Flexible and efficient simulation of stochastic reaction-diffusion processes in cells

The reaction-diffusion master equation (RDME) is a popular model in systems biology. In the RDME, diffusion is modeled as discrete jumps between voxels in the computational domain. However, it has been demonstrated that a more fine-grained model is required to resolve all the dynamics of some highly diffusion-limited systems.

In Greenʼs Function Reaction Dynamics (GFRD), a method based on the Smoluchowski model, diffusion is modeled continuously in space.

This will be more accurate at fine scales, but also less efficient than a discrete-space model.

We have developed a hybrid method, combining the RDME and the GFRD method, making it possible to do the more expensive fine-grained simulations only for the species and in the parts of space where it is required in order to resolve all the dynamics, and more coarse-grained simulations where possible. We have applied this method to a model of a MAPK-pathway, and managed to reduce the number of molecules simulated with GFRD by orders of magnitude and without an appreciable loss of accuracy.