Space-time histories approach to fast stochastic simulation of bimolecular reactions.

Abstract

Computational models of reaction-diffusion systems involving low copy numbers or strongly heterogeneous molecular spatial distributions, such as those frequently found in cellular signaling pathways, require approaches that account for the stochastic dynamics of individual particles, as opposed to approaches representing them through their average concentrations. Efforts to remedy the high computational cost associated with particle-based stochastic approaches by taking advantage of Green's functions are hampered by the need to draw random numbers from complicated, and therefore costly, non-standard probability distributions to update particle positions. Here, we introduce an approach that permits the reconstruction of entire molecular trajectories, including bimolecular encounters, in retrospect, after a simulated time step, while avoiding inefficient draws from non-standard distributions. This means that highly accurate stochastic simulations can be performed for system sizes that would be prohibitively costly to simulate with conventional Green's function based methods. The algorithm applies equally well to one, two, and three dimensional systems and can be readily extended to include deterministic forces specified by an interaction potential, such as the Coulomb potential.