Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting.

ABSTRACT: The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing

SUBMITTER: Hellander A 

PROVIDER: S-EPMC4746020 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature