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1887

access icon free Excluded volume effects in on- and off-lattice reaction–diffusion models

© The Institution of Engineering and Technology
Received 26/05/2016, Accepted 25/10/2016, Revised 24/10/2016, Published 01/11/2016

Mathematical models are important tools to study the excluded volume effects on reaction–diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off-lattice Brownian dynamics become computationally expensive in crowded environments. In this study, the authors therefore investigate to which extent on-lattice approximations, the so-called cellular automata models, can be used to simulate reactions and diffusion in the presence of crowding molecules. They show that the diffusion is most severely slowed down in the off-lattice model, since randomly distributed obstacles effectively exclude more volume than those ordered on an artificial grid. Crowded reaction rates can be both increased and decreased by the grid structure and it proves important to model the molecules with realistic sizes when excluded volume is taken into account. The grid artefacts increase with increasing crowder density and they conclude that the computationally more efficient on-lattice simulations are accurate approximations only for low crowder densities.

Inspec keywords: cellular automata; molecular biophysics; biodiffusion; reaction-diffusion systems; cellular biophysics; Brownian motion; molecular configurations

Other keywords: mathematical models; off-lattice reaction-diffusion models; detailed microscopic simulations; artificial grid; living cells; off-lattice Brownian dynamics; on-lattice reaction-diffusion models; cellular automata models; grid structure; grid artefacts; randomly distributed obstacles; crowding molecules; excluded volume effects; on-lattice approximations; crowded reaction rates; crowder density; crowded environments

Subjects: Nonlinear dynamical systems and bifurcations; Biomolecular structure, configuration, conformation, and active sites; Fluctuation phenomena, random processes, and Brownian motion; Function theory, analysis; Biomolecular dynamics, molecular probes, molecular pattern recognition; Model reactions in molecular biophysics; Macromolecular configuration (bonds, dimensions); Biological transport; cellular and subcellular transmembrane physics

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