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.
%0 Journal Article
%1 Wang_2003_491
%A Wang, Hongyun
%A Peskin, Charles S
%A Elston, Timothy C
%D 2003
%J J. Theor. Biol.
%K Active; Algorithms; Animals; Biological Chains; Diffusion; Markov Models, Transport,
%N 4
%P 491--511
%T A robust numerical algorithm for studying biomolecular transport
processes.
%U http://dx.doi.org/10.1006/jtbi.2003.3200
%V 221
%X 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.
@article{Wang_2003_491,
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.},
added-at = {2009-06-03T11:20:58.000+0200},
author = {Wang, Hongyun and Peskin, Charles S and Elston, Timothy C},
biburl = {https://www.bibsonomy.org/bibtex/262d997b2c5fc5338909b364c9c1ee285/hake},
description = {The whole bibliography file I use.},
file = {Wang_2003_491.pdf:Wang_2003_491.pdf:PDF},
interhash = {6c1db648826262d7b52176350861f7c9},
intrahash = {62d997b2c5fc5338909b364c9c1ee285},
journal = {J. Theor. Biol.},
keywords = {Active; Algorithms; Animals; Biological Chains; Diffusion; Markov Models, Transport,},
month = Apr,
number = 4,
pages = {491--511},
pii = {S0022519303932000},
pmid = {12713936},
timestamp = {2009-06-03T11:21:36.000+0200},
title = {A robust numerical algorithm for studying biomolecular transport
processes.},
url = {http://dx.doi.org/10.1006/jtbi.2003.3200},
volume = 221,
year = 2003
}