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0704.0021 | Yuichi Togashi | Vanessa Casagrande, Yuichi Togashi, Alexander S. Mikhailov | Molecular Synchronization Waves in Arrays of Allosterically Regulated
Enzymes | 5 pages, 4 figures | Phys. Rev. Lett. 99, 048301 (2007) | 10.1103/PhysRevLett.99.048301 | null | nlin.PS physics.chem-ph q-bio.MN | null | Spatiotemporal pattern formation in a product-activated enzymic reaction at
high enzyme concentrations is investigated. Stochastic simulations show that
catalytic turnover cycles of individual enzymes can become coherent and that
complex wave patterns of molecular synchronization can develop. The analysis
based on th... | 2007-07-24 |
0704.0034 | Vasily Ogryzko V | Vasily Ogryzko | Origin of adaptive mutants: a quantum measurement? | 5 pages | null | null | null | q-bio.PE q-bio.CB quant-ph | null | This is a supplement to the paper arXiv:q-bio/0701050, containing the text of
correspondence sent to Nature in 1990.
| 2007-05-23 |
0704.0036 | Eduardo D. Sontag | Liming Wang and Eduardo D. Sontag | A remark on the number of steady states in a multiple futile cycle | Resubmit with new results on the upper bound of the number of steady
states. 20 pages, 2 figures, See
http://www.math.rutgers.edu/~sontag/PUBDIR/index.html for online preprints
and reprints of related work | null | null | null | q-bio.QM q-bio.MN | null | The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly
used in cell signaling. This motif itself can generate a variety of dynamic
behaviors like bistability and ultrasensitivity without direct positive
feedbacks. In this paper, we study the number of positive steady states of a
general multisite... | 2011-11-09 |
0704.0158 | Huijie Yang | Fangcui Zhao, Huijie Yang, and Binghong Wang | Complexities of Human Promoter Sequences | 5 pages, 3 figures, To appear in Journal of Theoretical Biology | Journal of Theoretical Biology 247 (2007) 645?C649 | 10.1016/j.jtbi.2007.03.035 | null | q-bio.OT | null | By means of the diffusion entropy approach, we detect the scale-invariance
characteristics embedded in the 4737 human promoter sequences. The exponent for
the scale-invariance is in a wide range of $[ {0.3,0.9} ]$, which centered at
$\delta_c = 0.66$. The distribution of the exponent can be separated into left
and ri... | 2011-11-09 |
0704.0191 | Peter Virnau | Peter Virnau (1), Leonid A. Mirny (1,2), Mehran Kardar (1) ((1)
Massachusetts Institute of Technology, Department of Physics, Cambridge, MA,
United States of America, (2) Massachusetts Institute of Technology,
Harvard-MIT Division of Health Science and Technology, Cambridge, MA, United
States of America) | Intricate Knots in Proteins: Function and Evolution | 6 pages, 2 figures, 1 table | P. Virnau, L. A. Mirny, M. Kardar, PLoS Comp Biol 2, 1074-1079
(2006) | null | null | physics.bio-ph physics.data-an q-bio.BM | null | A number of recently discovered protein structures incorporate a rather
unexpected structural feature: a knot in the polypeptide backbone. These knots
are extremely rare, but their occurrence is likely connected to protein
function in as yet unexplored fashion. Our analysis of the complete Protein
Data Bank reveals s... | 2007-05-23 |
0704.0271 | Edgardo Brigatti | E. Brigatti, V. Schwammle and Minos A. Neto | An individual based model with global competition interaction:
fluctuations effects in pattern formation | 9 pages, 9 figures, minor changes | Physical Review E 77, 021914 (2008) | 10.1103/PhysRevE.77.021914 | null | cond-mat.stat-mech q-bio.PE | null | We present some numerical results obtained from a simple individual based
model that describes clustering of organisms caused by competition. Our aim is
to show how, even when a deterministic description developed for continuum
models predicts no pattern formation, an individual based model displays well
defined patt... | 2009-11-13 |
0704.0304 | Carlos Gershenson | Carlos Gershenson | The World as Evolving Information | 16 pages. Extended version, three more laws of information, two
classifications, and discussion added. To be published (soon) in
International Conference on Complex Systems 2007 Proceedings | Minai, A., Braha, D., and Bar-Yam, Y., eds. Unifying Themes in
Complex Systems VII, pp. 100-115. Springer, Berlin Heidelberg, 2012 | 10.1007/978-3-642-18003-3_10 | null | cs.IT cs.AI math.IT q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper discusses the benefits of describing the world as information,
especially in the study of the evolution of life and cognition. Traditional
studies encounter problems because it is difficult to describe life and
cognition in terms of matter and energy, since their laws are valid only at the
physical scale. ... | 2013-04-05 |
0704.0305 | Yongxing Guo | Yongxing Guo, Yifeng Liu, Jay X. Tang, and James M. Valles Jr | Polymerization Force Driven Buckling of Microtubule Bundles Determines
the Wavelength of Patterns Formed in Tubulin Solutions | 4 pages, 4 figures | Phys. Rev. Lett. 98, 198103 (2007) | 10.1103/PhysRevLett.98.198103 | null | physics.bio-ph | null | We present a model for the spontaneous formation of a striated pattern in
polymerizing microtubule solutions. It describes the buckling of a single
microtubule (MT) bundle within an elastic network formed by other similarly
aligned and buckling bundles and unaligned MTs. Phase contrast and polarization
microscopy stu... | 2007-06-13 |
0704.0322 | Liu Quanxing | Quan-Xing Liu, Gui-Quan Sun, Bai-Lian Li and Zhen Jin | Emergence of spatiotemporal chaos driven by far-field breakup of spiral
waves in the plankton ecological systems | 9 Figures and 11 pages, REVTeX 4 | 2009 Chinese Phys. B 18 506-515 | 10.1088/1674-1056/18/2/021 | null | nlin.PS nlin.CD q-bio.PE | null | Alexander B. Medvinsky \emph{et al} [A. B. Medvinsky, I. A. Tikhonova, R. R.
Aliev, B.-L. Li, Z.-S. Lin, and H. Malchow, Phys. Rev. E \textbf{64}, 021915
(2001)] and Marcus R. Garvie \emph{et al} [M. R. Garvie and C. Trenchea, SIAM
J. Control. Optim. \textbf{46}, 775-791 (2007)] shown that the minimal
spatially exten... | 2009-05-29 |
0704.0331 | C. Soule | J.-L. Jestin, C. Soule (IHES) | Symmetries by base substitutions in the genetic code predict 2' or 3'
aminoacylation of tRNAs | Accepted for publication in the Journal of Theoretical Biology | null | null | null | q-bio.OT | null | This letter reports complete sets of two-fold symmetries between partitions
of the universal genetic code. By substituting bases at each position of the
codons according to a fixed rule, it happens that properties of the degeneracy
pattern or of tRNA aminoacylation specificity are exchanged.
| 2007-05-23 |
0704.0357 | Gergely J Sz\"oll\H{o}si | Gergely J Szollosi and Imre Derenyi | Evolutionary games on minimally structured populations | Supporting information available as EPAPS Document No.
E-PLEEE8-78-144809 at http://ftp.aip.org/epaps/phys_rev_e/E-PLEEE8-78-144809/ | PHYSICAL REVIEW E 78, 031919 (2008) | 10.1103/PhysRevE.78.031919 | null | q-bio.PE q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Population structure induced by both spatial embedding and more general
networks of interaction, such as model social networks, have been shown to have
a fundamental effect on the dynamics and outcome of evolutionary games. These
effects have, however, proved to be sensitive to the details of the underlying
topology ... | 2009-11-13 |
0704.0392 | Marcus Kaiser | Marcus Kaiser, Robert Martin, Peter Andras and Malcolm P. Young | Simulation of Robustness against Lesions of Cortical Networks | submitted to European Journal of Neuroscience (under review) | European Journal of Neuroscience, 25:3185--3192, 2007 | 10.1111/j.1460-9568.2007.05574.x | null | q-bio.NC cond-mat.dis-nn physics.soc-ph | null | Structure entails function and thus a structural description of the brain
will help to understand its function and may provide insights into many
properties of brain systems, from their robustness and recovery from damage, to
their dynamics and even their evolution. Advances in the analysis of complex
networks provid... | 2008-08-27 |
0704.0429 | Ping Ao | P. Ao | Quantitative Resolution to some "Absolute Discrepancies" in Cancer
Theories: a View from Phage lambda Genetic Switch | latex, 7 pages | CellularOncology29:67-69,2007 | null | null | q-bio.SC q-bio.CB | null | Is it possible to understand cancer? Or more specifically, is it possible to
understand cancer from genetic side? There already many answers in literature.
The most optimistic one has claimed that it is mission-possible. Duesberg and
his colleagues reviewed the impressive amount of research results on cancer
accumula... | 2008-11-26 |
0704.0464 | Edward Lyman Ph.D. | Edward Lyman and Daniel M. Zuckerman | Annealed importance sampling of dileucine peptide | null | null | 10.1063/1.2754267 | null | q-bio.BM | null | Annealed importance sampling is a means to assign equilibrium weights to a
nonequilibrium sample that was generated by a simulated annealing protocol. The
weights may then be used to calculate equilibrium averages, and also serve as
an ``adiabatic signature'' of the chosen cooling schedule. In this paper we
demonstra... | 2009-11-13 |
0704.0598 | Ignazio Licata | Ignazio Licata, Luigi Lella | Evolutionary Neural Gas (ENG): A Model of Self Organizing Network from
Input Categorization | 16 pages, 8 figures | EJTP,vol.4,, No.14 (2007),31-50 | null | null | physics.gen-ph q-bio.PE | null | Despite their claimed biological plausibility, most self organizing networks
have strict topological constraints and consequently they cannot take into
account a wide range of external stimuli. Furthermore their evolution is
conditioned by deterministic laws which often are not correlated with the
structural paramete... | 2010-04-26 |
0704.0615 | Trevor Bruen TB | Trevor Bruen, David Bryant | Parsimony via concensus | Final published version of article | Systematic Biology (2008), 57(2): 251-56 | 10.1080/10635150802040597 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The parsimony score of a character on a tree equals the number of state
changes required to fit that character onto the tree. We show that for
unordered, reversible characters this score equals the number of tree
rearrangements required to fit the tree onto the character. We discuss
implications of this connection fo... | 2013-10-02 |
0704.0634 | Mark Bathe | Mark Bathe | A Finite Element framework for computation of protein normal modes and
mechanical response | null | null | null | null | q-bio.BM q-bio.QM | null | A coarse-grained computational procedure based on the Finite Element Method
is proposed to calculate the normal modes and mechanical response of proteins
and their supramolecular assemblies. Motivated by the elastic network model,
proteins are modeled as homogeneous isotropic elastic solids with volume
defined by the... | 2007-05-23 |
0704.0648 | Kaushik Majumdar | Kaushik Majumdar | Behavioral response to strong aversive stimuli: A neurodynamical model | Submitted to journal | null | null | null | q-bio.NC | null | In this paper a theoretical model of functioning of a neural circuit during a
behavioral response has been proposed. A neural circuit can be thought of as a
directed multigraph whose each vertex is a neuron and each edge is a synapse.
It has been assumed in this paper that the behavior of such circuits is
manifested ... | 2007-05-23 |
0704.0673 | Mark McDonnell | Mark D. McDonnell, Nigel G. Stocks and Derek Abbott | Optimal stimulus and noise distributions for information transmission
via suprathreshold stochastic resonance | Accepted for publication by Physical Review E, 28 pages of text and
references, 5 figures, 2 tables | Phys. Rev. E 75, 061105 (2007) | 10.1103/PhysRevE.75.061105 | null | cond-mat.stat-mech q-bio.NC | null | Suprathreshold stochastic resonance (SSR) is a form of noise enhanced signal
transmission that occurs in a parallel array of independently noisy identical
threshold nonlinearities, including model neurons. Unlike most forms of
stochastic resonance, the output response to suprathreshold random input
signals of arbitra... | 2007-07-02 |
0704.1147 | Giulio Ruffini | Giulio Ruffini | Information, complexity, brains and reality (Kolmogorov Manifesto) | This is a live essay, kind of a mental log book on a series of topics
under the theme of information and compression | null | null | Starlab TN00054 | physics.gen-ph physics.bio-ph | null | I discuss several aspects of information theory and its relationship to
physics and neuroscience. The unifying thread of this somewhat chaotic essay is
the concept of Kolmogorov or algorithmic complexity (Kolmogorov Complexity, for
short). I argue that it is natural to interpret cognition as the art of finding
algori... | 2007-05-23 |
0704.1169 | Dirson Jian Li | Dirson Jian Li, Shengli Zhang | Holographic bound and protein linguistics | 4 pages, 4 figures. A trial application of holographic bound in life
science | null | null | null | q-bio.GN hep-th q-bio.QM | null | The holographic bound in physics constrains the complexity of life. The
finite storage capability of information in the observable universe requires
the protein linguistics in the evolution of life. We find that the evolution of
genetic code determines the variance of amino acid frequencies and genomic GC
content amo... | 2007-05-23 |
0704.1362 | J.H. van Hateren | J. H. van Hateren | Fast recursive filters for simulating nonlinear dynamic systems | 20 pages, 8 figures, 1 table. A comparison with 4th-order Runge-Kutta
integration shows that the new algorithm is 1-2 orders of magnitude faster.
The paper is in press now at Neural Computation | Neural Computation 20:1821-1846 (2008) | null | null | q-bio.QM q-bio.NC | null | A fast and accurate computational scheme for simulating nonlinear dynamic
systems is presented. The scheme assumes that the system can be represented by
a combination of components of only two different types: first-order low-pass
filters and static nonlinearities. The parameters of these filters and
nonlinearities m... | 2008-06-20 |
0704.1390 | Azam Gholami | Azam Gholami, Martin Falcke, Erwin Frey | Velocity oscillations in actin-based motility | 5 pages, 6 figures | null | 10.1088/1367-2630/10/3/033022 | HMI 18779, LMU-ASC 18/07 | q-bio.CB | null | We present a simple and generic theoretical description of actin-based
motility, where polymerization of filaments maintains propulsion. The dynamics
is driven by polymerization kinetics at the filaments' free ends, crosslinking
of the actin network, attachment and detachment of filaments to the obstacle
interfaces a... | 2015-05-13 |
0704.1546 | Richard A Neher | Richard A. Neher, Wolfram Mobius, Erwin Frey, Ulrich Gerland | Optimal flexibility for conformational transitions in macromolecules | 4 pages, 4 figures | null | 10.1103/PhysRevLett.99.178101 | LMU-ASC 22/07 | q-bio.BM | null | Conformational transitions in macromolecular complexes often involve the
reorientation of lever-like structures. Using a simple theoretical model, we
show that the rate of such transitions is drastically enhanced if the lever is
bendable, e.g. at a localized "hinge''. Surprisingly, the transition is fastest
with an i... | 2009-11-13 |
0704.1547 | Martin Castelnovo | Fabien Montel, Emeline Fontaine, Philippe St-Jean, Martin Castelnovo,
Cendrine Moskalenko-Faivre | AFM Imaging of SWI/SNF action: mapping the nucleosome remodeling and
sliding | 25 pages,5 figures, to appear in Biophysical Journal | null | 10.1529/biophysj.107.105569 | null | physics.bio-ph cond-mat.soft q-bio.BM | null | We propose a combined experimental (Atomic Force Microscopy) and theoretical
study of the structural and dynamical properties of nucleosomes. In contrast to
biochemical approaches, this method allows to determine simultaneously the DNA
complexed length distribution and nucleosome position in various contexts.
First, ... | 2009-11-13 |
0704.1571 | Philippe Gambette | Philippe Gambette (LIAFA), St\'ephane Vialette (LRI) | On restrictions of balanced 2-interval graphs | null | Dans Lecture Notes In Computer Science - 33rd International
Workshop on Graph-Theoretic Concepts in Computer Science (WG'07), Dornburg :
Allemagne (2007) | 10.1007/978-3-540-74839-7_6 | null | cs.DM q-bio.QM | null | The class of 2-interval graphs has been introduced for modelling scheduling
and allocation problems, and more recently for specific bioinformatic problems.
Some of those applications imply restrictions on the 2-interval graphs, and
justify the introduction of a hierarchy of subclasses of 2-interval graphs that
genera... | 2008-02-04 |
0704.1667 | Erel Levine | Erel Levine and Terence Hwa | Stochastic fluctuations in metabolic pathways | null | PNAS 2007 | 10.1073/pnas.0610987104 | null | q-bio.MN cond-mat.stat-mech | null | Fluctuations in the abundance of molecules in the living cell may affect its
growth and well being. For regulatory molecules (e.g., signaling proteins or
transcription factors), fluctuations in their expression can affect the levels
of downstream targets in a network. Here, we develop an analytic framework to
investi... | 2009-11-13 |
0704.1672 | Ilia Solov'yov | Ilia A. Solov'yov, Alexander V. Yakubovich, Andrey V. Solov'yov and
Walter Greiner | Two center multipole expansion method: application to macromolecular
systems | 23 pages, 7 figures, 1 table | null | 10.1103/PhysRevE.75.051912 | null | physics.bio-ph physics.comp-ph | null | We propose a new theoretical method for the calculation of the interaction
energy between macromolecular systems at large distances. The method provides a
linear scaling of the computing time with the system size and is considered as
an alternative to the well known fast multipole method. Its efficiency,
accuracy and... | 2009-11-13 |
0704.1763 | Ilia Solov'yov | Ilia A. Solov'yov, Walter Greiner | Towards understanding of birds magnetoreceptor mechanism | 10 pages, 4 figures | null | null | null | physics.bio-ph | null | In the present letter we suggest a new theoretical model for a quantitative
description of the magnetoreception mechanism in birds. The considered
mechanism involves two types of iron minerals (magnetite and maghemite) which
were found in subcellular compartments within sensory dendrites of the upper
beak of several ... | 2007-05-23 |
0704.1811 | Samarth Swarup | Samarth Swarup and Les Gasser | Unifying Evolutionary and Network Dynamics | 11 pages, 12 figures, Accepted for publication in Physical Review E | null | 10.1103/PhysRevE.75.066114 | null | q-bio.QM q-bio.PE | null | Many important real-world networks manifest "small-world" properties such as
scale-free degree distributions, small diameters, and clustering. The most
common model of growth for these networks is "preferential attachment", where
nodes acquire new links with probability proportional to the number of links
they alread... | 2009-11-13 |
0704.1885 | Jesse Bloom | Jesse D. Bloom, Zhongyi Lu, David Chen, Alpan Raval, Ophelia S.
Venturelli, and Frances H. Arnold | Evolution favors protein mutational robustness in sufficiently large
populations | null | BMC Biology 5:29 (2007) | 10.1186/1741-7007-5-29 | null | q-bio.PE q-bio.BM | null | BACKGROUND: An important question is whether evolution favors properties such
as mutational robustness or evolvability that do not directly benefit any
individual, but can influence the course of future evolution. Functionally
similar proteins can differ substantially in their robustness to mutations and
capacity to ... | 2009-04-16 |
0704.1908 | Radek Erban | Radek Erban, Jonathan Chapman and Philip Maini | A practical guide to stochastic simulations of reaction-diffusion
processes | 35 pages | null | null | null | q-bio.SC physics.ed-ph q-bio.QM | null | A practical introduction to stochastic modelling of reaction-diffusion
processes is presented. No prior knowledge of stochastic simulations is
assumed. The methods are explained using illustrative examples. The article
starts with the classical Gillespie algorithm for the stochastic modelling of
chemical reactions. T... | 2007-11-19 |
0704.1912 | Adrian Melott | L.C. Natarajan, A.L. Melott, B.M. Rothschild, and L.D. Martin
(University of Kansas) | Bone Cancer Rates in Dinosaurs Compared with Modern Vertebrates | As published in Transactions of the Kansas Academy of Science | TKAS 110, 155-158 (2007) | null | null | q-bio.PE astro-ph physics.geo-ph | null | Data on the prevalence of bone cancer in dinosaurs is available from past
radiological examination of preserved bones. We statistically test this data
for consistency with rates extrapolated from information on bone cancer in
modern vertebrates, and find that there is no evidence of a different rate.
Thus, this test ... | 2007-10-16 |
0704.2114 | A. Mary Selvam | A. M. Selvam | Universal spectrum for DNA base CG frequency distribution in Takifugu
rubripes (Puffer fish) genome | 32 pages, 8 figures | null | null | null | physics.gen-ph physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The frequency distribution of DNA bases A, C, G, T exhibit fractal
fluctuations ubiquitous to dynamical systems in nature. The power spectra of
fractal fluctuations exhibit inverse power law form signifying long-range
correlations between local (small-scale) and global (large-scale)
perturbations. The author has deve... | 2011-03-07 |
0704.2132 | Roberto Chignola | C. Tomelleri, E. Milotti, C. Dalla Pellegrina, O. Perbellini, A. Del
Fabbro, M. T. Scupoli and R. Chignola | A quantitative study on the growth variability of tumour cell clones in
vitro | 31 pages, 5 figures | null | null | null | q-bio.CB q-bio.QM | null | Objectives: In this study, we quantify the growth variability of tumour cell
clones from a human leukemia cell line. Materials and methods: We have used
microplate spectrophotometry to measure the growth kinetics of hundreds of
individual cell clones from the Molt3 cell line. The growth rate of each clonal
population... | 2007-05-23 |
0704.2191 | Bo Deng | Bo Deng | Mismatch Repair Error Implies Chargaff's Second Parity Rule | null | null | null | null | q-bio.GN | null | Chargaff's second parity rule holds empirically for most types of DNA that
along single strands of DNA the base contents are equal for complimentary
bases, A = T, G = C. A Markov chain model is constructed to track the evolution
of any single base position along single strands of genomes whose organisms are
equipped ... | 2007-09-20 |
0704.2200 | Stefan Bornholdt | Maria I. Davidich, Stefan Bornholdt | Boolean network model predicts cell cycle sequence of fission yeast | 10 pages, 3 figures | null | 10.1371/journal.pone.0001672 | null | q-bio.MN | null | A Boolean network model of the cell-cycle regulatory network of fission yeast
(Schizosaccharomyces Pombe) is constructed solely on the basis of the known
biochemical interaction topology. Simulating the model in the computer,
faithfully reproduces the known sequence of regulatory activity patterns along
the cell cycl... | 2015-05-13 |
0704.2260 | Frederick Matsen IV | Frederick A. Matsen and Mike Steel | Phylogenetic mixtures on a single tree can mimic a tree of another
topology | null | null | null | null | q-bio.PE | null | Phylogenetic mixtures model the inhomogeneous molecular evolution commonly
observed in data. The performance of phylogenetic reconstruction methods where
the underlying data is generated by a mixture model has stimulated considerable
recent debate. Much of the controversy stems from simulations of mixture model
data ... | 2007-06-30 |
0704.2346 | Marcio Rocha | M. S. Rocha, M. C. Ferreira, and O. N. Mesquita | Transition on the entropic elasticity of DNA induced by intercalating
molecules | This experimental article shows and discuss a transition observed in
the persistence length of DNA molecules when studied as a function of some
intercalating drug concentrations, like daunomycin and ethidium bromide. It
has 15 pages and 4 figures. The article presented here is in preprint format | null | 10.1063/1.2768945 | null | physics.bio-ph physics.chem-ph | null | We use optical tweezers to perform stretching experiments on DNA molecules
when interacting with the drugs daunomycin and ethidium bromide, which
intercalate the DNA molecule. These experiments are performed in the low-force
regime from zero up to 2 pN. Our results show that the persistence length of
the DNA-drug com... | 2009-11-13 |
0704.2409 | Jose Vilar | Leonor Saiz and Jose M.G. Vilar | Multilevel Deconstruction of the In Vivo Behavior of Looped DNA-Protein
Complexes | Open Access article available at
http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000355 | PLoS ONE 2(4): e355 (2007) | 10.1371/journal.pone.0000355 | null | q-bio.BM q-bio.SC | null | Protein-DNA complexes with loops play a fundamental role in a wide variety of
cellular processes, ranging from the regulation of DNA transcription to
telomere maintenance. As ubiquitous as they are, their precise in vivo
properties and their integration into the cellular function still remain
largely unexplored. Here... | 2007-05-23 |
0704.2454 | Vahid Rezania | Vahid Rezania, Jack Tuszynski, Michael Hendzel | Modeling transcription factor binding events to DNA using a random
walker/jumper representation on a 1D/2D lattice with different affinity sites | 24 pages, 9 figures | Physical Biology, 4, 256-267 (2007) | 10.1088/1478-3975/4/4/003 | null | q-bio.QM q-bio.BM | null | Surviving in a diverse environment requires corresponding organism responses.
At the cellular level, such adjustment relies on the transcription factors
(TFs) which must rapidly find their target sequences amidst a vast amount of
non-relevant sequences on DNA molecules. Whether these transcription factors
locate thei... | 2009-11-13 |
0704.2474 | Yi Xiao | Changjun Chen and Yi Xiao | Observation of Multiple folding Pathways of beta-hairpin Trpzip2 from
Independent Continuous Folding Trajectories | 13 pages, 8 figures | null | null | null | q-bio.BM | null | We report 10 successfully folding events of trpzip2 by molecular dynamics
simulation. It is found that the trizip2 can fold into its native state through
different zipper pathways, depending on the ways of forming hydrophobic core.
We also find a very fast non-zipper pathway. This indicates that there may be
no incon... | 2007-05-23 |
0704.2533 | Frank Schweitzer | Frank Schweitzer | Multi-Agent Approach to the Self-Organization of Networks | 20 papges, to appear in: F. Reed-Tsochas, N. F. Johnson, J.
Efstathiou: Understanding and Managing Complex Agent-Based Dynamical
Networks, Singapore: World Scientific (2007) | null | null | null | nlin.AO physics.bio-ph q-bio.QM | null | Is it possible to link a set of nodes without using preexisting positional
information or any kind of long-range attraction of the nodes? Can the process
of generating positional information, i.e. the detection of ``unknown'' nodes
and the estabishment of chemical gradients, \emph{and} the process of network
formatio... | 2007-05-23 |
0704.2547 | Remi Monasson | Valentina Baldazzi (LPS), Serena Bradde (LPS), Simona Cocco (LPS),
Enzo Marinari, Remi Monasson (LPTENS) | Inferring DNA sequences from mechanical unzipping data: the
large-bandwidth case | null | Phys. Rev. E 75 (2007) 011904 | 10.1103/PhysRevE.75.011904 | null | q-bio.BM cond-mat.stat-mech | null | The complementary strands of DNA molecules can be separated when stretched
apart by a force; the unzipping signal is correlated to the base content of the
sequence but is affected by thermal and instrumental noise. We consider here
the ideal case where opening events are known to a very good time resolution
(very lar... | 2015-05-13 |
0704.2551 | Sophie Lebre | Sophie L\`ebre (SG) | Inferring dynamic genetic networks with low order independencies | null | null | null | null | math.ST q-bio.QM stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we propose a novel inference method for dynamic genetic
networks which makes it possible to face with a number of time measurements n
much smaller than the number of genes p. The approach is based on the concept
of low order conditional dependence graph that we extend here in the case of
Dynamic Bayesi... | 2009-05-29 |
0704.2554 | Yannick Brohard | Brigitte Meyer-Berthaud (AMAP), Anne-Laure Decombeix (AMAP) | A tree without leaves | null | Nature 446, 7138 (2006) 861-862 | 10.1038/446861a | A-07-09 | q-bio.PE | null | The puzzle presented by the famous stumps of Gilboa, New York, finds a
solution in the discovery of two fossil specimens that allow the entire
structure of these early trees to be reconstructed.
| 2007-05-23 |
0704.2649 | Mike Steel Prof. | Mike Steel, Aki Mimoto, Arne O. Mooers | Hedging our bets: the expected contribution of species to future
phylogenetic diversity | 19 pages, 2 figures | null | null | null | q-bio.PE | null | If predictions for species extinctions hold, then the `tree of life' today
may be quite different to that in (say) 100 years. We describe a technique to
quantify how much each species is likely to contribute to future biodiversity,
as measured by its expected contribution to phylogenetic diversity. Our
approach consi... | 2007-05-23 |
0704.2700 | Ivan Degtyarenko Mr. | Ivan Degtyarenko, Karl J. Jalkanen, Andrey A. Gurtovenko and Risto M.
Nieminen | The aqueous and crystalline forms of L-alanine zwitterion | preprint of 22 pages, 7 figures, and 2 tables | null | null | null | physics.bio-ph physics.chem-ph physics.comp-ph | null | The structural properties of L-alanine amino acid in aqueous solution and in
crystalline phase have been studied by means of density-functional
electronic-structure and molecular dynamics simulations. The solvated
zwitterionic structure of L-alanine (+NH3-C2H4-COO-) was systematically
compared to the structure of its... | 2007-05-23 |
0704.2750 | Nikolai Lebovka I | Nikolai Lebovka, Eugene Vorobiev | The kinetics of inactivation of spheroidal microbial cells by pulsed
electric fields | 12 pages, 10 figures | null | null | null | physics.bio-ph | null | The nature of non-exponential kinetics in microbial cells inactivation by
pulsed electric fields (PEF) is discussed. It was demonstrated that possible
mechanism of non-exponential kinetics can be related to orientational disorder
in suspension of microbial cells of anisotropic form. A numerical studies of
spheroidal ... | 2007-05-23 |
0704.2793 | Matthew Scott | Matthew Scott, Terence Hwa and Brian Ingalls | Deterministic characterization of stochastic genetic circuits | 6 pages (Supplementary Information is appended) | Proceedings of the National Academy of Sciences USA (2007), vol.
104(18): 7402-7407 | 10.1073/pnas.0610468104 | null | q-bio.MN q-bio.QM | null | For cellular biochemical reaction systems where the numbers of molecules is
small, significant noise is associated with chemical reaction events. This
molecular noise can give rise to behavior that is very different from the
predictions of deterministic rate equation models. Unfortunately, there are few
analytic meth... | 2009-11-13 |
0704.2794 | Rafael Quintero-Torres | R. Quintero-Torres and J.L. Aragon, M. Torres, M. Estrada and L. Cros | Strong far field coherent scattering of ultraviolet radiation by
holococcolithophores | 4 pages and 4 figures | Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Sep;74:2006 Sep 12 | null | null | physics.bio-ph | null | By considering the structure of holococcoliths (calcite plates that cover
holococcolithophores, a haploid phase of the coccolithophore life cycle) as a
photonic structure, we apply a discrete dipolar approximation to study the
light backscattering properties of these algae. We show that some holococcolith
structures ... | 2007-05-23 |
0704.2896 | Adrian Melott | Bruce S.Lieberman and Adrian L. Melott (University of Kansas) | Considering the Case for Biodiversity Cycles: Reexamining the Evidence
for Periodicity in the Fossil Record | Minor modifications to reflect final published version | PLoS ONE 2(8): e759 (2007) | 10.1371/journal.pone.0000759 | null | q-bio.PE astro-ph physics.geo-ph | null | Medvedev and Melott (2007) have suggested that periodicity in fossil
biodiversity may be induced by cosmic rays which vary as the Solar System
oscillates normal to the galactic disk. We re-examine the evidence for a 62
million year (Myr) periodicity in biodiversity throughout the Phanerozoic
history of animal life re... | 2007-08-22 |
0704.2964 | Ashok Palaniappan | Ashok Palaniappan | Fourier Analysis of Biological Evolution: Concept of Selection Moment | null | null | null | null | q-bio.BM q-bio.QM | null | Secondary structure elements of many protein families exhibit differential
conservation on their opposing faces. Amphipathic helices and beta-sheets by
definition possess this property, and play crucial functional roles. This type
of evolutionary trajectory of a protein family is usually critical to the
functions of ... | 2007-05-23 |
0704.3005 | Yasser Roudi | Yasser Roudi, Peter E. Latham | A balanced memory network | Accepted for publications in PLoS Comp. Biol | null | 10.1371/journal.pcbi.0030141 | null | q-bio.NC cond-mat.dis-nn | null | A fundamental problem in neuroscience is understanding how working memory --
the ability to store information at intermediate timescales, like 10s of
seconds -- is implemented in realistic neuronal networks. The most likely
candidate mechanism is the attractor network, and a great deal of effort has
gone toward inves... | 2015-05-13 |
0704.3049 | Ryan Gutenkunst | Ryan N. Gutenkunst, Fergal P. Casey, Joshua J. Waterfall, Christopher
R. Myers, James P. Sethna | Extracting falsifiable predictions from sloppy models | 4 pages, 2 figures. Submitted to the Annals of the New York Academy
of Sciences for publication in "Reverse Engineering Biological Networks:
Opportunities and Challenges in Computational Methods for Pathway Inference" | Annals of the New York Academy of Sciences 1115:203-211 (2007) | 10.1196/annals.1407.003 | null | q-bio.QM | null | Successful predictions are among the most compelling validations of any
model. Extracting falsifiable predictions from nonlinear multiparameter models
is complicated by the fact that such models are commonly sloppy, possessing
sensitivities to different parameter combinations that range over many decades.
Here we dis... | 2007-11-24 |
0704.3071 | Karina Mazzitello | K. I. Mazzitello, C. M. Arizmendi, and H. G. E. Hentschel | Converting genetic network oscillations into somite spatial pattern | 7 pages, 7 figures | null | 10.1103/PhysRevE.78.021906 | null | q-bio.QM | null | In most vertebrate species, the body axis is generated by the formation of
repeated transient structures called somites. This spatial periodicity in
somitogenesis has been related to the temporally sustained oscillations in
certain mRNAs and their associated gene products in the cells forming the
presomatic mesoderm.... | 2009-11-13 |
0704.3079 | Ilia Solov'yov | Alexander V. Yakubovich, Ilia A. Solov'yov, Andrey V. Solov'yov and
Walter Greiner | Ab initio theory of helix-coil phase transition | 24 pages, 3 figures | null | 10.1140/epjd/e2007-00328-9 | null | physics.bio-ph physics.chem-ph | null | In this paper we suggest a theoretical method based on the statistical
mechanics for treating the alpha-helix-random coil transition in alanine
polypeptides. We consider this process as a first-order phase transition and
develop a theory which is free of model parameters and is based solely on
fundamental physical pr... | 2009-11-13 |
0704.3085 | Ilia Solov'yov | Ilia A. Solov'yov, Alexander V. Yakubovich, Andrey V. Solov'yov and
Walter Greiner | Alpha helix-coil phase transition: analysis of ab initio theory
predictions | 34 pages, 12 figures | null | 10.1140/epjd/e2007-00327-x | null | physics.bio-ph physics.chem-ph | null | In the present paper we present results of calculations obtained with the use
of the theoretical method described in our preceding paper [1] and perform
detail analysis of alpha helix-random coil transition in alanine polypeptides
of different length. We have calculated the potential energy surfaces of
polypeptides w... | 2009-11-13 |
0704.3138 | Branislav Brutovsky | Branislav Brutovsky, Denis Horvath and Vladimir Lisy | Inverse Geometric Approach to the Simulation of the Circular Growth. The
Case of Multicellular Tumor Spheroids | null | null | 10.1016/j.physa.2007.10.036 | null | q-bio.CB | null | We demonstrate the power of the genetic algorithms to construct the cellular
automata model simulating the growth of 2-dimensional close-to-circular
clusters revealing the desired properties, such as the growth rate and, at the
same time, the fractal behavior of their contours. The possible application of
the approac... | 2009-11-13 |
0704.3172 | Debaprasad Giri | Sanjay Kumar and Debaprasad Giri | Force induced conformational transition in a system of interacting stiff
polymer: Application to unfolding | RevTeX v4, 9 pages with 6 eps figures | Phys. Rev. E 72, 052901 (2005) | 10.1103/PhysRevE.72.052901 | BHU-PHY/CMPT/05-01 | cond-mat.soft cond-mat.stat-mech physics.bio-ph | null | We consider a stiff polymer chain in poor solvent and apply a force at one
end of the chain. We find that by varying the stiffness parameter, polymer
undergoes a transition from the globule state to the folded like state. The
conformation of folded state mimics the $\beta$-sheet as seen in titin
molecule. Using exact... | 2015-05-13 |
0704.3174 | Ma\'ira Aguiar | Ma\'ira Aguiar, Nico Stollenwerk | A new chaotic attractor in a basic multi-strain epidemiological model
with temporary cross-immunity | 16 pages, 15 figures | null | null | null | nlin.CD q-bio.PE | null | An epidemic multi-strain model with temporary cross-immunity shows chaos,
even in a previously unexpected parameter region. Especially dengue fever
models with strong enhanced infectivity on secondary infection have previously
shown deterministic chaos motivated by experimental findings of
antibody-dependent-enhancem... | 2007-06-25 |
0704.3175 | Debaprasad Giri | Debaprasad Giri and Sanjay Kumar | Effects of Eye-phase in DNA unzipping | RevTeX v4, 9 pages with 7 eps figures | Phys. Rev. E 73, 050903(R) (2006) | 10.1103/PhysRevE.73.050903 | BHU-PHY/CMPT/05-03 | cond-mat.soft cond-mat.stat-mech physics.bio-ph | null | The onset of an "eye-phase" and its role during the DNA unzipping is studied
when a force is applied to the interior of the chain. The directionality of the
hydrogen bond introduced here shows oscillations in force-extension curve
similar to a "saw-tooth" kind of oscillations seen in the protein unfolding
experiments... | 2015-05-13 |
0704.3193 | Elsa Henriques S | Elsa S. Henriques, Andrey V. Solov'yov | A Rational Method for Probing Macromolecules Dissociation: The
Antibody-Hapten System | 22 pages, 10 figures | null | 10.1140/epjd/e2008-00009-3 | null | physics.bio-ph physics.chem-ph | null | The unbinding process of a protein-ligand complex of major biological
interest was investigated by means of a computational approach at atomistic
classical mechanical level. An energy minimisation-based technique was used to
determine the dissociation paths of the system by probing only a relevant set
of generalized ... | 2009-11-13 |
0704.3221 | Manuel Lladser | Manuel Lladser, M. D. Betterton, Rob Knight | Multiple pattern matching: A Markov chain approach | Final version to appear in the Journal of Mathematical Biology | null | null | null | math.PR math.CO math.ST q-bio.GN q-bio.QM stat.TH | null | RNA motifs typically consist of short, modular patterns that include base
pairs formed within and between modules. Estimating the abundance of these
patterns is of fundamental importance for assessing the statistical
significance of matches in genomewide searches, and for predicting whether a
given function has evolv... | 2007-05-23 |
0704.3223 | Benedikt Obermayer | Benedikt Obermayer and Oskar Hallatschek | Coupling of transverse and longitudinal response in stiff polymers | 4 pages, 3 figures, 1 table; final version | Phys. Rev. Lett. 99 (2007) 098302 | 10.1103/PhysRevLett.99.098302 | LMU-ASC 25/07 | cond-mat.soft q-bio.BM | null | The time-dependent transverse response of stiff polymers, represented as
weakly-bending wormlike chains (WLCs), is well-understood on the linear level,
where transverse degrees of freedom evolve independently from the longitudinal
ones. We show that, beyond a characteristic time scale, the nonlinear coupling
of trans... | 2007-09-03 |
0704.3226 | Radhakrishnan Nagarajan | Radhakrishnan Nagarajan | Delay estimation in a two-node acyclic network | 33 Pages, 6 Figures | Physica A: Volume 376, 15 March 2007, Pages 725-737 | 10.1016/j.physa.2006.10.067 | null | q-bio.QM q-bio.MN | null | Linear measures such as cross-correlation have been used successfully to
determine time delays from the given processes. Such an analysis often precedes
identifying possible causal relationships between the observed processes. The
present study investigates the impact of a positively correlated driver whose
correlati... | 2015-05-13 |
0704.3259 | James P. Sethna | Christopher R. Myers, Ryan N. Gutenkunst, and James. P. Sethna | Python Unleashed on Systems Biology | Submitted to special issue of CiSE | null | null | null | q-bio.QM q-bio.MN | null | We have built an open-source software system for the modeling of biomolecular
reaction networks, SloppyCell, which is written in Python and makes substantial
use of third-party libraries for numerics, visualization, and parallel
programming. We highlight here some of the powerful features that Python
provides that en... | 2007-05-23 |
0704.3263 | Dominique Jean-Marie Mornet | Karim Hnia, G\'erald Hugon, Ahmed Masmoudi, Jacques Mercier,
Fran\c{c}ois Rivier, Dominique Jean-Marie Mornet | Effect of beta-Dystroglycan Processing on Utrophin / DP116 Anchorage in
Normal and MDX Mouse Schwann Cell Membrane | null | Neuroscience 141 (18/04/2006) 607-620 | 10.1016/J.neuroscience.2006.04.043 | null | q-bio.NC | null | In the peripheral nervous system, utrophin and the short dystrophin isoform
(Dp116) are co-localized at the outermost layer of the myelin sheath of nerve
fibers; together with the dystroglycan complex. In peripheral nerve, matrix
metalloproteinase (MMP) creates a 30 kDa fragment of beta-dystroglycan, leading
to a dis... | 2007-05-23 |
0704.3264 | Jose Vilar | Leonor Saiz and Jose M. G. Vilar | Efficiency and versatility of distal multisite transcription regulation | null | null | null | null | q-bio.SC q-bio.MN | null | Transcription regulation typically involves the binding of proteins over long
distances on multiple DNA sites that are brought close to each other by the
formation of DNA loops. The inherent complexity of the assembly of regulatory
complexes on looped DNA challenges the understanding of even the simplest
genetic syst... | 2007-05-23 |
0704.3312 | Yohan Payan | Nicolas Vuillerme (TIMC - IMAG), Olivier Chenu (TIMC - IMAG),
Alexandre Moreau-Gaudry (TIMC - IMAG), Jacques Demongeot (TIMC - IMAG), Yohan
Payan (TIMC - IMAG) | Artificial Tongue-Placed Tactile Biofeedback for perceptual
supplementation: application to human disability and biomedical engineering | null | Human Machine iNteraction Conference Human'07 (2007) 105-112 | null | null | physics.med-ph q-bio.NC | null | The present paper aims at introducing the innovative technologies, based on
the concept of "sensory substitution" or "perceptual supplementation", we are
developing in the fields of human disability and biomedical engineering.
Precisely, our goal is to design, develop and validate practical assistive
biomedical and/t... | 2007-05-23 |
0704.3321 | Chikara Furusawa | Chikara Furusawa and Kunihiko Kaneko | A generic mechanism for adaptive growth rate regulation | 14 pages, 5 figures, submitted to PLoS Computational Biology | null | 10.1371/journal.pcbi.0040003 | null | q-bio.MN | null | How can a microorganism adapt to a variety of environmental conditions
despite there exists a limited number of signal transduction machineries? We
show that for any growing cells whose gene expression is under stochastic
fluctuations, adaptive cellular state is inevitably selected by noise, even
without specific sig... | 2015-05-13 |
0704.3356 | Yohan Payan | Alexandre Moreau-Gaudry (TIMC - IMAG), Anne Prince (CMUDD), Jacques
Demongeot (TIMC - IMAG), Yohan Payan (TIMC - IMAG) | Pr\'evention des escarres chez les parapl\'egiques : une nouvelle
approche par \'electrostimulation linguale | null | Actes de la 4\`eme Conf\'erence Handicap 2006 "Nouvelles
Technologies au service de l'homme" (2006) 216-220 | null | null | physics.med-ph q-bio.NC | null | Pressure ulcers are recognized as a major health issue in individuals with
spinal cord injuries and new approaches to prevent this pathology are
necessary. An innovative health strategy is being developed through the use of
computer and sensory substitution via the tongue in order to compensate for the
sensory loss i... | 2007-05-23 |
0704.3365 | Takehiro Nagasima | Takehiro Nagasima, Akira R. Kinjo, Takashi Mitsui, Ken Nishikawa | Wang-Landau molecular dynamics technique to search for low-energy
conformational space of proteins | 8 pages, 7 figures, accepted for publication in Physical Review E | Phys. Rev. E 75, 066706 (2007) | 10.1103/PhysRevE.75.066706 | null | physics.comp-ph physics.bio-ph | null | Multicanonical molecular dynamics (MD) is a powerful technique for sampling
conformations on rugged potential surfaces such as protein. However, it is
notoriously difficult to estimate the multicanonical temperature effectively.
Wang and Landau developed a convenient method for estimating the density of
states based ... | 2007-11-01 |
0704.3406 | Martin Weigt | Hamed Mahmoudi, Andrea Pagnani, Martin Weigt, Riccardo Zecchina | Propagation of external regulation and asynchronous dynamics in random
Boolean networks | 19 pages, 14 figures, to appear in Chaos | Chaos 17, 026109 (2007) | 10.1063/1.2742931 | null | cond-mat.stat-mech cond-mat.dis-nn q-bio.MN | null | Boolean Networks and their dynamics are of great interest as abstract
modeling schemes in various disciplines, ranging from biology to computer
science. Whereas parallel update schemes have been studied extensively in past
years, the level of understanding of asynchronous updates schemes is still very
poor. In this p... | 2007-07-19 |
0704.3453 | Tshilidzi Marwala | S. Mohamed, D. Rubin, and T. Marwala | An Adaptive Strategy for the Classification of G-Protein Coupled
Receptors | 9 pages, 5 tables, 3 figures | null | null | null | cs.AI q-bio.QM | null | One of the major problems in computational biology is the inability of
existing classification models to incorporate expanding and new domain
knowledge. This problem of static classification models is addressed in this
paper by the introduction of incremental learning for problems in
bioinformatics. Many machine lear... | 2007-06-25 |
0704.3551 | J\"org Langowski | Annika Wedemeier, Holger Merlitz, Chen-Xu Wu, and J\"org Langowski | Modelling diffusional transport in the interphase cell nucleus | 9 pages, 8 figures | null | 10.1063/1.2753158 | null | physics.bio-ph physics.comp-ph | null | In this paper a lattice model for diffusional transport of particles in the
interphase cell nucleus is proposed. Dense networks of chromatin fibers are
created by three different methods: randomly distributed, non-interconnected
obstacles, a random walk chain model, and a self avoiding random walk chain
model with pe... | 2009-11-13 |
0704.3560 | Christian Blum | Christian Blum, Willem L. Vos, and Vinod Subramaniam | Tuning Spontaneous Emission versus Forster Energy Transfer in Biological
Systems by Manipulating the Density of Photonic States | 12 pages, 3 figures, pdf | null | null | null | physics.chem-ph physics.bio-ph | null | We theoretically discuss how to tune the competition between Forster transfer
and spontaneous emission in a continuous and nondestructive fashion. The
proposed approach is especially suitable for delicate biological systems like
light harvesting complexes and fluorescent protein oligomers. We demonstrate
that the man... | 2007-06-19 |
0704.3619 | Marcus Kaiser | Luciano da F Costa, Marcus Kaiser, Claus C Hilgetag | Predicting the connectivity of primate cortical networks from
topological and spatial node properties | null | BMC Systems Biology 2007, 1:16 | 10.1186/1752-0509-1-16 | null | q-bio.NC physics.soc-ph | null | The organization of the connectivity between mammalian cortical areas has
become a major subject of study, because of its important role in scaffolding
the macroscopic aspects of animal behavior and intelligence. In this study we
present a computational reconstruction approach to the problem of network
organization, ... | 2007-05-23 |
0704.3639 | Filipe Tostevin | Filipe Tostevin, Pieter Rein ten Wolde, Martin Howard | Fundamental Limits to Position Determination by Concentration Gradients | 24 pages, 2 figures | PLoS Computational Biology 3 e78 (2007) | 10.1371/journal.pcbi.0030078 | null | q-bio.SC cond-mat.stat-mech | null | Position determination in biological systems is often achieved through
protein concentration gradients. Measuring the local concentration of such a
protein with a spatially-varying distribution allows the measurement of
position within the system. In order for these systems to work effectively,
position determination... | 2007-05-23 |
0704.3640 | Dennis Wylie | Dennis Cates Wylie | Linked by Loops: Network Structure and Switch Integration in Complex
Dynamical Systems | 21 pages, 5 figures. Paper simplified and shortened. Quantities
presented in table 1 are different, though related, to quantities previously
presented in table 1 | null | null | null | q-bio.QM cond-mat.dis-nn math.DS nlin.CD | null | Simple nonlinear dynamical systems with multiple stable stationary states are
often taken as models for switchlike biological systems. This paper considers
the interaction of multiple such simple multistable systems when they are
embedded together into a larger dynamical "supersystem." Attention is focused
on the net... | 2008-04-10 |
0704.3715 | Pablo Echenique | Pablo Echenique, J. L. Alonso | Efficient model chemistries for peptides. I. Split-valence Gaussian
basis sets and the heterolevel approximation in RHF and MP2 | 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Chem | J. Comp. Chem. (2008) 1408-1422 | 10.1002/jcc.20900 | null | q-bio.QM cond-mat.soft q-bio.BM | null | We present an exhaustive study of more than 250 ab initio potential energy
surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries
(MCs) used are constructed as homo- and heterolevels involving possibly
different RHF and MP2 calculations for the geometry and the energy. The basis
sets used belong ... | 2013-06-21 |
0704.3724 | Paul Smolen | Paul Smolen | A Model of Late Long-Term Potentiation Simulates Aspects of Memory
Maintenance | Accepted to PLoS One. 8 figures at end | null | 10.1371/journal.pone.0000445 | null | q-bio.NC q-bio.MN | null | Late long-term potentiation (L-LTP) appears essential for the formation of
long-term memory, with memories at least partly encoded by patterns of
strengthened synapses. How memories are preserved for months or years, despite
molecular turnover, is not well understood. Ongoing recurrent neuronal
activity, during memor... | 2015-05-13 |
0704.3730 | Volkan Sevim | Volkan Sevim, Per Arne Rikvold | Network Growth with Preferential Attachment for High Indegree and Low
Outdegree | null | Physica A, Volume 387, Issue 11, 2631-2636 (2008) | 10.1016/j.physa.2008.01.034 | null | cond-mat.stat-mech q-bio.PE | null | We study the growth of a directed transportation network, such as a food web,
in which links carry resources. We propose a growth process in which new nodes
(or species) preferentially attach to existing nodes with high indegree (in
food-web language, number of prey) and low outdegree (or number of predators).
This s... | 2008-03-17 |
0704.3748 | Gerald A. Miller | Gerald A. Miller, Yi Y. Shi, Hong Qian, and Karol Bomsztyk | Clustering Coefficients of Protein-Protein Interaction Networks | 16 pages, 3 figures, in Press PRE uses pdflatex | Phys. Rev. E 75, 051910 (2007) | 10.1103/PhysRevE.75.051910 | null | q-bio.QM cond-mat.stat-mech physics.bio-ph q-bio.MN | null | The properties of certain networks are determined by hidden variables that
are not explicitly measured. The conditional probability (propagator) that a
vertex with a given value of the hidden variable is connected to k of other
vertices determines all measurable properties. We study hidden variable models
and find an... | 2009-11-13 |
0704.3771 | James P. Crutchfield | Olof Gornerup and James P. Crutchfield | Primordial Evolution in the Finitary Process Soup | 7 pages, 10 figures;
http://cse.ucdavis.edu/~cmg/compmech/pubs/pefps.htm | null | 10.1142/9789812779953_0012 | null | q-bio.PE q-bio.MN | null | A general and basic model of primordial evolution--a soup of reacting
finitary and discrete processes--is employed to identify and analyze
fundamental mechanisms that generate and maintain complex structures in
prebiotic systems. The processes--$\epsilon$-machines as defined in
computational mechanics--and their inte... | 2016-11-23 |
0704.3808 | Jakob Enemark | Jakob Enemark and Kim Sneppen | On Gene Duplication Models for Evolving Regulatory Networks | 14 pages, 7 figures | null | 10.1088/1742-5468/2007/11/P11007 | null | q-bio.PE q-bio.OT | null | Background: Duplication of genes is important for evolution of molecular
networks. Many authors have therefore considered gene duplication as a driving
force in shaping the topology of molecular networks. In particular it has been
noted that growth via duplication would act as an implicit way of preferential
attachme... | 2009-11-13 |
0704.3809 | Laurent Cognet | David Lasne (CPMOH), Gerhard A. Blab (CPMOH), St\'ephane Berciaud
(CPMOH), Martin Heine (PCS), Laurent Groc (PCS), Daniel Choquet (PCS),
Laurent Cognet (CPMOH), Brahim Lounis (CPMOH) | Single NanoParticle Photothermal Tracking (SNaPT) of 5 nm gold beads in
live cells | null | Biophysical Journal 91, 12 (15/12/2006) 4598 | 10.1529/biophysj.106.089771 | null | physics.bio-ph physics.optics | null | Tracking individual nano-objets in live cells during arbitrary long times is
an ubiquitous need in modern biology. We present here a method for tracking
individual 5 nm gold nanoparticles on live cells. It relies on the photothermal
effect and the detection of the Laser Induced Scattering around a NanoAbsorber
(LISNA... | 2007-05-23 |
0704.3816 | Laurent Cognet | Laurent Cognet (CPMOH), Catherine Tardin (CPMOH), David Boyer (CPMOH),
Daniel Choquet (PCS), Philippe Tamarat (CPMOH), Brahim Lounis (CPMOH) | Single metallic nanoparticle imaging for protein detection in cells | null | Proceeding of the national academy of sciences 100, 20
(30/09/2003) 11350 | 10.1073/pnas.1534635100 | null | physics.optics physics.bio-ph | null | We performed a visualization of membrane proteins labeled with 10-nm gold
nanoparticles in cells, using an all-optical method based on photothermal
interference contrast. The high sensitivity of the method and the stability of
the signals allows 3D imaging of individual nanoparticles without the drawbacks
of photoble... | 2007-05-23 |
0704.3826 | Mark Ya. Azbel' | Mark Ya. Azbel | Non-coding DNA programs express adaptation and its universal law | Refined version 19 pages, 10 figs | null | null | null | q-bio.GN cond-mat.other nlin.AO q-bio.OT q-bio.PE q-bio.QM | null | Significant fraction (98.5% in humans) of most animal genomes is non- coding
dark matter. Its largely unknown function (1-5) is related to programming
(rather than to spontaneous mutations) of accurate adaptation to rapidly
changing environment. Programmed adaptation to the same universal law for
non-competing animal... | 2007-08-02 |
0704.3853 | Laurent Cognet | Laurent Cognet (CPMOH), Fran\c{c}oise Coussen (PCS), Daniel Choquet
(PCS), Brahim Lounis (CPMOH) | Fluorescence microscopy of single autofluorescent proteins for cellular
biology | null | Comptes Rendus de l Acad\'emie des Sciences - Series IV - Physics
3 (15/08/2002) 645 | null | null | physics.optics physics.bio-ph | null | In this paper we review the applicability of autofluorescent proteins for
single-molecule imaging in biology. The photophysical characteristics of
several mutants of the Green Fluorescent Protein (GFP) and those of DsRed are
compared and critically discussed for their use in cellular biology. The
alternative use of t... | 2007-05-23 |
0704.3854 | Laurent Cognet | Laurent Cognet (CPMOH), Laurent Groc (PCS), Brahim Lounis (CPMOH),
Daniel Choquet (PCS) | Multiple Routes for Glutamate Receptor Trafficking: Surface Diffusion
and Membrane Traffic Cooperate to Bring Receptors to Synapses | null | Science's STKE (electronic resource) : signal transduction
knowledge environment 327 (21/03/2006) 13 | null | null | physics.optics physics.bio-ph | null | Trafficking of glutamate receptors into and out of synapses is critically
involved in the plasticity of excitatory synaptic transmission. Endocytosis and
exocytosis of receptors have initially been thought to account alone for this
trafficking. However, membrane proteins also traffic through surface lateral
diffusion... | 2007-05-23 |
0704.3855 | Laurent Cognet | Piet H M Lommerse, Gerhard A Blab, Laurent Cognet, Gregory S Harms, B
Ewa Snaar-Jagalska, Herman P Spaink, Thomas Schmidt | Single-molecule imaging of the H-ras membrane-anchor reveals domains in
the cytoplasmic leaflet of the cell membrane | null | Biophys J 86, 1 Pt 1 (01/2004) 609-16 | null | null | physics.optics physics.bio-ph | null | In the last decade evidence has accumulated that small domains of 50-700 nm
in diameter are located in the exoplasmic leaflet of the plasma membrane. Most
of these domains supposedly consist of specific sets of lipids and proteins,
and are believed to coordinate signal transduction cascades. Whether similar
domains a... | 2007-05-23 |
0704.3858 | Laurent Cognet | Catherine Tardin (CPMOH), Laurent Cognet (CPMOH), C\'ecile Bats (PCS),
Brahim Lounis (CPMOH), Daniel Choquet (PCS) | Direct imaging of lateral movements of AMPA receptors inside synapses | null | EMBO J 22, 18 (15/09/2003) 4656-65 | 10.1093/emboj/cdg463 | null | physics.optics physics.bio-ph | null | Trafficking of AMPA receptors in and out of synapses is crucial for synaptic
plasticity. Previous studies have focused on the role of endo/exocytosis
processes or that of lateral diffusion of extra-synaptic receptors. We have now
directly imaged AMPAR movements inside and outside synapses of live neurons
using single... | 2007-05-23 |
0704.3948 | Alexey Mazur K | Alexey K. Mazur | The Worm-Like Chain Theory And Bending Of Short DNA | 4 pages, 3 figures, to appear in PRL | Phys. Rev. Lett. 98, 218102, 2007. | 10.1103/PhysRevLett.98.218102 | null | q-bio.BM cond-mat.soft physics.bio-ph | null | The probability distributions for bending angles in double helical DNA
obtained in all-atom molecular dynamics simulations are compared with
theoretical predictions. The computed distributions remarkably agree with the
worm-like chain theory for double helices of one helical turn and longer, and
qualitatively differ ... | 2009-11-13 |
0704.3957 | Vasily Ogryzko V | Vasily Ogryzko | Erwin Schroedinger, Francis Crick and epigenetic stability | New and improved version of the essay, now published in the online
journal 'Biology Direct'. Contains more expanded discussion on entanglement.
18 pages, 2 figures. The file includes open reviews by E.Koonin, V.Vedral and
E.Karsenti | Biol Direct. 2008 Apr 17;3(1):15 | null | null | physics.gen-ph q-bio.MN | null | Schroedinger's book 'What is Life?' is widely credited for having played a
crucial role in development of molecular and cellular biology. My essay
revisits the issues raised by this book from the modern perspective of
epigenetics and systems biology. I contrast two classes of potential mechanisms
of epigenetic stabil... | 2008-05-30 |
0705.0078 | Claudius Gros | Claudius Gros | Neural networks with transient state dynamics | null | New J.Phys.9:109,2007 | 10.1088/1367-2630/9/4/109 | null | cond-mat.dis-nn astro-ph cond-mat.other nlin.AO q-bio.NC | null | We investigate dynamical systems characterized by a time series of distinct
semi-stable activity patterns, as they are observed in cortical neural activity
patterns. We propose and discuss a general mechanism allowing for an adiabatic
continuation between attractor networks and a specific adjoined transient-state
net... | 2010-02-11 |
0705.0201 | Jesse Bloom | Jesse D Bloom, Philip A Romero, Zhongyi Lu, and Frances H Arnold | Neutral genetic drift can aid functional protein evolution | null | Biology Direct 2:17 (2007) | 10.1186/1745-6150-2-17 | null | q-bio.PE q-bio.BM | null | BACKGROUND: Many of the mutations accumulated by naturally evolving proteins
are neutral in the sense that they do not significantly alter a protein's
ability to perform its primary biological function. However, new protein
functions evolve when selection begins to favor other, "promiscuous" functions
that are incide... | 2007-07-18 |
0705.0227 | Graeme J. Ackland | Graeme J. Ackland, Richard D.L.Hanes, Morrel H. Cohen | Self assembly of a model multicellular organism resembling the
Dictyostelium slime molds | null | null | null | null | q-bio.CB q-bio.PE | null | The evolution of multicellular organisms from monocellular ancestors
represents one of the greatest advances of the history of life. The assembly of
such multicellular organisms requires signalling and response between cells:
over millions of years these signalling processes have become extremely
sophisticated and re... | 2007-05-23 |
0705.0313 | Gasper Tkacik | Gasper Tkacik, Curtis G Callan Jr, William Bialek | Information flow and optimization in transcriptional control | 5 pages, 4 figures | Proc Natl Acad Sci USA 105 (2008): 12265-12270 | 10.1073/pnas.0806077105 | null | q-bio.MN | null | In the simplest view of transcriptional regulation, the expression of a gene
is turned on or off by changes in the concentration of a transcription factor
(TF). We use recent data on noise levels in gene expression to show that it
should be possible to transmit much more than just one regulatory bit.
Realizing this o... | 2013-08-01 |
0705.0374 | Razvan Radulescu M.D. | Razvan T. Radulescu, Angelika Jahn, Daniela Hellmann and Gregor
Weirich | Immunohistochemical pitfalls in the demonstration of insulin-degrading
enzyme in normal and neoplastic human tissues | 17 pages, 6 figures | null | null | null | q-bio.TO q-bio.QM | null | Previously, we have identified the cytoplasmic zinc metalloprotease
insulin-degrading enzyme(IDE) in human tissues by an immunohistochemical method
involving no antigen retrieval (AR) by pressure cooking to avoid artifacts by
endogenous biotin exposure and a detection kit based on the labeled
streptavidin biotin (LSA... | 2007-05-23 |
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