Fast exact stochastic simulation algorithms using partial propensities
Publikation: Beitrag in Fachzeitschrift › Konferenzartikel › Beigetragen › Begutachtung
Beitragende
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.
Details
Originalsprache | Englisch |
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Seiten (von - bis) | 1338-1341 |
Seitenumfang | 4 |
Fachzeitschrift | AIP Conference Proceedings |
Jahrgang | 1281 |
Publikationsstatus | Veröffentlicht - 30 Sept. 2010 |
Peer-Review-Status | Ja |
Extern publiziert | Ja |
Konferenz
Titel | International Conference on Numerical Analysis and Applied Mathematics 2010, ICNAAM-2010 |
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Dauer | 19 - 25 September 2010 |
Stadt | Rhodes |
Land | Griechenland |
Externe IDs
ORCID | /0000-0003-4414-4340/work/159608315 |
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Schlagworte
ASJC Scopus Sachgebiete
Schlagwörter
- chemical reactions, partial propensities, partial propensity methods, SSA, stochastic simulation algorithm