Simulation of stochastic reaction-diffusion processes on unstructured meshes
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Brownian motionchemical systemdiffusionfinite element methodhybrid algorithmhybrid methodmaster equationmolecular biologynumerical examplesreaction rate equationsunstructured mesh
Reaction-diffusion equations (35K57) PDEs with randomness, stochastic partial differential equations (35R60) Stochastic partial differential equations (aspects of stochastic analysis) (60H15) Computational methods for stochastic equations (aspects of stochastic analysis) (60H35) Biochemistry, molecular biology (92C40)
Abstract: Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic level, the master equation for a well stirred chemical system is combined with Brownian motion in space to obtain the reaction-diffusion master equation. The space is covered by an unstructured mesh and the diffusion coefficients on the mesoscale are obtained from a finite element discretization of the Laplace operator on the macroscale. The resulting method is a flexible hybrid algorithm in that the diffusion can be handled either on the meso- or on the macroscale level. The accuracy and the efficiency of the method are illustrated in three numerical examples inspired by molecular biology.
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