Linked Life Data

18698893

Source:http://linkedlifedata.com/resource/pubmed/id/18698893

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
5
pubmed:dateCreated
2008-8-13
pubmed:abstractText
Brownian Dynamics algorithms have been widely used for simulating systems in soft-condensed matter physics. In recent times, their application has been extended to the simulation of coarse-grained models of biochemical networks. In these models, components move by diffusion and interact with one another upon contact. However, when reactions are incorporated into a Brownian dynamics algorithm, care must be taken to avoid violations of the detailed-balance rule, which would introduce systematic errors in the simulation. We present a Brownian dynamics algorithm for simulating reaction-diffusion systems that rigorously obeys detailed balance for equilibrium reactions. By comparing the simulation results to exact analytical results for a bimolecular reaction, we show that the algorithm correctly reproduces both equilibrium and dynamical quantities. We apply our scheme to a "push-pull" network in which two antagonistic enzymes covalently modify a substrate. Our results highlight that spatial fluctuations of the network components can strongly reduce the gain of the response of a biochemical network.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
1089-7690
pubmed:author
pubmed:issnType
Electronic
pubmed:day
7
pubmed:volume
129
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
054112
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network.
pubmed:affiliation
FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't