Quantitative Biology

Authors and titles for July 2003

[1] arXiv:astro-ph/0307543 (cross-list from astro-ph) [pdf, other]

Title: Importance of Biologically Active Aurora-like Ultraviolet Emission: Stochastic Irradiation of Earth and Mars by Flares and Explosions

David S. Smith (1), John Scalo (1), J. Craig Wheeler (1) ((1) Univ. Texas at Austin)

Comments: 21 pages, 2 figures, accepted for publication in Origins of Life and Evolution of the Biosphere

Journal-ref: Origins of life and evolution of the biosphere October 2004, Volume 34, Issue 5, pp 513-532

Subjects: Astrophysics (astro-ph); Populations and Evolution (q-bio.PE)

[2] arXiv:cond-mat/0307006 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Energetics of Protein Thermodynamic Cooperativity: Contributions of Local and Nonlocal Interactions

Michael Knott, Huseyin Kaya, Hue Sun Chan

Comments: 23 pages, 8 postscript figures (will appear in Polymer)

Journal-ref: Polymer 45 (2004) 623-632.

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

[3] arXiv:cond-mat/0307046 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Unified "micro"- and "macro-" evolution of eco-systems: Self-organization of a dynamic network

Dietrich Stauffer, Debashish Chowdhury

Comments: 7 pages with 3 figures; for Max Born Symposium, Poland, Sept. 2003

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

[4] arXiv:cond-mat/0307060 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Single Stranded DNA Translocation Through A Nanopore: A Master Equation Approach

O. Flomenbom, J. Klafter

Comments: 7 pages submitted to PRE

Journal-ref: Phys. Rev. E 68, 041910 (2003)

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

[5] arXiv:cond-mat/0307079 (cross-list from cond-mat.soft) [pdf, other]

Title: Adsorption of mono- and multivalent cat- and anions on DNA molecules

E. Allahyarov, H. Löwen, G. Gompper

Comments: 34 pages with 14 figures

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

[6] arXiv:cond-mat/0307104 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Multi-state neural networks based upon spin-glasses: a biased overview

D. Bolle

Comments: Review chapter to appear in Advances in Condensed Matter and Statistical Mechanics, ed. by E. Korutcheva and R. Cuerno, Nova Science Publishers (38 pages Latex with 12 eps-figures)

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Quantitative Biology (q-bio)

[7] arXiv:cond-mat/0307105 (cross-list from cond-mat.soft) [pdf, other]

Title: Simultaneous surface acoustic wave and surface plasmon resonance measurements: electrodeposition and biological interactions monitoring

J.-M. Friedt, L. Francis, G. Reekmans, R. De Palma, A. Campitelli, U.B. Sleytr

Comments: 13 pages, 4 figures

Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)

[8] arXiv:cond-mat/0307114 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Network properties, species abundance and evolution in a model of evolutionary ecology

Paul Anderson, Henrik Jeldtoft Jensen

Comments: 12 pages, 4 figures

Journal-ref: J Theor Biol Vol. 232, p. 551 (2005)

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

[9] arXiv:cond-mat/0307132 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Synchronous Dynamics of a Hopfield Model with Random Asymmetric Interactions

Manoranjan P. Singh

Comments: 15 pages, 1 figure, revtex

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Quantitative Biology (q-bio)

[10] arXiv:cond-mat/0307135 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Mechanisms of recoverable prevalence and extinction of viruses on linearly growing scale-free networks

Yukio Hayashi

Comments: 4 pages, 2 figures

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

[11] arXiv:cond-mat/0307242 (cross-list from cond-mat.soft) [pdf, other]

Title: Dynamics of Pulsed Flow in an Elastic Tube

Amit K. Chattopadhyay, Shreekantha Sil

Comments: 6 pages and 4 figures

Journal-ref: "Propagation of pulse through elastic tubes" in International Journal of Modern Physics B 17 (26), 4619-4629 (2003)

Subjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Tissues and Organs (q-bio.TO)

[12] arXiv:cond-mat/0307317 (cross-list from cond-mat) [pdf, other]

Title: Modes of speciation in heterogeneous space

Martin Rost, Michael Lässig

Comments: 13 pages latex, 6 eps-figures, some typos corrected (if ps file has corrupt figures, try pdf)

Subjects: Condensed Matter (cond-mat); Populations and Evolution (q-bio.PE)

[13] arXiv:cond-mat/0307319 (cross-list from cond-mat.soft) [pdf, other]

Title: Dynamics of polymer chain collapse into compact states

D. C. Rapaport

Comments: 11 pages, 11 figures (some low resolution)

Journal-ref: Phys. Rev. E 68 (2003) 041801

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

[14] arXiv:cond-mat/0307380 (cross-list from cond-mat.soft) [pdf, other]

Title: Helicase activity on DNA as a propagating front

Somendra M. Bhattacharjee

Comments: 5 pages, 5 eps figures; replaced by the published version

Journal-ref: Europhysics Letts. 65, 574 (2004)

Subjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Quantitative Biology (q-bio)

[15] arXiv:cond-mat/0307439 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: The emergent properties of a dolphin social network

David Lusseau

Comments: 5 pages, 4 figures. Available online from the journal's web-site (See this http URL) as well. To be printed this year

Journal-ref: published in Biology Letters: Lusseau, D. 2003 The emergent properties of a dolphin social network. Proceedings of the Royal Society of London- Series B (Suppl.) DOI 10.1098/rsbl.2003.0057

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

[16] arXiv:cond-mat/0307557 (cross-list from cond-mat.soft) [pdf, other]

Title: Far Infrared Sensing Of The Oxidation State Of Heme Proteins

J.-Y. Chen, J. Cerne, A. G. Markelz

Comments: single pdf file containing figures, 4 pages

Subjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci); Quantitative Biology (q-bio)

[17] arXiv:cond-mat/0307558 (cross-list from cond-mat.soft) [pdf, other]

Title: Xerogel Protein Substrates for Far Infrared Studies

J.-Y. Chen, W. Cox, E. Tehan, F.V. Bright, J. Cerne, A. G. Markelz

Comments: single pdf file, 5 pages, 4 figures

Subjects: Soft Condensed Matter (cond-mat.soft); Quantitative Biology (q-bio)

[18] arXiv:cond-mat/0307567 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Maximisation Principles and Daisyworld

G.J.Ackland

Comments: 17 pages 6 figures

Subjects: Statistical Mechanics (cond-mat.stat-mech); Disordered Systems and Neural Networks (cond-mat.dis-nn); Quantitative Biology (q-bio)

[19] arXiv:cond-mat/0307574 (cross-list from cond-mat) [pdf, other]

Title: Neuromorphometric characterization with shape functionals

Marconi Soares Barbosa, Luciano da Fontoura Costa, Esmerindo de Sousa Bernardes

Journal-ref: Physical Review E 67 061910 (2003)

Subjects: Condensed Matter (cond-mat); Neurons and Cognition (q-bio.NC)

[20] arXiv:cond-mat/0307577 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Thermally activated processes in polymer dynamics

Lorenzo Bongini, Roberto Livi, Alessandro Torcini, Antonio Politi

Comments: 16 pages, Revtex - 19 EPS Figs - Submitted to Phys. Rev. E

Journal-ref: Phys. Rev. E, 68 (2003) 061111

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

[21] arXiv:cond-mat/0307666 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: A novel stochastic Hebb-like learning rule for neural networks

Frank Emmert-Streib

Comments: 10 pages, 7 figures

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Quantitative Biology (q-bio)

[22] arXiv:cond-mat/0307667 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Bidirectional communication in neural networks moderated by a Hebb-like learning rule

Frank Emmert-Streib

Comments: 7 pages, 4 figures

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Quantitative Biology (q-bio)

[23] arXiv:cond-mat/0307717 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Some asymptotic properties of duplication graphs

Alpan Raval

Comments: 19 pages, including 3 figures

Subjects: Statistical Mechanics (cond-mat.stat-mech); Molecular Networks (q-bio.MN)

[24] arXiv:cond-mat/0307720 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Self-organized Pattern Formation in Motor-Microtubule Mixtures

Sumithra Sankararaman, Gautam I. Menon (IMSc, Chennai), P.B. Sunil Kumar (IITM, Chennai)

Comments: 11 pages Latex file, 2 figures included

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

[25] arXiv:cond-mat/0307742 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Nonlinear Voter Models: The Transition from Invasion to Coexistence

Frank Schweitzer, Laxmidhar Behera

Comments: Completely revised and extended version, new results and interpretation. 39 pages, 24 figures. European Physical Journal B, vol 67 (2009)

Journal-ref: European Physical Journal B, vol 67 (2009) 301-318

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

[26] arXiv:cond-mat/0307747 (cross-list from cond-mat.soft) [pdf, other]

Title: Towards the Understanding of Stability Puzzles in Phage lambda

P. Ao, L. Yin

Comments: latex, 2 pages

Subjects: Soft Condensed Matter (cond-mat.soft); Quantitative Biology (q-bio)

[27] arXiv:nlin/0307006 (cross-list from nlin.AO) [pdf, other]

Title: Crossover Behaviour of 3-Species Systems with Mutations or Migrations

Margarita Ifti, Birger Bergersen

Comments: 2nd version revised and refereed 14 pages, 5 figures

Journal-ref: European Physical Journal B37, 101-107 (2004)

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

[28] arXiv:nlin/0307007 (cross-list from nlin.CD) [pdf, other]

Title: Sound and Image Processing with Optical Biocomputers

Cameron L. Jones

Comments: 6 pages, 8 figures, Paper presented at ICIAM - 5th International Congress on Industrial and Applied Mathematics, 7-11th July, 2003 Sydney, Australia. For the 6th Engineering Mathematics and Applications Conference. EMAC EML150N-007, 11th July, 2003 Sydney. Australia

Subjects: Chaotic Dynamics (nlin.CD); Pattern Formation and Solitons (nlin.PS); Quantitative Methods (q-bio.QM)

[29] arXiv:nlin/0307014 (cross-list from nlin.CD) [pdf, other]

Title: A propensity criterion for networking in an array of coupled chaotic systems

F.T. Arecchi, E. Allaria, I. Leyva

Comments: 4 pages, 3 figures

Subjects: Chaotic Dynamics (nlin.CD); Pattern Formation and Solitons (nlin.PS); Neurons and Cognition (q-bio.NC)

[30] arXiv:nlin/0307015 (cross-list from nlin.AO) [pdf, other]

Title: Methods and Techniques of Complex Systems Science: An Overview

Cosma Rohilla Shalizi (Center for the Study of Complex Systems, University of Michigan)

Comments: 96 pages, 8 figures. Versions 2 and 3: corrects minor typographical errors. Version 4: Expanded examples, updated references (through late 2004), matches published version up to changes in formatting

Journal-ref: Chapter 1 (pp. 33--114) in Thomas S. Deisboeck and J. Yasha Kresh (eds.),_Complex Systems Science in Biomedicine_ (New York: Springer, 2006)

Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Statistical Mechanics (cond-mat.stat-mech); Chaotic Dynamics (nlin.CD); Cellular Automata and Lattice Gases (nlin.CG); Data Analysis, Statistics and Probability (physics.data-an); Quantitative Methods (q-bio.QM)

[31] arXiv:nlin/0307031 (cross-list from nlin.PS) [pdf, other]

Title: Effect of base-pair inhomogeneities on charge transport along DNA mediated by twist and radial polarons

F. Palmero, J.F.R. Archilla, D. Hennig, F.R. Romero

Comments: 21 pages, 10 figures

Journal-ref: New. Jou. Phys. 6:13.1-13.16, 2004.

Subjects: Pattern Formation and Solitons (nlin.PS); Soft Condensed Matter (cond-mat.soft); Biomolecules (q-bio.BM)

[32] arXiv:physics/0307001 (cross-list from physics.bio-ph) [pdf, other]

Title: Scaling laws in the functional content of genomes

Erik van Nimwegen

Subjects: Biological Physics (physics.bio-ph); Genomics (q-bio.GN)

[33] arXiv:physics/0307007 (cross-list from physics.bio-ph) [pdf, other]

Title: Keynote Paper: Cell-Surface Adhesive Interactions in Microchannels and Microvessels

Michael R. King

Comments: 6 pages, 4 figures

Journal-ref: Proceedings of the First International Conference on Microchannels and Minichannels, ASME, pp. 103-108, 2003

Subjects: Biological Physics (physics.bio-ph); Fluid Dynamics (physics.flu-dyn); Cell Behavior (q-bio.CB)

[34] arXiv:physics/0307013 (cross-list from physics.bio-ph) [pdf, other]

Title: A Microscopic Mechanism for Muscle's Motion

Bao-Quan Ai, Xian-Ju Wang, Guo-Tao Liu, Liang-Gang Liu, M Nakano, H Matsuura

Comments: 9 pages, 6 figures

Journal-ref: Chin. Phys. Lett. 19 (2002)137

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

[35] arXiv:physics/0307014 (cross-list from physics.bio-ph) [pdf, other]

Title: Internal Motility in Stiffening Actin-Myosin Networks

Joerg Uhde, Manfred Keller, Erich Sackmann, Andrea Parmeggiani, Erwin Frey

Comments: 4 pages, 3 figures

Journal-ref: Phys. Rev. Lett. 93, 268101 (2004)

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Quantitative Biology (q-bio)

[36] arXiv:physics/0307031 (cross-list from physics.bio-ph) [pdf, other]

Title: A Possible Mechanism of Biological Memories in terms of Quantum Fluids

Tsunehiro Kobayashi

Comments: 8 pages

Subjects: Biological Physics (physics.bio-ph); Fluid Dynamics (physics.flu-dyn); Quantitative Biology (q-bio)

[37] arXiv:physics/0307043 (cross-list from physics.bio-ph) [pdf, other]

Title: Unexpected trends in termite survival

Og DeSouza, Octavio Miramontes

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

[38] arXiv:physics/0307045 (cross-list from physics.bio-ph) [pdf, other]

Title: Spatiotemporal Pattern Formation in BioFluids I: Cell Shape Perturbants As Evidence of Spatially-Organised Membrane Flows

J.T.Lofthouse

Comments: 22 pages, 5 figures. Accepted Physica D, 2003

Subjects: Biological Physics (physics.bio-ph); Fluid Dynamics (physics.flu-dyn); Cell Behavior (q-bio.CB); Other Quantitative Biology (q-bio.OT)

[39] arXiv:physics/0307051 (cross-list from physics.bio-ph) [pdf, other]

Title: Simulations of Oligomeric Intermediates in Prion Diseases

David L. Mobley, Daniel L. Cox, Rajiv R. P. Singh, Rahul V. Kulkarni, Alexander Slepoy

Comments: 8 pages, 10 figures For larger versions of several figures, see this http URL and click on the prion paper link

Journal-ref: Biophys. J. 85:2213-2223 (Oct. 2003)

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

[40] arXiv:physics/0307065 (cross-list from physics.bio-ph) [pdf, other]

Title: Has the Brain Maximized its Information Storage Capacity?

Armen Stepanyants

Comments: 6 pages, 2 figures, 1 table

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); General Physics (physics.gen-ph); Neurons and Cognition (q-bio.NC)

[41] arXiv:physics/0307072 (cross-list from physics.bio-ph) [pdf, other]

Title: Network information and connected correlations

Elad Schneidman, Susanne Still, Michael J. Berry II, William Bialek

Comments: 4 pages, 3 figures

Journal-ref: Phys. Rev. Lett. 91, 238701:1-4 (2003)

Subjects: Biological Physics (physics.bio-ph); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Neurons and Cognition (q-bio.NC)

[42] arXiv:physics/0307076 (cross-list from physics.bio-ph) [pdf, other]

Title: Protein secondary structure prediction based on quintuplets

Wei-Mou Zheng

Comments: 10 pages with 6 tables

Subjects: Biological Physics (physics.bio-ph); Data Analysis, Statistics and Probability (physics.data-an); Biomolecules (q-bio.BM)

[43] arXiv:physics/0307107 (cross-list from physics.bio-ph) [pdf, other]

Title: A stochastic model for retinocollicular map development

Alexei A. Koulakov, Dmitry N. Tsigankov

Comments: 19 pages, 11 color figures

Subjects: Biological Physics (physics.bio-ph); Disordered Systems and Neural Networks (cond-mat.dis-nn); Quantitative Biology (q-bio)

[44] arXiv:physics/0307121 (cross-list from physics.bio-ph) [pdf, other]

Title: Free Energy Transduction in a Chemical Motor Model

Josh E. Baker

Comments: 26 pages, 6 figures

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

[45] arXiv:physics/0307135 (cross-list from physics.bio-ph) [pdf, other]

Title: The Intrinsic Time Scale of Transient Neuronal Responses

Bjoern Naundorf, Theo Geisel, Fred Wolf

Comments: 5 pages, 4 figures

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

[46] arXiv:physics/0307136 (cross-list from physics.bio-ph) [pdf, other]

Title: A Growth Model for Multicellular Tumor Spheroids

Pier Paolo Delsanto, Caterina Guiot, Piero Giorgio Degiorgis, Carlos A. Condat, Yuri Mansury, Thomas S. Deisboeck

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

[47] arXiv:physics/0307143 (cross-list from physics.bio-ph) [pdf, other]

Title: Modeling Amyloid Beta Peptide Insertion into Lipid Bilayers

David L. Mobley, Daniel L. Cox, Rajiv R. P. Singh, Michael W. Maddox, Marjorie L. Longo

Comments: 14 pages; 8 figures; 2nd revision

Subjects: Biological Physics (physics.bio-ph); Computational Physics (physics.comp-ph); Medical Physics (physics.med-ph); Biomolecules (q-bio.BM)

[48] arXiv:physics/0307155 (cross-list from physics.bio-ph) [pdf, other]

Title: Synchronization of active mechanical oscillators by an inertial load

Andrej Vilfan, Thomas Duke

Comments: 5 pages, 4 figures, To appear in Phys. Rev. Lett

Journal-ref: Phys. Rev. Lett. 91, 114101 (2003)

Subjects: Biological Physics (physics.bio-ph); Adaptation and Self-Organizing Systems (nlin.AO); Quantitative Biology (q-bio)