Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes in similar manners as in real biochemical systems.
Smoldyn was initially released in 2003 as a simulator that represented chemical reactions between diffusing particles in rectilinear volumes.
[3] Further development added support for surfaces,[1] multiscale simulation[4] molecules with excluded volume,[2] rule-based modeling[5] and C/C++ and Python APIs.
Smoldyn has been developed primarily by Steve Andrews, over the course of multiple research and teaching positions.
[7] Smoldyn has been refactored twice to run on GPUs, each time offering approximately 200-fold speed improvements.