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Fast simulation of Brownian dynamics in a crowded environment

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Original languageEnglish
Article number024105
JournalThe Journal of Chemical Physics
Volume146
DOIs
Publication statusPublished - 11 Jan 2017

Abstract

Brownian dynamics simulations are an increasingly popular tool for understanding spatiallyextended biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion e_ects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into threedimensional 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 \crowderfree" method to dramatically increase simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the case 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.

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