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.

WWW: http://www.smoldyn.org/