What Smoldyn is
Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds 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 easy to use and easy to install. It is 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.
Smoldyn 2.31 released September 9, 2013
BBSRC/NSF proposal for chromatin dynamics
Steve Andrews is on the job market
Oscillations of Min-proteins in micropatterned environments: a three-dimensional particle-based stochastic simulation approach
Max Hoffmann and Ulrich S. Schwarz, Soft Matter 10:2388, 2014One way in which
Smoldyn is written and maintained by Steve Andrews. Development has been supported by the National Institutes of Health, the U.S. Department of Energy, the National Science Foundation, and the MITRE Corporation, albeit never by funding that was dedicated specifically for this purpose.