Fast exact stochastic simulation algorithms using partial propensities

Research output: Contribution to journalConference articleContributedpeer-review

Contributors

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

Original languageEnglish
Pages (from-to)1338-1341
Number of pages4
JournalAIP Conference Proceedings
Volume1281
Publication statusPublished - 30 Sept 2010
Peer-reviewedYes
Externally publishedYes

Conference

TitleInternational Conference on Numerical Analysis and Applied Mathematics 2010, ICNAAM-2010
Duration19 - 25 September 2010
CityRhodes
CountryGreece

External IDs

ORCID /0000-0003-4414-4340/work/159608315

Keywords

ASJC Scopus subject areas

Keywords

  • chemical reactions, partial propensities, partial propensity methods, SSA, stochastic simulation algorithm