title: The subtle business of model reduction for stochastic chemical kinetics.
abstract: 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 S(1)<=>S(2)-->S(3), whose simplicity allows all the mathematics to be done exactly. The advantages and disadvantages of replacing this reaction set with a single S(3)-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.
authors.affiliation: Dan T. Gillespie Consulting, 30504 Cordoba Place, Castaic, California 91384, USA. gillespiedt@mailaps.org
authors.forename: Dan T
authors.initials: DT
authors.lastname: Gillespie
authors.forename: Yang
authors.initials: Y
authors.lastname: Cao
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Sanft
authors.forename: Linda R
authors.initials: LR
authors.lastname: Petzold
mesh_terms: D007700:Kinetics; D008956:Models, Chemical; D012680:Sensitivity and Specificity; D013269:Stochastic Processes