Quantitative Biology

Authors and titles for November 2005

[51] arXiv:q-bio/0511051 [pdf, other]

Title: Quasispecies and recombination

Martin Nilsson Jacobi, Mats Nordahl

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

[52] arXiv:cond-mat/0511119 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Electronic transport and localization in short and long DNA

H. Wang, R. Marsh, J.P. Lewis, R.A. Roemer

Comments: 26 pages, 12 .eps figures using the elsevier style files (enclosed); to appear in an Elsevier Review Book on Biopolymers

Journal-ref: Modern Methods for Theoretical Physical Chemistry of Biopolymers (pp. 407-427), 2006

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Soft Condensed Matter (cond-mat.soft); Quantitative Methods (q-bio.QM)

[53] arXiv:cond-mat/0511128 (cross-list from cond-mat.soft) [pdf, other]

Title: Lengthscales and Cooperativity in DNA Bubble Formation

Z. Rapti, A. Smerzi, K. Ø. Rasmussen, A. R. Bishop

Journal-ref: Europhys. Lett., 74 (3), pp. 540-546 (2006)

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

[54] arXiv:cond-mat/0511159 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Learning by message-passing in networks of discrete synapses

Alfredo Braunstein, Riccardo Zecchina

Comments: 4 pages, 3 figures; references updated and minor corrections; accepted in PRL

Journal-ref: Phys. Rev. Lett. 96, 030201 (2006)

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

[55] arXiv:cond-mat/0511255 (cross-list from cond-mat.soft) [pdf, other]

Title: Reversible mesoscopic model of protein adsorption: From equilibrium to dynamics

Gergely J. Szollosi, Imre Derenyi, Janos Voros

Journal-ref: Physica A 343, 359-375 (2004).

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

[56] arXiv:cond-mat/0511379 (cross-list from cond-mat.soft) [pdf, other]

Title: Polymer translocation through a nanopore under an applied external field

Kaifu Luo, Ilkka Huopaniemi, Tapio Ala-Nissila, See-Chen Ying

Comments: 25 Pages, 10 figures. Submitted to J. Chem. Phys. J. Chem. Phys. 124, in press (2006)

Journal-ref: J. Chem. Phys. 124, 114704 (2006)

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

[57] arXiv:cond-mat/0511474 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: A Simple Noise Model with Memory for Biological Systems

O. Chichigina, D. Valenti, B. Spagnolo

Comments: 8 pages, 4 figures

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

[58] arXiv:cond-mat/0511532 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Modelling Disorder: the Cases of Wetting and DNA Denaturation

Saul Ares, Angel Sanchez

Comments: Final published version. Title and discussion modified. 6 pages, 3 figures

Journal-ref: Eur. Phys. J. B 56, 253 (2007)

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

[59] arXiv:cond-mat/0511630 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Kernel method for clustering based on optimal target vector

Leonardo Angelini, Daniele Marinazzo, Mario Pellicoro, Sebastiano Stramaglia

Comments: 4 pages, 4 figures

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Data Analysis, Statistics and Probability (physics.data-an); Quantitative Methods (q-bio.QM)

[60] arXiv:math/0511246 (cross-list from math.PR) [pdf, other]

Title: Probabilities on cladograms: introduction to the alpha model

Daniel J. Ford

Comments: 75 pages, 29 figures; material presented at Annual New Zealand Phylogenetics Conference 2005; part of a PhD thesis (in preparation)

Subjects: Probability (math.PR); Combinatorics (math.CO); Populations and Evolution (q-bio.PE)

[61] arXiv:math/0511346 (cross-list from math.PR) [pdf, other]

Title: Sequential and asynchronous processes driven by stochastic or quantum grammars and their application to genomics: a survey

Dimitri Petritis (IRMAR)

Comments: Presented at the European Congress on Mathematical and Theoretical Biology, Dresden 18--22 July 2005

Subjects: Probability (math.PR); Genomics (q-bio.GN)

[62] arXiv:math/0511743 (cross-list from math.PR) [pdf, other]

Title: The process of most recent common ancestors in an evolving coalescent

P. Pfaffelhuber, A. Wakolbinger

Subjects: Probability (math.PR); Populations and Evolution (q-bio.PE)

[63] arXiv:nlin/0511018 (cross-list from nlin.AO) [pdf, other]

Title: The Role of Redundancy in the Robustness of Random Boolean Networks

Carlos Gershenson, Stuart A. Kauffman, Ilya Shmulevich

Comments: v2 improved with referee comments. 7 pages, 4 figures. To be published in Artificial Life X, Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems. MIT Press

Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Statistical Mechanics (cond-mat.stat-mech); Computational Complexity (cs.CC); Cellular Automata and Lattice Gases (nlin.CG); Biological Physics (physics.bio-ph); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[64] arXiv:nlin/0511040 (cross-list from nlin.PS) [pdf, other]

Title: Distributed Sources, Accelerated Universe, Consciousness and Quantum Entanglement

E. A. Novikov

Comments: 5 pages

Subjects: Pattern Formation and Solitons (nlin.PS); Astrophysics (astro-ph); Neurons and Cognition (q-bio.NC)

[65] arXiv:physics/0511137 (cross-list from physics.bio-ph) [pdf, other]

Title: Complex networks in brain electrical activity

G. Ruffini, C. Ray, J. Marco, L. Fuentemilla, C. Grau

Comments: 22 pages, 5 figures. Starlab preprint. This version is an attempt to include better figures (no content change)

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