期刊
JOURNAL OF CHEMICAL PHYSICS
卷 130, 期 6, 页码 -出版社
AIP Publishing
DOI: 10.1063/1.3072704
关键词
reaction kinetics theory; reduction (chemical); stochastic processes
资金
- California Institute of Technology [102-1080890]
- National Institute of General Medical Sciences [R01GM078992]
- National Institute of Biomedical Imaging and Bioengineering [R01EB007511]
- University of California at Santa Barbara [054281A20]
- National Science Foundation [CCF-0726763]
- National Institutes of Health [GM073744, GM078989]
- Pfizer Inc.
- DOE [DE-FG02-04ER25621]
- NSF [IGERT DG02-21715]
- U.S. Army Research Office [DFR3A-8-447850-23002]
- [82-1083250]
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.
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