Computer Simulation System for Modeling of Reaction-Diffusion of Biochemical Pathways

We have been developing a computer simulation system for an efficient modeling and analysis of intracellular processes involving transportation of molecules. Recently, many experimental studies focus on spatio-temporal dynamics of molecules that contribute to functions of biological pathways such as signal transduction pathways. A number of these studies reported localization of molecules. However, conventional modeling techniques which are based on simulations of ordinary differential equations (ODE) could only describe averaged dynamics since they assume that molecules are uniformly distributed. To improve the treatment of spatial information, partial differential equation (PDE) [3] and stochastic simulation methods [1, 4] were developed. Here we present our method and technology for stochastic simulation of reaction-diffusion problems of biochemical pathways. In particular, we introduce a plan to develop a special purpose computer which enables us to simulate reaction-diffusion problems involving more than 10 molecules.