Quantitative Biology

Authors and titles for April 2005

[1] arXiv:q-bio/0504001 [pdf, other]

Title: A nonlocal continuum model for biological aggregation

Chad M. Topaz, Andrea L. Bertozzi, Mark A. Lewis

Comments: 25 pages, 9 figures

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

[2] arXiv:q-bio/0504002 [pdf, other]

Title: Brush Effects on DNA Chips: Thermodynamics, Kinetics and Design Guidlines

A. Halperin, A. Buhot, E. B. Zhulina

Comments: 20 pages, 5 figures (one figure in PNG format : figure1)

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

[3] arXiv:q-bio/0504003 [pdf, other]

Title: Metabolic Network Modelling: Including Stochastic Effects

P. Ao

Comments: 7 pages, latex

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

[4] arXiv:q-bio/0504004 [pdf, other]

Title: Electronic Transport in DNA

Daphne Klotsa, Rudolf A. Roemer, Matthew S. Turner

Comments: 12 pages RevTeX4 with 17 figures, submitted to Biophysical Journal

Journal-ref: Biophys. J. 89, 2187-2198 (2005)

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

[5] arXiv:q-bio/0504005 [pdf, other]

Title: Geometrical constraints in a gene network model and pattern formation

L. Diambra, Luciano da Fontoura Costa

Comments: 30 pages, 11 figures

Subjects: Molecular Networks (q-bio.MN)

[6] arXiv:q-bio/0504006 [pdf, other]

Title: Computer Simulations to Study Sympatric Speciation Processes

K. Luz-Burgoa

Comments: Doctoral Thesis defended on 28th March, 2005 at the "Universidade Federal Fluminense" Federal University in Niteroi, Brazil. Version in Portuguese

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

[7] arXiv:q-bio/0504007 [pdf, other]

Title: A methodology for determining amino-acid substitution matrices from set covers

A. H. L. Porto, V. C. Barbosa

Journal-ref: Lecture Notes in Computer Science 3907 (2006), 138-148

Subjects: Quantitative Methods (q-bio.QM)

[8] arXiv:q-bio/0504008 [pdf, other]

Title: L-selectin mediated leukocyte tethering in shear flow is controlled by multiple contacts and cytoskeletal anchorage facilitating fast rebinding events

Ulrich S. Schwarz (1), Ronen Alon (2) ((1) MPI Colloids and Interfaces, (2) Weizmann Institute)

Comments: 9 pages, Revtex, 4 Postscript figures included

Journal-ref: PNAS 101: 6940-6945 (2004)

Subjects: Subcellular Processes (q-bio.SC)

[9] arXiv:q-bio/0504009 [pdf, other]

Title: Dynamics of conduction blocks in a model of paced cardiac tissue

Herve Henry, Wouter-Jan Rappel

Comments: 8 pages 6 figures

Subjects: Tissues and Organs (q-bio.TO); Other Condensed Matter (cond-mat.other); Pattern Formation and Solitons (nlin.PS); Biological Physics (physics.bio-ph); Other Quantitative Biology (q-bio.OT)

[10] arXiv:q-bio/0504010 [pdf, other]

Title: Statistical modeling of primary Ewing tumours of the bone

Sreepurna Malakar, Florentin Smarandache, Sukanto Bhattacharya

Comments: 12 pages

Journal-ref: International Journal of Tomography & Statistics, Vol. 3, No. JJ05, 81-88, 2005.

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

[11] arXiv:q-bio/0504011 [pdf, other]

Title: Design of HIV-1-PR inhibitors which do not create resistance: blocking the folding of single monomers

R. A. Broglia, G. Tiana, L. Sutto, D. Provasi, F. Simona

Subjects: Biomolecules (q-bio.BM)

[12] arXiv:q-bio/0504012 [pdf, other]

Title: Mimivirus Gene Promoters Exhibit an Unprecedented Conservation among all Eukaryotes

Karsten Suhre (IGS), Stéphane Audic (IGS), Jean-Michel Claverie (IGS)

Subjects: Genomics (q-bio.GN)

[13] arXiv:q-bio/0504013 [pdf, other]

Title: PCA and K-Means decipher genome

A.N. Gorban, A. Y. Zinovyev

Comments: 18 pages, with program listings for MatLab, PCA analysis of genomes and additional animated 3D PCA plots

Journal-ref: A.N. Gorban, B. Kegl, D.C. Wunsch, A. Zinovyev (eds.) Principal Manifolds for Data Visualization and Dimension Reduction, Lecture Notes in Computational Science and Engineering 58, Springer, Berlin - Heidelberg, 2008, 307-323

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

[14] arXiv:q-bio/0504014 [pdf, other]

Title: Mimivirus Relatives in the Sargasso Sea

Elodie Ghedin, Jean-Michel Claverie (IGS)

Comments: see also this http URL

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

[15] arXiv:q-bio/0504015 [pdf, other]

Title: Evidence of a universal power law characterizing the evolution of metabolic networks

Shalini, Areejit Samal, Varun Giri, Sandeep Krishna, N. Raghuram, Sanjay Jain

Comments: 7 pages, 3 figures

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

[16] arXiv:q-bio/0504016 [pdf, other]

Title: On Recursive Production and Evolvabilty of Cells: Catalytic Reaction Network Approach

Kunihiko Kaneko

Comments: 46 pages 28 figures

Journal-ref: Adv Chem. Phys 130 (2005) 543-598

Subjects: Molecular Networks (q-bio.MN); Statistical Mechanics (cond-mat.stat-mech); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

[17] arXiv:q-bio/0504017 [pdf, other]

Title: Min-oscillations in Escherichia coli induced by interactions of membrane-bound proteins

G. Meacci, K. Kruse

Comments: 17 pages, 5 figures. Submitted to Physical Biology

Journal-ref: Phys. Biol. 2 (2005) 89-97

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

[18] arXiv:q-bio/0504018 [pdf, other]

Title: Neutral Theory and Relative Species Abundance in Ecology

Igor Volkov, Jayanth R. Banavar, Stephen P. Hubbell, Amos Maritan

Comments: 19 pages, 1 figure

Journal-ref: Nature, 424, 1035-1037 (28 August 2003)

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

[19] arXiv:q-bio/0504019 [pdf, other]

Title: Scaling properties of the Penna model

E. Brigatti, J.S. Sa' Martins, I. Roditi

Comments: 4 pages, 4 figures

Journal-ref: European Physical Journal B, 42 431-434 (2004)

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

[20] arXiv:q-bio/0504020 [pdf, other]

Title: Evolutionary ecology in-silico: Does mathematical modelling help in understanding the "generic" trends?

Debashish Chowdhury, Dietrich Stauffer

Comments: 28 pages, LATEX, 4 eps figures

Journal-ref: Review Article in "Journal of Biosciences", vol.30, 277-287 (2005)

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

[21] arXiv:q-bio/0504021 [pdf, other]

Title: Sharp gene pool transition in a population affected by phenotype-based selective hunting

E. Brigatti, J.S. Sa' Martins, I. Roditi

Comments: 5 pages, 4 figures

Journal-ref: European Physical Journal B 45 (2005) 529

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

[22] arXiv:q-bio/0504022 [pdf, other]

Title: Density-Dependence as a Size-Independent Regulatory Mechanism

Harold P. de Vladar

Comments: 41 Pages, 5 figures Submitted to JTB

Journal-ref: H.P. de Vladar. Density-dependence as a size-independent regulatory mechanism. J. Theor. Biol. (2006) vol. 238 (2) pp. 245-256

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

[23] arXiv:q-bio/0504023 [pdf, other]

Title: On Myosin II dynamics in the presence of external loads

A. Buonocore, L. Caputo, Y. Ishii, E. Pirozzi, T. Yanagida, L. M. Ricciardi

Comments: 6 figures, 8 tables, to appear on Biosystems

Subjects: Subcellular Processes (q-bio.SC)

[24] arXiv:q-bio/0504024 [pdf, other]

Title: Comment on ``Critical branching captures activity in living neural networks and maximizes the number of metastable states''

Dietmar Plenz

Comments: Submitted Comment to PRL

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

[25] arXiv:q-bio/0504025 [pdf, other]

Title: Self-organization of gene regulatory network motifs enriched with short transcript's half-life transcription factors

Edwin Wang, Enrico Purisima

Comments: Trends Genet (in press), main text 1, supplementary notes 1, 40 pages, 7 tables, 4 figs, minor modifications

Journal-ref: Trends Genet, 21:492-495, 2005

Subjects: Molecular Networks (q-bio.MN)

[26] arXiv:q-bio/0504026 [pdf, other]

Title: Low Degree Metabolites Explain Essential Reactions and Enhance Modularity in Biological Networks

Areejit Samal, Shalini Singh, Varun Giri, Sandeep Krishna, N. Raghuram, Sanjay Jain

Comments: 12 pages main text with 2 figures and 2 tables. 16 pages of Supplementary material. Revised version has title changed and contains study of 3 organisms instead of 1 earlier

Journal-ref: BMC Bioinformatics 7:118 (2006)

Subjects: Molecular Networks (q-bio.MN)

[27] arXiv:q-bio/0504027 [pdf, other]

Title: Extraclassical receptive field phenomena & short-range connectivity in V1

Jim Wielaard, Paul Sajda

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

[28] arXiv:q-bio/0504028 [pdf, other]

Title: Modeling multi-cellular systems using sub-cellular elements

T. J. Newman

Comments: 20 pages, 4 figures

Subjects: Quantitative Methods (q-bio.QM)

[29] arXiv:q-bio/0504029 [pdf, other]

Title: A physically meaningful method for the comparison of potential energy functions

J. L. Alonso, Pablo Echenique

Comments: 30 pages, 7 figures, LaTeX, BibTeX. v2: A misspelling in the author's name has been corrected. v3: A new application of the method has been added at the end of section 9 and minor modifications have also been made in other sections. v4: Journal reference and minor corrections added

Journal-ref: J. Comp. Chem. 27 (2006) 238-252

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

[30] arXiv:q-bio/0504030 [pdf, other]

Title: Modeling of negative autoregulated genetic networks in single cells

Azi Lipshtat, Hagai B. Perets, Nathalie Q. Balaban, Ofer Biham

Comments: 15 pages, 4 figures. Published in Gene

Journal-ref: Gene, Vol. 347, Issue 2, 14 March 2005, Pages 265-271

Subjects: Molecular Networks (q-bio.MN); Biological Physics (physics.bio-ph)

[31] arXiv:q-bio/0504031 [pdf, other]

Title: Parametric Resonance May Explain Virologic Failure to HIV Treatment Interruptions

Romulus Breban, Sally Blower

Comments: 15 pages, 2 figures, 1 table

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

[32] arXiv:q-bio/0504032 [pdf, other]

Title: Evolutionary origin of power-laws in Biochemical Reaction Network; embedding abundance distribution into topology

Chikara Furusawa, Kunihiko Kaneko

Comments: 11 pages, 3 figures

Subjects: Populations and Evolution (q-bio.PE); Molecular Networks (q-bio.MN)

[33] arXiv:q-bio/0504033 [pdf, other]

Title: Geometric and physical considerations for realistic protein models

Isaac A. Hubner, Eugene I. Shakhnovich

Subjects: Biomolecules (q-bio.BM)

[34] arXiv:q-bio/0504034 [pdf, other]

Title: tRNA-alike in Nanoarchaeum equitans ?

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

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

[35] arXiv:cond-mat/0504025 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Point process model of 1/f noise versus a sum of Lorentzians

B. Kaulakys, V. Gontis, M. Alaburda

Comments: 23 pages, 10 figures, to be published in Phys. Rev. E

Journal-ref: Phys.Rev. E71 (2005) 051105

Subjects: Statistical Mechanics (cond-mat.stat-mech); Astrophysics (astro-ph); Disordered Systems and Neural Networks (cond-mat.dis-nn); Computational Engineering, Finance, and Science (cs.CE); Statistics Theory (math.ST); Adaptation and Self-Organizing Systems (nlin.AO); Data Analysis, Statistics and Probability (physics.data-an); Neurons and Cognition (q-bio.NC)

[36] arXiv:cond-mat/0504097 (cross-list from cond-mat.soft) [pdf, other]

Title: Effect of Poisson ratio on cellular structure formation

Ilka B. Bischofs, Ulrich S. Schwarz (Heidelberg University and MPI Colloids and Interfaces)

Comments: 4 pages, Revtex, 4 Postscript figures included

Journal-ref: Phys. Rev. Lett. 95: 068102 (2005)

Subjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci); Cell Behavior (q-bio.CB)

[37] arXiv:cond-mat/0504107 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Optimal search strategies for hidden targets

O. Benichou, M. Coppey, M. Moreau, P-H. Suet, R. Voituriez

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

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

[38] arXiv:cond-mat/0504329 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Multi-state epidemic processes on complex networks

Naoki Masuda, Norio Konno

Comments: 7 figures, 1 table

Journal-ref: Journal of Theoretical Biology, 243, 64-75 (2006)

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Populations and Evolution (q-bio.PE)

[39] arXiv:cond-mat/0504508 (cross-list from cond-mat.soft) [pdf, other]

Title: Inferring the diameter of a biopolymer from its stretching response

Ngo Minh Toan, Davide Marenduzzo, Cristian Micheletti

Comments: Revtex, 9 pages, 5 figures, to appear in the Biophysical Journal

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

[40] arXiv:cond-mat/0504652 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: A "Burnt Bridge'' Brownian Ratchet

T. Antal, P. L. Krapivsky

Comments: 11 pages, 7 figures

Journal-ref: Phys. Rev. E 72, 046104 (2005)

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

[41] arXiv:cond-mat/0504654 (cross-list from cond-mat.soft) [pdf, other]

Title: Elasticity of semiflexible polymers in two dimensions

Ashok Prasad, Yuko Hori, Jane' Kondev

Comments: 16 pages, 3 figures

Journal-ref: Phys. Rev. E 72, 041918 (2005)

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

[42] arXiv:cond-mat/0504708 (cross-list from cond-mat.soft) [pdf, other]

Title: Structural Polymorphism of the Cytoskeleton: A Model of Linker-Assisted Filament Aggregation

Itamar Borukhov (Compugen Ltd.), Robijn F. Bruinsma (UCLA), William M. Gelbart (UCLA), Andrea J. Liu (UPenn)

Comments: 17 pages, 3 figures

Journal-ref: Proc. Natl. Acad. Sci., vol. 102, 3673-3678 (2005)

Subjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Chemical Physics (physics.chem-ph); Biomolecules (q-bio.BM)

[43] arXiv:math/0504378 (cross-list from math.PR) [pdf, other]

Title: A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood is Hard

S. Roch

Comments: 6 pages; Corrected typos and notational problem

Subjects: Probability (math.PR); Computational Complexity (cs.CC); Computational Engineering, Finance, and Science (cs.CE); Statistics Theory (math.ST); Populations and Evolution (q-bio.PE)

[44] arXiv:math/0504477 (cross-list from math.ST) [pdf, other]

Title: On hybrid simulation schemes for stochastic reaction dynamics

Sergey Plyasunov

Comments: 21 pages, 3 EPS figures, uses this http URL

Subjects: Statistics Theory (math.ST); Quantitative Methods (q-bio.QM)

[45] arXiv:nlin/0504028 (cross-list from nlin.CD) [pdf, other]

Title: Periodic and Chaotic Events in a Discrete Model of Logistic Type for the Competitive Interaction of Two Species

Ricardo Lopez-Ruiz, Daniele Fournier-Prunaret

Comments: 18 pages, 13 figures

Subjects: Chaotic Dynamics (nlin.CD); Dynamical Systems (math.DS); Pattern Formation and Solitons (nlin.PS); Populations and Evolution (q-bio.PE)

[46] arXiv:physics/0504015 (cross-list from physics.bio-ph) [pdf, other]

Title: Measurement of the cell membrane capacitance and conductance of colonic crypt cells of the rat using the patch clamp technique

C. Schill

Comments: Diploma thesis, University of Freiburg, Germany (in German)

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

[47] arXiv:physics/0504051 (cross-list from physics.bio-ph) [pdf, other]

Title: Power-law rheology and mechano-sensing in a cytoskeleton model with forced protein unfolding

Brenton D. Hoffman, Gladys Massiera, John C. Crocker

Comments: 4 pages, 4 figures, revtex4

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

[48] arXiv:physics/0504058 (cross-list from physics.bio-ph) [pdf, other]

Title: Budding and Fission of a multiphase vesicle

Jean-Marc Allain (LPS), Martine Ben Amar (LPS)

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

[49] arXiv:physics/0504084 (cross-list from physics.bio-ph) [pdf, other]

Title: Fluctuations in type IV pilus retraction

Martin Linden, Emil Johansson, Ann-Beth Jonsson, Mats Wallin

Comments: 10 pages, 2 figures, 1 table

Subjects: Biological Physics (physics.bio-ph); Other Condensed Matter (cond-mat.other); Other Quantitative Biology (q-bio.OT); Subcellular Processes (q-bio.SC)

[50] arXiv:physics/0504140 (cross-list from physics.bio-ph) [pdf, other]

Title: Model for Folding and Aggregation in RNA Secondary Structures

Vishwesha Guttal, Ralf Bundschuh

Comments: Revtex, 4 pages; 3 Figures; Final published version

Journal-ref: Phys. Rev. Lett. 96, 018105 (2006)

Subjects: Biological Physics (physics.bio-ph); Statistical Mechanics (cond-mat.stat-mech); Biomolecules (q-bio.BM)