Brownian dynamics simulations of an idealized chemical reaction network under spatial confinement and crowding conditions

Abstract

We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of inert crowders has a non-nontrivial effect on the dynamics of the network and, consequently, that effective modeling efforts aiming at a general understanding of the behavior of biochemical networks in vivo should be stochastic in nature and based on an explicit representation of both spatial confinement and macromolecular crowding.

arXiv comment20 pages, 8 figures, 1 table

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Cited by in corpus (2)

• Learning Dynamic Boltzmann Distributions as Reduced Models of Spatial Chemical Kinetics
• Learning Moment Closure in Reaction-Diffusion Systems with Spatial Dynamic Boltzmann Distributions