MesoRD - Mesoscopic Reaction Diffusion Simulator
MesoRD - Mesoscopic Reaction Diffusion Simulator |
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AboutMesoRD is a tool for stochastic simulation of reactions and diffusion [2]. In particular, it is an implementation of the Next Subvolume Method [3, 4], which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation [5, 6, 7]. Following version 0.2.0 MesoRD also supports mean-field simulations. Starting with version 1.0, MesoRD supports high spatial resolution for bi-molecular reactions [8]. Simulation of the Min-system in E. coliMesoRD has been used to model the stochastic contribution to different mutant phenotypes in the Min-system in E. coli [1]. Visualisation of a stochastic simulation of a wild type E. coli cell is shown below. MinD on the cell membrane is shown in red and MinE in complex with MinD on the membrane is shown in blue. 
Citing MesoRDPlease use reference [2] when citing MesoRD and reference [3] when citing the Next Subvolume Method. Contact InformationIf you have questions and/or comments, or just want to compliment the software, please send e-mail to either david or johan. References[1] David Fange and Johan Elf (2006) Noise induced Min phenotypes in E. coli. PLoS Comp. Biol. link [2] Johan Hattne, David Fange and Johan Elf (2005) Stochastic reaction-diffusion simulation with MesoRD Bioinfomatics. pdf [3] Elf and Ehrenberg (2004) Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases Systems Biology 2. pdf, Supplementary material: Next Subvolume Method algorithm [4] Elf et al. (2003) Mesoscopic reaction-diffusion in intracellular signaling SPIE 5110 114-124 2003. pdf [5] Gardiner, C.: Handbook of stochastic Methods. Second edition (Springer-Verlag. Berlin, 1985). [6] Nicolis, G. and Prigogine, I.: Self-organization in nonequilibrium systems. (John Wiley & sons. New York, 1977). [7] Baras, F. and Mansour, M.M. (1997) Microscopic simulation of chemical instabilities, Advances in Chemical Physics, 100:393-475. [8] Fange D., Berg O.G., Sjöberg P., Elf J. (2010) Stochastic reaction-diffusion kinetics in the microscopic limit. PNAS, 107:19820-5. [9] Takahashi K, Tanase-Nicola S, Ten Wolde PR (2010) Spatio-temporal correlations can drastically change the response of a MAPK pathway. PNAS, 107:2473-2478 AcknowledgementsThe development of MesoRD up to version 0.2.1 was funded by grants from the Swedish Research Council (Vetenskapsrådet) to Måns Ehrenberg, Uppsala University. The development of later versions has been funded by ERC grant "TF kinetics in vivo" and SciLifeLab-Uppsala. 
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