Quantitative Biology

Authors and titles for July 2005

[1] arXiv:q-bio/0507001 [pdf, other]

Title: Characterizing Polygonality in Biological Structures

Luciano da Fontoura Costa, Fernando Rocha, Silene Araujo de Lima

Comments: 14 pages, 11 figures

Journal-ref: Phys. Rev. E 73, 011913 (2006)

Subjects: Tissues and Organs (q-bio.TO); Disordered Systems and Neural Networks (cond-mat.dis-nn)

[2] arXiv:q-bio/0507002 [pdf, other]

Title: A learning rule for place fields in a cortical model: theta phase precession as a network effect

Silvia Scarpetta, Maria Marinaro

Comments: 10 pages, 7 figures, to be published in Hippocampus

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn)

[3] arXiv:q-bio/0507003 [pdf, other]

Title: The Mediterranean deep-sea fauna: historical evolution, bathymetric variations and geographical changes

Christian Emig (DIMAR), Patrick Geistdoerfer (LOV)

Journal-ref: Carnets de G\'{e}ologie / Notebooks on Geology Article 2004/01 (CG2004_A01_CCE-PG) (2004) 10 p., 4 fig., 3 tabl

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

[4] arXiv:q-bio/0507004 [pdf, other]

Title: Life in solid ice

P. Buford Price

Comments: 21 pages, no figures, presented at Workshop on Life in Ancient Ice, June 30, 2001

Subjects: Populations and Evolution (q-bio.PE); Cell Behavior (q-bio.CB)

[5] arXiv:q-bio/0507005 [pdf, other]

Title: Probability Models for Degree Distributions of Protein Interaction Networks

Michael P.H. Stumpf, Piers J. Ingram

Journal-ref: Europhys.Lett., 71 (1), pp. 152-158 (2005)

Subjects: Molecular Networks (q-bio.MN)

[6] arXiv:q-bio/0507006 [pdf, other]

Title: Does telomere elongation lead to a longer lifespan if cancer is considered?

Michael Masa, Stanislaw Cebrat, Dietrich Stauffer

Comments: 9 pages including 5 figures

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

[7] arXiv:q-bio/0507007 [pdf, other]

Title: Stochastic model for Soj relocation dynamics in Bacillus subtilis

Konstantin Doubrovinski, Martin Howard

Comments: 45 pages

Journal-ref: Proc. Natl. Acad. Sci. 102 9808-9813 (2005)

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

[8] arXiv:q-bio/0507008 [pdf, other]

Title: Introns Restructure tRNA Genes of Archaea

Zhumur Ghosh, Smarajit Das, Jayprokas Chakrabarti, Bibekanand Mallick, Satyabrata Sahoo

Comments: This paper has been withdrawn

Subjects: Genomics (q-bio.GN)

[9] arXiv:q-bio/0507009 [pdf, other]

Title: Quantitative Measure of Stability in Gene Regulatory Networks

P. Ao

Subjects: Quantitative Methods (q-bio.QM)

[10] arXiv:q-bio/0507010 [pdf, other]

Title: Integrin activation - the importance of a positive feedback

Dagmar Iber, Iain D Campbell

Comments: in press in Bulletin of Mathematical Biology

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

[11] arXiv:q-bio/0507011 [pdf, other]

Title: Power laws of complex systems from Extreme physical information

B. Roy Frieden, Robert A. Gatenby

Subjects: Cell Behavior (q-bio.CB)

[12] arXiv:q-bio/0507012 [pdf, other]

Title: Activation and Protonation of Dinitrogen at the FeMo-Cofactor of Nitrogenase

Johannes Kaestner (1 and 2), Sascha Hemmen (1), Peter E. Bloechl (1) ((1) Clausthal University of Technology, Germany, (2) Max-Planck-Institue for Coal Research, Germany)

Comments: 9 Pages, 6 figures, accepted in J. Chem. Phys. Typos corrected according to the galley proofs of JCP

Journal-ref: J. Chem. Phys. 123, 074306 (2005)

Subjects: Biomolecules (q-bio.BM)

[13] arXiv:q-bio/0507013 [pdf, other]

Title: Does host contact structure reduce pathogen diversity?

A. Nunes, M. M. Telo da Gama, M. G. M. Gomes

Comments: 28 pages, 7 figures

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

[14] arXiv:q-bio/0507014 [pdf, other]

Title: Nonlinear brain dynamics and many-body field dynamics

Walter J. Freeman, Giuseppe Vitiello

Comments: 8 pages, Invited talk presented at Fröhlich Centenary International Symposium "Coherence and Electromagnetic Fields in Biological Systems", July 1-4, 2005, Prague, Czech Republic

Subjects: Neurons and Cognition (q-bio.NC); Other Quantitative Biology (q-bio.OT)

[15] arXiv:q-bio/0507015 [pdf, other]

Title: Differential gene expression in Bacillus subtilis

Dagmar Iber, Joanna Clarkson, Michael D Yudkin, Iain D Campbell

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

[16] arXiv:q-bio/0507016 [pdf, other]

Title: Spectral Detrended Fluctuation Analysis and Its Application to Heart Rate Variability Assessment

Luciano da Fontoura Costa, Ruth Caldeira de Melo, Ester da Silva, Audrey Borghi-Silva, Aparecida Maria Catai

Comments: 10 pages, 4 figures

Subjects: Quantitative Methods (q-bio.QM); Disordered Systems and Neural Networks (cond-mat.dis-nn); Tissues and Organs (q-bio.TO)

[17] arXiv:q-bio/0507017 [pdf, other]

Title: New data on the systematics and interrelationships of sawfishes (Elasmobranchii, Batoidea, Pristiformes)

Pascal Deynat (DMPA)

Journal-ref: Journal of Fish Biology 66 (2005) 1447-1458

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

[18] arXiv:q-bio/0507018 [pdf, other]

Title: Bayesian Method for Disease QTL Detection and Mapping, using a Case and Control Design and DNA Pooling

Toby Johnson

Journal-ref: Biostatistics (2007) 8:546--565

Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)

[19] arXiv:q-bio/0507019 [pdf, other]

Title: Modeling genome evolution with a diffusion approximation of a birth-and-death process

Georgy P. Karev, Faina S. Berezovskaya, Eugene V. Koonin

Comments: 22pages, 9 figures; submitted to Bioinformatics

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

[20] arXiv:q-bio/0507020 [pdf, other]

Title: Simple stochastic birth and death models of genome evolution: Was there enough time for us to evolve?

Georgy P. Karev, Yuri I. Wolf, Eugene V. Koonin

Comments: 25 pages, 9 figures, 4 Tables

Journal-ref: Bioinformatics 2003, 19(15):1889-1900

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

[21] arXiv:q-bio/0507021 [pdf, other]

Title: Spontaneous polarization in eukaryotic gradient sensing: A mathematical model based on mutual inhibition of frontness and backness pathways

Atul Narang

Comments: 20 pages, 11 figures

Subjects: Cell Behavior (q-bio.CB)

[22] arXiv:q-bio/0507022 [pdf, other]

Title: Dynamics of DNA Ejection From Bacteriophage

Mandar M. Inamdar, William M. Gelbart, Rob Phillips

Comments: 17 pages, 5 figures

Subjects: Biomolecules (q-bio.BM)

[23] arXiv:q-bio/0507023 [pdf, other]

Title: Synchronization and spindle oscillation in noisy integrate-and-fire-or-burst neurons with inhibitory coupling

H.Sakaguchi, S.Tobiishi

Comments: 18pages, 8figures

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

[24] arXiv:q-bio/0507024 [pdf, other]

Title: Modeling Human Erythrocyte Shape and Size Abnormalities

S. Munoz, J.L. Sebastian, M. Sancho, G. Alvarez

Comments: submitted to Bioelectromagnetics

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

[25] arXiv:q-bio/0507025 [pdf, other]

Title: Phi-values in protein folding kinetics have energetic and structural components

Claudia Merlo, Ken A. Dill, Thomas R. Weikl

Comments: 15 pages, 3 figures, 1 table

Journal-ref: PNAS 102, 10171 (2005)

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

[26] arXiv:q-bio/0507026 [pdf, other]

Title: Biological applications of the theory of birth-and-death processes

Artem S. Novozhilov, Georgy P. Karev, Eugene V. Koonin

Comments: 29 pages, 4 figures; submitted to "Briefings in Bioinformatics"

Subjects: Quantitative Methods (q-bio.QM); Genomics (q-bio.GN)

[27] arXiv:q-bio/0507027 [pdf, other]

Title: Modeling the Role of the Cell Cycle in Regulating Proteus mirabilis Swarm-Colony Development

Bruce P. Ayati

Journal-ref: Applied Mathematics Letters, Vol. 20, 2007, pp. 913-918

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

[28] arXiv:q-bio/0507028 [pdf, other]

Title: Dynamics of Heterogeneous Populations and Communities and Evolution of Distributions

Georgy P. Karev

Comments: 11 pages; submitted to Discrete and Continuous Dynamical Systems

Subjects: Populations and Evolution (q-bio.PE); Other Quantitative Biology (q-bio.OT)

[29] arXiv:q-bio/0507029 [pdf, other]

Title: Prediction and predictability of global epidemics: the role of the airline transportation network

Vittoria Colizza, Alain Barrat, Marc Barthelemy, Alessandro Vespignani

Comments: 20 pages, 5 figures

Journal-ref: Proc. Natl. Acad. Sci. USA 103, 2015 (2006)

Subjects: Other Quantitative Biology (q-bio.OT); Biological Physics (physics.bio-ph)

[30] arXiv:q-bio/0507030 [pdf, other]

Title: Conspiracy in bacterial genomes

Luc Frappat, Antonino Sciarrino

Comments: revised version: introduction and conclusion enhanced, references added, figures added, some tables removed

Subjects: Genomics (q-bio.GN)

[31] arXiv:q-bio/0507031 [pdf, other]

Title: Detection of confinement and jumps in single molecule membrane trajectories

N. Meilhac, L. Le Guyader, L. Salome, N. Destainville

Comments: 4 pages, 3 figures

Journal-ref: Phys. Rev. E 73, 011915 (2006)

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

[32] arXiv:q-bio/0507032 [pdf, other]

Title: Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

Jacob Bock Axelsen, Koon-Kiu Yan, Sergei Maslov

Comments: 42 pages, 6 figures, 2 supplementary figure

Journal-ref: Biology Direct 2:32,(2007)

Subjects: Genomics (q-bio.GN); Soft Condensed Matter (cond-mat.soft)

[33] arXiv:q-bio/0507033 [pdf, other]

Title: Simulation of Rapoport's rule for latitudinal species spread

Dietrich Stauffer, Klaus Rohde

Comments: 14 pages including 6 figures

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

[34] arXiv:q-bio/0507034 [pdf, other]

Title: Dynamics and pattern formation in invasive tumor growth

Evgeniy Khain, Leonard M. Sander

Comments: 4 pages, 4 figures

Subjects: Cell Behavior (q-bio.CB)

[35] arXiv:q-bio/0507035 [pdf, other]

Title: A stochastic model for wound healing

Thomas Callaghan, Evgeniy Khain, Leonard M. Sander, Robert M. Ziff

Comments: 16 pages, 7 figures

Subjects: Cell Behavior (q-bio.CB)

[36] arXiv:q-bio/0507036 [pdf, other]

Title: A helicoidal transfer matrix model for inhomogeneous DNA melting

Tom Michoel, Yves Van de Peer

Comments: v3: Matlab toolbox included with source file; article unchanged, 12 pages, 11 figures, RevTeX

Journal-ref: Phys. Rev. E 73, 011908 (2006)

Subjects: Biomolecules (q-bio.BM); Quantitative Methods (q-bio.QM)

[37] arXiv:q-bio/0507037 [pdf, other]

Title: Neuromodulation Influences Synchronization and Intrinsic Read-out

Gabriele Scheler

Comments: 14 pages, 12 figures

Journal-ref: F1000Research 2018, 7:1277

Subjects: Neurons and Cognition (q-bio.NC); Neural and Evolutionary Computing (cs.NE); Adaptation and Self-Organizing Systems (nlin.AO)

[38] arXiv:q-bio/0507038 [pdf, other]

Title: Bacteriophage-mediated competition in Bordetella bacteria

Jaewook Joo, Michelle Gunny, Marisa Cases, Peter Hudson, Reka Albert, Eric Harvill

Comments: 10pages, 8 figures

Journal-ref: Proceedings of the Royal Society B: Biological Sciences (2006)

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

[39] arXiv:q-bio/0507039 [pdf, other]

Title: A complex adaptive systems approach to the kinetic folding of RNA

Wilfred Ndifon

Comments: 23 pages, 4 figures, 2 tables, to be published in BioSystems (Note: updated 2 references)

Subjects: Biomolecules (q-bio.BM); Adaptation and Self-Organizing Systems (nlin.AO)

[40] arXiv:q-bio/0507040 [pdf, other]

Title: Effects of correlated interactions in a biological coevolution model with individual-based dynamics

Volkan Sevim, Per Arne Rikvold

Comments: 17 pages, 10 figures. Submitted to Physical Biology

Journal-ref: J. Phys. A: Math. Gen. 38 No 43 (28 October 2005) 9475-9489

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

[41] arXiv:q-bio/0507041 [pdf, other]

Title: A base pairing model of duplex formation I: Watson-Crick pairing geometries

J.D. Bashford, P.D. Jarvis

Comments: Latex file, 13 pages, no figures. Refereed draft of manuscript submitted to Biopolymers

Journal-ref: Biopolymers 78: 287-297, 2005

Subjects: Biomolecules (q-bio.BM)

[42] arXiv:q-bio/0507042 [pdf, other]

Title: Signal analysis of impulse response functions in MR- and CT-measurements of cerebral blood flow

Evelyn Rost (Greifswald), Ralf Geske (Neubrandenburg), Michael Baake (Bielefeld)

Comments: 15 pages, 6 figures

Journal-ref: J. Theor. Biol. 240 (2006) 451-458

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

[43] arXiv:q-bio/0507043 [pdf, other]

Title: Flow correlated percolation during vascular network formation in tumors

D.-S. Lee, H. Rieger, K. Bartha

Comments: 4 pages, 3 figures (higher resolution at this http URL)

Journal-ref: Phys. Rev. Lett. 96, 058104 (2006)

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

[44] arXiv:q-bio/0507044 [pdf, other]

Title: A core genetic module : the Mixed Feedback Loop

Paul Francois, Vincent Hakim

Comments: To be published in Physical Review E

Subjects: Molecular Networks (q-bio.MN); Other Quantitative Biology (q-bio.OT)

[45] arXiv:q-bio/0507045 [pdf, other]

Title: A framework for detection and classification of events in neural activity

Hemant Bokil, Bijan Pesaran, R.A. Andersen, Partha P. Mitra

Comments: 30 pages, 6 figures; This version submitted to the IEEE Transactions in Biomedical Engineering

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

[46] arXiv:q-bio/0507046 [pdf, other]

Title: Chromosome Oscillations in Mitosis

Otger Campas, Pierre Sens

Comments: this http URL

Subjects: Subcellular Processes (q-bio.SC); Biological Physics (physics.bio-ph)

[47] arXiv:cond-mat/0507418 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Birth, death and diffusion of interacting particles

Emilio Hernandez-Garcia, Cristobal Lopez

Comments: 15 pages, 6 figures, Iop style. To appear in Journal of Physics A: Condensed matter

Journal-ref: J. Phys.: Condens. Matter 17 (2005) S4263-S4274

Subjects: Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)

[48] arXiv:cond-mat/0507464 (cross-list from cond-mat.soft) [pdf, other]

Title: Field Theoretic Study of Bilayer Membrane Fusion: II. Mechanism of a Stalk-Hole Complex

Kirill Katsov, Marcus Mueller, Michael Schick

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

[49] arXiv:cond-mat/0507477 (cross-list from cond-mat.soft) [pdf, other]

Title: Analytic theory of DNA condensation

Yukitaka Ishimoto (RIKEN), Norio Kikuchi (U. Mainz)

Comments: RevTex4, 4 pages, 1 figure (colour), typo fixed

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

[50] arXiv:cond-mat/0507542 (cross-list from cond-mat.soft) [pdf, other]

Title: TransPath: A Computational Method to Study the Ion Transit Pathways in Membrane Channels

Z. Kuang, A. Liu, T. L. Beck

Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Chemical Physics (physics.chem-ph); Biomolecules (q-bio.BM)