MesoRD is a tool for stochastic simulation of reactions and diffusion . 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 .
MesoRD source code is hosted at Sourceforge. Pre-built binaries are available for Windows.
Please use reference  when citing MesoRD and reference  when citing the Next Subvolume Method.
Have you used MesoRD? Let us know what you think!
Visualize your model results with our MATLAB toolbox.
- David Fange and Johan Elf (2006) Noise induced Min phenotypes in
E. coli. PLoS Comp. Biol.
- Johan Hattne, David Fange and Johan Elf (2005) Stochastic reaction-diffusion
simulation with MesoRD. Bioinfomatics
- Elf and Ehrenberg (2004) Spontaneous separation of bi-stable
biochemical systems into spatial domains of opposite phases. Systems Biolog.
Next Subvolume Method algorithm
- Elf et al. (2003) Mesoscopic reaction-diffusion in
intracellular signaling. SPIE
- Gardiner, C.: Handbook of stochastic Methods. Second edition
(Springer-Verlag. Berlin, 1985).
- Nicolis, G. and Prigogine, I.: Self-organization in
nonequilibrium systems. (John Wiley & sons. New York,
- Baras, F. and Mansour, M.M. (1997) Microscopic simulation of chemical
instabilities, Advances in Chemical Physics, 100:393-475.
- Fange D., Berg O.G., Sjöberg P., Elf J. (2010) Stochastic
reaction-diffusion kinetics in the microscopic limit. PNAS,
- 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.