Quantitative Biology

Authors and titles for June 2008

[51] arXiv:0806.2840 [pdf, other]

Title: Cluster structure of functional networks estimated from high-resolution EEG data

Roberta Sinatra, Fabrizio De Vico Fallani, Laura Astolfi, Fabio Babiloni, Febo Cincotti, Vito Latora, Donatella Mattia

Comments: 21 pages, 4 figures

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

[52] arXiv:0806.2888 [pdf, other]

Title: Spread of infectious diseases through clustered populations

Joel C. Miller

Comments: Updated version

Subjects: Quantitative Methods (q-bio.QM)

[53] arXiv:0806.3048 [pdf, other]

Title: A fast and efficient gene-network reconstruction method from multiple over-expression experiments

Dejan Stokic, Rudolf Hanel, Stefan Thurner

Comments: 10 pages, 3 figures

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

[54] arXiv:0806.3064 [pdf, other]

Title: Identifying critical residues in protein folding: Insights from phi-value and Pfold analysis

P.F.N. Faisca, R.D.M. Travasso, R.C. Ball, E.I. Shakhnovich

Comments: Submitted for publication with minor changes (abstract & higher resolution figures)

Journal-ref: J. Chem. Phys. 129, 095108 (2008)

Subjects: Biomolecules (q-bio.BM)

[55] arXiv:0806.3130 [pdf, other]

Title: Do quantum effects hold together DNA condensates?

Alfredo Iorio, Samik Sen, Siddhartha Sen

Comments: 8 pages, 6 figures

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

[56] arXiv:0806.3274 [pdf, other]

Title: Significance tests for comparing digital gene expression profiles

Leonardo Varuzza, Arthur Gruber, Carlos A. de B. Pereira

Comments: 16 pages, 5 figures. Implementations of both tests are available under the GNU General Public License at this http URL

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

[57] arXiv:0806.3340 [pdf, other]

Title: New Mechanics of Spinal Injury

Vladimir G. Ivancevic

Comments: 14 pages, 1 figure, Latex

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

[58] arXiv:0806.3479 [pdf, other]

Title: Comment of Global dynamics of biological systems

Radhakrishnan Nagarajan

Comments: 6 pages, 2 figures

Subjects: Genomics (q-bio.GN)

[59] arXiv:0806.3489 [pdf, other]

Title: Line-Defect Patterns of Unstable Spiral Waves in Cardiac Tissue

Juan G. Restrepo, Alain Karma

Comments: 4 pages, 5 figures

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

[60] arXiv:0806.3591 [pdf, other]

Title: Detecting Robust Patterns in the Spread of Epidemics: A Case Study of Influenza in the United States and France

Pascal Crépey, Marc Barthélemy

Comments: 8 pages, 7 figures, 3 tables

Journal-ref: Am J Epidemiol. 2007 Dec 1;166(11):1244-51. Epub 2007 Oct 15

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

[61] arXiv:0806.3652 [pdf, other]

Title: Protein Structure Prediction Using Basin-Hopping

Michael C. Prentiss, David J. Wales, Peter G. Wolynes

Journal-ref: J. Chem. Phys. 128, 225106 (2008)

Subjects: Biomolecules (q-bio.BM)

[62] arXiv:0806.3734 [pdf, other]

Title: Characterization of Protein Folding by Dominant Reaction Pathways

Pietro Faccioli

Comments: 14 pages, 11 figures

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

[63] arXiv:0806.3738 [pdf, other]

Title: The Influence of Sodium and Potassium Dynamics on Excitability, Seizures, and the Stability of Persistent States: I. Single Neuron Dynamics

John R. Cressman Jr., Ghanim Ullah, Jokubas Ziburkus, Steven J. Schiff, Ernest Barreto

Comments: Post-review revision. 8 figures. This is the first of a pair of related papers; see also arXiv:0806.3741

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

[64] arXiv:0806.3741 [pdf, other]

Title: The Influence of Sodium and Potassium Dynamics on Excitability, Seizures, and the Stability of Persistent States: II. Network and Glial Dynamics

Ghanim Ullah, John R. Cressman Jr., Ernest Barreto, Steven J. Schiff

Comments: Post-review revision. 5 figures. This is the second of a pair of related papers; see also arXiv:0806.3738

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

[65] arXiv:0806.3772 [pdf, other]

Title: Emergence of mutationally robust proteins in a microscopic model of evolution

Konstantin B. Zeldovich, Eugene I. Shakhnovich

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

[66] arXiv:0806.3823 [pdf, other]

Title: Annotation of Tribolium nuclear receptors reveals an evolutionary overacceleration of a network controlling the ecdysone cascade

François Bonneton (IGFL), Arnaud Chaumot (UR BELY), Vincent Laudet (IGFL)

Journal-ref: Insect Biochemistry and Molecular Biology 4, 38 (2008) 416-429

Subjects: Quantitative Methods (q-bio.QM)

[67] arXiv:0806.3845 [pdf, other]

Title: Traffic of cytoskeletal motors with disordered attachment rates

H. Grzeschik, R. J. Harris, L. Santen

Comments: 15 pages, 13 figures; revised version (to appear in Phys. Rev. E)

Journal-ref: Phys. Rev. E 81, 031929 (2010)

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

[68] arXiv:0806.3897 [pdf, other]

Title: Cytoskeleton mediated effective elastic properties of model red blood cell membranes

Rui Zhang, Frank L. H. Brown

Comments: 38 pages, 1 table, 12 figures. To be published in Journal of Chemical Physics

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

[69] arXiv:0806.3978 [pdf, other]

Title: Information In The Non-Stationary Case

Vincent Q. Vu, Bin Yu, Robert E. Kass

Subjects: Neurons and Cognition (q-bio.NC); Information Theory (cs.IT); Quantitative Methods (q-bio.QM); Methodology (stat.ME)

[70] arXiv:0806.3980 [pdf, other]

Title: Multi-Scale, Multi-Resolution Brain Cancer Modeling

Le Zhang, L. Leon Chen, Thomas S. Deisboeck

Comments: 26 pages, 7 figures

Subjects: Cell Behavior (q-bio.CB); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM); Tissues and Organs (q-bio.TO)

[71] arXiv:0806.4154 [pdf, other]

Title: Cancer Cell Motility: Optimizing Spatial Search Strategies

L. Leon Chen, Le Zhang, Jeongah Yoon, Thomas S. Deisboeck

Comments: 31 pages, 8 figures

Subjects: Cell Behavior (q-bio.CB); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM); Tissues and Organs (q-bio.TO)

[72] arXiv:0806.4161 [pdf, other]

Title: Two Potential Mechanisms of Spatial Attention in Early Visual Areas

Erez Persi

Comments: 15 pages, 4 figures, part of this work was presented in the 34th SFN annual meeting (2004)

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

[73] arXiv:0806.4276 [pdf, other]

Title: Communities recognition in the Chesapeake Bay ecosystem by dynamical clustering algorithms based on different oscillators systems

Alessandro Pluchino, Andrea Rapisarda, Vito Latora

Comments: 8 pages, 7 figures, Proceedings of the International Workshop on "Ecological Complex Systems: Stochastic Dynamics and Patterns", 22-26 July 2007 - Terrasini (Palermo), Italy

Subjects: Populations and Evolution (q-bio.PE); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Physics and Society (physics.soc-ph)

[74] arXiv:0806.4444 [pdf, other]

Title: Mean encounter times for cell adhesion in hydrodynamic flow: analytical progress by dimensional reduction

C. B. Korn, U. S. Schwarz

Comments: Reftex, postscript figures included

Journal-ref: EPL 83:28007 (2008)

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

[75] arXiv:0806.4449 [pdf, other]

Title: Impact of road mitigation measures on amphibian populations: A stage-class population mathematical model

Renaud Jolivet, Michel Antoniazza, Catherine Strehler-Perrin, Antoine Gander

Comments: 18 pages, 3 figures, 2 tables and 4 supplementary figures

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

[76] arXiv:0806.4518 [pdf, other]

Title: The motility of normal and cancer cells in response to the combined influence of substrate rigidity and anisotropic microstructure

Tzvetelina Tzvetkova-Chevolleau (LTM, TIMC), Angélique Stéphanou (TIMC), David Fuard (LTM), Jacques Ohayon (TIMC), Patrick Schiavone (LTM, TIMC), Philippe Tracqui (TIMC)

Journal-ref: Biomaterials 29, 10 (2008) 1541--1551

Subjects: Cell Behavior (q-bio.CB)

[77] arXiv:0806.4576 [pdf, other]

Title: Torus bifurcations, isolas and chaotic attractors in a simple dengue model with ADE and temporary cross immunity

Maira Aguiar, Nico Stollenwerk, Bob W. Kooi

Comments: 13 pages, 4 fugures; proceedings of CMMSE 2008, ISBN 978-84-612-1982-7

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

[78] arXiv:0806.4662 [pdf, other]

Title: On the statistical significance of temporal firing patterns in multi-neuronal spike trains

C. O. Diekman, P. S. Sastry, K. P. Unnikrishnan

Comments: 17 pages, 7 figures

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

[79] arXiv:0806.4838 [pdf, other]

Title: On the performance of combined dichotomic predictors of natively unfolded proteins

Antonio Deiana, Andrea Giansanti

Comments: The title of the paper has been changed to convey the focus of the work. The text has been slightly modified to clarify the subject. A more extended version of the paper has been published in BMC Bioinformatics 2010, 11:198 (21 April 2010)

Subjects: Biomolecules (q-bio.BM)

[80] arXiv:0806.4845 [pdf, other]

Title: Localization of Simultaneous Multiple Sources using SMS-LORETA

Avni Pllana, Herbert Bauer

Comments: 6 pages, 1 figure. From a talk available at this http URL

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

[81] arXiv:0806.0186 (cross-list from cond-mat.other) [pdf, other]

Title: Stochastic Dynamical Structure (SDS) of Nonequilibrium Processes in the Absence of Detailed Balance. IV: Emerging of Stochastic Dynamical Equalities and Steady State Thermodynamics from Darwinian Dynamics

P Ao

Comments: latex, 49 pages

Journal-ref: Emerging of Stochastic Dynamical Equalities and Steady State Thermodynamics. P. Ao, Communications in Theoretical Physics 49 (2008) 1073-1090

Subjects: Other Condensed Matter (cond-mat.other); Statistical Mechanics (cond-mat.stat-mech); Dynamical Systems (math.DS); Adaptation and Self-Organizing Systems (nlin.AO); Populations and Evolution (q-bio.PE)

[82] arXiv:0806.0263 (cross-list from math-ph) [pdf, other]

Title: On Some Perturbation Approaches to Population Dynamics

Francisco M. Fernandez

Subjects: Mathematical Physics (math-ph); Populations and Evolution (q-bio.PE)

[83] arXiv:0806.0505 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Stretching chimeric DNA: a test for the putative S-form

Stephen Whitelam, Sander Pronk, Phillip L. Geissler

Journal-ref: J. Chem. Phys. 129 205101 (2008)

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

[84] arXiv:0806.0739 (cross-list from quant-ph) [pdf, other]

Title: Quantum Zeno Effect Explains Magnetic-Sensitive Radical-Ion-Pair Reactions

I. K. Kominis

Comments: 10 pages, 5 figures

Journal-ref: Phys. Rev. E 80, 056115 (2009)

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

[85] arXiv:0806.1186 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Intricate dynamics of a deterministic walk confined in a strip

Denis Boyer

Comments: 6 pages, 5 figures

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

[86] arXiv:0806.2341 (cross-list from physics.bio-ph) [pdf, other]

Title: Structure from Fleeting Illumination of Faint Spinning Objects in Flight with Application to Single Molecules

Russell Fung, Valentin Shneerson, Dilano K. Saldin, Abbas Ourmazd

Comments: 11 pages, 3 figures

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

[87] arXiv:0806.3233 (cross-list from cond-mat.other) [pdf, other]

Title: Shuttle-mediated proton pumping across the inner mitochondrial membrane

Anatoly Yu. Smirnov, Sergey E. Savel'ev, Franco Nori

Comments: 22 pages, 6 figures

Subjects: Other Condensed Matter (cond-mat.other); Biological Physics (physics.bio-ph); Subcellular Processes (q-bio.SC)

[88] arXiv:0806.3326 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Probing microscopic origins of confined subdiffusion by first-passage observables

S. Condamin, V. Tejedor, R. Voituriez, O. Benichou, J. Klafter

Comments: 21 pages, 3 figures. Submitted version

Journal-ref: PNAS 105, 5675 (2008)

Subjects: Statistical Mechanics (cond-mat.stat-mech); Disordered Systems and Neural Networks (cond-mat.dis-nn); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)

[89] arXiv:0806.3424 (cross-list from math.AP) [pdf, other]

Title: Existence, multiplicity and stability of endemic states for an age-structured S-I epidemic model

D. Breda, D. Visetti

Comments: changed content, i.e. added well-posedness, stability change and Hopf bifurcation

Subjects: Analysis of PDEs (math.AP); Populations and Evolution (q-bio.PE)

[90] arXiv:0806.3835 (cross-list from physics.bio-ph) [pdf, other]

Title: Osmotic pressure: resisting or promoting DNA ejection from phage

Meerim Jeembaeva (L.U.), Martin Castelnovo (Phys-ENS), Frida Larsson (L.U.), Alex Evilevitch (L.U.)

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

[91] arXiv:0806.4440 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Exact solution of a stochastic SIR model

Gunter M. Schütz, Marian Brandau, Steffen Trimper

Comments: 19 pages, 4 figures

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

[92] arXiv:0806.4552 (cross-list from quant-ph) [pdf, other]

Title: Entanglement and intra-molecular cooling in biological systems? - A quantum thermodynamic perspective

Hans J. Briegel, Sandu Popescu

Comments: Section 2 expanded. A few references added. 20 pages, 6 figures

Subjects: Quantum Physics (quant-ph); Biomolecules (q-bio.BM)

[93] arXiv:0806.4565 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: The SIRI stochastic model with creation and annihilation operators

Nico Stollenwerk, Maira Aguiar

Comments: 10 pages

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