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cottrell's biorefs [75 articles]

Recent papers added to cottrell's library classified by the tag biorefs. You can also see everyone's biorefs.
  • Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach
    (23 Dec 2007)
    by Jérémie Bourdon, Damien Eveillard, Samuel Gabillard, Theo Merle
    posted to biomath biorefs by cottrell on 2008-01-02 19:41:48 as **
  • Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites
    (9 Aug 2007)
    by Vahid Rezania, Jack Tuszynski, Michael Hendzel
    posted to binding biorefs spatial-simulation by cottrell on 2007-08-31 00:38:25 as **
  • Enzyme localization can drastically affect signal amplification in signal transduction pathways
    (27 Aug 2007)
    by Siebe B van Albada, Pieter
    posted to biorefs enzyme gene_expression localization by cottrell on 2007-08-28 15:09:20 as **
  • A modified Next Reaction Method for simulating systems with time varying rate constants and systems with delays
    (2 Aug 2007)
    by David F Anderson
    posted to biorefs next-reaction-method simulation by cottrell on 2007-08-03 14:37:22 as **
  • An accurate and efficient tau-leaping procedure for the simulation of chemical reaction systems
    (2 Aug 2007)
    by David F Anderson
    posted to biorefs reaction simulation tau-leaping by cottrell on 2007-08-03 14:36:50 as ** along with 1 person margaritis
  • Particle Systems and Reaction-Diffusion Equations
    The Annals of Probability, Vol. 22, No. 1. (1994), pp. 289-333.
    by R Durrett, C Neuhauser
    posted to biorefs reaction-diffusion by cottrell on 2007-08-02 21:05:42 as **
  • Systematic analysis of the multivariate master equation for a reaction-diffusion system
    Journal of Statistical Physics, Vol. 22, No. 4. (1 April 1980), pp. 495-512.
    by G Nicolis, M Malek-Mansour
    posted to biorefs master-equation reaction-diffusion by cottrell on 2007-08-02 20:19:26 as **
  • Spatial Epidemics: Critical Behavior in One Dimension
    (25 Jul 2007)
    by Steven P Lalley
    posted to biorefs interacting-particles spatial stochastic by cottrell on 2007-07-27 23:04:05 as **
  • Stochastic Interacting Systems: Contact, Voter and Exclusion Processes (Grundlehren der mathematischen Wissenschaften)
    (15 November 1999)
    by Thomas M Liggett
    posted to biorefs interacting-diffusion interacting-particles by cottrell on 2007-07-27 22:06:41 as **
  • Interacting Particle Systems (Classics in Mathematics)
    (22 December 2004)
    by Thomas M Liggett
    posted to biorefs interacting-diffusion interacting-particles by cottrell on 2007-07-27 22:05:59 as **
  • Nonlinear Stochastic PDE's: Hydrodynamic Limit and Burgers' Turbulence (The IMA Volumes in Mathematics and its Applications)
    (01 December 1995)
    by Tadahisa Funaki, Wojbor A Woyczynski
    posted to biorefs reaction-diffusion spde by cottrell on 2007-07-27 19:48:27 as **
  • A model for the interaction of two chemicals
    Journal of Theoretical Biology, Vol. 238, No. 3. (7 February 2006), pp. 652-656.
    by Pali Sen, Denis Bell
    posted to biorefs reaction-diffusion by cottrell on 2007-07-26 14:51:17 as **
  • Coarse-grained stochastic processes and Monte Carlo simulations in lattice systems
    Journal of Computational Physics, Vol. 186, No. 1. (20 March 2003), pp. 250-278.
    by Markos A Katsoulakis, Andrew J Majda, Dionisios G Vlachos
    posted to biorefs reaction-diffusion by cottrell on 2007-07-03 16:56:15 as **
  • Temporal acceleration of spatially distributed kinetic Monte Carlo simulations
    Journal of Computational Physics, Vol. 211, No. 2. (20 January 2006), pp. 596-615.
    by Abhijit Chatterjee, Dionisios G Vlachos
    posted to biorefs reaction-diffusion by cottrell on 2007-07-03 16:56:02 as **
  • Monte Carlo Algorithms for Complex Surface Reaction Mechanisms: Efficiency and Accuracy
    Journal of Computational Physics, Vol. 173, No. 1. (10 October 2001), pp. 302-321.
    by JS Reese, S Raimondeau, DG Vlachos
    posted to biorefs reaction-diffusion by cottrell on 2007-07-03 16:55:10 as **
  • Mesoscopic reaction-diffusion in intracellular signaling
    Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems, Vol. 5110, No. 1. (2003), pp. 114-124.
    by Johan Elf, Andreas Doncic, Mans Ehrenberg
    edited by Sergey M Bezrukov, Hans Frauenfelder, Frank Moss
    posted to biorefs reaction-diffusion by cottrell on 2007-06-26 20:23:22 as **
  • Analysis of reaction-diffusion systems by the method of linear determining equations
    Computational Mathematics and Mathematical Physics, Vol. 47, No. 2. (11 February 2007), pp. 249-261.
    by A Schmidt
    posted to biorefs reaction-diffusion by cottrell on 2007-06-26 19:32:44 as **
  • Pullback attractors and extremal complete trajectories for non-autonomous reaction-diffusion problems
    Journal of Differential Equations, Vol. 238, No. 2. (15 July 2007), pp. 289-337.
    by James C Robinson, Anibal Rodriguez-Bernal, Alejandro Vidal-Lopez
    posted to biorefs reaction-diffusion by cottrell on 2007-06-26 17:54:18 as *****
  • Coarse-grained models for proteins.
    Curr Opin Struct Biol, Vol. 15, No. 2. (April 2005), pp. 144-150.
    by V Tozzini
    posted to biorefs by cottrell on 2007-06-08 18:43:30 as ** along with 6 people baaden aqeel ltrabuco simone choonpeng iantunbridge
  • Bridging from molecular simulation to biochemical networks
    Current Opinion in Structural Biology, Vol. 17, No. 2. (April 2007), pp. 166-172.
    by Matthias Stein, Razif R Gabdoulline, Rebecca C Wade
    posted to biorefs simulation by cottrell on 2007-06-08 17:52:39 as read
  • Computer simulation of steady-state diffusion-controlled reaction rates in dispersions of static sinks: Effect of sink sizes
    The Journal of Chemical Physics, Vol. 93, No. 4. (1990), pp. 2658-2663.
    by Lihua Zheng, Yee C Chiew
    posted to biorefs reaction_rates by cottrell on 2007-06-08 17:44:58 as **
  • Coarse-graining approximation for simulating surface reaction kinetics in particulate systems
    Computational Materials Science, Vol. 38, No. 2. (December 2006), pp. 369-373.
    by Jeffrey W Bullard
    posted to biorefs coarse_graining reaction_rates by cottrell on 2007-06-08 17:41:10 as **
  • Introducing effective reaction rates to account for the inefficient mixing of the convective boundary layer
    Atmospheric Environment, Vol. 39, No. 3. (January 2005), pp. 445-461.
    by JF Vinuesa, Vila-Guerau
    posted to biorefs reaction_rates by cottrell on 2007-06-08 17:38:13 as **
  • A Reaction-Diffusion Model to Study RNA Motion by Quantitative Fluorescence Recovery after Photobleaching
    Biophys. J., Vol. 92, No. 8. (15 April 2007), pp. 2694-2703.
    by Jose Braga, James G Mcnally, Maria Carmo-Fonseca
    posted to biorefs by cottrell on 2007-04-19 21:39:43 as **
  • Stochastic mRNA Synthesis in Mammalian Cells
    PLoS Biology, Vol. 4, No. 10. (1 October 2006), e309.
    by Arjun Raj, Charles S Peskin, Daniel Tranchina, Diana Y Vargas, Sanjay Tyagi
    posted to biorefs by cottrell on 2007-04-19 19:30:45 as ** along with 7 people jjray nirfriedman madhadron balabu qfwills johncumbers margaritis
  • Statistical Methods for Biostatistics and Related Fields
    posted to biorefs biostatistical by cottrell on 2007-03-07 20:08:18 as **
  • A method for estimating stochastic noise in large genetic regulatory networks
    Bioinformatics, Vol. 21, No. 2., 208.
    by David Orrell, Stephen Ramsey, Pedro d de Atauri, Hamid Bolouri
    posted to biorefs dizzy simulation stochastic by cottrell on 2007-03-03 15:31:33 as ** along with 1 person csgillespie
  • On a Fourier space master equation for Navier-Stokes turbulence
    Zeitschrift für Physik B Condensed Matter, Vol. V100, No. 3. (17 June 1996), pp. 461-468.
    by Heinz-Peter Breuer, Francesco Petruccione, Frithjof Weber
    posted to stochastic navier-stokes master-equation biorefs by cottrell on 2007-01-25 17:17:44 as **
  • Discrete Green's functions for products of regular graphs
    (8 Sep 2003)
    by Robert B Ellis
    posted to torus random-walk hitting-time graph biorefs by cottrell on 2007-01-21 06:54:26 as **
  • Particle-Based Stochastic Simulation in Systems Biology
    Current Bioinformatics, Vol. 1, No. 3. (August 2006), pp. 315-320.
    by P Tolle, Dominic, Le Novere, Nicolas
    posted to simulation particle-based biorefs by cottrell on 2007-01-20 22:16:24 as **
  • Perfect Sampling of the Chemical Master Equation for Gene Regulatory Networks
    (27 Oct 2006)
    by Martin Hemberg, Mauricio Barahona
    posted to ssa sampling biorefs by cottrell on 2007-01-20 22:15:53 as **
  • Wick-Stochastic Finite Element Solution of Reaction-Diffusion Problems
    J. Comp. Applied Math
    by Manouzi
    posted to wick-stochastic spde finite-element biorefs by cottrell on 2007-01-20 22:09:06 as **
  • A general method for the computation of probabilities in systems of first order chemical reactions
    The Journal of Chemical Physics, Vol. 122, No. 10. (2005)
    by Xueying Zhang, Katrien De Cock, Monica F Bugallo, Petar M Djuric
    posted to biorefs by cottrell on 2007-01-20 21:43:25 as **
  • Bayesian Inference for Stochastic Kinetic Models Using a Diffusion Approximation
    Biometrics, Vol. 61, No. 3. (2005), pp. 781-788.
    by A Golightly, DJ Wilkinson
    posted to biorefs by cottrell on 2007-01-20 21:42:14 as ** along with 1 person petermilner
  • Moment equations for a spatially extended system of two competing species
    The European Physical Journal B - Condensed Matter and Complex Systems, Vol. V50, No. 1. (March 2006), pp. 199-203.
    by D Valenti, L Schimansky-Geier, X Sailer, B Spagnolo
    posted to biorefs networks queing by cottrell on 2006-11-21 21:40:06 as **
  • Statistical Modeling and Analysis for Complex Data Problems (Gerad 25th Anniversary Series)
    (01 January 2005)
    by P Duchesne, B Remillard
    posted to biorefs book process stochastic by cottrell on 2006-10-30 19:43:14 as **
  • Feynman-Kac Formulae - Genealogical and Interacting Particle Systems with Applications
    by Piere Del Moral
    posted to biorefs book process stochastic by cottrell on 2006-10-30 19:41:35 as **
  • Stochastics in Finite and Infinite Dimensions (Trends in Mathematics)
    (15 October 2000)
    by Takeyuki Hida
    posted to biorefs book process stochastic by cottrell on 2006-10-30 19:39:44 as **
  • On the large scale behavior of super-Brownian motion in three dimensions with a single point source
    (26 Jul 2006)
    by Klaus Fleischmann, Carl Mueller, Pascal Vogt
    posted to biorefs branching-diffusion by cottrell on 2006-10-06 21:02:20 as **
  • Reaction volume statistics for rate processes in disordered systems. Thermodynamic analogies and extracting information from experimental data
    Chemical Physics, Vol. 243, No. 3. (15 May 1999), pp. 273-294.
    by Marcel O Vlad, John Ross, Andrzej Plonka
    posted to biorefs reaction-diffusion by cottrell on 2006-10-06 01:45:07 as **
  • Microscopic spatial correlations induced by external noise in a reaction-diffusion system
    Physica A: Statistical and Theoretical Physics, Vol. 188, No. 1-3. (1 September 1992), pp. 386-403.
    by Charles R Doering
    posted to biorefs reaction-diffusion by cottrell on 2006-10-06 01:41:16 as **
  • Fluctuations and correlations in a diffusion-reaction system: Exact hydrodynamics
    Journal of Statistical Physics, Vol. V65, No. 5. (1 December 1991), pp. 953-970.
    by Charles R Doering, Martin A Burschka, Werner Horsthemke
    posted to biorefs reaction-diffusion by cottrell on 2006-10-06 01:30:32 as **
  • On Exact Solutions of a Class of Reaction-Diffusion Equations
    IMA J Appl Math, Vol. 33, No. 2. (1 September 1984), pp. 153-168.
    by BD Sleeman, E Tuma
    posted to biorefs reaction-diffusion by cottrell on 2006-10-06 01:24:24 as **
  • Stochastic gene expression in a single cell.
    Science, Vol. 297, No. 5584. (16 August 2002), pp. 1183-1186.
    by MB Elowitz, AJ Levine, ED Siggia, PS Swain
    posted to biorefs gene_expression by cottrell on 2006-10-02 19:01:54 as ** along with 16 people and 3 groups mjoach austin jjray dylanwalker tvdbulck balicea jiny wilvc madhadron mmt litam mhucka timflutre margaritis roland_ewald ptupper UWNICU dIEMoSIRIS MoSi-Rostock
  • The role of proofreading in signal transduction specificity.
    Biophys J, Vol. 82, No. 6. (June 2002), pp. 2928-2933.
    by PS Swain, ED Siggia
    posted to biorefs gene_expression by cottrell on 2006-10-02 19:00:28 as **
  • Viscosity solutions for the porous medium equation
    Vol. 65 (1999), pp. 13-26.
    by Luis Caffarelli, Juan L Vazquez
    posted to biorefs medium pde porous by cottrell on 2006-09-13 19:24:46 as **
  • Viscosity solutions for quasilinear degenerate parabolic equations of porous medium type
    Indiana Univ. Math. J., Vol. 54, No. 3. (2005), pp. 817-860.
    by Cristina Brändle, Juan L Vázquez
    posted to biorefs medium pde porous by cottrell on 2006-09-12 23:11:10 as **
  • Perspectives in Nonlinear Diffusion. Between Analysis, Physics and Geometry
    by Vázquez
    posted to biorefs medium pde porous by cottrell on 2006-09-12 23:00:22 as **
  • The Evolution and Measurement of a Population of Pairs
    Journal of Applied Probability, Vol. 32, No. 4. (1995), pp. 1048-1062.
    by Eric Jakeman, Sean Phayre, Eric Renshaw
    posted to biorefs networks by cottrell on 2006-09-08 22:22:14 as **
  • The evolution of a batch-immigration death process subject to counts
    by Colin Gillespie, Renshaw
    posted to biorefs networks by cottrell on 2006-09-08 22:11:21 as **
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