Excluded volume effects in on‐ and off‐lattice reaction–diffusion models. Issue 2 (28th March 2017)

• Record Type: Journal Article
• Authors: Meinecke, Lina; Eriksson, Markus
• Is Part Of: IET systems biology. Volume 11:Issue 2(2017)
• Page Start: 55
• Page End: 64
• Publication Date: 2017-03-28
• Subjects: reaction‐diffusion systems -- cellular biophysics -- biodiffusion -- Brownian motion -- cellular automata -- molecular biophysics -- molecular configurations; crowder density -- grid artefacts -- grid structure -- crowded reaction rates -- artificial grid -- randomly distributed obstacles -- crowding molecules -- cellular automata models -- on‐lattice approximations -- crowded environments -- off‐lattice Brownian dynamics -- detailed microscopic simulations -- living cells -- mathematical models -- off‐lattice reaction‐diffusion models -- on‐lattice reaction‐diffusion models -- excluded volume effects; Systems biology -- Periodicals; Cell physiology -- Periodicals; Biological systems -- Mathematical models -- Periodicals; Genetics -- Mathematical models -- Periodicals; Computational biology -- Periodicals; 573
• DOI: 10.1049/iet-syb.2016.0021
• Languages: English
• ISSNs: 1751-8849

Abstract

Abstract : 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.