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0708.0840 | Luciano da Fontoura Costa | Luis Enrique Correa da Rocha and Luciano da Fontoura Costa | Multiple complex networks emerging from individual interactions | 26 pages, 14 figures. A working manuscript, comments welcomed | null | null | null | physics.bio-ph physics.comp-ph | null | Systems composed of distinct complex networks are present in many real-world
environments, from society to ecological systems. In the present paper, we
propose a network model obtained as a consequence of interactions between two
species (e.g. predator and prey). Fields are produced and sensed by the
individuals, defining spatio-temporal patterns which are strongly affected by
the attraction intensity between individuals from the same species. The
dynamical evolution of the system, including the change of individuals between
different clusters, is investigated by building two complex networks having the
individuals as nodes. In the first network, the edge weight is given by the
Euclidean distance between every two individuals and, in the case of the second
network, by the amount of time two individuals stay close one another. A third
network is obtained from the two previous networks whose nodes correspond to
the spatially congruent groups. The system evolves to an organized state where
Gaussian and scale-free-like strength distributions emerge, respectively, in
the predator and prey networks. Such a different connectivity is mainly a
consequence of preys elimination. Some configurations favor the survival of
preys or higher efficiency of predator activity.
| 2007-08-08 |
0708.0862 | Jun-nosuke Teramae | Jun-nosuke Teramae and Tomoki Fukai | Reliability of temporal coding on pulse-coupled networks of oscillators | 4 pages, 3 figures | null | null | null | nlin.AO cond-mat.dis-nn q-bio.NC | null | We study the reliability of spike output in a general class of pulse-coupled
oscillators receiving a fluctuating input. Showing that this problem is
equivalent to noise-induced synchronization between identical networks of
oscillators, we employ the phase reduction method to analytically derive the
average Lyapunov exponent of the synchronized state. We show that a transition
occurs between reliable and unreliable responses at a critical coupling
strength, which is determined through the competition between the external
input and recurrent input. To our surprise, the critical value does not depend
on intrinsic properties of oscillators.
| 2007-08-08 |
0708.0987 | Ping Ao | P Ao | Darwinian Dynamics Implies Developmental Ascendency | 3 pages, latex | Biological Theory 2 (1) (2007) 113-115 | null | null | q-bio.PE q-bio.OT | null | A tendency in biological theorizing is to formulate principles above or equal
to Evolution by Variation and Selection of Darwin and Wallace. In this letter I
analyze one such recent proposal which did so for the developmental ascendency.
I show that though the idea of developmental ascendency is brilliant, this is
in wrong order in the hierarchical structure of biological theories and can
easily generate confusing. Several other examples are also briefly discussed in
the note added.
| 2007-08-08 |
0708.1067 | Debashish Chowdhury | Tripti Tripathi and Debashish Chowdhury | Interacting RNA polymerase motors on DNA track: effects of traffic
congestion and intrinsic noise on RNA synthesis | 13 pages, including 6 EPS figures; accepted for publication in
Physical Review E | Physical Review E 77, 011921 (2008) | 10.1103/PhysRevE.77.011921 | null | physics.bio-ph q-bio.BM | null | RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA)
strand which is complementary to a single-stranded DNA template. From the
perspective of physicists, an RNAP is a molecular motor that utilizes chemical
energy input to move along the track formed by a DNA. In many circumstances,
which are described in this paper, a large number of RNAPs move simultaneously
along the same track; we refer to such collective movements of the RNAPs as
RNAP traffic. Here we develop a theoretical model for RNAP traffic by
incorporating the steric interactions between RNAPs as well as the
mechano-chemical cycle of individual RNAPs during the elongation of the mRNA.
By a combination of analytical and numerical techniques, we calculate the rates
of mRNA synthesis and the average density profile of the RNAPs on the DNA
track. We also introduce, and compute, two new measures of fluctuations in the
synthesis of RNA. Analyzing these fluctuations, we show how the level of {\it
intrinsic noise} in mRNA synthesis depends on the concentrations of the RNAPs
as well as on those of some of the reactants and the products of the enzymatic
reactions catalyzed by RNAP. We suggest appropriate experimental systems and
techniques for testing our theoretical predictions.
| 2008-02-06 |
0708.1136 | Zeba Wunderlich | Zeba Wunderlich, Leonid A. Mirny | Spatial effects on the speed and reliability of protein-DNA search | 16 pages, 4 figures | Nucleic Acids Res. 2008 May 3 | 10.1093/nar/gkn173 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Strong experimental and theoretical evidence shows that transcription factors
and other specific DNA-binding proteins find their sites using a two-mode
search: alternating between 3D diffusion through the cell and 1D sliding along
the DNA. We consider the role spatial effects in the mechanism on two different
scales. First, we reconcile recent experimental findings by showing that the 3D
diffusion of the transcription factor is often local, i.e. the transcription
factor lands quite near its dissociation site. Second, we discriminate between
two types of searches: global searches and local searches. We show that these
searches differ significantly in average search time and the variability of
search time. Using experimentally measured parameter values, we also show that
1D and 3D search is not optimally balanced, leading to much larger estimates of
search time. Together, these results lead to a number of biological
implications including suggestions of how prokaryotes and eukaryotes achieve
rapid gene regulation and the relationship between the search mechanism and
noise in gene expression.
| 2008-06-11 |
0708.1173 | Nikolai Rulkov | Nikolai F. Rulkov | A Map-Based Model of the Cardiac Action Potential | 6 pages, 9 figures, submitted to PRE | null | null | null | q-bio.CB | null | A discrete time model that is capable of replicating the basic features of
cardiac cell action potentials is suggested. The paper shows how the map-based
approaches can be used to design highly efficient computational models
(algorithms) that enable large-scale simulations and analysis of discrete
network models of cardiac activity.
| 2007-08-10 |
0708.1256 | Jose-Luis Aragon | J. L\'opez-Sauceda and J.L. Arag\'on | Eutacticity in sea urchin evolution | 17 pages, 6 figures | Bulletin of Mathematical Biology, 70 (2008) 625-634 | 10.1007/s11538-007-9273-2 | null | q-bio.QM | null | An eutactic star, in a n-dimensional space, is a set of N vectors which can
be viewed as the projection of N orthogonal vectors in a N-dimensional space.
By adequately associating a star of vectors to a particular sea urchin we
propose that a measure of the eutacticity of the star constitutes a measure of
the regularity of the sea urchin. Then we study changes of regularity
(eutacticity) in a macroevolutive and taxonomic level of sea urchins belonging
to the Echinoidea Class. An analysis considering changes through geological
time suggests a high degree of regularity in the shape of these organisms
through their evolution. Rare deviations from regularity measured in
Holasteroida order are discussed.
| 2021-11-05 |
0708.1341 | David Hsu | David Hsu, Murielle Hsu, He Huang and Erwin B. Montgomery, Jr | An algorithm for detecting oscillatory behavior in discretized data: the
damped-oscillator oscillator detector | 20 pages, 6 figures | null | null | null | q-bio.QM q-bio.NC | null | We present a simple algorithm for detecting oscillatory behavior in discrete
data. The data is used as an input driving force acting on a set of simulated
damped oscillators. By monitoring the energy of the simulated oscillators, we
can detect oscillatory behavior in data. In application to in vivo deep brain
basal ganglia recordings, we found sharp peaks in the spectrum at 20 and 70 Hz.
The algorithm is also compared to the conventional fast Fourier transform and
circular statistics techniques using computer generated model data, and is
found to be comparable to or better than fast Fourier transform in test cases.
Circular statistics performed poorly in our tests.
| 2012-08-27 |
0708.1439 | Walton Gutierrez | Walton R. Gutierrez | The Optimal Form of Distribution Networks Applied to the Kidney and Lung | 12 pages, 6 figures | null | null | null | q-bio.TO q-bio.QM | null | A model is proposed to minimize the total volume of the main distribution
networks of fluids in relation to the organ form. The minimization analysis
shows that the overall exterior form of distribution networks is a modified
ellipsoid, a geometric form that is a good approximation to the external
anatomy of the kidney and lung. The variational procedure implementing this
minimization is similar to the traditional isoperimetric theorems of geometry.
A revised version of this preprint that expands Section 4 will be published
in the Journal of Biological Systems, World Scientific Publishing.
| 2007-08-13 |
0708.1449 | Hendrik Ulbricht | Sarayut Deachapunya, Paul J. Fagan, Andras G. Major, Elisabeth Reiger,
Helmut Ritsch, Andre Stefanov, Hendrik Ulbricht and Markus Arndt | Slow beams of massive molecules | 7 pages, 6 figures | Eur. Phys. J. D 46, 307 (2008) | 10.1140/epjd/e2007-00301-8 | null | quant-ph physics.atm-clus physics.bio-ph physics.chem-ph | null | Slow beams of neutral molecules are of great interest for a wide range of
applications, from cold chemistry through precision measurements to tests of
the foundations of quantum mechanics. We report on the quantitative observation
of thermal beams of perfluorinated macromolecules with masses up to 6000 amu,
reaching velocities down to 11 m/s. Such slow, heavy and neutral molecular
beams are of importance for a new class of experiments in matter-wave
interferometry and we also discuss the requirements for further manipulation
and cooling schemes with molecules in this unprecedented mass range.
| 2009-11-13 |
0708.1598 | HC Paul Lee | Sing-Guan Kong, Hong-Da Chen, Wen-Lang Fan, Jan Wigger, Andrew Torda,
and HC Lee | Genomes: at the edge of chaos with maximum information capacity | 4 pages, 3 figures, paper | null | null | null | q-bio.GN | null | We propose an order index, phi, which quantifies the notion of ``life at the
edge of chaos'' when applied to genome sequences. It maps genomes to a number
from 0 (random and of infinite length) to 1 (fully ordered) and applies
regardless of sequence length. The 786 complete genomic sequences in GenBank
were found to have phi values in a very narrow range, 0.037+/-0.027. We show
this implies that genomes are halfway towards being completely random, namely,
at the edge of chaos. We argue that this narrow range represents the
neighborhood of a fixed-point in the space of sequences, and genomes are driven
there by the dynamics of a robust, predominantly neutral evolution process.
| 2007-08-14 |
0708.1637 | Thimo Rohlf | Thimo Rohlf | Self-organization of heterogeneous topology and symmetry breaking in
networks with adaptive thresholds and rewiring | 4 pages revtex, 6 figures | null | 10.1209/0295-5075/84/10004 | null | cond-mat.dis-nn cond-mat.stat-mech nlin.AO q-bio.MN | null | We study an evolutionary algorithm that locally adapts thresholds and wiring
in Random Threshold Networks, based on measurements of a dynamical order
parameter. A control parameter $p$ determines the probability of threshold
adaptations vs. link rewiring. For any $p < 1$, we find spontaneous symmetry
breaking into a new class of self-organized networks, characterized by a much
higher average connectivity $\bar{K}_{evo}$ than networks without threshold
adaptation ($p =1$). While $\bar{K}_{evo}$ and evolved out-degree distributions
are independent from $p$ for $p <1$, in-degree distributions become broader
when $p \to 1$, approaching a power-law. In this limit, time scale separation
between threshold adaptions and rewiring also leads to strong correlations
between thresholds and in-degree. Finally, evidence is presented that networks
converge to self-organized criticality for large $N$.
| 2009-11-13 |
0708.1746 | Attila Szolnoki | Matjaz Perc and Attila Szolnoki | Social diversity and promotion of cooperation in the spatial prisoner's
dilemma game | 5 two-column pages, 5 figures | Phys. Rev. E 77 (2008) 011904 | 10.1103/PhysRevE.77.011904 | null | physics.soc-ph physics.gen-ph q-bio.PE | null | The diversity in wealth and social status is present not only among humans,
but throughout the animal world. We account for this observation by generating
random variables that determ ine the social diversity of players engaging in
the prisoner's dilemma game. Here the term social diversity is used to address
extrinsic factors that determine the mapping of game pay offs to individual
fitness. These factors may increase or decrease the fitness of a player
depending on its location on the spatial grid. We consider different
distributions of extrin sic factors that determine the social diversity of
players, and find that the power-law distribution enables the best promotion of
cooperation. The facilitation of the cooperative str ategy relies mostly on the
inhomogeneous social state of players, resulting in the formation of
cooperative clusters which are ruled by socially high-ranking players that are
able to prevail against the defectors even when there is a large temptation to
defect. To confirm this, we also study the impact of spatially correlated
social diversity and find that coopera tion deteriorates as the spatial
correlation length increases. Our results suggest that the distribution of
wealth and social status might have played a crucial role by the evolution of
cooperation amongst egoistic individuals.
| 2008-03-29 |
0708.1781 | Eduardo Candelario-Jalil | A. Gonzalez-Falcon, E. Candelario-Jalil, M. Garcia-Cabrera, O. S. Leon | Effects of pyruvate administration on infarct volume and neurological
deficits following permanent focal cerebral ischemia in rats | null | Brain Research 990(1-2): 1-7 (2003) | null | null | q-bio.TO | null | Recent experimental evidences indicate that pyruvate, the final metabolite of
glycolysis, has a remarkable protective effect against different types of brain
injury. The purpose of this study was to assess the neuroprotective effect and
the neurological outcome after pyruvate administration in a model of ischemic
stroke induced by permanent middle cerebral artery occlusion (pMCAO) in rats.
Three doses of pyruvate (250, 500 and 1000 mg/kg, i.p.) or vehicle were
administered intraperitoneally 30 min after pMCAO. In other set of experiments,
pyruvate was given either before, immediately after ischemia or in a long-term
administration paradigm. Functional outcome, mortality and infarct volume were
determined 24 h after stroke. Even when the lowest doses of pyruvate reduced
mortality and neurological deficits, no concomitant reduction in infarct volume
was observed. The highest dose of pyruvate increased cortical infarction by 27%
when administered 30 min after pMCAO. In addition, when pyruvate was given
before pMCAO, a significant increase in neurological deficits was noticed.
Surprisingly, on the contrary of what was found in the case of transient global
ischemia, present findings do not support a great neuroprotective role for
pyruvate in permanent focal cerebral ischemia, suggesting two distinct
mechanisms involved in the effects of this glycolytic metabolite in the
ischemic brain.
| 2007-08-15 |
0708.1791 | Joshua Shaevitz | Joshua W. Shaevitz, Daniel A. Fletcher | Load fluctuations drive actin network growth | To be published in PNAS | null | 10.1073/pnas.0702601104 | null | physics.bio-ph | null | The growth of actin filament networks is a fundamental biological process
that drives a variety of cellular and intracellular motions. During motility,
eukaryotic cells and intracellular pathogens are propelled by actin networks
organized by nucleation-promoting factors, which trigger the formation of
nascent filaments off the side of existing filaments in the network. A Brownian
ratchet (BR) mechanism has been proposed to couple actin polymerization to
cellular movements, whereby thermal motions are rectified by the addition of
actin monomers at the end of growing filaments. Here, by following
actin--propelled microspheres using three--dimensional laser tracking, we find
that beads adhered to the growing network move via an object--fluctuating BR.
Velocity varies with the amplitude of thermal fluctuation and inversely with
viscosity as predicted for a BR. In addition, motion is saltatory with a broad
distribution of step sizes that is correlated in time. These data point to a
model in which thermal fluctuations of the microsphere or entire actin network,
and not individual filaments, govern motility. This conclusion is supported by
Monte Carlo simulations of an adhesion--based BR and suggests an important role
for membrane tension in the control of actin--based cellular protrusions.
| 2009-11-13 |
0708.1794 | Jan Karbowski | Jan Karbowski, Gary Schindelman, Chris J. Cronin, Adeline Seah, Paul
W. Sternberg | Systems level circuit model of C. elegans undulatory locomotion:
mathematical modeling and molecular genetics | Neural control of C. elegans motion with genetic perturbations | Journal of Computational Neuroscience 24, 253-276 (2008) | null | null | q-bio.NC q-bio.GN | null | To establish the relationship between locomotory behavior and dynamics of
neural circuits in the nematode C. elegans we combined molecular and
theoretical approaches. In particular, we quantitatively analyzed the motion of
C. elegans with defective synaptic GABA and acetylcholine transmission,
defective muscle calcium signaling, and defective muscles and cuticle
structures, and compared the data with our systems level circuit model. The
major experimental findings are: (i) anterior-to-posterior gradients of body
bending flex for almost all strains both for forward and backward motion, and
for neuronal mutants, also analogous weak gradients of undulatory frequency,
(ii) existence of some form of neuromuscular (stretch receptor) feedback, (iii)
invariance of neuromuscular wavelength, (iv) biphasic dependence of frequency
on synaptic signaling, and (v) decrease of frequency with increase of the
muscle time constant. Based on (i) we hypothesize that the Central Pattern
Generator (CPG) is located in the head both for forward and backward motion.
Points (i) and (ii) are the starting assumptions for our theoretical model,
whose dynamical patterns are qualitatively insensitive to the details of the
CPG design if stretch receptor feedback is sufficiently strong and slow. The
model reveals that stretch receptor coupling in the body wall is critical for
generation of the neuromuscular wave. Our model agrees with our behavioral
data(iii), (iv), and (v), and with other pertinent published data, e.g., that
frequency is an increasing function of muscle gap-junction coupling.
| 2008-06-10 |
0708.1802 | Vijay Kumar Krishna Murthy | K. Vijay Kumar, Sriram Ramaswamy, Madan Rao | Active elastic dimers: self-propulsion and current reversal on a
featureless track | 4 pages | null | null | null | cond-mat.stat-mech cond-mat.soft q-bio.BM | null | We present a Brownian inchworm model of a self-propelled elastic dimer in the
absence of an external potential. Nonequilibrium noise together with a
stretch-dependent damping form the propulsion mechanism. Our model connects
three key nonequilibrium features -- position-velocity correlations, a nonzero
mean internal force, and a drift velocity. Our analytical results, including
striking current reversals, compare very well with numerical simulations. The
model unifies the propulsion mechanisms of DNA helicases, polar rods on a
vibrated surface, crawling keratocytes and Myosin VI. We suggest experimental
realizations and tests of the model.
| 2011-11-10 |
0708.1823 | Francoise Heres-Renzetti | V. Petrenko, J. Brigati, J. Sykora, Eric V. Olsen, I. Sorokulova, G.
Kouzmitcheva, I-Hsuan Chen, J. Barbaree, B. Chin, V. Vodyanoy | Landscape phage, phage display, stripped phage, biosensors, detection,
affinity reagent, nanotechnology, Salmonella typhimurium, Bacillus anthracis | Submitted on behalf of TIMA Editions
(http://irevues.inist.fr/tima-editions) | Dans European Nano Systems Worshop - ENS 2005, Paris : France
(2005) | null | null | cond-mat.mtrl-sci q-bio.CB | null | Filamentous phage, such as fd used in this study, are thread-shaped bacterial
viruses. Their outer coat is a tube formed by thousands equal copies of the
major coat protein pVIII. We constructed libraries of random peptides fused to
all pVIII domains and selected phages that act as probes specific for a panel
of test antigens and biological threat agents. Because the viral carrier is
infective, phage borne bio-selective probes can be cloned individually and
propagated indefinitely without needs of their chemical synthesis or
reconstructing. We demonstrated the feasibility of using landscape phages and
their stripped fusion proteins as new bioselective materials that combine
unique characteristics of affinity reagents and self assembling membrane
proteins. Biorecognition layers fabricated from phage-derived probes bind
biological agents and generate detectable signals. The performance of
phage-derived materials as biorecognition films was illustrated by detection of
streptavidin-coated beads, Bacillus anthracis spores and Salmonella typhimurium
cells. With further refinement, the phage-derived analytical platforms for
detecting and monitoring of numerous threat agents may be developed, since the
biodetector films may be obtained from landscape phages selected against any
bacteria, virus or toxin. As elements of field-use detectors, they are superior
to antibodies, since they are inexpensive, highly specific and strong binders,
resistant to high temperatures and environmental stresses.
| 2007-08-15 |
0708.1839 | Francoise Heres-Renzetti | Satoshi Hiyama, Y. Isogawa, T. Suda, Y. Moritani, Kazuo Sutoh | A Design of an Autonomous Molecule Loading/Transporting/Unloading System
Using DNA Hybridization and Biomolecular Linear Motors | Submitted on behalf of TIMA Editions
(http://irevues.inist.fr/tima-editions) | Dans European Nano Systems Worshop - ENS 2005, Paris : France
(2005) | null | null | physics.bio-ph q-bio.MN | null | This paper describes a design of a molecular propagation system in molecular
communication. Molecular communication is a new communication paradigm where
biological and artificially-created nanomachines communicate over a short
distance using molecules. A molecular propagation system in molecular
communication directionally transports molecules from a sender to a receiver.
In the design described in this paper, protein filaments glide over immobilized
motor proteins along preconfigured microlithographic tracks, and the gliding
protein filaments carry and transport molecules from a sender to a receiver. In
the design, DNA hybridization is used to load and unload the molecules onto and
from the carriers at a sender and a receiver. In the design,
loading/transporting/unloading processes are autonomous and require no external
control.
| 2007-08-15 |
0708.1840 | Francoise Heres-Renzetti | Mustapha Hamdi (LVR), Gaurav Sharma, A. Ferreira (LVR), Constantinos
Mavroidis | Prototyping Bio-Nanorobots using Molecular Dynamics Simulation | Submitted on behalf of TIMA Editions
(http://irevues.inist.fr/tima-editions) | Dans European Nano Systems Worshop - ENS 2005, Paris : France
(2005) | null | null | physics.bio-ph | null | This paper presents a molecular mechanics study using a molecular dynamics
software (NAMD) coupled to virtual reality (VR) techniques for intuitive
Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the
operator can design and characterize through physical simulation and 3-D
visualization the behavior of Bio-NanoRobotic components and structures. The
main novelty of the proposed simulations is based on the characterization of
stiffness performances of passive joints-based deca-alanine protein molecule
and active joints-based viral protein motor (VPL) in their native environment.
Their use as elementary Bio-NanoRobotic components (1 dof platform) are also
simulated and the results discussed.
| 2007-08-15 |
0708.1849 | Francoise Heres-Renzetti | Ching-Ting Lin, En-Kuang Tien, Szu-Yuan Lee, Long-Sheng Lu, Chau-Chung
Wu, Chen-Yuan Dong, Chii-Wann Lin | Effects of Ox-LDL on Macrophages NAD(P)H Autofluorescence Changes by
Two-photon Microscopy | Submitted on behalf of TIMA Editions
(http://irevues.inist.fr/tima-editions) | Dans European Nano Systems Worshop - ENS 2005, Paris : France
(2005) | null | null | physics.bio-ph | null | Ox-LDL uptakes by macrophage play a critical role in the happening of
atherosclerosis. Because of its low damage on observed cells and better
signal-to- background ratio, two-photon excitation fluorescence microscopy is
used to observe NAD(P)H autofluorescence of macrophage under difference
cultured conditions- bare cover glass, coated with fibronectin or
poly-D-lysine. The results show that the optimal condition is fibronectin
coated surface, on which, macrophages profile can be clearly identified on
NAD(P)H autofluorescence images collected by two-photon microscopy. Moreover,
different morphology and intensities of autofluorescence under different
conditions were observed as well. In the future, effects of ox-LDL on
macrophages will be investigated by purposed system to research etiology of
atherosclerosis.
| 2007-08-15 |
0708.1865 | Pan-Jun Kim | Pan-Jun Kim, Dong-Yup Lee, Tae Yong Kim, Kwang Ho Lee, Hawoong Jeong,
Sang Yup Lee, Sunwon Park | Metabolite essentiality elucidates robustness of Escherichia coli
metabolism | Supplements available at
http://stat.kaist.ac.kr/publication/2007/PJKim_pnas_supplement.pdf | Proc. Natl. Acad. Sci. USA. 104 13638 (2007) | 10.1073/pnas.0703262104 | null | q-bio.MN physics.bio-ph q-bio.QM | null | Complex biological systems are very robust to genetic and environmental
changes at all levels of organization. Many biological functions of Escherichia
coli metabolism can be sustained against single-gene or even multiple-gene
mutations by using redundant or alternative pathways. Thus, only a limited
number of genes have been identified to be lethal to the cell. In this regard,
the reaction-centric gene deletion study has a limitation in understanding the
metabolic robustness. Here, we report the use of flux-sum, which is the
summation of all incoming or outgoing fluxes around a particular metabolite
under pseudo-steady state conditions, as a good conserved property for
elucidating such robustness of E. coli from the metabolite point of view. The
functional behavior, as well as the structural and evolutionary properties of
metabolites essential to the cell survival, was investigated by means of a
constraints-based flux analysis under perturbed conditions. The essential
metabolites are capable of maintaining a steady flux-sum even against severe
perturbation by actively redistributing the relevant fluxes. Disrupting the
flux-sum maintenance was found to suppress cell growth. This approach of
analyzing metabolite essentiality provides insight into cellular robustness and
concomitant fragility, which can be used for several applications, including
the development of new drugs for treating pathogens.
| 2007-08-30 |
0708.1899 | Hernan Garcia | Hernan G. Garcia, Jan\'e Kondev, Nigel Orme, Julie A. Theriot, Rob
Phillips | A First Exposure to Statistical Mechanics for Life Scientists | 27 pages, 16 figures. Submitted to American Journal of Physics | null | null | null | q-bio.QM | null | Statistical mechanics is one of the most powerful and elegant tools in the
quantitative sciences. One key virtue of statistical mechanics is that it is
designed to examine large systems with many interacting degrees of freedom,
providing a clue that it might have some bearing on the analysis of the
molecules of living matter. As a result of data on biological systems becoming
increasingly quantitative, there is a concomitant demand that the models set
forth to describe biological systems be themselves quantitative. We describe
how statistical mechanics is part of the quantitative toolkit that is needed to
respond to such data. The power of statistical mechanics is not limited to
traditional physical and chemical problems and there are a host of interesting
ways in which these ideas can be applied in biology. This article reports on
our efforts to teach statistical mechanics to life science students and
provides a framework for others interested in bringing these tools to a
nontraditional audience in the life sciences.
| 2007-08-15 |
0708.1928 | Katja Taute | Katja M. Taute, Francesco Pampaloni, Erwin Frey and Ernst-Ludwig
Florin | Microtubule dynamics depart from wormlike chain model | 4 pages, 4 figures. Updated content, added reference, corrected typos | Physical Review Letters (2008), 100:028102. | 10.1103/PhysRevLett.100.028102 | null | q-bio.BM | null | Thermal shape fluctuations of grafted microtubules were studied using high
resolution particle tracking of attached fluorescent beads. First mode
relaxation times were extracted from the mean square displacement in the
transverse coordinate. For microtubules shorter than 10 um, the relaxation
times were found to follow an L^2 dependence instead of L^4 as expected from
the standard wormlike chain model. This length dependence is shown to result
from a complex length dependence of the bending stiffness which can be
understood as a result of the molecular architecture of microtubules. For
microtubules shorter than 5 um, high drag coefficients indicate contributions
from internal friction to the fluctuation dynamics.
| 2008-09-09 |
0708.1931 | Debanjan Chowdhury | Debanjan Chowdhury | Searching for targets on a model DNA: Effects of inter-segment hopping,
detachment and re-attachment | Final published version | International Journal of Modern Physics C 20 (6), 817-830 (2009) | 10.1142/S0129183109014023 | null | cond-mat.stat-mech q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For most of the important processes in DNA metabolism, a protein has to reach
a specific binding site on the DNA. The specific binding site may consist of
just a few base pairs while the DNA is usually several millions of base pairs
long. How does the protein search for the target site? What is the most
efficient mechanism for a successful search? Motivated by these fundamental
questions on intracellular biological processes, we have developed a model for
searching a specific site on a model DNA by a single protein. We have made a
comparative quantitative study of the efficiencies of sliding, inter-segmental
hoppings and detachment/re-attachments of the particle during its search for
the specific site on the DNA. We also introduce some new quantitative measures
of {\it efficiency} of a search process by defining a relevant quantity, which
can be measured in {\it in-vitro} experiments.
| 2010-01-10 |
0708.1936 | Hendrik Ulbricht | Hendrik Ulbricht, Martin Berninger, Sarayut Deachapunya, Andre
Stefanov and Markus Arndt | Gas phase sorting of nanoparticles | 6 pages, 5 figures | Nanotechnology 19, 045502 (2008) | 10.1088/0957-4484/19/04/045502 | null | quant-ph cond-mat.mtrl-sci physics.atm-clus physics.bio-ph physics.chem-ph | null | We discuss Stark deflectometry of micro-modulated molecular beams for the
enrichment of biomolecular isomers as well as single-wall carbon nanotubes and
we demonstrate the working principle of this idea with fullerenes. The sorting
is based on the species-dependent polarizability-to-mass ratio $\alpha/m$. The
device is compatible with a high molecular throughput, and the spatial
micro-modulation of the beam permits to obtain a fine spatial resolution and a
high sorting sensitivity.
| 2016-09-21 |
0708.1971 | Eduardo Candelario-Jalil | E. Candelario-Jalil, H. H. Ajamieh, S. Sam, G. Martinez, O. S. Leon | Nimesulide limits kainate-induced oxidative damage in the rat
hippocampus | null | European Journal of Pharmacology 390(3): 295-298 (2000) | null | null | q-bio.TO | null | Kainate induces a marked expression of cyclooxygenase-2 after its systemic
administration. Because cyclooxygenase-2 activity is associated to the
production of reactive oxygen species, we investigated the effects of
nimesulide, a selective cyclooxygenase-2 inhibitor, on kainate-induced in vivo
oxidative damage in the rat hippocampus. A clinically relevant dose of
nimesulide (6 mg/kg, i.p.) was administered three times following kainate
application (9 mg/kg, i.p.). After 24 h of kainate administration, the drastic
decrease in hippocampal glutathione content and the significant increase in
lipid peroxidation were attenuated in nimesulide-treated rats, suggesting that
the induction of cyclooxygenase-2 is involved in kainate-mediated free radicals
formation.
| 2007-08-16 |
0708.1991 | Niranjan Joshi Dr. | N. V. Joshi | Conditions for the Trivers-Willard hypothesis to be valid: A minimal
population-genetic model | 14 pages including 4 figures | Journal of Genetics, Vol 79 issue 1, page 9-15 (2000) | null | null | q-bio.PE | null | The very insightful Trivers-Willard hypothesis, proposed in the early 1970s,
states that females in good physiological conditions are more likely to produce
male offspring, when the variance of reproductive success amongst males is
high. A number of studies, aimed at its experimental verification, have found
adequate supportive evidence in its favour. Theoretical investigations,
however, have been few, perhaps because formulating a population-genetic model
for describing the Trivers-Willard hypothesis turns out to be surprisingly
complex. The present study describes a minimal population genetic model to
explore one specific scenario, viz. how is the preference for a male offspring
by females in good condition altered when 'g', the proportion of such females
in the population changes from a low to a high value. As expected, when the
proportion of such females is low, i.e., for low values of 'g', the
Trivers-Willard (TW) strategy goes to fixation against the equal investment
strategy. This holds true up to gmax, a critical value of 'g', above which the
two strategies coexist, but the proportion of the TW strategy steadily
decreases as 'g' increases to unity. Similarly, when the effect of well-endowed
males attaining disproportionately high number of matings is more pronounced,
the TW strategy is more likely to go to fixation. Interestingly, the success of
the TW strategy has a complex dependence on the variance in the physiological
condition of females. If the difference in the two types of conditions is not
large, TW strategy is favoured, and its success is more likely as the
difference increases. However, beyond a critical value of the difference, the
TW strategy is found to be less and less likely to succeed as the difference
becomes larger. Possible reasons for these effects are discussed.
| 2007-08-16 |
0708.1993 | Zhao Lu | Zhao Lu and Michael A Lee | Dynamics of glucose-lactose diauxic growth in E. coli | This paper has been withdrawn by the author because it was a part of
the author's thesis | null | null | null | q-bio.OT q-bio.CB | null | We present a mathematical model of glucose-lactose diauxic growth in
Escherichia coli including both the postive and negative regulation mechanisms
of the lactose operon as well as the inducer exclusion. To validate this model,
we first calculated the time evolution of beta-galactosidase for only the
lactose nutrient and compared the numerical results with experimental data.
Second, we compared the calculated cell biomass of the glucose-lactose diauxic
growth with the experimental optical density of the diauxic growth for a
particular E. coli MG 1655. For both cases, the numerical calculations from
this model are in good agreement with these two experiments' data. The diauxic
growth pattern of a wild type E. coli was also investigated.
| 2011-01-31 |
0708.2038 | Julius Lucks | Julius B. Lucks, David R. Nelson, Grzegorz Kudla, Joshua B. Plotkin | Genome landscapes and bacteriophage codon usage | 9 Color Figures, 5 Tables, 53 References | Lucks JB, Nelson DR, Kudla GR, Plotkin JB (2008) Genome Landscapes
and Bacteriophage Codon Usage. PLoS Computational Biology 4(2): e1000001 | 10.1371/journal.pcbi.1000001 | null | q-bio.GN | null | Across all kingdoms of biological life, protein-coding genes exhibit unequal
usage of synonmous codons. Although alternative theories abound, translational
selection has been accepted as an important mechanism that shapes the patterns
of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns
of codon usage across 74 diverse bacteriophages that infect E. coli, P.
aeruginosa and L. lactis as their primary host. We introduce the concept of a
`genome landscape,' which helps reveal non-trivial, long-range patterns in
codon usage across a genome. We develop a series of randomization tests that
allow us to interrogate the significance of one aspect of codon usage, such a
GC content, while controlling for another aspect, such as adaptation to
host-preferred codons. We find that 33 phage genomes exhibit highly non-random
patterns in their GC3-content, use of host-preferred codons, or both. We show
that the head and tail proteins of these phages exhibit significant bias
towards host-preferred codons, relative to the non-structural phage proteins.
Our results support the hypothesis of translational selection on viral genes
for host-preferred codons, over a broad range of bacteriophages.
| 2008-03-04 |
0708.2061 | Eduardo Candelario-Jalil | E. Candelario-Jalil, S. M. Al-Dalain, R. Castillo, G. Martinez, O. S.
Fernandez | Selective vulnerability to kainate-induced oxidative damage in different
rat brain regions | null | Journal of Applied Toxicology 21(5): 403-407 (2001) | null | null | q-bio.TO | null | Some markers of oxidative injury were measured in different rat brain areas
(hippocampus, cerebral cortex, striatum, hypothalamus, amygdala/piriform cortex
and cerebellum) after the systemic administration of an excitotoxic dose of
kainic acid (KA, 9 mg kg(-1) i.p.) at two different sampling times (24 and 48
h). Kainic acid was able to lower markedly (P < 0.05) the glutathione (GSH)
levels in hippocampus, cerebellum and amygdala/piriform cortex (maximal
reduction at 24 h). In a similar way, lipid peroxidation, as assessed by
malonaldehyde and 4-hydroxyalkenal levels, significantly increased (P < 0.05)
in hippocampus, cerebellum and amygdala/piriform cortex mainly at 24 h after
KA. In addition, hippocampal superoxide dismutase (SOD) activity decreased
significantly (P < 0.05) with respect to basal levels by 24 h after KA
application. On the other hand, brain areas such as hypothalamus, striatum and
cerebral cortex seem to be less susceptible to KA excitotoxicity. According to
these findings, the pattern of oxidative injury induced by systemically
administered KA seems to be highly region-specific. Further, our results have
shown that a lower antioxidant status (GSH and SOD) seems not to play an
important role in the selective vulnerability of certain brain regions because
it correlates poorly with increases in markers of oxidative damage.
| 2007-08-16 |
0708.2083 | Jie Chen | Jie Chen, Ruxandra I. Dima and D. Thirumalai | Allosteric communication in Dihydrofolate Reductase: Signaling network
and pathways for closed to occluded transition and back | 43 pages, 12 figures | null | null | null | q-bio.BM | null | E. Coli. dihydrofolate reductase (DHFR) undergoes conformational transitions
between the closed (CS) and occluded (OS) states which, respectively, describe
whether the active site is closed or occluded by the Met20 loop. A
sequence-based approach is used to identify a network of residues that
represents the allostery wiring diagram. We also use a self-organized polymer
model to monitor the kinetics of the CS->OS and the reverse transitions. a
sliding motion of Met20 loop is observed. The residues that facilitate the
Met20 loop motion are part of the network of residues that transmit allosteric
signals during the CS->OS transition.
| 2007-08-16 |
0708.2121 | Ashok Palaniappan | Ashok Palaniappan | Detection of an ancient principle and an elegant solution to the protein
classification problem | 13p | null | null | null | q-bio.GN q-bio.BM q-bio.QM | null | This work is concerned with the development of a well-founded, theoretically
justified, and least complicated metric for the classification of proteins with
reference to enzymes. As the signature of an enzyme family, a catalytic domain
is easily fingerprinted. Given that the classification problem has so far
seemed intractable, a classification schema derived from the catalytic domain
would be satisfying. Here I show that there exists a natural ab initio if
nonobvious basis to theorize that the catalytic domain of an enzyme is uniquely
informative about its regulation. This annotates its function. Based on this
hypothesis, a method that correctly classifies potassium ion channels into
their respective subfamilies is described. To put the principle on firmer
ground, extra validation was sought and obtained through co-evolutionary
analyses. The co-evolutionary analyses reveal a departure from the notion that
potassium ion channel proteins are functionally modular. This finding is
discussed in light of the prevailing notion of domain. These studies establish
that significant co-evolution of the catalytic domain of a gene with its
conjoint domain is a specialized, necessary process following fusion and
swapping events in evolution. Instances of this discovery are likely to be
found pervasive in protein science.
| 2007-08-17 |
0708.2124 | Mike Steel Prof. | Mike Steel and Allen Rodrigo | Maximum Likelihood Supertrees | 13 pages, 0 figures | null | null | null | q-bio.PE q-bio.QM | null | We analyse a maximum-likelihood approach for combining phylogenetic trees
into a larger `supertree'. This is based on a simple exponential model of
phylogenetic error, which ensures that ML supertrees have a simple
combinatorial description (as a median tree, minimising a weighted sum of
distances to the input trees). We show that this approach to ML supertree
reconstruction is statistically consistent (it converges on the true species
supertree as more input trees are combined), in contrast to the widely-used MRP
method, which we show can be statistically inconsistent under the exponential
error model. We also show that this statistical consistency extends to an ML
approach for constructing species supertrees from gene trees. In this setting,
incomplete lineage sorting (due to coalescence rates of homologous genes being
lower than speciation rates) has been shown to lead to gene trees that are
frequently different from species trees, and this can confound efforts to
reconstruct the species phylogeny correctly.
| 2007-08-17 |
0708.2141 | Shyamal Lakshminarayanan | Shyamal Lakshminarayanan | A model for exploring bird morphology | 7 pages, 1 table, 3 figures | null | null | null | q-bio.OT | null | A simplified model of the bird skeleton along with elongation parameters for
the flight feathers is used to explore the diversity of bird shapes. Varying a
small number of parameters simulates a wide range of observed bird silhouettes.
The model may serve to examine developmental factors involved, help museum
curators develop computational approaches to bird morphometry and has
applications in computer generated illustration.
| 2007-08-17 |
0708.2147 | Dalius Balciunas | Dalius Balciunas | The logistic equation and a critique of the theory of natural selection | 31 pages, 5 figures, appendix | null | null | null | q-bio.PE | null | Species coexistence is one of the central themes in modern ecology.
Coexistence is a prerequisite of biological diversity. However, the question
arises how biodiversity can be reconciled with the statement of competition
theory, which asserts that competing species cannot coexist. To solve this
problem natural selection theory is rejected because it contradicts kinetic
models of interacting populations. Biological evolution is presented as a
process equivalent to a chemical reaction. The main point is that interactions
occur between self-replicating units. Under these assumptions biodiversity is
possible if and only if species are identical with respect to the patterns of
energy flow in which individuals are involved.
| 2007-08-17 |
0708.2244 | Volkan Sevim | Volkan Sevim, Per Arne Rikvold | Unbiased Random Threshold Networks Are Chaotic or Critical | null | null | null | null | cond-mat.dis-nn cond-mat.stat-mech nlin.CG q-bio.MN | null | This paper has been withdrawn.
| 2008-05-08 |
0708.2294 | Maria A. Avino-Diaz | Maria A. Avino-Diaz | A probabilistic regulatory network for the human immune system | 9 pages | null | null | null | q-bio.CB q-bio.BM | null | In this paper we made a review of some papers about probabilistic regulatory
networks (PRN), in particular we introduce our concept of homomorphisms of PRN
with an example of projection of a regulatory network to a smaller one. We
apply the model PRN (or Probabilistic Boolean Network) to the immune system,
the PRN works with two functions. The model called ""The B/T-cells
interaction"" is Boolean, so we are really working with a Probabilistic Boolean
Network. Using Markov Chains we determine the state of equilibrium of the
immune response.
| 2007-08-20 |
0708.2308 | Takahiro Harada | Tomomi Yokogawa and Takahiro Harada | Intermittent dynamics and 1/f^beta noise in single cardiac muscle cells | 5 pages, 5 figures | null | null | null | q-bio.CB | null | Fluctuations in the spontaneous beating activity of isolated cardiac cells
were studied over a timescale of six decades. The beat dynamics of single
cardiac cells were heterogeneous and intermittent. The interbeat intervals
(IBIs) were power-law distributed in a long-time regime. Furthermore, for long
timescales up to the experimental window, the autocorrelation of IBIs exhibits
a scaling behavior of 1/f^beta-noise type. These observations suggest that
1/f^beta noise is an intrinsic characteristic of spontaneous activity of single
cardiac cells.
| 2007-08-20 |
0708.2384 | Indranil Mitra Mr | Indranil Mitra, Sisir Roy, Gary Hastings | Co-operativity in neurons and the role of noise in brain | 12 Pages, Updated Version, SPIE 2007 Conference | null | null | null | q-bio.NC q-bio.QM | null | In view of some recent results in case of the dopaminergic neurons exhibiting
long range correlations in VTA of the limbic brain we are interested to find
out whether any stochastic nonlinear response may be reproducible in the nano
scales usimg the results of quantum mechanics. We have developed a scheme to
investigate this situation in this paper by taking into consideration the
Schrodinger equation (SE) in an arbitrary manifold with a metric, which is in
some sense a special case of the heat kernel equation. The special case of this
heat kernel equation is the diffusion equation, which may reproduce some key
phenomena of the neural activities. We make a dual equivalent circuit model of
SE and incorporate non commutativity and noise inside the circuit scheme. The
behaviour of the circuit elements with interesting limits are investigated. The
most bizarre part is the long range response of the model by dint of the
Central Limit Theorem, which is responsible for coherent behaviour of a large
assembly of neurons.
| 2007-08-20 |
0708.2421 | Sergei Maslov | Sergei Maslov, I. Ispolatov | Propagation of large concentration changes in reversible protein binding
networks | 5 pages, 7 figures | Proc Nat Acad Sci U S A 104(34): 13655-13660 (2007) | 10.1073/pnas.0702905104 | null | q-bio.MN q-bio.BM | null | We study how the dynamic equilibrium of the reversible protein-protein
binding network in yeast Saccharomyces cerevisiae responds to large changes in
abundances of individual proteins. The magnitude of shifts between free and
bound concentrations of their immediate and more distant neighbors in the
network is influenced by such factors as the network topology, the distribution
of protein concentrations among its nodes, and the average binding strength.
Our primary conclusion is that, on average, the effects of a perturbation are
strongly localized and exponentially decay with the network distance away from
the perturbed node, which explains why, despite globally connected topology,
individual functional modules in such networks are able to operate fairly
independently. We also found that under specific favorable conditions, realized
in a significant number of paths in the yeast network, concentration
perturbations can selectively propagate over considerable network distances (up
to four steps). Such "action-at-a-distance" requires high concentrations of
heterodimers along the path as well as low free (unbound) concentration of
intermediate proteins.
| 2007-08-20 |
0708.2452 | Nicholas Licata | Nicholas A. Licata and Alexei V. Tkachenko | Kinetic limitations of cooperativity based drug delivery systems | 4 pages, 4 figures, v3: minor revisions | null | 10.1103/PhysRevLett.100.158102 | null | cond-mat.soft q-bio.CB | null | We study theoretically a novel drug delivery system that utilizes the
overexpression of certain proteins in cancerous cells for cell specific
chemotherapy. The system consists of dendrimers conjugated with "keys" (ex:
folic acid) which "key-lock" bind to particular cell membrane proteins (ex:
folate receptor). The increased concentration of "locks" on the surface leads
to a longer residence time for the dendrimer and greater incorporation into the
cell. Cooperative binding of the nanocomplexes leads to an enhancement of cell
specificity. However, both our theory and detailed analysis of in-vitro
experiments indicate that the degree of cooperativity is kinetically limited.
We demonstrate that cooperativity and hence the specificity to particular cell
type can be increased by making the strength of individual bonds weaker, and
suggest a particular implementation of this idea. The implications of the work
for optimizing the design of drug delivery vehicles are discussed.
| 2009-11-13 |
0708.2527 | Ping Xie | Ping Xie | Model for processive nucleotide and repeat additions by the telomerase | 28 pages, 5 figures | null | null | null | q-bio.BM | null | A model is presented to describe the nucleotide and repeat addition
processivity by the telomerase. In the model, the processive nucleotide
addition is implemented on the basis of two requirements: One is that stem IV
loop stimulates the chemical reaction of nucleotide incorporation, and the
other one is the existence of an ssRNA-binding site adjacent to the polymerase
site that has a high affinity for the unpaired base of the template. The
unpairing of DNA:RNA hybrid after the incorporation of the nucleotide paired
with the last base on the template, which is the prerequisite for repeat
addition processivity, is caused by a force acting on the primer. The force is
resulted from the unfolding of stem III pseudoknot that is induced by the
swinging of stem IV loop towards the nucleotide-bound polymerase site. Based on
the model, the dynamics of processive nucleotide and repeat additions by
Tetrahymena telomerase are quantitatively studied, which give good explanations
to the previous experimental results. Moreover, some predictions are presented.
In particular, it is predicted that the repeat addition processivity is mainly
determined by the difference between the free energy required to disrupt the
DNA:RNA hybrid and that required to unfold the stem III pseudoknot, with the
large difference corresponding to a low repeat addition processivity while the
small one corresponding to a high repeat addition processivity.
| 2007-08-21 |
0708.2594 | Michel Salzet | M. Salzet (NA) | Molecular Aspect of Annelid Neuroendocrine system | null | Invertebrate Neuropeptides and Hormones: Basic Knowledge and
Recent Advances, Transworld Research Network (Ed.) (2007) 19 | null | null | q-bio.NC | null | Hormonal processes along with enzymatic processing similar to that found in
vertebrates occur in annelids. Amino acid sequence determination of annelids
precursor gene products reveals the presence of the respective peptides that
exhibit high sequence identity to their mammalian counterparts. Furthermore,
these neuropeptides exert similar physiological function in annelids than the
ones found in vertebrates. In this respect, the high conservation in course of
evolution of these molecules families reflects their importance. Nevertheless,
some specific neuropeptides to annelids or invertebrates have also been in
these animals.
| 2007-08-21 |
0708.2647 | David Hochberg | David Hochberg and Maria-Paz Zorzano | Mirror symmetry breaking as a problem in dynamical critical phenomena | 9 pages, 3 figures | Physical Review E76, 021109 (2007) | 10.1103/PhysRevE.76.021109 | null | q-bio.PE cond-mat.stat-mech | null | The critical properties of the Frank model of spontaneous chiral synthesis
are discussed by applying results from the field theoretic renormalization
group (RG). The long time and long wavelength features of this microscopic
reaction scheme belong to the same universality class as multi-colored directed
percolation processes. Thus, the following RG fixed points (FP) govern the
critical dynamics of the Frank model for d<4: one unstable FP that corresponds
to complete decoupling between the two enantiomers, a saddle-point that
corresponds to symmetric interspecies coupling, and two stable FPs that
individually correspond to unidirectional couplings between the two chiral
molecules. These latter two FPs are associated with the breakdown of mirror or
chiral symmetry. In this simplified model of molecular synthesis, homochirality
is a natural consequence of the intrinsic reaction noise in the critical
regime, which corresponds to extremely dilute chemical systems.
| 2007-08-23 |
0708.2707 | Peter Csermely | Shijun Wang, Mate S. Szalay, Changshui Zhang, Peter Csermely | Learning and innovative elements of strategy adoption rules expand
cooperative network topologies | 14 pages, 3 Figures + a Supplementary Material with 25 pages, 3
Tables, 12 Figures and 116 references | PLoS ONE 3, e1917 (2008) | 10.1371/journal.pone.0001917 | null | q-bio.MN cond-mat.dis-nn nlin.AO physics.bio-ph | null | Cooperation plays a key role in the evolution of complex systems. However,
the level of cooperation extensively varies with the topology of agent networks
in the widely used models of repeated games. Here we show that cooperation
remains rather stable by applying the reinforcement learning strategy adoption
rule, Q-learning on a variety of random, regular, small-word, scale-free and
modular network models in repeated, multi-agent Prisoners Dilemma and Hawk-Dove
games. Furthermore, we found that using the above model systems other long-term
learning strategy adoption rules also promote cooperation, while introducing a
low level of noise (as a model of innovation) to the strategy adoption rules
makes the level of cooperation less dependent on the actual network topology.
Our results demonstrate that long-term learning and random elements in the
strategy adoption rules, when acting together, extend the range of network
topologies enabling the development of cooperation at a wider range of costs
and temptations. These results suggest that a balanced duo of learning and
innovation may help to preserve cooperation during the re-organization of
real-world networks, and may play a prominent role in the evolution of
self-organizing, complex systems.
| 2012-03-01 |
0708.2724 | Michael Zwolak | Michael Zwolak, Massimiliano Di Ventra | Physical approaches to DNA sequencing and detection | 26 pages, 22 figures | Rev. Mod. Phys. 80, 141 (2008) | 10.1103/RevModPhys.80.141 | LAUR-07-5650 | physics.bio-ph cond-mat.soft q-bio.BM | null | With the continued improvement of sequencing technologies, the prospect of
genome-based medicine is now at the forefront of scientific research. To
realize this potential, however, we need a revolutionary sequencing method for
the cost-effective and rapid interrogation of individual genomes. This
capability is likely to be provided by a physical approach to probing DNA at
the single nucleotide level. This is in sharp contrast to current techniques
and instruments which probe, through chemical elongation, electrophoresis, and
optical detection, length differences and terminating bases of strands of DNA.
In this Colloquium we review several physical approaches to DNA detection that
have the potential to deliver fast and low-cost sequencing. Center-fold to
these approaches is the concept of nanochannels or nanopores which allow for
the spatial confinement of DNA molecules. In addition to their possible impact
in medicine and biology, the methods offer ideal test beds to study open
scientific issues and challenges in the relatively unexplored area at the
interface between solids, liquids, and biomolecules at the nanometer length
scale. We emphasize the physics behind these methods and ideas, critically
describe their advantages and drawbacks, and discuss future research
opportunities in this field.
| 2008-01-03 |
0708.2931 | Douglas Galvao | Fernando Sato, Scheila F. Braga, Helio F. dos Santos, and Douglas S.
Galvao | Structure-Activity Relationship Investigation of Some New Tetracyclines
by Electronic Index Methodology | 18 pages, 8 figures | null | null | null | q-bio.BM physics.bio-ph | null | Tetracyclines are an old class of molecules that constitute a broad-spectrum
antibiotics. Since the first member of tetracycline family were isolated, the
clinical importance of these compounds as therapeutic and prophylactic agents
against a wide range of infections has stimulated efforts to define their mode
of action as inhibitors of bacterial reproduction. We used three SAR
methodologies for the analysis of biological activity of a set of 104
tetracycline compounds. Our calculation were carried out using the
semi-empirical Austin Method One (AM1) and Parametric Method 3 (PM3).
Electronic Indices Methodology (EIM), Principal Component Analysis (PCA) and
Artificial Neural Networks (ANN) were applied to the classification of 14 old
and 90 new proposed derivatives of tetracyclines. Our results make evident the
importance of EIM descriptors in pattern recognition and also show that the EIM
can be effectively used to predict the biological activity of Tetracyclines.
| 2007-09-13 |
0708.2953 | David K. Lubensky | David K. Lubensky | Equilibrium-like behavior in far-from-equilibrium chemical reaction
networks | 5 pages, 2 figures; brief discussion of non-mass-action kinetics
added | null | 10.1103/PhysRevE.81.060102 | null | cond-mat.stat-mech cond-mat.soft q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In an equilibrium chemical reaction mixture, the number of molecules present
obeys a Poisson distribution. We ask when the same is true of the steady state
of a nonequilibrium reaction network and obtain an essentially complete answer.
In particular, we show that networks with certain topological features must
have a Poisson distribution, whatever the reaction rates. Such driven systems
also obey an analog of the fluctuation-dissipation theorem. Our results may be
relevant to biological systems and to the larger question of how equilibrium
concepts might apply to nonequilibrium systems.
| 2013-05-29 |
0708.2971 | Filippo Petroni | Maurizio Serva and Filippo Petroni | Indo-European languages tree by Levenshtein distance | null | null | 10.1209/0295-5075/81/68005 | null | physics.soc-ph physics.data-an q-bio.PE | null | The evolution of languages closely resembles the evolution of haploid
organisms. This similarity has been recently exploited \cite{GA,GJ} to
construct language trees. The key point is the definition of a distance among
all pairs of languages which is the analogous of a genetic distance. Many
methods have been proposed to define these distances, one of this, used by
glottochronology, compute distance from the percentage of shared ``cognates''.
Cognates are words inferred to have a common historical origin, and subjective
judgment plays a relevant role in the identification process. Here we push
closer the analogy with evolutionary biology and we introduce a genetic
distance among language pairs by considering a renormalized Levenshtein
distance among words with same meaning and averaging on all the words contained
in a Swadesh list \cite{Sw}. The subjectivity of process is consistently
reduced and the reproducibility is highly facilitated. We test our method
against the Indo-European group considering fifty different languages and the
two hundred words of the Swadesh list for any of them. We find out a tree which
closely resembles the one published in \cite{GA} with some significant
differences.
| 2009-11-13 |
0708.3061 | Kevin Lin | Kevin K. Lin, Eric Shea-Brown, Lai-Sang Young | Reliability of Coupled Oscillators I: Two-Oscillator Systems | Part 1 of 2. Part 2 can be found at 0708.3063 | null | null | null | nlin.CD q-bio.NC | null | This paper concerns the reliability of a pair of coupled oscillators in
response to fluctuating inputs. Reliability means that an input elicits
essentially identical responses upon repeated presentations regardless of the
network's initial condition. Our main result is that both reliable and
unreliable behaviors occur in this network for broad ranges of coupling
strengths, even though individual oscillators are always reliable when
uncoupled. A new finding is that at low input amplitudes, the system is highly
susceptible to unreliable responses when the feedforward and feedback couplings
are roughly comparable. A geometric explanation based on shear-induced chaos at
the onset of phase-locking is proposed.
| 2007-08-23 |
0708.3063 | Kevin Lin | Kevin K. Lin, Eric Shea-Brown, Lai-Sang Young | Reliability of Coupled Oscillators II: Larger Networks | Part 2 of 2. Part 1 can be found at 0708.3061 | null | null | null | nlin.CD q-bio.NC | null | We study the reliability of phase oscillator networks in response to
fluctuating inputs. Reliability means that an input elicits essentially
identical responses upon repeated presentations, regardless of the network's
initial condition. In this paper, we extend previous results on two-cell
networks to larger systems. The first issue that arises is chaos in the absence
of inputs, which we demonstrate and interpret in terms of reliability. We give
a mathematical analysis of networks that can be decomposed into modules
connected by an acyclic graph. For this class of networks, we show how to
localize the source of unreliability, and address questions concerning
downstream propagation of unreliability once it is produced.
| 2007-08-23 |
0708.3096 | Cynthia J. Olson Reichhardt | M. B. Wan, C. J. Olson Reichhardt, Z. Nussinov and C. Reichhardt | Rectification of Swimming Bacteria and Self Driven Particle Systems by
Arrays of Asymmetric Barriers | 4 pages, 4 postscript figures. Version to appear in Phys. Rev. Lett | Phys. Rev. Lett. 101, 018102 (2008) | 10.1103/PhysRevLett.101.018102 | null | cond-mat.soft cond-mat.stat-mech q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show that the recent experimental observation of the rectification of
swimming bacteria in a system with an array of asymmetric barriers occurs due
to the ballistic component of the bacteria trajectories introduced by the
bacterial "motor." Each bacteria selects a random direction for motion and then
moves in this direction for a fixed period of time before randomly changing its
orientation and moving in a new direction. In the limit where the bacteria
undergo only Brownian motion, rectification by the barriers does not occur. We
also examine the effects of steric interactions between the bacteria and
observe a clogging effect upon increasing the bacteria density.
| 2009-11-13 |
0708.3098 | Sourav Chatterji | Sourav Chatterji, Ichitaro Yamazaki, Zhaojun Bai and Jonathan Eisen | CompostBin: A DNA composition-based algorithm for binning environmental
shotgun reads | null | null | null | null | q-bio.GN | null | A major hindrance to studies of microbial diversity has been that the vast
majority of microbes cannot be cultured in the laboratory and thus are not
amenable to traditional methods of characterization. Environmental shotgun
sequencing (ESS) overcomes this hurdle by sequencing the DNA from the organisms
present in a microbial community. The interpretation of this metagenomic data
can be greatly facilitated by associating every sequence read with its source
organism. We report the development of CompostBin, a DNA composition-based
algorithm for analyzing metagenomic sequence reads and distributing them into
taxon-specific bins. Unlike previous methods that seek to bin assembled contigs
and often require training on known reference genomes, CompostBin has the
ability to accurately bin raw sequence reads without need for assembly or
training. It applies principal component analysis to project the data into an
informative lower-dimensional space, and then uses the normalized cut
clustering algorithm on this filtered data set to classify sequences into
taxon-specific bins. We demonstrate the algorithm's accuracy on a variety of
simulated data sets and on one metagenomic data set with known species
assignments. CompostBin is a work in progress, with several refinements of the
algorithm planned for the future.
| 2007-08-24 |
0708.3103 | Karen Luz Burgoa K. Luz-Burgoa | K. Luz-Burgoa, S. Moss de Oliveira and J. S. Sa Martins | Computer simulations on the sympatric speciation modes for the Midas
cichlid species complex | 6 pages and 8 figures. Submitted | null | null | null | q-bio.PE | null | Cichlid fishes are one of the best model system for the study of evolution of
the species. Inspired by them, in this paper we simulated the splitting of a
single species into two separate ones via random mutations, with both
populations living together in sympatry, sharing the same habitat. We study the
ecological, mating and genetic conditions needed to reproduce the
polychromatism and polymorphism of three species of the Midas Cichlid species
complex. Our results show two scenarios for the A. Citrinellus speciation
process, one with and the other without disruptive natural selection. In the
first scenario, the ecological and genetic conditions are sufficient to create
two new species, while in the second the mating and genetic conditions must be
synchronized in order to control the velocity of genetic drift.
| 2007-08-24 |
0708.3134 | Emma Jin | Emma Y. Jin and Christian M. Reidys | Pseudoknot RNA Structures with Arc-Length $\ge 3$ | 18 pages, 4 figures | null | null | null | math.CO q-bio.BM | null | In this paper we study $k$-noncrossing RNA structures with arc-length $\ge
3$, i.e. RNA molecules in which for any $i$, the nucleotides labeled $i$ and
$i+j$ ($j=1,2$) cannot form a bond and in which there are at most $k-1$
mutually crossing arcs. Let ${\sf S}_{k,3}(n)$ denote their number. Based on a
novel functional equation for the generating function $\sum_{n\ge 0}{\sf
S}_{k,3}(n)z^n$, we derive for arbitrary $k\ge 3$ exponential growth factors
and for $k=3$ the subexponential factor. Our main result is the derivation of
the formula ${\sf S}_{3,3}(n) \sim \frac{6.11170\cdot 4!}{n(n-1)...(n-4)}
4.54920^n$.
| 2007-08-24 |
0708.3163 | Pierre-Henri Chavanis | Pierre-Henri Chavanis and Clement Sire | Jeans type analysis of chemotactic collapse | null | Physica A, 387, 4033 (2008) | 10.1016/j.physa.2008.02.025 | null | physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We perform a linear dynamical stability analysis of a general hydrodynamic
model of chemotactic aggregation [Chavanis & Sire, Physica A, in press (2007)].
Specifically, we study the stability of an infinite and homogeneous
distribution of cells against "chemotactic collapse". We discuss the analogy
between the chemotactic collapse of biological populations and the
gravitational collapse (Jeans instability) of self-gravitating systems. Our
hydrodynamic model involves a pressure force which can take into account
several effects like anomalous diffusion or the fact that the organisms cannot
interpenetrate. We also take into account the degradation of the chemical which
leads to a shielding of the interaction like for a Yukawa potential. Finally,
our hydrodynamic model involves a friction force which quantifies the
importance of inertial effects. In the strong friction limit, we obtain a
generalized Keller-Segel model similar to the generalized Smoluchowski-Poisson
system describing self-gravitating Langevin particles. For small frictions, we
obtain a hydrodynamic model of chemotaxis similar to the Euler-Poisson system
describing a self-gravitating barotropic gas. We show that an infinite and
homogeneous distribution of cells is unstable against chemotactic collapse when
the "velocity of sound" in the medium is smaller than a critical value. We
study in detail the linear development of the instability and determine the
range of unstable wavelengths, the growth rate of the unstable modes and the
damping rate, or the pulsation frequency, of the stable modes as a function of
the friction parameter and shielding length. For specific equations of state,
we express the stability criterion in terms of the density of cells.
| 2009-11-13 |
0708.3171 | Bhaswar Ghosh | Indrani Bose and Bhaswar Ghosh | The p53-MDM2 network: from oscillations to apoptosis | null | null | null | null | q-bio.MN | null | The p53 protein is well-known for its tumour suppressor function. The
p53-MDM2 negative feedback loop constitutes the core module of a network of
regulatory interactions activated under cellular stress. In normal cells, the
level of p53 proteins is kept low by MDM2, i.e. MDM2 negatively regulates the
activity of p53. In the case of DNA damage,the p53-mediated pathways are
activated leading to cell cycle arrest and repair of the DNA. If repair is not
possible due to excessive damage, the p53-mediated apoptotic pathway is
activated bringing about cell death. In this paper, we give an overview of our
studies on the p53-MDM2 module and the associated pathways from a systems
biology perspective. We discuss a number of key predictions, related to some
specific aspects of cell cycle arrest and cell death, which could be tested in
experiments.
| 2007-08-24 |
0708.3181 | Rudolf A. Roemer | Chi-Tin Shih, Stephan Roche, Rudolf A. R\"omer | Point Mutations Effects on Charge Transport Properties of the
Tumor-Suppressor Gene p53 | 4.1 PR style pages with 5 figures included | Phys. Rev. Lett. 100, 018105 (2008) | 10.1103/PhysRevLett.100.018105 | null | q-bio.GN cond-mat.soft q-bio.QM | null | We report on a theoretical study of point mutations effects on charge
transfer properties in the DNA sequence of the tumor-suppressor p53 gene. On
the basis of effective single-strand or double-strand tight-binding models
which simulate hole propagation along the DNA, a statistical analysis of charge
transmission modulations associated with all possible point mutations is
performed. We find that in contrast to non-cancerous mutations, mutation
hotspots tend to result in significantly weaker {\em changes of transmission
properties}. This suggests that charge transport could play a significant role
for DNA-repairing deficiency yielding carcinogenesis.
| 2008-01-09 |
0708.3271 | T. R. Krishna Mohan | T. R. Krishna Mohan | Simulation of Spread and Control of Lesions in Brain | 5 pages, 3 postscript figures, submitted for publication | null | null | null | physics.bio-ph physics.comp-ph q-bio.NC | null | A simulation model for the spread and control of lesions in the brain is
constructed using a planar network (graph) representation for the Central
Nervous System (CNS). The model is inspired by the lesion structures observed
in the case of Multiple Sclerosis (MS), a chronic disease of the CNS. The
initial lesion site is at the center of a unit square and spreads outwards
based on the success rate in damaging edges (axons) of the network. The damaged
edges send out alarm signals which, at appropriate intensity levels, generate
programmed cell death. Depending on the extent and timing of the programmed
cell death, the lesion may get controlled or aggravated akin to the control of
wild fires by burning of peripheral vegetation. The parameter phase space of
the model shows smooth transition from uncontrolled situation to controlled
situation. The simulations show that the model is capable of generating a wide
variety of lesion growth and arrest scenarios.
| 2007-08-27 |
0708.3336 | James Rice Dr | James H. Rice | Far-field fluorescence microscopy beyond the diffraction limit:
Fluorescence imaging with ultrahigh resolution | 27 pages, 2 figures, 2 tables, review of devlopments in super
resolution fluorescence microscopy | null | null | null | physics.bio-ph | null | Fluorescence microscopy is an important and extensively utilised tool for
imaging biological systems. However, the image resolution that can be obtained
has a limit as defined through the laws of diffraction. Demand for improved
resolution has stimulated research into developing methods to image beyond the
diffraction limit based on far-field fluorescence microscopy techniques. Rapid
progress is being made in this area of science with methods emerging that
enable fluorescence imaging in the far-field to possess a resolution well
beyond the diffraction limit. This review outlines developments in far-field
fluorescence methods which enable ultrahigh resolution imaging and application
of these techniques to biology. Future possible trends and directions in
far-field fluorescence imaging with ultrahigh resolution are also outlined.
| 2007-08-27 |
0708.3499 | Francesc Rossell\'o | Gabriel Cardona, Francesc Rossello, Gabriel Valiente | Comparison of Tree-Child Phylogenetic Networks | 37 pages | null | null | null | q-bio.PE cs.CE cs.DM | null | Phylogenetic networks are a generalization of phylogenetic trees that allow
for the representation of non-treelike evolutionary events, like recombination,
hybridization, or lateral gene transfer. In this paper, we present and study a
new class of phylogenetic networks, called tree-child phylogenetic networks,
where every non-extant species has some descendant through mutation. We provide
an injective representation of these networks as multisets of vectors of
natural numbers, their path multiplicity vectors, and we use this
representation to define a distance on this class and to give an alignment
method for pairs of these networks. To the best of our knowledge, they are
respectively the first true distance and the first alignment method defined on
a meaningful class of phylogenetic networks strictly extending the class of
phylogenetic trees. Simple, polynomial algorithms for reconstructing a
tree-child phylogenetic network from its path multiplicity vectors, for
computing the distance between two tree-child phylogenetic networks, and for
aligning a pair of tree-child phylogenetic networks, are provided, and they
have been implemented as a Perl package and a Java applet, and they are
available at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance
| 2007-08-28 |
0708.3502 | Dietrich Stauffer | D. Stauffer and S. Moss de Oliveira | Child mortality in Penna ageing model | To pages including one figure | null | null | null | q-bio.PE | null | Assuming the deleterious mutations in the Penna ageing model to affect mainly
the young ages, we get an enhanced mortality at very young age, followed by a
minimum of the mortality, and then the usual exponential increase of mortality
with age.
| 2007-08-28 |
0708.3509 | Vahid Rezania | Vahid Rezania and Jack Tuszynski | Modeling polymerization of microtubules: a quantum mechanical approach | 19 pages, 1 figure | Physica A, Vol. 387, 5795 - 5809 (2008) | null | null | q-bio.BM cond-mat.stat-mech q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper a quantum mechanical description of the assembly/disassembly
process for microtubules is proposed. We introduce creation and annihilation
operators that raise or lower the microtubule length by a tubulin layer.
Following that, the Hamiltonian and corresponding equations of motion for the
quantum fields are derived that describe the dynamics of microtubules. These
Heisenberg-type equations are then transformed to semi-classical equations
using the method of coherent structures. We find that the dynamics of a
microtubule can be mathematically expressed via a cubic-quintic nonlinear
Schr\"{o}dinger (NLS) equation. We show that a vortex filament, a generic
solution of the NLS equation, exhibits linear growth/shrinkage in time as well
as temporal fluctuations about some mean value which is qualitatively similar
to the dynamic instability of microtubules.
| 2008-10-22 |
0708.3599 | Siebe van Albada | Siebe B. van Albada and Pieter Rein ten Wolde | Enzyme localization can drastically affect signal amplification in
signal transduction pathways | PLoS Comp Biol, in press. 32 pages including 6 figures and supporting
information | null | 10.1371/journal.pcbi.0030195.eor | null | q-bio.MN | null | Push-pull networks are ubiquitous in signal transduction pathways in both
prokaryotic and eukaryotic cells. They allow cells to strongly amplify signals
via the mechanism of zero-order ultrasensitivity. In a push-pull network, two
antagonistic enzymes control the activity of a protein by covalent
modification. These enzymes are often uniformly distributed in the cytoplasm.
They can, however, also be colocalized in space, for instance, near the pole of
the cell. Moreover, it is increasingly recognized that these enzymes can also
be spatially separated, leading to gradients of the active form of the
messenger protein. Here, we investigate the consequences of the spatial
distributions of the enzymes for the amplification properties of push-pull
networks. Our calculations reveal that enzyme localization by itself can have a
dramatic effect on the gain. The gain is maximized when the two enzymes are
either uniformly distributed or colocalized in one region in the cell.
Depending on the diffusion constants, however, the sharpness of the response
can be strongly reduced when the enzymes are spatially separated. We discuss
how our predictions could be tested experimentally.
| 2007-08-28 |
0708.3627 | Walter Nadler | Walter Nadler, Ulrich H. E. Hansmann | Optimizing Replica Exchange Moves For Molecular Dynamics | 4 pages, 3 figures; revised version (1 figure added), PRE in press | null | 10.1103/PhysRevE.76.057102 | null | q-bio.QM cond-mat.stat-mech physics.comp-ph q-bio.BM | null | In this short note we sketch the statistical physics framework of the replica
exchange technique when applied to molecular dynamics simulations. In
particular, we draw attention to generalized move sets that allow a variety of
optimizations as well as new applications of the method.
| 2009-11-13 |
0708.3739 | Andrea Corsi | P. D. Gujrati, Bradley P. Lambeth Jr, Andrea Corsi and Evan Askanazi | Exact Statistical Mechanical Investigation of a Finite Model Protein in
its environment: A Small System Paradigm | null | null | null | UATP/07-03 | cond-mat.stat-mech q-bio.BM | null | We consider a general incompressible finite model protein of size M in its
environment, which we represent by a semiflexible copolymer consisting of amino
acid residues classified into only two species (H and P, see text) following
Lau and Dill. We allow various interactions between chemically unbonded
residues in a given sequence and the solvent (water), and exactly enumerate the
number of conformations W(E) as a function of the energy E on an infinite
lattice under two different conditions: (i) we allow conformations that are
restricted to be compact (known as Hamilton walk conformations), and (ii) we
allow unrestricted conformations that can also be non-compact. It is easily
demonstrated using plausible arguments that our model does not possess any
energy gap even though it is supposed to exhibit a sharp folding transition in
the thermodynamic limit. The enumeration allows us to investigate exactly the
effects of energetics on the native state(s), and the effect of small size on
protein thermodynamics and, in particular, on the differences between the
microcanonical and canonical ensembles. We find that the canonical entropy is
much larger than the microcanonical entropy for finite systems. We investigate
the property of self-averaging and conclude that small proteins do not
self-average. We also present results that (i) provide some understanding of
the energy landscape, and (ii) shed light on the free energy landscape at
different temperatures.
| 2008-01-16 |
0708.3825 | Ana Nunes | M. Sim\~oes, M. M. Telo da Gama and A. Nunes | Stochastic Fluctuations in Epidemics on Networks | 29 pages, 8 figures | null | null | null | q-bio.PE | null | The effects of demographic stochasticity in the long term behaviour of
endemic infectious diseases have been considered for long as a necessary
addition to an underlying deterministic theory. The latter would explain the
regular behaviour of recurrent epidemics, and the former the superimposed noise
of observed incidence patterns. Recently, a stochastic theory based on a
mechanism of resonance with internal noise has shifted the role of
stochasticity closer to the center stage, by showing that the major dynamic
patterns found in the incidence data can be explained as resonant fluctuations,
whose behaviour is largely independent of the amplitude of seasonal forcing,
and by contrast very sensitive to the basic epidemiological parameters. Here we
elaborate on that approach, by adding an ingredient which is missing in
standard epidemic models, the 'mixing network' through which infection may
propagate. We find that spatial correlations have a major effect in the
enhancement of the amplitude and the coherence of the resonant stochastic
fluctuations, providing the ordered patterns of recurrent epidemics, whose
period may differ significantly from that of the small oscillations around the
deterministic equilibrium. We also show that the inclusion of a more realistic,
time correlated, recovery profile instead of exponentially distributed
infectious periods may, even in the random-mixing limit, contribute to the same
effect.
| 2007-08-29 |
0708.3869 | Guy Katriel | Guy Katriel | Existence of periodic solutions for enzyme-catalysed reactions with
periodic substrate input | null | Discrete & Continuous Dynamical Systems - Supplements, September
2007 | null | null | q-bio.BM nlin.AO | null | Considering a basic enzyme-catalysed reaction, in which the rate of input of
the substrate varies periodically in time, we give a necessary and sufficient
condition for the existence of a periodic solution of the reaction equations.
The proof employs the Leray-Schauder degree, applied to an appropriately
constructed homotopy.
| 2011-11-10 |
0708.3910 | Michael B\"orsch | N. Zarrabi, M. G. Dueser, S. Ernst, R. Reuter, G. D. Glick, S. D.
Dunn, J. Wrachtrup, M. Boersch | Monitoring the rotary motors of single FoF1-ATP synthase by synchronized
multi channel TCSPC | 12 pages, 9 figures | null | 10.1117/12.734301 | null | physics.bio-ph | null | Confocal time resolved single-molecule spectroscopy using pulsed laser
excitation and synchronized multi channel time correlated single photon
counting (TCSPC) provides detailed information about the conformational changes
of a biological motor in real time. We studied the formation of adenosine
triphosphate, ATP, from ADP and phosphate by FoF1-ATP synthase. The reaction is
performed by a stepwise internal rotation of subunits of the lipid
membrane-embedded enzyme. Using fluorescence resonance energy transfer, FRET,
we detected rotation of this biological motor by sequential changes of
intramolecular distances within a single FoF1-ATP synthase. Prolonged
observation times of single enzymes were achieved by functional immobilization
to the glass surface. The stepwise rotary subunit movements were identified by
Hidden Markov Models (HMM) which were trained with single-molecule FRET
trajectories. To improve the accuracy of the HMM analysis we included the
single-molecule fluorescence lifetime of the FRET donor and used alternating
laser excitation to co-localize the FRET acceptor independently within a photon
burst. The HMM analysis yielded the orientations and dwell times of rotary
subunits during stepwise rotation. In addition, the action mode of bactericidal
drugs, i.e. inhibitors of FoF1-ATP synthase like aurovertin, could be
investigated by the time resolved single-molecule FRET approach.
| 2009-11-13 |
0708.4011 | Ralph Scheicher | Haiying He, Ralph H. Scheicher, Ravindra Pandey, Alexandre Reily
Rocha, Stefano Sanvito, Anton Grigoriev, Rajeev Ahuja, Shashi P. Karna | Functionalized nanopore-embedded electrodes for rapid DNA sequencing | 12 pages, 5 figures | J. Phys. Chem. C, 112 (10), 3456 -3459, 2008. | 10.1021/jp7115142 | null | physics.bio-ph cond-mat.soft q-bio.BM | null | The determination of a patient's DNA sequence can, in principle, reveal an
increased risk to fall ill with particular diseases [1,2] and help to design
"personalized medicine" [3]. Moreover, statistical studies and comparison of
genomes [4] of a large number of individuals are crucial for the analysis of
mutations [5] and hereditary diseases, paving the way to preventive medicine
[6]. DNA sequencing is, however, currently still a vastly time-consuming and
very expensive task [4], consisting of pre-processing steps, the actual
sequencing using the Sanger method, and post-processing in the form of data
analysis [7]. Here we propose a new approach that relies on functionalized
nanopore-embedded electrodes to achieve an unambiguous distinction of the four
nucleic acid bases in the DNA sequencing process. This represents a significant
improvement over previously studied designs [8,9] which cannot reliably
distinguish all four bases of DNA. The transport properties of the setup
investigated by us, employing state-of-the-art density functional theory
together with the non-equilibrium Green's Function method, leads to current
responses that differ by at least one order of magnitude for different bases
and can thus provide a much more robust read-out of the base sequence. The
implementation of our proposed setup could thus lead to a viable protocol for
rapid DNA sequencing with significant consequences for the future of genome
related research in particular and health care in general.
| 2008-03-06 |
0708.4065 | Manoj Gopalakrishnan | Shivam Ghosh (St.Stephens College, Delhi), Manoj Gopalakrishnan (HRI,
Allahabad), Kimberly Forsten-Williams (Virginia Tech) | Self-consistent theory of reversible ligand binding to a spherical cell | 23 pages with 4 figures | Phys. Biol. 4 344-354 (2007) | 10.1088/1478-3975/4/4/010 | null | q-bio.SC cond-mat.stat-mech q-bio.QM | null | In this article, we study the kinetics of reversible ligand binding to
receptors on a spherical cell surface using a self-consistent stochastic
theory. Binding, dissociation, diffusion and rebinding of ligands are
incorporated into the theory in a systematic manner. We derive explicitly the
time evolution of the ligand-bound receptor fraction p(t) in various regimes .
Contrary to the commonly accepted view, we find that the well-known
Berg-Purcell scaling for the association rate is modified as a function of
time. Specifically, the effective on-rate changes non-monotonically as a
function of time and equals the intrinsic rate at very early as well as late
times, while being approximately equal to the Berg-Purcell value at
intermediate times. The effective dissociation rate, as it appears in the
binding curve or measured in a dissociation experiment, is strongly modified by
rebinding events and assumes the Berg-Purcell value except at very late times,
where the decay is algebraic and not exponential. In equilibrium, the ligand
concentration everywhere in the solution is the same and equals its spatial
mean, thus ensuring that there is no depletion in the vicinity of the cell.
Implications of our results for binding experiments and numerical simulations
of ligand-receptor systems are also discussed.
| 2009-11-13 |
0708.4212 | Frank Schweitzer | Adrian M. Seufert, Frank Schweitzer | Aggregate Dynamics in an Evolutionary Network Model | null | International Journal of Modern Physics C, vol. 18, no. 10 (2007),
pp. 1659-1674 | 10.1142/S0129183107011649 | null | q-bio.PE nlin.AO q-bio.MN q-bio.QM | null | We analyze a model of interacting agents (e.g. prebiotic chemical species)
which are represended by nodes of a network, whereas their interactions are
mapped onto directed links between these nodes. On a fast time scale, each
agent follows an eigendynamics based on catalytic support from other nodes,
whereas on a much slower time scale the network evolves through selection and
mutation of its nodes-agent. In the first part of the paper, we explain the
dynamics of the model by means of characteristic snapshots of the network
evolution and confirm earlier findings on crashes an recoveries in the network
structure. In the second part, we focus on the aggregate behavior of the
network dynamics. We show that the disruptions in the network structure are
smoothed out, so that the average evolution can be described by a growth regime
followed by a saturation regime, without an initial random regime. For the
saturation regime, we obtain a logarithmic scaling between the average
connectivity per node $\mean{l}_{s}$ and a parameter $m$, describing the
average incoming connectivity, which is independent of the system size $N$.
| 2009-11-13 |
0709.0024 | Miodrag Krmar | Vladan Pankovic, Nikola Vunduk, Milan Predojevic | Population Dynamics of Children and Adolescents without Problematic
Behavior | two pages, no figures | null | null | null | q-bio.PE | null | In this work we suggest a simple mathematical model for the dynamics of the
population of children and adolescents without problematic behavior (criminal
activities etc.). This model represents a typical population growth equation
but with time dependent (linearly decreasing) population growth coefficient.
Given equation admits definition of the half-life time of the non-problematic
children behavior as well as a criterion for estimation of the social
regulation of the children behavior.
| 2007-09-04 |
0709.0025 | Ping Ao | P Ao | Borges Dilemma, Fundamental Laws, and Systems Biology | 4 pages | null | null | null | q-bio.QM q-bio.OT | null | I reason here that the known folk law in biology that there is no general law
in biology because of exceptions is false. The (quantitative) systems biology
offers the potential to solve the Borges Dilemma, by transcending it. There
have already a plenty of indications on this trend.
| 2007-09-04 |
0709.0125 | Mark Lipson | Mark Lipson (Harvard University) | Differential and graphical approaches to multistability theory for
chemical reaction networks | 28 pages, no figures | null | null | null | q-bio.MN q-bio.QM | null | The use of mathematical models has helped to shed light on countless
phenomena in chemistry and biology. Often, though, one finds that systems of
interest in these fields are dauntingly complex. In this paper, we attempt to
synthesize and expand upon the body of mathematical results pertaining to the
theory of multiple equilibria in chemical reaction networks (CRNs), which has
yielded surprising insights with minimal computational effort. Our central
focus is a recent, cycle-based theorem by Gheorghe Craciun and Martin Feinberg,
which is of significant interest in its own right and also serves, in a
somewhat restated form, as the basis for a number of fruitful connections among
related results.
| 2007-09-04 |
0709.0217 | Tobias Reichenbach | Tobias Reichenbach, Mauro Mobilia and Erwin Frey | Mobility promotes and jeopardizes biodiversity in rock-paper-scissors
games | Final submitted version; the printed version can be found at
http://dx.doi.org/10.1038/nature06095 Supplementary movies are available at
http://www.theorie.physik.uni-muenchen.de/lsfrey/images_content/movie1.AVI
and
http://www.theorie.physik.uni-muenchen.de/lsfrey/images_content/movie2.AVI | Nature 448, 1046-1049 (2007) | 10.1038/nature06095 | LMU-ASC 62/07 | q-bio.PE cond-mat.stat-mech physics.bio-ph | null | Biodiversity is essential to the viability of ecological systems. Species
diversity in ecosystems is promoted by cyclic, non-hierarchical interactions
among competing populations. Such non-transitive relations lead to an evolution
with central features represented by the `rock-paper-scissors' game, where rock
crushes scissors, scissors cut paper, and paper wraps rock. In combination with
spatial dispersal of static populations, this type of competition results in
the stable coexistence of all species and the long-term maintenance of
biodiversity. However, population mobility is a central feature of real
ecosystems: animals migrate, bacteria run and tumble. Here, we observe a
critical influence of mobility on species diversity. When mobility exceeds a
certain value, biodiversity is jeopardized and lost. In contrast, below this
critical threshold all subpopulations coexist and an entanglement of travelling
spiral waves forms in the course of temporal evolution. We establish that this
phenomenon is robust, it does not depend on the details of cyclic competition
or spatial environment. These findings have important implications for
maintenance and evolution of ecological systems and are relevant for the
formation and propagation of patterns in excitable media, such as chemical
kinetics or epidemic outbreaks.
| 2008-04-09 |
0709.0218 | Debprakash Patnaik | Debprakash Patnaik (Electrical Engg. Dept., Indian Institute of
Science), P. S. Sastry (Electrical Engg. Dept., Indian Institute of Science),
K. P. Unnikrishnan (General Motors R&D) | Inferring Neuronal Network Connectivity using Time-constrained Episodes | 9 pages. See also http://neural-code.cs.vt.edu/ | null | null | null | cs.DB q-bio.NC | null | Discovering frequent episodes in event sequences is an interesting data
mining task. In this paper, we argue that this framework is very effective for
analyzing multi-neuronal spike train data. Analyzing spike train data is an
important problem in neuroscience though there are no data mining approaches
reported for this. Motivated by this application, we introduce different
temporal constraints on the occurrences of episodes. We present algorithms for
discovering frequent episodes under temporal constraints. Through simulations,
we show that our method is very effective for analyzing spike train data for
unearthing underlying connectivity patterns.
| 2008-03-10 |
0709.0225 | Jonas Cremer | Jonas Cremer, Tobias Reichenbach, Erwin Frey | Anomalous finite-size effects in the Battle of the Sexes | 8 pages, 5 figures. To appear in the ECCS '07 issue, Eur. Phys. J. B
(2008) | Eur. Phys. J. B 63, 373-380 (2008) | 10.1140/epjb/e2008-00036-x | LMU-ASC 67/07 | q-bio.PE cond-mat.stat-mech physics.bio-ph | null | The Battle of the Sexes describes asymmetric conflicts in mating behavior of
males and females. Males can be philanderer or faithful, while females are
either fast or coy, leading to a cyclic dynamics. The adjusted replicator
equation predicts stable coexistence of all four strategies. In this situation,
we consider the effects of fluctuations stemming from a finite population size.
We show that they unavoidably lead to extinction of two strategies in the
population. However, the typical time until extinction occurs strongly prolongs
with increasing system size. In the meantime, a quasi-stationary probability
distribution forms that is anomalously flat in the vicinity of the coexistence
state. This behavior originates in a vanishing linear deterministic drift near
the fixed point. We provide numerical data as well as an analytical approach to
the mean extinction time and the quasi-stationary probability distribution.
| 2008-08-31 |
0709.0329 | Anca Radulescu | Anca R. Radulescu | Schizophrenia - a parameters' game? | The manuscript is 23 pages long (14 pages of text and 9 of
references). It contains five figures, two of which in color | null | null | null | q-bio.QM q-bio.TO | null | Schizophrenia is a severe, currently incurable, relatively common mental
condition. Its symptoms are complex and widespread. It structurally and
functionally affects cortical and subcortical regions involved in cognitive,
emotional and motivational aspects of behavior. Its cause is unknown, its
diagnosis is based on statistical behavior and its treatment is elusive.
Our paradigm addresses the complexity of schizophrenic symptoms. Building
upon recent neural vulnerability and limbic dysregulation hypotheses, it offers
a mathematical model for the evolution of the limbic system under perturbation.
Dependence on parameters and the concept of "bifurcation" could be the key to
understanding the threshold between "normality" and "disease".
| 2007-09-05 |
0709.0346 | Akira Kinjo | Akira R. Kinjo and Sanzo Miyazawa | On the optimal contact potential of proteins | 5 pages, text only | Chemical Physics Letters, Vol. 451 pp. 132-135 (2008) | 10.1016/j.cplett.2007.12.005 | null | q-bio.BM physics.bio-ph physics.chem-ph | null | We analytically derive the lower bound of the total conformational energy of
a protein structure by assuming that the total conformational energy is well
approximated by the sum of sequence-dependent pairwise contact energies. The
condition for the native structure achieving the lower bound leads to the
contact energy matrix that is a scalar multiple of the native contact matrix,
i.e., the so-called Go potential. We also derive spectral relations between
contact matrix and energy matrix, and approximations related to one-dimensional
protein structures. Implications for protein structure prediction are
discussed.
| 2008-01-03 |
0709.0418 | Antonio Siber | Antonio Siber and Rudolf Podgornik | Role of electrostatic interactions in the assembly of empty spherical
viral capsids | Sent to publication | Phys. Rev. E 76, 061906 (2007) | 10.1103/PhysRevE.76.061906 | null | physics.bio-ph | null | We examine the role of electrostatic interactions in the assembly of empty
spherical viral capsids. The charges on the protein subunits that make the
viral capsid mutually interact and are expected to yield electrostatic
repulsion acting against the assembly of capsids. Thus, attractive
protein-protein interactions of non-electrostatic origin must act to enable the
capsid formation. We investigate whether the interplay of repulsive
electrostatic and attractive interactions between the protein subunits can
result in the formation of spherical viral capsids of a preferred radius. For
this to be the case, we find that the attractive interactions must depend on
the angle between the neighboring protein subunits (i.e. on the mean curvature
of the viral capsid) so that a particular angle(s) is (are) preferred
energywise. Our results for the electrostatic contributions to energetics of
viral capsids nicely correlate with recent experimental determinations of the
energetics of protein-protein contacts in Hepatitis B virus [P. Ceres and A.
Zlotnick, Biochemistry {\bf 41}, 11525 (2002).
| 2007-12-24 |
0709.0443 | Diana Marco | D. E. Marco, S. A. Cannas, M. A. Montemurro, B. Hu and S. Cheng | Similar self-organizing scale-invariant properties characterize early
cancer invasion and long range species spread | 21 pages, 2 figures | Journal of Theoretical Biology 256: 65-75 (2008) | 10.1016/j.jtbi.2008.09.011 | null | q-bio.PE q-bio.CB | null | Occupancy of new habitats through dispersion is a central process in nature.
In particular, long range dispersal is involved in the spread of species and
epidemics, although it has not been previously related with cancer invasion, a
process that involves spread to new tissues. We show that the early spread of
cancer cells is similar to the species individuals spread and that both
processes are represented by a common spatio-temporal signature, characterized
by a particular fractal geometry of the boundaries of patches generated, and a
power law-scaled, disrupted patch size distribution. We show that both
properties are a direct result of long-distance dispersal, and that they
reflect homologous ecological processes of population self-organization. Our
results are significant for processes involving long-range dispersal like
biological invasions, epidemics and cancer metastasis.
| 2009-02-16 |
0709.0531 | John Rhodes | Elizabeth S. Allman, Cecile Ane, John A. Rhodes | Identifiability of a Markovian model of molecular evolution with
Gamma-distributed rates | 35 pages, 3 figures; Minor revisions and reformatting to reflect
version to be published | null | null | null | math.ST q-bio.PE stat.TH | null | Inference of evolutionary trees and rates from biological sequences is
commonly performed using continuous-time Markov models of character change. The
Markov process evolves along an unknown tree while observations arise only from
the tips of the tree. Rate heterogeneity is present in most real data sets and
is accounted for by the use of flexible mixture models where each site is
allowed its own rate. Very little has been rigorously established concerning
the identifiability of the models currently in common use in data analysis,
although non-identifiability was proven for a semi-parametric model and an
incorrect proof of identifiability was published for a general parametric model
(GTR+Gamma+I). Here we prove that one of the most widely used models
(GTR+Gamma) is identifiable for generic parameters, and for all parameter
choices in the case of 4-state (DNA) models. This is the first proof of
identifiability of a phylogenetic model with a continuous distribution of
rates.
| 2008-02-01 |
0709.0552 | Ping Ao | P. Ao, D. Galas, L. Hood, X.-M. Zhu | Cancer Genesis and Progression as Dynamics in Functional Landscape of
Endogenous Molecular-Cellular Network | 13 pages | null | null | null | q-bio.SC q-bio.MN | null | An endogenous molecular-cellular network for both normal and abnormal
functions is assumed to exist. This endogenous network forms a nonlinear
stochastic dynamical system, with many stable attractors in its functional
landscape. Normal or abnormal robust states can be decided by this network in a
manner similar to the neural network. In this context cancer is hypothesized as
one of its robust intrinsic states. This hypothesis implies that a nonlinear
stochastic mathematical cancer model is constructible based on available
experimental data and its quantitative prediction is directly testable. Within
such model the genesis and progression of cancer may be viewed as stochastic
transitions between different attractors. Thus it further suggests that
progressions are not arbitrary. Other important issues on cancer, such as
genetic vs epigenetics, double-edge effect, dormancy, are discussed in the
light of present hypothesis. A different set of strategies for cancer
prevention, cure, and care, is therefore suggested.
| 2007-09-06 |
0709.0561 | Leonard Harris | Leonard A. Harris, Aaron M. Piccirilli, Emily R. Majusiak and Paulette
Clancy | Quantifying Stochastic Effects in Biochemical Reaction Networks using
Partitioned Leaping | v3: Final accepted version. 15 pages, 9 figures, 3 tables. SSA
results included for comparison to PLA | Phys. Rev. E 79 (2009) 051906 | 10.1103/PhysRevE.79.051906 | null | q-bio.SC physics.chem-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | "Leaping" methods show great promise for significantly accelerating
stochastic simulations of complex biochemical reaction networks. However, few
practical applications of leaping have appeared in the literature to date.
Here, we address this issue using the "partitioned leaping algorithm" (PLA)
[L.A. Harris and P. Clancy, J. Chem. Phys. 125, 144107 (2006)], a
recently-introduced multiscale leaping approach. We use the PLA to investigate
stochastic effects in two model biochemical reaction networks. The networks
that we consider are simple enough so as to be accessible to our intuition but
sufficiently complex so as to be generally representative of real biological
systems. We demonstrate how the PLA allows us to quantify subtle effects of
stochasticity in these systems that would be difficult to ascertain otherwise
as well as not-so-subtle behaviors that would strain commonly-used "exact"
stochastic methods. We also illustrate bottlenecks that can hinder the approach
and exemplify and discuss possible strategies for overcoming them. Overall, our
aim is to aid and motivate future applications of leaping by providing stark
illustrations of the benefits of the method while at the same time elucidating
obstacles that are often encountered in practice.
| 2009-07-06 |
0709.0566 | Debprakash Patnaik | K.P.Unnikrishnan (General Motors R&D Center, Warren, MI), Debprakash
Patnaik (Dept. Elecetrical Engineering, Indian Institute of Science,
Bangalore), P.S.Sastry (Dept. Elecetrical Engineering, Indian Institute of
Science, Bangalore) | Discovering Patterns in Multi-neuronal Spike Trains using the Frequent
Episode Method | Also see http://neural-code.cs.vt.edu/ | null | null | null | cs.DB q-bio.NC | null | Discovering the 'Neural Code' from multi-neuronal spike trains is an
important task in neuroscience. For such an analysis, it is important to
unearth interesting regularities in the spiking patterns. In this report, we
present an efficient method for automatically discovering synchrony, synfire
chains, and more general sequences of neuronal firings. We use the Frequent
Episode Discovery framework of Laxman, Sastry, and Unnikrishnan (2005), in
which the episodes are represented and recognized using finite-state automata.
Many aspects of functional connectivity between neuronal populations can be
inferred from the episodes. We demonstrate these using simulated multi-neuronal
data from a Poisson model. We also present a method to assess the statistical
significance of the discovered episodes. Since the Temporal Data Mining (TDM)
methods used in this report can analyze data from hundreds and potentially
thousands of neurons, we argue that this framework is appropriate for
discovering the `Neural Code'.
| 2008-03-10 |
0709.0625 | Kateryna Mishchenko | Kateryna Mishchenko, Sverker Holmgren and Lars Ronnegard | Efficient Implementation of the AI-REML Iteration for Variance Component
QTL Analysis | 14 pages, 2 figures | null | null | Research report MDH/IMA ISSN 1404-4978 | q-bio.QM q-bio.OT | null | Regions in the genome that affect complex traits, quantitative trait loci
(QTL), can be identified using statistical analysis of genetic and phenotypic
data. When restricted maximum-likelihood (REML) models are used, the mapping
procedure is normally computationally demanding. We develop a new efficient
computational scheme for QTL mapping using variance component analysis and the
AI-REML algorithm. The algorithm uses an exact or approximative low-rank
representation of the identity-by-descent matrix, which combined with the
Woodbury formula for matrix inversion results in that the computations in the
AI-REML iteration body can be performed more efficiently. For cases where an
exact low-rank representation of the IBD matrix is available a-priori, the
improved AI-REML algorithm normally runs almost twice as fast compared to the
standard version. When an exact low-rank representation is not available, a
truncated spectral decomposition is used to determine a low-rank approximation.
We show that also in this case, the computational efficiency of the AI-REML
scheme can often be significantly improved.
| 2008-02-11 |
0709.0679 | Joshua Shaevitz | Joshua W. Shaevitz, Daniel A. Fletcher | Curvature and torsion in growing actin networks | null | null | 10.1088/1478-3975/5/2/026006 | null | q-bio.BM physics.bio-ph q-bio.CB | null | Intracellular pathogens such as Listeria monocytogenes and Rickettsia
rickettsii move within a host cell by polymerizing a comet-tail of actin fibers
that ultimately pushes the cell forward. This dense network of cross-linked
actin polymers typically exhibits a striking curvature that causes bacteria to
move in gently looping paths. Theoretically, tail curvature has been linked to
details of motility by considering force and torque balances from a finite
number of polymerizing filaments. Here we track beads coated with a prokaryotic
activator of actin polymerization in three dimensions to directly quantify the
curvature and torsion of bead motility paths. We find that bead paths are more
likely to have low rather than high curvature at any given time. Furthermore,
path curvature changes very slowly in time, with an autocorrelation decay time
of 200 seconds. Paths with a small radius of curvature, therefore, remain so
for an extended period resulting in loops when confined to two dimensions. When
allowed to explore a 3D space, path loops are less evident. Finally, we
quantify the torsion in the bead paths and show that beads do not exhibit a
significant left- or right-handed bias to their motion in 3D. These results
suggest that paths of actin-propelled objects may be attributed to slow changes
in curvature rather than a fixed torque.
| 2009-11-13 |
0709.0682 | Yohan Payan | Nicolas Vuillerme (TIMC - IMAG), Olivier Chenu (TIMC - IMAG), Nicolas
Pinsault (TIMC - IMAG), Alexandre Moreau-Gaudry (TIMC - IMAG), Anthony Fleury
(TIMC - IMAG), Jacques Demongeot (TIMC - IMAG), Yohan Payan (TIMC - IMAG) | Pressure sensor-based tongue-placed electrotactile biofeedback for
balance improvement - Biomedical application to prevent pressure sores
formation and falls | null | Dans Proceedings - 29th Annual International Conference of the
IEEE Engineering in Medicine and Biology Society., Lyon : France (2007) | null | null | physics.med-ph q-bio.NC | null | We introduce the innovative technologies, based on the concept of "sensory
substitution", we are developing in the fields of biomedical engineering and
human disability. Precisely, our goal is to design, develop and validate
practical assistive biomedical and/or technical devices and/or rehabilitating
procedures for persons with disabilities, using artificial tongue-placed
tactile biofeedback systems. Proposed applications are dealing with: (1)
pressure sores prevention in case of spinal cord injuries (persons with
paraplegia, or tetraplegia); and (2) balance control improvement to prevent
fall in older and/or disabled adults. This paper describes the architecture and
the functioning principle of these biofeedback systems and presents preliminary
results of two feasibility studies performed on young healthy adults.
| 2007-09-06 |
0709.0689 | Yohan Payan | Nicolas Vuillerme (TIMC - IMAG), Olivier Chenu (TIMC - IMAG), Nicolas
Pinsault (TIMC - IMAG), Anthony Fleury (TIMC - IMAG), Jacques Demongeot (TIMC
- IMAG), Yohan Payan (TIMC - IMAG) | A Plantar-pressure Based Tongue-placed Tactile Biofeedback System for
Balance Improvement | null | Computer Methods in Biomechanics and Biomedical Engineering
Supplement 1 (2007) 63-64 | null | null | physics.med-ph q-bio.NC | null | Maintaining an upright stance represents a complex task, which is achieved by
integrating sensory information from the visual, vestibular and somatosensory
systems. When one of these sensory inputs becomes unavailable and/or inaccurate
and/or unreliable, postural control generally is degraded. One way to solve
this problem is to supplement and/or substitute limited/altered/missing sensory
information by providing additional sensory information to the central nervous
system via an alternative sensory modality. Along these lines, we developed an
original biofeedback system [1] whose underlying principle consists in
supplying the user with supplementary sensory information related to foot sole
pressure distribution through a tongue-placed output device (Tongue Display
Unit, "TDU" [2]). The purpose of the present experiment was to assess its
effectiveness in improving balance in young healthy adults.
| 2007-09-06 |
0709.0719 | Alexander K. Vidybida | Alexander K. Vidybida | Estimation of Possible Selectivity and Sensitivity of a Cooperative
System to Low-Intensive Microwave Radiation | 4 pages, 8 references, talk made on the Electromagnetic
Hypersensitivity, 2nd Copenhagen Conference | Physics of the Alive, Volume 3, Issue 1, 1995, Pages 38-39 | null | null | physics.bio-ph | null | Recently, origins of non-deterministic behavior and free will in living
systems obtain growing interest (see, e.g. Maye A, Hsieh C, Sugihara G, Brembs
B (2007) Order in Spontaneous Behavior. PLoS ONE 2(5): e443.
doi:10.1371/journal.pone.0000443). In this text, devoted to electromagnetic
hypersensitivity, in n.2 and n.4, a possible physical mechanism of free will
and consequent indeterminacy in behavior is discussed.
| 2007-09-06 |
0709.0723 | William Klug | Lin Ma and William S. Klug | Viscous regularization and r-adaptive remeshing for finite element
analysis of lipid membrane mechanics | null | null | 10.1016/j.jcp.2008.02.019 | null | physics.bio-ph physics.comp-ph | null | As two-dimensional fluid shells, lipid bilayer membranes resist bending and
stretching but are unable to sustain shear stresses. This property gives
membranes the ability to adopt dramatic shape changes. In this paper, a finite
element model is developed to study static equilibrium mechanics of membranes.
In particular, a viscous regularization method is proposed to stabilize
tangential mesh deformations and improve the convergence rate of nonlinear
solvers. The Augmented Lagrangian method is used to enforce global constraints
on area and volume during membrane deformations. As a validation of the method,
equilibrium shapes for a shape-phase diagram of lipid bilayer vesicle are
calculated. These numerical techniques are also shown to be useful for
simulations of three-dimensional large-deformation problems: the formation of
tethers (long tube-like exetensions); and Ginzburg-Landau phase separation of a
two-lipid-component vesicle. To deal with the large mesh distortions of the
two-phase model, modification of vicous regularization is explored to achieve
r-adaptive mesh optimization.
| 2009-11-13 |
0709.0778 | Zhao Jing | Jing Zhao, Guo-Hui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jian-Hua Luo,
Zhi-Wei Cao, Yi-Xue Li | Modular co-evolution of metabolic networks | 26 pages, 7 figures | BMC Bioinformatics, 2007, 8:311 | null | null | q-bio.MN | null | The architecture of biological networks has been reported to exhibit high
level of modularity, and to some extent, topological modules of networks
overlap with known functional modules. However, how the modular topology of the
molecular network affects the evolution of its member proteins remains unclear.
In this work, the functional and evolutionary modularity of Homo sapiens (H.
sapiens) metabolic network were investigated from a topological point of view.
Network decomposition shows that the metabolic network is organized in a highly
modular core-periphery way, in which the core modules are tightly linked
together and perform basic metabolism functions, whereas the periphery modules
only interact with few modules and accomplish relatively independent and
specialized functions. Moreover, over half of the modules exhibit
co-evolutionary feature and belong to specific evolutionary ages. Peripheral
modules tend to evolve more cohesively and faster than core modules do. The
correlation between functional, evolutionary and topological modularity
suggests that the evolutionary history and functional requirements of metabolic
systems have been imprinted in the architecture of metabolic networks. Such
systems level analysis could demonstrate how the evolution of genes may be
placed in a genome-scale network context, giving a novel perspective on
molecular evolution.
| 2007-09-07 |
0709.0792 | Vladimir Lobaskin | Vladimir Lobaskin, Dmitry Lobaskin, Igor M. Kulic | Brownian dynamics of a microswimmer | Submitted | Eur. Phys. J. Special Topics 157, 149 (2008) | 10.1140/epjst/e2008-00637-7 | null | physics.flu-dyn physics.bio-ph | null | We report on dynamic properties of a simple model microswimmer composed of
three spheres and propelling itself in a viscous fluid by spinning motion of
the spheres under zero net torque constraint. At a fixed temperature and
increasing the spinning frequency, the swimmer demonstrates a transition from
dissipation-dominated to a pumping-dominated motion regime characterized by
negative effective friction coefficient. In the limit of high frequencies, the
diffusion of the swimmer can be described by a model of an active particle with
constant velocity.
| 2008-05-08 |
0709.0823 | Carsten Marr | Carsten Marr, Mark Mueller-Linow, Marc-Thorsten Huett | Reply to ''Comment on 'Regularizing Capacity of Metabolic Networks' '' | 2 pages, 2 figures | null | 10.1103/PhysRevE.77.023902 | null | q-bio.MN nlin.CG | null | In a recent paper [C. Marr, M. Mueller-Linow, and M.-T. Huett, Phys. Rev. E
75, 041917 (2007)] we discuss the pronounced potential of real metabolic
network topologies, compared to randomized counterparts, to regularize complex
binary dynamics. In their comment [P. Holme and M. Huss, arXiv:0705.4084v1],
Holme and Huss criticize our approach and repeat our study with more realistic
dynamics, where stylized reaction kinetics are implemented on sets of pairwise
reactions. The authors find no dynamic difference between the reaction sets
recreated from the metabolic networks and randomized counterparts. We reproduce
the author's observation and find that their algorithm leads to a dynamical
fragmentation and thus eliminates the topological information contained in the
graphs. Hence, their approach cannot rule out a connection between the topology
of metabolic networks and the ubiquity of steady states.
| 2009-11-13 |
0709.0830 | Julian Oberdisse | Anna Salvati (UNIFI), Sandra Ristori (UNIFI), Julian Oberdisse (LCVN),
Olivier Spalla (LIONS), Giampaolo Ricciardi, Daniela Pietrangeli, Mauro
Giustini, Giacomo Martini (UNIFI) | Small Angle Scattering and Zeta Potential of Liposomes Loaded with
Octa(carboranyl)porphyrazine | null | The Journal of Physical Chemistry B 111 (2007) 10357-10364 | 10.1021/jp0731710 | null | cond-mat.soft physics.bio-ph | null | In this work the physicochemical characterization of liposomes loaded with a
newly synthesised carboranyl porphyrazine (H2HECASPz) is described. This
molecule represents a potential drug for different anticancer therapies, such
as Boron Neutron Capture Therapy, Photodynamic Therapy and Photothermal
Therapy. Different loading methods and different lipid mixtures were tested.
The corresponding loaded vectors were studied by Small Angle Scattering (SANS
and SAXS), light scattering and zeta potential. The combined analysis of
structural data at various length scales and the measurement of the surface
charge allowed to obtain a detailed characterization of the investigated
systems. The mechanisms underlying the onset of differences in relevant
physicochemical parameters (size, polydispersity and charge) were also
critically discussed.
| 2007-09-07 |
0709.0922 | Andrea Pagnani | Alfredo Braunstein, Roberto Mulet, Andrea Pagnani | Estimating the size of the solution space of metabolic networks | 8 pages, 7 pdf figures | BMC Bioinformatics. 2008;9:240 | null | null | cond-mat.dis-nn cond-mat.stat-mech q-bio.MN q-bio.QM | null | In this work we propose a novel algorithmic strategy that allows for an
efficient characterization of the whole set of stable fluxes compatible with
the metabolic constraints. The algorithm, based on the well-known Bethe
approximation, allows the computation in polynomial time of the volume of a non
full-dimensional convex polytope in high dimensions. The result of our
algorithm match closely the prediction of Monte Carlo based estimations of the
flux distributions of the Red Blood Cell metabolic network but in incomparably
shorter time. We also analyze the statistical properties of the average fluxes
of the reactions in the E-Coli metabolic network and finally to test the effect
of gene knock-outs on the size of the solution space of the E-Coli central
metabolism.
| 2010-04-02 |
0709.1012 | Julian Oberdisse | Anna Salvati (UNIFI), Sandra Ristori (UNIFI), Daniela Pietrangeli,
Julian Oberdisse (LCVN), Luca Calamai, Giacomo Martini (UNIFI), Giampaolo
Ricciardi | Insertion of a magnesium(II)-octacarboranyl(hexylsulfanyl) porphyrazine
into liposomes: a physico-chemical study | null | null | null | null | cond-mat.soft physics.bio-ph | null | The synthesis, characterization and liposome insertion of a novel
magnesium(II) carboranyl-porphyrazine, i.e. [2,3,7,8,12,13,17,18-octakis-
(1,2-dicarba-closo-dodecaboranyl)-hexylthio-5,10,15,20-
porphyrazine]magnesium(II) complex, MgHECSPz, is described. MgHECSPz was
designed to improve the potentiality in multiple approach anticancer therapy.
Liposomal formulations with different surface charge were prepared as
delivering agents. The obtained loaded vectors were characterized by DLS, SAXS,
SANS and \zeta potential measurements in order to define the overall properties
and structural details of loaded liposomes.
| 2007-09-11 |
0709.1148 | Alexander Leshansky | Alexander Leshansky, Oded Kenneth | Surface tank-treading: propulsion of Purcell's toroidal swimmer | null | null | 10.1063/1.2939069 | null | physics.flu-dyn physics.bio-ph | null | In this work we address the "smoking ring" propulsion technique, originally
proposed by E. M. Purcell. We first consider self-locomotion of a
doughnut-shaped swimmer powered by surface tank-treading. Different modes of
surface motion are assumed and propulsion velocity and swimming efficiency are
determined. The swimmer is propelled against the direction of its outer surface
motion, the inner surface having very little affect. The simplest swimming mode
corresponding to constant angular velocity, can achieve propulsion speeds of up
to 66% of the surface tank-treading velocity and swimming efficiency of up to
13%. Higher efficiency is possible for more complicated modes powered by
twirling of extensible surface. A potential practical design of a swimmer
motivated by Purcell's idea is proposed and demonstrated numerically. Lastly,
the explicit solution is found for a two-dimensional swimmer composed of two
counter-rotating disks, using complex variable techniques.
| 2009-11-13 |
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