Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics

doi:10.1088/1674-1056/25/4/048201

Abstract

Most biochemical processes in cells are usually modeled by reaction-diffusion (RD) equations. In these RD models, the diffusive process is assumed to be Gaussian. However, a growing number of studies have noted that intracellular diffusion is anomalous at some or all times, which may result from a crowded environment and chemical kinetics. This work aims to computationally study the effects of chemical reactions on the diffusive dynamics of RD systems by using both stochastic and deterministic algorithms. Numerical method to estimate the mean-square displacement (MSD) from a deterministic algorithm is also investigated. Our computational results show that anomalous diffusion can be solely due to chemical reactions. The chemical reactions alone can cause anomalous sub-diffusion in the RD system at some or all times. The time-dependent anomalous diffusion exponent is found to depend on many parameters, including chemical reaction rates, reaction orders, and chemical concentrations.

Keywords: reaction-diffusion system anomalous diffusion exponent MCell

Received: 10 October 2015
Revised: 10 December 2015
Accepted manuscript online:

PACS:	82.39.Rt	(Reactions in complex biological systems)
	87.16.A-	(Theory, modeling, and simulations)

Fund:

Project supported by the Thailand Research Fund and Mahidol University (Grant No. TRG5880157), the Thailand Center of Excellence in Physics (ThEP), CHE, Thailand, and the Development Promotion of Science and Technology.

Corresponding Authors: Charin Modchang
E-mail: charin.mod@mahidol.edu

Cite this article:

Naruemon Rueangkham, Charin Modchang Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics 2016 Chin. Phys. B 25 048201

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