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Three-Dimensional Icosahedral Phase Field Quasicrystal
NASA Astrophysics Data System (ADS)
Subramanian, P.; Archer, A. J.; Knobloch, E.; Rucklidge, A. M.
We investigate the formation and stability of icosahedral quasicrystalline structures using a dynamic phase field crystal model. Nonlinear interactions between density waves at two length scales stabilize three-dimensional quasicrystals. We determine the phase diagram and parameter values required for the quasicrystal to be the global minimum free energy state. We demonstrate that traits that promote the formation of two-dimensional quasicrystals are extant in three dimensions, and highlight the characteristics required for three-dimensional soft matter quasicrystal formation.
About the atomic structures of icosahedral quasicrystals
NASA Astrophysics Data System (ADS)
Quiquandon, Marianne; Gratias, Denis
This paper is a survey of the crystallographic methods that have been developed these last twenty five years to decipher the atomic structures of the icosahedral stable quasicrystals since their discovery in 1982 by D. Shechtman. After a brief recall of the notion of quasiperiodicity and the natural description of Z-modules in 3-dim as projection of regular lattices in N>3-dim spaces, we give the basic geometrical ingredients useful to describe icosahedral quasicrystals as irrational 3-dim cuts of ordinary crystals in 6-dim space. Atoms are described by atomic surfaces (ASs) that are bounded volumes in the internal (or perpendicular) 3-dim space and the intersections of which with the physical space are the actual atomic positions. The main part of the paper is devoted to finding the major properties of quasicrystalline icosahedral structures. As experimentally demonstrated, they can be described with a surprisingly few high symmetry ASs located at high symmetry special points in 6-dim space. The atomic structures are best described by aggregations and intersections of high symmetry compact interpenetrating atomic clusters. We show here that the experimentally relevant clusters are derived from one generic cluster made of two concentric triacontahedra scaled by τ and an external icosidodecahedron. Depending on which ones of the orbits of this cluster are eventually occupied by atoms, the actual atomic clusters are of type Bergman, Mackay, Tsai and others….
Magnetism in icosahedral quasicrystals: current status and open questions
Goldman, Alan I.
Progress in our understanding of the magnetic properties of R-containing icosahedral quasicrystals (R = rare earth element) from over 20 years of experimental effort is reviewed. This includes the much studied R-Mg-Zn and R-Mg-Cd ternary systems, as well as several magnetic quasicrystals that have been discovered and investigated more recently including Sc-Fe-Zn, R-Ag-In, Yb-Au-Al, the recently synthesized R-Cd binary quasicrystals, and their periodic approximants. In many ways, the magnetic properties among these quasicrystals are very similar. However, differences are observed that suggest new experiments and promising directions for future research.
Magnetism in icosahedral quasicrystals: current status and open questions
NASA Astrophysics Data System (ADS)
Goldman, Alan I.
Progress in our understanding of the magnetic properties of R-containing icosahedral quasicrystals (R = rare earth element) from over 20 years of experimental effort is reviewed. This includes the much studied R-Mg-Zn and R-Mg-Cd ternary systems, as well as several magnetic quasicrystals that have been discovered and investigated more recently including Sc-Fe-Zn, R-Ag-In, Yb-Au-Al, the recently synthesized R-Cd binary quasicrystals, and their periodic approximants. In many ways, the magnetic properties among these quasicrystals are very similar. However, differences are observed that suggest new experiments and promising directions for future research.
The quasiperiodic average structure of highly disordered decagonal Zn-Mg-Dy and its temperature dependence.
Ors, Taylan; Takakura, Hiroyuki; Abe, Eiji; Steurer, Walter
A single-crystal X-ray diffraction structure analysis of decagonal Zn-Mg-Dy, a Frank-Kasper-type quasicrystal, was performed using the higher-dimensional approach. For this first Frank-Kasper (F-K) decagonal quasicrystal studied so far, significant differences to the decagonal Al-TM-based (TM: transition metal) phases were found. A new type of twofold occupation domain is located on certain edge centers of the five-dimensional unit cell. The structure can be described in terms of a two-cluster model based on a decagonal cluster (∼ 23 Å diameter) arranged on the vertices of a pentagon-Penrose tiling (PPT) and a star-like cluster covering the remaining space. This model is used for the five-dimensional refinements, which converged to an R value of 0.126. The arrangement of clusters is significantly disordered as indicated by high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). In order to check the structure and stability at higher temperatures, in-situ high-temperature (HT) single-crystal X-ray diffraction experiments were conducted at 598 and 648 K (i.e. slightly below the decomposition temperature). The structure does not change significantly, however, the best quasiperiodic order is found at 598 K. The implication of these results on the stabilization mechanism of quasicrystals is discussed. PMID:24675601
Partial spectra of atomic thermal vibrations in decagonal and icosahedral quasicrystals
Parshin, P. P.; Zemlyanov, M. G. Brand, R. A.
The atomic dynamics of an Al-Ni-Fe decagonal quasicrystal and an Al-Cu-Fe icosahedral quasicrystal are investigated experimentally using the isotopic contrast method in inelastic neutron scattering. The partial spectra of thermal vibrations of copper, nickel, iron, and aluminum atoms in the decagonal and icosahedral quasicrystals are reconstructed directly from the experimental data without recourse to model concepts. The limiting energies and positions of the main features in the partial spectra of atomic thermal vibrations in decagonal and icosahedral quasicrystals are determined. It is established that, in the quasicrystals under investigation, the copper and nickel atoms are bound more weakly than the iron atoms and that the partial vibrational spectrum of aluminum atoms in the quasicrystals is considerably harder than the spectrum of pure metallic aluminum.
Multiple diffraction in an icosahedral Al-Cu-Fe quasicrystal
NASA Astrophysics Data System (ADS)
Fan, C. Z.; Weber, Th.; Deloudi, S.; Steurer, W.
In order to reveal its influence on quasicrystal structure analysis, multiple diffraction (MD) effects in an icosahedral Al-Cu-Fe quasicrystal have been investigated in-house on an Oxford Diffraction four-circle diffractometer equipped with an Onyx™ CCD area detector and MoKα radiation. For that purpose, an automated approach for Renninger scans (ψ-scans) has been developed. Two weak reflections were chosen as the main reflections (called P) in the present measurements. As is well known for periodic crystals, it is also observed for this quasicrystal that the intensity of the main reflection may significantly increase if the simultaneous (H) and the coupling (P-H) reflections are both strong, while there is no obvious MD effect if one of them is weak. The occurrence of MD events during ψ-scans has been studied based on an ideal structure model and the kinematical MD theory. The reliability of the approach is revealed by the good agreement between simulation and experiment. It shows that the multiple diffraction effect is quite significant.
Anisotropic Spin Correlations in the Zn-Mg-Ho Icosahedral Quasicrystal
NASA Astrophysics Data System (ADS)
Sato, Taku J.; Takakura, Hiroyuki; Tsai, An Pang; Shibata, Kaoru
Neutron scattering experiments have been performed on the Zn-Mg-Ho icosahedral quasicrystal using powder and single-crystalline samples. In contrast to a previous Letter [Charrier et al., Phys. Rev. Lett. 78, 4637 (1997)], the magnetic long-range order could not be detected in the icosahedral quasicrystal. It instead exhibits highly anisotropic diffuse scattering, which appears as satellite ridges of intense nuclear Bragg reflections, running parallel to the fivefold axis. The result suggests that quasi-five-dimensional spin correlations develop on a six-dimensional hypercubic lattice.
Speculation of equilibrium pressure of Ti36Zr40Ni20Pd4 icosahedral quasicrystal
NASA Astrophysics Data System (ADS)
Huang, Huogen; Chen, Liang
Ti-Zr-Ni quasicrystals have been demonstrated to store a large number of hydrogen atoms, which implies strong potential application in hydrogen energy field for them. However, the desorption of hydrogen atoms in the quasicrystals is quite difficult, with the indication of high desorption temperature and slow desorption rate. The shortage limits their use in the field to a large extent. But this kind of quasicrystals might be used in nuclear fusion energy field, because tritium as a coral fuel for nuclear fusion needs tight storage. However, equilibrium pressure at room temperature of Ti-Zr-Ni quasicrystals, important for their application in fusion energy field, has not been clear yet. In this work, we designed a gas-solid reaction system with the pressure resolution of 10-8Pa and carried out hydrogen desorption investigation at different temperatures on Ti36Zr40Ni20Pd4 icosahedral quasicrystal. Based on three Pressure-Composition-Temperature desorption curves, we speculate according to Van't Hoff theory about hydrogen storage that its equilibrium pressure at room temperature could be at the magnitude of 10-6Pa, displaying good stability of hydrogen in the quasicrystal and also implying application prospects in fusion energy field for quasicrystals of this type.
Dynamical x-ray diffraction from an icosahedral Al-Pd-Mn quasicrystal
Kycia, S.
Primary extinction effects in diffraction from single grains of Al-Pd- Mn, and presumably many other FCI alloys, may be significant and should be corrected for prior to use of diffraction data in structural determinations. Probes based on dynamical diffraction effects, such as x-ray standing wave fluorescence, multiple beam interference, and x-ray transmission topographs, may now be used to study the bulk and surface structure of some quasicrystals. The observation of dynamical diffraction from icosahedral Al-Pd-Mn is a striking confirmation of the fact that quasicrystals can present a degree of structural perfection comparable to that found in the best periodic intermetallic crystals.
A group theoretical approach to structural transitions of icosahedral quasicrystals and point arrays
NASA Astrophysics Data System (ADS)
Zappa, Emilio; Dykeman, Eric C.; Geraets, James A.; Twarock, Reidun
In this paper we describe a group theoretical approach to the study of structural transitions of icosahedral quasicrystals and point arrays. We apply the concept of Schur rotations, originally proposed by Kramer, to the case of aperiodic structures with icosahedral symmetry; these rotations induce a rotation of the physical and orthogonal spaces invariant under the icosahedral group, and hence, via the cut-and-project method, a continuous transformation of the corresponding model sets. We prove that this approach allows for a characterisation of such transitions in a purely group theoretical framework, and provide explicit computations and specific examples. Moreover, we prove that this approach can be used in the case of finite point sets with icosahedral symmetry, which have a wide range of applications in carbon chemistry (fullerenes) and biology (viral capsids).
Adsorption sites on icosahedral quasicrystal surfaces: Dark stars and white flowers
Unal, B.; Jenks, C.J.; Thiel, P.A.
From other work, two preferred sites have been suggested for metals and semimetals adsorbed on the fivefold surfaces of icosahedral, Al-based quasicrystals. Because of their appearance in scanning tunneling microscopy (STM) images, these sites are known as dark stars and white flowers. In this paper, we analyze four bulk structural models in physical space to determine the types, chemical decorations, and densities of the dark star - and, to a lesser extent, the white flower - adsorption sites for the fivefold planes of icosahedral Al-Pd-Mn. We find that the chemical decorations of these sites are heterogeneous, even within a single model. Both features are also structurally heterogeneous, according to STM measurements, and the structural variation is consistent with the bulk structure models. Finally, from the models, the density of dark stars in the planes correlates with the step height. This may explain previous experimental observations of different properties for different terraces.
Ab initio Ti-Zr-Ni phase diagram predicts stability of icosahedral TiZrNi quasicrystals
NASA Astrophysics Data System (ADS)
Hennig, R. G.; Carlsson, A. E.; Kelton, K. F.; Henley, C. L.
The ab initio phase diagram determines the energetic stability of the icosahedral TiZrNi quasicrystal. The complete ab initio zero-temperature ternary phase diagram is constructed from the calculated energies of the elemental, binary and ternary Ti-Zr-Ni phases. For this, the icosahedral i -TiZrNi quasicrystal is approximated by periodic structures of up to 123 atoms/unit cell, based on a decorated-tiling model [R. G. Hennig, K. F. Kelton, A. E. Carlsson, and C. L. Henley, Phys. Rev. B 67, 134202 (2003)]. The approximant structures containing the 45-atom Bergman cluster are nearly degenerate in energy, and are all energetically stable against the competing phases. It is concluded that i -TiZrNi is a ground-state quasicrystal, as it is experimentally the low-temperature phase for its composition.
Unified structure theory of icosahedral quasicrystals: Evidence from neutron powder diffraction patterns that AlCrFeMnSi, AlCuLiMg, and TiNiFeSi icosahedral quasicrystals are twins of cubic crystals containing about 820 or 1012 atoms in a primitive unit cube
Pauling, Linus
A unified structure theory of icosahedral quasicrystals, combining the twinned-cubic-crystal theory and the Penrose-tiling-six-dimensional-projection theory, is described. Values of the primitive-cubic lattice constant for several quasicrystals are evaluated from x-ray and neutron diffraction data. The fact that the low-angle diffraction maxima can be indexed with cubic unit cells provides additional support for the twinned-cubic-crystal theory of icosahedral quasicrystals. PMID:16593990
Unified structure theory of icosahedral quasicrystals: Evidence from neutron powder diffraction patterns that AlCrFeMnSi, AlCuLiMg, and TiNiFeSi icosahedral quasicrystals are twins of cubic crystals containing about 820 or 1,012 atoms in a primitive unit cube
Pauling, L. )
A unified structure theory of icosahedral quasicrystals, combining the twinned-cubic-crystal theory and the Penrose-tiling-six-dimensional-projection theory, is described. Values of the primitive-cubic lattice constant for several quasicrystals are evaluated from x-ray and neutron diffraction data. The fact that the low-angle diffraction maxima can be indexed with cubic unit cells provides additional support for the twinned-cubic-crystal theory of icosahedral quasicrystals.
Observation of Quasimagnetic Structures in Rare-Earth-Based Icosahedral Quasicrystals
Charrier, B.; Schmitt, D.; Ouladdiaf, B.
The first observation of long-range quasiperiodic antiferromagnetic structures in quasicrystals, namely the heavy rare-earth-based icosahedral R{sub 8}Mg{sub 42}Zn{sub 50} compounds (R=Tb , Dy, Ho, Er), is reported. This {ital quasimagnetic} ordering is characterized by the propagation vector {bold Q}=((1)/(4),0,0,0,0,0) in the six-dimensional notation. Simultaneously, broad magnetic peaks appear in the neutron diffraction patterns, characteristic of a short-range ordering. The coexistence of two different magnetic correlation lengths suggests the presence of two types of crystallographic sites for the rare-earth atoms. {copyright} {ital 1997} {ital The American Physical Society}
Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal
Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc
The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye–Waller factor, which explains the vanishing of 'high-Q perp' reflections. PMID:27437112
Valence band structure of the icosahedral Ag-In-Yb quasicrystal
Sharma, H. R.; Simutis, G.; Dhanak, V. R.; Nugent, P. J.; McGrath, R.; Cui, C.; Shimoda, M.; Tsai, A. P.; Ishii, Y.
The valence band structure of the icosahedral (i) Ag-In-Yb quasicrystal, which is isostructural to the binary i-Cd-Yb system, is investigated by ultraviolet photoemission spectroscopy (UPS). Experimental results are compared with electronic-structure calculations of a cubic approximant of the same phase. UPS spectra from the fivefold, threefold, and twofold i-Ag-In-Yb surfaces reveal that the valence band near to the Fermi level is dominated by Yb 4f-derived states, in agreement with calculations. The spectra also exhibit peaks which are surface core level shifted, caused by changes in the electronic structure in surface layers. Calculations yield a pseudogap in the density of states due to a hybridization of the Yb 5d band with the Ag 5p and In 5p bands. Both experimental and calculated band features are very similar to those of Cd-Yb. The modification of the band structure after surface treatment by sputtering and by oxidation is also studied. Additionally, the work function of i-Ag-In-Yb measured from the width of UPS spectrum is found to be almost unaffected by surface orientation, but increases after sputtering or oxidation.
Structural stability of the icosahedral AlCuFe quasicrystal under high-pressure and high-temperature
NASA Astrophysics Data System (ADS)
Takagi, S.; Kyono, A.; Nakamoto, Y.; Hirao, N.
We report high-pressure and high-temperature in-situ X-ray diffraction study of icosahedral (i)-AlCuFe quasicrystal "icosahedrite" which is the first known naturally occurring quasicrystal mineral discovered in the Khatyrka meteorite. The i-AlCuFe quasicrystal was synthesized in laboratory from a powder mixture with an atomic ratio of Al : Cu : Fe = 65 : 20 : 15. The high-temperature and high-pressure X-ray diffraction experiments were performed using the laser-heated diamond anvil cell system installed at BL10XU, SPring-8, Japan. The i-AlCuFe showed a characteristic X-ray diffraction pattern of quasicrystal. With only compression, the diffraction patterns of the i-AlCuFe were continued until 75 GPa. At a pressure of 87 GPa two small new peaks occurred and then kept up to the maximum pressure of 104 GPa in the study. The results indicate that the pressure-induced structural phase transition of the i-AlCuFe occurs above 87 GPa, and the structure of the i-AlCuFe remains unchanged at least up to 75 GPa. Under simultaneously high pressure and high temperature, on the other hand, the i-AlCuFe was readily transformed to crystalline phase. It can be characterized by an irreversible transformation process. The structure of the i-AlCuFe is therefore more affected by thermal metamorphism than by pressure metamorphism. The present high-pressure and high-temperature experiments clearly revealed the thermal and pressure stability of the i-AlCuFe quasicrystal which may help to explain the formation of the naturally occurring quasicrystal in the solar system.
Icosahedral AlCuFe quasicrystal at high pressure and temperature and its implications for the stability of icosahedrite.
Stagno, Vincenzo; Bindi, Luca; Shibazaki, Yuki; Tange, Yoshinori; Higo, Yuji; Mao, H-K; Steinhardt, Paul J; Fei, Yingwei
The first natural-occurring quasicrystal, icosahedrite, was recently discovered in the Khatyrka meteorite, a new CV3 carbonaceous chondrite. Its finding raised fundamental questions regarding the effects of pressure and temperature on the kinetic and thermodynamic stability of the quasicrystal structure relative to possible isochemical crystalline or amorphous phases. Although several studies showed the stability at ambient temperature of synthetic icosahedral AlCuFe up to ~35 GPa, the simultaneous effect of temperature and pressure relevant for the formation of icosahedrite has been never investigated so far. Here we present in situ synchrotron X-ray diffraction experiments on synthetic icosahedral AlCuFe using multianvil device to explore possible temperature-induced phase transformations at pressures of 5 GPa and temperature up to 1773 K. Results show the structural stability of i-AlCuFe phase with a negligible effect of pressure on the volumetric thermal expansion properties. In addition, the structural analysis of the recovered sample excludes the transformation of AlCuFe quasicrystalline phase to possible approximant phases, which is in contrast with previous predictions at ambient pressure. Results from this study extend our knowledge on the stability of icosahedral AlCuFe at higher temperature and pressure than previously examined, and provide a new constraint on the stability of icosahedrite. PMID:25070248
Diffuse scattering and phason fluctuations in the Zn-Mg-Sc icosahedral quasicrystal and its Zn-Sc periodic approximant.
de Boissieu, M; Francoual, S; Kaneko, Y; Ishimasa, T
We report on the absolute scale measurement of the x-ray diffuse scattering in the ZnMgSc icosahedral quasicrystal and its periodic approximant. Whereas the diffuse scattering in the approximant is purely accounted for by thermal diffuse scattering, an additional signal is observed in the quasicrystal. It is related to phason fluctuations as indicated by its Q(2)(per) dependence. Moreover, when compared to previous measurements carried out on the i-AlPdMn phase, we find that the amount of diffuse scattering is smaller in the i-ZnMgSc phase, in agreement with larger phason elastic constants in this phase. This is confirmed by the observation of a large number of weak Bragg peaks having a high Q(per) reciprocal space component. PMID:16196940
Additional evidence from x-ray powder diffraction patterns that icosahedral quasi-crystals of intermetallic compounds are twinned cubic crystals
Pauling, L. )
Analysis of the measured values of Q for the weak peaks (small maxima, usually considered to be background fluctuations, noise) on the x-ray powder diffraction curves for 17 rapidly quenched alloys leads directly to the conclusion that they are formed by an 820-atom or 1012-atom primitive cubic structure that by icosahedral twinning produces the so-called icosahedral quasi-crystals.
Development of thermal rectifier using unusual electron thermal conductivity of icosahedral quasicrystals
NASA Astrophysics Data System (ADS)
Takeuchi, Tsunehiro
The bulk thermal rectifiers usable at high temperature were developed using the unusual increase of electron thermal conductivity of icosahedral quasicrystals (ICQ's) at high temperature. Our previously performed analyses in terms of linear response theory suggested that the unusual increase of electron thermal conductivity of ICQ was brought about by the synergy effect of quasiperiodicity and narrow pseudogap at the Fermi level. Since the linear response theory suggests that the unusual increase of electron thermal conductivity is coupled with the small magnitude of Seebeck coefficient, the composition of Al-Cu-Fe ICQ, where the thermal conductivity shows the most significant increase with increasing temperature, was determined with a great help of Seebeck coefficient measurements. Consequently obtained Al61.5Cu26.5Fe12.0 ICQ, which was characterized by the small magnitude of Seebeck coefficient, possessed 9 times larger value of thermal conductivity at 1000 K than that observed at 300 K. The increasing tendency of electron thermal conductivity with increasing temperature was further enhanced by means of small amount of Re substitution for Fe. This substitution definitely reduced the lattice thermal conductivity while the electron thermal conductivity was kept unchanged. The lattice thermal conductivity was reduced by 35 % under the presence of 0.5 at.% Re, and the thermal conductivity at 1000 K consequently became about 11 times larger than that at 300 K. The thermal rectifiers were constructed using our newly developed ICQ (Al61.5Cu26.5Fe12.0 or Al61.0Si0.5Cu26.5Fe11.5Re0.5) together with one of the selected materials (Si, Al2O3, CuGeTe2 or Ag2Te) that possess thermal conductivity decreasing with increasing temperature. The heat current flowing in the rectifiers was confirmed to show significant direction dependence. The consequently obtained TRR =|
Influence of leaching on surface composition, microstructure, and valence band of single grain icosahedral Al-Cu-Fe quasicrystal
NASA Astrophysics Data System (ADS)
Lowe, M.; Yadav, T. P.; Fournée, V.; Ledieu, J.; McGrath, R.; Sharma, H. R.
The use of quasicrystals as precursors to catalysts for the steam reforming of methanol is potentially one of the most important applications of these new materials. To develop application as a technology requires a detailed understanding of the microscopic behavior of the catalyst. Here, we report the effect of leaching treatments on the surface microstructure, chemical composition, and valence band of the icosahedral (i-) Al-Cu-Fe quasicrystal in an attempt to prepare a model catalyst. The high symmetry fivefold surface of a single grain i-Al-Cu-Fe quasicrystal was leached with NaOH solution for varying times, and the resulting surface was characterized by x-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), scanning electron microscopy (SEM), and atomic force microscopy (AFM). The leaching treatments preferentially remove Al producing a capping layer consisting of Fe and Cu oxides. The subsurface layer contains elemental Fe and Cu in addition to the oxides. The quasicrystalline bulk structure beneath remains unchanged. The subsurface gradually becomes Fe3O4 rich with increasing leaching time. The surface after leaching exhibits micron sized dodecahedral cavities due to preferential leaching along the fivefold axis. Nanoparticles of the transition metals and their oxides are precipitated on the surface after leaching. The size of the nanoparticles is estimated by high resolution transmission microscopy to be 5-20 nm, which is in agreement with the AFM results. Selected area electron diffraction (SAED) confirms the crystalline nature of the nanoparticles. SAED further reveals the formation of an interface between the high atomic density lattice planes of nanoparticles and the quasicrystal. These results provide an important insight into the preparation of model catalysts of nanoparticles for steam reforming of methanol.
Influence of leaching on surface composition, microstructure, and valence band of single grain icosahedral Al-Cu-Fe quasicrystal
Lowe, M.; McGrath, R.; Sharma, H. R.; Yadav, T. P.; Fournée, V.; Ledieu, J.
The use of quasicrystals as precursors to catalysts for the steam reforming of methanol is potentially one of the most important applications of these new materials. To develop application as a technology requires a detailed understanding of the microscopic behavior of the catalyst. Here, we report the effect of leaching treatments on the surface microstructure, chemical composition, and valence band of the icosahedral (i-) Al-Cu-Fe quasicrystal in an attempt to prepare a model catalyst. The high symmetry fivefold surface of a single grain i-Al-Cu-Fe quasicrystal was leached with NaOH solution for varying times, and the resulting surface was characterized by x-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), scanning electron microscopy (SEM), and atomic force microscopy (AFM). The leaching treatments preferentially remove Al producing a capping layer consisting of Fe and Cu oxides. The subsurface layer contains elemental Fe and Cu in addition to the oxides. The quasicrystalline bulk structure beneath remains unchanged. The subsurface gradually becomes Fe{sub 3}O{sub 4} rich with increasing leaching time. The surface after leaching exhibits micron sized dodecahedral cavities due to preferential leaching along the fivefold axis. Nanoparticles of the transition metals and their oxides are precipitated on the surface after leaching. The size of the nanoparticles is estimated by high resolution transmission microscopy to be 5-20 nm, which is in agreement with the AFM results. Selected area electron diffraction (SAED) confirms the crystalline nature of the nanoparticles. SAED further reveals the formation of an interface between the high atomic density lattice planes of nanoparticles and the quasicrystal. These results provide an important insight into the preparation of model catalysts of nanoparticles for steam reforming of methanol.
Speculation of equilibrium pressure of Ti{sub 36}Zr{sub 40}Ni{sub 20}Pd{sub 4} icosahedral quasicrystal
Huang, Huogen; Chen, Liang
Ti-Zr-Ni quasicrystals have been demonstrated to store a large number of hydrogen atoms, which implies strong potential application in hydrogen energy field for them. However, the desorption of hydrogen atoms in the quasicrystals is quite difficult, with the indication of high desorption temperature and slow desorption rate. The shortage limits their use in the field to a large extent. But this kind of quasicrystals might be used in nuclear fusion energy field, because tritium as a coral fuel for nuclear fusion needs tight storage. However, equilibrium pressure at room temperature of Ti-Zr-Ni quasicrystals, important for their application in fusion energy field, has not been clear yet. In this work, we designed a gas-solid reaction system with the pressure resolution of 10{sup −8}Pa and carried out hydrogen desorption investigation at different temperatures on Ti{sub 36}Zr{sub 40}Ni{sub 20}Pd{sub 4} icosahedral quasicrystal. Based on three Pressure-Composition-Temperature desorption curves, we speculate according to Van't Hoff theory about hydrogen storage that its equilibrium pressure at room temperature could be at the magnitude of 10{sup −6}Pa, displaying good stability of hydrogen in the quasicrystal and also implying application prospects in fusion energy field for quasicrystals of this type.
Step-terrace morphology and reactivity to C60 of the five-fold icosahedral Ag-In-Yb quasicrystal
NASA Astrophysics Data System (ADS)
Nugent, P. J.; Smerdon, J. A.; McGrath, R.; Shimoda, M.; Cui, C.; Tsai, A. P.; Sharma, H. R.
The surface of the icosahedral i-Ag-In-Yb quasicrystal provides one of the first non-Al-based aperiodic surfaces that is suitable for study under ultra-high vacuum conditions. We present a scanning tunnelling microscopy (STM) study of the five-fold surface of this new quasicrystal demonstrating detailed structure of the terraces and steps. The analysis of the autocorrelation functions of STM images at opposite bias polarities and of the in-plane structure of the bulk model of i-Cd-Yb, which is isostructural to i-Ag-In-Yb, reveals that the surface terminations occur at the centres of the rhombic triacontrahedral (RTH) clusters, which are the basic building blocks of this material. The study further confirms that the unoccupied electronic states are located on Yb sites. Step edges display a Fibonacci sequence of truncated clusters, which can also be explained in terms of the model structure. Occasionally, a single terrace is found to display different structures at negative bias, whereas the same terrace shows a uniform structure at positive bias. Depositing C60 creates a disordered overlayer on the surface with no resulting FFT or LEED patterns.
Schottky effect in the i -Zn-Ag-Sc-Tm icosahedral quasicrystal and its 1/1 Zn-Sc-Tm approximant
NASA Astrophysics Data System (ADS)
Jazbec, S.; Kashimoto, S.; Koželj, P.; Vrtnik, S.; Jagodič, M.; Jagličić, Z.; Dolinšek, J.
The analysis of low-temperature specific heat of rare-earth (RE)-containing quasicrystals and periodic approximants and consequent interpretation of their electronic properties in the T →0 limit is frequently hampered by the Schottky effect, where crystalline electric fields lift the degeneracy of the RE-ion Hund's rule ground state and introduce additional contribution to the specific heat. In this paper we study the low-temperature specific heat of a thulium-containing i -Zn-Ag-Sc-Tm icosahedral quasicrystal and its 1/1 Zn-Sc-Tm approximant, both being classified as "Schottky" systems. We have derived the crystal-field Hamiltonian for pentagonal symmetry of the crystalline electric field, pertinent to the class of Tsai-type icosahedral quasicrystals and their approximants, where the RE ions are located on fivefold axes of the icosahedral atomic cluster. Using the leading term of this Hamiltonian, we have calculated analytically the Schottky specific heat in the presence of an external magnetic field and made comparison to the experimental specific heat of the investigated quasicrystal and approximant. When the low-temperature specific heat C is analyzed in a C /T versus T2 scale (as it is customarily done for metallic specimens), the Schottky specific heat yields an upturn in the T →0 limit that cannot be easily distinguished from a similar upturn produced by the electron-electron interactions in exchange-enhanced systems and strongly correlated systems. Our results show that extraction of the electronic properties of RE-containing quasicrystals from their low-temperature specific heat may be uncertain in the presence of the Schottky effect.
Cahn, John W.
The discretely diffracting aperiodic crystals termed quasicrystals, discovered at NBS in the early 1980s, have led to much interdisciplinary activity involving mainly materials science, physics, mathematics, and crystallography. It led to a new understanding of how atoms can arrange themselves, the role of periodicity in nature, and has created a new branch of crystallography.
Scanning Tunneling Microscopy Studies of Surface Structures of Icosahedral Al-Cu-Fe Quasicrystals
Tanhong Cai
Three papers are included in this dissertation. The first paper: ''Structural aspects of the fivefold quasicrystalline Al-Cu-Fe surface from STM and dynamical LEED studies'', is in press with ''Surface Science''. The second paper: ''An STM study of the atomic structure of the icosahedral Al-Cu-Fe fivefold surface'' is submitted to ''Physical Review B, Rapid Communication''. The third paper: ''Pseudomorphic starfish: arrangement of extrinsic metal atoms on a quasicrystalline substrate'' is submitted to ''Nature''. Following the third paper are general conclusions and appendices that document the published paper ''Structural aspects of the three-fold surface of icosahedral Al-Pd-Mn'' (appearing in volume 461, issue 1-3 of ''Surface Science'' on page L521-L527, 2000), the design as well as the specifications of the aluminum evaporator used in the aluminum deposition study in this dissertation, an extended discussion of the aluminum deposition on the quasicrystalline surface, and the STM database.
Unoccupied electronic states of icosahedral Al-Pd-Mn quasicrystals: Evidence of image potential resonance and pseudogap
Maniraj, M; Rai, Abhishek; Barman, S R; Krajci, M; Schlagel, Deborah L; Lograsso, Thomas A; Horn, K
We study the unoccupied region of the electronic structure of the fivefold symmetric surface of an icosahedral (i) Al-Pd-Mn quasicrystal. A feature that exhibits parabolic dispersion with an effective mass of (1.15±0.1)me and tracks the change in the work function is assigned to an image potential resonance because our density functional calculation shows an absence of band gap in the respective energy region. We show that Sn grows pseudomorphically on i-Al-Pd-Mn as predicted by density functional theory calculations, and the energy of the image potential resonance tracks the change in the work function with Sn coverage. The image potential resonance appears much weaker in the spectrum from the related crystalline Al-Pd-Mn surface, demonstrating that its strength is related to the compatibility of the quasiperiodic wave functions in i-Al-Pd-Mn with the free-electron-like image potential states. Our investigation of the energy region immediately above EF provides unambiguous evidence for the presence of a pseudogap, in agreement with our density functional theory calculations.
Terrace-dependent nucleation of small Ag clusters on a five-fold icosahedral quasicrystal surface
Unal, B.; Evans, J.W.; Lograsso, T.A.; Ross, A.R.; Jenks, C.J.; Thiel, P.A.
Nucleation of Ag islands on the five-fold surface of icosahedral Al-Pd-Mn is influenced strongly by trap sites. Submonolayers of Ag prepared by deposition at 365 K and with a flux of 1 x 10{sup -3} monolayers/s exhibit a variation in Ag island densities across different terraces. Comparisons with previous work and with rate equation analysis indicate that trap sites are not saturated under these experimental conditions and that the difference in island densities is not necessarily due to variation in trap densities. While it could have a number of different origins, our results point to a terrace-dependent value of the effective diffusion barrier for Ag adatoms.
Magnetoresistance in i-R-Cd icosahedral quasicrystals (R=Y, Gd)
NASA Astrophysics Data System (ADS)
Saraswat, Garima; Popović, Dragana; Kong, Tai; Bud'Ko, Sergey L.; Canfield, Paul C.
We use magnetoresistance (MR) to probe the electronic properties of the recently discovered binary quasicrystals (QCs) i-Gd-Cd and i-Y-Cd, with and without local magnetic moments, respectively. DC magnetization has revealed spin-glass freezing in i-Gd-Cd at a temperature Tf = 4 . 6 K. MR was measured at 1 . 6 <= T (K) <= 300 and in magnetic fields H up to 12 T. The most interesting behavior is observed in i-Gd-Cd, in which the MR exhibits thermo-magnetic history dependence at low T. In particular, there is a clear difference between the ZFC and FC values of the low-field positive MR. In contrast, the i-Y-Cd MR does not depend on magnetic history. The onset of the history dependent MR at T ~ 20 K >Tf , when the QC with local magnetic moments is cooled in a high field of 12 T, may be related to the formation of magnetic clusters above Tf, as inferred from the magnetization and specific heat studies. Possible mechanisms responsible for the striking coupling between charge transport and local magnetic environment observed in the MR will be discussed. Work at the NHMFL supported by NSF Grant No. DMR-1307075, the NSF Cooperative Agreement No. DMR-0654118 and the State of Florida. Work at Ames Lab (TK, SLB and PCC) supported by the U.S. D.O.E / B.E.S under Contract No. DE-AC02-07CH11358.
Development of an icosahedral quasicrystal and two approximants in the Ca-Au-Sn system: syntheses and structural analyses.
Lin, Qisheng; Corbett, John D
The realm of Tsai-type (YCd(6)-type) quasicrystals (QCs) and their approximants (ACs) continues to expand to the east in the periodic table. The heavy tetrel Sn is now one of the major components in the new Ca(15.0(5))Au(60.0(4))Sn(25.0(2)) (atom %) icosahedral QC and in the corresponding 1/1 and 2/1 ACs. (The 2/1 AC with Yb is also established.) Single-crystal X-ray diffraction on a 1/1 AC gives the refined formula of Ca(3)Au(14.36(3))Sn(4.38(5)) in space group Im3, a = 15.131(1) Å, whereas a representative 2/1 AC gives Ca(13)Au(47.2(1))Sn(28.1(1)), Pa3 and a = 24.444(1) Å. Both ACs contain five-shell multiply endohedral triacontahedral clusters as the common building blocks, as in the parent structure of YCd(6). The 2/1 AC also contains four Ca(2)-dimer-centered prolate rhombohedra (PRs) in the unit cell. The long-range order between triacontahedra and PRs in the 2/1 AC is the same as those in Bergman-type 2/1 ACs. A TB-LMTO-ASA calculation on an ideal 1/1 AC model reveals a shallow pseudogap in the total densities-of-states data around the Fermi energy, as expected. The depth of the pseudogap is considerably enhanced through interactions between the Ca 3d states and s and p states of Au and Sn. PMID:20939550
Investigation of the surface terminations of icosahedral AlPdMn quasicrystal based on a modified non-spherical model
NASA Astrophysics Data System (ADS)
Yu, Fengmei; Zou, Huamin; Wang, Jianbo; Wang, Renhui
The atomic positions are obtained from a modified non-spherical model of icosahedral AlPdMn quasicrystal (Fang et al 2003 J. Phys.: Condens. Matter 15 4947) by the cut method. The four-shell pseudo-Mackay clusters (PMCs) were searched for in a box of 400 Å × 400 Å × 400 Å. The results show that the number of atoms in the fourth shell, an icosidodecahedron, of the pseudo-Mackay cluster can vary from 15 to 30 because of the cluster overlap, and about 99.96% of the total atoms are included in such incomplete pseudo-Mackay clusters. The characteristics of the atom distribution in the planes perpendicular to a fivefold axis indicate that the planes, which are 1.56 Å apart from their neighbouring planes, are expected to be the terminal surfaces. If one such a plane and its closest neighbouring plane, between which the spacing is 0.48 Å, are considered as a thin layer or a corrugated surface, these layers are also the layers with the maximum density. The pair of corrugated surfaces that are 1.56 Å apart have almost identical chemical composition. These planes form terraces that follow the rule of the Fibonacci sequence with two step heights, 6.60 and 4.08 Å. On the corrugated surfaces perpendicular to a fivefold axis the pentagonal holes arise from the interspaces of adjacent incomplete PMCs. For the atomic planes normal to a twofold axis, the planes with spacing of 1.48 Å from their adjacent planes might be expected to be the terminal surfaces, which form terraces with step heights of 6.28 and 3.88 Å following the rule of the Fibonacci sequence. For the atomic planes normal to a threefold axis, the planes with spacing of 0.86 Å from their adjacent planes might be expected to be the terminal surfaces. No similar results were found for the atomic layers perpendicular to a pseudo-twofold axis.
Medium-range icosahedral order in quasicrystal-forming Zr{sub 2}Pd binary metallic glass
Huang Li; Fang, X. W.; Wang, C. Z.; Ho, K. M.; Kramer, M. J.; Ding, Z. J.
Medium-range order in Zr{sub 2}Pd metallic glass was studied using a combination of x-ray diffraction experiment and atomistic simulations. We show that, in contrast to earlier experimental interpretations, the icosahedral-like polyhedron is centered around Pd, rather than Zr. Furthermore, we find that the ordered icosahedral packing around Pd extends to the third shell in the way similar to that in the Bergman-type clusters. The existence of Bergman-type clusters sheds interesting light into the formation of nanoquasicrystal phase during crystallization process of Zr{sub 2}Pd metallic glass.
Scanning tuneeling microscopy studies of fivefold surfaces of icosahedral Al-Pd-Mn quasicrystals and of thin silver films on those surfaces
Unal, Baris
The present work in this dissertation mainly focuses on the clean fivefold surfaces of i-Al-Pd-Mn quasicrystals as well as the nucleation and growth of Ag films on these surfaces. In addition, Ag film growth on NiAl(110) has been explored in the frame of this dissertation. First, we have investigated the equilibration of a fivefold surface of icosahedral Al-Pd-Mn quasicrystal at 900-915 K and 925-950 K, using Omicron variable temperature scanning tunneling microscope (STM). Annealing at low temperatures resulted in many voids on some terraces while the others were almost void-free. After annealing at 925-950K, void-rich terraces became much rarer. Our STM images suggest that through growth and coalescence of the voids, a different termination becomes exposed on host terraces. All of these observations in our study indicate that even after the quasicrystalline terrace-step structure appears, it evolves with time and temperature. More specifically, based on the STM observations, we conclude that during the annealing a wide range of energetically similar layers nucleate as surface terminations, however, with increasing temperature (and time) this distribution gets narrower via elimination of the metastable void-rich terraces. Next, we have examined the bulk structural models of icosahedral Al-Pd-Mn quasicrystal in terms of the densities, compositions and interplanar spacings for the fivefold planes that might represent physical surface terminations. In our analyses, we mainly have focused on four deterministic models which have no partial or mixed occupancy but we have made some comparisons with an undeterministic model. We have compared the models with each other and also with the available experimental data including STM, LEED-IV, XPD and LEIS. In all deterministic models, there are two different families of layers (a pair of planes), and the nondeterministic model contains similar group of planes. These two families differ in terms of the chemical decoration of
Magnetic and transport properties of i-R-Cd icosahedral quasicrystals (R=Y, Gd-Tm)
Kong, Tai; Bud'ko, Sergey L.; Jesche, Anton; McArthur, John; Kreyssig, Andreas; Goldman, Alan I.; Canfield, Paul C.
We present a detailed characterization of the recently discovered i-R-Cd (R=Y,Gd-Tm) binary quasicrystals by means of x-ray diffraction, temperature-dependent dc and ac magnetization, temperature-dependent resistance, and temperature-dependent specific heat measurements. Structurally, the broadening of x-ray diffraction peaks found for i-R-Cd is dominated by frozen-in phason strain, which is essentially independent of R. i-Y-Cd is weakly diamagnetic and manifests a temperature-independent susceptibility. i-Gd-Cd can be characterized as a spin glass below 4.6 K via dc magnetization cusp, a third order nonlinear magnetic susceptibility peak, a frequency-dependent freezing temperature, and a broad maximum in the specific heat. i-R-Cd (R=Ho-Tm) is similar to i-Gd-Cd in terms of features observed in thermodynamic measurements. i-Tb-Cd and i-Dy-Cd do not show a clear cusp in their zero-field-cooled dc magnetization data, but instead show a more rounded, broad local maximum. The resistivity for i-R-Cd is of order 300μΩ cm and weakly temperature dependent. The characteristic freezing temperatures for i-R-Cd (R=Gd-Tm) deviate from the de Gennes scaling, in a manner consistent with crystal electric field splitting induced local moment anisotropy.
Approximant phases and an icosahedral quasicrystal in the Ca-Au-Ga system: the influence of size of gallium versus indium.
Lin, Qisheng; Corbett, John D
Two crystalline approximants (ACs) and their corresponding icosahedral quasicrystal (i-QC) are obtained in the Ca-Au-Ga system through conventional solid-state exploratory syntheses. Single crystal structural analyses reveal that the 1/1 AC, Ca 3Au x Ga 19- x ( x = approximately 9.3-12.1) [ Im3, a = 14.6941(6)-14.7594(6) A], has the empty cubes in the prototypic YCd 6 (= Y 3Cd 18) now fully occupied by Ga, resulting in a 3:19 stoichiometry. In parallel, the distorted cubes in the 2/1 AC, Ca 13Au 57.1Ga 23.4 [ Pa3, a = 23.9377(8) A] are fully or fractionally occupied by Ga. The valence electron count per atom ( e/ a) for the 2/1 AC (1.64) is smaller than that over the 1/1 AC composition range (1.76-2.02), and the e/ a of the Ca 15.2Au 50.3Ga 34.5 i-QC, 1.84, is somewhat distant from typical values for Tsai-type i-QCs ( approximately 2.0). Comparisons of the gallium results with the corresponding In phases suggest that the structural differences result mainly from size rather than electronic factors. The 1/1 and 2/1 appear to be thermodynamically stable on slow cooling, as usual, whereas the i-QC isolated by quenching decomposes on heating at approximately 660 degrees C, mainly into 2/1 AC and Ca 3(Au,Ga) 11. Calculations of the electronic structure of 1/1 AC suggest that the Fermi sphere-Brillouin zone interactions remain important for the Ca-Au-Ga i-QC. PMID:18672875
Crystal chemistry and chemical order in ternary quasicrystals and approximants
NASA Astrophysics Data System (ADS)
Gómez, Cesar Pay; Tsai, An Pang
In this work we review our current understanding of structure, stability and formation of icosahedral quasicrystals and approximants. The work has special emphasis on Cd-Yb type phases, but several concepts are generalized to other families of icosahedral quasicrystals and approximants. The paper handles topics such as chemical order and site preference at the cluster level for ternary phases, valence electron concentration and its influence on formation and composition, fundamental building blocks and cluster linkages, and the similarities and differences between different families of icosahedral quasicrystals and approximants.
Symmetry of Magnetically Ordered Quasicrystals
NASA Astrophysics Data System (ADS)
Lifshitz, Ron
The notion of magnetic symmetry is reexamined in light of the recent observation of long-range magnetic order in icosahedral quasicrystals [Charrier et al., Phys. Rev. Lett. 78, 4637 (1997)]. The relation between the symmetry of a magnetically ordered (periodic or quasiperiodic) crystal, given in terms of a ``spin space group,'' and its neutron diffraction diagram is established. In doing so, an outline of a symmetry classification scheme for magnetically ordered quasiperiodic crystals, is provided. Predictions are given for the expected diffraction patterns of magnetically ordered icosahedral crystals, provided their symmetry is well described by icosahedral spin space groups.
Interatomic force interaction in an i-AlCuFe quasicrystal
Parshin, P. P.; Zemlyanov, M. G. Brand, R. A.
Partial spectra of thermal vibrations of Al, Cu, and Fe atoms in an icosahedral quasicrystal have been obtained by the isotopic-contrast method in inelastic neutron scattering. Joint analysis of these results and the published data on the atomic and electronic structures of the icosahedral i-AlCuFe quasicrystal has been performed. A physical model of the quasicrystal structure is proposed that is in agreement with the existing experimental data and qualitatively describes the peculiarities of interatomic interaction.
Electronic properties of quasicrystals
NASA Astrophysics Data System (ADS)
Berger, C.; Gozlan, A.; Fourcaudot, G.; Cyrot-Lackmann, F.; Lasjaunias, J. C.
The electronic properties of quasi-crystals are discussed using experimental data with particular attention given to the AlMn(Si) system. A comparison is made of the electronic properties of AlMn samples of the same composition for amorphous, icosahedral, decagonal and crystalline structures. It is concluded that, for AlMn, the measured properties are very similar in the quasi-crystalline and amorphous phases but are in all respects different from those of the crystalline compound. It is suggested that this is due to the presence of many defects in these metastable quasi-crystalline structures obtained by rapid solidification. Some preliminary experiments on single grain of the new thermodynamically stable AlCuFe quasi-crystals are presented.
A crystallographic approach to structural transitions in icosahedral viruses.
Indelicato, Giuliana; Cermelli, Paolo; Salthouse, David G; Racca, Simone; Zanzotto, Giovanni; Twarock, Reidun
Viruses with icosahedral capsids, which form the largest class of all viruses and contain a number of important human pathogens, can be modelled via suitable icosahedrally invariant finite subsets of icosahedral 3D quasicrystals. We combine concepts from the theory of 3D quasicrystals, and from the theory of structural phase transformations in crystalline solids, to give a framework for the study of the structural transitions occurring in icosahedral viral capsids during maturation or infection. As 3D quasicrystals are in a one-to-one correspondence with suitable subsets of 6D icosahedral Bravais lattices, we study systematically the 6D-analogs of the classical Bain deformations in 3D, characterized by minimal symmetry loss at intermediate configurations, and use this information to infer putative viral-capsid transition paths in 3D via the cut-and-project method used for the construction of quasicrystals. We apply our approach to the Cowpea Chlorotic Mottle virus (CCMV) and show that the putative transition path between the experimentally observed initial and final CCMV structures is most likely to preserve one threefold axis. Our procedure suggests a general method for the investigation and prediction of symmetry constraints on the capsids of icosahedral viruses during structural transitions, and thus provides insights into the mechanisms underlying structural transitions of these pathogens. PMID:21611828
Approximation of virus structure by icosahedral tilings.
Salthouse, D G; Indelicato, G; Cermelli, P; Keef, T; Twarock, R
Viruses are remarkable examples of order at the nanoscale, exhibiting protein containers that in the vast majority of cases are organized with icosahedral symmetry. Janner used lattice theory to provide blueprints for the organization of material in viruses. An alternative approach is provided here in terms of icosahedral tilings, motivated by the fact that icosahedral symmetry is non-crystallographic in three dimensions. In particular, a numerical procedure is developed to approximate the capsid of icosahedral viruses by icosahedral tiles via projection of high-dimensional tiles based on the cut-and-project scheme for the construction of three-dimensional quasicrystals. The goodness of fit of our approximation is assessed using techniques related to the theory of polygonal approximation of curves. The approach is applied to a number of viral capsids and it is shown that detailed features of the capsid surface can indeed be satisfactorily described by icosahedral tilings. This work complements previous studies in which the geometry of the capsid is described by point sets generated as orbits of extensions of the icosahedral group, as such point sets are by construction related to the vertex sets of icosahedral tilings. The approximations of virus geometry derived here can serve as coarse-grained models of viral capsids as a basis for the study of virus assembly and structural transitions of viral capsids, and also provide a new perspective on the design of protein containers for nanotechnology applications. PMID:26131897
Quantum critical state in a magnetic quasicrystal.
Deguchi, Kazuhiko; Matsukawa, Shuya; Sato, Noriaki K; Hattori, Taisuke; Ishida, Kenji; Takakura, Hiroyuki; Ishimasa, Tsutomu
Quasicrystals are metallic alloys that possess long-range, aperiodic structures with diffraction symmetries forbidden to conventional crystals. Since the discovery of quasicrystals by Schechtman et al. in 1984, there has been considerable progress in resolving their geometric structure. For example, it is well known that the golden ratio of mathematics and art occurs over and over again in their crystal structure. However, the characteristic properties of the electronic states--whether they are extended as in periodic crystals or localized as in amorphous materials--are still unresolved. Here we report the first observation of quantum (T = 0) critical phenomena of the Au-Al-Yb quasicrystal--the magnetic susceptibility and the electronic specific heat coefficient arising from strongly correlated 4f electrons of the Yb atoms diverge as T→0. Furthermore, we observe that this quantum critical phenomenon is robust against hydrostatic pressure. By contrast, there is no such divergence in a crystalline approximant, a phase whose composition is close to that of the quasicrystal and whose unit cell has atomic decorations (that is, icosahedral clusters of atoms) that look like the quasicrystal. These results clearly indicate that the quantum criticality is associated with the unique electronic state of the quasicrystal, that is, a spatially confined critical state. Finally we discuss the possibility that there is a general law underlying the conventional crystals and the quasicrystals. PMID:23042414
Computer Simulated Growth of Icosahedral Glass
NASA Astrophysics Data System (ADS)
Leino, Y. A. J.; Salomaa, M. M.
One possible model for materials displaying classically forbidden symmetry properties (apart from perfect quasicrystals) is the icosahedral glass model. We simulate the random growth of two types of two-dimensional icosahedral glasses consisting of the Penrose tiles, First we restrict the growth with the arrow rules, then we let the structure develop totally freely. The diffraction patterns have a clear five-fold symmetry in both cases. The diffraction peak intensities do not differ, but shapes of the central peaks vary depending on whether the arrow rules are imposed or not. Finally, we show that the half-width of the central peak decreases when the size of the simulation increases until a finite disorder-limited value is achieved. This phenomenon is in agreement with the behaviour of physical quasicrystallites and in contradiction with perfect mathematical quasicrystals which have Bragg peaks of zero width.
Atomic dynamics and interatomic interaction in quasicrystals
Parshin, P. P.; Zemlyanov, M. G.; Brand, R. A.
The previous experimental data on the partial spectra of thermal atomic vibrations in icosahedral (Al{sub 62}Cu{sub 25.5}Fe{sub 12.5}) and decagonal (Al{sub 71.3}Ni{sub 24}Fe{sub 4.7}) quasicrystals have been used to perform a comparative analysis of the atomic dynamics features and determine the role that Al, Cu, Ni, and Fe atoms play in the formation of interatomic interaction in the alloys studied. A physical model of the decagonal quasicrystal structure is proposed.
Multiple scattering of light in three-dimensional photonic quasicrystals.
Ledermann, Alexandra; Wiersma, Diederik S; Wegener, Martin; von Freymann, Georg
Recent experiments on three-dimensional icosahedral dielectric photonic quasicrystals have shown several unexpected features: transmitted femtosecond pulses developed a trailing "diffusive" exponential tail and the sum of (zeroth-order) transmittance and reflectance was well below unity. These experimental findings have previously been ascribed to sample imperfections. Here, we analyze these findings by using 3D periodic approximants of the ideal photonic quasicrystals. We show that the experimental observations can be explained in terms of multiple scattering of light within these structures, i.e., in terms of intrinsic rather than purely extrinsic quasicrystal properties. PMID:19189014
Magnetism of Al-Mn quasicrystals
Liu, F.; Khanna, S.N.; Magaud, L.; Jena, P. ); de Coulon, V.; Reuse, F. ); Jaswal, S.S.; He, X. ); Cyrot-Lackman, F. )
The effect of symmetry and concentration of Mn on the magnetism of Al-Mn quasicrystals has been investigated through self-consistent density-functional calculations using molecular clusters and supercell band-structure schemes. A single Mn atom surrounded by 54 Al atoms in an icosahedral or a cuboctahedral structure is found to be nonmagnetic. However, as the Mn concentration is increased, moments develop on Mn sites whose magnitude and coupling depend on their location.
Local growth of icosahedral quasicrystalline tilings
NASA Astrophysics Data System (ADS)
Hann, Connor T.; Socolar, Joshua E. S.; Steinhardt, Paul J.
Icosahedral quasicrystals (IQCs) with extremely high degrees of translational order have been produced in the laboratory and found in naturally occurring minerals, yet questions remain about how IQCs form. In particular, the fundamental question of how locally determined additions to a growing cluster can lead to the intricate long-range correlations in IQCs remains open. In answer to this question, we have developed an algorithm that is capable of producing a perfectly ordered IQC yet relies exclusively on local rules for sequential, face-to-face addition of tiles to a cluster. When the algorithm is seeded with a special type of cluster containing a defect, we find that growth is forced to infinity with high probability and that the resultant IQC has a vanishing density of defects. The geometric features underlying this algorithm can inform analyses of experimental systems and numerical models that generate highly ordered quasicrystals.
Direct observation of solid-state reversed transformation from crystals to quasicrystals in a Mg alloy
NASA Astrophysics Data System (ADS)
Liu, Jian-Fang; Yang, Zhi-Qing; Ye, Heng-Qiang
Phase transformation of quasicrystals is of interest in various fields of science and technology. Interestingly, we directly observed unexpected solid-state epitaxial nucleation and growth of Zn6Mg3Y icosahedral quasicrystals in a Mg alloy at about 573 K which is about 300 K below the melting point of Zn6Mg3Y, in contrast to formation of quasicrystals through solidification that was usually found in many alloys. Maximizing local packing density of atoms associated with segregation of Y and Zn in Mg adjacent to Mg/Zn3MgY interfaces triggered atomic rearrangement in Mg to form icosahedra coupled epitaxially with surface distorted icosahedra of Zn3MgY, which plays a critical role in the nucleation of icosahedral clusters. A local Zn:Mg:Y ratio close to 6:3:1, corresponding to a valence electron concentration of about 2.15, should have been reached to trigger the formation of quasicrystals at Mg/Zn3MgY interfaces. The solid-state icosahedral ordering in crystals opens a new window for growing quasicrystals and understanding their atomic origin mechanisms. Epitaxial growth of quasicrystals onto crystals can modify the surface/interface structures and properties of crystalline materials.
Direct observation of solid-state reversed transformation from crystals to quasicrystals in a Mg alloy
Liu, Jian-Fang; Yang, Zhi-Qing; Ye, Heng-Qiang
Phase transformation of quasicrystals is of interest in various fields of science and technology. Interestingly, we directly observed unexpected solid-state epitaxial nucleation and growth of Zn 6 Mg 3 Y icosahedral quasicrystals in a Mg alloy at about 573 K which is about 300 K below the melting point of Zn 6 Mg 3 Y, in contrast to formation of quasicrystals through solidification that was usually found in many alloys. Maximizing local packing density of atoms associated with segregation of Y and Zn in Mg adjacent to Mg/Zn 3 MgY interfaces triggered atomic rearrangement in Mg to form icosahedra coupled epitaxially with surface distorted icosahedra of Zn 3 MgY, which plays a critical role in the nucleation of icosahedral clusters. A local Zn:Mg:Y ratio close to 6:3:1, corresponding to a valence electron concentration of about 2.15, should have been reached to trigger the formation of quasicrystals at Mg/Zn 3 MgY interfaces. The solid-state icosahedral ordering in crystals opens a new window for growing quasicrystals and understanding their atomic origin mechanisms. Epitaxial growth of quasicrystals onto crystals can modify the surface/interface structures and properties of crystalline materials. PMID:26066096
Direct observation of solid-state reversed transformation from crystals to quasicrystals in a Mg alloy.
Liu, Jian-Fang; Yang, Zhi-Qing; Ye, Heng-Qiang
Phase transformation of quasicrystals is of interest in various fields of science and technology. Interestingly, we directly observed unexpected solid-state epitaxial nucleation and growth of Zn6Mg3Y icosahedral quasicrystals in a Mg alloy at about 573 K which is about 300 K below the melting point of Zn6Mg3Y, in contrast to formation of quasicrystals through solidification that was usually found in many alloys. Maximizing local packing density of atoms associated with segregation of Y and Zn in Mg adjacent to Mg/Zn3MgY interfaces triggered atomic rearrangement in Mg to form icosahedra coupled epitaxially with surface distorted icosahedra of Zn3MgY, which plays a critical role in the nucleation of icosahedral clusters. A local Zn:Mg:Y ratio close to 6:3:1, corresponding to a valence electron concentration of about 2.15, should have been reached to trigger the formation of quasicrystals at Mg/Zn3MgY interfaces. The solid-state icosahedral ordering in crystals opens a new window for growing quasicrystals and understanding their atomic origin mechanisms. Epitaxial growth of quasicrystals onto crystals can modify the surface/interface structures and properties of crystalline materials. PMID:26066096
NASA Astrophysics Data System (ADS)
Samavat, F.; Kiani, M.
Quasicrystals (QCs) are aperiodic intermetallic alloys that possess a long range positional order. They often exhibit crystallographically forbidden symmetries, most commonly fivefold and tenfold. The forbidden symmetry is related to the fact that the atoms are arranged quasiperiodically. Quasiperiodic translational order has physical consequences. For example, since electrons and phonons in quasicrystals do not encounter a periodic potential, quasicrystals have unusual resistive and elastic properties, and these have been exploited in several applications. The purpose of this introduction is to present certain properties that are relevant to the surface science of quasicrystals, as a launching point for the other articles in this special issue of progress in surface science.
Entropy-driven formation of large icosahedral colloidal clusters by spherical confinement
NASA Astrophysics Data System (ADS)
de Nijs, Bart; Dussi, Simone; Smallenburg, Frank; Meeldijk, Johannes D.; Groenendijk, Dirk J.; Filion, Laura; Imhof, Arnout; van Blaaderen, Alfons; Dijkstra, Marjolein
Icosahedral symmetry, which is not compatible with truly long-range order, can be found in many systems, such as liquids, glasses, atomic clusters, quasicrystals and virus-capsids. To obtain arrangements with a high degree of icosahedral order from tens of particles or more, interparticle attractive interactions are considered to be essential. Here, we report that entropy and spherical confinement suffice for the formation of icosahedral clusters consisting of up to 100,000 particles. Specifically, by using real-space measurements on nanometre- and micrometre-sized colloids, as well as computer simulations, we show that tens of thousands of hard spheres compressed under spherical confinement spontaneously crystallize into icosahedral clusters that are entropically favoured over the bulk face-centred cubic crystal structure. Our findings provide insights into the interplay between confinement and crystallization and into how these are connected to the formation of icosahedral structures.
X-Ray and Electrostatic Levitation Undercooling Studies in Ti-Zr-Ni Quasicrystals Forming Alloys
NASA Technical Reports Server (NTRS)
Rogers, J. R.; Hyers, R. W.; Rathz, T. J.; Kelton, K. F.; Gangopadhyay, A. K.; Woo, G. L.; Hannet, L.; Krishnan, S.; Curreri, Peter A. (Technical Monitor)
The first undercooling nucleation measurements of electrostatic-levitated droplets of TiZrNi alloys that form the icosahedral quasicrystal phase (i-phase) are presented. The reduced undercooling for crystallization decreases with an increasing polytetrahedral order of the primary solidifying phase, supporting the existence of a developing icosahedral short-range order in the undercooled liquid. X-ray diffraction measurements made at the Advance Photon Source on levitated liquid droplets of these alloys at their liquidus temperatures, however, show no evidence for increased icosahedral order. This suggests that significant ordering only occurs below the melting temperature.
Synthesis and characterization of quasicrystals in an Al-Fe-W alloy
Mukhopadhyay, N.K.; Weatherly, G.C.; Embury, J.D. ); Lloyd, D.J. )
After the discovery of quasicrystals (QC) in an al-14% Mn alloy, many attempts have been made to find alloy systems which form quasicrystals. Much effort has been devoted to the study of the Al-Fe system and its modification by Cu and other elements such as Mn, Cr, Mo and Ta to improve the ease of forming icosahedral quasicrystals (IQC). Although the Al-Fe system does not form IQC, the formation of a decagonal quasicrystal (DQC) being favored, these elements promote the IQC phase. This paper considers the Al-Fe system and its modification by W and demonstrates the existence of IQC in an Al-Fe-W ternary alloy.
Studies of Nucleation and Growth, Specific Heat and Viscosity of Undercooled Melts of Quasicrystals and Polytetrahedral-Phase-Forming Alloys
NASA Technical Reports Server (NTRS)
Kelton, K. F.; Gangopadhyay, A. K.; Lee, G. W.; Hyers, R. W.; Rogers, J. R.; Robinson, M. B.; Rathz, T. J.; Krishnan, S.; Curreri, Peter A. (Technical Monitor)
The local atomic structures of undercooled liquid metals are presumed to be icosahedral; this order is incompatible with translational periodicity, constituting a barrier to the nucleation of the crystal phase. The extended atomic structure of the icosahedral quasicrystal (i-phase) is similar to that presumed in the undercooled liquid. Therefore, a comparison of the maximum undercooling in alloys that form the i-phase with those that form crystal phases provides a probe of the liquid structure.
Quasicrystals: diversity and complexity
NASA Astrophysics Data System (ADS)
Dubois, Jean-Marie; Lifshitz, Ron
Scientific presentations at ICQ11 - the 11th International Conference on Quasicrystals, which took place in Sapporo, Japan, in June 2010 - offered a variety of stimulating new experimental data and novel theoretical results. New aperiodic crystals were presented; new theoretical ideas were described; exciting experimental results were revealed; and potential applications of quasicrystals were reviewed, showing an unprecedented level of development. ICQ11 was a great success thanks to the high standard of its scientific content and to the efficiency of its organization. ICQ11 proved that quasicrystal research is sure to continue offering diverse challenges and profound insights into the complexity of matter.
Quasicrystals: Making invisible materials
NASA Astrophysics Data System (ADS)
Boriskina, Svetlana V.
All-dielectric photonic quasicrystals may act as zero-refractive-index homogeneous materials despite their lack of translational symmetry and periodicity, stretching wavelengths to infinity and offering applications in light wavefront sculpting and optical cloaking.
Crystal electric field excitations in quasicrystal approximant TbCd6 studied by inelastic neutron scattering
NASA Astrophysics Data System (ADS)
Das, Pinaki; Flint, R.; Kong, T.; Canfield, P. C.; Kreyssig, A.; Goldman, A. I.; de Boissieu, M.; Lory, P.-F.; Beutier, G.; Hiroto, T.
All of the known quasicrystals with local moments exhibit frustration and spin glass-like behavior at low temperature. The onset of the spin freezing temperature is believed to be affected by the crystal electric field (CEF) splitting of the local moments. The quasicrystal approximant TbCd6 and its related icosahedral quasicrystal phase, i-Tb-Cd, form a set of model systems to explore how magnetism evolves from a conventional lattice (approximant phase) to an aperiodic quasicrystal. Though TbCd6 shows long-range antiferromagnetic ordering (TN = 24 K), only spin glass like behavior is observed in i-Tb-Cd with a spin freezing temperature of TF = 6 K. To investigate further, we have performed inelastic neutron scattering measurements on powder samples of TbCd6 and observed two distinct CEF excitations at low energies which points to a high degeneracy of the CEF levels related to the Tb surrounding with almost icosahedral symmetry. Work at Ames Laboratory was supported by the DOE, BES, Division of Materials Sciences & Engineering, under Contract No. DE-AC02-07CH11358. This research used resources at Institut Laue-Langevin, France.
The Crystallography of Quasicrystals
NASA Astrophysics Data System (ADS)
Rabson, David Alan
A century ago, E. S. Fedorov, A. Schonflies, and W. Barlow, working independently, classified the 230 distinct symmetry groups of objects repeated periodically in three-dimensional space. The 230 space groups determine the symmetries of macroscopic properties and provide crystallographers with their most important tool in deducing structure; as such, they find use in biology, organic chemistry, and virology as well as in physics, geology, and materials science. With the discovery in 1984 of quasicrystals, well-ordered but aperiodic metallic alloys with crystallographically forbidden rotational symmetries, the need arose to develop a space-group theory for these new materials. Based on the work by Rokhsar, Wright, and Mermin^1 in two dimensions, Rabson, Mermin, Rokhsar, and Wright have classified all quasicrystal and crystal three -dimensional axial space groups.^2 Our classification, proceeding in reciprocal space, is elementary, does not rely on projecting higher-dimensional crystallographic space groups, and is valid for arbitrary rotational symmetry. As an additional illustration of quasicrystallographic space groups, I derive and demonstrate algorithms that produce two-dimensional tilings of rhombi with each of the possible plane-group symmetries.^3 While the analogous task for crystallographic plane groups is trivial, the lack of translational symmetry in a quasicrystal tiling makes these constructions interesting. Since the symmetry of a quasicrystal appears more naturally in reciprocal than in direct space, it is not surprising that some of the resulting tilings seem intricate, although in fact their symmetries are quite simple. ftn^1 Acta Cryst. A44, 197-211 (1988). ^2 "The Space Groups of Axial Crystals and Quasicrystals," preprint. ^3See also Rabson, Ho, and Mermin, Acta Cryst. A44, 678 (1988) and Acta Cryst. A45, 538 (1989).
Optics of photonic quasicrystals
NASA Astrophysics Data System (ADS)
Vardeny, Z. Valy; Nahata, Ajay; Agrawal, Amit
The physics of periodic systems are of fundamental importance and result in various phenomena that govern wave transport and interference. However, deviations from periodicity may result in higher complexity and give rise to a number of surprising effects. One such deviation can be found in the field of optics in the realization of photonic quasicrystals, a class of structures made from building blocks that are arranged using well-designed patterns but lack translational symmetry. Nevertheless, these structures, which lie between periodic and disordered structures, still show sharp diffraction patterns that confirm the existence of wave interference resulting from their long-range order. In this Review, we discuss the beautiful physics unravelled in photonic quasicrystals of one, two and three dimensions, and describe how they can influence optical transmission and reflectivity, photoluminescence, light transport, plasmonics and laser action.
Crystallography of icosahedral crystals
NASA Astrophysics Data System (ADS)
Bak, P.
The crystallography of icosahedral crystals is constructed. The actual three-dimensional crystal is represented by a three-dimensional cut in a regular six-dimensional periodic crystal with symmetry described by a six-dimensional space group, and the positions of atoms correspond to an arrangement of hypersurface segments. The resulting crystal cannot in general be viewed as a space-filling arrangemment of a small number of different Penrose tiles. The intensities of Bragg spots are given directly as the intensities of Bragg spots of the six-dimensional crystal.
Quasicrystals and Instabilities of the Two-Dimensional Wigner Crystal.
NASA Astrophysics Data System (ADS)
Cockayne, Eric James
This work concerns two unrelated topics: quasicrystals and the two-dimensional Wigner crystal. Despite a great deal of effort since the discovery of quasicrystals in 1984 determine their atomic structures, it remains an only partially solved problem. One approach to solving the quasicrystal structure problem is to determine the structure of a finite-unit cell crystalline approximant whose structure is related to that of the quasicrystal. The structure of the approximant can be refined with respect to experimental diffraction data. This approach is developed here and then applied to the case of icosahedral AlCuFe, where large single-grain X-ray and neutron diffraction data sets are used in comparing several different models for the structure. A geometry problem that is also of interest in quasicrystallography is the problem: given a sphere radius and a desired quasiperiodic point group, how can one pack these spheres without overlap so as to achieve the highest packing fraction? A technique is, the "pinwheel construction" is given in detail that can increase the packing fraction of certain dodecagonal, octagonal and icosahedral sphere packings over those based on the "cut and project" method that use simpler shapes for the projection window. The ground state of the two-dimensional electron system is a fundamental and difficult problem in physics. Of interest is the transition between the "Wigner crystal" and fluid states and the magnetic state of the crystal. This system is first investigated in the semiclassical limit where the energies of point defects are calculated. These point defects could play a role in the melting transition, although the critical density calculated here is not in agreement with published estimates of the critical density. Then the quantum electron system is considered. Trial wavefunctions for the ground state are used that are linear superpositions of "multigaussians", where a multigaussian is a Slater determinant of gaussian one
Shock synthesis of quasicrystals with implications for their origin in asteroid collisions
NASA Astrophysics Data System (ADS)
Asimow, Paul D.; Lin, Chaney; Bindi, Luca; Ma, Chi; Tschauner, Oliver; Hollister, Lincoln S.; Steinhardt, Paul J.
We designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg0.75Fe2+0.25)2SiO4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al68–73Fe11–16Cu10–12Cr1–4Ni1–2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystal in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors.
Shock synthesis of quasicrystals with implications for their origin in asteroid collisions.
Asimow, Paul D; Lin, Chaney; Bindi, Luca; Ma, Chi; Tschauner, Oliver; Hollister, Lincoln S; Steinhardt, Paul J
We designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg0.75Fe(2+) 0.25)2SiO4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al68-73Fe11-16Cu10-12Cr1-4Ni1-2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystal in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors. PMID:27298357
Single crystal growth of Al-based intermetallic phases being approximants to quasicrystals
NASA Astrophysics Data System (ADS)
Gille, Peter; Bauer, Birgitta; Hahne, Michael; Smontara, Ana; Dolinšek, Janez
Decagonal (d) quasicrystals are formed in a number of Al-based ternary systems with d-AlCoNi being the best studied decagonal phase. They are highly anisotropic showing unusual properties of e.g. electric and thermal transport when measured along the periodic or quasiperiodic directions. For a long time, this has been attributed to the lack of periodicity in certain crystallographic orientations. Some neighbouring phases in the Al-Co-Ni system as well as in related ternaries consist of the same type of large icosahedral clusters, but are periodic in all three directions, sometimes with very large unit cells. Therefore, they are called approximants to the decagonal quasicrystals. They allow comparative studies of these phases as to judge whether some unusual properties of quasicrystals arise from the lack of periodicity or from the common atomic arrangements. Additional to decagonal AlCoNi quasicrystals, various approximants (monoclinic Al13(Co,Ni)4, orthorhombic Al13Co4, orthorhombic Al4(Cr,Fe), monoclinic Al13Fe4 and its ternary extensions Al13(Fe,Cr)4 and Al13(Fe,Ni)4) were grown by the Czochralski method as large single crystals as to carry out transport orientation-dependent measurements. It could be found that transport properties show remarkably similar anisotropic features when comparing corresponding crystallographic directions in these phases that can be related to the periodic stacking of layers.
NMR and NQR study of the thermodynamically stable quasicrystals
Shastri, A.
{sup 27}Al and {sup 61,65}Cu NMR measurements are reported for powder samples of stable AlCuFe and AlCuRu icosahedral quasicrystals and their crystalline approximants, and for a AlPdMn single grain quasicrystal. Furthermore, {sup 27}Al NQR spectra at 4.2 K have been observed in the AlCuFe and AlCuRu samples. From the quadrupole perturbed NMR spectra at different magnetic fields, and from the zero field NQR spectra, a wide distribution of local electric field gradient (EFG) tensor components and principal axis system orientations was found at the Al site. A model EFG calculation based on a 1/1 AlCuFe approximant was successful in explaining the observed NQR spectra. It is concluded that the average local gradient is largely determined by the p-electron wave function at the Al site, while the width of the distribution is due to the lattice contribution to the EFG. Comparison of {sup 63}Cu NMR with {sup 27}Al NMR shows that the EFG distribution at the two sites is similar, but that the electronic contribution to the EFG is considerably smaller at the Cu site, in agreement with a more s-type wave function of the conduction electrons.
Evidence for the extraterrestrial origin of a natural quasicrystal
Bindi, Luca; Eiler, John M.; Guan, Yunbin; Hollister, Lincoln S.; MacPherson, Glenn; Steinhardt, Paul J.; Yao, Nan
We present evidence that a rock sample found in the Koryak Mountains in Russia and containing icosahedrite, an icosahedral quasicrystalline phase with composition Al63Cu24Fe13, is part of a meteorite, likely formed in the early solar system about 4.5 Gya. The quasicrystal grains are intergrown with diopside, forsterite, stishovite, and additional metallic phases [khatyrkite (CuAl2), cupalite (CuAl), and β-phase (AlCuFe)]. This assemblage, in turn, is enclosed in a white rind consisting of diopside, hedenbergite, spinel (MgAl2O4), nepheline, and forsterite. Particularly notable is a grain of stishovite (from the interior), a tetragonal polymorph of silica that only occurs at ultrahigh pressures (≥10 Gpa), that contains an inclusion of quasicrystal. An extraterrestrial origin is inferred from secondary ion mass spectrometry 18O/16O and 17O/16O measurements of the pyroxene and olivine intergrown with the metal that show them to have isotopic compositions unlike any terrestrial minerals and instead overlap those of anhydrous phases in carbonaceous chondrite meteorites. The spinel from the white rind has an isotopic composition suggesting that it was part of a calcium-aluminum-rich inclusion similar to those found in CV3 chondrites. The mechanism that produced this exotic assemblage is not yet understood. The assemblage (metallic copper-aluminum alloy) is extremely reduced, and the close association of aluminum (high temperature refractory lithophile) with copper (low temperature chalcophile) is unexpected. Nevertheless, our evidence indicates that quasicrystals can form naturally under astrophysical conditions and remain stable over cosmic timescales, giving unique insights on their existence in nature and stability. PMID:22215583
Evidence for the extraterrestrial origin of a natural quasicrystal.
Bindi, Luca; Eiler, John M; Guan, Yunbin; Hollister, Lincoln S; MacPherson, Glenn; Steinhardt, Paul J; Yao, Nan
We present evidence that a rock sample found in the Koryak Mountains in Russia and containing icosahedrite, an icosahedral quasicrystalline phase with composition Al(63)Cu(24)Fe(13), is part of a meteorite, likely formed in the early solar system about 4.5 Gya. The quasicrystal grains are intergrown with diopside, forsterite, stishovite, and additional metallic phases [khatyrkite (CuAl(2)), cupalite (CuAl), and β-phase (AlCuFe)]. This assemblage, in turn, is enclosed in a white rind consisting of diopside, hedenbergite, spinel (MgAl(2)O(4)), nepheline, and forsterite. Particularly notable is a grain of stishovite (from the interior), a tetragonal polymorph of silica that only occurs at ultrahigh pressures (≥ 10 Gpa), that contains an inclusion of quasicrystal. An extraterrestrial origin is inferred from secondary ion mass spectrometry (18)O/(16)O and (17)O/(16)O measurements of the pyroxene and olivine intergrown with the metal that show them to have isotopic compositions unlike any terrestrial minerals and instead overlap those of anhydrous phases in carbonaceous chondrite meteorites. The spinel from the white rind has an isotopic composition suggesting that it was part of a calcium-aluminum-rich inclusion similar to those found in CV3 chondrites. The mechanism that produced this exotic assemblage is not yet understood. The assemblage (metallic copper-aluminum alloy) is extremely reduced, and the close association of aluminum (high temperature refractory lithophile) with copper (low temperature chalcophile) is unexpected. Nevertheless, our evidence indicates that quasicrystals can form naturally under astrophysical conditions and remain stable over cosmic timescales, giving unique insights on their existence in nature and stability. PMID:22215583
Natural quasicrystal with decagonal symmetry
Bindi, Luca; Yao, Nan; Lin, Chaney; Hollister, Lincoln S.; Andronicos, Christopher L.; Distler, Vadim V.; Eddy, Michael P.; Kostin, Alexander; Kryachko, Valery; MacPherson, Glenn J.; Steinhardt, William M.; Yudovskaya, Marina; Steinhardt, Paul J.
We report the first occurrence of a natural quasicrystal with decagonal symmetry. The quasicrystal, with composition Al71Ni24Fe5, was discovered in the Khatyrka meteorite, a recently described CV3 carbonaceous chondrite. Icosahedrite, Al63Cu24Fe13, the first natural quasicrystal to be identified, was found in the same meteorite. The new quasicrystal was found associated with steinhardtite (Al38Ni32Fe30), Fe-poor steinhardtite (Al50Ni40Fe10), Al-bearing trevorite (NiFe2O4) and Al-bearing taenite (FeNi). Laboratory studies of decagonal Al71Ni24Fe5 have shown that it is stable over a narrow range of temperatures, 1120 K to 1200 K at standard pressure, providing support for our earlier conclusion that the Khatyrka meteorite reached heterogeneous high temperatures [1100 < T(K) ≤ 1500] and then rapidly cooled after being heated during an impact-induced shock that occurred in outer space 4.5 Gya. The occurrences of metallic Al alloyed with Cu, Ni, and Fe raises new questions regarding conditions that can be achieved in the early solar nebula. PMID:25765857
Natural quasicrystal with decagonal symmetry.
Bindi, Luca; Yao, Nan; Lin, Chaney; Hollister, Lincoln S; Andronicos, Christopher L; Distler, Vadim V; Eddy, Michael P; Kostin, Alexander; Kryachko, Valery; MacPherson, Glenn J; Steinhardt, William M; Yudovskaya, Marina; Steinhardt, Paul J
We report the first occurrence of a natural quasicrystal with decagonal symmetry. The quasicrystal, with composition Al71Ni24Fe5, was discovered in the Khatyrka meteorite, a recently described CV3 carbonaceous chondrite. Icosahedrite, Al63Cu24Fe13, the first natural quasicrystal to be identified, was found in the same meteorite. The new quasicrystal was found associated with steinhardtite (Al38Ni32Fe30), Fe-poor steinhardtite (Al50Ni40Fe10), Al-bearing trevorite (NiFe2O4) and Al-bearing taenite (FeNi). Laboratory studies of decagonal Al71Ni24Fe5 have shown that it is stable over a narrow range of temperatures, 1120 K to 1200 K at standard pressure, providing support for our earlier conclusion that the Khatyrka meteorite reached heterogeneous high temperatures [1100 < T(K) ≤ 1500] and then rapidly cooled after being heated during an impact-induced shock that occurred in outer space 4.5 Gya. The occurrences of metallic Al alloyed with Cu, Ni, and Fe raises new questions regarding conditions that can be achieved in the early solar nebula. PMID:25765857
Pressure-Driven Quantum Criticality and T/H Scaling in the Icosahedral Au-Al-Yb Approximant
NASA Astrophysics Data System (ADS)
Matsukawa, Shuya; Deguchi, Kazuhiko; Imura, Keiichiro; Ishimasa, Tsutomu; Sato, Noriaki K.
We report on ac magnetic susceptibility measurements under pressure of the Au-Al-Yb alloy, a crystalline approximant to the icosahedral quasicrystal that shows unconventional quantum criticality. In describing the susceptibility as χ(T)-1 - χ(0)-1 ∝ Tγ, we find that χ(0)-1 decreases with increasing pressure and vanishes to zero at the critical pressure P{c} ≃ 2 GPa, with γ ( ≃ 0.5) unchanged. We suggest that this quantum criticality emerges owing to critical valence fluctuations. Above Pc, the approximant undergoes a magnetic transition at T ≃ 100 mK. These results are contrasted with the fact that, in the quasicrystal, the quantum criticality is robust against the application of pressure. The applicability of the so-called T/H scaling to the approximant is also discussed.
Formation ranges of icosahedral, amorphous and crystalline phases in rapidly solidified Ti-Zr-Hf-Ni alloys
Chen, N. . E-mail: email@example.com; Louzguine, D.V.; Ranganathan, S.; Inoue, A.
From the quaternary Ti-Zr-Hf-Ni phase diagram, the cross-section at 20 at.% Ni was selected for investigation. The icosahedral quasicrystalline, crystalline and amorphous phases were observed to form in nine kinds of rapidly solidified (Ti{sub x}Zr{sub y}Hf{sub z}){sub 80}Ni{sub 20} (x + y + z = 1) alloys at different compositions. The quasilattice constants of 0.519 and 0.531 nm were obtained for the icosahedral phase formed in the melt-spun Ti{sub 40}Zr{sub 20}Hf{sub 20}Ni{sub 20} and Ti{sub 20}Zr{sub 40}Hf{sub 20}Ni{sub 20} alloys, respectively. The icosahedral phase formed in the melt-spun Ti{sub 40}Zr{sub 20}Hf{sub 20}Ni{sub 20} alloy especially is thermodynamically stable. The supercooled liquid region of the Ti{sub 20}Zr{sub 20}Hf{sub 40}Ni{sub 20} glassy alloy reached 64 K. From these results a comparison of quasicrystal-forming and glass-forming abilities was carried out. The quasicrystal-forming ability was reduced and glass-forming ability was improved with an increase in Hf and Zr contents in the (Ti{sub x}Zr{sub y}Hf{sub z}){sub 80}Ni{sub 20} alloys. On the other hand, an increase in Ti content caused an improvement in quasicrystal-forming ability.
Subcellular neuronal quasicrystals: Implications for consciousness
Gardiner, John
Neuron neurotransmitter receptors are in general pentameric. This enables them to form pentagonal components in biological quasicrystals (similar to mathematical aperiodic tilings). As quasicrystals have been proposed to require quantum effects to exist this might introduce such effects as a component of neurotransmission and thus consciousness. Microtubules may play a role in the clustering of the receptors into quasicrystals, thus modulating their function and may even form quasicrystals themselves. Other quaiscrystals in neurons are potentially formed by water, cholera toxin complexes, and the cytoskeletal components actin and ankyrin. PMID:26478770
Subcellular neuronal quasicrystals: Implications for consciousness
Gardiner, John
Neuron neurotransmitter receptors are in general pentameric. This enables them to form pentagonal components in biological quasicrystals (similar to mathematical aperiodic tilings). As quasicrystals have been proposed to require quantum effects to exist this might introduce such effects as a component of neurotransmission and thus consciousness. Microtubules may play a role in the clustering of the receptors into quasicrystals, thus modulating their function and may even form quasicrystals themselves. Other quaiscrystals in neurons are potentially formed by water, cholera toxin complexes, and the cytoskeletal components actin and ankyrin. PMID:26629259
Atomic structure of the i-R -Cd quasicrystals and consequences for magnetism
NASA Astrophysics Data System (ADS)
Yamada, T.; Takakura, H.; Kong, T.; Das, P.; Jayasekara, W. T.; Kreyssig, A.; Beutier, G.; Canfield, P. C.; de Boissieu, M.; Goldman, A. I.
We report on the six-dimensional (6D) structural refinement of three members of the i-R -Cd quasicrystals (R = Gd, Dy, Tm) via synchrotron x-ray diffraction from single-grain samples, and show that this series is isostructural to the i-YbCd5.7 quasicrystal. However, our refinements suggest that the R occupancy on the Yb icosahedron sites within the Tsai-type atomic cluster is approximately 80%, with the balance taken up by Cd. Similarities between the i-R -Cd series and i-ScZn7.33, and their differences with i-YbCd5.7 and i-Ca15Cd85 , indicate that there are at least two subclasses of Tsai-type icosahedral quasicrystals. We further show from x-ray resonant magnetic scattering (XRMS) measurements on a set of closely related Tb1 -xYxCd6 1/1 approximants that the dilution of the magnetic R ions on the icosahedron within the Tsai-type cluster by nonmagnetic Y disrupts the commensurate magnetic ordering in the approximant phase.
Mosaic two-lengthscale quasicrystals.
Dotera, T; Oshiro, T; Ziherl, P
Over the past decade, quasicrystalline order has been observed in many soft-matter systems: in dendritic micelles, in star and tetrablock terpolymer melts and in diblock copolymer and surfactant micelles. The formation of quasicrystals from such a broad range of 'soft' macromolecular micelles suggests that they assemble by a generic mechanism rather than being dependent on the specific chemistry of each system. Indeed, micellar softness has been postulated and shown to lead to quasicrystalline order. Here we theoretically explore this link by studying two-dimensional hard disks decorated with step-like square-shoulder repulsion that mimics, for example, the soft alkyl shell around the aromatic core in dendritic micelles. We find a family of quasicrystals with 10-, 12-, 18- and 24-fold bond orientational order which originate from mosaics of equilateral and isosceles triangles formed by particles arranged core-to-core and shoulder-to-shoulder. The pair interaction responsible for these phases highlights the role of local packing geometry in generating quasicrystallinity in soft matter, complementing the principles that lead to quasicrystal formation in hard tetrahedra. Based on simple interparticle potentials, quasicrystalline mosaics may well find use in diverse applications ranging from improved image reproduction to advanced photonic materials. PMID:24487618
High-Temperature NMR Studies of Quasicrystals and Polymers
NASA Astrophysics Data System (ADS)
Hill, Edward Arthur
Icosahedral alloys such as rm Al _{65}Cu_{20}Ru_ {15}, Al_{62.5}Cu_ {24.5}Fe_{13}, and rm Al_{70}Pd_{20}Re _{10} have motivated a great deal of experimental and theoretical effort to understand fundamental issues such as the electronic structure, "lattice" dynamics, and thermodynamic stability of quasicrystalline materials. It has been shown here that Nuclear Magnetic Resonance (NMR) is a useful tool for exploring many of the essential properties of quasicrystal alloys and the so-called approximant phase alloys. Specifically, the ^{27 }Al Knight shift has been used here to study the electronic density of states in these alloys up to temperatures of 1200 K. Furthermore, ^{27}Al nuclear spin-lattice and spin-spin relaxation measurements across a wide temperature range have been used to show that the dynamic processes found in quasicrystals are quite different from those found in some crystalline alloys of similar compositions. In addition, two-dimensional exchange experiments have been employed to study the dynamics of these materials. Finally, the semiconducting alloy rm Al_2Ru has also been studied by the techniques mentioned above. It has also been demonstrated here that high temperature NMR techniques are useful in the study of organic polymers. These experiments focus on determining the timescales and other aspects of molecular motion for several specific samples. ^2H NMR measurements, including the ^2H two-dimensional exchange technique, on the high temperature polymer polybenzamidazole (PBI) are described here. ^2H NMR results for high melting temperature copolyester liquid crystals of the PCnNBB family will also be discussed. An assessment of the high temperature motion in these samples is relevant to an understanding of the physical properties that influence their high temperature applications and high temperature processing.
Synthesis and Characterization of Bulk Al-Cu-Fe Based Quasicrystals and Composites by Spray Forming
NASA Astrophysics Data System (ADS)
Mukhopadhyay, N. K.; Uhlenwinkel, V.; Srivastava, V. C.
The bulk quasicrystalline (QC) materials and their composites have attracted considerable interest due to their promising mechanical properties. In the present investigation, spray forming has been used to synthesize bulk single-phase icosahedral quasicrystals and composites in Al62.5Cu25Fe12.5 system as well as in quaternary system containing 10% Sn. The elemental materials were induction melted under nitrogen cover and a billet of 250 mm in diameter and 350 mm in height was spray formed. The phase constitution of the spray-formed materials showed a bulk single-phase icosahedral quasicrystal as a major phase along with other crystalline phases. A large number of annealing twins were observed in the microstructure in ternary AlCuFe alloys. It is interesting to note that due to addition of Sn, the volume fraction of β-Al(CuFe) phase was found to increase and annealing twins were almost absent. The hardness of the single-phase AlCuFe alloy and Sn-containing composites was found to be 8.6 and 6.0 GPa, respectively, at a load of 300 g. In general, the hardness decreases with heat treatment at high temperatures. However, in case of Sn-containing alloy, hardness increases with low-temperature heat treatment. Long and hair-like cracks (Palmqvist type) are observed to form from the corner of the indentations of the ternary alloys, whereas in Sn-containing composites, the cracks are not sharp and long suggesting the enhancement of fracture toughness in the composites. Attempts have been made to understand the effect of Sn on the evolution of icosahedral phase, other crystalline phases and their composite effects on the mechanical properties.
Precipitates in a quasicrystal-strengthened Al–Mn–Be–Cu alloy
Zupanič, Franc; Wang, Di; Gspan, Cristian; Bončina, Tonica
In this work, an Al–Mn–Be–Cu alloy was studied containing a primary and eutectic icosahedral quasicrystalline phase in the as-cast microstructure. Special attention was given to a transmission electron microscopy investigation of precipitates formed within the aluminium solid solution (Al{sub ss}) at different temperatures. At 200 °C, only binary Al–Cu precipitates (θ′) were formed. At 300 °C, icosahedral quasicrystalline (IQC) precipitates prevailed with a crystallographic orientation relationship with the Al{sub ss.} The rods of the T-phase (Al{sub 20}Mn{sub 3}Cu{sub 2}) which were precipitated above 400 °C, also had a specific orientation relationship with the Al{sub ss}. The primary and eutectic IQC microstructural constituent started to transform rapidly to the T-phase and Be{sub 4}Al(Mn,Cu) at 500 °C. - Highlights: • In a quasicrystal-strengthened Al-alloy several types of precipitates can form. • At 200 °C, only binary Al–Cu precipitates formed (Al{sub 2}Cu-θ′). • The icosahedral quasicrystalline (IQC) precipitates prevailed at 300 °C. • T-phase (Al{sub 20}Mn{sub 3}Cu{sub 2}) precipitated at temperatures above 400 °C. • The precipitation of different phases did not have a strong effect on hardness.
Faceting and roughening in quasicrystals
NASA Technical Reports Server (NTRS)
Garg, Anupam; Levine, Dov
The question whether quasi-crystal shapes should be faceted is studied in a simple model of quasi-crystalline order. At T = 0, the model is proved to yield a completely faceted equilibrium shape in both two and three dimensions. At T greater than 0, an interface model is derived for a two-dimensional Penrose tiling. By mapping it onto a one-dimensional quasi-periodic Schroedinger equation, it is shown that the roughness exponent varies continuously with T at low T.
Dynamics of phason fluctuations in the i-AlPdMn quasicrystal.
Francoual, S; Livet, F; de Boissieu, M; Yakhou, F; Bley, F; Létoublon, A; Caudron, R; Gastaldi, J
We report on the study of the dynamics of long wavelength phason fluctuations in the i-AlPdMn icosahedral phase using coherent x-ray scattering. When measured with a coherent x-ray beam, the diffuse intensity due to phasons presents strong fluctuations or speckles pattern. From room temperature to 500 degrees C the speckle pattern is time independent. At 650 degrees C the time correlation of the speckle pattern exhibits an exponential time decay, from which a characteristic time tau is extracted. We find that tau is proportional to the square of the phason wavelength, which demonstrates that phasons are collective diffusive modes in quasicrystals, in agreement with theoretical predictions. PMID:14683248
Quasicrystals in Medieval Islamic Architecture
NASA Astrophysics Data System (ADS)
Lu, Peter
The conventional view holds that girih (geometric star-and-polygon) patterns in medieval Islamic architecture were conceived by their designers as a network of zigzagging lines, and drafted directly with a straightedge and a compass. I discuss our recent findings that, by 1200 A. D., a conceptual breakthrough occurred in which girih patterns were reconceived as tessellations of a special set of equilateral polygons (girih tiles) decorated with lines. These girih tiles enabled the creation of increasingly complex periodic girih patterns, and by the 15th century, the tessellation approach was combined with self-similar transformations to construct nearly-perfect quasicrystalline patterns. These patterns have remarkable properties; they do not repeat periodically, and have special symmetry---and were not understood in the West until the 1970s. I will discuss some of the properties of Islamic quasicrystalline tilings, and their relation to the Penrose tiling, perhaps the best known quasicrystal pattern.
Surface Characteristics of Quasicrystal Thin Films of AlCuFe
NASA Astrophysics Data System (ADS)
Symko, Orest G.; Abdel-Rahman, Ehab; Emmi, Matthew; Zudova, Snezhana
We have investigated the surface energy and surface structure of thin films of i-AlCuFe. Such films are important for applications and in particular for coatings. The films investigated ranged in thickness from 10 nm to 300 nm; they were deposited on various substrates such as sapphire, silicon, stainless steel, and others. The surface energy was determined by contact angle measurements using the drop method. Results show contact angles comparable to Teflon. Studies were extended to the surface structure using an Atomic Force Microscope at ambient conditions. Images show extremely smooth surfaces which at certain locations provide evidence for the icosahedral symmetries of the quasicrystal. Such images were enhanced by auto-correlation techniques thus revealing more clearly the symmetries at the surface of the films. Other techniques such as x-ray diffraction, TEM, XPS and ToF-SIMS were used to determine the quality of the quasicrystal films and the nature of the surface. This characterization is essential for biomedical applications of our QC coatings.
Observation of topological phase transitions in photonic quasicrystals.
Verbin, Mor; Zilberberg, Oded; Kraus, Yaacov E; Lahini, Yoav; Silberberg, Yaron
Topological insulators and topological superconductors are distinguished by their bulk phase transitions and gapless states at a sharp boundary with the vacuum. Quasicrystals have recently been found to be topologically nontrivial. In quasicrystals, the bulk phase transitions occur in the same manner as standard topological materials, but their boundary phenomena are more subtle. In this Letter we directly observe bulk phase transitions, using photonic quasicrystals, by constructing a smooth boundary between topologically distinct one-dimensional quasicrystals. Moreover, we use the same method to experimentally confirm the topological equivalence between the Harper and Fibonacci quasicrystals. PMID:25166388
Generalized dynamics of moving dislocations in quasicrystals
NASA Astrophysics Data System (ADS)
Agiasofitou, Eleni; Lazar, Markus; Kirchner, Helmut
A theoretical framework for dislocation dynamics in quasicrystals is provided according to the continuum theory of dislocations. Firstly, we present the fundamental theory for moving dislocations in quasicrystals giving the dislocation density tensors and introducing the dislocation current tensors for the phonon and phason fields, including the Bianchi identities. Next, we give the equations of motion for the incompatible elastodynamics as well as for the incompatible elasto-hydrodynamics of quasicrystals. We continue with the derivation of the balance law of pseudomomentum thereby obtaining the generalized forms of the Eshelby stress tensor, the pseudomomentum vector, the dynamical Peach-Koehler force density and the Cherepanov force density for quasicrystals. The form of the dynamical Peach-Koehler force for a straight dislocation is obtained as well. Moreover, we deduce the balance law of energy that gives rise to the generalized forms of the field intensity vector and the elastic power density of quasicrystals. The above balance laws are produced for both models. The differences between the two models and their consequences are revealed. The influences of the phason fields as well as of the dynamical terms are also discussed.
Generalized dynamics of moving dislocations in quasicrystals.
Agiasofitou, Eleni; Lazar, Markus; Kirchner, Helmut
A theoretical framework for dislocation dynamics in quasicrystals is provided according to the continuum theory of dislocations. Firstly, we present the fundamental theory for moving dislocations in quasicrystals giving the dislocation density tensors and introducing the dislocation current tensors for the phonon and phason fields, including the Bianchi identities. Next, we give the equations of motion for the incompatible elastodynamics as well as for the incompatible elasto-hydrodynamics of quasicrystals. We continue with the derivation of the balance law of pseudomomentum thereby obtaining the generalized forms of the Eshelby stress tensor, the pseudomomentum vector, the dynamical Peach-Koehler force density and the Cherepanov force density for quasicrystals. The form of the dynamical Peach-Koehler force for a straight dislocation is obtained as well. Moreover, we deduce the balance law of energy that gives rise to the generalized forms of the field intensity vector and the elastic power density of quasicrystals. The above balance laws are produced for both models. The differences between the two models and their consequences are revealed. The influences of the phason fields as well as of the dynamical terms are also discussed. PMID:21406784
Luminescence properties of a Fibonacci photonic quasicrystal.
Passias, V; Valappil, N V; Shi, Z; Deych, L; Lisyansky, A A; Menon, V M
An active one-dimensional Fibonacci photonic quasi-crystal is realized via spin coating. Luminescence properties of an organic dye embedded in the quasi-crystal are studied experimentally and compared to theoretical simulations. The luminescence occurs via the pseudo-bandedge mode and follows the dispersion properties of the Fibonacci crystal. Time resolved luminescence measurement of the active structure shows faster spontaneous emission rate, indicating the effect of the large photon densities available at the bandedge due to the presence of critically localized states. The experimental results are in good agreement with the theoretical calculations for steady-state luminescence spectra. PMID:19365490
Crystalline and quasicrystalline allotropes of Pb formed on the fivefold surface of icosahedral Ag-In-Yb
Sharma, H. R. Smerdon, J. A.; Nugent, P. J.; Ribeiro, A.; McGrath, R.; McLeod, I.; Dhanak, V. R.; Shimoda, M.; Tsai, A. P.
Crystalline and quasicrystalline allotropes of Pb are formed by evaporation on the fivefold surface of the icosahedral (i) Ag-In-Yb quasicrystal under ultra-high vacuum. Lead grows in three dimensional quasicrystalline order and subsequently forms fivefold-twinned islands with the fcc(111) surface orientation atop of the quasicrystalline Pb. The islands exhibit specific heights (magic heights), possibly due to the confinement of electrons in the islands. We also study the adsorption behavior of C{sub 60} on the two allotropes of Pb. Scanning tunneling microcopy reveals that a high corrugation of the quasicrystalline Pb limits the diffusion of the C{sub 60} molecules and thus produces a disordered film, similar to adsorption behavior of the same molecules on the clean substrate surface. However, the sticking coefficient of C{sub 60} molecules atop the Pb islands approaches zero, regardless of the overall C{sub 60} coverage.
Surfaces of Intermetallics: Quasicrystals and Beyond
Yuen, Chad
The goal of this work is to characterize surfaces of intermetallics, including quasicrystals. In this work, surface characterization is primarily focused on composition and structure using X-ray photoelectron spectroscopy (XPS) and scanning tunneling microscopy (STM) performed under ultrahigh vacuum (UHV) conditions.
Omnidirectional reflection from generalized Fibonacci quasicrystals.
Barriuso, Alberto G; Monzón, Juan J; Yonte, Teresa; Felipe, Angel; Sánchez-Soto, Luis L
We determine the optimal thicknesses for which omnidirectional reflection from generalized Fibonacci quasicrystals occurs. By capitalizing on the idea of wavelength- and angle-averaged reflectance, we assess in a consistent way the performance of the different systems. Our results indicate that some of these aperiodic arrangements can largely over-perform the conventional photonic crystals as omnidirectional reflection is concerned. PMID:24514554
Two-Band Fibonacci Quasicrystal with Hybridization:. Exact Local GREEN'S Function Using the Renormalization-Group Method
NASA Astrophysics Data System (ADS)
Chakrabarti, A.; Karmakar, S. N.; Moitra, R. K.
In this paper we present a study of the electronic properties of a one-dimensional Fibonacci chain with two hybridizing bands. Our study is motivated by recent experiments with quasicrystals in which transition metal atoms occupy positions of icosahedral symmetry. Using a recently proposed real space renormalization group scheme we make an exact analytical study of the two-band problem. We examine the effect of hybridization on the energy spectrum, the wave functions and the density of states of the Fibonacci chain. We find that the spectrum continues to remain a Cantor set even in the presence of hybridization. We conclude therefore this property of the spectrum is a purely structural effect. We present our results on the electronic density of states and show how hybridization produces additional structures in the energy spectrum.
Theoretical study on icosahedral water clusters
NASA Astrophysics Data System (ADS)
Loboda, Oleksandr; Goncharuk, Vladyslav
Here we present a structural study of different gas hydrates using the B3LYP hybrid DFT exchange-correlation functional. A new concept for viewing the icosahedral cluster as an expansion of dodecahedral subclusters is introduced. The investigated structures consist of 280 water molecules. Structural and orientational features of various guest molecules occupying the central cavity of the clusters are established. It was found that water as the guest molecule has the highest stabilization energy in studied clusters. The conformational changes in dimer and trimer water molecules upon incorporation into hydrate cavity are discussed. The influence of second- and third-order solvent shells is illustrated on example of icosahedral water cluster derivatives.
Icosahedral inclusions (carboxysomes) of Nitrobacter agilis.
Shively, J M; Bock, E; Westphal, K; Cannon, G C
The icosahedral bodies of Nitrobacter agilis are about 120 nm in diameter and, as viewed by electron microscopy, consist of an outer shell enclosing 10-nm particles. The inner 10-nm particle is the enzyme D-ribulose 1,5-bisphosphate carboxylase. The bodies isolated from cells incubated 1 month without nitrite had a specific activity for the enzyme of 0.54 mu mol of CO2 fixed per min per mg of protein. Images PMID:199579
DNA Cages with Icosahedral Symmetry in Bionanotechnology
NASA Astrophysics Data System (ADS)
Jonoska, Nataša; Taormina, Anne; Twarock, Reidun
Blueprints for polyhedral cages with icosahedral symmetry made of circular DNA molecules are provided. The basic rule is that every edge of the cage is met twice in opposite directions by the DNA strand(s), and vertex junctions are realized by a set of admissible junction types. As nanocontainers for cargo storage and delivery, the icosidodecahedral cages are of special interest because they have the largest volume per surface ratio of all cages discussed here.
Discussion on the surface science of quasicrystals
Thiel, P.A.
This paper contains a short review of four aspects of the surface science of quasicrystals, together with a list of challenges for the scientific community in the near future. The first issue concerns the ability of surface science to shed light on bulk atomic structure. The second is the use of surfaces as quasiperiodic templates, particularly for films of periodic metals. Here, enforcing quasiperiodicity in the film may lead to unusual magnetic, tribological or adsorption properties. The third aspect concerns the effects of surface phasons and phonons on dynamical interactions with adsorbates, such as sticking coefficient, as well as on diffusion between the surface and near-surface region. The final area is tribology, where studies of quasicrystals have suggested that both adhesion and phononic friction may be important.
Eighteenth-century forms of quasicrystals.
Pina, Carlos M; López-Acevedo, Victoria
A careful inspection of the drawings and baked clay models created by the mineralogist Romé de L'Isle in the 18th century has revealed the existence of a number of intriguing forms with pentagonal symmetries. These forms cannot be classified in any of the 32 crystal classes. They can thus be considered the first crystallographic descriptions of polyhedral forms found in quasicrystals two centuries later. This paper presents a symmetry analysis of the fascinating drawings and clay models with pentagonal symmetries described in the book Cristallographie published in 1783 by Romé de L'Isle, as well as a comparison with quasicrystals recently synthesized. The paper also briefly discusses what could induce Romé de L'Isle to consider forms with pentagonal symmetries as plausible crystal forms. PMID:26697870
Fibonacci, quasicrystals and the beauty of flowers
Gardiner, John
The appearance of Fibonacci sequences and the golden ratio in plant structures is one of the great outstanding puzzles of biology. Here I suggest that quasicrystals, which naturally pack in the golden ratio, may be ubiquitous in biological systems and introduce the golden ratio into plant phyllotaxy. The appearance of golden ratio-based structures as beautiful indicates that the golden ratio may play a role in the development of consciousness and lead to the aesthetic natural selection of flowering plants. PMID:23072998
Photonic quasi-crystal terahertz lasers
Vitiello, Miriam Serena; Nobile, Michele; Ronzani, Alberto; Tredicucci, Alessandro; Castellano, Fabrizio; Talora, Valerio; Li, Lianhe; Linfield, Edmund H.; Davies, A. Giles
Quasi-crystal structures do not present a full spatial periodicity but are nevertheless constructed starting from deterministic generation rules. When made of different dielectric materials, they often possess fascinating optical properties, which lie between those of periodic photonic crystals and those of a random arrangement of scatterers. Indeed, they can support extended band-like states with pseudogaps in the energy spectrum, but lacking translational invariance, they also intrinsically feature a pattern of 'defects', which can give rise to critically localized modes confined in space, similar to Anderson modes in random structures. If used as laser resonators, photonic quasi-crystals open up design possibilities that are simply not possible in a conventional periodic photonic crystal. In this letter, we exploit the concept of a 2D photonic quasi crystal in an electrically injected laser; specifically, we pattern the top surface of a terahertz quantum-cascade laser with a Penrose tiling of pentagonal rotational symmetry, reaching 0.1–0.2% wall-plug efficiencies and 65 mW peak output powers with characteristic surface-emitting conical beam profiles, result of the rich quasi-crystal Fourier spectrum. PMID:25523102
Levitated crystals and quasicrystals of metamaterials
Wang, Zhehui; Morris, Christopher; Goree, John A
New scientific and technological opportunities exist by marrying dusty plasma research with metamaterials. Specifically, by balancing control and self-assembly, certain laboratory plasmas can become a generic levitation platform for novel structure formation and nanomaterial synthesis. We propose to experimentally investigate two dimensional (2D) and three dimensional (3D) levitated structures of metamaterials and their properties. Such structures can self assemble in laboratory plasmas, similar to levitated dust crystals which were discovered in the mid 1990's. Laboratory plasma platform for metamaterial formation eliminates substrates upon which most metamaterials have to be supported. Three types of experiments, with similar setups, are discussed here. Levitated crystal structures of metamaterials using anisotropic microparticles are the most basic of the three. The second experiment examines whether quasicrystals of metamaterials are possible. Quasicrystals, discovered in the 1980's, possess so-called forbidden symmetries according to the conventional crystallography. The proposed experiment could answer many fundamental questions about structural, thermal and dynamical properties of quasicrystals. And finally, how to use nanoparticle coated microparticles to synthesize very long carbon nanotubes is also described. All of the experiments can fit inside a standard International Space Station locker with dimensions of 8-inch x 17-inch X 18-inch. Microgravity environment is deemed essential in particular for large 3D structures and very long carbon nanotube synthesis.
Confessions of an icosahedral virus crystallographer
Johnson, John E.
This is a personal history of my structural studies of icosahedral viruses that evolved from crystallographic studies, to hybrid methods with electron cryo-microscopy and image reconstruction (cryoEM) and then developed further by incorporating a variety of physical methods to augment the high resolution crystallographic studies. It is not meant to be comprehensive, even for my own work, but hopefully provides some perspective on the growth of our understanding of these remarkable biologic assemblies. The goal is to provide a historical perspective for those new to the field and to emphasize the limitations of any one method, even those that provide atomic resolution information about viruses. PMID:23291268
Method of making an icosahedral boride structure
Hersee, Stephen D.; Wang, Ronghua; Zubia, David; Aselage, Terrance L.; Emin, David
A method for fabricating thin films of an icosahedral boride on a silicon carbide (SiC) substrate is provided. Preferably the icosahedral boride layer is comprised of either boron phosphide (B.sub.12 P.sub.2) or boron arsenide (B.sub.12 As.sub.2). The provided method achieves improved film crystallinity and lowered impurity concentrations. In one aspect, an epitaxially grown layer of B.sub.12 P.sub.2 with a base layer or substrate of SiC is provided. In another aspect, an epitaxially grown layer of B.sub.12 As.sub.2 with a base layer or substrate of SiC is provided. In yet another aspect, thin films of B.sub.12 P.sub.2 or B.sub.12 As.sub.2 are formed on SiC using CVD or other vapor deposition means. If CVD techniques are employed, preferably the deposition temperature is above 1050.degree. C., more preferably in the range of 1100.degree. C. to 1400.degree. C., and still more preferably approximately 1150.degree. C.
Gabor frames for quasicrystals and K-theory
NASA Astrophysics Data System (ADS)
Kreisel, Michael
We study the connection between Gabor frames for quasicrystals, the topology of the hull of a quasicrystal, and the K-theory of an associated twisted groupoid algebra. In particular, we construct a finitely generated projective module over this algebra, and multiwindow Gabor frames can be used to construct an idempotent representing the module in K-theory. For lattice subsets in dimension two, this allows us to prove a twisted version of Bellissard's gap labeling theorem. By viewing Gabor frames in this operator algebraic framework, we are also able to show that for certain quasicrystals it is not possible to construct a tight multiwindow Gabor frame.
Fibonacci optical lattices for tunable quantum quasicrystals
NASA Astrophysics Data System (ADS)
Singh, K.; Saha, K.; Parameswaran, S. A.; Weld, D. M.
We describe a quasiperiodic optical lattice, created by a physical realization of the abstract cut-and-project construction underlying all quasicrystals. The resulting potential is a generalization of the Fibonacci tiling. Calculation of the energies and wave functions of ultracold atoms loaded into such a lattice demonstrate a multifractal energy spectrum, a singular continuous momentum-space structure, and the existence of controllable edge states. These results open the door to cold atom quantum simulation experiments in tunable or dynamic quasicrystalline potentials, including topological pumping of edge states and phasonic spectroscopy.
Preparation and wear resistance of Ti-Zr-Ni quasicrystal and polyamide composite materials
NASA Astrophysics Data System (ADS)
Wang, Xinlu; Li, Xuesong; Zhang, Zhenjiang; Zhang, Shanshan; Liu, Wanqiang; Wang, Limin
Ti-Zr-Ni icosahedral quasicrystal powders (Ti-QC), prepared by mechanical alloying and then annealing in a vacuum furnace, were used as a novel filler material in polyamide 12 (PA12). The melt processability of the composite was studied using a Haake torque rheometer. This indicates that PA12/Ti-QC composites can be melt-processed into a wear-resistant material. Further, these composites, fabricated by compression molding, were tested in sliding wear against a polished bearing steel counterface. The results from wear testing show that the addition of Ti-QC filler to PA12 enhances wear resistance and reduces volume loss by half compared with neat PA12. Furthermore, it is found that the hardness of the composite increases with increasing content of Ti-QC filler. In addition, PA12/Ti-QC composites exhibit a slightly higher crystallization temperature and better thermal stability than PA12. These combined results demonstrate that Ti-QC filler may be a desirable alternative when attempting to increase the wear resistance of PA12.
Emergent quasicrystals in strongly correlated systems
NASA Astrophysics Data System (ADS)
Sagi, Eran; Nussinov, Zohar
Commensurability is of paramount importance in numerous strongly interacting electronic systems. In the fractional quantum Hall effect, a rich cascade of increasingly narrow plateaux appear at larger denominator filling fractions. Rich commensurate structures also emerge, at certain filling fractions, in high temperature superconductors and other electronic systems. A natural question concerns the character of these and other electronic systems at irrational filling fractions. Here we demonstrate that quasicrystalline structures naturally emerge in these situations, and trigger behaviors not typically expected of periodic systems. We first show that irrationally filled quantum Hall systems cross over into quasiperiodically ordered configuration in the thin-torus limit. Using known properties of quasicrystals, we argue that these states are unstable against the effects of disorder, in agreement with the existence of quantum Hall plateaux. We then study analogous physical situations in a system of cold Rydberg atoms placed on an optical lattice. Such an experimental setup is generally disorder free, and can therefore be used to detect the emergent quasicrystals we predict. We discuss similar situations in the Falicov-Kimball model, where known exact results can be used to establish quasicrystalline structures in one and two dimensions. We briefly speculate on possible relations between our theoretical findings and the existence of glassy dynamics and other features of strongly correlated electronic systems.
One-Dimensional Quasicrystals from Incommensurate Charge Order
NASA Astrophysics Data System (ADS)
Flicker, Felix; van Wezel, Jasper
Artificial quasicrystals are nowadays routinely manufactured, yet only two naturally occurring examples are known. We present a class of systems with the potential to be realized both artificially and in nature, in which the lowest energy state is a one-dimensional quasicrystal. These systems are based on incommensurately charge-ordered materials, in which the quasicrystalline phase competes with the formation of a regular array of discommensurations as a way of interpolating between incommensurate charge order at high temperatures and commensurate order at low temperatures. The nonlocal correlations characteristic of the quasicrystalline state emerge from a free-energy contribution localized in reciprocal space. We present a theoretical phase diagram showing that the required material properties for the appearance of such a ground state allow for one-dimensional quasicrystals to form in real materials. The result is a potentially wide class of one-dimensional quasicrystals.
Mechanical properties of icosahedral virus capsids
NASA Astrophysics Data System (ADS)
Vliegenthart, G. A.; Gompper, G.
Virus capsids are self-assembled protein shells in the size range of 10 to 100 nanometers. The shells of DNA-viruses have to sustain large internal pressures while encapsulating and protecting the viral DNA. We employ computer simulations to study the mechanical properties of crystalline shells with icosahedral symmetry that serve as a model for virus capsids. The shells are positioned on a substrate and deformed by a uni-axial force excerted by a small bead. We predict the elastic response for small deformations, and the buckling transitions at large deformations. Both are found to depend strongly on the number N of elementary building blocks (capsomers), and the Föppl-von Kármán number γ which characterizes the relative importance of shear and bending elasticity.
Topological Photonic Quasicrystals: Fractal Topological Spectrum and Protected Transport
NASA Astrophysics Data System (ADS)
Bandres, Miguel A.; Rechtsman, Mikael C.; Segev, Mordechai
We show that it is possible to have a topological phase in two-dimensional quasicrystals without any magnetic field applied, but instead introducing an artificial gauge field via dynamic modulation. This topological quasicrystal exhibits scatter-free unidirectional edge states that are extended along the system's perimeter, contrary to the states of an ordinary quasicrystal system, which are characterized by power-law decay. We find that the spectrum of this Floquet topological quasicrystal exhibits a rich fractal (self-similar) structure of topological "minigaps," manifesting an entirely new phenomenon: fractal topological systems. These topological minigaps form only when the system size is sufficiently large because their gapless edge states penetrate deep into the bulk. Hence, the topological structure emerges as a function of the system size, contrary to periodic systems where the topological phase can be completely characterized by the unit cell. We demonstrate the existence of this topological phase both by using a topological index (Bott index) and by studying the unidirectional transport of the gapless edge states and its robustness in the presence of defects. Our specific model is a Penrose lattice of helical optical waveguides—a photonic Floquet quasicrystal; however, we expect this new topological quasicrystal phase to be universal.
Pentagonal and icosahedral order in rapidly cooled metals
NASA Astrophysics Data System (ADS)
Nelson, D. R.; Halperin, B. I.
The discovery of an alloy of aluminum and manganese with sharp Bragg diffraction spots and an icosahedral point group symmetry was announced last year. The icosahedral symmetry appears to be an intrinsic property fo the material and not an artifact of twinning. There are remarkable similarities between the observed diffraction patterns and aperiodic tesselations of space called Penrose tiles. The relation between the experiments and Penrose tiles, as well as phenomenological descriptions of the icosahedral aluminum-manganese alloy as a superposition of incommensurate density waves, are reviewed. Other types of exotic crystallography are also discussed.
Generation of optical crystals and quasicrystal beams: Kaleidoscopic patterns and phase singularity
Chen, Y. F.; Liang, H. C.; Lin, Y. C.; Tzeng, Y. S.; Su, K. W.; Huang, K. F.
We explore the feasibility of the generation of pseudonondiffracting optical beams related to crystal and quasicrystal structures. It is experimentally confirmed that optical crystal and quasicrystal beams can be remarkably generated with a collimated light to illuminate a high-precision mask with multiple apertures regularly distributed on a ring. We also found that exotic kaleidoscopic patterns can be exhibited with the high-order quasicrystal beams. More importantly, the structures of phase singularities in optical quasicrystal beams are manifested.
Dynamical Diffraction and X-Ray Standing Waves from Atomic Planes Normal to a Twofold Symmetry Axis of the Quasicrystal AlPdMn
Jach, T.; Zhang, Y.; Colella, R.; de Boissieu, M.; Boudard, M.; Goldman, A.I.; Lograsso, T.A.; Delaney, D.W.; Kycia, S.
We have observed dynamical diffraction in the
A pseudo-icosahedral cage {Gd12} based on aminomethylphosphonate.
Zhang, Ze-Min; Zangana, Karzan H; Kostopoulos, Andreas K; Tong, Ming-Liang; Winpenny, Richard E P
Reaction of (aminomethyl)phosphonic acid (ampH2) with a mixture of gadolinium and cobalt pivalates under solvothermal conditions, led to a pseudo-icosahedral cage {Gd12}, which shows a large magnetocaloric effect (MCE). PMID:27188600
Nanotechnology and Quasicrystals: From Self-Assembly to Photonic Applications
NASA Astrophysics Data System (ADS)
Lifshitz, R.
After providing a concise overview on quasicrystals and their discovery more than a quarter of a century ago, I consider the unexpected interplay between nano-technology and quasiperiodic crystals. Of particular relevance are efforts to fabricate artificial functional micro- or nanostructures, as well as efforts to control the self-assembly of nanostructures, where current knowledge about the possibility of having long-range order without periodicity can provide significant advantages. I discuss examples of systems ranging from artificial metamaterials for photonic applications, through self-assembled soft matter, to surface waves and optically-induced nonlinear photonic quasicrystals.
Magnetic moments and non-Fermi-liquid behavior in quasicrystals
NASA Astrophysics Data System (ADS)
Andrade, Eric
Motivated by the intrinsic non-Fermi-liquid behavior observed in the heavy-fermion quasicrystal Au51Al34Yb15, we study the low-temperature behavior of dilute magnetic impurities placed in metallic quasicrystals. We find that a large fraction of the magnetic moments are not quenched down to very low temperatures, leading to a power-law distribution of Kondo temperatures, accompanied by a non-Fermi-liquid behavior, in a remarkable similarity to the Kondo-disorder scenario found in disordered heavy-fermion metals. This work was supported by FAPESP (Brazil) Grant No. 2013/00681-8.
Spin waves in one-dimensional bicomponent magnonic quasicrystals
NASA Astrophysics Data System (ADS)
Rychły, J.; Kłos, J. W.; Mruczkiewicz, M.; Krawczyk, M.
We studied a finite Fibonacci sequence of Co and Py stripes aligned side by side and in direct contact with each other. Calculations based on a continuous model, including exchange and dipole interactions, were performed for structures feasible for fabrication and characterization of the main properties of magnonic quasicrystals. We have shown the fractal structure of the magnonic spectrum with a number of magnonic gaps of different widths. Moreover, localization of spin waves in quasicrystals and the existence of surface spin waves in finite quaiscrystal structure is demonstrated.
The RNA of turnip yellow mosaic virus exhibits icosahedral order
Larson, Steven B.; Lucas, Robert W.; Greenwood, Aaron; McPherson, Alexander . E-mail: firstname.lastname@example.com
Difference electron density maps, based on structure factor amplitudes and experimental phases from crystals of wild-type turnip yellow mosaic virus and those of empty capsids prepared by freeze-thawing, show a large portion of the encapsidated RNA to have an icosahedral distribution. Four unique segments of base-paired, double-helical RNA, one to two turns in length, lie between 33-A and 101-A radius and are organized about either 2-fold or 5-fold icosahedral axes. In addition, single-stranded loops of RNA invade the pentameric and hexameric capsomeres where they contact the interior capsid surface. The remaining RNA, not seen in electron density maps, must serve as connecting links between these secondary structural elements and is likely icosahedrally disordered. The distribution of RNA observed crystallographically appears to be in agreement with models based on biochemical data and secondary structural analyses.
Prediction of stability changes upon mutation in an icosahedral capsid.
Hickman, Samuel J; Ross, James F; Paci, Emanuele
Identifying the contributions to thermodynamic stability of capsids is of fundamental and practical importance. Here we use simulation to assess how mutations affect the stability of lumazine synthase from the hyperthermophile Aquifex aeolicus, a T = 1 icosahedral capsid; in the simulations the icosahedral symmetry of the capsid is preserved by simulating a single pentamer and imposing crystal symmetry, in effect simulating an infinite cubic lattice of icosahedral capsids. The stability is assessed by estimating the free energy of association using an empirical method previously proposed to identify biological units in crystal structures. We investigate the effect on capsid formation of seven mutations, for which it has been experimentally assessed whether they disrupt capsid formation or not. With one exception, our approach predicts the effect of the mutations on the capsid stability. The method allows the identification of interaction networks, which drive capsid assembly, and highlights the plasticity of the interfaces between subunits in the capsid. PMID:26178267
Broadband linear and nonlinear optical response of plasmonic quasicrystals
NASA Astrophysics Data System (ADS)
Ravishankar, Ajith P.; Yallapragada, V. J.; Kasture, S.; Nagarajan, Arvind; Achanta, Venu Gopal
Plasmonic quasicrystals with 5-fold rotation symmetry are shown to offer broadband transmission enhancement. The observed linear transmission enhancement leads to broadband second harmonic generation in a wide incident angle range contrary to unpatterned gold film. From the measured linear and harmonic transmitted powers, we estimate the 2nd order susceptibility values in the 760-840 nm range.
Periodic almost-Schrödinger equation for quasicrystals
Blinov, Igor V.
A new method for finding electronic structure and wavefunctions of electrons in quasiperiodic potential is introduced. To obtain results it uses slightly modified Schrödinger equation in spaces of dimensionality higher than physical space. It enables to get exact results for quasicrystals without expensive non-exact calculations. PMID:26205845
Properties- and applications of quasicrystals and complex metallic alloys.
Dubois, Jean-Marie
This article aims at an account of what is known about the potential for applications of quasicrystals and related compounds, the so-called family of Complex Metallic Alloys (CMAs‡). Attention is focused at aluminium-based CMAs, which comprise a large number of crystalline compounds and quasicrystals made of aluminium alloyed with transition metals (like Fe or Cu) or normal metals like Mg. Depending on composition, the structural complexity varies from a few atoms per unit cell up to thousands of atoms. Quasicrystals appear then as CMAs of ultimate complexity and exhibit a lattice that shows no periodicity anymore in the usual 3-dimensional space. Properties change dramatically with lattice complexity and turn the metal-type behaviour of simple Al-based crystals into a far more complex behaviour, with a fingerprint of semi-conductors that may be exploited in various applications, potential or realised. An account of the ones known to the author is given in the light of the relevant properties, namely light absorption, reduced adhesion and friction, heat insulation, reinforcement of composites for mechanical devices, and few more exotic ones. The role played by the search for applications of quasicrystals in the development of the field is briefly addressed in the concluding section. PMID:22933085
Stability of two-dimensional soft quasicrystals in systems with two length scales.
Jiang, Kai; Tong, Jiajun; Zhang, Pingwen; Shi, An-Chang
The relative stability of two-dimensional soft quasicrystals in systems with two length scales is examined using a recently developed projection method, which provides a unified numerical framework to compute the free energy of periodic crystal and quasicrystals. Accurate free energies of numerous ordered phases, including dodecagonal, decagonal, and octagonal quasicrystals, are obtained for a simple model, i.e., the Lifshitz-Petrich free-energy functional, of soft quasicrystals with two length scales. The availability of the free energy allows us to construct phase diagrams of the system, demonstrating that, for the Lifshitz-Petrich model, the dodecagonal and decagonal quasicrystals can become stable phases, whereas the octagonal quasicrystal stays as a metastable phase. PMID:26565220
Crystallography of decahedral and icosahedral particles. II - High symmetry orientations
NASA Technical Reports Server (NTRS)
Yang, C. Y.; Yacaman, M. J.; Heinemann, K.
Based on the exact crystal structure of decahedral and icosahedral particles, high energy electron diffraction patterns and image profiles have been derived for various high symmetry orientations of the particles with respect to the incident beam. These results form a basis for the identification of small metal particle structures with advanced methods of transmission electron microscopy.
Coherent coexistence of nanodiamonds and carbon onions in icosahedral core-shell particles
Shevchenko, Vladimir Ya. Madison, Alexey E.; Mackay, Alan L.
In icosahedral carbon nanoparticles, the diamond-like core can undergo a reversible topological transition into and coexist coherently with the onion shells. The general approach for describing and designing complex hierarchical icosahedral structures is discussed. Structural models of icosahedral carbon nanoparticles in which the local arrangement of atoms is virtually identical to that in diamond are derived. It is shown that icosahedral diamond-like particles can be transformed into onion-like shell structures (and vice versa) by the consecutive smoothing (puckering) of atomic networks without disturbance of their topological integrity. The possibility of coherent coexistence of icosahedral diamond-like core with onion shells is shown.
Green's functions of one-dimensional quasicrystal bi-material with piezoelectric effect
NASA Astrophysics Data System (ADS)
Zhang, Liangliang; Wu, Di; Xu, Wenshuai; Yang, Lianzhi; Ricoeur, Andreas; Wang, Zhibin; Gao, Yang
Based on the Stroh formalism of one-dimensional quasicrystals with piezoelectric effect, the problems of an infinite plane composed of two different quasicrystal half-planes are taken into account. The solutions of the internal and interfacial Green's functions of quasicrystal bi-material are obtained. Moreover, numerical examples are analyzed for a quasicrystal bi-material subjected to line forces or line dislocations, showing the contour maps of the coupled fields. The impacts of changing material constants on the coupled field components are investigated.
Composition-driven spin glass to ferromagnetic transition in the quasicrystal approximant Au-Al-Gd
NASA Astrophysics Data System (ADS)
Ishikawa, A.; Hiroto, T.; Tokiwa, K.; Fujii, T.; Tamura, R.
We investigated the composition dependence of the magnetic susceptibility of the quasicrystal approximant Au-Al-Gd. A composition-driven ferromagnetic transition is observed in a quasicrystal approximant, which is attributed to the Ruderman-Kittel-Kasuya-Yosida (RKKY) oscillation via a variation in the Fermi wave vector. The ferromagnetic transition is most simply understood as a result of the close matching of the nearest and second-nearest spin distances with the maximum positions of the RKKY potential. The present work provides an idea that allows us to tailor the magnetic order via the electron concentration in quasicrystal approximants as well as in quasicrystals.
The Energetics and Symmetry of Quasicrystals.
NASA Astrophysics Data System (ADS)
Narasimhan, Subha
In a dramatic experiment in 1984, Shechtman and co-workers observed electron diffraction patterns in rapidly cooled Al-Mn alloys, exhibiting non-crystallographic symmetry, contrary to the conventional wisdom that solid structures could be broadly classified as glassy or amorphous, and crystalline. This and subsequent experiments have spurred an intense effort by the condensed matter physics community into understanding the nature and origin of solid structures, particularly in the light of earlier abstract mathematical structures ("tilings"), invented by Penrose and others, that are space filling but non-periodic and non-random in nature. This dissertation aims at understanding the energetics and symmetry of these "quasi-crystalline" structures. It consists of two parts. In the first part, the energetics of various observed quasi-crystalline phases have been studied by using a type of phenomenological Ginzburg-Landau theory that has been successful in predicting the qualitative features of a wide variety of phase transitions. It is found that qualitative agreement with experiment can indeed be had regarding the relative stability of these phases. The model also predicts the most likely equilibrium structure in various regimes of parameter space. The second part is focussed towards understanding the symmetries of the density function of these phases, the symmetry of the hydrodynamic degrees of freedom, the structure of the reciprocal lattice and so on. The harmonic elastic energy, invariant under the point group of the diffraction pattern is constructed for each of the observed phases. Finally, a formalism is developed for determining the various reciprocal lattices possible with a given arbitrary point group symmetry. It is then applied to the cases of 2D Pentagonal and 3D Icosahedral structures.
New roles for icosahedral clusters in intermetallic phases: micelle-like segregation of Ca-Cd and Cu-Cd interactions in Ca10Cd27Cu2.
Hadler, Amelia B; Harris, Nicholas A; Fredrickson, Daniel C
Despite significant progress in the structural characterization of the quasicrystalline state, the chemical origins of long- and short-range icosahedral order remain mysterious and a subject of debate. In this Article, we present the crystal structure of a new complex intermetallic phase, Ca10Cd27Cu2 (mC234.24), whose geometrical features offer clues to the driving forces underlying the icosahedral clusters that occur in Bergman-type quasicrystals. Ca10Cd27Cu2 adopts a C-centered monoclinic superstructure of the 1/1 Bergman approximant structure, in which [110] layers of Bergman clusters in the 1/1 structure are separated through the insertion of additional atoms (accompanied by substantial positional disorder). An examination of the coordination environments of Ca and Cu (in the ordered regions) reveals that the structure can be viewed as a combination of coordination polyhedra present in the nearest binary phases in the Ca-Cd-Cu compositional space. A notable feature is the separation of Ca-Cd and Cu-Cd interactions, with Bergman clusters emerging as Ca-Cd Friauf polyhedra (derived from the MgZn2-type CaCd2 phase) encapsulate a Cu-Cd icosahedron similar to those appearing in Cu2Cd5. DFT chemical pressure calculations on nearby binary phases point to the importance of this segregation of Ca-Cd and Cu-Cd interactions. The mismatch in atomic size between Cu and Cd leads to an inability to satisfy Ca-Cu and Ca-Cd interactions simultaneously in the Friauf polyhedra of the nearby Laves phase CaCd2. The relegation of the Cu atoms to icosahedra prevents this frustration while nucleating the formation of Bergman clusters. PMID:24147875
Distributed Hybridization Model for Quantum Critical Behavior in Magnetic Quasicrystals
NASA Astrophysics Data System (ADS)
Otsuki, Junya; Kusunose, Hiroaki
A quantum critical behavior of the magnetic susceptibility was observed in a quasicrystal containing ytterbium. At the same time, a mixed-valence feature of Yb ions was reported, which appears to be incompatible with the magnetic instability. We derive the magnetic susceptibility by expressing the quasiperiodicity as the distributed hybridization strength between Yb 4f and conduction electrons. Assuming a wide distribution of the hybridization strength, the most f electrons behave as renormalized paramagnetic states in the Kondo or mixed-valence regime, but a small number of f moments remain unscreened. As a result, the bulk magnetic susceptibility exhibits a nontrivial power-law-like behavior, while the average f-electron occupation is that of mixed-valence systems. This model thus resolves two contradictory properties of Yb quasicrystals.
Optical Mode Control by Geometric Phase in Quasicrystal Metasurface
NASA Astrophysics Data System (ADS)
Yulevich, Igor; Maguid, Elhanan; Shitrit, Nir; Veksler, Dekel; Kleiner, Vladimir; Hasman, Erez
We report on the observation of optical spin-controlled modes from a quasicrystalline metasurface as a result of an aperiodic geometric phase induced by anisotropic subwavelength structure. When geometric phase defects are introduced in the aperiodic structured surface, the modes exhibit polarization helicity dependence resulting in the optical spin-Hall effect. The radiative thermal dispersion bands from a quasicrystal structure are studied where the observed bands arise from the optical spin-orbit interaction induced by the aperiodic space-variant orientations of anisotropic antennas. The optical spin-flip behavior of the revealed modes that arise from the geometric phase pickup is experimentally observed within the visible spectrum by measuring the spin-projected diffraction patterns. The introduced ability to manipulate the light-matter interaction of quasicrystals in a spin-dependent manner provides the route for molding light via spin-optical aperiodic artificial planar surfaces.
Optical Mode Control by Geometric Phase in Quasicrystal Metasurface.
Yulevich, Igor; Maguid, Elhanan; Shitrit, Nir; Veksler, Dekel; Kleiner, Vladimir; Hasman, Erez
We report on the observation of optical spin-controlled modes from a quasicrystalline metasurface as a result of an aperiodic geometric phase induced by anisotropic subwavelength structure. When geometric phase defects are introduced in the aperiodic structured surface, the modes exhibit polarization helicity dependence resulting in the optical spin-Hall effect. The radiative thermal dispersion bands from a quasicrystal structure are studied where the observed bands arise from the optical spin-orbit interaction induced by the aperiodic space-variant orientations of anisotropic antennas. The optical spin-flip behavior of the revealed modes that arise from the geometric phase pickup is experimentally observed within the visible spectrum by measuring the spin-projected diffraction patterns. The introduced ability to manipulate the light-matter interaction of quasicrystals in a spin-dependent manner provides the route for molding light via spin-optical aperiodic artificial planar surfaces. PMID:26613450
Virus templated plasmonic nanoclusters with icosahedral symmetry via directed assembly
NASA Astrophysics Data System (ADS)
Ratna, Banahalli; Fontana, Jake; Dressick, Walter; Phelps, Jamie; Johnson, John; Sampson, Travian; Rendell, Ronald; Soto, Carissa
Controlling the spatial and orientational order of plasmonic nanoparticles may lead to structures with novel electromagnetic properties and applications such as sub-wavelength imaging and ultra-sensitive chemical sensors. Here we report the directed assembly of three-dimensional, icosahedral plasmonic nanoclusters with resonances at visible wavelengths. We show using transmission electron microcopy and in situ dynamic light scattering the nanoclusters consist of twelve gold nanospheres attached to thiol groups at predefined locations on the surface of a genetically engineered cowpea mosaic virus with icosahedral symmetry. We measured the bulk absorbance from aqueous suspensions of nanoclusters and reproduced the major features of the spectrum using finite-element simulations. Furthermore, because the viruses are easily produced in gram quantities the directed assembly approach is capable of high-throughput, providing a strategy to realize large quantities for applications. NRL summer intern under the HBCU/MI Summer Research Program.
Electronic transport in polycrystalline samples of icosahedral phases
NASA Astrophysics Data System (ADS)
Vekilov, Yu. Kh.; Chernikov, M. A.; Dolinichek, Ya.
The low-temperature electronic transport in polycrystals of quasicrystalline phases with an icosahedral structure has been analyzed within the model of the granular electronic system. In this model, the grains (drops) of a metallic icosahedral phase are surrounded by extended defects and grain boundaries, which create an insulating environment. The electron transport in this model is determined by the size quantization of electronic states inside metallic grains, by intergranular tunneling, and by electrostatic barriers. Depending on the temperature and structural state of the system, the hopping conductivity with variable lengths of jumps in the Efros-Shklovskii or Mott regime is observed with predominantly elastic cotunneling. In the case of strong intergranular coupling, the system passes into the metallic regime with the exponential temperature dependence of the electrical conductivity.
Forging Unsupported Metal-Boryl Bonds with Icosahedral Carboranes.
Saleh, Liban M A; Dziedzic, Rafal M; Khan, Saeed I; Spokoyny, Alexander M
In contrast to the plethora of metal-catalyzed cross-coupling methods available for the installation of functional groups on aromatic hydrocarbons, a comparable variety of methods are currently not available for icosahedral carboranes, which are boron-rich three-dimensional aromatic analogues of aryl groups. Part of this is due to the limited understanding of the elementary steps for cross-coupling involving carboranes. Here, we report our efforts in isolating metal-boryl complexes to further our understanding of one of these elementary steps, oxidative addition. Structurally characterized examples of group 10 M-B bonds featuring icosahedral carboranes are completely unknown. Use of mercurocarboranes as a reagent to deliver M-B bonds saw divergent reactivity for platinum and palladium, with a Pt-B bond being isolated for the former, and a rare Pd-Hg bond being formed for the latter. PMID:27017293
Encapsulation of a polymer by an icosahedral virus
Elrad, Oren M.; Hagan, Michael F.
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication and enable use of capsids in nanomaterials applications. To this end, we perform Brownian dynamics on a coarse-grained model that describes the dynamics of icosahedral capsid assembly around a flexible polymer. We identify several mechanisms by which the polymer plays an active role in its encapsulation, including cooperative polymer-protein motions. These mechanisms are related to experimentally controllable parameters such as polymer length, protein concentration, and solution conditions. Furthermore, the simulations demonstrate that assembly mechanisms are correlated to encapsulation efficiency, and we present a phase diagram that predicts assembly outcomes as a function of experimental parameters. We anticipate that our simulation results will provide a framework for designing in vitro assembly experiments on single-stranded RNA virus capsids. PMID:21149971
Crystallography of decahedral and icosahedral particles. I - Geometry of twinning
NASA Technical Reports Server (NTRS)
Yang, C. Y.
The crystal structure of the tetrahedral twins in multiply-twinned particles with decahedral and icosahedral point group symmetries has been examined and correlated with the face-centered cubic structure. Details on the crystal structure as well as the geometrical relationships among twins in each particle are presented. These crystallographic facts serve as a basis for the interpretation of small particle images obtained with advanced methods of transmission electron microscopy.
Prediction of stability changes upon mutation in an icosahedral capsid
Hickman, Samuel J.
ABSTRACT Identifying the contributions to thermodynamic stability of capsids is of fundamental and practical importance. Here we use simulation to assess how mutations affect the stability of lumazine synthase from the hyperthermophile Aquifex aeolicus, a T = 1 icosahedral capsid; in the simulations the icosahedral symmetry of the capsid is preserved by simulating a single pentamer and imposing crystal symmetry, in effect simulating an infinite cubic lattice of icosahedral capsids. The stability is assessed by estimating the free energy of association using an empirical method previously proposed to identify biological units in crystal structures. We investigate the effect on capsid formation of seven mutations, for which it has been experimentally assessed whether they disrupt capsid formation or not. With one exception, our approach predicts the effect of the mutations on the capsid stability. The method allows the identification of interaction networks, which drive capsid assembly, and highlights the plasticity of the interfaces between subunits in the capsid. Proteins 2015; 83:1733–1741. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc PMID:26178267
Soft materials design via self assembly of functionalized icosahedral particles
NASA Astrophysics Data System (ADS)
Muthukumar, Vidyalakshmi Chockalingam
In this work we simulate self assembly of icosahedral building blocks using a coarse grained model of the icosahedral capsid of virus 1m1c. With significant advancements in site-directed functionalization of these macromolecules [1], we propose possible application of such self-assembled materials for drug delivery. While there have been some reports on organization of viral particles in solution through functionalization, exploiting this behaviour for obtaining well-ordered stoichiometric structures has not yet been explored. Our work is in well agreement with the earlier simulation studies of icosahedral gold nanocrystals, giving chain like patterns [5] and also broadly in agreement with the wet lab works of Finn, M.G. et al., who have shown small predominantly chain-like aggregates with mannose-decorated Cowpea Mosaic Virus (CPMV) [22] and small two dimensional aggregates with oligonucleotide functionalization on the CPMV capsid [1]. To quantify the results of our Coarse Grained Molecular Dynamics Simulations I developed analysis routines in MATLAB using which we found the most preferable nearest neighbour distances (from the radial distribution function (RDF) calculations) for different lengths of the functional groups and under different implicit solvent conditions, and the most frequent coordination number for a virus particle (histogram plots further using the information from RDF). Visual inspection suggests that our results most likely span the low temperature limits explored in the works of Finn, M.G. et al., and show a good degree of agreement with the experimental results in [1] at an annealing temperature of 4°C. Our work also reveals the possibility of novel stoichiometric N-mer type aggregates which could be synthesized using these capsids with appropriate functionalization and solvent conditions.
Dynamic and Kinetic Assembly Studies of an Icosahedral Virus Capsid
NASA Astrophysics Data System (ADS)
Lee, Kelly
Hepatitis B virus has an icosahedrally symmetrical core particle (capsid), composed of either 90 or 120 copies of a dimeric protein building block. We are using time-resolved, solution small-angle X-ray scattering and single-molecule fluorescence microscopy to probe the core particle assembly reaction at the ensemble and individual assembly levels. Our experiments to date reveal the assembly process to be highly cooperative with minimal population of stable intermediate species. Solution conditions, particularly salt concentration, appears to influence the partitioning of assembly products into the two sizes of shells. Funding from NIH R00-GM080352 and University of Washington.
Structures of giant icosahedral eukaryotic dsDNA viruses
Xiao, Chuan; Rossmann, Michael G.
In the last twenty years, numerous giant, dsDNA, icosahedral viruses have been discovered and assigned to the nucleocytoplasmic large dsDNA virus (NCLDV) clade. The major capsid proteins of these viruses consist of two consecutive jelly-roll domains, assembled into trimers, with pseudo 6-fold symmetry. The capsomers are assembled into arrays that have either p6 (as in Paramecium bursaria Chlorella virus-1) or p3 symmetry (as in Mimivirus). Most of the NCLDV viruses have a membrane that separates the nucleocapsid from the external capsid. PMID:21909343
Platonic solids back in the sky: icosahedral inflation
NASA Astrophysics Data System (ADS)
Kang, Jonghee; Nicolis, Alberto
We generalize the model of solid inflation to an anisotropic cosmic solid. Barring fine tunings, the observed isotropy of the cosmological background and of the scalar two-point function isolate the icosahedral group as the only possible symmetry group of such a solid. In such a case, higher-point correlation functions—starting with the three-point one—are naturally maximally anisotropic, which makes the standard detection strategies highly inefficient and calls for a dedicated analysis of CMB data. The tensor two-point function can also be highly anisotropic, but only in the presence of sizable higher-derivative couplings.
A silicon photonic quasi-crystal structure obtained by interference lithography
NASA Astrophysics Data System (ADS)
Lis, S.; Zakrzewski, A.; Gryglewicz, J.; Oleszkiewicz, W.; Patela, S.
Photonic quasi-crystal structures have been prepared and investigated. Symmetrical patterns were fabricated by interference lithography in negative tone photoresist and transferred to silicon by reactive ion etching. Theoretical influences of pattern detail (radius of hole) on the photonic band gap have been studied. Three types of 2D photonic quasi-crystals have been prepared: 8-fold, 10-fold and 12-fold pattern. Finally, finite-difference time-domain method was used for theoretically prediction of transmission spectrum for fabricated 12-fold quasi-crystal.
Modeling liquid-liquid phase transitions and quasicrystal formation
NASA Astrophysics Data System (ADS)
Skibinsky, Anna
In this thesis, studies which concern two different subjects related to phase transitions in fluids and crystalline solids are presented. Condensed matter formation, structure, and phase transitions are modeled using molecular dynamics simulations of simple discontinuous potentials with attractive and repulsive interactions. Novel phase diagrams are proposed for quasicrystals, crystals, and liquids. In the first part of the thesis, the formation of a quasicrystal in a two dimensional monodisperse system is investigated using molecular dynamics simulations of hard sphere particles interacting via a two-dimensional square-well potential. It is found that for certain values of the square-well parameters more than one stable crystalline phase can form. By quenching the liquid phase at a very low temperature, an amorphous phase is obtained. When this the amorphous phase is heated, a quasicrystalline structure with five-fold symmetry forms. From estimations of the Helmholtz potentials of the stable crystalline phases and of the quasicrystal, it is concluded that within a specific temperature range, the observed quasicrystal phase can be the stable phase. The second part of the thesis concerns a study of the liquid-liquid phase transition for a single-component system in three dimensions, interacting via an isotropic potential with a repulsive soft-core shoulder at short distance and an attractive well at an intermediate distance. The potential is similar to potentials used to describe such liquid systems as colloids, protein solutions, or liquid metals. It is shown that the phase diagram for such a potential can have two lines of first-order fluid-fluid phase transitions: one separating a gas and a low-density liquid (LDL), and another between the LDL and a high-density liquid (HDL). Both phase transition lines end in a critical point, a gas-LDL critical point and, depending on the potential parameters, either a gas-HDL critical point or a LDL-HDL critical point. A
Observation and Structure Determination of an Oxide Quasicrystal Approximant.
Förster, S; Trautmann, M; Roy, S; Adeagbo, W A; Zollner, E M; Hammer, R; Schumann, F O; Meinel, K; Nayak, S K; Mohseni, K; Hergert, W; Meyerheim, H L; Widdra, W
We report on the first observation of an approximant structure to the recently discovered two-dimensional oxide quasicrystal. Using scanning tunneling microscopy, low-energy electron diffraction, and surface x-ray diffraction in combination with ab initio calculations, the atomic structure and the bonding scheme are determined. The oxide approximant follows a 3^{2}.4.3.4 Archimedean tiling. Ti atoms reside at the corners of each tiling element and are threefold coordinated to oxygen atoms. Ba atoms separate the TiO_{3} clusters, leading to a fundamental edge length of the tiling 6.7 Å. PMID:27610863
What periodicities can be found in diffraction patterns of quasicrystals?
Wolny, Janusz; Kozakowski, Bartlomiej; Kuczera, Pawel; Pytlik, Lucjan; Strzalka, Radoslaw
The structure of quasicrystals is aperiodic. Their diffraction patterns, however, can be considered periodic. They are composed solely of series of peaks which exhibit a fully periodic arrangement in reciprocal space. Furthermore, the peak intensities in each series define the so-called `envelope function'. A Fourier transform of the envelope function gives an average unit cell, whose definition is based on the statistical distribution of atomic coordinates in physical space. If such a distribution is lifted to higher-dimensional space, it becomes the so-called atomic surface - the most fundamental feature of higher-dimensional analysis. PMID:24572319
Photonic quasi-crystal fiber with high birefringence
NASA Astrophysics Data System (ADS)
Liu, Hongfei; Xiao, Wei; Cai, Weicheng; Liu, Exian; Feng, Bo; Wang, Ziming; Liang, Taiyuan; Wang, Shuo; Liu, Jianjun
A high-birefringence photonic quasi-crystal fiber (HB-PQF) based on SiO2 is proposed. The relationships between birefringence and structure parameters and between beat length and structure parameters are researched by finite difference beam propagation method. With the optimization of fiber structure parameters, the birefringence is 1.4207×10-2, which is two orders of magnitude higher than the normally used fiber when the wavelength is 1.55 μm. The radius of the fiber is 6.5 μm. The HB-PQF in a communication sensor will have important application prospects.
Nonhydrostatic icosahedral atmospheric model (NICAM) for global cloud resolving simulations
NASA Astrophysics Data System (ADS)
Satoh, M.; Matsuno, T.; Tomita, H.; Miura, H.; Nasuno, T.; Iga, S.
A new type of ultra-high resolution atmospheric global circulation model is developed. The new model is designed to perform "cloud resolving simulations" by directly calculating deep convection and meso-scale circulations, which play key roles not only in the tropical circulations but in the global circulations of the atmosphere. Since cores of deep convection have a few km in horizontal size, they have not directly been resolved by existing atmospheric general circulation models (AGCMs). In order to drastically enhance horizontal resolution, a new framework of a global atmospheric model is required; we adopted nonhydrostatic governing equations and icosahedral grids to the new model, and call it Nonhydrostatic ICosahedral Atmospheric Model (NICAM). In this article, we review governing equations and numerical techniques employed, and present the results from the unique 3.5-km mesh global experiments—with O(10 9) computational nodes—using realistic topography and land/ocean surface thermal forcing. The results show realistic behaviors of multi-scale convective systems in the tropics, which have not been captured by AGCMs. We also argue future perspective of the roles of the new model in the next generation atmospheric sciences.
Unusual properties of icosahedral boron-rich solids
Emin, David . E-mail: email@example.com
Icosahedral boron-rich solids are materials containing boron-rich units in which atoms reside at an icosahedron's 12 vertices. These materials are known for their exceptional bonding and the unusual structures that result. This article describes how the unusual bonding generates other distinctive and useful effects. In particular, radiation-induced atomic vacancies and interstitials spontaneously recombine to produce the 'self-healing' that underlies these materials' extraordinary radiation tolerance. Furthermore, boron carbides, a group of icosahedral boron-rich solids, possess unusual electronic, magnetic and thermal properties. For example, the charge carriers, holes, localize as singlet pairs on icosahedra. The unusual origin of this localization is indicated by the absence of a concomitant photo-ionization. The thermally assisted hopping of singlet pairs between icosahedra produces Seebeck coefficients that are unexpectedly large and only weakly dependent on carrier concentration. These properties are exploited in devices: (1) long-lived high-power high-capacity beta-voltaic cells (2) very high temperature thermoelectrics and (3) solid-state neutron detectors. - Graphical abstract: Very high-resolution transmission electron microscopy shows no damage to B{sub 12}P{sub 2} after an intense bombardment (10{sup 18} electrons/cm{sup 2} s) by 400 keV electrons to a net dose of about 10{sup 23} electrons/cm{sup 2}.
Vortex quasi-crystals in mesoscopic superconducting samples
NASA Astrophysics Data System (ADS)
Wang, Jing-Kun; Zhang, Wei; R, Sá de Melo C. A.
There seems to be a one to one correspondence between the phases of atomic and molecular matter (AMOM) and vortex matter (VM) in superfluids and superconductors. Crystals, liquids, and glasses have been experimentally observed in both AMOM and VM. Here, we propose a vortex quasi-crystal state which can be stabilized due to boundary and surface energy effects for samples of special shapes and sizes. For finite sized pentagonal samples, it is proposed that a phase transition between a vortex crystal and a vortex quasi-crystal occurs as a function of magnetic field and temperature as the sample size is reduced. Project supported by the National Natural Science Foundation of China (Grant Nos. 11274009, 11434011, and 111522436), the National Key Basic Research Program of China (Grant No. 2013CB922000), the Research Funds of Renmin University of China (Grant Nos. 10XNL016 and 16XNLQ03), and the Program of State Key Laboratory of Quantum Optics and Quantum Optics Devices (Grant No. KF201404).
Self-similarity and self-inversion of quasicrystals
NASA Astrophysics Data System (ADS)
Madison, A. E.
The discovery of quasicrystals played a revolutionary role in the condensed matter science and forced to renounce the dogma of the classical crystallography that the regular filling of the space by identical blocks is reduced solely to the Fedorov space groups. It is shown that aperiodic crystals, apart from the similarity, exhibit the self-inversion property. In a broadened sense, the self-inversion implies the possible composition of the inversion with translations, rotations, and homothety, whereas pure reflection by itself in a circle can be absent as an independent symmetry element. It is demonstrated that the symmetry of aperiodic tilings is described by Schottky groups (which belong to a particular type of Kleinian groups generated by the linear fractional Möbius transformations); in the theory of aperiodic crystals, the Schottky groups play the same role that the Fedorov groups play in the theory of crystal lattices. The local matching rules for the Penrose fractal tiling are derived, the problem of choice of the fundamental region of the group of motions of a quasicrystal is discussed, and the relation between the symmetry of aperiodic tilings and the symmetry of constructive fractals is analyzed.
Strongly localized modes in one-dimensional defect-free magnonic quasicrystals
Chen, C. H.; Qiu, R. Z.; Chang, C. H.; Hsueh, W. J.
Signal storage in magnonic quasicrystals using a slow spin-wave mode, rather than the quasinormal mode of traditional periodic magnonic crystals, is proposed, which is analogous to the slow light mode in the field of optics. Compared to traditional materials, richer and more wavelength-selective sharp resonances are achieved using the quasicrystals with a fewer number of layers, because of the peculiar fractal transmission spectra of quasicrystals. The number of sharp resonance and the quality factor for the sharp resonances in the transmission spectra also increases as the generation order of the magnonic quasicrystal increases. This generic nature allows the storage of signals using spin wave, for a wide range of quasiperiodic systems.
Lasing from organic quasicrystal fabricated by seven- and nine-beam interference.
Luo, D; Li, Y; Xu, X W; Du, Q G
We demonstrate mirrorless lasers based on all organic nanostructure fabricated by seven- and nine-beam interference using low contrast material, holographic polymer dispersed liquid crystals (H-PDLC). A finite-difference time-domain (FDTD) simulation is used to study the transmission of quasicrystal. The wavelengths of lasing peak are determined by both of local structure of quasicrystal that the pumping light experienced as well as the photoluminescence of laser dye doped. Features of mirrorless laser from quasicrystal based on H-PDLC include directional light source, low threshold, simple fabrication process, low cost and tunability. These properties make H-PDLC photonic quasicrystal promising for a new type of all organic miniature lasers. PMID:27410148
Association of broad icosahedral Raman bands with substitutional disorder in SiB{sub 3} and boron carbide
Aselage, T.L.; Tallant, D.R.
The structure of silicon boride, SiB{sub 3}, is based on 12-atom, boron-rich icosahedra in which silicon atoms substitute for some boron atoms. Raman bands associated with vibrations of icosahedral atoms in SiB{sub 3} are quite broad, reflecting this substitutional disorder. Comparing the Raman spectra of other icosahedral borides with SiB{sub 3}, only boron carbides have similarly broad icosahedral Raman bands. The direct correlation of broad icosahedral Raman bands with substitutional disorder supports the proposition that carbon atoms replace icosahedral boron atoms in boron carbides of all compositions. {copyright} {ital 1998} {ital The American Physical Society}
A Convenient Route to Diversely Substituted Icosahedral Closomer Nanoscaffolds
Jalisatgi, Satish S.; Kulkarni, Vikas S.; Tang, Betty; Houston, Zachary H.; Lee, Mark W.; Hawthorne, M. Frederick
The design and synthesis of icosahedral polyhedral borane closomer motifs based upon carbonate and carbamate anchoring groups for biomedical applications are described. Dodecacarbamate closomers containing easily accessible groups of interest at their linker termini were synthesized via activation of the B-OH vertices as aryl carbonates and their subsequent reaction with primary amines. Novel dodecacarbonate closomers were successfully synthesized for the first time by reacting [closo-B12(OH)12]2− with an excess of respective aryl chloroformates, utilizing relatively short reaction times, mild conditions and simple purification strategies, all of which had previously presented difficulties in closomer chemistry. This methodology for the 12-fold degenerate synthesis of carbonate and carbamate closomers will greatly facilitate further exploration of closomers as monodisperse nanomolecular delivery platforms. PMID:21766843
Icosahedral capsid formation by capsomers and short polyions
NASA Astrophysics Data System (ADS)
Zhang, Ran; Linse, Per
Kinetical and structural aspects of the capsomer-polyion co-assembly into icosahedral viruses have been simulated by molecular dynamics using a coarse-grained model comprising cationic capsomers and short anionic polyions. Conditions were found at which the presence of polyions of a minimum length was necessary for capsomer formation. The largest yield of correctly formed capsids was obtained at which the driving force for capsid formation was relatively weak. Relatively stronger driving forces, i.e., stronger capsomer-capsomer short-range attraction and/or stronger electrostatic interaction, lead to larger fraction of kinetically trapped structures and aberrant capsids. The intermediate formation was investigated and different evolving scenarios were found by just varying the polyion length.
Radial vibrations of a sodium ion inside icosahedral C60
NASA Technical Reports Server (NTRS)
Ballester, J. L.; Dunlap, B. I.
The very high symmetry of icosahedral C60 suggests that, as a first approximation, an atom trapped inside C60 would be subject to a potential that is radially symmetric about the center. All-electron local-density-functional calculations of the total energy of a sodium ion as a function of radial displacement from the center along the fivefold axis of C60 serve to refine such a radial potential. In particular, the calculations suggest studying potentials that have minima displaced from the center. An analytic functional form for a radial potential having a positive cusp at the origin is proposed, and the s-wave radial solutions of the corresponding Schroedinger equation are examined.
Dynamico, an Icosahedral Dynamical Core Designed for Consistency and Versatility
NASA Astrophysics Data System (ADS)
Dubos, T.
The design of the icosahedral-hexagonal dynamical core DYNAMICO is presented. DYNAMICO solves the multi-layer rotating shallow-water equations, a compressible variant of the same equivalent to a discretization of the hydrostatic primitive equations (HPE) in a Lagrangian vertical coordinate, and the HPE in a hybrid mass-based vertical coordinate. In line with more general lines of thought known as physics-preserving discretizations and discrete differential geometry, kinematics and dynamics are separated as strictly as possible. This separation means that the transport of mass, scalars and potential temperature uses no information regarding the specific momentum equation being solved. This disregarded information includes the equation of state as well as any metric information, and is used only for certain terms of the momentum budget, written in Hamiltonian, vector-invariant form. The common Hamiltonian structure of the various equations of motion (Tort and Dubos, 2014 ; Dubos and Tort, 2014) is exploited to formulate energy-conserving spatial discretizations in a unified way. Furthermore most of the model code is common to the three sets of equations solved, making it easier to develop and validate each piece of the model separately. This design permits to consider several extensions in the near future, especially to deep-atmosphere, moist and non-hydrostatic equations. Representative academic three-dimensional benchmarks are run and analyzed, showing correctness of the model (Figure : time-zonal statistics from Held and Suarez (1994) simulations). Hopefully preliminary full-physics results will be presented as well. References : T. Dubos and M. Tort, "Equations of atmospheric motion in non-Eulerian vertical coordinates : vector-invariant form and Hamiltonian formulation", accepted by Mon. Wea. Rev. M. Tort and T. Dubos, "Usual approximations to the equations of atmospheric motion : a variational perspective" accepted by J. Atmos. Sci T. Dubos et al., "DYNAMICO
Archaeal Haloarcula californiae Icosahedral Virus 1 Highlights Conserved Elements in Icosahedral Membrane-Containing DNA Viruses from Extreme Environments
Demina, Tatiana A.; Pietilä, Maija K.; Svirskaitė, Julija; Ravantti, Janne J.; Atanasova, Nina S.; Bamford, Dennis H.
ABSTRACT Despite their high genomic diversity, all known viruses are structurally constrained to a limited number of virion morphotypes. One morphotype of viruses infecting bacteria, archaea, and eukaryotes is the tailless icosahedral morphotype with an internal membrane. Although it is considered an abundant morphotype in extreme environments, only seven such archaeal viruses are known. Here, we introduce Haloarcula californiae icosahedral virus 1 (HCIV-1), a halophilic euryarchaeal virus originating from salt crystals. HCIV-1 also retains its infectivity under low-salinity conditions, showing that it is able to adapt to environmental changes. The release of progeny virions resulting from cell lysis was evidenced by reduced cellular oxygen consumption, leakage of intracellular ATP, and binding of an indicator ion to ruptured cell membranes. The virion contains at least 12 different protein species, lipids selectively acquired from the host cell membrane, and a 31,314-bp-long linear double-stranded DNA (dsDNA). The overall genome organization and sequence show high similarity to the genomes of archaeal viruses in the Sphaerolipoviridae family. Phylogenetic analysis based on the major conserved components needed for virion assembly—the major capsid proteins and the packaging ATPase—placed HCIV-1 along with the alphasphaerolipoviruses in a distinct, well-supported clade. On the basis of its virion morphology and sequence similarities, most notably, those of its core virion components, we propose that HCIV-1 is a member of the PRD1-adenovirus structure-based lineage together with other sphaerolipoviruses. This addition to the lineage reinforces the notion of the ancient evolutionary links observed between the viruses and further highlights the limits of the choices found in nature for formation of a virion. PMID:27435460
Renormalization, Thermodynamic Formalism and Quasi-Crystals in Subshifts
NASA Astrophysics Data System (ADS)
Bruin, Henk; Leplaideur, Renaud
We examine the thermodynamic formalism for a class of renormalizable dynamical systems which in the symbolic space is generated by the Thue-Morse substitution, and in complex dynamics by the Feigenbaum-Coullet-Tresser map. The basic question addressed is whether fixed points V of a renormalization operator {{R}} acting on the space of potentials are such that the pressure function {β mapsto {P}(-β V)} exhibits phase transitions. This extends the work by Baraviera, Leplaideur and Lopes on the Manneville-Pomeau map, where such phase transitions were indeed detected. In this paper, however, the attractor of renormalization is a Cantor set (rather than a single fixed point), which admits various classes of fixed points of {{R}}, some of which do and some of which do not exhibit phase transitions. In particular, we show it is possible to reach, as a ground state, a quasi-crystal before temperature zero by freezing a dynamical system.
Friction Anisotropy: A unique and intrinsic property of decagonal quasicrystals
Mulleregan, Alice; Park, Jeong Young; Salmeron, Miquel; Ogetree, D.F.; Jenks, C.J.; Thiel, P.A.; Brenner, J.; Dubois, J.M.
We show that friction anisotropy is an intrinsic property of the atomic structure of Al-Ni-Co decagonal quasicrystals and not only of clean and well-ordered surfaces that can be prepared in vacuum [J.Y. Park et al., Science (2005)]. Friction anisotropy is manifested both in nanometer size contacts obtained with sharp atomic force microscope (AFM) tips as well as in macroscopic contacts produced in pin-on-disc tribometers. We show that the friction anisotropy, which is not observed when an amorphous oxide film covers the surface, is recovered when the film is removed due to wear. Equally important is the loss of the friction anisotropy when the quasicrystalline order is destroyed due to cumulative wear. These results reveal the intimate connection between the mechanical properties of these materials and their peculiar atomic structure.
Atomistic simulation of frictional anisotropy on quasicrystal approximant surfaces
NASA Astrophysics Data System (ADS)
Ye, Zhijiang; Martini, Ashlie; Thiel, Patricia; Lovelady, Heather H.; McLaughlin, Keith; Rabson, David A.
J. Y. Park et al. [Science 309, 1354 (2005), 10.1126/science.1113239] have reported eight times greater atomic-scale friction in the periodic than in the quasiperiodic direction on the twofold face of a decagonal Al-Ni-Co quasicrystal. We present results of molecular-dynamics simulations intended to elucidate mechanisms behind this giant frictional anisotropy. Simulations of a bare atomic-force-microscope tip on several model substrates and under a variety of conditions failed to reproduce experimental results. On the other hand, including the experimental passivation of the tip with chains of hexadecane thiol, we reproduce qualitatively the experimental anisotropy in friction, finding evidence for entrainment of the organic chains in surface furrows parallel to the periodic direction.
Acid-base chemistry in the formation of Mackay-type icosahedral clusters: μ3-acidity analysis of Sc-rich phases of the Sc-Ir system.
Guo, Yiming; Stacey, Timothy E; Fredrickson, Daniel C
The crystal structures of intermetallic phases offer a wealth of geometrical features (helices, multishelled clusters, and host-guest motifs) whose formation has yet to be explained or predicted by chemical theory. A recently developed extension of the acid-base concept to metallic systems, the μ3-acidity model, provides an avenue for developing this understanding for intermetallics formed from transition metals. In this Article, we illustrate how this approach can be used to understand one of the most striking geometrical entities to emerge in intermetallic chemistry, the Mackay cluster of icosahedral quasicrystals. We present μ3-acidity analyses, based on DFT-calibrated Hückel calculations, for a series of Sc-Ir intermetallics: ScIr (CsCl-type), Sc2Ir (Ti2Ni-type), Sc11Ir4, and the Mackay cluster containing phases Sc57Ir13 and Sc44Ir7. We begin by illustrating that a μ3-acidity model correctly predicts that each of these phases is stable relative to disproportionation into their neighboring compounds when a common set of Hückel parameters and d-orbital occupancies is used. Next, we explain these results by developing a relationship between the distance distribution of homoatomic contacts within an atom's coordination sphere and the μ3-neutralization it experiences. For a given average homoatomic distance, the role of heteroatomic contacts is higher when the distribution of homoatomic contacts is narrower. This effect is key to the strength of the acid-base neutralization of the Sc-rich phases, where the Sc atoms find a scarcity of Ir atoms from which to obtain neutralization. Under these circumstances, Sc-Ir contacts should be maximized, whereas the number and distance variations of the Sc-Sc contacts should be minimized. These expectations are borne out by the observed crystal structures. In particular, the Mackay clusters of Sc57Ir13 and Sc44Ir7, in which a central Ir atom is icosahedrally coordinated by a pentagonal dodecahedral array of face-sharing Sc
Classification of Voronoi and Delone tiles in quasicrystals: I. General method
NASA Astrophysics Data System (ADS)
Masáková, Z.; Patera, J.; Zich, J.
A new general method is presented which allows one to find all distinct Voronoi and Delone tiles in any quasicrystal from a large family. This includes the tiles which may be present with arbitrarily low density >0. At all stages, the method requires only consideration of a (possibly large) finite number of cases. Our method is applicable, in principle, to quasicrystals in any dimension and with any irrationality. This is the first of three papers where the Voronoi and Delone tilings are studied. Two-dimensional point sets, 'quasicrystals', arising from the A4-root lattice by means of the standard projection to a two-dimensional plane with the irrationality tau = 1/2(1 + surd5), are considered. In general, we require that the acceptance window be bounded with non-empty interior. Specific results are provided here for rhombic acceptance windows of any size oriented along the direction of simple roots of the Coxeter group H2. Within one quasicrystal the tiles are distinguished by their shape, size and orientation. The rhombic window case is indispensable for subsequent classification of Voronoi and Delone tiles in quasicrystals with general shape of the acceptance window. Voronoi and Delone tiles of quasicrystals with circular and decagonal windows of any size are given in subsequent papers. Let VT denote the set of distinct Voronoi tiles making up a quasicrystal with a given acceptance window. There are three VT sets of the 'generic' type and three of the 'singular' type. The latter occur for one precise value of the size of the acceptance window. Any other VT set is a uniform scaling of the tiles listed here. Similar results, differing in detail, are provided for the sets of distinct Delone tiles DT. Altogether there are four different sets DT of Delone tiles.
Metal-organic framework materials based on icosahedral boranes and carboranes
Mirkin, Chad A.; Hupp, Joseph T.; Farha, Omar K.; Spokoyny, Alexander M.; Mulfort, Karen L.
Disclosed herein are metal-organic frameworks of metals and boron rich ligands, such as carboranes and icosahedral boranes. Methods of synthesizing and using these materials in gas uptake are disclosed.
Speckle in the diffraction patterns of Hendricks-Teller and icosahedral glass models
NASA Technical Reports Server (NTRS)
Garg, Anupam; Levine, Dov
It is shown that the X-ray diffraction patterns from the Hendricks-Teller model for layered systems and the icosahedral glass models for the icosahedral phases show large fluctuations between nearby scattering wave vectors and from sample to sample, that are quite analogous to laser speckle. The statistics of these fluctuations are studied analytically for the first model and via computer simulations for the second. The observability of these effects is discussed briefly.
Superior room-temperature ductility of typically brittle quasicrystals at small sizes.
Zou, Yu; Kuczera, Pawel; Sologubenko, Alla; Sumigawa, Takashi; Kitamura, Takayuki; Steurer, Walter; Spolenak, Ralph
The discovery of quasicrystals three decades ago unveiled a class of matter that exhibits long-range order but lacks translational periodicity. Owing to their unique structures, quasicrystals possess many unusual properties. However, a well-known bottleneck that impedes their widespread application is their intrinsic brittleness: plastic deformation has been found to only be possible at high temperatures or under hydrostatic pressures, and their deformation mechanism at low temperatures is still unclear. Here, we report that typically brittle quasicrystals can exhibit remarkable ductility of over 50% strains and high strengths of ∼4.5 GPa at room temperature and sub-micrometer scales. In contrast to the generally accepted dominant deformation mechanism in quasicrystals-dislocation climb, our observation suggests that dislocation glide may govern plasticity under high-stress and low-temperature conditions. The ability to plastically deform quasicrystals at room temperature should lead to an improved understanding of their deformation mechanism and application in small-scale devices. PMID:27515779
Thermal expansion of a Au-Al-Yb intermediate valence quasicrystal
NASA Astrophysics Data System (ADS)
Watanuki, T.; Kashimoto, S.; Ishimasa, T.; Machida, A.; Yamamoto, S.; Tanaka, Y.; Mizumaki, M.; Kawamura, N.; Watanabe, S.
The thermal expansion of a Au-Al-Yb intermediate-valence quasicrystal has been studied. X-ray diffraction measurements showed zero thermal expansion below 50 K. By comparison with an isostructural Au-Al-Tm quasicrystal, the contribution of the Yb valence variation was extracted, and it was shown that its negative thermal expansion component compensated for the positive thermal expansion of the original lattice. On cooling, the Yb contribution grew steeply below approximately 155 K down to the lowest experimental temperature of 5 K, due to enlargement of the Yb atomic radius, which was caused by the valence shift toward the divalent state. Additionally, a larger Yb contribution to the thermal expansion was demonstrated in a crystalline approximant to this quasicrystal. The magnitude of this contribution was approximately 1.4 times larger than in the case of the quasicrystal itself, resulting in a slight negative thermal expansion below 50 K. A heterogeneous valence model for the quasicrystal that we proposed previously accounts for this magnitude difference.
Quantum transport through single and multilayer icosahedral fullerenes
NASA Astrophysics Data System (ADS)
Lovey, Daniel A.; Romero, Rodolfo H.
We use a tight-binding Hamiltonian and Green functions methods to calculate the quantum transmission through single-wall fullerenes and bilayered and trilayered onions of icosahedral symmetry attached to metallic leads. The electronic structure of the onion-like fullerenes takes into account the curvature and finite size of the fullerenes layers as well as the strength of the intershell interactions depending on to the number of interacting atom pairs belonging to adjacent shells. Misalignment of the symmetry axes of the concentric iscosahedral shells produces breaking of the level degeneracies of the individual shells, giving rise some narrow quasi-continuum bands instead of the localized discrete peaks of the individual fullerenes. As a result, the transmission function for non symmetrical onions is rapidly varying functions of the Fermi energy. Furthermore, we found that most of the features of the transmission through the onions are due to the electronic structure of the outer shell with additional Fano-like antiresonances arising from coupling with or between the inner shells.
Many-molecule encapsulation by an icosahedral shell
Perlmutter, Jason D; Mohajerani, Farzaneh; Hagan, Michael F
We computationally study how an icosahedral shell assembles around hundreds of molecules. Such a process occurs during the formation of the carboxysome, a bacterial microcompartment that assembles around many copies of the enzymes ribulose 1,5-bisphosphate carboxylase/ oxygenase and carbonic anhydrase to facilitate carbon fixation in cyanobacteria. Our simulations identify two classes of assembly pathways leading to encapsulation of many-molecule cargoes. In one, shell assembly proceeds concomitantly with cargo condensation. In the other, the cargo first forms a dense globule; then, shell proteins assemble around and bud from the condensed cargo complex. Although the model is simplified, the simulations predict intermediates and closure mechanisms not accessible in experiments, and show how assembly can be tuned between these two pathways by modulating protein interactions. In addition to elucidating assembly pathways and critical control parameters for microcompartment assembly, our results may guide the reengineering of viruses as nanoreactors that self-assemble around their reactants. DOI: http://dx.doi.org/10.7554/eLife.14078.001 PMID:27166515
Electronic Properties of Ordered Quasicrystals and Related Phases
NASA Astrophysics Data System (ADS)
Biggs, Byron Davis
An extensive, systematic study of the electronic properties of the well-ordered icosahedral (i-) phases and related crystalline and amorphous phases is presented. Barely metallic behavior is observed in the ordered i-crystals, including high resistivities with large temperature coefficients, low electronic densities of states at the Fermi energy, large values of the low-temperature Hall coefficients, and unusual temperature dependences of the Hall coefficients and the thermoelectric powers. In addition, rapid variations of these properties with small changes in composition are observed. Similar behavior is seen in crystalline approximant structures, which are close crystalline analogues of the i-phase. With increasing structural disorder in disordered i-phases and in the totally disordered amorphous (a-) phases, the familiar metallic-glass-like electronic properties are restored. This striking electronic behavior is shown to be due to band structure effects. The high resistivities, low densities of states, and low carrier densities are shown to be due to the structural scattering mechanism of the Fermi-surface-Jones-zone interaction, which is enhanced due to the high degree of structural ordering and, in the i-phases, due to the icosahedral symmetry. The unusual temperature dependences of the Hall coefficients and thermoelectric powers, as well as the rapid variation of the electronic properties with small changes in composition, support the existence of a rapidly varying density of states on a fine energy scale, on the order of 26 meV. The existence of these band structure effects is further supported by the effects of structural disorder on the electronic properties, with disorder restoring the free-electron metallic-glass -like electronic properties. The temperature dependence of the conductivity at high temperatures displays novel concave upward curvature in a wide variety of icosahedral, amorphous, and crystalline phases which have high resistivity values
TOPICAL REVIEW: The various modes of growth of metals on quasicrystals
NASA Astrophysics Data System (ADS)
Smerdon, J. A.
Quasicrystals are fascinating intermetallic compounds composed of two or more elements. They differ from conventional crystals in that they possess long-range order, but no translational symmetry—that is, they are aperiodic. Much effort has been expended on identifying routes towards exploiting and exploring the properties of such systems due to their aperiodic nature. One such route is concerned with the deposition of thin films, particularly of metals, to investigate how their growth progresses in this inherently frustrated scenario. This topical review will examine the various epitaxial relationships observed in quasicrystal research with particular emphasis on single-element metallic films deposited under ultrahigh-vacuum conditions.
Excitation of Bloch-like surface waves in quasi-crystals and aperiodic dielectric multilayers.
Koju, Vijay; Robertson, William M
The existence of Bloch surface waves in periodic dielectric multilayer structures with a surface defect is well known. Not yet recognized is that quasi-crystals and aperiodic dielectric multilayers can also support Bloch-like surface waves. In this work, we numerically show the excitation of Bloch-like surface waves in Fibonacci quasi-crystals and Thue-Morse aperiodic dielectric multilayers using the prism coupling method. We report improved surface electric field intensity and penetration depth of Bloch-like surface waves in the air side in such structures compared to their periodic counterparts. PMID:27367064
Surface Tension and Viscosity of Quasicrystal-Forming Ti-Zr-Ni Alloys
NASA Technical Reports Server (NTRS)
Hyers, R. W.; Bradshaw, R. C.; Rogers, J. R.; Rathz, T. J.; Lee, G. W.; Kelton, K. F.; Gangopadhyay, A. K.
The surface tension and viscosity of quasicrystal-forming Ti-Zr-Ni alloys were measured over a range of temperature, including both stable and undercooled liquids by an Electrostatic Levitation (ESL) technique. ESL is a containerless technique which allows processing of samples without contact, greatly reducing contamination and increasing access to the metastable undercooled liquid. The measured viscosity is typical of glass-forming alloys of similar composition to the quasicrystal-forming alloys studied here, while the surface tension shows an anomaly at deep undercoolings.
Comparative Study of Non-Enveloped Icosahedral Viruses Size
Nikitin, Nikolai; Trifonova, Ekaterina; Evtushenko, Evgeniy; Kirpichnikov, Mikhail; Atabekov, Joseph; Karpova, Olga
Now, as before, transmission electron microscopy (TEM) is a widely used technique for the determination of virions size. In some studies, dynamic light scattering (DLS) has also been applied for this purpose. Data obtained by different authors and using different methods could vary significantly. The process of TEM sample preparation involves drying on the substrate, which can cause virions to undergo morphology changes. Therefore, other techniques should be used for measurements of virions size in liquid, (i.e. under conditions closer to native). DLS and nanoparticle tracking analysis (NTA) provide supplementary data about the virions hydrodynamic diameter and aggregation state in liquid. In contrast to DLS, NTA data have a higher resolution and also are less sensitive to minor admixtures. In the present work, the size of non-enveloped icosahedral viruses of different nature was analyzed by TEM, DLS and NTA: the viruses used were the encephalomyocarditis virus (animal virus), and cauliflower mosaic virus, brome mosaic virus and bean mild mosaic virus (plant viruses). The same, freshly purified, samples of each virus were used for analysis using the different techniques. The results were compared with earlier published data and description databases. DLS data about the hydrodynamic diameter of bean mild mosaic virus, and NTA data for all examined viruses, were obtained for the first time. For all virus samples, the values of size obtained by TEM were less than virions sizes determined by DLS and NTA. The contribution of the electrical double layer (EDL) in virions hydrodynamic diameter was evaluated. DLS and NTA data adjusted for EDL thickness were in better agreement with TEM results. PMID:26545232
Studies of Nucleation and Growth, Specific Heat and Viscosity of Undercooled Melts of Quasicrystals and Polytetrehedral-Phase-Forming Alloys
NASA Technical Reports Server (NTRS)
By investigating the properties of quasicrystals and quasicrystal-forming liquid alloys, we may determine the role of ordering of the liquid phase in the formation of quasicrystals, leading to a better fundamental understanding of both the quasicrystal and the liquid. A quasicrystal is solid characterized by a symmetric but non-periodic arrangement of atoms, usually in the form of an icosahedron (12 atoms, 20 triangular faces). It is theorized that the short-range order in liquids takes this same form. The degree of ordering depends on the temperature of the liquid, and affects many of the liquid s properties, including specific heat, viscosity, and electrical resistivity. The MSFC role in this project includes solidification studies, phase diagram determination, and thermophysical property measurements on the liquid quasicrystal-forming alloys, all by electrostatic levitation (ESL). The viscosity of liquid quasicrystal-forming alloys is measured by the oscillating drop method, both in the stable and undercooled liquid state. The specific heat of solid, undercooled liquid, and stable liquid are measured by the radiative cooling rate of the droplets.
Soft spherical nanostructures with a dodecagonal quasicrystal-like order.
Rochal, S B; Konevtsova, O V; Shevchenko, I A; Lorman, V L
We develop a theory which predicts curvature-related structural peculiarities of soft spherical nanostructures with a dodecagonal local arrangement of subunits. Spherical templates coated with a thin film of a soft quasicrystal (QC)-forming material constitute the most promising direction to realize these nanostructures. Disordered and perfect spherical nanostructures are simulated using two approaches. The first of them models a random QC-like spherical nanostructure with extended curvature-induced topological defects similar to scars in colloidal spherical crystals. The second approach is inspired by the physics of viral capsids. It deals with the most regular spherical nanostructures with a local QC-like order derived from three well-known planar dodecagonal tilings. We explain how the additional QC-like degrees of freedom assist the nanostructure stabilization and determine the point defect number and location without extended scar formation. Unusual for nanoassemblies snub cube geometry is shown to be the most energetically favorable global organization of these spherical QC nanostructures. PMID:26592422
Dodecagonal Quasicrystal Phase in a Diblock Copolymer Melt
NASA Astrophysics Data System (ADS)
Bates, Frank; Gillard, Timothy; Lee, Sangwoo
Recent experiments with low molecular weight asymmetric poly(isoprene- b-lactide) (PI-PLA) diblock copolymers have established an equilibrium Frank-Kasper σ-phase at compositions between 18 and 22 percent by volume PLA, which transforms to a BCC phase followed by disordering with increasing temperature. This presentation will describe synchrotron small-angle x-ray scattering and dynamic mechanical spectroscopy experiments conducted following rapid temperature quenches from the disordered state to temperatures associated with the σ-phase. We document the development of a long-lived dodecagonal quasicrystalline (DQC) phase that transforms with time into the associated quasicrystal approximate σ-phase at a rate that is highly temperature dependent. Remarkably, the DQC does not form from either the σ-phase or BCC state. These finding will be discussed in the context of an apparent spontaneous structural transition that occurs when the disordered melt is supercooled below a threshold temperature coincident with the BCC to σ-phase order-order transition temperature. Support provided by the National Science Foundation (1104368).
The Connection Between Local Icosahedral Order in Metallic Liquids and the Nucleation of Ordered Phases
NASA Technical Reports Server (NTRS)
Curreri, Peter A. (Technical Monitor); Kelton, K. F.; Gangopadhyay, A.; Lee, G. W.; Hyers, R. W.; Rathz, R. J.; Rogers, J.; Schenk, T.; Simonet, V.; Holland-Moritz, D.
Over fifty years ago, David Turnbull showed that the temperature of many metallic liquids could be decreased far below their equilibrium melting temperature before crystallization occurred. To explain those surprising results, Charles Frank hypothesized that the local structures of undercooled metallic liquids are different from those of crystal phases, containing a significant degree of icosahedral order that is incompatible with extended periodicity. Such structural differences must create a barrier to the formation crystal phases, explaining the observed undercooling behavior. If true, the nucleation from the liquid of phases with extended icosahedral order should be easier. Icosahedral order is often favored in small clusters, as observed recently in liquid-like clusters of pure Pb on the (111) surface of Si, for example. However, it has never been shown that an increasing preference for icosahedral phase formation can be directly linked with the development of icosahedral order in the undercooled liquid. Owing to the combination of very recent advances in levitation techniques and the availability of synchrotron x-ray and high flux neutron facilities, this is shown here.
The Connection Between Local Icosahedral Order in Metallic Liquids and the Nucleation of Ordered Phases
NASA Technical Reports Server (NTRS)
Kelton, K. F.; Gangopadhyay, A. K.; Lee, G. W.; Hyers, R. W.; Rathz, T. J.; Rogers, J. R.; Robinson, M. B.; Schenk, T.; Simonet, V.; Holland-Moritz, D.; Curreri, Peter A. (Technical Monitor)
Over fifty years ago, David Turnbull showed that the temperature of many metallic liquids could be decreased far below their equilibrium melting temperature before crystallization occurred. To explain those surprising results, Charles Frank hypothesized that the local structures of undercooled metallic liquids are different from those of crystal phases, containing a significant degree of icosahedral order that is incompatible with extended periodicity. Such structural differences must create a barrier to the formation crystal phases, explaining the observed undercooling behavior. If true, the nucleation from the liquid of phases with extended icosahedral order should be easier. Icosahedral order is often favored in small clusters, as observed recently in liquid-like clusters of pure Pb on the (111) surface of Si(3), for example. However, it has never been shown that an increasing preference for icosahedral phase formation can be directly linked with the development of icosahedral order in the undercooled liquid. Owing to the combination of very recent advances in levitation techniques and the availability of synchrotron X-ray and high flux neutron facilities.
The Connection Between Local Icosahedral Order in Metallic Liquids and the Nucleation Behavior of Ordered Phases
NASA Technical Reports Server (NTRS)
Kelton, K. F.; Gangopadhyay, A. K.; Lee, G. W.; Hyers, R. W.; Rathz, T. J.; Rogers, J. R.; Robinson, M. B.; Schenk, T.; Simonet, V.
Over fifty years ago, David Turnbull showed that the temperature of many metallic liquids could be decreased far below their equilibrium melting temperature before crystallization occurred. To explain those surprising results, Charles Frank hypothesized that the local structures of undercooled metallic liquids are different from those of crystal phases, containing a significant degree of icosahedral order that is incompatible with extended periodicity. Such structural differences must create a barrier to the formation crystal phases, explaining the observed undercooling behavior. If true, the nucleation from the liquid of phases with extended icosahedral order should be easier. Icosahedral order is often favored in small clusters, as observed recently in liquid-like clusters of pure Pb on the (111) surface of Si[3], for example. However, it has never been shown that an increasing preference for icosahedral phase formation can be directly linked with the development of icosahedral order in the undercooled liquid. Owing to the combination of very recent advances in levitation techniques and the availability of synchrotron x-ray and high flux neutron facilities, this is shown here.
Accurate design of megadalton-scale two-component icosahedral protein complexes.
Bale, Jacob B; Gonen, Shane; Liu, Yuxi; Sheffler, William; Ellis, Daniel; Thomas, Chantz; Cascio, Duilio; Yeates, Todd O; Gonen, Tamir; King, Neil P; Baker, David
Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines. PMID:27463675
Ultrathin Icosahedral Pt-Enriched Nanocage with Excellent Oxygen Reduction Reaction Activity.
He, Dong Sheng; He, Daping; Wang, Jing; Lin, Yue; Yin, Peiqun; Hong, Xun; Wu, Yuen; Li, Yadong
Cost-efficient utilization of Pt in the oxygen reduction reaction (ORR) is of great importance for the potential industrial scale demand of proton-exchange membrane fuel cells. Designing a hollow structure of a Pt catalyst offers a great opportunity to enhance the electrocatalytic performance and maximize the use of precious Pt. Herein we report a routine to synthesize ultrathin icosahedral Pt-enriched nanocages. In detail, the Pt atoms were conformally deposited on the surface of Pd icosahedral seeds, followed by selective removal of the Pd core by a concentrated HNO3 solution. The icosahedral Pt-enriched nanocage that is a few atomic layers thick includes the merits of abundant twin defects, an ultrahigh surface/volume ratio, and an ORR-favored Pt{111} facet, all of which have been demonstrated to be promoting factors for ORR. With a 10 times higher specific activity and 7 times higher mass activity, this catalyst shows more extraordinary ORR activity than the commercial Pt/C. The ORR activity of icosahedral Pt-enriched nanocages outperforms the cubic and octahedral nanocages reported in the literature, demonstrating the superiority of the icosahedral nanocage structure. PMID:26808073
Superior room-temperature ductility of typically brittle quasicrystals at small sizes
Zou, Yu; Kuczera, Pawel; Sologubenko, Alla; Sumigawa, Takashi; Kitamura, Takayuki; Steurer, Walter; Spolenak, Ralph
The discovery of quasicrystals three decades ago unveiled a class of matter that exhibits long-range order but lacks translational periodicity. Owing to their unique structures, quasicrystals possess many unusual properties. However, a well-known bottleneck that impedes their widespread application is their intrinsic brittleness: plastic deformation has been found to only be possible at high temperatures or under hydrostatic pressures, and their deformation mechanism at low temperatures is still unclear. Here, we report that typically brittle quasicrystals can exhibit remarkable ductility of over 50% strains and high strengths of ∼4.5 GPa at room temperature and sub-micrometer scales. In contrast to the generally accepted dominant deformation mechanism in quasicrystals—dislocation climb, our observation suggests that dislocation glide may govern plasticity under high-stress and low-temperature conditions. The ability to plastically deform quasicrystals at room temperature should lead to an improved understanding of their deformation mechanism and application in small-scale devices. PMID:27515779
Interactions among K+-Ca2+ Exchange, Sorption of m-Dinitrobenzene, and Smectite Quasicrystal Dynamics
Technology Transfer Automated Retrieval System (TEKTRAN)
The fate of organic compounds in soils and sediments is influenced by sorption of the compounds on surfaces of soil materials. We investigated the interaction among sorption of an organic compound, cation exchange reactions, and both the size and swelling of smectite quasicrystals. Two reference sme...
Study of the structure and physical properties of quasicrystals using large scale facilities
NASA Astrophysics Data System (ADS)
de Boissieu, Marc
Quasicrystals have been puzzling scientists since their discovery. In this article we review some of the recent advances in this field and show how the use of large scale facilities has brought in decisive information for the understanding of their structure and physical properties.
Group theory of icosahedral virus capsid vibrations: a top-down approach.
Peeters, Kasper; Taormina, Anne
We explore the use of a top-down approach to analyse the dynamics of icosahedral virus capsids and complement the information obtained from bottom-up studies of viral vibrations available in the literature. A normal mode analysis based on protein association energies is used to study the frequency spectrum, in which we reveal a universal plateau of low-frequency modes shared by a large class of Caspar-Klug capsids. These modes break icosahedral symmetry and are potentially relevant to the genome release mechanism. We comment on the role of viral tiling theory in such dynamical considerations. PMID:19014954
Global ocean simulations by HYCOM on icosahedral and logically rectangular grids
NASA Astrophysics Data System (ADS)
Sun, Shan; Bleck, Rainer
iHYCOM, short for "icosahedral HYbrid Coordinate Ocean Model", is being developed at the NOAA Earth System Research Laboratory. The purpose of formulating HYCOM on an icosahedral grid is to allow coupling to an existing icosahedral weather prediction model ("FIM", see http://fim.noaa.gov) unencumbered by interpolation problems at the air-sea-ice interface. We have tested the traditional HYCOM, formulated on a Mercator grid augmented by a bipolar pole patch, with iHYCOM for several decades at comparable horizontal mesh sizes in the 0.5-1.0 deg range, employing the same vertical resolution of 26 potential density (sigma_1) layers. These comparison runs were forced by CORE (Common Ocean-Ice Reference Experiment) fields. Several performance measures indicate that formulating HYCOM on an icosahedral mesh is feasible, although a numerically stable barotropic-baroclinic mode splitting scheme is not available yet. We compare the large scale circulations simulated by both model versions and investigate the model sensitivity to different horizontal grids.
Studies of Inactivation Mechanism of non-enveloped icosahedral viruses by a visible ultrashort pulsed laser
Technology Transfer Automated Retrieval System (TEKTRAN)
The inactivation mechanism of ultrashort pulsed laser irradiation at a wavelength of 425 nm has been studied using two different-sized, non-enveloped icosahedral viruses, murine norovirus-1 (MNV-1) and human papillomavirus-16 (HPV-16) pseudovirions. Our experimental results are consistent with a mo...
Capping-agent-free synthesis of substrate-supported porous icosahedral gold nanoparticles
NASA Astrophysics Data System (ADS)
Wu, Ji Hong; Guan, Zhenping; Yang, Su Ke; Yuan, Peiyan; Xu, Qing-Hua; Xu, Guo Qin
We report a new capping-agent-free strategy for the synthesis of substrate-supported porous icosahedral Au nanoparticles (NPs) with rough naked surfaces, based on the crystallization from substrate-supported thin solution layers followed by solid-phase thermolysis. The plasmonic properties of icosahedral Au NPs have been studied using single particle dark-field scattering microscopy and spectroscopy. The two distinct localized surface plasmon resonance (LSPR) bands observed in the single particle dark-field spectra can be ascribed to the quadrupole resonance at ca. 425 nm and the size-dependent dipole resonance in the red region (645-708 nm). The unique rough naked surface, the facile synthesis, together with the ability to control the nanoparticle size and to vary the LSPR frequency in the red region, would make the substrate-supported porous icosahedral Au NPs promising on multiple levels in the applications of catalysis, ultrasensitive biosensors, and in surface-enhanced Raman scattering (SERS).We report a new capping-agent-free strategy for the synthesis of substrate-supported porous icosahedral Au nanoparticles (NPs) with rough naked surfaces, based on the crystallization from substrate-supported thin solution layers followed by solid-phase thermolysis. The plasmonic properties of icosahedral Au NPs have been studied using single particle dark-field scattering microscopy and spectroscopy. The two distinct localized surface plasmon resonance (LSPR) bands observed in the single particle dark-field spectra can be ascribed to the quadrupole resonance at ca. 425 nm and the size-dependent dipole resonance in the red region (645-708 nm). The unique rough naked surface, the facile synthesis, together with the ability to control the nanoparticle size and to vary the LSPR frequency in the red region, would make the substrate-supported porous icosahedral Au NPs promising on multiple levels in the applications of catalysis, ultrasensitive biosensors, and in surface
Formation of quasi-icosahedral structures with multi-conjoint fivefold deformation twins in fivefold twinned metallic nanowires
NASA Astrophysics Data System (ADS)
Jiang, Shan; Shen, Yonggang; Zheng, Yonggang; Chen, Zhen
We show by molecular dynamics simulations that symmetrical quasi-icosahedral structures can be formed in fivefold twinned metallic nanowires (Cu, Au, and Ag) under dynamic tensile loading. The quasi-icosahedral structure, different from the icosahedral nanoclusters found in the past, consists of a twisted original fivefold twinned axis and ten secondary fivefold deformation twins, with five preexisting prismatic and fifteen tetrahedral subunits joined adjacently. Formation of these structures is observed in the necking region during the plastic deformation with successive twinning processes and is found to be independent on the cross-sectional shape as well as the tensile strain rate of the nanowires.
A simple configuration for fabrication of 2D and 3D photonic quasicrystals with complex structures
NASA Astrophysics Data System (ADS)
Sun, XiaoHong; Wang, Shuai; Liu, Wei; Jiang, LiuDi
A simple method using a single-prism common-path interferometer is presented for the fabrication of complex quasicrystals in sub-micrometer scales. Multiple types of two-dimensional (2D) and three-dimensional (3D) quasicrystalline structures are designed and their diffraction patterns are obtained by using Fourier Transform method. Multi-fold rotational symmetries are demonstrated and compared. By using this method, a wide range of quasicrystals types can be produced with arbitrary complexities and rotational symmetries. The transmittance studies of 12-fold and 18-fold structures also reveal the existence of complete photonic bandgaps, which also demonstrates increased symmetry and significantly improved characteristics of photonic band-gaps.
Non-Fermi-Liquid Behavior in Metallic Quasicrystals with Local Magnetic Moments.
Andrade, Eric C; Jagannathan, Anuradha; Miranda, Eduardo; Vojta, Matthias; Dobrosavljević, Vladimir
Motivated by the intrinsic non-Fermi-liquid behavior observed in the heavy-fermion quasicrystal Au51Al34Yb15, we study the low-temperature behavior of dilute magnetic impurities placed in metallic quasicrystals. We find that a large fraction of the magnetic moments are not quenched down to very low temperatures T, leading to a power-law distribution of Kondo temperatures P(T(K))∼T(K)(α-1), with a nonuniversal exponent α, in a remarkable similarity to the Kondo-disorder scenario found in disordered heavy-fermion metals. For α<1, the resulting singular P(T(K)) induces non-Fermi-liquid behavior with diverging thermodynamic responses as T→0. PMID:26230810
Non-Fermi-Liquid Behavior in Metallic Quasicrystals with Local Magnetic Moments
NASA Astrophysics Data System (ADS)
Andrade, Eric C.; Jagannathan, Anuradha; Miranda, Eduardo; Vojta, Matthias; Dobrosavljević, Vladimir
Motivated by the intrinsic non-Fermi-liquid behavior observed in the heavy-fermion quasicrystal Au51Al34Yb15 , we study the low-temperature behavior of dilute magnetic impurities placed in metallic quasicrystals. We find that a large fraction of the magnetic moments are not quenched down to very low temperatures T , leading to a power-law distribution of Kondo temperatures P (TK)˜TKα -1, with a nonuniversal exponent α , in a remarkable similarity to the Kondo-disorder scenario found in disordered heavy-fermion metals. For α <1 , the resulting singular P (TK) induces non-Fermi-liquid behavior with diverging thermodynamic responses as T →0 .
Harmonic response of multilayered one-dimensional quasicrystal plates subjected to patch loading
NASA Astrophysics Data System (ADS)
Waksmanski, Natalie; Pan, Ernian; Yang, Lian-Zhi; Gao, Yang
Dynamic analyses of a multilayered one-dimensional quasicrystal plate subjected to a patch harmonic loading with simply supported lateral boundary conditions are presented. The pseudo-Stroh formulation and propagator matrix method are used to obtain the exact three-dimensional response of the plate. In order to avoid resonance, the frequency of the patch loading is chosen away from the natural frequencies by introducing a small imaginary part. The patch loading is expressed in the form of a double Fourier series expansion. Comprehensive numerical results are shown for a sandwich plate with two different stacking sequences. The results reveal the influence of layering, loading area, phonon-phason coupling coefficient and input frequency. This work is the first step towards understanding quasicrystals under intricate loading conditions such as indentation and impact, and the exact closed-form solution can serve as a reference in convergence studies of other numerical methods and for verification of existing or future plate theories.
Icosahedral stereographic projections in three dimensions for use in dark field TEM.
Bourdillon, Antony J
Thermodynamics require that rapidly cooled crystals and quasicrystals are relatively defective. Yet, without convenient 3-dimensional indexation both at crystal poles and in diffraction planes, or Kikuchi maps, it is difficult to identify the defects by dark field transmission electron microscopy. For two phase Al6Mn, these maps are derived. They relate i-Al6Mn to the standard face centered cubic, matrix crystals. An example of their usefulness in determining interfacial characteristics is described. Indices are integral powers on an irrational number. PMID:23850135
Opening of an icosahedral boron framework: A combined infrared spectroscopic and computational study
NASA Astrophysics Data System (ADS)
Fagiani, Matias R.; Liu Zeonjuk, L.; Esser, Tim K.; Gabel, Detlef; Heine, Thomas; Asmis, Knut R.; Warneke, Jonas
The opening of an icosahderal boron cage in the periodinated closo-dodecaborate B12I122- upon deiodination is studied using cryogenic ion trap vibrational spectroscopy combined with electronic structure calculations. Comparison of simulated vibrational spectra to the infrared photodissociation spectra of messenger-tagged B12I122- and B12In- (n = 7-9) formed by skimmer collision induced dissociation shows that the larger clusters absorb exclusively below 975 cm-1 and hence exhibit quasi-icosahedral B12-cage structures, while the higher energy absorptions in-between 1000 and 1300 cm-1 observed for n = 7 can only be recovered by considering a breakup of the icosahedral cage upon deiodination from n = 8 to n = 7.
Dual-phase glassy/nanoscale icosahedral phase materials in Cu–Zr–Ti–Pd system alloys
Louzguine-Luzgin, Dmitri V.; Churyumov, A.Yu.
The present work is devoted to an investigation of the formation kinetics, stability and homogeneity area of the nanoscale icosahedral phase formed on heating in the dual-phase glassy/quasicrystalline phase Cu–Zr–Ti–Pd alloys. The data obtained indicate that the Cu–Zr–Ti–Pd icosahedral phase is not a Cu-rich part of the compositional homogeneity area of the Zr–Cu–Pd one. Moreover, Ti, as well as Pd, is found to be an important element stabilizing quasicrystalline phase in the Cu–Zr–Ti–Pd alloys. The formation criteria for Cu- and Zr/Hf-based icosahedral phases are discussed based on the quasilattice constant to average atomic diameter ratio. Deviation from a certain ratio leads to destabilization of the icosahedral phase. By using the isothermal calorimetry traces transformation kinetics above and below the glass-transition region was analyzed. Some difference in the transformation kinetics above and below the glass-transition region allows us to suggest that possible structure changes occur upon glass-transition. - Highlights: • Formation kinetics, stability and homogeneity area of nanoscale icosahedral phase • Cu–Zr–Ti–Pd icosahedral phase is not a Cu-rich part of Zr–Cu–Pd one. • Ti, as well as Pd, is an important element stabilizing quasicrystalline phase. • Difference in transformation kinetics above and below glass-transition region.
Vibration isolation support system for a truncated icosahedral gravitational wave antenna
NASA Astrophysics Data System (ADS)
Velloso, W. F.; Melo, J. L.; Aguiar, O. D.
We designed a mechanical isolation system for an icosahedral resonant gravitational wave detector we plan to construct in Brazil. We have used the NASTRAN finite element software to perform the numerical analysis. Our results show that the designed system could allow a damping factor better than -200 dB in the spectral range of interest, which is adequate to the sensibility level we want for the antenna.
Icosahedral symmetry breaking: C(60) to C(84), C(108) and to related nanotubes.
Bodner, Mark; Bourret, Emmanuel; Patera, Jiri; Szajewska, Marzena
This paper completes the series of three independent articles [Bodner et al. (2013). Acta Cryst. A69, 583-591, (2014), PLOS ONE, 10.1371/journal.pone.0084079] describing the breaking of icosahedral symmetry to subgroups generated by reflections in three-dimensional Euclidean space {\\bb R}^3 as a mechanism of generating higher fullerenes from C60. The icosahedral symmetry of C60 can be seen as the junction of 17 orbits of a symmetric subgroup of order 4 of the icosahedral group of order 120. This subgroup is noted by A1 × A1, because it is isomorphic to the Weyl group of the semi-simple Lie algebra A1 × A1. Thirteen of the A1 × A1 orbits are rectangles and four are line segments. The orbits form a stack of parallel layers centered on the axis of C60 passing through the centers of two opposite edges between two hexagons on the surface of C60. These two edges are the only two line segment layers to appear on the surface shell. Among the 24 convex polytopes with shell formed by hexagons and 12 pentagons, having 84 vertices [Fowler & Manolopoulos (1992). Nature (London), 355, 428-430; Fowler & Manolopoulos (2007). An Atlas of Fullerenes. Dover Publications Inc.; Zhang et al. (1993). J. Chem. Phys. 98, 3095-3102], there are only two that can be identified with breaking of the H3 symmetry to A1 × A1. The remaining ones are just convex shells formed by regular hexagons and 12 pentagons without the involvement of the icosahedral symmetry. PMID:25921498
Binary icosahedral flavor symmetry for four generations of quarks and leptons
NASA Astrophysics Data System (ADS)
Chen, Chian-Shu; Kephart, Thomas W.; Yuan, Tzu-Chiang
To include the quark sector, the A5≡ I (icosahedron) four generation lepton model is extended to a binary icosahedral symmetry I' flavor model. We find that the masses of fermions, including the heavy sectors, can be accommodated. At leading order the Cabibbo-Kobayashi-Maskawa (CKM) matrix is the identity and the Pontecorvo-Maki-Nakagawa-Sakata (PMNS) matrix, resulting from the same set of vacua, corresponds to tribimaximal mixings.
Virus-Templated Plasmonic Nanoclusters with Icosahedral Symmetry via Directed Self-Assembly
Fontana, Jake; Dressick, Walter J; Phelps, Jamie; Johnson, John E; Rendell, Ronald W; Sampson, Travian; Ratna, Banahalli R; Soto, Carissa M
The assembly of plasmonic nanoparticles with precise spatial and orientational order may lead to structures with new electromagnetic properties at optical frequencies. The directed self-assembly method presented controls the interparticle-spacing and symmetry of the resulting nanometer-sized elements in solution. The self-assembly of three-dimensional (3D), icosahedral plasmonic nanosclusters (NCs) with resonances at visible wavelengths is demonstrated experimentally. The ideal NCs consist of twelve gold (Au) nanospheres (NSs) attached to thiol groups at predefined locations on the surface of a genetically engineered cowpea mosaic virus with icosahedral symmetry. In situ dynamic light scattering (DLS) measurements confirm the NSs assembly on the virus. Transmission electron micrographs (TEM) demonstrate the ability of the self-assembly method to control the nanoscopic symmetry of the bound NSs, which reflects the icosahedral symmetry of the virus. Both, TEM and DLS show that the NCs comprise of a distribution of capsids mostly covered (i.e., 6–12 NS/capsid) with NSs. 3D finite-element simulations of aqueous suspensions of NCs reproduce the experimental bulk absorbance measurements and major features of the spectra. Simulations results show that the fully assembled NCs give rise to a 10-fold surface-averaged enhancement of the local electromagnetic field. PMID:24733721
Photonic band gaps and planar cavity of two-dimensional eightfold symmetric void-channel photonic quasicrystals
NASA Astrophysics Data System (ADS)
Zhou, Guangyong; Gu, Min
By using the femtosecond laser induced microexplosion method, high-quality two-dimensional eightfold photonic quasicrystals have been fabricated in a solid transparent polymer material. Multiorder band gaps have been observed in a 25-layer structure with a suppression rate of up to 72% for the fundamental gap. Polarization measurements show that the photonic quasicrystal has a strong anisotropic effect, showing that the transverse electric is the favorite polarization. Fabry-Pérot cavities have been fabricated by removing the central layer of channels. Based on the cavity mode position, the order of the mode and the effective cavity size have been determined.
Structural and electronic properties of Li- and Cu-doped β-rhombohedral boron constructed from icosahedral and truncated icosahedral clusters
NASA Astrophysics Data System (ADS)
Matsuda, H.; Nakayama, T.; Kimura, K.; Murakami, Y.; Suematsu, H.; Kobayashi, M.; Higashi, I.
This study performs dc conductivity and static magnetic-susceptibility measurements on Li- and Cu-doped β-rhombohedral boron (β-rhombohedral B), which is a unique polymorphic semiconducting (group III) material composed of B12 icosahedral clusters. dc conductivity results show a variable-range-hopping (VRH)-type temperature dependence with a typical localization length of about ~1 Å. In addition, the density of states (DOS) at the Fermi energy, which is calculated from fitted parameters of VRH conduction, was found to have a peak with respect to metal concentration, such that at the highest concentration (Li7.9B105 and Cu4.2B105), metal-doped β-rhombohedral B appears to revert back to an insulator, instead of showing insulator-to-metal transition. Corresponding static magnetic-susceptibility results, however, show a contribution from Pauli paramagnetism in the temperature-independent component χ0, where a similar concentration dependence is shows to that in the DOS of VRH conduction. Based on these properties, we discuss the possibility of filling the intrinsic acceptor band, which originates from the uppermost molecular bonding orbital of the B12 icosahedral cluster that is split by the Jahn-Teller effect. β-rhombohedral B's crystalline structure can also be viewed as a slightly distorted face-centered cubic (fcc) packing of B84 soccer-ball-shaped clusters covalently bound to each other and containing a relatively large number of large-size interstitial doping sites. This structure is considered to be topologically similar to that of fcc C60, although the bonding mechanisms of their clusters are different, and therefore we also describe the similarities and differences between them.
Fundamental solutions in a half space of two-dimensional hexagonal quasicrystal and their applications
Wang, T.; Li, X. Y.; Zhang, X.; Müller, R.
Fundamental phonon-phason field in a half-infinite space of two-dimensional hexagonal quasicrystal is derived, on the basis of general solutions in terms of quasi-harmonic functions, by virtue of the trial-and-error technique. Extended Boussinesq and Cerruti problems are studied. Appropriate potential functions are assumed and corresponding fundamental solutions are explicitly derived in terms of elementary functions. The boundary integral equations governing the contact and crack problems are constructed from the present fundament solutions. The obtained analytical solutions can serve as guidelines for future indentation tests via scanning probe microscopy and atomic force microscopy methods.
Direct imaging of coexisting ordered and frustrated sublattices in artificial ferromagnetic quasicrystals
NASA Astrophysics Data System (ADS)
Farmer, B.; Bhat, V. S.; Balk, A.; Teipel, E.; Smith, N.; Unguris, J.; Keavney, D. J.; Hastings, J. T.; De Long, L. E.
We have used scanning electron microscopy with polarization analysis and photoemission electron microscopy to image the two-dimensional magnetization of permalloy films patterned into Penrose P2 tilings (P2T). The interplay of exchange interactions in asymmetrically coordinated vertices and short-range dipole interactions among connected film segments stabilize magnetically ordered, spatially distinct sublattices that coexist with frustrated sublattices at room temperature. Numerical simulations that include long-range dipole interactions between sublattices agree with images of as-grown P2T samples and predict a magnetically ordered ground state for a two-dimensional quasicrystal lattice of classical Ising spins.
A 3-D Finite-Volume Non-hydrostatic Icosahedral Model (NIM)
NASA Astrophysics Data System (ADS)
Lee, Jin
The Nonhydrostatic Icosahedral Model (NIM) formulates the latest numerical innovation of the three-dimensional finite-volume control volume on the quasi-uniform icosahedral grid suitable for ultra-high resolution simulations. NIM's modeling goal is to improve numerical accuracy for weather and climate simulations as well as to utilize the state-of-art computing architecture such as massive parallel CPUs and GPUs to deliver routine high-resolution forecasts in timely manner. NIM dynamic corel innovations include: * A local coordinate system remapped spherical surface to plane for numerical accuracy (Lee and MacDonald, 2009), * Grid points in a table-driven horizontal loop that allow any horizontal point sequence (A.E. MacDonald, et al., 2010), * Flux-Corrected Transport formulated on finite-volume operators to maintain conservative positive definite transport (J.-L, Lee, ET. Al., 2010), *Icosahedral grid optimization (Wang and Lee, 2011), * All differentials evaluated as three-dimensional finite-volume integrals around the control volume. The three-dimensional finite-volume solver in NIM is designed to improve pressure gradient calculation and orographic precipitation over complex terrain. NIM dynamical core has been successfully verified with various non-hydrostatic benchmark test cases such as internal gravity wave, and mountain waves in Dynamical Cores Model Inter-comparisons Projects (DCMIP). Physical parameterizations suitable for NWP are incorporated into NIM dynamical core and successfully tested with multimonth aqua-planet simulations. Recently, NIM has started real data simulations using GFS initial conditions. Results from the idealized tests as well as real-data simulations will be shown in the conference.
3-dimensional indexation of the icosahedral diffraction pattern using the techniques of electron microscopy
NASA Astrophysics Data System (ADS)
Bourdillon, Antony
The following facts about icosahedra need wider attention. 1) The golden section τ is as fundamental to the icosahedral structure (length /edge) as π is to the sphere (circumference /diameter). 2) The diffraction series are in restricted Fibonacci order because the ratio of adjacent terms fn/fn-1 does not vary, but is the constant τ. The series is therefore geometric. 3) Because of the tetragonal subgroup in the icosahedral point group symmetry, many axes in the icosahedral structure have identical orientation to axes in the face centered cubic matrix of Al6Mn [1] (e.g. [100] and [111]). On these bases, a three dimensional stereographic projection will be presented. 4) A quasi-Bragg law is derived that correctly represents the diffraction series in powers of τ [2]. Furthermore, by employing the normal conventions of electron microscopy, all diffraction patterns are completely indexed in three dimensions. These are the topic of this presentation. Significant consequences will be presented elsewhere: 1) The diffraction pattern intensities near all main axes are correctly simulated, and all atoms are located on a specimen image. 2) The quasi-Bragg law has a special metric. Atomic locations are consistently calculated for the first time. 3) Whereas the Bragg law transforms a crystal lattice in real space into a reciprocal lattice in diffraction space, the quasi-Bragg law transforms a geometric diffraction pattern into a hierarchic structure. 4) Hyperspatial indexation [3] is superceded. [1] Shechtman, D.; Blech, I.; Gratias, D.; Cahn, J.W., Metallic phase with long-range orientational order and no translational symmetry, Phys. Rev. Lett., 1984, 53, 1951-3. [2] Bourdillon, A. J., Nearly free electron band structures in a logarithmically periodic solid, Sol. State Comm. 2009, 149, 1221-1225. [3] Duneau, M., and Katz, A., Phys Rev Lett 54, 2688-2691
3 nj-symbols and harmonic superposition coefficients: an icosahedral abacus
NASA Astrophysics Data System (ADS)
Aquilanti, Vincenzo; Coletti, Cecilia
Angular momentum recoupling coefficients of angular momentum theory and matrix elements for basis set transformation of hyperspherical harmonics enjoy properties and sum rules crucial for applications but complicated without the guidance of graphical techniques. These coefficients being related to Racah's polynomials, the graphs also apply to polynomials of the hypergeometric family, their q-analogues and their `elliptic' extensions. A useful `abacus' exploiting the connections with presentations of icosahedral and related symmetries is introduced. Particular and limiting cases, such as those of the semiclassical type, allow a unified view of properties of angular and hyperangular momentum algebra, including relationships among vector coupling coefficients and rotation matrix elements.
Human Rhinovirus Subviral A Particle Binds to Lipid Membranes over a Twofold Axis of Icosahedral Symmetry
Kumar, Mohit
Minor group human rhinoviruses bind low-density lipoprotein (LDL) receptors for endocytosis. Once they are inside endosomes, the acidic pH triggers their dissociation from the receptors and conversion into hydrophobic subviral A particles; these attach to the membrane and transfer their single-strand, positive-sense RNA genome into the cytosol. Here, we allowed human rhinovirus 2 (HRV2) A particles, produced in vitro by incubation at pH 5.4, to attach to liposomes; cryo-electron microscopy 3-dimensional single-particle image reconstruction revealed that they bind to the membrane around a 2-fold icosahedral symmetry axis. PMID:23946453
Studies of inactivation mechanism of non-enveloped icosahedral virus by a visible ultrashort pulsed laser
Background Low-power ultrashort pulsed (USP) lasers operating at wavelengths of 425 nm and near infrared region have been shown to effectively inactivate viruses such as human immunodeficiency virus (HIV), M13 bacteriophage, and murine cytomegalovirus (MCMV). It was shown previously that non-enveloped, helical viruses such as M13 bacteriophage, were inactivated by a USP laser through an impulsive stimulated Raman scattering (ISRS) process. Recently, enveloped virus like MCMV has been shown to be inactivated by a USP laser via protein aggregation induced by an ISRS process. However, the inactivation mechanism for a clinically important class of viruses – non-enveloped, icosahedral viruses remains unknown. Results and discussions We have ruled out the following four possible inactivation mechanisms for non-enveloped, icosahedral viruses, namely, (1) inactivation due to ultraviolet C (UVC) photons produced by non-linear optical process of the intense, fundamental laser beam at 425 nm; (2) inactivation caused by thermal heating generated by the direct laser absorption/heating of the virion; (3) inactivation resulting from a one-photon absorption process via chromophores such as porphyrin molecules, or indicator dyes, potentially producing reactive oxygen or other species; (4) inactivation by the USP lasers in which the extremely intense laser pulse produces shock wave-like vibrations upon impact with the viral particle. We present data which support that the inactivation mechanism for non-enveloped, icosahedral viruses is the impulsive stimulated Raman scattering process. Real-time PCR experiments show that, within the amplicon size of 273 bp tested, there is no damage on the genome of MNV-1 caused by the USP laser irradiation. Conclusion We conclude that our model non-enveloped virus, MNV-1, is inactivated by the ISRS process. These studies provide fundamental knowledge on photon-virus interactions on femtosecond time scales. From the analysis of the transmission
Experimentally Founded Charge Transport Model for Icosahedral Boron-Rich Solids
NASA Astrophysics Data System (ADS)
Werheit, Helmut
Charge transport in icosahedral boron-rich solids, in particular in boron carbide, has been controversially discussed. Theoretical band structure calculations, based on idealized instead of real structures, yield qualitatively wrong results; metallic instead of semiconducting behavior in consequence of neglecting intrinsic structural defects. The theoretical bipolaron hypothesis is not compatible with numerous experimental results. In contrast, the actual energy band schemes of β-rhombohedral boron and boron carbide mainly derived from optical investigations allows the consistent description of most of the experimental results. Electronic transport is a superposition of hopping-type and band-type transport, whose share depends on the actual conditions and the antecedent.
First observation of ferromagnetic order in an artificial 2D quasicrystal
NASA Astrophysics Data System (ADS)
Farmer, Barry; Bhat, Vinayak; Balk, Andrew; Unguris, John; de Long, Lance
Magnetic order in bulk quasicrystals is not well understood and known materials exhibit short-range, spin-glass order. We patterned ferromagnetic (FM) thin films into artificial quasicrystals, a new class of metamaterials that exhibits complex magnetic reversal and dynamics that can be controlled via tiling design. We analyzed two-dimensional SEMPA images of magnetization textures of Penrose P2 tilings (P2T) patterned into Permalloy. The diverse, asymmetric vertex coordinations drive novel, non-stochastic switching and complex spin-ice behaviors that reflect the influence of vertex domain wall energies. Monte Carlo and OOMMF simulation analyses of SEMPA images of slowly grown, never-field-cycled P2T reveal low energy, long-range ordered sublattices that form building blocks of a ground state. A fully ordered ground state is unresolved without long-range dipolar interactions that stabilize a magnetically ordered state with a net moment. Our P2T constitute a set of quasicrystalline metamaterials in which frustration and magnetic order among classical Ising spins can be directly studied. Kentucky research supported by U.S. DoE Grant DE-FG02-97ER45653 and NSF Grant EPS-0814194. ALB acknowledges support under the Cooperative Research Agreement between the University of Maryland and NIST.
Origin of Quantum Criticality in Yb-Al-Au Approximant Crystal and Quasicrystal
NASA Astrophysics Data System (ADS)
Watanabe, Shinji; Miyake, Kazumasa
To get insight into the mechanism of emergence of unconventional quantum criticality observed in quasicrystal Yb15Al34Au51, the approximant crystal Yb14Al35Au51 is analyzed theoretically. By constructing a minimal model for the approximant crystal, the heavy quasiparticle band is shown to emerge near the Fermi level because of strong correlation of 4f electrons at Yb. We find that charge-transfer mode between 4f electron at Yb on the 3rd shell and 3p electron at Al on the 4th shell in Tsai-type cluster is considerably enhanced with almost flat momentum dependence. The mode-coupling theory shows that magnetic as well as valence susceptibility exhibits χ ˜ T-0.5 for zero-field limit and is expressed as a single scaling function of the ratio of temperature to magnetic field T/B over four decades even in the approximant crystal when some condition is satisfied by varying parameters, e.g., by applying pressure. The key origin is clarified to be due to strong locality of the critical Yb-valence fluctuation and small Brillouin zone reflecting the large unit cell, giving rise to the extremely-small characteristic energy scale. This also gives a natural explanation for the quantum criticality in the quasicrystal corresponding to the infinite limit of the unit-cell size.
David Adler Lectureship Award in the Field of Materials Physics Talk: Surfaces of Quasicrystals
NASA Astrophysics Data System (ADS)
Thiel, Patricia
Quasiperiodic order is recognized (in a utilitarian, rather than a mathematical sense) by the absence of periodicity, concurrent with a classically-forbidden rotational symmetry. It is quite beautiful, having captured the attention of scientists and artists alike. Following the discovery of quasiperiodic order in a real system,footnotetextD. Shechtman, I. Blech, D. Gratias, and J.W. Cahn, Phys. Rev. Lett. 53, 1951 (1984). many metallic alloys and intermetallics were found to exhibit this type of order on the atomic scale. More recently ``soft'' quasicrystals were discovered,footnotetextL. Bindi, P.J. Steinhardt, N. Yao, and P.J. Lu, Science 324, 1306 (2009). and nanocrystalline arrays were found to spontaneously adopt quasiperiodic order.footnotetextD.V. Talapin, E.V. Shevchenko, M.I. Bodnarchuk, X. Ye, J. Chen, and C.B. Murray, Nature 461 , 964 (2009). From a scientific perspective, quasicrystals are alluring because they allow us to test the relationship between atomic structure and physical properties. This talk deals with the ways in which our understanding of solid surfaces has been both enriched and challenged by these complex materials.footnotetextP. Thiel, Annu. Rev. Phys. Chem. (2008).^,footnotetextV. Fourn'ee, J. Ledieu, and P. Thiel, J. Phys: Condens. Matter. 20, 3310301 (2008). properties of the metallic quasicrystals originally generated interest because they were unusual.footnotetextJ.M. Dubois, Useful Quasicrystals(World Scientific, Singapore, 2005). For instance, among Al-rich alloys, the Al-based quasicrystalline phases exhibit puzzling resistance to surface oxidation. Also, Al-rich quasicrystals have surprisingly good and promising catalytic properties (e.g. for steam reforming of methanol).footnotetextA.P. Tsai and M. Yoshimura, Appl. Cat. A: General 214 , 237 (2001). Perhaps most famously, they exhibit low friction.^7 Comparisons with crystalline materials have established that these features are deeply related to the quasiperiodic atomic
A Vertically Flow-Following, Icosahedral Grid Model for Medium-Range and Seasonal Prediction. Part 1: Model Description
NASA Technical Reports Server (NTRS)
Bleck, Rainer; Bao, Jian-Wen; Benjamin, Stanley G.; Brown, John M.; Fiorino, Michael; Henderson, Thomas B.; Lee, Jin-Luen; MacDonald, Alexander E.; Madden, Paul; Middlecoff, Jacques; Rosinski, James; Smirnova, Tanya G.; Sun, Shan; Wang, Ning
A hydrostatic global weather prediction model based on an icosahedral horizontal grid and a hybrid terrain following/ isentropic vertical coordinate is described. The model is an extension to three spatial dimensions of a previously developed, icosahedral, shallow-water model featuring user-selectable horizontal resolution and employing indirect addressing techniques. The vertical grid is adaptive to maximize the portion of the atmosphere mapped into the isentropic coordinate subdomain. The model, best described as a stacked shallow-water model, is being tested extensively on real-time medium-range forecasts to ready it for possible inclusion in operational multimodel ensembles for medium-range to seasonal prediction.
Molecular dynamics simulation of radiation damage in CaCd{sub 6} quasicrystal cubic approximant up to 10 keV
Chen, P. H.; Avchachov, K.; Nordlund, K.; Pussi, K.
Due to the peculiar nature of the atomic order in quasicrystals, examining phase transitions in this class of materials is of particular interest. Energetic particle irradiation can provide a way to modify the structure locally in a quasicrystal. To examine irradiation-induced phase transitions in quasicrystals on the atomic scale, we have carried out molecular dynamics simulations of collision cascades in CaCd{sub 6} quasicrystal cubic approximant with energies up to 10 keV at 0 and 300 K. The results show that the threshold energies depend surprisingly strongly on the local coordination environments. The energy dependence of stable defect formation exhibits a power-law dependence on cascade energy, and surviving defects are dominated by Cd interstitials and vacancies. Only a modest effect of temperature is observed on defect survival, while irradiation temperature increases lead to a slight increase in the average size of both vacancy clusters and interstitial clusters.
Icosahedral Gold Cage Clusters: M@Au₁₂⁻ (M = V, Nb, and Ta)
Zhai, Hua JIN.; Li, Jun; Wang, Lai S.
We report the observation and characterization of a series of stable bimetallic 18-valence-electron clusters containing a highly symmetric 12-atom icosahedral Au cage with an encapsulated central heteroatom of group VB transition metals, M-Au??? (M = V, Nb, Ta). Electronic and structural properties of these clusters were probed by anion photoelectron spectroscopy and theoretical calculations. Characteristics of the M-Au??? species include their remarkably high binding energies and relatively simple spectral features, which reflect their high symmetry and stability. The adiabatic electronic binding energies of M-Au??? were measured to be 3.70 ? 0.03, 3.77 ? 0.03, and 3.76 ? 0.03 eV for M = V, Nb, and Ta, respectively. Comparison of density functional calculations with experimental data established the highly symmetric icosahedral structures for the 18-electron cluster anions, which may be promising building blocks for cluster-assembled nanomaterials in the form of stoichiometric [M-Au???]X? salts.
Hierarchy of bond stiffnesses within icosahedral-based gold clusters protected by thiolates
Yamazoe, Seiji; Takano, Shinjiro; Kurashige, Wataru; Yokoyama, Toshihiko; Nitta, Kiyofumi; Negishi, Yuichi; Tsukuda, Tatsuya
Unique thermal properties of metal clusters are believed to originate from the hierarchy of the bonding. However, an atomic-level understanding of how the bond stiffnesses are affected by the atomic packing of a metal cluster and the interfacial structure with the surrounding environment has not been attained to date. Here we elucidate the hierarchy in the bond stiffness in thiolate-protected, icosahedral-based gold clusters Au25(SC2H4Ph)18, Au38(SC2H4Ph)24 and Au144(SC2H4Ph)60 by analysing Au L3-edge extended X-ray absorption fine structure data. The Au–Au bonds have different stiffnesses depending on their lengths. The long Au–Au bonds, which are more flexible than those in the bulk metal, are located at the icosahedral-based gold core surface. The short Au–Au bonds, which are stiffer than those in the bulk metal, are mainly distributed along the radial direction and form a cyclic structural backbone with the rigid Au–SR oligomers. PMID:26778685
Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses.
Janner, A
Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article. PMID:27126109
Coupled ocean-atmosphere modeling on horizontally icosahedral and vertically hybrid-isentropic/isopycnic grids.
NASA Astrophysics Data System (ADS)
Bleck, Rainer; Sun, Shan; Li, Haiqin; Benjamin, Stan
Current efforts to close the gap between weather prediction and climate models have led to the construction of a coupled ocean-atmosphere system consisting of two high-resolution component models, operating on matching icosahedral grids and utilizing adaptive, near-isentropic/isopycnic vertical coordinates. The two components models, FIM and HYCOM (the latter converted to an icosahedral mesh for this purpose), have been tested extensively in twice-daily global medium-range weather prediction (http://fim.noaa.gov) and in real-time ocean data assimilation (http://hycom.org), respectively. The use of matching horizontal grids, currently at resolutions of 15km, 30km and 60km, avoids coastline ambiguities and interpolation errors at the air-sea interface. The intended purpose of the coupled model being subseasonal-to-seasonal prediction, our focus is on mid-term precipitation biases and the statistical steadiness of the atmospheric circulation (blocking frequency, Rossby wave breaking, meridional heat transport, etc.), as well as on possible causes of ocean model drift. An attempt is made to isolate the weather model's role in modifying water mass properties and ocean circulations (including meridional overturning) by comparing coupled model results to ocean-only experiments forced by observed atmospheric boundary conditions. A multi-decadal run at 60km resolution is used to illustrate ENSO variability in the coupled system.
Hierarchy of bond stiffnesses within icosahedral-based gold clusters protected by thiolates.
Yamazoe, Seiji; Takano, Shinjiro; Kurashige, Wataru; Yokoyama, Toshihiko; Nitta, Kiyofumi; Negishi, Yuichi; Tsukuda, Tatsuya
Unique thermal properties of metal clusters are believed to originate from the hierarchy of the bonding. However, an atomic-level understanding of how the bond stiffnesses are affected by the atomic packing of a metal cluster and the interfacial structure with the surrounding environment has not been attained to date. Here we elucidate the hierarchy in the bond stiffness in thiolate-protected, icosahedral-based gold clusters Au25(SC2H4Ph)18, Au38(SC2H4Ph)24 and Au144(SC2H4Ph)60 by analysing Au L3-edge extended X-ray absorption fine structure data. The Au-Au bonds have different stiffnesses depending on their lengths. The long Au-Au bonds, which are more flexible than those in the bulk metal, are located at the icosahedral-based gold core surface. The short Au-Au bonds, which are stiffer than those in the bulk metal, are mainly distributed along the radial direction and form a cyclic structural backbone with the rigid Au-SR oligomers. PMID:26778685
Performance Analysis of high-order remap-type advection scheme on icosahedral-hexagonal grid
NASA Astrophysics Data System (ADS)
Mittal, Rashmi; Dubey, Sarvesh; Saxena, Vaibhav; Meurdesoif, Yann
A comparative performance analysis on computational cost of second order advection schemes FF-CSLAM (Flux form conservative semi-Lagrangian multi-tracer transport scheme) and it's two simplifications on Icosahedral grid has been presented. Tracer transport is one of the main building blocks in atmospheric models and hence their performance greatly determines the overall performance of the model. FF-CSLAM falls in the category of arbitrary Lagrangian Eulerian (ALE) scheme. It exploits the finite volume formulation and therefore it is inherently conservative. Flux-area through edges are approximated with great circle arcs in an upwind fashion. Bi-quadratic sub-grid scale reconstructions using weighted least-squares method is employed to approximate trace field. Area integrals on the overlapped region of flux-area and static Eulerian meshes are evaluated via line-integrals. A brief description of implementation of FF-CSLAM on icosahedral -hexagonal meshes along with and its numerical accuracy in terms of standard test cases will be presented. A comparative analysis of the computational overhead is necessary to assess the suitability of FF-CSLAM for massively parallel and multi-threading computer architectures in comparison to other advection schemes implemented on icosahedral grids. The main focus of this work is to present the implementation of the shared memory parallelization and to describe the memory access pattern of the numerical scheme. FF-CSLAM is a remap-type advection scheme, thus extra calculation are done in comparison to the other advection schemes. The additional computations are associated with the search required to find the overlap area between the area swept through the edge and the underlining grid. But the experiments shows that the associated computational overhead is minimal for multi-tracer transport. It will be shown that for the Courant Number less than one, FF-CSLAM, the computations are not expensive. Since the grid cells are arranged in
The Three-Dimensional Finite-Volume Non-Hydrostatic Icosahedral Model (NIM)
NASA Astrophysics Data System (ADS)
Lee, J. L.; MacDonald, A. E.
A multi-scales Non-hydrostatic Icosahedral Model (NIM) has been developed at Earth System Research Laboratory (ESRL) to meet NOAA's future prediction mission ranging from mesoscale short-range, high-impact weather forecasts to longer-term intra-seasonal climate prediction. NIM formulates the latest numerical innovation of the three-dimensional finite-volume control volume on the quasi-uniform icosahedral grid suitable for ultra-high resolution simulations. NIM is designed to utilize the state-of-art computing architecture such as Graphic Processing Units (GPU) processors to run globally at kilometer scale resolution to explicitly resolve convective storms and complex terrains. The novel features of NIM numerical design include: 1.1. A local coordinate system upon which finite-volume integrations are undertaken. The use of a local Cartesian coordinate greatly simplifies the mathematic formulation of the finite-volume operators and leads to the finite-volume integration along straight lines on the plane, rather than along curved lines on the spherical surface. 1.2. A general indirect addressing scheme developed for modeling on irregular grid. It arranges the icosahedral grid with a one-dimensional vector loop structure, table specified memory order, and an indirect addressing scheme that yields very compact code despite the complexities of this grid. 1.3. Use of three-dimensional finite-volume integration over control volumes constructed on the height coordinates. Three-dimensional finite-volume integration accurately represents the Newton Third Law over terrain and improves pressure gradient force over complex terrain. 1.4. Use of the Runge-Kutta 4th order conservative and positive-definite transport scheme 1.5. NIM dynamical solver has been implemented on CPU as well as GPU. As one of the potential candidates for NWS next generation models, NIM dynamical core has been successfully verified with various benchmark test cases including those proposed by DCMIP
Protruding Features of Viral Capsids Are Clustered on Icosahedral Great Circles
Wilson, David P.
Spherical viruses are remarkably well characterized by the Triangulation (T) number developed by Casper and Klug. The T-number specifies how many viral capsid proteins are required to cover the virus, as well as how they are further subdivided into pentamer and hexamer subunits. The T-number however does not constrain the orientations of these proteins within the subunits or dictate where the proteins should place their protruding features. These protrusions often take the form of loops, spires and helices, and are significant because they aid in stability of the capsid as well as recognition by the host organism. Until now there has be no overall understanding of the placement of protrusions for spherical viruses, other than they have icosahedral symmetry. We constructed a set of gauge points based upon the work affine extensions of Keef and Twarock, which have fixed relative angular locations with which to measure the locations of these features. This work adds a new element to our understanding of the geometric arrangement of spherical viral capsid proteins; chiefly that the locations of protruding features are not found stochastically distributed in an icosahedral manner across the viral surface, but instead these features are found only in specific locations along the 15 icosahedral great circles. We have found that this result holds true as the T number and viral capsids size increases, suggesting an underlying geometric constraint on their locations. This is in spite of the fact that the constraints on the pentamers and hexamer orientations change as a function of T-number, as you need to accommodate more hexamers in the same solid angle between pentamers. The existence of this angular constraint of viral capsids suggests that there is a fitness or energetic benefit to the virus placing its protrusions in this manner. This discovery may have profound impacts on identifying and eliminating viral pathogens, understanding evolutionary constraints as well as
Protruding Features of Viral Capsids Are Clustered on Icosahedral Great Circles.
Wilson, David P
Spherical viruses are remarkably well characterized by the Triangulation (T) number developed by Casper and Klug. The T-number specifies how many viral capsid proteins are required to cover the virus, as well as how they are further subdivided into pentamer and hexamer subunits. The T-number however does not constrain the orientations of these proteins within the subunits or dictate where the proteins should place their protruding features. These protrusions often take the form of loops, spires and helices, and are significant because they aid in stability of the capsid as well as recognition by the host organism. Until now there has be no overall understanding of the placement of protrusions for spherical viruses, other than they have icosahedral symmetry. We constructed a set of gauge points based upon the work affine extensions of Keef and Twarock, which have fixed relative angular locations with which to measure the locations of these features. This work adds a new element to our understanding of the geometric arrangement of spherical viral capsid proteins; chiefly that the locations of protruding features are not found stochastically distributed in an icosahedral manner across the viral surface, but instead these features are found only in specific locations along the 15 icosahedral great circles. We have found that this result holds true as the T number and viral capsids size increases, suggesting an underlying geometric constraint on their locations. This is in spite of the fact that the constraints on the pentamers and hexamer orientations change as a function of T-number, as you need to accommodate more hexamers in the same solid angle between pentamers. The existence of this angular constraint of viral capsids suggests that there is a fitness or energetic benefit to the virus placing its protrusions in this manner. This discovery may have profound impacts on identifying and eliminating viral pathogens, understanding evolutionary constraints as well as
Statistical analysis of the formation of icosahedral metallic nanowires under stretching
NASA Astrophysics Data System (ADS)
Peláez, S.; Serena, P. A.; García-Mochales, P.; Paredes, R.; Guerrero, C.
Icosahedral or pentagonal nanowires are formed by subsequent staggered parallel pentagonal rings (with a relative rotation of π/5) connected with single atoms, showing a characteristic -5-1-5-1- ordering. These structures have been found on simulated nanowires of different species [1-3]. However, the statistical study of their formation from stretching of metallic samples has been only addressed for Ni up to date [3,4]. In this work we present an algorithm that allows the automatic identification of pentagonal ring structures. With this methodology we are able to differentiate pentagonal and non-pentagonal regions along the nanowire axis, as well as their lengths. We have obtained for many different nanowires (Al, Ni and Cu, hundreds of ruptures with different crystalline orientations, sizes and temperatures), the distribution of lengths of the pentagonal region Lp as well as the distribution of the number of pentagonal rings np before the nanowire breaks.
Thermal Conductivity and Seebeck Coefficients of Icosahedral Boron Arsenide Films on Silicon Carbide
Y Gong; Y Zhang; M Dudley; Y Zhang; J Edgar; P Heard; M Kuball
The thermal conductivity of icosahedral boron arsenide (B{sub 12}As{sub 2}) films grown on (0001) 6H-SiC substrates by chemical vapor deposition was studied by the 3{omega} technique. The room temperature thermal conductivity decreased from 27.0 to 15.3 W/m K as the growth temperature was decreased from 1450 to 1275 C. This is mainly attributed to the differences in the impurity concentration and microstructure, determined from secondary ion mass spectrometry and high resolution transmission electron microscopy, respectively. Callaway's theory was applied to calculate the temperature-dependent thermal conductivity, and the results are in good agreement with the experimental data. Seebeck coefficients were determined as 107 {micro}V/K and 136 {micro}V/K for samples grown at 1350 C with AsH{sub 3}/B{sub 2}H{sub 6} flow ratio equals to 1:1 and 3:5, respectively.
Defining criteria for oligomannose immunogens for HIV using icosahedral virus capsid scaffolds.
Astronomo, Rena D; Kaltgrad, Eiton; Udit, Andrew K; Wang, Sheng-Kai; Doores, Katie J; Huang, Cheng-Yuan; Pantophlet, Ralph; Paulson, James C; Wong, Chi-Huey; Finn, M G; Burton, Dennis R
The broadly neutralizing antibody 2G12 recognizes a conserved cluster of high-mannose glycans on the surface envelope spike of HIV, suggesting that the "glycan shield" defense of the virus can be breached and may, under the right circumstances, serve as a vaccine target. In an attempt to recreate features of the glycan shield semisynthetically, oligomannosides were coupled to surface lysines on the icosahedral capsids of bacteriophage Q beta and cowpea mosaic virus (CPMV). The Q beta glycoconjugates, but not CPMV, presented oligomannose clusters that bind the antibody 2G12 with high affinity. However, antibodies against these 2G12 epitopes were not detected in immunized rabbits. Rather, alternative oligomannose epitopes on the conjugates were immunodominant and elicited high titers of anti-mannose antibodies that do not crossreact with the HIV envelope. The results presented reveal important design considerations for a carbohydrate-based vaccine component for HIV. PMID:20416507
Reinvestigation of long-range magnetic ordering in icosahedral Tb-Mg-Zn
NASA Astrophysics Data System (ADS)
Islam, Z.; Fisher, I. R.; Zarestky, J.; Canfield, P. C.; Stassis, C.; Goldman, A. I.
We present results of a study of possible magnetic ordering in the icosahedral phase of Tb-Mg-Zn probed by bulk magnetization measurements and neutron diffraction. Measurements on both crushed single grains and cast polycrystalline samples of Tb-Mg-Zn were performed. Magnetization measurements on both samples reveal only a spin-glass-like transition at approximately 5.8 K. Neutron diffraction from the crushed single grains reveals only short-range magnetic ordering at low temperatures, with no evidence of the long-range magnetic ordering reported previously [Charrier, Ouladdiaf, and Schmitt, Phys. Rev. Lett. 78, 4637 (1997)]. Likewise, the cast polycrystalline samples exhibit primarily diffuse magnetic scattering at low temperature, but at least one relatively sharp diffraction peak was observed. Our results indicate that for single grain samples there is no long-range magnetic ordering and that, at best, the magnetic ordering in these quasicrystalline alloys is not very robust.
Structure, Chirality, and Formation of Giant Icosahedral Fullerenes and Spherical Graphitic Onions
Terrones, Mauricio; Terrones, Guillermo ); Terrones, Humberto
We describe the topology, structure, and stability of giant fullerenes exhibiting various symmetries (I, Ih, D2h, T). Our results demonstrate that it is also possible to create two new families of nested-chiral-icosahedral (I) fullerenes namely C260@ C560@ C980@ C1520@..and C140@ C380@ C740@ C1220@..., which exhibit interlayer separations of ca. 3.4. These chiral fullerenes are thought to possess non semiconducting properties. Finally, we study in detail the transformation of polyhedral graphitic particles into quasi-spherical nested giant fullerenes by reorganization of carbon atoms which result in the formation of additional pentagonal and heptagonal carbon rings. These spherical structures are metastable and we believe they could be formed if conditions during formation are extreme such as high energy electron irradiation. There is circumstantial experimental evidence for the presence of heptagonal rings within these spherical fullerenes.
Reinterpretation of the zero-temperature conductivity in icosahedral AlPdRe
NASA Astrophysics Data System (ADS)
Rapp, Ö.
The zero-temperature conductivity σ (0 ) of icosahedral (i )-AlPdRe has been found to be simply related to the resistance ratio R =ρ4.2 K/ρ295 K by a power law, σ (0 ) ˜R-1.74 , over four orders of magnitude in σ (0 ) . This relation includes metallic single grain samples, and polygrain samples of different morphologies which are metallic for small R values, and insulatinglike at large R . Electronic transport properties of single grain i -AlPdRe samples are thus found to be on common ground with polygrain i -AlPdRe. The relation between R and σ (0 ) can be qualitatively understood from published band-structure calculations on quasicrystalline approximants.
Development of a genetic system for the archaeal virus Sulfolobus turreted icosahedral virus (STIV).
Wirth, Jennifer Fulton; Snyder, Jamie C; Hochstein, Rebecca A; Ortmann, Alice C; Willits, Deborah A; Douglas, Trevor; Young, Mark J
Our understanding of archaeal viruses has been limited by the lack of genetic systems for examining viral function. We describe the construction of an infectious clone for the archaeal virus Sulfolobus turreted icosahedral virus (STIV). STIV was isolated from a high temperature (82°C) acidic (pH 2.2) hot spring in Yellowstone National Park and replicates in the archaeal model organism Sulfolobus solfataricus (Rice et al., 2004). While STIV is one of most studied archaeal viruses, little is known about its replication cycle. The development of an STIV infectious clone allows for directed gene disruptions and detailed genetic analysis of the virus. The utility of the STIV infectious clone was demonstrated by gene disruption of STIV open reading frame (ORF) B116 which resulted in crippled virus replication, while disruption of ORFs A197, C381 and B345 was lethal for virus replication. PMID:21496857
Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology.
Legendre, Matthieu; Bartoli, Julia; Shmakova, Lyubov; Jeudy, Sandra; Labadie, Karine; Adrait, Annie; Lescot, Magali; Poirot, Olivier; Bertaux, Lionel; Bruley, Christophe; Couté, Yohann; Rivkina, Elizaveta; Abergel, Chantal; Claverie, Jean-Michel
The largest known DNA viruses infect Acanthamoeba and belong to two markedly different families. The Megaviridae exhibit pseudo-icosahedral virions up to 0.7 μm in diameter and adenine-thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand proteins. Like their Mimivirus prototype discovered 10 y ago, they entirely replicate within cytoplasmic virion factories. In contrast, the recently discovered Pandoraviruses exhibit larger amphora-shaped virions 1 μm in length and guanine-cytosine-rich genomes up to 2.8 Mb long encoding up to 2,500 proteins. Their replication involves the host nucleus. Whereas the Megaviridae share some general features with the previously described icosahedral large DNA viruses, the Pandoraviruses appear unrelated to them. Here we report the discovery of a third type of giant virus combining an even larger pandoravirus-like particle 1.5 μm in length with a surprisingly smaller 600 kb AT-rich genome, a gene content more similar to Iridoviruses and Marseillevirus, and a fully cytoplasmic replication reminiscent of the Megaviridae. This suggests that pandoravirus-like particles may be associated with a variety of virus families more diverse than previously envisioned. This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated a survey of the virome of Siberian permafrost. The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health. PMID:24591590
DYNAMICO-1.0, an icosahedral hydrostatic dynamical core designed for consistency and versatility
NASA Astrophysics Data System (ADS)
Dubos, T.; Dubey, S.; Tort, M.; Mittal, R.; Meurdesoif, Y.; Hourdin, F.
The design of the icosahedral dynamical core DYNAMICO is presented. DYNAMICO solves the multi-layer rotating shallow-water equations, a compressible variant of the same equivalent to a discretization of the hydrostatic primitive equations in a Lagrangian vertical coordinate, and the primitive equations in a hybrid mass-based vertical coordinate. The common Hamiltonian structure of these sets of equations is exploited to formulate energy-conserving spatial discretizations in a unified way. The horizontal mesh is a quasi-uniform icosahedral C-grid obtained by subdivision of a regular icosahedron. Control volumes for mass, tracers and entropy/potential temperature are the hexagonal cells of the Voronoi mesh to avoid the fast numerical modes of the triangular C-grid. The horizontal discretization is that of Ringler et al. (2010), whose discrete quasi-Hamiltonian structure is identified. The prognostic variables are arranged vertically on a Lorenz grid with all thermodynamical variables collocated with mass. The vertical discretization is obtained from the three-dimensional Hamiltonian formulation. Tracers are transported using a second-order finite-volume scheme with slope limiting for positivity. Explicit Runge-Kutta time integration is used for dynamics, and forward-in-time integration with horizontal/vertical splitting is used for tracers. Most of the model code is common to the three sets of equations solved, making it easier to develop and validate each piece of the model separately. Representative three-dimensional test cases are run and analyzed, showing correctness of the model. The design permits to consider several extensions in the near future, from higher-order transport to more general dynamics, especially deep-atmosphere and non-hydrostatic equations.
Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology
Legendre, Matthieu; Bartoli, Julia; Shmakova, Lyubov; Jeudy, Sandra; Labadie, Karine; Adrait, Annie; Lescot, Magali; Poirot, Olivier; Bertaux, Lionel; Bruley, Christophe; Couté, Yohann; Rivkina, Elizaveta; Abergel, Chantal; Claverie, Jean-Michel
The largest known DNA viruses infect Acanthamoeba and belong to two markedly different families. The Megaviridae exhibit pseudo-icosahedral virions up to 0.7 μm in diameter and adenine–thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand proteins. Like their Mimivirus prototype discovered 10 y ago, they entirely replicate within cytoplasmic virion factories. In contrast, the recently discovered Pandoraviruses exhibit larger amphora-shaped virions 1 μm in length and guanine–cytosine-rich genomes up to 2.8 Mb long encoding up to 2,500 proteins. Their replication involves the host nucleus. Whereas the Megaviridae share some general features with the previously described icosahedral large DNA viruses, the Pandoraviruses appear unrelated to them. Here we report the discovery of a third type of giant virus combining an even larger pandoravirus-like particle 1.5 μm in length with a surprisingly smaller 600 kb AT-rich genome, a gene content more similar to Iridoviruses and Marseillevirus, and a fully cytoplasmic replication reminiscent of the Megaviridae. This suggests that pandoravirus-like particles may be associated with a variety of virus families more diverse than previously envisioned. This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated a survey of the virome of Siberian permafrost. The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health. PMID:24591590
Structure of Periodic Crystals and Quasicrystals in Ultrathin Films of Ba-Ti-O
Cockayne, Eric; Mihalkovič, Marek; Henley, Christopher L.
We model the remarkable thin-film Ba-Ti-O structures formed by heat treatment of an initial perovskite BaTiO3 thin film on a Pt(111) surface. All structures contain a rumpled Ti-O network with all Ti threefold coordinated with O, and with Ba occupying the larger. mainly Ti7O7, pores. The quasicrystal structue is a simple decoration of three types of tiles: square, triangle and 30° rhombus, with edge lengths 6.85 Å, joined edge-to-edge in a quasicrystalline pattern; observed periodic crystals in ultrathin film Ba-Ti-O are built from these and other tiles. Simulated STM images reproduce the patterns seen experimentally, and identify the bright protrusions as Ba atoms. The models are consistent with all experimental observations. PMID:26998528
Simultaneous large band gaps and localization of electromagnetic and elastic waves in defect-free quasicrystals.
Yu, Tianbao; Wang, Zhong; Liu, Wenxing; Wang, Tongbiao; Liu, Nianhua; Liao, Qinghua
We report numerically large and complete photonic and phononic band gaps that simultaneously exist in eight-fold phoxonic quasicrystals (PhXQCs). PhXQCs can possess simultaneous photonic and phononic band gaps over a wide range of geometric parameters. Abundant localized modes can be achieved in defect-free PhXQCs for all photonic and phononic polarizations. These defect-free localized modes exhibit multiform spatial distributions and can confine simultaneously electromagnetic and elastic waves in a large area, thereby providing rich selectivity and enlarging the interaction space of optical and elastic waves. The simulated results based on finite element method show that quasiperiodic structures formed of both solid rods in air and holes in solid materials can simultaneously confine and tailor electromagnetic and elastic waves; these structures showed advantages over the periodic counterparts. PMID:27137236
Magnetism in the i- R-Cd (R = Y, Gd-Tm) binary quasicrystals
NASA Astrophysics Data System (ADS)
Goldman, Alan; Kong, Tai; Kreyssig, Andreas; Yamada, Tsunetomo; Takakura, Hiroyuki; Bud'Ko, Sergey; Das, Pinaki; Jayasekara, Wageesha; Canfield, Paul; de Boissieu, Marc
Progress in our understanding of the consequences of aperiodicity for physical phenomena such as the electronic, magnetic, and optical properties has recently seen a surge of activity and new results. A new family of i- R-Cd binary magnetic quasicrystals, exhibiting spin-glass-like behavior, and the closely related RCd6 crystalline approximants , which manifest long-range magnetic order at low temperature, offer new opportunities for studies of the impact of aperiodicity on magnetic interactions in compounds that have similar local structures. I will discuss their magnetic behavior, as well as recent x-ray diffraction and elastic magnetic neutron scattering investigations that provide some insight into their structural and magnetic properties. The research was supported by the Office of the Basic Energy Sciences, Materials Sciences Division, US Department of Energy (DOE).
A parametric study of the lensing properties of dodecagonal photonic quasicrystals
NASA Astrophysics Data System (ADS)
Di Gennaro, E.; Morello, D.; Miletto, C.; Savo, S.; Andreone, A.; Castaldi, G.; Galdi, V.; Pierro, V.
We present a study of the lensing properties of two-dimensional (2-D) photonic quasicrystal (PQC) slabs made of dielectric cylinders arranged according to a 12-fold-symmetric square-triangle aperiodic tiling. Our full-wave numerical analysis confirms the results recently emerged in the technical literature and, in particular, the possibility of achieving focusing effects within several frequency regions. However, contrary to the original interpretation, such focusing effects turn out to be critically associated to local symmetry points in the PQC slab, and strongly dependent on its thickness and termination. Nevertheless, our study reveals the presence of some peculiar properties, like the ability to focus the light even for slabs with a reduced lateral width, or beaming effects, which render PQC slabs potentially interesting and worth of deeper investigation.
Self-generation of dissipative solitons in magnonic quasicrystal active ring resonator
Grishin, S. V. Beginin, E. N.; Morozova, M. A.; Sharaevskii, Yu. P.; Nikitov, S. A.
Self-generation of dissipative solitons in the magnonic quasicrystal (MQC) active ring resonator is studied theoretically and experimentally. The developed magnonic crystal has quasiperiodic Fibonacci type structure. Frequency selectivity of the MQC together with the parametric three-wave decay of magnetostatic surface spin wave (MSSW) leads to the dissipative soliton self-generation. The transfer matrix method is used to describe MQC transmission responses. Besides, the model of MQC active ring resonator is suggested. The model includes three coupled differential equations describing the parametric decay of MSSW and two differential equations of linear oscillators describing the frequency selectivity of MQC. Numerical simulation results of dissipative soliton self-generation are in a fair agreement with experimental data.
Long-range magnetic order in models for rare-earth quasicrystals
NASA Astrophysics Data System (ADS)
Thiem, Stefanie; Chalker, J. T.
We take a two-step theoretical approach to study magnetism of rare-earth quasicrystals by considering Ising spins on quasiperiodic tilings, coupled via Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions. First, we compute RKKY interactions from a tight-binding Hamiltonian defined on the two-dimensional quasiperiodic tilings. We find that the magnetic interactions are frustrated and strongly dependent on the local environment. This results in the formation of clusters with strong bonds at certain patterns of the tilings that repeat quasiperiodically. Second, we examine the statistical mechanics of Ising spins with these RKKY interactions, using extensive Monte Carlo simulations. Although models that have frustrated interactions and lack translational invariance might be expected to display spin-glass behavior, we show that the spin system has a phase transition to low-temperature states with long-range quasiperiodic magnetic order. Additionally, we find that in some of the systems spin clusters can fluctuate much below the ordering temperature.
Thermoelectric properties of (α-, δ-, ζ-) Ti-Ru-B approximants for the decagonal quasicrystal
NASA Astrophysics Data System (ADS)
Takagiwa, Y.; Miyazaki, Y.; Yoshida, T.; Yanagihara, D.; Ueda, S.; Kitahara, K.; Kimura, K.
The electronic structure and the thermoelectric properties of (α-, δ-, ζ-) Ti-Ru-B approximants related to its decagonal quasicrystal phase were investigated. The band structure calculation reveals that they form pseudogaps in the electronic density of states across the Fermi level. The samples were synthesized by arc-melting, followed by spark plasma sintering. The electrical conductivity at 373 K varies from 1600 to 4200 Ω-1 cm-1 and their temperature coefficients are negative. All measured compounds show n-type properties, judging from the sign of the Seebeck coefficient; however, the magnitudes are rather low of less than 25 μV K-1. The phonon thermal conductivity at 373 K have a range 3-5 W m-1 K-1 resulting from complex crystal structures with large unit cell volumes. The maximum dimensionless figure-of-merit of 0.008 is evaluated at 773 K for δ-Ti-Ru-B.
Complex antiferromagnetic order in the Cd6 R approximants to the i- R-Cd quasicrystals
NASA Astrophysics Data System (ADS)
Kreyssig, A.; Beutier, G.; Hoffmann, J.-U.; Kong, T.; Kim, M. G.; Tucker, G. S.; Ueland, B. G.; Hiroto, T.; Liu, D.; Yamada, T.; Boissieu, M. De; Tamura, R.; Bud'Ko, S. L.; Canfield, P. C.; Goldman, A. I.
The observation of antiferromagnetic order in the Cd6 R (R = rare earths) approximants to the recently discovered related i- R-Cd quasicrystals provides new and exciting opportunities to unravel the nature of magnetism in these materials. We present single-crystal studies employing x-ray and neutron scattering that revealed complex antiferromagnetism in the Cd6 R approximants. Resolution-limited magnetic Bragg peaks have been observed at lattice points forbidden by the center-symmetry and at incommensurate positions demonstrating long-range antiferromagnetic correlations between the R moments. The work at the Ames Laboratory was supported by US DOE, Office of Basic Energy Sciences, DMSE, contract DE-AC02-07CH11358. Work at the Tokyo University of Science was supported by KAKENHI (Grant No. 20045017).
Evidence from x-ray and neutron powder diffraction patterns that the so-called icosahedral and decagonal quasicrystals of MnAl/sub 6/ and other alloys are twinned cubic crystals
Pauling, L.
It is shown that the x-ray powder diffraction patterns of rapidly quenched MnAl/sub 6/ and Mg/sub 32/(Al,Zn)/sub 49/ and the neutron powder diffraction pattern of MnAl/sub 5/ are compatible with the proposed 820-atom primitive cubic structure. The values found for the edge of the unit cube are 23.365 A (x-ray) and 23.416 A (neutron) for MnAl/sub 6/ and 24.313 A (x-ray) for Mg/sub 32/(Al,Zn)/sub 49/.
Shock waves in complex binary solids: Cubic Laves crystals, quasicrystals, and amorphous solids
NASA Astrophysics Data System (ADS)
Roth, Johannes
Shock waves have been simulated by molecular dynamics in the cubic Laves phase C15, in related Frank-Kasper-type (AlCu)Li quasicrystals, and in an amorphous solid of the same composition and potential parameters. The goal of this study was to generate shock waves in periodic and aperiodic structures and to compare their behavior. The expectation was that new types of defects would show up in aperiodic materials. Three regimes are observed in the Laves phase: at low shock wave intensity the system reacts elastically, at high intensities it turns disordered. In the intermediate region the velocity of the elastic wave saturates and an additional plastic wave appears. Extended defects are created which form a network of walls of finite width. The crystallites in between are rotated by the shock wave. If the samples are quenched a polycrystalline phase is obtained. The size of the grains decreases with increasing shock wave intensity until complete fragmentation occurs in the third regime. The behavior of the quasicrystal models is similar, except that there is a continuous transition from a quasielastic behavior to the plastic regime. Ring processes are observed which break up into open paths when the shock wave energy grows. The transition to a complete destruction of the structure is continuous. In the amorphous solid a linear us-up relation is found over the whole range of piston velocities. Two regimes are present, with unsteady plastic waves at weak shock strengths and steady waves in the range coinciding with the upper regime in the ordered structures.
Atomic Scale coexistence of Periodic and quasiperiodic order in a2-fold A1-Ni-Co decagonal quasicrystal surface
Park, Jeong Young; Ogletree, D. Frank; Salmeron, Miquel; Ribeiro,R.A.; Canfield, P.C.; Jenks, C.J.; Thiel, P.A.
Decagonal quasicrystals are made of pairs of atomic planes with pentagonal symmetry periodically stacked along a 10-fold axis. We have investigated the atomic structure of the 2-fold surface of a decagonal Al-Ni-Co quasicrystal using scanning tunneling microscopy (STM). The surface consists of terraces separated by steps of heights 1.9, 4.7, 7.8, and 12.6{angstrom} containing rows of atoms parallel to the 10-fold direction with an internal periodicity of 4{angstrom}. The rows are arranged aperiodically, with separations that follow a Fibonacci sequence and inflation symmetry. The results indicate that the surfaces are preferentially Al-terminated and in general agreement with bulk models.
Electronic densities of states close to the surface of quasicrystals in relation with their low adhesion properties
NASA Astrophysics Data System (ADS)
Belin-Ferre, Esther; Dubois, Vincent
Quasicrystalline alloys exhibit low adhesion properties in comparison to normal metals and even to purpose designed polymers like PTFEs. The physical origin of this effect is still a matter of research but is presumably related on the one hand to a substantial resistance to oxidation that prevents the formation of a thick alumina film at the surface (since oxides have a large surface energy, wetting is easy and therefore adhesion to organic matters is important on aluminium-based alloys). On the other hand, the density of states (DOS) at the Fermi level is dramatically reduced in quasicrystals. Our experiments show that this reduction extends towards the top atomic layers and therefore the low DOSs goes up to the surface. This effect cancels any gradient of the DOS from the surface down to the bulk and contributes significantly to the low surface energy of quasicrystals. Experimental evidence will be reported to support this view. by emailing it to the address below:
Studies of Nucleation, Growth, Specific Heat, and Viscosity of Undercooled Melts of Quasicrystals and Polytetrahedral-Phase-Forming Alloys
NASA Technical Reports Server (NTRS)
Kelton, K. F.; Croat, T. K.; Gangopadhyay, A.; Holland-Moritz, D.; Hyers, Robert W.; Rathz, Thomas J.; Robinson, Michael B.; Rogers, Jan R.
Undercooling experiments and thermal physical property measurements of metallic alloys on the International Space Station (ISS) are planned. This recently-funded research focuses on fundamental issues of the formation and structure of highly-ordered non-crystallographic phases (quasicrystals) and related crystal phases (crystal approximants), and the connections between the atomic structures of these phases and those of liquids and glasses. It extends studies made previously by us of the composition dependence of crystal nucleation processes in silicate and metallic glasses, to the case of nucleation from the liquid phase. Motivating results from rf-levitation and drop-tube measurements of the undercooling of Ti/Zr-based liquids that form quasicrystals and crystal approximants are discussed. Preliminary measurements by electrostatic levitation (ESL) are presented.
Quasilattice-conserved molecular dynamics study of the atomic structure of decagonal Al-Co-Ni quasicrystals
NASA Astrophysics Data System (ADS)
Zhao, Yu-Jun; Li, Xiaotian; Advisor-student Collaboration
The detailed atomic structure of quasicrystals has been an open question for decades. In this paper, we present a quasilattice-conserved molecular dynamics method (quasiMD), with particular quasiperiodic boundary conditions. As the atomic coordinates are described by basic cells and quasilattices, we are able to maintain the self-similarity characteristics of qusicrystals with the atomic structure of the boundary region updated timely following the relaxing region. Exemplified with the study of decagonal Al-Co-Ni (d-Al-Co-Ni), we propose a more stable atomic structure model based on Penrose quasilattice and our quasiMD simulations. In particular, ``rectangle-triangle'' rules are suggested for the local atomic structures of d-Al-Co-Ni quasicrystals.
High-voltage electron microscope high-temperature in situ straining experiments to study dislocation dynamics in intermetallics and quasicrystals.
Messerschmidt, U
The dynamic behaviour of dislocations in several intermetallic alloys, studied by in situ straining experiments in a high-voltage electron microscope, is compared at room temperature and at high temperatures. In contrast to room temperature, the dislocations move viscously at high temperatures, which is explained by diffusion processes in the dislocation cores. In quasicrystals, the viscous dislocation motion can be interpreted by models on the cluster scale. PMID:11454156
Phason space analysis and structure modelling of 100 Å-scale dodecagonal quasicrystal in Mn-based alloy
NASA Astrophysics Data System (ADS)
Ishimasa, Tsutomu; Iwami, Shuhei; Sakaguchi, Norihito; Oota, Ryo; Mihalkovič, Marek
The dodecagonal quasicrystal classified into the five-dimensional space group P126/mmc, recently discovered in a Mn-Cr-Ni-Si alloy, has been analysed using atomic-resolution spherical aberration-corrected electron microscopy, i.e. high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) and conventional transmission electron microscopy. By observing along the 12-fold axis, non-periodic tiling consisting of an equilateral triangle and a square has been revealed, of which common edge length is a = 4.560 Å. These tiles tend to form a network of dodecagons of which size is ?a ≈ 17 Å in diameter. The tiling was interpreted as an aggregate of 100 Å-scale oriented domains of high- and low-quality quasicrystals with small crystallites appearing at their boundaries. The quasicrystal domains exhibited a densely filled circular acceptance region in the phason space. This is the first observation of the acceptance region in an actual dodecagonal quasicrystal. Atomic structure model consistent with the electron microscopy images is a standard Frank-Kasper decoration of the triangle and square tiles that can be inferred from the crystal structures of Zr4Al3 and Cr3Si. Four kinds of layers located at z = 0, ±1/4 and 1/2 are stacked periodically along the 12-fold axis, and the atoms at z = 0 and 1/2 form hexagonal anti-prisms consistently with the 126-screw axis. The validity of this structure model was examined by means of powder X-ray diffraction.
Fundamentals in generalized elasticity and dislocation theory of quasicrystals: Green tensor, dislocation key-formulas and dislocation loops
NASA Astrophysics Data System (ADS)
Lazar, Markus; Agiasofitou, Eleni
The present work provides fundamental quantities in generalized elasticity and dislocation theory of quasicrystals. In a clear and straightforward manner, the three-dimensional Green tensor of generalized elasticity theory and the extended displacement vector for an arbitrary extended force are derived. Next, in the framework of dislocation theory of quasicrystals, the solutions of the field equations for the extended displacement vector and the extended elastic distortion tensor are given; that is, the generalized Burgers equation for arbitrary sources and the generalized Mura-Willis formula, respectively. Moreover, important quantities of the theory of dislocations as the Eshelby stress tensor, Peach-Koehler force, stress function tensor and the interaction energy are derived for general dislocations. The application to dislocation loops gives rise to the generalized Burgers equation, where the displacement vector can be written as a sum of a line integral plus a purely geometric part. Finally, using the Green tensor, all other dislocation key-formulas for loops, known from the theory of anisotropic elasticity, like the Peach-Koehler stress formula, Mura-Willis equation, Volterra equation, stress function tensor and the interaction energy are derived for quasicrystals.
Point contact tunneling spectroscopy of the density of states in Tb-Mg-Zn quasicrystals
NASA Astrophysics Data System (ADS)
Escudero, R.; Morales, F.
According to theoretical predictions the quasicrystalline (QC) electronic density of states (DOS) must have a rich and fine spiky structure which actually has resulted elusive. The problem with its absence may be related to poor structural characteristics of the studied specimens, and/or to the non-existence of this spike characteristic. Recent calculations have shown that the fine structure indeed exists, but only for two dimensional approximants phases. The aim of the present study is to show our recent experimental studies with point contacts tunnel junction spectroscopy performed in samples of very high quality. The studies were performed in icosahedral QC alloys with composition Tb$_9$Mg$_{35}$Zn$_{56}$. We found the presence of a pseudogap feature at the Fermi level, small as compared to the pseudogap of other icosahedral materials. This study made in different spots on the QC shows quite different spectroscopic features, where the observed DOS was a fine non-spiky structure, distinct to theoretical predictions. In some regions of the specimens the spectroscopic features could be related to Kondo characteristics due to Tb magnetic atoms acting as impurities. Additionally, we observed that the spectroscopic features vanished under magnetic field.
Systematic study of the electronic structure and optical properties of icosahedral boron and boron compounds
NASA Astrophysics Data System (ADS)
Li, Dong
A systematic study of the electronic structures, total energies and optical properties of B12-based boron and boron-rich compounds and boron oxide compounds has been conducted by the first-principles orthogonalized linear combination of atomic orbitals method. The materials involved are: α-r-B12, B12As2,/ B12P2,/ B11C(CBC)/ (or/ B4C),/ B13C2,/ B12O2,/ (B10Si2)Si2,/ (B10Si2)Si2-I, B2O3-I and B2O3-II. The band structures show that α-r-B12,/ B12As2,/ B12P2,/ B11C(CBC),/ B12O2,/ (B10Si2)Si2, and (B10Si2)Si2-I are semiconductors with band gaps ranging from 1.29 eV to 3.04 eV while B13C2 is a metal with an intrinsic hole at the top of the valence band below a semiconductor-like gap. The study also shows that B2O3-I and B2O3-II are wide gap insulators with calculated LDA gaps of 6.20 eV and 8.85 eV separately. The calculated density of states are resolved into atomic and orbital partial components and the valence-charge distributions are also studied. The natural bonding characteristics in these crystals are illuminated by evaluating the Mulliken effective charges on each atom and overlap populations between pairs of atoms. It is shown that inter-icosahedral bonding is much stronger than the intra-icosahedral bonding in the B12- based crystals. The chain elements in B12As2,/ B12P2,/ (B10Si2)Si2 and (B10Si2)Si2-I donate electrons to the icosahedra, while B11C(CBC),/ B13C2 and B12O2 gain a slight amount of charge in forming strong covalent bonds. For boron oxide compounds, B2O3-II is found to be more ionic than B2O3-I. It is also concluded that the sp2 planar bonding in B2O3-I is stronger than the sp3 tetrahedral bonding in B2O3-II. The bulk moduli of α-r-B12,/ B12As2,/ B12P2,/ B11C(CBC),/ B13C2 and B12O2 are estimated by means of total energy calculation as a function of crystal volume, and are to be considered as upper limits. We have also calculated the interband optical conductivities and the complex dielectric functions. Static dielectric constants for icosahedral
"Quasi-Antiferromagnetic" Ordering in the R-Mg-Zn Icosahedral Alloys? The Case of Tb-Mg-Zn
NASA Astrophysics Data System (ADS)
Goldman, A. I.; Islam, Z.; Fisher, I. R.; Panchula, A. F.; Cheon, K. O.; Canfield, P. C.; Stassis, C.; Zarestky, J.
Recently, it was reported that long-range magnetic ordering was observed in several of the new rare earth containing icosahedral alloys, R-Mg-Zn (R=Tb, Dy, Ho, Er) (B. Charrier et al., Phys. Rev. Lett. 78, 4637, 1997.). At low temperatures, the antiferromagnetic Bragg peaks, while weak, could be indexed to the icosahedral parent phase with good accuracy. In addition, significant magnetic diffuse scattering, indicating only short-range magnetic order, was also observed. However, bulk magnetization measurements have evidenced only a spin-glass transition at low temperatures, and no antiferromagnetic transition. We will report on new neutron scattering measurements of the magnetic order in Tb-Mg-Zn powder samples produced from crushed single-crystals, used to improve sample purity. Our results for these samples show only the diffuse component of the magnetic scattering at low temperature, and no antiferromagnetic Bragg peaks. We will discuss several possibilities for the discrepencies between the two experiments.
A control volume method on an icosahedral grid for numerical integration of the shallow-water equations on the sphere
Chern, I-Liang
Two versions of a control volume method on a symmetrized icosahedral grid are proposed for solving the shallow-water equations on a sphere. One version expresses of the equations in the 3-D Cartersian coordinate system, while the other expresses the equations in the northern/southern polar sterographic coordinate systems. The pole problem is avoided because of these expressions in both versions and the quasi-homogenity of the icosahedral grid. Truncation errors and convergence tests of the numerical gradient and divergent operators associated with this method are studied. A convergence tests of the numerical gradient and divergent operators associated with this method are studied. A convergence test for a steady zonal flow is demonstrated. Several simulations of Rossby-Haurwitz waves with various numbers are also performed.
Pattern formation in icosahedral virus capsids: the papova viruses and Nudaurelia capensis beta virus.
Marzec, C J; Day, L A
The capsids of the spherical viruses all show underlying icosahedral symmetry, yet they differ markedly in capsomere shape and in capsomere position and orientation. The capsid patterns presented by the capsomere shapes, positions, and orientations of three viruses (papilloma, SV40, and N beta V) have been generated dynamically through a bottom-up procedure which provides a basis for understanding the patterns. A capsomere shape is represented in two-dimensional cross-section by a mass or charge density on the surface of a sphere, given by an expansion in spherical harmonics, and referred to herein as a morphological unit (MU). A capsid pattern is represented by an icosahedrally symmetrical superposition of such densities, determined by the positions and orientations of its MUs on the spherical surface. The fitness of an arrangement of MUs is measured by an interaction integral through which all capsid elements interact with each other via an arbitrary function of distance. A capsid pattern is generated by allowing the correct number of approximately shaped MUs to move dynamically on the sphere, positioning themselves until an extremum of the fitness function is attained. The resulting patterns are largely independent of the details of both the capsomere representation and the interaction function; thus the patterns produced are generic. The simplest useful fitness function is sigma 2, the average square of the mass (or charge) density, a minimum of which corresponds to a "uniformly spaced" MU distribution; to good approximation, the electrostatic free energy of charged capsomeres, calculated from the linearized Poisson-Boltzmann equation, is proportional to sigma 2. With disks as MUs, the model generates the coordinated lattices familiar from the quasi-equivalence theory, indexed by triangulation numbers. Using fivefold MUs, the model generates the patterns observed at different radii within the T = 7 capsid of papilloma and at the surface of SV40; threefold MUs
Wide quantum critical region of valence fluctuations: Origin of robust quantum criticality in quasicrystal Yb15Al34Au51 under pressure
NASA Astrophysics Data System (ADS)
Watanabe, Shinji; Miyake, Kazumasa
The mechanism of the emergence of robust quantum criticality in the heavy- electron quasicrystal YR15Al34Au51 is analyzed theoretically. By constructing a minimal model for the quasicrystal and its crystalline approximant, which contain concentric shell structures with Yb and Al-Au clusters, we show that a set of quantum critical points of the first-order valence transition of Yb appears as spots in the ground-state phase diagram. Their critical regions overlap each other, giving rise to a wide quantum critical region. This well explains the robust criticality observed in YR15Al34Au51 under pressure, and predicts the emergence of the common criticality in the crystalline approximant under pressure. The wider critical region in the quasicrystal than that in the crystalline approximant in the T-P phase diagram and the field-induced valence-crossover "region" in the T-H phase diagram are predicted to appear.
Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids
NASA Astrophysics Data System (ADS)
Dykeman, Eric C.; Sankey, Otto F.
We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (˜10) low-frequency modes that are global and cooperative.
Reinvestigation of long-range magnetic ordering in icosahedral Tb-Mg-Zn
Islam, Z.; Fisher, I.R.; Zarestky, J.; Canfield, P.C.; Stassis, C.; Goldman, A.I.
We present results of a study of possible magnetic ordering in the icosahedral phase of Tb-Mg-Zn probed by bulk magnetization measurements and neutron diffraction. Measurements on both crushed single grains and cast polycrystalline samples of Tb-Mg-Zn were performed. Magnetization measurements on both samples reveal only a spin-glass-like transition at approximately 5.8K. Neutron diffraction from the crushed single grains reveals only short-range magnetic ordering at low temperatures, with no evidence of the long-range magnetic ordering reported previously [Charrier, Ouladdiaf, and Schmitt, Phys. Rev. Lett. {bold 78}, 4637 (1997)]. Likewise, the cast polycrystalline samples exhibit primarily diffuse magnetic scattering at low temperature, but at least one relatively sharp diffraction peak was observed. Our results indicate that for single grain samples there is no long-range magnetic ordering and that, at best, the magnetic ordering in these quasicrystalline alloys is not very robust. {copyright} {ital 1998} {ital The American Physical Society}
Thermal conductivity and Seebeck coefficients of icosahedral boron arsenide films on silicon carbide
Gong, Y.; Kuball, M.; Zhang, Y.; Dudley, M.; Zhang, Y.; Edgar, J. H.; Heard, P. J.
The thermal conductivity of icosahedral boron arsenide (B{sub 12}As{sub 2}) films grown on (0001) 6H-SiC substrates by chemical vapor deposition was studied by the 3{omega} technique. The room temperature thermal conductivity decreased from 27.0 to 15.3 W/m K as the growth temperature was decreased from 1450 to 1275 deg. C. This is mainly attributed to the differences in the impurity concentration and microstructure, determined from secondary ion mass spectrometry and high resolution transmission electron microscopy, respectively. Callaway's theory was applied to calculate the temperature-dependent thermal conductivity, and the results are in good agreement with the experimental data. Seebeck coefficients were determined as 107 {mu}V/K and 136 {mu}V/K for samples grown at 1350 deg. C with AsH{sub 3}/B{sub 2}H{sub 6} flow ratio equals to 1:1 and 3:5, respectively.
Photonic quasi-crystals in Fourier and Fourier-Bessel space
NASA Astrophysics Data System (ADS)
Newman, S. R.; Gauthier, R. C.
Photonic crystals that are aperiodic or quasi-crystalline in nature have been the focus of research due to their complex spatial distributions, resulting in high order rotational symmetries. Recently we proposed aperiodic patterns that were rotationally symmetric while being random in the radial direction. The structures are designed by segmenting the circular design space, randomly populating one segment, and repeating that segment about a center of rotation. Studying the symmetries and geometrical attributes of aperiodic structures is typically performed in reciprocal Fourier space by examining the distribution of the Fourier coefficients. This allows the translational symmetry to be directly extracted and the rotational nature to be interpreted. Instead we propose comparing the typical Fourier analysis with the use of a Fourier-Bessel space. The Fourier-Bessel approach expands the dielectric layout in cylindrical coordinates using exponential and Bessel functions as the angular and radial basis functions. The coefficients obtained in this fashion directly provide the rotational symmetries that are present. This work will examine both the Fourier and Fourier-Bessel distributions of the proposed structures as well as other quasi-crystals in order to explore the strengths and weaknesses of both techniques.
Impact-induced shock and the formation of natural quasicrystals in the early solar system.
Hollister, Lincoln S; Bindi, Luca; Yao, Nan; Poirier, Gerald R; Andronicos, Christopher L; MacPherson, Glenn J; Lin, Chaney; Distler, Vadim V; Eddy, Michael P; Kostin, Alexander; Kryachko, Valery; Steinhardt, William M; Yudovskaya, Marina; Eiler, John M; Guan, Yunbin; Clarke, Jamil J; Steinhardt, Paul J
The discovery of a natural quasicrystal, icosahedrite (Al63Cu24Fe13), accompanied by khatyrkite (CuAl2) and cupalite (CuAl) in the CV3 carbonaceous chondrite Khatyrka has posed a mystery as to what extraterrestrial processes led to the formation and preservation of these metal alloys. Here we present a range of evidence, including the discovery of high-pressure phases never observed before in a CV3 chondrite, indicating that an impact shock generated a heterogeneous distribution of pressures and temperatures in which some portions reached at least 5 GPa and 1,200 °C. The conditions were sufficient to melt Al-Cu-bearing minerals, which then rapidly solidified into icosahedrite and other Al-Cu metal phases. The meteorite also contains heretofore unobserved phases of iron-nickel and iron sulphide with substantial amounts of Al and Cu. The presence of these phases in Khatyrka provides further proof that the Al-Cu alloys are natural products of unusual processes that occurred in the early solar system. PMID:24925481
Nanoscale SEMPA imaging of an artificial quasicrystal spin ice at remanence
NASA Astrophysics Data System (ADS)
Balk, Andrew; Bhat, Vinayak; Farmer, Barry; Delong, Lance; Unguris, John; Electron Physics Group, CNST Team
Artificial spin ice has emerged in the past decade as a model metamaterial for studying frustrated magnetic ordering at length scales large enough to be experimentally probed in real space. Recently, complex designs have been engineered to explore exotic behavior in non-square lattices. However, direct measurements of the actual moment directions have not been very common, and interpretation from techniques such as magnetic force microscopy and magneto-optical Kerr effect magnetometry can be complicated by the more complex geometries. Here we demonstrate using SEMPA (scanning electron microscopy with polarization analysis) as a method to robustly measure the ordering direction of elements in a connected artificial quasicrystal. We discuss the applicability of SEMPA to this system, details of the imaging and potential artifacts, and conclusions that can be drawn from the nanoscale two dimensional maps of the moment direction. This work is partially funded by DoE Grant #DE-FG02-97ER45653. ALB acknowledges support of this research under the Cooperative Research Agreement between the University of Maryland and NIST.
Multiple Bragg diffraction in quasicrystals: The issue of centrosymmetry in Al-Pd-Mn
Lee, H.; Colella, R.; Shen, Q.
When a crystal is rotated around the scattering vector for a Bragg reflection {bold P}, another reflection {bold H} may be simultaneously excited for a particular value {psi} of the azimuthal angle. The plot of the intensity {ital I}{sub {bold P}} vs {psi} (called the {open_quote}{open_quote}azimuthal plot{close_quote}{close_quote}) shows peaks with asymmetric features from which phases of structure factors can be obtained. Multibeam diffraction data have been obtained with a high-quality Al-Pd-Mn quasicrystal using synchrotron x rays. Rocking widths of 36 arcsec have been obtained, which made it possible to obtain data that could be interpreted using dynamical theory without any need of smearing functions to take into account the mosaic spread or other instrumental resolution effects. The asymmetric features and the peak intensity of all azimuthal plots could be fitted with phases consistent with a noncentrosymmetric structure. This conclusion was reinforced by the results of a multibeam experiment with circularly polarized x rays. This is in contrast with several other diffraction experiments based on intensity measurements in the two-beam case. Possible reasons for this discrepancy are discussed. {copyright} {ital 1996 The American Physical Society.}
THOR-ICO: a General Circulation Model for Exoplanets on an Icosahedral Grid
NASA Astrophysics Data System (ADS)
Mendonca, J.; Heng, K.; Grimm, S.
The study of extrasolar planets has become important since the discovery of a large number of these astronomical objects. The diversity of planetary characteristics observed raises questions about the variety of climates. The influence of the astronomical and planetary bulk parameters in driving the atmospheric circulations continues to be poorly understood. In the solar system the results from planetary spacecraft missions have demonstrated how different the planetary climate and atmospheric circulations can be. The study of exoplanets is going to require a study of a far greater range of physical and orbital parameters than the ones that characterise our neighbour planets (in the solar system). For this reason the study of exoplanets will involve an even greater diversity of circulation and climate regimes. We are developing a dedicated General Circulation Model (GCM) for extrasolar planets called "Exoclimes Simulation Platform". This model will solve the complex physical and dynamical equations that include fundamental principles of atmospheric fluid dynamics and various idealisations of, for example, radiative transfer [1] and dry or moist convection. The interpretation and analysis of the results from this complex model will help us to have a better understanding on the diversity of climates and atmospheric circulations. Here we present the first results of our recent scheme which represents the fluid dynamical phenomena in the atmosphere. This new code solves the atmospheric fluid equations in a rotating sphere (fully compressible - elastic - nonhydrostatic system) using an icosahedral grid. The grid is also modified to improve the uniformity of the grid point distribution applying a method called spring dynamics [2]. The results shown include 3D experiments of gravity and acustic waves, Held-Suarez test case [3] and an idealized hot-Jupiter case.
Stable Icosahedral Hollow Cage Clusters: Stannapherene (Sn12 2-) and Plumbaspherene (Pb12 2-)
Cui, Lifeng; Wang, Lai S.
One of the major objectives of cluster science is to discover stable atomic clusters, which may be used as building blocks for cluster-assembled nanomaterials. The discovery and bulk synthesis of the fullerenes have sprouted new research disciplines in chemistry and nanoscience and precipitated intense interests to search for other similar stable clusters. However, despite major research efforts, no other analogous gas-phase clusters have been found and yielded to bulk syntheses. In this article, we review our recent discoveries in cluster beam experiments of stannaspherene (Sn12 2–) and plumbaspherene (Pb12 2–), which are highly stable and symmetric cage clusters. The names for these two clusters derive from their icosahedral (Ih) symmetry and delocalized spherical π-bonding that are characteristics of buckminsterfullerene C60. Stannaspherene and plumbaspherene have diameters comparable to that of C60 and can be considered as inorganic analogs of the buckyball. The large internal space in Sn12 2– has been shown to be able to trap any transition metal atom to form new endohedral cage clusters, M@Sn12 –, analogous to endohedral fullerenes. The doped atom in M@Sn12 – keeps its quasi-atomic nature with large magnetic moments. These endohedral cages form a rich class of new building blocks for cluster-assembled materials with tunable magnetic, electronic, and chemical properties. During our attempt to synthesize endohedral stannaspherenes, we crystallized a new Pd2@Sn18 4– cluster, which can be viewed as the fusion of two Pd@Sn12 2– clusters. This result suggests that stannaspherene, plumbaspherene, and a large number of their endohedrally doped species can be synthesized in the bulk.
Analysis of structure and P-c-T curve of hydrogenated Ti53Zr27xNi20Pd(x) quasicrystals.
Jo, Youngsoo; Lee, Sang-Hwa; Shin, Hong Sik; Kim, Jaeyong
The potential application of TiZrNi quasicrystals was evaluated by measuring the pressure-composition-temperature curves after replacing Zr by Pd to the limit maintaining the host structure for the samples made with Ti53Zr27(-x)Ni20Pd(x), where 0 < or = x < or = 8. The results of X-ray diffraction data revealed that the samples keep the pure quasicrystal structure to the maximum value of x = 8. All diffracted peaks uniformly shifted to the low angle of 2 theta in X-ray diffraction pattern suggesting that hydrogen atoms homogeneously diffuse in the quasicrystals and uniformly expand the quasilattice constants without modification of the structure. After hydrogenation at elevated temperature, the quasi-lattice constants increased from 5.12 to 5.34 angstroms for the samples made with x = 0 without appearing an impurity phase. When Zr was replaced by 8 at.% of Pd, the equilibrium vapor pressures significantly increased to 3.41 from 0.41 Torr at 300 degrees C although the total amount of hydrogen decreased as increasing Pd concentration. These results demonstrate that Pd will play a critical role in application for the TiZrNi quasicrystals as hydrogen storage materials. PMID:24266172
Icosahedral short-range order in amorphous Cu80Si20 by ab initio molecular dynamics simulation study
Wu, S.; Kramer, Matthew J.; Fang, Xiaowei; Wang, Shy-Guey; Wang, Cai-Zhuang; Ho, Kai-Ming; Ding, Z.J.; Chen, L.Y.
Short-range order in liquid and amorphous structures of Cu80Si20 is studied by ab initio molecular dynamics simulations. We performed the simulations at 1140 and 300 K respectively to investigate the local structure change from liquid to amorphous. The result of structure factor in comparison with experimental data indicates that our simulation of amorphous Cu80Si20 is reliable. By using the bond-angle distribution function, Honeycutt–Andersen index, Voronoi tessellation method, and the atomistic cluster alignment method, the icosahedral short-range order in the system is revealed. Strong Cu–Si interaction was also observed.
Icositetrahedral and icosahedral atomic configurations observed in the Nb-Ag metallic glasses synthesized by ion beam mixing
Tai, K. P.; Gao, N.; Dai, X. D.; Li, J. H.; Lai, W. S.; Liu, B. X.
Metallic glasses are obtained in an immiscible Nb-Ag system by ion beam mixing and an atomic configuration in the amorphous structure is discovered, i.e., an icositetrahedral ordering, which, together with an icosahedral ordering also observed in the Nb-Ag metallic glasses and in some previously reported systems, helps in formulating a structural spectrum of the amorphous solids. The experimental characterization and atomistic modeling with an ab initio derived Nb-Ag potential demonstrate the significance of structural heredity, i.e., the crystalline structures of the constituent metals play a decisive role in determining the atomic structure of the metallic glasses in the system.
Deuterium dynamics in the icosahedral and amorphous phases of the Ti40Zr40Ni20 hydrogen-absorbing alloy studied by 2H NMR
NASA Astrophysics Data System (ADS)
Gradišek, A.; Kocjan, A.; McGuiness, P. J.; Apih, T.; Kim, Hae Jin; Dolinšek, J.
The Ti40Zr40Ni20 hydrogen-absorbing alloy was prepared in the icosahedral and amorphous phases by controlling the rotation speed of the melt-spinning method of sample preparation, and the deuterium dynamics was investigated by 2H NMR dynamic lineshape and spin-lattice relaxation. The results were analysed by the lineshape and relaxation models that assume deuterium thermally activated hopping within a manifold of different chemical environments. The observed 8% larger activation energy for the deuterium hopping over the interstitial sites and the 10% larger static spectrum width of the amorphous phase, as compared to the icosahedral phase, can be accounted for by the larger deuterium content of the investigated amorphous sample. From the deuterium dynamics point of view, the icosahedral phase is not special with respect to the amorphous modification of the same material.
Effect of LiH on electrochemical hydrogen storage properties of Ti55V10Ni35 quasicrystal
NASA Astrophysics Data System (ADS)
Liu, Dongyan; Zhao, Zhen; Luo, Tianhao; Xing, Cheng; Fei, Liang; Lin, Jing; Hou, Jianhua; Jiang, Dayong; Liu, Wanqiang; Wang, Limin
The electrochemical hydrogen storage properties and mechanisms of the Ti55V10Ni35 quasicrystal + xLiH(x = 3, 6 and 9 wt.%) system are investigated and discussed in this paper. A composite material in the Ti55V10Ni35 quasicrystal and system has been synthesized moderately by means of mechanical milling under an argon atmosphere, which can avoid reaction of releasing of hydrogen during the process of milling. The results indicate that the addition of LiH significantly improves the electrochemical characteristics of composite material. The maximum discharge capacity increases from 220.1 mAh/g to 292.3 mAh/g on Ti55V10Ni35 + 6 wt.% LiH, and the cycling stability is also enhanced too. In addition, the high rate dischargeability (HRD) is ameliorated remarkably, and the value of HRD value at 240 mA/g rises by 78.1%-87.8% for Ti55V10Ni35 + 6 wt.% LiH alloy electrodes. The improvement of characteristics of the electrochemical hydrogen storage characteristics may be attributed to LiH, which has excellent electrochemical activity.
Antiferromagnetic order and the structural order-disorder transition in the Cd6Ho quasicrystal approximant
Kreyssig, Andreas; Beutier, Guillaume; Hiroto, Takanobu; Kim, Min Gyu; Tucker, Gregory S.; de Boissieu, Marc; Tamura, Ryuji; Goldman, Alan I.
It has generally been accepted that the orientational ordering of the Cd4 tetrahedron within the Cd6 R quasicrystal approximants is kinetically inhibited for R = Ho, Er, Tm and Lu by steric constraints. Our high-resolution X-ray scattering measurements of the Cd6Ho quasicrystal approximant, however, reveal an abrupt (first-order) transition to a monoclinic structure below T S = 178 K for samples that have 'aged' at room temperature for approximately one year, reopening this question. Using X-ray resonant magnetic scattering at the Ho L 3-edge we have elucidated the nature of the antiferromagnetic ordering below T N = 8.5 K in Cd6Ho. The magnetic Bragg peaks are found at the charge forbidden H + K + L = 2n + 1 positions, referenced to the high-temperature body-centred cubic structure. In general terms, this corresponds to antiferromagnetic arrangements of the Ho moments on adjacent clusters in the unit cell as previously found for Cd6Tb.
Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs
Baker, T. S.; Olson, N. H.; Fuller, S. D.
Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-Å) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical. PMID:10585969
Simulations of the Structure and Properties of Large Icosahedral Boron Clusters Based on a Novel Semi-Empirical Hamiltonian
NASA Astrophysics Data System (ADS)
Tandy, Paul; Yu, Ming; Jayanthi, C. S.; Wu, Shi-Yu; Condensed Matter Theory Group Team
A successful development of a parameterized semi-empirical Hamiltonian (SCED-LCAO) for boron based on a LCAO framework using a sp3 basis set will be discussed. The semi-empirical Hamiltonian contains environment-dependency and electron screening effects of a many-body Hamiltonian and allows for charge self-consistency. We have optimized the parameters of the SCED-LCAO Hamiltonian for boron by fitting the properties (e.g., the binding energy, bond length, etc.) of boron sheets, small clusters and boron alpha to first-principles calculations based on DFT calculations. Although extended phases of boron alpha and beta have been studied, large clusters of boron with icosahedral structures such as those cut from boron alpha are difficult if not impossible to simulate with ab initio methods. We will demonstrate the effectiveness of the SCED-LCAO Hamiltonian in studying icosahedral boron clusters containing up to 800 atoms and will report on some novel boron clusters and computational speed. Support has been provided by the Dillion Fellowship.
Electrochemically shape-controlled synthesis in deep eutectic solvents: triambic icosahedral platinum nanocrystals with high-index facets and their enhanced catalytic activity.
Wei, Lu; Zhou, Zhi-You; Chen, Sheng-Pei; Xu, Chang-Deng; Su, Dangsheng; Schuster, Manfred Erwin; Sun, Shi-Gang
Pt triambic icosahedral nanocrystals (TIH NCs) enclosed by {771} high-index facets were successfully synthesized electrochemically, for the first time, in ChCl-urea based deep eutectic solvents, and exhibited higher electrocatalytic activity and stability towards ethanol electrooxidation than a commercial Pt black catalyst. PMID:24084858
Planar scanning method for detecting refraction characteristics of two-dimensional photonic quasi-crystal wedge-shaped prisms.
Liu, Jianjun; Tan, Wei; Liu, Exian; Hu, Haili; Fan, Zhigang; Zhang, Tianhua; Zhang, Xiong
In this study, a planar scanning method is proposed. This novel method adapts two monitors moving along double planar tracks that can be used to detect refraction characteristics of two-dimensional (2D) photonic quasi-crystal (PQC) wedge-shaped prisms. Refraction of a decagonal Penrose-type PQC prism is analyzed for a given incident beam and two polarization modes at different incident positions in the prism using this method. Refraction from the prism is irregular, indicating that nonuniformity in the arrangement of scatterers in the prism causes Bragg-like scattering irregularities. Numerical results show that this method can be used for guiding the design of a 2D PQC prism and for the analysis of its refraction characteristics. PMID:27140896
New type of Al-based decagonal quasicrystal in Al60Cr20Fe10Si10 alloy
NASA Astrophysics Data System (ADS)
He, Zhanbing; Ma, Haikun; Li, Hua; Li, Xingzhong; Ma, Xiuliang
A new kind of decagonal quasicrystal (DQC) with a periodicity of 1.23 nm was observed in the as-cast quaternary Al60Cr20Fe10Si10 alloy. The intensity distribution of some spots in the selected-area electron diffraction pattern along the tenfold zone axis was found to be different from other Al-based DQCs. High-angle annular dark-field scanning transmission electron microscopy was adopted to reveal the structural features at an atomic level. Both the tenfold symmetry and symmetry-broken decagonal (D) clusters of 1.91 nm in diameter were found, but with structural characteristics different from the corresponding D clusters in the other Al-based DQCs. The neighboring D clusters are connected by sharing one edge rather than covering, suggesting the tiling model is better than the covering model for structural description.
Low index-contrast aperiodically ordered photonic quasicrystals for the development of isotropic photonic band-gap devices
NASA Astrophysics Data System (ADS)
Priya Rose, T.; Di Gennaro, E.; Andreone, A.; Abbate, G.
Photonic quasicrystals (PQCs) have neither true periodicity nor translational symmetry, however they can exhibit symmetries that are not achievable by conventional periodic structures. The arbitrarily high rotational symmetry of these materials can be practically exploited to manufacture isotropic band gap materials, which are perfectly suitable for hosting waveguides or cavities. In this work, formation and development of the photonic bandgap (PBG) in twodimensional 8-, 10- and 12-fold symmetry quasicrystalline lattices of low dielectric contrast (0.4-0.6) were measured in the microwave region and compared with the PBG properties of a conventional hexagonal crystal. Band-gap properties were also investigated by changing the direction of propagation of the incident beam inside the crystal. Various angles of incidence from 0° to 30° were used in order to investigate the isotropic nature of the band-gap.
Self-imaging effect in photonic quasicrystal waveguides: Application to 3 dB power splitter for terahertz waves
NASA Astrophysics Data System (ADS)
Xu, Feixiang; Zou, Qiushun; Zhou, Quancheng; Wang, Tongbiao; Yu, Tianbao; Liu, Nianhua
We report that self-imaging effect still can be achieved in photonic quasicrystal waveguides (PtQCWs) just as it does in photonic crystal waveguides. As a possible application of the results, a new kind of compact 3 dB PtQCWs-based power splitters based on this effect for terahertz waves with symmetric interference is presented and analyzed. The finite element method is used to calculate the distributions of stable-state electric field and evaluate transmission efficiency of these structures. The calculated results show that the proposed device provides a new compact model for exporting efficiently THz wave with a broad bandwidth to two channels averagely and can be extended to new designs of PtQCW devices.
New type of Al-based decagonal quasicrystal in Al60Cr20Fe10Si10 alloy
He, Zhanbing; Ma, Haikun; Li, Hua; Li, Xingzhong; Ma, Xiuliang
A new kind of decagonal quasicrystal (DQC) with a periodicity of 1.23 nm was observed in the as-cast quaternary Al60Cr20Fe10Si10 alloy. The intensity distribution of some spots in the selected-area electron diffraction pattern along the tenfold zone axis was found to be different from other Al-based DQCs. High-angle annular dark-field scanning transmission electron microscopy was adopted to reveal the structural features at an atomic level. Both the tenfold symmetry and symmetry-broken decagonal (D) clusters of 1.91 nm in diameter were found, but with structural characteristics different from the corresponding D clusters in the other Al-based DQCs. The neighboring D clusters are connected by sharing one edge rather than covering, suggesting the tiling model is better than the covering model for structural description. PMID:26928759
A flux-form conservative semi-Lagrangian multitracer transport scheme (FF-CSLAM) for icosahedral-hexagonal grids
NASA Astrophysics Data System (ADS)
Dubey, Sarvesh; Mittal, Rashmi; Lauritzen, Peter H.
A high-order incremental "remap-type" transport scheme is presented (FF-CSLAM). The scheme utilizes bi-quadratic polynomial subgrid-cell reconstruction functions based on the weighted least squares method. The integration of the reconstruction functions over flux areas, which is inherent in remap schemes, makes use of CSLAM approach of line integration. Though the formal order of the scheme is second order, yet quadratic subgrid scale polynomial reconstruction does lead to improvement in the overall accuracy of the scheme. Since the rigorous search for overlap areas between flux areas and grid cells is cumbersome, two simplifications have been suggested in the literature. The main objectives of this paper are (a) to formulate flux-form CSLAM for the icosahedral-hexagonal grid and (b) to assess the accuracy of two flux-integral simplifications.
A Winged-Helix Protein From Sulfolobus Turreted Icosahedral Virus Points Toward Stabilizing Disulfide Bonds in the Intracellular Proteins of a Hyperthermophilic Virus
Larson, E.T.; Eilers, B.; Menon, S.; Reiter, D.; Ortmann, A.; Young, M.J.; Lawrence, C.M.
Sulfolobus turreted icosahedral virus (STIV) was the first non-tailed icosahedral virus to be isolated from an archaeal host. Like other archaeal viruses, its 37 open reading frames generally lack sequence similarity to genes with known function. The roles of the gene products in this and other archaeal viruses are thus largely unknown. However, a protein's three-dimensional structure may provide functional and evolutionary insight in cases of minimal sequence similarity. In this vein, the structure of STIV F93 reveals a homodimer with strong similarity to the winged-helix family of DNA-binding proteins. Importantly, an interchain disulfide bond is found at the dimer interface, prompting analysis of the cysteine distribution in the putative intracellular proteins of the viral proteome. The analysis suggests that intracellular disulfide bonds are common in cellular STIV proteins, where they enhance the thermostability of the viral proteome.
The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea.
Jalasvuori, Matti; Jaatinen, Silja T; Laurinavicius, Simonas; Ahola-Iivarinen, Elina; Kalkkinen, Nisse; Bamford, Dennis H; Bamford, Jaana K H
We have sequenced the genome and identified the structural proteins and lipids of the novel membrane-containing, icosahedral virus P23-77 of Thermus thermophilus. P23-77 has an approximately 17-kb circular double-stranded DNA genome, which was annotated to contain 37 putative genes. Virions were subjected to dissociation analysis, and five protein species were shown to associate with the internal viral membrane, while three were constituents of the protein capsid. Analysis of the bacteriophage genome revealed it to be evolutionarily related to another Thermus phage (IN93), archaeal Halobacterium plasmid (pHH205), a genetic element integrated into Haloarcula genome (designated here as IHP for integrated Haloarcula provirus), and the Haloarcula virus SH1. These genetic elements share two major capsid proteins and a putative packaging ATPase. The ATPase is similar with the ATPases found in the PRD1-type viruses, thus providing an evolutionary link to these viruses and furthering our knowledge on the origin of viruses. PMID:19587059
A molecular dynamics study on the structural and electronic properties of two-dimensional icosahedral B12 cluster based structures
NASA Astrophysics Data System (ADS)
Kah, Cherno Baba; Yu, M.; Jayanthi, C. S.; Wu, S. Y.
Our previous study on one-dimensional icosahedral B12 cluster (α-B12) based chain [Bulletin of APS Annual Meeting, p265 (2013)] and ring structures has prompted us to study the two-dimensional (2D) α-B12 based structures. Recently, we have carried out a systematic molecular dynamics study on the structural stabilities and electronic properties of the 2D α-B12 based structures using the SCED-LCAO method [PRB 74, 15540 (2006)]. We have considered several types of symmetry for these 2D structures such as δ3, δ4, δ6 (flat triangular), and α' types. We have found that the optimized structures are energetically in the order of δ6 < α' < δ3 < δ4 which is different from the energy order of α'< δ6 < δ4 < δ3 found in the 2D boron monolayer sheets [ACS Nano 6, 7443 (2012)]. A detailed discussion of this study will be presented. The first author acknowledges the McSweeny Fellowship for supporting his research in this work.
Reconstruction of the Disassembly Pathway of an Icosahedral Viral Capsid and Shape Determination of Two Successive Intermediates.
Law-Hine, Didier; Sahoo, Anil K; Bailleux, Virginie; Zeghal, Mehdi; Prevost, Sylvain; Maiti, Prabal K; Bressanelli, Stéphane; Constantin, Doru; Tresset, Guillaume
Viral capsids derived from an icosahedral plant virus widely used in physical and nanotechnological investigations were fully dissociated into dimers by a rapid change of pH. The process was probed in vitro at high spatiotemporal resolution by time-resolved small-angle X-ray scattering using a high brilliance synchrotron source. A powerful custom-made global fitting algorithm allowed us to reconstruct the most likely pathway parametrized by a set of stoichiometric coefficients and to determine the shape of two successive intermediates by ab initio calculations. None of these two unexpected intermediates was previously identified in self-assembly experiments, which suggests that the disassembly pathway is not a mirror image of the assembly pathway. These findings shed new light on the mechanisms and the reversibility of the assembly/disassembly of natural and synthetic virus-based systems. They also demonstrate that both the structure and dynamics of an increasing number of intermediate species become accessible to experiments. PMID:27120684
A study of optical reflectance and localization modes of 1-D Fibonacci photonic quasicrystals using different graded dielectric materials
NASA Astrophysics Data System (ADS)
Singh, Bipin K.; Pandey, Praveen C.
In this paper, we present an analytical study on the reflection properties of light through one-dimensional (1-D) quasi-periodic multilayer structures. The considered structures are as follows: F7, F8, F9, (F2)10, (F3)10 and some combinations such as: [(F2)10 (F7) (F2)10], [(F2)10 (F8) (F2)10], [(F3)10 (F7) (F3)10], [(F3)10 (F8) (F3)10], [(F2)10(F3)10], [(F2)10 (F7) (F3)10] and [(F2)10 (F8) (F3)10], where (Fj)n represents n period of the Fibonacci sequence of jth generation. These multilayer structures are considered of two types of layers. One type of layer is considered of graded material like normal, linear or exponential graded material, and the second type of layer is considered of constant refractive index material. Transfer matrix method is utilized to calculate the reflection spectra and localization modes of such structures in the frequency range 150-450 THz. This work would provide the basis of understanding of the effect of graded materials on the reflection and localization modes in Fibonacci photonic quasicrystal structures and obtained spectra can be used in the recognition of grading of materials. The considered heterostructures provide the broad reflection band and some localization modes in the calculated region.
Optical reflectance and omnidirectional bandgaps in Fibonacci quasicrystals type 1-D multilayer structures containing exponentially graded material
NASA Astrophysics Data System (ADS)
Singh, Bipin K.; Thapa, Khem B.; Pandey, Praveen C.
A theoretical study of optical reflectance and reflection bands of 1-D photonic quasi-crystals (Fibonacci type arrangement) composed of exponentially graded material is presented. The proposed structures consist of two different layers, one of them is of constant refractive index (L) and the other one is of exponentially graded refractive index (S) dielectric materials. Four different generations (2nd, 3rd, 4th and 5th) of the Fibonacci sequence for 10 periods in one dimension (1-D) are considered and compared in view of their optical reflectance and bandgaps for both TE and TM polarisations. Also, we proposed some heterostructures made by the combination of different Fibonacci generations and their periods to obtain suitable omnidirectional reflection band. We used the transfer matrix method (TMM) to obtain the reflectance, bandgaps and omnidirectional reflectional bandgaps (ODR) of such structures in near infrared spectrum (800-2200 nm) at different angles of incidence. We show that ODR exists in these types of structures. The number of ODRs and total bandgap depend on the Fibonacci generations. Extraordinary ODR bandgaps are obtained in the case of heterostructures formed by the combination of different generations of the Fibonacci sequence. The ODR for these structures is similar to the ODR of photonic crystals containing left-handed materials. This work would be useful to study the Fibonacci type photonic crystals having graded index materials and also it will open new window to design several photonic crystal devices like sensors, reflectors, etc. in the infrared region.
Atomic structure solution of the complex quasicrystal approximant Al77Rh15Ru8 from electron diffraction data.
Samuha, Shmuel; Mugnaioli, Enrico; Grushko, Benjamin; Kolb, Ute; Meshi, Louisa
The crystal structure of the novel Al77Rh15Ru8 phase (which is an approximant of decagonal quasicrystals) was determined using modern direct methods (MDM) applied to automated electron diffraction tomography (ADT) data. The Al77Rh15Ru8 E-phase is orthorhombic [Pbma, a = 23.40 (5), b = 16.20 (4) and c = 20.00 (5) Å] and has one of the most complicated intermetallic structures solved solely by electron diffraction methods. Its structural model consists of 78 unique atomic positions in the unit cell (19 Rh/Ru and 59 Al). Precession electron diffraction (PED) patterns and high-resolution electron microscopy (HRTEM) images were used for the validation of the proposed atomic model. The structure of the E-phase is described using hierarchical packing of polyhedra and a single type of tiling in the form of a parallelogram. Based on this description, the structure of the E-phase is compared with that of the ε6-phase formed in Al-Rh-Ru at close compositions. PMID:25449623
Giant Surfactants based on Precisely Functionalized POSS Nano-atoms: Tuning from Crystals to Frank-Kasper Phases and Quasicrystals
NASA Astrophysics Data System (ADS)
Cheng, Stephen Z. D.
In creating new functional materials for advanced technologies, precisely control over functionality and their hierarchical ordered structures are vital for obtaining the desired properties. Giant polyhedra are a class of materials which are designed and constructed via deliberately placing precisely functionalized polyhedral oligomeric silsesquioxane (POSS) and fullerene (C60) molecular nano-particles (MNPs) (so-called ``nano-atoms'') at the vertices of a polyhedron. Giant surfactants are consisted of polymer tail-tethered ``nano-atoms'' which are deliberately and precisely functionalized POSS or C60 molecular nano-particles (MNPs). The ``nano-atom'' heads and polymer tails thus have drastic chemical differences to impart amphiphilicity. These giant surfactants capture the essential structural features of their small-molecule counterparts in many ways but possess much larger sizes, and therefore, they are recognized as size-amplified versions of small molecule surfactants. Two of the most illustrating examples are a series of novel giant tetrahedra and a series of giant giant surfactants as building blocks to construct into hierarchical ordered super-lattice structures ranging from crystals, Frank-Kasper phases and quasicrystals in the condensed bulk states, reveals evidently the interconnections between soft matters and hard matters in sharing their common structures and fundamental knowledge. This work was supported by National Science Foundation (DMR-1409972).
Designing photonic quasi-crystal fibers of various folds: onto optimization of efficiency and bandwidth of second harmonic generation.
Bhattacharjee, Ritapa; Senthilnathan, K; Sivabalan, S; Ramesh Babu, P
We design photonic quasi-crystal fibers (PQFs) of six-, eight-, ten-, and twelve-folds for determining the optimized efficiency as well as the bandwidth of second harmonic generation (SHG). We report a maximum SHG relative efficiency of 941.36% W⁻¹ cm⁻² for a twelve-fold PQF of 2 μm pitch. The detailed numerical results reveal that, while the relative efficiency increases appreciably, the phase-matching bandwidth increases marginally, as and when the number of folds increases. As the primary interest of this work is to enhance the relative efficiency, we focus our analysis with a twelve-fold PQF for which the efficiency turns a maximum. In line with the practical feasibility of poling, we keep the pitch at 7 μm and report an optimized relative efficiency and phase-matching bandwidth as 95.28% W⁻¹ cm⁻² and 50.51 nm.cm, respectively. PMID:24921878
Energetics, relative stabilities, and size-dependent properties of nanosized carbon clusters of different families: fullerenes, bucky-diamond, icosahedral, and bulk-truncated structures.
Yu, M; Chaudhuri, I; Leahy, C; Wu, S Y; Jayanthi, C S
Structures and relative stabilities of carbon clusters belonging to different families have been investigated for diameters d < or = 5 nm based on an efficient semiempirical molecular dynamics (MD) scheme as well as a density functional theory based simulation. Carbon clusters studied include fullerenes and fullerene-derived structures (e.g., cages and onions), icosahedral structures, bucky-diamond structures, and clusters cut from the bulk diamond with spherical and facetted truncations. The reason for using a semiempirical MD is partly due to the large number of different cases (or carbon allotropes) investigated and partly due to the size of the clusters investigated in this work. The particular flavor of the semiempirical MD scheme is based on a self-consistent and environment-dependent Hamiltonian developed in the framework of linear combination of atomic orbitals. We find that (i) among the families of carbon clusters investigated, fullerene structures have the lowest energy with the relative energy ordering being E(fullerene) < E(onion) < E(icosahedral) < E(bucky-diamond) < E(bulk-truncated), (ii) a crossover between bucky-diamond and icosahedral structures is likely at d approximately 8 nm, (iii) the highest occupied molecular orbital-lowest unoccupied molecular orbital gap as a function of the diameter for the case of fullerenes shows an oscillatory behavior with the gap ranging from 2 eV to 6 meV, and the gap approaching that of gapless graphite for d > 3.5 nm, and (iv) there can be three types of phase transformations depending on the manner of heating and cooling in our simulated annealing studies: (a) a bucky-diamond structure --> an onionlike structure, (b) an onionlike --> a cage structure, and (c) a bucky-diamond --> a cage structure. PMID:19449944
Carbon-rich icosahedral boron carbides beyond B4C and their thermodynamic stabilities at high temperature and pressure from first principles
NASA Astrophysics Data System (ADS)
Ektarawong, A.; Simak, S. I.; Alling, B.
We investigate the thermodynamic stability of carbon-rich icosahedral boron carbide at different compositions, ranging from B4C to B2C , using first-principles calculations. Apart from B4C , generally addressed in the literature, B2.5C , represented by B10C2p (C-C), where Cp and (C-C) denote a carbon atom occupying the polar site of the icosahedral cluster and a diatomic carbon chain, respectively, is predicted to be thermodynamically stable under high pressures with respect to B4C as well as pure boron and carbon phases. The thermodynamic stability of B2.5C is determined by the Gibbs free energy G as a function of pressure p and temperature T , in which the contributions from the lattice vibrations and the configurational disorder are obtained within the quasiharmonic and the mean-field approximations, respectively. The stability range of B2.5C is then illustrated through the p -T phase diagrams. Depending on the temperatures, the stability range of B2.5C is predicted to be within the range between 40 and 67 GPa. At T ≳ 500 K, the icosahedral Cp atoms in B2.5C configurationally disorder at the polar sites. By investigating the properties of B2.5C , e.g., elastic constants and phonon and electronic density of states, we demonstrate that B2.5C is both mechanically and dynamically stable at zero pressure, and is an electrical semiconductor. Furthermore, based on the sketched phase diagrams, a possible route for experimental synthesis of B2.5C as well as a fingerprint for its characterization from the simulations of x-ray powder diffraction pattern are suggested.
Atomic scale structure of the 5-fold surface of an AlPdMn quasicrystal: A quantitative X-Ray photoelectron diffraction analysis
Zheng, Jin-Cheng; Huan, C.H.A.; Wee, A.T.S.; Van Hove, M.A.; Fadley, C.S.; Shi, F.J.; Rotenberg, E.; Barman, S.R.; Paggel, J.J.; Horn, K.; Ebert, Ph.; Urban, K.
The atomic scale structure of the 5-fold symmetric surface of an AlPdMn quasicrystal is investigated quantitatively by comparing x-ray photoelectron diffraction (XPD) simulations to experiment. The observed 5-fold symmetry of the diffraction patterns indicates that the surface is quasicrystalline with no hint of a reconstruction from the bulk structure. In analyzing the experimental data, many possible bulk terminations have been tested. Those few that fit best to the data have in common that they contain an Al-rich surface layer followed by a dense mixed Al/Pd/Mn layer. These best terminations, while not identical to each other, are suggested to form terraces coexisting on a real surface. Structural relaxations of the quasicrystal surface are also analyzed: mixing several best-fit terminations gives average best-fit interlayer spacing changes of Dd12 = -0.057 Angstrom, Dd24 = +0.159 Angstrom. These results are in good agreement with a prior structure determination by LEED on a sample that was prepared in a different manner.
Studies of Nucleation and Growth, Specific Heat and Viscosity of Undercooled Melts of Quasicrystal and Polytetrahedral-Phase Forming Alloys
NASA Technical Reports Server (NTRS)
Kelton, K. F.; Gangopadhyay, Anup K.; Lee, G. W.; Hyers, Robert W.; Rathz, T. J.; Robinson, Michael B.; Rogers, Jan R.
From extensive ground based work on the phase diagram and undercooling studies of Ti-Zr-Ni alloys, have clearly identified the composition of three different phases with progressively increasing polytetrahedral order such as, (Ti/Zr), the C14 Laves phase, and the i-phase, that nucleate directly from the undercooled liquid. The reduced undercooling decreases progressively with increasing polytetrahedral order in the solid, supporting Frank s hypothesis. A new facility for direct measurements of the structures and phase transitions in undercooled liquids (BESL) was developed and has provided direct proof of the primary nucleation of a metastable icosahedral phase in some Ti-Zr-Ni alloys. The first measurements of specific heat and viscosity in the undercooled liquid of this alloy system have been completed. Other than the importance of thermo-physical properties for modeling nucleation and growth processes in these materials, these studies have also revealed some interesting new results (such as a maximum of C(sup q, sub p) in the undercooled state). These ground-based results have clearly established the necessary background and the need for conducting benchmark nucleation experiments at the ISS on this alloy system.
Design of Three-shell Icosahedral Matryoshka Clusters A@B12@A20 (A = Sn, Pb; B = Mg, Zn, Cd, Mn)
Huang, Xiaoming; Zhao, Jijun; Su, Yan; Chen, Zhongfang; King, R. Bruce
We propose a series of icosahedral matryoshka clusters of A@B12@A20 (A = Sn, Pb; B = Mg, Zn, Cd), which possess large HOMO-LUMO gaps (1.29 to 1.54 eV) and low formation energies (0.06 to 0.21 eV/atom). A global minimum search using a genetic algorithm and density functional theory calculations confirms that such onion-like three-shell structures are the ground states for these A21B12 binary clusters. All of these icosahedral matryoshka clusters, including two previously found ones, i.e., [As@Ni12@As20]3− and [Sn@Cu12@Sn20]12−, follow the 108-electron rule, which originates from the high Ih symmetry and consequently the splitting of superatom orbitals of high angular momentum. More interestingly, two magnetic matryoshka clusters, i.e., Sn@Mn12@Sn20 and Pb@Mn12@Pb20, are designed, which combine a large magnetic moment of 28 µB, a moderate HOMO-LUMO gap, and weak inter-cluster interaction energy, making them ideal building blocks in novel magnetic materials and devices. PMID:25376938
Design of Three-shell Icosahedral Matryoshka Clusters A@B12@A20 (A = Sn, Pb; B = Mg, Zn, Cd, Mn)
NASA Astrophysics Data System (ADS)
Huang, Xiaoming; Zhao, Jijun; Su, Yan; Chen, Zhongfang; King, R. Bruce
We propose a series of icosahedral matryoshka clusters of A@B12@A20 (A = Sn, Pb; B = Mg, Zn, Cd), which possess large HOMO-LUMO gaps (1.29 to 1.54 eV) and low formation energies (0.06 to 0.21 eV/atom). A global minimum search using a genetic algorithm and density functional theory calculations confirms that such onion-like three-shell structures are the ground states for these A21B12 binary clusters. All of these icosahedral matryoshka clusters, including two previously found ones, i.e., [As@Ni12@As20]3- and [Sn@Cu12@Sn20]12-, follow the 108-electron rule, which originates from the high Ih symmetry and consequently the splitting of superatom orbitals of high angular momentum. More interestingly, two magnetic matryoshka clusters, i.e., Sn@Mn12@Sn20 and Pb@Mn12@Pb20, are designed, which combine a large magnetic moment of 28 µB, a moderate HOMO-LUMO gap, and weak inter-cluster interaction energy, making them ideal building blocks in novel magnetic materials and devices.
Improvement of aerosol optical properties modeling over Eastern Asia with MODIS AOD assimilation in a global non-hydrostatic icosahedral aerosol transport model.
Dai, Tie; Schutgens, Nick A J; Goto, Daisuke; Shi, Guangyu; Nakajima, Teruyuki
A new global aerosol assimilation system adopting a more complex icosahedral grid configuration is developed. Sensitivity tests for the assimilation system are performed utilizing satellite retrieved aerosol optical depth (AOD) from the Moderate Resolution Imaging Spectroradiometer (MODIS), and the results over Eastern Asia are analyzed. The assimilated results are validated through independent Aerosol Robotic Network (AERONET) observations. Our results reveal that the ensemble and local patch sizes have little effect on the assimilation performance, whereas the ensemble perturbation method has the largest effect. Assimilation leads to significantly positive effect on the simulated AOD field, improving agreement with all of the 12 AERONET sites over the Eastern Asia based on both the correlation coefficient and the root mean square difference (assimilation efficiency). Meanwhile, better agreement of the Ångström Exponent (AE) field is achieved for 8 of the 12 sites due to the assimilation of AOD only. PMID:25017412
Form, symmetry and packing of biomacromolecules. V. Shells with boundaries at anti-nodes of resonant vibrations in icosahedral RNA viruses.
Janner, A
The RNA viruses cowpea chlorotic mottle, satellite tobacco mosaic, pariacoto and MS2, already considered in part IV of this series of papers [Janner, A. (2011a), Acta Cryst. A67, 517-520], are investigated further, with the aim to arrive at a possible physical basis for their structural properties. The shell structure of the filled capsid is analyzed in terms of successive spherical boundaries of the sets of icosahedral equivalent chains. By inversion in the sphere enclosing the capsid, the internal boundaries are transformed into external ones, which are more easily visualized. This graphical procedure reveals the presence of regularly spaced shells with boundaries fitting with anti-nodal surfaces of the virus considered as an elastic resonator. The centers of gravity of the various chains occur in the nodal regions of eigenvibrations with wavelength λ = R(0)/K(0), where R(0) is the radius of the virus and K(0) takes one of the values 12, 6, 4, 3, depending on the mode. The resonator model is consistent with practically all spherical shell boundaries, whereas deviations are observed for the icosahedral axial modes, which apparently play a secondary role with respect to the spherical ones. Both the spherical and the axial anti-nodal surfaces fit very well with the packed structure of the viruses in the crystal which, accordingly, is expected to have eigenfrequencies related to those of the virus. These results open the way to a better understanding of the possibility of breaking the capsid using resonant forced oscillations excited, for example, by an applied elastic shock or by irradiation with femtosecond laser pulses, as already realised by K.-T. Tsen and co-workers. An alternative `plywood' model connected to the extreme elastic properties of the capsid is also considered. PMID:22011468
Undercooling and solidification behavior of melts of the quasicrystal-forming alloys Al-Cu-Fe and Al-Cu-Co
Holland-Moritz, D.; Schroers, J.; Herlach, D.M.; Grushko, B.; Urban, K.
Al-Cu-Fe, Al-Fe and Al-Cu-Co melts of different compositions were undercooled by containerless processing in an electromagnetic levitation facility. The phase selection during solidification from the undercooled melt was determined by direct measurements of the temperature changes during recalescence. Complimentarily, the phase selection and microstructure development was studied by scanning- and transmission electron microscopy (SEM, TEM) and X-ray diffraction (XRD) on the as-solidified samples with the undercooling and the alloy composition as experimental parameters. For comparison, rapidly quenched samples of the same alloys were produced by splat-cooling and investigated by TEM and XRD. The undercooling results were analyzed within the framework of classical nucleation theory. The activation threshold for the nucleation was found to be small for the icosahedral quasicrystalline phase in Al-Cu-Fe, medium for the decagonal D-phase in Al-Cu-Co and crystalline phases with polytetrahedral symmetry elements (Al{sub 13}Fe{sub 4} and Al{sub 5}Fe{sub 2}), but large for the cubic phase of Al{sub 50}(CuCo){sub 50} with non-polytetrahedral crystalline symmetry. These results are explained assuming of an icosahedral short-range order that prevails in the undercooled melt and gives rise to an interfacial energy decreasing with increasing degree of polytetrahedral order in the solid nucleus.
Coating of a layer of Au on Al13 : The findings of icosahedral Al@Al12Au20- and Al12Au202- fullerenes using ab initio pseudopotential calculations
NASA Astrophysics Data System (ADS)
Kumar, Vijay
We report results of ab initio pseudopotential calculations on the nanocoating of gold on an icosahedral Al13 cluster and the findings of icosahedrally symmetric endohedral Al@Al12Au20- and empty cage Al12Au202- compound fullerenes formed of metal atoms. Twelve Al atoms cap the pentagonal faces of a dodecahedral Au20 cage in which each Au atom has three Al atoms and three Au atoms as nearest neighbors. Mixing of Al13 and Au20 magic clusters leads to a large heat of formation of 0.55 eV/atom and high stability of the Al@Al12Au20 compound fullerene. The binding energies of Al12Au20 and Al@Al12Au20 are 3.017 and 3.007 eV/atom, respectively, which are much larger than 2.457 eV/atom for Au32 fullerene, leading to the possibility of their high abundance.
Identification of a major intermediate along the self-assembly pathway of an icosahedral viral capsid by using an analytical model of a spherical patch.
Law-Hine, Didier; Zeghal, Mehdi; Bressanelli, Stéphane; Constantin, Doru; Tresset, Guillaume
Viruses are astonishing edifices in which hundreds of molecular building blocks fit into the final structure with pinpoint accuracy. We established a robust kinetic model accounting for the in vitro self-assembly of a capsid shell derived from an icosahedral plant virus by using time-resolved small-angle X-ray scattering (TR-SAXS) data at high spatiotemporal resolution. By implementing an analytical model of a spherical patch into a global fitting algorithm, we managed to identify a major intermediate species along the self-assembly pathway. With a series of data collected at different protein concentrations, we showed that free dimers self-assembled into a capsid through an intermediate resembling a half-capsid. The typical lifetime of the intermediate was a few seconds and yet the presence of so large an oligomer was not reported before. The progress in instrumental detection along with the development of powerful algorithms for data processing contribute to shedding light on nonequilibrium processes in highly complex systems such as viruses. PMID:27444997
Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes.
Miyazaki, Naoyuki; Higashiura, Akifumi; Higashiura, Tomoko; Akita, Fusamichi; Hibino, Hiroyuki; Omura, Toshihiro; Nakagawa, Atsushi; Iwasaki, Kenji
The minor outer capsid protein P2 of Rice dwarf virus (RDV), a member of the genus Phytoreovirus in the family Reoviridae, is essential for viral cell entry. Here, we clarified the structure of P2 and the interactions to host insect cells. Negative stain electron microscopy (EM) showed that P2 proteins are monomeric and flexible L-shaped filamentous structures of ∼20 nm in length. Cryo-EM structure revealed the spatial arrangement of P2 in the capsid, which was prescribed by the characteristic virion structure. The P2 proteins were visualized as partial rod-shaped structures of ∼10 nm in length in the cryo-EM map and accommodated in crevasses on the viral surface around icosahedral 5-fold axes with hydrophobic interactions. The remaining disordered region of P2 assumed to be extended to the radial direction towards exterior. Electron tomography clearly showed that RDV particles were away from the cellular membrane at a uniform distance and several spike-like densities, probably corresponding to P2, connecting a viral particle to the host cellular membrane during cell entry. By combining the in vitro and in vivo structural information, we could gain new insights into the detailed mechanism of the cell entry of RDV. PMID:26374901
Correlation between dynamic slowing down and local icosahedral ordering in undercooled liquid Al{sub 80}Ni{sub 20} alloy
Jakse, N.; Pasturel, A.
We use ab initio molecular dynamics simulations to study the correlation between the local ordering and the dynamic properties of liquid Al{sub 80}Ni{sub 20} alloy upon cooling. Our results evidence a huge increase of local icosahedral ordering (ISRO) in the undercooled regime which is more developed around Ni than Al atoms. We show that ISRO has a strong impact on self-diffusion coefficients of both species and is at the origin of their crossover from Arrhenius to non-Arrhenius behavior around a crossover temperature T{sub X} = 1000 K, located in the undercooled region. We also clearly identify that this temperature corresponds to the development of dynamic heterogeneities and to the breakdown of the Stokes-Einstein relation. At temperatures below this crossover, we find that the behavior of the diffusion and relaxation dynamics is mostly incompatible with predictions of the mode-coupling theory. Finally, an analysis of the van Hove function indicates that the crossover temperature T{sub X} marks the onset of a change in the diffusion mechanism from a normal flow to an activated process with hopping. From these results, the glass-forming ability of the alloy is discussed.
Development of an aerosol-chemistry transport model coupled to non-hydrostatic icosahedral atmospheric model (NICAM) through applying a stretched grid system to regional simulations around Japan
NASA Astrophysics Data System (ADS)
Goto, D.; Nakajima, T.; Masaki, S.
Air pollution has a great impact on both climate change and human health. One effective way to tackle with these issues is a use of atmospheric aerosol-chemistry models with high-resolution in a global scale. For this purpose, we have developed an aerosol-chemistry model based on a global cloud-resolving model (GCRM), Nonhydrostatic Icosahedral Atmospheric Model (NICAM; Tomita and Satoh, Fluid. Dyn. Res. 2004; Satoh et al., J. Comput. Phys. 2008, PEPS, 2014) under MEXT/RECCA/SALSA project. In the present study, we have simulated aerosols and tropospheric ozone over Japan by our aerosol-chemistry model "NICAM-Chem" with a stretched-grid system of approximately 10 km resolution, for saving the computer resources. The aerosol and chemistry modules are based on Spectral Radiation-Transport Model for Aerosol Species (SPRINTARS; Takemura et al., J. Geophys. Res., 2005) and Chemical AGCM for Study of Atmospheric Environment and Radiative Forcing (CHASER; Sudo et al., J. Geophys. Res., 2002). We found that our model can generally reproduce both aerosols and ozone, in terms of temporal variations (daily variations of aerosols and diurnal variations of ozone). Under MEXT/RECCA/SALSA project, we also have used these results obtained by NICAM-Chem for the assessment of their impact on human health.
A hybrid simulated method for analyzing the optical efficiency of a head-mounted display with a quasi-crystal OLED panel.
Chang, Kao-Der; Li, Chang-Yi; Pan, Jui-Wen; Cheng, Kuei-Yuan
Organic light emitting diodes (OLEDs) with a quasi-crystal (QC) structure are analyzed and applied in a head-mounted display (HMD) system in this study. We adopt a hybrid simulated method to evaluate the light extraction efficiency (LEE) and far-field pattern in the air, and study the relationship between them. The simulation results show that OLEDs implanted with the QC structure can provide a collimated far-field pattern to increase the brightness. Using this 10-fold QC arrangement the maxima LEE of the OLEDs can be increased by 1.20 times. Compared with conventional OLEDs, the viewing angle of the OLED panel decreases from 120 degrees to 26 degrees with an improvement in the optical efficiency of the HMD system by 2.66 times. Moreover, the normalized on-axis intensity in the pupil of the eyepiece can be enlarged up to 3.95 times which suggests that the OLED panel can save 74.68% energy while achieving the same on-axis intensity as conventional OLEDs. PMID:24922267
Quantum diffusion of electrons in quasiperiodic and periodic approximant lattices in the rare earth-cadmium system
NASA Astrophysics Data System (ADS)
Armstrong, N. M. R.; Mortimer, K. D.; Kong, T.; Bud'ko, S. L.; Canfield, P. C.; Basov, D. N.; Timusk, T.
Icosahedral quasicrystals are characterised by the absence of a distinct Drude peak in their low-frequency optical conductivity and the same is true of their crystalline approximants. We have measured the optical conductivity of i-GdCd?, an icosahedral quasicrystal, and two approximants, GdCd? and YCd?. We find that there is a significant difference in the optical properties of these compounds. The approximants have a zero frequency peak, characteristic of a metal, whereas the quasicrystal has a striking minimum. This is the first example where the transport properties of a quasicrystal and its approximant differ in such a fundamental way. Using a generalised Drude model introduced by Mayou, we find that our data are well described by this model. It implies that the quantum diffusion of electron wave packets through the periodic and quasiperiodic lattices is responsible for these dramatic differences: in the approximants, the transport is superdiffusive, whereas the quasicrystals show subdiffusive motion of the electrons.
A hybrid plant RNA virus made by transferring the noncapsid movement protein from a rod-shaped to an icosahedral virus is competent for systemic infection.
De Jong, W; Ahlquist, P
For many plant RNA viruses, multiple viral gene products, including noncapsid movement proteins and capsid proteins, contribute to the spread of infection within plants. The extent to which these factors interact to support infection spread is not known, but, for movement protein mutants of certain viruses, the inability of coinoculated "helper" viruses to complement defective movement has suggested a possible requirement for coadaptation between noncapsid movement proteins and other virus factors. To test directly for required coadaptation, the 3a movement protein gene of cowpea chlorotic mottle virus, an icosahedral bromovirus, was replaced with the nonhomologous 30-kDa movement protein gene of sunn-hemp mosaic virus, a rod-shaped, cowpea-adapted tobamovirus. The resulting hybrid virus is competent for systemic infection of cowpea, with systemic infection dependent upon expression of the 30-kDa gene. In view of the dramatic differences between cowpea chlorotic mottle virus and sunn-hemp mosaic virus in genetic organization and particle morphology, the ability of the hybrid to systemically infect cowpea implies that the tobamovirus 30-kDa movement protein functions independently of sequence-specific interactions with other viral components or sequences. Similarly, the required contribution of bromovirus capsid protein to infection movement appears to be independent of specific interaction with the natural 3a movement protein. In addition to other implications concerning movement protein and coat protein function, the results are consistent with the possibility that two or more distinguishable transfer processes may be involved in crossing different tissue barriers to achieve full systemic spread of infection. PMID:1495969
Interpenetration of a 3D Icosahedral M@Ni12 (M=Al, Ga) Framework with Porphyrin-Reminiscent Boron Layers in MNi9 B8.
Zheng, Qiang; Wagner, Frank R; Ormeci, Alim; Prots, Yurii; Burkhardt, Ulrich; Schmidt, Marcus; Schnelle, Walter; Grin, Yuri; Leithe-Jasper, Andreas
Two ternary borides MNi9 B8 (M=Al, Ga) were synthesized by thermal treatment of mixtures of the elements. Single-crystal X-ray diffraction data reveal AlNi9 B8 and GaNi9 B8 crystallizing in a new type of structure within the space group Cmcm and the lattice parameters a=7.0896(3) Å, b=8.1181(3) Å, c=10.6497(4) Å and a=7.0897(5) Å, b=8.1579(4) Å, c=10.6648(7) Å, respectively. The boron atoms build up two-dimensional layers, which consist of puckered [B16 ] rings with two tailing B atoms, whereas the M atoms reside in distorted vertices-condensed [Ni12 ] icosahedra, which form a three-dimensional framework interpenetrated by boron porphyrin-reminiscent layers. An unusual local arrangement resembling a giant metallo-porphyrin entity is formed by the [B16 ] rings, which, due to their large annular size of approximately 8 Å, chelate four of the twelve icosahedral Ni atoms. An analysis of the chemical bonding by means of the electron localizability approach reveals strong covalent B-B interactions and weak Ni-Ni interactions. Multi-center dative B-Ni interaction occurs between the Al-Ni framework and the boron layers. In agreement with the chemical bonding analysis and band structure calculations, AlNi9 B8 is a Pauli-paramagnetic metal. PMID:26418894
The structure of an Al-Rh-Cu decagonal quasicrystal studied by spherical aberration (Cs)-corrected scanning transmission electron microscopy
NASA Astrophysics Data System (ADS)
Hiraga, Kenji; Yasuhara, Akira; Yamamoto, Kazuki; Yubuta, Kunio
The structure of an Al-Rh-Cu decagonal quasicrystal formed with two quasiperiodic planes along the periodic axis in an Al63Rh18.5Cu18.5 alloy has been studied by spherical aberration (Cs)-corrected high-angle annular detector dark-field (HAADF)- and annular bright-field (ABF)-scanning transmission electron microscopy (STEM). Heavy atoms of Rh and mixed sites (MSs) of Al and Cu atoms projected along the periodic axis can be clearly represented as separate bright dots in observed HAADF-STEM images, and consequently arrangements of Rh atoms and MSs on the two quasiperiodic planes can be directly determined from those of bright dots in the observed HAADF-STEM image. The Rh atoms are arranged in pentagonal tiling formed with pentagonal and star-shaped pentagonal tiles with an edge-length of 0.76 nm, and also MSs with a pentagonal arrangement are located in the pentagonal tiles with definite orientations. The star-shaped pentagonal tiles in the pentagonal tiling are arranged in τ2(τ: golden ratio)-inflated pentagonal tiling with a bond-length of 2 nm. From arrangements of Rh atoms placed in pentagonal tilings with a bond-length of 2 nm, which are generated by the projection of a five-dimensional hyper-cubic lattice, occupation domains in the perpendicular space are derived. Al atoms as well as Rh atoms and MSs are represented as dark dots in an observed ABF-STEM image, and arrangements of Al atoms in well-symmetric regions are discussed.
Gravitational wave detection by a spherical antenna: The angular sensitivity of resonators in the truncated icosahedral gravitational wave antenna configuration and its variation with sidereal time and galactic longitude
NASA Astrophysics Data System (ADS)
Gasparini, Maria Alice
Experimental projects using spherical antennas to detect gravitational waves are nowadays a concrete reality. The main purpose of this paper is to give a possible way of interpreting output data from such a system. Responses of the five fundamental quadrupole modes and of the six resonators in truncated icosahedral gravitational wave antenna (TIGA) collocations are shown as a function of the incoming direction of the incident wave. Then, for a source lying in the galactic plane, sidereal time and galactic longitude dependence is given. Thus, once a candidate source of gravitational waves is considered, we can exactly predict the resonators' response as a function of time.
Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase
Dellas, Nikki; Snyder, Jamie C.; Dills, Michael; Nicolay, Sheena J.; Kerchner, Keshia M.; Brumfield, Susan K.; Lawrence, C. Martin
ABSTRACT Sulfolobus turreted icosahedral virus (STIV), an archaeal virus that infects the hyperthermoacidophile Sulfolobus solfataricus, is one of the most well-studied viruses of the domain Archaea. STIV shares structural, morphological, and sequence similarities with viruses from other domains of life, all of which are thought to belong to the same viral lineage. Several of these common features include a conserved coat protein fold, an internal lipid membrane, and a DNA-packaging ATPase. B204 is the ATPase encoded by STIV and is thought to drive packaging of viral DNA during the replication process. Here, we report the crystal structure of B204 along with the biochemical analysis of B204 mutants chosen based on structural information and sequence conservation patterns observed among members of the same viral lineage and the larger FtsK/HerA superfamily to which B204 belongs. Both in vitro ATPase activity assays and transfection assays with mutant forms of B204 confirmed the essentiality of conserved and nonconserved positions. We also have identified two distinct particle morphologies during an STIV infection that differ in the presence or absence of the B204 protein. The biochemical and structural data presented here are not only informative for the STIV replication process but also can be useful in deciphering DNA-packaging mechanisms for other viruses belonging to this lineage. IMPORTANCE STIV is a virus that infects a host from the domain Archaea that replicates in high-temperature, acidic environments. While STIV has many unique features, there exist several striking similarities between this virus and others that replicate in different environments and infect a broad range of hosts from Bacteria and Eukarya. Aside from structural features shared by viruses from this lineage, there exists a significant level of sequence similarity between the ATPase genes carried by these different viruses; this gene encodes an enzyme thought to provide energy that drives
Enhancement of light output power of GaN-based light-emitting diodes with photonic quasi-crystal patterned on p-GaN surface and n-side sidewall roughing
In this paper, GaN-based light-emitting diodes (LEDs) with photonic quasi-crystal (PQC) structure on p-GaN surface and n-side roughing by nano-imprint lithography are fabricated and investigated. At an injection current of 20 mA, the LED with PQC structure on p-GaN surface and n-side roughing increased the light output power of the InGaN/GaN multiple quantum well LEDs by a factor of 1.42, and the wall-plug efficiency is 26% higher than the conventional GaN-based LED type. After 500-h life test (55°C/50 mA), it was found that the normalized output power of GaN-based LED with PQC structure on p-GaN surface and n-side roughing only decreased by 6%. These results offer promising potential to enhance the light output powers of commercial light-emitting devices using the technique of nano-imprint lithography. PMID:23683526
Diffraction studies of the structure of glasses and liquids
Moss, S.C.
At the University of Houston, our program on glasses and liquids has continued with emphasis on melanin; vitreous TiO{sub 2}; metallic glasses/quasicrystals, including the computer modelling of quasicrystals via icosahedral glass models; and the structure of C{sup +} ion-beam deposited carbon films. The development of a dedicated glass and liquid diffractometer (GLAD) at the Argonne IPNS, under the direction of Dr. David L. Price, has entered the prototype stage. We are now quite close to a fully operating facility and commissioning should take place in the Spring 1990 with beam time available for participating scientists, on state-of-the-art experiments, shortly thereafter.
Quasicrystal Ising chain and automata theory
Allouche, J.P.; France, M.M.
An automatic sequence is generated by a finite machine (automaton). These sequences can be periodic or not; in the latter case, however, they are not random, but rather ''quasicrystalline.'' The authors consider an Ising chain with variable interaction in a uniform external field, at zero temperature, and prove that, if this interaction is automatic, then the induced magnetic field is also automatic.
Basis for Synthesis of Spiral Lattice Quasicrystals
NASA Astrophysics Data System (ADS)
Bursill, L. A.; Ryan, George; Fan, Xudong; Rouse, J. L.; Peng, Julin; Perkins, Anne
Observations of the sunflower Helianthus tuberosus reveal the occurrence of both Fibonacci and Lucas numbers of visible spirals (parastichies). This species is multi-headed, allowing a quantitative study of the relative abundance of these two types of phyllotaxis. The florets follow a spiral arrangement. It is remarkable that the Lucas series occurred, almost invariably, in the first-flowering heads of individual plants. The occurrence of left-and right-handed chirality was found to be random, within experimental error, using an appropriate chirality convention. Quantitative crystallographic studies allow the average growth law to be derived (r = alτ-1 θ = 2πl/(τ + 1), where a is a constant, l is the seed cell number and τ is the golden mean (1 +√ {5})/2). They also reveal departures from classical theoretical models of phyllotaxis, taking the form of persistent oscillations in both divergence angle and radius. The experimental results are discussed in terms of a new theoretical model for the close-packing of growing discs. Finally, a basis for synthesis of (inorganic) spiral lattice structures is proposed.
Carbon-rich icosahedral boron carbide designed from first principles
Jay, Antoine; Vast, Nathalie; Sjakste, Jelena; Duparc, Olivier Hardouin
The carbon-rich boron-carbide (B{sub 11}C)C-C has been designed from first principles within the density functional theory. With respect to the most common boron carbide at 20% carbon concentration B{sub 4}C, the structural modification consists in removing boron atoms from the chains linking (B{sub 11}C) icosahedra. With C-C instead of C-B-C chains, the formation of vacancies is shown to be hindered, leading to enhanced mechanical strength with respect to B{sub 4}C. The phonon frequencies and elastic constants turn out to prove the stability of the carbon-rich phase, and important fingerprints for its characterization have been identified.
Hall constant on the Icosahedral t-J model
NASA Astrophysics Data System (ADS)
Haerter, Jan; Peterson, Michael; Shastry, Sriram
We investigate the Hall constant RH in the zero field limit through the exact diagonalization technique on small clusters within the triangular lattice t-J model. As a model system we study the icosahedron, a 12-site Platonic solid consisting solely of five fold coordinated triangles. We compare results with toroidal geometries up to 12 sites. While the high-temperature behavior of the high-frequency RH^* is quite well understood analytically, our objective is to explain the complete T-dependence of RH in Na.68CoO2 as observed in experiments (Ong et al), especially in the low-T regime. Furthermore, we investigate RH as function of frequency by explicit evaluation of Kubo formulae. We compare results with existing studies of RH on square lattices.
Mackay icosahedron explaining orientation relationship of dispersoids in aluminium alloys.
Muggerud, Astrid Marie F; Li, Yanjun; Holmestad, Randi; Andersen, Sigmund J
The orientation relations (ORs) of the cubic icosahedral quasicrystal approximant phase α-Al(Fe,Mn)Si have been studied after low temperature annealing of a 3xxx wrought aluminium alloy by transmission electron microscopy. From diffraction studies it was verified that the most commonly observed OR for the α-Al(Fe,Mn)Si dispersoids is [1\\bar 11]α // [1\\bar 11]Al, (5\\bar 2\\bar 7)α // (011)Al. This orientation could be explained by assuming that the internal Mackay icosahedron (MI) in the α-phase has a fixed orientation in relation to Al, similar to that of the icosahedral quasi-crystals existing in this alloy system. It is shown that mirroring of the normal-to-high-symmetry icosahedral directions of the MI explains the alternative orientations, which are therefore likely to be caused by twinning of the fixed MI. Only one exception was found, which was related to the Bergman icosahedron internal to the T-phase of the Al-Mg-Zn system. PMID:25274523
Isolation and Structural Characterization of a Mackay 55-Metal-Atom Two-Shell Icosahedron of Pseudo-Ih Symmetry, Pd55L12(μ3-CO)20 (L = PR3, R = Isopropyl): Comparative Analysis with Interior Two-Shell Icosahedral Geometries in Capped Three-Shell Pd145, Pt-Centered Four-Shell Pd-Pt M165, and Four-Shell Au133 Nanoclusters.
Erickson, Jeremiah D; Mednikov, Evgueni G; Ivanov, Sergei A; Dahl, Lawrence F
We present the first successful isolation and crystallographic characterization of a Mackay 55-metal-atom two-shell icosahedron, Pd55L12(μ3-CO)20 (L = PPr(i)3) (1). Its two-shell icosahedron of pseudo-Ih symmetry (without isopropyl substituents) enables a structural/bonding comparison with interior 55-metal-atom two-shell icosahedral geometries observed within the multi-shell capped 145-metal-atom three-shell Pd145(CO)72(PEt3)30 and 165-metal-atom four-shell Pt-centered (μ12-Pt)Pd164-xPtx(CO)72(PPh3)20 (x ≈ 7) nanoclusters, and within the recently reported four-shell Au133(SC6H4-p-Bu(t))52 nanocluster. DFT calculations carried out on a Pd55(CO)20(PH3)12 model analogue, with triisopropyl phosphine substituents replaced by H atoms, revealed a positive +0.84 e charge for the entire Pd55 core, with a highly positive second-shell Pd42 surface of +1.93 e. PMID:26790717
The determination of the solidification paths and the liquidus surface in the quasicrystalline region of the Al-Cu-Ru systems
Haines, S.
Objective is to determine if conventional slow-growth methods will be successful for growing single quasicrystals in this system. Reaction schemes, isopleths, and a ternary liquidus diagram were constructed using DTA, XRD, microscopy, and energy dispersive spectroscopy. Results suggest a peak in the liquidus near the predicted compositions of Al{sub 65}Cu{sub 23}Ru{sub 12} or Al{sub 65}Cu{sub 20}Ru{sub 15} in the face-centered icosahedral phase field. Further study is needed to verify the existence of a congruently melting phase. There appears to be composition for which slow-growth methods will produce a single-quasicrystal. Directional solidification studies were done on 65Al25Cu10Ru.
Dynamical implications of Viral Tiling Theory.
ElSawy, K M; Taormina, A; Twarock, R; Vaughan, L
The Caspar-Klug classification of viruses whose protein shell, called viral capsid, exhibits icosahedral symmetry, has recently been extended to incorporate viruses whose capsid proteins are exclusively organised in pentamers. The approach, named 'Viral Tiling Theory', is inspired by the theory of quasicrystals, where aperiodic Penrose tilings enjoy 5-fold and 10-fold local symmetries. This paper analyses the extent to which this classification approach informs dynamical properties of the viral capsids, in particular the pattern of Raman active modes of vibrations, which can be observed experimentally. PMID:18353372
Spectrum of Lebesgue Measure Zero for Jacobi Matrices of Quasicrystals
NASA Astrophysics Data System (ADS)
Beckus, Siegfried; Pogorzelski, Felix
We study one-dimensional random Jacobi operators corresponding to strictly ergodic dynamical systems. We characterize the spectrum of these operators via non-uniformity of the transfer matrices and vanishing of the Lyapunov exponent. For aperiodic, minimal subshifts satisfying the so-called Boshernitzan condition this gives that the spectrum is supported on a Cantor set with Lebesgue measure zero. This generalizes earlier results for Schrödinger operators.
Method of making quasicrystal alloy powder, protective coatings and articles
Shield, J.E.; Goldman, A.I.; Anderson, I.E.; Ellis, T.W.; McCallum, R.W.; Sordelet, D.J.
A method of making quasicrystalline alloy particulates is disclosed wherein an alloy is superheated and the melt is atomized to form generally spherical alloy particulates free of mechanical fracture and exhibiting a predominantly quasicrystalline in the atomized condition structure. The particulates can be plasma sprayed to form a coating or consolidated to form an article of manufacture. 3 figs.
An Attempt to Prepare Metallic Glasses from Quasicrystals
NASA Astrophysics Data System (ADS)
Zi-Jing, Li; Lin-Ran, Zhao; Yu-Ting, Wang; Ze-Ming, Chen; Wen-Kang, Tu; Ya-Qi, Zhang; Hong, Bo; Ying-Dan, Liu; Li-Min, Wang
Not Available Supported by the National Basic Research Program of China under Grant No 2010CB731604, the National Natural Science Foundation of China under Grant Nos 51131002, 51071138 and 51271160, and the Program of Qinhuangdao Science and Technology Bureau under Grant No 201401A051.
No inherent glassiness in a Penrose tiling quasicrystal
Strandburg, K.J.; Dressel, P.R.
Consideration of the structure of the Penrose pattern has led to speculation that a system with a Penrose tiling ground state might be subject to inherent glassy behavior. Monte Carol simulations show, using a simple model of the energetics, that there is no inherent glassiness in the Penrose tiling. Thermodynamic quantities measured are completely reversible, displaying no observable hysterisis, and the system may be easily cooled from a highly disordered configuration into its lowest energy state. 11 refs., 7 figs.
Method of making quasicrystal alloy powder, protective coatings and articles
Shield, Jeffrey E.; Goldman, Alan I.; Anderson, Iver E.; Ellis, Timothy W.; McCallum, R. William; Sordelet, Daniel J.
A method of making quasicrystalline alloy particulates wherein an alloy is superheated and the melt is atomized to form generally spherical alloy particulates free of mechanical fracture and exhibiting a predominantly quasicrystalline in the atomized condition structure. The particulates can be plasma sprayed to form a coating or consolidated to form an article of manufacture.
Bandgap isotropy in photonic quasicrystals with low-index contrast
NASA Astrophysics Data System (ADS)
Andreone, Antonello; Abbate, Giancarlo; Di Gennaro, Emiliano; Rose Thankamani, Priya
Formation and development of the photonic band gap in two-dimensional 8-, 10-, and 12-fold symmetry quasicrystalline lattices of low-index contrast are reported. Finite-size structures made of dielectric cylindrical rods are studied and measured in the microwave region, and their properties are compared with a conventional hexagonal crystal. Band-gap characteristics are investigated by changing the direction of propagation of the incident beam inside the crystal. Various angles of incidence are used to investigate the isotropic nature of the band gap.
Electrically tunable graphene plasmonic quasicrystal metasurfaces for transformation optics
Zeng, Chao; Liu, Xueming; Wang, Guoxi
The past few years have witnessed tremendous achievements of transformation optics applied to metallic plasmonic systems. Due to the poor tunability of metals, however, the ultimate control over surface plasmons remains a challenge. Here we propose a new type of graphene plasmonic (GP) metasurfaces by shaping the dielectrics underneath monolayer graphene into specific photonic crystals. The radial and axial gradient-index (GRIN) lenses are implemented to demonstrate the feasibility and versatility of the proposal. It is found that the designed GP-GRIN lenses work perfectly well for focusing, collimating, and guiding the GP waves. Especially, they exhibit excellent performances in the THz regime as diverse as ultra-small focusing spot (λ0/60) and broadband electrical tunability. The proposed method offers potential opportunities in exploiting active transformational plasmonic elements operating at THz frequencies. PMID:25042132
The Mpemba Effect, Shechtman's Quasicrystals and Student Exploration Activities
ERIC Educational Resources Information Center
Balazovic, Marek; Tomasik, Boris
In the 1960s, Tanzanian student Erasto Mpemba and his teacher published a paper with the title "Cool?" in this journal (Mpemba and Osborne 1969 "Phys. Educ." 4 172-5). They claimed that hot water freezes more quickly than cold water. The paper not only led to a wave of discussion, and more publications about this topic, but also to a whole series…
Electrically tunable graphene plasmonic quasicrystal metasurfaces for transformation optics
NASA Astrophysics Data System (ADS)
Zeng, Chao; Liu, Xueming; Wang, Guoxi
The past few years have witnessed tremendous achievements of transformation optics applied to metallic plasmonic systems. Due to the poor tunability of metals, however, the ultimate control over surface plasmons remains a challenge. Here we propose a new type of graphene plasmonic (GP) metasurfaces by shaping the dielectrics underneath monolayer graphene into specific photonic crystals. The radial and axial gradient-index (GRIN) lenses are implemented to demonstrate the feasibility and versatility of the proposal. It is found that the designed GP-GRIN lenses work perfectly well for focusing, collimating, and guiding the GP waves. Especially, they exhibit excellent performances in the THz regime as diverse as ultra-small focusing spot (λ0/60) and broadband electrical tunability. The proposed method offers potential opportunities in exploiting active transformational plasmonic elements operating at THz frequencies.
Role of Smectite Quasicrystal Dynamics in Adsorption of Dinitrophenol
Technology Transfer Automated Retrieval System (TEKTRAN)
Understanding sorption mechanisms and processes is critical for predicting the fate of organic pollutants in soils and for development of effective remediation strategies for contaminated soils. Novel X-ray diffraction (XRD) techniques were used to investigate processes associated with the adsorptio...
Novel Kac-Moody-type affine extensions of non-crystallographic Coxeter groups
NASA Astrophysics Data System (ADS)
Dechant, Pierre-Philippe; Bœhm, Céline; Twarock, Reidun
Motivated by recent results in mathematical virology, we present novel asymmetric {Z}[\\tau ]-integer-valued affine extensions of the non-crystallographic Coxeter groups H2, H3 and H4 derived in a Kac-Moody-type formalism. In particular, we show that the affine reflection planes which extend the Coxeter group H3 generate (twist) translations along two-, three- and five-fold axes of icosahedral symmetry, and we classify these translations in terms of the Fibonacci recursion relation applied to different start values. We thus provide an explanation of previous results concerning affine extensions of icosahedral symmetry in a Coxeter group context, and extend this analysis to the case of the non-crystallographic Coxeter groups H2 and H4. These results will enable new applications of group theory in physics (quasicrystals), biology (viruses) and chemistry (fullerenes).
Quasicrystallinity Studies on Conventionally Solidified Aluminum-Technetium and Aluminum-Uranium Based Alloys
NASA Astrophysics Data System (ADS)
Athanasiou, N. S.
We present quasicrystallinity investigations on conventionally solidified binary Al-Tc, ternary Al-Tc-M (M = Mn, Ni, Cu, Ru, Rh, Pd, Re, Ir, Pt), Al-Cu-U, as well as quaternary Al-Cu-Ru-U alloys. By conventional cooling (dT/dt≈103 to 102 Ksec-1) crystalline phases were formed in all the systems, except for Al-Tc-Ir system, where only icosahedral quasicrystalline phases were found. A new large (1-1.5 mm in size) icosahedral (F-type structure) quasicrystal with a pentaprismatic growth morphology was obtained in the sample with the nominal composition Al77.6Tc10Ir12.4. The characterization of the quasicrystalline state was examined by X-ray diffractometry, scanning electron microscopy (SEM) and energy-dispersive X-ray microanalysis (EDXA).
Phenomenological Magnetic Model in Tsai-Type Approximants
NASA Astrophysics Data System (ADS)
Sugimoto, Takanori; Tohyama, Takami; Hiroto, Takanobu; Tamura, Ryuji
Recent neutron diffraction study has reported a curious ferromagnetism in Tsai-type approximants Au-Si-RE (RE=Tb,Dy,Ho), which have the same local structure as quasi-crystals with a translational symmetry simultaneously. In these materials, magnetic moments of rare-earth atoms have a single-ion anisotropy determined locally via spin-orbit coupling around crystal fields satisfying a distorted icosahedral crystal structure. We phenomenologically propose a possible magnetic model reproducing the magnetic structure and the thermodynamical quantities. The corresponding energies of the single-ion anisotropy and RKKY exchange couplings are also estimated by comparing magnetization curves and susceptibility of our model and experiments. Moreover, simulated annealing calculations with the energies in our model coincide with the strange ferromagnetism. In conclusion, a distortion of icosahedral cluster in body-centered cubic structure plays a key role to emerge the peculiar magnetic structure. Our magnetic model does not only explain magnetic behaviors in quasi-crystal approximants, but also can approach to a coexistence of a long-ranged order and a quasi-periodicity.
Three problems in soft condensed phases
NASA Astrophysics Data System (ADS)
Roan, Jiunn-Ren
Dynamics of dilute heteropolymer solution, thermodynamic stability of quasicrystal phases of diblock copolymer melt, and phase separation of a critically quenched binary fluid/surfactant system are studied. For the dynamics of dilute heteropolymer chain, using functional-integral representation, a mean-field equation of motion is obtained, from which the slowest relaxation mode is derived. In addition to the usual excluded-volume and hydrodynamic contributions, it is found that heterogeneity of the chain also renormalizes the mode. However, the breaking of fluctuation-dissipation relation responsible for the freezing transition in spin-glass systems is found to have no effect to the renormalization due to heterogeneity. This implies that when using spin-glass analogy to study heteropolymers, popularized by protein folding problem, care should be taken when dynamic issues are addressed. For the stability study of diblock copolymer melt, motivated by the fact that there are two complementary approaches (packing of Penrose tiles and density-wave mean filed theory) in the theoretical study of icosahedral quasicrystals while there exists only one approach (Caspar-Klug packing theory) to understanding the icosahedral morphology of virus shells, the icosahedral phases are examined using Landau free energy expansion (Leibler's theory) with multiple harmonics. Treating the packing units (proteins) like amphiphilic copolymers, the free energies of icosahedral phases are calculated at different compositions. Compared to those of stable conventional phases, the icosahedral phases are found always less stable. For the phase separation of a binary fluid/surfactant system, hydrodynamic effect in a Hele-Shaw cell is studied numerically using a recently proposed model. When the quench is deep, so that thermal fluctuations are ineffective, it is found that surfactants tend to be trapped in domains of binary fluid. The trapping of surfactant clusters, however, does not occur when
Investigations of the electronic properties and surface structures of aluminum-rich quasicrystalline alloys
NASA Astrophysics Data System (ADS)
Barrow, Jason Allen
The work in this dissertation presents studies of three distinct areas of interest in the field of quasicrystals: bulk structure, transport properties, and electronic structure. First, we describe the results of a study which explored the fundamental interactions between the atomic species of the icosahedral Al-Pd-Mn quasicrystal. This study was done using laser vaporization to create gas-phase metal clusters, which were then ionized and analyzed using time-of-flight mass spectrometry. Both the kinetic and thermodynamic stabilities of the clusters were probed. Second, we report our investigations of the bulk thermal transport properties of a decagonal Al-Ni-Co quasicrystal in the temperature range 373K--873K. The properties of a sample oriented along the periodic, aperiodic, and 45° axes were measured. A high degree of anisotropy was observed between the aperiodic and periodic directions. The results of the 45° off-axis data were compared with theoretically predicted values. Transport behavior is described in terms of charge carriers and the mean-free time between carrier collisions. It is concluded that the mean-free time is much longer in the periodic direction than in the aperiodic direction, producing the observed anisotropy in thermal transport. The third study presents a detailed analysis of the sputter-induced phase transformation which occurs on the 5-fold surface of an icosahedral Al-Cu-Fe quasicrystal. Reflection high-energy electron diffraction, x-ray photoemission spectroscopy, and ultra-violet photoemission spectroscopy data were collected as a function of annealing temperature and were used to probe surface structure, surface composition, and electronic structure, respectively. The composition and structure of the sputtered surface are consistent with a transformation to the beta-Al-Cu-Fe cubic structure, and shows a sharp metallic cut-off in the spectral intensity of the electronic structure at the Fermi edge. Upon annealing the surface reverts to
Science Using an Electrostatic Levitation Furnace in the MUCAT Sector at the APS
NASA Technical Reports Server (NTRS)
Goldman, A.; Kelton, K. F.; Rogers, J. R.
The original motivation for the construction of the BESL prototype was to obtain the first proof of a 50-year-old hypothesis regarding the solidification of liquid metals. Since the 1950s it has been known that under proper conditions liquid metals can be cooled below their melting temperature (undercooled) without crystallizing to the stable solid phase. In 1952 Frank proposed that this was because the atoms in the metallic liquid were arranged with the symmetry of an icosahedron, a Platonic solid consisting of 20 tetrahedra (4-sided pyramid-shaped polyhedra) arranged around a common center. Since this local atomic order is incompatible with the long-range translational periodicity of crystal phases, a barrier is formed to the formation of small regions of the crystal phase, the nucleation barrier. A proof of Frank's hypothesis required a direct correlation between measured icosahedral order in the undercooled liquid and the nucleation barrier. The tendency of sample containers to catalyze nucleation obscured this relation, requiring containerless techniques. Combining containerless processing techniques for electrostatically levitated droplets (ESL) with x-ray synchrotron methods, a team from Washington University, St. Louis, MO, NASA Marshall Space Flight Center, and MUCAT at the APS demonstrated an increasing icosahedral order in TiZrNi liquids with decreasing temperature below the melting temperature. The increased icosahedral order caused the transformation of the liquid to a metastable icosahedral quasicrystal phase, instead of the stable tetrahedrally-coordinated crystal intermetallic, giving the first clear demonstration of the connection between the nucleation barrier and the local structure of the liquid, verifying Frank's hypothesis for this alloy.
Na9K16TI~25: A New Phase Containing Naked Icosahedral Cluster Fragments Ti99-
Li, Bin; Corbett, John D.
The phase Na{sub 9}K{sub 16}Tl{sub 25.25(2)} was synthesized by fusion of the elements in sealed Ta containers followed by quenching and annealing at 250 C. The structure established by single crystal X-ray diffraction means (P6{sub 3}/m, Z = 2, a = 19.376(3) {angstrom}, c = 11.480(2) {angstrom}) features Tl{sub 9}{sup 9-} clusters. These are well separated by cations that bridge between, faces, edges, and vertices of the clusters; sodium appears to be essential in this role. This is the third compound known to contain Tl{sub 9} clusters, but here two of nine sites are partially occupied, which can be interpreted as a 70:30 mixture of Tl{sub 9} and Tl{sub 7} units in the same cavity. This Tl{sub 9} example also displays lower symmetry (C{sub s}) but requires the same 2n skeletal electrons. EHTB electronic structure calculations indicate that the Fermi level intersects a finite densities-of-states (DOS), and only some bonds are optimized at E{sub F}, giving some insight regarding the site of Tl deficiency. Direct geometric relationships are found among Tl{sub 13}, Tl{sub 9}, Tl{sub 7} and Tl{sub 5} clusters through systematic removal of vertices.
Heat capacity and thermal expansion of icosahedral lutetium boride LuB66
Novikov, V V; Avdashchenko, D V; Matovnikov, A V; Mitroshenkov, N V; Bud'ko, S L
The experimental values of heat capacity and thermal expansion for lutetium boride LuB66 in the temperature range of 2-300 K were analysed in the Debye-Einstein approximation. It was found that the vibration of the boron sub-lattice can be considered within the Debye model with high characteristic temperatures; low-frequency vibration of weakly connected metal atoms is described by the Einstein model.
Protruding knob-like proteins violate local symmetries in an icosahedral marine virus
Gipson, Preeti; Baker, Matthew L.; Raytcheva, Desislava; Haase-Pettingell, Cameron; Piret, Jacqueline; King, Jonathan A.; Chiu, Wah
Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by electron cryo-microscopy and modelling. A Cα backbone trace of the major capsid protein (gp39) reveals a classic phage protein fold. In addition, two knob-like proteins protruding from the capsid surface are also observed. Using bioinformatics and structure analysis tools, these proteins are identified to correspond to gp55 and gp58 (each with two copies per asymmetric unit). The non 1:1 stoichiometric distribution of gp55/58 to gp39 breaks all expected local symmetries and leads to non-quasi-equivalence of the capsid subunits, suggesting a role in capsid stabilization. Such a structural arrangement has not yet been observed in any known virus structures. PMID:24985522
Synonymous Mutations Reduce Genome Compactness in Icosahedral ssRNA Viruses
Tubiana, Luca; Božič, Anže Lošdorfer; Micheletti, Cristian; Podgornik, Rudolf
Recent studies have shown that single-stranded (ss) viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison, it has been suggested that wild-type viral RNA may have evolved to be atypically compact so as to aid its encapsidation and assist the viral assembly process. To further explore the compactness selection hypothesis, we systematically compare the predicted sizes of >100 wild-type viral sequences with those of their mutants, which are evolved in silico and subject to a number of known evolutionary constraints. In particular, we enforce mutation synonynimity, preserve the codon-bias, and leave untranslated regions intact. It is found that progressive accumulation of these restricted mutations still suffices to completely erase the characteristic compactness imprint of the viral RNA genomes, making them in this respect physically indistinguishable from randomly shuffled RNAs. This shows that maintaining the physical compactness of the genome is indeed a primary factor among ssRNA viruses' evolutionary constraints, contributing also to the evidence that synonymous mutations in viral ssRNA genomes are not strictly neutral. PMID:25564866
Extremely Electron-Rich, Boron-Functionalized, Icosahedral Carborane-Based Phosphinoboranes
Spokoyny, Alexander M.; Lewis, Calvin D.; Teverovskiy, Georgiy; Buchwald, Stephen L.
We have prepared the first examples of B9-connected trivalent aryl and alkyl phosphinoborane species via Pd-catalyzed phosphination of 9-iodo-meta-carborane. Our studies highlight the unique electronic features of the B9-connected meta-carboranyl moiety as compared to its C1-based analogue. This work suggests that the B9-functionalized meta-carboranyl substituent in these ligands exhibits more electron-releasing character than any other known carbon-based substituent, ultimately laying the foundation for a new class of phosphine ligands with extremely electron-rich character. PMID:23667288
Icosahedral metallacarborane/carborane species derived from 1,1'-bis(o-carborane).
Thiripuranathar, Gobika; Man, Wing Y; Palmero, Cesar; Chan, Antony P Y; Leube, Bernhard T; Ellis, David; McKay, David; Macgregor, Stuart A; Jourdan, Laure; Rosair, Georgina M; Welch, Alan J
Examples of singly-metallated derivatives of 1,1'-bis(o-carborane) have been prepared and spectroscopically and structurally characterised. Metallation of [7-(1'-1',2'-closo-C2B10H11)-7,8-nido-C2B9H10](2-) with a {Ru(p-cymene)}(2+) fragment affords both the unisomerised species [1-(1'-1',2'-closo-C2B10H11)-3-(p-cymene)-3,1,2-closo-RuC2B9H10] (2) and the isomerised [8-(1'-1',2'-closo-C2B10H11)-2-(p-cymene)-2,1,8-closo-RuC2B9H10] (3), and 2 is easily transformed into 3 with mild heating. Metallation with a preformed {CoCp}(2+) fragment also affords a 3,1,2-MC2B9-1',2'-C2B10 product [1-(1'-1',2'-closo-C2B10H11)-3-Cp-3,1,2-closo-CoC2B9H10] (4), but if CoCl2/NaCp is used followed by oxidation the result is the 2,1,8-CoC2B9-1',2'-C2B10 species [8-(1'-1',2'-closo-C2B10H11)-2-Cp-2,1,8-closo-CoC2B9H10] (5). Compound 4 does not convert into 5 in refluxing toluene, but does do so if it is reduced and then reoxidised, perhaps highlighting the importance of the basicity of the metal fragment in the isomerisation of metallacarboranes. A computational study of 1,1'-bis(o-carborane) is in excellent agreement with a recently-determined precise crystallographic study and establishes that the {1',2'-closo-C2B10H11} fragment is electron-withdrawing compared to H. PMID:25702632
Protruding knob-like proteins violate local symmetries in an icosahedral marine virus
NASA Astrophysics Data System (ADS)
Gipson, Preeti; Baker, Matthew L.; Raytcheva, Desislava; Haase-Pettingell, Cameron; Piret, Jacqueline; King, Jonathan A.; Chiu, Wah
Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by electron cryo-microscopy and modelling. A Cα backbone trace of the major capsid protein (gp39) reveals a classic phage protein fold. In addition, two knob-like proteins protruding from the capsid surface are also observed. Using bioinformatics and structure analysis tools, these proteins are identified to correspond to gp55 and gp58 (each with two copies per asymmetric unit). The non 1:1 stoichiometric distribution of gp55/58 to gp39 breaks all expected local symmetries and leads to non-quasi-equivalence of the capsid subunits, suggesting a role in capsid stabilization. Such a structural arrangement has not yet been observed in any known virus structures.
THOR-ISO: a Global Circulation Model for Exoplanets on an Icosahedral Grid
NASA Astrophysics Data System (ADS)
Mendonca, J.; Grimm, S.; Heng, K.
In this presentation I will describe the details and first results of our new dynamical code for exoplanet atmospheres. This model is part of the Exoclimes Simulation Platform (ESP), and is a project of the Exoplanet and Exoclimes Group (see www.exoclime.org). The model I will present solves the complex physical and dynamical equations that include fundamental principles of atmospheric fluid dynamics and various idealisations of radiative transfer and dry convection, among others. I will also show the results of the first successful benchmark tests for this model, where we explore the results of the model for Earth-like and Hot-Jupiter like conditions. The analysis of the results from this complex and detailed model, will help us to have a better understanding of the diversity of climates and atmospheric circulations that we expect to find in the multitude of exoplanets already discovered.
Virus-like particles not previously described were observed in a human gastroenteritis stool using negative-stain TEM. The stool was among a number of acute-phase illness stools which had been collected in Egypt during 1980. The particles measured 65-70 nm in diameter, and it was...
Synonymous Mutations Reduce Genome Compactness in Icosahedral ssRNA Viruses
NASA Astrophysics Data System (ADS)
Tubiana, Luca; Božič, Anže Lošdorfer; Micheletti, Cristian; Podgornik, Rudolf
Recent studies have shown that single-stranded viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison it has been suggested that wild-type viral RNA may have evolved to be atypically compact so as to aid its encapsidation and assist the viral assembly process. In order to further explore the compactness selection hypothesis, we systematically compare the predicted sizes of more than one hundred wild-type viral sequences with those of their mutants, which are evolved in silico and subject to a number of known evolutionary constraints. In particular, we enforce mutation synonynimity, preserve the codon-bias, and leave untranslated regions intact. It is found that progressive accumulation of these restricted mutations still suffices to completely erase the characteristic compactness imprint of the viral RNA genomes, making them in this respect physically indistinguishable from randomly shuffled RNAs. This shows that maintaining the physical compactness of the genome is indeed a primary factor among ssRNA viruses evolutionary constraints, contributing also to the evidence that synonymous mutations in viral ssRNA genomes are not strictly neutral.
Diffraction studies of the structure of glasses and liquids: Technical progress report
Moss, S.C.
The Houston program on glasses and liquids has continued over the year with an expanded activity into vitreous TiO/sub 2/ and amorphous metals/quasicrystals. The modeling study of vitreous SiO/sub 2/ has been published and the study of amorphous melanin is well underway in-house. We have also begun some promising modeling work on the icosahedral glass model (IGM) for quasicrystals and have completed a preliminary study of epitaxial diamond crystal growth on the (111) silicon crystal surface (initially undertaken to study the expected ''amorphous'' diamond-like phase). The work on GLAD at the Argonne IPNS continues on schedule under the direction of Dr. David L. Price. The status of the Phase I instrument has been published and the Phase II development is underway with an evacuated flight path, additional detectors and a final data acquisition system in progress. It is our expectation that the final instrument will be the most advanced of its kind in the world for the study of a wide variety of problems in glasses, liquids and amorphous materials.
Hydriding of TiZrNiFe nanocompounds
NASA Astrophysics Data System (ADS)
Żywczak, A.; Shinya, Daigo; Gondek, Ł.; Takasaki, Akito; Figiel, H.
Ti-based quasicrystals belong to the second largest group of the stable quasicrystals, showing attractive properties as hydrogen storage materials. The Ti 45Zr 38Ni 17 intermetallic compound forms an icosahedral ( i-phase) structure, in which Ti and Zr atoms possess very good chemical affinity for hydrogen absorption. We modified the Ti 45Zr 38Ni 17 compounds by substituting 3d metals (iron) for Ni to obtain amorphous phase. The samples were produced by mechanical alloying. The 3d metal atoms are located in the same positions as nickel. The structural characterization was made by means of XRD measurements. Thermodynamic properties were studied by differential scanning calorimetry (DSC) and thermal desorption spectroscopy (TDS). The obtained amorphous phases Ti 45Zr 38Ni (9,13)Fe (8,4) transform to the i-phase at the similar temperature range as Ti 45Zr 38Ni 17. The final concentration of absorbed hydrogen depends on the amount of Fe. When increasing the amount of iron, the hydrogen release temperature becomes lower. After hydriding, the samples decompose into simple metal hydrides.
Imaging Magnetic Order and Frustration on Distinct Sublattices in Artificial Quasicrystals
NASA Astrophysics Data System (ADS)
Farmer, Barry; Balk, Andrew; Bhat, Vinayaka; Teipel, Eric; Smith, Nathan; Unguris, John; Hastings, Jeffrey Todd; de Long, Lance
Scanning electron microscopy with polarization analysis (SEMPA) was used to acquire direct images of as-grown magnetization textures for Permalloy thin films patterned into Penrose P2 tilings (P2T). Simulations yield a low-energy manifold of textures composed of two distinct, perfectly ordered sublattices and two sublattices that remain frustrated. As-grown P2T samples exhibited large domains of the two ordered sublattices in the room-temperature SEMPA images. Higher resolution Monte Carlo simulations based on long-range dipolar interactions predict the two frustrated sublattices will order. These results indicate 3rd generation P2T will offer the first example of magnetic order in a quasicrystalline material. Research at University of Kentucky supported by U.S. Department of Energy Grant No. DE-FG02-97ER-45653, and U.S. National Science Foundation Grant No. DMR-1506979.
The Mpemba effect, Shechtman's quasicrystals and student exploration activities
NASA Astrophysics Data System (ADS)
Balážovič, Marek; Tomášik, Boris
In the 1960s, Tanzanian student Erasto Mpemba and his teacher published a paper with the title 'Cool?' in this journal (Mpemba and Osborne 1969 Phys. Educ. 4 172-5). They claimed that hot water freezes more quickly than cold water. The paper not only led to a wave of discussion, and more publications about this topic, but also to a whole series of new experiments, with the aim of verifying this apparent thermodynamic absurdity and finding an adequate explanation. Here we give a review with references to explanations and we offer some proposals for experimental student work in this area. We not only introduce the Mpemba effect as a paradoxical physics phenomenon, but also present a strong educational message that the Mpemba story brings to teachers and their students. This message also creates a bridge between this phenomenon and the discovery for which the 2011 Nobel Prize in Chemistry was awarded. It leads to critical adoption of traditional knowledge and encourages resilience in investigative exploration of new things.
Ionic Strength-Induced Formation of Smectite Quasicrystals Enhances Nitroaromatic Compound Sorption
Technology Transfer Automated Retrieval System (TEKTRAN)
The influence of ionic strength on nitroaromatic compound sorption from water by K+- and Ca2+-saturated smectite (SWy-2) was examined. The results indicated that sorption of 1,3-dinitrobenzene by K-SWy-2 increased up to 2.2 times as KCl ionic strength increased from 0.01 to 0.30 M. In contrast, sorp...
Evidence of local effects in anomalous refraction and focusing properties of dodecagonal photonic quasicrystals
NASA Astrophysics Data System (ADS)
di Gennaro, Emiliano; Miletto, Carlo; Savo, Salvatore; Andreone, Antonello; Morello, Davide; Galdi, Vincenzo; Castaldi, Giuseppe; Pierro, Vincenzo
We present the key results from a comprehensive study of the refraction and focusing properties of a two-dimensional dodecagonal photonic "quasicrystal" (PQC), which was carried out via both full-wave numerical simulations and microwave measurements on a slab made of alumina rods inserted in a parallel-plate waveguide. We observe an anomalous refraction and focusing in several frequency regions, which confirm some recently published results. However, our interpretation, which is based on numerical and experimental evidence, substantially differs from the one in terms of "effective negative refractive index" that was originally proposed. Instead, our study highlights the critical role played by short-range interactions associated with local order and symmetry.
Mode confinement in photonic quasicrystal point-defect cavities for particle accelerators
NASA Astrophysics Data System (ADS)
Di Gennaro, E.; Savo, S.; Andreone, A.; Galdi, V.; Castaldi, G.; Pierro, V.; Masullo, M. Rosaria
In this letter, we present a study of the confinement properties of point-defect resonators in finite-size photonic-bandgap structures composed of aperiodic arrangements of dielectric rods, with special emphasis on their use for the design of cavities for particle accelerators. Specifically, for representative geometries, we study the properties of the fundamental mode (as a function of the filling fraction, structure size, and losses) via two-dimensional and three-dimensional full-wave numerical simulations, as well as microwave measurements at room temperature. Results indicate that for reduced-size structures, aperiodic geometries exhibit superior confinement properties by comparison with periodic ones.
Isotropic properties of the photonic band gap in quasicrystals with low-index contrast
NASA Astrophysics Data System (ADS)
Priya Rose, T.; di Gennaro, E.; Abbate, G.; Andreone, A.
We report on the formation and development of the photonic band gap in two-dimensional 8-, 10-, and 12-fold symmetry quasicrystalline lattices of low-index contrast. Finite-size structures made of dielectric cylindrical rods were studied and measured in the microwave region, and their properties were compared with a conventional hexagonal crystal. Band-gap characteristics were investigated by changing the direction of propagation of the incident beam inside the crystal. Various angles of incidence from 0∘ to 30∘ were used to investigate the isotropic nature of the band gap. The arbitrarily high rotational symmetry of aperiodically ordered structures could be practically exploited to manufacture isotropic band-gap materials, which are perfectly suitable for hosting waveguides or cavities.
Generalized Penrose tiling as a quasilattice for decagonal quasicrystal structure analysis.
Chodyn, Maciej; Kuczera, Pawel; Wolny, Janusz
The generalized Penrose tiling is, in fact, an infinite set of decagonal tilings. It is constructed with the same rhombs (thick and thin) as the conventional Penrose tiling, but its long-range order depends on the so-called shift parameter (s ∈ 〈0; 1)). The structure factor is derived for the arbitrarily decorated generalized Penrose tiling within the average unit cell approach. The final formula works in physical space only and is directly dependent on the s parameter. It allows one to straightforwardly change the long-range order of the refined structure just by changing the s parameter and keeping the tile decoration unchanged. This gives a great advantage over the higher-dimensional method, where every change of the tiling (change in the s parameter) requires the structure model to be built from scratch, i.e. the fine division of the atomic surfaces has to be redone. PMID:25727864
Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.
Hafner, Jürgen
During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures. PMID:21386539
Quasicrystals and the Penrose Patterns: A Geometric Activity with a Scientific Application.
ERIC Educational Resources Information Center
Clason, Robert; And Others
Penrose tile patterns are created using regular pentagon-based rhombi. Provides instructions for assembling Penrose patterns, plus activities for secondary school students and preservice elementary teachers. Compares the two-dimensional process of placing pattern blocks to form Penrose patterns to the symmetries of crystals formed in nature.…
A Sodium-Containing Quasicrystal: Using Gold To Enhance Sodium's Covalency in Intermetallic Compounds
Smetana, Volodymyr; Lin, Qisheng; Pratt, Daniel K.; Kreyssig, Andreas; Ramazanoglu, Mehmet; Corbett, John D.; Goldman, Alan I.; Miller, Gordon J.
Gold macht stabil: Na13Au12Ga15, ein natriumhaltiges thermodynamisch stabiles quasikristallines Material, wurde bei einer systematischen Studie des polaren Na-Au-Ga-Intermetallsystems entdeckt. Sein Elektron/Atom-Verhältnis von 1.75 ist für Bergman-Ikosaederphasen extrem klein, doch der substanzielle Au-Anteil sorgt für eine Hume-Rothery-Stabilisierung und neuartige polar-kovalente Na-Au-Wechselwirkungen.
Structure and properties of the ceramics based on quasicrystal powders processed by plasma coating method
NASA Astrophysics Data System (ADS)
Ekimov, E. A.; Ivanov, A. S.; Pal, A. F.; Petrzhik, M. I.; Ryabinkin, A. N.; Serov, A. O.
Homogeneous incorporation of a small amount of binding material or modifying agent in the batch consisting of micron size particles is a problem of a composite material production process. In this work the problem is solved by deposition of a thin coating consisting of binding material on the initial powder particles by means of high-rate magnetron sputtering. The confinement of dusty particles in plasma was used in fine powder processing procedure. Composite powders based on the Al-Cu-Fe quasicrystalline particles with nickel coating were obtained. Their investigation showed that the method provides uniform incorporation of small quantities of additives (at concentration of about 3 wt. %) to fine powders. The powders were pressed at room temperature under quasi-hydrostatic conditions at high pressures. After pressing the samples were sintered in hydrogen at normal pressure. Structure and mechanical properties of the sintered samples were studied. The conditions of sintering the composite powder, which provide producing compacts with improved performance data, were established.
Surfaces of complex intermetallic compounds: insights from density functional calculations.
Hafner, Jürgen; Krajčí, Marian
. Detailed results are presented for two intermetallic compounds that have recently attracted much attention as active and highly selective catalysts for the semihydrogenation of alkynes to alkenes, but the identification of the catalytically active surfaces was found to be very difficult. The crystal structure of B20-type GaPd can be interpreted as the lowest order approximant of icosahedral Al-Pd-Mn quasicrystals. Among the low-index surfaces, the {100} surface shows 2-fold symmetry and the {210} surface pseudo-5-fold symmetry; for both the surface stoichiometry is identical to that of the bulk. Because the structure lacks inversion symmetry, the {111} surfaces have polar character and permit terminations of widely different chemical composition. Results for all three surfaces are presented and compared with the available experiments. The crystal structure of orthorhombic Al13Co4 is built by pentagonal clusters similar to those found in decagonal Al-Co and Al-Ni-Co quasicrystals. A simulated cleavage experiment shows that the constituent clusters remain intact upon cleavage, resulting in the formation of a highly corrugated (100) surface. The calculated STM images are found to be in very good agreement with experiment and permit in addition identification of possible surface modifications by the desorption of individual atoms. Pentagonal motifs on the {210} surface of GaPd and on the (100) surface of Al13Co4 consisting of simple- and transition-metal atoms have been identified as the catalytically active centers for the semihydrogenation of acetylene to ethylene. PMID:24741993
Charge Detection Mass Spectrometry Identifies Preferred Non-Icosahedral Polymorphs in the Self-Assembly of Woodchuck Hepatitis Virus Capsids.
Pierson, Elizabeth E; Keifer, David Z; Kukreja, Alexander A; Wang, Joseph C-Y; Zlotnick, Adam; Jarrold, Martin F
Woodchuck hepatitis virus (WHV) is prone to aberrant assembly in vitro and can form a broad distribution of oversized particles. Characterizing aberrant assembly products is challenging because they are both large and heterogeneous. In this work, charge detection mass spectrometry (CDMS) is used to measure the distribution of WHV assembly products. CDMS is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of each ion's charge and m/z (mass-to-charge) ratio. Under relatively aggressive, assembly promoting conditions, roughly half of the WHV assembly products are T=4 capsids composed of exactly 120 dimers while the other half are a broad distribution of larger species that extends to beyond 210 dimers. There are prominent peaks at around 132 dimers and at 150 dimers. In part, the 150 dimer complex can be attributed to elongating a T=4 capsid along its 5-fold axis by adding a ring of hexamers. However, most of the other features cannot be explained by existing models for hexameric defects. Cryo-electron microscopy provides evidence of elongated capsids. However, image analysis reveals that many of them are not closed but have "spiral-like" morphologies. The CDMS data indicate that oversized capsids have a preference for growth by addition of 3 or 4 dimers, probably by completion of hexameric vertices. PMID:26151485
Investigations of the Electronic Properties and Surface Structures of Aluminium-Rich Quasicrystalline Alloys
Jason A. Barrow
The work presented in this dissertation has investigated three distinct areas of interest in the field of quasicrystals: bulk structure, transport properties, and electronic structure. First, they have described the results of a study which explored the fundamental interactions between the atomic species of the icosahedral Al-Pd-Mn quasicrystal. The goal of this work was to determine whether the pseudo-MacKay or Bergman type clusters have a special stability or are merely a geometric coincidence. This was carried out by using laser vaporization to produce gas-phase metal clusters, which were analyzed using time-of-flight mass spectrometry. Both the kinetic and thermodynamic stabilities of the clusters were probed. The data indicated no special stability for either pseudo-MacKay or Bergman type clusters as isolated units. This, however, is not proof that these clusters are simply a geometric coincidence. It is possible that such clusters only have stability in the framework of the bulk matrix and do not exist as isolated units. Next, they have reported their investigations of the bulk thermal transport properties of a decagonal Al-Ni-Co two dimensional quasicrystal in the temperature range 373K-873K. The properties of a sample oriented along the periodic axis and another oriented along the aperiodic axis were measured. A high degree of anisotropy was observed between the aperiodic and periodic directions. Additionally, the properties were measured for a sample miscut to an orientation 45{sup o} off-axis. The properties of the miscut sample were shown to have good agreement with a theoretical model used to describe thermal transport in metallic single crystals. This model only considers thermal transport by a free-electron gas; therefore, agreement with experimental data suggests the validity of the Drude free-electron model for the decagonal Al-Ni-Co at these temperatures. Consequently, the observed anisotropy may be adequately described using classical transport
Na8Au9.8(4)Ga7.2 and Na17Au15.87(2)Ga46.63: The diversity of pseudo 5-fold 0 Cross Mark symmetries in the Na-Au-Ga system
Smetana, Volodymyr; Corbett, John D.; Miller, Gordon J.
The Na-rich part (similar to 30% Na) of the Na-Au-Ga system between NaAu2, NaGa4, and Na(22)Ga39 has been found to contain the ternary phases NasAug(8)(4)Ga-7.2 (I) and NavAu(5.87(2))Ga46.63 (II), according to the results of single crystal X-ray diffraction measurements. I is orthorhombic, Cmcm, a= 5.3040(1), b=24.519(5), c=14.573(3) A, and contains a network of clusters with local 5-fold symmetry along the a-axis. Such clusters are frequent building units in decagonal quasicrystals and their approximants. II is rhombohedral, a =16.325(2), c=35.242(7) A, and contains building blocks that are structurally. identical to the Bergman-type clusters as well as fused icosahedral units known with active metals, triels and late transition elements. II also contains a polycationic network with elements of the clathrate V type structure. Tight-binding electronic structure calculations using linear muffin-tin-orbital (LMTO) methods on idealized models of I and II indicate that both compounds are metallic with evident pseudogaps at the corresponding Fermi levels. The overall Hamilton bond populations are generally dominated by Au-Ga and Au-Au bonds in I and by Ga-Ga bonds in II; moreover, the Na-Au and Na-Ga contributions in I are unexpectedly large, 20% of the total. A similar involvement of sodium in covalent bonding has also been found in the electron-richer i-Nai(3)Aui(2)Gai(5) quasicrystal approximant. (C) 2013 Elsevier Inc. All rights reserved.
Na{sub 8}Au{sub 9.8(4)}Ga{sub 7.2} and Na{sub 17}Au{sub 5.87(2)}Ga{sub 46.63}: The diversity of pseudo 5-fold symmetries in the Na–Au–Ga system
Smetana, Volodymyr; Corbett, John D. Miller, Gordon J.
The Na-rich part (∼30% Na) of the Na–Au–Ga system between NaAu{sub 2}, NaGa{sub 4}, and Na{sub 22}Ga{sub 39} has been found to contain the ternary phases Na{sub 8}Au{sub 9.8(4)}Ga{sub 7.2} (I) and Na{sub 17}Au{sub 5.87(2)}Ga{sub 46.63} (II), according to the results of single crystal X-ray diffraction measurements. I is orthorhombic, Cmcm, a=5.3040(1), b=24.519(5), c=14.573(3) Å, and contains a network of clusters with local 5-fold symmetry along the a-axis. Such clusters are frequent building units in decagonal quasicrystals and their approximants. II is rhombohedral, R3{sup ¯}m, a=16.325(2), c=35.242(7) Å, and contains building blocks that are structurally identical to the Bergman-type clusters as well as fused icosahedral units known with active metals, triels and late transition elements. II also contains a polycationic network with elements of the clathrate V type structure. Tight-binding electronic structure calculations using linear muffin–tin-orbital (LMTO) methods on idealized models of I and II indicate that both compounds are metallic with evident pseudogaps at the corresponding Fermi levels. The overall Hamilton bond populations are generally dominated by Au–Ga and Au–Au bonds in I and by Ga–Ga bonds in II; moreover, the Na–Au and Na–Ga contributions in I are unexpectedly large, ∼20% of the total. A similar involvement of sodium in covalent bonding has also been found in the electron-richer i-Na{sub 13}Au{sub 12}Ga{sub 15} quasicrystal approximant. - Graphical abstract: Multiply-endohedral Bergman-related clusters in the structure of Na{sub 17}Au{sub 5.9(1)}Ga{sub 46.6.} Display Omitted - Highlights: • Two new compounds with the local 5-fold symmetry have been investigated. • Na{sub 8}Au{sub 9.8(4)}Ga{sub 7.2} is an orthorhombic approximant of the Na{sub 13}Au{sub 12}Ga{sub 15} quasicrystal. • Na{sub 17}Au{sub 5.87(2)}Ga{sub 46.63} represents a rhombohedral distortion of the Bergman-type phases.
Band gaps and transmission spectra in generalized Fibonacci σ(p,q) one-dimensional magnonic quasicrystals.
Costa, C H O; Vasconcelos, M S
We employ a microscopic theory to investigate spin wave (magnon) propagation through their dispersion and transmission spectra in magnonic crystals arranged to display deterministic disorder. In this work the quasiperiodic arrangement investigated is the well-known generalized Fibonacci sequence, which is characterized by the σ(p,q) parameter, where p and q are non-zero integers. In order to determine the bulk modes and transmission spectra of the spin waves, the calculations are carried out for the exchange dominated regime within the framework of the Heisenberg model and taking into account the random phase approximation. We have considered magnetic materials that have a ferromagnetic order, and the transfer-matrix treatment is applied to simplify the algebra. The results reveal that spin wave spectra display a rich and interesting magnonic pass- and stop-bands structures, including an almost symmetric band gap distribution around of a mid-gap frequency, which depends on the Fibonacci sequence type. PMID:23779133
Huygens and Barrow, Newton and Hooke. Pioneers in mathematical analysis and catastrophe theory from evolvents to quasicrystals.
NASA Astrophysics Data System (ADS)
Arnol'D, V. I.
This book is an English translation of the Russian original of 1989. It is based on a college lecture commemorating the tercentenary of Newton's book Philosophiae Naturalis Principia Mathematica. The author retraces the beginnings of mathematical analysis and theoretical physics in the works of the great scientists of the 17th century, and recounts the history of the discovery of the law of gravitation, discussions Newton had with Hooke and Leibniz, and much more. Some of Huygens' and Newton's ideas, several centuries ahead of their time, were developed only recently. The author follows the link between their inception and the break-throughs in contemporary mathematics and physics. The book provides present-day generalizations of Newton's theorems on the elliptical shape of orbits, attraction of spheres, and on the transcendence of Abelian integrals; it offers a brief review of the theory of regular and chaotic movement in celestial mechanics, including, for example, the problem of ports in the distribution of smaller planets and a discussion of the structure of planetary rings.
Thermal Evaporation Loss Measurements on Quasicrystal (Ti-Zr-Ni) and Glass Forming (Vit 106 and Vit 106a) Liquids
NASA Astrophysics Data System (ADS)
Blodgett, M. E.; Gangopadhyay, A. K.; Kelton, K. F.
Thermal evaporation loss measurements made using the electrostatic levitation (ESL) technique for one binary Ti-Zr, two ternary Ti-Zr-Ni, and two glass-forming (Vit 106 and Vit 106a) alloy liquids are reported. The containerless environment enables measurements not only for the equilibrium liquids but also for the metastable supercooled liquids. The data follow the Langmuir equation when the activity coefficient of the solute atoms, a measure for the deviation from the ideal solution behavior, is taken into account. An estimate for the activity coefficient of Ni in the Ti-Zr liquid is made from these data, demonstrating the effectiveness of ESL for such measurements.
Structural aspects of the fivefold quasicrystalline Al-Cu-Fe surface from STM and dynamical LEED Studies
Cai, T.; Shi, F.; Shen, Z.; Gierer, M.; Goldman, A.I.; Kramer, M.J.; Jenks, C.J.; Lograsso, T.A.; Delaney, D.W.; Thiel, P.A.; Van, M.A.
We investigate the atomic structure of the fivefold surface of an icosahedral Al-Cu-Fe alloy, using scanning tunneling microscopy (STM) imaging and a special dynamical low energy-electron diffraction (LEED) method. STM indicates that the step heights adopt (primarily) two values in the ratio of tau, but the spatial distribution of these two values does not follow a Fibonacci sequence, thus breaking the ideal bulk-like quasicrystalline layer stacking order perpendicular to the surface. The appearance of screw dislocations in the STM images is another indication of imperfect quasicrystallinity. On the other hand, the LEED analysis, which was successfully applied to Al-Pd-Mn in a previous study, is equally successful for Al-Cu-Fe. Similar structural features are found for both materials, in particular for interlayer relaxations and surface terminations. Although there is no structural periodicity, there are clear atomic planes in the bulk of the quasicrystal, some of which can be grouped in recurring patterns. The surface tends to form between these grouped layers in both alloys. For Al-Cu-Fe, the step heights measured by STM are consistent with the thicknesses of the grouped layers favored in LEED. These results suggest that the fivefold Al-Cu-Fe surface exhibits a quasicrystalline layering structure, but with stacking defects.
Use of frit-disc crucibles for routine and exploratory solution growth of single crystalline samples
NASA Astrophysics Data System (ADS)
Canfield, Paul C.; Kong, Tai; Kaluarachchi, Udhara S.; Jo, Na Hyun
Solution growth of single crystals from high temperature solutions often involves the separation of residual solution from the grown crystals. For many growths of intermetallic compounds, this separation has historically been achieved with the use of plugs of silica wool. Whereas this is generally efficient in a mechanical sense, it leads to a significant contamination of the decanted liquid with silica fibres. In this paper, we present a simple design for frit-disc alumina crucible sets that has made their use in the growth single crystals from high temperature solutions both simple and affordable. An alumina frit-disc allows for the clean separation of the residual liquid from the solid phase. This allows for the reuse of the decanted liquid, either for further growth of the same phase, or for subsequent growth of other, related phases. In this paper, we provide examples of the growth of isotopically substituted TbCd? and icosahedral i-RCd quasicrystals, as well as the separation of (i) the closely related ? and ? phases and (ii) ? and ?.
Digital Alchemy for Materials Design: Colloids and Beyond.
van Anders, Greg; Klotsa, Daphne; Karas, Andrew S; Dodd, Paul M; Glotzer, Sharon C
Starting with the early alchemists, a holy grail of science has been to make desired materials by modifying the attributes of basic building blocks. Building blocks that show promise for assembling new complex materials can be synthesized at the nanoscale with attributes that would astonish the ancient alchemists in their versatility. However, this versatility means that making a direct connection between building-block attributes and bulk structure is both necessary for rationally engineering materials and difficult because building block attributes can be altered in many ways. Here we show how to exploit the malleability of the valence of colloidal nanoparticle "elements" to directly and quantitatively link building-block attributes to bulk structure through a statistical thermodynamic framework we term "digital alchemy". We use this framework to optimize building blocks for a given target structure and to determine which building-block attributes are most important to control for self-assembly, through a set of novel thermodynamic response functions, moduli, and susceptibilities. We thereby establish direct links between the attributes of colloidal building blocks and the bulk structures they form. Moreover, our results give concrete solutions to the more general conceptual challenge of optimizing emergent behaviors in nature and can be applied to other types of matter. As examples, we apply digital alchemy to systems of truncated tetrahedra, rhombic dodecahedra, and isotropically interacting spheres that self-assemble diamond, fcc, and icosahedral quasicrystal structures, respectively. Although our focus is on colloidal systems, our methods generalize to any building blocks with adjustable interactions. PMID:26401754
Cluster self-organization of intermetallic systems: Quasi-spherical nanocluster precursors with internal Friauf polyhedra (A-172) and icosahedra (B-137) in the Li{sub 19}Na{sub 8}Ba{sub 15} (hP842) crystal structure
Ilyushin, G. D.; Blatov, V. A.
A combinatorial and topological analysis of Li{sub 19}Na{sub 8}Ba{sub 15} (hP842, a = 20 A, c = 93 A, V = 33552 A{sup 3}, P3-bar) has been performed using computer methods (the TOPOS program package). Two types of crystal-forming quasi-spherical nanoclusters about 20 A in diameter with internal Friauf polyhedra (A-172) and icosahedra (B-137) have been established by the complete decomposition of the 3D factor graph of the structure into cluster substructures. Each type of nanoclusters forms close-packed 2D layers 3{sup 6}, which alternate along the c axis. The B-137 and A-172 nanoclusters are composed of three layers and have shell compositions (1 + 12 + 32 + 92) and (1 + 16 + 59 + 103) with local symmetries 3 and 3-bar, respectively; they were revealed for the first time in crystal structures as cluster precursors. The icosahedral B-137 nanocluster contains a 104-atom quasicrystal approximant (Samson cluster).
Orbits of crystallographic embedding of non-crystallographic groups and applications to virology.
Twarock, Reidun; Valiunas, Motiejus; Zappa, Emilio
The architecture of infinite structures with non-crystallographic symmetries can be modelled via aperiodic tilings, but a systematic construction method for finite structures with non-crystallographic symmetry at different radial levels is still lacking. This paper presents a group theoretical method for the construction of finite nested point sets with non-crystallographic symmetry. Akin to the construction of quasicrystals, a non-crystallographic group G is embedded into the point group P of a higher-dimensional lattice and the chains of all G-containing subgroups are constructed. The orbits of lattice points under such subgroups are determined, and it is shown that their projection into a lower-dimensional G-invariant subspace consists of nested point sets with G-symmetry at each radial level. The number of different radial levels is bounded by the index of G in the subgroup of P. In the case of icosahedral symmetry, all subgroup chains are determined explicitly and it is illustrated that these point sets in projection provide blueprints that approximate the organization of simple viral capsids, encoding information on the structural organization of capsid proteins and the genomic material collectively, based on two case studies. Contrary to the affine extensions previously introduced, these orbits endow virus architecture with an underlying finite group structure, which lends itself better to the modelling of dynamic properties than its infinite-dimensional counterpart. PMID:26522406
Use of frit-disc crucibles for routine and exploratory solution growth of single crystalline samples
Canfield, Paul C.; Kong, Tai; Kaluarachchi, Udhara S.; Jo, Na Hyun
Solution growth of single crystals from high temperature solutions often involves the separation of residual solution from the grown crystals. For many growths of intermetallic compounds, this separation has historically been achieved with the use of plugs of silica wool. Whereas this is generally efficient in a mechanical sense, it leads to a significant contamination of the decanted liquid with silica fibres. In this paper, we present a simple design for frit-disc alumina crucible sets that has made their use in the growth single crystals from high temperature solutions both simple and affordable. An alumina frit-disc allows for the cleanmore » separation of the residual liquid from the solid phase. This allows for the reuse of the decanted liquid, either for further growth of the same phase, or for subsequent growth of other, related phases. In this article, we provide examples of the growth of isotopically substituted TbCd6 and icosahedral i-RCd quasicrystals, as well as the separation of (i) the closely related Bi2Rh3S2 and Bi2Rh3.5S2 phases and (ii) and PrZn11 and PrZn17.« less
PREFACE: 6th International Conference on Aperiodic Crystals (APERIODIC'09)
NASA Astrophysics Data System (ADS)
Grimm, Uwe; McGrath, Rónán; Degtyareva, Olga; Sharma, Hem Raj
on quasicrystals (Eiji Abe), complex metal alloys (Alessandra Beni) and incommensurately modulated structures (Gervais Chapuis). While these were mainly aimed at younger researchers in the field, the lectures were very well attended and appreciated by the participants. The main programme ran from Monday morning until Friday lunchtime. It comprised 13 invited and 40 contributed plenary talks, and more than 40 posters, which were presented at two afternoon/evening poster sessions. The topics covered in the programme range from mathematical foundations, mathematical models, new materials, sample preparation, structure determination, physical properties and surface properties to industrial applications. Every presenter was invited to submit an article for this proceedings volume, and the 36 peer-reviewed papers in this volume present a cross-section of the range of presentations at the conference. They have been arranged into four categories, (i) quasicrystals, (ii) modulated structures, (iii) mathematical and theoretical aspects of aperiodic order, and (iv) approximants and complex phases. Prizes for best student presentations were awarded to Heinrich Orsini-Rosenberg (ETH Zurich) for his poster Tailor-made sevenfold approximants: ab-initio investigations on formation and stability and to Holger Euchner (Universität Stuttgart) for his contributed talk on Lattice dynamics in complex metallic alloys - vibrational properties of Zn11Mg2. In addition to a cash prize, Heinrich Orsini-Rosenberg received an icosahedral teapot, which was manufactured and donated by David Warrington, and Holger Euchner received a book prize. The meeting started with a welcome reception in the University's recently refurbished Victoria Gallery and Museum. A public lecture Simple sets of shapes that tile the plane but cannot ever repeat by Professor Sir Roger Penrose FRS attracted a wide audience and gave a fascinating insight into the discovery of the Penrose tiling, which is still the paradigm
A distorted tetrahedral metal oxide cluster inside an icosahedral carbon cage. Synthesis, isolation, and structural characterization of Sc4(mu3-O)2@Ih-C80.
Stevenson, Steven; Mackey, Mary A; Stuart, Melissa A; Phillips, J Paige; Easterling, Michael L; Chancellor, Christopher J; Olmstead, Marilyn M; Balch, Alan L
The remarkably large cluster Sc4(mu3-O)2 has been obtained trapped inside an Ih-C80 cage by conducting the vaporization of graphite rods doped with copper(II) nitrate and scandium(III) oxide in an electric arc under a low pressure helium atmosphere with an added flow of air. The product has been isolated by chromatography and identified by high-resolution mass spectrometry. The structure of Sc4(mu3-O)2@Ih-C80 has been determined by X-ray crystallography on a crystal of Sc4(mu3-O)firstname.lastname@example.com(OEP).2(C6H6). The Sc4(mu3-O)2 unit consists of a distorted tetrahedron of scandium atoms with oxygen atoms bridging two of its faces. The Sc-Sc distances range from 2.946(7) to 3.379(7) A. PMID:18702488
A Novel Liquid-Liquid Transition in Undercooled Ti-Zr-Ni Liquids
NASA Technical Reports Server (NTRS)
Lee, G. W.; Gangopadhyay, A. K.; Kelton, K. F.; Bradshaw, R. C.; Hyers, R. W.; Rathz, T. J.; Rogers, J. R.
If crystallization can be avoided, liquids enter a metastable (undercooled) state below their equilibrium liquidus temperatures, T(sub l), finally 'freezing' into a glass below a characteristic temperature called the glass transition temperature, T(sub g). In rare cases, the undercooled liquid may undergo a liquid-liquid phase transition (liquid polymorphism) before entering the glassy state. This has been suggested from experimental studies of H2O and Si. Such phase transitions have been predicted in some stable liquids, ie. above T(sub l) at atmospheric pressure, for SiO2 and BeF2, but these have not been verified experimentally. They have been observed in liquids of P, Si and C, but only under high pressure. In this letter we present the first experimental evidence for a phase transition in a low viscosity metallic liquid that is driven by an approach to a constant entropy configuration state and correlated with a growing icosahedral order in the liquid. A maximum in the specific heat at constant pressure, similar to what is normally observed near T(sub g), is reported for undercooled liquids of quasicrystal-forming Ti-Zr-Ni alloys. A two-state excitation model that includes cooperativity by incorporating a temperature-dependent excitation energy, fits the specific heat data well, signaling a phase transition. An inflection in the liquid density with decreasing temperature instead of a discontinuity indicates that this is not a typical first order phase transition; it could be a weakly first order or higher order transition. While showing many similarities to a glass transition, this liquid-liquid phase transition occurs in a mobile liquid, making it novel.
Containerless measurements of thermophysical properties of Zr54Ti8Cu20Al10Ni8.
Bradshaw, R C; Warren, M E; Rogers, J R; Rathz, T J; Gangopadhyay, A K; Kelton, K F; Hyers, R W
High-temperature measurement and study of reactive materials can be difficult with conventional processing methods because contamination from the measuring apparatus and container walls can adversely affect measurements. Containerless processing techniques can be employed to isolate samples from their environment, reducing contamination. Benefits of containerless processing include reduction in heterogeneous nucleation sites, which in turn delays the onset of solidification and allows the study of meta-stable undercooled phases. However, property measurements must use noncontact methods as well. Fortunately, several optical-based methods have been developed and successfully employed to measure thermophysical properties, including surface tension, viscosity, density, and thermal expansion. Combining these techniques with the electrostatic levitator (ESL) located at the NASA Marshall Space Flight Center (MSFC) has resulted in an excellent facility to perform containerless material studies which support microgravity flight projects. Currently, studies of the thermophysical properties of liquid quasi-crystal forming and related alloys ranging from superheated to deeply undercooled states are being done with this facility in support of the NASA-funded flight project Quasi-crystalline Undercooled Alloys for Space Investigation (QUASI). While the primary purpose of these measurements is to support planned flight experiments, they are also a desirable resource for future manufacturing considerations and for fundamental insight in the physics of icosahedral ordering in liquids and solids. Presented here is an overview of the contactless measuring methods for surface tension, viscosity, density, and thermal expansion applied to Zr54Ti8Cu20Al10Ni8, for the superheated and meta-stable undercooled liquid phases, in support of QUASI. PMID:17124115
Role of Hf on Phase Formation in Ti45Zr(38-x)Hf(x)Ni17 Liquids and Solids
NASA Technical Reports Server (NTRS)
Wessels, V.; Sahu, K. K.; Gangopadhyay, A. K.; Huett, V. T.; Canepari, S.; Goldman, A. I.; Hyers, R. W.; Kramer, M. J.; Rogers, J. R.; Kelton, K. F.; Robinson, D.
Hafnium and zirconium are very similar, with almost identical sizes and chemical bonding characteristics. However, they behave differently when alloyed with Ti and Ni. A sharp phase formation boundary near 18-21 at.% Hf is observed in rapidly-quenched and as-cast Ti45Zr38-xHfxNi17 alloys. Rapidly-quenched samples that contain less than 18 at.% Hf form the icosahedral quasicrystal phase, whiles samples containing more than 21 at.% form the 3/2 rational approximant phase. In cast alloys, a C14 structure is observed for alloys with Hf lower than the boundary concentration, while a large-cell (11.93 ) FCC Ti2Ni-type structure is found in alloys with Hf concentrations above the boundary. To better understand the role of Hf on phase formation, the structural evolution with supercooling and the solidification behavior of liquid Ti45Zr38-xHfxNi17 alloys (x=0, 12, 18, 21, 38) were studied using the Beamline Electrostatic Levitation (BESL) technique using 125keV x-rays on the 6ID-D beamline at the Advanced Photon Source, Argonne National Laboratory. For all liquids primary crystallization was to a BCC solid solution phase; interestly, an increase in Hf concentration leads to a decrease in the BCC lattice parameter in spite of the chemical similarity between Zr and Hf. A Reitveld analysis confirmed that as in the cast alloys, the secondary phase that formed was the C14 below the phase formation boundary and a Ti2Ni-type structure at higher Hf concentrations. Both the liquidus temperature and the reduced undercooling change sharply on traversing the phase formation boundary concentration, suggesting a change in the liquid structure. Structural information from a Honeycutt-Anderson index analysis of reverse Monte Carlo fits to the S(q) liquid data will be presented to address this issue.
Nanoclusters based on pentagondodecahedra with shells in the form of D32, D42, and D50 deltahedra in crystal structures of intermetallic compounds
Pankova, A. A.; Ilyushin, G. D.; Blatov, V. A.
The TOPOS software package has been used to form a database of intermetallic compounds containing pentagondodecahedral d clusters (528 crystal structures of intermetallic compounds, 111 topological types, and 47 space symmetry groups). On the whole, 606 atomic d configurations have been selected which are described by 14 point symmetry groups. Examples of nanoclusters are presented which are precursors of the crystal structures of intermetallic compounds with the outer shell in the form of deltahedra D, which are formed above dodecahedra. These nanoclusters are identified in the automatic mode of structural data processing: D32 (K{sub 8}In{sub 6}Ge{sub 40}, Cs{sub 30}Na{sub 3}Sn{sub 162}), D{sub 42} (Ru{sub 3}Be{sub 17}, Y{sub 3}Cd{sub 18}, Ca{sub 3}(Cd{sub 17}Al)), and D{sub 50} (Yb{sub 3}Zn{sub 18}, Ce{sub 3}(Au{sub 14}Sn{sub 3}), Pr{sub 3}Cd{sub 18}, Eu{sub 4}Cd{sub 25}), where 32, 42, and 50 are the numbers of atoms in the shell. Similar deltahedra were found previously in icosahedral nanoclusters (precursors of intermetallic compounds). Structures with the dodecahedral nanocluster precursors containing D42 and D50 deltahedra are approximants of MCd{sub 5.7} (M = Yb or Ca) quasicrystals and belong to the family of MCd{sub 6} (M = Ce, Pr, Nd, Sm, Eu, Gd, Dy, Yb, Y, or Ca).
Formation of the icosahedral quasicrystalline phase in a rapidly solidified Al{sub 52}Cu{sub 25.5}Fe{sub 12.5}Si{sub 1} alloy
Wang Yan; Zhang Zhonghua . E-mail: firstname.lastname@example.com; Geng Haoran; Yang Zhongxi
In the present work, the effect of wheel speed (quenching rate) on the formation of the quasicrystalline phase in a rapidly solidified Al{sub 52}Cu{sub 25.5}Fe{sub 12.5}Si{sub 1} alloy has been investigated using X-ray diffraction (XRD), differential thermal analysis (DTA), differential scanning calorimetry (DSC) and transmission electron microscopy (TEM). The results show that rapid solidification has no effect on the phase constitution of the Al{sub 52}Cu{sub 25.5}Fe{sub 12.5}Si{sub 1} alloy. The addition of Si decreases the stability of the quasicrystalline phase in the conventionally cast Al{sub 52}Cu{sub 25.5}Fe{sub 12.5}Si{sub 1} alloy. The thermal stability of the quasicrystalline phase in the melt-spun alloy depends upon the quenching rate. Moderate-rate rapid solidification can improve the thermal stability of the quasicrystalline phase in the melt-spun alloy. Higher quenching rate instigates the transformation of the quasicrystalline phase into the cubic approximant phase and decreases the stability of the quasicrystalline phase. Furthermore, the transformation temperature decreases with increasing Si addition into the Al{sub (62-x)}Cu{sub 25.5}Fe{sub 12.5}Si{sub x}.
Preparation and structural characterization of the Ih and the D5h isomers of the endohedral fullerenes Tm3N@C80: icosahedral C80 cage encapsulation of a trimetallic nitride magnetic cluster with three uncoupled Tm3+ ions.
Zuo, Tianming; Olmstead, Marilyn M; Beavers, Christine M; Balch, Alan L; Wang, Guangbin; Yee, Gordon T; Shu, Chunying; Xu, Liaosa; Elliott, Bevan; Echegoyen, Luis; Duchamp, James C; Dorn, Harry C
We report an efficient method for the preparation and purification of the Ih and the D5h isomers of Tm3N@C80. Following preparation in a Kratschmer-Huffman electric-arc generator, the Tm3N@C80 isomers were obtained by a chemical separation process followed by a one-stage isomer selective chromatographic high-performance liquid chromatography (HPLC) separation (pyrenyl, 5PYE column). The HPLC chromatographic retention behavior on a pentabromobenzyl (5PBB) column suggests a charge transfer of approximately 6 electrons; [M3N] 6+@C80(6-) and the chromatographic retention mechanisms of the Ih and the D5h isomers of Tm3N@C80 on both 5PBB and 5PYE columns are discussed. Single-crystal X-ray diffraction data demonstrate that the Tm3N cluster has a planar structure but represents a tight fit for trapping the Tm3N cluster inside the I h - and the D 5h -C 80 cages. Specifically, the Tm atoms punch out the cage carbon atoms adjacent to them. The "punched out" effect can be demonstrated by cage radii and pyramidal angles at cage carbon atoms near the Tm atoms. The magnetic susceptibility (chiT) for Tm3N@ Ih -C80 was found to exhibit Curie-Weiss behavior with C = 23.4 emu.K/mol, which is consistent with the calculated value for three uncoupled Tm3+ ions by considering the spin and orbital contributions with no quenching of the orbital angular momentum ( L = 5, S = 1, and J = 6; Ccalcd = 23.3 emu.K/mol). The electrochemical measurements demonstrate that both the Ih and the D5h isomers of Tm3N@C80 have a large electrochemical gap. PMID:18447327
Effects of configurational disorder on the elastic properties of icosahedral boron-rich alloys based on B6O, B13C2, and B4C, and their mixing thermodynamics
NASA Astrophysics Data System (ADS)
Ektarawong, A.; Simak, S. I.; Hultman, L.; Birch, J.; Tasnádi, F.; Wang, F.; Alling, B.
The elastic properties of alloys between boron suboxide (B6O) and boron carbide (B13C2), denoted by (B6O)1-x(B13C2)x, as well as boron carbide with variable carbon content, ranging from B13C2 to B4C are calculated from first-principles. Furthermore, the mixing thermodynamics of (B6O)1-x(B13C2)x is studied. A superatom-special quasirandom structure approach is used for modeling different atomic configurations, in which effects of configurational disorder between the carbide and suboxide structural units, as well as between boron and carbon atoms within the units, are taken into account. Elastic properties calculations demonstrate that configurational disorder in B13C2, where a part of the C atoms in the CBC chains substitute for B atoms in the B12 icosahedra, drastically increase the Young's and shear modulus, as compared to an atomically ordered state, B12(CBC). These calculated elastic moduli of the disordered state are in excellent agreement with experiments. Configurational disorder between boron and carbon can also explain the experimentally observed almost constant elastic moduli of boron carbide as the carbon content is changed from B4C to B13C2. The elastic moduli of the (B6O)1-x(B13C2)x system are also practically unchanged with composition if boron-carbon disorder is taken into account. By investigating the mixing thermodynamics of the alloys, in which the Gibbs free energy is determined within the mean-field approximation for the configurational entropy, we outline the pseudo-binary phase diagram of (B6O)1-x(B13C2)x. The phase diagram reveals the existence of a miscibility gap at all temperatures up to the melting point. Also, the coexistence of B6O-rich as well as ordered or disordered B13C2-rich domains in the material prepared through equilibrium routes is predicted.
Isolation of CeLu2 N@Ih -C80 through a Non-Chromatographic, Two-Step Chemical Process and Crystallographic Characterization of the Pyramidalized CeLu2 N within the Icosahedral Cage.
Stevenson, Steven; Thompson, Hannah R; Arvola, Kristine D; Ghiassi, Kamran B; Olmstead, Marilyn M; Balch, Alan L
By combining two chemical methods of purification, 4 mg of purified CeLu2 N@C80 was readily isolated from 500 mg of carbon soot extract without the use of recycling HPLC, a method which has previously been necessary to obtain pure samples of endohedral fullerenes. In stage 1, CeLu2 N@C80 was selectively precipitated by virtue of its low first oxidation potential (+0.01 V) and the judicious choice of MgCl2 as the Lewis acid precipitant. For stage 2, we used a stir and filter approach (SAFA), which employed the electron-rich NH2 groups immobilized on silica gel to selectively bind residual endohedrals and higher cage fullerenes that were contaminants from stage 1. Crystallographic analysis of CeLu2 N@C80 in the co-crystal CeLu2 N@Ih -C80 ⋅Ni(octaethylporphyrin)⋅2(toluene) reveals that the Ih -C80 cage is present with a pyramidalized CeLu2 N unit inside. PMID:26059441
[Non-empirical interatomic potentials for transition metals
Not Available
The report is divided into the following sections: potential-energy functions for d-band metals, potential-energy functions for aluminides and quasicrystals, electronic structure of complex structures and quasicrystals, potential-energy functions in transition-metal oxides, applications to defect structure and mechanical properties, and basic theory of interatomic potentials.
[Non-empirical interatomic potentials for transition metals]. Progress report
Not Available
The report is divided into the following sections: potential-energy functions for d-band metals, potential-energy functions for aluminides and quasicrystals, electronic structure of complex structures and quasicrystals, potential-energy functions in transition-metal oxides, applications to defect structure and mechanical properties, and basic theory of interatomic potentials.
Crystallization of Zr2PdxCu1-x and Zr2NixCu1-x Metallic Glass
Xu, Min
One interesting aspect of rretallic glasses is the numerous instances of the deviation of the phase selection from the amorphous state to thermodynamically stable phases during the crystallization process. Their devitrification pathways allow us to study the relationship between the original amorphous structure and their crystalline counter parts. Among the various factors of phase selections, size and electronic effects have been most extensively studied. Elucidating the phase selection process of a glassy alloy will be helpful to fill in the puzzle of the changes from disordered to ordered structures. In this thesis, Two model Zr2PdxCu1-x and Zr2NixCu1-x (x = 0, 0.25, 0.5, 0.75 and 1) glassy systems were investigated since: (1) All of the samples can be made into a homogenous metallic glass; (2) The atomic radii differ from Pd to Cu is by 11%, while Ni has nearly the identical atomic size compare to Cu. Moreover, Pd and Ni differ by only one valence electron from Cu. Thus, these systems are ideal to test the idea of the effects of electronic structure and size factors; (3) The small number of components in these pseudo binary systems readily lend themselves to theoretical modeling. Using high temperature X-ray diffraction (HTXRD) and thermal analysis, topological, size, electronic, bond and chemical distribution factors on crystallization selections in Zr2PdxCu1-x and Zr2NixCu1-x metallic glass have been explored. All Zr2PdxCu1-x compositions share the same Cu11b phase with different pathways of meta-stable, icosahedral quasicrystalline phase (i-phase), and C16 phase formations. The quasicrystal phase formation is topologically related to the increasing icosahedral short range order (SRO) with Pd content in Zr2PdxCu1-x system. Meta-stable C16 phase is competitive with
Low-dimensional boron structures based on icosahedron B12
NASA Astrophysics Data System (ADS)
Kah, C. B.; Yu, M.; Tandy, P.; Jayanthi, C. S.; Wu, S. Y.
One-dimensional icosahedral boron chains and two-dimensional icosahedral boron sheets (icosahedral α, δ6, and δ4 sheets) that contain icosahedra B12 as their building units have been predicted in a computer simulation study using a state-of-the-art semi-empirical Hamiltonian. These novel low-dimensional icosahedral structures exhibit interesting bonding and electronic properties. Specifically, the three-center, two-electron bonding between icosahedra B12 of the boron bulk (rhombohedral boron) transforms into a two-center bonding in these new allotropes of boron sheets. In contrast to the previously reported stable buckled α and triangular boron monolayer sheets, these new allotropes of boron sheets form a planar network. Calculations of electronic density of states (DOS) reveal a semiconducting nature for both the icosahedral chain and the icosahedral δ6 and δ4 sheets, as well as a nearly gapless (or metallic-like) feature in the DOS for the icosahedral α sheet. The results for the energy barrier per atom between the icosahedral δ6 and α sheets (0.17 eV), the icosahedral δ6 and δ4 sheets (0.38 eV), and the icosahedral α and δ4 sheets (0.27 eV), as indicated in the respective parentheses, suggest that these new allotropes of boron sheets are relatively stable.
Multi-body forces and the energetics of transition metals, alloys, and semiconductors. Annual progress report, (1991--1992)
Carlsson, A.E.
Progress over the past year is divided into 3 areas: potential-energy functions for transition-metal aluminides; electronic structure and energetics of complex structures and quasicrystals; and ceramic materials (PdO, PtO).
Multi-body forces and the energetics of transition metals, alloys, and semiconductors
Carlsson, A.E.
Progress over the past year is divided into 3 areas: potential-energy functions for transition-metal aluminides; electronic structure and energetics of complex structures and quasicrystals; and ceramic materials (PdO, PtO).
L'Oréal and UNESCO Award Women Physicists $500 000
NASA Astrophysics Data System (ADS)
Feder, Toni
Not just cosmetic: L'Oréal and UNESCO are rewarding five women from around the globe for their scientific contributions in crystallography, disordered materials, scaling laws of fluids and complex systems, and electron microscopy of crystals and quasicrystals.
Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways.
May, Eric R; Feng, Jun; Brooks, Charles L
Many icosahedral viruses undergo large-scale conformational transitions between icosahedrally symmetric conformations during their life cycles. However, whether icosahedral symmetry is maintained along the transition pathways for this process is unknown. By employing a simplified and directed structure-based potential we compute an ensemble of transition pathways for the maturation transition of bacteriophage HK97. We observe localized symmetry-breaking events, but find that the large-scale displacements are dominated by icosahedrally symmetric deformation modes. We find that all pathways obey a common mechanism characterized by formation of pentameric contacts early in the transition. PMID:22325284
Synthesis of unsymmetrical N-carboranyl NHCs: directing effect of the carborane anion.
Asay, Matthew J; Fisher, Steven P; Lee, Sarah E; Tham, Fook S; Borchardt, Dan; Lavallo, Vincent
The syntheses of unsymmetrical N-heterocyclic carbenes (NHCs) that contain a single N-bound icosahedral carborane anion substituent are reported. Both anionic C-2 and doubly deprotonated dianionic C-2/C-5 NHC lithium complexes are isolated. The latter species is formed selectively, which reveals a surprising directing effect conveyed by icosahedral carborane anion substituents. PMID:25387660
Cubic Icosahedra? A Problem in Assigning Symmetry
ERIC Educational Resources Information Center
Lloyd, D. R.
There is a standard convention that the icosahedral groups are classified separately from the cubic groups, but these two symmetry types have been conflated as "cubic" in some chemistry textbooks. In this note, the connection between cubic and icosahedral symmetries is examined, using a simple pictorial model. It is shown that octahedral and…
Single Particle Cryo-electron Microscopy and 3-D Reconstruction of Viruses
Guo, Fei; Jiang, Wen
With fast progresses in instrumentation, image processing algorithms, and computational resources, single particle electron cryo-microscopy (cryo-EM) 3-D reconstruction of icosahedral viruses has now reached near-atomic resolutions (3–4 Å). With comparable resolutions and more predictable outcomes, cryo-EM is now considered a preferred method over X-ray crystallography for determination of atomic structure of icosahedral viruses. At near-atomic resolutions, all-atom models or backbone models can be reliably built that allow residue level understanding of viral assembly and conformational changes among different stages of viral life cycle. With the developments of asymmetric reconstruction, it is now possible to visualize the complete structure of a complex virus with not only its icosahedral shell but also its multiple non-icosahedral structural features. In this chapter, we will describe single particle cryo-EM experimental and computational procedures for both near-atomic resolution reconstruction of icosahedral viruses and asymmetric reconstruction of viruses with both icosahedral and non-icosahedral structure components. Procedures for rigorous validation of the reconstructions and resolution evaluations using truly independent de novo initial models and refinements are also introduced. PMID:24357374
Modeling quasi-lattice with octagonal symmetry
Girzhon, V. V.; Smolyakov, O. V.; Zakharenko, M. I.
We prove the possibility to use the method of modeling of a quasi-lattice with octagonal symmetry similar to that proposed earlier for the decagonal quasicrystal. The method is based on the multiplication of the groups of basis sites according to specified rules. This model is shown to be equivalent to the method of the periodic lattice projection, but is simpler because it considers merely two-dimensional site groups. The application of the proposed modeling procedure to the reciprocal lattice of octagonal quasicrystals shows a fairly good matching with the electron diffraction pattern. Similarly to the decagonal quasicrystals, the possibility of three-index labeling of the diffraction reflections is exhibited in this case. Moreover, the ascertained ratio of indices provides information on the intensity of diffraction reflections.
The geometry of disorder: Report 1987--1990
Henley, C.L. )
This report is organized into four sections by topic. Each section and subsection has an introduction, followed by summaries of each publication. Summaries of works in progress, with expected completion by July 1, are included labeled by the item number in the list at the bottom of the publications list. This paper includes work on the geometry, i.e. how are structural units packed together in space, including the single most significant accomplishment under this grant: the development of the random tiling'' picture of quasicrystal ordering. This is followed by quasicrystal atomic structure (including work on quasicrystal faceting). Then I turn to random frustrated magnetic systems, where we have worked out ground state selection -- ordering due to disorder'' -- in some 2D model systems, and are currently studying the Wolff Monte Carlo algorithm. finally I summarize results on a new self-organized percolation'' model with a non-equilibrium dynamics representing epidemics'', forest fires'', or other self-catalytic reactions.
Superlubricity in quasicrystalline twisted bilayer graphene
NASA Astrophysics Data System (ADS)
Koren, Elad; Duerig, Urs
The unique atomic positions in quasicrystals lead to peculiar self-similarity and fractal-like structural morphology. Accordingly, many of the material properties are supposed to manifest exceptional characteristics. In this Rapid Communication, we explain through numerical simulations the fundamental and peculiar aspects of quasicrystals wearless friction manifested in a 30° twisted bilayer graphene system. In particular, the sliding force exhibits a fractal structure with distinct area correlations due to the natural mixture between both periodic and aperiodic lateral modulations. In addition, zero power scaling of the sliding force with respect to the contact area is demonstrated for a geometric sequence of dodecagonal elements.
Grain size softening effect in Al{sub 62.5}Cu{sub 25}Fe{sub 12.5} nanoquasicrystals
Mukhopadhyay, N. K.; Ali, F.; Scudino, S. Samadi Khoshkhoo, M. Stoica, M.; Srivastava, V. C.; Uhlenwinkel, V.; Vaughan, G.; Suryanarayana, C.; Eckert, J.
Inverse Hall-Petch (IHP) behavior in nano-quasicrystalline Al{sub 62.5}Cu{sub 25}Fe{sub 12.5} is reported. Powders with varying grain sizes were produced by mechanical milling of spray-formed quasicrystals. The hardness of the milled powders increased with decreasing grain size down to about 40 nm and decreased with further refinement, demonstrating the IHP behavior. This critical grain size was found to be larger compared to other metallic nanocrystalline alloys. This IHP behaviour has been attributed to the structural complexity in quasicrystals and to thermally activated shearing events of atoms at the grain boundaries.
Fabrication of ten-fold photonic quasicrystalline structures
Sun, XiaoHong Wu, YuLong; Liu, Wen; Liu, Wei; Han, Juan; Jiang, Lei
Compared to periodic crystals, quasicrystals have higher point group symmetry and are more favorable in achieving complete band-gaps. In this report, a top-cut prism interferometer is designed to fabricate ten-fold photonic quasicrystalline structures. By optimizing the exposing conditions and material characteristics, appropriate quasicrystals have been obtained in the SU8 photoresist films. Atomic Force Microscopy and laser diffraction are used to characterize the fabricated structures. The measurement results show the consistence between the theoretical design and experiments. This will provide guidance for the large-area and fast production of ten-fold quasicrystalline structures with high quality.
Origin of the log-periodic oscillations in the quantum dynamics of electrons in quasiperiodic systems
NASA Astrophysics Data System (ADS)
Thiem, Stefanie
Recently, the occurrence of log-periodic oscillations in the quantum dynamics of electrons was reported for the one-dimensional Fibonacci quasicrystal by Lifshitz and Even-Dar Mandel. We apply a real-space renormalization group approach to show that these log-periodic oscillations are related to the underlying quasiperiodic structure of the Fibonacci quasicrystal. We find that they originate from the superposition of bonding and antibonding states associated to strongly coupled atoms in the chains, and that they show a hierarchical structure closely related to the atomic configurations.
Scaling in the Optical Characteristics of Aperiodic Structures with Self-Similarity Symmetry
Zotov, A. M.; Korolenko, P. V. Mishin, A. Yu.
The properties of diffraction gratings and multilayered systems constructed using 1D models of quasicrystals are considered based on numerical simulation. It is shown that there is a direct relationship between the self-similarity symmetry of quasicrystals and scaling in the characteristics of the above-mentioned optical devices. The degree of structural correspondence between the graphical representations of the geometric properties of crystals, light diffraction patterns of gratings, and the transmission spectra of multilayered systems is estimated. It is shown that certain types of self-similarity symmetry make the characteristics of aperiodic diffraction gratings highly stable to a change in the size ratio of forming elements.
Phenomenological Magnetic Model in Tsai-Type Approximants
NASA Astrophysics Data System (ADS)
Sugimoto, Takanori; Tohyama, Takami; Hiroto, Takanobu; Tamura, Ryuji
Motivated by recent discovery of canted ferromagnetism in Tsai-type approximants Au-Si-RE (RE = Tb, Dy, Ho), we propose a phenomenological magnetic model reproducing their magnetic structure and thermodynamic quantities. In the model, cubic symmetry ($m\\bar{3}$) of the approximately-regular icosahedra plays a key role in the peculiar magnetic structure determined by a neutron diffraction experiment. Our magnetic model does not only explain magnetic behaviors in the quasicrystal approximants, but also provides a good starting point for the possibility of coexistence between magnetic long-range order and aperiodicity in quasicrystals.
Raman spectroscopy of carboranes and polycarboranesiloxanes
Shelnutt, J.A.
Raman spectra of some m-carboranesiloxane polymers are compared with each other and with the spectrum of o-carborane and boron carbide. The comparisons and additional polarization studies allow the assignment of some vibrations to the icosahedral 1,7-dicarboranyl units, siloxy polymer connecting units, and substituent groups of the silicon atoms. The Raman investigation is directed toward understanding the interaction of carborane icosahedral units of boron-carbide semiconductor materials.
Flexible generation of optical beams with quasicrystalline structures via astigmatism induced by a tilted lens
NASA Astrophysics Data System (ADS)
Tung, J. C.; Liang, H. C.; Tsou, C. H.; Su, K. W.; Chen, Y. F.
We theoretically show that a family of optical beams with vortex-lattice structures can be reliably generated by tilting the focal lens to introduce the relative phases between the interfering beams. We also experimentally generate the quasicrystal beams to confirm the theoretical analysis. With the analytical wave functions and experimental patterns, a variety of vortex-lattice structures are manifested.
(X-ray diffraction experiments with condenser matter)
Coppens, P.
This report discusses research on the following topics: high-{Tc} superconductors; The response of crystal to an applied electric field; quasicrystals; surface structure and kinetics of surface layer formation; EXAFS studies of superconductors and heterostructures; effect of iron on the crystal structure of perovskite; x-ray detector development; and SAXS experiments. (LSP)
Band-gap boundaries and fundamental solitons in complex two-dimensional nonlinear lattices
Ablowitz, Mark J.; Antar, Nalan; Bakirtas, Ilkay; Ilan, Boaz
Nonlinear Schroedinger (NLS) equation with external potentials (lattices) possessing crystal and quasicrystal structures are studied. The fundamental solitons and band gaps are computed using a spectral fixed-point numerical scheme. Nonlinear and linear stability properties of the fundamental solitons are investigated by direct simulations and the linear stability properties of the fundamental solitons are confirmed by analysis the linearized eigenvalue problem.
Hyperinflation Approach to a Tight-Binding Model in Quasiperiodic Chains
NASA Astrophysics Data System (ADS)
Odagaki, Takashi
The hyperinflation technique is shown to be an efficient way to obtain the energy bands, the density and integrated density of states for a tight-binding electron in one-dimensional quasicrystals and their approximants. Within the semiclassical treatment of a carrier dynamics, the approximant crystals are shown to exhibit negative differential conductivity for sufficiently strong fields.
Clay-humic Complexes in Soil Microaggregates of a Prairie Soil
Technology Transfer Automated Retrieval System (TEKTRAN)
Microaggregates (5 to 50 um) in Midwestern prairie soils are composed primarily of intimate associations of diffuse filamentous humic substances and smectite. The humic material coats surfaces of the smectites and bridges from one smectite quasicrystal to another and between different locations on t...
NASA Astrophysics Data System (ADS)
Volfson, Boris
The hypothesis of transition from a chaotic Dirac Sea, via highly unstable positronium, into a Simhony Model of stable face-centered cubic lattice structure of electrons and positrons securely bound in vacuum space, is considered. 13.75 Billion years ago, the new lattice, which, unlike a Dirac Sea, is permeable by photons and phonons, made the Universe detectable. Many electrons and positrons ended up annihilating each other producing energy quanta and neutrino-antineutrino pairs. The weak force of the electron-positron crystal lattice, bombarded by the chirality-changing neutrinos, may have started capturing these neutrinos thus transforming from cubic crystals into a quasicrystal lattice. Unlike cubic crystal lattice, clusters of quasicrystals are "slippery" allowing the formation of centers of local torsion, where gravity condenses matter into galaxies, stars and planets. In the presence of quanta, in a quasicrystal lattice, the Majorana neutrinos' rotation flips to the opposite direction causing natural transformations in a category comprised of three components; two others being positron and electron. In other words, each particle-antiparticle pair "e-" and "e+", in an individual crystal unit, could become either a quasi- component "e- ve e+", or a quasi- component "e+ - ve e-". Five-to-six six billion years ago, a continuous stimulation of the quasicrystal aetherial lattice by the same, similar, or different, astronomical events, could have triggered Hebbian and anti-Hebbian learning processes. The Universe may have started writing script into its own aether in a code most appropriate for the quasicrystal aether "hardware": Eight three-dimensional "alphabet" characters, each corresponding to the individual quasi-crystal unit shape. They could be expressed as quantum Turing machine qubits, or, alternatively, in a binary code. The code numerals could contain terminal and nonterminal symbols of the Chomsky's hierarchy, wherein, the showers of quanta, forming the
From structure of the complex to understanding of the biology
Rossmann, Michael G.; Arisaka, Fumio; Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan; Kanamaru, Shuji; Kostyuchenko, Victor A.; Mesyanzhinov, Vadim V.; Shneider, Mikhail M.; Palermo, Laura M.; Parrish, Colin R.; Xiao, Chuan
The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.
Analysis of boron carbides' electronic structure
NASA Technical Reports Server (NTRS)
Howard, Iris A.; Beckel, Charles L.
The electronic properties of boron-rich icosahedral clusters were studied as a means of understanding the electronic structure of the icosahedral borides such as boron carbide. A lower bound was estimated on bipolaron formation energies in B12 and B11C icosahedra, and the associated distortions. While the magnitude of the distortion associated with bipolaron formation is similar in both cases, the calculated formation energies differ greatly, formation being much more favorable on B11C icosahedra. The stable positions of a divalent atom relative to an icosahedral borane was also investigated, with the result that a stable energy minimum was found when the atom is at the center of the borane, internal to the B12 cage. If incorporation of dopant atoms into B12 cages in icosahedral boride solids is feasible, novel materials might result. In addition, the normal modes of a B12H12 cluster, of the C2B10 cage in para-carborane, and of a B12 icosahedron of reduced (D sub 3d) symmetry, such as is found in the icosahedral borides, were calculated. The nature of these vibrational modes will be important in determining, for instance, the character of the electron-lattice coupling in the borides, and in analyzing the lattice contribution to the thermal conductivity.
Analysis of boron carbides' electronic structure. Final technical report, 18 July 1984-17 August 1986
Howard, I.A.; Beckel, C.L.
The electronic properties of boron-rich icosahedral clusters were studied as a means of understanding the electronic structure of the icosahedral borides such as boron carbide. A lower bound was estimated on bipolaron formation energies in B/sub 12/ and B/sub 11/C icosahedra, and the associated distortions. While the magnitude of the distortion associated with bipolaron formation is similar in both cases, the calculated formation energies differ greatly, formation being much more favorable on B11C icosahedra. The stable positions of a divalent atom relative to an icosahedral borane was also investigated, with the result that a stable energy minimum was found when the atom is at the center of the borane, internal to the B/sub 12/ cage. If incorporation of dopant atoms into B/sub 12/ cages in icosahedral boride solids is feasible, novel materials might result. In addition, the normal modes of a B/sub 12/H/sub 12/ cluster, of the C/sub 2/B/sub 10/ cage in para-carborane, and of a B/sub 12/ icosahedron of reduced (D sub 3d) symmetry, such as is found in the icosahedral borides, were calculated. The nature of these vibrational modes will be important in determining, for instance, the character of the electron-lattice coupling in the borides, and in analyzing the lattice contribution to the thermal conductivity.
NASA Astrophysics Data System (ADS)
Tanda, Satoshi; Matsuyama, Toyoki; Oda, Migaku; Asano, Yasuhiro; Yakubo, Kousuke
.]. Nanofibers of hydrogen storage alloy / I. Saita ... [et al.]. Synthesis of stable icosahedral quasicrystals in Zn-Sc based alloys and their magnetic properties / S. Kashimoto and T. Ishimasa. One-armed spiral wave excited by eam pressure in accretion disks in Be/X-Ray binaries / K. Hayasaki and A. T. Okazaki -- IV. Topological defects and excitations. Topological excitations in the ground state of charge density wave systems / P. Monceau. Soliton transport in nanoscale charge-density-wave systems / K. Inagaki, T. Toshima and S. Tanda. Topological defects in triplet superconductors UPt3, Sr[symbol]RuO[symbol], etc. / K. Maki ... [et al.]. Microscopic structure of vortices in type II superconductors / K. Machida ... [et al.]. Microscopic neutron investigation of the Abrikosov state of high-temperature superconductors / J. Mesot. Energy dissipation at nano-scale topological defects of high-Tc superconductors: microwave study / A. Maeda. Pressure induced topological phase transition in the heavy Fermion compound CeAl[symbol] / H. Miyagawa ... [et al.]. Explanation for the unusual orientation of LSCO square vortex lattice in terms of nodal superconductivity / M. Oda. Local electronic states in Bi[symbol]Sr[symbol]CaCu[symbol]O[symbol] / A. Hashimoto ... [et al.] -- V. Topology in quantum phenomena. Topological vortex formation in a Bose-Einstein condensate of alkali-metal atoms / M. Nakahara. Quantum phase transition of [symbol]He confined in nano-porous media / K. Shirahama, K. Yamamoto and Y. Shibayama. A new mean-field theory for Bose-Einstein condensates / T. Kita. Spin current in topological cristals / Y. Asano. Antiferromagnetic defects in non-magnetic hidden order of the heavy-electron system URu[symbol]Si[symbol] / H. Amitsuka, K. Tenya and M. Yokoyama. Magnetic-field dependences of thermodynamic quantities in the vortex state of Type-II superconductors / K. Watanabe, T. Kita and M. Arai. Three-magnon-mediated nuclear spin relaxation in quantum ferrimagnets of topological
Anomalous electronic transport in boron carbides
NASA Astrophysics Data System (ADS)
Emin, D.; Samara, G. A.; Wood, C.
The boron carbides are composed of icosahedral units, B12 and B11C1, linked together by strong intericosahedral bonds. With such distributions of icosahedral and intericosahedral compositions, boron carbides, B/sub 1-x/C/sub x/, are single phase over 0.1 less than or equal to x less than or equal to 0.2. The electronic transport properties of the boron carbides were examined within this single-phase region. Results are inconsistent with conventional analyses of both itinerant and hopping transport. Most striking are Seebeck coefficients which are both large and rapidly increasing functions of temperature despite thermally activated dc conductivities. These results manifest the hopping of small bipolaronic holes between carbon-containing icosahedral that are inequivalent in energy and electron-lattice coupling strength. Under hydrostatic pressures up to approx. 25 kbar, the dc conductivities increase with pressure. This anomalous behavior for hopping conduction reflects the distinctive structure and bonding of these materials.
Anomalous structure-property relationships in metallic glasses through pressure-mediated glass formation
NASA Astrophysics Data System (ADS)
Ding, Jun; Asta, Mark; Ritchie, Robert O.
Metallic glasses are commonly found to favor denser packing structures and icosahedral order in experiments, simulations, and theoretical models. Here we present a molecular dynamics simulation study of Cu-Zr metallic glasses, prepared through a pressure-mediated pathway. The resulting glasses exhibit anomalous structure-property relationships; these glasses are less energetically stable, concomitant with a denser atomic packing and a significant increase in icosahedral short-range order. The enhanced icosahedral order is shown to be accompanied by a pressure-mediated change in chemical short-range order. The results demonstrate that in amorphous alloys (nonmonatomic), theoretical frameworks of the two-order-parameter model must be generalized to account for chemical degrees of freedom.
Formation of fivefold axes in the FCC-metal nanoclusters
NASA Astrophysics Data System (ADS)
Myasnichenko, Vladimir S.; Starostenkov, Mikhail D.
Formation of atomistic structures of metallic Cu, Au, Ag clusters and bimetallic Cu-Au clusters was studied with the help of molecular dynamics using the many-body tight-binding interatomic potential. The simulation of the crystallization process of clusters with the number of atoms ranging from 300 to 1092 was carried out. The most stable configurations of atoms in the system, corresponding to the minimum of potential energy, was found during super-fast cooling from 1000 K. Atoms corresponding to fcc, hcp, and Ih phases were identified by the method of common neighbor analysis. Incomplete icosahedral core can be discovered at the intersection of one of the Ih axes with the surface of monometallic cluster. The decahedron-shaped structure of bimetallic Cu-Au cluster with seven completed icosahedral cores was obtained. The principles of the construction of small bimetallic clusters with icosahedral symmetry and increased fractal dimensionality were offered.
NASA Technical Reports Server (NTRS)
Bates, Kevin R.; Scuseria, Gustavo E.
Multi-layered round carbon particles (onions) containing tens to hundreds of thousands of atoms form during electron irradiation of graphite. However. theoretical models or large icosahedral fullerenes predict highly faceted shapes for molecules with more than a few hundred atoms. This discrepancy in shape may be explained by the presence of defects during the formation of carbon onions. Here, we use the semi-empirical tight-binding method for carbon to simulate the incorporation of pentagon-heptagon defects on to the surface of large icosahedral fullerenes. We show a simple mechanism that results in energetically competitive derivative structures and a global change in molecular shape from faceted to round. Our results provide a plausible explanation of the apparent discrepancy between experimental observations or round buckyonions and theoretical predictions of faceted icosahedral fullerenes.
NASA Technical Reports Server (NTRS)
Bates, Kevin R.; Scuseria, Gustavo E.
Multi-layered round carbon particles (onions) containing tens to hundreds of thousands of atoms form during electron irradiation of graphite carbon. However, theoretical models of large icosahedral fullerenes predict highly faceted shapes for molecules with more than a few hundred atoms. This discrepancy in shape may be explained by the presence of defects during the formation of carbon onions. Here, we use the semi-empirical tight-binding method for carbon to simulate the incorporation of pentagon-heptagon defects on to the surface of large icosahedral fullerenes. We show a simple mechanism that results in energetically competitive derivative structures and a global change in molecular shape from faceted to round. Our results provide a plausible explanation of the apparent discrepancy between experimental observations of round buckyonions and theoretical predictions of faceted icosahedral fullerenes.
Unlocking Internal Prestress from Protein Nanoshells
NASA Astrophysics Data System (ADS)
Klug, W. S.; Roos, W. H.; Wuite, G. J. L.
The capsids of icosahedral viruses are closed shells assembled from a hexagonal lattice of proteins with fivefold angular defects located at the icosahedral vertices. Elasticity theory predicts that these disclinations are subject to an internal compressive prestress, which provides an explanation for the link between size and shape of capsids. Using a combination of experiment and elasticity theory we investigate the question of whether macromolecular assemblies are subject to residual prestress, due to basic geometric incompatibility of the subunits. Here we report the first direct experimental test of the theory: by controlled removal of protein pentamers from the icosahedral vertices, we measure the mechanical response of so-called "whiffle ball" capsids of herpes simplex virus, and demonstrate the signature of internal prestress locked into wild-type capsids during assembly.
NASA Astrophysics Data System (ADS)
Vidal, A. J.; Astrakharchik, G. E.; Vranješ Markić, L.; Boronat, J.
The ground-state properties of one-dimensional electron-spin-polarized hydrogen 1H, deuterium 2H, and tritium 3H are obtained by means of quantum Monte Carlo methods. The equations of state of the three isotopes are calculated for a wide range of linear densities. The pair correlation function and the static structure factor are obtained and interpreted within the framework of the Luttinger liquid theory. We report the density dependence of the Luttinger parameter and use it to identify different physical regimes: Bogoliubov Bose gas, super-Tonks–Girardeau gas, and quasi-crystal regimes for bosons; repulsive, attractive Fermi gas, and quasi-crystal regimes for fermions. We find that the tritium isotope is the one with the richest behavior. Our results show unambiguously the relevant role of the isotope mass in the properties of this quantum system.
Fabrication of photonic quasicrystalline structures in the sub-micrometer scale
NASA Astrophysics Data System (ADS)
Wang, Shuai; Sun, XiaoHong; Li, WenYang; Liu, Wei; Jiang, Lei; Han, Juan
Compared to periodic crystals, photonic quasicrystals (PQC) have higher point group symmetry and are more favorable in achieving complete band-gaps. In this report, a top-cut prism interferometer is designed to fabricate ten-fold photonic quasicrystalline structures in the sub-micro scale. Based on the difference of production conditions, a variety of quasicrystals have been obtained in the SU8 photoresist films. Scanning Probe Microscopy and laser diffraction are used to characterize the produced structures. The corresponding theoretical analysis is also provided to compare with the experimental results. This will provide guidance for the large-area and fast production of ten-fold quasicrystalline structures with high quality.
Structures of pseudo-decagonal approximants in Al-Co-Ni.
Hovmöller, Sven; Hovmöller Zou, Linus; Zou, Xiaodong; Grushko, Benjamin
Quasi-crystals shocked the crystallographic world when they were reported in 1984. We now know that they are not a rare exception, and can be found in many alloy systems. One of the richer systems for quasi-crystals and their approximants is Al-Co-Ni. A large series of pseudo-decagonal (PD) approximants have been found. Only two of them, PD4 and PD8, have been solved by X-ray crystallography. We report here the structures of PD1, PD2, PD3 and PD5, solved from the limited information that is provided by electron diffraction patterns, unit cell dimensions and high-resolution electron microscopy images. PMID:22615470
A Density Functional Theory Study on the Deformation Behaviors of Fe-Si-B Metallic Glasses
Zheng, Guang-Ping
Density functional theory has been employed to investigate the deformation behaviors of glassy Fe-Si-B model systems prepared by ab initio molecular dynamics. The atomistic deformation defects which are closely related to the local dilation volumes or excess volumes and unstable bonding have been systematically analyzed. It has been found that the icosahedral structures are relatively stable under shear deformation until fracture occurs. Plastic flow is indicated by interruption of percolating icosahedral structures, caused by unstable Fe-Si bonding of p-s hybridization in nature. PMID:22949869
Determination of three-dimensional low-resolution viral structure from solution x-ray scattering data.
Zheng, Y; Doerschuk, P C; Johnson, J E
The capsid is modeled as a region of constant electron density located between inner and outer envelopes that exhibit icosahedral symmetry. For computational purposes the envelopes are represented as truncated sums of weighted icosahedral harmonics. Methods are described for estimating the weights from x-ray solution scattering patterns based on nonlinear least squares, and two examples of the procedure, for viruses with known atomic-resolution structures, are given. Images FIGURE 8 FIGURE 9 FIGURE 14 FIGURE 17 FIGURE 20 FIGURE 23 PMID:8527677
Annealing effects on the optical properties of semiconducting boron carbide
Billa, R. B.; Robertson, B. W.; Hofmann, T.; Schubert, M.
Infrared vibrations of as-deposited and annealed semiconducting boron carbide thin films were investigated by midinfrared spectroscopic ellipsometry. The strong boron-hydrogen resonance at approx2560 cm{sup -1} in as-deposited films reveals considerable hydrogen incorporation during plasma-enhanced chemical vapor deposition. Extended annealing at 600 deg. C caused significant reduction in film thickness, substantial reduction of boron-hydrogen bond resonance absorption, and development of distinct blue-shifted boron-carbon and icosahedral vibration mode resonances. Our findings suggest that annealing results in substantial loss of hydrogen and in development of icosahedral structure, accompanied by strain relaxation and densification.
Structure determination of enterovirus 71
Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G.
Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.
Quantum and spectral properties of the Labyrinth model
NASA Astrophysics Data System (ADS)
Takahashi, Yuki
We consider the Labyrinth model, which is a two-dimensional quasicrystal model. We show that the spectrum of this model, which is known to be a product of two Cantor sets, is an interval for small values of the coupling constant. We also consider the density of states measure of the Labyrinth model and show that it is absolutely continuous with respect to Lebesgue measure for almost all values of coupling constants in the small coupling regime.
NASA Astrophysics Data System (ADS)
Hughes, Barry D.; Ninham, Barry W.
A single mathematical theme underpins disparate physical phenomena in classical, quantum and statistical mechanical contexts. This mathematical "correspondence principle", a kind of wave-particle duality with glorious realizations in classical and modern mathematical analysis, embodies fundamental geometrical and physical order, and yet in some sense sits on the edge of chaos. Illustrative cases discussed are drawn from classical and anomalous diffusion, quantum mechanics of single particles and ideal gases, quasicrystals and Casimir forces.
Quasicrystalline particulate reinforced aluminum composite
Anderson, I.E.; Biner, S.B.; Sordelet, D.J.; Unal, O.
Particulate reinforced aluminum and aluminum alloy composites are rapidly emerging as new commercial materials for aerospace, automotive, electronic packaging and other high performance applications. However, their low processing ductility and difficulty in recyclability have been the key concern. In this study, two composite systems having the same aluminum alloy matrix, one reinforced with quasicrystals and the other reinforced with the conventional SiC reinforcements were produced with identical processing routes. Their processing characteristics and tensile mechanical properties were compared.
Towards quantum simulation and quantum sensing with strontium and lithium
NASA Astrophysics Data System (ADS)
Senaratne, Ruwan; Rajagopal, Shankari; Geiger, Zachary; Lebedev, Vyacheslav; Weld, David
In this poster we describe progress towards the construction of two ultracold atomic physics experiments, based on bosonic and fermionic strontium and lithium. Applications of the experiments will include quantum simulation of quasicrystals, the development of novel cooling techniques, and force sensing on small length scales. We discuss hardware design, experimental features, and scientific goals. Work supported in part by AFOSR via a YIP award.
Quasi crystals: Studies of stability and phason relaxation
Gronlund, L.D.
This dissertation is in two distinct parts. In chapter I the author considers a simple model of solidification based on Landau theory and investigates whether this model can have stable or metastable quasicrystalline solutions. The model is that proposed by Kalugin, Kitaev, and Levitov with an additional local quartic term in the free energy. In this case, the body-centered cubic (bcc) crystal is the global minimum. He assesses the stability of the quasicrystalline solutions and shows that they are not even metastable, being unstable against a collapse to the bcc crystal. In chapter II he proposes a simple model for phason dynamics in quasicrystals. Phason shifts in the Penrose tiling model of quasicrystals appear as flips of rows of tiles, known as worms. When worms cross one another a hierarchy is established in which some of the worms cannot flip until others have. A complex set of constraints on worm flips is thereby introduced by the intricate pattern of worm crossings in quasicrystalline tilings. He introduces a simple model of interacting sets of one-dimensional Ising chains that mimics this set of constraints and study the possible consequences of these constraints for phason dynamics and the relaxation of phason strain in quasicrystals.
Diffraction pattern of modulated structures described by Bessel functions
NASA Astrophysics Data System (ADS)
Wolny, Janusz; Buganski, Ireneusz; Strzalka, Radoslaw
We performed detailed analysis of 1D modulated structure (MS) with harmonic modulation within the statistical approach. By applying two-mode Fourier transform, we were able to derive analytically the structure factor for MS with single harmonic modulation component. We confirmed in a very smooth way that ordinary Bessel functions of the first kind define envelopes tuning the intensities of the diffraction peaks. This applies not only to main reflections of the diffraction pattern but also to all satellites. In the second part, we discussed in details the similarities between harmonically modulated structures with multiple modulations and 1D model quasicrystal. The Fourier expansion of the nodes' positions in the Fibonacci chain gives direct numerical definition of the atomic arrangement in MS. In that sense, we can define 1D quasicrystal as a MS with infinite number of harmonic modulations. We prove that characteristic measures (like v(u) relation typical for statistical approach and diffraction pattern) calculated for MS asymptotically approach their counterparts for 1D quasicrystal as large enough number of modulation terms is taken into account.
Analysis of Hydrogenated Ti-Zr-Ni alloys.
NASA Astrophysics Data System (ADS)
Majzoub, E. H.; Viano, A. M.; Kelton, K. F.; Yelon, W. B.; Goldman, A. I.
The polytetrahedral order in quasicrystals deserves close attention for pragmatic reasons. It is well known that hydrogen atoms prefer to sit in tetrahedral interstitial sites in transition metals and their alloys. Since the number of tetrahedral intersticies is presumed large in quasicrystals, it is interesting to see how much hydrogen can be stored in them. Additionally, hydrogen in quasicrystals can be of great help in locating tetrahedral sites, since neutron diffraction of a loaded sample will determine the position of the hydrogen atoms. We present results of elastic neutron scattering studies of deuterated tzn453817. Samples were deuterated using the gas phase method, samples were hydrogenated using both the gas phase method and by electrochemical means. Differential scanning calorimetry (DSC) was performed on loaded samples to determine stability of phases formed and to estimate transition enthalpies. Approximate binding energies of hydrogen in the host alloy were determined using DSC enthalpies and are shown to be in the range of 1eV/H atom for tzn453817 alloys. Chemical variations in the alloy tvzn45-xx3817 are shown to affect this binding energy quite dramatically.
Effects of Oxygen Impurities on Glass-Formation Ability in Zr2Cu Alloy.
Wang, Zhanyu; Huang, Li; Yue, G Q; Shen, B; Dong, F; Zhang, R J; Zheng, Y X; Wang, S Y; Wang, C Z; Kramer, M J; Ho, K M; Chen, L Y
Using ab initio molecular dynamics simulations, we show that oxygen (O) impurities have a noticeable influence on the glass-formation ability (GFA) in Zr2Cu alloy. Cu-centered icosahedral clusters and Zr-centered Kasper polyhedra are the dominate short-range orders in undercooled Zr2Cu liquid which are most likely to be responsible for the glass formation in Zr2Cu systems. When O is introduced, a Zr octahedron is formed around the O impurity. Most of the Zr atoms in the octahedron also serve as the bridging atoms for cross-linked Kasper polyhedral network, resulting in an O-centered medium range order (MRO) structure. Meanwhile, Cu atoms are moved away from the first shell of O-centered octahedral clusters. With 1 at. % O impurities, the fractions of Zr-centered clusters are less affected, while the increase of ideal icosahedral order and decrease of distorted icosahedral order lead to a more stable atomic structure. This result suggests that a low concentration of O impurities would improve the GFA in Zr2Cu alloy. However, when ∼5 at. % O impurities are included, the ideal icosahedral clusters and Zr-centered Kasper polyhedra are seriously suppressed by the formation of O-centered MRO, which can lead to deterioration of GFA. Our analyses provide useful insight into glass formation behavior in O-doped metallic alloy systems. PMID:27509394
Theory of morphological transformation of viral capsid shell during the maturation process in the HK97 bacteriophage and similar viruses.
Konevtsova, O V; Lorman, V L; Rochal, S B
We consider the symmetry and physical origin of collective displacement modes playing a crucial role in the morphological transformation during the maturation of the HK97 bacteriophage and similar viruses. It is shown that the experimentally observed hexamer deformation and pentamer twist in the HK97 procapsid correspond to the simplest irreducible shear strain mode of a spherical shell. We also show that the icosahedral faceting of the bacteriophage capsid shell is driven by the simplest irreducible radial displacement field. The shear field has the rotational icosahedral symmetry group I while the radial field has the full icosahedral symmetry I_{h}. This difference makes their actions independent. The radial field sign discriminates between the icosahedral and the dodecahedral shapes of the faceted capsid shell, thus making the approach relevant not only for the HK97-like viruses but also for the parvovirus family. In the frame of the Landau-Ginzburg formalism we propose a simple phenomenological model valid for the first reversible step of the HK97 maturation process. The calculated phase diagram illustrates the discontinuous character of the virus shape transformation. The characteristics of the virus shell faceting and expansion obtained in the in vitro and in vivo experiments are related to the decrease in the capsid shell thickness and to the increase of the internal capsid pressure. PMID:27300929
Draft Genome Sequence of Tokyovirus, a Member of the Family Marseilleviridae Isolated from the Arakawa River of Tokyo, Japan
Members of the Marseilleviridae family are large DNA viruses with icosahedral particles that infect Acanthamoeba cells. This report presents a new Marseilleviridae family member discovered in a water/soil sample from a river in Tokyo, named Tokyovirus, with genome size of 370 to 380 kb. PMID:27284144
The diversity of the orthoreoviruses: molecular taxonomy and phylogentic divides.
Technology Transfer Automated Retrieval System (TEKTRAN)
The family Reoviridae is a diverse group of viruses with double-stranded ribonucleic acid (RNA) genomes contained within icosahedral, layered protein capsids. Within the Reoviridae, the Orthoreovirus genus includes viruses that infect reptiles, birds and mammals (including humans). Recent sequencing...
Theory of morphological transformation of viral capsid shell during the maturation process in the HK97 bacteriophage and similar viruses
NASA Astrophysics Data System (ADS)
Konevtsova, O. V.; Lorman, V. L.; Rochal, S. B.
We consider the symmetry and physical origin of collective displacement modes playing a crucial role in the morphological transformation during the maturation of the HK97 bacteriophage and similar viruses. It is shown that the experimentally observed hexamer deformation and pentamer twist in the HK97 procapsid correspond to the simplest irreducible shear strain mode of a spherical shell. We also show that the icosahedral faceting of the bacteriophage capsid shell is driven by the simplest irreducible radial displacement field. The shear field has the rotational icosahedral symmetry group I while the radial field has the full icosahedral symmetry Ih. This difference makes their actions independent. The radial field sign discriminates between the icosahedral and the dodecahedral shapes of the faceted capsid shell, thus making the approach relevant not only for the HK97-like viruses but also for the parvovirus family. In the frame of the Landau-Ginzburg formalism we propose a simple phenomenological model valid for the first reversible step of the HK97 maturation process. The calculated phase diagram illustrates the discontinuous character of the virus shape transformation. The characteristics of the virus shell faceting and expansion obtained in the in vitro and in vivo experiments are related to the decrease in the capsid shell thickness and to the increase of the internal capsid pressure.
Advanced quadratures and periodic boundary conditions in parallel 3D S{sub n} transport
Manalo, K.; Yi, C.; Huang, M.; Sjoden, G.
Significant updates in numerical quadratures have warranted investigation with 3D Sn discrete ordinates transport. We show new applications of quadrature departing from level symmetric (
S{sub 2}o). investigating 3 recently developed quadratures: Even-Odd (EO), Linear-Discontinuous Finite Element - Surface Area (LDFE-SA), and the non-symmetric Icosahedral Quadrature (IC). We discuss implementation changes to 3D Sn codes (applied to Hybrid MOC-Sn TITAN and 3D parallel PENTRAN) that can be performed to accommodate Icosahedral Quadrature, as this quadrature is not 90-degree rotation invariant. In particular, as demonstrated using PENTRAN, the properties of Icosahedral Quadrature are suitable for trivial application using periodic BCs versus that of reflective BCs. In addition to implementing periodic BCs for 3D Sn PENTRAN, we implemented a technique termed 'angular re-sweep' which properly conditions periodic BCs for outer eigenvalue iterative loop convergence. As demonstrated by two simple transport problems (3-group fixed source and 3-group reflected/periodic eigenvalue pin cell), we remark that all of the quadratures we investigated are generally superior to level symmetric quadrature, with Icosahedral Quadrature performing the most efficiently for problems tested. (authors)
Design of a hyperstable 60-subunit protein icosahedron.
Hsia, Yang; Bale, Jacob B; Gonen, Shane; Shi, Dan; Sheffler, William; Fong, Kimberly K; Nattermann, Una; Xu, Chunfu; Huang, Po-Ssu; Ravichandran, Rashmi; Yi, Sue; Davis, Trisha N; Gonen, Tamir; King, Neil P; Baker, David
The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport. There has been considerable interest in repurposing such structures for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, highly ordered icosahedral structures would open the door to a new generation of protein containers with properties custom-tailored to specific applications. Here we describe the computational design of a 25-nanometre icosahedral nanocage that self-assembles from trimeric protein building blocks. The designed protein was produced in Escherichia coli, and found by electron microscopy to assemble into a homogenous population of icosahedral particles nearly identical to the design model. The particles are stable in 6.7 molar guanidine hydrochloride at up to 80 degrees Celsius, and undergo extremely abrupt, but reversible, disassembly between 2 molar and 2.25 molar guanidinium thiocyanate. The icosahedron is robust to genetic fusions: one or two copies of green fluorescent protein (GFP) can be fused to each of the 60 subunits to create highly fluorescent 'standard candles' for use in light microscopy, and a designed protein pentamer can be placed in the centre of each of the 20 pentameric faces to modulate the size of the entrance/exit channels of the cage. Such robust and customizable nanocages should have considerable utility in targeted drug delivery, vaccine design and synthetic biology. PMID:27309817
Complete genome sequence of the podoviral bacteriophage CP24R virulent for Clostridium perfringens
Technology Transfer Automated Retrieval System (TEKTRAN)
Bacteriophage 'CP24R was isolated from raw sewage of a waste treatment plant and lytic activity was observed against a type C Clostridium perfringens isolate. Electron microscopy revealed a small virion (44nm diameter icosahedral capsid) with a short, non-contractile tail, indicative of the family ...
Deoxyribonucleic acid in Nitrobacter carboxysomes.
Westphal, K; Bock, E; Cannon, G; Shively, J M
Carboxysomes were isolated from Nitrobacter winogradskyi and Nitrobacter agilis. The icosahedral particles contained double-stranded deoxyribonucleic acid (DNA). In the presence of ethidium bromide and cesium chloride, the particle-bound DNA had a buoyant density of rho 25 = 1.701 g/cm3. Electron microscopy revealed the DNA to be a 14-micron circular molecule. Images PMID:227833
First record of a mosquito iridescent virus in Culex pipiens L. (Diptera: Culicidae)
Technology Transfer Automated Retrieval System (TEKTRAN)
The mosquito iridescent viruses (MIVs) are large icosahedral DNA viruses that replicate and assemble in the cytoplasm of the host. Paracrystalline arrangements of virions that accumulate in the cytoplasm produce an iridescent color that is symptomatic of acute infections. In August 2010, we found ...
Complete Genome Sequence of Caulobacter crescentus Siphophage Sansa
Vara, Leonardo; Kane, Ashley A.; Cahill, Jesse L.; Rasche, Eric S.
Caulobacter crescentus is a Gram-negative dimorphic model organism used to study cell differentiation. Siphophage Sansa is a newly isolated siphophage with an icosahedral capsid that infects C. crescentus. Sansa shares no sequence similarity to other phages deposited in GenBank. Here, we describe its genome sequence and general features. PMID:26450723
Complete Genome Sequence of Caulobacter crescentus Siphophage Sansa.
Vara, Leonardo; Kane, Ashley A; Cahill, Jesse L; Rasche, Eric S; Kuty Everett, Gabriel F
Caulobacter crescentus is a Gram-negative dimorphic model organism used to study cell differentiation. Siphophage Sansa is a newly isolated siphophage with an icosahedral capsid that infects C. crescentus. Sansa shares no sequence similarity to other phages deposited in GenBank. Here, we describe its genome sequence and general features. PMID:26450723
Complete Genome Sequence of Caulobacter crescentus Siphophage Seuss
Sloan, Jordan M.; Keene, Jennifer L.; Cahill, Jesse L.; Rasche, Eric S.
Caulobacter crescentus is a water-dwelling bacterium known to have a dimorphic life cycle. Here, we announce the complete genome of Seuss, a C. crescentus icosahedral siphophage, and describe key features. Seuss is unique among phages deposited in GenBank, with genes encoding novel hypothetical proteins composing 45% of its genome. PMID:26430045
Complete Genome Sequence of Caulobacter crescentus Siphophage Seuss.
Sloan, Jordan M; Keene, Jennifer L; Cahill, Jesse L; Rasche, Eric S; Kuty Everett, Gabriel F
Caulobacter crescentus is a water-dwelling bacterium known to have a dimorphic life cycle. Here, we announce the complete genome of Seuss, a C. crescentus icosahedral siphophage, and describe key features. Seuss is unique among phages deposited in GenBank, with genes encoding novel hypothetical proteins composing 45% of its genome. PMID:26430045
Structure of Epsilon15 Phage Reveals Organization of Genome and DNA Packaging/Injection Apparatus
Jiang, Wen; Chang, Juan; Jakana, Joanita; Weigele, Peter; King, Jonathan; Chiu, Wah
Using single particle electron cryomicroscopy that does not impose icosahedral averaging, we determined the structure of the entire infectious Salmonella phage Epsilon151, including both icosahedral and non-icosahedral components. At least three layers of condensed viral DNA were observed to pack in coaxial coils with local 25 Å hexagonal inter-strand spacing. At one of the five-fold vertices, a portal complex with twelve subunits replaces a capsid pentamer. A tail hub with six projecting trimeric tailspikes sits on the external face of the portal. Below the portal is a cylindrical protein core. An extended shaft of density fills the central channel of the protein core and the portal complex and appears to consist of about 90 nucleotides at the terminus of the packaged DNA poised for injection. Using an icosahedral symmetry imposed reconstruction, the fold of the capsid shell protein is seen to resemble the capsid protein fold of other tailed double-stranded DNA phages2–5 and human herpesvirus6. These common structural features suggest a common evolutionary origin among these viruses. PMID:16452981
Design of a hyperstable 60-subunit protein icosahedron
NASA Astrophysics Data System (ADS)
Hsia, Yang; Bale, Jacob B.; Gonen, Shane; Shi, Dan; Sheffler, William; Fong, Kimberly K.; Nattermann, Una; Xu, Chunfu; Huang, Po-Ssu; Ravichandran, Rashmi; Yi, Sue; Davis, Trisha N.; Gonen, Tamir; King, Neil P.; Baker, David
The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport. There has been considerable interest in repurposing such structures for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, highly ordered icosahedral structures would open the door to a new generation of protein containers with properties custom-tailored to specific applications. Here we describe the computational design of a 25-nanometre icosahedral nanocage that self-assembles from trimeric protein building blocks. The designed protein was produced in Escherichia coli, and found by electron microscopy to assemble into a homogenous population of icosahedral particles nearly identical to the design model. The particles are stable in 6.7 molar guanidine hydrochloride at up to 80 degrees Celsius, and undergo extremely abrupt, but reversible, disassembly between 2 molar and 2.25 molar guanidinium thiocyanate. The icosahedron is robust to genetic fusions: one or two copies of green fluorescent protein (GFP) can be fused to each of the 60 subunits to create highly fluorescent 'standard candles' for use in light microscopy, and a designed protein pentamer can be placed in the centre of each of the 20 pentameric faces to modulate the size of the entrance/exit channels of the cage. Such robust and customizable nanocages should have considerable utility in targeted drug delivery, vaccine design and synthetic biology.
Twenty-four near-instabilities of Caspar-Klug viruses
NASA Astrophysics Data System (ADS)
Englert, François; Peeters, Kasper; Taormina, Anne
Group theoretical arguments combined with normal mode analysis techniques are applied to a coarse-grained approximation of icosahedral viral capsids which incorporates areas of variable flexibility. This highlights a remarkable structure of the low-frequency spectrum in this approximation, namely, the existence of a plateau of 24 near zero modes with universal group theory content.
Twenty-four near-instabilities of Caspar-Klug viruses.
Englert, François; Peeters, Kasper; Taormina, Anne
Group theoretical arguments combined with normal mode analysis techniques are applied to a coarse-grained approximation of icosahedral viral capsids which incorporates areas of variable flexibility. This highlights a remarkable structure of the low-frequency spectrum in this approximation, namely, the existence of a plateau of 24 near zero modes with universal group theory content. PMID:18851066
Irregular and Semi-Regular Polyhedral Models for Rous Sarcoma Virus Cores
Heymann, J. Bernard; Butan, Carmen; Winkler, Dennis C.; Craven, Rebecca C.; Steven, Alasdair C.
Whereas many viruses have capsids of uniquely defined sizes that observe icosahedral symmetry, retrovirus capsids are highly polymorphic. Nevertheless, they may also be described as polyhedral foldings of a fullerene lattice on which the capsid protein (CA) is arrayed. Lacking the high order of symmetry that facilitates the reconstruction of icosahedral capsids from cryo-electron micrographs, the three-dimensional structures of individual retrovirus capsids may be determined by cryo-electron tomography, albeit at lower resolution. Here we describe computational and graphical methods to construct polyhedral models that match in size and shape, capsids of Rous sarcoma virus (RSV) observed within intact virions [8]. The capsids fall into several shape classes, including tubes, "lozenges", and "coffins". The extent to which a capsid departs from icosahedral symmetry reflects the irregularity of the distribution of pentamers, which are always 12 in number for a closed polyhedral capsid. The number of geometrically distinct polyhedra grows rapidly with increasing quotas of hexamers, and ranks in the millions for RSV capsids, which typically have 150 – 300 hexamers. Unlike the capsid proteins of icosahedral viruses that assume a minimal number of quasi-equivalent conformations equal to the triangulation number (T), retroviral CAs exhibit a near-continuum of quasi-equivalent conformations – a property that may be attributed to the flexible hinge linking the N- and C-terminal domains. PMID:19122884
Draft Genome Sequence of Tokyovirus, a Member of the Family Marseilleviridae Isolated from the Arakawa River of Tokyo, Japan.
Takemura, Masaharu
Members of the Marseilleviridae family are large DNA viruses with icosahedral particles that infect Acanthamoeba cells. This report presents a new Marseilleviridae family member discovered in a water/soil sample from a river in Tokyo, named Tokyovirus, with genome size of 370 to 380 kb. PMID:27284144
New insights into the enigma of boron carbide inverse molecular behavior
Dera, Przemyslaw; Manghnani, Murli H.; Hushur, Anwar; Hu, Yi; Tkachev, Sergey
Equation of state and compression mechanism of nearly stoichiometric boron carbide B{sub 4}C were investigated using diamond anvil cell single crystal synchrotron X-ray diffraction technique up to a maximum quasi-hydrostatic pressure of 74.0(1) GPa in neon pressure transmitting medium at ambient temperature. No signatures of structural phase transitions were observed on compression. Crystal structure refinements indicate that the icosahedral units are less compressible (13% volume reduction at 60 GPa) than the unit cell volume (18% volume reduction at 60 GPa), contrary to expectations based on the inverse molecular behavior hypothesis, but consistent with spectroscopic evidence and first principles calculations. The high-pressure crystallographic refinements reveal that the nature of the chemical bonds (two, versus three centered character) has marginal effect on the bond compressibility and the compression of the crystal is mainly governed by the force transfer between the rigid icosahedral structural units. - Graphical abstract: Single crystal measurements of equation of state and compression mechanism of B{sub 4}C show that the icosahedral units are less compressibe than the unit cell volume, despite the threei-ceneterd nature of some icosahedral bonds. - Highlights: • Equation of state and compression mechanism of B{sub 4}C were measured to 75 GPa. • No signatures of structural phase transitions were observed on compression. • Icosahedral units are less compressibe than the unit cell volume. • The nature of the chemical bonds has mariginal effect on the bond compressibility. • The compression is governed by force transfer between the rigid icosahedra.
Absolutely continuous spectrum and ballistic transport in a one-dimensional quasiperiodic system
NASA Astrophysics Data System (ADS)
Pal, Biplab; Chakrabarti, Arunava
We analyse a quasiperiodic arrangement of four atomic sites sitting at the vertices of a diamond shaped plaquette and single isolated sites, occupying a one dimensional backbone following a Fibonacci quasicrystal pattern. We work within a tight binding formalism. It is shown that, even with this simple deviation from pure one dimension, a definite relation between the numerical values of the system parameters will render all the single particle states completely extended. The spectrum will be absolutely continuous with the transmission completely ballistic throughout the band, completely violating the Cantor set character of the usual Fibonacci quasiperiodic chains.
Anomalies in the Thermophysical Properties of Undercooled Glass-Forming Alloys
NASA Technical Reports Server (NTRS)
Hyers, Robert W.; Rogers, Jan R.; Kelton, Kenneth F.; Gangopadhyay, Anup
The surface tension, viscosity, and density of several bulk metallic glass-forming alloys have been measured using noncontact techniques in the electrostatic levitation facility (ESL) at NASA Marshall Space Flight Center. All three properties show unexpected behavior in the undercooled regime. Similar deviations were previously observed in titanium-based quasicrystal-forming alloys,but the deviations in the properties of the glass-forming alloys are much more pronounced. New results for anomalous thermophysical properties in undercooled glass-forming alloys will be presented and discussed.
Quantum pumping induced by disorder in one dimension
NASA Astrophysics Data System (ADS)
Qin, Jihong; Guo, Huaiming
The topological property in one dimension is protected by symmetry. Based on a concrete model, we study the effect of disorder preserving or breaking the symmetry and show the nature of symmetry protecting in the one dimensional topological phase. A stable quantum pumping can be constructed within the topological model. It is shown that an integer charge is pumped across a periodic chain in a cyclic process. Furthermore we find that not only the quantum pumping is stable to on-site disorder, but also can be induced by it. These results may be realized experimentally using quasicrystals.
A self-similar transformation for a dodecagonal quasiperiodic covering with T-clusters
NASA Astrophysics Data System (ADS)
Liao, Longguang; Zhang, Wenbin; Yu, Tongxu; Cao, Zexian
A single cluster covering for the ship tiling of a dodecagonal quasiperiodic structure is obtained via a self-similar transformation, by which a turtle-like cluster, dubbed as a T-cluster, comprising seven squares, twenty regular triangles and two 30°-rhombuses, is changed into twenty scaled-down T-clusters, each centering at a vertex of the original one. Remarkably, there are three types of transformations according to the distinct configuration of the 20 scaled-down T-clusters. Detailed data for the transformations are specified. The results are expected to be helpful for the study of the physical and structural properties of dodecagonal quasicrystals.
On the generation of point groups in spaces of various dimensions.
Pokorny, A; Herzig, P; Altmann, S L
In this paper the use of Clifford algebra in the parametrization of point groups in spaces of various dimensions is shown. Higher-dimensional spaces are of great interest especially when modulated crystals or quasicrystals are studied. While the quaternion units, which are useful to parametrize rotations in 3 dimensions, can be identified with rotations, the basic Clifford units may be regarded as mirrors from which all proper and improper symmetry operations can be generated. The practical implementation of this method of parametrization is demonstrated for the group of the hypercube in the 4-dimensional space, and generalisations to spaces of dimensions higher than 4 are suggested. PMID:11666073
Photonic Choke-Joints for Dual-Polarization Waveguides
NASA Technical Reports Server (NTRS)
Wollack, Edward J.; U-yen, Kongpop; Chuss, David T.
Photonic choke joint (PCJ) structures for dual-polarization waveguides have been investigated for use in device and component packaging. This interface enables the realization of a high performance non-contacting waveguide joint without degrading the in-band signal propagation properties. The choke properties of two tiling approaches, symmetric square Cartesian and octagonal quasi-crystal lattices of metallic posts, are explored and optimal PCJ design parameters are presented. For each of these schemes, the experimental results for structures with finite tilings demonstrate near ideal transmission and reflection performance over a full waveguide band.
The structure of small penta-twinned gold particles
NASA Astrophysics Data System (ADS)
Gao, Pei-Yu; Kunath, W.; Gleiter, H.; Weiss, K.
The structural feathers of penta-twinned gold particles (size between 2 and 6 nm) generated by gas evaporation have been investigated by high resolution TEM. The structural characteristic of penta-twinned particles is different from that of quasi-crystals that the five coherent or incoherent twin boundaries separating the twin oriented segments do not join up along a common edge. The lattice parameter is reduced by 4 5% in comparison to that of bulk gold. The formation of the penta-twinned particles is proposed to occur by particle collision. The particles were observed to be crystalline at ambient temperature.
Reformulation of the Fourier-Bessel steady state mode solver
NASA Astrophysics Data System (ADS)
Gauthier, Robert C.
The Fourier-Bessel resonator state mode solver is reformulated using Maxwell's field coupled curl equations. The matrix generating expressions are greatly simplified as well as a reduction in the number of pre-computed tables making the technique simpler to implement on a desktop computer. The reformulation maintains the theoretical equivalence of the permittivity and permeability and as such structures containing both electric and magnetic properties can be examined. Computation examples are presented for a surface nanoscale axial photonic resonator and hybrid { ε , μ } quasi-crystal resonator.
Self-assembly of a space-tessellating structure in the binary system of hard tetrahedra and octahedra.
Cadotte, A T; Dshemuchadse, J; Damasceno, P F; Newman, R S; Glotzer, S C
We report the formation of a binary crystal of hard polyhedra due solely to entropic forces. Although the alternating arrangement of octahedra and tetrahedra is a known space-tessellation, it had not previously been observed in self-assembly simulations. Both known one-component phases - the dodecagonal quasicrystal of tetrahedra and the densest-packing of octahedra in the Minkowski lattice - are found to coexist with the binary phase. Apart from an alternative, monoclinic packing of octahedra, no additional crystalline phases were observed. PMID:27387490
Design and optimizations of quasiperiodic microcavity with high-quality factor and its application in quantum dot lasers
NASA Astrophysics Data System (ADS)
Mosallanezhad, Gholamreza; Keshavarz, Alireza
We propose an optimized quasiperiodic microcavity with the aim of achieving the highest quality factor. The proposed structure consists of two quasicrystal rings with different geometries. By performing several optimizations on the structure, the highest quality factor of 8.16×107 for a femtosecond laser with a wavelength of 1040 nm can be achieved. The quasiperiodic microcavity is used for a quantum dot laser application that obtained the highest output power of 3800 W/m2. The most important characteristics of this structure are the improvement of the quality factor and a simultaneously stable cavity wavelength.
Crystallization of nickel nanoclusters by molecular dynamics
NASA Astrophysics Data System (ADS)
Chamati, H.; Gaminchev, K.
We investigated the melting properties of bulk nickel and the crystallization of nickel nanocrystals via molecular dynamics using a potential in the framework of the second moment approximation of tight-binding theory. The melting behavior was simulated with the hysteresis approach by subsequently heating and cooling gradually the system over a wide range of temperatures. The crystallization of nickel nanoclusters consisting of 55, 147 and 309 atoms was achieved after repeatedly annealing and quenching the corresponding quasicrystals several times to avoid being trapped in a local energy minimum. The time over which the global minimum was reached was found to increase with the cluster size.
Giant regular polyhedra from calixarene carboxylates and uranyl
Pasquale, Sara; Sattin, Sara; Escudero-Adán, Eduardo C.; Martínez-Belmonte, Marta; de Mendoza, Javier
Self-assembly of large multi-component systems is a common strategy for the bottom-up construction of discrete, well-defined, nanoscopic-sized cages. Icosahedral or pseudospherical viral capsids, built up from hundreds of identical proteins, constitute typical examples of the complexity attained by biological self-assembly. Chemical versions of the so-called 5 Platonic regular or 13 Archimedean semi-regular polyhedra are usually assembled combining molecular platforms with metals with commensurate coordination spheres. Here we report novel, self-assembled cages, using the conical-shaped carboxylic acid derivatives of calix[4]arene and calix[5]arene as ligands, and the uranyl cation UO22+ as a metallic counterpart, which coordinates with three carboxylates at the equatorial plane, giving rise to hexagonal bipyramidal architectures. As a result, octahedral and icosahedral anionic metallocages of nanoscopic dimensions are formed with an unusually small number of components. PMID:22510690
Structure of Cytoplasmic Polyhedrosis Virus from Bombyx mori.
Yu, Xue-Kui; Lu, Xin-Yin; Zhang, Hong; Zhou, Zhen-Hong; Zhang, Qin-Fen; Zhang, Xing; Zhang, Jing-Qiang
The structures of full and empty capsids of CPV were studied by negative staining and electron cryomicroscopy and computer reconstruction techniques. By comparing the structures and biochemical compositions, the CPV was identified as a single-layered capsid with its five structural proteins located on it. This single capsid is arranged according to T=1 icosahedral symmetry with 12 turret-like spikes at its icosahedral vertices. The empty and full CPV show identical capsid but differ inside. The dense and ordered genomic dsRNA is located inside the full CPV. The internal space of the empty CPV has almost no electron density except for 12 electron densities attributed the transcriptional enzyme complexes extending inward from the base part of CPV spikes. PMID:12114971
Structural and electronic properties of a single layered α-tetragonal B50 sheet
NASA Astrophysics Data System (ADS)
Kah, Cherno; Yu, Ming; Jayanthi, Chakram S.; Wu, Shiyu
Ultrathin single-crystalline boron nanosheets with α-tetragonal B50 symmetry (α-t-B50) have recently been synthesized. In this presentation, the relaxed structure of this new type of boron sheet is determined using a robust self-consistent and environment-dependent semi-empirical Hamiltonian developed within the LCAO framework that includes MD and power quenching schemes. Upon relaxation, the sheet symmetry is broken and the icosahedral B12 units in the sheet are found to be distorted. This stability of the sheet was investigated through a calculation of the vibrational frequencies. The sheet electronic density of states exhibits no energy gap at the Fermi level, suggesting a metallic character similar to that of the bulk α-t-B50. Finally, the cohesive energy of the α-t-B50 sheet is found to be higher than that of the recently reported icosahedral B12-δ6 sheet.
Freezing structures of free silver nanodroplets: A molecular dynamics simulation study
NASA Astrophysics Data System (ADS)
Tian, Ze-An; Liu, Rang-Su; Peng, Ping; Hou, Zhao-Yang; Liu, Hai-Rong; Zheng, Cai-Xing; Dong, Ke-Jun; Yu, Ai-Bing
Freezing structures of free silver nanodroplets containing different numbers of atoms have been studied by using MD simulation and adopting quantum Sutton-Chen (QSC) potential. It is demonstrated that during most of the solidification processes there are a first order and a continuous phase transitions. By means of the cluster-type index method (CTIM-2) and three dimension graphic techniques, the internal structures of final nanoparticles have been investigated intensively. Besides regular crystalline, decahedral and icosahedral nanoparticles, some very interesting novelty morphologies have also been found. From geometrical views, these novelty structures can be called surface-isomers, because they can be constructed on the base of regular crystalline, decahedral or icosahedral nanoparticles by adding few layers with specific atomic arrangement. These new morphologies have well global (three- or five-fold) symmetry and lower energy than other structures, with same size and one of them is in agreement with the observation in experiment [Phys. Rev. Lett. 92 (2004) 196102].
Cui, Li-Feng; Huang, Xin; Wang, Lei-Ming; Li, Jun; Wang, Lai-Sheng
Although Si or Ge is not known to form empty cage clusters such as the fullerenes, we recently found a unique 12-atom icosahedral tin cluster, Sn12 2- (stannaspherene). Here we report photoelectron spectroscopy and theoretical evidence that Pb12 2- is also a highly stable icosahedral cage cluster and bonded by four delocalized radial pi bonds and nine delocalized on-sphere sigma bonds from the 6p orbitals of the Pb atoms. Following Sn12 2-, we coin a name, plumbaspherene, for the highly stable and nearly spherical Pb12 2- cluster, which is expected to be stable in solution and the solid state. Plumbaspherene has a diameter of approximately 6.3 A with an empty interior volume large enough to host most transition metal atoms, affording a new class of endohedral clusters. PMID:16928103
Single-particle cryo-electron microscopy of Rift Valley fever virus
Sherman, Michael B.; Freiberg, Alexander N.; Holbrook, Michael R.; Watowich, Stanley J.
Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human and veterinary pathogen causing acute hepatitis in ruminants and has the potential to cause hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T = 12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure provides a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit vaccines.
A Flexible Atmospheric Modeling Framework for the CESM
Randall, David; Heikes, Ross; Konor, Celal
We have created two global dynamical cores based on the unified system of equations and Z-grid staggering on an icosahedral grid, which are collectively called UZIM (Unified Z-grid Icosahedral Model). The z-coordinate version (UZIM-height) can be run in hydrostatic and nonhydrostatic modes. The sigma-coordinate version (UZIM-sigma) runs in only hydrostatic mode. The super-parameterization has been included as a physics option in both models. The UZIM versions with the super-parameterization are called SUZI. With SUZI-height, we have completed aquaplanet runs. With SUZI-sigma, we are making aquaplanet runs and realistic climate simulations. SUZI-sigma includes realistic topography and a SiB3 model to parameterize the land-surface processes.
The local environment of Co in B{sub 5}CH{sub x}
Dowben, P. A.; Lui Jing; Skomski, Ralph; Ignatov, A. Yu.
Cobalt-doped boron carbides produced by simultaneous plasma-enhanced chemical vapor deposition of carborane and cobaltocene are investigated. Cobalt does not dope plasma-enhanced chemical vapor deposition grown boron carbides as a random fragment of the cobaltocene source gas. The Co atoms are fivefold boron coordinated (R=2.1 A) and chemically bonded to the icosahedral cages of B{sub 10}CH{sub x} or B{sub 9}C{sub 2}H{sub y}. Pairwise Co doping occurs with the cobalt atoms favoring sites about 5.3 A apart. The cobalt strongly hybridizes with the molecular orbitals of the icosahedral cage, and the states in the region of the band gap probably have a strong cobalt weight.
Scattering functions of Platonic solids
Li, Xin; Shew, Chwen-Yang; He, Lilin; Meilleur, Flora; Myles, Dean A A; Liu, Emily; Zhang, Yang; Smith, Greg; Herwig, Kenneth W; Pynn, Roger; Chen, Wei-Ren
The single-particle small-angle scattering properties of five Platonic solids, including the tetrahedron, hexahedron, octahedron, dodecahedron and icosahedron, are systematically investigated. For each given geometry, the Debye spatial autocorrelation function, pair distance distribution function and intraparticle structure factor (form factor) are calculated and compared with the corresponding scattering function of a spherical reference system. From the theoretical models, the empirical relationship between the dodecahedral and icosahedral structural characteristics and those of the equivalent spheres is found. Moreover, the single-particle scattering properties of icosahedral and spherical shells with identical volume are investigated, and the prospect of using different data analysis approaches to explore their structural differences is presented and discussed.
Scattering functions of Platonic solids
Chen, Wei-Ren; Herwig, Kenneth W; Li, Xin; Liu, Emily; Pynn, Roger; Shew, Chwen-Yang; Smith, Gregory Scott; Myles, Dean A A; He, Lilin; Meilleur, Flora
In this report the single-particle scattering properties of five Platonic solids, including tetrahedron, hexahedron, octahedron, dodecahedron and icosahedron, are investigated in a systematic manner. For each given geometry, the Debye spatial autocorrelation function (r), pair distance distribution function (PDDF) p (r) and intraparticle structure factor (form factor) P (Q) are respectively calculated and compared to the corresponding scattering function of the spherical referential system. Based on our theoretical models, the empirical relationship between the dodecahedral and icosahedral structural characteristics and those of the equivalent spheres is found. Moreover, the single-particle scattering properties of the icosahedral and the spherical shells with the same volume are further investigated and the prospect of using different data analysis approaches to explore their structural difference is also presented and discussed.
Structure of Dengue Virus: Implications for Flavivirus Organization, Maturation, and Fusion
Kuhn, Richard J.; Zhang, Wei; Rossmann, Michael G.; Pletnev, Sergei V.; Corver, Jeroen; Lenches, Edith; Jones, Christopher T.; Mukhopadhyay, Suchetana; Chipman, Paul R.; Strauss, Ellen G.; Baker, Timothy S.; Strauss, James H.
Summary The first structure of a flavivirus has been determined by using a comThe first structure of a flavivirus has been determined by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron density map. The virus core, within a lipid bilayer, has a less-ordered structure than the external, icosahedral scaffold of 90 glycoprotein E dimers. The three E monomers per icosahedral asymmetric unit do not have quasiequivalent symmetric environments. Difference maps indicate the location of the small membrane protein M relative to the overlaying scaffold of E dimers. The structure suggests that flaviviruses, and by analogy also alphaviruses, employ a fusion mechanism in which the distal β barrels of domain II of the glycoprotein E are inserted into the cellular membrane. PMID:11893341
Monitoring Physiological Changes in Haloarchaeal Cell during Virus Release
Svirskaitė, Julija; Oksanen, Hanna M.; Daugelavičius, Rimantas; Bamford, Dennis H.
The slow rate of adsorption and non-synchronous release of some archaeal viruses have hindered more thorough analyses of the mechanisms of archaeal virus release. To address this deficit, we utilized four viruses that infect Haloarcula hispanica that represent the four virion morphotypes currently known for halophilic euryarchaeal viruses: (1) icosahedral internal membrane-containing SH1; (2) icosahedral tailed HHTV-1; (3) spindle-shaped His1; and (4) pleomorphic His2. To discern the events occurring as the progeny viruses exit, we monitored culture turbidity, as well as viable cell and progeny virus counts of infected and uninfected cultures. In addition to these traditional metrics, we measured three parameters associated with membrane integrity: the binding of the lipophilic anion phenyldicarbaundecaborane, oxygen consumption, and both intra- and extra-cellular ATP levels. PMID:26927156
Synthesis of perhydroxydodecaborate salts and related species
Hawthorne, M. Frederick; Peymann, Toralf; Herzog, Axel Hans-Joachim
New icosahedral borohydrates Cs.sub.2 [closo-B.sub.12 (OH).sub.12 ]; Cs[closo-1-H-1-CB.sub.11 (OH).sub.11 ]; and closo-1,12-H.sub.2 -1,12-C.sub.2 B.sub.10 (OH).sub.10 are disclosed. Also set forth are their preparation by refluxing the icosahedral boranes [closo-B.sub.12 H.sub.12 ].sup.2-, [closo-1-CB.sub.11 H.sub.12 ].sup.- and closo-1,12-(CH.sub.2 OH).sub.2 -1,12-C.sub.2 B.sub.10 H.sub.10 with a hydroxylating agent, preferably 30%.sub.w hydrogen peroxide.
Isotopic phonon effects in β-rhombohedral boron—non-statistical isotope distribution
NASA Astrophysics Data System (ADS)
Werheit, H.; Filipov, V.; Kuhlmann, U.; Schwarz, U.; Armbrüster, M.; Antadze, M.
On the basis of the spectra of IR- and Raman-active phonons, the isotopic phonon effects in β-rhombohedral boron are analysed for polycrystalline 10B- and 11B-enriched samples of different origin and high-purity natB single crystals. Intra- and inter-icosahedral B-B vibrations are harmonic, hence meeting the virtual crystal approximation (VCA) requirements. Deviations from the phonon shift expected according to the VCA are attributed to the anharmonic share of the lattice vibrations. In the case of icosahedral vibrations, the agreement with calculations on α-rhombohedral boron by Shirai and Katayama-Yoshida is quite satisfactory. Phonon shifts due to isotopic disorder in natB are separated and determined. Some phonon frequencies are sensitive to impurities. The isotopic phonon effects yield valuable specific information on the nature of the different phonon modes. The occupation of regular boron sites by isotopes deviates significantly from the random distribution.
Historical review: viruses, crystals and geodesic domes.
Morgan, Gregory J
In the mid 1950s, Francis Crick and James Watson attempted to explain the structure of spherical viruses. They hypothesized that spherical viruses consist of 60 identical equivalently situated subunits. Such an arrangement has icosahedral symmetry. Subsequent biophysical and electron micrographic data suggested that many viruses had >60 subunits. Drawing inspiration from architecture, Donald Caspar and Aaron Klug discovered a solution to the problem - they proposed that spherical viruses were structured like miniature geodesic domes. PMID:12575996
Synthesis of boron suboxide from boron and boric acid under mild pressure and temperature conditions
Jiao, Xiaopeng; Jin, Hua; Ding, Zhanhui; Yang, Bin; Lu, Fengguo; Zhao, Xudong; Liu, Xiaoyang; Peng, Liping
Graphical abstract: Well-crystallized and icosahedral B{sub 6}O crystals were prepared by reacting boron and boric acid at milder reaction conditions (1 GPa and 1300 {sup o}C for 2 h) as compared to previous work.. Research highlights: {yields} Well-crystallized icosahedral B{sub 6}O was synthesized by reacting boric acid and boron. {yields} The synthesis conditions (1 GPa and 1300 {sup o}C for 2 h) are milder in comparison with previous work. {yields} The more practical synthesis method may make B{sub 6}O as a potential substitute for diamond in industry. -- Abstract: Boron suboxide (B{sub 6}O) was synthesized by reacting boron and boric acid (H{sub 3}BO{sub 3}) at pressures between 1 and 10 GPa, and at temperatures between 1300 and 1400 {sup o}C. The B{sub 6}O samples prepared were icosahedral with diameters ranging from 20 to 300 nm. Well-crystallized and icosahedral crystals with an average size of {approx}100 nm can be obtained at milder reaction conditions (1 GPa and 1300 {sup o}C for 2 h) as compared to previous work. The bulk B{sub 6}O sample was stable in air at 600 {sup o}C and then slowly oxidized up to 1000 {sup o}C. The relatively mild synthetic conditions developed in this study provide a more practical synthesis of B{sub 6}O, which may potentially be used as a substitute for diamond in industry as a new superhard material.
Structure and replication of geminivirus genomes.
Davies, J W; Stanley, J; Donson, J; Mullineaux, P M; Boulton, M I
The geminiviruses are a group of plant viruses containing single-stranded (ss) DNA in particles comprising two quasi-icosahedral units. Some are transmitted by whiteflies, others by leafhoppers. Comparisons were made of the genome organization and expression of cassava latent virus (CLV) and maize streak virus (MSV) and beet curly top virus (BCTV), each with distinct host range and insect vector species characteristics. From these studies, several indications as to the replication mechanism(s) are suggested. PMID:3503890
Reconstruction of viruses from solution x-ray scattering data
NASA Astrophysics Data System (ADS)
Zheng, Yibin; Doerschuk, Peter C.; Johnson, John E.
A model-based method for reconstructing the 3D structure of icosahedrally-symmetric viruses from solution x-ray scattering is presented. An example of the reconstruction, for data from cowpea mosaic virus, is described. The major opportunity provided by solution x-ray scattering is the ability to study the dynamics of virus particles in solution, information that is not accessible to crystal x-ray diffraction experiments.
A first-principles core-level XPS study on the boron impurities in germanium crystal
Yamauchi, Jun; Yoshimoto, Yoshihide; Suwa, Yuji
We systematically investigated the x-ray photoelectron spectroscopy (XPS) core-level shifts and formation energies of boron defects in germanium crystals and compared the results to those in silicon crystals. Both for XPS core-level shifts and formation energies, relationship between defects in Si and Ge is roughly linear. From the similarity in the formation energy, it is expected that the exotic clusters like icosahedral B12 exist in Ge as well as in Si.
Isolation and characterization of a bacteriophage lytic for Desulfovibrio salexigens, a salt-requiring, sulfate-reducing bacterium
Kamimura, Kazuo; Araki, Michio )
A bacteriophage that lysed Desulfovibrio salexigens cells was isolated from marine sediments and preliminarily characterized by electron microscopy and electrophoretic analysis of structural proteins and genomic nucleic acid. The bacteriophage had an icosahedral head and a long flexible tail, and the buoyant density of the bacteriophage particles was 1.468 g/ml in cesium chloride. The particles consisted of a double-stranded DNA molecule about 33 kilobase pairs long and at least 11 structural proteins.
Key roles of carbon solubility in single-walled carbon nanotube nucleation and growth
NASA Astrophysics Data System (ADS)
He, Maoshuai; Amara, Hakim; Jiang, Hua; Hassinen, Jukka; Bichara, Christophe; Ras, Robin H. A.; Lehtonen, Juha; Kauppinen, Esko I.; Loiseau, Annick
Elucidating the roles played by carbon solubility in catalyst nanoparticles is required to better understand the growth mechanisms of single-walled carbon nanotubes (SWNTs). Here, we highlight that controlling the level of dissolved carbon is of key importance to enable nucleation and growth. We first performed tight binding based atomistic computer simulations to study carbon incorporation in metal nanoparticles with low solubilities. For such metals, carbon incorporation strongly depends on their structures (face centered cubic or icosahedral), leading to different amounts of carbon close to the nanoparticle surface. Following this idea, we then show experimentally that Au nanoparticles effectively catalyze SWNT growth when in a face centered cubic structure, and fail to do so when icosahedral. Both approaches emphasize that the presence of subsurface carbon in the nanoparticles is necessary to enable the cap lift-off, making the nucleation of SWNTs possible.Elucidating the roles played by carbon solubility in catalyst nanoparticles is required to better understand the growth mechanisms of single-walled carbon nanotubes (SWNTs). Here, we highlight that controlling the level of dissolved carbon is of key importance to enable nucleation and growth. We first performed tight binding based atomistic computer simulations to study carbon incorporation in metal nanoparticles with low solubilities. For such metals, carbon incorporation strongly depends on their structures (face centered cubic or icosahedral), leading to different amounts of carbon close to the nanoparticle surface. Following this idea, we then show experimentally that Au nanoparticles effectively catalyze SWNT growth when in a face centered cubic structure, and fail to do so when icosahedral. Both approaches emphasize that the presence of subsurface carbon in the nanoparticles is necessary to enable the cap lift-off, making the nucleation of SWNTs possible. Electronic supplementary information (ESI
A first-principles core-level XPS study on the boron impurities in germanium crystal
NASA Astrophysics Data System (ADS)
Yamauchi, Jun; Yoshimoto, Yoshihide; Suwa, Yuji
We systematically investigated the x-ray photoelectron spectroscopy (XPS) core-level shifts and formation energies of boron defects in germanium crystals and compared the results to those in silicon crystals. Both for XPS core-level shifts and formation energies, relationship between defects in Si and Ge is roughly linear. From the similarity in the formation energy, it is expected that the exotic clusters like icosahedral B12 exist in Ge as well as in Si.
Cui, Li-Feng; Huang, Xin; Wang, Lei-Ming; Zubarev, Dmitry Yu; Boldyrev, Alexander I; Li, Jun; Wang, Lai-Sheng
Stannaspherene. The Sn122- cluster is discovered to be a highly stable and highly symmetric icosahedral cage bonded by four delocalized radial pi bonds and nine delocalized on-sphere sigma bonds from the 5p orbitals of the Sn atoms. It has a diameter of 6.1 A, with a large empty interior volume, and can host most transition metal atoms inside, giving rise to a large class of endohedral chemical building blocks for cluster-assembled nanomaterials. PMID:16802791
First-principles study of configurational disorder in B4C using a superatom-special quasirandom structure method
NASA Astrophysics Data System (ADS)
Ektarawong, A.; Simak, S. I.; Hultman, L.; Birch, J.; Alling, B.
Configurationally disordered crystalline boron carbide, with the composition B4C, is studied using first-principles calculations. We investigate both dilute and high concentrations of carbon-boron substitutional defects. For the latter purpose, we suggest a superatom's picture of the complex structure and combine it with a special quasirandom structure approach for disorder. In this way, we model a random distribution of high concentrations of the identified low-energy defects: (1) bipolar defects and (2) rotation of icosahedral carbon among the three polar-up sites. Additionally, the substitutional disorder of the icosahedral carbon at all six polar sites, as previously discussed in the literature, is also considered. Two configurational phase transitions from the ordered to the disordered configurations are predicted to take place upon an increase in temperature using a mean-field approximation for the entropy. The first transition, at 870 K, induces substitutional disorder of the icosahedral carbon atoms among the three polar-up sites; meanwhile the second transition, at 2325 K, reveals the random substitution of the icosahedral carbon atoms at all six polar sites coexisting with bipolar defects. Already the first transition removes the monoclinic distortion existing in the ordered ground-state configuration and restore the rhombohedral system (R3m). The restoration of inversion symmetry yielding the full rhombohedral symmetry (R3¯m ) on average, corresponding to what is reported in the literature, is achieved after the second transition. Investigating the effects of high pressure on the configurational stability of the disordered B4C phases reveals a tendency to stabilize the ordered ground-state configuration as the configurationally ordering/disordering transition temperature increases with pressure exerted on B4C. The electronic density of states, obtained from the disordered phases, indicates a sensitivity of the band gap to the degree of configurational
Evolution of Pentagonal Nano- and Micro-Objects in Temperature Fields
NASA Astrophysics Data System (ADS)
Dorogov, M. V.; Vikarchuk, A. A.; Romanov, A. E.
The effect of temperature and annealing atmosphere on the structure and morphology of small icosahedral copper particles and filamentary pentagonal crystals has been investigated. Particles and filamentary crystals were obtained by electrodeposition of metal, and their structure and morphology were investigated by electron microscopy and x-ray diffraction. It has been shown that during annealing, whiskers are formed on the surface of the particles together with porous and "flake" structures, and cavities are formed inside them.
Shell structure in faceted metal clusters
NASA Astrophysics Data System (ADS)
Pavloff, Nicolas; Creagh, Stephen C.
We study the quantized electronic energy levels in a three-dimensional icosahedral billiard modeling a faceted metal cluster. The first 2000 levels are determined numerically. The magic numbers are compared with experimental data and with the results for a spherical model. We discuss the supershell structure and propose its study as a test of cluster sphericity. We compare our results with the predictions of the semiclassical trace formula and point out the relevance of diffractive orbits.
Morphological Variants of Sindbis Virus Obtained from Infected Mosquito Tissue Culture Cells
Brown, Dennis T.; Gliedman, Jeffrey B.
Tissue-cultured Aedes albopictus cells infected with morphologically homogeneous Sindbis virus were found to produce progeny virions which could be divided into three classes based on size. The thickness of the envelope was constant on all three sizes of progeny virions suggesting that the variability in size rested with the viral nucleocapsid. It is suggested that the three classes of virions have icosahedral nucleocapsids composed of common subunits organized in decreasing triangulation numbers. Images PMID:4128381
Elastic Lennard-Jones polymers meet clusters: Differences and similarities
NASA Astrophysics Data System (ADS)
Schnabel, Stefan; Bachmann, Michael; Janke, Wolfhard
We investigate solid-solid and solid-liquid transitions of elastic flexible off-lattice polymers with Lennard-Jones monomer-monomer interaction and anharmonic springs by means of sophisticated variants of multicanonical Monte Carlo methods. We find that the low-temperature behavior depends strongly and nonmonotonically on the system size and exhibits broad similarities to unbound atomic clusters. Particular emphasis is dedicated to the classification of icosahedral and nonicosahedral low-energy polymer morphologies.
Virus Assembly and Maturation: Auto-regulation Through Allosteric Molecular Switches
Domitrovic, Tatiana; Movahed, Navid; Brian, Bothner; Matsui, Tsutomu; Wang, Qiu; Doerschuk, Peter; Johnson, John E.
We generalize the concept of allostery from the traditional non active-site control of enzymes to virus maturation. Virtually all animal viruses transition from a procapsid, non infectious state, to a mature infectious state. The procapsid contains an encoded chemical program that is executed following an environmental cue. We developed an exceptionally accessible virus system for the study of the activators of maturation and the down stream consequences that result in particle stability and infectivity. Nudaurelia Capensis Omegavirus (NωV) is a T=4 icosahedral virus that undergoes a dramatic maturation in which the 490Å spherical procapsid condenses to a 400Å icosahedral shaped capsid with associated specific auto-proteolysis and stabilization. Employing X-ray crystallography, time resolved electron cryo-microscopy and hydrogen/deuterium exchange as well as biochemistry it was possible to define the mechanisms of allosteric communication among the 4 quasi-equivalent subunits in the icosahedral asymmetric unit. These gene products undergo proteolysis at different rates, dependent on quaternary structure environment, while particle stability is conferred globally following only a few local subunit transitions. We show that there is a close similarity between the concepts of tensegrity, associated with geodesic domes and mechanical engineering, and allostery, associated with biochemical control mechanisms. PMID:23485419
Virus assembly and maturation: auto-regulation through allosteric molecular switches.
Domitrovic, Tatiana; Movahed, Navid; Bothner, Brian; Matsui, Tsutomu; Wang, Qiu; Doerschuk, Peter C; Johnson, John E
We generalize the concept of allostery from the traditional non-active-site control of enzymes to virus maturation. Virtually, all animal viruses transition from a procapsid noninfectious state to a mature infectious state. The procapsid contains an encoded chemical program that is executed following an environmental cue. We developed an exceptionally accessible virus system for the study of the activators of maturation and the downstream consequences that result in particle stability and infectivity. Nudaurelia capensis omega virus (NωV) is a T=4 icosahedral virus that undergoes a dramatic maturation in which the 490-Å spherical procapsid condenses to a 400-Å icosahedral-shaped capsid with associated specific auto-proteolysis and stabilization. Employing X-ray crystallography, time-resolved electron cryo-microscopy and hydrogen/deuterium exchange as well as biochemistry, it was possible to define the mechanisms of allosteric communication among the four quasi-equivalent subunits in the icosahedral asymmetric unit. These gene products undergo proteolysis at different rates, dependent on quaternary structure environment, while particle stability is conferred globally following only a few local subunit transitions. We show that there is a close similarity between the concepts of tensegrity (associated with geodesic domes and mechanical engineering) and allostery (associated with biochemical control mechanisms). PMID:23485419