Literature DB >> 15817692

Stochastic reaction-diffusion simulation with MesoRD.

Johan Hattne1, David Fange, Johan Elf.   

Abstract

UNLABELLED: MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular, it is an implementation of the next subvolume method, which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation. AVAILABILITY: MesoRD is free software, written in C++ and licensed under the GNU general public license (GPL). MesoRD runs on Linux, Mac OS X, NetBSD, Solaris and Windows XP. It can be downloaded from http://mesord.sourceforge.net. CONTACT: johan.elf@icm.uu.se; johan.hattne@embl-hamburg.de SUPPLEMENTARY INFORMATION: 'MesoRD User's Guide' and other documents are available at http://mesord.sourceforge.net.

Mesh：

Year:  2005        PMID： 15817692     DOI： 10.1093/bioinformatics/bti431

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  110 in total

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5.  Reaction rates for a generalized reaction-diffusion master equation.

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6.  Discrete-continuous reaction-diffusion model with mobile point-like sources and sinks.

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7.  Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase.

Authors:  Mats H M Olsson; Arieh Warshel
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8.  Hybrid stochastic and deterministic simulations of calcium blips.

Authors:  S Rüdiger; J W Shuai; W Huisinga; C Nagaiah; G Warnecke; I Parker; M Falcke
Journal:  Biophys J       Date:  2007-05-11       Impact factor: 4.033

9.  Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm.

Authors:  Douglas Ridgway; Gordon Broderick; Ana Lopez-Campistrous; Melania Ru'aini; Philip Winter; Matthew Hamilton; Pierre Boulanger; Andriy Kovalenko; Michael J Ellison
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10.  A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation.

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