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A Robust Numerical Algorithm for Studying Biomolecular Transport Processes

✍ Scribed by HONGYUN WANG; CHARLES S. PESKIN; TIMOTHY C. ELSTON

Publisher: Elsevier Science
Year: 2003
Tongue: English
Weight: 335 KB
Volume: 221
Category: Article
ISSN: 0022-5193
DOI: 10.1006/jtbi.2003.3200

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✦ Synopsis

We present a numerical algorithm that is well suited for the study of biomolecular transport processes. In the algorithm a continuous Markov process is discretized as a jump process and the jump rates are derived from local solutions of the continuous system. Consequently, the algorithm has two advantages over standard numerical methods: (1) it preserves detailed balance for equilibrium processes, (2) it is able to handle discontinuous potentials. The formulation of the algorithm also allows us to calculate the effective diffusion coefficient or, equivalently, the randomness parameter. We provide several simple examples of how to implement the algorithm. All the MATLAB functions files needed to reproduce the results presented in the article are available from www.amath.unc.edu/Faculty/telston/matlab_functions.

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