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