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An exact accelerated stochastic simulation algorithm

Bibliographic reference Mjolsness, Eric ; Orendorff, David ; Chatelain, Philippe ; Koumoutsakos, Petros. An exact accelerated stochastic simulation algorithm. In: Journal of Chemical Physics, Vol. 130, no.14, p. 144110 (2009)
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  1. Gillespie Daniel T., Exact stochastic simulation of coupled chemical reactions, 10.1021/j100540a008
  2. Gillespie Daniel T., Approximate accelerated stochastic simulation of chemically reacting systems, 10.1063/1.1378322
  3. Chatterjee A., Mayawala K., Edwards J. S., Vlachos D. G., Time accelerated Monte Carlo simulations of biological networks using the binomial  -leap method, 10.1093/bioinformatics/bti308
  4. Cao Yang, Gillespie Daniel T., Petzold Linda R., Avoiding negative populations in explicit Poisson tau-leaping, 10.1063/1.1992473
  5. Cao Yang, Gillespie Daniel T., Petzold Linda R., Efficient step size selection for the tau-leaping simulation method, 10.1063/1.2159468
  6. E Weinan, Liu Di, Vanden-Eijnden Eric, Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates, 10.1063/1.2109987
  7. Samant A., Vlachos D. G., Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm, 10.1063/1.2046628
  8. Salis Howard, Kaznessis Yiannis N., An equation-free probabilistic steady-state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks, 10.1063/1.2131050
  9. Cao Yang, Gillespie Daniel T., Petzold Linda R., The slow-scale stochastic simulation algorithm, 10.1063/1.1824902
  10. Slepoy Alexander, Thompson Aidan P., Plimpton Steven J., A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks, 10.1063/1.2919546
  11. Auger Anne, Chatelain Philippe, Koumoutsakos Petros, R-leaping: Accelerating the stochastic simulation algorithm by reaction leaps, 10.1063/1.2218339
  12. Van Kampen N. G., Stochastic Processes in Physics and Chemistry (2007)
  13. Yosiphon G., Learning and Inference in Computational Systems Biology (2008)
  14. Wilkinson D. J., Stochastic Modelling for Systems Biology (Mathematical and Computational Biology) (2006)
  15. Mjolsness Eric, Yosiphon Guy, Stochastic process semantics for dynamical grammars, 10.1007/s10472-006-9034-1
  16. J. von Neumann, Various Techniques Used in Connection with Random Graphs (U.S. Government Printing Office, Washington, 1951), pp. 36–38.
  17. Evans T. W., Gillespie C. S., Wilkinson D. J., The SBML discrete stochastic models test suite, 10.1093/bioinformatics/btm566
  18. Wang Hongli, Li Qianshu, Master equation analysis of deterministic chemical chaos, 10.1063/1.476189
  19. Gibson Michael A., Bruck Jehoshua, Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels, 10.1021/jp993732q
  20. Rossinelli Diego, Bayati Basil, Koumoutsakos Petros, Accelerated stochastic and hybrid methods for spatial simulations of reaction–diffusion systems, 10.1016/j.cplett.2007.11.055
  21. Bayati Basil, Chatelain Philippe, Koumoutsakos Petros, Multiresolution stochastic simulations of reaction–diffusion processes, 10.1039/b810795e