technical report Notes on stochastic simulation of chemical kinetics with cycle-leaping


In this report we review the Riedel-Bruck stochastic simulation algorithm, which makes use of a cycle-leaping strategy to improve the simulation performance. We implemented the algorithmi and tested our implementation on some stochastic models, such as the Lotka-Volterra model of predation, the Brusselator model, and the Michaelis-Menten model of enzymatic catalysis. We discuss the advantages and the disadvantages of this algorithm from the viewpoint of its use in a systemic approach to modeling and simulation of biochemical and biological processes.

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P. Lecca,  S. Teso