About

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]. Since version 0.2.0 MesoRD also supports mean-field simulations.

Simulation of the Min-system in E. coli

MesoRD 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 MesoRD

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

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.

Acknowledgements

The development of MesoRD was funded by a research grant from the Swedish Research Council (Vetenskapsrådet) to Måns Ehrenberg, Uppsala University.