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The Journal of Chemical Physics
Article . 2009 . Peer-reviewed
Data sources: Crossref
https://dx.doi.org/10.5167/uzh...
Other literature type . 2009
Data sources: Datacite
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An exact accelerated stochastic simulation algorithm

Authors: Mjolsness, E; Orendorff, D; Chatelain, P; Koumoutsakos, P;

An exact accelerated stochastic simulation algorithm

Abstract

An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm (SSA), is proposed. The present “ER-leap” algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 2∕3 power of the number of reaction events in a Galton–Watson process.

Countries
Switzerland, Belgium
Keywords

Stochastic Processes, SX00 SystemsX.ch, Models, Chemical, SX15 WingX, SX20 Research, Technology and Development Projects, 570 Life sciences; biology, Computer Simulation, 1606 Physical and Theoretical Chemistry, 3100 General Physics and Astronomy, Algorithms

  • BIP!
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    citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    16
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
16
Average
Average
Top 10%
Green
bronze