|Author||Thanh, Vo Hong ♦ Priami, Corrado ♦ Zunino, Roberto|
|Source||United States Department of Energy Office of Scientific and Technical Information|
|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.|
|Learning Resource Type||Article|
|Publisher Place||United States|
|Journal||Journal of Chemical Physics|
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