A Gaussian jump process formulation of the reaction-diffusion master equation enables faster exact stochastic simulations

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

Abstract

We propose a Gaussian jump process model on a regular Cartesian lattice for the diffusion part of the Reaction-Diffusion Master Equation (RDME). We derive the resulting Gaussian RDME (GRDME) formulation from analogy with a kernel-based discretization scheme for continuous diffusion processes and quantify the limits of its validity relative to the classic RDME. We then present an exact stochastic simulation algorithm for the GRDME, showing that the accuracies of GRDME and RDME are comparable, but exact simulations of the GRDME require only a fraction of the computational cost of exact RDME simulations. We analyze the origin of this speedup and its scaling with problem dimension. The benchmarks suggest that the GRDME is a particularly beneficial model for diffusion-dominated systems in three dimensional spaces, often occurring in systems biology and cell biology.

Details

Original languageEnglish
Article number194110
JournalJournal of Chemical Physics
Volume157
Issue number19
Publication statusPublished - 21 Nov 2022
Peer-reviewedYes

External IDs

PubMed 36414462
ORCID /0000-0003-4414-4340/work/159608275