Quantitative Biology

Authors and titles for February 2005

[1] arXiv:q-bio/0502001 [pdf, other]

Title: The Dynamic Evolution of the Power Exponent in a Universal Growth Model of Tumors

Caterina Guiot, Pier Paolo Delsanto, Alberto Carpinteri, Nicola Pugno Yuri Mansury, Thomas S. Deisboeck

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

[2] arXiv:q-bio/0502002 [pdf, other]

Title: The Effects of EGF-Receptor Density on Multiscale Tumor Growth Patterns

Chaitanya A. Athale, Thomas S. Deisboeck

Subjects: Cell Behavior (q-bio.CB); Molecular Networks (q-bio.MN); Other Quantitative Biology (q-bio.OT)

[3] arXiv:q-bio/0502003 [pdf, other]

Title: Autoassociative Memory Retrieval and Spontaneous Activity Bumps in Small-World Networks of Integrate-and-Fire Neurons

A. Anishchenko (1), E. Bienenstock (1), A. Treves (2) ((1) Brown University, (2) SISSA)

Comments: 25 pages, 7 figures; submitted to Neural Computation

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

[4] arXiv:q-bio/0502004 [pdf, other]

Title: Telomere loss limits the rate of human epithelial tumor formation

Hermann B. Frieboes, James P. Brody

Comments: 15 pages, includes 7 figures

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

[5] arXiv:q-bio/0502005 [pdf, other]

Title: Cliques and duplication-divergence network growth

I. Ispolatov, P. L. Krapivsky, I. Mazo, A. Yuryev

Comments: 7 pages, 6 figures

Journal-ref: New J. Phys. v. 7 (2005) 145

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

[6] arXiv:q-bio/0502006 [pdf, other]

Title: What can one learn from two-state single molecule trajectories?

Ophir Flomenbom, Joseph Klafter, Attila Szabo

Comments: Biophys. J., in press (2005)

Journal-ref: Biophys. J. 88, 3780-3783 (2005)

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

[7] arXiv:q-bio/0502007 [pdf, other]

Title: Some Properties of the Speciation Model for Food-Web Structure - Mechanisms for Degree Distributions and Intervality

A. G. Rossberg, H. Matsuda, T. Amemiya, K. Itoh

Comments: 23 pages, 6 figures, minor rewrites

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

[8] arXiv:q-bio/0502008 [pdf, other]

Title: Dissociation in a polymerization model of homochirality

A. Brandenburg, A.C. Andersen, M. Nilsson

Comments: 16 pages, 6 figures, submitted to Orig. Life Evol. Biosph

Journal-ref: Orig. Life Evol. Biosph. 35, 507-521 (2005)

Subjects: Biomolecules (q-bio.BM); Other Condensed Matter (cond-mat.other); Other Quantitative Biology (q-bio.OT)

[9] arXiv:q-bio/0502009 [pdf, other]

Title: Statistical analysis of simple repeats in the human genome

Francesco Piazza, Pietro Lio

Journal-ref: Physica A 347 (2005) 472-488

Subjects: Genomics (q-bio.GN)

[10] arXiv:q-bio/0502010 [pdf, other]

Title: Sympatric Speciation in a Simple Food Web

K. Luz-Burgoa, Tony Dell, Toshinori Okuyama

Comments: Contribution to the Proceedings of the Complex Systems Summer School 2004, organized by the Santa Fe Institute (9 pages and 6 figures)

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

[11] arXiv:q-bio/0502011 [pdf, other]

Title: Determination of barrier heights and prefactors from protein folding rate data

Steven S. Plotkin

Comments: 11 pages, 5 figures, 1 table, Accepted Biophys J

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

[12] arXiv:q-bio/0502012 [pdf, other]

Title: Short-range spectroscopic ruler based on a single-molecule optical switch

Mark Bates, Timothy R. Blosser, Xiaowei Zhuang

Comments: Article contains 4 pages and 4 figures. Accepted for publication in Physical Review Letters. Supplementary material and movie file will be available through the PRL web site at the time of publication

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph); Chemical Physics (physics.chem-ph); Biomolecules (q-bio.BM)

[13] arXiv:q-bio/0502013 [pdf, other]

Title: Accelerating, hyper-accelerating, and decelerating probabilistic networks

M. J. Gagen, J. S. Mattick

Comments: 13 pages, 9 figures

Journal-ref: Physical Review E, 72, 016123 (2005)

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

[14] arXiv:q-bio/0502014 [pdf, other]

Title: Resolution exchange simulation

Edward Lyman, F. Marty Ytreberg, Daniel M. Zuckerman

Comments: revised manuscript: 4.2 pages, 3 figures

Journal-ref: Phys. Rev. Lett. v.96:028105(2006)

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

[15] arXiv:q-bio/0502015 [pdf, other]

Title: A stochastic approach to multi-gene expression dynamics

T. Ochiai, J.C. Nacher, T. Akutsu

Comments: 17 pages, 2 figures, Latex, v2 includes minor modifications

Subjects: Biomolecules (q-bio.BM)

[16] arXiv:q-bio/0502016 [pdf, other]

Title: Loop-closure events during protein folding: Rationalizing the shape of Phi-value distributions

Thomas R. Weikl

Comments: 24 pages, 3 figures, 2 tables; to appear in "Proteins: Structure, Function, and Bioinformatics"

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

[17] arXiv:q-bio/0502017 [pdf, other]

Title: The large-scale logico-chemical structure of a transcriptional regulation network

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

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

[18] arXiv:q-bio/0502018 [pdf, other]

Title: Graph theoretic analysis of protein interaction networks of eukaryotes

K.-I. Goh, B. Kahng, D. Kim (Seoul National University)

Comments: 7 pages, 6 figures, 2 tables

Journal-ref: Physica A 357, 512 (2005).

Subjects: Molecular Networks (q-bio.MN)

[19] arXiv:q-bio/0502019 [pdf, other]

Title: Early events in insulin fibrillization studied by time-lapse atomic force microscopy

A. Podesta', G. Tiana, P. Milani, M. Manno

Subjects: Biomolecules (q-bio.BM)

[20] arXiv:q-bio/0502020 [pdf, other]

Title: Pairwise alignment incorporating dipeptide covariation

Gavin E. Crooks, Richard E. Green, Steven E. Brenner

Journal-ref: Bioinformatics 21 3704-3710 (2005)

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

[21] arXiv:q-bio/0502021 [pdf, other]

Title: Biodiversity in model ecosystems, I: Coexistence conditions for competing species

Ugo Bastolla, Michael Lässig, Susanna C. Manrubia, Angelo Valleriani

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

[22] arXiv:q-bio/0502022 [pdf, other]

Title: Biodiversity in model ecosystems, II: Species assembly and food web structure

Ugo Bastolla, Michael Lässig, Susanna C. Manrubia, Angelo Valleriani

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

[23] arXiv:q-bio/0502023 [pdf, other]

Title: Learning intrinsic excitability in medium spiny neurons

Gabriele Scheler

Comments: 20 pages, 8 figures

Journal-ref: F1000Research 2014, 2:88

Subjects: Neurons and Cognition (q-bio.NC); Neural and Evolutionary Computing (cs.NE)

[24] arXiv:q-bio/0502024 [pdf, other]

Title: Self-organized density patterns of molecular motors in arrays of cytoskeletal filaments

Stefan Klumpp, Theo M. Nieuwenhuizen, Reinhard Lipowsky

Comments: 48 pages, 8 figures

Journal-ref: Biophys. J. 88, 3118-3132 (2005)

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

[25] arXiv:q-bio/0502025 [pdf, other]

Title: On the role of chemical synapses in coupled neurons with noise

Pablo Balenzuela Jordi Garcia-Ojalvo

Comments: 7 pages, 7 figures

Subjects: Neurons and Cognition (q-bio.NC); Other Condensed Matter (cond-mat.other); Biological Physics (physics.bio-ph); Other Quantitative Biology (q-bio.OT)

[26] arXiv:q-bio/0502026 [pdf, other]

Title: Stochastic gene expression in switching environments

Martin Gander, Christian Mazza, Hansklaus Rummler

Comments: 14 pages, 5 figures

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

[27] arXiv:q-bio/0502027 [pdf, other]

Title: Simulations of a mortality plateau in the sexual Penna model for biological ageing

Veit Schwämmle, Suzana M. de Oliveira

Comments: submitted to Phys. Rev. E

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

[28] arXiv:q-bio/0502028 [pdf, other]

Title: Release of Brain Mitochondrial Hexokinase by Acidic Proteins and Macromolecular Polyanions

F. Moller

Comments: 29 pages,3 figures. Figures and page number revised(28 pages)

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

[29] arXiv:q-bio/0502029 [pdf, other]

Title: The Species Abundances Distribution in a new perspective

M. Ravasz, A. Balog, V. Marko, Z. Neda

Comments: 8 pages, 4 figures

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

[30] arXiv:q-bio/0502030 [pdf, other]

Title: Transient Information Flow in a Network of Excitatory and Inhibitory Model Neurons: Role of Noise and Signal Autocorrelation

Julien Mayor, Wulfram Gerstner

Comments: 27 pages, 7 figures, to appear in J. Physiology (Paris) Vol. 98

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

[31] arXiv:q-bio/0502031 [pdf, other]

Title: Signal buffering in random networks of spiking neurons: microscopic vs. macroscopic phenomena

Julien Mayor, Wulfram Gerstner

Comments: 5 pages, 3 figures

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

[32] arXiv:q-bio/0502032 [pdf, other]

Title: Cellular organization by self-organization : mechanisms and models for Min protein dynamics

Martin Howard, Karsten Kruse

Comments: 20 pages, 1 figure

Journal-ref: J. Cell Biol. 168 533-536 (2005)

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

[33] arXiv:q-bio/0502033 [pdf, other]

Title: The use of oscillatory signals in the study of genetic networks

Ovidiu Lipan, Wing H. Wong

Comments: 46 pages, 5 figures. Submitted to PNAS on May 27th 2004. The paper is under consideration

Subjects: Molecular Networks (q-bio.MN)

[34] arXiv:q-bio/0502034 [pdf, other]

Title: Kinetics of target site localization of a protein on DNA: a stochastic approach

M. Coppey, O. Benichou, R. Voituriez, M. Moreau

Comments: 10 pages, 8 figures

Journal-ref: Biophys. J., September 1, 2004; 87(3): 1640 - 1649

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

[35] arXiv:q-bio/0502035 [pdf, other]

Title: Functional cartography of complex metabolic networks

Roger Guimera, Luis A. Nunes Amaral

Comments: 17 pages, 4 figures. Go to this http URL for the PDF file of the reprint

Journal-ref: Nature 433, 895-900 (2005)

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

[36] arXiv:q-bio/0502036 [pdf, other]

Title: Morphogen Gradient from a Noisy Source

Jeremy L. England, John Cardy

Comments: Four pages, three figures

Journal-ref: PRL 94, 078101 (2005)

Subjects: Tissues and Organs (q-bio.TO); Other Condensed Matter (cond-mat.other); Molecular Networks (q-bio.MN); Other Quantitative Biology (q-bio.OT)

[37] arXiv:q-bio/0502037 [pdf, other]

Title: Optimal Spike-Timing Dependent Plasticity for Precise Action Potential Firing

Jean-Pascal Pfister, Taro Toyoizumi, David Barber, Wulfram Gerstner

Comments: 27 pages, 10 figures

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

[38] arXiv:q-bio/0502038 [pdf, other]

Title: Modelling butterfly wing eyespot patterns

Rui Dilao, Joaquim Sainhas

Comments: 12 pages, 3 figures

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

[39] arXiv:q-bio/0502039 [pdf, other]

Title: Spectral representation: analyzing single-unit activity in extracellularly recorded neuronal data without spike sorting

Artur Luczak, Nandakumar S. Narayanan

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

[40] arXiv:q-bio/0502040 [pdf, other]

Title: A new model for the immune clonal networks

V. V. Gafiychuk, A. K. Prykarpatsky

Comments: 15 pages, 4 figures

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

[41] arXiv:q-bio/0502041 [pdf, other]

Title: The reaction-diffusion approach to morphogenesis

Rui Dilao

Comments: 22 pages, 11 figures

Subjects: Cell Behavior (q-bio.CB)

[42] arXiv:q-bio/0502042 [pdf, other]

Title: Harvesting in a resource dependent age structured Leslie type population model

Rui Dilao, Tiago Domingos, Elman M. Shahverdiev

Comments: 26 pages, 4 figures

Journal-ref: Math. Biosciences vol. 189 (2004) 141-151

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

[43] arXiv:q-bio/0502043 [pdf, other]

Title: Helices in Biomolecules

Kevin Cahill

Comments: five pages, no figures

Journal-ref: Physical Review E 72, 062901 (2005)

Subjects: Biomolecules (q-bio.BM)

[44] arXiv:q-bio/0502044 [pdf, other]

Title: DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise

Jose M. G. Vilar, Leonor Saiz

Comments: To appear in Current Opinion in Genetics & Development

Journal-ref: Current Opinion in Genetics & Development, 15, 136-144 (2005)

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

[45] arXiv:q-bio/0502045 [pdf, other]

Title: Evolutionarily conserved human targets of adenosine to inosine RNA editing

Erez Y. Levanon, Martina Hallegger, Yaron Kinar, Ronen Shemesh, Kristina Djinovic-Carugo, Gideon Rechavi, Michael F. Jantsch, Eli Eisenberg

Journal-ref: Nucleic Acids Research, Vol. 33, 1162-1168 (2005)

Subjects: Genomics (q-bio.GN)

[46] arXiv:q-bio/0502046 [pdf, other]

Title: Fluctuations in models of biological macroevolution

Per Arne Rikvold

Comments: 7 pages, 5 figures

Journal-ref: Proceedings of SPIE -- Volume 5845, Noise in Complex Systems and Stochastic Dynamics III, edited by L.B. Kish, K. Lindenberg, and Z. Gingl (SPIE, Bellingham, WA, 2005), pp. 148-155.

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

[47] arXiv:cond-mat/0502389 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Stationary distributions of a noisy logistic process

P. F. Gora

Comments: 15 pages in LaTeX incl. 4 PostScript figures. Submitted to Acta Physica Polonica B

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

[48] arXiv:cond-mat/0502527 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Movements of molecular motors: Ratchets, random walks and traffic phenomena

Stefan Klumpp, Theo M. Nieuwenhuizen, Reinhard Lipowsky

Comments: latex, uses this http URL and this http URL (included), 10 pages, 6 figures, to appear in the proceedings of FQMT'04, Prague

Journal-ref: Physica E 29, 380-389 (2005)

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

[49] arXiv:cs/0502076 (cross-list from cs.LG) [pdf, other]

Title: Learning nonsingular phylogenies and hidden Markov models

Elchanan Mossel, Sébastien Roch

Comments: Published at this http URL in the Annals of Applied Probability (this http URL) by the Institute of Mathematical Statistics (this http URL)

Journal-ref: Annals of Applied Probability 2006, Vol. 16, No. 2, 583-614

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

[50] arXiv:math/0502226 (cross-list from math.PR) [pdf, other]

Title: Subtree prune and regraft: a reversible real tree-valued Markov process

Steven N. Evans, Anita Winter

Comments: Published at this http URL in the Annals of Probability (this http URL) by the Institute of Mathematical Statistics (this http URL)

Journal-ref: Annals of Probability 2006, Vol. 34, No. 3, 918-961

Subjects: Probability (math.PR); Metric Geometry (math.MG); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)