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Crystal structure prediction via particle-swarm optimization
NASA Astrophysics Data System (ADS)
Wang, Yanchao; Lv, Jian; Zhu, Li; Ma, Yanming
We have developed a method for crystal structure prediction from "scratch" through particle-swarm optimization (PSO) algorithm within the evolutionary scheme. PSO technique is different with the genetic algorithm and has apparently avoided the use of evolution operators (e.g., crossover and mutation). The approach is based on an efficient global minimization of free-energy surfaces merging total-energy calculations via PSO technique and requires only chemical compositions for a given compound to predict stable or metastable structures at given external conditions (e.g., pressure). A particularly devised geometrical structure parameter which allows the elimination of similar structures during structure evolution was implemented to enhance the structure search efficiency. The application of designed variable unit-cell size technique has greatly reduced the computational cost. Moreover, the symmetry constraint imposed in the structure generation enables the realization of diverse structures, leads to significantly reduced search space and optimization variables, and thus fastens the global structure convergence. The PSO algorithm has been successfully applied to the prediction of many known systems (e.g., elemental, binary, and ternary compounds) with various chemical-bonding environments (e.g., metallic, ionic, and covalent bonding). The high success rate demonstrates the reliability of this methodology and illustrates the promise of PSO as a major technique on crystal structure determination.
Structural memory effect in liquid crystal phases stabilised by silica particle aggregates
L. Almásy; A. Jákli; L. Rosta; G. Pépy
A SANS study revealed the orientational stabilisation of the smectic structure by non-mesogenic polymer networks dispersed in a liquid crystal matrix. In the present experiment, hydrophobic silica particles were dispersed in liquid crystal 8CB. The Bragg reflections from smectic layers show that the alignment of the layers is perfect if the system is cooled down in a magnetic field. After
Structural memory effect in liquid crystal phases stabilised by silica particle aggregates
L. Almásy; A. Jákli; L. Rosta; G. Pépy
A SANS study revealed the orientational stabilisation of the smectic structure by non-mesogenic polymer networks dispersed in a liquid crystal matrix. In the present experiment, hydrophobic silica particles were dispersed in liquid crystal 8CB. The Bragg reflections from smectic layers show that the alignment of the layers is perfect if the system is cooled down in a magnetic field. After
Dependence of the crystal structure on particle size in barium titanate
Kenji Uchino; T. Hirose; E. Sadanaga
The authors discuss the effect of the sample particle size on the crystal structure and the Curie temperature of BaTiOâ powder investigated in the particle size range 0.1 to 1.0 μm. The transformation from tetragonal to cubic symmetry occurs at a critical particle size of 0.12 μm at room temperature, and the Curie temperature drops below room temperature at the
Crystal structure of the ribonucleoprotein core of the signal recognition particle.
Batey, R T; Rambo, R P; Lucast, L; Rha, B; Doudna, J A
The signal recognition particle (SRP), a protein-RNA complex conserved in all three kingdoms of life, recognizes and transports specific proteins to cellular membranes for insertion or secretion. We describe here the 1.8 angstrom crystal structure of the universal core of the SRP, revealing protein recognition of a distorted RNA minor groove. Nucleotide analog interference mapping demonstrates the biological importance of observed interactions, and genetic results show that this core is functional in vivo. The structure explains why the conserved residues in the protein and RNA are required for SRP assembly and defines a signal sequence recognition surface composed of both protein and RNA. PMID:10678824
Crystal structures of enterovirus 71 (EV71) recombinant virus particles provide insights into vaccine design.
Lyu, Ke; Wang, Guang-Chuan; He, Ya-Ling; Han, Jian-Feng; Ye, Qing; Qin, Cheng-Feng; Chen, Rong
Hand-foot-and-mouth disease (HFMD) remains a major health concern in the Asia-Pacific regions, and its major causative agents include human enterovirus 71 (EV71) and coxsackievirus A16. A desirable vaccine against HFMD would be multivalent and able to elicit protective responses against multiple HFMD causative agents. Previously, we have demonstrated that a thermostable recombinant EV71 vaccine candidate can be produced by the insertion of a foreign peptide into the BC loop of VP1 without affecting viral replication. Here we present crystal structures of two different naturally occurring empty particles, one from a clinical C4 strain EV71 and the other from its recombinant virus containing an insertion in the VP1 BC loop. Crystal structure analysis demonstrated that the inserted foreign peptide is well exposed on the particle surface without significant structural changes in the capsid. Importantly, such insertions do not seem to affect the virus uncoating process as illustrated by the conformational similarity between an uncoating intermediate of another recombinant virus and that of EV71. Especially, at least 18 residues from the N terminus of VP1 are transiently externalized. Altogether, our study provides insights into vaccine development against HFMD. PMID:25492868
Biological and immunological characteristics of hepatitis E virus-like particles based on the crystal structure
Yamashita, Tetsuo; Mori, Yoshio; Miyazaki, Naoyuki; Cheng, R. Holland; Yoshimura, Masato; Unno, Hideaki; Shima, Ryoichi; Moriishi, Kohji; Tsukihara, Tomitake; Li, Tian Cheng; Takeda, Naokazu; Miyamura, Tatsuo; Matsuura, Yoshiharu
Hepatitis E virus (HEV) is a causative agent of acute hepatitis. The crystal structure of HEV-like particles (HEV-LP) consisting of capsid protein was determined at 3.5-? resolution. The capsid protein exhibited a quite different folding at the protruding and middle domains from the members of the families of Caliciviridae and Tombusviridae, while the shell domain shared the common folding. Tyr-288 at the 5-fold axis plays key roles in the assembly of HEV-LP, and aromatic amino acid residues are well conserved among the structurally related viruses. Mutational analyses indicated that the protruding domain is involved in the binding to the cells susceptive to HEV infection and has some neutralization epitopes. These structural and biological findings are important for understanding the molecular mechanisms of assembly and entry of HEV and also provide clues in the development of preventive and prophylactic measures for hepatitis E. PMID:19620712
Single crystal structure analysis of a single Sm{sub 2}Fe{sub 17}N{sub 3} particle
Inami, Nobuhito, E-mail: email@example.com; Takeichi, Yasuo; Saito, Kotaro; Sagayama, Ryoko; Kumai, Reiji; Ono, Kanta [High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801 (Japan); Ueno, Tetsuro [National Institute for Materials Science (NIMS), Tsukuba 305-0047 (Japan)
We performed single crystal structure analysis of Sm{sub 2}Fe{sub 17}N{sub 3} using X-ray diffraction. A pick-up system combined with a micromanipulation tool driven by piezoelectric actuators and a microgripper was used. A single Sm{sub 2}Fe{sub 17}N{sub x} particle with the diameter of about 20??m was picked up, and X-ray diffraction was measured using an X-ray diffractometer at the synchrotron radiation beamline at the Photon Factory, KEK. Single crystal structure analysis of a Sm{sub 2}Fe{sub 17}N{sub 3} particle was performed and the structure was successfully determined from X-ray diffraction patterns. The space group and the lattice constants were determined to be R-3m (number sign166) a?=?b?=?8.7206?Å and c?=?12.6345?Å, respectively. Atomic positions of Sm and Fe atoms were accurately determined by single crystal structure analysis of only one particle.
Colloidal Particles at Chiral Liquid Crystal Interfaces
Anne Claire Pawsey; Juho Lintuvuori
Colloidal particles trapped at an interface between two fluids can form a wide range of different structures. Replacing one of the fluid with a liquid crystal increases the complexity of interactions and results in a greater range of possible structures. New behaviour emerges when colloidal particles interact with defects in the liquid crystal phases. Here we discuss the templating of colloids at a cholesteric isotropic interface.
Crystal structure and prediction.
Thakur, Tejender S; Dubey, Ritesh; Desiraju, Gautam R
The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape. PMID:25422850
Exclusion of impurity particles in charged colloidal crystals.
Yoshizawa, Koki; Toyotama, Akiko; Okuzono, Tohru; Yamanaka, Junpei
Uniformly shaped, charged colloidal particles dispersed in water form ordered "crystal" structures when the interaction between the particles is sufficiently strong. Herein, we report the behavior of "impurity" particles, whose sizes and/or charge numbers are different from those of the bulk, on addition to the charged colloidal crystals. These impurities were excluded from the crystals during the homogeneous crystallization, crystal grain growth, and unidirectional crystallization processes. Such systems will be useful as models for studying the refinement of materials and crystal defects. PMID:24807633
Crystal Structure of Yeast Rpn14, a Chaperone of the 19 S Regulatory Particle of the Proteasome*
Kim, Sangwoo; Saeki, Yasushi; Fukunaga, Keisuke; Suzuki, Atsuo; Takagi, Kenji; Yamane, Takashi; Tanaka, Keiji; Mizushima, Tsunehiro; Kato, Koichi
The ubiquitin-proteasome pathway is a major proteolytic system in eukaryotic cells and regulates various cellular processes. The 26 S proteasome, the central enzyme of this pathway, consists of a proteolytic core particle and two 19 S regulatory particles (RPs) composed of ATPase (Rpt) and non-ATPase (Rpn) subunits. Growing evidence indicates that proteasome assembly is assisted by a variety of chaperones. In particular, it has been reported recently that Nas2, Nas6, Rpn14, and Hsm3 bind specific Rpt subunits, thereby contributing to the formation of 19 S RP. Rpn14 transiently binds to the C-terminal domain of the Rpt6 subunit (Rpt6-C) during maturation of the ATPase ring of 19 S RP. In this study, we determined the crystal structure of yeast Rpn14 at 2.0 Å resolution, which revealed that this chaperone consists of a unique N-terminal domain with unknown function and a C-terminal domain assuming a canonical seven-bladed ?-propeller fold. The Rpt6-binding site on Rpn14 was predicted based on structural comparison with the complex formed between Nas6 and Rpt3-C. The top face of Rpn14 exhibits a highly acidic surface area, whereas the putative interacting surface of Rpt6-C is basic. By inspection of structural data along with genetic and biochemical data, we determined the specific residues of Rpn14 and Rpt6 for complementary charge interactions that are required for 19 S RP assembly. PMID:20236927
Characterization of synthetic nanocrystalline mackinawite: crystal structure, particle size, and specific surface area
Jeong, Hoon Y.; Lee, Jun H.; Hayes, Kim F.
Iron sulfide was synthesized by reacting aqueous solutions of sodium sulfide and ferrous chloride for 3 days. By X-ray powder diffraction (XRPD), the resultant phase was determined to be primarily nanocrystalline mackinawite (space group: P4/nmm) with unit cell parameters a = b = 3.67 Å and c = 5.20 Å. Iron K-edge XAS analysis also indicated the dominance of mackinawite. Lattice expansion of synthetic mackinawite was observed along the c-axis relative to well-crystalline mackinawite. Compared with relatively short-aged phase, the mackinawite prepared here was composed of larger crystallites with less elongated lattice spacings. The direct observation of lattice fringes by HR-TEM verified the applicability of Bragg diffraction in determining the lattice parameters of nanocrystalline mackinawite from XRPD patterns. Estimated particle size and external specific surface area (SSAext) of nanocrystalline mackinawite varied significantly with the methods used. The use of Scherrer equation for measuring crystallite size based on XRPD patterns is limited by uncertainty of the Scherrer constant (K) due to the presence of polydisperse particles. The presence of polycrystalline particles may also lead to inaccurate particle size estimation by Scherrer equation, given that crystallite and particle sizes are not equivalent. The TEM observation yielded the smallest SSAext of 103 m2/g. This measurement was not representative of dispersed particles due to particle aggregation from drying during sample preparation. In contrast, EGME method and PCS measurement yielded higher SSAext (276–345 m2/g by EGME and 424 ± 130 m2/g by PCS). These were in reasonable agreement with those previously measured by the methods insensitive to particle aggregation. PMID:21085620
Periodic dynamics, localization metastability, and elastic interaction of colloidal particles with confining surfaces and helicoidal structure of cholesteric liquid crystals
NASA Astrophysics Data System (ADS)
Varney, Michael C. M.; Zhang, Qiaoxuan; Tasinkevych, Mykola; Silvestre, Nuno M.; Bertness, Kris A.; Smalyukh, Ivan I.
Nematic and cholesteric liquid crystals are three-dimensional fluids that possess long-range orientational ordering and can support both topological defects and chiral superstructures. Implications of this ordering remain unexplored even for simple dynamic processes such as the ones found in so-called "fall experiments," or motion of a spherical inclusion under the effects of gravity. Here we show that elastic and surface anchoring interactions prompt periodic dynamics of colloidal microparticles in confined cholesterics when gravity acts along the helical axis. We explore elastic interactions between colloidal microparticles and confining surfaces as well as with an aligned ground-state helical structure of cholesterics for different sizes of spheres relative to the cholesteric pitch, demonstrating unexpected departures from Stokes-like behavior at very low Reynolds numbers. We characterize metastable localization of microspheres under the effects of elastic and surface anchoring periodic potential landscapes seen by moving spheres, demonstrating the important roles played by anchoring memory, confinement, and topological defect transformation. These experimental findings are consistent with the results of numerical modeling performed through minimizing the total free energy due to colloidal inclusions at different locations along the helical axis and with respect to the confining substrates. A potential application emerging from this work is colloidal sorting based on particle shapes and sizes.
Periodic dynamics, localization metastability, and elastic interaction of colloidal particles with confining surfaces and helicoidal structure of cholesteric liquid crystals.
Varney, Michael C M; Zhang, Qiaoxuan; Tasinkevych, Mykola; Silvestre, Nuno M; Bertness, Kris A; Smalyukh, Ivan I
Nematic and cholesteric liquid crystals are three-dimensional fluids that possess long-range orientational ordering and can support both topological defects and chiral superstructures. Implications of this ordering remain unexplored even for simple dynamic processes such as the ones found in so-called "fall experiments," or motion of a spherical inclusion under the effects of gravity. Here we show that elastic and surface anchoring interactions prompt periodic dynamics of colloidal microparticles in confined cholesterics when gravity acts along the helical axis. We explore elastic interactions between colloidal microparticles and confining surfaces as well as with an aligned ground-state helical structure of cholesterics for different sizes of spheres relative to the cholesteric pitch, demonstrating unexpected departures from Stokes-like behavior at very low Reynolds numbers. We characterize metastable localization of microspheres under the effects of elastic and surface anchoring periodic potential landscapes seen by moving spheres, demonstrating the important roles played by anchoring memory, confinement, and topological defect transformation. These experimental findings are consistent with the results of numerical modeling performed through minimizing the total free energy due to colloidal inclusions at different locations along the helical axis and with respect to the confining substrates. A potential application emerging from this work is colloidal sorting based on particle shapes and sizes. PMID:25615114
Direct visualization of spatiotemporal structure of self-assembled colloidal particles in electrohydrodynamic flow of a nematic liquid crystal.
Sasaki, Yuji; Hoshikawa, Hikaru; Seto, Takafumi; Kobayashi, Fumiaki; Jampani, V S R; Herminghaus, Stephan; Bahr, Christian; Orihara, Hiroshi
Characterization of spatiotemporal dynamics is of vital importance to soft matter systems far from equilibrium. Using a confocal laser scanning microscopy, we directly reveal three-dimensional motion of surface-modified particles in the electrohydrodynamic convection of a nematic liquid crystal. Particularly, visualizing a caterpillar-like motion of a self-assembled colloidal chain demonstrates the mechanism of the persistent transport enabled by the elastic, electric, and hydrodynamic contributions. We also precisely show how the particles' trajectory is spatially modified by simply changing the surface boundary condition. PMID:25774695
D. M. Donaldson; J. Monteath Robertson
THE synthesis of the hydrocarbon ovalene, or octabenzonaphthalene (Fig. 1) has recently been described by E. Clar1. We have now examined the crystal structure of this compound and find it to be remarkably similar to that of the analogous hydrocarbon coronene2,3. We are indebted to Dr. Clar for some very beautiful crystal specimens of ovalene, which made this work possible.
Teaching with Crystal Structures: Helping Students Recognize and Classify the Smallest Repeating Particle in a Given Substance
ERIC Educational Resources Information Center
Smithenry, Dennis W.
Classifying a particle requires an understanding of the type of bonding that exists within and among the particles, which requires an understanding of atomic structure and electron configurations, which requires an understanding of the elements of periodic properties, and so on. Rather than getting tangled up in all of these concepts at the start…
Anisotropic colloidal crystal particles from microfluidics.
Cheng, Yao; Zhu, Cun; Xie, Zhuoying; Gu, Hongcheng; Tian, Tian; Zhao, Yuanjin; Gu, Zhongze
Anisotropic colloidal crystal particles (CCPs) have showed their great potential in biotechnology and structural materials due to their anisotropic shapes and tunable optical property. However, their controllable generation is still a challenge. Here, a novel microfluidic approach is developed to generate anisotropic CCPs. The microfluidic device is composed of an injection capillary and a collection capillary with available size and shape. Based on the device, the anisotropic particles with non-close-packed colloidal crystal structures are achieved by photo-polymerizing droplet templates in a confined collection capillary with different shapes and sizes. Moreover, anisotropic close-packed CCPs can be made from non-close-packed CCPs through a thermal process. It is demonstrated that the anisotropic CCPs in different sizes, structural colors and shapes (rods, cuboids and disks) can be generated. These distinguishable features of resultant particles make them ideal barcodes for high-throughput bioassays. In order to prove it, DNA multiplex detection is carried out. The experimental results indicate that achieved particles have a great encoding capacity and are highly practical for multiplex coding bioassays. Therefore, we believe that the anisotropic CCPs would be highly promising barcodes in biomedical applications, including high-throughput bioassays and cell culture research where multiplexing is needed. PMID:24594033
X-ray Crystal Structure of the Vault, Largest Ribonucleoprotein Particle, with a Molecular Weight of 10 MDa
NASA Astrophysics Data System (ADS)
Tanaka, Hideaki; Kato, Koji; Yamashita, Eiki
Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Although roles in multidrug resistance and innate immunity have been suggested, the cellular function remains unclear. We have determined the X-ray structure of rat liver vault at 3.5 Å resolution. A vault particle shell was composed of 78 MVP (Major vault protein) chains with 39-fold dihedral symmetry. The shoulder domain of MVP is structurally similar to SPFH (stomatin/prohibitin/flotillin/HflK/C) domain involved in lipid raft association.
Passive particle dosimetry. [silver halide crystal growth
NASA Technical Reports Server (NTRS)
Childs, C. B.
Present methods of dosimetry are reviewed with emphasis on the processes using silver chloride crystals for ionizing particle dosimetry. Differences between the ability of various crystals to record ionizing particle paths are directly related to impurities in the range of a few ppm (parts per million). To understand the roles of these impurities in the process, a method for consistent production of high purity silver chloride, and silver bromide was developed which yields silver halides with detectable impurity content less than 1 ppm. This high purity silver chloride was used in growing crystals with controlled doping. Crystals were grown by both the Czochalski method and the Bridgman method, and the Bridgman grown crystals were used for the experiments discussed. The distribution coefficients of ten divalent cations were determined for the Bridgman crystals. The best dosimeters were made with silver chloride crystals containing 5 to 10 ppm of lead; other impurities tested did not produce proper dosimeters.
Monodispersed Ultrafine Zeolite Crystal Particles by Microwave Hydrothermal Synthesis
Hu, Michael Z. [ORNL; Harris, Michael Tyrone [ORNL; Khatri, Lubna [ORNL
Microwave hydrothermal synthesis of zeolites is reviewed. Monodispersed ultrafine crystal particles of zeolite (Silicalite-1) have been synthesized in batch reactor vessels by microwave irradiation heating of aqueous basic silicate precursor solutions with tetra propyl ammonium hydroxide as the templating molecule. The effects of major process parameters (such as synthesis temperature, microwave heating rate, volume ratio (i.e., the volume of the initial synthesis solution over the total volume of the reactor vessel), and synthesis time on the zeolite particle characteristics are studied using a computer-controlled microwave reactor system that allows real-time monitoring and control of reaction medium temperature. The changes in the morphology, size and crystal structure of the particles are investigated using scanning electron microscope, dynamic light scattering, X-ray diffraction, and BET surface analysis. We have found that the synthesis temperature, volume ratio, and heating rate play a significant role in controlling the particle size, uniformity, and morphology. Microwave processing has generated new morphologies of zeolite particles (i.e., uniform block-shaped particles that contain mixed gel-nanocrystallites and agglomerated crystal particles) that could not be made by a conventional hydrothermal process. At higher synthesis temperature and lower volume ratio, irregular block-shaped particles were produced, whereas increasing the volume ratio promoted the formation of monodispersed single-crystal particles with uniform shape. Our results clearly demonstrate that faster microwave heating is advantageous to enhance the zeolite crystallization kinetics and produces larger-size crystal particles in shorter time. In addition, zeolite crystallization mechanisms, depending on the microwave heating rate, were also discussed.
Structural Color Painting by Rubbing Particle Powder
Park, ChooJin; Koh, Kunsuk; Jeong, Unyong
Structural colors originate from purely physical structures. Scientists have been inspired to mimic the structures found in nature, the realization of these structures still presents a great challenge. We have recently introduced unidirectional rubbing of a dry particle powder on a rubbery surface as a quick, highly reproducible means to fabricate a single crystal monolayer assembly of particles over an unlimited area. This study extends the particle-rubbing process to a novel fine-art painting, structural color painting (SCP). SCP is based on structural coloring with varying iridescence according to the crystal orientation, as controlled by the rubbing direction. This painting technique can be applied on curved surfaces, which enriches the objects to be painted and helps the painter mimic the structures found in nature. It also allows for quick fabrication of complicated particle-assembly patterns, which enables replication of paintings. PMID:25661669
Structural Color Painting by Rubbing Particle Powder
NASA Astrophysics Data System (ADS)
Park, Choojin; Koh, Kunsuk; Jeong, Unyong
Structural colors originate from purely physical structures. Scientists have been inspired to mimic the structures found in nature, the realization of these structures still presents a great challenge. We have recently introduced unidirectional rubbing of a dry particle powder on a rubbery surface as a quick, highly reproducible means to fabricate a single crystal monolayer assembly of particles over an unlimited area. This study extends the particle-rubbing process to a novel fine-art painting, structural color painting (SCP). SCP is based on structural coloring with varying iridescence according to the crystal orientation, as controlled by the rubbing direction. This painting technique can be applied on curved surfaces, which enriches the objects to be painted and helps the painter mimic the structures found in nature. It also allows for quick fabrication of complicated particle-assembly patterns, which enables replication of paintings.
Inorganic Crystal Structure Database (ICSD)
National Institute of Standards and Technology Data Gateway
SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase) The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.
Directed Discovery of Crystal Structures
NSDL National Science Digital Library
Dave Mogk
This contribution is modified from a published exercise "Directed Discovery of Crystal Structures Using Ball-and-Stick Models" [Mogk, 1997] . While the published exercise is based on student exploration of traditional ball-and-stick models of crystal structures, this modified version uses a similar "discovery-based" approach and the latest online crystallographic information and visualization software to teach the spatial relationships and crystal-chemical rules that govern the crystal structures of common minerals and crystalline solids. A few changes in the content have been made from the published exercise, mainly to accommodate the new digital media.
Restricted Dislocation Motion in Crystals of Colloidal Dimer Particles
Sharon J. Gerbode; Stephanie H. Lee; Chekesha M. Liddell; Itai Cohen
At high area fractions, monolayers of colloidal dimer particles form a degenerate crystal (DC) structure in which the particle lobes occupy triangular lattice sites while the particles are oriented randomly along any of the three lattice directions. We report that dislocation glide in DCs is blocked by certain particle orientations. The mean number of lattice constants between such obstacles is 4.6 +/- 0.2 in experimentally observed DC grains and 6.18 +/- 0.01 in simulated monocrystalline DCs. Dislocation propagation beyond these obstacles is observed to proceed through dislocation reactions. We estimate that the energetic cost of dislocation pair separation via such reactions in an otherwise defect free DC grows linearly with final separation, hinting that the material properties of DCs may be dramatically different from those of 2-D crystals of spheres.
Effect of the crystal structure of small precursor particles on the growth of ?-NaREF4 (RE = Sm, Eu, Gd, Tb) nanocrystals
NASA Astrophysics Data System (ADS)
Voß, Benjamin; Nordmann, Jörg; Uhl, Andreas; Komban, Rajesh; Haase, Markus
The origin of the narrow particle size distributions obtained in the oleic acid-based synthesis of hexagonal phase ?-NaREF4 nanocrystals (RE = Sm, Eu, Gd, Tb) has been investigated. Compared to the standard synthesis, the growth conditions were simplified by using small purified particles of either ?-NaREF4 (cubic phase) or ?-NaREF4 (hexagonal phase) as single-source precursors, thereby avoiding the complications arising from the simultaneous presence of molecular educts and intermediately formed small particles. The study shows that ?-phase as well as ?-phase particles grow by Ostwald-ripening but narrow particle size distributions of the ?-NaREF4 product particles are only obtained when ?-phase precursor particles are employed. Since the small particles are also formed as intermediate products in the standard synthesis of ?-NaSmF4, ?-NaEuF4, ?-NaGdF4 and ?-NaTbF4 particles, their crystal phase is an important parameter to obtain a narrow size distribution in these systems.The origin of the narrow particle size distributions obtained in the oleic acid-based synthesis of hexagonal phase ?-NaREF4 nanocrystals (RE = Sm, Eu, Gd, Tb) has been investigated. Compared to the standard synthesis, the growth conditions were simplified by using small purified particles of either ?-NaREF4 (cubic phase) or ?-NaREF4 (hexagonal phase) as single-source precursors, thereby avoiding the complications arising from the simultaneous presence of molecular educts and intermediately formed small particles. The study shows that ?-phase as well as ?-phase particles grow by Ostwald-ripening but narrow particle size distributions of the ?-NaREF4 product particles are only obtained when ?-phase precursor particles are employed. Since the small particles are also formed as intermediate products in the standard synthesis of ?-NaSmF4, ?-NaEuF4, ?-NaGdF4 and ?-NaTbF4 particles, their crystal phase is an important parameter to obtain a narrow size distribution in these systems. Electronic supplementary information (ESI) available: XRD patterns of the samples, particle size histograms from TEM and DLS measurements, Rietveld fits, emission spectra of NaGdF4:Eu particles with different Eu3+ concentrations and weighted amounts of NaREF4 precursor particles for the synthesis of the final products. See DOI: 10.1039/c2nr33083k
Soap Froths and Crystal Structures
Primoz Ziherl; Randall D. Kamien
We propose a physical mechanism to explain the crystal symmetries found in macromolecular and supramolecular micellar materials. We argue that the packing entropy of the hard micellar cores is frustrated by the entropic interaction of their brush-like coronas. The latter interaction is treated as a surface effect between neighboring Voronoi cells. The observed crystal structures correspond to the Kelvin and Weaire-Phelan minimal foams. We show that these structures are stable for reasonable areal entropy densities.
Symmetry Considerations for the Targeted Assembly of Entropically Stabilized Colloidal Crystals via Voronoi Particles.
Schultz, Benjamin A; Damasceno, Pablo F; Engel, Michael; Glotzer, Sharon C
The relationship between colloidal building blocks and their assemblies is an active field of research. As a strategy for targeting novel crystal structures, we examine the use of Voronoi particles, which are hard, space-filling particles in the shape of Voronoi cells of a target structure. Although Voronoi particles stabilize their target structure in the limit of high pressure by construction, the thermodynamic assembly of the same structure at moderate pressure, close to the onset of crystallization, is not guaranteed. Indeed, we find that a more symmetric crystal is often preferred due to additional entropic contributions arising from configurational or occupational degeneracy. We characterize the assembly behavior of the Voronoi particles in terms of the symmetries of the building blocks as well as the symmetries of crystal structures and demonstrate how controlling the degeneracies through a modification of particle shape and field-directed assembly can significantly improve the assembly propensity. PMID:25692863
Dense packing crystal structures of physical tetrahedra
Yoav Kallus; Veit Elser
We present a method for discovering dense packings of general convex hard particles and apply it to study the dense packing behavior of a one-parameter family of particles with tetrahedral symmetry representing a deformation of the ideal mathematical tetrahedron into a less ideal, physical, tetrahedron and all the way to the sphere. Thus, we also connect the two well studied problems of sphere packing and tetrahedron packing on a single axis. Our numerical results uncover a rich optimal-packing behavior, compared to that of other continuous families of particles previously studied. We present four structures as candidates for the optimal packing at different values of the parameter, providing an atlas of crystal structures which might be observed in systems of nano-particles with tetrahedral symmetry.
Dense packing crystal structures of physical tetrahedra
Kallus, Yoav
We present a method for discovering dense packings of general convex hard particles and apply it to study the dense packing behavior of a one-parameter family of particles with tetrahedral symmetry representing a deformation of the ideal mathematical tetrahedron into a less ideal, physical, tetrahedron and all the way to the sphere. Thus, we also connect the two well studied problems of sphere packing and tetrahedron packing on a single axis. Our numerical results uncover a rich optimal-packing behavior, compared to that of other continuous families of particles previously studied. We present four structures as candidates for the optimal packing at different values of the parameter, providing an atlas of crystal structures which might be observed in systems of nano-particles with tetrahedral symmetry.
CALYPSO: A method for crystal structure prediction
NASA Astrophysics Data System (ADS)
Wang, Yanchao; Lv, Jian; Zhu, Li; Ma, Yanming
We have developed a software package CALYPSO (Crystal structure AnaLYsis by Particle Swarm Optimization) to predict the energetically stable/metastable crystal structures of materials at given chemical compositions and external conditions (e.g., pressure). The CALYPSO method is based on several major techniques (e.g. particle-swarm optimization algorithm, symmetry constraints on structural generation, bond characterization matrix on elimination of similar structures, partial random structures per generation on enhancing structural diversity, and penalty function, etc.) for global structural minimization from scratch. All of these techniques have been demonstrated to be critical to the prediction of global stable structure. We have implemented these techniques into the CALYPSO code. Testing of the code on many known and unknown systems shows high efficiency and the highly successful rate of this CALYPSO method [Y. Wang, J. Lv, L. Zhu, Y. Ma, Phys. Rev. B 82 (2010) 094116] [29]. In this paper, we focus on descriptions of the implementation of CALYPSO code and why it works.
Photonic crystal devices formed by a charged-particle beam
S. Y. Lin; H. W. P. Koops
A photonic crystal device and method are disclosed. The photonic crystal device comprises a substrate with at least one photonic crystal formed thereon by a charged-particle beam deposition method. Each photonic crystal comprises a plurality of spaced elements having a composition different from the substrate, and may further include one or more impurity elements substituted for spaced elements. Embodiments of
Photonic crystal devices formed by a charged-particle beam
Shawn-Yu Lin; Hans W. P. Koops
A photonic crystal device and method. The photonic crystal device comprises a substrate with at least one photonic crystal formed thereon by a charged-particle beam deposition method. Each photonic crystal comprises a plurality of spaced elements having a composition different from the substrate, and may further include one or more impurity elements substituted for spaced elements. Embodiments of the present
Crystal structure refinement with SHELXL.
Sheldrick, George M
The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors. PMID:25567568
Crystal structure refinement with SHELXL
Sheldrick, George M.
The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as 'a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors. PMID:25567568
Crystal structure of fenpropathrin
Kang, Gihaeng; Jeon, Youngeun; Lee, Sangjin; Kim, Tae Ho
In the title compound [systematic name: cyano(3-phenoxyphenyl)methyl 2,2,3,3-tetramethylcyclopropanecarboxylate], C22H23NO3, which is the pyrethroid insecticide fenpropathrin, the dihedral angle between the cyclopropane ring plane and the carboxylate group plane is 88.25?(11)°. The dihedral angle between the benzene and phenyl rings in the phenoxybenzyl group is 82.99?(4)°. In the crystal, C—H?N hydrogen bonds and weak C—H?? interactions link adjacent molecules, forming loop chains along the b-axis direction. PMID:25553036
Crystallization of Brownian Particles in a Pyramidal Pit by a Uniform External Force
NASA Astrophysics Data System (ADS)
Kanatsu, Youhei; Sato, Masahide
We carry out Brownian dynamics simulations and study the crystallization of particles in an inverse pyramidal-shaped container induced by an external force. Owing to the side walls of the container, the face-centered cubic (fcc) structure is mainly formed. In the bulk, both disordered solidlike particles and hexagonal close-packed (hcp) structured particles are hardly formed. These two types of particle appear near the central axis of the container. Their numbers increase with increasing strength of the external force.
Photonic Crystal Laser-Driven Accelerator Structures
Cowan, Benjamin M.
Laser-driven acceleration holds great promise for significantly improving accelerating gradient. However, scaling the conventional process of structure-based acceleration in vacuum down to optical wavelengths requires a substantially different kind of structure. We require an optical waveguide that (1) is constructed out of dielectric materials, (2) has transverse size on the order of a wavelength, and (3) supports a mode with speed-of-light phase velocity in vacuum. Photonic crystals---structures whose electromagnetic properties are spatially periodic---can meet these requirements. We discuss simulated photonic crystal accelerator structures and describe their properties. We begin with a class of two-dimensional structures which serves to illustrate the design considerations and trade-offs involved. We then present a three-dimensional structure, and describe its performance in terms of accelerating gradient and efficiency. We discuss particle beam dynamics in this structure, demonstrating a method for keeping a beam confined to the waveguide. We also discuss material and fabrication considerations. Since accelerating gradient is limited by optical damage to the structure, the damage threshold of the dielectric is a critical parameter. We experimentally measure the damage threshold of silicon for picosecond pulses in the infrared, and determine that our structure is capable of sustaining an accelerating gradient of 300 MV/m at 1550 nm. Finally, we discuss possibilities for manufacturing these structures using common microfabrication techniques.
Crystal structure of chlorfluazuron.
Cho, Seonghwa; Kim, Jineun; Lee, Sangjin; Kim, Tae Ho
The title compound (systematic name: 1-{3,5-di-chloro-4-[3-chloro-5-(tri-fluoro-meth-yl)pyridin-2-yl-oxy]phen-yl}-3-(2,6-difluoro-benzo-yl)urea), C20H9Cl3F5N3O3, is a benzoyl-phenyl-urea insecticide. The dihedral angles between the planes of the central di-chloro-phenyl and the terminal di-fluoro-phenyl and chloro-pyridyl rings are 79.51?(6) and 78.84 6)°, respectively. In the crystal, pairs of N-H?O hydrogen bonds link adjacent mol-ecules, forming R 2 (2)(8) inversion dimers. In addition, the dimers are linked by short F?Cl [3.1060?(16)?Å] and Cl?Cl [3.2837?(7)?Å] contacts, as well as weak inter-molecular ?-? inter-actions [ring centroid separation = 3.6100?(11) and 3.7764?(13)?Å], resulting in a two-dimensional architecture parallel to (111). PMID:25705506
Crystal structure of chlorfluazuron
Cho, Seonghwa; Kim, Jineun; Lee, Sangjin; Kim, Tae Ho
The title compound (systematic name: 1-{3,5-dichloro-4-[3-chloro-5-(trifluoromethyl)pyridin-2-yloxy]phenyl}-3-(2,6-difluorobenzoyl)urea), C20H9Cl3F5N3O3, is a benzoylphenylurea insecticide. The dihedral angles between the planes of the central dichlorophenyl and the terminal difluorophenyl and chloropyridyl rings are 79.51?(6) and 78.84 6)°, respectively. In the crystal, pairs of N—H?O hydrogen bonds link adjacent molecules, forming R 2 2(8) inversion dimers. In addition, the dimers are linked by short F?Cl [3.1060?(16)?Å] and Cl?Cl [3.2837?(7)?Å] contacts, as well as weak intermolecular ?–? interactions [ring centroid separation = 3.6100?(11) and 3.7764?(13)?Å], resulting in a two-dimensional architecture parallel to (111). PMID:25705506
Crystal structure of difenoconazole
Cho, Seonghwa; Kang, Gihaeng; Lee, Sangjin; Kim, Tae Ho
In the title compound difenoconazole [systematic name: 1-({2-[2-chloro-4-(4-chlorophenoxy)phenyl]-4-methyl-1,3-dioxolan-2-yl}methyl)-1H-1,2,4-triazole], C19H17Cl2N3O3, the dihedral angle between the planes of the 4-chlorophenyl and 2-chlorophenyl rings is 79.34?(9)°, while the dihedral angle between the planes of the triazole ring and the dioxolanyl group is 59.45?(19)°. In the crystal, pairs of C—H?N hydrogen bonds link adjacent molecules, forming dimers with R 2 2(6) loops. In addition, the dimers are linked by C—H?O hydrogen bonds, resulting in a three-dimensional architecture. Disorder was modeled for one C atom of the dioxolanyl group over two sets of sites with an occupancy ratio of 0.566?(17):0.434?(17). PMID:25484812
The crystal structure of katayamalite
Toshio KATO; Nobuhide MURAKAMI
The crystal structure of katayamalite has been determined by Patterson method and refined by the least-squares method using single crystal diffractometer data, giving R = 0.057 for 5785 reflections. Formula: (K,Na)Li.Ca,(Ti,Fe'+,Mn)2(Si60'8).(OH,F)2' Cell dimensions: a 9.721(2), b 16.923(3), c 19.942(3)A, a 91.43(10t, iJ 104.15(11t, 'Y 89.94(10t, space group Cl, Z = 4; or a 9.763(2), b 9.721(2), c 19.942(3)A, a 104.15(11t,
Crystal structures of tungsten disulfide and diselenide
NASA Astrophysics Data System (ADS)
Schutte, W. J.; De Boer, J. L.; Jellinek, F.
The crystal structures of the 2 H- and 3 R-forms of WS 2 have been refined from single-crystal data. The results are summarized and the interatomic distances are compared with those in related compounds.
Crystal structures of tungsten disulfide and diselenide
W. J. Schutte; J. L. de Boer; F. Jellinek
The crystal structures of the 2H- and 3R-forms of WS2 have been refined from single-crystal data. The results are summarized and the interatomic distances are compared with those in related compounds.
Crystal structure of lignin peroxidase
Edwards, S.L. (Center for Advanced Research in Biotechnology, Rockville, MD (United States) National Institutes of Health, Bethesda, MD (United States)); Raag, R. (Center for Advanced Research in Biotechnology, Rockville, MD (United States)); Wariishi, Hiroyuki; Gold, M.H. (Oregon Graduate Institute of Science and Technology, Beaverton (United States)); Poulos, T.L. (Center for Advanced Reseaarch in Biotechnology, Rockville, MD (United States) Univ. of California, Irvine (United States))
The crystal structure of lignin peroxidase (LiP) from the basidiomycete Phanerochaete chrysosporium has been determined to 2.6 [Angstrom] resolution by using multiple isomorphous replacement methods and simulated annealing refinement. Of the 343 residues, residues 3-335 have been accounted for in the electron density map, including four disulfide bonds. The overall three-dimensional structure is very similar to the only other peroxidase in this group for which a high-resolution crystal structure is available, cytochrome c peroxidase, despite the fact that the sequence identity is only [approx]20%, LiP has four disulfide bonds, while cytochrome c peroxidase has none, and Lip is larger (343 vs. 294 residues). The basic helical fold and connectivity defined by 11 helical segments with the heme sandwiched between the distal and proximal helices found in cytochrome c peroxidase is maintained in LiP. Both enzymes have a histidine as a proximal heme ligand, which is hydrogen bonded to a buried aspartic acid side chain. The distal or peroxide binding pocket also is similar, including the distal arginine and histidine. The most striking difference is that, whereas cytochrome c peroxidase has tryptophans contacting the distal and proximal heme surfaces, LiP has phenylalanines. This in part explains why, in the reaction with peroxides, cytochrome c peroxidase forms an amino acid-centered free radical, whereas LiP forms a porphyrin [pi] cation radical. 42 refs., 4 figs., 2 tabs.
Crystal Structure Effect on Electrical Properties of Ysz Ceramics
NASA Astrophysics Data System (ADS)
Zhang, Chunxia; Gong, Shengkai; Zhou, Chungen; Xu, Huibin
YSZ samples were prepared by Plasma Spray (PS) and Electron Beam Physical Vapor Deposition (EB-PVD) respectively. Microstructure and morphology were observed by SEM and XRD. Grain size of PS-YSZ was non-uniform caused by the inclusion of nano particle by molten particle and column crystal structure was observed for EB-PVD-YSZ. The Arrhenius plots of two samples were graphed by analysis of the measurement results of AC impedance spectra. The conductive mechanisms for EB-PVD and PS YSZ were different due to the crystal structure.
Structural Dynamics of the Vault Ribonucleoprotein Particle
NASA Astrophysics Data System (ADS)
Casañas, Arnau; Querol, Jordi; Fita, Ignasi; Verdaguer, Núria
Vaults are ubiquitous, highly conserved, 13 MDa ribonucleoprotein particles, involved in a diversity of cellular processes, including multidrug resistance, transport mechanisms and signal transmission. There are between 104 and 106 vault particles per mammalian cell and they do not trigger autoimmunity. The vault particle shows a hollow barrel-shaped structure organized in two identical moieties, each consisting of 39 copies of the major vault protein (MVP). Other data indicated that vault halves can dissociate at acidic pH. The high resolution, crystal structure of the of the seven N-terminal domains (R1-R7) of MVP, forming the central vault barrel, together with that of the native vault particle (solved at 8 Å resolution), revealed the interactions governing vault association and suggested a pH-dependent mechanism for a reversible dissociation induced by low pH. Vault particles posses many features making them very promising vehicles for the delivery of therapeutic agents including self-assembly, 100 nm size range, emerging atomic-level structural information, natural presence in humans ensuring biocompability, recombinant production system, existing features for targeting species to the large lumen and a dynamic structure that may be controlled for manipulation of drug release kinetics. All these attributes provide vaults with enormous potential as a drug/gene delivery platform.
Isomorph invariance of the structure and dynamics of classical crystals
NASA Astrophysics Data System (ADS)
Albrechtsen, Dan E.; Olsen, Andreas E.; Pedersen, Ulf R.; Schrøder, Thomas B.; Dyre, Jeppe C.
This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles interacting via the Buckingham pair potential and via a purely repulsive pair potential diverging at a finite separation, an ortho-terphenyl molecular model crystal, and SPC/E hexagonal ice. Except for NaCl and ice, the crystals simulated all have isomorphs. Based on previous simulations of liquid models, we conjecture that crystalline solids with isomorphs include most or all formed by atoms or molecules interacting via metallic or van der Waals forces, whereas covalently bonded or hydrogen-bonded crystals are not expected to have isomorphs; crystals of ions or dipolar molecules constitute a limiting case for which isomorphs are only expected when the Coulomb interactions are relatively weak. We briefly discuss the consequences of the findings for theories of melting and crystallization.
Simulations of Photonic Crystal and Dielectric Structures
Werner, G. R. [Center for Integrated Plasma Studies, University of Colorado, Boulder, CO 80309 (United States)
Dielectric materials and photonic crystal structures have electromagnetic properties that could potentially offer great benefits for accelerators. Computer simulation plays a critical role in designing, understanding, and optimizing these structures, especially the non-intuitive photonic crystal structures for which there is no relevant zeroth-order analytic model.
Binary hard-sphere crystals with the cesium chloride structure
NASA Astrophysics Data System (ADS)
Schofield, A. B.
The possibility of binary hard-sphere colloids crystallizing with the cesium chloride (CsCl) structure was examined experimentally using poly (methyl methacrylate) particles dispersed in organic solvents. Towards this end, two dispersions were prepared that contained particles with a radius ratio ?=RB/RA, where A refers to the large particles and B the small, of 0.736. This is close to the optimum ratio of 0.732 at which this structure is predicted to form as determined by space-filling calculations. The phases found within the binary mixture were examined using laser light crystallography and scanning electromicroscopy, and some were shown to have the CsCl structure. Over a period of time some of the CsCl crystals disappeared indicating that they were metastable and that this structure may not be the most enduring phase at this size ratio.
Formation of a Columnar Liquid Crystal in a Simple One-Component System of Particles
Alfredo Metere; Tomas Oppelstrup; Sten Sarman; Mikhail Dzugutov
We report a molecular dynamics simulation demonstrating that a columnar liquid crystal, commonly formed by disc-shaped molecules, can be formed by identical particles interacting via a spherically symmetric potential. Upon isochoric cooling from a low-density isotropic liquid state the simulated system performed a weak first order phase transition which produced a liquid crystal phase composed of parallel particle columns arranged in a hexagonal pattern in the plane perpendicular to the column axis. The particles within columns formed a liquid structure and demonstrated a significant intracolumn diffusion. Further cooling resulted in another first-order transition whereby the column structure became periodically ordered in three dimensions transforming the liquid-crystal phase into a crystal. This result is the first observation of a liquid crystal formation in a simple one-component system of particles. Its conceptual significance is in that it demonstrated that liquid crystals that have so far only been produced in systems of anisometric molecules, can also be formed by mesoscopic soft-matter and colloidal systems of spherical particles with appropriately tuned interatomic potential.
New crystal structure maps for intermetallic compounds
NASA Astrophysics Data System (ADS)
Harada, Yoshihisa; Morinaga, Masahiko; Saito, Jun-ichi; Takagi, Yasuharu
New crystal structure maps have been proposed on the basis of the 0953-8984/9/38/008/img6 molecular orbital calculations of electronic structures. Two electronic parameters have been introduced and employed as new parameters for the classification of crystal structures. One is the bond order and the other is the d-orbital energy level of elements. Both of them change following the position of elements in the periodic table. With these parameters crystal structure maps have been constructed for aluminides, silicides, and some transition-metal-based compounds. There is a clear separation of the crystal structures on the maps. These maps are found to be applicable to the prediction of crystal structures not only for binary compounds but also for ternary compounds. The possibilities of structural modification of 0953-8984/9/38/008/img7 and 0953-8984/9/38/008/img8 by alloying are also discussed with the aid of these maps.
Crystal Structure of the Carboxyltransferase Domain of
Tong, Liang
Crystal Structure of the Carboxyltransferase Domain of AcetylÂCoenzyme A Carboxylase Hailong Zhang, Zhiru Yang,* Yang Shen,* Liang Tong AcetylÂcoenzyme A carboxylases (ACCs) are required determined the crystal structure of the free enzyme and the coenzyme A complex of yeast CT at 2.7 angstrom
Crystal structure analysis of intermetallic compounds
NASA Technical Reports Server (NTRS)
Conner, R. A., Jr.; Downey, J. W.; Dwight, A. E.
Study concerns crystal structures and lattice parameters for a number of new intermetallic compounds. Crystal structure data have been collected on equiatomic compounds, formed between an element of the Sc, Ti, V, or Cr group and an element of the Co or Ni group. The data, obtained by conventional methods, are presented in an easily usable tabular form.
Photonic crystal devices formed by a charged-particle beam
Lin, Shawn-Yu (Albuquerque, NM); Koops, Hans W. P. (Ober-Ramstadt, DE)
A photonic crystal device and method. The photonic crystal device comprises a substrate with at least one photonic crystal formed thereon by a charged-particle beam deposition method. Each photonic crystal comprises a plurality of spaced elements having a composition different from the substrate, and may further include one or more impurity elements substituted for spaced elements. Embodiments of the present invention may be provided as electromagnetic wave filters, polarizers, resonators, sources, mirrors, beam directors and antennas for use at wavelengths in the range from about 0.2 to 200 microns or longer. Additionally, photonic crystal devices may be provided with one or more electromagnetic waveguides adjacent to a photonic crystal for forming integrated electromagnetic circuits for use at optical, infrared, or millimeter-wave frequencies.
Crystal growth, spectral, structural and optical studies of ?-conjugated stilbazolium crystal: 4-Bromobenzaldehyde-4?-N?-methylstilbazolium tosylate
NASA Astrophysics Data System (ADS)
Krishna Kumar, M.; Sudhahar, S.; Bhagavannarayana, G.; Mohan Kumar, R.
Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4?-N?-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from 1H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (0 0 1) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (?) and energy band gap (Eg) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser.
Crystal growth, spectral, structural and optical studies of ?-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.
Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R
Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (?) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser. PMID:24531108
Self-organized assemblies of colloidal particles obtained from an aligned chromonic liquid crystal dispersion.
Zimmermann, Natalie; Jünnemann-Held, Gisela; Collings, Peter J; Kitzerow, Heinz-S
The behavior of mono-disperse colloidal particles in a chromonic liquid crystal was investigated. Poly(methyl methacrylate) spherical particles with three different functionalizations, with and without surface charges, were utilized in the nematic and columnar phases of disodium cromoglycate solutions. The nematic phase was completely aligned parallel to the glass substrates by a simple rubbing technique, and the columnar phase showed regions of similar alignment. The behavior of the colloidal particles in the chromonic liquid crystal depended critically on the functionality, with bromine functionalized particles not dispersing at all, and cationic trimethylammonium and epoxy functionalized particles dispersing well in the isotropic phase of the liquid crystal. At the transition to the nematic and especially the columnar phase, the colloidal particles were expelled into the remaining isotropic phase. Since the columnar phase grew in parallel ribbons, the colloidal particles ended up in chain-like assemblies. Such behavior opens the possibility of producing patterned assemblies of colloidal particles by taking advantage of the self-organized structure of chromonic liquid crystals. PMID:25589441
Draft Crystal Structure of the Vault Shell at 9-Å Resolution
Daniel H Anderson; Valerie A Kickhoefer; Stuart A Sievers; Leonard H Rome; David Eisenberg
Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed
Old and New Particle Structure
NASA Astrophysics Data System (ADS)
Wolff, Milo
This discussion will compare the old concept of the structure of matter with Nature. How did the ancient model affect scientific thinking leading science down blind pathways producing paradoxes? What instead is the simple logic and surprising consequences of Nature's choice, the Wave Structure of Matter? The old concept due to the Greek Democritus was a discrete particle like a grain of sand. It has survived almost unchanged. Even today, we prefer to regard mathematical entities, the 'photon' and quarks, as tiny grains. Only recently has the wave structure of particles been determined. Human emotions prefer explanations that agree with personal experience. We know that atomic sizes are much smaller than our senses can reveal, but most people, including scientists, prefer to imagine the electron like a baseball or a bullet. It is not. The quantum Wave Structure of Matter reveals the origin of the Natural laws, and opens a door to research in chemistry, biology, energy, and micro-electronics. Why had this not been found before? Because the Democritus particle agreed with emotions. Few people looked elsewhere. Modern structure is at www.QuantumMatter.com
Design of a Highly Focused Photonic Crystal Lens Using Boolean Particle Swarm Optimization
Alireza Marandi; Farzaneh Afshinmanesh; Poman P. M. So
The Boolean particle swarm optimization technique in conjunction with the scattering matrix method is proposed to design two dimensional photonic crystal based structures. The potential of this approach is illustrated in a lens design problem. The resulting lens has a superb F-number of 0.39. Furthermore, the effectiveness of this method in comparison with a genetic algorithm based optimization procedure is
Introduction to Crystal Structure: Bond Strength
NSDL National Science Digital Library
Dexter Perkins
This exercise is designed to familiarize students with some basic crystal structures The exercise helps students fully understand the nature and significance of ionic bonds and Pauling's second rule It also builds a bit on Pauling's first rule (radius ratio principle) It is one of several related activities, all of which are intended to help students understand the nature of ionic crystals
Metal oxide superconducting powder comprised of flake-like single crystal particles
Capone, D.W.; Dusek, J.
Powder of a ceramic superconducting material is synthesized such that each particle of the powder is a single crystal having a flake-like, nonsymmetric morphology such that the c-axis is aligned parallel to the short dimension of the flake. Nonflake powder is synthesized by the normal methods and is pressed into pellets or other shapes and fired for excessive times to produce a coarse grained structure. The fired products are then crushed and ground producing the flake-like powder particles which exhibit superconducting characteristics when aligned with the crystal lattice. 3 figs.
Metal oxide superconducting powder comprised of flake-like single crystal particles
Capone, Donald W. (Bolingbrook, IL); Dusek, Joseph (Downers Grove, IL)
Powder of a ceramic superconducting material is synthesized such that each particle of the powder is a single crystal having a flake-like, nonsymmetric morphology such that the c-axis is aligned parallel to the short dimension of the flake. Nonflake powder is synthesized by the normal methods and is pressed into pellets or other shapes and fired for excessive times to produce a coarse grained structure. The fired products are then crushed and ground producing the flake-like powder particles which exhibit superconducting characteristics when aligned with the crystal lattice.
Compact Couplers for Photonic Crystal Laser-Driven Accelerator Structures
Cowan, Benjamin; /Tech-X, Boulder; Lin, M.C.; /Tech-X, Boulder; Schwartz, Brian; /Tech-X, Boulder; Byer, Robert; /Stanford U., Phys. Dept.; McGuinness, Christopher; /Stanford U., Phys. Dept.; Colby, Eric; /SLAC; England, Robert; /SLAC; Noble, Robert; /SLAC; Spencer, James; /SLAC
Photonic crystal waveguides are promising candidates for laser-driven accelerator structures because of their ability to confine a speed-of-light mode in an all-dielectric structure. Because of the difference between the group velocity of the waveguide mode and the particle bunch velocity, fields must be coupled into the accelerating waveguide at frequent intervals. Therefore efficient, compact couplers are critical to overall accelerator efficiency. We present designs and simulations of high-efficiency coupling to the accelerating mode in a three-dimensional photonic crystal waveguide from a waveguide adjoining it at 90{sup o}. We discuss details of the computation and the resulting transmission. We include some background on the accelerator structure and photonic crystal-based optical acceleration in general.
Strategies for crystallizing a chromatin protein in complex with the nucleosome core particle
Makde, Ravindra D.; Tan, Song
The molecular details for how chromatin factors and enzymes interact with the nucleosome are critical to understand fundamental genetic processes including cell division and gene regulation. A structural understanding of such processes has been hindered by the difficulty producing diffraction quality crystals of chromatin proteins in complex with the nucleosome. We describe here the steps used to grow crystals of the 300 kDa RCC1 chromatin factor/nucleosome core particle complex which diffract to 2.9 Å resolution. These steps included both pre- and post-crystallization strategies potentially useful to other complexes. We screened multiple variant RCC1-nucleosome core particle complexes assembled using different RCC1 homologs and deletion variants, and nucleosomes containing nucleosomal DNA with different sequences and lengths as well as histone deletion variants. We found that using RCC1 from different species produced different crystal forms of the RCC1-nucleosome complex consistent with key crystal packing interactions mediated by RCC1. Optimization of post-crystallization soaks to dehydrate the crystals dramatically improved the diffraction quality of the RCC1/nucleosome crystal from 5.0 to 2.9 Å resolution. PMID:23928047
Process to make structured particles
Knapp, Angela Michelle; Richard, Monique N; Luhrs, Claudia; Blada, Timothy; Phillips, Jonathan
Disclosed is a process for making a composite material that contains structured particles. The process includes providing a first precursor in the form of a dry precursor powder, a precursor liquid, a precursor vapor of a liquid and/or a precursor gas. The process also includes providing a plasma that has a high field zone and passing the first precursor through the high field zone of the plasma. As the first precursor passes through the high field zone of the plasma, at least part of the first precursor is decomposed. An aerosol having a second precursor is provided downstream of the high field zone of the plasma and the decomposed first material is allowed to condense onto the second precursor to from structured particles.
ICSD Web: the Inorganic Crystal Structure Database
NSDL National Science Digital Library
Hewat Alan
This site contains a free demonstration version of the Inorganic Crystal Structure Database. This database contains a 3325 structure subset of the 76,480 inorganic structures as of 2004. The demo version can be queried and accessed by a web-interface which allows multiple methods of searching, and the resulting crystal structures can then be viewed online (with the CHIME plug-in) or downloaded for viewing with other visualization software. Also included on the site are updates of bug fixes, conditions of use and prices, tips for displaying the structures, a gallery of images, a flash movie, and instructions for installing a ICSD server.
Formation of the structure of gold nanoclusters during crystallization
Gafner, Yu. Ya., E-mail: email@example.com; Goloven'ko, Zh. V.; Gafner, S. L. [Khakassian State University (Russian Federation)] [Khakassian State University (Russian Federation)
The structure formation in gold nanoparticles 1.6-5.0 nm in diameter is studied by molecular dynamics simulation using a tight-binding potential. The simulation shows that the initial fcc phase in small Au clusters transforms into other structural modifications as temperature changes. As the cluster size increases, the transition temperature shifts toward the melting temperature of the cluster. The effect of various crystallization conditions on the formation of the internal structure of gold nanoclusters is studied in terms of microcanonical and canonical ensembles. The stability boundaries of various crystalline isomers are analyzed. The obtained dependences are compared with the corresponding data obtained for copper and nickel nanoparticles. The structure formation during crystallization is found to be characterized by a clear effect of the particle size on the stability of a certain isomer modification. Nickel and copper clusters are shown to exhibit common features in the formation of their structural properties, whereas gold clusters demonstrate much more complex behavior.
Interaction between two spherical particles in a nematic liquid crystal
NASA Astrophysics Data System (ADS)
Fukuda, Jun-Ichi; Stark, Holger; Yoneya, Makoto; Yokoyama, Hiroshi
We numerically investigate the interaction between two spherical particles in a nematic liquid crystal mediated by elastic distortions in the orientational order. We pay attention to the cases where two particles with equal radii R0 impose rigid normal anchoring on their surfaces and carry a pointlike topological defect referred to as a hyperbolic hedgehog. To describe the geometry of our system, we use bispherical coordinates, which prove useful in the implementation of boundary conditions at the particle surfaces and at infinity. We adopt the Landau de Gennes continuum theory in terms of a second-rank tensor order parameter Qij for the description of the orientational order of a nematic liquid crystal. We also utilize an adaptive mesh refinement scheme that has proven to be an efficient way of dealing with topological defects whose core size is much smaller than the particle size. When the two "dipoles," composed of a particle and a hyperbolic hedgehog, are in parallel directions, the two-particle interaction potential is attractive for large interparticle distances D and proportional to D-3 as expected from the form of the dipole-dipole interaction, until the well-defined potential minimum at D?2.46 R0 is reached. For the antiparallel configuration with no hedgehogs between the two particles, the interaction potential is repulsive and behaves as D-2 for D?10 R0 , which is stronger than the dipole-dipole repulsion ( ˜ D-3 ) expected theoretically as an asymptotic behavior for large D .
Crystal-originated particles in germanium-doped Czochralski silicon crystal
Jiahe Chen; Deren Yang; Hong Li; Xiangyang Ma; Daxi Tian; Liben Li; Duainlin Que
Grown-in distribution and annealing behavior of crystal-originated particles (COPs) in Czochralski silicon (Cz-Si) wafer with germanium doping have been investigated. It was found that COPs with high density but small sizes were inclined to generate in germanium-doped Cz-Si (GCz-Si) wafer. The increase of boron atoms in Cz-Si crystal with the germanium doping could benefit the formation of COPs while the
Experimental studies of two-dimensional and three-dimensional structure in a crystallized dusty plasma
Goree, John
of strongly coupled interactions between plasma components, including those in- volving dust grains of the crystal structures formed by monodisperse polymer particles of 9.4 m diameter, in a rf plasma reactor
Pholcodine monohydrate: Crystal structure and polymorphism
NASA Astrophysics Data System (ADS)
Petruševski, Gjorgji; Zba?nik, Marija; Kajdžanoska, Marina; Ugarkovic, Sonja; Trim?eski, Vase; Kaitner, Branko; Jovanovski, Gligor; Makreski, Petre
The first crystal structure elucidation of pholcodine monohydrate, an important antitussive active pharmaceutical ingredient is reported herein. The studied compound crystallizes in the orthorhombic system in the space group P212121. Each H2O molecule is shared by two pholcodine molecules via three strong hydrogen bonds. The detailed crystallization screening from several different organic solvents afforded single crystals with various quality, all exhibiting prism-to-needlelike micro morphology. The investigation of the obtained single crystals by means of several physico-chemical, solid-state instrumental techniques (FT-IR, DSC, TG/DTG and XRPD) proved that pholcodine monohydrate exists in a single crystalline modification, identical to the commercial form of the compound.
Fabrication and characterization of non-Brownian particle-based crystals.
Lash, Melissa H; Fedorchak, Morgan V; Little, Steven R; McCarthy, Joseph J
Particle-based crystals have been explored in the literature for applications in molecular electronics, photonics, sensors, and drug delivery. However, much of the research on these crystals has been focused on particles of nano- and submicrometer dimensions (so-called colloidal crystals) with limited attention directed toward building blocks with dimensions ranging from tens to hundreds of micrometers. This can be attributed, in part, to the fact that the underlying thermal effects in these larger systems typically cannot naturally overcome kinetic barriers at the meso- and macroscales so that many of the methods used for nanoscale particle assembly cannot be directly applied to larger components, as they become kinetically arrested in nonequilibrium states. In this work, ultrasonic agitation is being explored as a means of allowing large, non-Brownian microparticles (18-750 ?m) to overcome the kinetic barriers to packing in the creation of close-packed, highly ordered, crystalline structures. In addition, we study how the energy input affects bulk particle behavior and describe several new ways to characterize particle-based crystals made from microparticles. PMID:24983125
Amphidynamic Crystals: Structural Blueprints for Molecular Machines
Steven D. Karlen; Miguel A. Garcia-Garibay
By considering the relation between molecular structure, molecular dynamics, and phase order,\\u000a we suggest that certain structures should be able to make up supramolecular assemblies with structurally\\u000a programmed molecular dynamics. Given that the simplest members of these structures should have the\\u000a elements required to form a rigid lattice with moving parts, we propose the term amphidynamic\\u000a crystals to describe them. We
Natural photonic crystals: formation, structure, function
NASA Astrophysics Data System (ADS)
Bartl, Michael H.; Dahlby, Michael R.; Barrows, Frank P.; Richens, Zachary J.; Terooatea, Tommy; Jorgensen, Matthew R.
The structure and properties of natural photonic crystals are discussed using the colored scales of the beetle Lamprocyphus augustus as an example. While the exact mechanism behind the formation of these biopolymeric photonic structures has yet to be fully explored, similarities of these structures to intracellular cubic membrane architectures are introduced. Some crucial parameters behind the formation of cubic membranes are discussed. Using these insights, intracellular cubic membrane structures are transformed into an extracellular environment.
Photoluminescence of Eu 3 + : Y 2 O 3 as an indication of crystal structure and particle size in nanoparticles synthesized by flame spray pyrolysis
Dosi Dosev; Bing Guo; Ian M. Kennedy
Nanoparticles of europium-doped yttrium oxide (Eu:Y2O3) were synthesized by flame spray pyrolysis. The nanoparticles were separated by centrifugation into two size groups (5–60nm and 50–200nm), each characterized by laser induced fluorescence spectroscopy, Transmission Electron Microscopy (TEM) and X-ray Diffraction (XRD). The fluorescence spectra, the electron diffraction pattern, and the XRD pattern of the large particles were typical of the stable
Transformation of the snow crystal to a particle of ice
NASA Astrophysics Data System (ADS)
Guseva-Lozinski, Elena
To study the physical properties of snow under different meteorological conditions a mathematical model and numerical computer program were created and applied for some numerical modelling estimates. The non-linear mathematical model consists of partial differential equations and can be subdivided into a thermal part with phase changes in porous media, diffusion, structural transformation and mechanical parts. The model was applied to simulate the evolution of structural, thermal and mechanical parameters in a snow profile subject to meteorological parameters (air temperature and moisture, wind velocity, precipitation, density). The snow structure is very sensitive to the temporal variations of all external parameters: temperature, humidity, precipitation and wind-pumping. Snow deposited in cold weather conditions is transformed through densification, metamorphism and recrystallisation. Snow crystals have unstable shapes. The tendency for mass and heat to be redistributed through sublimation is to minimise the surface free energy. The result of these processes is to change the shape of a snow crystal to that of a sphere. The transformation of the initial singular stellar crystal to a number of small grains with the same mass as the original crystal is described mathematically. It gives the rates of the transformations. Based on this mathematical approach we can predict changes of the crystal shapes, number of crystals and other physical properties inside a snowpack subject to different meteorological conditions.
Crystal structure of plant photosystem I
Adam Ben-Shem; Felix Frolow; Nathan Nelson
Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4Å resolution. Its intricate structure shows
Building Crystal Structure Ball Models Using Pre-Drilled Templates: Sheet Structures, Tridymite, and Cristobalite
NSDL National Science Digital Library
Kurt Hollocher
This activity involves building crystal structure ball models in order to strengthen students' understanding of crystalline order, relative atomic size, atomic coordination, crystal chemistry, and crystal symmetry.
Data mining chemistry and crystal structure
NASA Astrophysics Data System (ADS)
Yang, Lusann W.
The availability of large amounts of data generated by high-throughput computing and experimentation has generated interest in the application of machine learning techniques to materials science. Machine learning of materials behavior requires the use of feature vectors that capture compositional or structural information influence a target property. We present methods for assessing the similarity of compositions, substructures, and crystal structures. Similarity measures are important for the classification and clustering of data points, allowing for the organization of data and the prediction of materials properties. The similarity functions between ions, compositions, substructures and crystal structure are based upon a data-mined probability with which two ions will substitute for each other within the same structure prototype. The composition similarity is validated via the prediction of crystal structure prototypes for oxides from the Inorganic Crystal Structure Database. It performs particularly well on the quaternary oxides, predicting the correct prototype within 5 guesses 90% of the time. The sustructural similarity is validated via the prediction of Li insertion sites in the oxides; it finds all of the Li sites with less than 8 incorrect guesses 90% of the time.
Phononic crystals of spherical particles: A tight binding approach
Mattarelli, M., E-mail: firstname.lastname@example.com [NiPS Laboratory, Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06100 Perugia (Italy); Secchi, M. [CMM - Fondazione Bruno Kessler, Via Sommarive 18, 38123 Trento (Italy) [CMM - Fondazione Bruno Kessler, Via Sommarive 18, 38123 Trento (Italy); Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy); Montagna, M. [Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy)] [Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy)
The vibrational dynamics of a fcc phononic crystal of spheres is studied and compared with that of a single free sphere, modelled either by a continuous homogeneous medium or by a finite cluster of atoms. For weak interaction among the spheres, the vibrational dynamics of the phononic crystal is described by shallow bands, with low degree of dispersion, corresponding to the acoustic spheroidal and torsional modes of the single sphere. The phonon displacements are therefore related to the vibrations of a sphere, as the electron wave functions in a crystal are related to the atomic wave functions in a tight binding model. Important dispersion is found for the two lowest phonon bands, which correspond to zero frequency free translation and rotation of a free sphere. Brillouin scattering spectra are calculated at some values of the exchanged wavevectors of the light, and compared with those of a single sphere. With weak interaction between particles, given the high acoustic impedance mismatch in dry systems, the density of phonon states consist of sharp bands separated by large gaps, which can be well accounted for by a single particle model. Based on the width of the frequency gaps, tunable with the particle size, and on the small number of dispersive acoustic phonons, such systems may provide excellent materials for application as sound or heat filters.
Crystal structure and chirality of natural floridoside.
Simon-Colin, Christelle; Michaud, François; Léger, Jean-Michel; Deslandes, Eric
The crystal structure and absolute configuration of natural floridoside (2-O-alpha-D-galactopyranosylglycerol) were determined by single-crystal X-ray diffraction analysis. The space group is orthorhombic P2(1)2(1)2(1) with Z=4, a=4.885(1), b=9.734(1), c=23.886(2) A at 296 +/- 2 K. The structure was solved by a direct method and refined to R=0.0351 from 1914 reflections of Cu Kalpha radiation. PMID:14572727
Critical single domain grain sizes in chains of interacting greigite particles: Implications for magnetosome crystals
NASA Astrophysics Data System (ADS)
Muxworthy, Adrian R.; Williams, Wyn; Roberts, Andrew P.; Winklhofer, Michael; Chang, Liao; Pósfai, Mihály
Magnetotactic bacteria contain chains of magnetically interacting crystals (magnetosomes), which aid navigation (magnetotaxis). To improve the efficiency of magnetotaxis, magnetosome crystals (which can consist of magnetite or greigite) should be magnetically stable single domain (SD) particles. Larger particles subdivide into nonuniform multidomain (MD) magnetic structures that produce weaker magnetic signals, while small SD particles become magnetically unstable due to thermal fluctuations and exhibit superparamagnetic (SP) behavior. In this study, we determined the stable SD range as a function of grain elongation and interparticle separation for chains of identical greigite grains using fundamental parameters recently determined for greigite. Interactions significantly increase the stable SD range. For example, for cube-shaped greigite grains the upper stable SD threshold size is increased from 107 nm for isolated grains to 204 nm for touching grains arranged in chains. The larger critical SD grain size for greigite means that, compared to magnetite magnetosomes, greigite magnetosomes can produce larger magnetic signals without the need for intergrain interactions.
Crystal structures and morphologies of fractionated milk fat in nanoemulsions.
Truong, Tuyen; Morgan, Garry P; Bansal, Nidhi; Palmer, Martin; Bhandari, Bhesh
The triacylglycerol (TAG) crystal structures and morphologies of fractionated milk lipids in nanoemulsions were investigated at 4°C. Droplet size (0.17 versus 1.20 ?m), lipid composition (stearin versus olein) and cooling rate (1 versus 10°C min(-1)) had an influence on the structural properties. Five crystal polymorphs (?, ?'1, ?'2, ?1, and ?2) were formed with either triple and/or double chain length structures in the solid phases of the emulsified systems. X-ray scattering peak intensities were reduced with the nanoemulsion particles. The internal structure of TAG exhibited stacking of individual lamellar layers (3.8-4.2 nm). Various anisometric shapes of fat nanoparticles were formed due to a highly sharp curvature of the nano-size droplets. The shape of olein nanoparticles was more polyhedral compared to the stearin. TAG crystals arranged in a planar-layered organisation at the slower cooling rate. These differences imply that the nanometric confinement of oil droplets modifies the fat crystal habit. PMID:25308656
Requirements for structure determination of aperiodic crystals
NASA Astrophysics Data System (ADS)
Li, Xiao-Ou; Stern, Edward A.; Ma, Yanjun
Using computer simulation, we compared the Patterson functions of one-dimensional (1D) randomly packed and quasiperiodic Fibonacci lattices with or without disorder, and a 2D Penrose lattice and random packing of pentagons (icosahedral glass model). Based on these comparisons, we derived some empirical guidelines for distinguishing ideal quasicrystals from aperiodic crystals with disorder using diffraction data. In contrast to periodic crystals, it is essential to include the background to obtain correct Patterson functions of the average structure since the background contains unresolved peaks. In particular, a Bragg peak scattering measurement cannot, in general, determine the structure of aperiodic crystals. Instead, a diffuse scattering measurement is required, which determines the absolute value of the diffraction background, in addition to the Bragg peaks. We further estimate that, dependent upon the disorder present, it is necessary to include up to 75% of the total diffracted intensity in any analysis.
Surface-induced structures in nematic liquid crystal colloids.
Chernyshuk, S B; Tovkach, O M; Lev, B I
We predict theoretically the existence of a class of colloidal structures in nematic liquid crystal (NLC) cells, which are induced by surface patterns on the plates of the cell (like cells with UV-irradiated polyamide surfaces using micron sized masks in front of the cell). These bulk structures arise from nonuniform boundary conditions for the director distortions at the confining surfaces. In particular, we demonstrate that quadrupole spherical particles (like spheres with boojums or Saturn-ring director configurations) form a square lattice inside a planar NLC cell, which has checkerboard patterns on both its plates. PMID:25215675
Surface induced structures in nematic liquid crystal colloids
S. B. Chernyshuk; O. M. Tovkach; B. I. Lev
We predict theoretically the existence of a class of colloidal structures in nematic liquid crystal (NLC) cells, which are induced by surface patterns on the plates of the cell (like cells with UV-irradiated polyimide surfaces using micron size masks). These bulk structures arise from non-zero boundary conditions for the director distortions at the confining surfaces. In particular, we demonstrate that quadrupole spherical particles (like spheres with boojums or Saturn-ring director configurations) form a square lattice inside a planar NLC cell, which has checkerboard patterns on both its plates.
Shear induced structures in crystallizing cocoa butter
NASA Astrophysics Data System (ADS)
Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.
Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.
Crystal structure of the anthrax lethal factor
Andrew D. Pannifer; Thiang Yian Wong; Robert Schwarzenbacher; Martin Renatus; Carlo Petosa; Jadwiga Bienkowska; D. Borden Lacy; R. John Collier; Stephen H. Leppla; Philip Hanna; Robert C. Liddington
Lethal factor (LF) is a protein (relative molecular mass 90,000) that is critical in the pathogenesis of anthrax. It is a highly specific protease that cleaves members of the mitogen-activated protein kinase kinase (MAPKK) family near to their amino termini, leading to the inhibition of one or more signalling pathways. Here we describe the crystal structure of LF and its
MURPHY, JAMES E [University of Nevada, Reno] [University of Nevada, Reno
The objective of this research project is to produce single crystal niobium (Nb) tubes for use as particle accelerator cavities for the Fermi laboratory's International Linear Collider project. Single crystal Nb tubes may have superior performance compared to a polycrystalline tubes because the absence of grain boundaries may permit the use of higher accelerating voltages. In addition, Nb tubes that are subjected to the high temperature, high vacuum crystallization process are very pure and well annealed. Any impurity with a significantly higher vapor pressure than Nb should be decreased by the relatively long exposure at high temperature to the high vacuum environment. After application of the single crystal process, the surfaces of the Nb tubes are bright and shiny, and the tube resembles an electro polished Nb tube. For these reasons, there is interest in single crystal Nb tubes and in a process that will produce single crystal tubes. To convert a polycrystalline niobium tube into a single crystal, the tube is heated to within a few hundred ?C of the melting temperature of niobium, which is 2477 ?C. RF heating is used to rapidly heat the tube in a narrow zone and after reaching the operating temperature, the hot zone is slowly passed along the length of the tube. For crystallization tests with Nb tubes, the traverse rate was in the range of 1-10 cm per hour. All the crystallization tests in this study were performed in a water-cooled, stainless steel chamber under a vacuum of 5 x10-6 torr or better. In earliest tests of the single crystal growth process, the Nb tubes had an OD of 1.9 cm and a wall thickness of 0.15 mm. With these relatively small Nb tubes, the single crystal process was always successful in producing single crystal tubes. In these early tests, the operating temperature was normally maintained at 2200 ?C, and the traverse rate was 5 cm per hour. In the next test series, the Nb tube size was increased to 3.8 cm OD and the wall thickness was increased 0.18 mm and eventually to 0.21 mm. Again, with these larger tubes, single crystal tubes were usually produced by the crystallization process. The power supply was generally operated at full output during these tests, and the traverse rate was 5 cm per hour. In a few tests, the traverse rate was increased to 10 cm per hour, and at the faster traverse rate, single crystal growth was not achieved. In these tests with a faster traverse rate, it was thought that the tube was not heated to a high enough temperature to achieve single crystal growth. In the next series of tests, the tube OD was unchanged at 3.8 cm and the wall thickness was increased to 0.30 mm. The increased wall thickness made it difficult to reach an operating temperature above 2,000 ?C, and although the single crystal process caused a large increase in the crystal grains, no single crystal tubes were produced. It was assumed that the operating temperature in these tests was not high enough to achieve single crystal growth. In FY 2012, a larger power supply was purchased and installed. With the new power supply, temperatures above the melting point of Nb were easily obtained regardless of the tube thickness. A series of crystallization tests was initiated to determine if indeed the operating temperature of the previous tests was too low to achieve single crystal growth. For these tests, the Nb tube OD remained at 3.8 cm and the wall thickness was 0.30 mm. The first test had an operating temperature of 2,000 ?C. and the operating temperature was increased by 50 ?C increments for each successive test. The final test was very near the Nb melting temperature, and indeed, the Nb tube eventually melted in the center of the tube. These tests showed that higher temperatures did yield larger grain sizes if the traverse rate was held constant at 5 cm per hour, but no single crystal tubes were produced even at the highest operating temperature. In addition, slowing the traverse rate to as low as 1 cm per hour did not yield a single crystal tube regardless of operating temperature. At this time, it
Crystal structure of a plectonemic RNA supercoil
Stagno, Jason R.; Ma, Buyong; Li, Jess; Altieri, Amanda S.; Byrd, R. Andrew; Ji, Xinhua (NCI); (Maryland)
Genome packaging is an essential housekeeping process in virtually all organisms for proper storage and maintenance of genetic information. Although the extent and mechanisms of packaging vary, the process involves the formation of nucleic-acid superstructures. Crystal structures of DNA coiled coils indicate that their geometries can vary according to sequence and/or the presence of stabilizers such as proteins or small molecules. However, such superstructures have not been revealed for RNA. Here we report the crystal structure of an RNA supercoil, which displays one level higher molecular organization than previously reported structures of DNA coiled coils. In the presence of an RNA-binding protein, two interlocking RNA coiled coils of double-stranded RNA, a 'coil of coiled coils', form a plectonemic supercoil. Molecular dynamics simulations suggest that protein-RNA interaction is required for the stability of the supercoiled RNA. This study provides structural insight into higher order packaging mechanisms of nucleic acids.
A hierarchical structure for apatite crystals
Sergey V. Dorozhkin
Based on the experimental results taken from the references, a reasonable hierarchical structure of apatite (both fluorapatite and hydroxyapatite) crystals has been proposed for the first time. The structure consists of four levels of the hierarchy: the smallest level is made of single unit-cells and\\/or Posner's clusters with the linear dimensions slightly below 1 nm, the second level comprises X-ray
Slip flow through colloidal crystals of varying particle diameter.
Rogers, Benjamin J; Wirth, Mary J
Slip flow of water through silica colloidal crystals was investigated experimentally for eight different particle diameters, which have hydraulic channel radii ranging from 15 to 800 nm. The particle surfaces were silylated to be low in energy, with a water contact angle of 83°, as determined for a silylated flat surface. Flow rates through centimeter lengths of colloidal crystal were measured using a commercial liquid chromatograph for accurate comparisons of water and toluene flow rates using pressure gradients as high as 10(10) Pa/m. Toluene exhibited no-slip Hagen-Poiseuille flow for all hydraulic channel radii. For water, the slip flow enhancement as a function of hydraulic channel radius was described well by the expected slip flow correction for Hagen-Poiseuille flow, and the data revealed a constant slip length of 63 ± 3 nm. A flow enhancement of 20 ± 2 was observed for the smallest hydraulic channel radius of 15 nm. The amount of slip flow was found to be independent of shear rate over a range of fluid velocities from 0.7 to 5.8 mm/s. The results support the applicability of the slip flow correction for channel radii as small as 15 nm. The work demonstrates that packed beds of submicrometer particles enable slip flow to be employed for high-volume flow rates. PMID:23237590
Crystallization and Melting Behavior of Nanopolymeric Particles Containing Single or a Few Chains
Samples of nanopolymeric particles, each containing a single chain or a few chains, were prepared by a freeze-drying method from dilute solutions of isotactic polystyrene (iPS) in benzene. Thermal analysis of the particle samples revealed that the cold crystallization temperature greatly decreases and the crystallization rate remarkably increases as the solution concentration decreases. The increase in crystallization rate can be
Predicting Polymeric Crystal Structures by Evolutionary Algorithms
Qiang Zhu; Vinit Sharma; Artem R Oganov; Rampi Ramprasad
The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures for a given chemical composition. Here we extend this method to predict the crystal structure of polymers by performing constrained evolutionary search, where each monomeric unit is treated as one or several building blocks with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings using these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely polyethylene (PE), polyacetylene (PA), poly(glycolic acid) (PGA), poly(vinyl chloride) (PVC), poly(oxymethylene) (POM), poly(phenylene oxide) (PPO), and poly (p-phenylene sulfide) (PPS). By fixing the orientation of polymeric chains, this method can be further extended to predict all polymorphs of poly(vinylidene fluoride) (PVDF), and the complex linear polymer crystals, such as nylon-6 and cellulose. The excellent agreement between predicted crystal structures and experimentally known structures assures a major role of this approach in the efficient design of the future polymeric materials.
Structure of nucleosome core particles of chromatin
J. T. Finch; L. C. Lutter; D. Rhodes; R. S. Brown; B. Rushton; M. Levitt; A. Klug
Crystals have been obtained of nucleosome cores and analysed by X-ray diffraction and electron microscopy. The core is a flat particle of dimensions about 110 × 110 × 57 Å, somewhat wedge shaped, and strongly divided into two `layers', consistent with the DNA being wound into about 1¾ turns of a fiat superhelix of a pitch about 28 Å. The
Crystal structure and magnetic structure of TbOOH
A. Nørlund Christensen; S. Quézel
The monoclinic modification of terbium oxide hydroxide, TbOOH, was prepared using hydrothermal technique. The crystal structure was investigated by three-dimensional single-crystal X-ray analysis and was refined to a conventional R-value of 8.1%. The space group is P21\\/m, No. 11, with a = 6.04 Å, b = 3.69 Å, c = 4.33 Å, and beta = 109.0°. The terbium atom is
Structure of the nucleosome core particle at 7 Å resolution
T. J. Richmond; J. T. Finch; B. Rushton; D. Rhodes; A. Klug
The crystal structure of the nucleosome core particle has been solved to 7 Å resolution. The right-handed B-DNA superhelix on the outside contains several sharp bends and makes numerous interactions with the histone octamer within. The central turn of superhelix and H3 . H4 tetramer have dyad symmetry, but the H2A . H2B dimers show departures due to interparticle associations.
5.841 Crystal Structure Refinement, Fall 2006
Mueller, Peter
This course in crystal structure refinement examines the practical aspects of crystal structure determination from data collection strategies to data reduction and basic and advanced refinement problems of organic and ...
5.067 Crystal Structure Refinement, Fall 2007
Mueller, Peter
This course in crystal structure refinement examines the practical aspects of crystal structure determination from data collection strategies to data reduction and basic and advanced refinement problems of organic and ...
Nonviscous motion of a slow particle in a dust crystal under microgravity conditions.
Zhukhovitskii, D I; Fortov, V E; Molotkov, V I; Lipaev, A M; Naumkin, V N; Thomas, H M; Ivlev, A V; Schwabe, M; Morfill, G E
Subsonic motion of a large particle moving through the bulk of a dust crystal formed by negatively charged small particles is investigated using the PK-3 Plus laboratory onboard the International Space Station. Tracing the particle trajectories shows that the large particle moves almost freely through the bulk of the plasma crystal, while dust particles move along characteristic ?-shaped pathways near the large particle. In the hydrodynamic approximation, we develop a theory of nonviscous dust particle motion about a large particle and calculate particle trajectories. Good agreement with experiment validates our approach. PMID:23005544
Crystal structure of riboflavin synthase
Liao, D.-I.; Wawrzak, Z.; Calabrese, J.C.; Viitanen, P.V.; Jordan, D.B. (DuPont); (NWU)
Riboflavin synthase catalyzes the dismutation of two molecules of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine to yield riboflavin and 4-ribitylamino-5-amino-2,6-dihydroxypyrimidine. The homotrimer of 23 kDa subunits has no cofactor requirements for catalysis. The enzyme is nonexistent in humans and is an attractive target for antimicrobial agents of organisms whose pathogenicity depends on their ability to biosynthesize riboflavin. The first three-dimensional structure of the enzyme was determined at 2.0 {angstrom} resolution using the multiwavelength anomalous diffraction (MAD) method on the Escherichia coli protein containing selenomethionine residues. The homotrimer consists of an asymmetric assembly of monomers, each of which comprises two similar {beta} barrels and a C-terminal {alpha} helix. The similar {beta} barrels within the monomer confirm a prediction of pseudo two-fold symmetry that is inferred from the sequence similarity between the two halves of the protein. The {beta} barrels closely resemble folds found in phthalate dioxygenase reductase and other flavoproteins. The three active sites of the trimer are proposed to lie between pairs of monomers in which residues conserved among species reside, including two Asp-His-Ser triads and dyads of Cys-Ser and His-Thr. The proposed active sites are located where FMN (an analog of riboflavin) is modeled from an overlay of the {beta} barrels of phthalate dioxygenase reductase and riboflavin synthase. In the trimer, one active site is formed, and the other two active sites are wide open and exposed to solvent. The nature of the trimer configuration suggests that only one active site can be formed and be catalytically competent at a time.
Particle beam and crabbing and deflecting structure
Delayen, Jean (Yorktown, VA)
A new type of structure for the deflection and crabbing of particle bunches in particle accelerators comprising a number of parallel transverse electromagnetic (TEM)-resonant) lines operating in opposite phase from each other. Such a structure is significantly more compact than conventional crabbing cavities operating the transverse magnetic TM mode, thus allowing low frequency designs.
Crystallization Pathways of Sulfate-Nitrate-Ammonium Aerosol Particles Julie C. Schlenker and Scot T. Martin*
Crystallization Pathways of Sulfate-Nitrate-Ammonium Aerosol Particles Julie C. Schlenker and Scot into the nonlinear crystallization pathways of sulfate-nitrate-ammonium aerosol particles. 1. Introduction The physicochemical behavior of the sulfate particles is strongly influenced by the presence of nitrate and ammonium.3
Wetting of a spherical particle by a nematic liquid crystal
NASA Astrophysics Data System (ADS)
Fukuda, Jun-Ichi; Stark, Holger; Yokoyama, Hiroshi
We discuss how the curvature of a substrate influences wetting by a nematic liquid crystal concentrating on the surface of a spherical particle. Our investigation is based on Landau de Gennes free energy formulated in terms of second-rank nematic order parameter Qij. We review the method to treat wetting transitions in curved geometries and calculate the wetting phase diagram in terms of the temperature and a surface coupling parameter. We find that the length of the prewetting line which corresponds to the boundary-layer transitions introduced by Sheng [Phys. Rev. A 26, 1610 (1982)] gradually decreases with a decrease in particle radius until it vanishes completely below a critical radius of about 100 nm. The prewetting line ends at a critical point which we study in detail. By interpreting the effect of curvature as an effective shift in temperature in Landau de Gennes theory, we are able to formulate a good estimate for the critical temperature as a function of the inverse particle radius. It demonstrates that splay deformations around the particle significantly influence nematic wetting of curved surfaces.
Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.
ERIC Educational Resources Information Center
Chesick, John P.
Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)
Exploring Crystal Structures with XtalDraw
NSDL National Science Digital Library
Wendy Panero
At the end of this exercise students will be able to use computer-based software to draw crystal structures and visualize symmetries present in minerals. By varying the way in which atoms or groups of atoms are displayed, they will begin to see how atoms link through bonds. Students will also begin to investigate the effects of variable composition on bonding on unit cell parameters.
Crystal Structures of the ?2-Adrenergic Receptor
NASA Astrophysics Data System (ADS)
Weis, William I.; Rosenbaum, Daniel M.; Rasmussen, Søren G. F.; Choi, Hee-Jung; Thian, Foon Sun; Kobilka, Tong Sun; Yao, Xiao-Jie; Day, Peter W.; Parnot, Charles; Fung, Juan J.; Ratnala, Venkata R. P.; Kobilka, Brian K.; Cherezov, Vadim; Hanson, Michael A.; Kuhn, Peter; Stevens, Raymond C.; Edwards, Patricia C.; Schertler, Gebhard F. X.; Burghammer, Manfred; Sanishvili, Ruslan; Fischetti, Robert F.; Masood, Asna; Rohrer, Daniel K.
G protein coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome, and are responsible for the majority of signal transduction events involving hormones and neuro-transmitters across the cell membrane. GPCRs that bind to diffusible ligands have low natural abundance, are relatively unstable in detergents, and display basal G protein activation even in the absence of ligands. To overcome these problems two approaches were taken to obtain crystal structures of the ?2-adrenergic receptor (?2AR), a well-characterized GPCR that binds cate-cholamine hormones. The receptor was bound to the partial inverse agonist carazolol and co-crystallized with a Fab made to a three-dimensional epitope formed by the third intracellular loop (ICL3), or by replacement of ICL3 with T4 lysozyme. Small crystals were obtained in lipid bicelles (?2AR-Fab) or lipidic cubic phase (?2AR-T4 lysozyme), and diffraction data were obtained using microfocus technology. The structures provide insights into the basal activity of the receptor, the structural features that enable binding of diffusible ligands, and the coupling between ligand binding and G-protein activation.
Predicting polymeric crystal structures by evolutionary algorithms
NASA Astrophysics Data System (ADS)
Zhu, Qiang; Sharma, Vinit; Oganov, Artem R.; Ramprasad, Ramamurthy
The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures. Here we extend this method to predict the crystal structure of polymers by constrained evolutionary search, where each monomeric unit is treated as a building block with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings of these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely, polyethylene, polyacetylene, poly(glycolic acid), poly(vinyl chloride), poly(oxymethylene), poly(phenylene oxide), and poly (p-phenylene sulfide). By fixing the orientation of polymeric chains, this method can be further extended to predict the structures of complex linear polymers, such as all polymorphs of poly(vinylidene fluoride), nylon-6 and cellulose. The excellent agreement between predicted crystal structures and experimentally known structures assures a major role of this approach in the efficient design of the future polymeric materials.
A hierarchical structure for apatite crystals.
Dorozhkin, Sergey V
Based on the experimental results taken from the references, a reasonable hierarchical structure of apatite (both fluorapatite and hydroxyapatite) crystals has been proposed for the first time. The structure consists of four levels of the hierarchy: the smallest level is made of single unit-cells and/or Posner's clusters with the linear dimensions slightly below 1 nm, the second level comprises X-ray coherent scattering blocks of 50-80 nm in size, the third level is represented by dislocation blocks of 0.3-2.0 microm in size and, finally, there are macroblocks of 35-50 microm in size. PMID:17323170
Large-area optoelastic manipulation of colloidal particles in liquid crystals using photoresponsive molecular surface monolayers
Martinez, Angel; Mireles, Hector C.; Smalyukh, Ivan I.
Noncontact optical trapping and manipulation of micrometer- and nanometer-sized particles are typically achieved by use of forces and torques exerted by tightly focused high-intensity laser beams. Although they were instrumental for many scientific breakthroughs, these approaches find few technological applications mainly because of the small-area manipulation capabilities, the need for using high laser powers, limited application to anisotropic fluids and low-refractive-index particles, as well as complexity of implementation. To overcome these limitations, recent research efforts have been directed toward extending the scope of noncontact optical control through the use of optically-guided electrokinetic forces, vortex laser beams, plasmonics, and optofluidics. Here we demonstrate manipulation of colloidal particles and self-assembled structures in nematic liquid crystals by means of single-molecule-thick, light-controlled surface monolayers. Using polarized light of intensity from 1,000 to 100,000 times smaller than that in conventional optical tweezers, we rotate, translate, localize, and assemble spherical and complex-shaped particles of various sizes and compositions. By controlling boundary conditions through the monolayer, we manipulate the liquid crystal director field and the landscape of ensuing elastic forces exerted on colloids by the host medium. This permits the centimeter-scale, massively parallel manipulation of particles and complex colloidal structures that can be dynamically controlled by changing illumination or assembled into stationary stable configurations dictated by the "memorized" optoelastic potential landscape due to the last illumination pattern. We characterize the strength of optically guided elastic forces and discuss the potential uses of this noncontact manipulation in fabrication of novel optically- and electrically-tunable composites from liquid crystals and colloids. PMID:22160673
Geometry of crystal structure with defects. I. Euclidean picture
Trzesowski, A.
Continuously distributed defects of crystal structure are considered. The starting point is the Euclidean geometry of the ideal crystal lattice and the topological description of the distortion of the crystal structure. It is shown how the non-Euclidean geometry of distorted crystal structure, as well as the basic assumptions of the phenomenological plasticity theory concerning the deformation of a continuum, are related to those theories. A form for an affine connection describing continuously distributed dislocations is proposed.
Crystal Structure of A-amylose: a Revisit from Synchrotron Microdiffraction Analysis of Single Crystals
Paris-Sud XI, Université de
1 Crystal Structure of A-amylose: a Revisit from Synchrotron Microdiffraction Analysis of Single;2 Abstract The three-dimensional structure of A-amylose crystals, as a model of the crystal domains of A the resolution of important new fine details. These include a distortion of the amylose double helices resulting
PROTEIN STRUCTURE REPORT Crystal structure of the Yersinia type III
, 2005; FINAL REVISION July 15, 2005; ACCEPTED July 27, 2005) Abstract The plague-causing bacterium of oligomerization is discussed. Keywords: Yersinia pestis; plague; type III secretion; YscE; crystal structure Yersinia pestis, the causative agent of plague, utilizes a type III secretion system (T3SS) to inject
Study on twin boundaries and Te particles in CdMnTe crystals for nuclear detector application
NASA Astrophysics Data System (ADS)
Du, Yuanyuan; Jie, Wanqi; Wang, Tao; Luo, Lin; Xu, Yadong; Luan, Lijun
Electron backscatter diffraction (EBSD) and Raman scattering were used to characterize twins and Te particles in CdMnTe crystals grown by the vertical Bridgman method. The size, concentration and phase structure of Te particles, as well as the orientation of twins were studied. {111} twins decorated with Te particles were identified by low and high magnitude EBSD mapping. Three type crystal phases of Te particles were observed, including hexagonal, monoclinic and high-pressure rhombohedral phase. Most of Te particles were preferentially oriented with the {110}CdMnTe//{112¯0}Te. The A1 (Te) and E (Te) modes in CdMnTe Raman scattering spectroscopy were found with red-shift than single Te phase due to the tensile stress effect.
Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus. Purification, Crystallization and Structure Determination
Clemons, William M.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki (MRC); (Utah); (MRC)
We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 {angstrom} resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 {angstrom} resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.
Exciton dynamics in alpha-particle tracks in organic crystals: Magnetic field study of the scintillation in tetracene crystals
Nicholas E. Geacintov; Michael Binder; Charles E. Swenberg; Martin Pope
The mechanisms of scintillation of organic crystals bombarded by alpha particles are discussed in terms of the current knowledge of exciton dynamics, which has been derived from a study of the photofluorescence of crystals such as anthracene and tetracene. The scintillation of tetracene excited by 4.4-MeV alpha particles incident in a direction perpendicular to the ab plane has been studied
Crystal structure of the Golgi casein kinase
Xiao, Junyu; Tagliabracci, Vincent S.; Wen, Jianzhong; Kim, Soo-A; Dixon, Jack E.
The family with sequence similarity 20 (Fam20) kinases phosphorylate extracellular substrates and play important roles in biomineralization. Fam20C is the Golgi casein kinase that phosphorylates secretory pathway proteins within Ser-x-Glu/pSer motifs. Mutations in Fam20C cause Raine syndrome, an osteosclerotic bone dysplasia. Here we report the crystal structure of the Fam20C ortholog from Caenorhabditis elegans. The nucleotide-free and Mn/ADP-bound structures unveil an atypical protein kinase-like fold and highlight residues critical for activity. The position of the regulatory ?C helix and the lack of an activation loop indicate an architecture primed for efficient catalysis. Furthermore, several distinct elements, including the presence of disulfide bonds, suggest that the Fam20 family diverged early in the evolution of the protein kinase superfamily. Our results reinforce the structural diversity of protein kinases and have important implications for patients with disorders of biomineralization. PMID:23754375
Crystal structure of plant photosystem I
NASA Astrophysics Data System (ADS)
Ben-Shem, Adam; Frolow, Felix; Nelson, Nathan
Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4Å resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.
Particle Mass Measurements and Strong Interaction Studies with Exotic Atoms using X-ray Crystal Spectrometer
Titov, Anatoly
with crystal spectrometer are discussed which aim to improve particle masses and to study hyperon- nucleus Deexcitation and Isotope Exchange of Excited Mesic Hydrogen A. V. Kravtsov, A. I. Mikhailov Àííîòàöèÿ ÏðîöåññûParticle Mass Measurements and Strong Interaction Studies with Exotic Atoms using X-ray Crystal
Tunability of LSPR using gold nano-particles embedded in a liquid crystal cell
NASA Astrophysics Data System (ADS)
Wang, Huan; Vial, Alexandre
Tunability of localized surface plasmon resonance (LSPR) of an ordered array of gold nano-particles is investigated in this paper. Herein, the array is embedded in a liquid crystal cell and then sandwiched with two glass substrates. The extinction spectra are computed using the Finite-Difference Time Domain (FDTD) method. The LSPR tunability of gold nanostructures is compromised by the anchoring effects of surrounding LC molecules, this effect can be compensated by optimizing geometric parameters of gold nanostructures. Interestingly, double resonant peaks are achieved with optimized structure. Meanwhile, the tunability of LSPR is improved up to 72 nm with anchoring effects taken into account.
Crystal structure of yeast Sco1
Abajian, Carnie; Rosenzweig, Amy C. (NWU)
The Sco family of proteins are involved in the assembly of the dinuclear CuA site in cytochrome c oxidase (COX), the terminal enzyme in aerobic respiration. These proteins, which are found in both eukaryotes and prokaryotes, are characterized by a conserved CXXXC sequence motif that binds copper ions and that has also been proposed to perform a thiol:disulfide oxidoreductase function. The crystal structures of Saccharomyces cerevisiae apo Sco1 (apo-ySco1) and Sco1 in the presence of copper ions (Cu-ySco1) were determined to 1.8- and 2.3-{angstrom} resolutions, respectively. Yeast Sco1 exhibits a thioredoxin-like fold, similar to that observed for human Sco1 and a homolog from Bacillus subtilis. The Cu-ySco1 structure, obtained by soaking apo-ySco1 crystals in copper ions, reveals an unexpected copper-binding site involving Cys181 and Cys216, cysteine residues present in ySco1 but not in other homologs. The conserved CXXXC cysteines, Cys148 and Cys152, can undergo redox chemistry in the crystal. An essential histidine residue, His239, is located on a highly flexible loop, denoted the Sco loop, and can adopt positions proximal to both pairs of cysteines. Interactions between ySco1 and its partner proteins yeast Cox17 and yeast COX2 are likely to occur via complementary electrostatic surfaces. This high-resolution model of a eukaryotic Sco protein provides new insight into Sco copper binding and function.
Continuous synthesis of polymer-coated drug particles by porous hollow fiber membrane-based antisolvent crystallization.
Chen, Dengyue; Singh, Dhananjay; Sirkar, Kamalesh K; Pfeffer, Robert
Using porous hollow fiber membranes, this study illustrates a novel technique to continuously synthesize polymer-coated drug crystals by antisolvent crystallization. The synthesized polymer-coated drug crystals involve crystals of the drug Griseofulvin (GF) coated by a thin layer of the polymer Eudragit RL100. The process feed, an acetone solution of the drug GF containing the dissolved polymer, was passed through the shell side of a membrane module containing many porous hollow fibers of Nylon-6. Through the lumen of the hollow fibers, the antisolvent water was passed at a higher pressure to inject water jets through every pore in the fiber wall into the shell-side acetone feed solution, creating an extremely high level of supersaturation and immediate crystallization. It appears that the GF crystals are formed first and serve as nuclei for the precipitation of the polymer Eudragit, which forms a thin coating around the GF crystals. The polymer-coated drug crystals were collected by a filtration device at the shell-side outlet of the membrane module, and the surface morphology, particle size distribution, and the polymer coating thickness were then characterized by scanning electron microscopy (SEM), scanning transmission electron microscopy (STEM), laser diffraction spectroscopy (LDS), and thermogravimetric analysis (TGA). To study the properties of the coated drug crystals, X-ray diffraction (XRD), Raman spectroscopy, and dissolution tests were implemented. These results indicate that a polymer-coated, free-flowing product was successfully developed under appropriate conditions in this novel porous hollow fiber antisolvent crystallization (PHFAC) method. The coated drug particles can be potentially used for controlled release. The molecular and the crystal structures of GF were not affected by the PHFAC method, which may be easily scaled up. PMID:25552289
Some Lower Valence Vanadium Fluorides: Their Crystal Distortions, Domain Structures, Modulated Structures, Ferrimagnetism, and Composition Dependence.
ERIC Educational Resources Information Center
Hong, Y. S.; And Others
Describes some contemporary concepts unique to the structure of advanced solids, i.e., their crystal distortions, domain structures, modulated structures, ferrimagnetism, and composition dependence. (Author/CS)
Short Article The Crystal Structure of the Intact E. coli
Passmore, Lori A.
the crystal structure of the intact Escherichia coli RelB2E2 complex at 2.8 A° resolution, comprising both The Escherichia coli relBE locus encodes a bacterial type II toxin- antitoxin (TA) complex consisting of a toxinStructure Short Article The Crystal Structure of the Intact E. coli RelBE Toxin-Antitoxin Complex
Aggregate Structure and Free Energy Changes in Chromonic Liquid Crystals
Collings, Peter
Aggregate Structure and Free Energy Changes in Chromonic Liquid Crystals Alexandra J. Dickinson, Swarthmore College, Swarthmore, PA, USA Past and recent x-ray and absorption data on chromonic liquid crystal phase forms at higher concentrations. Keywords: aggregation; chromonic; liquid crystals
Crystal structure of Junin virus nucleoprotein.
Zhang, Yinjie; Li, Le; Liu, Xiang; Dong, Shishang; Wang, Wenming; Huo, Tong; Guo, Yu; Rao, Zihe; Yang, Cheng
Junin virus (JUNV) has been identified as the aetiological agent of Argentine haemorrhagic fever (AHF), which is a serious public health problem with approximately 5 million people at risk. It is treated as a potential bioterrorism agent because of its rapid transmission by aerosols. JUNV is a negative-sense ssRNA virus that belongs to the genus Arenavirus within the family Arenaviridae, and its genomic RNA contains two segments encoding four proteins. Among these, the nucleoprotein (NP) has essential roles in viral RNA synthesis and immune suppression, but the molecular mechanisms of its actions are only partially understood. Here, we determined a 2.2 Å crystal structure of the C-terminal domain of JUNV NP. This structure showed high similarity to the Lassa fever virus (LASV) NP C-terminal domain. However, both the structure and function of JUNV NP showed differences compared with LASV NP. This study extends our structural insight into the negative-sense ssRNA virus NPs. PMID:23884367
Crystal structures of the human adiponectin receptors.
Tanabe, Hiroaki; Fujii, Yoshifumi; Okada-Iwabu, Miki; Iwabu, Masato; Nakamura, Yoshihiro; Hosaka, Toshiaki; Motoyama, Kanna; Ikeda, Mariko; Wakiyama, Motoaki; Terada, Takaho; Ohsawa, Noboru; Hato, Masakatsu; Ogasawara, Satoshi; Hino, Tomoya; Murata, Takeshi; Iwata, So; Hirata, Kunio; Kawano, Yoshiaki; Yamamoto, Masaki; Kimura-Someya, Tomomi; Shirouzu, Mikako; Yamauchi, Toshimasa; Kadowaki, Takashi; Yokoyama, Shigeyuki
Adiponectin stimulation of its receptors, AdipoR1 and AdipoR2, increases the activities of 5' AMP-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor (PPAR), respectively, thereby contributing to healthy longevity as key anti-diabetic molecules. AdipoR1 and AdipoR2 were predicted to contain seven transmembrane helices with the opposite topology to G-protein-coupled receptors. Here we report the crystal structures of human AdipoR1 and AdipoR2 at 2.9 and 2.4 Å resolution, respectively, which represent a novel class of receptor structure. The seven-transmembrane helices, conformationally distinct from those of G-protein-coupled receptors, enclose a large cavity where three conserved histidine residues coordinate a zinc ion. The zinc-binding structure may have a role in the adiponectin-stimulated AMPK phosphorylation and UCP2 upregulation. Adiponectin may broadly interact with the extracellular face, rather than the carboxy-terminal tail, of the receptors. The present information will facilitate the understanding of novel structure-function relationships and the development and optimization of AdipoR agonists for the treatment of obesity-related diseases, such as type 2 diabetes. PMID:25855295
Magnetism and Crystal Structure of Zirconium Compound with Laves Structure
K. Kanematsu
Magnetic studies were performed on intermetallic compounds with Laves-type structure, (Zr, Nb)Fe2, (Zr, Mo)Fe2, Zr(Fe, Mn)2, Zr(Fe, V)2, and Zr(Fe, Co)2. The crystal structure of all the compounds except Zr(Fe, Co)2 changes from the MgCu2 type to MgZn2 type with decreasing ZrFe2 content. The magnetism changes from ferromagnetism to paramagnetism with change from MgCu2 type to MgZn2 type, and it
Structural, Spectral And Optical Characterization Of Calcium Barium Tartrate Crystals
NASA Astrophysics Data System (ADS)
Freeda, M. Mary; Priya, R. Krishna; Freeda, T. H.; Delphine, S. Mary
Single crystals of Calcium Barium tartrate (CBT) were grown by controlled diffusion in silica gel at ambient temperature. The structural characterization of the grown crystals was carried out by Powder X-ray diffraction analysis. The functional groups present in the crystals were identified using Fourier Transform Infrared spectral analysis. The UV-Vis-NIR transmission spectrum was recorded to study the optical transparency of the grown crystals.
Crystal structure of human uroporphyrinogen decarboxylase.
Whitby, F G; Phillips, J D; Kushner, J P; Hill, C P
Uroporphyrinogen decarboxylase (URO-D) catalyzes the fifth step in the heme biosynthetic pathway, converting uroporphyrinogen to coproporphyrinogen by decarboxylating the four acetate side chains of the substrate. This activity is essential in all organisms, and subnormal activity of URO-D leads to the most common form of porphyria in humans, porphyria cutanea tarda (PCT). We have determined the crystal structure of recombinant human URO-D at 1.60 A resolution. The 40.8 kDa protein is comprised of a single domain containing a (beta/alpha)8-barrel with a deep active site cleft formed by loops at the C-terminal ends of the barrel strands. Many conserved residues cluster at this cleft, including the invariant side chains of Arg37, Arg41 and His339, which probably function in substrate binding, and Asp86, Tyr164 and Ser219, which may function in either binding or catalysis. URO-D is a dimer in solution (Kd = 0.1 microM), and this dimer also appears to be formed in the crystal. Assembly of the dimer juxtaposes the active site clefts of the monomers, suggesting a functionally important interaction between the catalytic centers. PMID:9564029
Crystal Structures of Respiratory Pathogen Neuraminidases
Hsiao, Y.; Parker, D; Ratner, A; Prince, A; Tong, L
Currently there is pressing need to develop novel therapeutic agents for the treatment of infections by the human respiratory pathogens Pseudomonas aeruginosa and Streptococcus pneumoniae. The neuraminidases of these pathogens are important for host colonization in animal models of infection and are attractive targets for drug discovery. To aid in the development of inhibitors against these neuraminidases, we have determined the crystal structures of the P. aeruginosa enzyme NanPs and S. pneumoniae enzyme NanA at 1.6 and 1.7 {angstrom} resolution, respectively. In situ proteolysis with trypsin was essential for the crystallization of our recombinant NanA. The active site regions of the two enzymes are strikingly different. NanA contains a deep pocket that is similar to that in canonical neuraminidases, while the NanPs active site is much more open. The comparative studies suggest that NanPs may not be a classical neuraminidase, and may have distinct natural substrates and physiological functions. This work represents an important step in the development of drugs to prevent respiratory tract colonization by these two pathogens.
Activation of the alternative pathway of complement by monosodium urate monohydrate crystals and other inflammatory particles.
Doherty, M; Whicher, J T; Dieppe, P A
Activation of serum C3 by monosodium urate monohydrate (MSU) crystals and other particles was determined by immunofixation following electrophoretic separation of C3 and its activation products. Densitometry allowed quantitation of results. MSU, hydroxyapatite, brushite, and calcium pyrophosphate dihydrate crystals split C3 under conditions which demonstrate activation via the alternative pathway (AP). Quantitatively similar results were obtained in immunoglobulin deficient serum. Activation was crystal specific and was reduced by heating, grinding, sonication, and aging of crystals. Other inflammatory particles (e.g., blackthorn) activated C3 via the AP: noninflammatory particles (e.g., diamond) caused insignificant activation. It is suggested that particle-induced activation of the alternative pathway of complement may be important in the initiation of crystal-induced synovitis. Images PMID:6407405
Colloidal particle-based surface nanotopography with high mechanical stability by thermal fixation for liquid crystal devices
NASA Astrophysics Data System (ADS)
Chul Park, Seung; Na, Jun-Hee; Lee, Sin-Doo
We develop a simple and versatile platform to construct the surface nanotopography of a substrate by thermal fixation of colloidal particles. The micrometer-size particles of polystyrene are dispersed in a random monolayer on a substrate by spin-coating and transformed into hemispherical nanostructures with high mechanical stability under thermal treatment. The experimental results for the structural change of the particles agree well with the calculations in a simple model of the constant-volume. The liquid crystal (LC) alignment on the nanotopographic surface with hemispherical structures is found to increase the symmetry of the electro-optic properties of the LC devices. The colloidal particle-based surface topography with size-scalable nanostructures provides a practical route to the control of interfacial structural orders of the functional molecules on a nanometer-to-micrometer scale.
Crystal structures of saposins A and C
Ahn, Victoria E.; Leyko, Paul; Alattia, Jean-René; Chen, Lu; Privé, Gilbert G.
Saposins A and C are sphingolipid activator proteins required for the lysosomal breakdown of galactosylceramide and glucosylceramide, respectively. The saposins interact with lipids, leading to an enhanced accessibility of the lipid headgroups to their cognate hydrolases. We have determined the crystal structures of human saposins A and C to 2.0 Å and 2.4 Å, respectively, and both reveal the compact, monomeric saposin fold. We confirmed that these two proteins were monomeric in solution at pH 7.0 by analytical centrifugation. However, at pH 4.8, in the presence of the detergent C8E5, saposin A assembled into dimers, while saposin C formed trimers. Saposin B was dimeric under all conditions tested. The self-association of the saposins is likely to be relevant to how these small proteins interact with lipids, membranes, and hydrolase enzymes. PMID:16823039
Crystal structure of betulinic acid methanol monosolvate.
Tang, Wei; Chen, Neng-Hua; Li, Guo-Qiang; Wang, Guo-Cai; Li, Yao-Lan
The title compound [systematic name: 3?-hy-droxy-lup-20(29)-en-28-oic acid methanol monosolvate], C30H48O3·CH3OH, is a solvent pseudopolymorph of a naturally occurring plant-derived lupane-type penta-cyclic triterpenoid, which was isolated from the traditional Chinese medicinal plant Syzygium jambos (L.) Alston. The dihedral angle between the planes of the carb-oxy-lic acid group and the olefinic group is 12.17?(18)°. The A/B, B/C, C/D and D/E ring junctions are all trans-fused. In the crystal, O-H?O hydrogen bonds involving the hy-droxy and carb-oxy-lic acid groups and the methanol solvent mol-ecule give rise to a two-dimensional network structure lying parallel to (001). PMID:25553022
Crystal structure of betulinic acid methanol monosolvate
Tang, Wei; Chen, Neng-Hua; Li, Guo-Qiang; Wang, Guo-Cai; Li, Yao-Lan
The title compound [systematic name: 3?-hydroxylup-20(29)-en-28-oic acid methanol monosolvate], C30H48O3·CH3OH, is a solvent pseudopolymorph of a naturally occurring plant-derived lupane-type pentacyclic triterpenoid, which was isolated from the traditional Chinese medicinal plant Syzygium jambos (L.) Alston. The dihedral angle between the planes of the carboxylic acid group and the olefinic group is 12.17?(18)°. The A/B, B/C, C/D and D/E ring junctions are all trans-fused. In the crystal, O—H?O hydrogen bonds involving the hydroxy and carboxylic acid groups and the methanol solvent molecule give rise to a two-dimensional network structure lying parallel to (001). PMID:25553022
Crystal structure of a snake venom cardiotoxin
Rees, B.; Samama, J.P.; Thierry, J.C.; Gilibert, M.; Fischer, J.; Schweitz, H.; Lazdunski, M.; Moras, D.
Cardiotoxin V/sup II/4 from Naja mossambica crystallizes in space group P6/sub 1/ (a = b = 73.9 A; c = 59.0 A) with two molecules of toxin (molecular mass = 6715 Da) in the asymmetric unit. The structure was solved by using a combination of multiple isomorphous replacement and density modification methods. Model building and least-squares refinement led to an agreement factor of 27% for a data set to 3-A resolution prior to any inclusion of solvent molecules. The topology of the molecule is similar to that found in short and long snake neurotoxins, which block the nicotinic acetylcholine receptor. Major differences occur in the conformation of the central loop, resulting in a change in the concavity of the molecule. Hydrophobic residues are clustered in two distinct areas. The existence of stable dimeric entities in the crystalline state, with the formation of a six-stranded antiparallel ..beta.. sheet, may be functionally relevant.
Formation of structured nanophases in halide crystals.
Kulveit, J; Demo, P; Polák, K; Sveshnikov, A M; Kožíšek, Z
When halide crystals KCl and NaCl are slightly doped by PbCl(2), (in orders of 10(-4)?mol/mol) the structurally stable nanophases ("quantum dots") are formed via nucleation within the bulks of their matrices. Using lattice modeling we have found in KCl-Pb system natural nucleation pathway from single impurity-vacancy complex to Suzuki phase, not demonstrated in previous analyses; further transition to PbCl(2) is difficult due to high stability of this phase. In the case of NaCl-Pb, no stable "end point" of aggregation was observed and our calculations suggest nucleation may readily proceed to large PbCl(2) clusters when initially formed platelike cluster reaches a certain critical thickness. These results coincide with our experimental data. PMID:21495761
Formation of structured nanophases in halide crystals
NASA Astrophysics Data System (ADS)
Kulveit, J.; Demo, P.; Polák, K.; Sveshnikov, A. M.; Kožíšek, Z.
When halide crystals KCl and NaCl are slightly doped by PbCl_2, (in orders of 10^{-4} mol/mol) the structurally stable nanophases ("quantum dots") are formed via nucleation within the bulks of their matrices. Using lattice modeling we have found in KCl-Pb system natural nucleation pathway from single impurity-vacancy complex to Suzuki phase, not demonstrated in previous analyses; further transition to PbCl_2 is difficult due to high stability of this phase. In the case of NaCl-Pb, no stable "end point" of aggregation was observed and our calculations suggest nucleation may readily proceed to large PbCl_2 clusters when initially formed platelike cluster reaches a certain critical thickness. These results coincide with our experimental data.
Structural studies of large nucleoprotein particles, vaults
TANAKA, Hideaki; TSUKIHARA, Tomitake
Vault is the largest nonicosahedral cytosolic nucleoprotein particle ever described. The widespread presence and evolutionary conservation of vaults suggest important biologic roles, although their functions have not been fully elucidated. X-ray structure of vault from rat liver was determined at 3.5 Å resolution. It exhibits an ovoid shape with a size of 40 × 40 × 67 nm3. The cage structure of vault consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The other components of vaults, telomerase-associated proteins, poly(ADP-ribose) polymerases and small RNAs, are in location in the vault particle by electron microscopy. PMID:23060231
Preface to some crystal structure communications
J. M. M. Smits; H. Behm; W. P. Bosman; Paul T. Beurskens
Crystals are prepared and\\/or recrystallized [solvent] in one of the chemistry departments of our university. One crystal is selected [approximate size] and used on an Enraf-Nonius CAD4 single-crystal diffractometer, employing Cu Ker (X = 1.54184 ,&) or Mo Ka (~ = 0.71073 ,~) radiation with a graphite crystal monochromator. The unit-cell dimensions are determined from the angular settings of 25
Superionics: crystal structures and conduction processes
NASA Astrophysics Data System (ADS)
Hull, Stephen
Superionic conductors are compounds that exhibit exceptionally high values of ionic conductivity within the solid state. Indeed, their conductivities often reach values of the order of 1 OHgr-1 cm-1, which are comparable to those observed in the molten state. Following Faraday's first observation of high ionic conductivity within the solids bgr-PbF2 and Ag2S in 1836, a fundamental understanding of the nature of the superionic state has provided one of the major challenges in the field of condensed matter science. However, experimental and theoretical approaches to their study are often made difficult by the extensive dynamic structural disorder which characterizes superionic conduction and the inapplicability of many of the commonly used approximations in solid state physics. Nevertheless, a clearer picture of the nature of the superionic state at the ionic level has emerged within the past few decades. Many different techniques have contributed to these advances, but the most significant insights have been provided by neutron scattering experiments and molecular dynamics simulations. This review will summarize the state of current knowledge concerning the crystal structures and conduction processes of superionic conductors, beginning with a comparison of the behaviour of two of the most widely studied binary compounds, AgI and bgr-PbF2. Each can be considered a parent of two larger families of highly conducting compounds which are related by either chemical or structural means. These include perovskite-structured oxides and Li+ containing spinel-structured compounds, which have important commercial applications in fuel cells and lightweight batteries, respectively. In parallel with these discussions, the relative importance of factors such as bonding character and the properties of the mobile and immobile ions (charge, size, polarizability, etc) in promoting the extensive lattice disorder which characterizes superionic behaviour will be assessed and the possibilities for predicting a priori which compounds will display high ionic conductivity discussed.
Analytical method for band structure calculation of photonic crystal fibers filled with liquid crystal.
Hu, Juan Juan; Ren, Guobin; Shum, Ping; Yu, Xia; Wang, Guanghui; Lu, Chao
An analytical method for band structure calculations of photonic crystal fibers with liquid crystal infiltrations is presented. The scalar eigenvalue equation is extended to treat both isotropic and anisotropic materials by introducing a coefficient to describe the index contrast between the extraordinary and ordinary refractive index of the liquid crystal. The simple model provides a fast insight into bandgap formation in photonic crystal fibers filled with anisotropic material such as liquid crystal, which would be useful to aid the design based on such fibers. PMID:18545370
Hierarchical structuring of liquid crystal polymer-Laponite hybrid materials.
Tritschler, Ulrich; Zlotnikov, Igor; Zaslansky, Paul; Aichmayer, Barbara; Fratzl, Peter; Schlaad, Helmut; Cölfen, Helmut
Biomimetic organic-inorganic composite materials were fabricated via one-step self-organization on three hierarchical levels. The organic component was a polyoxazoline with pendent cholesteryl and carboxyl (N-Boc-protected amino acid) side chains that was able to form a chiral nematic lyotropic phase and bind to positively charged inorganic faces of Laponite. The Laponite particles formed a mesocrystalline arrangement within the liquid-crystal (LC) polymer phase upon shearing a viscous dispersion of Laponite nanoparticles and LC polymer in DMF. Complementary analytical and mechanical characterization techniques (AUC, POM, TEM, SEM, SAXS, ?CT, and nanoindentation) covering the millimeter, micrometer, and nanometer length scales reveal the hierarchical structures and properties of the composite materials consisting of different ratios of Laponite nanoparticles and liquid-crystalline polymer. PMID:23790152
Single-crystal CVD diamond detector for high-resolution particle spectrometry
NASA Astrophysics Data System (ADS)
Sato, Y.; Murakami, H.; Shimaoka, T.; Tsubota, M.; Kaneko, J. H.
The performance of a single-crystal diamond detector, grown by chemical vapour deposition, as an energy spectrometer for charged particles was studied. The detector was able to identify four different energies of 241\\text{Am} ? -particles (5.389, 5.443, 5.486, and 5.545 MeV) thanks to a superior intrinsic energy resolution of ˜0.4{%} (full width at half maximum). The electrode configuration, specifically the electric field configuration inside the diamond crystal, and the electrode materials, strongly affect the energy resolution for charged particles. The charge collection efficiency inside the diamond crystal was ˜97{%} for both electrons and holes.
Undergraduates Improve upon Published Crystal Structure in Class Assignment
ERIC Educational Resources Information Center
Horowitz, Scott; Koldewey, Philipp; Bardwell, James C.
Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the…
Neutron-diffraction studies of magnetic structures of crystals
Yurii A Izyumov
The contemporary state of neutron diffraction of magnetic structures is analyzed from the standpoint of the theory of symmetry of crystals. It is shown that the varied and numerous structures determined in neutron-diffraction studies can be classified and described by the theory of representations of space groups of crystals. This approach is based on expanding the spin density of the
Crystal Structure of Adenosine 5-Phosphosulfate Kinase from Penicillium chrysogenum,
Fisher, Andrew J.
Crystal Structure of Adenosine 5-Phosphosulfate Kinase from Penicillium chrysogenum, Ian J. Mac crystal structure of ligand-free APS kinase from the filamentous fungus, Penicillium chrysogenum focuses on APS kinase from the filamentous fungus, Penicillium chrysogenum, an enzyme possessing several
The structure of particle cloud premixed flames
NASA Technical Reports Server (NTRS)
Seshadri, K.; Berlad, A. L.
The structure of premixed flames propagating in combustible systems containing uniformly distributed volatile fuel particles in an oxidizing gas mixture is analyzed. This analysis is motivated by experiments conducted at NASA Lewis Research Center on the structure of flames propagating in combustible mixtures of lycopodium particles and air. Several interesting modes of flame propagation were observed in these experiments depending on the number density and the initial size of the fuel particle. The experimental results show that steady flame propagation occurs even if the initial equivalence ratio of the combustible mixture based on the gaseous fuel available in the particles, phi sub u, is substantially larger than unity. A model is developed to explain these experimental observations. In the model, it is presumed that the fuel particles vaporize first to yield a gaseous fuel of known chemical composition which then reacts with oxygen in a one-step overall process. The activation energy of the chemical reaction is presumed to be large. The activation energy characterizing the kinetics of vaporization is also presumed to be large. The equations governing the structure of the flame were integrated numerically. It is shown that the interplay of vaporization kinetics and oxidation process can result in steady flame propagation in combustible mixtures where the value of phi sub u is substantially larger than unity. This prediction is in agreement with experimental observations.
Track-Structure Simulations for Charged Particles
Dingfelder, Michael
Monte-Carlo track-structure simulations provide a detailed and accurate picture of radiation transport of charged particles through condensed matter of biological interest. Liquid water serves as surrogate for soft tissue and is used in most Monte-Carlo track-structure codes. Basic theories of radiation transport and track-structure simulations are discussed and differences to condensed history codes highlighted. Interaction cross sections for electrons, protons, alpha particles, light and heavy ions are required input data for track-structure simulations. Different calculation methods, including the plane-wave Born approximation, the dielectric theory, and semi-empirical approaches are presented using liquid water as a target. Low-energy electron transport and light ion transport are discussed as areas of special interest. PMID:23032889
Growth and crystal structure of the BeAl 6O 10 single crystals
NASA Astrophysics Data System (ADS)
Alimpiev, A. I.; Merkulov, A. A.; Solntsev, V. P.; Tsvetkov, E. G.; Matrosov, V. N.; Pestryakov, E. V.
Unlike earlier published works we have established incongruent melting for the compound BeAl 6O 10 (BHA). The conditions of growing crystals from their own melt with a superstoichiometric excess of BeO, using the Czochralski method, have been determined. The nature of inclusions in grown BHA crystals is described. On the basis of X-ray crystal structure analysis and data of spectroscopic studies the symmetry and space group of BHA crystal structure have been refined, as well as uncertainties arising in their interpretation are discussed.
High-speed prediction of crystal structures for organic molecules
NASA Astrophysics Data System (ADS)
Obata, Shigeaki; Goto, Hitoshi
We developed a master-worker type parallel algorithm for allocating tasks of crystal structure optimizations to distributed compute nodes, in order to improve a performance of simulations for crystal structure predictions. The performance experiments were demonstrated on TUT-ADSIM supercomputer system (HITACHI HA8000-tc/HT210). The experimental results show that our parallel algorithm could achieve speed-ups of 214 and 179 times using 256 processor cores on crystal structure optimizations in predictions of crystal structures for 3-aza-bicyclo(3.3.1)nonane-2,4-dione and 2-diazo-3,5-cyclohexadiene-1-one, respectively. We expect that this parallel algorithm is always possible to reduce computational costs of any crystal structure predictions.
Large scale structures in liquid crystal/clay colloids
NASA Astrophysics Data System (ADS)
van Duijneveldt, Jeroen S.; Klein, Susanne; Leach, Edward; Pizzey, Claire; Richardson, Robert M.
Suspensions of three different clays in K15, a thermotropic liquid crystal, have been studied by optical microscopy and small angle x-ray scattering. The three clays were claytone AF, a surface treated natural montmorillonite, laponite RD, a synthetic hectorite, and mined sepiolite. The claytone and laponite were sterically stabilized whereas sepiolite formed a relatively stable suspension in K15 without any surface treatment. Micrographs of the different suspensions revealed that all three suspensions contained large scale structures. The nature of these aggregates was investigated using small angle x-ray scattering. For the clays with sheet-like particles, claytone and laponite, the flocs contain a mixture of stacked and single platelets. The basal spacing in the stacks was independent of particle concentration in the suspension and the phase of the solvent. The number of platelets in the stack and their percentage in the suspension varied with concentration and the aspect ratio of the platelets. The lath shaped sepiolite did not show any tendency to organize into ordered structures. Here the aggregates are networks of randomly oriented single rods.
Multiresponsive hydrogel photonic crystal microparticles with inverse-opal structure.
Wang, Jianying; Hu, Yuandu; Deng, Renhua; Liang, Ruijing; Li, Weikun; Liu, Shanqin; Zhu, Jintao
Hydrogel photonic crystal microparticles (HPCMs) with inverse-opal structure are generated through a combination of microfluidic and templating technique. Temperature and pH responsive HPCMs have firstly been prepared by copolymerizing functional monomers, for example, N-isopropylacrylamide (NIPAm) and methacrylic acid (MAA). HPCMs not only show tunable color variation almost covering the entire wavelength of visible light (above 150 nm of stop-band shift) by simply tailoring temperature or pH value of the solution, but also display rapid response (less than 1 min) due to the small volume and well-ordered porous structure. Importantly, the temperature sensing window of the HPCMs can be enlarged by controlling the transition temperature of the hydrogel matrix, and the HPCMs also exhibit good reversibility and reproducibility for pH response. Moreover, functional species or particles (such as azobenzene derivative or magnetic nanoparticles) can be further introduced into the hydrogel matrix by using post-treatment process. These functionalized HPCMs can respond to the UV/visible light without significantly influencing the temperature and pH response, and thus, multiresponsive capability within one single particle can be realized. The presence of magnetic nanoparticles may facilitate secondary assembly, which has potential applications in advanced optical devices. PMID:23768084
Crystal and magnetic structure of Mn3IrSi
T. Eriksson; R. Lizárraga; S. Felton; L. Bergqvist; Y. Andersson; P. Nordblad; O. Eriksson
A new ternary Ir-Mn-Si phase with stoichiometry Mn3IrSi has been synthesized and found to crystallize in the cubic AlAu4-type structure, space group P213 with Z=4, which is an ordered form of the beta-Mn structure. The unit cell dimension was determined by x-ray powder diffraction to a=6.4973(3) Å. In addition to the crystal structure, we have determined the magnetic structure and
Particle yoyos and their quark structures
Yi Lin; Xiaoya He
Purpose – The purpose of this paper is to investigate such fundamental concepts as mass, charge, and quark structure of the general systemic yoyo model so that this model could be more widely applied in studies of various scientific disciplines. Design\\/methodology\\/approach – Laboratory experiments well documented in quantum mechanics and particle physics are employed as supporting evidence. Findings – A
Liquid-crystal patterns of rectangular particles in a square nanocavity
NASA Astrophysics Data System (ADS)
González-Pinto, Miguel; Martínez-Ratón, Yuri; Velasco, Enrique
Using density-functional theory in the restricted-orientation approximation, we analyze the liquid-crystal patterns and phase behavior of a fluid of hard rectangular particles confined in a two-dimensional square nanocavity of side length H composed of hard inner walls. Patterning in the cavity is governed by surface-induced order as well as capillary and frustration effects and depends on the relative values of the particle aspect ratio ??L/?, with L the length and ? the width of the rectangles (L??), and cavity size H. Ordering may be very different from bulk (H??) behavior when H is a few times the particle length L (nanocavity). Bulk and confinement properties are obtained for the cases ?=1, 3, and 6. In bulk the isotropic phase is always stable at low packing fractions ?=L??0 (with ?0 the average density) and nematic, smectic, columnar, and crystal phases can be stabilized at higher ? depending on ?: For increasing ? the sequence of isotropic to columnar is obtained for ?=1 and 3, whereas for ?=6 we obtain isotropic to nematic to smectic (the crystal being unstable in all three cases for the density range explored). In the confined fluid surface-induced frustration leads to fourfold symmetry breaking in all phases (which become twofold symmetric). Since no director distortion can arise in our model by construction, frustration in the director orientation is relaxed by the creation of domain walls (where the director changes by 90?); this configuration is necessary to stabilize periodic phases. For ?=1 the crystal becomes stable with commensurate transitions taking place as H is varied. These transitions involve structures with different number of peaks in the local density. In the case ?=3 the commensurate transitions involve columnar phases with different number of columns. In the case ?=6 the high-density region of the phase diagram is dominated by commensurate transitions between smectic structures; at lower densities there is a symmetry-breaking isotropic to nematic transition exhibiting nonmonotonic behavior with cavity size. Apart from the present application in a confinement setup, our model could be used to explore the bulk region near close packing in order to elucidate the possible existence of disordered phases at close packing.
Liquid-crystal patterns of rectangular particles in a square nanocavity.
González-Pinto, Miguel; Martínez-Ratón, Yuri; Velasco, Enrique
Using density-functional theory in the restricted-orientation approximation, we analyze the liquid-crystal patterns and phase behavior of a fluid of hard rectangular particles confined in a two-dimensional square nanocavity of side length H composed of hard inner walls. Patterning in the cavity is governed by surface-induced order as well as capillary and frustration effects and depends on the relative values of the particle aspect ratio ??L/?, with L the length and ? the width of the rectangles (L??), and cavity size H. Ordering may be very different from bulk (H??) behavior when H is a few times the particle length L (nanocavity). Bulk and confinement properties are obtained for the cases ?=1, 3, and 6. In bulk the isotropic phase is always stable at low packing fractions ?=L??_{0} (with ?_{0} the average density) and nematic, smectic, columnar, and crystal phases can be stabilized at higher ? depending on ?: For increasing ? the sequence of isotropic to columnar is obtained for ?=1 and 3, whereas for ?=6 we obtain isotropic to nematic to smectic (the crystal being unstable in all three cases for the density range explored). In the confined fluid surface-induced frustration leads to fourfold symmetry breaking in all phases (which become twofold symmetric). Since no director distortion can arise in our model by construction, frustration in the director orientation is relaxed by the creation of domain walls (where the director changes by 90^{?}); this configuration is necessary to stabilize periodic phases. For ?=1 the crystal becomes stable with commensurate transitions taking place as H is varied. These transitions involve structures with different number of peaks in the local density. In the case ?=3 the commensurate transitions involve columnar phases with different number of columns. In the case ?=6 the high-density region of the phase diagram is dominated by commensurate transitions between smectic structures; at lower densities there is a symmetry-breaking isotropic to nematic transition exhibiting nonmonotonic behavior with cavity size. Apart from the present application in a confinement setup, our model could be used to explore the bulk region near close packing in order to elucidate the possible existence of disordered phases at close packing. PMID:24125284
Diffraction phenomena in spontaneous and stimulated radiation by relativistic particles in crystals (Review)
Baryshevsky, V.G. (Inst. of Nuclear Problems, Minsk (Belarus)); Dubovskaya, I.Ya. (Lawrence Berkeley Lab., CA (United States))
This report discusses: the dispersion characteristics of parametric x-ray radiation (PXR) and diffraction radiation of oscillator; cooperative effects in x-radiation by charged particles in crystals; and diffraction x-radiation by relativistic oscillator.
Ultrastructure of Calcareous Dinophytes (Thoracosphaeraceae, Peridiniales) with a Focus on Vacuolar Crystal-Like Particles
Zinssmeister, Carmen; Keupp, Helmut; Tischendorf, Gilbert; Kaulbars, Freya; Gottschling, Marc
Biomineralization in calcareous dinophytes (Thoracosphaeracaea, Peridiniales) takes place in coccoid cells and is presently poorly understood. Vacuolar crystal-like particles as well as collection sites within the prospective calcareous shell may play a crucial role during this process at the ultrastructural level. Using transmission electron microscopy, we investigated the ultrastructure of coccoid cells at an early developmental stage in fourteen calcareous dinophyte strains (corresponding to at least ten species of Calciodinellum, Calcigonellum, Leonella, Pernambugia, Scrippsiella, and Thoracosphaera). The shell of the coccoid cells consisted either of one (Leonella, Thoracosphaera) or two matrices (Scrippsiella and its relatives) of unknown element composition, whereas calcite is deposited in the only or the outer layer, respectively. We observed crystal-like particles in cytoplasmic vacuoles in cells of nine of the strains investigated and assume that they are widespread among calcareous dinophytes. However, similar structures are also found outside the Thoracosphaeraceae, and we postulate an evolutionarily old physiological pathway (possibly involved in detoxification) that later was specialized for calcification. We aim to contribute to a deeper knowledge of the biomineralization process in calcareous dinophytes. PMID:23320120
Multiscale models of colloidal dispersion of particles in nematic liquid crystals
NASA Astrophysics Data System (ADS)
Bennett, T. P.; D'Alessandro, G.; Daly, K. R.
We use homogenization theory to develop a multiscale model of colloidal dispersion of particles in nematic liquid crystals under weak-anchoring conditions. We validate the model by comparing it with simulations by using the Landau-de Gennes free energy and show that the agreement is excellent. We then use the multiscale model to study the effect that particle anisotropy has on the liquid crystal: spherically symmetric particles always reduce the effective elastic constant. Asymmetric particles introduce an effective alignment field that can increase the Fredericks threshold and decrease the switch-off time.
Flash Nanoprecipitation: Particle Structure and Stability
Pustulka, Kevin M.; Wohl, Adam R.; Lee, Han Seung; Michel, Andrew R.; Han, Jing; Hoye, Thomas R.; McCormick, Alon V.; Panyam, Jayanth; Macosko, Christopher W.
Flash nanoprecipitation (FNP) is a process that, through rapid mixing, stabilizes an insoluble low molecular weight compound in a nano-sized, polymer-stabilized delivery vehicle. The polymeric components are typically amphiphilic diblock copolymers (BCPs). In order to fully exploit the potential of FNP, factors affecting particle structure, size, and stability must be understood. Here we show that polymer type, hydrophobicity and crystallinity of the small molecule, and small molecule loading levels all affect particle size and stability. Of the four block copolymers (BCP) that we have studied here, poly(ethylene glycol)-b-poly(lactic-co-glycolic acid) (PEG-b-PLGA) was most suitable for potential drug delivery applications due to its ability to give rise to stable nanoparticles, its biocompatibility, and its degradability. We found little difference in particle size when using PLGA block sizes over the range of 5 to 15kDa. The choice of hydrophobic small molecule was important, as molecules with a calculated water-octanol partition coefficient (clogP) below 6 gave rise to particles that were unstable and underwent rapid Ostwald ripening. Studies probing the internal structure of nanoparticles were also performed. Analysis of differential scanning calorimetry (DSC), cryogenic transmission electron microscopy (cryo-TEM), and 1H-NMR experiments support a three-layer core-shell-corona nanoparticle structure. PMID:24053447
Crystal structure of 2-pentyloxybenzamide
Bugenhagen, Bernhard; Al Jasem, Yosef; Thiemann, Thies
In the title molecule, C12H17NO2, the amide NH2 group is oriented toward the pentyloxy substituent and an intramolecular N—H?O hydrogen bond is formed with the pentyloxy O atom. The benzene ring forms dihedral angles of 2.93?(2) and 5.60?(2)° with the amide group and the pentyloxy group mean planes, respectively. In the crystal, molecules are linked by pairs of N—H?O hydrogen bonds, forming inversion dimers with their molecular planes parallel, but at an offset of 0.45?(1)?Å to each other. These dimers are ordered into two types of symmetry-related columns extended along the a axis, with the mean plane of one set of dimers in a column approximately parallel to (121) and the other in a column approximately parallel to (1-21). The two planes form a dihedral angle of 85.31?(2)°, and are linked via C—H?O hydrogen bonds and C—H?? interactions, forming a three-dimensional framework structure. PMID:25484660
Crystal structure of lithium beryllium hydride
NASA Astrophysics Data System (ADS)
Overhauser, A. W.
Analysis of powder diffraction data, published by Bell and Coates, reveals that LiBeH3 and Li2BeH4 both have an fcc translation group with lattice constants 5.09 and 5.14 Å, respectively. The cubic cell of each contains eight formula units; so the total atomic concentrations, 3.03×1023 and 4.12×1023 cm-3, exceed that of diamond by factors of 1.7 and 2.3. The computed densities are 1.91 and 2.63 g/cm3. Both crystals have a modified perovskite structure involving cubes with edges half the size of the lattice constant. The (otherwise) sc lattice is broken by a chemical superstructure in LiBeH3 and by an orientational superstructure in Li2BeH4. The ``conduction''-electron density of the latter is 4.71×1023 cm3; so the equivalent-sphere-radius parameter is rs=1.51 Bohr, a value in the range typically assumed for metallic hydrogen. Infrared absorption at 1600 cm-1 (~=2300 K) was reported. Consequently, these compounds, if metallic, may manifest the high-temperature superconductivity often envisioned for metallic hydrogen.
Photonic crystals for monitoring fatigue phenomena in steel structures
NASA Astrophysics Data System (ADS)
Zonta, Daniele; Chiappini, Andrea; Chiasera, Alessandro; Ferrari, Maurizio; Pozzi, Matteo; Battisti, Lorenzo; Benedetti, Matteo
This paper introduces the concept and development of a strain sensing system for structural application based on the properties of photonic crystals. Photonic crystals are artificially created periodic structures, usually produced in the thinfilm form, where optical properties are tailored by a periodicity in the refractive index. The idea of using the crystal as a sensor is based on the observation that a distortion in the crystal structure produces a change in the reflected bandwidth. When a photonic crystal is designed to operate in the visible part of the spectrum, a permanent distortion of the film results in a change in its apparent color. This property makes photonic crystals suitable for permanent monitoring of structural elements, as any critical changes in the strain field can be promptly and easily detected by visual inspection. A simple and low-cost example of photonic crystals consists of opals synthesized by vertical deposition. In this contribution we introduce a target application for the fatigue monitoring of wind turbines, and then provide the reader with some basic information concerning modeling of the crystal architecture and fabrication of these structures. Next we discuss their application to strain measurement, specifying how reflection and transmission properties of the opals have to be designed to satisfy the expected strain response of the sensor. Finally, we present the preliminary results of a laboratory validation carried out on thin films applied to a rubber support.
The influence of silica matrix on the crystal structure and high frequency performance of cobalt nanoparticles
Xuegang Lu; Gongying Liang; Qianjin Sun; Caihua Yang
Cobalt–SiO2 nanocomposites were successfully synthesized by chemical precipitation combined H2 reduction method. The influence of SiO2 matrix on the crystal structure and high frequency magnetic properties of cobalt nanoparticles was investigated. Amorphous SiO2 layer, which is adhered to Co particle surface through Si–O–Co bonds, inhibits the growth of the nanoparticles and stabilizes the face-centered-cubic (FCC) structured Co. The FCC-cobalt\\/SiO2 nanocomposites
Synthesis, characterization, crystal structure determination, computational study, and thermal decomposition into NiO nano-particles of a new NiIIL2 Schiff base complex (L = 2-{(E)-[2-chloroethyl)imino]methylphenolate)
NASA Astrophysics Data System (ADS)
Grivani, Gholamhossein; Vakili, Mohammad; Khalaji, Aliakbar Dehno; Bruno, Giuseppe; Rudbari, Hadi Amiri; Taghavi, Maedeh; Tahmasebi, Vida
The Nickel (II) Schiff base complex of NiL2, (L = 2-{(E)-[2-chloroethyl) imino]methylphenolate) have been synthesized and characterized by elemental (CHN) analysis, UV-vis and FT-IR spectroscopy. The molecular structure of [NiL2] was determined by single crystal X-ray diffraction technique. The Schiff base ligand HL acts as a chelating ligand and coordinates via one nitrogen atom and one oxygen atom to the metal center. The nickel (II) center is coordinated by two nitrogen and two oxygen atoms from two Schiff base ligands in an approximately square planar trans-[MN2O2] coordination geometry. Thermogravimetric analysis of NiL2 showed that it decomposed in three stages. In addition, complex NiL2 thermally decomposed in air at 660 °C and the XRD pattern of the obtained solid showed the formation of NiO nanoparticles with an average size of 43 nm. In addition, the conformational analysis and molecular structures of NiL2 were investigated by means of density functional theory (DFT) calculations at B3LYP/6-311G* level and the calculated geometrical parameters were compared with the experimental results.
Evolutionary Crystal Structure Prediction and Novel High-Pressure Phases
Artem R. Oganov; Yanming Ma; Andriy O. Lyakhov; Mario Valle; Carlo Gatti
\\u000a Prediction of stable crystal structures at given pressure-temperature conditions, based only on the knowledge of the chemical\\u000a composition, is a central problem of condensed matter physics. This extremely challenging problem is often termed "crystal\\u000a structure prediction problem", and recently developed evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary\\u000a Xtallography) made an important progress in solving it, enabling efficient and reliable prediction
In vivo protein crystallization opens new routes in structural biology
Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars; Nass, Karol; DePonte, Daniel P; White, Thomas A; Stellato, Francesco; Rehders, Dirk; Liang, Mengning; Andreasson, Jakob; Aquila, Andrew; Bajt, Sasa; Barthelmess, Miriam; Barty, Anton; Bogan, Michael J; Bostedt, Christoph; Boutet, Sébastien; Bozek, John D; Caleman, Carl; Coppola, Nicola; Davidsson, Jan; Doak, R Bruce; Ekeberg, Tomas; Epp, Sascha W; Erk, Benjamin; Fleckenstein, Holger; Foucar, Lutz; Graafsma, Heinz; Gumprecht, Lars; Hajdu, Janos; Hampton, Christina Y; Hartmann, Andreas; Hartmann, Robert; Hauser, Günter; Hirsemann, Helmut; Holl, Peter; Hunter, Mark S; Kassemeyer, Stephan; Kirian, Richard A; Lomb, Lukas; Maia, Filipe R N C; Kimmel, Nils; Martin, Andrew V; Messerschmidt, Marc; Reich, Christian; Rolles, Daniel; Rudek, Benedikt; Rudenko, Artem; Schlichting, Ilme; Schulz, Joachim; Seibert, M Marvin; Shoeman, Robert L; Sierra, Raymond G; Soltau, Heike; Stern, Stephan; Strüder, Lothar; Timneanu, Nicusor; Ullrich, Joachim; Wang, Xiaoyu; Weidenspointner, Georg; Weierstall, Uwe; Williams, Garth J; Wunderer, Cornelia B; Fromme, Petra; Spence, John C H; Stehle, Thilo; Chapman, Henry N; Betzel, Christian; Duszenko, Michael
Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology. PMID:22286384
Crystal structure and characterization of pyrroloquinoline quinone disodium trihydrate
Background Pyrroloquinoline quinone (PQQ), a tricarboxylic acid, has attracted attention as a growth factor, and its application to supplements and cosmetics is underway. The product used for these purposes is a water-soluble salt of PQQ disodium. Although in the past, PQQ disodiumpentahydrates with a high water concentration were used, currently, low hydration crystals of PQQ disodiumpentahydrates are preferred. Results We prepared a crystal of PQQ disodium trihydrate in a solution of ethanol and water, studied its structure, and analyzed its properties. In the prepared crystal, the sodium atom interacted with the oxygen atom of two carboxylic acids as well as two quinones of the PQQ disodium trihydrate. In addition, the hydration water of the prepared crystal was less than that of the conventional PQQ disodium crystal. From the results of this study, it was found that the color and the near-infrared (NIR) spectrum of the prepared crystal changed depending on the water content in the dried samples. Conclusions The water content in the dried samples was restored to that in the trihydrate crystal by placing the samples in a humid environment. In addition, the results of X-ray diffraction (XRD) and X-ray diffraction-differential calorimetry (XRD-DSC) analyses show that the phase of the trihydrate crystal changed when the crystallization water was eliminated. The dried crystal has two crystalline forms that are restored to the original trihydrate crystals in 20% relative humidity (RH). This crystalline (PQQ disodium trihydrate) is stable under normal environment. PMID:22713213
Synthesis and textural evolution of alumina particles with mesoporous structures
Liu Xun [College of Chemistry and Molecular Science, Wuhan University, Wuhan 430072 (China); Peng Tianyou, E-mail: email@example.com [College of Chemistry and Molecular Science, Wuhan University, Wuhan 430072 (China); Yao Jinchun; Lv Hongjin; Huang Cheng [College of Chemistry and Molecular Science, Wuhan University, Wuhan 430072 (China)
Alumina particles with mesostructures were synthesized through a chemical precipitation method by using different inorganic aluminum salts followed by a heterogeneous azeotropic distillation and calcination process. The obtained mesoporous {gamma}-alumina particles were systematically characterized by the X-ray diffraction, transmission electron microscopy and nitrogen adsorption-desorption measurement. Effects of the aluminum salt counter anion, pH value and the azeotropic distillation process on the structural or textural evolution of alumina particles were investigated. It is found that Cl{sup -} in the reaction solution can restrain the textural evolution of the resultant precipitates into two-dimensional crystallized pseudoboehmite lamellae during the heterogeneous azeotropic distillation, and then transformed into {gamma}-Al{sub 2}O{sub 3} particles with mesostructures after further calcination at 1173 K, whereas coexisting SO{sub 4}{sup 2-} can promote above morphology evolution and then transformed into {gamma}-Al{sub 2}O{sub 3} nanofibers after calcination at 1173 K. Moreover nearly all materials retain relatively high specific surface areas larger than 100 m{sup 2} g{sup -1} even after calcinations at 1173 K. - Graphical abstract: Co-existing Cl{sup -} is beneficial for the formation of {gamma}-alumina nanoparticles with mesostructures during the precipitation process. Interparticle and intraparticle mesopores can be derived from acidic solution and near neutral solution, respectively.
Enhanced flux pinning in Bi2212 single crystal embedded with MgO particles
NASA Astrophysics Data System (ADS)
Zhao, B.; Song, W. H.; Wu, X. C.; Huang, W. D.; Pu, M. H.; Du, J. J.; Sun, Y. P.; Ku, H. C.
Bi2Sr2CaCu2O8+icons/Journals/Common/delta" ALT="delta" ALIGN="MIDDLE"/> single crystals embedded with MgO particles were successfully synthesized. Preliminary results indicate that MgO particles introduced during the single crystal growth process have little effect on Tc of the Bi2212 superconductor. The critical current density of the MgO-added single crystal has been increased by over a factor of three at low temperatures below 20 K with high magnetic fields parallel to the c -axis as compared with samples without MgO added. The underlying flux pinning mechanism is discussed in detail.
Photonic Crystal Structures with Tunable Structure Color as Colorimetric Sensors
Wang, Hui; Zhang, Ke-Qin
Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors. PMID:23539027
Infrared response from metallic particles embedded in a single-crystal Si matrix - The layered internal photoemission sensor
NASA Technical Reports Server (NTRS)
Fathauer, R. W.; Iannelli, J. M.; Nieh, C. W.; Hashimoto, Shin
Infrared radiation at wavelengths of 1-2 microns has been detected in a new device labeled the layered internal photoemission sensor. The device structure, which is grown by molecular beam epitaxy, incorporates epitaxial CoSi2 particles with dimensions of 10-50 nm. Radiation absorbed by these particles photoexcites carriers into a surrounding single-crystal silicon matrix. A peak quantum efficiency of 1.3 percent is measured, which is approximately six times higher than in planar CoSi2 Schottky diodes with 5-nm silicide thickness.
Novel photonic crystal cavities and related structures.
Luk, Ting Shan
The key accomplishment of this project is to achieve a much more in-depth understanding of the thermal emission physics of metallic photonic crystal through theoretical modeling and experimental measurements. An improved transfer matrix technique was developed to enable incorporation of complex dielectric function. Together with microscopic theory describing emitter radiative and non-radiative relaxation dynamics, a non-equilibrium thermal emission model is developed. Finally, experimental methodology was developed to measure absolute emissivity of photonic crystal at high temperatures with accuracy of +/-2%. Accurate emissivity measurements allow us to validate the procedure to treat the effect of the photonic crystal substrate.
Crystal structure of ?-d,l-allose
Ishii, Tomohiko; Senoo, Tatsuya; Kozakai, Taro; Fukada, Kazuhiro; Sakane, Genta
The title compound, C6H12O6, a C-3 position epimer of glucose, was crystallized from an equimolar mixture of d- and l-allose. It was confirmed that d-allose (l-allose) formed ?-pyranose with a 4 C 1 (1 C 4) conformation in the crystal. In the crystal, molecules are linked by O—H?O hydrogen bond, forming a three-dimensional framework. The cell volume of the racemic ?-d,l-allose is 739.36?(3)?Å3, which is about 10?Å3 smaller than that of chiral ?-d-allose [V = 751.0?(2)?Å3].
Band structure analysis of crystals with discontinuous metallic wires
Halim Boutayeb; Tayeb A. Denidni; Abdel Razik Sebak; Larbi Talbi
The band structure for normal propagation of crystals with finite straight metallic wires is studied for different wire diameters and lengths. The crystal is considered as a set of parallel grids. Dispersion characteristics are obtained by using a transmission line model where the parameters are calculated from the reflection and transmission coefficients of the grids. These coefficients are computed rigorously
Theoretical Determination of the Efficiency of Aerosol Particle Collection by Falling Columnar Ice Crystals
N. L. Miller; P. K. Wano
A theoretical model for the removal of aerosol particles by falling columnar ice crystals which incorporates gravitational, inertial, thermophoreic, diffusiophoretic, and electrostatic mechanisms has been formulated. The results of this trajectory model, combined with earlier resuslts, determine the collection efficiency for submicron particles as a flux onto a collector surface for any geometry and due to Brownian diffusion, thermo- and
Hydroflux synthesis and crystal structure of new lanthanide tungstate oxyhydroxides
NASA Astrophysics Data System (ADS)
Latshaw, Allison M.; Smith, Mark D.; Chance, W. Michael; zur Loye, Hans-Conrad
Single crystals of Na5Ln(OH)6WO4 where Ln = Er, Tm, and Yb were grown out of a NaOH hydroflux. The crystals were characterized by single crystal X-ray diffraction and were found to crystallize in the monoclinic space group I2/a. The lattice parameter ranges for the three structures are a = 11.2024(7) Å-11.2412(6) Å, b = 16.1850(10) Å-16.2220(10) Å, and c = 11.9913(7) Å-12.0323(7) Å while the ? angle range is 101.999(2)°-102.025(2)°.
The Crystal Structures of the Tryparedoxin-Tryparedoxin Peroxidase Couple Unveil the Structural Determinants of
Paris-Sud XI, Université de
The Crystal Structures of the Tryparedoxin-Tryparedoxin Peroxidase Couple Unveil the Structural of electrons by the tryparedoxin/tryparedoxin peroxidase system (TXN/TXNPx) to reduce the hydroperoxides A (2012) The Crystal Structures of the Tryparedoxin-Tryparedoxin Peroxidase Couple Unveil the Structural
Programmably structured plasma waveguide for development of table-top photon and particle sources
Hung, T.-S.; Ho, Y.-C.; Wong, S.-J.; Chen, S.-Y. [Department of Physics, National Central University, Jhong-Li 320, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Chang, Y.-L. [Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Department of Physics, National Chung Cheng University, Chia-Yi 621, Taiwan (China); Chu, H.-H. [Department of Physics, National Central University, Jhong-Li 320, Taiwan (China); Lin, J.-Y. [Department of Physics, National Chung Cheng University, Chia-Yi 621, Taiwan (China); Wang, J. [Department of Physics, National Central University, Jhong-Li 320, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Department of Physics, National Taiwan University, Taipei 106, Taiwan (China)
Programmable fabrication of longitudinal spatial structures in an optically preformed plasma waveguide in a gas jet was achieved, by using laser machining with a liquid-crystal spatial light modulator as the pattern mask. Fabrication of periodic structures with a minimal period of 200 {mu}m and density-ramp structures with a minimal slope length of 100 {mu}m was attained. The technique is useful for the optimization of various laser-plasma-based photon and particle sources.
Crystal Structure of Human Plasma Platelet-Activating Factor Acetylhydrolase
Samanta, U.; Bahnson, B
Human plasma platelet-activating factor (PAF) acetylhydrolase functions by reducing PAF levels as a general anti-inflammatory scavenger and is linked to anaphylactic shock, asthma, and allergic reactions. The enzyme has also been implicated in hydrolytic activities of other pro-inflammatory agents, such as sn-2 oxidatively fragmented phospholipids. This plasma enzyme is tightly bound to low and high density lipoprotein particles and is also referred to as lipoprotein-associated phospholipase A{sub 2}. The crystal structure of this enzyme has been solved from x-ray diffraction data collected to a resolution of 1.5{angstrom}. It has a classic lipase {alpha}/{beta}-hydrolase fold, and it contains a catalytic triad of Ser{sup 273}, His{sup 351}, and Asp{sup 296}. Two clusters of hydrophobic residues define the probable interface-binding region, and a prediction is given of how the enzyme is bound to lipoproteins. Additionally, an acidic patch of 10 carboxylate residues and a neighboring basic patch of three residues are suggested to play a role in high density lipoprotein/low density lipoprotein partitioning. A crystal structure is also presented of PAF acetylhydrolase reacted with the organophosphate compound paraoxon via its active site Ser{sup 273}. The resulting diethyl phosphoryl complex was used to model the tetrahedral intermediate of the substrate PAF to the active site. The model of interface binding begins to explain the known specificity of lipoprotein-bound substrates and how the active site can be both close to the hydrophobic-hydrophilic interface and at the same time be accessible to the aqueous phase.
Optically Generated Reconfigurable Photonic Structures of Elastic Quasiparticles in Frustrated Cholesteric Liquid Crystals
Smalyukh,, I. I.; Kaputa, D.; Kachynski, A. V.; Kuzmin, A. N.; Ackerman, P. J.; Twombly, C. W.; Lee, T.; Trivedi, R. P.; Prasad, P. N.
We describe laser-induced two-dimensional periodic photonic structures formed by localized particle-like excitations in an untwisted confined cholesteric liquid crystal. The individual particle-like excitations (dubbed 'Torons') contain three-dimensional twist of the liquid crystal director matched to the uniform background director field by topological point defects. Using both single-beam-steering and holographic pattern generation approaches, the periodic crystal lattices are tailored by tuning their periodicity, reorienting their crystallographic axes, and introducing defects. Moreover, these lattices can be dynamically reconfigurable: generated, modified, erased and then recreated, depending on the needs of a particular photonic application. This robust control is performed by tightly focused laser beams of power 10-100 mW and by low-frequency electric fields at voltages {approx}10 V applied to the transparent electrodes.
Crystallization, melting, and structure of water nanoparticles at atmospherically relevant temperatures.
Johnston, Jessica C; Molinero, Valeria
Water nanoparticles play an important role in atmospheric processes, yet their equilibrium and nonequilibrium liquid-ice phase transitions and the structures they form on freezing are not yet fully elucidated. Here we use molecular dynamics simulations with the mW water model to investigate the nonequilibrium freezing and equilibrium melting of water nanoparticles with radii R between 1 and 4.7 nm and the structure of the ice formed by crystallization at temperatures between 150 and 200 K. The ice crystallized in the particles is a hybrid form of ice I with stacked layers of the cubic and hexagonal ice polymorphs in a ratio approximately 2:1. The ratio of cubic ice to hexagonal ice is insensitive to the radius of the water particle and is comparable to that found in simulations of bulk water around the same temperature. Heating frozen particles that contain multiple crystallites leads to Ostwald ripening and annealing of the ice structures, accompanied by an increase in the amount of ice at the expense of the liquid water, before the particles finally melt from the hybrid ice I to liquid, without a transition to hexagonal ice. The melting temperatures T(m) of the nanoparticles are not affected by the ratio of cubic to hexagonal layers in the crystal. T(m) of the ice particles decreases from 255 to 170 K with the particle size and is well described by the Gibbs-Thomson equation, T(m)(R) = T(m)(bulk) - K(GT)/(R - d), with constant K(GT) = 82 ± 5 K·nm and a premelted liquid of width d = 0.26 ± 0.05 nm, about one monolayer. The freezing temperatures also decrease with the particles' radii. These results are important for understanding the composition, freezing, and melting properties of ice and liquid water particles under atmospheric conditions. PMID:22452637
Metal insulator semiconductor structure single crystal silicon liquid crystal light valve
NASA Astrophysics Data System (ADS)
Gao, JiaoBo; Ye, Ke-fei; Feng, Yue-you
Detailed description of the structure, operation, fabrication, and performance of a fast-response metal- insulator-semiconductor structure single crystal silicon liquid crystal light valve (MIS-Si-LCLV) is given. A 45 degree(s) twisted nematic liquid crystal configuration has been utilized. A MIS-Si-LCLV is demonstrated with a limiting resolution of 40 lp/mm over a 45 mm aperture and contrast ratios of > 50:1, input light sensitivities at (lambda) equals 930 nm ((Delta) (lambda) equals 40 nm) of better than 30 (mu) W/cm2 and response times as fast as 20 ms have been measured.
Enhanced high-temperature ice nucleation ability of crystallized aerosol particles after preactivation at low temperature
NASA Astrophysics Data System (ADS)
Wagner, Robert; Möhler, Ottmar; Saathoff, Harald; Schnaiter, Martin
In cloud chamber experiments with crystallized aqueous ammonium sulfate, oxalic acid, and succinic acid solution droplets, we have studied a preactivation mechanism that markedly enhances the particles' heterogeneous ice nucleation ability. First cloud expansion experiments were performed at a high temperature (267-244 K) where the crystallized particles did not promote any heterogeneous ice nucleation. Ice nucleation at this temperature, however, could be triggered by temporarily cooling the crystallized particles to a lower temperature. This is because upon crystallization, residuals of the aqueous solution are trapped within the crystals. These captured liquids can freeze when cooled below their respective homogeneous or heterogeneous freezing temperature, leading to the formation of ice pockets in the crystalline particles. When warmed again to the higher temperature, ice formation by the preactivated particles occurred via depositional and deliquescence-induced ice growth, with ice active fractions ranging from 1 to 4% and from 4 to 20%, respectively. Preactivation disappeared above the eutectic temperature, which for the organic acids are close to the melting point of ice. This mechanism could therefore contribute to the very small fraction of atmospheric aerosol particles that are still ice active well above 263 K.
Structural, optical and electrical characteristics of a new NLO crystal
NASA Astrophysics Data System (ADS)
D'silva, E. D.; Krishna Podagatlapalli, G.; Venugopal Rao, S.; Dharmaprakash, S. M.
A new nonlinear optical (NLO) organic crystal 1-[4-({(E)-[4-(methylsulfanyl)phenyl]methylidene}amino)phenyl]ethanone (MMP) has been grown by slow evaporation technique at ambient temperature. The crystal structure of MMP was determined by single crystal X-ray diffraction. MMP crystallizes in non-centrosymmetric monoclinic system with space group P21. The FT-IR spectrum recorded for new crystal confirmed the presence of various functional groups in the material. MMP was found to be thermally stable up to 300 °C. The grown crystal was optically transparent in the wavelength range of 400-1100 nm. The second harmonic generation (SHG) efficiency of the crystal was measured by the classical powder technique using Nd:YAG laser and was found to be 4.13 times more efficient than reference material, urea. Third order nonlinear parameters were measured by employing the Z-scan technique. The laser damage threshold for MMP crystal was determined to be 4.26 GW/cm2. The Brewster angle technique was employed to measure the refractive index of the crystal and the values for green and red wavelengths were found to be 1.35 and 1.33, respectively. The dielectric and electrical measurements were carried out to study the different polarization mechanisms and conductivity of the crystal.
The Effect of High Pressure on Crystal Structure Topology
Wood, Peter Andrew
This thesis describes the effects of the application of high pressure to single crystals of small organic compounds. A range of different structural analysis techniques have been used with the emphasis on whole molecule interactions rather than atom...
A machine learning approach to crystal structure prediction
Fischer, Christopher Carl
This thesis develops a machine learning framework for predicting crystal structure and applies it to binary metallic alloys. As computational materials science turns a promising eye towards design, routine encounters with ...
Slow light performance enhancement of Bragg slot photonic crystal waveguide with particle swarm optimization algorithm
NASA Astrophysics Data System (ADS)
Abedi, Kambiz; Mirjalili, Seyed Mohammad
Recently, majority of current research in the field of designing Phonic Crystal Waveguides (PCW) focus in extracting the relations between output slow light properties of PCW and structural parameters through a huge number of tedious non-systematic simulations in order to introduce better designs. This paper proposes a novel systematic approach which can be considered as a shortcut to alleviate the difficulties and human involvements in designing PCWs. In the proposed method, the problem of PCW design is first formulated as an optimization problem. Then, an optimizer is employed in order to automatically find the optimum design for the formulated PCWs. Meanwhile, different constraints are also considered during optimization with the purpose of applying physical limitations to the final optimum structure. As a case study, the structure of a Bragg-like Corrugation Slotted PCWs (BCSPCW) is optimized by using the proposed method. One of the most computationally powerful techniques in Computational Intelligence (CI) called Particle Swarm Optimization (PSO) is employed as an optimizer to automatically find the optimum structure for BCSPCW. The optimization process is done by considering five constraints to guarantee the feasibility of the final optimized structures and avoid band mixing. Numerical results demonstrate that the proposed method is able to find an optimum structure for BCSPCW with 172% and 100% substantial improvements in the bandwidth and Normalized Delay-Bandwidth Product (NDBP) respectively compared to the best current structure in the literature. Moreover, there is a time domain analysis at the end of the paper which verifies the performance of the optimized structure and proves that this structure has low distortion and attenuation simultaneously.
Improvement of the theory of heterogeneous crystallization of metals and choice of the nanomodifier particle sizes
NASA Astrophysics Data System (ADS)
Kats, A. M.
A numerical analysis of the joint effect that the radii of the nucleus and the insoluble impurity particle have on the nucleation work and the nucleation rate of crystallization centers has been performed. The extreme dependence of these parameters on the impurity particle size has been established for the first time and scientifically justified practical recommendations on the choice of nanomodifier particle sizes have been elaborated.
Crystal morphology characteristics of the domain structure and superconducting properties of 123 single crystals
A. I. Otko; A. A. Nosenko; O. P. Bal'Va; M. B. Kosmyna; S. F. Prokopovich; A. S. Chernyi
The characteristics of the domain structure of YBa(2-x)Sr(x)Cu3O(7-delta) single crystals are investigated for x = 0, 0.2, 0.4. and 0.5. A domain structure analysis is also carried out for TmBa(1.5)Sr(0.5)Cu3O(7-delta) single crystals. Various types of domain structure in these materials are identified, and a relationship is established between the domain structure type and the characteristics of the superconducting transition.
The crystal structure of faustite and its copper analogue turquoise
U. Kolitsch; G. Giester
The crystal structure of faustite, ZnAI6(P04MOHhAH20, was determined using single-crystal data (Mo-KIX X-radiation, CCD area detector, 1624 unique reflections, RI = 4.91 %, wR2 = 9.23%), and compared with results of a reinvestigation of the structure of its copper analogue turquoise, CuAI6(P04MOH)gAH20 (2737 unique reflections, RI = 2.81%, wR2 = 6.90%). Both are isostructural and crystallize in space group PI,
Crystal structure of a actinide metals at high compression
Fast, L. [Condensed Matter Theory Group, Physics Department, Uppsala University, Box 530 (Sweden); Soederlind, P. [Physics Department, Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)
The crystal structures of some light actinide metals are studied theoretically as a function of applied pressure. The first principles electronic structure theory is formulated in the framework of density functional theory, with the gradient corrected local density approximation of the exchange-correlation functional. The light actinide metals are shown to be well described as itinerant (metallic) f-electron metals and generally, they display a crystal structure which have, in agreement with previous theoretical suggestions, increasing degree of symmetry and closed-packing upon compression. The theoretical calculations agree well with available experimental data. At very high compression, the theory predicts closed-packed structures such as the fcc or the hcp structures or the nearly closed-packed bcc structure for the light actinide metals. A simple canonical band picture is presented to explain in which particular closed-packed form these metals will crystallize at ultra-high pressure. {copyright} {ital 1996 American Institute of Physics.}
Transport of particles by a thermally induced gradient of the order parameter in nematic liquid crystals
NASA Astrophysics Data System (ADS)
Škarabot, M.; Lokar, Ž.; Muševi?, I.
We demonstrate manipulation and transport of microparticles and even fluorescent molecules by the thermally induced gradient of the order parameter in the nematic liquid crystal. We use IR light absorption of the tightly focused beam of laser tweezers to heat locally a thin layer of the nematic liquid crystal by several degrees. This creates a spatial gradient of temperature of the nematic liquid crystal over separations of several tens of micrometers. We show that a dipolar colloidal particle is attracted into the hot spot of the laser tweezers. The depth of the trapping potential scales linearly with particle radius, indicating that the trapping mechanism is due to elastic self-energy of the distorted nematic liquid crystal around the particle and softening of the elasticity with increased temperature of the liquid crystal. We also demonstrate that this thermal trapping mechanism is efficient down to the nanoscale, as fluorescent molecules are also transported into hotter regions of the liquid crystal. This effect is absent in the isotropic phase, which calls into question particle transport due to the Soret effect.
An enzyme immobilization platform for biosensor designs of direct electrochemistry using flower-like ZnO crystals and nano-sized gold particles
Yuwei Zhang; Yun Zhang; Hua Wang; Bani Yan; Guoli Shen; Ruqin Yu
A novel immobilization platform has been developed for fabricating enzyme-based biosensors of direct electrochemistry by synergistically using ZnO crystals and nano-sized gold particles (Nanogold). ZnO crystals were synthesized with flower-like structure to be casted on the electrode mediated by chitosan so as to provide larger surface area for anchoring horseradish peroxidase (HRP)-labeled Nanogold. The resultant enzyme biosensor was tested for
The Crystal and Molecular Structure of Dianhydrogossypol
Samat A. Talipov; Azimjon A. Mamadrakhimov; Zavkibek G. Tiljakov; Michael K. Dowd; Bakhtiyar T. Ibragimov; Muhabbat T. Xonkeldieva
Dianhydrogossypol (4,4?-dihydroxy-5,5?-diisopropyl-7,7?-dimethyl-bis(3H-naphtho[1,8-bc]furan-3-one)) was made by refluxing gossypol in m-xylene. Proton NMR spectroscopy was used to confirm that complete conversion was achieved over a time period of several hours.\\u000a Single crystals of the compound were obtained by slow evaporation from dichloromethane. Diffraction studies indicate that\\u000a this crystal form is tetragonal with a I41\\/a space group and with cell dimensions of a = b = 33.8265(4) Å,
Crystal Structure of DL-Alanine Sulfate
Yu. I. Smolin; A. E. Lapshin; G. A. Pankova; Yu. N. Osipova
Crystals of [(C3NO2H7)2·H2SO4] composition were analyzed by single-crystal X-ray diffraction (triclinic, P\\u000a$${\\\\bar 1}$$\\u000a, a = 7.431(3), b = 9.826(3), c = 10.081(3) Å, a = 120.07(5), ß = 104.73(5), ? = 94.24(5)°). The independent part of the unit cell contains two alanine molecules and one sulfate ion. The amino group is additionally protonated in both molecules. One of
Studies on Crystals of Intact Bacterial Ribosomal Particles
Yonath, Ada E.
(Shevack et aI., 1985) and from Bacillus stearothermophilus (Yonath et aI., 1980, 1982a, b, 1983a, bI., 1984a, b; Leonard et aI., 1984). Large crystals of the 50S subunits from B. stearothermophilus and H
Colloidal particles in liquid crystal films and at interfaces
Mykola Tasinkevych; Denis Andrienko
This mini-review discusses the recent contribution of theoretical and computational physics as well as experimental efforts to the understanding of the behavior of colloidal particles in confined geometries and at liquid crystalline interfaces. Theoretical approaches used to study trapping, long- and short-range interactions, and assembly of solid particles and liquid inclusions are outlined. As an example, an interaction of a spherical colloidal particle with a nematic-isotropic interface and a pair interaction potential between two colloids at this interface are obtained by minimizing the Landau-de Gennes free energy functional using the finite-element method with adaptive meshes.
The Crystal and Molecular Structure of Dianhydrogossypol
Technology Transfer Automated Retrieval System (TEKTRAN)
Dianhydrogossypol (4,4'-dihydroxy-5,5'-diisopropyl-7,7'-dimethyl-bis(3H-naphtho[1,8-bc]furan-3-one)) was made by refluxing gossypol in m-xylene. Proton NMR confirmed that complete conversion was achieved over several hours. Single crystals were obtained by slow evaporation of the product from dichl...
The local structure and crystallization of FeB nanoparticle
NASA Astrophysics Data System (ADS)
Kien, P. H.; Thao, N. T.; Hung, P. K.
Using molecular dynamics simulation, we have studied the structural evolution of FeB nanoparticle under annealing and the physical properties of its polymorphs such as crystalline, amorphous and mixed samples. The main focus of present work is the crystallization mechanism and the local structure of polymorphs of FeB nanoparticle. The simulation result shows that the amorphous sample undergoes the crystallization via the nucleation mechanism. During the crystallization, B atoms move out the places where the Fe crystal locates, and diffuse to the boundary region of Fe crystal. The crystal growth proceeds when this boundary region attains specific properties which are defined by the fraction of B atoms and the energies of AB-atoms and CB-atoms. Further our study indicates that unlike amorphous sample, the crystalline and mixed samples consist of three distinct parts including Fe crystalline and two FeB amorphous parts (B-poor and B-rich amorphous part). The different polymorphs of FeB nanoparticle differ in the local structure, size of Fe crystal and energies of different type atoms.
Structural Aspects of Saltatory Particle Movement
Rebhun, Lionel I.
A variety of cells possess particles which show movements statistically different from Brownian movements. They are characterized by discontinuous jumps of 2–30 µ at velocities of 0.5–5 µ/sec or more. A detailed analysis of these saltatory, jumplike movements makes it most likely that they are caused by transmission of force to the particles by a fiber system in the cell outside of the particle itself. Work with isolated droplets of cytoplasm from algae demonstrates a set of fibers involved in both cytoplasmic streaming and saltatory motion, suggesting that both phenomena are related to the same force-generating set of fibers. Analysis of a variety of systems in which streaming and/or saltatory movement occurs reveals two types of fiber systems spatially correlated with the movement, microtubules and 50 A microfilaments. The fibers in Nitella (alga) are of the microfilament type. In other systems (melanocyte processes, mitotic apparatus, nerve axons) microtubules occur. A suggestion is made, based on work on cilia, that a microtubule-microfilament complex may be present in those cases in which only microtubules appear to be present, with the microfilament closely associated with or buried in the microtubule wall. If so, then microfilaments, structurally similar to smooth muscle filaments, may be a force-generating element in a very wide variety of saltatory and streaming phenomena. PMID:6069914
Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal
NASA Astrophysics Data System (ADS)
Marchewka, M. K.; Pietraszko, A.
The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2 1/ c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H⋯O and N-H⋯O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-H⋯? type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.
Single-crystal growth, crystal and electronic structure of NaCoO 2
Yasuhiko Takahashi; Yoshito Gotoh; Junji Akimoto
Single crystals of NaCoO2 have been successfully synthesized for the first time by a flux method at 1323K. A single-crystal X-ray diffraction study confirmed the trigonal R3?m space group and the lattice parameters a=2.8897(15)A?, c=15.609(3)A?. The crystal structure has been refined to the conventional values R=1.9% and wR=2.1% for 309 independent observed reflections. The electron density distribution of NaCoO2 has
Crystal Structure and Interaction Dependence of the Crystal-Melt Interfacial Free Energy
Ruslan L. Davidchack; Brian B. Laird
We examine via molecular simulation the dependence of the crystal-melt interfacial free energy gamma on molecular interaction and crystal structure (fcc vs bcc) for systems interacting with inverse-power repulsive potentials, u(r)=?(sigma\\/r)n, 6<=n<=100. Both the magnitude and anisotropy of gamma are found to increase as the range of the potential increases. Also we find that gammabcc
Datamining protein structure databanks for crystallization patterns of proteins.
Valafar, Homayoun; Prestegard, James H; Valafar, Faramarz
A study of 345 protein structures selected among 1,500 structures determined by nuclear magnetic resonance (NMR) methods, revealed useful correlations between crystallization properties and several parameters for the studied proteins. NMR methods of structure determination do not require the growth of protein crystals, and hence allow comparison of properties of proteins that have or have not been the subject of crystallographic approaches. One- and two-dimensional statistical analyses of the data confirmed a hypothesized relation between the size of the molecule and its crystallization potential. Furthermore, two-dimensional Bayesian analysis revealed a significant relationship between relative ratio of different secondary structures and the likelihood of success for crystallization trials. The most immediate result is an apparent correlation of crystallization potential with protein size. Further analysis of the data revealed a relationship between the unstructured fraction of proteins and the success of its crystallization. Utilization of Bayesian analysis on the latter correlation resulted in a prediction performance of about 64%, whereas a two-dimensional Bayesian analysis succeeded with a performance of about 75%. PMID:12594078
Liquid Crystal Phase Behaviour of Attractive Disc-Like Particles
Wu, Liang; Jackson, George; Müller, Erich A.
We employ a generalized van der Waals-Onsager perturbation theory to construct a free energy functional capable of describing the thermodynamic properties and orientational order of the isotropic and nematic phases of attractive disc particles. The model mesogen is a hard (purely repulsive) cylindrical disc particle decorated with an anisotropic square-well attractive potential placed at the centre of mass. Even for isotropic attractive interactions, the resulting overall inter-particle potential is anisotropic, due to the orientation-dependent excluded volume of the underlying hard core. An algebraic equation of state for attractive disc particles is developed by adopting the Onsager trial function to characterize the orientational order in the nematic phase. The theory is then used to represent the fluid-phase behaviour (vapour-liquid, isotropic-nematic, and nematic-nematic) of the oblate attractive particles for varying values of the molecular aspect ratio and parameters of the attractive potential. When compared to the phase diagram of their athermal analogues, it is seen that the addition of an attractive interaction facilitates the formation of orientationally-ordered phases. Most interestingly, for certain aspect ratios, a coexistence between two anisotropic nematic phases is exhibited by the attractive disc-like fluids. PMID:23965962
Crystal structure of a nematode-infecting virus
Guo, Yusong R.; Hryc, Corey F.; Jakana, Joanita; Jiang, Hongbing; Wang, David; Chiu, Wah; Zhong, Weiwei; Tao, Yizhi J.
Orsay, the first virus discovered to naturally infect Caenorhabditis elegans or any nematode, has a bipartite, positive-sense RNA genome. Sequence analyses show that Orsay is related to nodaviruses, but molecular characterizations of Orsay reveal several unique features, such as the expression of a capsid–? fusion protein and the use of an ATG-independent mechanism for translation initiation. Here we report the crystal structure of an Orsay virus-like particle assembled from recombinant capsid protein (CP). Orsay capsid has a T = 3 icosahedral symmetry with 60 trimeric surface spikes. Each CP can be divided into three regions: an N-terminal arm that forms an extended protein interaction network at the capsid interior, an S domain with a jelly-roll, ?-barrel fold forming the continuous capsid, and a P domain that forms surface spike projections. The structure of the Orsay S domain is best aligned to T = 3 plant RNA viruses but exhibits substantial differences compared with the insect-infecting alphanodaviruses, which also lack the P domain in their CPs. The Orsay P domain is remotely related to the P1 domain in calicivirus and hepatitis E virus, suggesting a possible evolutionary relationship. Removing the N-terminal arm produced a slightly expanded capsid with fewer nucleic acids packaged, suggesting that the arm is important for capsid stability and genome packaging. Because C. elegans-Orsay serves as a highly tractable model for studying viral pathogenesis, our results should provide a valuable structural framework for further studies of Orsay replication and infection. PMID:25136116
Effects of Nano-Particle Doping on the Physical Properties of Ferroelectric Liquid Crystals
NASA Astrophysics Data System (ADS)
Neeraj, Neeraj; Raina, K. K.
Ferroelectric liquid crystals (FLCs) are special class of lamellar crystal materials. They are used as optical materials in several display devices. The fast switching responses have made them best suited over conventional nematic and chiral nematic systems. Electro-optic studies have been carried out on silica nano-particles (SiO2) dispersed FLC mixture in planer aligned sample cells. The effect of temperature and bias field on the switching characteristics of FLC composites were studied and compared. These studies suggest high contrast over undoped system. Our results indicate that the doped FLC composites are promising materials for electro-optical and liquid crystal display (LCD) devices.
Predicting crystal structure by merging data mining with quantum mechanics
Ceder, Gerbrand
ARTICLES Predicting crystal structure by merging data mining with quantum mechanics CHRISTOPHER email@example.com Published online: 9 July 2006; doi:10.1038/nmat1691 Modern methods of quantum mechanics have proved with quantum mechanics if an algorithm to direct the search through the large space of possible structures
Structures of Four Crystal Forms of Decaplanin by Christopher Lehmanna
birthday The glycopeptide antibiotic decaplanin (1; formerly known as MM 47761 and M86-1410) crystallizes facilitated the MAD structure solution. The structures contain the dimer units typical of antibiotics related threat presented by pathogens that have developed multiple resistance to antibiotics [1], in particular
Hexagonal structures for two-dimensional photonic crystals
D. Cassagne; C. Jouanin; D. Bertho
Periodic dielectric structures have been recently proposed to inhibit spontaneous emission in semiconductors. From this suggestion, the new concepts of photonic band gap and photonic crystal have been developed. Zero-threshold lasers, waveguides, antenna substrates, filters and polarizers are promising applications. We propose a new class of two-dimensional periodic dielectric structures with hexagonal symmetry. We study the gap opening according to
Optimization of liquid crystal structures for real time holography applications.
Sahraoui, B; Anczykowska, A; Bartkiewicz, S; Mysliwiec, J
In this paper we present results of experiments designed to increase our understanding of the photorefractive effect occurring during processes of dynamic hologram generation in Hybrid Photorefractive Liquid Crystal Structures (HPLCS). We also propose equivalent mathematical model which can be used to optimize those structures in order to obtain the highest diffraction efficiency in possibly shortest time. PMID:22109472
Boron-oxygen polyanion in the crystal structure of tunellite
Clark, J.R.
The crystal structure of tunellite, SrO??3B2O 3??4H2O, with infinite sheets of composition n[B6O9(OH)2]2-, has cations and water molecules in the spaces within the sheets. Adjacent sheets are held together by hydrogen bonding through the water molecules. The boron-oxygen polyanions provide the first example in hydrated borate crystals of one oxygen linked to three borons.
Crystal Structure of L-Histidinium 2-Nitrobenzoate
Natarajan, Subramanian; Moovendaran, Kalimuthu; Kalyana Sundar, Jeyaperumal; Ravikumar, Krishnan
A new nonlinear optical organic compound, namely, L-histidinium 2-nitrobenzoate (abbreviated as LH2NB (I); ([C6H10N3O2]+ [C7H4NO4]?)), was synthesized. The molecular structure of LH2NB (I) was elucidated using single crystal X-ray diffraction technique. The second harmonic generation (SHG) efficiency of this compound is about two times that of the standard potassium dihydrogen phosphate crystals. PMID:22536482
Crystal Structures of Two Putative Phosphoheptose
Seetharaman,J.; Rajashankar, K.; Solarzano, V.; Kniewel, R.; Lima, C.; Bonanno, J.; Burley, S.; Swaminathan, S.
Structural genomic centers use both NMR spectroscopic and X-ray crystallographic methods to determine three-dimensional structures of proteins on a genomic scale in a high-throughput mode and to deposit in the PDB. The main goal of structural genomics is to determine a large number of protein structures to complement the ever-expanding database of genome sequences. Another role of structural genomics is to delineate the correspondence between sequence and structure space; a number of protein structures from otherwise unrelated (i.e., 8-10% sequence identity) families often prove to have remarkably similar folds. This finding, in turn, allows better understanding of the structure-function relationships in those proteins for which either structures are not available or cannot be experimentally determined.
Crystal engineering with thioureas: A structure-based inquiry
NASA Astrophysics Data System (ADS)
Paisner, Kathryn A.
Structural trends applicable to crystal engineering were studied in three classes of thiourea-based compounds. The aim of the study was to identify, predict, and ultimately design reliable single-molecule structural features, which could then be used to engineer crystals with desirable properties. In one class of compounds, this goal was achieved: N-alkyl and N-aryl derivatives of N,N'-bis(3-thioureidopropyl)piperazine adopted an identical conformation in the solid state, which resulted in near-identical crystal packing. A second class of closely related compounds, N-substituted tris(2-thioureidoethyl)amines, showed no such reliability in the solid state, likely because the parent structure lacked hydrogen-bonding functionalities sufficient to control intramolecular structure. In the third class of compounds that we studied, 1-benzoyl-3-(2-pyridyl)thioureas, substitution patterns were often predictive of molecular conformation; however, these intramolecular trends did not lead to recognizable crystal packing motifs. Nevertheless, certain physical properties observed in this last class of compounds---color, solubility, and often crystallinity---were conformer-specific, interestingly without any apparent relevance to crystal lattice structure. Solution-state and solid-state conformational trends in these 1-benzoyl-3-(2-pyridyl)thioureas have been documented, and speculations as to the source of color in one of the two observed conformations have been noted.
Ice crystallization in ultrafine water-salt aerosols: nucleation, ice-solution equilibrium, and internal structure.
Hudait, Arpa; Molinero, Valeria
Atmospheric aerosols have a strong influence on Earth's climate. Elucidating the physical state and internal structure of atmospheric aqueous aerosols is essential to predict their gas and water uptake, and the locus and rate of atmospherically important heterogeneous reactions. Ultrafine aerosols with sizes between 3 and 15 nm have been detected in large numbers in the troposphere and tropopause. Nanoscopic aerosols arising from bubble bursting of natural and artificial seawater have been identified in laboratory and field experiments. The internal structure and phase state of these aerosols, however, cannot yet be determined in experiments. Here we use molecular simulations to investigate the phase behavior and internal structure of liquid, vitrified, and crystallized water-salt ultrafine aerosols with radii from 2.5 to 9.5 nm and with up to 10% moles of ions. We find that both ice crystallization and vitrification of the nanodroplets lead to demixing of pure water from the solutions. Vitrification of aqueous nanodroplets yields nanodomains of pure low-density amorphous ice in coexistence with vitrified solute rich aqueous glass. The melting temperature of ice in the aerosols decreases monotonically with an increase of solute fraction and decrease of radius. The simulations reveal that nucleation of ice occurs homogeneously at the subsurface of the water-salt nanoparticles. Subsequent ice growth yields phase-segregated, internally mixed, aerosols with two phases in equilibrium: a concentrated water-salt amorphous mixture and a spherical cap-like ice nanophase. The surface of the crystallized aerosols is heterogeneous, with ice and solution exposed to the vapor. Free energy calculations indicate that as the concentration of salt in the particles, the advance of the crystallization, or the size of the particles increase, the stability of the spherical cap structure increases with respect to the alternative structure in which a core of ice is fully surrounded by solution. We predict that micrometer-sized particles and nanoparticles have the same equilibrium internal structure. The variation of liquid-vapor surface tension with solute concentration is a key factor in determining whether a solution-embedded ice core or vapor-exposed ice cap is the equilibrium structure of the aerosols. In agreement with experiments, we predict that the structure of mixed-phase HNO3-water particles, representative of polar stratospheric clouds, consists of an ice core surrounded by freeze-concentrated solution. The results of this work are important to determine the phase state and internal structure of sea spray ultrafine aerosols and other mixed-phase particles under atmospherically relevant conditions. PMID:24820354
Model solution for volume reflection of relativistic particles in a bent crystal
Bondarenco, M. V. [Kharkov Institute of Physics and Technology, 1 Academic St., 61108 Kharkov (Ukraine)
For volume reflection process in a bent crystal, exact analytic expressions for positively- and negatively-charged particle trajectories are obtained within a model of parabolic continuous potential in each interplanar interval, with the neglect of incoherent multiple scattering. In the limit of the crystal bending radius greatly exceeding the critical value, asymptotic formulas are obtained for the particle mean deflection angle in units of Lindhard's critical angle, and for the final beam profile. Volume reflection of negatively charged particles is shown to contain effects of rainbow scattering and orbiting, whereas with positively charged particles none of these effects arise within the given model. The model predictions are compared with experimental results and numerical simulations. Estimates of the volume reflection mean angle and the final beam profile robustness under multiple scattering are performed.
Crystal structures of bile salts: Sodium taurocholate
Anna Rita Campanelli; Sofia Candeloro De Sanctis; Angelo Antonio D'Archivio; Edoardo Giglio; Lucid Scaramuzza
Crystals of sodium taurocholate (NaC26H44NO7S · 2.5 H2O) belonging to the triclinic space groupP1 have unit cell parametersa = 12.731 (2),b = 16.104 (2),c = 7.628 (1) ?A, a =83.40 (1),ß = 101.20 (1), ? = 105.35 (1)°, and two molecules in the asymmetric unit. The refinement, carried out on 4424 observed reflections, gaveR = 0.059 andRw = 0.066. The
Application of multispectral data processing techniques to cholesteric liquid crystal tracer particles
Wilcox, Neal Allen
), and the color film model used to calculate the exposure vector, (2) particle tracking, which gives a brief discription of the sof tware developed by Chang [1] for automated particle tracking, and (3) liquid crystal thermography, which gives a description... that the reference coordinates are the same in all the frames. This translation corrects for film misregistration during exposure and digitization. program TRACKMAT performs two major functions: (I) the tracking of partic)es from frame to frame and (2...
Volume Reflection and Volume Refraction of Relativistic Particles in a Uniformly Bent Crystal
Gennady V. Kovalev
The scattering of fast charged particles in a bent crystal has been analyzed in the framework of relativistic classical mechanics. The expressions obtained for the deflection function are in satisfactory agreement with the experimental data for the volume reflection of relativistic protons obtained in [1,2,3]. The features of the scattering of the particles on ring potentials are considered in a wide range of impact parameters
Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure
Payne, S.A.; Kway, W.L.; DeLoach, L.D.; Krupke, W.F.; Chai, B.H.T.
Yb[sup 3+] and Nd[sup 3+] doped Sr[sub 5](VO[sub 4])[sub 3]F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr[sub 5](VO[sub 4])[sub 3]F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr[sub 5](VO[sub 4])[sub 3]F, where the Sr[sup 2+] and F[sup [minus
Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure
Payne, Stephen A. (Castro Valley, CA); Kway, Wayne L. (Fremont, CA); DeLoach, Laura D. (Manteca, CA); Krupke, William F. (Pleasanton, CA); Chai, Bruce H. T. (Oviedo, FL)
Yb.sup.3+ and Nd.sup.3+ doped Sr.sub.5 (VO.sub.4).sub.3 F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr.sub.5 (VO.sub.4).sub.3 F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr.sub.5 (VO.sub.4).sub.3 F, where the Sr.sup.2+ and F.sup.- ions are replaced by related chemical species, have similar properties.
Toxicity of TiO2 Nanoparticles to Escherichia coli: Effects of Particle Size, Crystal Phase and Water Chemistry
Lin, Xiuchun; Li, Jingyi; Ma, Si; Liu, Gesheng; Yang, Kun; Tong, Meiping; Lin, Daohui
Controversial and inconsistent results on the eco-toxicity of TiO2 nanoparticles (NPs) are commonly found in recorded studies and more experimental works are therefore warranted to elucidate the nanotoxicity and its underlying precise mechanisms. Toxicities of five types of TiO2 NPs with different particle sizes (10?50 nm) and crystal phases were investigated using Escherichia coli as a test organism. The effect of water chemistry on the nanotoxicity was also examined. The antibacterial effects of TiO2 NPs as revealed by dose-effect experiments decreased with increasing particle size and rutile content of the TiO2 NPs. More bacteria could survive at higher solution pH (5.0–10.0) and ionic strength (50–200 mg L?1 NaCl) as affected by the anatase TiO2 NPs. The TiO2 NPs with anatase crystal structure and smaller particle size produced higher content of intracellular reactive oxygen species and malondialdehyde, in line with their greater antibacterial effect. Transmission electron microscopic observations showed the concentration buildup of the anatase TiO2 NPs especially those with smaller particle sizes on the cell surfaces, leading to membrane damage and internalization. These research results will shed new light on the understanding of ecological effects of TiO2 NPs. PMID:25310452
Structure of ice crystallized from supercooled water
Malkin, Tamsin L.; Murray, Benjamin J.; Brukhno, Andrey V.; Anwar, Jamshed; Salzmann, Christoph G.
The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples. PMID:22232652
Band-structure determination for finite 3-D photonic crystals
NASA Astrophysics Data System (ADS)
Botey, M.; Maymó, M.; Martorell, J.
The partial band structure from a finite photonic crystal is determined using a model based on light diffraction and the transfer-matrix formalism. The predictions from such a model are compared to an experimental measurement of the bands in the LU direction of a face centered cubic colloidal crystal. Then, both the theoretical predictions and the experimental measurements are compared with the usual band-structure calculation based on a plane-wave expansion with perfectly periodic boundary conditions. As in measurements performed in the past, discrepancies between the predictions of this later model and the experimentally determined bands are observed. On the contrary, using the model presented based on light propagation through a finite crystal, where no periodicity is imposed in the direction perpendicular to any of the set of planes considered to determine a specific branch of the band structure, we found a very good agreement between the experimentally determined and the predicted bandwidths.
Gas accumulation in particle-rich suspensions and implications for bubble populations in crystal-rich magma
Rempel, Alan W.
in particle-aided bubble coalescence. However, these studies demon- strate that the effect of particles on gasGas accumulation in particle-rich suspensions and implications for bubble populations in crystal between rising bubbles and particles. We observe different interaction styles as the ratio of bubble
Crystal growth of lead carbonates: Influence of the medium and relationship between structure and habit
NASA Astrophysics Data System (ADS)
Sánchez-Navas, Antonio; López-Cruz, Olimpia; Velilla, Nicolás; Vidal, Isaac
The crystal-growth features of cerussite and hydrocerussite formed by two different chemical reactions are studied. With respect to the former, acid-vapour oxidation and latter carbonation of metallic lead produced a nanocrystalline precipitate for the lead carbonates. In the latter, cerussite and hydrocerusite are precipitated after mixing two mother solutions in liquid and solid porous media, forming diverse polyhedral morphologies. Crystal growth in gel medium gives rise to pseudo-cubic morphologies by the aggregation of one-micron-sized particles of cerussite. Skeletal morphologies composed of cyclically twinned crystals of cerussite also occur in gel-growth experiments. These morphologies were determined by kinetic factors, in particular by high supersaturation conditions that led to high growth rates. Kinetics also favoured the predominance of weak over strong interactions during crystal growth. The habit observed for cerussite crystals has been explained based on crystal-structure considerations and quantum-mechanical calculations. In particular, the crystal growth along the a direction in cyclically twinned crystals is explained by the binding forces between the CO32- molecular group and Pb2+, defining an uninterrupted chain of strong bonds along that direction. However, the preferred growth along the c direction observed for the cerussite crystal formed in gel media is here attributed to an intermolecular interaction through C-C bonds. The occurrence of a chemical bonding between the C atoms of the CO32- molecular groups aligned along the c direction is clearly shown by the theoretical analysis of the electron density with the quantum theory of atoms in molecules (QTAIM).
Crystal structure of an amphiphilic foldamer reveals a 48-mer assembly comprising a hollow truncated octahedron
Pavone, Vincenzo; Zhang, Shao-Qing; Merlino, Antonello; Lombardi, Angela; Wu, Yibing; DeGrado, William F.
Foldamers provide an attractive medium to test the mechanisms by which biological macromolecules fold into complex three-dimensional structures, and ultimately to design novel protein-like architectures with properties unprecedented in nature. Here, we describe a large cage-like structure formed from an amphiphilic arylamide foldamer crystallized from aqueous solution. Forty eight copies of the foldamer assemble into a 5 nm cage-like structure, an omnitruncated octahedron filled with well-ordered ice-like water molecules. The assembly is stabilised by a mix of arylamide stacking interaction, hydrogen bonding and hydrophobic forces. The omnitruncated octahedra tessellate to form a cubic crystal. These findings may provide an important step towards the design of nanostructured particles resembling spherical viruses. PMID:24705140
Crystal chemistry and structure refinement of five hydrated calcium borates
Clark, J.R.; Appleman, D.E.; Christ, C.L.
The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.
Influence of particles on the functional properties of single crystals of high-strength ferromagnetic alloys
NASA Astrophysics Data System (ADS)
Kretinina, I. V.; Kuts, O. A.; Kuksgauzen, D. A.; Poklonov, V. V.; Pobedennaya, Z. V.; Platonova, Yu N.
Single crystals of the ordered ferromagnetic Co49Ni21Ga30 (at.%) alloy with B2-L10 martensitic transformation and of the disordered iron-based Fe41Ni28Co17Al11.5X2.5 (X=Ta, Ti) (at.%) alloys, which undergo thermoelastic ?-a' martensitic transformations, were studied in terms of the influence of chemical composition, size and volume fraction of the dispersed ?'- phase particles on functional properties – shape memory effect and superelasticity. Single crystals of Co49Ni21Ga30 alloy showed that the precipitation of nanometric ?'-phase particles changes the martensitic transformation characteristic temperature, reduces the value of the shape memory effect and superelasticity, increases thermal and stress hysteresis, and leads to hardening of the high temperature phase, which promotes superelasticity at a wide temperature range and at high temperatures at T>373K compared with the crystals without particles. Single crystals of FeNiCoAlX (X=Ta, Ti) alloys have experimentally demonstrated that the precipitation of ordered ?'-phase particles at a size of d=5-10 nm during aging at T=973 K, 3 h, leads to the occurrence of the shape memory effect and superelasticity.
Effect of particle size on hydroxyapatite crystal-induced tumor necrosis factor alpha secretion by macrophages
Imad Nadra; Aldo R. Boccaccini; Pandelis Philippidis; Linda C. Whelan; Geraldine M. McCarthy; Dorian O. Haskard; R. Clive Landis
Macrophages may promote a vicious cycle of inflammation and calcification in the vessel wall by ingesting neointimal calcific deposits (predominantly hydroxyapatite) and secreting tumor necrosis factor (TNF)?, itself a vascular calcifying agent. Here we have investigated whether particle size affects the proinflammatory potential of hydroxyapatite crystals in vitro and whether the nuclear factor (NF)-?B pathway plays a role in the
Optical particle trapping with computer-generated holograms written on a liquid-crystal display.
Reicherter, M; Haist, T; Wagemann, E U; Tiziani, H J
Computer-generated holograms written on a liquid-crystal display can be used to generate dynamic light fields of arbitrary shape. This method was used to simultaneously trap polystyrene particles laterally and to displace them independently of one another. PMID:18073798
Possibility of Observing Spiral Scattering of Relativistic Particles in a Bent Crystal
Gennady V. Kovalev
The peak position, impact-parameter range, and optimal conditions for observing spiral scattering of relativistic particles in a uniformly bent crystal are estimated. The existence of spiral scattering with a square-root singularity is pointed out. In this case, the secondary process of volume capture to the channeling mode is absent and the conditions for observing this effect are most favorable.
Crystal Structures of Monomeric Actin Bound to Cytochalasin D
Nair, Usha B.; Joel, Peteranne B.; Wan, Qun; Lowey, Susan; Rould, Mark A.; Trybus, Kathleen M.
The fungal toxin cytochalasin D (CD) interferes with the normal dynamics of the actin cytoskeleton by binding to the barbed end of actin filaments. Despite its widespread use as a tool for studying actin-mediated processes, the exact location and nature of its binding to actin has not been previously determined. Here we describe two crystal structures of an expressed monomeric actin in complex with CD, one obtained by soaking preformed actin crystals with CD, and the other by co-crystallization. The binding site for CD, in the hydrophobic cleft between actin subdomains 1 and 3, is the same in the two structures. Polar and hydrophobic contacts play an equally important role in CD binding, and six hydrogen bonds stabilize the actin-CD complex. Many unrelated actin-binding proteins and marine toxins target this cleft, and the hydrophobic pocket at the front end of the cleft (viewing actin with subdomain 2 in the upper right corner). CD differs in that it binds to the back half of the cleft. The ability of CD to induce actin dimer formation and actin-catalyzed ATP hydrolysis may be related to its unique binding site, and the necessity to fit its bulky macrocycle into this cleft. Contacts with residues lining this cleft appear to be crucial to capping and/or severing. The co-crystallized actin-CD structure also revealed changes in actin conformation. A rotation of ~6° of the smaller actin domain (subdomains 1 and 2) with respect to the larger domain (subdomains 3 and 4) results in small changes in crystal packing that allow the D-loop to adopt an extended loop structure, instead of being disordered as it is in most crystal structures of actin. We speculate that these changes represent a potential conformation that the actin monomer can adopt on the pathway to polymerization or in the filament. PMID:18938176
Crystal structure of the human spastin AAA domain
Taylor, Jennifer L.; White, Susan Roehl; Lauring, Brett; Kull, F. Jon
Hereditary spastic paraplegia (HSP) is a motor neuron disease caused by a progressive degeneration of the motor axons of the corticospinal tract. Point mutations or exon deletions in the microtubule-severing ATPase, spastin, are responsible for approximately 40% of cases of autosomal dominant HSP. Here, we report the 3.3 Å X-ray crystal structure of a hydrolysis- deficient mutant (E442Q) of the human spastin protein AAA domain. This structure is analyzed in the context of the existing Drosophila melanogaster spastin AAA domain structure and crystal structures of other closely related proteins in order to build a more unifying framework for understanding the structural features of this group of microtubule-severing ATPases. PMID:22446388
Crystal structure of the human spastin AAA domain.
Taylor, Jennifer L; White, Susan Roehl; Lauring, Brett; Kull, F Jon
Hereditary spastic paraplegia (HSP) is a motor neuron disease caused by a progressive degeneration of the motor axons of the corticospinal tract. Point mutations or exon deletions in the microtubule-severing ATPase, spastin, are responsible for approximately 40% of cases of autosomal dominant HSP. Here, we report the 3.3 Å X-ray crystal structure of a hydrolysis-deficient mutant (E442Q) of the human spastin protein AAA domain. This structure is analyzed in the context of the existing Drosophila melanogaster spastin AAA domain structure and crystal structures of other closely related proteins in order to build a more unifying framework for understanding the structural features of this group of microtubule-severing ATPases. PMID:22446388
Baig, M.; Brown, A.; Eswaramoorthy, S.; Swaminathan, S.
Klebsiella pneumoniae, a gram-negative enteric bacterium, is found in nosocomial infections which are acquired during hospital stays for about 10% of hospital patients in the United States. The crystal structure of a putative oxidoreductase from K. pneumoniae has been determined. The structural information of this K. pneumoniae protein was used to understand its function. Crystals of the putative oxidoreductase enzyme were obtained by the sitting drop vapor diffusion method using Polyethylene glycol (PEG) 3350, Bis-Tris buffer, pH 5.5 as precipitant. These crystals were used to collect X-ray data at beam line X12C of the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL). The crystal structure was determined using the SHELX program and refi ned with CNS 1.1. This protein, which is involved in the catalysis of an oxidation-reduction (redox) reaction, has an alpha/beta structure. It utilizes nicotinamide adenine dinucleotide phosphate (NADP) or nicotine adenine dinucleotide (NAD) to perform its function. This structure could be used to determine the active and co-factor binding sites of the protein, information that could help pharmaceutical companies in drug design and in determining the protein's relationship to disease treatment such as that for pneumonia and other related pathologies.
Crystal structures of carbonates up to Mbar pressures determined by single crystal synchrotron radiation diffraction
NASA Astrophysics Data System (ADS)
Merlini, M.
The recent improvements at synchrotron beamlines, currently allow single crystal diffraction experiments at extreme pressures and temperatures [1,2] on very small single crystal domains. We successfully applied such technique to determine the crystal structure adopted by carbonates at mantle pressures. The knowledge of carbon-bearing phases is in fact fundamental for any quantitative modelling of global carbon cycle. The major technical difficulty arises after first order transitions or decomposition reactions, since original crystal (apx. 10x10x5 ?m3) is transformed in much smaller crystalline domains often with random orientation. The use of 3D reciprocal space visualization software and the improved resolution of new generation flat panel detectors, however, allow both identification and integration of each single crystal domain, with suitable accuracy for ab-initio structure solution, performed with direct and charge-flipping methods and successive structure refinements. The results obtained on carbonates, indicate two major crystal-chemistry trends established at high pressures. The CO32- units, planar and parallel in ambient pressure calcite and dolomite structures, becomes non parallel in calcite- and dolomite-II and III phases, allowing more flexibility in the structures with possibility to accommodate strain arising from different cation sizes (Ca and Mg in particular). Dolomite-III is therefore also observed to be thermodynamically stable at lower mantle pressures and temperatures, differently from dolomite, which undergoes decomposition into pure end-members in upper mantle. At higher pressure, towards Mbar (lowermost mantle and D'' region) in agreement with theoretical calculations [3,4] and other experimental results [5], carbon coordination transform into 4-fold CO4 units, with different polymerisation in the structure depending on carbonate composition. The second important crystal chemistry feature detected is related to Fe2+ in Fe-bearing magnesite, which spontaneously oxidises at HP/HT, forming Fe3+ carbonates, Fe3+ oxides and reduced carbon (diamonds). Single crystal diffraction approach allowed full structure determination of these phases, yielding to the discovery of few unpredicted structures, such as Mg2Fe2C4O13 and Fe13O19, which can be well reproduced in different experiments. Mg2Fe2C4O13 carbonate present truncated chain C4O13 groups, and Fe13O19 oxide, whose stoichiometry is intermediate between magnetite and hematite, is a one-layer structure, with features encountered in superconducting materials. The results fully support the ideas of unexpected complexities in the mineralogy of the lowermost mantle, and single crystal technique, once properly optimized in ad-hoc synchrotron beamlines, is fundamental for extracting accurate structural information, otherwise rarely accessible with other experimental techniques. References: [1] Merlini M., Hanfland M. (2013). Single crystal diffraction at Mbar conditions by synchrotron radiation. High Pressure Research, in press. [2] Dubrovinsky et al., (2010). High Pressure Research, 30, 620-633. [3] Arapan et al. (1997). Phys. Rev. Lett., 98, 268501. [4] Oganov et al. (2008) EPSL, 273, 38-47. [5] Boulard et al. (2011) PNAS, 108, 5184-5187.
Crystal Structure Representations for Machine Learning Models of Formation Energies
Faber, Felix; von Lilienfeld, O Anatole; Armiento, Rickard
We introduce and evaluate a set of feature vector representations of crystal structures for machine learning (ML) models of formation energies of solids. ML models of atomization energies of organic molecules have been successful using a Coulomb matrix representation of the molecule. We consider three ways to generalize such representations to periodic systems: (i) a matrix where each element is related to the Ewald sum of the electrostatic interaction between two different atoms in the unit cell repeated over the lattice; (ii) an extended Coulomb-like matrix that takes into account a number of neighboring unit cells; and (iii) an Ansatz that mimics the periodicity and the basic features of the elements in the Ewald sum matrix by using a sine function of the crystal coordinates of the atoms. The representations are compared for a Laplacian kernel with Manhattan norm, trained to reproduce formation energies using a data set of 3938 crystal structures obtained from the Materials Project. For training sets consi...
Self-powdering and nonlinear optical domain structures in ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals formed in glass
Tsukada, Y.; Honma, T. [Department of Materials Science and Technology, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka 940-2188 (Japan); Komatsu, T., E-mail: email@example.com [Department of Materials Science and Technology, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka 940-2188 (Japan)
Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3}, (GMO), crystals are formed through the crystallization of 21.25Gd{sub 2}O{sub 3}-63.75MoO{sub 3}-15B{sub 2}O{sub 3} glass (mol%), and two scientific curious phenomena are observed. (1) GMO crystals formed in the crystallization break into small pieces with a triangular prism or pyramid shape having a length of 50-500 {mu}m spontaneously during the crystallizations in the inside of an electric furnace, not during the cooling in air after the crystallization. This phenomenon is called 'self-powdering phenomenon during crystallization' in this paper. (2) Each self-powdered GMO crystal grain shows a periodic domain structure with different refractive indices, and a spatially periodic second harmonic generation (SHG) depending on the domain structure is observed. It is proposed from polarized micro-Raman scattering spectra and the azimuthal dependence of second harmonic intensities that GMO crystals are oriented in each crystal grain and the orientation of (MoO{sub 4}){sup 2-} tetrahedra in GMO crystals changes periodically due to spontaneous strains in ferroelastic GMO crystals. - Graphical abstract: This figure shows the polarized optical photograph at room temperature for a particle (piece) obtained by a heat treatment of the glass at 590 deg. C for 2 h in an electric furnace in air. This particle was obtained through the self-powdering behavior in the crystallization of glass. The periodic domain structure is observed. Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals are formed in the particle, and second harmonic generations are detected, depending on the domain structure.
Viral capsomere structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy
NASA Astrophysics Data System (ADS)
Malkin, A. J.; Kuznetsov, Yu. G.; McPherson, A.
In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV), cucumber mosaic virus (CMV) and glucose isomerase. Growth of these crystals proceeded by two-dimensional (2D) nucleation. For glucose isomerase, from supersaturation dependencies of tangential step rates and critical step length, the kinetic coefficients of the steps and the surface free energy of the step edge were calculated for different crystallographic directions. The molecular structure of the step edges, the adsorption of individual virus particles and their aggregates, and the initial stages of formation of 2D nuclei on the surfaces of TYMV and CMV crystals were recorded. The surfaces of individual TYMV virions within crystals were visualized, and hexameric and pentameric capsomers of the T=3 capsids were clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the TYMV crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions.
Structures of Yukawa and Coulomb particles in cylinders: simulations for fine particle plasmas and colloidal suspensions.
Totsuji, Hiroo; Totsuji, Chieko
Low-temperature structures of Yukawa particles in systems with cylindrical symmetry are analyzed by numerical simulations. Particles are organized into well-defined thin concentric shells forming triangular lattices with defects on each shell and structural parameters are expressed by simple interpolation formulas including the limiting case of Coulomb particles. In outer shells, the local structure can be regarded as three-dimensional closest packing as in the case of the background of uniform spheres. These formulas can be directly compared with fine particle experiments in long cylindrical chambers under microgravity or colloidal suspensions in cylinders and may be useful as a basis of structural analyses in cylindrical systems. PMID:21867249
Lactose particle engineering: Influence of ultrasound and anti-solvent on crystal habit and particle size
NASA Astrophysics Data System (ADS)
Kougoulos, E.; Marziano, I.; Miller, P. R.
This study focuses on ultrasound-assisted anti-solvent crystallization of lactose, expanding on previous studies and presenting, for the first time, the results of large scale implementation of sonocrystallization for lactose. The results further clarify the interplay between solution chemistry - namely the role of ?-lactose - and crystallization, representing a step forward in the fine tuning of lactose properties for pharmaceutical manufacturing applications. Batches manufactured at laboratory and pilot scales were extensively characterised, including an approach for the quantification of ?-lactose in ?-lactose based on powder X-ray diffraction (PXRD), which is described here.
Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal
NASA Astrophysics Data System (ADS)
Sankari, R. Siva; Perumal, Rajesh Narayana
Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.
Synthesis and Crystallization of Nano-Ceria Particles by Solvothermal Routes
NASA Astrophysics Data System (ADS)
Fu, Cong; Li, Ruixing; Zhang, Yue
Cerium oxides (CeO2) were synthesized by two steps solvothermal routes. First, a precursor was precipitated using solutions of cerium (III) nitrate and ammonia, and then this precursor was treated via solvothermal techniques in an autoclave. Narrow distribution of CeO2 particle size, between 10 to 15 nm, was achieved in different solvents. Hard agglomerates of nano-CeO2 were mitigated in an ethanol solvent. Most of crystal particles were in the shape of a quadrangle for the precursor. Morphology of CeO2 particles gradually changed after the precursor was treated by solvothermal techniques. There were both quadrangular and symmetrically hexagonal particles at an alkaline pH value. Alternatively, the quadrangular particles disappeared, instead of geometrically unsymmetrical hexagon with decreasing pH to a more acid value. The evolution mechanism of the morphology was discussed. These results have important implications for recognizing and controlling the crystalline shape by solvothermal techniques.
Crystal structure of a human GABAA receptor
Miller, Paul S.; Aricescu, A. Radu
Summary Type-A ?-aminobutyric acid receptors (GABAARs) are the principal mediators of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signalling triggers hyperactive neurological disorders such as insomnia, anxiety and epilepsy. Here we present the first three-dimensional structure of a GABAAR, the human ?3 homopentamer, at 3 Å resolution. This structure reveals architectural elements unique to eukaryotic Cys-loop receptors, explains the mechanistic consequences of multiple human disease mutations and shows a surprising structural role for a conserved N-linked glycan. The receptor was crystallised bound to a previously unknown agonist, benzamidine, opening a new avenue for the rational design of GABAAR modulators. The channel region forms a closed gate at the base of the pore, representative of a desensitised state. These results offer new insights into the signalling mechanisms of pentameric ligand-gated ion channels and enhance current understanding of GABAergic neurotransmission. PMID:24909990
Crystal structures of two engineered thiol trypsins.
McGrath, M E; Wilke, M E; Higaki, J N; Craik, C S; Fletterick, R J
We have determined the three-dimensional structures of engineered rat trypsins which mimic the active sites of two classes of cysteine proteases. The catalytic serine was replaced with cysteine (S195C) to test the ability of sulfur to function as a nucleophile in a serine protease environment. This variant mimics the cysteine trypsin class of thiol proteases. An additional mutation of the active site aspartate to an asparagine (D102N) created the catalytic triad of the papain-type cysteine proteases. Rat trypsins S195C and D102N,S195C were solved to 2.5 and 2.0 A, respectively. The refined structures were analyzed to determine the structural basis for the 10(6)-fold loss of activity of trypsin S195C and the 10(8)-fold loss of activity of trypsin D102N,S195C, relative to rat trypsin. The active site thiols were found in a reduced state in contrast to the oxidized thiols found in previous thiol protease structures. These are the first reported structures of serine proteases with the catalytic centers of sulfhydryl proteases. Structure analysis revealed only subtle global changes in enzyme conformation. The substrate binding pocket is unaltered, and active site amino acid 102 forms hydrogen bonds to H57 and S214 as well as to the backbone amides of A56 and H57. In trypsin S195C, D102 is a hydrogen-bond acceptor for H57 which allows the other imidazole nitrogen to function as a base during catalysis. In trypsin D102N,S195C, the asparagine at position 102 is a hydrogen-bond donor to H57 which places a proton on the imidazole nitrogen proximal to the nucleophile. This tautomer of H57 is unable to act as a base in catalysis.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2611228
Effect of local structures on structural evolution during crystallization in undercooled metallic glass-forming liquids.
Wu, Z W; Li, M Z; Wang, W H; Song, W J; Liu, K X
The effect of local structures on structural evolution during the crystallization of undercooled ZrCu metallic glass-forming liquid was studied via molecular dynamics simulations. It is found that body-centered-cubic (bcc)-like clusters play a key role in structural evolution during crystallization. In contrast to previous speculations, the number of bcc-like crystal nuclei does not change much before the onset of crystallization. Instead, the development of a bcc-like critical nucleus during annealing leads to a strong spatial correlation with other nuclei in its surroundings, forming a crystalline structure template. It is also found that the size distribution of bcc-like nuclei follows a power-law form with an exponential cutoff in the early stage of annealing, but changes to a pure power-law behavior just before the onset of crystallization. This implies that the crystalline structure template has fractal feature and the undercooled liquids evolve to a self-organized critical state before the onset of crystallization, which might trigger the subsequent rapid crystallization. According to the graph theory analysis, it is also found that the observed large scatter of the onset time of crystallization in different liquid samples results from the connectivity of the bcc-like clusters. PMID:23445019
Effect of local structures on structural evolution during crystallization in undercooled metallic glass-forming liquids
NASA Astrophysics Data System (ADS)
Wu, Z. W.; Li, M. Z.; Wang, W. H.; Song, W. J.; Liu, K. X.
The effect of local structures on structural evolution during the crystallization of undercooled ZrCu metallic glass-forming liquid was studied via molecular dynamics simulations. It is found that body-centered-cubic (bcc)-like clusters play a key role in structural evolution during crystallization. In contrast to previous speculations, the number of bcc-like crystal nuclei does not change much before the onset of crystallization. Instead, the development of a bcc-like critical nucleus during annealing leads to a strong spatial correlation with other nuclei in its surroundings, forming a crystalline structure template. It is also found that the size distribution of bcc-like nuclei follows a power-law form with an exponential cutoff in the early stage of annealing, but changes to a pure power-law behavior just before the onset of crystallization. This implies that the crystalline structure template has fractal feature and the undercooled liquids evolve to a self-organized critical state before the onset of crystallization, which might trigger the subsequent rapid crystallization. According to the graph theory analysis, it is also found that the observed large scatter of the onset time of crystallization in different liquid samples results from the connectivity of the bcc-like clusters.
Materials research at Stanford University. [composite materials, crystal structure, acoustics
NASA Technical Reports Server (NTRS)
Research activity related to the science of materials is described. The following areas are included: elastic and thermal properties of composite materials, acoustic waves and devices, amorphous materials, crystal structure, synthesis of metal-metal bonds, interactions of solids with solutions, electrochemistry, fatigue damage, superconductivity and molecular physics and phase transition kinetics.
The Crystal Structure of the Human Hepatitis B Virus Capsid
S. A Wynne; R. A Crowther; A. G. W Leslie
Hepatitis B is a small enveloped DNA virus that poses a major hazard to human health. The crystal structure of the T = 4 capsid has been solved at 3.3 Å resolution, revealing a largely helical protein fold that is unusual for icosahedral viruses. The monomer fold is stabilized by a hydrophobic core that is highly conserved among human viral
Crystal structure of S-glutathiolated carbonic anhydrase III
Robert J. Mallis; Bradley W. Poland; Tapan K. Chatterjee; Rory A. Fisher; Steven Darmawan; Richard B. Honzatko; James A. Thomas
S-Glutathiolation of carbonic anhydrase III (CAIII) occurs rapidly in hepatocytes under oxidative stress. The crystal structure of the S-glutathiolated CAIII from rat liver reveals covalent adducts on cysteines 183 and 188. Electrostatic charge and steric contacts at each modification site inversely correlate with the relative rates of reactivity of these cysteines toward glutathione (GSH). Diffuse electron density associated with the
Crystal structure of the Anabaena sensory rhodopsin transducer
Vogeley, Lutz; Trivedi, Vishwa D.; Sineshchekov, Oleg A.; Spudich, Elena N.; Spudich, John L.; Luecke, Hartmut
Presented in this paper are crystal structures of the Anabaena sensory rhodopsin transducer (ASRT), a soluble cytoplasmic protein that interacts with the first structurally characterized eubacterial retinylidene photoreceptor Anabaena sensory rhodopsin (ASR). Four crystal structures of ASRT from three different spacegroups were obtained, in all of which ASRT is present as a planar (C4) tetramer, consistent with our characterization of ASRT as a tetramer in solution. The ASRT tetramer is tightly packed with large interfaces where the well-structured ?-sandwich portion of the monomers provides the bulk of the tetramer-forming interactions and forms a flat, stable surface on one side of the tetramer (the "?-face"). Only one of our four different ASRT crystals reveals a C-terminal ?-helix in the otherwise all-? protein, together with a large loop from each monomer on the opposite face of the tetramer (the "?-face"), which is flexible and largely disordered in the other three crystal forms. Gel filtration demonstrates that ASRT forms stable tetramers in solution and isothermal microcalorimetry shows that the ASRT tetramer binds to ASR with a stoichiometry of one ASRT tetramer per one ASR photoreceptor with a Kd of 8 ?M. Possible mechanisms for the interaction of this transducer tetramer with the ASR photoreceptor via its flexible ?-face to mediate transduction of the light signal are discussed. PMID:17289074
COMMUNICATION Crystal Structure of Apaf-1 Caspase Recruitment
Joshua-Tor, Leemor
a proteolytic cascade that leads to apoptotic cell death. We report the crystal structure of the Apaf-1 CARD). It triggers the proteolytic cascade by activating caspase-9 (Thornberry & Lazebnik, 1998) in response as molecules that bind to them like Apaf-1 and RAIDD. DEDs often occur as tandem repeats and are found
Unusual Features of Crystal Structures of Some Simple Copper Compounds
ERIC Educational Resources Information Center
Douglas, Bodie
Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…
Classification, representation and prediction of crystal structures of ionic compounds
E. W. Gorter
The aim of this paper is to show that with the aid of a qualitative model of ionic bonding, including polarizability, many crystal structures, mainly of halides and chalcogenides, can be explained or even predicted. Polarization of O2- and F- ions may be neglected unless these ions have very small, or small and highly charged cation neighbours. The polarizability of
~ Animation of Crystal Structure Variations with Pressure, Temperature and Composition
Downs, Robert T.
~ Animation of Crystal Structure Variations with Pressure, Temperature and Composition Robert T as a function of temperature, pressure and composition. Examples of these animations are found on the cover another is an effective way to make the computer animations. This paper presents an outline
Magnetic activity at infrared frequencies in structured metallic photonic crystals
J B Pendry
We derive the effective permeability and permittivity of a nanostructured metallic photonic crystal by analysing the complex reflection and transmission coefficients for slabs of various thicknesses. These quantities were calculated using the transfer matrix method. Our results indicate that these structures could be used to realize a negative effective permeability, at least up to infrared frequencies. The origin of the
Light propagation in liquid crystals and liquid crystalline structures
Haijun Yuan
Liquid crystals are optically complex materials, characterized in general by anisotropy, loss and chirality. Understanding light propagation both in uniform samples, and in stratified structures consisting of layers of such materials is of considerable interest for fundamental reasons. It is also essential for the effective use of these materials in technology. Light propagation in matter can be understood classically in
Exotic behavior and crystal structures of calcium under pressure
Oganov, Artem R.
Exotic behavior and crystal structures of calcium under pressure Artem R. Oganova,b,1 , Yanming Mac that calcium undergoes sev- eral counterintuitive transitions under pressure: fcc bcc simple cubic Ca-IV Ca-V, and becomes a good superconductor in the simple cubic and higher-pressure phases. Here, using ab initio
[Band electronic structures and crystal packing forces
Not Available
We investigated the electronic and structural properties of low-dimensional materials and explored the structure-property correlations governing their physical properties. Progress was made on how to interpret the scanning tunneling microscopy and atomic force microscopy images of layered materials and on how to account for charge density wave instabilities in 2-D metals. Materials studied included transition metal chalcogenides, transition metal halides, organic conducting salts, Mo bronzes, A[sub 2]PdH[sub 2], fullerenes, squarate tetrahydrate polymers Fe, Cu(C[sub 4]O[sub 4])4[center dot]H[sub 2]O, BEDT salts, etc.
Structure of the trigonal crystal form of bovine annexin IV.
Zanotti, G; Malpeli, G; Gliubich, F; Folli, C; Stoppini, M; Olivi, L; Savoia, A; Berni, R
The structure of a trigonal crystal form of N-terminally truncated [des-(1-9)] bovine annexin IV, an annexin variant that exhibits the distinctive property of binding both phospholipids and carbohydrates in a Ca2+-dependent manner, has been determined at 3 A (0.3 nm) resolution -space group: R3; cell parameters: a=b=118.560 (8) A and c=82.233 (6) A-. The overall structure of annexin IV, crystallized in the absence of Ca2+ ions, is highly homologous to that of the other known members of the annexin family. The trimeric assembly in the trigonal crystals of annexin IV is quite similar to that found previously in non-isomorphous crystals of human, chicken and rat annexin V and to the subunit arrangement in half of the hexamer of hydra annexin XII. Moreover, it resembles that found in two-dimensional crystals of human annexin V bound to phospholipid monolayers. The propensity of several annexins to generate similar trimeric arrays supports the hypothesis that trimeric complexes of such annexins, including annexin IV, may represent the functional units that interact with membranes. PMID:9405281
Crystal structures of two engineered thiol trypsins
Mary E. McGrath; Marjorie E. Wilke; Jeffrey N. Higaki; Charles S. Craik; Robert J. Fletterick
We have determined the three-dimensional structures of engineered rat trypsins which mimic the active sites of two classes of cysteine proteases. The catalytic serine was replaced with cysteine (S195C) to test the ability of sulfur to function as a nucleophile in a serine protease environment. This variant mimics the cysteine trypsin class of thiol proteases. An additional mutation of the
Use of Particle Flow Algorithms in a Dual Readout Crystal Calorimeter
NASA Astrophysics Data System (ADS)
Magill, Stephen
The ability to grow clear, dense scintillating crystals presents an opportunity for development of a total absorption calorimeter that could contain multi-GeV hadrons in a detector volume similar to that of present-day calorimeters. With appropriate crystals and optimized readout elements, both scintillation and Cerenkov photons can be produced and detected separately. This dual readout approach allows one to selectively correct particle energies, resulting in significant gains in energy resolution ?20%/?E or even better for hadrons. An R&D program is underway to 1) develop appropriate clear, dense crystals, 2) test innovative readout methods for both scintillation and Cerenkov light, and 3) provide test beam capability for crystal and readout sensor testing and simulation verification. As part of this effort, simulation studies have been done assuming a dual readout crystal calorimeter implementation for a future e+e- linear collider detector. By using the dual readout correction, corrections for magnetic field effects on low momentum charged hadrons, and particle flow techniques, substantial improvements in dijet mass resolution are obtained.
Crystal structure of new AsS2 compound
NASA Astrophysics Data System (ADS)
Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Lityagina, L. M.; Kulikova, L. F.; Nikolaev, N. A.; Verin, I. A.
AsS2 single crystals have been obtained for the first time from an As2S3 melt at pressures above 6 GPa and temperatures above 800 K in the As2S3 ? AsS + AsS2 reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.
Photonic-band structure of magnetic photonic crystal slabs
Hasan Ajam; Mahmoud Shahabadi
In this paper, we introduce a rigorous computational method for the evaluation of the band structure of magnetic photonic crystal (MPC) slabs. With the help of this method, the full-wave analysis of the structure can be reduced to the analysis of an equivalent multi-conductor transmission line. In this work, we present a semi-analytical characteristic equation for the evaluation of the
Crystal Structure of Mistletoe Lectin I from Viscum album
Ruth Krauspenhaar; Susanne Eschenburg; Markus Perbandt; Vjacheslav Kornilov; Nina Konareva; Inna Mikailova; Stanka Stoeva; Roland Wacker; Timm Maier; Tej Singh; Albert Mikhailov; Wolfgang Voelter; Christian Betzel
The crystal structure of the ribosome-inactivating protein (RIP) mistletoe lectin I (ML-I) fromViscum albumhas been solved by molecular replacement techniques. The structure has been refined to a crystallographic R-factor of 24.5% using X-ray diffraction data to 2.8 Å resolution. The heterodimeric 63-kDa protein consists of a toxic A subunit which exhibits RNA-glycosidase activity and a galactose-specific lectin B subunit. The
Synthesis, crystal structure, and photoluminescence of a zinc metalloporphyrin
NASA Astrophysics Data System (ADS)
Chen, Wen-Tong; Yi, Xiu-Guang; Luo, Zhi-Gang; Fu, Hong-Ru; Liu, Juan
A zinc metalloporphyrin, ZnTCPP(acetone) ( 1) (TCPP = meso-tetra(4-carboxyphenyl)porphyrin), has been prepared via a solvothermal reaction and structurally characterized by single-crystal X-ray diffraction. Compound 1 features an isolated structure with a planar macrocycle and an embedded zinc ion binded to four pyrrole nitrogen atoms and one acetone oxygen atom. Photoluminescent investigation reveals that compound 1 displays an intensive emission in the red region.
Modeling liquid crystal bilayer structures with minimal surfaces J. D. Enlowa)
Gruner, Sol M.
.1063/1.1635811 I. INTRODUCTION The term ``liquid crystal'' is commonly associated with the simple polymer liquidModeling liquid crystal bilayer structures with minimal surfaces J. D. Enlowa) and R. L. Enlow crystal phase used in familiar liquid crystal displays, but the term also refers to structures with far
Drying dissipative structures of lycopodium spore particles in aqueous dispersion
Tsuneo Okubo; Etsuo Kokufuta; Masaharu Nakamuro; Kohji Yoshinaga; Masashi Mizutani; Akira Tsuchida
Drying dissipative structures of aqueous dispersions of lycopodium particles (31?m in average diameter) from the spores of Lycopodium clavatum were studied as a function of the particle concentrations in the presence and the absence of sodium chloride. The drying patterns formed on a cover glass, a watch glass and a Petri glass dish were observed macroscopically and microscopically. Lycopodium particles
Intermetallic crystal structures as foams. Beyond Frank-Kasper.
Bonneau, Charlotte; O'Keeffe, Michael
In many intermetallic structures, the atoms and bonds divide space into tilings by tetrahedra. The well-known Frank-Kasper phases are examples. The dual tilings divide space into a tiling by polyhedra that is topologically a foam. The number of faces of the dual polyhedron corresponds to the atom coordination number in the direct structure, and face sharing by adjacent polyhedra corresponds to bonds in the direct structure. A number of commonly occurring intermetallic crystal structures are shown as their duals. A major advantage of this alternative mode of depiction is that coordination of all of the atoms can be seen simultaneously. PMID:25247234
Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal.
Marchewka, M K; Pietraszko, A
The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2(1)/c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H...O and N-H...O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-Hcdots, three dots, centeredpi type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown. PMID:17627870
Disclination loops, standing alone and around solid particles, in nematic liquid crystals
NASA Astrophysics Data System (ADS)
Terentjev, E. M.
A suspended particle with specific director anchoring on its surface introduces a complex distortion field in a nematic liquid crystal matrix. Topological defects-disclination loops, boojums, and hedgehogs, are needed to match the director near the particle surface with that at the far distance, which is determined by boundary conditions on the sample. This paper analyzes the elastic energy and stability of a singular loop of wedge disclination and the first-order transition of the radial hedgehog into a wide singular loop, driven by an external magnetic field. The far field of distortions, created by a ``Saturn ring'' of disclination around the spherical radial particle, allows one to calculate the potential of interaction between such particles and with the surface of the liquid crystal. Particles are repelled from each other and from the rigidly anchored surface with the potential U~1/r3. If the sample surface has soft anchoring, the particle is attracted to it at close distances and is repelled, if beyond the anchoring coherence length ?w. Several experiments to test these conclusions are suggested.
Nanoscale structural features determined by AFM for single virus particles
NASA Astrophysics Data System (ADS)
Chen, Shu-Wen W.; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc
In this work, we propose ``single-image analysis'', as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis.
In situ observations of aerosol particles remaining from evaporated cirrus crystals: Comparing clean and polluted air masses
NASA Astrophysics Data System (ADS)
Seifert, M.; Ström, J.; Krejci, R.; Minikin, A.; Petzold, A.; Gayet, J.-F.; Schumann, U.; Ovarlez, J.
In situ observations of aerosol particles contained in cirrus crystals are presented and compared to interstitial aerosol size distributions (non-activated particles in between the cirrus crystals). The observations were conducted in cirrus clouds in the Southern and Northern Hemisphere mid-latitudes during the INCA project. The first campaign in March and April 2000 was performed from Punta Arenas, Chile (54° S) in pristine air. The second campaign in September and October 2000 was performed from Prestwick, Scotland (53° N) in the vicinity of the North Atlantic flight corridor. Size distribution measurements of crystal residuals (particles remaining after evaporation of the crystals) show that small aerosol particles (Dp < 0.1µm) dominate the number density of residuals. The crystal residual size distributions were significantly different in the two campaigns. On average the residual size distributions were shifted towards larger sizes in the Southern Hemisphere. For a given integral residual number density, the calculated particle volume was on average three times larger in the Southern Hemisphere. This may be of significance to the vertical redistribution of aerosol mass by clouds in the tropopause region. In both campaigns the mean residual size increased with increasing crystal number density. The observations of ambient aerosol particles were consistent with the expected higher pollution level in the Northern Hemisphere. The fraction of residual particles only contributes to approximately a percent or less of the total number of particles, which is the sum of the residual and interstitial particles.
Structural diversity and the role of particle shape and dense fluid behavior in assemblies of hard polyhedra
Pablo F. Damasceno; Michael Engel; Sharon C. Glotzer
A fundamental characteristic of matter is its ability to form ordered structures under the right thermodynamic conditions. Predicting these structures - and their properties - from the attributes of a material's building blocks is the holy grail of materials science. Here, we investigate the self-assembly of 145 hard convex polyhedra whose thermodynamic behavior arises solely from their anisotropic shape. Our results extend previous works on entropy-driven crystallization by demonstrating a remarkably high propensity for self-assembly and an unprecedented structural diversity, including some of the most complex crystalline phases yet observed in a non-atomic system. In addition to 22 Bravais and non-Bravais crystals, we report 66 plastic crystals (both Bravais and topologically close-packed), 21 liquid crystals (nematic, smectic, and columnar), and 44 glasses. We show that from simple measures of particle shape and local order in the disordered fluid, the class of ordered structure can be predicted.
Crystal structure and mechanistic investigation of the twister ribozyme.
Liu, Yijin; Wilson, Timothy J; McPhee, Scott A; Lilley, David M J
We present a crystal structure at 2.3-Å resolution of the recently described nucleolytic ribozyme twister. The RNA adopts a previously uncharacterized compact fold based on a double-pseudoknot structure, with the active site at its center. Eight highly conserved nucleobases stabilize the core of the ribozyme through the formation of one Watson-Crick and three noncanonical base pairs, and the highly conserved adenine 3' of the scissile phosphate is bound in the major groove of an adjacent pseudoknot. A strongly conserved guanine nucleobase directs its Watson-Crick edge toward the scissile phosphate in the crystal structure, and mechanistic evidence supports a role for this guanine as either a general base or acid in a concerted, general acid-base-catalyzed cleavage reaction. PMID:25038788
A method for hierarchical comparative analysis of crystal structures.
Blatov, Vladislav A
A geometrical-topological description of crystal structure as a three-dimensional graph with coloured nodes, weighted and coloured edges is used to generate a hierarchical sequence of the structure representations. The solid angles of Voronoi-Dirichlet polyhedra of atoms are used as the edge weights and the nodes and edges are coloured according to chemical reasons. Two operations are defined to derive the representations: contracting an atom to other atoms keeping the local connectivity, and removing an atom together with all its bonds. The atoms of the crystal structure are called origin, removed, contracted or target according to their roles in the operations. Each structure representation is described as a labelled quotient graph and determined by (i) colours of the graph nodes and edges, (ii) some level for edge weights, and (iii) an arrangement of atoms according to their roles. The computer enumeration and topological comparative analysis of all representations for crystal structures of any composition and complexity are implemented into the TOPOS program package. The advantages of the method are shown by the analysis of typical inorganic compounds and a molecular packing. PMID:16926484
The crystal structure and the phase transitions of pyridinium trifluoromethanesulfonate
NASA Astrophysics Data System (ADS)
Jesariew, Dominik; Ilczyszyn, Maria M.; Pietraszko, Adam
The calorimetric and optical studies and the structural properties of pyridinium trifluoromethanesulfonate (abbreviated as PyHOTf) are reported. A sequence of four fully reversible solid-solid phase transitions, at 223.0, 309.0, 359.9 and 394.3 K, has been discovered. The phase transition sequence was confirmed by x-ray diffraction data. The crystal structures of three phases (V, IV and III) have been determined from the single crystal x-ray diffraction data. Structural properties of the high temperature phases are characterized using powder x-ray diffraction data measured in the 290-425 K temperature range. The structural changes triggered by the temperature change are discussed in relation to the phase transitions. Two low temperature phases (V and IV) belong to the P43212 space group of the tetragonal system. The intermediate phases (III and II) are monoclinic and the prototype high temperature phase (I) is a pseudo-cubic (tetragonal) one. The low temperature phases (V and IV) are well ordered. The crystal structure of intermediate (III and II) and prototype (I) phases are characterized by high disorder of the pyridinium cations and triflate anions.
Structure and melting behavior of classical bilayer crystals of dipoles
Lu Xin; Wu Changqin; Micheli, Andrea; Pupillo, Guido [Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, Shanghai 200433 (China); Institute for Theoretical Physics, University of Innsbruck, A-6020 Innsbruck (Austria) and Institute for Quantum Optics and Quantum Information, Austrian Academy of Sciences, A-6020 Innsbruck (Austria)
We study the structure and melting of a classical bilayer system of dipoles in a setup where the dipoles are oriented perpendicular to the planes of the layers and the density of dipoles is the same in each layer. Due to the anisotropic character of the dipole-dipole interactions, we find that the ground-state configuration is given by two hexagonal crystals positioned on top of each other, independent of the interlayer spacing and dipolar density. For large interlayer distances these crystals are independent, while in the opposite limit of small interlayer distances the system behaves as a two-dimensional crystal of paired dipoles. Within the harmonic approximation for the phonon excitations, the melting temperature of these crystalline configurations displays a nonmonotonic dependence on the interlayer distance, which is associated with a re-entrant melting behavior in the form of solid-liquid-solid-liquid transitions at fixed temperature.
Thermally Triggered Solid-State Single-Crystal-to-Single-Crystal Structural Transformation Accompanies Property Changes.
Li, Quan-Quan; Ren, Chun-Yan; Huang, Yang-Yang; Li, Jian-Li; Liu, Ping; Liu, Bin; Liu, Yang; Wang, Yao-Yu
The 1D complex [(CuL0.5 H2 O)?H2 O]n (1) (H4 L=2,2'-bipyridine-3,3',6,6'-tetracarboxylic acid) undergoes an irreversible thermally triggered single-crystal-to-single-crystal (SCSC) transformation to produce the 3D anhydrous complex [CuL0.5 ]n (2). This SCSC structural transformation was confirmed by single-crystal X-ray diffraction analysis, thermogravimetric (TG) analysis, powder X-ray diffraction (PXRD) patterns, variable-temperature powder X-ray diffraction (VT-PXRD) patterns, and IR spectroscopy. Structural analyses reveal that in complex 2, though the initial 1D chain is still retained as in complex 1, accompanied with the Cu-bound H2 O removed and new O(carboxyl)?Cu bond forming, the coordination geometries around the Cu(II) ions vary from a distorted trigonal bipyramid to a distorted square pyramid. With the drastic structural transition, significant property changes are observed. Magnetic analyses show prominent changes from antiferromagnetism to weak ferromagnetism due to the new formed Cu1-O-C-O-Cu4 bridge. The catalytic results demonstrate that, even though both solid-state materials present high catalytic activity for the synthesis of 2-imidazolines derivatives and can be reused, the activation temperature of complex 1 is higher than that of complex 2. In addition, a possible pathway for the SCSC structural transformations is proposed. PMID:25663637
Crystallization of atmospheric sulfate-nitrate-ammonium particles Scot T. Martin, Julie C. Schlenker, Adam Malinowski, and Hui-Ming Hung
Crystallization of atmospheric sulfate-nitrate-ammonium particles Scot T. Martin, Julie C the crystallization RH (CRH) at 293 K of particles throughout the entire sulfate-nitrate-ammonium composition space to ammonium sulfate crystallize near 30% RH. Such particles are common in the boundary layer, including
Self-consistent three-dimensional model of dust particle transport and formation of Coulomb crystals in plasma processing reactors
Kushner, Mark
Self-consistent three-dimensional model of dust particle transport and formation of Coulomb of Illinois, Urbana, Illinois 61801 Received 24 June 2002; accepted 30 August 2002 Dust particle transport plasmas. Dust particles in radio frequency discharges form Coulomb crystals and display collective
Collective aspects of charged particle track structure
G. Basbas; A. Howie; R. H. Ritchie
A plasmon generated by a swift charged particle constitutes a coherent excitation about the particle track. We discuss the representation of collective modes in impact parameter space when created by a swift ion or a fast electron, and the decay of these modes into localized excitations. Several alternative spatial representations are considered. We show that the high spatial resolution found
Equilibrium state of a cylindrical particle with flat ends in nematic liquid crystals
NASA Astrophysics Data System (ADS)
Hashemi, S. Masoomeh; Ejtehadi, Mohammad Reza
A continuum theory is employed to numerically study the equilibrium orientation and defect structures of a circular cylindrical particle with flat ends under a homeotropic anchoring condition in a uniform nematic medium. Different aspect ratios of this colloidal geometry from thin discotic to long rodlike shapes and several colloidal length scales ranging from mesoscale to nanoscale are investigated. We show that the equilibrium state of this colloidal geometry is sensitive to the two geometrical parameters: aspect ratio and length scale of the particle. For a large enough mesoscopic particle, there is a specific asymptotic equilibrium angle associated to each aspect ratio. Upon reducing the particle size to nanoscale, the equilibrium angle follows a descending or ascending trend in such a way that the equilibrium angle of a particle with the aspect ratio bigger than 1:1 (a discotic particle) goes to a parallel alignment with respect to the far-field nematic, whereas the equilibrium angle for a particle with the aspect ratio 1:1 and smaller (a rodlike particle) tends toward a perpendicular alignment to the uniform nematic direction. The discrepancy between the equilibrium angles of the mesoscopic and nanoscopic particles originates from the significant differences between their defect structures. The possible defect structures related to mesoscopic and nanoscopic colloidal particles of this geometry are also introduced.
Edinburgh Research Explorer Europium-IV: An Incommensurately Modulated Crystal Structure
Millar, Andrew J.
Edinburgh Research Explorer Europium-IV: An Incommensurately Modulated Crystal Structure 2012, 'Europium-IV: An Incommensurately Modulated Crystal Structure in the Lanthanides' Physical Review to the work immediately and investigate your claim. Download date: 27. Jun. 2014 #12;Europium
Crystal and molecular structure of N-methylpiperidine betaine hydrochloride
NASA Astrophysics Data System (ADS)
Dega-Szafran, Z.; Szafran, M.; Dulewicz, E.; Addlagatta, A.; Jaskólski, M.
A 1:1 complex between N-methylpiperidine betaine and hydrochloric acid, MPBH·Cl, has been characterized by single crystal X-ray analysis, FTIR spectroscopy, and DFT calculations. The crystals are monoclinic, space group P2 1/ n, with a=6.0644(3), b=13.0220(6), c=12.7653(7) Å, ?=101.925(5)°. The piperidine ring adopts a chair conformation with the -CH 2COOH group in an axial and the-CH 3 group in an equatorial position. In the crystal, the Cl -anion is engaged in a medium-strong hydrogen bond with the COOH group (O-H⋯Cl -=2.9503(7) Å), in several C-H⋯Cl - contacts and, additionally, in three N +⋯Cl -intermolecular interactions. Four conformations (axial and equatorial, both protonated and unprotonated) of MPBHCl were examined by the B3LYP/6-31G(d,p) method. The calculated structure of MPBH·Cl(ax) is very similar to that in the crystal, except the N(1)-C(8)-C(9)-O(1) and N(1)-C(8)-C(9)-O(2) units, which are planar in the crystal but nonplanar in the isolated molecule. Powder FTIR spectra of MPBH·Cl and its deuterated analogue (MPBD·Cl) were measured and assignments of the observed bands to vibrations of the hydrogen bond and to internal vibrations are proposed.
Two new bismuth thiourea bromides: crystal structure, growth, and characterization.
Li, Ming; Li, R K
Crystals of two new bismuth thiourea bromides, bismuth trithiourea bromide (Bi[CS(NH2)2]3Br3, BTB) and bismuth protonated-hexathiourea bromide (Bi[CS(NH2)2H]6Br9, BHB), have been successfully grown from hydrobromic acid solution with different pH values by slow evaporation. Single crystal X-ray diffraction reveals that BTB is isostructural to its Cl-analog crystallizing in a monoclinic space group Cc with unit cell dimensions of a = 8.6238(7) Å, b = 12.2506(11) Å, c = 15.5040(13) Å, ? = 90.7810(10)° and Z = 4. In contrast, BHB crystallizes in a trigonal space group R3[combining macron]c with unit cell dimensions of a = b = 12.748(17) Å, c = 40.45(11) Å, and Z = 6. The protonation of the thiourea in BHB is confirmed by the structure solution, IR and Raman spectroscopy. The UV diffuse reflection spectra clearly indicate that both of the two crystals have good optical transparency in the range below 2000 nm. Both compounds decompose above 190 °C, and BHB melts at around 140 °C while BTB possesses a phase transition at 145 °C as indicated by thermogravimetric (TG) and differential thermal analysis (DTA). PMID:24316978
Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica.
Goral, Anna M; Tkaczuk, Karolina L; Chruszcz, Maksymilian; Kagan, Olga; Savchenko, Alexei; Minor, Wladek
Isochorismatase-like hydrolases (IHL) constitute a large family of enzymes divided into five structural families (by SCOP). IHLs are crucial for siderophore-mediated ferric iron acquisition by cells. Knowledge of the structural characteristics of these molecules will enhance the understanding of the molecular basis of iron transport, and perhaps resolve which of the mechanisms previously proposed in the literature is the correct one. We determined the crystal structure of the apo-form of a putative isochorismatase hydrolase OaIHL (PDB code: 3LQY) from the antarctic ?-proteobacterium Oleispira antarctica, and did comparative sequential and structural analysis of its closest homologs. The characteristic features of all analyzed structures were identified and discussed. We also docked isochorismate to the determined crystal structure by in silico methods, to highlight the interactions of the active center with the substrate. The putative isochorismate hydrolase OaIHL from O. antarctica possesses the typical catalytic triad for IHL proteins. Its active center resembles those IHLs with a D-K-C catalytic triad, rather than those variants with a D-K-X triad. OaIHL shares some structural and sequential features with other members of the IHL superfamily. In silico docking results showed that despite small differences in active site composition, isochorismate binds to in the structure of OaIHL in a similar mode to its binding in phenazine biosynthesis protein PhzD (PDB code 1NF8). PMID:22350524
Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica
Goral, Anna M.; Tkaczuk, Karolina L.; Chruszcz, Maksymilian; Kagan, Olga; Savchenko, Alexei; Minor, Wladek
Isochorismatase-like hydrolases (IHL) constitute a large family of enzymes divided into five structural families (by SCOP). IHLs are crucial for siderophore-mediated ferric iron acquisition by cells. Knowledge of the structural characteristics of these molecules will enhance the understanding of the molecular basis of iron transport, and perhaps resolve which of the mechanisms previously proposed in the literature is the correct one. We determined the crystal structure of the apo-form of a putative isochorismatase hydrolase OaIHL (PDB code: 3LQY) from the antarctic ?-proteobacterium Oleispira antarctica, and did comparative sequential and structural analysis of its closest homologs. The characteristic features of all analyzed structures were identified and discussed. We also docked isochorismate to the solved crystal structure by in silico methods, to highlight the interactions of the active center with the substrate. The putative isochorismate hydrolase OaIHL from Oleispira antarctica possesses the typical catalytic triad for IHL proteins. Its active center resembles those IHLs with a D-K-C catalytic triad, rather than those variants with a D-K-X triad. OaIHL shares some structural and sequential features with other members of the IHL superfamily. In silico docking results showed that despite small differences in active site composition, isochorismate binds to in the structure of OaIHL in a similar mode to its binding in phenazine biosynthesis protein PhzD (PDB code 1NF8). PMID:22350524
The Resonance Scattering Phenomenon of Fast Negatively Charged Particles in a Single Crystal
Gennady V. Kovalev
The energy spectrum of the extended attractive potential of a crystallographic row for negatively charged particles has quasi-bound states. It follows that a negatively charged particle with small transversal momentum component ($p_{\\bot} R <<1$) may undergo resonance scattering. Thus the resonance scattering phenomenon can be observed in a single crystal, when fast electrons move with a small glancing angle ($\\theta_0 << 1/pR$) to a crystallographic axis. The calculated results for the electrons and angular widths of resonance peaks are consistent with experimental data.
The Resonance Scattering Phenomenon of Fast Negatively Charged Particles in a Single Crystal
Kovalev, Gennady V
The energy spectrum of the extended attractive potential of a crystallographic row for negatively charged particles has quasi-bound states. It follows that a negatively charged particle with small transversal momentum component ($p_{\\bot} R <<1$) may undergo resonance scattering. Thus the resonance scattering phenomenon can be observed in a single crystal, when fast electrons move with a small glancing angle ($\\theta_0 << 1/pR$) to a crystallographic axis. The calculated results for the electrons and angular widths of resonance peaks are consistent with experimental data.
Crystal structure and microstructure of ?-Er 2S 3
A. R Landa-Cánovas; U Amador; L. C Otero-D??az
The atomic structure of Er2S3 was refined by single-crystal X-ray diffraction methods. The compound is isostructural to the ?-Ho2S3 structure type, which has monoclinic symmetry and space group P21\\/m, a=10.072 (1) Å, b=3.976 (2) Å, c=17.389 (2) Å, ?=98.66(1)°, Z=6. Refinement proceeded to R=0.037 for 1745 observed reflections. Experimental high-resolution micrographs (structural images) were obtained along the [010] zone axis
Crystal structure of four-stranded Oxytricha telomeric DNA
NASA Technical Reports Server (NTRS)
Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.
The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.
The Rapid Crystallization Strategy for Structure-Based Inhibitor Design
NASA Astrophysics Data System (ADS)
Bergfors, Terese
RAPID (Rapid Approaches to Pathogen Inhibitor Discovery) is an integrated center for structural biology, computational chemistry, and medicinal chemistry at Uppsala University, Sweden. The main target of the structural biology section is Mycobacterium tuberculosis. Key concepts in the crystallization strategy include minimal screening and buffer optimization. Examples are presented showing how these concepts have been successful in RAPID projects. Three screening methods are used: vapor-diffusion, micro-batch, and microfluidics. Our experiences may be relevant for other small, academic laboratories involved in structure-based inhibitor design.
Soft Particle Suspensions Near Jamming: Structure, Diffusion,
McGaughey, Alan
solids: crystallization, dynamical arrest, and development of a bona-fied shear modulus and yield stress play the role of temperature in conventional solids. In particular, the random close packing volume frequency shear modulus and a corresponding yield stress. This -controlled transition from a fluid
Effects of nematic polymer liquid crystal on crystallization and structure of PET\\/Vectra blends
G. Georgiev; P. Cebe; M. Capel
We investigate the effects of a nematic liquid crystalline polymer, Vectra A, on the structure and properties of its blends with a semicrystalline polymer, poly(ethylene terephthalate),PET. PET\\/Vectra blend composition ranged from 100\\/0 to 60\\/40. Real-time, in situ studies ofisothermal and non-isothermal melt crystallizations of these blends were conducted usingsimultaneous wide and small angle X-ray scattering (WAXS and SAXS), differentialscanning calorimetry
Synthesis of polycrystalline platelike KNbO 3 particles by the topochemical micro-crystal conversion method and fabrication of grain-oriented (K 0.5Na 0.5)NbO 3 ceramics
Yasuyoshi Saito; Hisaaki Takao
Polycrystalline rectangular-platelike KNbO3 particles with an orthorhombic perovskite structure were synthesized by the topochemical micro-crystal conversion (TMC) method from rectangular-platelike precursor particles of layer-structured K4Nb6O17 at 850°C in molten KCl-salt. TMC-synthesized KNbO3 particles preserved the shape of precursor particles, and had a thickness of about 1?m, a width of 5–10?m and a length of 20–40?m. However, TMC-synthesized rectangular-platelike KNbO3 particles
Effect of Gravity Level on the Particle Shape and Size During Zeolite Crystal Growth
NASA Technical Reports Server (NTRS)
Song, Hong-Wei; Ilebusi, Olusegun J.; Sacco, Albert, Jr.
A microscopic diffusion model is developed to represent solute transport in the boundary layer of a growing zeolite crystal. This model is used to describe the effect of gravity on particle shape and solute distribution. Particle dynamics and crystal growth kinetics serve as the boundary conditions of flow and convection-diffusion equations. A statistical rate theory is used to obtain the rate of solute transport across the growing interface, which is expressed in terms of concentration and velocity of solute species. Microgravity can significantly decrease the solute velocity across the growing interface compared to its earth-based counterpart. The extent of this reduction highly depends on solute diffusion constant in solution. Under gravity, the flow towards the crystal enhances solute transport rate across the growing interface while the flow away from crystals reduces this rate, suggesting a non-uniform growth rate and thus an elliptic final shape. However, microgravity can significantly reduce the influence of flow and obtain a final product with perfect spherical shape. The model predictions compare favorably with the data of space experiment of zeolites grown in space.
Revisiting the crystal structure of rhombohedral lead metaniobate.
Olsen, Gerhard Henning; Sørby, Magnus Helgerud; Hauback, Bjørn Christian; Selbach, Sverre Magnus; Grande, Tor
Lead metaniobate (PbNb2O6) can exist both as a stable rhombohedral and a metastable orthorhombic tungsten-bronze-type polymorph. Although the orthorhombic is a well-known ferroelectric material, the rhombohedral polymorph has been far less studied. The crystal structure and energetic stability of the stable rhombohedral polymorph of lead metaniobate is re-examined by powder X-ray diffraction and powder neutron diffraction in combination with ab initio calculations. We show that this structure is described by the polar space group R3, in contradiction to the previously reported space group R3m. The crystal structure is unusual, consisting of edge-sharing dimers of NbO(6/2) octahedra forming layers with 6- and 3-fold rings of octahedra and lead ions in channels formed by these rings. The layers are connected by corner-sharing between octahedra. Finally, the crystal structure is discussed in relation to other AB2O6 compounds with B = Nb, Ta. PMID:25167129
The effect of crystal tilt on high resolution micrographs of small metal particles
Malm, J.O. [Lund Univ. (Sweden). Dept. of Inorganic Chemistry 2; O`Keefe, M.A. [Lawrence Berkeley Lab., CA (United States)
The structure of small (1.5-5 nm) metal particles has been studied by high resolution transmission electron microscopy. For particles of this size, it is not possible to use tilting techniques (selected area diffraction), which means that the microscopist has to rely on the image when deciding in which direction the particle is viewed. This work points out some of the problems of intuitive determination of the viewing direction. (DLC)
838 nature structural biology volume 8 number 10 october 2001 Crystal structure of the
Glover, Mark
functions. Here we determine the crystal structure of the BRCT domain of human BRCA1 at 2.5 Å resolution to DNA damage. The structure provides a basis to predict the structural consequences of uncharacter- ized suppressor function of BRCA1. We predict that a similar packing arrange- ment exists in other DNA repair
EVO—Evolutionary algorithm for crystal structure prediction
NASA Astrophysics Data System (ADS)
Bahmann, Silvia; Kortus, Jens
We present EVO—an evolution strategy designed for crystal structure search and prediction. The concept and main features of biological evolution such as creation of diversity and survival of the fittest have been transferred to crystal structure prediction. EVO successfully demonstrates its applicability to find crystal structures of the elements of the 3rd main group with their different spacegroups. For this we used the number of atoms in the conventional cell and multiples of it. Running EVO with different numbers of carbon atoms per unit cell yields graphite as the lowest energy structure as well as a diamond-like structure, both in one run. Our implementation also supports the search for 2D structures and was able to find a boron sheet with structural features so far not considered in literature. Program summaryProgram title: EVO Catalogue identifier: AEOZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 23488 No. of bytes in distributed program, including test data, etc.: 1830122 Distribution format: tar.gz Programming language: Python. Computer: No limitations known. Operating system: Linux. RAM: Negligible compared to the requirements of the electronic structure programs used Classification: 7.8. External routines: Quantum ESPRESSO (http://www.quantum-espresso.org/), GULP (https://projects.ivec.org/gulp/) Nature of problem: Crystal structure search is a global optimisation problem in 3N+3 dimensions where N is the number of atoms in the unit cell. The high dimensional search space is accompanied by an unknown energy landscape. Solution method: Evolutionary algorithms transfer the main features of biological evolution to use them in global searches. The combination of the "survival of the fittest" (deterministic) and the randomised choice of the parents and normally distributed mutation steps (non-deterministic) provides a thorough search. Restrictions: The algorithm is in principle only restricted by a huge search space and simultaneously increasing calculation time (memory, etc.), which is not a problem for our piece of code but for the used electronic structure programs. Running time: The simplest provided case runs serially and takes 30 minutes to one hour. All other calculations run for significantly longer time depending on the parameters like the number and sort of atoms and the electronic structure program in use as well as the level of parallelism included.
Dipole Parallel Alignment in the Crystal Structure of a Polar Biphenyl: 4-Acetyl-4-Methoxybiphenyl (AMB)
Glaser, Rainer
-aligned polar molecules bearing biphenyl spacers. We are aware of only two reports of crystal structuresDipole Parallel Alignment in the Crystal Structure of a Polar Biphenyl: 4-Acetyl-4-Methoxybiphenyl.4 D and affords about 53% of maximal polar alignment. The polar crystal structure of syn-AMB contrasts
Fabrication of three-dimensional photonic crystal structures by interferometric lithography and nanoparticle self-assembly
New Mexico, University of
Fabrication of three-dimensional photonic crystal structures by interferometric lithography 2008 We report a simple approach to fabrication of three-dimensional photonic crystal structures. One to fabricate three-dimensional photonic crystals with void channels in a woodpile structure. The optical
Coherent effects of high-energy particles in a graded Si(1-x)Ge(x) crystal.
Bagli, E; Bandiera, L; Guidi, V; Mazzolari, A; De Salvador, D; Maggioni, G; Berra, A; Lietti, D; Prest, M; Vallazza, E; Abrosimov, N V
A graded Si(1-x)Ge(x) crystal has been manufactured for operation with high-energy protons to excite coherent interactions of the particles with the crystal such as channeling and volume reflection. The crystal had the shape of a parallelepiped though its (111) atomic planes were curved at a radius of 25.6 m because of the graded Ge content. The crystal was exposed to a 400??GeV/c proton beam at the external lines of CERN Super Proton Synchrotron to probe its capability to steer high-energy particles. Measured deflection efficiency was 62.0% under planar channeling and 96.0% under volume reflection. Such values are critically compared to their counterparts for a standard bent Si crystal under peer conditions. A Monte Carlo simulation of the dynamics of channeled and volume reflected particles in a graded crystal including the effect of Ge impurities and of lattice dislocations has been carried out. We found that the effect of crystal imperfections spoiled the efficiency of channeling while it negligibly affected the performance of volume reflection. We finally propose the usage of the graded crystal as a primary scatterer to aid halo collimation for the new generation of hadronic machines. As a unique feature, a properly cut graded crystal circumvents the problem of the miscut angle, which is currently a severe limitation for implementation of crystal-assisted collimation. PMID:23679744
Phase Transitions in Liquid Crystal Doped with Magnetic Particles of Different Shapes in Combined Electric and Magnetic Fields
NASA Astrophysics Data System (ADS)
Tomašovi?ová, Natália; Timko, Milan; Závišová, Vlasta; Hashim, Anežka; Jadzyn, Jan; Chaud, Xavier; Beaugnon, Eric; Kop?anský, Peter
We have studied the influence of electric and magnetic fields on the orientational structure of ferronematics based on a thermotropic nematic 4- trans-4- n-hexylcyclohexyl-isothiocyanato-benzene (6CHBT). The 6CHBT liquid crystal has been dissolved in phenyl isothiocyanate and doped with rod-like or chain-like magnetic particles. In such a mixture, the phase transition from an isotropic to a nematic phase is via a droplet state, i.e., coexistence of nematic and isotropic phases. The obtained results showed that a combination of the electric and magnetic fields can change the character of a phase transition from the isotropic to the nematic phase via the droplet state in such systems. Moreover, magneto-dielectric measurements of structural transitions showed the magnetic field induced a shift of the phase transition temperature from the isotropic to the droplet state.
Micro-spectroscopic mapping: revealing internal structures of zircon crystals
NASA Astrophysics Data System (ADS)
Nasdala, L.; Reiners, P. W.; Hanchar, J. M.
Natural zircon crystals typically deviate from perfect crystallinity and ideal chemical composition. If non-ideality features are not homogeneously distributed within a crystal but show a heterogeneity pattern, this is referred to as its "internal structure". Internal structures of zircon are mostly first caused by the heterogeneous incorporation of trace elements during crystal growth. Over time, these primary patterns may become more complex after being overprinted by radioactive self-irradiation and heterogeneous alteration or recrystallization. Internal structures may provide valuable information about the origin and post-growth history of zircon crystals. Further, they need to be recognized for sound microprobe dating, for instance to avoid biased results when straddling zones of different age. Revealing internal structures has thus become an important tool in zircon research. It is mostly done by means of backscattered electrons or cathodoluminescence imaging. These two techniques are advantageous over optical microscopy in the cross-polarized mode as the volume resolution is better and simple polished mounts instead of doubly-sided sections are needed. A disadvantage, however, is that the impact of electron beam during analysis causes local structural changes. Quantitative studies of the real structure of zircon samples, such as determination of the degree of the radiation damage, is therefore tainted with potential uncertainty when being done after electron probe analysis. As an alternative, we present images of internal zircon structures generated through visible laser excitation and mapping of the Raman and photoluminescence light. Due to the time-consuming mapping procedure, such images will perhaps not be routinely used. For detailed studies, however, they may provide most valuable information. Photoluminescence maps provide, for instance, information on both the distribution of rare earth elements (band integrals) and the short-range order (band broadening) whereas Raman-based images are most sensitive for revealing patterns of heterogeneous radiation damage. Application of micro-spectroscopic mappings to the study of zircon crystals from the Gold Butte block, Nevada, and the Adirondack Mountains, New York State, are presented.
How evolutionary crystal structure prediction works--and why.
Oganov, Artem R; Lyakhov, Andriy O; Valle, Mario
Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult. Crystal structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or conformations of the molecules; therefore ranking becomes the main challenge. For inorganic crystals, quantum mechanical methods often provide correct relative energies, making search the most critical problem. Recent developments provide useful practical methods for solving the search problem to a considerable extent. One can use simulated annealing, metadynamics, random sampling, basin hopping, minima hopping, and data mining. Genetic algorithms have been applied to crystals since 1995, but with limited success, which necessitated the development of a very different evolutionary algorithm. This Account reviews CSP using one of the major techniques, the hybrid evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography). Using recent developments in the theory of energy landscapes, we unravel the reasons evolutionary techniques work for CSP and point out their limitations. We demonstrate that the energy landscapes of chemical systems have an overall shape and explore their intrinsic dimensionalities. Because of the inverse relationships between order and energy and between the dimensionality and diversity of an ensemble of crystal structures, the chances that a random search will find the ground state decrease exponentially with increasing system size. A well-designed evolutionary algorithm allows for much greater computational efficiency. We illustrate the power of evolutionary CSP through applications that examine matter at high pressure, where new, unexpected phenomena take place. Evolutionary CSP has allowed researchers to make unexpected discoveries such as a transparent phase of sodium, a partially ionic form of boron, complex superconducting forms of calcium, a novel superhard allotrope of carbon, polymeric modifications of nitrogen, and a new class of compounds, perhydrides. These methods have also led to the discovery of novel hydride superconductors including the "impossible" LiH(n) (n=2, 6, 8) compounds, and CaLi(2). We discuss extensions of the method to molecular crystals, systems of variable composition, and the targeted optimization of specific physical properties. PMID:21361336
Crystal structure of bis(pyridine betaine) hydrochloride monohydrate
NASA Astrophysics Data System (ADS)
Xiao-Ming, Chen; Mak, Thomas C. W.
Bis(pyridine betaine) hydrochloride monohydrate, 2C 5H 5NCH 2COO·HCl·H 2O, crystallizes in space group Pnna (No. 52), with a=15.623(3), b=19.707(3), c=5.069(1) Å, and Z=4. The structure has been refined to RF=0.067 for 1207 observed (| F0|>6?| F0|) Mo K? data. The carboxylate groups of a pair of pyridine betaine molecules are bridged by a proton to form a centrosymmetric dimer featuring a very strong hydrogen bond of length 2.436(6) Å. The crystal structure comprises a packing of such [(C 5H 5NCH 2COO) 2H] + moieties and hydrogen-bonded (Cl -{dH 2O} ?) zigzag chains running parallel to the c axis.
Crystal structure of BIS(Betaine) hydrochloride monohydrate
NASA Astrophysics Data System (ADS)
Chen, Xiao-Ming; Mak, Thomas C. W.
Bis(betaine) hydrochloride monohydrate, 2Me 3NCH 2COO·HCI·H 2O, crystallizes in space group Pnma (No. 62), with a=11.904(1), b=22.454(5), c=5.624(1) Å, and Z=4. The structure has been refined to RinF=0.046 for 863 observed (| Fo||>6?| Fo|) Mo K? data. the carboxylate groups of a pair of betaine molecules are bridged by a proton to form a centrosymmetric dimer featuring a very strong hydrogen bond of length 2.454(4) Å. The crystal structure comprises a packing of such [(Me 3NCH 2COO) 2H] + moieties and hydrogen-bonded (Cl -·H 2O) ? zigzag chains running parallel to the c axis.
Crystal structures and properties of nylon polymers from theory
Dasgupta, S.; Goddard, W.A. III [California Inst. of Technology, Pasadena, CA (United States)] [California Inst. of Technology, Pasadena, CA (United States); Hammond, W.B. [Allied Signal Inc., Morristown, NJ (United States)] [Allied Signal Inc., Morristown, NJ (United States)
A complete force field (MSXX) for simulation of all nylon polymers is derived from ab initio quantum calculations. Special emphasis is given to the accuracy of the hydrogen bond potential for the amide unit and the torsional potential between the peptide and alkane fragments. The MSXX force field was used to predict the structures, moduli, and detailed geometries of all nine nylons for which there are experimental crystal data plus one other. For nylon-(2n) with 2n = 6, the {alpha} crystal structure (with all-trans CH{sub 2} chains nearly coplanar with the hydrogen bonding plane) is more stable, while for 2n > 6, {gamma} (with the alkane plane twisted by 70{degree}) is more stable. This change results from the increased importance of methylene packing interactions over H bonds for larger 2n. We find the highest Young`s modulus for nylon-7. 51 refs., 6 figs., 7 tabs.
Crystal structure of naturally occurring mercury(II) amidonitrate
NASA Astrophysics Data System (ADS)
Randall, Charles J.; Peacor, Donald R.; Rouse, Roland C.; Dunn, Pete J.
A naturally-occurring mercuroammonium compound from Pitkin County, Colorado, is shown to be the natural analog of synthetic HgNH 2NO 3. The crystals are isometric, P4 132 or P4 332, with a = 10.254(1)Å and twelve formula weights per cell. Using 437 symmetry-independent reflections, the crystal structure was partially determined and refined to a residual of 0.090. The positions of the Hg atoms and the N and O atoms of the nitrate group were determined, but the amide ion could not be located, probably due to positional disorder. The structure contains mercury atoms arranged in equilateral triangles 3.421(1) Å on a side. These triangles are linked through shared vertices into helical chains wound around the fourfold screw axes. Similar triangular units occur in other inorganic Hg(II) compounds. The distortion of the nitrate ion from trigonal planar symmetry is also discussed.
Crystal structure of frustrated antiferromagnet UNi4B
NASA Astrophysics Data System (ADS)
Haga, Y.; Oyamada, A.; Matsuda, T. D.; Ikeda, S.; ?unki, Y.
Crystal structure of a frustrated antiferomagnet UNi4B was investigated precisely by the X-ray diffraction on a Czochralski-grown high-quality single crystal. The unit cell was unambiguously determined as orthorhombic with the lattice parameters a=6.968, b=17.1377, and c=14.8882 Å. These orthorhombic lattice parameters are approximately related to the reported hexagonal unit cell parameters ahex and chex as a=2chex, b=2?{3}ahex and c=3ahex. They are also consistent with the previously reported weak superlattice reflections measured by the neutron scattering assuming the hexagonal lattice. We have found that four different uranium sites with the different local environment exist. Therefore UNi4B can no more be regarded as a pure frustrated system as previously assumed and its magnetic properties should be reanalyzed based on the correct structure.
Models for the aggregate structure of soot particles
Patterson, Robert I.A.; Kraft, Markus [Department of Chemical Engineering, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA (United Kingdom)
New bivariate models for soot particle structure are introduced to qualitatively replicate observed particle shapes and are found to offer quantitative improvements over older single-variable models. Models for the development of particle shape during surface growth and for particle collision diameters are described and implemented along with two models taken from other published work. Using a stochastic approach, bivariate soot particle distributions are calculated for the first time. Distributions calculated for the new models are found to be insensitive to the collision diameter model used for coagulation. The total mass of soot produced in a laminar premixed flame is found to vary by no more than 20% as the model for the geometric effects of chemical reactions on the surface of particles is changed. Histories of individual particles are analyzed and show the limitations of collector particle techniques for predicting the evolution of aggregate shape descriptors. (author)
Mechanism and kinetics of organic matter degradation based on particle structure variation during pig manure aerobic composting.
Ge, Jinyi; Huang, Guangqun; Huang, Jing; Zeng, Jianfei; Han, Lujia
Characterization of the dynamic structure of composting particles may facilitate our understanding of the mechanisms of organic matter degradation during pig manure-wheat straw aerobic composting. In this study, changes in the size, shape, pores, chemical compositions, and crystal structures of pig manure particles during composting were investigated. The results showed that the median diameter (D50) decreased exponentially, while the particle aspect ratio and sphericity were unchanged, suggesting that particles were degraded uniformly along different radial directions. Pores had a mean diameter of 15-30?m and were elliptical. The particle porosity increased linearly mainly because of hemicellulose degradation. Furthermore, the influence of particle structure variation on the first order rate constant (k) of organic matter degradation was corrected, which may facilitate the optimization of operation conditions. The k value was proportional to the reciprocal of D50 according to the specific surface area of particles, and it decreased with increased porosity due to the stabilized chemical compositions and crystal structures of particles. However, the applicability of these data to other composting materials should be verified. PMID:25781372
Clustering of low-valence particles: Structure and kinetics
NASA Astrophysics Data System (ADS)
Markova, Olga; Alberts, Jonathan; Munro, Edwin; Lenne, Pierre-François
We compute the structure and kinetics of two systems of low-valence particles with three or six freely oriented bonds in two dimensions. The structure of clusters formed by trivalent particles is complex with loops and holes, while hexavalent particles self-organize into regular and compact structures. We identify the elementary structures which compose the clusters of trivalent particles. At initial stages of clustering, the clusters of trivalent particles grow with a power-law time dependence. Yet at longer times fusion and fission of clusters equilibrates and clusters form a heterogeneous phase with polydispersed sizes. These results emphasize the role of valence in the kinetics and stability of finite-size clusters.
Structure of RCC1 chromatin factor bound to the nucleosome core particle
Makde, Ravindra D.; England, Joseph R.; Yennawar, Hemant P.; Tan, Song (Penn)
The small GTPase Ran enzyme regulates critical eukaryotic cellular functions including nuclear transport and mitosis through the creation of a RanGTP gradient around the chromosomes. This concentration gradient is created by the chromatin-bound RCC1 (regulator of chromosome condensation) protein, which recruits Ran to nucleosomes and activates Ran's nucleotide exchange activity. Although RCC1 has been shown to bind directly with the nucleosome, the molecular details of this interaction were not known. Here we determine the crystal structure of a complex of Drosophila RCC1 and the nucleosome core particle at 2.9 {angstrom} resolution, providing an atomic view of how a chromatin protein interacts with the histone and DNA components of the nucleosome. Our structure also suggests that the Widom 601 DNA positioning sequence present in the nucleosomes forms a 145-base-pair nucleosome core particle, not the expected canonical 147-base-pair particle.
Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase
Han,Q.; Robinson, H.; Gao, Y.; Vogelaar, N.; Wilson, S.; Rizzi, M.; Li, J.
Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75{angstrom} high-resolution three-dimensional crystal structure of AGT from the mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1{angstrom} resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.
Crystal structures and conducting properties of TTM-TTP salts
Y. Misaki; H. Nishikawa; T. Yamabe; T. Mori; H. Mori; S. Tanaka
Conducting properties of various cation radical salts of the title donor have been investigated. Among them (TTM-TTP)I3 and ?-(TTM-TTP)2I3 show metallic conductivity down to TMI = 160 and 20 K, respectively. The results of X-ray crystal structure analysis of (TTM-TTP)I3 and (TTM-TTP)(PF6)0.267(THF)0.6 are also presented.
Crystal Structures of Cisplatin Bound to a Human Copper Chaperone
Boal, Amie K.; Rosenzweig, Amy C.; (NWU)
Copper trafficking proteins, including the chaperone Atox1 and the P{sub 1B}-type ATPase ATP7B, have been implicated in cellular resistance to the anticancer drug cisplatin. We have determined two crystal structures of cisplatin-Atox1 adducts that reveal platinum coordination by the conserved CXXC copper-binding motif. Direct interaction of cisplatin with this functionally relevant site has significant implications for understanding the molecular basis for resistance mediated by copper transport pathways.
Topological structure of disclination lines in 2-dimensional liquid crystals
Hui Zhang; Guo-Hong Yang
Using ?-mapping method and topological current theory, the topological structure of disclination lines in 2-dimensional liquid\\u000a crystals is studied. By introducing the strength density and the topological current of many disclination lines, it is pointed\\u000a out that the disclination lines are determined by the singulaities of the director field, and topologically quantized by the\\u000a Hopf indices and Brouwer degrees. Due
Incommensurate composite crystal structure of scandium-II
Fujihisa, Hiroshi; Gotoh, Yoshito; Yamawaki, Hiroshi; Sakashita, Mami; Takeya, Satoshi; Honda, Kazumasa [National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565 (Japan); Akahama, Yuichi; Kawamura, Haruki [Graduate School of Material Science, University of Hyogo, 3-2-1 Koto, Kamigohri, Hyogo 678-1297 (Japan)
The long-unknown crystal structure of the high pressure phase scandium-II was solved by powder x-ray diffraction and was found to have tetragonal host channels along the c axis and guest chains that are incommensurate with the host, as well as the high pressure phases of Ba, Sr, Bi, and Sb. The pressure dependences of the lattice constants, the incommensurability, the atomic distances, and the atomic volume were investigated.
Crystal structures explain functional properties of two E. coli porins
S. W. Cowan; T. Schirmer; G. Rummel; M. Steiert; R. Ghosh; R. A. Pauptit; J. N. Jansonius; J. P. Rosenbusch
Porins form aqueous channels that aid the diffusion of small hydrophilic molecules across the outer membrane of Gram-negative bacteria. The crystal structures of matrix porin and phosphoporin both reveal trimers of identical subunits, each subunit consisting of a 16-stranded anti-parallel beta-barrel containing a pore. A long loop inside the barrel contributes to a constriction of the channel where the charge
On structure and twist in ZnS crystal whiskers
S. Mardix; A. R. Lang; G. Kowalski; A. P. W. Makepeace
ZnS crystal whiskers grown from the vapour at about 1450 K, with typical lengths of about 20 mm and diameters about 100 ?m, have been studied by synchrotron X-ray topography. Crystallographic structure and texture have been compared with morphological and optical characteristics point-by-point along whisker axes. Using continuous radiation and cylindrical camera geometry, entire diffraction patterns from zones of type
Lithium niobate: Summary of physical properties and crystal structure
R. S. Weis; T. K. Gaylord
Ferroelectric lithium niobate (LiNbO3) is widely used in integrated and guided-wave optics because of its favorable optical, piezoelectric, electro-optic, elastic, photoelastic, and photorefractive properties. However, detailed summaries of its pertinent physical properties and crystal structure are not readily available. In this tutorial paper, the important tensor physical properties and their mathematical descriptions are compiled and presented. The essential features of
The crystal structure of alpha-SrMnO3
Koji Kuroda; Nobuo Ishizawa; Nobuyasu Mizutani; Masanori Kato
alpha-SrMnO3 crystallizes in the hexagonal system with unit-cell dimensions a = 5.454(1) Å, c = 9.092(2)Å, space group P63\\/mmc, Z = 4. The structure was solved by the heavy-atom method; of 404 unique reflections measured by counter method, 203 that obeyed the condition F0 >= 3sigma (F0) were used in the refinement to a conventional R value of 0.043. The
The Crystal and Molecular Structure of Adenosine Triphosphate
Olga Kennard; N. W. Isaacs; W. D. S. Motherwell; J. C. Coppola; D. L. Wampler; A. C. Larson; D. G. Watson
The three-dimensional structure of the hydrated disodium salt of adenosine triphosphate (Na2ATP) has been determined from an X-ray diffraction study to a resolution of 0.9 angstrom. The crystals are orthorhombic, space group P212121, with a = 30.45(4), b = 20.88(3), c = 7.07(1) angstrom. There are two molecules of ATP, four sodium ions, and six water molecules in the asymmetric
Polymer crystallization enabled nanotube functionalization: Morphology, structure and applications
NASA Astrophysics Data System (ADS)
Li, Lingyu
Carbon Nanotubes (CNT) have attracted tremendous attention and numerous potential applications have been proposed. In this thesis study, a unique means to modify CNT surface with polymer crystals via controlled polymer crystallization method has been developed. CNTs were wrapped in polymer single crystal lamellae in a periodic manner, resulting in nano hybrid shish-kebab (NHSK) structures. The periodicity of the polymer lamellae can be varied from 20-150 nm. The kebabs are ˜5 nm thick (along CNT direction) with a lateral size of ˜20 nm to micrometers, which can be readily controlled by varying crystallization conditions. PE, Nylon 66 and PE-b-SBR were successfully decorated on single-walled carbon nanotubes (SWNT), multi-walled carbon nanotubes (MWNT), as well as vapor grown carbon nanofibers (CNF). The formation mechanism was attributed to "size dependent soft epitaxy". Efforts were focused on PE/SWNT system to understand the growth mechanism and the effect of experimental parameters on the periodicity. It was found that weight ratio of SWNT and PE (defined as R) played an important role and periodicity increases with increasing R. This was attributed to a reduced polymer concentration at the crystal growth front. Since NHSK formation conditions depend upon CNT structures, it further provides a unique opportunity for CNT separation. Applications of using NHSK in CNT dispersions, separation and nanocomposites have also been successfully developed. This unique means is different from all the reported methods and it opens a gateway to achieving periodically functionalized CNT for a variety of applications ranging from nanocomposites, sensors, fuel cells etc.
Structural contribution to the roughness of supersmooth crystal surface
Butashin, A. V.; Muslimov, A. E., E-mail: email@example.com; Kanevsky, V. M.; Deryabin, A. N.; Pavlov, V. A.; Asadchikov, V. E. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)
Technological advances in processing crystals (Si, sapphire {alpha}-Al{sub 2}O{sub 3}, SiC, GaN, LiNbO{sub 3}, SrTiO{sub 3}, etc.) of substrate materials and X-ray optics elements make it possible to obtain supersmooth surfaces with a periodicity characteristic of the crystal structure. These periodic structures are formed by atomically smooth terraces and steps of nano- and subnanometer sizes, respectively. A model surface with such nanostructures is proposed, and the relations between its roughness parameters and the height of atomic steps are determined. The roughness parameters calculated from these relations almost coincide with the experimental atomic force microscopy (AFM) data obtained from 1 Multiplication-Sign 1 and 10 Multiplication-Sign 10 {mu}m areas on the surface of sapphire plates with steps. The minimum roughness parameters for vicinal crystal surfaces, which are due to the structural contribution, are calculated based on the approach proposed. A comparative analysis of the relief and roughness parameters of sapphire plate surfaces with different degrees of polishing is performed. A size effect is established: the relief height distribution changes from stochastic to regular with a decrease in the surface roughness.
Crystal structure of the integral membrane diacylglycerol kinase
Li, Dianfan; Lyons, Joseph A.; Pye, Valerie E.; Vogeley, Lutz; Aragão, David; Kenyon, Colin P.; Shah, Syed T. A.; Doherty, Christine; Aherne, Margaret; Caffrey, Martin
Diacylglycerol kinase (DgkA) catalyzes the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid for use in shuttling water-soluble components to membrane derived oligosaccharide and lipopolysaccharide in the cell envelope of Gram-negative bacteria1. For half a century, this 121-residue kinase has served as a paradigm for investigating membrane protein enzymology1,3-7, folding8,9, assembly10-13, and stability1,14. Here, we present crystal structures for three functional forms of this unique and paradigmatic kinase, one of which is wild type (WT). These reveal a homo-trimeric enzyme with three transmembrane helices and an N-terminal amphiphilic helix per monomer. Bound lipid substrate and docked ATP identify the putative active site which is of the composite, shared site type. The crystal structures rationalize extensive biochemical and biophysical data on the enzyme. They are however at variance with a published solution NMR model2 in that domain swapping, a key feature of the solution form, is not observed in the crystal structures. PMID:23676677
Crystal structure of lead(II) tartrate: a redetermination
Weil, Matthias
Single crystals of poly[?4-tartrato-?6 O 1,O 3:O 1?:O 2,O 4:O 4?-lead], [Pb(C4H4O6)]n, were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ?). Acta Cryst. C58, m596–m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb2+ cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb2+ cations. The resulting three-dimensional framework is stabilized by O—H?O hydrogen bonds between the OH groups of one tartrate anion and the carboxylate O atoms of adjacent anions. PMID:25705458
Crystal structure of lead(II) tartrate: a redetermination.
Weil, Matthias
Single crystals of poly[?4-tartrato-?(6) O (1),O (3):O (1'):O (2),O (4):O (4')-lead], [Pb(C4H4O6)] n , were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ?). Acta Cryst. C58, m596-m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb(2+) cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb(2+) cations. The resulting three-dimensional framework is stabilized by O-H?O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl-ate O atoms of adjacent anions. PMID:25705458
Nanoconfinement-Induced Structures in Chiral Liquid Crystals
Melle, Michael; Theile, Madlona; Hall, Carol K.; Schoen, Martin
We employ Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality. Our model potential consists of a simple Lennard-Jones potential, where the attractive contribution has been modified to represent the orientation dependence of the interaction between a pair of chiral liquid-crystal molecules. The liquid crystal is confined between a pair of planar and atomically smooth substrates onto which molecules are anchored in a hybrid fashion. Hybrid anchoring allows for the formation of helical structures in the direction perpendicular to the substrate plane without exposing the helix to spurious strains. At low chirality, we observe a cholesteric phase, which is transformed into a blue phase at higher chirality. More specifically, by studying the unit cell and the spatial arrangement of disclination lines, this blue phase can be established as blue phase II. If the distance between the confining substrates and molecular chirality are chosen properly, we see a third structure, which may be thought of as a hybrid, exhibiting mixed features of a cholesteric and a blue phase. PMID:23989605
Influence of particle aspect ratio on the midinfrared extinction spectra of wavelength-sized ice crystals.
Wagner, Robert; Benz, Stefan; Möhler, Ottmar; Saathoff, Harald; Schnaiter, Martin; Leisner, Thomas
We have used the T-matrix method and the discrete dipole approximation to compute the midinfrared extinction cross-sections (4500-800 cm(-1)) of randomly oriented circular ice cylinders for aspect ratios extending up to 10 for oblate and down to 1/6 for prolate particle shapes. Equal-volume sphere diameters ranged from 0.1 to 10 microm for both particle classes. A high degree of particle asphericity provokes a strong distortion of the spectral habitus compared to the extinction spectrum of compactly shaped ice crystals with an aspect ratio around 1. The magnitude and the sign (increase or diminution) of the shape-related changes in both the absorption and the scattering cross-sections crucially depend on the particle size and the values for the real and imaginary part of the complex refractive index. When increasing the particle asphericity for a given equal-volume sphere diameter, the values for the overall extinction cross-sections may change in opposite directions for different parts of the spectrum. We have applied our calculations to the analysis of recent expansion cooling experiments on the formation of cirrus clouds, performed in the large coolable aerosol and cloud chamber AIDA of Forschungszentrum Karlsruhe at a temperature of 210 K. Depending on the nature of the seed particles and the temperature and relative humidity characteristics during the expansion, ice crystals of various shapes and aspect ratios could be produced. For a particular expansion experiment, using Illite mineral dust particles coated with a layer of secondary organic matter as seed aerosol, we have clearly detected the spectral signatures characteristic of strongly aspherical ice crystal habits in the recorded infrared extinction spectra. We demonstrate that the number size distributions and total number concentrations of the ice particles that were generated in this expansion run can only be accurately derived from the recorded infrared spectra when employing aspect ratios as high as 10 in the retrieval approach. Remarkably, the measured spectra could also be accurately fitted when employing an aspect ratio of 1 in the retrieval. The so-deduced ice particle number concentrations, however, exceeded the true values, determined with an optical particle counter, by more than 1 order of magnitude. Thus, the shape-induced spectral changes between the extinction spectra of platelike ice crystals of aspect ratio 10 and compactly shaped particles of aspect ratio 1 can be efficiently balanced by deforming the true number size distribution of the ice cloud. As a result of this severe size/shape ambiguity in the spectral analysis, we consider it indispensable to cross-check the infrared retrieval results of wavelength-sized ice particles with independent reference measurements of either the number size distribution or the particle morphology. PMID:18004822
In-situ observations of aerosol particles remaining from evaporated cirrus crystals: Comparing clean and polluted air masses
NASA Astrophysics Data System (ADS)
Seifert, M.; Ström, J.; Krejci, R.; Minikin, A.; Petzold, A.; Gayet, J.-F.; Schumann, U.; Ovarlez, J.
In-situ observations of aerosol particles contained in cirrus crystals are presented and compared to interstitial aerosol size distributions (non-activated particles in between the cirrus crystals). The observations were conducted in cirrus clouds in the Southern and Northern Hemisphere mid-latitudes during the INCA project. The first campaign in March and April 2000 was performed from Punta Arenas, Chile (54°S) in pristine air. The second campaign in September and October 2000 was performed from Prestwick, Scotland (53°N) in the vicinity of the North Atlantic flight corridor. Size distribution measurements of crystal residuals (particles remaining after evaporation of the crystals) show that small aerosol particles (Dp< 0.1 mm) dominate the number density of residuals. The crystal residual size distributions were significantly different in the two campaigns. On average the residual size distributions were shifted towards larger sizes in the Southern Hemisphere. For a given integral residual number density, the calculated particle volume was on average three times larger in the Southern Hemisphere. This may be of significance to the vertical redistribution of aerosol mass by clouds in the tropopause region. In both campaigns the mean residual size increased slightly with increasing crystal number density. The form of the residual size distribution did not depend on temperature as one might have expected considering different modes of nucleation. The observations of ambient aerosol particles were consistent with the expected higher pollution level in the Northern Hemisphere. The fraction of residual particles only contributes to approximately a percent or less of the total number of particles, which is the sum of the residual and interstitial particles. Excellent agreement between the CVI and FSSP-300 probes was found supporting the assumption that each crystal is associated with only one residual particle.
Ab initio molecular crystal structures, spectra, and phase diagrams.
Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni
Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher. PMID:24754304
Crystal structure of inactive form of Rab3B
Zhang, Wei [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China)] [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China); Shen, Yang [Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7 (Canada)] [Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7 (Canada); Jiao, Ronghong [Department of Function Inspection, Hebei Provincial People's Hospital, Shijiazhuang 050051 (China)] [Department of Function Inspection, Hebei Provincial People's Hospital, Shijiazhuang 050051 (China); Liu, Yanli; Deng, Lingfu [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China)] [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China); Qi, Chao, E-mail: email@example.com [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China)] [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China)
Highlights: Black-Right-Pointing-Pointer This is the first structural information of human Rab3B. Black-Right-Pointing-Pointer To provides a structural basis for the GDP/GTP switch in controlling the activity of Rab3. Black-Right-Pointing-Pointer The charge distribution of Rab3B indicates its unique roles in vesicular trafficking. -- Abstract: Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 A resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.
Crystal structure of a soluble cleaved HIV-1 envelope trimer
Julien, Jean-Philippe; Cupo, Albert; Sok, Devin; Stanfield, Robyn L.; Lyumkis, Dmitry; Deller, Marc C.; Klasse, Per-Johan; Burton, Dennis R.; Sanders, Rogier W.; Moore, John P.; Ward, Andrew B.; Wilson, Ian A.
HIV-1 entry into CD4+ target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 Å of an antigenically near-native, cleaved, stabilized, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a pre-fusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the three-fold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3 and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design. PMID:24179159
Gyroid cuticular structures in butterfly wing scales: biological photonic crystals.
Michielsen, K; Stavenga, D G
We present a systematic study of the cuticular structure in the butterfly wing scales of some papilionids (Parides sesostris and Teinopalpus imperialis) and lycaenids (Callophrys rubi, Cyanophrys remus, Mitoura gryneus and Callophrys dumetorum). Using published scanning and transmission electron microscopy (TEM) images, analytical modelling and computer-generated TEM micrographs, we find that the three-dimensional cuticular structures can be modelled by gyroid structures with various filling fractions and lattice parameters. We give a brief discussion of the formation of cubic gyroid membranes from the smooth endoplasmic reticulum in the scale's cell, which dry and harden to leave the cuticular structure behind when the cell dies. The scales of C. rubi are a potentially attractive biotemplate for producing three-dimensional optical photonic crystals since for these scales the cuticle-filling fraction is nearly optimal for obtaining the largest photonic band gap in a gyroid structure. PMID:17567555
Nanoscale potassium niobate crystal structure and phase transition
Nanoscale potassium niobate (KNbO3) powders of orthorhombic structure were synthesized using the sol-gel method. The heat-treatment temperature of the gels had a pronounced effect on KNbO3 particle size and morphology. Field emission scanning electron microscopy and transmission electron microscopy were used to determine particle size and morphology. The average KNbO3 grain size was estimated to be less than 100 nm, and transmission electron microscopy images indicated that KNbO3 particles had a brick-like morphology. Synchrotron X-ray diffraction was used to identify the room-temperature structures using Rietveld refinement. The ferroelectric orthorhombic phase was retained even for particles smaller than 50 nm. The orthorhombic to tetragonal and tetragonal to cubic phase transitions of nanocrystalline KNbO3 were investigated using temperature-dependent powder X-ray diffraction. Differential scanning calorimetry was used to examine the temperature dependence of KNbO3 phase transition. The Curie temperature and phase transition were independent of particle size, and Rietveld analyses showed increasing distortions with decreasing particle size. PMID:21943345
Crystal structure, microstructure and magnetic properties of Ni nanoparticles elaborated by hydrothermal route
NASA Astrophysics Data System (ADS)
Bouremana, A.; Guittoum, A.; Hemmous, M.; Rahal, B.; Sunol, J. J.; Martínez-Blanco, D.; Blanco, J. A.; Gorria, Pedro; Benrekaa, N.
We report on the crystal structure, microstructure and magnetic properties of Ni nanoparticles (NPs), with an average diameter of around 40 nm, produced by hydrothermal method. A series of Ni powders was synthesized at relatively low temperature (140 °C) by varying the NaOH concentration. The crystal structure, microstructure and magnetic properties were investigated by means of XRD, MEB coupled to EDX and VSM magnetometry. The XRD patterns show Bragg reflections corresponding to Ni with face centred cubic (fcc) crystal structure. EDX spectra confirm the purity of Ni powders. Moreover, the SEM micrographs show that the Ni-NPs are agglomerated forming entities of 1-5 ?m in average size with different morphologies that change as the NaOH concentration increases. While those entities exhibit a flower-like form at the lowest concentration, a dendritic shape appears for the highest one. The room temperature values for the coercive field (<200 Oe) and saturation magnetization (?52 Am2/kg) were obtained from the magnetic hysteresis loops. We discuss about the influence of the particle morphology on the magnetic behaviour.
Synthesis, crystal growth, structural, thermal, optical and mechanical properties of solution grown 4-methylpyridinium 4-hydroxybenzoate single crystal.
Sudhahar, S; Krishna Kumar, M; Sornamurthy, B M; Mohan Kumar, R
Organic nonlinear optical material, 4-methylpyridinium 4-hydroxybenzoate (4MPHB) was synthesized and single crystal was grown by slow evaporation solution growth method. Single crystal and powder X-ray diffraction analyses confirm the structure and crystalline perfection of 4MPHB crystal. Infrared, Raman and NMR spectroscopy techniques were used to elucidate the functional groups present in the compound. TG-DTA analysis was carried out in nitrogen atmosphere to study the decomposition stages, endothermic and exothermic reactions. UV-visible and Photoluminescence spectra were recorded for the grown crystal to estimate the transmittance and band gap energy respectively. Linear refractive index, birefringence, and SHG efficiency of the grown crystal were studied. Laser induced surface damage threshold and mechanical properties of grown crystal were studied to assess the suitability of the grown crystals for device applications. PMID:24184578
Synthesis, crystal growth, structural, thermal, optical and mechanical properties of solution grown 4-methylpyridinium 4-hydroxybenzoate single crystal
NASA Astrophysics Data System (ADS)
Sudhahar, S.; Krishna Kumar, M.; Sornamurthy, B. M.; Mohan Kumar, R.
Organic nonlinear optical material, 4-methylpyridinium 4-hydroxybenzoate (4MPHB) was synthesized and single crystal was grown by slow evaporation solution growth method. Single crystal and powder X-ray diffraction analyses confirm the structure and crystalline perfection of 4MPHB crystal. Infrared, Raman and NMR spectroscopy techniques were used to elucidate the functional groups present in the compound. TG-DTA analysis was carried out in nitrogen atmosphere to study the decomposition stages, endothermic and exothermic reactions. UV-visible and Photoluminescence spectra were recorded for the grown crystal to estimate the transmittance and band gap energy respectively. Linear refractive index, birefringence, and SHG efficiency of the grown crystal were studied. Laser induced surface damage threshold and mechanical properties of grown crystal were studied to assess the suitability of the grown crystals for device applications.
Crystal structure of new AsS{sub 2} compound
Bolotina, N. B., E-mail: email@example.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Brazhkin, V. V.; Dyuzheva, T. I.; Lityagina, L. M.; Kulikova, L. F.; Nikolaev, N. A. [Russian Academy of Sciences, Vereshchagin Institute for High Pressure Physics (Russian Federation)] [Russian Academy of Sciences, Vereshchagin Institute for High Pressure Physics (Russian Federation); Verin, I. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)] [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)
AsS{sub 2} single crystals have been obtained for the first time from an As{sub 2}S{sub 3} melt at pressures above 6 GPa and temperatures above 800 K in the As{sub 2}S{sub 3} {yields} AsS + AsS{sub 2} reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.
Fusion proteins as alternate crystallization paths to difficult structure problems
NASA Technical Reports Server (NTRS)
Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua
The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.
Manganese oxide minerals: Crystal structures and economic and environmental significance
Post, Jeffrey E.
Manganese oxide minerals have been used for thousands of years—by the ancients for pigments and to clarify glass, and today as ores of Mn metal, catalysts, and battery material. More than 30 Mn oxide minerals occur in a wide variety of geological settings. They are major components of Mn nodules that pave huge areas of the ocean floor and bottoms of many fresh-water lakes. Mn oxide minerals are ubiquitous in soils and sediments and participate in a variety of chemical reactions that affect groundwater and bulk soil composition. Their typical occurrence as fine-grained mixtures makes it difficult to study their atomic structures and crystal chemistries. In recent years, however, investigations using transmission electron microscopy and powder x-ray and neutron diffraction methods have provided important new insights into the structures and properties of these materials. The crystal structures for todorokite and birnessite, two of the more common Mn oxide minerals in terrestrial deposits and ocean nodules, were determined by using powder x-ray diffraction data and the Rietveld refinement method. Because of the large tunnels in todorokite and related structures there is considerable interest in the use of these materials and synthetic analogues as catalysts and cation exchange agents. Birnessite-group minerals have layer structures and readily undergo oxidation reduction and cation-exchange reactions and play a major role in controlling groundwater chemistry. PMID:10097056
Substrate selectivity of bacterial monoacylglycerol lipase based on crystal structure.
Tsurumura, Toshiharu; Tsuge, Hideaki
Lipases, which are conserved from bacteria to mammals, catalyze the hydrolysis of acylglycerol to free fatty acids and glycerol. Monoacylglycerol lipase (MGL) specifically catalyzes the hydrolysis of monoacylglycerol. Although there have been numerous studies of the structure of lipases, there have been few studies of MGL. Here, we report the crystal structure of authentic MGL isolated from Bacillus sp. H257 (bMGL). The crystal diffracts to 1.96 Å resolution. It belongs to space group P21212, and the unit cell parameters are a=99.7 Å, b=106.1 Å and c=43.0 Å. As in other lipases, three structural features for lipase activity are conserved in bMGL: the glycine-X-serine-X-glycine motif, catalytic triad and cap region. The structure of bMGL appears to be closed, as the cap region covers the active site entrance. The isolated bMGL hydrolyzed 2-AG, a known human MGL-specific substrate. Based on a 2-AG bound model, we discuss the substrate selectivity. The functional and structural features of bMGL provide insight how its substrate selectivity is determined and how specific inhibitors of bacterial MGL could be designed, which may be useful for development of novel antibiotics. PMID:24894647
The crystal structure of human GDP-L-fucose synthase.
Zhou, Huan; Sun, Lihua; Li, Jian; Xu, Chunyan; Yu, Feng; Liu, Yahui; Ji, Chaoneng; He, Jianhua
Human GDP-l-fucose synthase, also known as FX protein, synthesizes GDP-l-fucose from its substrate GDP-4-keto-6-deoxy-d-mannose. The reaction involves epimerization at both C-3 and C-5 followed by an NADPH-dependent reduction of the carbonyl at C-4. In this paper, the first crystal structure of human FX protein was determined at 2.37 Å resolution. The asymmetric unit of the crystal structure contains four molecules which form two homodimers. Each molecule consists of two domains, a Rossmann-fold NADPH-binding motif and a carboxyl terminal domain. Compared with the Escherichia coli GDP-l-fucose synthase, the overall structures of these two enzymes have four major differences. There are four loops in the structure of human FX protein corresponding to two ?-helices and two ?-sheets in that of the E. coli enzyme. Besides, there are seven different amino acid residues binding with NAPDH comparing human FX protein with that from E. coli. The structure of human FX reveals the key catalytic residues and could be useful for the design of drugs for the treatment of inflammation, auto-immune diseases, and possibly certain types of cancer. PMID:23774504
Crystal structure and crystal chemistry of melanovanadite, a natural vanadium bronze.
Konnert, J.A.; Evans, H.T., Jr.
The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.
Identifying duplicate crystal structures: XTALCOMP, an open-source solution
NASA Astrophysics Data System (ADS)
Lonie, David C.; Zurek, Eva
We describe the implementation of XTALCOMP, an efficient, reliable, and open-source library that tests if two crystal descriptions describe the same underlying structure. The algorithm has been tested and found to correctly identify duplicate structures in spite of the "real-world" difficulties that arise from working with numeric crystal representations: degenerate unit cell lattices, numerical noise, periodic boundaries, and the lack of a canonical coordinate origin. The library is portable, open, and not dependent on any external packages. A web interface to the algorithm is publicly accessible at http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html. Program summaryProgram title: XtalComp Catalogue identifier: AEKV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: "New" (3-clause) BSD [1] No. of lines in distributed program, including test data, etc.: 3148 No. of bytes in distributed program, including test data, etc.: 21 860 Distribution format: tar.gz Programming language: C++ Computer: No restrictions Operating system: All operating systems with a compliant C++ compiler. Classification: 7.8 Nature of problem: Computationally identifying duplicate crystal structures taken from the output of modern solid state calculations is a non-trivial exercise for many reasons. The translation vectors in the description are not unique — they may be transformed into linear combinations of themselves and continue to describe the same extended structure. The coordinates and cell parameters contain numerical noise. The periodic boundary conditions at the unit cell faces, edges, and corners can cause very small displacements of atomic coordinates to result in very different representations. The positions of all atoms may be uniformly translated by an arbitrary vector without modifying the underlying structure. Additionally, certain applications may consider enantiomorphic structures to be identical. Solution method: The XtalComp algorithm overcomes these issues to detect duplicate structures regardless of differences in representation. It begins by performing a Niggli reduction on the inputs, standardizing the translation vectors and orientations. A transform search is performed to identify candidate sets of rotations, reflections, and translations that potentially map the description of one crystal onto the other, solving the problems of enantiomorphs and rotationally degenerate lattices. The atomic positions resulting from each candidate transform are then compared, using a cell-expansion technique to remove periodic boundary issues. Computational noise is treated by comparing non-integer quantities using a specified tolerance. Running time: The test run provided takes less than a second to complete.
Hierarchical Structure-Ferroelectricity Relationships of Barium Titanate Particles
Aksay, Ilhan A.
Review Hierarchical Structure-Ferroelectricity Relationships of Barium Titanate Particles Tu Lee structural levels and to thoroughly review the corresponding structure- ferroelectricity relationships at all). However, the inconsistency of the critical size in the literature, ranging from 15 to 200 nm in diameter,4
The Low-Temperature Crystal Structure of RS-Camphor
NASA Astrophysics Data System (ADS)
Mora, Asiloé J.; Fitch, Andrew N.
The crystal structure of the low-temperature phase of RS-camphor (1,7,7-trimethylbicyclo[2.2.1]heptan-2-one, C 10H 16O) has been solved at 100 K by high-resolution powder X-ray diffraction using synchrotron radiation. The structure is orthorhombic, space group Cmcm, with a=6.8341(2) Å, b=11.6584(3) Å, c=11.5000(3) Å, and Z=4. The structure has four-fold disorder of the molecules. Left-handed and right-handed molecules are situated on the same crystallographic site, with an additional two-fold rotational disorder of the molecules. The structure was obtained from a combination of auto indexing, direct methods, and a grid search of molecular orientations.
Crystal Structure of a Fructokinase Homolog from Halothermothrix orenii
Khiang, C.; Seetharaman, J; Kasprzak, J; Cherlyn, N; Patel, B; Love, C; Bujnicki, J; Sivaraman, J
Fructokinase (FRK; EC 220.127.116.11) catalyzes the phosphorylation of D-fructose to D-fructose 6-phosphate (F6P). This irreversible and near rate-limiting step is a central and regulatory process in plants and bacteria, which channels fructose into a metabolically active state for glycolysis. Towards understanding the mechanism of FRK, here we report the crystal structure of a FRK homolog from a thermohalophilic bacterium Halothermothrix orenii (Hore{_}18220 in sequence databases). The structure of the Hore{_}18220 protein reveals a catalytic domain with a Rossmann-like fold and a b-sheet 'lid' for dimerization. Based on comparison of Hore{_}18220 to structures of related proteins, we propose its mechanism of action, in which the lid serves to regulate access to the substrate binding sites. Close relationship of Hore{_}18220 and plant FRK enzymes allows us to propose a model for the structure and function of FRKs.
Structure and magnetic properties of aerosol synthesized barium ferrite particles
W. A. Kaczmarek; B. W. Ninham; A. Calka
The aerosol synthesis technique has been employed to produce barium ferrite particles. X-ray and electron diffraction, scanning and transmission microscopy methods were used to find detailed information on crystallography, morphology and chemical composition of as prepared and annealed powders. A detailed study has been made of the correlation between magnetic hysteresis parameters and the inner structure of submicrometer ferrite particles.
Monomer structure of a hyperthermophilic ?-glucosidase mutant forming a dodecameric structure in the crystal form.
Nakabayashi, Makoto; Kataoka, Misumi; Watanabe, Masahiro; Ishikawa, Kazuhiko
One of the ?-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8?Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability. PMID:25005077
Monomer structure of a hyperthermophilic ?-glucosidase mutant forming a dodecameric structure in the crystal form
Nakabayashi, Makoto; Kataoka, Misumi; Watanabe, Masahiro; Ishikawa, Kazuhiko
One of the ?-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8?Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability. PMID:25005077
Morphology, crystal structure and hydration of calcined and modified anhydrite
NASA Astrophysics Data System (ADS)
Niu, Xiao-qing; Chen, Ji-chun
The effects of calcination and modification on the morphology (shapes and textures) and crystal structure of anhydrite powders were studied. The results show that, calcination at 100°C causes anhydrite to disintegrate into smaller crystals, accompanied by a slight increase in d-spacing. Without calcination and modification, the solidification time and curing time of anhydrite are 15 and 77 h, respectively. After the treatment, however, the solidification time and curing time are shortened significantly to 9.5 and 14 min, respectively. The compressive and flexural strengths of hydration products made from the treated anhydrite reach 10.2 and 2.0 MPa, respectively. The much shorter solidification and curing time make it possible to use anhydrite as a building and construction material.
Crystal structure and encapsulation dynamics of ice II-structured neon hydrate
Wang, Wei Hua
Crystal structure and encapsulation dynamics of ice II-structured neon hydrate Xiaohui Yua. Francisco, June 9, 2014 (sent for review April 24, 2014) Neon hydrate was synthesized and studied by in situ knowledge, we demonstrate that neon atoms can be enclathrated in water molecules to form ice II
Banded Structure and Domain Arrangements in PbTiO3 Single Crystals
NASA Astrophysics Data System (ADS)
Chou, Chen-Chia; Chen, Cheng-Sao
In the present work we report the ferroelectric domain arrangements and characteristics of banded structures observed in flux-grown PbTiO3 single crystals. Investigations of etched crystals indicate that most of the specimens show banded structures which may correspond to surface relief characteristics of as-grown crystals. Banded structures, which are different from domain structures, possess structural characteristics similar to those of martensite variants in various alloys and ceramics. The stresses produced during transformation were relieved by the formation of the banded structures and the 90° domain structures, suggesting that the band structures and 90° domains are the products of self-accommodation in as-grown PbTiO3 crystals during the cubic/tetragonal (C/T) transformation. Image characteristics imply that banded-structure-induced domain intersections may store high strain energy in lead titanate crystals and therefore hinder polarization switching of the crystals.
Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise
ERIC Educational Resources Information Center
Bindel, Thomas H.
A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…
Surface Structure of Zeolite (MFI) Crystals Isabel Diaz,, Efrosini Kokkoli, Osamu Terasaki, and Michael Tsapatsis*,
Kokkoli, Efie
Articles Surface Structure of Zeolite (MFI) Crystals Isabel Di´az,,§ Efrosini Kokkoli, Osamu type MFI) is an important zeolite that, in addition to conventional applications such as adsorption in studies of zeolite crystal growth. The surface structure of silicalite-1 crystals with two different
The crystal structure of superoxide dismutase from Plasmodium falciparum
Boucher, Ian W; Brzozowski, Andrzej M; Brannigan, James A; Schnick, Claudia; Smith, Derek J; Kyes, Sue A; Wilkinson, Anthony J
Background Superoxide dismutases (SODs) are important enzymes in defence against oxidative stress. In Plasmodium falciparum, they may be expected to have special significance since part of the parasite life cycle is spent in red blood cells where the formation of reactive oxygen species is likely to be promoted by the products of haemoglobin breakdown. Thus, inhibitors of P. falciparum SODs have potential as anti-malarial compounds. As a step towards their development we have determined the crystal structure of the parasite's cytosolic iron superoxide dismutase. Results The cytosolic iron superoxide dismutase from P. falciparum (PfFeSOD) has been overexpressed in E. coli in a catalytically active form. Its crystal structure has been solved by molecular replacement and refined against data extending to 2.5 Å resolution. The structure reveals a two-domain organisation and an iron centre in which the metal is coordinated by three histidines, an aspartate and a solvent molecule. Consistent with ultracentrifugation analysis the enzyme is a dimer in which a hydrogen bonding lattice links the two active centres. Conclusion The tertiary structure of PfFeSOD is very similar to those of a number of other iron-and manganese-dependent superoxide dismutases, moreover the active site residues are conserved suggesting a common mechanism of action. Comparison of the dimer interfaces of PfFeSOD with the human manganese-dependent superoxide dismutase reveals a number of differences, which may underpin the design of parasite-selective superoxide dismutase inhibitors. PMID:17020617
Diterbium hepta-nickel: a crystal structure redetermination.
Levytskyy, Volodymyr; Babizhetskyy, Volodymyr; Kotur, Bohdan; Smetana, Volodymyr
The crystal structure of the title compound, Tb2Ni7, was redetermined from single-crystal X-ray diffraction data. In comparison with previous studies based on powder X-ray diffraction data [Lemaire et al. (1967). C. R. Acad. Sci. Ser. B, 265, 1280-1282; Lemaire & Paccard (1969). Bull. Soc. Fr. Mineral. Cristallogr. 92, 9-16; Buschow & van der Goot (1970). J. Less-Common Met. 22, 419-428], the present redetermination affords refined coordinates and anisotropic displacement parameters for all atoms. A partial occupation for one Tb atom results in the non-stoichiometric composition Tb1.962?(4)Ni7. The title compound adopts the Ce2Ni7 structure type and can also be derived from the CaCu5 structure type as an inter-growth structure. The asymmetric unit contains two Tb sites (both site symmetries 3m.) and five Ni sites (.m., mm2, 3m., 3m., -3m.). The two different coordination polyhedra of Tb are a Frank-Kasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo Frank-Kasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are Frank-Kasper icosa-hedra formed by five Tb and seven Ni atoms, four Tb and eight Ni atoms, three Tb and nine Ni atoms, and six Tb and six Ni atoms, respectively. PMID:25249871
Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis
Chan, Siu Kit; Kitajima-Ihara, Tomomi; Fujii, Ryudoh; Gotoh, Toshiaki; Murakami, Midori; Ihara, Kunio; Kouyama, Tsutomu
Cruxrhodopsin-3 (cR3), a retinylidene protein found in the claret membrane of Haloarcula vallismortis, functions as a light-driven proton pump. In this study, the membrane fusion method was applied to crystallize cR3 into a crystal belonging to space group P321. Diffraction data at 2.1 Å resolution show that cR3 forms a trimeric assembly with bacterioruberin bound to the crevice between neighboring subunits. Although the structure of the proton-release pathway is conserved among proton-pumping archaeal rhodopsins, cR3 possesses the following peculiar structural features: 1) The DE loop is long enough to interact with a neighboring subunit, strengthening the trimeric assembly; 2) Three positive charges are distributed at the cytoplasmic end of helix F, affecting the higher order structure of cR3; 3) The cytoplasmic vicinity of retinal is more rigid in cR3 than in bacteriorhodopsin, affecting the early reaction step in the proton-pumping cycle; 4) the cytoplasmic part of helix E is greatly bent, influencing the proton uptake process. Meanwhile, it was observed that the photobleaching of retinal, which scarcely occurred in the membrane state, became significant when the trimeric assembly of cR3 was dissociated into monomers in the presence of an excess amount of detergent. On the basis of these observations, we discuss structural factors affecting the photostabilities of ion-pumping rhodopsins. PMID:25268964
Crystal Structure of Rat Carnitine Palmitoyltransferase II (CPT-II)
Hsiao,Y.; Jogl, G.; Esser, V.; Tong, L.
Carnitine palmitoyltransferase II (CPT-II) has a crucial role in the {beta}-oxidation of long-chain fatty acids in mitochondria. We report here the crystal structure of rat CPT-II at 1.9 Angstroms resolution. The overall structure shares strong similarity to those of short- and medium-chain carnitine acyltransferases, although detailed structural differences in the active site region have a significant impact on the substrate selectivity of CPT-II. Three aliphatic chains, possibly from a detergent that is used for the crystallization, were found in the structure. Two of them are located in the carnitine and CoA binding sites, respectively. The third aliphatic chain may mimic the long-chain acyl group in the substrate of CPT-II. The binding site for this aliphatic chain does not exist in the short- and medium-chain carnitine acyltransferases, due to conformational differences among the enzymes. A unique insert in CPT-II is positioned on the surface of the enzyme, with a highly hydrophobic surface. It is likely that this surface patch mediates the association of CPT-II with the inner membrane of the mitochondria.
Diterbium heptanickel: a crystal structure redetermination
Levytskyy, Volodymyr; Babizhetskyy, Volodymyr; Kotur, Bohdan; Smetana, Volodymyr
The crystal structure of the title compound, Tb2Ni7, was redetermined from single-crystal X-ray diffraction data. In comparison with previous studies based on powder X-ray diffraction data [Lemaire et al. (1967). C. R. Acad. Sci. Ser. B, 265, 1280–1282; Lemaire & Paccard (1969). Bull. Soc. Fr. Mineral. Cristallogr. 92, 9–16; Buschow & van der Goot (1970). J. Less-Common Met. 22, 419–428], the present redetermination affords refined coordinates and anisotropic displacement parameters for all atoms. A partial occupation for one Tb atom results in the non-stoichiometric composition Tb1.962?(4)Ni7. The title compound adopts the Ce2Ni7 structure type and can also be derived from the CaCu5 structure type as an intergrowth structure. The asymmetric unit contains two Tb sites (both site symmetries 3m.) and five Ni sites (.m., mm2, 3m., 3m., -3m.). The two different coordination polyhedra of Tb are a Frank–Kasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo Frank–Kasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are Frank–Kasper icosahedra formed by five Tb and seven Ni atoms, four Tb and eight Ni atoms, three Tb and nine Ni atoms, and six Tb and six Ni atoms, respectively. PMID:25249871
Crystal structure of Cruxrhodopsin-3 from Haloarcula vallismortis.
Chan, Siu Kit; Kitajima-Ihara, Tomomi; Fujii, Ryudoh; Gotoh, Toshiaki; Murakami, Midori; Ihara, Kunio; Kouyama, Tsutomu
Cruxrhodopsin-3 (cR3), a retinylidene protein found in the claret membrane of Haloarcula vallismortis, functions as a light-driven proton pump. In this study, the membrane fusion method was applied to crystallize cR3 into a crystal belonging to space group P321. Diffraction data at 2.1 Å resolution show that cR3 forms a trimeric assembly with bacterioruberin bound to the crevice between neighboring subunits. Although the structure of the proton-release pathway is conserved among proton-pumping archaeal rhodopsins, cR3 possesses the following peculiar structural features: 1) The DE loop is long enough to interact with a neighboring subunit, strengthening the trimeric assembly; 2) Three positive charges are distributed at the cytoplasmic end of helix F, affecting the higher order structure of cR3; 3) The cytoplasmic vicinity of retinal is more rigid in cR3 than in bacteriorhodopsin, affecting the early reaction step in the proton-pumping cycle; 4) the cytoplasmic part of helix E is greatly bent, influencing the proton uptake process. Meanwhile, it was observed that the photobleaching of retinal, which scarcely occurred in the membrane state, became significant when the trimeric assembly of cR3 was dissociated into monomers in the presence of an excess amount of detergent. On the basis of these observations, we discuss structural factors affecting the photostabilities of ion-pumping rhodopsins. PMID:25268964
Crystal Structure of Baculovirus RNA Triphosphatase Complexed with Phosphate
Changela, Anita; Martin, Alexandra; Shuman, Stewart; Mondragon, Alfonso (NWU); (SKI)
Baculovirus RNA 5'-triphosphatase (BVP) exemplifies a family of RNA-specific cysteine phosphatases that includes the RNA triphosphatase domains of metazoan and plant mRNA capping enzymes. Here we report the crystal structure of BVP in a phosphate-bound state at 1.5 {angstrom} resolution. BVP adopts the characteristic cysteine-phosphatase {alpha}/{beta} fold and binds two phosphate ions in the active site region, one of which is proposed to mimic the phosphate of the product complex after hydrolysis of the covalent phosphoenzyme intermediate. The crystal structure highlights the role of backbone amides and side chains of the P-loop motif {sup 118}HCTHGXNRT{sup 126} in binding the cleavable phosphate and stabilizing the transition state. Comparison of the BVP structure to the apoenzyme of mammalian RNA triphosphatase reveals a concerted movement of the Arg-125 side chain (to engage the phosphate directly) and closure of an associated surface loop over the phosphate in the active site. The structure highlights a direct catalytic role of Asn-124, which is the signature P-loop residue of the RNA triphosphatase family and a likely determinant of the specificity of BVP for hydrolysis of phosphoanhydride linkages.
Crystal Structure of the Japanese Encephalitis Virus Envelope Protein
Luca, Vincent C.; AbiMansour, Jad; Nelson, Christopher A.; Fremont, Daved H. (WU-MED)
Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-{angstrom} resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimer in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.
Crystal structure of the human CSN6 MPN domain.
Ma, Xiao-li; Xu, Min; Jiang, Tao
The mammalian COP9 signalosome is an eight-subunit (CSN1-CSN8) complex that plays essential roles in multiple cellular and physiological processes. CSN5 and CSN6 are the only two MPN (Mpr1-Pad1-N-terminal) domain-containing subunits in the complex. Unlike the CSN5 MPN domain, CSN6 lacks a metal-binding site and isopeptidase activity. Here, we report the crystal structure of the human CSN6 MPN domain. Each CSN6 monomer contains nine ? sheets surrounded by three helices. Two forms of dimers are observed in the crystal structure. Interestingly, a domain swapping of ?8 and ?9 strands occurs between two neighboring monomers to complete a typical MPN fold. Analyses of the pseudo metal-binding motif in CSN6 suggest that the loss of two key histidine residues may contribute to the lack of catalytic activity in CSN6. Comparing the MPN domain of our CSN6 with that in the CSN complex shows that apart from the different ?8-?9 conformation, they have minor conformational differences at two insertion regions (Ins-1 and Ins-2). Besides, the interacting mode of CSN6-CSN6 in our structure is distinct from that of CSN5-CSN6 in the CSN complex structure. Moreover, the functional implications for Ins-1 and Ins-2 are discussed. PMID:25242525
STRUCTURE NOTE Crystal Structure of Stilbene Synthase From Arachis
Suh, Dae-Yeon
for the synthesis of resveratrol utilized in the stilbenoid biosynthesis.2 The members of CHS superfam- ily and Claisen condensation of the tetraketide, resulting in 2 different final products, resveratrol and chalcone final product resveratrol at 2.4 Ã? and 2.9 Ã?, respectively. Detailed structural comparisons of STS from
Structural-chemical transformations during organic self-propagating high-temperature synthesis. Crystal structure of piperazine malonate and its crystal hydrate
V. I. Ponomarev; E. G. Klimchuk; A. G. Merzhanov; O. S. Filipenko
An organic salt, piperazine malonate, was prepared by self-propagating high-temperature synthesis (SHS) in a solid-phase piperazine-malonic\\u000a acid (P-M) system. Triclinic crystals of piperazine malonate (PM) hydrate (I) were isolated from an aqueous solution. Monoclinic\\u000a crystals of anhydrous piperazine malonate (2) were isolated from a solution in DMSO. Crystals 1 and 2 were studied by X-ray\\u000a structural analysis. Structures 1 and
Azimuthal structures of produced particles in heavy-ion interactions
Vokal, S., E-mail: firstname.lastname@example.com; Orlova, G. I. [VBLHEP, JINR (Russian Federation); Lehocka, S. [University of P. J. Safarik (Slovakia)
The angular structures of particles produced in {sup 208}Pb at 158 A GeV/c and {sup 197}Au at 11.6 A GeV/c induced interactions with Ag(Br) nuclei in emulsion detector have been investigated. Nonstatistical well-ordered ring-like structures of produced particles in azimuthal plane of a collision have been found, and their parameters have been determined.
Anisotropy in Packing Structure and Elasticity of Sintered Spherical Particles
Hiroshi Kato; Chikako Matsunaga; Michio Kurashige; Kazuwo Imai
By computer simulation, we estimated macroscopic elastic moduli of sintered equal-sized spherical particles. The simulation is composed of sequential accumulation of spheres and structural analysis of a ``random network of 6-degree-freedom springs'', which is a mechanical model of ``sintered particles''. From the examination of statistical characteristics of the random packings of spheres, we discovered that their packing structure is affected
Investigation of crystal structure and associated electronic structure of Sr 6BP 5O 20
NASA Astrophysics Data System (ADS)
Ehrenberg, Helmut; Laubach, Sonja; Schmidt, P. C.; McSweeney, R.; Knapp, M.; Mishra, K. C.
Strontium borophosphate phosphate (Sr 6BP 5O 20, SrBP), activated by divalent europium ions is a bluish-green phosphor emitting in a broad band with the emission peak near 480 nm. In this paper, we report the crystal structure of SrBP determined from an analysis of the X-ray diffraction pattern of a prismatic single crystal (size 60 ?m×50 ?m×40 ?m). This crystal was chosen from undoped phosphor powder samples prepared for this purpose by solid-state reaction. SrBP is observed to crystallize in a body-centered tetragonal lattice with the lattice parameters a=9.7895(7) Å and c=19.032(3) Å, the associated space group being I4¯c2 (space group 120). Using the structural data from this study, we have also calculated its electronic structure using the augmented spherical wave method and the local density approximation (LDA). We show the ordering of the electronic states by the density of states (DOS) and the partial DOS plots. The LDA gives a direct optical band gap at the ? point of about 5 eV. The significance of the crystal structure and associated electronic structure is discussed with respect to maintenance of this phosphor in Hg-discharge lamps.
Lithium-cation conductivity and crystal structure of lithium diphosphate
Voronin, V.I., E-mail: firstname.lastname@example.com [Institute of Metal Physics Urals Branch RAS, S.Kovalevskoy Street 18, 620041 Ekaterinburg (Russian Federation); Sherstobitova, E.A. [Institute of Metal Physics Urals Branch RAS, S.Kovalevskoy Street 18, 620041 Ekaterinburg (Russian Federation); Blatov, V.A., E-mail: email@example.com [Samara Center for Theoretical Materials Science (SCTMS), Samara State University, Ac.Pavlov Street 1, 443011 Samara (Russian Federation); Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589 (Saudi Arabia); Shekhtman, G.Sh., E-mail: firstname.lastname@example.com [Institute of High Temperature Electrochemistry Urals Branch RAS, Akademicheskaya 20, 620990 Ekaterinburg (Russian Federation)
The electrical conductivity of lithium diphosphate Li{sub 4}P{sub 2}O{sub 7} has been measured and jump-like increasing of ionic conductivity at 913 K has been found. The crystal structure of Li{sub 4}P{sub 2}O{sub 7} has been refined using high temperature neutron diffraction at 300–1050 K. At 913 K low temperature triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one, space group P2{sub 1}/n, a=8.8261(4) Å, b=5.2028(4) Å, c=13.3119(2) Å, ?=104.372(6)°. The migration maps of Li{sup +} cations based on experimental data implemented into program package TOPOS have been explored. It was found that lithium cations in both low- and high temperature forms of Li{sub 4}P{sub 2}O{sub 7} migrate in three dimensions. Cross sections of the migrations channels extend as the temperature rises, but at the phase transition point have a sharp growth showing a strong "crystal structure – ion conductivity" correlation. -- Graphical abstract: Crystal structure of Li{sub 4}P{sub 2}O{sub 7} at 950 K. Red balls represent oxygen atoms; black lines show Li{sup +} ion migration channels in the layers perpendicular to [001] direction. Highlights: • Structure of Li{sub 4}P{sub 2}O{sub 7} has been refined using high temperature neutron diffraction. • At 913 K triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one. • The migration maps of Li{sup +} implemented into program package TOPOS have been explored. • Cross sections of the migrations channels at the phase transition have a sharp growth.
Structure, Hydrodynamics, and Phase Transition of Freely Suspended Liquid Crystals
NASA Technical Reports Server (NTRS)
Clark, Noel A.
Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enable the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable condensed phase fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new liquid crystal physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and Kosterlitz Thouless phase transition has been observed and 2D XY quasi long range order verified. Smectic films have enabled the precise determination of smectic layer electron density and positional fluctuation profile and have been used to show that the interlayer interactions in anti-ferroelectric tilted smectics do not extend significantly beyond nearest neighbors. The interactions which are operative in liquid crystals are generally weak in comparison to those in crystalline phases, leading to the facile manipulation of the order in liquid crystals by external agents such as applied fields and surfaces. Effects arising from weak ordering are significantly enhanced in ultrathin free films and filaments wherein the intermolecular coupling is effectively reduced by loss of neighbors. Over the past four years this research, which we now detail, has produced a host of exciting new discoveries and unexpected results, maintaining the position of the study of freely suspended liquid crystal structures as one of most exciting and fruitful areas of complex fluid physics. In addition, several potentially interesting microgravity free film experiments have been identified.
Phase behavior of lyotropic rigid-chain polymer liquid crystal studied by dissipative particle dynamics.
Zhao, Tongyang; Wang, Xiaogong
The phase behavior of lyotropic rigid-chain liquid crystal polymer was studied by dissipative particle dynamics (DPD) with variations of the solution concentration and temperature. A chain of fused DPD particles was used to represent each mesogenic polymer backbone surrounded with the strongly interacted solvent molecules. The free solvent molecules were modeled as independent DPD particles, where each particle includes a lump of solvent molecules with the volume roughly equal to the solvated polymer segment. The simulation shows that smectic-B (S(B)), smectic-A (S(A)), nematic (N), and isotropic (I) phases exist within certain regions in the temperature and concentration parameter space. The temperature-dependent S(B)?S(A), S(A)?N, and N?I phase transitions occur in the high concentration range. In the intermediate concentration range, the simulation shows coexistence of the anisotropic phases and isotropic phase, where the anisotropic phases can be the S(B), S(A), or N phases. Mole fraction and compositions of the coexisted phases are determined from the simulation, which indicates that concentration of rigid rods in isotropic phase increases as the temperature increases. By fitting the orientational distribution function of the systems, the biphasic coexistence is further confirmed. From the parameter ? obtained for the simulation, the distribution of the rigid rods in the two coexistence phases is quantitatively evaluated. By using model and simulation methods developed in this work, the phase diagrams of the lyotropic rigid-chain polymer liquid crystal are obtained. Incorporating the solvent particles in the DPD simulation is critical to predict the phase coexistence and obtain the phase diagrams. PMID:22225183
Phase behavior of lyotropic rigid-chain polymer liquid crystal studied by dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Zhao, Tongyang; Wang, Xiaogong
The phase behavior of lyotropic rigid-chain liquid crystal polymer was studied by dissipative particle dynamics (DPD) with variations of the solution concentration and temperature. A chain of fused DPD particles was used to represent each mesogenic polymer backbone surrounded with the strongly interacted solvent molecules. The free solvent molecules were modeled as independent DPD particles, where each particle includes a lump of solvent molecules with the volume roughly equal to the solvated polymer segment. The simulation shows that smectic-B (SB), smectic-A (SA), nematic (N), and isotropic (I) phases exist within certain regions in the temperature and concentration parameter space. The temperature-dependent SB/SA, SA/N, and N/I phase transitions occur in the high concentration range. In the intermediate concentration range, the simulation shows coexistence of the anisotropic phases and isotropic phase, where the anisotropic phases can be the SB, SA, or N phases. Mole fraction and compositions of the coexisted phases are determined from the simulation, which indicates that concentration of rigid rods in isotropic phase increases as the temperature increases. By fitting the orientational distribution function of the systems, the biphasic coexistence is further confirmed. From the parameter ? obtained for the simulation, the distribution of the rigid rods in the two coexistence phases is quantitatively evaluated. By using model and simulation methods developed in this work, the phase diagrams of the lyotropic rigid-chain polymer liquid crystal are obtained. Incorporating the solvent particles in the DPD simulation is critical to predict the phase coexistence and obtain the phase diagrams.
Structure and Optical Properties of Liquid Crystal Dispersed Polymers
Antal Jákli
Liquid crystal polymer composite systems can be divided into two main subgroups. The first consists of the polymer dispersed liquid crystals (PDLC), where the liquid crystal is dispersed in the continuous polymer matrix. The second contains the liquid crystal dispersed polymer (LCDP) systems (sometimes called as liquid crystal\\/gel dispersions), where only a small amount of polymer is dispersed in a
Synthesis, Crystal Structure, and Colloidal Dispersions of Vanadium Tetrasulfide (VS4 ).
Kozlova, Mariia N; Mironov, Yuri V; Grayfer, Ekaterina D; Smolentsev, Anton I; Zaikovskii, Vladimir I; Nebogatikova, Nadezhda A; Podlipskaya, Tatyana Yu; Fedorov, Vladimir E
Although many of the layered metal chalcogenides, such as MoS2 , are well-studied, some other chalcogenides have received less attention by comparison. In particular, there has been an emerging interest in vanadium tetrasulfide (VS4 ), which displays useful properties as a component of hybrids. However, the synthetic methods and characteristics of individual VS4 are not yet well defined, and there is no report on its solution processability. Here we have synthesized VS4 by a simple and fast direct reaction between elements. Reinvestigation of the VS4 crystal structure yielded more precise atomic coordinates and interatomic distances, thereby confirming the crystallization of VS4 in the monoclinic C2/c group and its quasi-1D chainlike structure. As the chains in VS4 are only bonded by weak van der Waals forces, we further demonstrate that bulk VS4 may be ultrasonically dispersed in appropriate solvents to form colloids, similarly to the layered chalcogenides. VS4 particles in colloids retain their phase identity and rod-shaped morphology with lengths in the range of hundreds of nanometers. Isopropanol dispersion exhibited the highest concentration and stability, which was achieved owing to the repulsion caused by high negative charges on the edges of the particles. PMID:25663043
Influence of colloidal particle transfer on the quality of self-assembling colloidal photonic crystal under confined condition
NASA Astrophysics Data System (ADS)
Zhao, Yong-Qiang; Li, Juan; Liu, Qiu-Yan; Dong, Wen-Jun; Chen, Ben-Yong; Li, Chao-Rong
The relationship between colloidal particle transfer and the quality of colloidal photonic crystal (CPC) is investigated by comparing colloidal particle self-assembling under the vertical channel (VC) and horizontal channel (HC) conditions. Both the theoretical analyses and the experimental measurements indicate that crystal quality depends on the stability of mass transfer. For the VC, colloidal particle transfer takes place in a stable laminar flow, which is conducive to forming high-quality crystal. In contrast, it happens in an unstable turbulent flow for the HC. Crystals with cracks and an uneven surface formed under the HC condition can be seen from the images of a field emission scanning electron microscope (SEM) and a three-dimensional (3D) laser scanning microscope (LSM), respectively. Project supported by the National Natural Science Foundation of China (Grant Nos. 91122022 and 51172209) and the Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT), China (Grant No. IRT13097).
Hypochromic and hyperchromic effects on the vibronic structure of molecular crystal spectra. The dimer model
NASA Astrophysics Data System (ADS)
Zgierski, M. Z.; Pawlikowski, M.
It is shown on model calculations that crystal-field mixing of Frenkel excition states in molecular crystals lead not only to a redistribution of their relative intensities but also to changes in the vibrational structure of weak exciton bands.
Drying dissipative structures of lycopodium spore particles in aqueous dispersion.
Okubo, Tsuneo; Kokufuta, Etsuo; Nakamuro, Masaharu; Yoshinaga, Kohji; Mizutani, Masashi; Tsuchida, Akira
Drying dissipative structures of aqueous dispersions of lycopodium particles (31 microm in average diameter) from the spores of Lycopodium clavatum were studied as a function of the particle concentrations in the presence and the absence of sodium chloride. The drying patterns formed on a cover glass, a watch glass and a Petri glass dish were observed macroscopically and microscopically. Lycopodium particles were the combination of hemisphere and tetrahedron in their shape and possessed the weakly acidic groups on their surfaces. The vague broad ring structure was observed even for the very large colloidal particles, and their size on a cover glass decreased as particle concentration decreased. Microscopic drying patterns almost disappeared except the short chain-like patterns. These observations support that the convectional contribution on the dissipative drying pattern formation is still effective in the lycopodium suspensions, though the convectional forces in the suspension are very weak compared with the sedimentation forces. PMID:20598865
Crystal Structure of a Self-Spliced Group II Intron
Toor, Navtej; Keating, Kevin S.; Taylor, Sean D.; Pyle, Anna Marie (Yale)
Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.
Crystal Structure of a Self-Spliced Group ll Intron
Toor,N.; Keating, K.; Taylor, S.; Pyle, A.
Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.
Crystal Structure of a Lipid G Protein?Coupled Receptor
Hanson, Michael A.; Roth, Christopher B.; Jo, Euijung; Griffith, Mark T.; Scott, Fiona L.; Reinhart, Greg; Desale, Hans; Clemons, Bryan; Cahalan, Stuart M.; Schuerer, Stephan C.; Sanna, M. Germana; Han, Gye Won; Kuhn, Peter; Rosen, Hugh; Stevens, Raymond C. (Scripps); (Receptos)
The lyso-phospholipid sphingosine 1-phosphate modulates lymphocyte trafficking, endothelial development and integrity, heart rate, and vascular tone and maturation by activating G protein-coupled sphingosine 1-phosphate receptors. Here, we present the crystal structure of the sphingosine 1-phosphate receptor 1 fused to T4-lysozyme (S1P{sub 1}-T4L) in complex with an antagonist sphingolipid mimic. Extracellular access to the binding pocket is occluded by the amino terminus and extracellular loops of the receptor. Access is gained by ligands entering laterally between helices I and VII within the transmembrane region of the receptor. This structure, along with mutagenesis, agonist structure-activity relationship data, and modeling, provides a detailed view of the molecular recognition and requirement for hydrophobic volume that activates S1P{sub 1}, resulting in the modulation of immune and stromal cell responses.
Crystal Structure of a Self-Spliced Group II Intron
Toor, Navtej; Keating, Kevin S.; Taylor, Sean D.; Pyle, Anna Marie
Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two–metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor. PMID:18388288
Tuning the self-assembled monolayer formation on nanoparticle surfaces with different curvatures: Investigations on spherical silica particles and plane-crystal-shaped zirconia particles
Feichtenschlager, Bernhard; Lomoschitz, Christoph J.; Kickelbick, Guido
The ordering of dodecyl-chain self-assembled monolayers (SAM) on different nanoscopic surfaces was investigated by FT-IR studies. As model systems plane-crystal-shaped ZrO2 nanoparticles and spherical SiO2 nanoparticles were examined. The type of capping agent was chosen dependent on the substrate, therefore dodecylphosphonic acid and octadecylphosphonic acid were used for ZrO2 and dodecyltrimethoxysilane for SiO2 samples. The plane ZrO2 nanocrystals yielded more ordered alkyl-chain structures whereas spherical SiO2 nanoparticles showed significantly lower alkyl-chain ordering. Submicron-sized silica spheres revealed a significantly higher alkyl chain ordering, comparable to an analogously prepared SAM on a non-curved plane oxidized Si-wafer. In the case of ZrO2 nanocrystals an intense alkyl-chain alignment could be disturbed by decreasing the grafting density from the maximum of 2.1 molecules/nm2 through the variation of coupling agent concentration to lower values. Furthermore, the co-adsorption of a different coupling agent, such as phenylphosphonic acid for ZrO2 and phenyltrimethoxysilane for SiO2, resulted in a significantly lower alkyl-chain ordering for ZrO2 plane crystals and for large SiO2 spherical particles at high grafting density. An increasing amount of order-disturbing molecules leads to a gradual decrease in alkyl-chain alignment on the surface of the inorganic nanoparticles. In the case of the ZrO2 nanoparticle system it is shown via dynamic light scattering (DLS) that the mixed monolayer formation on the particle surface impacts the dispersion quality in organic solvents such as n-hexane. PMID:21549385
Crystal structure of deglycosylated human IgG4-Fc
Davies, Anna M.; Jefferis, Roy; Sutton, Brian J.
The Fc region of IgG antibodies, important for effector functions such as antibody-dependent cell-mediated cytotoxicity, antibody-dependent cellular phagocytosis and complement activation, contains an oligosaccharide moiety covalently attached to each CH2 domain. The oligosaccharide not only orients the CH2 domains but plays an important role in influencing IgG effector function, and engineering the IgG-Fc oligosaccharide moiety is an important aspect in the design of therapeutic monoclonal IgG antibodies. Recently we reported the crystal structure of glycosylated IgG4-Fc, revealing structural features that could explain the anti-inflammatory biological properties of IgG4 compared with IgG1. We now report the crystal structure of enzymatically deglycosylated IgG4-Fc, derived from human serum, at 2.7 ? resolution. Intermolecular CH2-CH2 domain interactions partially bury the CH2 domain surface that would otherwise be exposed by the absence of oligosaccharide, and two Fc molecules are interlocked in a symmetric, open conformation. The conformation of the CH2 domain DE loop, to which oligosaccharide is attached, is altered in the absence of carbohydrate. Furthermore, the CH2 domain FG loop, important for Fc? receptor and C1q binding, adopts two different conformations. One loop conformation is unique to IgG4 and would disrupt binding, consistent with IgG4's anti-inflammatory properties. The second is similar to the conserved conformation found in IgG1, suggesting that in contrast to IgG1, the IgG4 CH2 FG loop is dynamic. Finally, crystal packing reveals a hexameric arrangement of IgG4-Fc molecules, providing further clues about the interaction between C1q and IgG. PMID:24956411
Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase.
Zhang, R.; Evans, G.; Rotella, F. J.; Westbrook, E. M.; Beno, D.; Huberman, E.; Joachimiak, A.; Collart, F. R.
IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the first step unique to GTP synthesis. To provide a basis for the evaluation of IMPDH inhibitors as antimicrobial agents, we have expressed and characterized IMPDH from the pathogenic bacterium Streptococcus pyogenes. Our results show that the biochemical and kinetic characteristics of S. pyogenes IMPDH are similar to other bacterial IMPDH enzymes. However, the lack of sensitivity to mycophenolic acid and the K{sub m} for NAD (1180 {mu}M) exemplify some of the differences between the bacterial and mammalian IMPDH enzymes, making it an attractive target for antimicrobial agents. To evaluate the basis for these differences, we determined the crystal structure of the bacterial enzyme at 1.9 {angstrom} with substrate bound in the catalytic site. The structure was determined using selenomethionine-substituted protein and multiwavelength anomalous (MAD) analysis of data obtained with synchrotron radiation from the undulator beamline (19ID) of the Structural Biology Center at Argonne's Advanced Photon Source. S. pyogenes IMPDH is a tetramer with its four subunits related by a crystallographic 4-fold axis. The protein is composed of two domains: a TIM barrel domain that embodies the catalytic framework and a cystathione {beta}-synthase (CBS) dimer domain of so far unknown function. Using information provided by sequence alignments and the crystal structure, we prepared several site-specific mutants to examine the role of various active site regions in catalysis. These variants implicate the active site flap as an essential catalytic element and indicate there are significant differences in the catalytic environment of bacterial and mammalian IMPDH enzymes. Comparison of the structure of bacterial IMPDH with the known partial structures from eukaryotic organisms will provide an explanation of their distinct properties and contribute to the design of specific bacterial IMPDH inhibitors.
Crystal Structure of Thioflavin T Bound to the Peripheral Site of Torpedo californica Acetylcholinesterase Reveals How
Sussman, Joel L.
Crystal Structure of Thioflavin T Bound to the Peripheral Site of Torpedo californica-ray structure of the complex of thioflavin T with Torpedo californica acetylcholinesterase. The two aromatic, Tyr334, and Phe330. Overlays of this structure with the crystal structures of Torpedo californica
Structural and optical properties of RbTiOPO4:Nb crystals
J. J. Carvajal; P. Segonds; A. Peña; J. Zaccaro; B. Boulanger; F. Díaz; M. Aguiló
When dealing with crystals showing self-frequency conversion properties, RbTiOPO4 doped with Nb5+ (RTP:Nb) is a better matrix than RTP for hosting luminescent ions in higher concentration. Therefore, we investigated the structural and the non-linear optical properties of RTP:Nb and RTP crystals for comparison. We used a new crystal growth process for RTP:Nb, which provides isometric inclusion- and crack-free crystals. Structural
Refinement of the crystal structure of lithium-bearing uvite
Rozhdestvenskaya, I. V., E-mail: email@example.com; Frank-Kamenetskaya, O. V. [St. Petersburg State University, Department of Crystallography (Russian Federation); Kuznetsova, L. G. [Russian Academy of Sciences, Vinogradov Institute of Geochemistry, Siberian Division (Russian Federation); Bannova, I. I.; Bronzova, Yu. M. [St. Petersburg State University, Department of Crystallography (Russian Federation)
The crystal structure of a natural calcium tourmaline, i.e., uvite with a high lithium content (0.51 au per formula (aupf) at the Y site, is refined to R = 0.019, R{sub w} = 0.020, and S = 1.11. It is shown that, in nature, there exist uvites in which the charge balance in the case where the Z site is occupied by trivalent cations is provided by the replacement of part of the divalent magnesium cations at the Y site by univalent cations, divalent calcium cations at the X site by sodium cations, and univalent anions at the W site by oxygen anions. The W site is found to be split into two sites, namely, the W1 and W11 sites (the W1-W11 distance is 0.14 A), which are partially occupied by the fluorine and oxygen anions, respectively. An analysis of the results obtained in this study and the data available in the literature on the crystal structure of uvites allows the conclusion that uvite can be considered a superspecies and that the nomenclature of this mineral group needs refinement with the use of structural data.
Analysis of the crystal structure of an active MCM hexamer.
Miller, Justin M; Arachea, Buenafe T; Epling, Leslie B; Enemark, Eric J
In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis. PMID:25262915
Analysis of the crystal structure of an active MCM hexamer
Miller, Justin M; Arachea, Buenafe T; Epling, Leslie B; Enemark, Eric J
In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis. DOI: http://dx.doi.org/10.7554/eLife.03433.001 PMID:25262915
Crystal Structure of the Yeast Nicotinamidase Pnc1p
Hu, Gang; Taylor, Alexander B.; McAlister-Henn, Lee; Hart, P. John
The yeast nicotinamidase Pnc1p acts in transcriptional silencing by reducing levels of nicotinamide, an inhibitor of the histone deacetylase Sir2p. The Pnc1p structure was determined at 2.9 Å resolution using MAD and MIRAS phasing methods after inadvertent crystallization during the pursuit of the structure of histidine-tagged yeast isocitrate dehydrogenase (IDH). Pnc1p displays a cluster of surface histidine residues likely responsible for its co-fractionation with IDH from Ni2+-coupled chromatography resins. Researchers expressing histidine-tagged proteins in yeast should be aware of the propensity of Pnc1p to crystallize, even when overwhelmed in concentration by the protein of interest. The protein assembles into extended helical arrays interwoven to form an unusually robust, yet porous superstructure. Comparison of the Pnc1p structure with those of three homologous bacterial proteins reveals a common core fold punctuated by amino acid insertions unique to each protein. These insertions mediate the self-interactions that define the distinct higher order oligomeric states attained by these molecules. Pnc1p also acts on pyrazinamide, a substrate analog converted by the nicotinamidase from Mycobacterium tuberculosis into a product toxic to that organism. However, we find no evidence for detrimental effects of the drug on yeast cell growth. PMID:17382284
Natural pseudowollastonite: Crystal structure, associated minerals, and geological context
NASA Astrophysics Data System (ADS)
Seryotkin, Yurii V.; Sokol, Ella V.; Kokh, Svetlana N.
Pseudowollastonite, an extremely rare constituent of ultrahigh-temperature combustion metamorphic and igneous rocks, has been found as a rock-forming mineral in Ca-rich paralava veins of Nabi Musa fossil mud volcano (Dead Sea area). Pseudowollastonite-bearing paralavas are the products of combustion metamorphism associated with spontaneous burning of methane. The melt began to crystallize at 1480-1500 °C about the ambient pressure. Pseudowollastonite enters two mineral assemblages: (1) rankinite, larnite, nagelschmidtite, wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, cuspidine, and fluorapatite; (2) parawollastonite (2M), wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, fluorellestadite. In this study we present the first single-crystal structure determination of natural pseudowollastonite. Pseudowollastonite from Nabi Musa dome is stoichiometric CaSiO3 and belongs to the most widespread four-layer polytype: a = 6.83556(10) Å, b = 11.86962(18) Å, c = 19.6255(3) Å, ? = 90.6805(13)°, V = 1592.21(4) Å3, space group C2/c. We argue that pseudowollastonite is so scarce in nature because its formation requires joint action of several uncommon factors: availability of hot melts of T > 1200 °C that bear free calcium but are poor in Mg and Fe (mostly as Fe3 +) and their crystallization in the shallow crust followed by quenching.
Self-assembly of hydrogensquarates: crystal structures and properties.
Koleva, B B; Kolev, T; Seidel, R W; Spiteller, M; Mayer-Figge, H; Sheldrick, W S
The self-assembly of the hydrogensquarates is elucidated by means of linear-polarized infrared (IR-LD) spectroscopy of oriented colloids in nematic host and the so-called reducing-difference procedure for polarized IR-LD spectra interpretation. The scopes and limitation are discussed on five novel derivatives of squaric acid and its anions, that is, 2-chloro-3-aminopyridinium hydrogensquarate (1), bis (1,2,3,4-tetrahydroquinolinium) squarate (2), bis hydrogensquarate dihydrate salt of 4-(aminomethyl)pyridine (3), N-(2-ammoniumethyl)-piperazinium monohydrate hydrogensquarate squarate (4), and 3-nitropyridinium hydrogensquarate monohydrate (5), respectively. The structures of these compounds 1-5 were solved by means of single-crystal X-ray diffraction, and the crystallographic data were used for the experimental elucidation of the corresponding IR spectra of crystals with respect to studying Fermi-resonance (FR), Davydov splitting (DS), and Fermi-Davydov (FD) as well as Evans' hole effects. The various motifs for self-assembly of squaric acid and its anions in the organic crystals are discussed together with their IR-spectroscopic properties. PMID:19278235
Synthesis and crystal structure of MgB{sub 12}
Adasch, Volker [DRONCO AG, Wiesenmuehle 1, D-95632 Wunsiedel (Germany); Hess, Kai-Uwe [Ludwig-Maximilians-Universitaet Muenchen, Institut fuer Mineralogie, Petrologie und Geochemie, Theresienstr. 41/III, D-80333 Munich (Germany); Ludwig, Thilo [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Anorganische und Analytische Chemie, Albertstr. 21, D-79104 Freiburg (Germany); Freiburger Materialforschungszentrum FMF, Stefan-Maier-Str. 25, D-79104 Freiburg (Germany); Vojteer, Natascha [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Anorganische und Analytische Chemie, Albertstr. 21, D-79104 Freiburg (Germany); Freiburger Materialforschungszentrum FMF, Stefan-Maier-Str. 25, D-79104 Freiburg (Germany); Hillebrecht, Harald [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Anorganische und Analytische Chemie, Albertstr. 21, D-79104 Freiburg (Germany) and Freiburger Materialforschungszentrum FMF, Stefan-Maier-Str. 25, D-79104 Freiburg (Germany)]. E-mail: firstname.lastname@example.com
Single crystals of MgB{sub 12} were synthesized from the elements in a Mg/Cu melt at 1600deg. C. MgB{sub 12} crystallizes orthorhombic in space group Pnma with a=16.632(3)A, b=17.803(4)A and c=10.396(2)A. The crystal structure (Z=30, 5796 reflections, 510 variables, R{sub 1}(F)=0.049, wR{sub 2}(I)=0.134) consists of a three dimensional net of B{sub 12} icosahedra and B{sub 21} units in a ratio 2:1. The B{sub 21} units are observed for the first time in a solid compound. Mg is on positions with partial occupation. The summation reveals the composition MgB{sub 12.35} or Mg{sub 0.97}B{sub 12} , respectively. This is in good agreement with the value of MgB{sub 11.25} as expected by electronic reasons to stabilize the boron polyhedra B{sub 12}{sup 2-} and B{sub 21}{sup 4-}.
Crystal structure of S,N-dibenzyl-d-penicillamine monohydrate
Yoshinari, Nobuto; Konno, Takumi
In the asymmetric unit of the title compound, C19H23NO2S·H2O, there are two independent organic molecules and two water molecules. Both organic molecules exist as the zwitterionic form. The dihedral angles between the planes of the rings in the organic molecules are 86.84?(10) and 88.77?(11)°. An intramolecular N—H?S hydrogen bond occurs. In the crystal, organic and water molecules are linked by N—H?O and O—H?O hydrogen bonds, generating a tape structure running along the b-axis direction. PMID:25484833
Crystal structure of S,N-dibenzyl-d-penicillamine monohydrate.
Yoshinari, Nobuto; Konno, Takumi
In the asymmetric unit of the title compound, C19H23NO2S·H2O, there are two independent organic mol-ecules and two water mol-ecules. Both organic mol-ecules exist as the zwitterionic form. The dihedral angles between the planes of the rings in the organic mol-ecules are 86.84?(10) and 88.77?(11)°. An intramolecular N-H?S hydrogen bond occurs. In the crystal, organic and water mol-ecules are linked by N-H?O and O-H?O hydrogen bonds, generating a tape structure running along the b-axis direction. PMID:25484833
Crystal chemistry and structural design of iron-based superconductors
NASA Astrophysics Data System (ADS)
Jiang, Hao; Sun, Yun-Lei; Xu, Zhu-An; Cao, Guang-Han
The second class of high-temperature superconductors (HTSCs), iron-based pnictides and chalcogenides, necessarily contain Fe2X2 ("X" refers to a pnictogen or a chalcogen element) layers, just like the first class of HTSCs which possess the essential CuO2 sheets. So far, dozens of iron-based HTSCs, classified into nine groups, have been discovered. In this article, the crystal-chemistry aspects of the known iron-based superconductors are reviewed and summarized by employing "hard and soft acids and bases (HSAB)" concept. Based on these understandings, we propose an alternative route to exploring new iron-based superconductors via rational structural design.
Crystal structure of 4-chloro-2-iodoaniline
Quinn, Taylor R.; Tanski, Joseph M.
In the crystal structure of the title compound, C6H5ClIN, the amino group engages in N—H?N hydrogen bonding, creating [100] chains. A Cl?I contact is observed [3.7850?(16)?Å]. The parallel planes of neigbouring molecules reveal highly offset ?-stacking characterized by a centroid–centroid distance of 4.154?(1), a centroid-to-plane distance of 3.553?(3) and ring-offset slippage of 2.151?(6)?Å. PMID:25309269
Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms
Leila M. Foroughi; You-Na Kang; Adam J. Matzger
Obtaining single crystals for X-ray diffraction remains a major bottleneck in structural biology; when existing crystal growth methods fail to yield suitable crystals, often the target rather than the crystallization approach is reconsidered. Here we demonstrate that polymer-induced heteronucleation, a powerful technique that has been used for small molecule crystallization form discovery, can be applied to protein crystallization by optimizing
Structure and Dynamics of Freely Suspended Liquid Crystals
NASA Technical Reports Server (NTRS)
Clark, Noel A.
Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1 D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline or quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enables the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new LC physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and Kosterlitz Thouless phase transition has been observed and 2D XY quasi long range order verified. Smectic films have enabled the precise determination of smectic layer electron density and positional fluctuation profiles and have been used to show that the interlayer interactions in antiferroelectric tilted smectics do not extend significantly beyond nearest neighbors. Freely suspended films played a pivotal role in the recent discovery of macroscopic chiral-polar ordering in fluids of achiral molecules. The interactions which are operative in liquid crystals are generally weak in comparison to those in crystalline phases, leading to the facile manipulation of the order in liquid crystals by external agents such as applied fields and surfaces. Effects arising from weak ordering are significantly enhanced in ultrathin free films and filaments, in which the intermolecular coupling is effectively further reduced by loss of neighbors. Over the past four years this research, which we now detail, has produced a host of exciting new discoveries and unexpected results, maintaining the study of freely suspended liquid crystal structures as one of most exciting and fruitful areas of complex fluid physics. In addition, a class of experiments on the behavior of 1D interfaces in 2D films have been pursued with results that point to potentially quite interesting effects in microgravity.
Synthesis and crystal structure of Sr2As2O7 from single-crystal data
NASA Astrophysics Data System (ADS)
Edhokkar, F.; Hadrich, A.; Graia, M.; Mhiri, T.
The title compound, strontium diarseniate Sr2As2O7, was prepared by solid-state method. This compound crystallizes in the tetragonal system, space group P41 with a = 7.142 (5) Å c = 25.693 (5) Å and Z = 8. Its structure is composed of SrO7-9 polyhedra and [As2O7] bitetrahedral units. These groups are linked together by corner and edge-sharing forming a three dimensional framework. The crystal structure of the title compound has been the subject of a previous investigation based on X-ray powder data [M. Weil, T. dordevic, C. L. Lengauer, U. Kolitsch Solid State Sciences 11 (2009), 2111-2117]. The present investigation confirms the previous study, but with higher precision and with all displacement parameters refined anisotropically. Sr2As2O7 is isotypic with the high-temperature polymorphs of Ca2P2O7 and Sr2V2O7.
Confinement effect on the interaction between colloidal particles in a nematic liquid crystal: An analytical study
NASA Astrophysics Data System (ADS)
Fukuda, Jun-Ichi; Žumer, Slobodan
Motivated by a recent experimental study on the interaction between colloidal particles in a confined nematic liquid crystal [M. Vilfan, N. Osterman, M. ?opi?, M. Ravnik, S. Žumer, J. Kotar, D. Babi?, and I. Poberaj, Phys. Rev. Lett. 101, 237801 (2008)], we discuss in an analytical manner how the interaction potential U between spherical colloidal particles in a confined nematic cell behaves as a function of the interparticle distance r . We show that the short-range potential follows a power law U(r)˜r-5 as expected from the quadrupolar nature of the interaction, while the long-range potential is dominated by an exponential function U(r)˜d/rexp(-2?r/d) , where d is the cell thickness. These two regimes are interchanged at r/d?0.8 . This behavior of U(r) is in a good semiquantitative agreement with the experimental finding.
Effects of Ice-Crystal Structure on Halo Formation: Cirrus Cloud Experimental and Ray-Tracing Modeling Studies
NASA Technical Reports Server (NTRS)
Sassen, Kenneth; Knight, Nancy C.; Takano, Yoshihide; Heymsfield, Andrew J.
During the 1986 Project FIRE (First International Satellite Cloud Climatology Project Regional Experiment) field campaign, four 22 deg halo-producing cirrus clouds were studied jointly from a ground-based polarization lidar and an instrumented aircraft. The lidar data show the vertical cloud structure and the relative position of the aircraft, which collected a total of 84 slides by impaction, preserving the ice crystals for later microscopic examination. Although many particles were too fragile to survive impaction intact, a large fraction of the identifiable crystals were columns and radial bullet rosettes, with both displaying internal cavitations and radial plate-column combinations. Particles that were solid or displayed only a slight amount of internal structure were relatively rare, which shows that the usual model postulated by halo theorists, i.e., the randomly oriented, solid hexagonal crystal, is inappropriate for typical cirrus clouds. With the aid of new ray-tracing simulations for hexagonal hollow-ended column and bullet-rosette models, we evaluate the effects of more realistic ice-crystal structures on halo formation and lidar depolarization and consider why the common halo is not more common in cirrus clouds.
The Crystal Structure of Diopside at Pressure to 10 Gpa
NASA Astrophysics Data System (ADS)
Thompson, R. M.; Downs, R. T.
Understanding the compression mechanisms of mantle minerals is important to predicting their behavior and properties beyond the range of conditions available in the laboratory. High-pressure experimental studies of C2/c pyroxenes have variously focused on different structural changes such as bond length changes, relative compression of different polyhedral components, and changes in the d-spacings of eutactic planes of oxygens. Recently, Thompson and Downs (2004) modeled the crystal structures of pyroxenes with regular tetrahedra and M1 octahedra to try and understand the observed changes in pyroxenes with changing P, T, and x. In this paper, we present new refinements of the crystal structure of diopside to 10.16 GPa, and analyze them using our model. A new parameter has been derived which quantifies the distortion of a C2/c pyroxene from its model equivalent (i.e. same unit cell volume and O3-O3-O3 angle, regular M1 and T), and this parameter is used to compare model and observed compression. Model and observed unit strain ellipsoids are compared. Compression mechanisms explored by previous investigators are placed in the context of our model. The data of Levien and Prewitt (1981) to 5 GPa is shown to be statistically consistent with our data. Thompson, R.M., and Downs, R.T. (2004) Model pyroxenes II: Structural variation as a function of tetrahedral rotation. American Mineralogist 89, 614-628. Levien, L. and Prewitt, C.T. (1981) High-pressure structural study of diopside. American Mineralogist, 66, 315- 323.
Analysis of zinc binding sites in protein crystal structures.
Alberts, I. L.; Nadassy, K.; Wodak, S. J.
The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations. PMID:10082367
ERIC Educational Resources Information Center
Bergsten, Ronald
Discusses the production and structure of a sequence of optical crystals which can serve as one-, two-, and three-dimensional diffraction plates to illustrate diffraction patterns by using light rather than x-rays or particles. Applications to qualitative presentations of Laue theory at the secondary and college levels are recommended. (CC)
Simulations of reversible protein aggregate and crystal structure.
Patro, S Y; Przybycien, T M
We simulated the structure of reversible protein aggregates as a function of protein surface characteristics, protein-protein interaction energies, and the entropic penalty accompanying the immobilization of protein in a solid phase. These simulations represent an extension of our previous work on kinetically irreversible protein aggregate structure and are based on an explicit accounting of the specific protein-protein interactions that occur within reversible aggregates and crystals. We considered protein monomers with a mixture of hydrophobic and hydrophilic surface regions suspended in a polar solvent; the energetic driving force for aggregation is provided by the burial of solvent-exposed hydrophobic surface area. We analyzed the physical properties of the generated aggregates, including density, protein-protein contact distributions, solvent accessible surface area, porosity, and order, and compared our results with the protein crystallization literature as well as with the kinetically irreversible case. The physical properties of reversible aggregates were consonant with those observed for the irreversible aggregates, although in general, reversible aggregates were more stable energetically and were more crystal-like in their order content than their irreversible counterparts. The reversible aggregates were less dense than the irreversible aggregates, indicating that the increased energetic stability is derived primarily from the optimality rather than the density of the packing in the solid phase. The extent of hydrophobic protein-protein contacts and solvent-exposed surface area within the aggregate phase depended on the aggregation pathway: reversible aggregates tended to have a greater proportion of hydrophobic-hydrophobic contacts and a smaller fraction of hydrophobic solvent-exposed surface area. Furthermore, the arrangement of hydrophobic patches on the protein surface played a major role in the distribution of protein contacts and solvent content. This was readily reflected in the order of the aggregates: the greater the contiguity of the hydrophobic patches on the monomer surface, the less ordered the aggregates became, despite the opportunities for rearrangement offered by a reversible pathway. These simulations have enhanced our understanding of the impact of protein structural motifs on aggregate properties and on the demarcation between aggregation and crystallization. Images FIGURE 4 FIGURE 5 FIGURE 7 PMID:8744327
The crystal structure of {pi}-ErBO{sub 3}: New single-crystal data for an old problem
Pitscheider, Almut [Institut fuer Allgemeine, Anorganische und Theoretische Chemie, Leopold-Franzens-Universitaet Innsbruck, Innrain 52a, A-6020 Innsbruck (Austria); Kaindl, Reinhard [Institut fuer Mineralogie und Petrographie, Leopold-Franzens-Universitaet Innsbruck, Innrain 52, A-6020 Innsbruck (Austria); Oeckler, Oliver [Department Chemie, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5-13, D-81377 Muenchen (Germany); Huppertz, Hubert, E-mail: firstname.lastname@example.com [Institut fuer Allgemeine, Anorganische und Theoretische Chemie, Leopold-Franzens-Universitaet Innsbruck, Innrain 52a, A-6020 Innsbruck (Austria)
Single crystals of the orthoborate {pi}-ErBO{sub 3} were synthesized from Er{sub 2}O{sub 3} and B{sub 2}O{sub 3} under high-pressure/high-temperature conditions of 2 GPa and 800 {sup o}C in a Walker-type multianvil apparatus. The crystal structure was determined on the basis of single-crystal X-ray diffraction data, collected at room temperature. The title compound crystallizes in the monoclinic pseudowollastonite-type structure, space group C2/c, with the lattice parameters a=1128.4(2) pm, b=652.6(2) pm, c=954.0(2) pm, and {beta}=112.8(1){sup o} (R{sub 1}=0.0124 and wR{sub 2}=0.0404 for all data). -- graphical abstract: The first satisfying single-crystal structure determination of {pi}-ErBO{sub 3} sheds light on the extensively discussed structure of {pi}-orthoborates. The application of light pressure during the solid state synthesis yielded in high-quality crystals, due to pressure-induced crystallization. Research highlights: {yields} High-quality single crystals of {pi}-ErBO{sub 3} were prepared via high-pressure-induced crystallization. {yields} At least five different space groups for the rare-earth {pi}-orthoborates are reported. {yields} {pi}-ErBO{sub 3} is isotypic to the pseudowollastonite-type CaSiO{sub 3}. {yields} Remaining ambiguities regarding the structure of the rare-earth {pi}-orthoborates are resolved.
Deflections of high energy channeled charged particles by elastically bent silicon single crystals
Salman, S.M.
The channeling and deflection of positively charged pions and protons by bent single silicon crystals was investigated over the range of momenta 10-200 GeV/c, and deflection angles in the range 0-28 milliradians. The critical radius of curvature was reached at least twice in the case of 180 GeV/c, under planer channeling conditions. The results of the experiment show that bending of channeled particles can be useful in some applications in high energy physics or accelerator technology. The results show a good agreement with the theory described by Ellison and Kudo in principle if one takes into account the effects of ordinary dechanneling. A difference with Ellison concernng the efficiency of (111)-S, (111)-L channels suggests an agreement with Kudo. Positive axial bending was investigated under limited conditions. The deflections are less than for the planar bending and the efficiency becomes less also. Feeding of the channeled particles into the planes is believed to be the reason. Negative particles channeling and bending shows very poor bending efficiency; this is explained in terms of breaking in the symmetry of the channels which has maximum effect for particles with low transverse energy.
Impact of surfactants on the crystallization of aqueous suspensions of celecoxib amorphous solid dispersion spray dried particles.
Chen, Jie; Ormes, James D; Higgins, John D; Taylor, Lynne S
Amorphous solid dispersions are frequently prepared by spray drying. It is important that the resultant spray dried particles do not crystallize during formulation, storage, and upon administration. The goal of the current study was to evaluate the impact of surfactants on the crystallization of celecoxib amorphous solid dispersions (ASD), suspended in aqueous media. Solid dispersions of celecoxib with hydroxypropylmethylcellulose acetate succinate were manufactured by spray drying, and aqueous suspensions were prepared by adding the particles to acidified media containing various surfactants. Nucleation induction times were evaluated for celecoxib in the presence and absence of surfactants. The impact of the surfactants on drug and polymer leaching from the solid dispersion particles was also evaluated. Sodium dodecyl sulfate and Polysorbate 80 were found to promote crystallization from the ASD suspensions, while other surfactants including sodium taurocholate and Triton X100 were found to inhibit crystallization. The promotion or inhibition of crystallization was found to be related to the impact of the surfactant on the nucleation behavior of celecoxib, as well as the tendency to promote leaching of the drug from the ASD particle into the suspending medium. It was concluded that surfactant choice is critical to avoid failure of amorphous solid dispersions through crystallization of the drug. PMID:25569461
The introduction of structure types into the Inorganic Crystal Structure Database ICSD
Allmann, Rudolf; Hinek, Roland
Both the approach used and the progress made in the assignment of structure types to the crystal structures contained in the ICSD database are reported. Extending earlier work, an hierarchical set of criteria for the separation of isopointal structures into isoconfigurational structure types is used. It is shown how these criteria, which include the space group (number), Wyckoff sequence and Pearson symbol, c/a ratio, ? ranges, ANX formulae and, in certain cases, the necessary elements and forbidden elements, may be used to uniquely identify the representative structure types of the compounds contained in the ICSD database. PMID:17703075
Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals
Ackerman, Paul J.; van de Lagemaat, Jao; Smalyukh, Ivan I.
Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called 'A-phase' in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called 'hopfions', or 'torons' when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields. PMID:25607778
Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals
NASA Astrophysics Data System (ADS)
Ackerman, Paul J.; van de Lagemaat, Jao; Smalyukh, Ivan I.
Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called 'A-phase' in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called 'hopfions', or 'torons' when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields.
Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals.
Ackerman, Paul J; van de Lagemaat, Jao; Smalyukh, Ivan I
Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called 'A-phase' in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called 'hopfions', or 'torons' when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields. PMID:25607778
Crystal Structure of 3S-hydroxy-7 Melleine
NASA Astrophysics Data System (ADS)
Liu, Xiao-hong; Xu, Fang; Zhang, Yi; Liu, Li-hong; Huang, Hua-rong; She, Zhi-gang; Lin, Yong-cheng; Chan, Winglai
A new compound, 3S-hydroxy-7 melleine was isolated from the endophytic fungus Xylariasp No.2508 from the mangrove tree on the South China Sea coast. It was the first time that this kind of compound was isolated from marine fungus. The structure was elucidated by NMR data, infrared spectrum (IR) and mass spectrometry (MS). In addition, its structure was determined by the single-crystal X-ray diffraction analysis. It crystallized in monoclinic, space group P21 with a=10.8884(19) Å, b=7.2284(13) Å, c=13.398(2) Å, ?=104.217(3)°, C10H10O4·H2O, Mr=212.20, V=1022.2(3) Å3, Z=4, Dc=1.379 mg/m3, F(000)=448, ?=0.112 mm-1, the final R=0.0498, ?R=0.101 for 2407 observed reflections (I>2?(I)). The molecular backbone of the compound includes a benzopyran ring. By comparing with the melting point and the optical rotation of the known 3R-hydroxy-7 melleine in literature, the absolute configuration of the compound was determined as 3S. It didn't exhibit antibacterial activity against Gram-positive bacterium Staphylococcus aureus at 200 ?g/disk in the preliminary test.
Crystal structure and thermal behaviour of pyridinium styphnate
Muthulakshmi, Selvarasu; Kalaivani, Doraisamyraja
In the crystal structure of the title molecular salt, C5H6N+·C6H2N3O8 ? (systematic name: pyridinium 3-hydroxy-2,4,6-trinitrophenolate), the pyridinium cation and the 3-hydroxy-2,4,6-trinitrophenolate anion are linked through bifurcated N—H?(O,O) hydrogen bonds, forming an R 1 2(6) ring motif. The nitro group para with respect to phenolate ion forms an intramolecular hydrogen bond with the adjacent phenolic –OH group, which results in an S(6) ring motif. The nitro group flanked by the phenolate ion and the phenolic –OH group deviates noticeably from the benzene ring, subtending a dihedral angle of 89.2?(4)°. The other two nitro groups deviate only slightly from the plane of the benzene ring, making dihedral angles of 2.8?(4) and 3.4?(3)°. In the crystal, the 3-hydroxy-2,4,6-trinitrophenolate anions are linked through O—H?O hydrogen bonds, forming chains along [100]. These anionic chains, to which the cations are attached, are linked via C—H?O hydrogen bonds, forming a three-dimensional structure. Impact friction sensitivity tests and TGA/DTA studies on the title molecular salt imply that it is an insensitive high-energy-density material.
Crystal structure of K[Hg(SCN)3] - a redetermination.
Weil, Matthias; Häusler, Thomas
The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium tri-thio-cyanato-mercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ?). Zh. Fiz. Khim. 26, 469-478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg-S bond lengths of 2.3954?(11), 2.4481?(8) and 2.7653?(6)?Å in comparison with values of 2.24, 2.43 and 2.77?Å. All atoms in the crystal structure are located on mirror planes. The Hg(2+) cation is surrounded by four S atoms in a seesaw shape [S-Hg-S angles range from 94.65?(2) to 154.06?(3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting (1) ?[HgS2/1S2/2] chains are also part of SCN(-) anions that link these chains with the K(+) cations into a three-dimensional network. The K-N bond lengths of the distorted KN7 polyhedra lie between 2.926?(2) and 3.051?(3)?Å. PMID:25309170
Crystal structure of K[Hg(SCN)3] – a redetermination
Weil, Matthias; Häusler, Thomas
The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium trithiocyanatomercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ?). Zh. Fiz. Khim. 26, 469–478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg—S bond lengths of 2.3954?(11), 2.4481?(8) and 2.7653?(6)?Å in comparison with values of 2.24, 2.43 and 2.77?Å. All atoms in the crystal structure are located on mirror planes. The Hg2+ cation is surrounded by four S atoms in a seesaw shape [S—Hg—S angles range from 94.65?(2) to 154.06?(3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting 1 ?[HgS2/1S2/2] chains are also part of SCN? anions that link these chains with the K+ cations into a three-dimensional network. The K—N bond lengths of the distorted KN7 polyhedra lie between 2.926?(2) and 3.051?(3)?Å. PMID:25309170
NSDL National Science Digital Library
Lawrence Hall of Science
In this earth science/math/art activity, learners use simple ingredients to grow crystals and examine the repeating geometric shapes and patterns. Learners compare the growth of crystals from four types of crystal-starters (table salt, Borax, sand, and Epsom salt) to see which starter grows the most crystals in 14 days. Learners report their results online and find out what other learners discovered. Afterward, learners can use the crystals they grew to create works of art.
Crystal structure of Hg2SO4 – a redetermination
Weil, Matthias
The crystal structure of mercury(I) sulfate (or mercurous sulfate), Hg2SO4, was re-determined based on modern CCD data. In comparison with the previous determination from Weissenberg film data [Dorm (1969 ?). Acta Chem. Scand. 23, 1607–1615], all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles [e.g. Hg—Hg = 2.5031?(7) compared to 2.500?(3)Å]. The structure consists of alternating rows along [001] of Hg2 2+ dumbbells (generated by inversion symmetry) and SO4 2? tetrahedra (symmetry 2). The dumbbells are linked via short O—Hg—Hg—O bonds to the sulfate tetrahedra into chains extending parallel to [20-1]. More remote O—Hg—Hg—O bonds connect these chains into a three-dimensional framework. PMID:25309168
Crystal Structure of a Phosphorylation-coupled Saccharide Transporter
Y Cao; X Jin; E Levin; H Huang; Y Zong; W Hendrickson; J Javitch; K Rajashankar; M Zhou; et al.
Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.
Crystal structure of prephenate dehydrogenase from Streptococcus mutans.
Ku, Hyung-Keun; Do, Nam Hyuk; Song, Jin Sue; Choi, Saehae; Yeon, Seung Hoon; Shin, Min Hyung; Kim, Kyung-Jin; Park, Sang-Ryoul; Park, Il-young; Kim, Sook-Kyung; Lee, Soo Jae
Prephenate dehydrogenase (PDH) is a bacterial enzyme that catalyzes conversion of prephenate to 4-hydroxyphenylpyruvate through the oxidative decarboxylation pathway for tyrosine biosynthesis. This enzymatic pathway exists in prokaryotes but is absent in mammals, indicating that it is a potential target for the development of new antibiotics. The crystal structure of PDH from Streptococcus mutans in a complex with NAD(+) shows that the enzyme exists as a homo-dimer, each monomer consisting of two domains, a modified nucleotide binding N-terminal domain and a helical prephenate C-terminal binding domain. The latter is the dimerization domain. A structural comparison of PDHs from mesophilic S. mutans and thermophilic Aquifex aeolicus showed differences in the long loop between ?6 and ?7, which may be a reason for the high K(m) values of PDH from Streptococcus mutans. PMID:21798280
Protein structure. Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism.
Li, Fei; Liu, Jian; Zheng, Yi; Garavito, R Michael; Ferguson-Miller, Shelagh
The 18-kilodalton translocator protein (TSPO), proposed to be a key player in cholesterol transport into mitochondria, is highly expressed in steroidogenic tissues, metastatic cancer, and inflammatory and neurological diseases such as Alzheimer's and Parkinson's. TSPO ligands, including benzodiazepine drugs, are implicated in regulating apoptosis and are extensively used in diagnostic imaging. We report crystal structures (at 1.8, 2.4, and 2.5 angstrom resolution) of TSPO from Rhodobacter sphaeroides and a mutant that mimics the human Ala(147)?Thr(147) polymorphism associated with psychiatric disorders and reduced pregnenolone production. Crystals obtained in the lipidic cubic phase reveal the binding site of an endogenous porphyrin ligand and conformational effects of the mutation. The three crystal structures show the same tightly interacting dimer and provide insights into the controversial physiological role of TSPO and how the mutation affects cholesterol binding. PMID:25635101
Effect of the Inhomogeneity of Ice Crystals on Retrieving Ice Cloud Optical Thickness and Effective Particle Size
NASA Technical Reports Server (NTRS)
Xie, Yu; Minnis, Patrick; Hu, Yong X.; Kattawar, George W.; Yang, Ping
Spherical or spheroidal air bubbles are generally trapped in the formation of rapidly growing ice crystals. In this study the single-scattering properties of inhomogeneous ice crystals containing air bubbles are investigated. Specifically, a computational model based on an improved geometric-optics method (IGOM) has been developed to simulate the scattering of light by randomly oriented hexagonal ice crystals containing spherical or spheroidal air bubbles. A combination of the ray-tracing technique and the Monte Carlo method is used. The effect of the air bubbles within ice crystals is to smooth the phase functions, diminish the 22deg and 46deg halo peaks, and substantially reduce the backscatter relative to bubble-free particles. These features vary with the number, sizes, locations and shapes of the air bubbles within ice crystals. Moreover, the asymmetry factors of inhomogeneous ice crystals decrease as the volume of air bubbles increases. Cloud reflectance lookup tables were generated at wavelengths 0.65 m and 2.13 m with different air-bubble conditions to examine the impact of the bubbles on retrieving ice cloud optical thickness and effective particle size. The reflectances simulated for inhomogeneous ice crystals are slightly larger than those computed for homogenous ice crystals at a wavelength of 0.65 microns. Thus, the retrieved cloud optical thicknesses are reduced by employing inhomogeneous ice cloud models. At a wavelength of 2.13 microns, including air bubbles in ice cloud models may also increase the reflectance. This effect implies that the retrieved effective particle sizes for inhomogeneous ice crystals are larger than those retrieved for homogeneous ice crystals, particularly, in the case of large air bubbles.
Crystal structure of the functional domain of the splicing factor Prp18
Jiang, Jianzhong; Horowitz, David S.; Xu, Rui-Ming
The splicing factor Prp18 is required for the second step of pre-mRNA splicing. We have isolated and determined the crystal structure of a large fragment of the Saccharomyces cerevisiae Prp18 that lacks the N-terminal 79 amino acids. This fragment, called Prp18?79, is fully active in yeast splicing in vitro and includes the sequences of Prp18 that have been evolutionarily conserved. The core structure of Prp18?79 is compact and globular, consisting of five ?-helices that adopt a novel fold that we have designated the five-helix X-bundle. The structure suggests that one face of Prp18 interacts with the splicing factor Slu7, whereas the more evolutionarily conserved amino acids in Prp18 form the opposite face. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two ?-helices and may interact with the U5 small nuclear ribonucleoprotein particles. The structure is consistent with a model in which Prp18 forms a bridge between Slu7 and the U5 small nuclear ribonucleoprotein particles. PMID:10737784
The crystal structure of NlpI A prokaryotic tetratricopeptide repeat protein with a globular fold
Mochrie, Simon
The crystal structure of NlpI A prokaryotic tetratricopeptide repeat protein with a globular fold-dimensional structure of a globular protein. The NlpI struc- ture is also the first TPR structure from a prokaryote
Structural properties of composites of polyvinylidene fluoride and mechanically activated BaTiO3 particles
NASA Astrophysics Data System (ADS)
Pavlovi?, V. P.; Pavlovi?, V. B.; Vlahovi?, B.; Božani?, D. K.; Pajovi?, J. D.; Doj?ilovi?, R.; Djokovi?, V.
Nanocomposites of electroactive ceramics and ferroelectric polymers exploit favorable features of the matrix polymer and the nanostructured filler to produce new functional materials for pressure and IR sensors. In this study, the influence of mechanical activation of barium titanate (BaTiO3) particles on the structural properties of BaTiO3/polyvinylidene fluoride (PVDF) nanocomposites was investigated. Nanocomposite films were prepared by the solution casting method and characterized by scanning electron microscopy, x-ray diffraction and Raman spectroscopy. It was found that mechanically activated fillers promote the formation of a ferroelectric ?-phase during crystallization of PVDF.
Chemical characterization of individual particles and residuals of cloud droplets and ice crystals collected on board research aircraft in the ISDAC 2008 study
NASA Astrophysics Data System (ADS)
Hiranuma, N.; Brooks, S. D.; Moffet, R. C.; Glen, A.; Laskin, A.; Gilles, M. K.; Liu, P.; MacDonald, A. M.; Strapp, J. W.; McFarquhar, G. M.
Ambient particles and the dry residuals of mixed-phase cloud droplets and ice crystals were collected during the Indirect and Semi-Direct Aerosol Campaign (ISDAC) near Barrow, Alaska, in spring of 2008. The collected particles were analyzed using Computer Controlled Scanning Electron Microscopy with Energy Dispersive X-ray analysis and Scanning Transmission X-ray Microscopy coupled with Near Edge X-ray Absorption Fine Structure spectroscopy to identify physico-chemical properties that differentiate cloud-nucleating particles from the total aerosol population. A wide range of individually mixed components was identified in the ambient particles and residuals including organic carbon compounds, inorganics, carbonates, and black carbon. Our results show that cloud droplet residuals differ from the ambient particles in both size and composition, suggesting that both properties may impact the cloud-nucleating ability of aerosols in mixed-phase clouds. The percentage of residual particles which contained carbonates (47%) was almost four times higher than those in ambient samples. Residual populations were also enhanced in sea salt and black carbon and reduced in organic compounds relative to the ambient particles. Further, our measurements suggest that chemical processing of aerosols may improve their cloud-nucleating ability. Comparison of results for various time periods within ISDAC suggests that the number and composition of cloud-nucleating particles over Alaska can be influenced by episodic events bringing aerosols from both the local vicinity and as far away as Siberia.
Crystal structure of the human GGA1 GAT domain.
Zhu, G.; Zhai, P.; He, X.; Terzyan, S.; Zhang, R.; Joachimiak, A.; Tang, J.; Zhang, X. C.; Biosciences Division; Oklahoma Medical Research Foundation; Oklahoma Univ. Medical Center
GGAs are a family of vesicle-coating regulatory proteins that function in intracellular protein transport. A GGA molecule contains four domains, each mediating interaction with other proteins in carrying out intracellular transport. The GAT domain of GGAs has been identified as the structural entity that binds membrane-bound ARF, a molecular switch regulating vesicle-coat assembly. It also directly interacts with rabaptin5, an essential component of endosome fusion. A 2.8 A resolution crystal structure of the human GGA1 GAT domain is reported here. The GAT domain contains four helices and has an elongated shape with the longest dimension exceeding 80 A. Its longest helix is involved in two structural motifs: an N-terminal helix-loop-helix motif and a C-terminal three-helix bundle. The N-terminal motif harbors the most conservative amino acid sequence in the GGA GAT domains. Within this conserved region, a cluster of residues previously implicated in ARF binding forms a hydrophobic surface patch, which is likely to be the ARF-binding site. In addition, a structure-based mutagenesis-biochemical analysis demonstrates that the C-terminal three-helix bundle of this GAT domain is responsible for the rabaptin5 binding. These structural characteristics are consistent with a model supporting multiple functional roles for the GAT domain.
Crystal structure of the Mus81-Eme1 complex.
Chang, Jeong Ho; Kim, Jeong Joo; Choi, Jung Min; Lee, Jung Hoon; Cho, Yunje
The Mus81-Eme1 complex is a structure-specific endonuclease that plays an important role in rescuing stalled replication forks and resolving the meiotic recombination intermediates in eukaryotes. We have determined the crystal structure of the Mus81-Eme1 complex. Both Mus81 and Eme1 consist of a central nuclease domain, two repeats of the helix-hairpin-helix (HhH) motif at their C-terminal region, and a linker helix. While each domain structure resembles archaeal XPF homologs, the overall structure is significantly different from those due to the structure of a linker helix. We show that a flexible intradomain linker that formed with 36 residues in the nuclease domain of Eme1 is essential for the recognition of DNA. We identified several basic residues lining the outer surface of the active site cleft of Mus81 that are involved in the interaction with a flexible arm of a nicked Holliday junction (HJ). These interactions might contribute to the optimal positioning of the opposite junction across the nick into the catalytic site, which provided the basis for the "nick and counternick" mechanism of Mus81-Eme1 and for the nicked HJ to be the favored in vitro substrate of this enzyme. PMID:18413719
Crystal structure of the human glucose transporter GLUT1
NASA Astrophysics Data System (ADS)
Deng, Dong; Xu, Chao; Sun, Pengcheng; Wu, Jianping; Yan, Chuangye; Hu, Mingxu; Yan, Nieng
The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation, the structure of GLUT1 remains unknown. Here we report the crystal structure of human GLUT1 at 3.2 Å resolution. The full-length protein, which has a canonical major facilitator superfamily fold, is captured in an inward-open conformation. This structure allows accurate mapping and potential mechanistic interpretation of disease-associated mutations in GLUT1. Structure-based analysis of these mutations provides an insight into the alternating access mechanism of GLUT1 and other members of the sugar porter subfamily. Structural comparison of the uniporter GLUT1 with its bacterial homologue XylE, a proton-coupled xylose symporter, allows examination of the transport mechanisms of both passive facilitators and active transporters.
A computational tool to design and generate crystal structures
NASA Astrophysics Data System (ADS)
Ferreira, R. C.; Vieira, M. B.; Dantas, S. O.; Lobosco, M.
The evolution of computers, more specifically regarding the increased storage and data processing capacity, allowed the construction of computational tools for the simulation of physical and chemical phenomena. Thus, practical experiments are being replaced, in some cases, by computational ones. In this context, we can highlight models used to simulate different phenomena on atomic scale. The construction of these simulators requires, by developers, the study and definition of accurate and reliable models. This complexity is often reflected in the construction of complex simulators, which simulate a limited group of structures. Such structures are sometimes expressed in a fixed manner using a limited set of geometric shapes. This work proposes a computational tool that aims to generate a set of crystal structures. The proposed tool consists of a) a programming language, which is used to describe the structures using for this purpose their characteristic functions and CSG (Constructive Solid Geometry) operators, and b) a compiler/interpreter that examines the source code written in the proposed language, and generates the objects accordingly. This tool enables the generation of an unrestricted number of structures, which can be incorporated in simulators such as the Monte Carlo Spin Engine, developed by our group at UFJF.
The crystal structures of potassium and cesium trivanadates
Evans, H.T., Jr.; Block, S.
Potassium and cesium trivanadates are monoclinic and isomorphous, space group P21/m, with the following dimensions (Z = 2): KV3O8, a = 7.640 A, b = 8.380 A, c = 4.979 A, ??= 96?? 57???; CsV3O8, a = 8.176 A, b = 8.519 A, c = 4.988 A, ?? = 95?? 32???. The crystal structure of KV3O8 has been determined from hk0, 0kl, and h0l Weissenberg data with an R factor of 0.15. The structure of CsV3O8 has been refined with 1273 hkl Weissenberg data to an R factor of 0.089. The structures consist of corrugated sheets based on a linkage of distorted VO6, octahedra. Two of the vanadium atoms lie in double, square-pyramid groups V2O8, which are linked through opposite basal corners into chains along the b axis. The chains are joined laterally along the c axis into sheets by the third vanadium atom in VO groups, also forming part of a square-pyramid coordination. Various aspects of these structures are compared with other known oxovanadate structures.
SHELXT – Integrated space-group and crystal-structure determination
Sheldrick, George M.
The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms. PMID:25537383
Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase
Fenglei Li
The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition, evaporation rate can be controlled or adjusted in this method during the crystallization process to favor either nucleation or growing processes for optimizing crystallization process. The protein crystals gotten by this method were experimentally proven to possess high x-ray diffraction qualities. Finally, we crystallized human lactate dehydrogenase 1 (H4) complexed with NADH and determined its structure by x-ray crystallography. The structure of LDH/NADH displays a significantly different structural feature, compared with LDH/NADH/inhibitor ternary complex structure, that subunits in LDH/NADH complex show open conformation or two conformations on the active site while the subunits in LDH/NADH/inhibitor are all in close conformation. Multiple LDH/NADH crystals were obtained and used for x-ray diffraction experiments. Difference in subunit conformation was observed among the structures independently solved from multiple individual LDH/NADH crystals. Structural differences observed among crystals suggest the existence of multiple conformers in solution.
Silicon crystals: Process for manufacturing wafer-like silicon crystals with a columnar structure
NASA Technical Reports Server (NTRS)
Authier, B.
Wafer-like crystals suitable for making solar cells are formed by pouring molten Si containing suitable dopants into a mold of the desired shape and allowing it to solidify in a temperature gradient, whereby the large surface of the melt in contact with the mold is kept at less than 200 D and the free surface is kept at a temperature of 200-1000 D higher, but below the melting point of Si. The mold can also be made in the form of a slit, whereby the 2 sides of the mold are kept at different temperatures. A mold was milled in the surface of a cylindrical graphite block 200 mm in diameter. The granite block was induction heated and the bottom of the mold was cooled by means of a water-cooled Cu plate, so that the surface of the mold in contact with one of the largest surfaces of the melt was held at approximately 800 D. The free surface of the melt was subjected to thermal radiation from a graphite plate located 2 mm from the surface and heated to 1500 D. The Si crystal formed after slow cooling to room temperature had a columnar structure and was cut with a diamond saw into wafers approximately 500 mm thick. Solar cells prepared from these wafers had efficiencies of 10 to 11%.
Hierarchical structures of ZnO spherical particles synthesized solvothermally
NASA Astrophysics Data System (ADS)
Saito, Noriko; Haneda, Hajime
We review the solvothermal synthesis, using a mixture of ethylene glycol (EG) and water as the solvent, of zinc oxide (ZnO) particles having spherical and flower-like shapes and hierarchical nanostructures. The preparation conditions of the ZnO particles and the microscopic characterization of the morphology are summarized. We found the following three effects of the ratio of EG to water on the formation of hierarchical structures: (i) EG restricts the growth of ZnO microcrystals, (ii) EG promotes the self-assembly of small crystallites into spheroidal particles and (iii) the high water content of EG results in hollow spheres.
Octa-O-propanoyl-B-maltose: crystal structure, acyl stacking, related structures and conformational anaylsis
Technology Transfer Automated Retrieval System (TEKTRAN)
The crystal structure of beta-maltose octapropanoate (1) was solved to increase knowledge of the influences on conformations of di-, oligo- and polysaccharides. The O6 and O6' atoms are in gg and gt conformations, respectively. Extrapolation of the coordinates of the non-reducing residue and observe...
Tessein, J. A.; Matthaeus, W. H.; Wan, M. [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States)] [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States); Osman, K. T. [Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry CV4 7AL (United Kingdom)] [Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry CV4 7AL (United Kingdom); Ruffolo, D. [Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand)] [Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand); Giacalone, J. [Department of Planetary Sciences and Lunar and Planetary Laboratory, University of Arizona, 1629 East University Boulevard, Tucson, AZ 85721 (United States)] [Department of Planetary Sciences and Lunar and Planetary Laboratory, University of Arizona, 1629 East University Boulevard, Tucson, AZ 85721 (United States)
Various mechanisms have been proposed to explain observed suprathermal particle populations in the solar wind, including direct acceleration at flares, stochastic acceleration, shock acceleration, and acceleration by random compression or reconnection sites. Using magnetic field and suprathermal particle data from the Advanced Composition Explorer (ACE), we identify coherent structures and interplanetary shocks, and analyze the temporal association of energetic particle fluxes with these coherent structures. Coherent structures having a range of intensities are identified using the magnetic Partial Variance of Increments statistic, essentially a normalized vector increment. A stronger association of energetic particle flux in the 0.047-4.75 MeV range is found with intense magnetic discontinuities than is found with shocks. Nevertheless, the average profile of suprathermals near shocks is quite consistent with standard models of diffusive shock acceleration, while a significant amount of the energetic particles measured and strong discontinuities are found by ACE within six hours of a shock. This evidence supports the view that multiple mechanisms contribute to the acceleration and transport of interplanetary suprathermal particles.
Crystal structure retrieval by maximum entropy analysis of atomic resolution incoherent images
Pennycook, Steve
Crystal structure retrieval by maximum entropy analysis of atomic resolution incoherent images A. J, TN 37831-6031, U.S.A. Key words. Atomic resolution, crystal structure retrieval, incoherent imaging be used to yield important information on unexpected atomic structures. Introduction The physical
Crystal structure of rabbit muscle creatine kinase J.K. Mohana RaoY
; Rabbit muscle; Enzyme; Crystal structure 1. Introduction Creatine kinase [1^3] (CK; adenosine 5PCrystal structure of rabbit muscle creatine kinase J.K. Mohana RaoY *, Grzegorz BujaczY , Alexander Abstract The crystal structure of rabbit muscle creatine kinase, solved at 2.35 Aî resolution by X
Classification of HIV-1 Protease Crystal Structures Using Random Forest, Linear Discriminant Analysis and Logistic Regression
Kumar, Sunil
Classification of HIV-1 Protease Crystal Structures Using Random Forest, Linear Discriminant of 70 HIV-1 protease crystal structures in terms of their structural descriptors to their complexed HIV on their complexed ligands. The selected descriptors would play a crucial role in understanding the HIV-1 protease
Band gap widening by photonic crystal heterostructures composed of two dimensional holes and diamond structure
NASA Astrophysics Data System (ADS)
Chen, Shibin; Li, Dichen; Zhi-Hui, Yuan
A new kind of heterostructures containing 3D diamond and 2D holes structures, and diamond-structure photonic crystals and 2D holes-structure photonic crystals fabricated by stereolithography and gel-casting with alumina were studied at microwave range, respectively. The heterostructures were designed by 2D holes structure embedded in 3D diamond structure, in which the lattice of three kinds of structures was equivalent. It was found that the band gaps of photonic crystal heterostructure were broadened by 124.6% and 150% comparing to that of diamond-structure crystal and 2D aerial holes structure. Experimental results showed the band gap broadened was not connected with a linear superposition of the band gap of 2D and 3D photonic crystals, which was the superposition of partial overlap.
Tunable all-optical switching in periodic structures with liquid-crystal defects
polymer dispersed liquid crystals," Opt. Lett. 28, 522-524 (2003). 10. E. Graugnard, J.S. King, S. Jain, CTunable all-optical switching in periodic structures with liquid-crystal defects Andrey E that tunable orientational nonlinearity of nematic liquid crystals can be employed for all-optical switching
PerspectiVes Good Crystals, Still a Challenge for Structural Biology
Tian, Weidong
crystallization strategies, structural genomics, and robotics and provided many examples where crystallogenesis crystallization, where the viscosity of the crystallizing samples plays a critical role. A Japanese team exploring imperfections.1 Particularly impressive were the results of two other Japanese scientists from Tohoku University
Nanoconfinement crystallization of frustrated alkyl groups: crossover of mesophase to crystalline structure.
Shi, Haifeng; Wang, Haixia; Xin, John H; Zhang, Xingxiang; Wang, Dujin
Crossover of mesophase to crystalline structure in the nanoconfinement crystallization process of frustrated side groups elucidates the critical crystal thickness d(c) or the length scale of side groups, which defines the transition process from mesophase (hexagonal and monoclinic phase) to crystalline phase (orthorhombic phase) of confined CH(2) sequences in a given crystal size restriction. PMID:21359343
Studies on synthesis, growth, structural, optical properties of organic 8-hydroxyquinolinium succinate single crystals
Thirumurugan, R., E-mail: firstname.lastname@example.com; Anitha, K., E-mail: email@example.com [School of Physics, Madurai Kamaraj University, Madurai-625021 (India)
8-hydroxyquinolinium succinate (8HQSU), an organic material has been synthesized and single crystals were grown by employing the technique of slow evaporation. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction analysis. 8HQSU crystal belongs to the monoclinic crystallographic system with non-centro symmetric space group of P2{sub 1}. FT-IR spectral investigation has been carried out to identify the various functional groups present in the grown crystal. UV–vis spectral studies reveal that 8HQSU crystals are transparent in the entire visible region and the cut-off wavelength has been found to be 220nm.
Manufacturing, structure and properties of recycled polyethylene terephthalate /liquid crystal polymer/montmorillonite clay nanocomposites
NASA Astrophysics Data System (ADS)
Japins, Guntis; Berzina, Rita; Zicans, Janis; Merijs Meri, Remo; Ivanova, Tatjana; Kalkis, Valdis; Reinholds, Ingars
Polyethylene terephthalate (PET)/liquid crystal polymer (LCP)/monthmorillonite clay (MMT) compositions were obtained by melt mixing. Their mechanical, structural, rheological and thermal properties were investigated.
Control of Polymer Structures in Phase-Separated Liquid Crystal-Polymer Composite Systems Qingbing WANG, Jung O. PARK1
Srinivasarao, Mohan
Control of Polymer Structures in Phase-Separated Liquid Crystal-Polymer Composite Systems Qingbing structure to a heterogeneous polymer dispersed liquid crystal (PDLC) structure. A variation in cell: liquid crystal, polymerization, phase separation, polymer morphology, polymer dispersed liquid crystal 1
Assessment of cigarette smoke particle deposition within the Vitrocell® exposure module using quartz crystal microbalances
Background Cigarette smoking is a cause of a variety of serious diseases, and to understand the toxicological impact of tobacco smoke in vitro, whole smoke exposure systems can be used. One of the main challenges of the different whole smoke exposure systems that are commercially available is that they dilute and deliver smoke in different ways, limiting/restricting the cross-comparison of biological responses. This is where dosimetry – dose quantification – can play a key role in data comparison. Quartz crystal microbalance (QCM) technology has been put forward as one such tool to quantify smoke particle deposition in vitro, in real-time. Results Using four identical QCMs, installed into the Vitrocell® mammalian 6/4 CF Stainless exposure module, we were able to quantify deposited smoke particle deposition, generated and diluted by a Vitrocell® VC 10 Smoking Robot. At diluting airflows 0.5-4.0 L/min and vacuum flow rate 5 ml/min/well through the exposure module, mean particle deposition was in the range 8.65?±?1.51 ?g/cm2-0.72?±?0.13 ?g/cm2. Additionally, the effect of varying vacuum flow rate on particle deposition was assessed from 5 ml/min/well - 100 ml/min/well. Mean deposited mass for all four airflows tested per vacuum decreased as vacuum rate was increased: mean deposition was 3.79, 2.75, 1.56 and 1.09 ?g/cm2 at vacuum rates of 5, 10, 50 and 100 ml/min/well respectively. Conclusions QCMs within the Vitrocell® exposure module have demonstrated applicability at defining particle dose ranges at various experimental conditions. This tool will prove useful for users of the Vitrocell® system for dose–response determination and QC purposes. PMID:23497606
Crystal structure of substrate free form of glycerol dehydratase
Liao, Der-Ing; Dotson, Garry; Turner, Jr., Ivan; Reiss, Lisa; Emptage, Mark (Du Pont)
Glycerol dehydratase (GDH) and diol dehydratase (DDH) are highly homologous isofunctional enzymes that catalyze the elimination of water from glycerol and 1,2-propanediol (1,2-PD) to the corresponding aldehyde via a coenzyme B{sub 12}-dependent radical mechanism. The crystal structure of substrate free form of GDH in complex with cobalamin and K{sup +} has been determined at 2.5 {angstrom} resolution. Its overall fold and the subunit assembly closely resemble those of DDH. Comparison of this structure and the DDH structure, available only in substrate bound form, shows the expected change of the coordination of the essential K{sup +} from hexacoordinate to heptacoordinate with the displacement of a single coordinated water by the substrate diol. In addition, there appears to be an increase in the rigidity of the K{sup +} coordination (as measured by lower B values) upon the binding of the substrate. Structural analysis of the locations of conserved residues among various GDH and DDH sequences has aided in identification of residues potentially important for substrate preference or specificity of protein-protein interactions.
Crystal structure of lipid phosphatase Escherichia coli phosphatidylglycerophosphate phosphatase B.
Fan, Junping; Jiang, Daohua; Zhao, Yan; Liu, Jianfeng; Zhang, Xuejun Cai
Membrane-integrated type II phosphatidic acid phosphatases (PAP2s) are important for numerous bacterial to human biological processes, including glucose transport, lipid metabolism, and signaling. Escherichia coli phosphatidylglycerol-phosphate phosphatase B (ecPgpB) catalyzes removing the terminal phosphate group from a lipid carrier, undecaprenyl pyrophosphate, and is essential for transport of many hydrophilic small molecules across the membrane. We determined the crystal structure of ecPgpB at a resolution of 3.2 Å. This structure shares a similar folding topology and a nearly identical active site with soluble PAP2 enzymes. However, the substrate binding mechanism appears to be fundamentally different from that in soluble PAP2 enzymes. In ecPgpB, the potential substrate entrance to the active site is located in a cleft formed by a V-shaped transmembrane helix pair, allowing lateral movement of the lipid substrate entering the active site from the membrane lipid bilayer. Activity assays of point mutations confirmed the importance of the catalytic residues and potential residues involved in phosphate binding. The structure also suggests an induced-fit mechanism for the substrate binding. The 3D structure of ecPgpB serves as a prototype to study eukaryotic PAP2 enzymes, including human glucose-6-phosphatase, a key enzyme in the homeostatic regulation of blood glucose concentrations. PMID:24821770
CsLiB 6O 10 crystals with Cs deficit: structure and properties
NASA Astrophysics Data System (ADS)
Isaenko, L.; Vasilyeva, I.; Merkulov, A.; Tomilenko, A.; Bogdanova, I.; Malakhov, V.; Drebushchak, V.
Cs-Li borate crystals (CLBO) grown from melts have been examined by chemical and thermal analysis and IR spectroscopy. Evaporation of cesium oxides from melt during growing resulted in crystals with Cs deficit. The defect structure of these crystals has been refined by means of single-crystal X-ray diffraction analysis, while two non equivalent Cs positions have been revealed. Using the close-packed spheres model, the volumes of the structural vacant spaces have been estimated, and the proof of their occupation by one or several water molecules has been given. The behavior of the defect CLBO crystals exposed to dry and moist atmospheres has been considered.
The interplanetary magnetic structure that guides solar relativistic particles
NASA Astrophysics Data System (ADS)
Masson, S.; Démoulin, P.; Dasso, S.; Klein, K.-L.
Context. Relating in-situ measurements of relativistic solar particles to their parent activity in the corona requires understanding the magnetic structures that guide them from their acceleration site to the Earth. Relativistic particle events are observed at times of high solar activity, when transient magnetic structures such as interplanetary coronal mass ejections (ICMEs) often shape the interplanetary magnetic field (IMF). They may introduce interplanetary paths that are longer than nominal, and magnetic connections rooted far from the nominal Parker spiral. Aims: We present a detailed study of the IMF configurations during ten relativistic solar particle events of the 23rd activity cycle to elucidate the actual IMF configuration that guides the particles to the Earth, where they are measured by neutron monitors. Methods: We used magnetic field (MAG) and plasma parameter measurements (SWEPAM) from the ACE spacecraft and determined the interplanetary path lengths of energetic particles through a modified version of the velocity dispersion analysis based on energetic particle measurements with SoHO/ERNE. Results: We find that the majority (7/10) of the events is detected in the vicinity of an ICME. Their interplanetary path lengths are found to be longer (1.5-2.6 AU) than those of the two events propagating in the slow solar wind (1.3 AU). The longest apparent path length is found in an event within the fast solar wind, probably caused by enhanced pitch angle scattering. The derived path lengths imply that the first energetic and relativistic protons are released at the Sun at the same time as electron beam emitting type III radio bursts. Conclusions: The timing of the first high-energy particle arrival on Earth is mainly determined by the type of IMF in which the particles propagate. Initial arrival times are as expected from Parker's model in the slow solar wind, and significantly longer in or near transient structures such as ICMEs.
Crystallization, crystal-structure refinement, and IR spectroscopy of a synthetic hexahydroborite analog
Yamnova, N. A., E-mail: firstname.lastname@example.com; Borovikova, E. Yu.; Dimitrova, O. V. [Moscow State University, Faculty of Geology (Russian Federation)
The crystal structure of the hexahydroborite analog Ca[B(OH){sub 4}]{sub 2} {center_dot} 2H{sub 2}O (a = 7.9941(3) Angstrom-Sign , b = 6.6321(2) Angstrom-Sign , c = 7.9871(3) Angstrom-Sign , {beta} = 104.166(4) Degree-Sign , V = 410.58(3) Angstrom-Sign {sup 3}, sp. gr. P2/c, Z = 2, {rho}{sub calc} = 1.891 g/cm{sup 3}; Xcalibur S CCD automated diffractometer, 1196 reflections with I > 2{sigma}(I), {lambda}MoK{sub {alpha}}), which was synthesized by the hydrothermal method via the recrystallization of calciborite CaB{sub 2}O{sub 4} (M) in the M - B{sub 2}O{sub 3} - H{sub 2}O system (t = 250 Degree-Sign C and P = 70-80 atm), was refined by the least-squares method with anisotropic displacement parameters (H atoms were located; R{sub 1} = 0.0260). The structure of synthetic hexahydroborite consists of infinite columns running along the c axis. The columns are formed by Ca polyhedra linked together and to [B(OH){sub 4}] orthotetrahedra by sharing edges. Along the two other axes, the translationally equivalent columns are linked only by hydrogen bonds. The presence of a stronger bond between the discrete (Ca-B-O) columns along the shortest (b = 6.6 Angstrom-Sign ) axis accounts for the possibility of the shift of the columns by 1/2T{sub b} and the formation of the second modification of Ca[B(OH){sub 4}]{sub 2} {center_dot} 2H{sub 2}O. The crystals of synthetic hexahydroborite were studied by IR spectroscopy. A crystal-chemical analysis was performed for a series of natural metaborates with the general formula CaB{sub 2}O{sub 4} {center_dot} nH{sub 2}O (CaO: B{sub 2}O{sub 3} = 1: 1, n = 0-6), including calciborite CaB{sub 2}O{sub 4} and hexahydroborite CaB{sub 2}O{sub 4} {center_dot} 6H{sub 2}O as the end members.
VO2 (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms
NASA Astrophysics Data System (ADS)
Rao Popuri, Srinivasa; Artemenko, Alla; Labrugere, Christine; Miclau, Marinela; Villesuzanne, Antoine; Pollet, Michaël
Well crystallized VO2 (A) microrods were grown via a single step hydrothermal reaction in the presence of V2O5 and oxalic acid. With the advantage of high crystalline samples, we propose P4/ncc as an appropriate space group at room temperature. From morphological studies, we found that the oriented attachment and layer by layer growth mechanisms are responsible for the formation of VO2 (A) micro rods. The structural and electronic transitions in VO2 (A) are strongly first order in nature, and a marked difference between the structural transition temperatures and electronic transitions temperature was evidenced. The reversible intra- (LTP-A to HTP-A) and irreversible inter- (HTP-A to VO2 (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO2 (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO2 (M1) are described.
Birefringence and band structure of CdP2 crystals
NASA Astrophysics Data System (ADS)
Beril, S. I.; Stamov, I. G.; Syrbu, N. N.; Zalamai, V. V.
The spatial dispersion in CdP2 crystals was investigated. The dispersion is positive (nk||?>nk||?) at ?>?0 and negative (nk||?
Crystal structure, thermal behavior and enzymatic degradation of poly(tetramethylene adipate) solution-grown chain-folded lamellar crystals.
Iwata, Tadahisa; Kobayashi, Shiomi; Tabata, Kenji; Yonezawa, Noriyuki; Doi, Yoshiharu
Solution-grown chain-folded lamellar single crystals of poly(tetramethylene adipate) (PTMA) were prepared from a dilute solution of 2-methyl-1-propanol by isothermal crystallization. PTMA crystals were hexagonal-shaped and polyethylene decoration of the crystals resulted in a "six cross-sector" surface morphology and showed that the average direction of chain folding is parallel to the crystal growth planes of [110] and [010]. Chain-folded lamellar crystals gave well-resolved electron diffraction diagrams corresponding to all the equatorial reflections of the X-ray fiber diagram obtained from stretched PTMA melt-quenched film (beta structure). The unit cell parameters of the beta structure of PTMA were determined as a = 0.503 nm, b = 0.732 nm and c (fiber axis) = 1.442 nm with an orthorhombic crystal system. The fiber repeat distance is appropriate for an all-trans backbone conformation for the straight stems. The setting angle, with respect to the a axis, is +/-46 degrees for the corner and center chains. Thermal behavior of lamellar crystals has been investigated by means of transmission electron microscopy (TEM) and atomic force microscopy (AFM). The lamellar thickness at the edges of the crystal increased after thermal treatment with taking the molecular chains into recrystallization parts; the holes then opened up at the thickening front of the crystal. The morphological changes of lamellar crystals after enzymatic degradation by Lipase type XIII from Pseudomonas sp. and water-soluble products were characterized by TEM, AFM, gel permeation chromatography, high performance liquid chromatography and fast atom bombardment mass spectrometry. The degradation progressed mainly from the edges of the lamellar crystals without decreasing the molecular weights and the lamellar thicknesses. The central portion of single crystals was often degraded by enzymatic attacks. This result combined with thermal behavior indicates that the loosely chain-packing region exists inside the single crystal, and that molecular chains in this region have higher mobility against thermal and enzymatic treatments. PMID:15468220
Synthesis, structure, crystal growth and characterization of a novel semiorganic nonlinear optical l-proline lithium bromide monohydrate single crystal.
Sathiskumar, S; Balakrishnan, T; Ramamurthi, K; Thamotharan, S
l-Proline lithium bromide monohydrate (LPLBM), a promising semiorganic nonlinear optical material, was synthesized and single crystals of LPLBM were grown from solution by slow evaporation technique. Single crystal X-ray structure solution reveals that the grown crystal belongs to monoclinic system with space group P21. Presence of various functional groups was identified by FT-IR and FT-Raman spectral analyses. UV-Vis-NIR spectroscopic study shows that the LPLBM crystal possesses 90% of transmittance in the range of 250-1100nm. Vickers microhardness values, the dielectric constant and dielectric loss of the LPLBM crystal were reported. Elemental analysis by energy dispersive X-ray analysis shows the presence of carbon, nitrogen, oxygen and bromine. The surface morphology of the crystal was investigated using scanning electron microscopic study. The thermal stability of the LPLBM crystal was studied from TGA and DSC analysis. Second harmonic generation efficiency of the LPLBM crystal measured by Kurtz and Perry powder technique using Nd:YAG laser is about 0.3 times that of urea. PMID:25498813
Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions
Qiu, Xiayang; Janson, Cheryl A. (GSK)
A topic of current interest is engineering surface mutations in order to improve the success rate of protein crystallization. This report explores the possibility of using metal-ion-mediated crystal-packing interactions to facilitate rational design. Escherichia coli apo acyl carrier protein was chosen as a test case because of its high content of negatively charged carboxylates suitable for metal binding with moderate affinity. The protein was successfully crystallized in the presence of zinc ions. The crystal structure was determined to 1.1 {angstrom} resolution with MAD phasing using anomalous signals from the co-crystallized Zn{sup 2+} ions. The case study suggested an integrated strategy for crystallization and structure solution of proteins via engineering surface Asp and Glu mutants, crystallizing them in the presence of metal ions such as Zn{sup 2+} and solving the structures using anomalous signals.
Change in crystal structure and electron density by introducing oxygen in YBaâCuâO{sub y} single crystal
Wen-Jye Jang; Hatsumi Mori; Setsuko Tajima
The electron density map of tetragonal YBaâCuâOâ (YBCOâ) single crystal was investigated, in comparison with that of orthorhombic YBaâCuâO{sub 6.9} (YBCO{sub 6.9}). The crystal structure was determined by using four-circle X-ray diffraction data. The final values of the weighted reliability factor (R{sub W}) and unweighted factor (R) were 0.027 and 0.024 for YBCOâ, which are small enough for analysis of
Crystal Structure of Cindoxin, the P450cin Redox Partner
The crystal structure of the flavin mononucleotide (FMN)-containing redox partner to P450cin, cindoxin (Cdx), has been determined to 1.3 Å resolution. The overall structure is similar to that of the FMN domain of human cytochrome P450 reductase. A Brownian dynamics–molecular dynamics docking method was used to produce a model of Cdx with its redox partner, P450cin. This Cdx–P450cin model highlights the potential importance of Cdx Tyr96 in bridging the FMN and heme cofactors as well P450cin Arg102 and Arg346. Each of the single-site Ala mutants exhibits ?10% of the wild-type activity, thus demonstrating the importance of these residues for binding and/or electron transfer. In the well-studied P450cam system, redox partner binding stabilizes the open low-spin conformation of P450cam and greatly decreases the stability of the oxy complex. In sharp contrast, Cdx does not shift P450cin to a low-spin state, although the stability of oxy-P450cin is decreased 10-fold in the presence of Cdx. This indicates that Cdx may have a modest effect on the open–closed equilibrium in P450cin compared to that in P450cam. It has been postulated that part of the effector role of Pdx on P450cam is to promote a significant structural change that makes available a proton relay network involving Asp251 required for O2 activation. The structure around the corresponding Asp in P450cin, Asp241, provides a possible structural reason for why P450cin is less dependent on its redox partner for functionally important structural changes. PMID:24533927
Structural conditionality of the piezoelectric properties of langasite family crystals
Dudka, A. P., E-mail: email@example.com; Simonov, V. I. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)
The atomic displacements upon isomorphic substitutions in crystals of the langasite family have been analyzed. The thermal parameters are determined and the probability density function of atoms is analyzed. Local potential energy minima are found which can be occupied by atoms under external effects. The contributions of cations in all four independent crystallographic positions and anions in all three such positions to the piezoelectric properties are established. One specific structural feature is the constant (at isomorphic substitutions) or possible (under external effects) but always opposite displacements of two cations along symmetry axis 2. Large cations in eight-vertex polyhedra make the main contribution to the piezoelectric properties. The cations in the tetrahedra on symmetry axis 2 weaken these properties. The cations in the octahedra in the origin of coordinates and in the tetrahedra on symmetry axes 3 only slightly affect the piezoelectricity.
Crystal Structure of Calcium-Deficient Carbonated Hydroxyapatite. Thermal Decomposition
T. I. Ivanova; O. V. Frank-Kamenetskaya; A. B. Kol'tsov; V. L. Ugolkov
Full Rietveld refinement of the crystal structure of the synthetic calcium-deficient carbonated apatite Ca13.40[Ca25.90 (NH4)0.10][(PO4)4.95(CO3)1.05(H2O)0.30][(OH)1.65(H2O)0.45] (space group P63\\/m; a=9.437(1), c=6.888(1) Å; Z=1; Rwp=5.23%) was carried out using X-ray powder diffraction data. The use of the model with the split position of O3 atom made it possible to find two orientations of CO3 triangles sharing one of their edges. They occupy
Crystal structure of a heterotetrameric NMDA receptor ion channel
Karakas, Erkan; Furukawa, Hiro
N -methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors, which mediate most excitatory synaptic transmission in mammalian brains. Calcium permeation triggered by activation of NMDA receptors is the pivotal event for initiation of neuronal plasticity. Here we show the crystal structure of the intact heterotetrameric GluN1/GluN2B NMDA receptor ion channel at 4 Å. The NMDA receptors are arranged as a dimer of GluN1-GluN2B heterodimers with the two-fold symmetry axis running through the entire molecule composed of an amino terminal domain (ATD), a ligand-binding domain (LBD), and a transmembrane domain (TMD). The ATD and LBD are much more highly packed in the NMDA receptors than non-NMDA receptors, which may explain why ATD regulates ion channel activity in NMDA receptors but not in non-NMDA receptors. PMID:24876489
Interfacial structure in epitaxial perovskite oxides on (001) Ge crystal
NASA Astrophysics Data System (ADS)
Shen, Xuan; Ahmadi-Majlan, K.; Ngai, Joseph H.; Wu, Di; Su, Dong
We investigated the interfacial structure of hetero-epitaxial SrZr0.68Ti0.32O3 thin film deposited on (001) Ge single crystal via transmission electron microscopy (TEM). The results from high-resolution scanning TEM and electron energy-loss spectroscopy show an atomically abrupt interface without secondary phase. We found misfit dislocations with Burgers vector of 1/2a <111> and threading dislocations with Burgers vector of a <100>. Furthermore, we observed the coupling between dislocation half-loop and anti-phase boundary induced by the lattice terrace of Ge along <100> direction and their decoupling after annealing. We proposed models based on half-loop theory to interpret the coupling and the dislocation reactions.
Crystal structure of a heterotetrameric NMDA receptor ion channel.
Karakas, Erkan; Furukawa, Hiro
N-Methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors, which mediate most excitatory synaptic transmission in mammalian brains. Calcium permeation triggered by activation of NMDA receptors is the pivotal event for initiation of neuronal plasticity. Here, we show the crystal structure of the intact heterotetrameric GluN1-GluN2B NMDA receptor ion channel at 4 angstroms. The NMDA receptors are arranged as a dimer of GluN1-GluN2B heterodimers with the twofold symmetry axis running through the entire molecule composed of an amino terminal domain (ATD), a ligand-binding domain (LBD), and a transmembrane domain (TMD). The ATD and LBD are much more highly packed in the NMDA receptors than non-NMDA receptors, which may explain why ATD regulates ion channel activity in NMDA receptors but not in non-NMDA receptors. PMID:24876489
Crystal structure of NLRC4 reveals its autoinhibition mechanism.
Hu, Zehan; Yan, Chuangye; Liu, Peiyuan; Huang, Zhiwei; Ma, Rui; Zhang, Chenlu; Wang, Ruiyong; Zhang, Yueteng; Martinon, Fabio; Miao, Di; Deng, Haiteng; Wang, Jiawei; Chang, Junbiao; Chai, Jijie
Nucleotide-binding and oligomerization domain-like receptor (NLR) proteins oligomerize into multiprotein complexes termed inflammasomes when activated. Their autoinhibition mechanism remains poorly defined. Here, we report the crystal structure of mouse NLRC4 in a closed form. The adenosine diphosphate-mediated interaction between the central nucleotide-binding domain (NBD) and the winged-helix domain (WHD) was critical for stabilizing the closed conformation of NLRC4. The helical domain HD2 repressively contacted a conserved and functionally important ?-helix of the NBD. The C-terminal leucine-rich repeat (LRR) domain is positioned to sterically occlude one side of the NBD domain and consequently sequester NLRC4 in a monomeric state. Disruption of ADP-mediated NBD-WHD or NBD-HD2/NBD-LRR interactions resulted in constitutive activation of NLRC4. Together, our data reveal the NBD-organized cooperative autoinhibition mechanism of NLRC4 and provide insight into its activation. PMID:23765277
Chemical composition, crystal structure, and their relationships with the intrinsic properties of spinel-type crystals based on bond valences.
Liu, Xiao; Wang, Hao; Lavina, Barbara; Tu, Bingtian; Wang, Weimin; Fu, Zhengyi
Spinel-type crystals may possess complex and versatile chemical composition and crystal structure, which leads to difficulty in constructing relationships among the chemical composition, crystal structure, and intrinsic properties. In this work, we develop new empirical methods based on bond valences to estimate the intrinsic properties, namely, compressibility and thermal expansion of complex spinel-type crystals. The composition-weighted average of bond force constants in tetrahedral and octahedral coordination polyhedra is derived as a function of the composition-weighted average of bond valences, which can be calculated according to the experimental chemical composition and crystal structural parameters. We discuss the coupled effects of tetrahedral and octahedral frameworks on the aforementioned intrinsic properties. The bulk modulus could be quantitatively calculated from the composition-weighted average of bond force constants in tetrahedral and octahedral coordination polyhedra. In contrast, a quantitative estimation of the thermal expansion coefficient could be obtained from the composition-weighted average of bond force constants in octahedral coordination polyhedra. These empirical methods have been validated by the results obtained for a new complex quaternary spinel-type oxynitride Mg0.268Al2.577O3.733N0.267 as well as MgAl2O4 and Al2.85O3.45N0.55 from the literature. Further, these empirical methods have the potential to be extensively applied in other types of complex crystals. PMID:24871452
Lagrangian coherent structures and the dynamics of inertial particles
NASA Astrophysics Data System (ADS)
Madhavan, Sudharsan
Dynamics of inertial particles in two-dimensional planar flow have been investigated by evaluating finite-time Lyapunov exponents (FTLE). The first part of our work deals with inertial particle dynamics. The Maxey-Riley equations have been employed to track particles. Patterns formed by inertial particles are reported along with their dependance on Strokes number and density of particles relative to the carrier-fluid density. Our results distinguish patterns formed by particles denser than the fluid (aerosols) from those formed by particles lighter than the fluid (bubbles). Preferential concentration of these particles at specific regions of the flow have been observed. The attenuating, low-pass filter effect of Stokes drag on bubbles are reported for the first time. The results from this part of the work motivated further investigations into the underlying organizing structures of the flow, namely the Lagrangian coherent structures (LCS). LCS is traditionally evaluated using FTLE. In the next part of the work, our objective was to interpret the dynamics of inertial particles by evaluating finite-time Lyapunov exponents on their trajectories. A main result is that aerosols were found to be attracted and preferentially concentrated along ridges of negative finite-time Lyapunov exponents (nFTLE) of the underlying flow. On the other hand bubbles were found to be repelled from these structures and were therefore observed preferentially concentrating away from these zones. These results, being reported for the first time, supplement the existing literature on preferential concentration of inertial particles. Despite having an effect on particle trajectories, increasing the Stokes number had very little effect on inertial finite-time Lyapunov exponents (iFTLE). Furthermore, increasing Stokes number resulted in an increase in the ridges of iFTLE contours for aerosols, whereas for bubbles the opposite was observed. These findings indicate that optimum mixing occurs at different Stokes numbers for aerosols and bubbles. The last part of the work focussed on comparing well-known dispersion measures with inertial finite-time Lyapunov exponents. We qualitatively show that two-point dispersion contours share dominant ridges with those from inertial finite-time Lyapunov exponents. This result numerically shows that material surfaces identified by inertial finite-time Lyapunov exponents are maximally dispersed in the flow. Applications and future directions based on our work are suggested.
Lidar inelastic multiple-scattering parameters of cirrus particle ensembles determined with geometrical-optics crystal phase functions.
Reichardt, J; Hess, M; Macke, A
Multiple-scattering correction factors for cirrus particle extinction coefficients measured with Raman and high spectral resolution lidars are calculated with a radiative-transfer model. Cirrus particle-ensemble phase functions are computed from single-crystal phase functions derived in a geometrical-optics approximation. Seven crystal types are considered. In cirrus clouds with height-independent particle extinction coefficients the general pattern of the multiple-scattering parameters has a steep onset at cloud base with values of 0.5-0.7 followed by a gradual and monotonic decrease to 0.1-0.2 at cloud top. The larger the scattering particles are, the more gradual is the rate of decrease. Multiple-scattering parameters of complex crystals and of imperfect hexagonal columns and plates can be well approximated by those of projected-area equivalent ice spheres, whereas perfect hexagonal crystals show values as much as 70% higher than those of spheres. The dependencies of the multiple-scattering parameters on cirrus particle spectrum, base height, and geometric depth and on the lidar parameters laser wavelength and receiver field of view, are discussed, and a set of multiple-scattering parameter profiles for the correction of extinction measurements in homogeneous cirrus is provided. PMID:18345086
Crystal structure of Bacillus anthracis transpeptidase enzyme CapD.
Wu, R.; Richter, S.; Zhang, R.; Anderson, V. J.; Missiakas, D.; Joachimiak, A.; Biosciences Division; Univ. of Chicago
Bacillus anthracis elaborates a poly-{gamma}-d-glutamic acid capsule that protects bacilli from phagocytic killing during infection. The enzyme CapD generates amide bonds with peptidoglycan cross-bridges to anchor capsular material within the cell wall envelope of B. anthracis. The capsular biosynthetic pathway is essential for virulence during anthrax infections and can be targeted for anti-infective inhibition with small molecules. Here, we present the crystal structures of the {gamma}-glutamyltranspeptidase CapD with and without {alpha}-l-Glu-l-Glu dipeptide, a non-hydrolyzable analog of poly-{gamma}-d-glutamic acid, in the active site. Purified CapD displays transpeptidation activity in vitro, and its structure reveals an active site broadly accessible for poly-{gamma}-glutamate binding and processing. Using structural and biochemical information, we derive a mechanistic model for CapD catalysis whereby Pro{sup 427}, Gly{sup 428}, and Gly{sup 429} activate the catalytic residue of the enzyme, Thr{sup 352}, and stabilize an oxyanion hole via main chain amide hydrogen bonds.
Crystal structure of the Nogo-receptor-2.
Semavina, Mariya; Saha, Nayanendu; Kolev, Momchil V; Goldgur, Yehuda; Giger, Roman J; Himanen, Juha P; Nikolov, Dimitar B
The inhibition of axon regeneration upon mechanical injury is dependent on interactions between Nogo receptors (NgRs) and their myelin-derived ligands. NgRs are composed of a leucine-rich repeat (LRR) region, thought to be structurally similar among the different isoforms of the receptor, and a divergent "stalk" region. It has been shown by others that the LRR and stalk regions of NgR1 and NgR2 have distinct roles in conferring binding affinity to the myelin associated glycoprotein (MAG) in vivo. Here, we show that purified recombinant full length NgR1 and NgR2 maintain significantly higher binding affinity for purified MAG as compared to the isolated LRR region of either NgR1 or NgR2. We also present the crystal structure of the LRR and part of the stalk regions of NgR2 and compare it to the previously reported NgR1 structure with respect to the distinct signaling properties of the two receptor isoforms. PMID:21308849
Crystal structure of the channelrhodopsin light-gated cation channel
Kato, Hideaki E.; Zhang, Feng; Yizhar, Ofer; Ramakrishnan, Charu; Nishizawa, Tomohiro; Hirata, Kunio; Ito, Jumpei; Aita, Yusuke; Tsukazaki, Tomoya; Hayashi, Shigehiko; Hegemann, Peter; Maturana, Andrés D.; Ishitani, Ryuichiro; Deisseroth, Karl; Nureki, Osamu
Channelrhodopsins (ChRs) are light-gated cation channels derived from algae that have shown experimental utility in optogenetics; for example, neurons expressing ChRs can be optically controlled with high temporal precision within systems as complex as freely moving mammals. Although ChRs have been broadly applied to neuroscience research, little is known about the molecular mechanisms by which these unusual and powerful proteins operate. Here we present the crystal structure of a ChR (a C1C2 chimaera between ChR1 and ChR2 from Chlamydomonas reinhardtii) at 2.3 Å resolution. The structure reveals the essential molecular architecture of ChRs, including the retinal-binding pocket and cation conduction pathway. This integration of structural and electrophysiological analyses provides insight into the molecular basis for the remarkable function of ChRs, and paves the way for the precise and principled design of ChR variants with novel properties. PMID:22266941
Crystal and magnetic structures of hexagonal YMnO3.
Howard, Christopher J; Campbell, Branton J; Stokes, Harold T; Carpenter, Michael A; Thomson, Richard I
The available data on the structural and magnetic transitions in multiferroic hexagonal YMnO3 have been reviewed, first making use of the computer programs from the group theoretical ISOTROPY software suite to list possible crystal and magnetic structures, then taking into account the capability of neutron diffraction and other physical methods to distinguish them. This leads to a clear view of the transformation sequence, as follows. Hexagonal YMnO3 is paraelectric in P63/mmc at elevated temperatures, and undergoes a single structural transition on cooling through 1250?K to a ferrielectric phase in P63cm that is retained through room temperature. At a much lower temperature, 70?K, there is a magnetic transition from paramagnetic to a triangular antiferromagnetic arrangement, most likely with symmetry P63'cm'. Comment is made on the unusual coupling of ferroelectric and magnetic domains reported to occur in this material, as well as on the so-called `giant magneto-elastic' effect. PMID:24253077
Crystal structure of complex natural aluminum magnesium calcium iron oxide
NASA Astrophysics Data System (ADS)
Rastsvetaeva, R. K.; Aksenov, S. M.; Verin, I. A.
The structure of a new natural oxide found near the Tashelga River (Eastern Siberia) was studied by X-ray diffraction. The pseudo-orthorhombic unit cell parameters are a = 5.6973(1) Å, b = 17.1823(4) Å, c = 23.5718(5) Å, ? = 90°, sp. gr. Pc. The structure was refined to R = 0.0516 based on 4773 reflections with | F| > 7?( F) taking into account the twin plane perpendicular to the z axis (the twin components are 0.47 and 0.53). The crystal-chemical formula ( Z = 4) is Ca2Mg{2/IV}Fe{2/(2+)IV}[Al{14/VI}O31(OH)][Al{2/IV}O][AlIV]ALIV(OH)], where the Roman numerals designate the coordination of the atoms. The structure of the mineral is based on wide ribbons of edge-sharing Al octahedra (an integral part of the spinel layer). The ribbons run along the shortest x axis and are inclined to the y and z axes. The adjacent ribbons are shifted with respect to each other along the y axis, resulting in the formation of step-like layers in which the two-ribbon thickness alternates with the three-ribbon thickness. Additional Al octahedra and Mg and Fe2+ tetrahedra are located between the ribbons. The layers are linked together to form a three-dimensional framework by Al tetrahedra, Ca polyhedra, and hydrogen bonds with the participation of OH groups.
Symmetry analysis in neutron diffraction studies of magnetic structures 1. A phase transition concept to describe magnetic structures in crystals
Yu. A. Izyumov; V. E. Naish
On the basis of phase transition symmetry theory there has been developed an efficient method of calculating the possible magnetic structures liable to arise from the paramagnetic phase of the crystal. Every magnetic structure is described by the superposition of the basis functions of the irreducible representation incorporated in the magnetic representation of the crystal symmetry group. Convenient formulas are
Likelihood-based modification of experimental crystal structure electron density maps
Terwilliger, Thomas C. (Sante Fe, NM)
A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.
Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe
Bulfer, Stacie L.; Hendershot, Jenna M.; Trievel, Raymond C. (Michigan); (UCSF)
Lysine biosynthesis in fungi, euglena, and certain archaebacteria occurs through the {alpha}-aminoadipate pathway. Enzymes in the first steps of this pathway have been proposed as potential targets for the development of antifungal therapies, as they are absent in animals but are conserved in several pathogenic fungi species, including Candida, Cryptococcus, and Aspergillus. One potential antifungal target in the {alpha}-aminoadipate pathway is the third enzyme in the pathway, homoisocitrate dehydrogenase (HICDH), which catalyzes the divalent metal-dependent conversion of homoisocitrate to 2-oxoadipate (2-OA) using nicotinamide adenine dinucleotide (NAD{sup +}) as a cofactor. HICDH belogns to a family of {beta}-hydroxyacid oxidative decarboxylases that includes malate dehydrogenase, tartrate dehydrogenase, 6-phosphogluconate dehydrogenase, isocitrate dehydrogenase (ICDH), and 3-isopropylmalte dehydrogenase (IPMDH). ICDH and IPMDH are well-characterized enzymes that catalyze the decarboxylation of isocitrate to yield 2-oxoglutarate (2-OG) in the citric acid cycle and the conversion of 3-isopropylmalate to 2-oxoisovalerate in the leucine biosynthetic pathway, respectively. Recent structural and biochemical studies of HICDH reveal that this enzyme shares sequence, structural, and mechanistic homology with ICDH and IPMDH. To date, the only published structures of HICDH are from the archaebacteria Thermus thermophilus (TtHICDH). Fungal HICDHs diverge from TtHICDH in several aspects, including their thermal stability, oligomerization state, and substrate specificity, thus warranting further characterization. To gain insights into these differences, they determined crystal structures of a fungal Schizosaccharomyces pombe HICDH (SpHICDH) as an apoenzyme and as a binary complex with additive tripeptide glycyl-glycyl-glycine (GGG) to 1.55 {angstrom} and 1.85 {angstrom} resolution, respectively. Finally, a comparison of the SpHICDH and TtHICDH structures reveal differences in their active sites that help explain the variations in their respective substrate specificities.
Local RNA structural changes induced by crystallization are revealed by SHAPE
Vicens, Quentin; Gooding, Anne R.; Laederach, Alain; Cech, Thomas R.
We present a simple approach to locate sites that undergo conformational changes upon crystallization by comparative structural mapping of the same RNA in three different environments. As a proof of principle, we probed the readily crystallized P4–P6?C209 domain from the Tetrahymena thermophila group I intron in a native solution, in a solution mimicking the crystallization drop, and in crystals. We chose the selective 2?-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, which monitors the flexibility and the conformation of each nucleotide. First, SHAPE successfully revealed the structural changes that occur during the crystallization process. Specifically, 64% of the nucleotides implicated in packing contacts and present in the portion of the molecule analyzed were identified. Second, reactivity differences for some of these nucleotides were already observed in the crystallization solution, suggesting that the crystallization buffer locked down a particular structure that was favorable to crystal formation. Third, the probing of a known structure extends our understanding of the structural basis for the SHAPE reaction by suggesting that reactivity is enhanced by a C2?-endo sugar pucker. Furthermore, by identifying local conformational changes of the RNA that take place during crystallization, SHAPE could be combined with the in vitro selection of stable mutants to rationalize the design of RNA candidates for crystallization. PMID:17299128
Influence of a random field on particle fractionation and solidification in liquid-crystal colloid mixtures.
Popa-Nita, V; van der Schoot, P; Kralj, S
The influence of a random-anisotropy (RA) type disorder on the phase separation of nematogen-colloid mixtures is studied theoretically by combining the phenomenological Landau-de Gennes, Carnahan-Starling, and hard-sphere crystal theories. We assume that the colloids enforce the RA disorder on the surrounding thermotropic liquid-crystal (LC) molecules. We adopt the Imry-Ma argument according to which the lower-temperature phase exhibits a domain-type pattern. The colloids impose a finite degree of orientational ordering even in the isotropic (paranematic) phase. In the ordered phase they give rise to a domain-type structure, resulting in the distorted nematic (speronematic) phase. The RA field opposes the phase separation tendency. With increasing disorder the difference between the paranematic and speronematic ordering decreases. Consequently there is a critical disorder, above which both phases become identical from the orientation point of view, but have different concentrations of colloids. We have also estimated another characteristic value of disorder above which the isotropic phase can exist only in a liquid state, the crystal phase being suppressed completely. PMID:17186160
Shock-Wave Structure in a Gas Containing Ablating Particles
Ali Hasan Nayfeh
The one-dimensional equations governing the structure of a shock wave in a mixture of a gas and an ablating dust using the transfer properties for free molecular flow are derived. The analysis takes into account the simultaneous effects of the solid particle drag, convective heat transfer, and ablation. These equations are programmed for numerical solution on an IBM 7094. The
Magnetic particles confined in a modulated channel: structural transitions tunable by tilting a magnetic field
J. E. Galván-Moya; D. Lucena; W. P. Ferreira; F. M. Peeters
The ground state of colloidal magnetic particles in a modulated channel are investigated as function of the tilt angle of an applied magnetic field. The particles are confined by a parabolic potential in the transversal direction while in the axial direction a periodic substrate potential is present. By using Monte Carlo (MC) simulations, we construct a phase diagram for the different crystal structures as a function of the magnetic field orientation, strength of the modulated potential and the commensurability factor of the system. Interestingly, we found first and second order phase transitions between different crystal structures, which can be manipulated by the orientation of the external magnetic field. A re-entrant behavior is found between two- and four-chain configurations, with continuous second order transitions. Novel configurations are found consisting of frozen in solitons. By changing the orientation and/or strength of the magnetic field and/or the strength and the spatial frequency of the periodic substrate potential, the system transits through different phases.
Synthesis, crystal growth, structural, optical, thermal and mechanical properties of novel organic NLO material: Ammonium malate
G. Anandha babu; G. Bhagavannarayana; P. Ramasamy
Ammonium malate (AM), an organic nonlinear optical material, has been synthesized and single crystals, with dimensions up to 38×35×27mm3, have been grown from aqueous solution. The crystal structure of AM has been determined, and it belongs to the non-centro symmetric space group Cc. The structural perfection of the grown crystals has been analysed by high-resolution X-ray diffraction (HRXRD) rocking curve
Multiple solvent crystal structures of ribonuclease A: An assessment of the method
Dechene, Michelle; Wink, Glenna; Smith, Mychal; Swartz, Paul; Mattos, Carla; (NCSU)
The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.
Advanced piezoelectric crystal Ca3TaGa3Si2O14: growth, crystal structure perfection, and acoustic properties
NASA Astrophysics Data System (ADS)
Roshchupkin, Dmitry; Ortega, Luc; Plotitcyna, Olga; Erko, Alexei; Zizak, Ivo; Irzhak, Dmitry; Fahrtdinov, Rashid; Buzanov, Oleg
A five-component crystal of the lanthanum-gallium silicate family Ca3TaGa3Si2O14 (CTGS) was grown by the Czochralski method. The CTGS crystal, like the langasite crystal (La3Ga5SiO14, LGS), possesses unique temperature properties and the fewer number of the Ga atoms in the unit cell makes the density much lower and, consequently, increases the velocity of acoustic wave propagation. The unit-cell parameters were determined by the powder diffraction technique. The defects in the CTGS crystal structure were studied by X-ray topography, which enables the visualization of growth banding characteristics of crystals grown by the Czochralski method. Surface acoustic wave (SAW) propagation in the CTGS crystal was investigated by the high-resolution X-ray diffraction method on the BESSY II synchrotron radiation source. The velocities of propagation and power flow angles of SAWs in the Y- and X-cuts of the CTGS crystal were determined from the X-ray diffraction spectra.