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0705.0666 | Tom Michoel | Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim
Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper,
Kathleen Marchal, Yves Van de Peer | Validating module network learning algorithms using simulated data | 13 pages, 6 figures + 2 pages, 2 figures supplementary information | BMC Bioinformatics 2007, 8(Suppl 2):S5 | 10.1186/1471-2105-8-S2-S5 | null | q-bio.QM q-bio.MN | null | In recent years, several authors have used probabilistic graphical models to
learn expression modules and their regulatory programs from gene expression
data. Here, we demonstrate the use of the synthetic data generator SynTReN for
the purpose of testing and comparing module network learning algorithms. We
introduce a software package for learning module networks, called LeMoNe, which
incorporates a novel strategy for learning regulatory programs. Novelties
include the use of a bottom-up Bayesian hierarchical clustering to construct
the regulatory programs, and the use of a conditional entropy measure to assign
regulators to the regulation program nodes. Using SynTReN data, we test the
performance of LeMoNe in a completely controlled situation and assess the
effect of the methodological changes we made with respect to an existing
software package, namely Genomica. Additionally, we assess the effect of
various parameters, such as the size of the data set and the amount of noise,
on the inference performance. Overall, application of Genomica and LeMoNe to
simulated data sets gave comparable results. However, LeMoNe offers some
advantages, one of them being that the learning process is considerably faster
for larger data sets. Additionally, we show that the location of the regulators
in the LeMoNe regulation programs and their conditional entropy may be used to
prioritize regulators for functional validation, and that the combination of
the bottom-up clustering strategy with the conditional entropy-based assignment
of regulators improves the handling of missing or hidden regulators.
| 2007-11-15 |
0705.0835 | Shyamsunder Erramilli | Logan Chieffo, Jason J. Amsden, Jeffrey Shattuck, Mi K. Hong, Lawrence
Ziegler, Shyamsunder Erramilli | Vibrational Infrared Lifetime of the Anesthetic nitrous oxide gas in
solution | 7 pages, 3 Figures, Presented at Biophysics conference in Singapore
2005 | Biophysical Review Letters, 1:309-316 (2006) | null | null | physics.bio-ph physics.chem-ph | null | The lifetime of the asymmetric fundamental stretching 2218 cm$^{-1}$
vibration of the anesthetic gas nitrous oxide (N$_2$O) dissolved in octanol and
olive oil is reported. These solvents are model systems commonly used to assess
anesthetic potency. Picosecond time-scale molecular dynamics simulations have
suggested that protein dynamics or membrane dynamics play a role in the
molecular mechanism of anesthetic action. Ultrafast infrared spectroscopy with
100 fs time resolution is an ideal tool to probe dynamics of anesthetic
molecules on such timescales. Pump-probe studies at the peak of the vibrational
band yield a lifetime of $55 \pm 1$ ps in olive oil and $52 \pm 1 ps$ in
octanol. The similarity of lifetimes suggests that energy relaxation of the
anesthetic is determined primarily by the hydrophobic nature of the
environment, consistent with models of anesthetic action. The results show that
nitrous oxide is a good model system for probing anesthetic-solvent
interactions using nonlinear infrared spectroscopy.
| 2007-05-23 |
0705.0902 | Maria Fabiana Laguna | M. F. Laguna, S. Bohn, E. A. Jagla | The role of elastic stresses on leaf venation morphogenesis | 10 figures, published in PLoS Computational Biology | null | 10.1371/journal.pcbi.1000055 | null | physics.bio-ph physics.comp-ph | null | We explore the possible role of elastic mismatch between epidermis and
mesophyll as a driving force for the development of leaf venation. The current
prevalent 'canalization' hypothesis for the formation of veins claims that the
transport of the hormone auxin out of the leaves triggers cell differentiation
to form veins. Although there is evidence that auxin plays a fundamental role
in vein formation, the simple canalization mechanism may not be enough to
explain some features observed in the vascular system of leaves, in particular,
the abundance of vein loops. We present a model based on the existence of
mechanical instabilities that leads very naturally to hierarchical patterns
with a large number of closed loops. When applied to the structure of high
order veins, the numerical results show the same qualitative features as actual
venation patterns and, furthermore, have the same statistical properties. We
argue that the agreement between actual and simulated patterns provides strong
evidence for the role of mechanical effects on venation development.
| 2008-05-02 |
0705.0912 | Erzs\'ebet Ravasz Regan | Erzsebet Ravasz, S. Gnanakaran and Zoltan Toroczkai | Network Structure of Protein Folding Pathways | 15 pages, 4 figures | null | null | null | q-bio.BM q-bio.MN | null | The classical approach to protein folding inspired by statistical mechanics
avoids the high dimensional structure of the conformation space by using
effective coordinates. Here we introduce a network approach to capture the
statistical properties of the structure of conformation spaces. Conformations
are represented as nodes of the network, while links are transitions via
elementary rotations around a chemical bond. Self-avoidance of a polypeptide
chain introduces degree correlations in the conformation network, which in turn
lead to energy landscape correlations. Folding can be interpreted as a biased
random walk on the conformation network. We show that the folding pathways
along energy gradients organize themselves into scale free networks, thus
explaining previous observations made via molecular dynamics simulations. We
also show that these energy landscape correlations are essential for recovering
the observed connectivity exponent, which belongs to a different universality
class than that of random energy models. In addition, we predict that the
exponent and therefore the structure of the folding network fundamentally
changes at high temperatures, as verified by our simulations on the AK peptide.
| 2007-05-23 |
0705.1019 | Shenbing Kuang | Shenbing Kuang, Jiafu Wang, Ting Zeng, Aiyin Cao | Theoretical Analysis of Subthreshold Oscillatory Behaviors in Nonlinear
Autonomous Systems | 4 pages, 2 figures | null | null | null | q-bio.QM | null | We have developed a linearization method to investigate the subthreshold
oscillatory behaviors in nonlinear autonomous systems. By considering firstly
the neuronal system as an example, we show that this theoretical approach can
predict quantitatively the subthreshold oscillatory activities, including the
damping coefficients and the oscillatory frequencies which are in good
agreement with those observed in experiments. Then we generalize the
linearization method to an arbitrary autonomous nonlinear system. The detailed
extension of this theoretical approach is also presented and further discussed.
| 2007-05-23 |
0705.1030 | Stephen Quake | H. Christina Fan and Stephen R. Quake | Detection of Aneuploidy with Digital PCR | null | null | null | null | q-bio.QM | null | The widespread use of genetic testing in high risk pregnancies has created
strong interest in rapid and accurate molecular diagnostics for common
chromosomal aneuploidies. We show here that digital polymerase chain reaction
(dPCR) can be used for accurate measurement of trisomy 21 (Down's Syndrome),
the most common human aneuploidy. dPCR is generally applicable to any
aneuploidy, does not depend on allelic distribution or gender, and is able to
detect signals in the presence of mosaics or contaminating maternal DNA.
| 2007-05-23 |
0705.1053 | Everaldo Arashiro | Kelly C. de Carvalho and T\^ania Tom\'e | Anisotropic probabilistic cellular automaton for a predator-prey system | 13 pages, 4 figures, accepted for publication in Brazilian Journal of
Physics | null | null | null | q-bio.PE | null | We consider a probabilistic cellular automaton to analyze the stochastic
dynamics of a predator-prey system. The local rules are Markovian and are based
in the Lotka-Volterra model. The individuals of each species reside on the
sites of a lattice and interact with an unsymmetrical neighborhood. We look for
the effect of the space anisotropy in the characterization of the oscillations
of the species population densities. Our study of the probabilistic cellular
automaton is based on simple and pair mean-field approximations and explicitly
takes into account spatial anisotropy.
| 2016-08-14 |
0705.1057 | Jos K\"afer | Jos K\"afer, Takashi Hayashi, Athanasius F.M. Mar\'ee, Richard W.
Carthew and Fran\c{c}ois Graner | Cell adhesion and cortex contractility determine cell patterning in the
Drosophila retina | revised manuscript; 8 pages, 6 figures; supplementary information not
included | Proc. Natl. Acad. Sci. U.S.A. (2007), 104 (47), 18549-18554 | 10.1073/pnas.0704235104 | null | q-bio.CB q-bio.TO | null | Hayashi and Carthew (Nature 431 [2004], 647) have shown that the packing of
cone cells in the Drosophila retina resembles soap bubble packing, and that
changing E- and N-cadherin expression can change this packing, as well as cell
shape.
The analogy with bubbles suggests that cell packing is driven by surface
minimization. We find that this assumption is insufficient to model the
experimentally observed shapes and packing of the cells based on their cadherin
expression. We then consider a model in which adhesion leads to a surface
increase, balanced by cell cortex contraction. Using the experimentally
observed distributions of E- and N-cadherin, we simulate the packing and cell
shapes in the wildtype eye. Furthermore, by changing only the corresponding
parameters, this model can describe the mutants with different numbers of
cells, or changes in cadherin expression.
| 2007-11-15 |
0705.1081 | Philip Gerlee | P. Gerlee, A.R.A Anderson | Stability Analysis of a Hybrid Cellular Automaton Model of Cell Colony
Growth | 8 pages, 6 figures | Phys. Rev. E 75, 051911 (2007) | 10.1103/PhysRevE.75.051911 | null | physics.bio-ph | null | Cell colonies of bacteria, tumour cells and fungi, under nutrient limited
growth conditions, exhibit complex branched growth patterns. In order to
investigate this phenomenon we present a simple hybrid cellular automaton model
of cell colony growth. In the model the growth of the colony is limited by a
nutrient that is consumed by the cells and which inhibits cell division if it
falls below a certain threshold. Using this model we have investigated how the
nutrient consumption rate of the cells affects the growth dynamics of the
colony. We found that for low consumption rates the colony takes on a Eden-like
morphology, while for higher consumption rates the morphology of the colony is
branched with a fractal geometry. These findings are in agreement with previous
results, but the simplicity of the model presented here allows for a linear
stability analysis of the system. By observing that the local growth of the
colony is proportional to the flux of the nutrient we derive an approximate
dispersion relation for the growth of the colony interface. This dispersion
relation shows that the stability of the growth depends on how far the nutrient
penetrates into the colony. For low nutrient consumption rates the penetration
distance is large, which stabilises the growth, while for high consumption
rates the penetration distance is small, which leads to unstable branched
growth. When the penetration distance vanishes the dispersion relation is
reduced to the one describing Laplacian growth without ultra-violet
regularisation. The dispersion relation was verified by measuring how the
average branch width depends on the consumption rate of the cells and shows
good agreement between theory and simulations.
| 2007-05-23 |
0705.1134 | Haret Rosu | H.C. Rosu, O. Cornejo-Perez, J.E. Perez-Terrazas | Supersymmetric methods in the traveling variable: inside neurons and at
the brain scale | 14 pages, 1 figure | null | 10.1142/9789812779953_0010 | null | physics.bio-ph | null | We apply the mathematical technique of factorization of differential
operators to two different problems. First we review our results related to the
supersymmetry of the Montroll kinks moving onto the microtubule walls as well
as mentioning the sine-Gordon model for the microtubule nonlinear excitations.
Second, we find analytic expressions for a class of one-parameter solutions of
a sort of diffusion equation of Bessel type that is obtained by supersymmetry
from the homogeneous form of a simple damped wave equations derived in the
works of P.A. Robinson and collaborators for the corticothalamic system. We
also present a possible interpretation of the diffusion equation in the brain
context
| 2016-11-23 |
0705.1232 | Jens Eisert | H.M. Wiseman and J. Eisert | Nontrivial quantum effects in biology: A skeptical physicists' view | 15 pages, minor typographical errors corrected | null | 10.1142/9781848162556_0017 | null | physics.gen-ph q-bio.OT quant-ph | null | Invited contribution to "Quantum Aspects of Life", D. Abbott Ed. (World
Scientific, Singapore, 2007).
| 2016-12-21 |
0705.1307 | Yohan Payan | Nicolas Vuillerme (TIMC - IMAG), Olivier Chenu (TIMC - IMAG), Jacques
Demongeot (TIMC - IMAG), Yohan Payan (TIMC - IMAG) | Controlling posture using a plantar pressure-based, tongue-placed
tactile biofeedback system | null | Experimental Brain Research 179, 3 (2007) 409-14 | 10.1007/s00221-006-0800-4 | null | physics.med-ph q-bio.NC | null | The present paper introduces an original biofeedback system for improving
human balance control, whose underlying principle consists in providing
additional sensory information related to foot sole pressure distribution to
the user through a tongue-placed tactile output device. To assess the effect of
this biofeedback system on postural control during quiet standing, ten young
healthy adults were asked to stand as immobile as possible with their eyes
closed in two conditions of No-biofeedback and Biofeedback. Centre of foot
pressure (CoP) displacements were recorded using a force platform. Results
showed reduced CoP displacements in the Biofeedback relative to the
No-biofeedback condition. The present findings evidenced the ability of the
central nervous system to efficiently integrate an artificial plantar-based,
tongue-placed tactile biofeedback for controlling control posture during quiet
standing.
| 2007-05-23 |
0705.1389 | Yurie Okabe | Yurie Okabe, Yuu Yagi, and Masaki Sasai | Effects of the DNA state fluctuation on single-cell dynamics of
self-regulating gene | 18 pages, 5 figures | null | 10.1063/1.2768353 | null | q-bio.MN q-bio.QM | null | A dynamical mean-field theory is developed to analyze stochastic single-cell
dynamics of gene expression. By explicitly taking account of nonequilibrium and
nonadiabatic features of the DNA state fluctuation, two-time correlation
functions and response functions of single-cell dynamics are derived. The
method is applied to a self-regulating gene to predict a rich variety of
dynamical phenomena such as anomalous increase of relaxation time and
oscillatory decay of correlations. Effective "temperature" defined as the ratio
of the correlation to the response in the protein number is small when the DNA
state change is frequent, while it grows large when the DNA state change is
infrequent, indicating the strong enhancement of noise in the latter case.
| 2009-11-13 |
0705.1435 | Pierre Collet | P.Collet S.Martinez | Asymptotic velocity of one dimensional diffusions with periodic drift | null | null | null | null | math.PR math.AP q-bio.SC | null | We consider the asymptotic behaviour of the solution of one dimensional
stochastic differential equations and Langevin equations in periodic
backgrounds with zero average. We prove that in several such models, there is
generically a non vanishing asymptotic velocity, despite of the fact that the
average of the background is zero.
| 2007-05-23 |
0705.1445 | Thomas Maeke | Rudolf M. Fuechslin, Thomas Maeke, John S. McCaskill | Multipolar Reactive DPD: A Novel Tool for Spatially Resolved Systems
Biology | submitted to CMSB 07 | null | 10.1140/epje/i2009-10482-x | null | q-bio.SC q-bio.CB | null | This article reports about a novel extension of dissipative particle dynamics
(DPD) that allows the study of the collective dynamics of complex chemical and
structural systems in a spatially resolved manner with a combinatorially
complex variety of different system constituents. We show that introducing
multipolar interactions between particles leads to extended membrane structures
emerging in a self-organized manner and exhibiting both the necessary
mechanical stability for transport and fluidity so as to provide a
two-dimensional self-organizing dynamic reaction environment for kinetic
studies in the context of cell biology. We further show that the emergent
dynamics of extended membrane bound objects is in accordance with scaling laws
imposed by physics.
| 2011-12-07 |
0705.1460 | Thomas Maeke | Rudolf M. Fuechslin, Thomas Maeke, Uwe Tangen, John S. McCaskill | Evolving inductive generalization via genetic self-assembly | null | Adv. Complex Syst., Vol. 9, Nos. 1&2 (2006) 1-29 | null | null | q-bio.PE q-bio.OT | null | We propose that genetic encoding of self-assembling components greatly
enhances the evolution of complex systems and provides an efficient platform
for inductive generalization, i.e. the inductive derivation of a solution to a
problem with a potentially infinite number of instances from a limited set of
test examples. We exemplify this in simulations by evolving scalable circuitry
for several problems. One of them, digital multiplication, has been intensively
studied in recent years, where hitherto the evolutionary design of only
specific small multipliers was achieved. The fact that this and other problems
can be solved in full generality employing self-assembly sheds light on the
evolutionary role of self-assembly in biology and is of relevance for the
design of complex systems in nano- and bionanotechnology.
| 2007-05-23 |
0705.1490 | Emidio Capriotti | Emidio Capriotti, Piero Fariselli, Ivan Rossi and Rita Casadio | A three-state prediction of single point mutations on protein stability
changes | Text: 9 pages, Figures: 9 pages, Tables: 1 page, Supplemetary
Material: 1 page | null | null | null | q-bio.BM q-bio.QM | null | A basic question of protein structural studies is to which extent mutations
affect the stability. This question may be addressed starting from sequence
and/or from structure. In proteomics and genomics studies prediction of protein
stability free energy change (DDG) upon single point mutation may also help the
annotation process. The experimental SSG values are affected by uncertainty as
measured by standard deviations. Most of the DDG values are nearly zero (about
32% of the DDG data set ranges from -0.5 to 0.5 Kcal/mol) and both the value
and sign of DDG may be either positive or negative for the same mutation
blurring the relationship among mutations and expected DDG value. In order to
overcome this problem we describe a new predictor that discriminates between 3
mutation classes: destabilizing mutations (DDG<-0.5 Kcal/mol), stabilizing
mutations (DDG>0.5 Kcal/mol) and neutral mutations (-0.5<=DDG<=0.5 Kcal/mol).
In this paper a support vector machine starting from the protein sequence or
structure discriminates between stabilizing, destabilizing and neutral
mutations. We rank all the possible substitutions according to a three state
classification system and show that the overall accuracy of our predictor is as
high as 52% when performed starting from sequence information and 58% when the
protein structure is available, with a mean value correlation coefficient of
0.30 and 0.39, respectively. These values are about 20 points per cent higher
than those of a random predictor.
| 2007-06-13 |
0705.1523 | Tobias Galla | Yoshimi Yoshino, Tobias Galla, Kei Tokita | Statistical mechanics and stability of a model eco-system | 23 pages, 13 figures; text of paper modified, discussion extended,
references added | J. Stat. Mech. (2007) P09003 | 10.1088/1742-5468/2007/09/P09003 | null | q-bio.PE cond-mat.dis-nn cond-mat.stat-mech | null | We study a model ecosystem by means of dynamical techniques from disordered
systems theory. The model describes a set of species subject to competitive
interactions through a background of resources, which they feed upon.
Additionally direct competitive or co-operative interaction between species may
occur through a random coupling matrix. We compute the order parameters of the
system in a fixed point regime, and identify the onset of instability and
compute the phase diagram. We focus on the effects of variability of resources,
direct interaction between species, co-operation pressure and dilution on the
stability and the diversity of the ecosystem. It is shown that resources can be
exploited optimally only in absence of co-operation pressure or direct
interaction between species.
| 2009-11-13 |
0705.1535 | Nicolas Ferey | Nicolas F\'erey (LIMSI), Pierre-Emmanuel Gros (LIMSI), Joan H\'erisson
(LIMSI), Rachid Gherbi (LIMSI) | Visual Data Mining of Genomic Databases by Immersive Graph-Based
Exploration | null | Visual Data Mining of Genomic Databases by Immersive Graph-Based
Exploration (2005) 4 | null | null | q-bio.QM | null | Biologists are leading current research on genome characterization
(sequencing, alignment, transcription), providing a huge quantity of raw data
about many genome organisms. Extracting knowledge from this raw data is an
important process for biologists, using usually data mining approaches.
However, it is difficult to deals with these genomic information using actual
bioinformatics data mining tools, because data are heterogeneous, huge in
quantity and geographically distributed. In this paper, we present a new
approach between data mining and virtual reality visualization, called visual
data mining. Indeed Virtual Reality becomes ripe, with efficient display
devices and intuitive interaction in an immersive context. Moreover, biologists
use to work with 3D representation of their molecules, but in a desktop
context. We present a software solution, Genome3DExplorer, which addresses the
problem of genomic data visualization, of scene management and interaction.
This solution is based on a well-adapted graphical and interaction paradigm,
where local and global topological characteristics of data are easily visible,
on the contrary to traditional genomic database browsers, always focused on the
zoom and details level.
| 2007-05-23 |
0705.1548 | Greg Stephens | Greg J Stephens, Bethany Johnson-Kerner, William Bialek and William S
Ryu | Dimensionality and dynamics in the behavior of C. elegans | 9 pages, 6 figures, minor corrections | PLoS Comput Biol 4(4): e1000028 (2008) | 10.1371/journal.pcbi.1000028 | null | q-bio.OT | null | A major challenge in analyzing animal behavior is to discover some underlying
simplicity in complex motor actions. Here we show that the space of shapes
adopted by the nematode C. elegans is surprisingly low dimensional, with just
four dimensions accounting for 95% of the shape variance, and we partially
reconstruct "equations of motion" for the dynamics in this space. These
dynamics have multiple attractors, and we find that the worm visits these in a
rapid and almost completely deterministic response to weak thermal stimuli.
Stimulus-dependent correlations among the different modes suggest that one can
generate more reliable behaviors by synchronizing stimuli to the state of the
worm in shape space. We confirm this prediction, effectively "steering" the
worm in real time.
| 2016-01-05 |
0705.1606 | Dennis C. Rapaport | D. C. Rapaport | Microscale swimming: The molecular dynamics approach | 5 pages, 3 figures (minor changes to text) | Phys. Rev.Lett. 99 (2007) 238101 | 10.1103/PhysRevLett.99.238101 | null | cond-mat.soft q-bio.SC | null | The self-propelled motion of microscopic bodies immersed in a fluid medium is
studied using molecular dynamics simulation. The advantage of the atomistic
approach is that the detailed level of description allows complete freedom in
specifying the swimmer design and its coupling with the surrounding fluid. A
series of two-dimensional swimming bodies employing a variety of propulsion
mechanisms -- motivated by biological and microrobotic designs -- is
investigated, including the use of moving limbs, changing body shapes and fluid
jets. The swimming efficiency and the nature of the induced, time-dependent
flow fields are found to differ widely among body designs and propulsion
mechanisms.
| 2007-12-06 |
0705.1656 | Manfred Bohn | Julio Mateos-Langerak, Osdilly Giromus, Wim de Leeuw, Manfred Bohn,
Pernette J. Verschure, Gregor Kreth, Dieter W. Heermann, Roel van Driel and
Sandra Goetze | Chromatin Folding in Relation to Human Genome Function | null | null | null | null | q-bio.GN | null | Three-dimensional (3D) chromatin structure is closely related to genome
function, in particular transcription. However, the folding path of the
chromatin fiber in the interphase nucleus is unknown. Here, we systematically
measured the 3D physical distance between pairwise labeled genomic positions in
gene-dense, highly transcribed domains and gene-poor less active areas on
chromosomes 1 and 11 in G1 nuclei of human primary fibroblasts, using
fluorescence in situ hybridization. Interpretation of our results and those
published by others, based on polymer physics, shows that the folding of the
chromatin fiber can be described as a polymer in a globular state (GS),
maintained by intra-polymer attractive interactions that counteract
self-avoidance forces. The GS polymer model is able to describe chromatin
folding in as well the highly expressed domains as the lowly expressed ones,
indicating that they differ in Kuhn length and chromatin compaction. Each type
of genomic domain constitutes an ensemble of relatively compact globular
folding states, resulting in a considerable cellto- cell variation between
otherwise identical cells. We present evidence for different polymer folding
regimes of the chromatin fiber on the length scale of a few mega base pairs and
on that of complete chromosome arms (several tens of Mb). Our results present a
novel view on the folding of the chromatin fiber in interphase and open the
possibility to explore the nature of the intra-chromatin fiber interactions.
| 2007-05-23 |
0705.1831 | Edward Furlani | E. P. Furlani | Continuous Magnetophoretic Separation of Blood Cells from Plasma at the
Microscale | Submitted to Journal of Applied Physics | null | 10.1088/0022-3727/40/5/001 | null | physics.bio-ph physics.med-ph | null | We present a method for the direct and continuous separation of red and white
blood cells from plasma at the microscale. The method is implemented in a
microfluidic system with magnetic functionality. The fluidic structure within
the microsystem consists of an inlet and a single microfluidic channel with
multiple outlets. The magnetic functionality is provided by an array of
integrated soft-magnetic elements that are embedded transverse and adjacent to
the microchannel. The elements are magnetized using an external field, and once
magnetized they produce a magnetic force on blood cells as they flow through
the microchannel. In whole blood, white blood cells (WBCs) behave as
diamagnetic microparticles, while red blood cells (RBCs) exhibit diamagnetic or
paramagnetic behavior depending on the oxygenation of their hemoglobin. We
study the motion of blood cells through the microchannel using a mathematical
model that takes into account the magnetic, fluidic and gravitational forces on
the cells. We use the model to study blood cell separation, and our analysis
indicates that the microsystem is capable of separating WBC-rich plasma,
deoxygenated RBC-rich plasma and cell-depleted plasma into respective outlets.
| 2009-11-13 |
0705.1845 | Pablo Echenique | Pablo Echenique | Introduction to protein folding for physicists | 53 pages, 18 figures, the figures are at a low resolution due to
arXiv restrictions, for high-res figures, go to http://www.pabloechenique.com | Contemporary Physics 48 (2007) 81-108 | 10.1080/00107510701520843 | null | physics.bio-ph cond-mat.soft physics.chem-ph q-bio.BM | null | The prediction of the three-dimensional native structure of proteins from the
knowledge of their amino acid sequence, known as the protein folding problem,
is one of the most important yet unsolved issues of modern science. Since the
conformational behaviour of flexible molecules is nothing more than a complex
physical problem, increasingly more physicists are moving into the study of
protein systems, bringing with them powerful mathematical and computational
tools, as well as the sharp intuition and deep images inherent to the physics
discipline. This work attempts to facilitate the first steps of such a
transition. In order to achieve this goal, we provide an exhaustive account of
the reasons underlying the protein folding problem enormous relevance and
summarize the present-day status of the methods aimed to solving it. We also
provide an introduction to the particular structure of these biological
heteropolymers, and we physically define the problem stating the assumptions
behind this (commonly implicit) definition. Finally, we review the 'special
flavor' of statistical mechanics that is typically used to study the
astronomically large phase spaces of macromolecules. Throughout the whole work,
much material that is found scattered in the literature has been put together
here to improve comprehension and to serve as a handy reference.
| 2008-11-24 |
0705.1974 | Franco Bagnoli | Franco Bagnoli, Pietro Lio, Luca Sguanci | Risk perception in epidemic modeling | 6 pages, 6 figures, completely new version | Phys. Rev. E 76, 061904 (2007) | 10.1103/PhysRevE.76.061904 | null | q-bio.PE q-bio.OT | null | We investigate the effects of risk perception in a simple model of epidemic
spreading. We assume that the perception of the risk of being infected depends
on the fraction of neighbors that are ill. The effect of this factor is to
decrease the infectivity, that therefore becomes a dynamical component of the
model. We study the problem in the mean-field approximation and by numerical
simulations for regular, random and scale-free networks.
We show that for homogeneous and random networks, there is always a value of
perception that stops the epidemics. In the ``worst-case'' scenario of a
scale-free network with diverging input connectivity, a linear perception
cannot stop the epidemics; however we show that a non-linear increase of the
perception risk may lead to the extinction of the disease. This transition is
discontinuous, and is not predicted by the mean-field analysis.
| 2007-12-06 |
0705.1997 | Patrick Huber | Patrick Huber, Klaus Knorr, and Andriy V. Kityk | Capillary Rise of Liquids in Nanopores | 4 pages, 1 figure, presented as a talk at the MRS Fall Meeting,
Boston (2005) in the session on "Dynamics in Confinement" | Mater. Res. Soc. Symp. Proc. 899E, N7.1 (2006) | null | null | physics.flu-dyn cond-mat.soft physics.bio-ph physics.chem-ph | null | We present measurements on the spontaneous imbibition (capillary rise) of
water, a linear hydrocarbon (n-C16H34) and a liquid crystal (8OCB) into the
pore space of monolithic, nanoporous Vycor glass (mean pore radius 5 nm).
Measurements on the mass uptake of the porous hosts as a function of time,
m(t), are in good agreement with the Lucas-Washburn square root of time
prediction, typical of imbibition of liquids into porous hosts. The relative
capillary rise velocities scale as expected from the bulk fluid parameters.
| 2007-05-23 |
0705.2032 | Andrei Paun | John Jack, Andrei Paun | Modeling the effects of HIV-1 virions and proteins on Fas-induced
apoptosis of infected cells | preliminary version | null | null | null | q-bio.MN q-bio.SC | null | We report a first in modeling and simulation of the effects of the HIV
proteins on the (caspase dependent) apoptotic pathway in infected cells. This
work is novel and is an extension on the recent reports and clarifications on
the FAS apoptotic pathway from the literature. We have gathered most of the
reaction rates and initial conditions from the literature, the rest of the
constants have been computed by fitting our model to the experimental results
reported. Using the model obtained we have then run the simulations for the
infected memory T cells, called also latent T cells, which, at the moment,
represent the major obstacle to finding a cure for HIV. We can now report that
the infected latent T cells have an estimated lifetime of about 42 hours from
the moment they are re-activated. As far as we know this is the first result of
this type obtained for the infected memory T cells.
| 2007-05-23 |
0705.2049 | Andrea Markelz | Andrea G. Markelz, Joseph R. Knab, Jing Yin Chen, and Yunfen He | Protein Dynamical Transition in Terahertz Dielectric Response | null | null | 10.1016/j.cplett.2007.05.080 | null | physics.bio-ph physics.chem-ph | null | The 200 K protein dynamical transition is observed for the first time in the
teraherz dielectric response. The complex dielectric permittivity $\epsilon$ =
$\epsilon$' + i$\epsilon$" is determined in the 0.2 - 2.0 THz and 80-294 K
ranges. $\epsilon$" has a linear temperature dependence up to 200 K then
sharply increases. The low temperature linear dependence in $\epsilon$"
indicates anharmonicity for temperatures 80 K < T < 180 K, challenging the
assumed harmonicity below 200K. The temperature dependence is consistent with
beta relaxation response and shows the protein motions involved in the
dynamical transition extend to subpicosecond time scales.
| 2009-11-13 |
0705.2057 | Nikolai Sinitsyn | N. A. Sinitsyn and I. Nemenman | The unified geometric theory of mesoscopic stochastic pumps and
reversible ratchets | 5 pages | Phys. Rev. Lett. 99, 220408 (2007) | 10.1103/PhysRevLett.99.220408 | LAUR- 07-0243 | cond-mat.stat-mech q-bio.QM | null | We construct a unifying theory of geometric effects in mesoscopic stochastic
kinetics. We demonstrate that the adiabatic pump and the reversible ratchet
effects, as well as similar new phenomena in other domains, such as in
epidemiology, all follow from geometric phase contributions to the effective
action in the stochastic path integral representation of the moment generating
function. The theory provides the universal technique for identification,
prediction and calculation of pump-like phenomena in an arbitrary mesoscopic
stochastic framework.
| 2009-11-13 |
0705.2092 | Erik Volz | Erik Volz | SIR dynamics in random networks with heterogeneous connectivity | 25 pages, 6 figures. Greatly revised version of arXiv:physics/0508160 | null | null | null | q-bio.PE q-bio.QM | null | Random networks with specified degree distributions have been proposed as
realistic models of population structure, yet the problem of dynamically
modeling SIR-type epidemics in random networks remains complex. I resolve this
dilemma by showing how the SIR dynamics can be modeled with a system of three
nonlinear ODE's. The method makes use of the probability generating function
(PGF) formalism for representing the degree distribution of a random network
and makes use of network-centric quantities such as the number of edges in a
well-defined category rather than node-centric quantities such as the number of
infecteds or susceptibles. The PGF provides a simple means of translating
between network and node-centric variables and determining the epidemic
incidence at any time. The theory also provides a simple means of tracking the
evolution of the degree distribution among susceptibles or infecteds. The
equations are used to demonstrate the dramatic effects that the degree
distribution plays on the final size of an epidemic as well as the speed with
which it spreads through the population. Power law degree distributions are
observed to generate an almost immediate expansion phase yet have a smaller
final size compared to homogeneous degree distributions such as the Poisson.
The equations are compared to stochastic simulations, which show good agreement
with the theory. Finally, the dynamic equations provide an alternative way of
determining the epidemic threshold where large-scale epidemics are expected to
occur, and below which epidemic behavior is limited to finite-sized outbreaks.
| 2007-05-23 |
0705.2105 | Erik Volz | Erik Volz and Lauren Ancel Meyers | SIR epidemics in dynamic contact networks | 20 pages, 4 figures. Submitted to Proc. Roy. Soc. B | null | null | null | q-bio.PE q-bio.QM | null | Contact patterns in populations fundamentally influence the spread of
infectious diseases. Current mathematical methods for epidemiological
forecasting on networks largely assume that contacts between individuals are
fixed, at least for the duration of an outbreak. In reality, contact patterns
may be quite fluid, with individuals frequently making and breaking social or
sexual relationships. Here we develop a mathematical approach to predicting
disease transmission on dynamic networks in which each individual has a
characteristic behavior (typical contact number), but the identities of their
contacts change in time. We show that dynamic contact patterns shape
epidemiological dynamics in ways that cannot be adequately captured in static
network models or mass-action models. Our new model interpolates smoothly
between static network models and mass-action models using a mixing parameter,
thereby providing a bridge between disparate classes of epidemiological models.
Using epidemiological and sexual contact data from an Atlanta high school, we
then demonstrate the utility of this method for forecasting and controlling
sexually transmitted disease outbreaks.
| 2007-05-23 |
0705.2143 | Fabrizio Lillo | Fabrizio Lillo and Marco Span\'o | Inverted and mirror repeats in model nucleotide sequences | 12 pages, 6 figures | null | 10.1103/PhysRevE.76.041914 | null | q-bio.GN q-bio.QM | null | We analytically and numerically study the probabilistic properties of
inverted and mirror repeats in model sequences of nucleic acids. We consider
both perfect and non-perfect repeats, i.e. repeats with mismatches and gaps.
The considered sequence models are independent identically distributed (i.i.d.)
sequences, Markov processes and long range sequences. We show that the number
of repeats in correlated sequences is significantly larger than in i.i.d.
sequences and that this discrepancy increases exponentially with the repeat
length for long range sequences.
| 2009-11-13 |
0705.2215 | Philipp Diesinger | P.M.Diesinger and D.W.Heermann | The influence of the cylindrical shape of the nucleosomes and H1 defects
on properties of chromatin | null | null | 10.1529/biophysj.107.113902 | null | cond-mat.soft cond-mat.stat-mech q-bio.SC | null | We present a model improving the two-angle model for interphase chromatin
(E2A model). This model takes into account the cylindrical shape of the histone
octamers, the H1 histones in front of the nucleosomes and the vertical distance
$d$ between the in and outgoing DNA strands. Factoring these chromatin features
in, one gets essential changes in the chromatin phase diagram: Not only the
shape of the excluded-volume borderline changes but also the vertical distance
$d$ has a dramatic influence on the forbidden area. Furthermore, we examined
the influence of H1 defects on the properties of the chromatin fiber. Thus we
present two possible strategies for chromatin compaction: The use of very dense
states in the phase diagram in the gaps in the excluded volume borderline or
missing H1 histones which can lead to very compact fibers. The chromatin fiber
might use both of these mechanisms to compact itself at least locally. Line
densities computed within the model coincident with the experimental values.
| 2009-11-13 |
0705.2281 | J\"urgen Sawinski | J. Sawinski, D. Debarre, W. Denk | Tunable Ti:Al2O3 oscillator optimized for high-repetition-rate and short
pulses | 14 pages, 5 figures | null | null | null | physics.optics physics.bio-ph | null | A laser was designed and constructed with the goal of producing ultra-short
pulses at a high repetition rate as needed for certain applications of
multi-photon microscopy. With pure prism-based dispersion compensation
repetition rates of up to 270MHz were achieved. The laser operates with hard-
and soft-aperturing at the third (diverging output) and the first (parallel
output) stability limits, respectively. At the third stability limit we found a
pulse width of 27fs (FWHM) at 800nm central wavelength. At the first stability
limit pulse widths of 23-40fs with tunability from 780nm to 920nm were reached.
| 2007-05-23 |
0705.2286 | Bernhard Mehlig | A. Eriksson, P. Fernstrom, B. Mehlig, and S. Sagitov | An accurate model for genetic hitch-hiking | 12 pages, 10 figures | Genetics 178, 439 (2008) | null | null | q-bio.PE | null | We suggest a simple deterministic approximation for the growth of the
favoured-allele frequency during a selective sweep. Using this approximation we
introduce an accurate model for genetic hitch-hiking. Only when Ns < 10 (N is
the population size and s denotes the selection coefficient), are discrepancies
between our approximation and direct numerical simulations of a Moran model
noticeable. Our model describes the gene genealogies of a contiguous segment of
neutral loci close to the selected one, and it does not assume that the
selective sweep happens instantaneously. This enables us to compute SNP
distributions on the neutral segment without bias.
| 2008-12-19 |
0705.2355 | Piero Fariselli | Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Ivan Rossi
and Rita Casadio | In silico evidence of the relationship between miRNAs and siRNAs | 8 pages, 2 figures | null | null | null | q-bio.BM q-bio.GN | null | Both short interfering RNAs (siRNAs) and microRNAs (miRNAs) mediate the
repression of specific sequences of mRNA through the RNA interference pathway.
In the last years several experiments have supported the hypothesis that siRNAs
and miRNAs may be functionally interchangeable, at least in cultured cells. In
this work we verify that this hypothesis is also supported by a computational
evidence. We show that a method specifically trained to predict the activity of
the exogenous siRNAs assigns a high silencing level to experimentally
determined human miRNAs. This result not only supports the idea of siRNAs and
miRNAs equivalence but indicates that it is possible to use computational tools
developed using synthetic small interference RNAs to investigate endogenous
miRNAs.
| 2007-05-23 |
0705.2485 | Bodie Crossingham | Bodie Crossingham and Tshilidzi Marwala | Using Genetic Algorithms to Optimise Rough Set Partition Sizes for HIV
Data Analysis | 10 pages, 1 figure, Update Bibliography | null | null | null | cs.NE cs.AI q-bio.QM | null | In this paper, we present a method to optimise rough set partition sizes, to
which rule extraction is performed on HIV data. The genetic algorithm
optimisation technique is used to determine the partition sizes of a rough set
in order to maximise the rough sets prediction accuracy. The proposed method is
tested on a set of demographic properties of individuals obtained from the
South African antenatal survey. Six demographic variables were used in the
analysis, these variables are; race, age of mother, education, gravidity,
parity, and age of father, with the outcome or decision being either HIV
positive or negative. Rough set theory is chosen based on the fact that it is
easy to interpret the extracted rules. The prediction accuracy of equal width
bin partitioning is 57.7% while the accuracy achieved after optimising the
partitions is 72.8%. Several other methods have been used to analyse the HIV
data and their results are stated and compared to that of rough set theory
(RST).
| 2007-06-25 |
0705.2491 | Kazuya Ishibashi | Kazuya Ishibashi, Kosuke Hamaguchi, and Masato Okada | Sparse and Dense Encoding in Layered Associative Network of Spiking
Neurons | null | null | 10.1143/JPSJ.76.124801 | null | q-bio.NC | null | A synfire chain is a simple neural network model which can propagate stable
synchronous spikes called a pulse packet and widely researched. However how
synfire chains coexist in one network remains to be elucidated. We have studied
the activity of a layered associative network of Leaky Integrate-and-Fire
neurons in which connection we embed memory patterns by the Hebbian Learning.
We analyzed their activity by the Fokker-Planck method. In our previous report,
when a half of neurons belongs to each memory pattern (memory pattern rate
$F=0.5$), the temporal profiles of the network activity is split into
temporally clustered groups called sublattices under certain input conditions.
In this study, we show that when the network is sparsely connected ($F<0.5$),
synchronous firings of the memory pattern are promoted. On the contrary, the
densely connected network ($F>0.5$) inhibit synchronous firings. The sparseness
and denseness also effect the basin of attraction and the storage capacity of
the embedded memory patterns. We show that the sparsely(densely) connected
networks enlarge(shrink) the basion of attraction and increase(decrease) the
storage capacity.
| 2009-11-13 |
0705.2504 | Yuichi Togashi | Yuichi Togashi, Alexander S. Mikhailov | Nonlinear Relaxation Dynamics in Elastic Networks and Design Principles
of Molecular Machines | 12 pages, 9 figures | Proc. Natl. Acad. Sci. (USA) 104, 8697 (2007) | 10.1073/pnas.0702950104 | null | q-bio.BM cond-mat.soft physics.chem-ph | null | Analyzing nonlinear conformational relaxation dynamics in elastic networks
corresponding to two classical motor proteins, we find that they respond by
well-defined internal mechanical motions to various initial deformations and
that these motions are robust against external perturbations. We show that this
behavior is not characteristic for random elastic networks. However, special
network architectures with such properties can be designed by evolutionary
optimization methods. Using them, an example of an artificial elastic network,
operating as a cyclic machine powered by ligand binding, is constructed.
| 2007-06-13 |
0705.2523 | Harshada Nagar | Srikanya Kundu, Harshada Nagar, S D Kulkarni, Renu Pasricha, A K Das,
G R Kulkarni and S V Bhoraskar | Applications of nanoparticles of gamma Fe2O3 for hyperthermia in E.coli
by Nd:YAG laser | 13 pages, 8 figures, communicated to Journal of Nanoparticle Research | null | null | null | physics.bio-ph | null | The paper explores the use of nanoparticles of gamma Fe2O3 for hyperthermia
treatment of living organisms by absorption of 1064 nm radiations from Nd:YAG
laser. Escherichia coli cells have been used as the model system for
demonstrating the effect wherein lysine is used as an interface between the
cell walls and the nanoparticles. Scanning Electron Microscopic observations
have, exclusively, proved that attachment of nanoparticles of iron oxide along
with lysine alone is responsible for absorption of above radiations. The
quantitative estimation has been provided by growth rate measurements and
protein assessment of the cells. The nanoparticles of gamma Fe2O3 were
synthesized by DC arc plasma assisted gas phase condensation.
| 2007-05-23 |
0705.2594 | Tibor Antal | Tibor Antal, P. L. Krapivsky, and Kirone Mallick | Molecular Spiders in One Dimension | 14 pages, 2 figures | Journal of Statistical Mechanics P08027 (2007) | 10.1088/1742-5468/2007/08/P08027 | null | cond-mat.stat-mech math.PR q-bio.QM | null | Molecular spiders are synthetic bio-molecular systems which have "legs" made
of short single-stranded segments of DNA. Spiders move on a surface covered
with single-stranded DNA segments complementary to legs. Different mappings are
established between various models of spiders and simple exclusion processes.
For spiders with simple gait and varying number of legs we compute the
diffusion coefficient; when the hopping is biased we also compute their
velocity.
| 2007-08-25 |
0705.2596 | Tibor Antal | Tibor Antal and P. L. Krapivsky | Molecular Spiders with Memory | 10 pages, 3 figures | Physical Review E 76, 021121 (2007) | 10.1103/PhysRevE.76.021121 | null | cond-mat.stat-mech math.PR q-bio.QM | null | Synthetic bio-molecular spiders with "legs" made of single-stranded segments
of DNA can move on a surface which is also covered by single-stranded segments
of DNA complementary to the leg DNA. In experimental realizations, when a leg
detaches from a segment of the surface for the first time it alters that
segment, and legs subsequently bound to these altered segments more weakly.
Inspired by these experiments we investigate spiders moving along a
one-dimensional substrate, whose legs leave newly visited sites at a slower
rate than revisited sites. For a random walk (one-leg spider) the slowdown does
not effect the long time behavior. For a bipedal spider, however, the slowdown
generates an effective bias towards unvisited sites, and the spider behaves
similarly to the excited walk. Surprisingly, the slowing down of the spider at
new sites increases the diffusion coefficient and accelerates the growth of the
number of visited sites.
| 2007-08-25 |
0705.2607 | Max Shpak | Max Shpak | Selection Against Demographic Stochasticity in Age-Structured
Populations | null | null | null | null | q-bio.PE | null | It has been shown that differences in fecundity variance can influence the
probability of invasion of a genotype in a population, i.e. a genotype with
lower variance in offspring number can be favored in finite populations even if
it has a somewhat lower mean fitness than a competitor. In this paper,
Gillespie's results are extended to population genetic systems with explicit
age structure, where the demographic variance (variance in growth rate)
calculated in the work of Engen and colleagues is used as a generalization of
"variance in offspring number" to predict the interaction between deterministic
and random forces driving change in allele frequency. By calculating the
variance from the life history parameters, it is shown that selection against
variance in the growth rate will favor a genotypes with lower stochasticity in
age specific survival and fertility rates. A diffusion approximation for
selection and drift in a population with two genotypes with different life
history matrices (and therefore, different growth rates and demographic
variances) is derived and shown to be consistent with individual based
simulations. It is also argued that for finite populations, perturbation
analyses of both the growth rate and demographic variances may be necessary to
determine the sensitivity of "fitness" (broadly defined) to changes in the life
history parameters.
| 2007-05-23 |
0705.2646 | Martin Weigt | Michele Leone, Sumedha, Martin Weigt | Clustering by soft-constraint affinity propagation: Applications to
gene-expression data | 11 pages, supplementary material:
http://isiosf.isi.it/~weigt/scap_supplement.pdf | Bioinformatics 23, 2708 (2007) | 10.1093/bioinformatics/btm414 | null | q-bio.QM cond-mat.stat-mech physics.data-an | null | Motivation: Similarity-measure based clustering is a crucial problem
appearing throughout scientific data analysis. Recently, a powerful new
algorithm called Affinity Propagation (AP) based on message-passing techniques
was proposed by Frey and Dueck \cite{Frey07}. In AP, each cluster is identified
by a common exemplar all other data points of the same cluster refer to, and
exemplars have to refer to themselves. Albeit its proved power, AP in its
present form suffers from a number of drawbacks. The hard constraint of having
exactly one exemplar per cluster restricts AP to classes of regularly shaped
clusters, and leads to suboptimal performance, {\it e.g.}, in analyzing gene
expression data. Results: This limitation can be overcome by relaxing the AP
hard constraints. A new parameter controls the importance of the constraints
compared to the aim of maximizing the overall similarity, and allows to
interpolate between the simple case where each data point selects its closest
neighbor as an exemplar and the original AP. The resulting soft-constraint
affinity propagation (SCAP) becomes more informative, accurate and leads to
more stable clustering. Even though a new {\it a priori} free-parameter is
introduced, the overall dependence of the algorithm on external tuning is
reduced, as robustness is increased and an optimal strategy for parameter
selection emerges more naturally. SCAP is tested on biological benchmark data,
including in particular microarray data related to various cancer types. We
show that the algorithm efficiently unveils the hierarchical cluster structure
present in the data sets. Further on, it allows to extract sparse gene
expression signatures for each cluster.
| 2007-11-29 |
0705.2704 | Danielle Rojas-Rousse | Auguste Ndoutoume, Danielle Rousse (IRBII), Roland Allemand | Rythmes d'activit\'e locomotrice chez deux insectes parasito\"ides
sympatriques : Eupelmus orientalis et Eupelmus vuilleti (Hym\'enopt\`ere,
Eupelmidae) | null | Comptes Rendus Biologies 329 (2006) 476-482 | null | null | q-bio.PE | null | With an automatic image analysis device, we studied the temporal distribution
of the locomotor activity of E. orientalis and E. vuilleti during 24 h, and
over several days to know whether the activity rhythms of these two Eupelmidae
play a role in their competitive interactions. The analysis of locomotor
activity rhythms of E. orientalis and E. vuilleti shows that the locomotor
activity of both species presents daily cyclic variations. These two Eupelmidae
have similar activity rhythms. Displacements of these parasitoids essentially
take place during the photophase. But the activity of E. vuilleti is earlier,
because the individuals of this species start their activity on average 4 to 5
h earlier than those of E. orientalis. E. vuilleti begins its displacements
several hours before the onset of lighting, whereas E. orientalis is active
only in the presence of the light. This shift of starting activity is thus a
factor allowing these concurrent species to minimize their interactions during
the cohabitation period in traditional granaries after the harvests of cowpea.
| 2007-05-23 |
0705.2706 | Massimo Sandal | Francesco Valle, Massimo Sandal, Bruno Samor\'i | The Interplay between Chemistry and Mechanics in the Transduction of a
Mechanical Signal into a Biochemical Function | 50 pages, 18 figures | null | 10.1016/j.plrev.2007.06.001 | null | q-bio.BM q-bio.MN | null | There are many processes in biology in which mechanical forces are generated.
Force-bearing networks can transduce locally developed mechanical signals very
extensively over different parts of the cell or tissues. In this article we
conduct an overview of this kind of mechanical transduction, focusing in
particular on the multiple layers of complexity displayed by the mechanisms
that control and trigger the conversion of a mechanical signal into a
biochemical function. Single molecule methodologies, through their capability
to introduce the force in studies of biological processes in which mechanical
stresses are developed, are unveiling subtle intertwining mechanisms between
chemistry and mechanics and in particular are revealing how chemistry can
control mechanics. The possibility that chemistry interplays with mechanics
should be always considered in biochemical studies.
| 2009-11-13 |
0705.2707 | Z. C. Tu | Z. C. Tu and U. Seifert | Concise theory of chiral lipid membranes | 14 pages, 7 figures | Phys. Rev. E 76, 031603 (2007) | 10.1103/PhysRevE.76.031603 | null | cond-mat.soft math-ph math.MP physics.bio-ph | null | A theory of chiral lipid membranes is proposed on the basis of a concise free
energy density which includes the contributions of the bending and the surface
tension of membranes, as well as the chirality and orientational variation of
tilting molecules. This theory is consistent with the previous experiments
[J.M. Schnur \textit{et al.}, Science \textbf{264}, 945 (1994); M.S. Spector
\textit{et al.}, Langmuir \textbf{14}, 3493 (1998); Y. Zhao, \textit{et al.},
Proc. Natl. Acad. Sci. USA \textbf{102}, 7438 (2005)] on self-assembled chiral
lipid membranes of DC$_{8,9}$PC. A torus with the ratio between its two
generated radii larger than $\sqrt{2}$ is predicted from the Euler-Lagrange
equations. It is found that tubules with helically modulated tilting state are
not admitted by the Euler-Lagrange equations, and that they are less
energetically favorable than helical ripples in tubules. The pitch angles of
helical ripples are theoretically estimated to be about 0$^\circ$ and
35$^\circ$, which are close to the most frequent values 5$^\circ$ and
28$^\circ$ observed in the experiment [N. Mahajan \textit{et al.}, Langmuir
\textbf{22}, 1973 (2006)]. Additionally, the present theory can explain twisted
ribbons of achiral cationic amphiphiles interacting with chiral tartrate
counterions. The ratio between the width and pitch of twisted ribbons is
predicted to be proportional to the relative concentration difference of left-
and right-handed enantiomers in the low relative concentration difference
region, which is in good agreement with the experiment [R. Oda \textit{et al.},
Nature (London) \textbf{399}, 566 (1999)].
| 2007-09-27 |
0705.2710 | Danielle Rojas-Rousse | Danielle Rojas-Rousse (IRBII), Karine Poitrineau, Cesar Basso | The potential of mass rearing of Monoksa dorsiplana (Pteromalidae) a
native gregarious ectoparasitoid of Pseudopachymeria spinipes (Bruchidae)in
South America | null | Biological Control 41 (30/04/2007) 348-353 | null | null | q-bio.PE | null | In Chile and Uruguay,the gregarious Pteromalidae (Monoksa dorsiplana) has
been discovered emerging from seeds of the persistent pods of Acacia caven
attacked by the univoltin bruchid Pseudopachymeria spinipes. We investigated
the potential for mass rearing of this gregarious ectoparasitoid on an
alternative bruchid host, Callosobruchus maculatus, to use it against the
bruchidae of native and cultured species of Leguminosea seeds in South America.
The mass rearing of M.dorsiplana was carried out in a population cage where the
density of egg-laying females per infested seed was increased from 1:1 on the
first day to 5:1 on the last (fifth) day. Under these experimental conditions
egg-clutch size per host increased, and at the same time the mortality of eggs
laid also increased. The density of egg-laying females influenced the sex ratio
which tended towards a balance of sons and daughters,in contrast to the sex
ratio of a single egg-laying female per host (1 son to 7 daughters). The mean
weight of adults emerging from a parasitized host was negatively correlated
with the egg-clutch size, i.e., as egg-clutch size increased, adult weight
decreased. All these results show that mass rearing of the gregarious
ectoparasitoid M.dorsiplana was possible under laboratory conditions on an
alternative bruchid host C.maculatus. As M.dorsiplana is a natural enemy of
larval and pupal stages of bruchidae, the next step was to investigate whether
the biological control of bruchid C.maculatus was possible in an experimental
structure of stored beans.
| 2007-05-23 |
0705.2711 | F\`elix Campelo | F. Campelo and A. Hernandez-Machado | Shape instabilities in vesicles: a phase-field model | null | Eur. Phys. J. Special Topics, 143: 101-108 (2007) | 10.1140/epjst/e2007-00077-y | null | cond-mat.soft q-bio.QM | null | A phase field model for dealing with shape instabilities in fluid membrane
vesicles is presented. This model takes into account the Canham-Helfrich
bending energy with spontaneous curvature. A dynamic equation for the
phase-field is also derived. With this model it is possible to see the vesicle
shape deformation dynamically, when some external agent instabilizes the
membrane, for instance, inducing an inhomogeneous spontaneous curvature. The
numerical scheme used is detailed and some stationary shapes are shown together
with a shape diagram for vesicles of spherical topology and no spontaneous
curvature, in agreement with known results.
| 2007-07-26 |
0705.2747 | Vladimir Gubernov | A.V. Kolobov, V.V. Gubernov, A.A. Polezhaev | Autowaves in the model of avascular tumour growth | 9 pages, 7 figures | null | null | null | q-bio.TO nlin.PS | null | A mathematical model of infiltrative tumour growth taking into account cell
proliferation, death and motility is considered. The model is formulated in
terms of local cell density and nutrient (oxygen) concentration. In the model
the rate of cell death depends on the local nutrient level. Thus heterogeneous
nutrient distribution in tissue affects tumour structure and development. The
existence of automodel solutions is demonstrated and their properties are
investigated. The results are compared to the properties of the
Kolmogorov-Petrovskii-Piskunov and Fisher equations. Influence of the nutrient
distribution on the autowave speed selection as well as on the relaxation to
automodel solution is demonstrated. The model adequately describes the data,
observed in experiments.
| 2007-05-23 |
0705.2811 | Alessandro Torcini | R\"udiger Zillmer, Roberto Livi, Antonio Politi, and Alessandro
Torcini | Stability of the splay state in pulse--coupled networks | 13 pages, 10 figures, submitted for pubblication to Physical Review E | Phys. Rev. E 76, 046102 (2007) | 10.1103/PhysRevE.76.046102 | null | cond-mat.dis-nn q-bio.NC | null | The stability of the dynamical states characterized by a uniform firing rate
({\it splay states}) is analyzed in a network of globally coupled leaky
integrate-and-fire neurons. This is done by reducing the set of differential
equations to a map that is investigated in the limit of large network size. We
show that the stability of the splay state depends crucially on the ratio
between the pulse--width and the inter-spike interval. More precisely, the
spectrum of Floquet exponents turns out to consist of three components: (i) one
that coincides with the predictions of the mean-field analysis [Abbott-van
Vreesvijk, 1993]; (ii) a component measuring the instability of
"finite-frequency" modes; (iii) a number of "isolated" eigenvalues that are
connected to the characteristics of the single pulse and may give rise to
strong instabilities (the Floquet exponent being proportional to the network
size). Finally, as a side result, we find that the splay state can be stable
even for inhibitory coupling.
| 2007-11-27 |
0705.2816 | Ginestra Bianconi | Ginestra Bianconi and Riccardo Zecchina | Viable flux distribution in metabolic networks | (10 pages, 1 figure) | null | null | null | q-bio.MN | null | The metabolic networks are very well characterized for a large set of
organisms, a unique case in within the large-scale biological networks. For
this reason they provide a a very interesting framework for the construction of
analytically tractable statistical mechanics models.
In this paper we introduce a solvable model for the distribution of fluxes in
the metabolic network. We show that the effect of the topology on the
distribution of fluxes is to allow for large fluctuations of their values, a
fact that should have implications on the robustness of the system.
| 2007-05-23 |
0705.2907 | Tom Chou | Tom Chou | Peeling and Sliding in Nucleosome Repositioning | 5 pp, 4 figs | Phys. Rev. Lett., 99, 058105, (2007) | 10.1103/PhysRevLett.99.058105 | null | q-bio.SC q-bio.BM | null | We investigate the mechanisms of histone sliding and detachment with a
stochastic model that couples thermally-induced, passive histone sliding with
active motor-driven histone unwrapping. Analysis of a passive loop or twist
defect-mediated histone sliding mechanism shows that diffusional sliding is
enhanced as larger portions of the DNA is peeled off the histone. The mean
times to histone detachment and the mean distance traveled by the motor complex
prior to histone detachment are computed as functions of the intrinsic speed of
the motor. Fast motors preferentially induce detachment over sliding. However,
for a fixed motor speed, increasing the histone-DNA affinity (and thereby
decreasing the passive sliding rate) increases the mean distance traveled by
the motor.
| 2009-11-13 |
0705.2913 | Jan Karbowski | Jan Karbowski | Global and regional brain metabolic scaling and its functional
consequences | Brain metabolism scales with its mass well above 3/4 exponent | BMC Biology 5:18 (2007) | null | null | q-bio.NC q-bio.TO | null | Background: Information processing in the brain requires large amounts of
metabolic energy, the spatial distribution of which is highly heterogeneous
reflecting complex activity patterns in the mammalian brain.
Results: Here, it is found based on empirical data that, despite this
heterogeneity, the volume-specific cerebral glucose metabolic rate of many
different brain structures scales with brain volume with almost the same
exponent around -0.15. The exception is white matter, the metabolism of which
seems to scale with a standard specific exponent -1/4. The scaling exponents
for the total oxygen and glucose consumptions in the brain in relation to its
volume are identical and equal to $0.86\pm 0.03$, which is significantly larger
than the exponents 3/4 and 2/3 suggested for whole body basal metabolism on
body mass.
Conclusions: These findings show explicitly that in mammals (i)
volume-specific scaling exponents of the cerebral energy expenditure in
different brain parts are approximately constant (except brain stem
structures), and (ii) the total cerebral metabolic exponent against brain
volume is greater than the much-cited Kleiber's 3/4 exponent. The
neurophysiological factors that might account for the regional uniformity of
the exponents and for the excessive scaling of the total brain metabolism are
discussed, along with the relationship between brain metabolic scaling and
computation.
| 2007-05-23 |
0705.3022 | M. Shane Hutson | M. Shane Hutson and Xiaoyan Ma | Plasma and cavitation dynamics during pulsed laser microsurgery in vivo | 9 pages, 5 figures | Phys. Rev. Lett. 99, 158104 (2007) | 10.1103/PhysRevLett.99.158104 | null | physics.bio-ph physics.med-ph | null | We compare the plasma and cavitation dynamics underlying pulsed laser
microsurgery in water and in fruit fly embryos (in vivo) - specifically for
nanosecond pulses at 355 and 532 nm. We find two key differences. First, the
plasma-formation thresholds are lower in vivo - especially at 355 nm - due to
the presence of endogenous chromophores that serve as additional sources for
plasma seed electrons. Second, the biological matrix constrains the growth of
laser-induced cavitation bubbles. Both effects reduce the disrupted region in
vivo when compared to extrapolations from measurements in water.
| 2008-10-24 |
0705.3188 | Eduardo D. Sontag | Murat Arcak and Eduardo D. Sontag | A passivity-based stability criterion for a class of interconnected
systems and applications to biochemical reaction networks | See http://www.math.rutgers.edu/~sontag/PUBDIR/index.html for related
(p)reprints | null | null | null | q-bio.QM | null | This paper presents a stability test for a class of interconnected nonlinear
systems motivated by biochemical reaction networks. One of the main results
determines global asymptotic stability of the network from the diagonal
stability of a "dissipativity matrix" which incorporates information about the
passivity properties of the subsystems, the interconnection structure of the
network, and the signs of the interconnection terms. This stability test
encompasses the "secant criterion" for cyclic networks presented in our
previous paper, and extends it to a general interconnection structure
represented by a graph. A second main result allows one to accommodate state
products. This extension makes the new stability criterion applicable to a
broader class of models, even in the case of cyclic systems. The new stability
test is illustrated on a mitogen activated protein kinase (MAPK) cascade model,
and on a branched interconnection structure motivated by metabolic networks.
Finally, another result addresses the robustness of stability in the presence
of diffusion terms in a compartmental system made out of identical systems.
| 2007-05-23 |
0705.3195 | Mendeli Vainstein | M. H. Vainstein, J. M. Rubi and J. M. G. Vilar | Stochastic population dynamics in turbulent fields | 11 pages, 9 figures. Submitted to EPJ Special Topics | null | 10.1140/epjst/e2007-00178-7 | null | q-bio.PE cond-mat.stat-mech | null | The behavior of interacting populations typically displays irregular temporal
and spatial patterns that are difficult to reconcile with an underlying
deterministic dynamics. A classical example is the heterogeneous distribution
of plankton communities, which has been observed to be patchy over a wide range
of spatial and temporal scales. Here, we use plankton communities as prototype
systems to present theoretical approaches for the analysis of the combined
effects of turbulent advection and stochastic growth in the spatiotemporal
dynamics of the population. Incorporation of these two factors into
mathematical models brings an extra level of realism to the description and
leads to better agreement with experimental data than that of previously
proposed models based on reaction-diffusion equations.
| 2009-11-13 |
0705.3218 | Jeffrey Buboltz | Jeffrey T. Buboltz, Charles Bwalya, Santiago Reyes, Dobromir Kamburov | Stern-Volmer Modeling of Steady-State Forster Energy Transfer Between
Dilute, Freely Diffusing Membrane-Bound Fluorophores | 6 pages, 4 figures, submitted to J Chem Phys | null | 10.1063/1.2800564 | null | physics.chem-ph physics.bio-ph | null | Two different metrics are used to assess Forster resonance energy transfer
(FRET) between fluorophores in the steady state: (1) acceptor-quenching of
donor fluorescence, E (a.k.a. transfer efficiency); and (ii) donor-excited
acceptor fluorescence, F-A-Dex. While E is still more widely used, F-A-Dex has
been gaining in popularity for practical reasons among experimentalists who
study biomembranes. Here, for the special case of membrane-bound fluorophores,
we present a substantial body of experimental evidence that justifies the use
of simple Stern-Volmer expressions when modeling either FRET metric under
dilute-probe conditions. We have also discovered a dilute-regime correspondence
between our Stern-Volmer expression for E and Wolber and Hudson's series
approximation for steady-state Forster quenching in 2D. This novel
correspondence allows us to interpret each of our 2D quenching constants in
terms of both (i) an effective Forster distance, and (ii) two maximum
acceptor-concentration limits, each of which defines its own useful
experimental regime. Taken together, our results suggest a three-step strategy
toward designing more effective steady-state FRET experiments for the study of
biomembranes.
| 2009-11-13 |
0705.3256 | Alberto Imparato | Alberto Imparato, Stefano Luccioli, Alessandro Torcini | Reconstructing the free energy landscape of a mechanically unfolded
model protein | null | Phys. Rev. Lett. 99, 168101 (2007) | 10.1103/PhysRevLett.99.168101 | null | cond-mat.stat-mech q-bio.BM | null | The equilibrium free energy landscape of an off-lattice model protein as a
function of an internal (reaction) coordinate is reconstructed from
out-of-equilibrium mechanical unfolding manipulations. This task is
accomplished via two independent methods: by employing an extended version of
the Jarzynski equality (EJE) and the protein inherent structures (ISs). In a
range of temperatures around the ``folding transition'' we find a good
quantitative agreement between the free energies obtained via EJE and IS
approaches. This indicates that the two methodologies are consistent and able
to reproduce equilibrium properties of the examined system. Moreover, for the
studied model the structural transitions induced by pulling can be related to
thermodynamical aspects of folding.
| 2007-10-17 |
0705.3373 | Anirban Banerjee | Anirban Banerjee and J\"urgen Jost | Laplacian Spectrum and Protein-Protein Interaction Networks | 7 pages, 3 figures | null | null | null | q-bio.QM physics.data-an q-bio.PE | null | From the spectral plot of the (normalized) graph Laplacian, the essential
qualitative properties of a network can be simultaneously deduced. Given a
class of empirical networks, reconstruction schemes for elucidating the
evolutionary dynamics leading to those particular data can then be developed.
This method is exemplified for protein-protein interaction networks. Traces of
their evolutionary history of duplication and divergence processes are
identified. In particular, we can identify typical specific features that
robustly distinguish protein-protein interaction networks from other classes of
networks, in spite of possible statistical fluctuations of the underlying data.
| 2007-05-24 |
0705.3473 | Alex Barnett | A. H. Barnett and P. R. Moorcroft | Analytic steady-state space use patterns and rapid computations in
mechanistic home range analysis | 14 pages, 7 figures, submit to J. Math. Biol | null | null | null | q-bio.QM | null | Mechanistic home range models are important tools in modeling animal dynamics
in spatially-complex environments. We introduce a class of stochastic models
for animal movement in a habitat of varying preference. Such models interpolate
between spatially-implicit resource selection analysis (RSA) and
advection-diffusion models, possessing these two models as limiting cases. We
find a closed-form solution for the steady-state (equilibrium) probability
distribution u* using a factorization of the redistribution operator into
symmetric and diagonal parts. How space use is controlled by the preference
function w then depends on the characteristic width of the redistribution
kernel: when w changes rapidly compared to this width, u* ~ w, whereas on
global scales large compared to this width, u* ~ w^2. We analyse the behavior
at discontinuities in w which occur at habitat type boundaries. We simulate the
dynamics of space use given two-dimensional prey-availability data and explore
the effect of the redistribution kernel width. Our factorization allows such
numerical simulations to be done extremely fast; we expect this to aid the
computationally-intensive task of model parameter fitting and inverse modeling.
| 2007-05-25 |
0705.3597 | Dennis Shasha | Dennis Shasha (Courant Institute, New York University) and Martyn Amos
(Computing and Mathematics, Manchester Metropolitan University) | DNA Hash Pooling and its Applications | 14 pages, 3 figures. To appear in the International Journal of
Nanotechnology and Molecular Computation. Improved background, analysis and
references | null | null | null | q-bio.BM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we describe a new technique for the comparison of populations
of DNA strands. Comparison is vital to the study of ecological systems, at both
the micro and macro scales. Existing methods make use of DNA sequencing and
cloning, which can prove costly and time consuming, even with current
sequencing techniques. Our overall objective is to address questions such as:
(i) (Genome detection) Is a known genome sequence present, at least in part, in
an environmental sample? (ii) (Sequence query) Is a specific fragment sequence
present in a sample? (iii) (Similarity discovery) How similar in terms of
sequence content are two unsequenced samples? We propose a method involving
multiple filtering criteria that result in "pools" of DNA of high or very high
purity. Because our method is similar in spirit to hashing in computer science,
we call it DNA hash pooling. To illustrate this method, we describe protocols
using pairs of restriction enzymes. The in silico empirical results we present
reflect a sensitivity to experimental error. Our method will normally be
performed as a filtering step prior to sequencing in order to reduce the amount
of sequencing required (generally by a factor of 10 or more). Even as
sequencing becomes cheaper, an order of magnitude remains important.
| 2008-07-02 |
0705.3612 | Christopher Pooley | C. M. Pooley, G. P. Alexander, and J. M. Yeomans | Swimming with a friend at low Reynolds number | 6 pages, 4 figures | null | null | null | cond-mat.soft cond-mat.other physics.bio-ph q-bio.OT | null | We investigate the hydrodynamic interactions between microorganisms swimming
at low Reynolds number. By considering simple model swimmers, and combining
analytic and numerical approaches, we investigate the time-averaged flow field
around a swimmer. At short distances the swimmer behaves like a pump. At large
distances the velocity field depends on whether the swimming stroke is
invariant under a combined time-reversal and parity transformation. We then
consider two swimmers and find that the interaction between them consists of
two parts; a dead term, independent of the motion of the second swimmer, which
takes the expected dipolar form and a live term resulting from the simultaneous
swimming action of both swimmers which does not. We argue that, in general, the
latter dominates. The swimmer--swimmer interaction is a complicated function of
their relative displacement, orientation and phase, leading to motion that can
be attractive, repulsive or oscillatory.
| 2007-05-25 |
0705.3660 | Robert Jack | Robert L. Jack, Michael F. Hagan, David Chandler | Fluctuation-dissipation ratios in the dynamics of self-assembly | 8 pages, 6 figures | Phys Rev E 76, 021119 (2007) | 10.1103/PhysRevE.76.021119 | null | cond-mat.stat-mech q-bio.BM | null | We consider two seemingly very different self-assembly processes: formation
of viral capsids, and crystallization of sticky discs. At low temperatures,
assembly is ineffective, since there are many metastable disordered states,
which are a source of kinetic frustration. We use fluctuation-dissipation
ratios to extract information about the degree of this frustration. We show
that our analysis is a useful indicator of the long term fate of the system,
based on the early stages of assembly.
| 2007-08-22 |
0705.3690 | Hugues Berry | Benoit Siri (INRIA Futurs), Hugues Berry (INRIA Futurs), Bruno Cessac
(INLN), Bruno Delord (ANIM), Mathias Quoy (ETIS) | A mathematical analysis of the effects of Hebbian learning rules on the
dynamics and structure of discrete-time random recurrent neural networks | null | null | null | null | nlin.CD q-bio.NC | null | We present a mathematical analysis of the effects of Hebbian learning in
random recurrent neural networks, with a generic Hebbian learning rule
including passive forgetting and different time scales for neuronal activity
and learning dynamics. Previous numerical works have reported that Hebbian
learning drives the system from chaos to a steady state through a sequence of
bifurcations. Here, we interpret these results mathematically and show that
these effects, involving a complex coupling between neuronal dynamics and
synaptic graph structure, can be analyzed using Jacobian matrices, which
introduce both a structural and a dynamical point of view on the neural network
evolution. Furthermore, we show that the sensitivity to a learned pattern is
maximal when the largest Lyapunov exponent is close to 0. We discuss how neural
networks may take advantage of this regime of high functional interest.
| 2008-04-07 |
0705.3691 | David Hsu | David Hsu (1), Aonan Tang (2), Murielle Hsu (1), and John M. Beggs (2)
((1) Department of Neurology, University of Wisconsin, Madison WI, (2)
Department of Physics, Indiana University, Bloomington IN) | A simple spontaneously active Hebbian learning model: homeostasis of
activity and connectivity, and consequences for learning and epileptogenesis | 37 pages, 1 table, 7 figures | Phys Rev E vol 76, October 2007 | 10.1103/PhysRevE.76.041909 | null | q-bio.NC | null | A spontaneously active neural system that is capable of continual learning
should also be capable of homeostasis of both firing rate and connectivity.
Experimental evidence suggests that both types of homeostasis exist, and that
connectivity is maintained at a state that is optimal for information
transmission and storage. This state is referred to as the critical state. We
present a simple stochastic computational Hebbian learning model that
incorporates both firing rate and critical homeostasis, and we explore its
stability and connectivity properties. We also examine the behavior of our
model with a simulated seizure and with simulated acute deafferentation. We
argue that a neural system that is more highly connected than the critical
state (i.e., one that is "supercritical") is epileptogenic. Based on our
simulations, we predict that the post-seizural and post-deafferentation states
should be supercritical and epileptogenic. Furthermore, interventions that
boost spontaneous activity should be protective against epileptogenesis.
| 2007-10-15 |
0705.3724 | Liu Quanxing | Quan-Xing Liu, Bai-Lian Li and Zhen Jin | Resonance and frequency-locking phenomena in spatially extended
phytoplankton-zooplankton system with additive noise and periodic forces | Some typos errors are proof, and some strong relate references are
added | J. Stat. Mech. (2008) P05011 | 10.1088/1742-5468/2008/05/P05011 | null | q-bio.PE cond-mat.stat-mech nlin.PS q-bio.OT | null | In this paper, we present a spatial version of phytoplankton-zooplankton
model that includes some important factors such as external periodic forces,
noise, and diffusion processes. The spatially extended
phytoplankton-zooplankton system is from the original study by Scheffer [M
Scheffer, Fish and nutrients interplay determines algal biomass: a minimal
model, Oikos \textbf{62} (1991) 271-282]. Our results show that the spatially
extended system exhibit a resonant patterns and frequency-locking phenomena.
The system also shows that the noise and the external periodic forces play a
constructive role in the Scheffer's model: first, the noise can enhance the
oscillation of phytoplankton species' density and format a large clusters in
the space when the noise intensity is within certain interval. Second, the
external periodic forces can induce 4:1 and 1:1 frequency-locking and spatially
homogeneous oscillation phenomena to appear. Finally, the resonant patterns are
observed in the system when the spatial noises and external periodic forces are
both turned on. Moreover, we found that the 4:1 frequency-locking transform
into 1:1 frequency-locking when the noise intensity increased. In addition to
elucidating our results outside the domain of Turing instability, we provide
further analysis of Turing linear stability with the help of the numerical
calculation by using the Maple software. Significantly, oscillations are
enhanced in the system when the noise term presents. These results indicate
that the oceanic plankton bloom may partly due to interplay between the
stochastic factors and external forces instead of deterministic factors. These
results also may help us to understand the effects arising from undeniable
subject to random fluctuations in oceanic plankton bloom.
| 2008-05-23 |
0705.3759 | Alain Destexhe | Claude Bedard and Alain Destexhe | A modified cable formalism for modeling neuronal membranes at high
frequencies | To appear in Biophysical Journal; Submitted on May 25, 2007; accepted
on Sept 11th, 2007 | Biophysical Journal 2008 Feb 15;94(4):1133-43. Epub 2007 Oct 5 | 10.1529/biophysj.107.113571 | null | q-bio.NC | null | Intracellular recordings of cortical neurons in vivo display intense
subthreshold membrane potential (Vm) activity. The power spectral density (PSD)
of the Vm displays a power-law structure at high frequencies (>50 Hz) with a
slope of about -2.5. This type of frequency scaling cannot be accounted for by
traditional models, as either single-compartment models or models based on
reconstructed cell morphologies display a frequency scaling with a slope close
to -4. This slope is due to the fact that the membrane resistance is
"short-circuited" by the capacitance for high frequencies, a situation which
may not be realistic. Here, we integrate non-ideal capacitors in cable
equations to reflect the fact that the capacitance cannot be charged
instantaneously. We show that the resulting "non-ideal" cable model can be
solved analytically using Fourier transforms. Numerical simulations using a
ball-and-stick model yield membrane potential activity with similar frequency
scaling as in the experiments. We also discuss the consequences of using
non-ideal capacitors on other cellular properties such as the transmission of
high frequencies, which is boosted in non-ideal cables, or voltage attenuation
in dendrites. These results suggest that cable equations based on non-ideal
capacitors should be used to capture the behavior of neuronal membranes at high
frequencies.
| 2009-11-13 |
0705.3869 | Eugene Shakhnovich | Konstantin Zeldovich, Peiqiu Chen, Boris Shakhnovich, Eugene
Shakhnovich | A first-principles model of early evolution: Emergence of gene families,
species and preferred protein folds | In press, PLoS Computational Biology | null | 10.1371/journal.pcbi.0030139 | null | q-bio.BM q-bio.PE | null | In this work we develop a microscopic physical model of early evolution,
where phenotype,organism life expectancy, is directly related to genotype, the
stability of its proteins in their native conformations which can be determined
exactly in the model. Simulating the model on a computer, we consistently
observe the Big Bang scenario whereby exponential population growth ensues as
soon as favorable sequence-structure combinations (precursors of stable
proteins) are discovered. Upon that, random diversity of the structural space
abruptly collapses into a small set of preferred proteins. We observe that
protein folds remain stable and abundant in the population at time scales much
greater than mutation or organism lifetime, and the distribution of the
lifetimes of dominant folds in a population approximately follows a power law.
The separation of evolutionary time scales between discovery of new folds and
generation of new sequences gives rise to emergence of protein families and
superfamilies whose sizes are power-law distributed, closely matching the same
distributions for real proteins. On the population level we observe emergence
of species, subpopulations which carry similar genomes. Further we present a
simple theory that relates stability of evolving proteins to the sizes of
emerging genomes. Together, these results provide a microscopic first
principles picture of how first gene families developed in the course of early
evolution
| 2015-05-13 |
0705.3895 | Apoorva Patel | Apoorva D. Patel | Towards Understanding the Origin of Genetic Languages | (v1) 33 pages, contributed chapter to "Quantum Aspects of Life",
edited by D. Abbott, P. Davies and A. Pati, (v2) published version with some
editing | null | 10.1142/9781848162556_0010 | null | q-bio.GN cs.IT math.IT physics.bio-ph quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular biology is a nanotechnology that works--it has worked for billions
of years and in an amazing variety of circumstances. At its core is a system
for acquiring, processing and communicating information that is universal, from
viruses and bacteria to human beings. Advances in genetics and experience in
designing computers have taken us to a stage where we can understand the
optimisation principles at the root of this system, from the availability of
basic building blocks to the execution of tasks. The languages of DNA and
proteins are argued to be the optimal solutions to the information processing
tasks they carry out. The analysis also suggests simpler predecessors to these
languages, and provides fascinating clues about their origin. Obviously, a
comprehensive unraveling of the puzzle of life would have a lot to say about
what we may design or convert ourselves into.
| 2016-12-21 |
0705.3983 | Emmanuel Tannenbaum | Yoav Raz, Emmanuel Tannenbaum | The influence of horizontal gene transfer on the mean fitness of
unicellular populations in static environments | 27 pages, 4 figures | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper develops a mathematical model describing the influence that
conjugation-mediated Horizontal Gene Transfer (HGT) has on the
mutation-selection balance in an asexually reproducing population of
unicellular, prokaryotic organisms. It is assumed that mutation-selection
balance is reached in the presence of a fixed background concentration of
antibiotic, to which the population must become resistant in order to survive.
We analyze the behavior of the model in the limit of low and high
antibiotic-induced first-order death rate constants, and find that the highest
mean fitness is obtained at low rates of bacterial conjugation. As the rate of
conjugation crosses a threshold, the mean fitness decreases to a minimum, and
then rises asymptotically to a limiting value as the rate of conjugation
becomes infinitely large. However, this limiting value is smaller than the mean
fitness obtained in the limit of low conjugation rate. This dependence of the
mean fitness on the conjugation rate is fairly small for the parameter ranges
we have considered, and disappears as the first-order death rate constant due
to the presence of antibiotic approaches zero. For large values of the
antibiotic death rate constant, we have obtained an analytical solution for the
behavior of the mean fitness that agrees well with the results of simulations.
The results of this paper suggest that conjugation-mediated HGT has a slightly
deleterious effect on the mean fitness of a population at mutation-selection
balance. Therefore, we argue that HGT confers a selective advantage by allowing
for faster adaptation to a new or changing environment. The results of this
paper are consistent with the observation that HGT can be promoted by
environmental stresses on a population.
| 2009-07-06 |
0705.3989 | Domenico Napoletani | D. Napoletani, T. Sauer, D. C. Struppa, E. Petricoin, L. Liotta | Augmented Sparse Reconstruction of Protein Signaling Networks | 24 pages, 6 figures | Journal of Theoretical Biology, vol. 255, Issue 1, 40-52 (2008) | null | null | physics.data-an q-bio.MN | null | The problem of reconstructing and identifying intracellular protein signaling
and biochemical networks is of critical importance in biology today. We sought
to develop a mathematical approach to this problem using, as a test case, one
of the most well-studied and clinically important signaling networks in biology
today, the epidermal growth factor receptor (EGFR) driven signaling cascade.
More specifically, we suggest a method, augmented sparse reconstruction, for
the identification of links among nodes of ordinary differential equation (ODE)
networks from a small set of trajectories with different initial conditions.
Our method builds a system of representation by using a collection of integrals
of all given trajectories and by attenuating block of terms in the
representation itself. The system of representation is then augmented with
random vectors, and minimization of the 1-norm is used to find sparse
representations for the dynamical interactions of each node. Augmentation by
random vectors is crucial, since sparsity alone is not able to handle the large
error-in-variables in the representation. Augmented sparse reconstruction
allows to consider potentially very large spaces of models and it is able to
detect with high accuracy the few relevant links among nodes, even when
moderate noise is added to the measured trajectories. After showing the
performance of our method on a model of the EGFR protein network, we sketch
briefly the potential future therapeutic applications of this approach.
| 2012-06-15 |
0705.4062 | Eugene Shakhnovich | Konstantin Zeldovich, Peiqiu Chen, Eugene Shakhnovich | The Hypercube of Life: How Protein Stability Imposes Limits on Organism
Complexity and Speed of Molecular Evolution | null | null | null | null | q-bio.BM q-bio.PE | null | Classical population genetics a priori assigns fitness to alleles without
considering molecular or functional properties of proteins that these alleles
encode. Here we study population dynamics in a model where fitness can be
inferred from physical properties of proteins under a physiological assumption
that loss of stability of any protein encoded by an essential gene confers a
lethal phenotype. Accumulation of mutations in organisms containing Gamma genes
can then be represented as diffusion within the Gamma dimensional hypercube
with adsorbing boundaries which are determined, in each dimension, by loss of a
protein stability and, at higher stability, by lack of protein sequences.
Solving the diffusion equation whose parameters are derived from the data on
point mutations in proteins, we determine a universal distribution of protein
stabilities, in agreement with existing data. The theory provides a fundamental
relation between mutation rate, maximal genome size and thermodynamic response
of proteins to point mutations. It establishes a universal speed limit on rate
of molecular evolution by predicting that populations go extinct (via lethal
mutagenesis) when mutation rate exceeds approximately 6 mutations per essential
part of genome per replication for mesophilic organisms and 1 to 2 mutations
per genome per replication for thermophilic ones. Further, our results suggest
that in absence of error correction, modern RNA viruses and primordial genomes
must necessarily be very short. Several RNA viruses function close to the
evolutionary speed limit while error correction mechanisms used by DNA viruses
and non-mutant strains of bacteria featuring various genome lengths and
mutation rates have brought these organisms universally about 1000 fold below
the natural speed limit.
| 2007-05-29 |
0705.4079 | Alpan Raval | Alpan Raval | Molecular Clock on a Neutral Network | 10 pages | null | 10.1103/PhysRevLett.99.138104 | null | q-bio.PE q-bio.MN | null | The number of fixed mutations accumulated in an evolving population often
displays a variance that is significantly larger than the mean (the
overdispersed molecular clock). By examining a generic evolutionary process on
a neutral network of high-fitness genotypes, we establish a formalism for
computing all cumulants of the full probability distribution of accumulated
mutations in terms of graph properties of the neutral network, and use the
formalism to prove overdispersion of the molecular clock. We further show that
significant overdispersion arises naturally in evolution when the neutral
network is highly sparse, exhibits large global fluctuations in neutrality, and
small local fluctuations in neutrality. The results are also relevant for
elucidating the topological structure of a neutral network from empirical
measurements of the substitution process.
| 2009-11-13 |
0705.4084 | Petter Holme | Petter Holme, Mikael Huss | Comment on "Regularizing capacity of metabolic networks" | null | Phys. Rev. E 77, 023901 (2008) | 10.1103/PhysRevE.77.023901 | null | q-bio.MN | null | In a recent paper, Marr, Muller-Linow and Hutt [Phys. Rev. E 75, 041917
(2007)] investigate an artificial dynamic system on metabolic networks. They
find a less complex time evolution of this dynamic system in real networks,
compared to networks of reference models. The authors argue that this suggests
that metabolic network structure is a major factor behind the stability of
biochemical steady states. We reanalyze the same kind of data using a dynamic
system modeling actual reaction kinetics. The conclusions about stability, from
our analysis, are inconsistent with those of Marr et al. We argue that this
issue calls for a more detailed type of modeling.
| 2008-02-06 |
0705.4274 | Brian Thomas | Brian C. Thomas (Washburn Univ.), Adrian L. Melott (Univ. of Kansas),
Brian D. Fields (Univ. of Illinois), and Barbara J. Anthony-Twarog (Univ. of
Kansas) | Superluminous supernovae: No threat from Eta Carinae | 19 pages, 2 figures; Revised version as accepted for publication in
Astrobiology | Astrobiology. February 1, 2008, 8(1): 9-16. | 10.1089/ast.2007.0181 | null | astro-ph physics.ao-ph q-bio.PE | null | Recently Supernova 2006gy was noted as the most luminous ever recorded, with
a total radiated energy of ~10^44 Joules. It was proposed that the progenitor
may have been a massive evolved star similar to eta Carinae, which resides in
our own galaxy at a distance of about 2.3 kpc. eta Carinae appears ready to
detonate. Although it is too distant to pose a serious threat as a normal
supernova, and given its rotation axis is unlikely to produce a Gamma-Ray Burst
oriented toward the Earth, eta Carinae is about 30,000 times nearer than
2006gy, and we re-evaluate it as a potential superluminous supernova. We find
that given the large ratio of emission in the optical to the X-ray, atmospheric
effects are negligible. Ionization of the atmosphere and concomitant ozone
depletion are unlikely to be important. Any cosmic ray effects should be spread
out over ~10^4 y, and similarly unlikely to produce any serious perturbation to
the biosphere. We also discuss a new possible effect of supernovae, endocrine
disruption induced by blue light near the peak of the optical spectrum. This is
a possibility for nearby supernovae at distances too large to be considered
"dangerous" for other reasons. However, due to reddening and extinction by the
interstellar medium, eta Carinae is unlikely to trigger such effects to any
significant degree.
| 2008-02-23 |
0705.4316 | Sungho Hong | Brian Nils Lundstrom, Sungho Hong, Matthew H. Higgs, and Adrienne L.
Fairhall (U. Washington) | Two computational regimes of a single-compartment neuron separated by a
planar boundary in conductance space | 18 pages, 5 figures, accepted version | null | null | null | q-bio.NC physics.bio-ph | null | Recent in vitro data show that neurons respond to input variance with varying
sensitivities. Here, we demonstrate that Hodgkin-Huxley (HH) neurons can
operate in two computational regimes, one that is more sensitive to input
variance (differentiating) and one that is less sensitive (integrating). A
boundary plane in the 3D conductance space separates these two regimes. For a
reduced HH model, this plane can be derived analytically from the V nullcline,
thus suggesting a means of relating biophysical parameters to neural
computation by analyzing the neuron's dynamical system.
| 2007-07-17 |
0705.4328 | Frederick Matsen IV | Frederick A. Matsen, Elchanan Mossel and Mike Steel | Mixed-up trees: the structure of phylogenetic mixtures | null | null | null | null | q-bio.PE | null | In this paper we apply new geometric and combinatorial methods to the study
of phylogenetic mixtures. The focus of the geometric approach is to describe
the geometry of phylogenetic mixture distributions for the two state random
cluster model, which is a generalization of the two state symmetric (CFN)
model. In particular, we show that the set of mixture distributions forms a
convex polytope and we calculate its dimension; corollaries include a simple
criterion for when a mixture of branch lengths on the star tree can mimic the
site pattern frequency vector of a resolved quartet tree. Furthermore, by
computing volumes of polytopes we can clarify how ``common'' non-identifiable
mixtures are under the CFN model. We also present a new combinatorial result
which extends any identifiability result for a specific pair of trees of size
six to arbitrary pairs of trees. Next we present a positive result showing
identifiability of rates-across-sites models. Finally, we answer a question
raised in a previous paper concerning ``mixed branch repulsion'' on trees
larger than quartet trees under the CFN model.
| 2007-11-08 |
0705.4416 | Zhihui Wang | Caterina Guiot, Nicola Pugno, Pier Paolo Delsanto, Thomas S. Deisboeck | Physical Aspects of Cancer Invasion | 20 pages, 2 figures | null | 10.1088/1478-3975/4/4/P01 | null | physics.bio-ph | null | Invasiveness, one of the hallmarks of tumor progression, represents the
tumor's ability to expand into the host tissue by means of several complex
biochemical and biomechanical processes. Since certain aspects of the problem
present a striking resemblance with well known physical mechanisms, such as the
mechanical insertion of a solid inclusion in an elastic material specimen [1,
2] or a water drop impinging on a surface [3], we propose here an analogy
between these physical processes and a cancer system's invasive branching into
the surrounding tissue. Accounting for its solid and viscous properties, we
present a unifying concept that the tumor behaves as a granular solid. While
our model has been explicitly formulated for multicellular tumor spheroids in
vitro, it should also contribute to a better understanding of tumor invasion in
vivo.
| 2009-11-13 |
0705.4427 | Dietrich Stauffer | M. A. Sumour, A. H. El-Astal, M. M. Shabat, and M. A. Radwan | Simulation of Demographic Change in Palestinian Territories | For Int. J. Mod. Phys. C 18, issue 11; 9 pages including figures and
program | null | 10.1142/S0129183107011686 | null | q-bio.PE | null | Mortality, birth rates and retirement play a major role in demographic
changes. In most cases, mortality rates decreased in the past century without
noticeable decrease in fertility rates, this leads to a significant increase in
population growth. In many poor countries like Palestinian territories the
number of births has fallen and the life expectancy increased.
In this article we concentrate on measuring, analyzing and extrapolating the
age structure in Palestine a few decades ago into future. A Fortran program has
been designed and used for the simulation and analysis of our statistical data.
This study of demographic change in Palestine has shown that Palestinians will
have in future problems as the strongest age cohorts are the above-60-year
olds. We therefore recommend the increase of both the retirement age and women
employment.
| 2009-11-13 |
0705.4429 | Stefano Marino | Stefano Marino | A successive sub-grouping method for multiple sequence alignments
analysis | 11 pages, 7 figures, the M_Al program is downloadable at
http://xoomer.alice.it/marinostefano/ | null | null | null | q-bio.OT q-bio.QM | null | A novel approach to protein multiple sequence alignment is discussed:
substantially this method counterparts with substitution matrix based methods
(like Blosum or PAM based methods), and implies a more deterministic approach
to chemical/physical sub-grouping of amino acids . Amino acids (aa) are divided
into sub-groups with successive derivations, that result in a clustering based
on the considered property. The properties can be user defined or chosen
between default schemes, like those used in the analysis described here.
Starting from an initial set of the 20 naturally occurring amino acids, they
are successively divided on the basis of their polarity/hydrophobic index, with
increasing resolution up to four level of subdivision. Other schemes of
subdivision are possible: in this thesis work it was employed also a scheme
based on physical/structural properties (solvent exposure, lateral chain
mobility and secondary structure tendency), that have been compared to the
chemical scheme with testing purposes. In the method described in this chapter,
the total score for each position in the alignment accounts for different
degree of similarity between amino acids. The scoring value result form the
contribution of each level of selectivity for every individual property
considered. Simply the method (called M_Al) analyse the n sequence alignment
position per position and assigns a score which have contributes by aa identity
plus a composed valuation of the chemical or of the structural affinity between
the n aligned amino acids. This method has been implemented in a series of
programs written in python language; these programs have been tested in some
biological cases, with benchmark purposes.
| 2007-06-07 |
0705.4630 | Danielle Rojas-Rousse | Auguste Ndoutoume-Ndong, Danielle Rojas-Rousse (IRBII) | Y a-t-il \'elimination d'Eupelmus orientalis Crawford par Eupelmus
vuilleti Crawford (Hymenoptera : Eupelmidae) des syst\`emes de stockage du
ni\'eb\'e (Vigna unguiculata Walp) ? | null | Annales de la Soci\'et\'e Entomologique de France 43, 2
(01/06/2007) 139-144 | null | null | q-bio.PE | null | Ni\'eb\'e is a food leguminous plant cultivated in tropical Africa for its
seeds rich in proteins. The main problem setted by its production is the
conservation of harvests. In the fields as in the stocks, the seeds are
destroyed by pests (bruchids). These bruchids are always associated with
several entomophagous species of hymenoptera. Four entomophagous species were
listed : an egg parasitoid (U lariophaga Stephan), and three solitary larval
and pupal ectoparasitoids (D. Basalis Rondoni, Pteromalidae; E. vuilleti
Crawford and E. orientalis Crawford, Eupelmidae). The survey of the populations
shows that at the beginning of storage, E orientalis is the most abundant
specie (72 %) whereas E. vuilleti and D. Basalis respectively represent 12 %
and 16 % of the hymenoptera. During storage, the E orientalis population
decreases gradually and it disappears completely in less than two months after
the beginning of storage. E. Vuilleti population becomes gradually more
important than D. basalis population which regress until less than 10 % of the
emerging parasitoids. E vuilleti adopts ovicide and larvicide behaviour against
D. Basalis. This behaviour explains its population regression inside granaries.
If the aggressive behaviour of this Eupelmidae is a constant, that could also
explain the disappearance of E orientalis. However if this species is
maintained in stocks, it would be an effective control agent of bruchids
according to their parasitic capacities. This study shows that ovicide and
larvicide behaviour of E vuilleti is not expressed against E orientalis. When
the females have exclusively the hosts already parasitized by E orientalis,
they do not lay eggs. The disappearance of E orientalis could not thus be
explained by the presence of E. vuilleti.
| 2007-06-01 |
0705.4634 | Carlo Piermarocchi | Diego Calzolari, Giovanni Paternostro, Patrick L. Harrington Jr.,
Carlo Piermarocchi, and Phillip M. Duxbury | Selective control of the apoptosis signaling network in heterogeneous
cell populations | 14 pages, 16 figures. Accepted for publication in PLoS ONE | PLoS ONE 2(6): e547 (2007) | 10.1371/journal.pone.0000547 | null | q-bio.QM cond-mat.stat-mech | null | Selective control in a population is the ability to control a member of the
population while leaving the other members relatively unaffected. The concept
of selective control is developed using cell death or apoptosis in
heterogeneous cell populations as an example. Apoptosis signaling in
heterogeneous cells is described by an ensemble of gene networks with identical
topology but different link strengths. Selective control depends on the
statistics of signaling in the ensemble of networks and we analyse the effects
of superposition, non-linearity and feedback on these statistics. Parallel
pathways promote normal statistics while series pathways promote skew
distributions which in the most extreme cases become log-normal. We also show
that feedback and non-linearity can produce bimodal signaling statistics, as
can discreteness and non-linearity. Two methods for optimizing selective
control are presented. The first is an exhaustive search method and the second
is a linear programming based approach. Though control of a single gene in the
signaling network yields little selectivity, control of a few genes typically
yields higher levels of selectivity. The statistics of gene combinations
susceptible to selective control is studied and is used to identify general
control strategies. We found that selectivity is promoted by acting on the
least sensitive nodes in the case of weak populations, while selective control
of robust populations is optimized through perturbations of more sensitive
nodes. High throughput experiments with heterogeneous cell lines could be
designed in an analogous manner, with the further possibility of incorporating
the selectivity optimization process into a closed-loop control system.
| 2014-07-29 |
0705.4635 | Thierry Emonet | Thierry Emonet and Philippe Cluzel | Relationship between cellular response and behavioral variability in
bacterial chemotaxis | 15 pages, 4 figures, Supporting information available here
http://cluzel.uchicago.edu/data/emonet/arxiv_070531_supp.pdf | null | 10.1073/pnas.0705463105 | null | q-bio.MN q-bio.CB q-bio.OT | null | Bacterial chemotaxis in Escherichia coli is a canonical system for the study
of signal transduction. A remarkable feature of this system is the coexistence
of precise adaptation in population with large fluctuating cellular behavior in
single cells (Korobkova et al. 2004, Nature, 428, 574). Using a stochastic
model, we found that the large behavioral variability experimentally observed
in non-stimulated cells is a direct consequence of the architecture of this
adaptive system. Reversible covalent modification cycles, in which methylation
and demethylation reactions antagonistically regulate the activity of
receptor-kinase complexes, operate outside the region of first-order kinetics.
As a result, the receptor-kinase that governs cellular behavior exhibits a
sigmoidal activation curve. This curve simultaneously amplifies the inherent
stochastic fluctuations in the system and lengthens the relaxation time in
response to stimulus. Because stochastic fluctuations cause large behavioral
variability and the relaxation time governs the average duration of runs in
response to small stimuli, cells with the greatest fluctuating behavior also
display the largest chemotactic response. Finally, Large-scale simulations of
digital bacteria suggest that the chemotaxis network is tuned to simultaneously
optimize the random spread of cells in absence of nutrients and the cellular
response to gradients of attractant.
| 2019-08-19 |
0705.4646 | Fernando Peruani | Fernando Peruani and Luis G. Morelli | Self-propelled particles with fluctuating speed and direction of motion | to appear in Phys. Rev. Lett | Phys. Rev. Lett. 99, 010602 (2007) | 10.1103/PhysRevLett.99.010602 | null | physics.bio-ph physics.gen-ph | null | We study general aspects of active motion with fluctuations in the speed and
the direction of motion in two dimensions. We consider the case in which
fluctuations in the speed are not correlated to fluctuations in the direction
of motion, and assume that both processes can be described by independent
characteristic time-scales. We show the occurrence of a complex transient that
can exhibit a series of alternating regimes of motion, for two different
angular dynamics which correspond to persistent and directed random walks. We
also show additive corrections to the diffusion coefficient. The characteristic
time-scales are also exposed in the velocity autocorrelation, which is a sum of
exponential forms.
| 2009-11-13 |
0705.4674 | Chris Adami | Arend Hintze and Christoph Adami (KGI) | Evolution of complex modular biological networks | 28 pages, 10 figures, 8 supplemental figures, and one supplementary
table. Final version to appear in PLoS Comp Bio | PLoS Computational Biology 4(2):e23 (2008) | 10.1371/journal.pcbi.0040023 | null | q-bio.MN q-bio.PE | null | Biological networks have evolved to be highly functional within uncertain
environments while remaining extremely adaptable. One of the main contributors
to the robustness and evolvability of biological networks is believed to be
their modularity of function, with modules defined as sets of genes that are
strongly interconnected but whose function is separable from those of other
modules. Here, we investigate the in silico evolution of modularity and
robustness in complex artificial metabolic networks that encode an increasing
amount of information about their environment while acquiring ubiquitous
features of biological, social, and engineering networks, such as scale-free
edge distribution, small-world property, and fault-tolerance. These networks
evolve in environments that differ in their predictability, and allow us to
study modularity from topological, information-theoretic, and gene-epistatic
points of view using new tools that do not depend on any preconceived notion of
modularity. We find that for our evolved complex networks as well as for the
yeast protein-protein interaction network, synthetic lethal pairs consist
mostly of redundant genes that lie close to each other and therefore within
modules, while knockdown suppressor pairs are farther apart and often straddle
modules, suggesting that knockdown rescue is mediated by alternative pathways
or modules. The combination of network modularity tools together with genetic
interaction data constitutes a powerful approach to study and dissect the role
of modularity in the evolution and function of biological networks.
| 2008-02-14 |
0706.0001 | Z. C. Tu | Z. C. Tu and Z. C. Ou-Yang | Elastic theory of low-dimensional continua and its applications in bio-
and nano-structures | Review article for J. Comput. Theor. Nanosci., 27 pages, 15 figures | J. Comput. Theor. Nanosci. 5, 422-448 (2008) | null | null | cond-mat.soft cond-mat.mtrl-sci math-ph math.MP physics.bio-ph q-bio.QM | null | This review presents the elastic theory of low-dimensional (one- and
two-dimensional) continua and its applications in bio- and nano-structures.
First, the curve and surface theory, as the geometric representation of the
low-dimensional continua, is briefly described through Cartan moving frame
method. The elastic theory of Kirchhoff rod, Helfrich rod, bending-soften rod,
fluid membrane, and solid shell is revisited. Secondly, the application and
availability of the elastic theory of low-dimensional continua in
bio-structures, including short DNA rings, lipid membranes, and cell membranes,
are discussed. The kink stability of short DNA rings is addressed by using the
theory of Kirchhoff rod, Helfrich rod, and bending-soften rod. The lipid
membranes obey the theory of fluid membrane. A cell membrane is simplified as a
composite shell of lipid bilayer and membrane skeleton, which is a little
similar to the solid shell. It is found that the membrane skeleton enhances
highly the mechanical stability of cell membranes. Thirdly, the application and
availability of the elastic theory of low-dimensional continua in
nano-structures, including graphene and carbon nanotubes, are discussed. A
revised Lenosky lattice model is proposed based on the local density
approximation. Its continuum form up to the second order terms of curvatures
and strains is the same as the free energy of 2D solid shells. Several typical
mechanical properties of carbon nanotubes are revisited and investigated based
on this continuum form. It is possible to avoid introducing the controversial
concepts, the Young's modulus and thickness of graphene and single-walled
carbon nanotubes, with this continuum form.
| 2015-01-20 |
0706.0076 | Hiroo Kenzaki | Hiroo Kenzaki, Macoto Kikuchi | Free-Energy Landscape of Kinesin by a Realistic Lattice Model | 15 pages, 4 figures | null | null | null | q-bio.BM | null | Structural fluctuations in the thermal equilibrium of the kinesin motor
domain are studied using a lattice protein model with Go interactions. By means
of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal
component analysis (PCA), the free-energy landscape is obtained. It is shown
that kinesins have two subdomains that exhibit partial folding/unfolding at
functionally important regions: one is located around the nucleotide binding
site and the other includes the main microtubule binding site. These subdomains
are consistent with structural variability that was reported recently based on
experimentally-obtained structures. On the other hand, such large structural
fluctuations have not been captured by B-factor or normal mode analyses. Thus,
they are beyond the elastic regime, and it is essential to take into account
chain connectivity for studying the function of kinesins.
| 2007-06-04 |
0706.0077 | Bruno. Cessac | B. Cessac | A discrete time neural network model with spiking neurons. Rigorous
results on the spontaneous dynamics | 56 pages, 1 Figure, to appear in Journal of Mathematical Biology | Journal of Mathematical Biology, Volume 56, Number 3, 311-345
(2008). | null | null | math.DS nlin.CD q-bio.NC | null | We derive rigorous results describing the asymptotic dynamics of a discrete
time model of spiking neurons introduced in \cite{BMS}. Using symbolic dynamic
techniques we show how the dynamics of membrane potential has a one to one
correspondence with sequences of spikes patterns (``raster plots''). Moreover,
though the dynamics is generically periodic, it has a weak form of initial
conditions sensitivity due to the presence of a sharp threshold in the model
definition. As a consequence, the model exhibits a dynamical regime
indistinguishable from chaos in numerical experiments.
| 2008-02-12 |
0706.0113 | Anirban Banerjee | Anirban Banerjee and J\"urgen Jost | Graph spectra as a systematic tool in computational biology | 12 pages, 3 figures, Discrete Applied Mathematics, to appear | Discrete Applied Mathematics, 157(10), 2425-2431,(2009) | null | null | nlin.AO q-bio.QM | null | We present the spectrum of the (normalized) graph Laplacian as a systematic
tool for the investigation of networks, and we describe basic properties of
eigenvalues and eigenfunctions. Processes of graph formation like motif joining
or duplication leave characteristic traces in the spectrum. This can suggest
hypotheses about the evolution of a graph representing biological data. To this
data, we analyze several biological networks in terms of rough qualitative data
of their spectra.
| 2012-10-19 |
0706.0117 | Toby Johnson | Toby Johnson | Reciprocal best hits are not a logically sufficient condition for
orthology | null | null | null | null | q-bio.GN | null | It is common to use reciprocal best hits, also known as a boomerang
criterion, for determining orthology between sequences. The best hits may be
found by blast, or by other more recently developed algorithms. Previous work
seems to have assumed that reciprocal best hits is a sufficient but not
necessary condition for orthology. In this article, I explain why reciprocal
best hits cannot logically be a sufficient condition for orthology. If
reciprocal best hits is neither sufficient nor necessary for orthology, it
would seem worthwhile to examine further the logical foundations of some
unsupervised algorithms that are used to identify orthologs.
| 2007-06-04 |
0706.0118 | Diana Fusco | D. Fusco, B. Bassetti, P. Jona, M. Cosentino Lagomarsino | DIA-MCIS. An Importance Sampling Network Randomizer for Network Motif
Discovery and Other Topological Observables in Transcription Networks | 6 pages and 1 figure, included supplementary mathematical notes | null | null | null | q-bio.QM | null | Transcription networks, and other directed networks can be characterized by
some topological observables such as for example subgraph occurrence (network
motifs). In order to perform such kind of analysis, it is necessary to be able
to generate suitable randomized network ensembles. Typically, one considers
null networks with the same degree sequences of the original ones. The commonly
used algorithms sometimes have long convergence times, and sampling problems.
We present here an alternative, based on a variant of the importance sampling
Montecarlo developed by Chen et al. [1].
| 2007-06-04 |
0706.0156 | Liane Gabora | Liane Gabora and Diederik Aerts | A Cross-disciplinary Framework for the Description of Contextually
Mediated Change | 19 pages. arXiv admin note: substantial text overlap with
arXiv:q-bio/0511007 | null | 10.1142/9789812779953_0005 | null | physics.gen-ph physics.bio-ph physics.pop-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a mathematical framework (referred to as Context-driven
Actualization of Potential, or CAP) for describing how entities change over
time under the influence of a context. The approach facilitates comparison of
change of state of entities studied in different disciplines. Processes are
seen to differ according to the degree of nondeterminism, and the degree to
which they are sensitive to, internalize, and depend upon a particular context.
Our analysis suggests that the dynamical evolution of a quantum entity
described by the Schrodinger equation is not fundamentally different from
change provoked by a measurement often referred to as collapse, but a limiting
case, with only one way to collapse. The biological transition to coded
replication is seen as a means of preserving structure in the fact of
context-driven change, and sextual replication as a means of increasing
potentiality thus enhancing diversity through interaction with context. The
framework sheds light on concepts like selection and fitness, reveals how
exceptional Darwinian evolution is as a means of 'change of state', and
clarifies in what sense culture, and the creative process underlying it, are
Darwinian.
| 2019-07-09 |
0706.0163 | Alexander K. Vidybida | Alexander K. Vidybida | Output Stream of Binding Neuron with Feedback | Version #1: 4 pages, 5 figures, manuscript submitted to Biological
Cybernetics. Version #2 (this version): added 3 pages of new text with
additional analytical and numerical calculations, 2 more figures, 11 more
references, added Discussion section | Eur. Phys. J. B 65, 577-584 (2008); Eur. Phys. J. B 69, 313 (2009) | 10.1140/epjb/e2008-00360-1 | null | q-bio.NC q-bio.OT | null | The binding neuron model is inspired by numerical simulation of
Hodgkin-Huxley-type point neuron, as well as by the leaky integrate-and-fire
model. In the binding neuron, the trace of an input is remembered for a fixed
period of time after which it disappears completely. This is in the contrast
with the above two models, where the postsynaptic potentials decay
exponentially and can be forgotten only after triggering. The finiteness of
memory in the binding neuron allows one to construct fast recurrent networks
for computer modeling. Recently, the finiteness is utilized for exact
mathematical description of the output stochastic process if the binding neuron
is driven with the Poissonian input stream. In this paper, the simplest
networking is considered for binding neuron. Namely, it is expected that every
output spike of single neuron is immediately fed into its input. For this
construction, externally fed with Poissonian stream, the output stream is
characterized in terms of interspike interval probability density distribution
if the binding neuron has threshold 2. For higher thresholds, the distribution
is calculated numerically. The distributions are compared with those found for
binding neuron without feedback, and for leaky integrator. Sample distributions
for leaky integrator with feedback are calculated numerically as well. It is
oncluded that even the simplest networking can radically alter spikng
statistics. Information condensation at the level of single neuron is
discussed.
| 2011-07-20 |
0706.0171 | Danielle Rojas-Rousse | Danielle Rousse (IRBII) | Persistent pods of the tree Acacia caven: a natural refuge for diverse
insects including Bruchid beetles and the parasitoids Trichogrammatidae,
Pteromalidae and Eulophidae | 9 pages | Journal of Insect Science, 8 (12/06/2006) 1-9 pages | null | www.insectscience.org ISSN:1536-2442 | q-bio.PE | null | The persistent pods of the tree, Acacia caven, that do not fall from the tree
provide opportunities for the appearance of a diverse group of insects the
following season. Such pods collected during the spring of 1999 in Chile were
indehiscent with highly sclerified pod walls. In contrast, persistent pods
collected in Uruguay after a wet winter and spring (2002) were partially
dehiscent, inducing the deterioration of the woody pods, and consequently
exposing the seeds. These persistent pods are a natural refuge for insect
species, namely two bruchid beetles (Pseudopachymeria spinipes, Stator
furcatus), one scolytidae (Dendroctonus sp), lepidopterous larvae, ant colonies
(Camponotus sp),one species of oophagous parasitoid (Uscana espinae group
senex), the gregarious larval-pupae parasitoid Monoksa dorsiplana
(Pteromalidae) and two species of Horismenus spp. (Eulophidae). The patriline
of M. dorsiplana is frequently formed by 1 son +7 daughters.
| 2007-06-04 |
0706.0185 | Xianghong Qi | Xianghong Qi and John J. Portman | Excluded volume, local structural cooperativity,and the polymer physics
of protein folding rates | 12 pages,6 figures,1 page supporting information.To be published in
Proc.Natl.Acad.Sci.(USA)(2007) | null | 10.1073/pnas.0609321104 | null | q-bio.BM physics.bio-ph physics.chem-ph | null | A coarse-grained variational model is used to investigate the polymer
dynamics of barrier crossing for a diverse set of two-state folding proteins.
The model gives reliable folding rate predictions provided excluded volume
terms that induce minor structural cooperativity are included in the
interaction potential. In general, the cooperative folding routes have sharper
interfaces between folded and unfolded regions of the folding nucleus and
higher free energy barriers. The calculated free energy barriers are strongly
correlated with native topology as characterized by contact order. Increasing
the rigidity of the folding nucleus changes the local structure of the
transition state ensemble non-uniformly across the set of protein studied.
Neverthless, the calculated prefactors k0 are found to be relatively uniform
across the protein set, with variation in 1/k0 less than a factor of five. This
direct calculation justifies the common assumption that the prefactor is
roughly the same for all small two-state folding proteins. Using the barrier
heights obtained from the model and the best fit monomer relaxation time 30ns,
we find that 1/k0 (1-5)us (with average 1/k0 4us). This model can be extended
to study subtle aspects of folding such as the variation of the folding rate
with stability or solvent viscosity, and the onset of downhill folding.
| 2009-11-13 |
0706.0194 | Andrea Sboner | Long J. Lu, Andrea Sboner, Yuanpeng J. Huang, Hao Xin Lu, Tara A.
Gianoulis, Kevin Y. Yip, Philip M. Kim, and Gaetano T. Montelione, Mark B.
Gerstein | Comparing Classical Pathways and Modern Networks: Towards the
Development of an Edge Ontology | 30 pages including 5 figures and supplemental material | null | null | null | q-bio.MN | null | Pathways are integral to systems biology. Their classical representation has
proven useful but is inconsistent in the meaning assigned to each arrow (or
edge) and inadvertently implies the isolation of one pathway from another.
Conversely, modern high-throughput experiments give rise to standardized
networks facilitating topological calculations. Combining these perspectives,
we can embed classical pathways within large-scale networks and thus
demonstrate the crosstalk between them. As more diverse types of
high-throughput data become available, we can effectively merge both
perspectives, embedding pathways simultaneously in multiple networks. However,
the original problem still remains - the current edge representation is
inadequate to accurately convey all the information in pathways. Therefore, we
suggest that a standardized, well-defined, edge ontology is necessary and
propose a prototype here, as a starting point for reaching this goal.
| 2007-06-04 |
0706.0196 | Maikel Rheinstadter | Arne Schafer, Tim Salditt, and Maikel C. Rheinstadter | Atomic force microscopy (AFM) study of thick lamellar stacks of
phospholipid bilayers | null | Phys. Rev. E 77, 021905 (2008) (8 pages). | 10.1103/PhysRevE.77.021905 | null | physics.bio-ph | null | We report an Atomic Force Microscopy (AFM) study on thick multi lamellar
stacks of approx. 10 mum thickness (about 1500 stacked membranes) of DMPC
(1,2-dimyristoyl-sn-glycero-3-phoshatidylcholine) deposited on silicon wafers.
These thick stacks could be stabilized for measurements under excess water or
solution. From force curves we determine the compressional modulus B and the
rupture force F_r of the bilayers in the gel (ripple), the fluid phase and in
the range of critical swelling close to the main transition. AFM allows to
measure the compressional modulus of stacked membrane systems and values for B
compare well to values reported in the literature. We observe pronounced
ripples on the top layer in the Pbeta' (ripple) phase and find an increasing
ripple period Lambda_r when approaching the temperature of the main phase
transition into the fluid Lalpha phase at about 24 C. Metastable ripples with
2Lambda_r are observed. Lambda_r also increases with increasing osmotic
pressure, i.e., for different concentrations of polyethylene glycol (PEG).
| 2009-10-02 |
0706.0229 | Christopher Haydock | Christopher Haydock | Conformational gel analysis and graphics: Measurement of side chain
rotational isomer populations by NMR and molecular mechanics | 9 pages, 6 figures, REVTeX v4 | null | null | null | physics.bio-ph | null | Conformational gel analysis and graphics systematically identifies and
evaluates plausible alternatives to the side chain conformations found by
conventional peptide or protein structure determination methods. The proposed
analysis determines the populations of side chain rotational isomers and the
probability distribution of these populations. The following steps are repeated
for each side chain of a peptide or protein: first, extract the local molecular
mechanics of side chain rotational isomerization from a single representative
global conformation; second, expand the predominant set of rotational isomers
to include all probable rotational isomers down to those that constitute just a
small percentage of the population; and third, evaluate the constraints vicinal
coupling constants and NOESY cross relaxation rates place on rotational isomer
populations. In this article we apply conformational gel analysis to the cobalt
glycyl-leucine dipeptide and detail the steps necessary to generalize the
analysis to other amino acid side chains in other peptides and proteins. For a
side chain buried within a protein interior, it is noteworthy that the set of
probable rotational isomers may contain one or more rotational isomers that are
not identified by conventional NMR structure determination methods. In cases
such as this the conformational gel graphics fully accounts for the interplay
of molecular mechanics and NMR data constraints on the population estimates.
The analysis is particularly suited to identifying side chain rotational
isomers that constitute a small percentage of the population, but nevertheless
might be structurally and functionally very significant.
| 2007-06-05 |
0706.0294 | Edoardo Airoldi | Edoardo M Airoldi, David M Blei, Stephen E Fienberg, Eric P Xing | Mixed membership analysis of high-throughput interaction studies:
Relational data | 22 pages, 6 figures, 2 tables | null | null | null | q-bio.MN q-bio.QM | null | In this paper, we consider the statistical analysis of a protein interaction
network. We propose a Bayesian model that uses a hierarchy of probabilistic
assumptions about the way proteins interact with one another in order to: (i)
identify the number of non-observable functional modules; (ii) estimate the
degree of membership of proteins to modules; and (iii) estimate typical
interaction patterns among the functional modules themselves. Our model
describes large amount of (relational) data using a relatively small set of
parameters that we can reliably estimate with an efficient inference algorithm.
We apply our methodology to data on protein-to-protein interactions in
saccharomyces cerevisiae to reveal proteins' diverse functional roles. The case
study provides the basis for an overview of which scientific questions can be
addressed using our methods, and for a discussion of technical issues.
| 2007-11-15 |
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