Quantitative Biology

Authors and titles for December 2005

[1] arXiv:q-bio/0512001 [pdf, other]

Title: Quantitative modeling and data analysis of SELEX experiments

Marko Djordjevic (1 and 2), Anirvan M. Sengupta (3) ((1) Columbia University Physics Department, (2) Mathematical Biosciences Institute, The Ohio State University, (3) Department of Physics and BioMaPS Institute, Rutgers University)

Comments: 29 pages, 8 figures, to appear in Physical Biology

Subjects: Genomics (q-bio.GN)

[2] arXiv:q-bio/0512002 [pdf, other]

Title: Characterization of a Branch of the Phylogenetic Tree

Stuart Samuel (Lawrence Berkeley National Laboratory)Gezhi Weng (Mount Sinai School of Medicine in New York)

Comments: LaTeX file, 10-page publication, 7 figures in jpeg format

Journal-ref: J. Theor. Biol. 220, 457 (2003)

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

[3] arXiv:q-bio/0512003 [pdf, other]

Title: Optimal strategies for fighting persistent bugs

Ole Steuernagel, Daniel Polani

Comments: 6 pages, 6 figures

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

[4] arXiv:q-bio/0512004 [pdf, other]

Title: Stretching of proteins in a force-clamp

Piotr Szymczak, Marek Cieplak

Comments: 14 pages, 6 figures; submitted to J. Phys. Cond. Matt

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

[5] arXiv:q-bio/0512005 [pdf, other]

Title: An RNA foldability metric; implications for the design of rapidly foldable RNA sequences

W. Ndifon, A. Nkwanta

Comments: To appear in Biophysical Chemistry

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

[6] arXiv:q-bio/0512006 [pdf, other]

Title: Transient pattern formation in a stochastic model of cancer growth

Anna Ochab-Marcinek

Comments: 9 pages, 2 figures

Journal-ref: Fluctuation and Noise Letters 5(2) (2005) L331

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

[7] arXiv:q-bio/0512007 [pdf, other]

Title: Efficiency, Robustness and Stochasticity of Gene Regulatory Networks in Systems Biology: lambda Switch as a Working Example

X. Zhu, L. Yin, L. Hood, D. Galas, P. Ao

Comments: 40 pages

Subjects: Subcellular Processes (q-bio.SC); Other Condensed Matter (cond-mat.other); Adaptation and Self-Organizing Systems (nlin.AO); Molecular Networks (q-bio.MN); Other Quantitative Biology (q-bio.OT)

[8] arXiv:q-bio/0512008 [pdf, other]

Title: Parametric Alignment of Drosophila Genomes

Colin Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter

Comments: 19 pages, 3 figures

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

[9] arXiv:q-bio/0512009 [pdf, other]

Title: A geometric approach to tree shape statistics

Frederick A. Matsen

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

[10] arXiv:q-bio/0512010 [pdf, other]

Title: Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials

Frederick A. Matsen, Steven N. Evans

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

[11] arXiv:q-bio/0512011 [pdf, other]

Title: Cooperative Cargo Transport by Several Molecular Motors

Stefan Klumpp, Reinhard Lipowsky

Comments: 24 pages, latex, 6 figures, includes Supporting Text

Journal-ref: PNAS 102, 17284-17289 (2005)

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

[12] arXiv:q-bio/0512012 [pdf, other]

Title: The Role of Life Cycle and Migration in Selection for Offspring Variance

Max Shpak, Stephen Proulx

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

[13] arXiv:q-bio/0512013 [pdf, other]

Title: Weak pairwise correlations imply strongly correlated network states in a neural population

Elad Schneidman, Michael J. Berry II, Ronen Segev, William Bialek

Comments: Full account of work presented at the conference on Computational and Systems Neuroscience (COSYNE), 17-20 March 2005, in Salt Lake City, Utah (this http URL)

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

[14] arXiv:q-bio/0512014 [pdf, other]

Title: Dynamics of networking agents competing for high centrality and low degree

Petter Holme, Gourab Ghoshal

Comments: v2: Fig. 3 fixed

Journal-ref: Phys. Rev. Lett. 96, 098701 (2006)

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

[15] arXiv:q-bio/0512015 [pdf, other]

Title: Distribution networks and the optimal form of the kidney and lung

Walton R. Gutierrez

Comments: 5 pages, 4 figures

Subjects: Tissues and Organs (q-bio.TO); Quantitative Methods (q-bio.QM)

[16] arXiv:q-bio/0512016 [pdf, other]

Title: Modeling stochastic gene expression under repression

Guilherme da C.P. Innocentini, Jose E. M. Hornos

Comments: 20 pages, 20 figures

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

[17] arXiv:q-bio/0512017 [pdf, other]

Title: Bacterial self-organisation and computation

Martyn Amos, David A. Hodgson, Alan Gibbons

Comments: Submitted to the International Journal of Unconventional Computing

Subjects: Cell Behavior (q-bio.CB)

[18] arXiv:q-bio/0512018 [pdf, other]

Title: Collective dynamics of molecular motors pulling on fluid membranes

O. Campas, Y. Kafri, K.B. Zeldovich, J. Casademunt, J.-F. Joanny

Comments: 5 pages, 5 figures

Journal-ref: Phys. Rev. Lett. 97, 038101 (2006)

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

[19] arXiv:q-bio/0512019 [pdf, other]

Title: Parametric inference of recombination in HIV genomes

Niko Beerenwinkel, Colin N. Dewey, Kevin M. Woods

Comments: 20 pages, 5 figures

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

[20] arXiv:q-bio/0512020 [pdf, other]

Title: Diversity in Free Energy Landscape of Proteins with the Same Native Topology

Hiroo Kenzaki, Macoto Kikuchi

Comments: 4 pages, 3 figures

Journal-ref: Chem. Phys. Lett. 427 (2006) 414-417

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

[21] arXiv:q-bio/0512021 [pdf, other]

Title: Attentional modulation of firing rate and synchrony in a model cortical network

Calin Buia, Paul Tiesinga

Comments: 36 pages, submitted to Journal of Computational Neuroscience

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

[22] arXiv:q-bio/0512022 [pdf, other]

Title: Mathematical modeling of anti-tumor virus therapy: Regimes with complete recovery within the framework of deterministic models

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

Comments: 24 pages, 8 figures; presented to ARCC workshop "The Modeling of Cancer Progression and Immunotherapy"

Subjects: Tissues and Organs (q-bio.TO); Populations and Evolution (q-bio.PE)

[23] arXiv:q-bio/0512023 [pdf, other]

Title: Co-transport-induced instability of membrane voltage in tip-growing cells

M. Leonetti, P. Marcq, J. Nuebler, F. Homble

Journal-ref: Phys. Rev. Lett. 95 (2005) 208105

Subjects: Quantitative Methods (q-bio.QM)

[24] arXiv:q-bio/0512024 [pdf, other]

Title: GIS-aided simulation of spatial distribution of some pollutants at "Stolby" state reservation

Marina G.Erunova, Michael G.Sadovsky, Anna A.Gosteva

Comments: 17 pages, 49 reference items, 12 figures

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

[25] arXiv:q-bio/0512025 [pdf, other]

Title: The energy cost of protein messages lead to a new protein information law

Robersy Sanchez, Ricardo Grau

Comments: 13 pages, 1 figure. Article process

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

[26] arXiv:q-bio/0512026 [pdf, other]

Title: A hypothesis on the selective advantage for sleep

Emmanuel Tannenbaum

Comments: 3 pages, no figures. This paper is a speculative note. I am still considering whether to submit it for publication

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

[27] arXiv:q-bio/0512027 [pdf, other]

Title: A Physical Model for the Condensation and Decondensation of Eukaryotic Chromosomes

Julien Mozziconacci, Christophe Lavelle, Maria Barbi, Annick Lesne, Jean-Marc Victor

Journal-ref: FEBS Letters 580 (2006) 368-372

Subjects: Subcellular Processes (q-bio.SC)

[28] arXiv:q-bio/0512028 [pdf, other]

Title: Cloning, expression and purification of the general stress protein Yhbo from Escherichia coli

Jad Abdallah (IJM), Renee Kern (IJM), Abderrahim Malki (IJM), Viola Eckey (IJM), Gilbert Richarme (IJM)

Journal-ref: Protein expression and purification. sous presse (2005) ?

Subjects: Genomics (q-bio.GN)

[29] arXiv:q-bio/0512029 [pdf, other]

Title: What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model

A. Amatori, J.Ferkinghoff-Borg, G. Tiana, R. A. Broglia

Subjects: Biomolecules (q-bio.BM)

[30] arXiv:q-bio/0512030 [pdf, other]

Title: Effect of Predators of Juvenile Rodents on the Spread of the Hantavirus Epidemic

G. Camelo-Neto, Ana T.C. Silva, L. Giuggioli, V.M. Kenkre

Comments: 13 pages, 5 figures, submitted to Physica A

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

[31] arXiv:q-bio/0512031 [pdf, other]

Title: Egocentric Path Integration Models and their Application to Desert Arthropods

Tobias Merkle, Martin Rost, Wolfgang Alt

Comments: 30 pages, 8 figures. Journal of Theoretical Biology (online available, paper in press)

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

[32] arXiv:q-bio/0512032 [pdf, other]

Title: The WHO surveillance threshold and the emergence of drug-resistant HIV strains in Botswana

Raffaele Vardavas, Sally Blower

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

[33] arXiv:q-bio/0512033 [pdf, other]

Title: Explicit factorization of external coordinates in constrained Statistical Mechanics models

Pablo Echenique, Ivan Calvo

Comments: 22 pages, 2 figures, LaTeX, AMSTeX. v2: Introduccion slightly extended. Version in arXiv is slightly larger than the published one

Journal-ref: J. Comp. Chem. 27 (2006) 1748-1755

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

[34] arXiv:q-bio/0512034 [pdf, other]

Title: Contextual Emergence of Mental States from Neurodynamics

H. Atmanspacher, P. beim Graben

Comments: 20 pages, no figures, accepted for publication in Chaos and Complexity Letters

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

[35] arXiv:q-bio/0512035 [pdf, other]

Title: An irreversible growth model for virus capsid assembly

Stephen D. Hicks, C. L. Henley

Comments: 19 pages, 19 figures; v2: two figures added, small changes to content; v3: minor content changes in response to referees

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

[36] arXiv:q-bio/0512036 [pdf, other]

Title: Inferring the in vivo looping properties of DNA

Leonor Saiz, J. Miguel Rubi, Jose M. G. Vilar

Comments: 20 pages, 4 figures

Journal-ref: Proc. Natl. Acad. Sci. USA 102, 17642-17645 (2005)

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

[37] arXiv:q-bio/0512037 [pdf, other]

Title: Epidemic dynamics on an adaptive network

Thilo Gross, Carlos Dommar D'Lima, Bernd Blasius

Comments: 4 pages, 4 figures, final version

Journal-ref: Phys. Rev. Lett. 96, 208701 (2006)

Subjects: Populations and Evolution (q-bio.PE); Soft Condensed Matter (cond-mat.soft); Physics and Society (physics.soc-ph)

[38] arXiv:q-bio/0512038 [pdf, other]

Title: Finding mesoscopic communities in sparse networks

I. Ispolatov, I. Mazo, A. Yuryev

Comments: 8 pages, 2 figure, typos corrected, 1 figure added

Journal-ref: J. Stat. Mech. (2006) P09014

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

[39] arXiv:q-bio/0512039 [pdf, other]

Title: Phase Transitions and Spatio-Temporal Fluctuations in Stochastic Lattice Lotka-Volterra Models

Mauro Mobilia, Ivan T. Georgiev, Uwe C. Tauber

Comments: 19 pages, 11 figures, 2-column revtex4 format. Minor modifications. Accepted in the Journal of Statistical Physics. Movies corresponding to Figures 2 and 3 are available at this http URL

Journal-ref: Journal of Statistical Physics, Vol.128 (Nos. 1/2), 447 (2007)

Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Adaptation and Self-Organizing Systems (nlin.AO); Quantitative Methods (q-bio.QM)

[40] arXiv:q-bio/0512040 [pdf, other]

Title: Ambiguous model learning made unambiguous with 1/f priors

Gurinder Singh Atwal, William Bialek

Comments: 8 pages, 2 figures

Journal-ref: NIPS 16, MIT Press, Cambridge (2004)

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

[41] arXiv:q-bio/0512041 [pdf, other]

Title: Exact results for noise power spectra in linear biochemical reaction networks

Patrick B. Warren, Sorin Tanase-Nicola, Pieter Rein ten Wolde

Comments: 10 pages, 2 figures, RevTeX 4

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

[42] arXiv:q-bio/0512042 [pdf, other]

Title: Abelian Finite Group of DNA Genomic Sequences

Robersy Sanchez, Jesus Barreto, Eberto Morgado, Ricardo Grau

Comments: 6 pages 1 figure. This paper was presented in the "IX Congreso Nacional de Matematica y Computacion", of the La Sociedad Cubana de Matematica y Computacion

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

[43] arXiv:q-bio/0512043 [pdf, other]

Title: Non-meanfield deterministic limits in chemical reaction kinetics far from equilibrium

R. E. Lee DeVille, Cyrill B. Muratov, Eric Vanden-Eijnden

Comments: 4 pages, 4 figures (submitted to Phys. Rev. Lett.)

Journal-ref: J. Chem. Phys. 124, 231102 (2006).

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

[44] arXiv:q-bio/0512044 [pdf, other]

Title: Short and Long-Term Dynamics of Childhood Diseases on Dynamic Small-World Networks

J. Verdasca

Comments: Proceedings of the II International Symposium on Mathematical and Computational Biology - BIOMAT 2005, Petropolis, RJ, Brasil, 03-08 Dec 2005. World Scientific Publishing co

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

[45] arXiv:q-bio/0512045 [pdf, other]

Title: The importance of selection rate in the evolution of cooperation

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

Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Adaptation and Self-Organizing Systems (nlin.AO); Physics and Society (physics.soc-ph); Quantitative Methods (q-bio.QM)

[46] arXiv:q-bio/0512046 [pdf, other]

Title: Uniqueness of steady states for a certain chemical reaction

Liming Wang, Eduardo Sontag

Subjects: Molecular Networks (q-bio.MN)

[47] arXiv:q-bio/0512047 [pdf, other]

Title: A new series of polyhedra as blueprints for viral capsids in the family of Papovaviridae

T. Keef, R. Twarock

Comments: 18 pages, 14 figures

Subjects: Biomolecules (q-bio.BM)

[48] arXiv:q-bio/0512048 [pdf, other]

Title: Two-state dynamics for replicating two-strand systems

Diederik Aerts, Marek Czachor

Comments: revtex, 3 eps figures

Journal-ref: Open Systems & Inf. Dynamics 14, 397-410 (2007)

Subjects: Populations and Evolution (q-bio.PE); Pattern Formation and Solitons (nlin.PS); Quantum Physics (quant-ph)

[49] arXiv:cond-mat/0512009 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Boundary-bulk interplay of molecular motor traffic flow through a compartment

M. Ebrahim Fouladvand, Modjtaba Salehi, Mostafa Yadegari

Comments: 9 pages, 17 eps figures, Revtex

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

[50] arXiv:cond-mat/0512089 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Computational core and fixed-point organisation in Boolean networks

L. Correale, M. Leone, A. Pagnani, M. Weigt, R. Zecchina

Comments: 29 pages, 18 figures, version accepted for publication in JSTAT

Journal-ref: J. Stat. Mech. (2006) P03002

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