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.
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.
