title: A robust numerical algorithm for studying biomolecular transport processes.
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.
authors.affiliation: Department of Applied Mathematics and Statistics, University of California, Santa Cruz, CA 95064, USA. hongwang@ams.ucsc.edu
authors.forename: Hongyun
authors.initials: H
authors.lastname: Wang
authors.forename: Charles S
authors.initials: CS
authors.lastname: Peskin
authors.forename: Timothy C
authors.initials: TC
authors.lastname: Elston
mesh_terms: D000465:Algorithms; D000818:Animals; D001693:Biological Transport, Active; D004058:Diffusion; D008390:Markov Chains; D008954:Models, Biological