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Author Thanh, Vo Hong ♦ Priami, Corrado ♦ Zunino, Roberto
Source United States Department of Energy Office of Scientific and Technical Information
Content type Text
Language English
Subject Keyword INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY ♦ ALGORITHMS ♦ BIOLOGICAL MODELS ♦ CALCULATION METHODS ♦ SIMULATION
Abstract 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.
ISSN 00219606
Educational Use Research
Learning Resource Type Article
Publisher Date 2014-10-07
Publisher Place United States
Journal Journal of Chemical Physics
Volume Number 141
Issue Number 13


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