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The subtle business of model reduction for stochastic chemical kinetics

By Dan T. Gillespie, Yang Cao, Kevin R. Sanft and Linda R. Petzold


This paper addresses the problem of simplifying chemical reaction networks by adroitly reducing the number of reaction channels and chemical species. The analysis adopts a discrete-stochastic point of view and focuses on the model reaction set S1⇌S2→S3, whose simplicity allows all the mathematics to be done exactly. The advantages and disadvantages of replacing this reaction set with a single S3-producing reaction are analyzed quantitatively using novel criteria for measuring simulation accuracy and simulation efficiency. It is shown that in all cases in which such a model reduction can be accomplished accurately and with a significant gain in simulation efficiency, a procedure called the slow-scale stochastic simulation algorithm provides a robust and theoretically transparent way of implementing the reduction

Topics: Theoretical Methods and Algorithms
Publisher: American Institute of Physics
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Provided by: PubMed Central
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