title: Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network.
abstract: Brownian Dynamics algorithms have been widely used for simulating systems in soft-condensed matter physics. In recent times, their application has been extended to the simulation of coarse-grained models of biochemical networks. In these models, components move by diffusion and interact with one another upon contact. However, when reactions are incorporated into a Brownian dynamics algorithm, care must be taken to avoid violations of the detailed-balance rule, which would introduce systematic errors in the simulation. We present a Brownian dynamics algorithm for simulating reaction-diffusion systems that rigorously obeys detailed balance for equilibrium reactions. By comparing the simulation results to exact analytical results for a bimolecular reaction, we show that the algorithm correctly reproduces both equilibrium and dynamical quantities. We apply our scheme to a "push-pull" network in which two antagonistic enzymes covalently modify a substrate. Our results highlight that spatial fluctuations of the network components can strongly reduce the gain of the response of a biochemical network.
authors.affiliation: FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.
authors.forename: Marco J
authors.initials: MJ
authors.lastname: Morelli
authors.forename: Pieter Rein
authors.initials: PR
authors.lastname: ten Wolde
mesh_terms: D000465:Algorithms; D004058:Diffusion; D008956:Models, Chemical; D013269:Stochastic Processes