Quantitative Biology

Authors and titles for May 2008

[1] arXiv:0805.0084 [pdf, other]

Title: Predicting the species abundance distribution using a model food web

Craig R. Powell, Alan J. McKane

Comments: 10 pages, 11 figures, 1 table

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

[2] arXiv:0805.0223 [pdf, other]

Title: Low energy defibrillation in human cardiac tissue: a simulation study

S. W. Morgan, G. Plank, I. V. Biktasheva, V. N. Biktashev

Comments: 17 pages, 7 figures, as accepted to Biophysical Journal 2008/11/25

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

[3] arXiv:0805.0484 [pdf, other]

Title: Evolution of the genetic code. From the CG- to the CGUA-alphabet, from RNA double helix to DNA

Denis A. Semenov

Comments: 19 pages, 7 tables

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

[4] arXiv:0805.0530 [pdf, other]

Title: Analytical Equations to the Chromaticity Cone: Algebraic Methods for Describing Color

Prashanth Alluvada

Comments: 20 pages, 17 figures, 1 table

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

[5] arXiv:0805.0532 [pdf, other]

Title: Inferring coupling strength from event-related dynamics

Szymon Leski, Daniel K. Wojcik

Comments: Final version published in Phys Rev E

Journal-ref: Phys. Rev. E 78, 041918 (2008)

Subjects: Neurons and Cognition (q-bio.NC); Chaotic Dynamics (nlin.CD)

[6] arXiv:0805.0592 [pdf, other]

Title: The silencing of neuronal activity by noise and the phenomenon of inverse stochastic resonance

Boris S. Gutkin, Juergen Jost, Henry C. Tuckwell

Comments: 12 pages, 4 figures

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

[7] arXiv:0805.0634 [pdf, other]

Title: To what extent does genealogical ancestry imply genetic ancestry?

Frederick A. Matsen, Steven N. Evans

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

[8] arXiv:0805.0695 [pdf, other]

Title: The genetic code Via Godel encoding

Tidjani Negadi

Journal-ref: The Open Physical Chemistry Journal, 2008, Vol.2, 1-5

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

[9] arXiv:0805.0696 [pdf, other]

Title: Observation of the DNA ion-phosphate vibrations

L.A. Bulavin, S.N. Volkov, S.Yu. Kutovy, S.M. Perepelytsya

Comments: 6 pages, 2 figures

Journal-ref: Reports of the National Academy of Science of Ukraine, 10, 69-73 (2007)

Subjects: Biomolecules (q-bio.BM)

[10] arXiv:0805.0819 [pdf, other]

Title: Prey-predator modeling of CO2 atmospheric concentration

Luis Augusto Trevisan, Fabiano Meira de Moura Luz

Comments: Key words:Prey Predator model, Photosynthesis rate, CO2 concentration

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

[11] arXiv:0805.0835 [pdf, other]

Title: Mechanism of robust circadian oscillation of KaiC phosphorylation in vitro

Kohei Eguchi, Mitsumasa Yoda, Tomoki P. Terada, Masaki Sasai

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

[12] arXiv:0805.1085 [pdf, other]

Title: On the Law of Directionality of Genome Evolution

Liaofu Luo

Comments: 18 pages

Subjects: Genomics (q-bio.GN); Cell Behavior (q-bio.CB)

[13] arXiv:0805.1128 [pdf, other]

Title: An algebraic hypothesis about the primeval genetic code

Robersy Sanchez, Ricardo Grau

Comments: A part of this article was presented in the Second international workshop IWOBI 08 (ISBN 978-959-250-394-6) at the Universidad Central de Las Villas, Santa Clara, Cuba. 25 pages, 2 figure and 3 Tables

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

[14] arXiv:0805.1289 [pdf, other]

Title: A limiting rule for the variability of coding sequence length in microbial genomes

Vasile V. Morariu

Subjects: Genomics (q-bio.GN)

[15] arXiv:0805.1395 [pdf, other]

Title: Inference of ecological interaction networks

Paola Vera-Licona, Reinhard Laubenbacher

Comments: To appear in Annales Zoologici Fennici

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

[16] arXiv:0805.1561 [pdf, other]

Title: Generalization of the event-based Carnevale-Hines integration scheme for integrate-and-fire models

Ronald A.J. van Elburg, Arjen van Ooyen

Comments: 11 pages with 2 figures included in main text

Journal-ref: Neural Computation, July 2009, Vol. 21, No. 7, Pages 1913-1930

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

[17] arXiv:0805.1640 [pdf, other]

Title: Connectivity and Dynamics of Neuronal Networks as Defined by the Shape of Individual Neurons

Sebastian Ahnert, Luciano da Fontoura Costa

Comments: 11 pages, 9 figures. A working manuscript

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

[18] arXiv:0805.1723 [pdf, other]

Title: A Wireless Embedded Tongue Tactile Biofeedback System for Balance Control

Nicolas Vuillerme (TIMC), Nicolas Pinsault (TIMC), Olivier Chenu (TIMC), Anthony Fleury (TIMC), Yohan Payan (TIMC), Jacques Demongeot (TIMC)

Comments: Pervasive and Mobile Computing (2008) in press

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

[19] arXiv:0805.1776 [pdf, other]

Title: Serially-regulated biological networks fully realize a constrained set of functions

Andrew Mugler, Etay Ziv, Ilya Nemenman, Chris H. Wiggins

Comments: 9 pages, 3 figures

Journal-ref: IET Sys. Bio. 2 (2008) 313-322

Subjects: Molecular Networks (q-bio.MN)

[20] arXiv:0805.1859 [pdf, other]

Title: Constructing the Simplest Possible Phylogenetic Network from Triplets

Leo van Iersel, Steven Kelk

Comments: The proof of Lemma 4 has been extended

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

[21] arXiv:0805.2071 [pdf, other]

Title: Evolving learning rules and emergence of cooperation in spatial Prisoner's Dilemma

Luis G. Moyano, Angel Sánchez

Comments: Final version, to appear in J. Theor. Biol

Subjects: Populations and Evolution (q-bio.PE); Physics and Society (physics.soc-ph)

[22] arXiv:0805.2288 [pdf, other]

Title: A comparative evolutionary study of transcription networks

A.L. Sellerio, B. Bassetti, H. Isambert, M. Cosentino Lagomarsino

Subjects: Molecular Networks (q-bio.MN)

[23] arXiv:0805.2298 [pdf, other]

Title: Characterizing the Diversity of Dynamics in Complex Networks Without Border Effects

Matheus P. Viana, Bruno A. N. Travencolo, E. Tanck, Luciano da F. Costa

Comments: 15 pages, 7 figures. A working manuscript

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

[24] arXiv:0805.2628 [pdf, other]

Title: Sloppiness, robustness, and evolvability in systems biology

Bryan C. Daniels, Yan-Jiun Chen, James P. Sethna, Ryan N. Gutenkunst, Christopher R. Myers

Comments: 12 pages, 7 figures, submitted to Current Opinion in Biotechnology

Subjects: Quantitative Methods (q-bio.QM)

[25] arXiv:0805.2796 [pdf, other]

Title: Intrinsic gain modulation and adaptive neural coding

Sungho Hong (University of Washington and Okinawa Institute of Science and Technology), Brian N. Lundstrom (University of Washington), Adrienne Fairhall (University of Washington)

Comments: 24 pages, 4 figures, 1 supporting information

Subjects: Neurons and Cognition (q-bio.NC); Biological Physics (physics.bio-ph)

[26] arXiv:0805.2936 [pdf, other]

Title: Markovian log-supermodularity, and its applications in phylogenetics

Mike Steel, Beata Faller

Comments: 8 pages, 2 figures

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

[27] arXiv:0805.3368 [pdf, other]

Title: A model of dissociated cortical tissue

M. Stiber, F. Kawasaki, D. Xu

Comments: 4 pages, 8 PDF figure files, uses graphicx, mathptmx, helvet, courier, amsmath, and 1 custom style file

Journal-ref: Proc. 7th Int. Workshop on Neural Coding, Montevideo, Uruguay, Nov. 7-12, 2007, pp. 24-27

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

[28] arXiv:0805.3523 [pdf, other]

Title: Reliability of Layered Neural Oscillator Networks

Kevin K. Lin, Eric Shea-Brown, Lai-Sang Young

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

[29] arXiv:0805.3544 [pdf, other]

Title: The cardiac Ca-sensitive regulatory switch, a system in dynamic equilibrium

John M. Robinson, Herbert C. Cheung, Wenji Dong

Comments: 49 pages, 9 figures, 2 supplemental figures

Subjects: Biomolecules (q-bio.BM)

[30] arXiv:0805.3578 [pdf, other]

Title: Macro- and Microscopic Self-Similarity in Neuro- and Psycho-Dynamics

Vladimir G. Ivancevic, Tijana T. Ivancevic

Comments: 8 pages, no figures, Latex - minor corrections

Subjects: Neurons and Cognition (q-bio.NC); Subcellular Processes (q-bio.SC)

[31] arXiv:0805.3583 [pdf, other]

Title: New Mechanics of Traumatic Brain Injury

Vladimir G. Ivancevic

Comments: 18 pages, 1 figure, Latex

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

[32] arXiv:0805.3588 [pdf, other]

Title: Human-Robot Biodynamics

Vladimir G. Ivancevic

Comments: 20 pages, 11 figures, Latex

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

[33] arXiv:0805.3675 [pdf, other]

Title: Allometric metabolic scaling and fetal and placental weight

Carolyn M. Salafia, Dawn P. Misra, Michael Yampolsky, Adrian K. Charles, Richard K. Miller

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

[34] arXiv:0805.3691 [pdf, other]

Title: Elucidation of differential response networks from toxicogenomics data

Z. Dezso, R. Welch, V. Kazandaev, A. Naito, J. Fuscoe, C. Melvin, Y. Dragan, Y. Nikolsky, T. Nikolskaya, A. Bugrim

Comments: 28 pages, 3 figures and 3 tables

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

[35] arXiv:0805.3757 [pdf, other]

Title: Drug absorption through a cell monolayer: a theoretical work on a non-linear three-compartment model

Niko Komin, Raúl Toral

Comments: 21 pages, 8 figures (v4: detailed definition of the treated model - additional information about limitations)

Journal-ref: European Journal of Pharmaceutical Sciences, 37 (2009), 106-114

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

[36] arXiv:0805.3841 [pdf, other]

Title: Diversity against adversity: How adaptive immunity evolves potent antibodies

Muyoung Heo, Konstantin B. Zeldovich, Eugene I. Shakhnovich

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

[37] arXiv:0805.3851 [pdf, other]

Title: Entomogenic Climate Change

David Dunn, James P. Crutchfield

Comments: 7 pages, 1 figure; this http URL

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

[38] arXiv:0805.3861 [pdf, other]

Title: Life-Space Foam: a Medium for Motivational and Cognitive Dynamics

Vladimir G. Ivancevic, Eugene V. Aidman

Comments: 25 pages, 2 figures, elsart

Journal-ref: Physica A 382, 616-630, (2007)

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

[39] arXiv:0805.4017 [pdf, other]

Title: Extrinsic and intrinsic nucleosome positioning signals

Alexandre V. Morozov, Karissa Fortney, Daria A. Gaykalova, Vasily M. Studitsky, Jonathan Widom, Eric D. Siggia

Comments: 20 pages and 6 figures in main text, plus supporting information

Subjects: Genomics (q-bio.GN); Biomolecules (q-bio.BM)

[40] arXiv:0805.4087 [pdf, other]

Title: Reliability of regulatory networks and its evolution

Stefan Braunewell, Stefan Bornholdt

Comments: 11 pages, 12 figures

Subjects: Molecular Networks (q-bio.MN)

[41] arXiv:0805.4315 [pdf, other]

Title: Microbial genome as a fluctuating system: Distribution and correlation of coding sequence lengths

V. V. Morariu

Comments: 13 pages, 8 figures

Subjects: Genomics (q-bio.GN)

[42] arXiv:0805.4316 [pdf, other]

Title: On two quantum approaches to adaptive mutations in bacteria

Vasily Ogryzko

Comments: 35 pages, 6 figures, 3 tables, 1 Appendix. This version was accepted in the NeuroQuantology Journal. Format has been adjusted accordingly, together with a number of clarifying modifications

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

[43] arXiv:0805.4455 [pdf, other]

Title: Sensitivity Regulation based on Noise Propagation in Stochastic Reaction Networks

Kyung Hyuk Kim, Hong Qian, Herbert M. Sauro

Comments: 16 pages. Acknowledgement is corrected

Subjects: Molecular Networks (q-bio.MN)

[44] arXiv:0805.4692 [pdf, other]

Title: Matrix genetics, part 3: the evolution of the genetic code from the viewpoint of the genetic octave Yin-Yang-algebra

Sergey V. Petoukhov

Comments: 22 pages, 7 figures. These materials were presented in the international symposium "2008 Molecular Informatics and Bioinformatics" at the Institute for Advanced Study, Collegium Budapest, Hungary, March 27-29, 2008. The abstract on their basis has been accepted into the program of XX International Congress of Genetics, Berlin, Germany, July 12-17, 2008

Subjects: Genomics (q-bio.GN); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)

[45] arXiv:0805.0275 (cross-list from math.CO) [pdf, other]

Title: The Dynamics of Conjunctive and Disjunctive Boolean Networks

Abdul Salam Jarrah, Reinhard Laubenbacher, Alan Veliz-Cuba

Subjects: Combinatorics (math.CO); Dynamical Systems (math.DS); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

[46] arXiv:0805.0326 (cross-list from physics.bio-ph) [pdf, other]

Title: Avalanches, branching ratios, and clustering of attractors in Random Boolean Networks and in the segment polarity network of \emph{Drosophila}

Andrew Berdahl, Amer Shreim, Vishal Sood, Joern Davidsen, Maya Paczuski

Subjects: Biological Physics (physics.bio-ph); Molecular Networks (q-bio.MN)

[47] arXiv:0805.1489 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Modeling and verifying a broad array of network properties

Vladimir Filkov, Zachary M. Saul, Soumen Roy, Raissa M. D'Souza, Premkumar T. Devanbu

Comments: To appear in Europhysics Letters

Journal-ref: Europhysics Letters, 86 (2009) 28003

Subjects: Statistical Mechanics (cond-mat.stat-mech); Software Engineering (cs.SE); Quantitative Methods (q-bio.QM); Applications (stat.AP)

[48] arXiv:0805.1607 (cross-list from nlin.AO) [pdf, other]

Title: How limit cycles and quasi-cycles are related in systems with intrinsic noise

Richard P. Boland, Tobias Galla, Alan J. McKane

Comments: 15 pages, 14 figures

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

[49] arXiv:0805.2522 (cross-list from nlin.AO) [pdf, other]

Title: Epigenetic Tracking, a Method to Generate Arbitrary Shapes By Using Evolutionary-Developmental Techniques

Alessandro Fontana

Comments: 12 pages, 11 figures

Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Cell Behavior (q-bio.CB)

[50] arXiv:0805.2695 (cross-list from math.DS) [pdf, other]

Title: Contractive piecewise continuous maps modeling networks of inhibitory neurons

E. Catsigeras, A. Rovella, R. Budelli

Comments: In this version we changed the section 2 to include a complete proof of the properties of the mathematical model from a physical model. In section 4 we added more details to the proof of the Lemmas and the main Theorem

Journal-ref: International Journal of Pure and Applied Mathematics, Volume 61 Number 4 2010, 381-407

Subjects: Dynamical Systems (math.DS); Neurons and Cognition (q-bio.NC)