Quantitative Biology

Authors and titles for June 2006

[1] arXiv:q-bio/0606001 [pdf, other]

Title: On Mathematical Theory of Selection: Discrete-Time Models

Georgy P. Karev

Comments: 8 pages, 3 figures; submitted to International Conference on Complex Systems 2006

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

[2] arXiv:q-bio/0606002 [pdf, other]

Title: Analytical Models of Forest Dynamics

Georgy P. Karev

Comments: 69 pages, 10 figures, 9 tables

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

[3] arXiv:q-bio/0606003 [pdf, other]

Title: Inhomogeneous maps: the basic theorems and some applications

Georgy P. Karev

Comments: 10 pages, 3 figures; submitted to Conference on Differential & Difference Equations and Applications, Florida Institute of Technology, 2005

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

[4] arXiv:q-bio/0606004 [pdf, other]

Title: Bifurcations of self-similar solutions of the Fokker-Plank Equation

F. Berezovskaya, G. Karev

Comments: 9 pages; submitted to Discrete and Continuous Dynamical Systems

Subjects: Quantitative Methods (q-bio.QM); Other Quantitative Biology (q-bio.OT)

[5] arXiv:q-bio/0606005 [pdf, other]

Title: Triangular lattice neurons may implement an advanced numeral system to precisely encode rat position over large ranges

Yoram Burak, Ted Brookings, Ila Fiete

Comments: 4 pages with one figure, and 2 pages of supplementary information

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

[6] arXiv:q-bio/0606006 [pdf, other]

Title: Spatially Distributed Stochastic Systems: equation-free and equation-assisted preconditioned computation

Liang Qiao, Radek Erban, C. T. Kelley, Ioannis G. Kevrekidis

Comments: 8 pages, 6 figures, submitted to Journal of Chemical Physics

Subjects: Quantitative Methods (q-bio.QM); Computational Physics (physics.comp-ph); Quantum Physics (quant-ph)

[7] arXiv:q-bio/0606007 [pdf, other]

Title: Model for unidirectional movement of axonemal and cytoplasmic dynein molecules

Ping Xie, Shuo-Xing Dou, Peng-Ye Wang

Journal-ref: Acta Biochimica Biophysica sinica 2006, 38 (10): 711-724

Subjects: Biomolecules (q-bio.BM)

[8] arXiv:q-bio/0606008 [pdf, other]

Title: Relevance of Quantum Mechanics in Circuit Implementation of Ion channels in Brain Dynamics

Indranil Mitra, Sisir Roy

Comments: 12 pages, Submitted to Physical Rev. E

Subjects: Neurons and Cognition (q-bio.NC); Quantum Physics (quant-ph)

[9] arXiv:q-bio/0606009 [pdf, other]

Title: A Bio-Polymer Transistor: Electrical Amplification by Microtubules

Avner Priel, Arnolt J. Ramos, Jack A. Tuszynski, Horacio F. Cantiello

Comments: This is the final submitted version. The published version should be downloaded from Biophysical Journal

Journal-ref: Biophys. J. 2006 90: 4639-4643

Subjects: Subcellular Processes (q-bio.SC); Biomolecules (q-bio.BM)

[10] arXiv:q-bio/0606010 [pdf, other]

Title: Probabilistic sequence alignments: realistic models with efficient algorithms

E. Yeramian, E. Debonneuil

Subjects: Genomics (q-bio.GN); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Computational Physics (physics.comp-ph)

[11] arXiv:q-bio/0606011 [pdf, other]

Title: Simulation in Biology

Jose Rodriguez

Comments: 40 pages. Introductory course to simulation

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

[12] arXiv:q-bio/0606012 [pdf, other]

Title: Protein Structure Prediction: The Next Generation

Michael C. Prentiss, Corey Hardin, Michael P. Eastwood, Chenghong Zong, Peter G. Wolynes

Journal-ref: Journal of Chemical Theory and Computation, Volume 2 Issue 3 (May 09, 2006)

Subjects: Biomolecules (q-bio.BM)

[13] arXiv:q-bio/0606013 [pdf, other]

Title: Nested Canalyzing, unate cascade, and polynomial functions

Abdul Salam Jarrah, Blessilda Raposa, Reinhard Laubenbacher

Comments: To appear in Physica D: Nonlinear Phenomena

Subjects: Quantitative Methods (q-bio.QM); Commutative Algebra (math.AC)

[14] arXiv:q-bio/0606014 [pdf, other]

Title: A Kinetic Model Describing the Processivity of Myosin-V

K. I. Skau, R. B. Hoyle, M. S Turner

Comments: 49 pages, 14 figures

Subjects: Biomolecules (q-bio.BM)

[15] arXiv:q-bio/0606015 [pdf, other]

Title: Ab initio simulations of Cu binding sites in the N-terminal region of PrP

S. Furlan, G. La Penna, F. Guerrieri, S. Morante, G.C. Rossi

Comments: 4 pages, conference proceeding

Subjects: Biomolecules (q-bio.BM)

[16] arXiv:q-bio/0606016 [pdf, other]

Title: Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21

Wentian Li, Pedro Miramontes

Comments: submitted to Physical Review E

Journal-ref: Physical Review E, 74:021912 (2006)

Subjects: Genomics (q-bio.GN)

[17] arXiv:q-bio/0606017 [pdf, other]

Title: Overlapping Probabilities of Top Ranking Gene Lists, Hypergeometric Distribution, and Stringency of Gene Selection Criterion

Wen Fury, Franak Batliwalla, Peter K. Gregersen, Wentian Li

Comments: submitted to IEEE/EMBS Conference'06

Journal-ref: Proceedings of 28th Annual International Conference of the Engineering in Medicine and Biology Society, IEEE (2006), pages 5531-5534

Subjects: Quantitative Methods (q-bio.QM)

[18] arXiv:q-bio/0606018 [pdf, other]

Title: Does Logarithm Transformation of Microarray Data Affect Ranking Order of Differentially Expressed Genes?

Wentian Li, Young Ju Suh, Jingshan Zhang

Comments: submitted to IEEE/EMBS Conference'06

Subjects: Quantitative Methods (q-bio.QM)

[19] arXiv:q-bio/0606019 [pdf, other]

Title: Scaling law for the transient behavior of type-II neuron models

Miguel Angel Durán Roa, Mauro Copelli, Osame Kinouchi, Nestor Caticha

Comments: 6 pages, 9 figures, accepted for publication in Phys. Rev. E

Journal-ref: Phys. Rev. E 75, 021911 (2007)

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

[20] arXiv:q-bio/0606020 [pdf, other]

Title: Perception proximale et distale \`{a} l'aide du dispositif de Lenay

Sylvain Hanneton (NPSM, JE 2378), Dounia Taleb-Kachour (NPSM), Marie-Martine Ramanantsoa (JE 2378), Bianca Hardy (JE 2378), Agnès Roby-Brami (NPSM)

Comments: 17 pages

Journal-ref: S\'{e}minaire PHITECO, France (27/10/2003)

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

[21] arXiv:q-bio/0606021 [pdf, other]

Title: Heterogeneous animal group models and their group-level alignment dynamics; an equation-free approach

Sung Joon Moon, B. Nabet, Naomi E. Leonard, Simon A. Levin, I. G. Kevrekidis

Comments: final form; accepted for publication in Journal of Theoretical Biology

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

[22] arXiv:q-bio/0606022 [pdf, other]

Title: Mean Field Model of Genetic Regulatory Networks

M. Andrecut, S. A. Kauffman

Comments: Changed content and notation

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

[23] arXiv:q-bio/0606023 [pdf, other]

Title: Subgraph Ensembles and Motif Discovery Using a New Heuristic for Graph Isomorphism

Kim Baskerville, Maya Paczuski

Comments: 13 pages, 14 figures

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

[24] arXiv:q-bio/0606024 [pdf, other]

Title: Bistable equilibrium points of mercury body burden

Houman Owhadi, Areen Boulos

Comments: To appear in Journal of Biological Systems

Subjects: Other Quantitative Biology (q-bio.OT)

[25] arXiv:q-bio/0606025 [pdf, other]

Title: Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes

Kavita Jain, Joachim Krug

Comments: Revised version, to appear in Genetics. Note on the role of selection in defining d_eff added; new figure 4 included

Journal-ref: Genetics 175, 1275 (2007)

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

[26] arXiv:q-bio/0606026 [pdf, other]

Title: Parametrization of the Hybrid Potential for Pairs of Neutral Atoms

Kevin Cahill

Comments: 7 pages, 11 figures, includes lithium, sodium, & potassium dimers, minor corrections

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

[27] arXiv:q-bio/0606027 [pdf, other]

Title: Conservation rules, their breakdown, and optimality in Caenorhabditis sinusoidal locomotion

Jan Karbowski, Christopher J. Cronin, Adeline Seah, Jane E. Mendel, Daniel Cleary, Paul W. Sternberg

Comments: Journal of Theoretical Biology, in press

Journal-ref: Journal of Theoretical Biology 242, 652-669 (2006)

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

[28] arXiv:q-bio/0606028 [pdf, other]

Title: Does the dynamics of sine-Gordon solitons predict active regions of DNA?

Sara Cuenda, Angel Sanchez, Niurka R. Quintero

Comments: 17 pages, 7 figures

Subjects: Genomics (q-bio.GN); Mathematical Physics (math-ph); Pattern Formation and Solitons (nlin.PS); Quantitative Methods (q-bio.QM)

[29] arXiv:q-bio/0606029 [pdf, other]

Title: Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein-protein interaction networks?

Santiago Schnell, Santo Fortunato, Sourav Roy (Indiana University School of Informatics)

Comments: 15 pages, 2 figures

Subjects: Genomics (q-bio.GN); Molecular Networks (q-bio.MN)

[30] arXiv:q-bio/0606030 [pdf, other]

Title: Diagnosis of rotator cuff lesions by FT-Raman spectroscopy: a biochemical study

Sergio Godoy Penteado, Claudio S. Meneses, Anderson de Oliveira Lobo, Airton Abrahao Martin, Herculano da Silva Martinho

Comments: 17 pages, presented on SPEC 2006-Heidelberg, Germany

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

[31] arXiv:q-bio/0606031 [pdf, other]

Title: Simple solvation potential for coarse-grained models of proteins

A. Bhattacharyay, A. Trovato, F. Seno

Comments: 18 pages, 8 tables, 3 figures

Subjects: Biomolecules (q-bio.BM)

[32] arXiv:q-bio/0606032 [pdf, other]

Title: Probabilistic Regulatory Networks: Modeling Genetic Networks

Maria A. Avino-Diaz, Oscar Moreno

Comments: 8 pages, 2 figures, International Congress of Matematicians, to be published in Proceedings of the Fifth International Conference on Engineering Computational Technology, 2006, Las Palmas, Gran Canaria

Subjects: Genomics (q-bio.GN); Dynamical Systems (math.DS)

[33] arXiv:q-bio/0606033 [pdf, other]

Title: Time Scales in Evolutionary Dynamics

Carlos P. Roca, Jose A. Cuesta y Angel Sanchez

Comments: Final version with minor changes, accepted for publication in Physical Review Letters

Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS); Adaptation and Self-Organizing Systems (nlin.AO); Physics and Society (physics.soc-ph); Quantitative Methods (q-bio.QM)

[34] arXiv:q-bio/0606034 [pdf, other]

Title: Why are diploid genomes widespread and dominant mutations rare?

Diana Garncarz, Stanislaw Cebrat, Dietrich Stauffer, Klaus Blindert

Comments: 11 pages including 10 figures, in prep. for Theoy in Biosci

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

[35] arXiv:q-bio/0606035 [pdf, other]

Title: A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies

Benjamin Ribba, Thierry Colin, Santiago Schnell

Comments: 19 pages, 14, figures. Article available at this http URL Copyright 2006 Ribba et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (this http URL), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Subjects: Tissues and Organs (q-bio.TO); Subcellular Processes (q-bio.SC)

[36] arXiv:q-bio/0606036 [pdf, other]

Title: Evolution of Protein Interaction Networks by Whole Genome Duplication and Domain Shuffling

K. Evlampiev, H. Isambert

Comments: 8 pages, 4 figures

Subjects: Molecular Networks (q-bio.MN)

[37] arXiv:q-bio/0606037 [pdf, other]

Title: The propagation of a cultural or biological trait by neutral genetic drift in a subdivided population

R A Blythe

Comments: 17 pages, 8 figures, requires this http URL; substantially revised and improved version; accepted for publication in Theoretical Population Biology

Journal-ref: Theoretical Population Biology (2007) 71 454

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

[38] arXiv:q-bio/0606038 [pdf, other]

Title: Use of the Metropolis algorithm to simulate the dynamics of protein chains

G. Tiana, L. Sutto, R. A. Broglia

Comments: corrections to the text and to the figures

Subjects: Other Quantitative Biology (q-bio.OT)

[39] arXiv:q-bio/0606039 [pdf, other]

Title: Randomization and Feedback Properties of Directed Graphs Inspired by Gene Networks

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

Comments: To appear in: Proceedings of the CMSB conference, Lecture Notes in Bioinformatics, Springer, 2006

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

[40] arXiv:q-bio/0606040 [pdf, other]

Title: Cerebellar Purkinje Cell Loss in Heterozygous Rora+/-Mice: A Longitudinal Study

Mohamed Doulazmi (NPA), Francesca Capone (NPA), Florence Frederic (NPA), JoËlle Bakouche (NPA), Yolande Lemaigre-Dubreuil (NPA), Jean Mariani (NPA)

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

[41] arXiv:q-bio/0606041 [pdf, other]

Title: Designing Complex Networks

Raoul-Martin Memmesheimer, Marc Timme

Comments: 42 pages, 12 figures

Journal-ref: Physica D 224:182 (2006)

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

[42] arXiv:q-bio/0606042 [pdf, other]

Title: Preventing extinction and outbreaks in chaotic populations

Frank M. Hilker, Frank H. Westerhoff

Comments: 10 pages, 6 figures

Journal-ref: American Naturalist 170, 232-241 (2007)

Subjects: Populations and Evolution (q-bio.PE); Chaotic Dynamics (nlin.CD)

[43] arXiv:q-bio/0606043 [pdf, other]

Title: Towards a model for protein production rates

J.J. Dong, B.Schmittmann, R.K.P.Zia

Comments: 8 pages, 8 figures; This submission is a duplicate of arXiv:q-bio/0602024, and has been removed

Journal-ref: Journal of Statistical Physics, Volume 128, Numbers 1-2 / July, 2007

Subjects: Quantitative Methods (q-bio.QM)

[44] arXiv:astro-ph/0606325 (cross-list from astro-ph) [pdf, other]

Title: Fossil Biodiversity: Red Noise Plus Signal

Adrian L. Melott, Bruce S. Lieberman (University of Kansas)

Comments: 3 page comment including one figure. corrected typo in abstract & figure caption

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

[45] arXiv:astro-ph/0606593 (cross-list from astro-ph) [pdf, other]

Title: Asymmetric Spatiotemporal Evolution of Prebiotic Homochirality

Marcelo Gleiser

Comments: Expanded version with added discussion, with 4 new figures and no modified results, in press in Origins of Life and Evolution of Biospheres. 12 pages in RevTeX

Journal-ref: Orig.LifeEvol.Biosph.37:235-251,2007

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

[46] arXiv:cond-mat/0606101 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Exact solution of a model of time-dependent evolutionary dynamics in a rugged fitness landscape

Clement Sire, Satya N. Majumdar, David S. Dean

Comments: 5 pages RevTex 2 figures .eps

Journal-ref: J. Stat. Mech., L07001 (2006)

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

[47] arXiv:cond-mat/0606210 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Spectral formulation and WKB approximation for rare-event statistics in reaction systems

Michael Assaf, Baruch Meerson

Comments: 11 pages, 10 eps figures

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

[48] arXiv:cond-mat/0606254 (cross-list from cond-mat.soft) [pdf, other]

Title: Force dependent fragility in RNA hairpins

M. Manosas, D. Collin, F. Ritort

Comments: Latex file, 4 pages+3 figures

Journal-ref: Phys. Rev. Lett. vol. 96, 218301 (2006)

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

[49] arXiv:cond-mat/0606378 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Complex noise in diffusion-limited reactions of replicating and competing species

David Hochberg, M.-P. Zorzano, Federico Moran

Comments: 10 pages, 2 composite figures

Journal-ref: Phys. Rev. E 73, 066109 (2006)

Subjects: Statistical Mechanics (cond-mat.stat-mech); Other Condensed Matter (cond-mat.other); Other Quantitative Biology (q-bio.OT); Populations and Evolution (q-bio.PE)

[50] arXiv:cond-mat/0606634 (cross-list from cond-mat.soft) [pdf, other]

Title: Reversible self-assembly of patchy particles into monodisperse icosahedral clusters

Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis, Eva G. Noya, Mark A. Miller, Pauline Wong

Comments: 12 pages, 12 figures

Journal-ref: J. Chem. Phys. 127, 085106 (2007)

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