GFRD decomposes the many-body reaction-diffusion problem into one- and two-body problems that can be solved analytically using Green’s Functions [1,2,3,4]. These Green’s Functions are then employed to set up an event-driven algorithm, which makes it possible to take large jumps in time and space when the particles are far apart from each other. GFRD can be up to 6 orders of magnitude faster than conventional algorithms based on Brownian Dynamics .
Movie 1. eGFRD in action.
The eGFRD algorithm is generic and can be applied to a wide variety of reaction-diffusion problems, including those in population dynamics, evolution, and soft-condensed matter physics. The scheme presented here has been specifically designed to simulate biochemical networks. Recently, we have completely rewritten the code in Modern C++, resulting a very fast simulator.
The eGFRD algorithm was originally developed by the group of Takahashi at the Riken institute in Japan and the group of Ten Wolde at AMOLF in The Netherlands.
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