Coupled Mesoscopic and Microscopic Simulation of Stochastic Reaction-Diffusion Processes in Mixed Dimensions

Andreas Hellander, Stefan Hellander, and Per Lötstedt

2011

Abstract:

We present a new simulation algorithm that allows for dynamic switching between a mesoscopic and a microscopic modeling framework for stochastic reaction-diffusion kinetics. The more expensive and more accurate microscopic model is used only for those species and in those regions in space where there is reason to believe that a microscopic model is needed to capture the dynamics correctly. The microscopic algorithm is extended to simulation on curved surfaces in order to model reaction and diffusion on membranes. The accuracy of the method on and near a spherical membrane is analyzed and evaluated in a numerical experiment. Two biologically motivated examples are simulated in which the need for microscopic simulation of parts of the system arises for different reasons. First, we apply the method to a model of the phosphorylation reactions in a MAPK signaling cascade where microscale methods are necessary to resolve fast rebinding events. Then a model is considered for transport of a species over a membrane coupled to reactions in the bulk. The new algorithm attains an accuracy similar to a full microscopic simulation by handling critical interactions on the microscale, but at a significantly reduced cost by using the mesoscale framework for most parts of the biological model.

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