Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays

V.H. Thanh, C. Priami, R. Zunino

Tutkimustuotos: LehtiartikkeliArticleScientificvertaisarvioitu

Abstrakti

We propose a new exact stochastic rejection-based simulation algorithm for biochemical reactions and extend it to systems with delays. Our algorithm accelerates the simulation by pre-computing reaction propensity bounds to select the next reaction to perform. Exploiting such bounds, we are able to avoid recomputing propensities every time a (delayed) reaction is initiated or finished, as is typically necessary in standard approaches. Propensity updates in our approach are still performed, but only infrequently and limited for a small number of reactions, saving computation time and without sacrificing exactness. We evaluate the performance improvement of our algorithm by experimenting with concrete biological models. © 2014 AIP Publishing LLC.
AlkuperäiskieliEnglanti
JulkaisuJournal of Chemical Physics
Vuosikerta141
Numero13
DOI - pysyväislinkit
TilaJulkaistu - 2014
OKM-julkaisutyyppiA1 Julkaistu artikkeli, soviteltu

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