A robust numerical algorithm for studying biomolecular transport processes

Hongyun Wang, Charles Peskin, Timothy C. Elston

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)491-511
Number of pages21
JournalJournal of Theoretical Biology
Volume221
Issue number4
DOIs
StatePublished - Apr 21 2003

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Transport Processes
Robust Algorithm
Numerical Algorithms
MATLAB
Detailed Balance
Jump Process
Local Solution
continuous systems
Continuous System
Markov Chains
Markov Process
Randomness
Diffusion Coefficient
Jump
diffusivity
Markov processes
Numerical Methods
preserves
Numerical methods
Calculate

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

A robust numerical algorithm for studying biomolecular transport processes. / Wang, Hongyun; Peskin, Charles; Elston, Timothy C.

In: Journal of Theoretical Biology, Vol. 221, No. 4, 21.04.2003, p. 491-511.

Research output: Contribution to journalArticle

Wang, Hongyun ; Peskin, Charles ; Elston, Timothy C. / A robust numerical algorithm for studying biomolecular transport processes. In: Journal of Theoretical Biology. 2003 ; Vol. 221, No. 4. pp. 491-511.
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