An adaptive algorithm for simulation of stochastic reaction-diffusion processes

作者：Ferm Lars; Hellander Andreas; Lotstedt Per^*

来源：Journal of Computational Physics, 2010, 229(2): 343-360.

DOI：10.1016/j.jcp.2009.09.030

• Master equation
• Chemical reactions
• Diffusion
• Hybrid method
• Adaptivity
• URDME

We propose an adaptive hybrid method suitable for stochastic simulation of diffusion dominated reaction-diffusion processes. For such systems, simulation of the diffusion requires the predominant part of the computing time. In order to reduce the computational work, the diffusion in parts of the domain is treated macroscopically, in other parts with the tau-leap method and in the remaining parts with Gillespie's stochastic simulation algorithm (SSA) as implemented in the next subvolume method (NSM). The chemical reactions are handled by SSA everywhere in the computational domain. A trajectory of the process is advanced in time by an operator splitting technique and the timesteps are chosen adaptively. The spatial adaptation is based on estimates of the errors in the tau-leap method and the macroscopic diffusion. The accuracy and efficiency of the method are demonstrated in examples from molecular biology where the domain is discretized by unstructured meshes.

• 出版日期2010-1-20