Quantitative Biology

Authors and titles for April 2006

[1] arXiv:q-bio/0604001 [pdf, other]

Title: Amplified biochemical oscillations in cellular systems

A. J. McKane, J. D. Nagy, T. J. Newman, M. O. Stefanini

Comments: 35 pages, 6 figures

Subjects: Cell Behavior (q-bio.CB); Statistical Mechanics (cond-mat.stat-mech); Biomolecules (q-bio.BM)

[2] arXiv:q-bio/0604002 [pdf, other]

Title: Conductance versus current noise in a neuronal model for noisy subthreshold oscillations and related spike generation

Martin Tobias Huber, Hans Albert Braun

Comments: accepted for publication in Biosystems; 10 pages, 2 figures

Subjects: Neurons and Cognition (q-bio.NC); Cell Behavior (q-bio.CB)

[3] arXiv:q-bio/0604003 [pdf, other]

Title: Solitons in the Yakushevich model of DNA beyond the contact approximation

G. Gaeta

Journal-ref: Phys. Rev. E 74 (2006), 021921

Subjects: Biomolecules (q-bio.BM)

[4] arXiv:q-bio/0604004 [pdf, other]

Title: Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential

G. Gaeta

Journal-ref: J. Nonlin. Math. Phys. 14 (2007), 57-81

Subjects: Biomolecules (q-bio.BM)

[5] arXiv:q-bio/0604005 [pdf, other]

Title: Diffusion of transcription factors can drastically enhance the noise in gene expression

Jeroen S. van Zon, Marco J. Morelli, Sorin Tanase-Nicola, Pieter Rein ten Wolde

Comments: 15 pages, 6 figures, REVTeX4

Subjects: Molecular Networks (q-bio.MN)

[6] arXiv:q-bio/0604006 [pdf, other]

Title: Graph Theory and Networks in Biology

Oliver Mason, Mark Verwoerd

Comments: 52 pages, 5 figures, Survey Paper

Subjects: Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[7] arXiv:q-bio/0604007 [pdf, other]

Title: Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data

Dmitry A. Kondrashov, Qiang Cui, George N. Phillips Jr

Comments: 18 pages, 4 figures, 1 supplemental file (this http URL)

Journal-ref: Biophysical Journal, vol 91 (8), 2006

Subjects: Biomolecules (q-bio.BM)

[8] arXiv:q-bio/0604008 [pdf, other]

Title: Tumors under periodic therapy -- Role of the immune response time delay

D. Rodriguez-Perez, Oscar Sotolongo-Grau, Ramon Espinosa Riquelme, Oscar Sotolongo-Costa, J. Antonio Santos Miranda, J.C. Antoranz

Comments: 6 pages, 2 figures

Subjects: Tissues and Organs (q-bio.TO)

[9] arXiv:q-bio/0604009 [pdf, other]

Title: Temporal and dimensional effects in evolutionary graph theory

C. J. Paley, S. N. Taraskin, S. R. Elliott

Comments: 6 pages, 4 figures Replaced after final round of peer review

Journal-ref: Phys. Rev. Lett. 98, 098103 (2007)

Subjects: Populations and Evolution (q-bio.PE)

[10] arXiv:q-bio/0604010 [pdf, other]

Title: Non-equilibrium theory of the allele frequency spectrum

Steven N. Evans, Yelena Shvets, Montgomery Slatkin

Comments: 24 pages, 7 figures, updated to accomodate referees' suggestions, to appear in Theoretical Population Biology

Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR)

[11] arXiv:q-bio/0604011 [pdf, other]

Title: A Surprising Clarification of the Mechanism of Ion-channel Voltage-Gating

Ashok Palaniappan

Comments: Indication of alternative mechanisms

Subjects: Biomolecules (q-bio.BM); Neurons and Cognition (q-bio.NC); Subcellular Processes (q-bio.SC)

[12] arXiv:q-bio/0604012 [pdf, other]

Title: The adaptive filter of the yeast galactose pathway

Serge Smidtas, Vincent Schachter, Francois Kepes

Journal-ref: J. Theor. Biol. 2005

Subjects: Molecular Networks (q-bio.MN); Cell Behavior (q-bio.CB)

[13] arXiv:q-bio/0604013 [pdf, other]

Title: CRNPRED: Highly Accurate Prediction of One-dimensional Protein Structures by Large-scale Critical Random Networks

Akira R. Kinjo, Ken Nishikawa

Comments: 10 pages, 1 figure, 2 tables

Journal-ref: BMC Bioinformatics, 7:401 (2006)

Subjects: Biomolecules (q-bio.BM)

[14] arXiv:q-bio/0604014 [pdf, other]

Title: A composite model for DNA torsion dynamics

M. Cadoni, R. De Leo, G. Gaeta

Comments: 29 pages

Journal-ref: Phys. Rev. E75 (2007), 021919

Subjects: Biomolecules (q-bio.BM); Biological Physics (physics.bio-ph)

[15] arXiv:q-bio/0604015 [pdf, other]

Title: Qualitative Assessment of Gene Expression in Affymetrix Genechip Arrays

Radhakrishnan Nagarajan, Meenakshi Upreti

Comments: 22 Pages, 7 Figures, 1 Table

Subjects: Genomics (q-bio.GN)

[16] arXiv:q-bio/0604016 [pdf, other]

Title: A mean-field analysis of community structure in social and kin networks

E. Durand, M.G.B Blum, O. Francois

Comments: 31 pages, 4 figures

Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR); Physics and Society (physics.soc-ph)

[17] arXiv:q-bio/0604017 [pdf, other]

Title: Complex Qualitative Models in Biology: a new approach

Philippe Veber, Michel Le_Borgne, Anne Siegel, Sandrine Lagarrigue, Ovidiu Radulescu

Comments: 15 pages, 2 figures, ECCS'05, to appear in Complexus

Subjects: Molecular Networks (q-bio.MN)

[18] arXiv:q-bio/0604018 [pdf, other]

Title: Algorithms for identification and categorization

J.M. Cortes, P.L. Garrido, H.J. Kappen, J. Marro, C. Morillas, D. Navidad, J.J. Torres

Comments: 6 pages, 5 figures

Journal-ref: AIP Conference Proceedings 779: 178-184, 2005

Subjects: Neurons and Cognition (q-bio.NC)

[19] arXiv:q-bio/0604019 [pdf, other]

Title: Competition between synaptic depression and facilitation in attractor neural networks

J. J. Torres, J.M. Cortes, J. Marro, H.J. Kappen

Comments: 14 pages, 7 figures

Subjects: Neurons and Cognition (q-bio.NC)

[20] arXiv:q-bio/0604020 [pdf, other]

Title: Chaotic hopping between attractors in neural networks

J. Marro, J.J. Torres, J.M. Cortes

Comments: 12 pages, 5 figures

Subjects: Neurons and Cognition (q-bio.NC)

[21] arXiv:q-bio/0604021 [pdf, other]

Title: Instability of attractors in autoassociative networks with bioinspired fast synaptic noise

J.J. Torres, J.M. Cortes, J. Marro

Comments: 6 pages, 2 figures

Journal-ref: LNCS 3512: 161-167, 2005

Subjects: Neurons and Cognition (q-bio.NC)

[22] arXiv:q-bio/0604022 [pdf, other]

Title: Information and Protein Interfaces

William W. Chen, Paul J. Choi, Jason E. Donald, Eugene I. Shakhnovich

Subjects: Biomolecules (q-bio.BM)

[23] arXiv:q-bio/0604023 [pdf, other]

Title: Analysis of a microscopic stochastic model of microtubule dynamic instability

Gennady Margolin, Ivan V. Gregoretti, Holly V. Goodson, Mark S. Alber

Comments: 14 pages, 7 figures

Journal-ref: PHYSICAL REVIEW E 74, 041920 (2006)

Subjects: Subcellular Processes (q-bio.SC); Cell Behavior (q-bio.CB); Quantitative Methods (q-bio.QM)

[24] arXiv:q-bio/0604024 [pdf, other]

Title: The transposition distance for phylogenetic trees

Francesc Rossello, Gabriel Valiente

Comments: 15 pages

Subjects: Populations and Evolution (q-bio.PE); Computational Engineering, Finance, and Science (cs.CE); Group Theory (math.GR); Other Quantitative Biology (q-bio.OT)

[25] arXiv:q-bio/0604025 [pdf, other]

Title: Combinatorial on/off Model for Olfactory Coding

A. Koulakov, A. Gelperin, D. Rinberg

Subjects: Neurons and Cognition (q-bio.NC)

[26] arXiv:q-bio/0604026 [pdf, other]

Title: Cross-species analysis of biological networks by Bayesian alignment

Johannes Berg, Michael Lässig

Comments: Published version - new title and figure, some changes to the text. 10 pages, 5 figures. Supporting text is available from the authors

Journal-ref: PNAS 103 (29), 10967-10972 (2006)

Subjects: Molecular Networks (q-bio.MN); Disordered Systems and Neural Networks (cond-mat.dis-nn); Genomics (q-bio.GN)

[27] arXiv:q-bio/0604027 [pdf, other]

Title: Solitons in a double pendulums chain model, and DNA roto-torsional dynamics

M. Cadoni, R. De Leo, G. Gaeta

Journal-ref: J. Nonlin. Math. Phys. 14 (2007), 128-146

Subjects: Biomolecules (q-bio.BM)

[28] arXiv:q-bio/0604028 [pdf, other]

Title: Synaptic plasticity of Inhibitory synapse promote synchrony in inhibitory network in presence of heterogeneity and noise

Sachin S Talathi

Comments: 5 pages, 4 figures

Subjects: Neurons and Cognition (q-bio.NC)

[29] arXiv:q-bio/0604029 [pdf, other]

Title: Structure and function of negative feedback loops at the interface of genetic and metabolic networks

Sandeep Krishna, Anna M. C. Andersson, Szabolcs Semsey, Kim Sneppen

Comments: 8 pages, 4 figures

Journal-ref: Nucleic Acids Res., 34: 2455 - 2462 (2006).

Subjects: Molecular Networks (q-bio.MN); Other Condensed Matter (cond-mat.other)

[30] arXiv:q-bio/0604030 [pdf, other]

Title: Self-organized patterns of coexistence out of a predator-prey cellular automaton

Kelly C. de Carvalho, Tania Tome

Comments: 19 pages, 11 figures

Subjects: Populations and Evolution (q-bio.PE)

[31] arXiv:q-bio/0604031 [pdf, other]

Title: Effects of Growth on Dinitrogen on the Transcriptome and Predicted Proteome of Nostoc PCC 7120

R. Wunschiers, R. Axelsson, P. Lindblad

Comments: 38 pages, including 9 figures and 6 tables

Subjects: Genomics (q-bio.GN)

[32] arXiv:q-bio/0604032 [pdf, other]

Title: Dynamics of Semiflexible Polymers in a Flow Field

Tobias Munk, Oskar Hallatschek, Chris H. Wiggins, Erwin Frey

Comments: Corrected Label in Fig. 2. 12 pages, 10 figures

Journal-ref: Physical Review E, Vol. 74, No. 4, 041911 (2006)

Subjects: Biomolecules (q-bio.BM); Soft Condensed Matter (cond-mat.soft)

[33] arXiv:q-bio/0604033 [pdf, other]

Title: Online detection and sorting of extracellularly recorded action potentials in human medial temporal lobe recordings, in vivo

Ueli Rutishauser, Erin M. Schuman, Adam N. Mamelak

Comments: 9 figures, 2 tables. Journal of Neuroscience Methods 2006 (in press). Journal of Neuroscience Methods, 2006 (in press)

Journal-ref: J Neurosci Methods, 2006; 154(1-2):204-224

Subjects: Quantitative Methods (q-bio.QM); Neurons and Cognition (q-bio.NC)

[34] arXiv:q-bio/0604034 [pdf, other]

Title: Virus evolution : the emergence of new ideas (and re-emergence of old ones)

Jean-Michel Claverie (IGS)

Comments: submitted

Subjects: Populations and Evolution (q-bio.PE)

[35] arXiv:q-bio/0604035 [pdf, other]

Title: On the weak solutions of the McKendrick equation: Existence of demography cycles

Rui Dilao, Abdelkader Lakmeche

Comments: 26 pages, 6 figures

Subjects: Populations and Evolution (q-bio.PE)

[36] arXiv:astro-ph/0604440 (cross-list from astro-ph) [pdf, other]

Title: Comment on: Protecting Life in the Milky Way: Metals Keep the GRBs Away by Stanek et al

Adrian L. Melott (University of Kansas)

Subjects: Astrophysics (astro-ph); Atmospheric and Oceanic Physics (physics.ao-ph); Geophysics (physics.geo-ph); Plasma Physics (physics.plasm-ph); Populations and Evolution (q-bio.PE)

[37] arXiv:astro-ph/0604556 (cross-list from astro-ph) [pdf, other]

Title: Terrestrial Consequences of Spectral and Temporal Variability in Ionizing Photon Events

Larissa M. Ejzak, Adrian L. Melott, Mikhail V. Medvedev, (University of Kansas), Brian C. Thomas (Washburn University)

Comments: 30 pages, to be published in ApJ. Replaced for conformity with published version, including correction of minor typos and updated references

Journal-ref: Astrophys.J.654:373-384,2007

Subjects: Astrophysics (astro-ph); Atmospheric and Oceanic Physics (physics.ao-ph); Biological Physics (physics.bio-ph); Geophysics (physics.geo-ph); Populations and Evolution (q-bio.PE)

[38] arXiv:cond-mat/0604024 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Random Networks Tossing Biased Coins

F. Bassetti, M. Cosentino Lagomarsino, B. Bassetti, P. Jona

Subjects: Statistical Mechanics (cond-mat.stat-mech); Quantitative Methods (q-bio.QM)

[39] arXiv:cond-mat/0604129 (cross-list from cond-mat.soft) [pdf, other]

Title: Finite-size effects in intracellular microrheology

I. Santamaria-Holek, J. M. Rubi

Comments: 6 pages 2 figures. To appear in the Journal of Chemical Physics

Subjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Subcellular Processes (q-bio.SC)

[40] arXiv:cond-mat/0604148 (cross-list from cond-mat.soft) [pdf, other]

Title: Self-energy limited ion transport in sub-nanometer channels

Douwe Jan Bonthuis, Jingshan Zhang, Breton Hornblower, Jerome Mathe, Boris I. Shklovskii, Amit Meller

Comments: more experimental material is added. 4 pages, 7 figures

Journal-ref: Phys. Rev. Lett. 97, 128104 (2006)

Subjects: Soft Condensed Matter (cond-mat.soft); Subcellular Processes (q-bio.SC)

[41] arXiv:cond-mat/0604275 (cross-list from cond-mat.soft) [pdf, other]

Title: Fluid-crystal coexistence for proteins and inorganic nanocolloids: dependence on ionic strength

Peter Prinsen, Theo Odijk

Comments: 15 pages, 9 figures

Subjects: Soft Condensed Matter (cond-mat.soft); Biomolecules (q-bio.BM)

[42] arXiv:math/0604041 (cross-list from math.PR) [pdf, other]

Title: Invasion and adaptive evolution for individual-based spatially structured populations

Nicolas Champagnat (WIAS), Sylvie Méléard (MODAL'X, FESE)

Subjects: Probability (math.PR); Populations and Evolution (q-bio.PE)

[43] arXiv:math/0604366 (cross-list from math.PR) [pdf, other]

Title: The Kesten-Stigum Reconstruction Bound Is Tight for Roughly Symmetric Binary Channels

Christian Borgs, Jennifer Chayes, Elchanan Mossel, Sebastien Roch

Subjects: Probability (math.PR); Computational Complexity (cs.CC); Populations and Evolution (q-bio.PE)

[44] arXiv:math/0604534 (cross-list from math.DS) [pdf, other]

Title: Finite Dynamical Systems, Linear Automata, and Finite Fields

Oscar Moreno, Dorothy Bollman, Maria A. Avino-Diaz

Comments: 5 pages, conference

Journal-ref: 2002 WSEAS Int. Conf. on System Science, Applied Mathematics & Computer Science and Power Engineering Systems, 1481-1483, October (2002)

Subjects: Dynamical Systems (math.DS); Rings and Algebras (math.RA); Genomics (q-bio.GN)

[45] arXiv:nlin/0604007 (cross-list from nlin.CD) [pdf, other]

Title: Fractional Generalization of Gradient Systems

Vasily E. Tarasov

Comments: 11 pages, LaTeX

Journal-ref: Letters in Mathematical Physics 73 (2005) 49-58

Subjects: Chaotic Dynamics (nlin.CD); Mathematical Physics (math-ph); Dynamical Systems (math.DS); Chemical Physics (physics.chem-ph); Classical Physics (physics.class-ph); Other Quantitative Biology (q-bio.OT)

[46] arXiv:nlin/0604042 (cross-list from nlin.CD) [pdf, other]

Title: Universal Scaling Laws for Large Events in Driven Nonequilibrium Systems

M. K. Verma, S. Manna, J. Banerjee, S. Ghosh

Comments: 9 pages, 5 figures

Journal-ref: Europhys. Lett., 76 (6), pp. 1050-1056 (2006)

Subjects: Chaotic Dynamics (nlin.CD); Statistical Mechanics (cond-mat.stat-mech); Quantitative Methods (q-bio.QM)

[47] arXiv:nlin/0604043 (cross-list from nlin.CD) [pdf, other]

Title: Self-organised criticality and 1/f noise in single-channel current of voltage-dependent anion channel

Jyotirmoy Banerjee, Mahendra. K. Verma, Smarajit Manna, Subhendu Ghosh

Comments: pdf file, 12 pages

Journal-ref: Europhys. Lett., v73, 457, 2006

Subjects: Chaotic Dynamics (nlin.CD); Statistical Mechanics (cond-mat.stat-mech); Quantitative Methods (q-bio.QM)

[48] arXiv:nlin/0604069 (cross-list from nlin.AO) [pdf, other]

Title: Evolution of Complexity: Introduction to the Workshop

Carlos Gershenson, Tom Lenaerts

Comments: to be held at ALife X. More info, full papers, and online discussion at this http URL

Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Populations and Evolution (q-bio.PE)

[49] arXiv:physics/0604075 (cross-list from physics.bio-ph) [pdf, other]

Title: Traffic of interacting ribosomes: effects of single-machine mechano-chemistry on protein synthesis

Aakash Basu, Debashish Chowdhury

Comments: 4 pages including 3 EPS figures

Subjects: Biological Physics (physics.bio-ph); Statistical Mechanics (cond-mat.stat-mech); Subcellular Processes (q-bio.SC)

[50] arXiv:physics/0604142 (cross-list from physics.soc-ph) [pdf, other]

Title: Pair Formation within Multi-Agent Populations

David M.D. Smith, Neil F. Johnson

Comments: Special Issue on Complex Networks, edited by Dirk Helbing

Journal-ref: Physica A, Vol. 363, p. 151-158 (2006)

Subjects: Physics and Society (physics.soc-ph); Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)