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

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

中国物理B ›› 2016, Vol. 25 ›› Issue (4): 48201-048201.doi: 10.1088/1674-1056/25/4/048201

• INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY • 上一篇下一篇

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

Naruemon Rueangkham, Charin Modchang

1 Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
2 Centre of Excellence in Mathematics, CHE, 328, Si Ayutthaya Road, Bangkok 10400, Thailand;
3 ThEP Center CHE, 328 Si Ayutthaya Road, Bangkok 10400, Thailand

收稿日期:2015-10-10 修回日期:2015-12-10 出版日期:2016-04-05 发布日期:2016-04-05
通讯作者: Charin Modchang E-mail:charin.mod@mahidol.edu
基金资助:
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.

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

Naruemon Rueangkham¹, Charin Modchang^1,2,3

1 Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
2 Centre of Excellence in Mathematics, CHE, 328, Si Ayutthaya Road, Bangkok 10400, Thailand;
3 ThEP Center CHE, 328 Si Ayutthaya Road, Bangkok 10400, Thailand

Received:2015-10-10 Revised:2015-12-10 Online:2016-04-05 Published:2016-04-05
Contact: Charin Modchang E-mail:charin.mod@mahidol.edu
Supported by:
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.

摘要/Abstract

摘要：

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.

关键词: reaction-diffusion system, anomalous diffusion exponent, MCell

Abstract:

Key words: reaction-diffusion system, anomalous diffusion exponent, MCell

中图分类号: (Reactions in complex biological systems)

82.39.Rt

87.16.A- (Theory, modeling, and simulations)

Naruemon Rueangkham, Charin Modchang. Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics[J]. 中国物理B, 2016, 25(4): 48201-048201.

Naruemon Rueangkham, Charin Modchang. Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics[J]. Chin. Phys. B, 2016, 25(4): 48201-048201.

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

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

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