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https://doi.org/10.1063/1.3497...
Article . 2010 . Peer-reviewed
Data sources: Crossref
https://dx.doi.org/10.5167/uzh...
Other literature type . 2010
Data sources: Datacite
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Fast Exact Stochastic Simulation Algorithms Using Partial Propensities

Authors: Rajesh Ramaswamy; Ivo F. Sbalzarini; Theodore E. Simos; George Psihoyios; Ch. Tsitouras;

Fast Exact Stochastic Simulation Algorithms Using Partial Propensities

Abstract

We review the class of partial‐propensity exact stochastic simulation algorithms (SSA) for chemical reaction networks. We show which modules partial‐propensity SSAs are composed of and how partial‐propensity variants of known SSAs can be constructed by adjusting the sampling strategy used. We demonstrate this on the example of two instances, namely the partial‐propensity variant of Gillespie’s original direct method and that of the SSA with composition‐rejection sampling (SSA‐CR). Partial‐propensity methods may outperform the corresponding classical SSA, particularly on strongly coupled reaction networks. Changing the different modules of partial‐propensity SSAs provides flexibility in tuning them to perform particularly well on certain classes of reaction networks. The framework presented here defines the design space of such adaptations.

Country
Switzerland
Related Organizations
Keywords

SX00 SystemsX.ch, SX15 WingX, 570 Life sciences; biology, 3100 General Physics and Astronomy

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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!
7
Average
Average
Average
Green