A Guide to Modeling Reaction-Diffusion of Molecules with the E-Cell System
The E-Cell System is an advanced platform intended for mathematical modeling and simulation of well-stirred biochemical systems. We have recently implemented the Spatiocyte method as a set of plug in modules to the E-Cell System, allowing simulations of complicated multicompartment dynamical processes with inhomogeneous molecular distributions. With Spatiocyte, the diffusion and reaction of each molecule can be handled individually at the microscopic scale. Here we describe the basic theory of the method and provide the installation and usage guides of the Spatiocyte modules. Where possible, model examples are also given to quickly familiarize the reader with spatiotemporal model building and simulation.
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