메뉴 건너뛰기




Volumn 226, Issue 1, 2007, Pages 818-835

A multiple time interval finite state projection algorithm for the solution to the chemical master equation

Author keywords

Chemical master equation; Markov processes; Stochastic gene regulatory networks

Indexed keywords

EFFICIENCY; ESCHERICHIA COLI; ORDINARY DIFFERENTIAL EQUATIONS; PROBABILITY DISTRIBUTIONS; STOCHASTIC SYSTEMS;

EID: 34548417080     PISSN: 00219991     EISSN: 10902716     Source Type: Journal    
DOI: 10.1016/j.jcp.2007.05.016     Document Type: Article
Times cited : (57)

References (23)
  • 1
    • 44049109914 scopus 로고
    • A rigorous derivation of the chemical master equation
    • Gillespie D.T. A rigorous derivation of the chemical master equation. Physica A 188 (1992) 404-425
    • (1992) Physica A , vol.188 , pp. 404-425
    • Gillespie, D.T.1
  • 2
    • 0001601301 scopus 로고
    • "Stochastic approach to chemical kinetics
    • McQuarrie D. "Stochastic approach to chemical kinetics. J. Appl. Probab. 4 (1967) 413-478
    • (1967) J. Appl. Probab. , vol.4 , pp. 413-478
    • McQuarrie, D.1
  • 4
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 May (1977) 2340-2360
    • (1977) J. Phys. Chem. , vol.81 , Issue.May , pp. 2340-2360
    • Gillespie, D.T.1
  • 5
    • 0037109565 scopus 로고    scopus 로고
    • Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
    • Haseltine E., and Rawlings J. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J. Chem. Phys. 117 Jul (2002) 6959-6969
    • (2002) J. Chem. Phys. , vol.117 , Issue.Jul , pp. 6959-6969
    • Haseltine, E.1    Rawlings, J.2
  • 6
    • 0037444724 scopus 로고    scopus 로고
    • Stochastic chemical kinetics and the quasi-steadystate assumption: application to the gillespie algorithm
    • Rao C.V., and Arkin A.P. Stochastic chemical kinetics and the quasi-steadystate assumption: application to the gillespie algorithm. J. Chem. Phys. 118 Mar (2003) 4999-5010
    • (2003) J. Chem. Phys. , vol.118 , Issue.Mar , pp. 4999-5010
    • Rao, C.V.1    Arkin, A.P.2
  • 7
    • 18144386494 scopus 로고    scopus 로고
    • Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
    • Cao Y., Gillespie D.T., and Petzold L.R. Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems. J. Comp. Phys. 206 July (2005) 395-411
    • (2005) J. Comp. Phys. , vol.206 , Issue.July , pp. 395-411
    • Cao, Y.1    Gillespie, D.T.2    Petzold, L.R.3
  • 8
    • 22944480262 scopus 로고    scopus 로고
    • The slow-scale stochastic simulation algorithm
    • Cao Y., Gillespie D., and Petzold L. The slow-scale stochastic simulation algorithm. J. Chem. Phys. 122 Jan (2005)
    • (2005) J. Chem. Phys. , vol.122 , Issue.Jan
    • Cao, Y.1    Gillespie, D.2    Petzold, L.3
  • 9
    • 22944451159 scopus 로고    scopus 로고
    • Accurate hybrid stochastic simulation of a system of coupled chemical or biological reactions
    • Salis H., and Kaznessis Y. Accurate hybrid stochastic simulation of a system of coupled chemical or biological reactions. J. Chem. Phys. 112 054103 (2005)
    • (2005) J. Chem. Phys. , vol.112 , Issue.054103
    • Salis, H.1    Kaznessis, Y.2
  • 10
    • 0035933994 scopus 로고    scopus 로고
    • Approximate accelerated stochastic simulation of chemically reacting systems
    • Gillespie D.T. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115 Jul (2001) 1716-1733
    • (2001) J. Chem. Phys. , vol.115 , Issue.Jul , pp. 1716-1733
    • Gillespie, D.T.1
  • 11
    • 0242425970 scopus 로고    scopus 로고
    • Improved leap-size selection for accelerated stochastic simulation
    • Gillespie D.T., and Petzold L.R. Improved leap-size selection for accelerated stochastic simulation. J. Chem. Phys. 119 Oct (2003) 8229-8234
    • (2003) J. Chem. Phys. , vol.119 , Issue.Oct , pp. 8229-8234
    • Gillespie, D.T.1    Petzold, L.R.2
  • 12
    • 0942279178 scopus 로고    scopus 로고
    • Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method
    • Rathinam M., Petzold L.R., Cao Y., and Gillespie D.T. Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method. J. Chem. Phys. 119 Dec (2003) 12784-12794
    • (2003) J. Chem. Phys. , vol.119 , Issue.Dec , pp. 12784-12794
    • Rathinam, M.1    Petzold, L.R.2    Cao, Y.3    Gillespie, D.T.4
  • 13
    • 3142543968 scopus 로고    scopus 로고
    • Binomial leap methods for simulating stochastic chemical kinetics
    • Tian T., and Burrage K. Binomial leap methods for simulating stochastic chemical kinetics. J. Chem. Phys. 121 Dec (2004) 10356-10364
    • (2004) J. Chem. Phys. , vol.121 , Issue.Dec , pp. 10356-10364
    • Tian, T.1    Burrage, K.2
  • 14
    • 23944491675 scopus 로고    scopus 로고
    • Avoiding negative populations in explicit poisson tau-leaping
    • Cao Y., Gillespie D.T., and Petzold L.R. Avoiding negative populations in explicit poisson tau-leaping. J. Chem. Phys. 123 054104 (2005)
    • (2005) J. Chem. Phys. , vol.123 , Issue.054104
    • Cao, Y.1    Gillespie, D.T.2    Petzold, L.R.3
  • 15
    • 29144488933 scopus 로고    scopus 로고
    • Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems
    • Cao Y., and Petzold L.R. Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems. J. Comp. Phys. 212 Feb (2006) 6-24
    • (2006) J. Comp. Phys. , vol.212 , Issue.Feb , pp. 6-24
    • Cao, Y.1    Petzold, L.R.2
  • 16
    • 33751347484 scopus 로고    scopus 로고
    • The finite state projection algorithm for the solution of the chemical master equation
    • Munsky B., and Khammash M. The finite state projection algorithm for the solution of the chemical master equation. J. Chem. Phys. 124 044104 (2006)
    • (2006) J. Chem. Phys. , vol.124 , Issue.044104
    • Munsky, B.1    Khammash, M.2
  • 17
    • 85190309527 scopus 로고    scopus 로고
    • B. Munsky, A. Hernday, D. Low, M. Khammash, Stochastic modeling of the pap-pili epigenetic switch, in: Proceedings of the FOSBE, August 2005, pp. 145-148.
  • 18
    • 85190290617 scopus 로고    scopus 로고
    • B. Munsky, M. Khammash, A reduced model solution for the chemical master equation arising in stochastic analyses of biological networks, in: Proceedings of the 45th IEEE CDC, Dec 2006.
  • 19
    • 85190264777 scopus 로고    scopus 로고
    • K. Burrage, M. Hegland, S. Macnamara, R. Sidje, A krylov-based finite state projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems, in: Proceedings of the A.A. Markov 150th Anniversary Meeting, 2006.
  • 20
    • 33751566347 scopus 로고    scopus 로고
    • Reduction and solution of the chemical master equation using time-scale separation and finite state projection
    • Peles S., Munsky B., and Khammash M. Reduction and solution of the chemical master equation using time-scale separation and finite state projection. J. Chem. Phys. 125 Nov (2006)
    • (2006) J. Chem. Phys. , vol.125 , Issue.Nov
    • Peles, S.1    Munsky, B.2    Khammash, M.3
  • 21
    • 85190257465 scopus 로고    scopus 로고
    • B. Munsky, S. Peles, M. Khammash, Stochastic analysis of gene regulatory networks using finite state projections and singular perturbation, in: Proceedings of the 26th American Control Conference, July 2007.
  • 22
    • 85190243714 scopus 로고    scopus 로고
    • H. El Samad, H. Kurata, J. Doyle, M. Khammash, C. Gross, Surviving heat shock: Control strategies for robustness and performance, PNAS 102 (8) (2005) 27362741.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.