The subtle business of model reduction for stochastic chemical kinetics
| Title | The subtle business of model reduction for stochastic chemical kinetics |
| Publication Type | Journal Article |
| Year of Publication | 2009 |
| Authors | Gillespie, D. T., Y. Cao, K. R. Sanft, and L. R. Petzold |
| Journal | JOURNAL OF CHEMICAL PHYSICS |
| Volume | 130 |
| Issue | 6 |
| Date Published | FEB 14 |
| Type of Article | Article |
| ISSN | 0021-9606 |
| 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.} |
| DOI | 10.1063/1.3072704 |
