title: Fast simulation of Brownian dynamics in a crowded environment.
abstract: Brownian dynamics simulations are an increasingly popular tool for understanding spatially extended biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics (BD) simulations; however these methods are extremely slow owing to the sheer number of possible collisions between particles. Here we propose a rigorous "crowder-free" method to dramatically increase the simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the cases where the reactive particles are point particles, and where they themselves occupy a volume. Using simulations of simple chemical reaction networks, we show that the "crowder-free" method is up to three orders of magnitude faster than conventional BD and yet leads to nearly indistinguishable results from the latter.
authors.affiliation: School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom.
authors.forename: Stephen
authors.initials: S
authors.lastname: Smith
authors.affiliation: School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom.
authors.forename: Ramon
authors.initials: R
authors.lastname: Grima
mesh_terms: D000465:Algorithms; D001669:Biochemical Phenomena; D002477:Cells / Q000737:chemistry; D004058:Diffusion; D056004:Molecular Dynamics Simulation; D011336:Probability