Fast simulation of Brownian dynamics in a crowded environment

TL;DR

This paper introduces a fast, crowder-free simulation method for Brownian dynamics in crowded biochemical environments, significantly reducing computation time while maintaining accuracy.

Contribution

The authors develop a novel crowder-free approach that eliminates explicit crowder simulation, enabling faster and equally accurate Brownian dynamics simulations in crowded cellular environments.

Findings

The crowder-free method achieves large speed increases.

Simulations show comparable accuracy to traditional methods.

Applicable to point particles and volume-occupying particles.

Abstract

Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed 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 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 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. We use simulations of simple chemical reaction networks to confirm that our simplification is just as accurate as the original algorithm, and that it corresponds to a large speed increase.