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Titolo:
Efficient exact stochastic simulation of chemical systems with many species and many channels
Autore:
Gibson, MA; Bruck, J;
Indirizzi:
CALTECH, Dept Computat & Neural Syst, Pasadena, CA 91125 USA CALTECH Pasadena CA USA 91125 putat & Neural Syst, Pasadena, CA 91125 USA
Titolo Testata:
JOURNAL OF PHYSICAL CHEMISTRY A
fascicolo: 9, volume: 104, anno: 2000,
pagine: 1876 - 1889
SICI:
1089-5639(20000309)104:9<1876:EESSOC>2.0.ZU;2-A
Fonte:
ISI
Lingua:
ENG
Soggetto:
SURFACE; LAMBDA;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
15
Recensione:
Indirizzi per estratti:
Indirizzo: Gibson, MA CALTECH, Dept Computat & Neural Syst, Mail Code 136-93, Pasadena, CA 91125USA CALTECH Mail Code 136-93 Pasadena CA USA 91125 ena, CA 91125USA
Citazione:
M.A. Gibson e J. Bruck, "Efficient exact stochastic simulation of chemical systems with many species and many channels", J PHYS CH A, 104(9), 2000, pp. 1876-1889

Abstract

There are two fundamental ways to view coupled systems of chemical equations: as continuous, represented by differential equations whose variables are concentrations, or as discrete, represented by stochastic processes whosevariables are numbers of molecules. Although the former is by far more common, systems with very small numbers of molecules are important in some applications (e.g., in small biological cells or in surface processes). In both views, most complicated systems with multiple reaction channels and multiple chemical species cannot be solved analytically. There are exact numerical simulation methods to simulate trajectories of discrete, stochastic systems, (methods that are rigorously equivalent to the Master Equation approach) but these do not scale well to systems with many reaction pathways. Thispaper presents the Next Reaction Method, an exact algorithm to simulate coupled chemical reactions that is also efficient: it (a) uses only a single random number per simulation event, and (b) takes time proportional to the-logarithm of the number of reactions, not to the number of reactions itself. The Next Reaction Method is extended to include time-dependent rate constants and non-Markov processes and is applied to a sample application in biology (the lysis/lysogeny decision circuit of lambda phage). The performanceof the Next Reaction Method on this application is compared with one standard method and an optimized version of that standard method.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 09/08/20 alle ore 22:29:23