Methods are presented for simulating chemical reaction networks with
a spatial resolution that is accurate to nearly the size scale of
individual molecules. Using an intuitive picture of chemical reaction
systems, each molecule is treated as a point-like particle that diffuses
freely in three-dimensional space. When a pair of reactive molecules
collide, such as an enzyme and its substrate, a reaction occurs and
the simulated reactants are replaced by products. Achieving accurate
bimolecular reaction kinetics is surprisingly difficult, requiring
a careful consideration of reaction processes that are often overlooked.
This includes whether the rate of a reaction is at steady-state and
the probability that multiple reaction products collide with each
other to yield a back reaction. Inputs to the simulation are experimental
reaction rates, diffusion coefficients and the simulation time step.
From these are calculated the simulation parameters, including the
'binding radius' and the 'unbinding radius', where the former defines
the separation for a molecular collision and the latter is the initial
separation between a pair of reaction products. Analytic solutions
are presented for some simulation parameters while others are calculated
using look-up tables. Capabilities of these methods are demonstrated
with simulations of a simple bimolecular reaction and the Lotka-Volterra
system.
%0 Journal Article
%1 Andr_2004_137
%A Andrews, Steven S
%A Bray, Dennis
%D 2004
%J Phys. Biol.
%K Algorithms; Extramural; Gov't, Kinetics; Models, Molecular; N.I.H., Non-P.H.S.; P.H.S.; Processes Research Stochastic Support, U.S.
%N 3-4
%P 137--151
%R 10.1088/1478-3967/1/3/001
%T Stochastic simulation of chemical reactions with spatial resolution
and single molecule detail.
%U http://dx.doi.org/10.1088/1478-3967/1/3/001
%V 1
%X Methods are presented for simulating chemical reaction networks with
a spatial resolution that is accurate to nearly the size scale of
individual molecules. Using an intuitive picture of chemical reaction
systems, each molecule is treated as a point-like particle that diffuses
freely in three-dimensional space. When a pair of reactive molecules
collide, such as an enzyme and its substrate, a reaction occurs and
the simulated reactants are replaced by products. Achieving accurate
bimolecular reaction kinetics is surprisingly difficult, requiring
a careful consideration of reaction processes that are often overlooked.
This includes whether the rate of a reaction is at steady-state and
the probability that multiple reaction products collide with each
other to yield a back reaction. Inputs to the simulation are experimental
reaction rates, diffusion coefficients and the simulation time step.
From these are calculated the simulation parameters, including the
'binding radius' and the 'unbinding radius', where the former defines
the separation for a molecular collision and the latter is the initial
separation between a pair of reaction products. Analytic solutions
are presented for some simulation parameters while others are calculated
using look-up tables. Capabilities of these methods are demonstrated
with simulations of a simple bimolecular reaction and the Lotka-Volterra
system.
@article{Andr_2004_137,
abstract = {Methods are presented for simulating chemical reaction networks with
a spatial resolution that is accurate to nearly the size scale of
individual molecules. Using an intuitive picture of chemical reaction
systems, each molecule is treated as a point-like particle that diffuses
freely in three-dimensional space. When a pair of reactive molecules
collide, such as an enzyme and its substrate, a reaction occurs and
the simulated reactants are replaced by products. Achieving accurate
bimolecular reaction kinetics is surprisingly difficult, requiring
a careful consideration of reaction processes that are often overlooked.
This includes whether the rate of a reaction is at steady-state and
the probability that multiple reaction products collide with each
other to yield a back reaction. Inputs to the simulation are experimental
reaction rates, diffusion coefficients and the simulation time step.
From these are calculated the simulation parameters, including the
'binding radius' and the 'unbinding radius', where the former defines
the separation for a molecular collision and the latter is the initial
separation between a pair of reaction products. Analytic solutions
are presented for some simulation parameters while others are calculated
using look-up tables. Capabilities of these methods are demonstrated
with simulations of a simple bimolecular reaction and the Lotka-Volterra
system.},
added-at = {2009-06-03T11:20:58.000+0200},
author = {Andrews, Steven S and Bray, Dennis},
biburl = {https://www.bibsonomy.org/bibtex/2fafb7f9c0f723c19f5ebd36019ee3419/hake},
description = {The whole bibliography file I use.},
doi = {10.1088/1478-3967/1/3/001},
file = {Andr_2004_137.pdf:Andr_2004_137.pdf:PDF},
interhash = {137c097b39ee22a924fb87d39bfc1534},
intrahash = {fafb7f9c0f723c19f5ebd36019ee3419},
journal = {Phys. Biol.},
keywords = {Algorithms; Extramural; Gov't, Kinetics; Models, Molecular; N.I.H., Non-P.H.S.; P.H.S.; Processes Research Stochastic Support, U.S.},
month = Dec,
number = {3-4},
pages = {137--151},
pii = {S1478-3967(04)83249-2},
pmid = {16204833},
timestamp = {2009-06-03T11:21:00.000+0200},
title = {Stochastic simulation of chemical reactions with spatial resolution
and single molecule detail.},
url = {http://dx.doi.org/10.1088/1478-3967/1/3/001},
volume = 1,
year = 2004
}