Mesoscopic Reaction Diffusion Simulator

About MesoRD

MesoRD 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].

Download MesoRD

MesoRD source code is hosted at Sourceforge. Pre-built binaries are available for Windows.

Citing MesoRD

Please use reference [2] when citing MesoRD and reference [3] when citing the Next Subvolume Method.

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MATLAB Toolbox

Visualize your model results with our MATLAB toolbox.

References

1. David Fange and Johan Elf (2006) Noise induced Min phenotypes in E. coli. PLoS Comp. Biol.
2. Johan Hattne, David Fange and Johan Elf (2005) Stochastic reaction-diffusion simulation with MesoRD. Bioinfomatics
3. Elf and Ehrenberg (2004) Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. Systems Biolog. Supplementary material: Next Subvolume Method algorithm
4. Elf et al. (2003) Mesoscopic reaction-diffusion in intracellular signaling. SPIE
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.