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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.
The rxnparam.c and SurfaceParam.c source code files are in the public domain. The Next Subvolume module is Copyright 2012 by Martin Robinson and is distributed under the Gnu LGPL license. The rest of the code is Copyright 2003-2015 by Steven Andrews and also distributed under the Gnu LGPL. Contact us if you would like Smoldyn to use a different license.