Fast exact stochastic simulation algorithms using partial propensities
Research output: Contribution to journal › Conference article › Contributed › peer-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 language | English |
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Pages (from-to) | 1338-1341 |
Number of pages | 4 |
Journal | AIP Conference Proceedings |
Volume | 1281 |
Publication status | Published - 30 Sept 2010 |
Peer-reviewed | Yes |
Externally published | Yes |
Conference
Title | International Conference on Numerical Analysis and Applied Mathematics 2010, ICNAAM-2010 |
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Duration | 19 - 25 September 2010 |
City | Rhodes |
Country | Greece |
External IDs
ORCID | /0000-0003-4414-4340/work/159608315 |
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Keywords
ASJC Scopus subject areas
Keywords
- chemical reactions, partial propensities, partial propensity methods, SSA, stochastic simulation algorithm