Smoldyn 2.61 – Cell-scale Biochemical Simulator

Smoldyn 2.61


Smoldyn is a spatial stochastic simulator for investigating chemical and biochemical reaction networks in complex geometries. It uses a Brownian dynamics algorithm for reaction-diffusion systems at the Smoluchowski level of approximation. A significant amount of effort has gone into making reaction kinetics as accurate as possible.It simulates each molecule of interest individually to capture natural stochasticity and for nanometer-scale spatial resolution. It treats other molecules implicity, so it can simulate tens of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system.


Smoldyn is both more accurate and faster than other particle-based simulators. Smoldyn’s unique features include: a “virtual experimenter” who can manipulate or measure the simulated system, support for spatial compartments, molecules with excluded volume, and simulations in 1, 2, or 3 dimensions.


Steve Andrews


Command Line


  • Windows / Linux / Mac OsX





Multiscale Reaction-Diffusion Simulations with Smoldyn.
Robinson M, Andrews SS, Erban R.
Bioinformatics. 2015 Mar 18. pii: btv149.

Detailed simulations of cell biology with Smoldyn 2.1.
Andrews SS, Addy NJ, Brent R, Arkin AP.
PLoS Comput Biol. 2010 Mar 12;6(3):e1000705. doi: 10.1371/journal.pcbi.1000705.

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