Free Simulation Tools

GFRD (Green's Function Reaction Dynamics) decomposes the many-body reaction-diffusion problem into one- and two-body problems that can be solved analytically using Green’s Function, and uses these functions to set up an event-driven algorithm.  Find it @ http://gfrd.org

MesoRD (Mesoscopic Reaction Diffusion Simulator) is a tool for stochastic simulation of reactions and diffusion. In particular, it is an implementation of the Next Subvolume Method, which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation.  Find it @ http://mesord.sourceforge.net/

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.  Find it @ http://www.smoldyn.org/