Quantitative Biology

Authors and titles for January 2006

[1] arXiv:q-bio/0601001 [pdf, other]

Title: Cooperativity, sensitivity and noise in biochemical signaling

William Bialek, Sima Setayeshgar

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

[2] arXiv:q-bio/0601002 [pdf, other]

Title: Regularization Strategies for Hyperplane Classifiers: Application to Cancer Classification with Gene Expression Data

Erik Andries (1 and 2), Thomas Hagstrom (1), Susan R. Atlas (3), Cheryl Willman (2 and 4) ((1) Department of Mathematics and Statistics, (2) Department of Pathology, (3) Center for Advanced Studies and Department of Physics and Astronomy, (4) Cancer Research and Treatment Center, University of New Mexico)

Comments: 22 pages, 3 figures; uses journal's this http URL; submitted to Journal of Bioinformatics and Computational Biology

Subjects: Genomics (q-bio.GN)

[3] arXiv:q-bio/0601003 [pdf, other]

Title: Designing the Dynamics of Spiking Neural Networks

Raoul-Martin Memmesheimer, Marc Timme

Comments: 4 pages, 3 figures

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

[4] arXiv:q-bio/0601004 [pdf, other]

Title: A Model of the Roles of Essential Kinases in the Induction and Expression of Late Long-Term Potentiation

Paul Smolen, Douglas A. Baxter, John H. Byrne

Comments: Accepted to Biophysical Journal. Single PDF, 7 figs included

Subjects: Neurons and Cognition (q-bio.NC); Molecular Networks (q-bio.MN)

[5] arXiv:q-bio/0601005 [pdf, other]

Title: Frequency and Viability of Diploid and Haploid Males Offsprings of Mated Females of Solitary Endoparasitoid (DIADROMUS Pulchellus) (Ichneumonidae)

Robert Kalmès (IRBII), Danielle Rojas-Rousse (IRBII)

Journal-ref: Comptes Rendus de l'Academie des Sciences. Serie 3, Sciences de la Vie 324 (2001) 149-158

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

[6] arXiv:q-bio/0601006 [pdf, other]

Title: Surprises in approximating Levenshtein distances

Michael Baake (Bielefeld), Uwe Grimm (Milton Keynes), Robert Giegerich (Bielefeld)

Comments: 7 pages, 4 figures; revised version

Journal-ref: Journal of Theoretical Biology 243 (2006) 279-282

Subjects: Quantitative Methods (q-bio.QM)

[7] arXiv:q-bio/0601007 [pdf, other]

Title: Waveform sample method of excitable sensory neuron

Sheng-Jun Wang, Xin-Jian Xu, Ying-Hai Wang

Comments: 4 pages, 4 figures

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

[8] arXiv:q-bio/0601008 [pdf, other]

Title: Sleep as the solution to an optimization problem

Emmanuel Tannenbaum

Comments: 7 pages, to be submitted to J. Theor. Biol. (figures included in journal submission)

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

[9] arXiv:q-bio/0601009 [pdf, other]

Title: Adhesion between cells, diffusion of growth factors, and elasticity of the AER produce the paddle shape of the chick limb

Nikodem J. Poplawski, Maciej Swat, J. Scott Gens, James A. Glazier

Comments: This paper has been withdrawn

Journal-ref: Physica A 373 (2007) 521-532

Subjects: Tissues and Organs (q-bio.TO); Cell Behavior (q-bio.CB)

[10] arXiv:q-bio/0601010 [pdf, other]

Title: Quantification and Correction of Systematic Errors Due to Detector Time-Averaging in Single-Molecule Tracking Experiments

Nicolas Destainville, Laurence Salome

Comments: 3 pages (Letter); 1 figure

Journal-ref: Biophys. J. 90, L17-L19 (2006)

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

[11] arXiv:q-bio/0601011 [pdf, other]

Title: Glial activation in white matter following ischemia in the neonatal P7 rat brain

Valérie Biran (NPA), Luc-Marie Joly (NPA), Anne Héron, Agnès Vernet (NPA), Céline Véga (NPA), Jean Mariani (NPA), Sylvain Renolleau (NPA), Christiane Charriaut-Marlangue (NPA)

Comments: 30 pages

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

[12] arXiv:q-bio/0601012 [pdf, other]

Title: Universal core modules govern the dynamics of cellular regulatory networks

Jing-Jing Li, Jie Ren, Zhi Liang, Meng Xu, Dan Xie, De-Shuang Huang, Bing-Hong Wang, Liwen Niu, Huanqing Feng, Wen-Xu Wang

Comments: 12 pages, 5 figures

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

[13] arXiv:q-bio/0601013 [pdf, other]

Title: Effect of channel block on the spiking activity of excitable membranes in a stochastic Hodgkin-Huxley model

Gerhard Schmid, Igor Goychuk, Peter Hanggi

Comments: 10 pages, 3 figures, published 2004

Journal-ref: PHYSICAL BIOLOGY 1, pp. 61-66 (2004)

Subjects: Subcellular Processes (q-bio.SC)

[14] arXiv:q-bio/0601014 [pdf, other]

Title: Biophysical analysis of electric current mediated nucleoprotein inactivation process

Jose E. Gonzalez, Robersy Sanchez, Aminael Sanchez

Comments: 12 pages. Presented in the First International Workshop on Bioinformatics Cuba-Flanders'2006 Santa Clara, Cuba February 7-10th, 2006

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

[15] arXiv:q-bio/0601015 [pdf, other]

Title: A dichotomy for a class of cyclic delay systems

G.A. Enciso

Comments: 19 pages, two figures

Subjects: Molecular Networks (q-bio.MN)

[16] arXiv:q-bio/0601016 [pdf, other]

Title: Pure multiplicative stochastic resonance of anti-tumor model with seasonal modulability

Wei-Rong Zhong, Yuan-Zhi Shao, Zhen-Hui He

Comments: 5 pages, 5 figures

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

[17] arXiv:q-bio/0601017 [pdf, other]

Title: Force Modulating Dynamic Disorder: Physical Theory of Catch-slip bond Transitions in Receptor-Ligand Forced Dissociation Experiments

Fei Liu, Zhong-can Ou-Yang

Comments: 8 pages, 3 figures, submitted

Subjects: Cell Behavior (q-bio.CB); Biomolecules (q-bio.BM)

[18] arXiv:q-bio/0601018 [pdf, other]

Title: Protein folding dynamics via quantification of kinematic energy landscape

Sëma Kachalo, Hsiao-Mei Lu, Jie Liang

Comments: 4 pages, 4 figures

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

[19] arXiv:q-bio/0601019 [pdf, other]

Title: Estimation of Amino Acid Residue Substitution Rates at Local Spatial Regions and Application in Protein Function Inference: A Bayesian Monte Carlo Approach

Yan Y. Tseng, Jie Liang

Comments: 27 pages, 7 figures

Journal-ref: Mol Biol Evol. 2006 Feb;23(2):421-36. Epub 2005 Oct 26

Subjects: Biomolecules (q-bio.BM)

[20] arXiv:q-bio/0601020 [pdf, other]

Title: Computation of protein geometry and its applications: Packing and function prediction

Jie Liang

Comments: 32 pages, 9 figures

Subjects: Biomolecules (q-bio.BM)

[21] arXiv:q-bio/0601021 [pdf, other]

Title: Does Cancer Growth Depend on Surface Extension?

Thomas S. Deisboeck, Caterina Guiot, Pier Paolo Delsanto, Nicola Pugno

Comments: 11 pages, 1 figure

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

[22] arXiv:q-bio/0601022 [pdf, other]

Title: Embryonic Pattern Scaling Achieved by Oppositely Directed Morphogen Gradients

Peter McHale, Wouter-Jan Rappel, Herbert Levine

Comments: 24 pages; 11 figures; uses iopart

Subjects: Subcellular Processes (q-bio.SC)

[23] arXiv:q-bio/0601023 [pdf, other]

Title: Effects of Noise on Ecological Invasion Processes: Bacteriophage-mediated Competition in Bacteria

Jaewook Joo, Eric Harvill, Reka Albert

Comments: 39 pages, 7 figures

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

[24] arXiv:q-bio/0601024 [pdf, other]

Title: Scale-free foraging by primates emerges from their interaction with a complex environment

Denis Boyer, Gabriel Ramos-Fernández, Octavio Miramontes, José L. Mateos, Germinal Cocho, Hernán Larralde, Humberto Ramos, Fernando Rojas

Comments: 31 pages, 4 figures. To appear in Proc. Roy. Soc. B. Minor revisions

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

[25] arXiv:q-bio/0601025 [pdf, other]

Title: Towards an understanding of lineage specification in hematopoietic stem cells: A mathematical model for the interaction of transcription factors GATA-1 and PU.1

Ingo Roeder, Ingmar Glauche

Comments: 27 pages, 8 figures, accepted for publication in Journal of Theoretical Biology

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

[26] arXiv:q-bio/0601026 [pdf, other]

Title: Knowledge-based energy functions for computational studies of proteins

Xiang Li, Jie Liang

Comments: 57 pages, 6 figures. To be published in a book by Springer

Subjects: Biomolecules (q-bio.BM)

[27] arXiv:q-bio/0601027 [pdf, other]

Title: Interstrand pairing patterns in $\beta$-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction

Ronald Jackups Jr., Jie Liang

Comments: 26 pages, 4 figures, and 4 tables

Journal-ref: J. Mol. Biol. (2005) 354:979--993

Subjects: Biomolecules (q-bio.BM)

[28] arXiv:q-bio/0601028 [pdf, other]

Title: Gradient learning in spiking neural networks by dynamic perturbation of conductances

Ila R. Fiete, H. Sebastian Seung

Comments: 5 pages; 1 figure; submitted to PRL

Journal-ref: Phys. Rev. Lett. 97, 048104 (2006)

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

[29] arXiv:q-bio/0601029 [pdf, other]

Title: Empirical Potential Function for Simplified Protein Models: Combining Contact and Local Sequence-Structure Descriptors

Jinfeng Zhang, Rong Chen, Jie Liang

Comments: 20 pages, 5 figures, 4 tables. In press, Proteins

Subjects: Biomolecules (q-bio.BM)

[30] arXiv:q-bio/0601030 [pdf, other]

Title: Magnetic Susceptibility: Solutions, Emulsions, and Cells

P. W. Kuchel, B. E. Chapman, W. A. Bubb, P. E. Hansen, C. J. Durrant, M. P. Hertzberg

Comments: 15 pages, 9 figures, v2: updated to resemble the published version

Journal-ref: Concepts in Magnetic Resonance Part A, Vol. 18A(1) 56-71 (2003)

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

[31] arXiv:q-bio/0601031 [pdf, other]

Title: Evolutionary dynamics on degree-heterogeneous graphs

T. Antal, S. Redner, V. Sood

Comments: 4 pages, 4 figures, 2 column revtex4 format. Revisions in response to referee comments for publication in PRL. The version on arxiv.org has one more figure than the published PRL

Journal-ref: Phys. Rev. Lett. 96, 188104 (2006)

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

[32] arXiv:q-bio/0601032 [pdf, other]

Title: Fuzzy Cognitive Maps Of Local People Impacted By Dam Construction: Their Demands Regarding Resettlement

Uygar Ozesmi

Comments: 23 pages, 4 tables, 7 figures

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

[33] arXiv:q-bio/0601033 [pdf, other]

Title: Perceptions of Complex Systems Are Governed by Power Laws

Uygar Ozesmi

Comments: 8 pages, 2 tables, 1 figure

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

[34] arXiv:q-bio/0601034 [pdf, other]

Title: Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins

Hiroshi Fujisaki, Yong Zhang, John E. Straub

Comments: 16 pages, 5 figures, 5 tables, submitted to J. Chem. Phys

Subjects: Biomolecules (q-bio.BM)

[35] arXiv:q-bio/0601035 [pdf, other]

Title: A Comparative Analysis of Influenza Vaccination Programs

Shweta Bansal, Babak Pourbohloul, Lauren Ancel Meyers

Journal-ref: PLoS Medicine, Vol 3 (10), 2006

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

[36] arXiv:q-bio/0601036 [pdf, other]

Title: Extinction in genetic bit-string model with sexual recombination

D. Stauffer, S. Cebrat

Comments: 11 pages including 6 figures

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

[37] arXiv:q-bio/0601037 [pdf, other]

Title: Optimal Dynamical Range of Excitable Networks at Criticality

Osame Kinouchi, Mauro Copelli

Comments: 2 figures, 6 pages

Journal-ref: Nature Physics, 2, 348-351 (2006)

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

[38] arXiv:q-bio/0601038 [pdf, other]

Title: Quantifying the information transmitted in a single stimulus

Michele Bezzi

Comments: 13 pages, 4 figures

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

[39] arXiv:q-bio/0601039 [pdf, other]

Title: Food-chain competition influences gene's size

Marta Dembska, M. R. Dudek, D. Stauffer

Comments: 11 pages including 7 figures

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

[40] arXiv:q-bio/0601040 [pdf, other]

Title: Mechanochemical coupling of kinesin studied with the neck linker swing model

Yaogen Shu, Hualin Shi

Comments: 5pages

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

[41] arXiv:q-bio/0601041 [pdf, other]

Title: The Activity Reaction Core and Plasticity of Metabolic Networks

E. Almaas, Z.N. Oltvai, A.-L. Barabasi

Comments: 21 pages, 4 figures, supp. mat. available at this http URL

Journal-ref: PLoS Comput Biol 1, e68 (2005)

Subjects: Molecular Networks (q-bio.MN); Disordered Systems and Neural Networks (cond-mat.dis-nn); Cell Behavior (q-bio.CB); Quantitative Methods (q-bio.QM)

[42] arXiv:q-bio/0601042 [pdf, other]

Title: Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the Alanine dipeptide

Pablo Echenique, Ivan Calvo, J. L. Alonso

Comments: 37 pages, 4 figures, LaTeX, BibTeX, AMSTeX

Journal-ref: J. Comp. Chem. 27 (2006) 1733-1747

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

[43] arXiv:q-bio/0601043 [pdf, other]

Title: Forced-unfolding and force-quench refolding of RNA hairpins

Changbong Hyeon, D. Thirumalai

Comments: 42 pages, 15 figures, Biophys. J. (in press)

Journal-ref: Biophys. J. (2006) 80 3410-3427

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

[44] arXiv:q-bio/0601044 [pdf, other]

Title: Hierarchy of events in protein folding: beyond the Go model

Ludovico Sutto, Guido Tiana, Ricardo A. Broglia

Subjects: Biomolecules (q-bio.BM)

[45] arXiv:q-bio/0601045 [pdf, other]

Title: Thresholds, long delays and stability from generalized allosteric effect in protein networks

Roberto Chignola, Chiara Dalla Pellegrina, Alessio Del Fabbro, Edoardo Milotti

Comments: 5 figures, submitted to Physica A

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

[46] arXiv:q-bio/0601046 [pdf, other]

Title: Substructural cooperativity and parallel versus sequential events during protein unfolding

Lothar Reich, Thomas R. Weikl

Comments: 8 pages, 7 figures (1 figure in color)

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

[47] arXiv:q-bio/0601047 [pdf, other]

Title: A simple measure of native-state topology and chain connectivity predicts the folding rates of two-state proteins with and without crosslinks

Purushottam D. Dixit, Thomas R. Weikl

Comments: 13 pages, 2 tables, and 2 figures

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

[48] arXiv:q-bio/0601048 [pdf, other]

Title: Taxis Equations for Amoeboid Cells

Radek Erban, Hans G. Othmer

Comments: 35 pages, submitted to the Journal of Mathematical Biology

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

[49] arXiv:q-bio/0601049 [pdf, other]

Title: Thermal unfolding of proteins

Marek Cieplak, Joanna I. Sulkowska

Comments: 3 figures, a text in latex

Journal-ref: J. Chem. Phys. 123, 194908 (2005)

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

[50] arXiv:q-bio/0601050 [pdf, other]

Title: Exploitation dynamics of fish stocks

Hiro-Sato Niwa

Comments: 27 pages, 19 figures

Journal-ref: Ecological Informatics 1 (2006) 87-99

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