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タグ: gillespie [21 articles]

Recent papers classified by the tag gillespie.
  • A practical guide to stochastic simulations of reaction-diffusion processes
    (15 Apr 2007)
    by Radek Erban, Jonathan Chapman, Philip Maini
    posted to biology gillespie simulation stochastic-simulation systems-biology by roland_ewald on 2007-07-23 09:07:13 as * along with 3 people and 3 groups cottrell dagmar csgillespie dIEMoSIRIS MoSi-Rostock compneur
  • Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales
    Journal of Computational Physics, Vol. 221, No. 1. (20 January 2007), pp. 158-180.
    by Weinan, Di Liu, Eric Vanden-Eijnden
    posted to gillespie ssa by ptupper on 2007-08-22 16:56:38 as ** along with 1 person khachsar
  • Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
    J. Comput. Phys., Vol. 206, No. 2. (2005), pp. 395-411.
    by Yang Cao, Dan Gillespie, Linda Petzold
    posted to gillespie multiscale ssa by ptupper on 2007-09-07 19:33:41 as ** along with 2 people LarryT pmendes
  • Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 71, No. 4. (2005)
    by David Bernstein
    posted to gillespie spatial ssa by ptupper on 2007-09-07 19:26:36 as **
  • Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
    The Journal of Chemical Physics, Vol. 117, No. 15. (2002), pp. 6959-6969.
    by Eric L Haseltine, James B Rawlings
    posted to gillespie simulation stochastic by ner25 on 2007-07-12 10:17:30 as ** along with 3 people and 1 group jstajic jjray dagmar compneur
  • Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli
    Bioinformatics, Vol. 22, No. 15. (1 August 2006), pp. 1895-1901.
    by Vidal J Rodriguez, Jaap A Kaandorp, Maciej Dobrzynski, Joke G Blom
    posted to ssa_alternative simulator reactions gillespie by m_j on 2008-09-09 15:56:22 as ** along with 1 person and 1 group dagmar compneur
  • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    Journal of Computational Physics, Vol. 22, No. 4. (December 1976), pp. 403-434.
    by Daniel T Gillespie
    posted to stochastic_simulation ssa gillespie by m_j on 2008-09-11 15:45:49 as ** along with 7 people and 1 group jberro rjoy mazzucco ptupper petermilner matthewhflamm jjray Projet_ENSIMAG
  • Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases.
    Syst Biol (Stevenage), Vol. 1, No. 2. (December 2004), pp. 230-236.
    by J Elf, M Ehrenberg
    posted to finite_elements gillespie spatial stochastic by lenov on 2007-09-26 09:08:34 as **
  • SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.
    Syst Biol (Stevenage), Vol. 1, No. 1. (June 2004), pp. 129-138.
    by M Ander, P Beltrao, B Di Ventura, J Ferkinghoff-Borg, M Foglierini, A Kaplan, C Lemerle, I Tomás-Oliveira, L Serrano
    posted to gillespie modelling spatial stochastic by lenov on 2007-09-26 09:19:04 as read along with 3 people Doug csanford arjunan
  • Stochastic reaction-diffusion simulation with MesoRD
    Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2923-2924.
    by Johan Hattne, David Fange, Johan Elf
    posted to finite_elements gillespie spatial stochastic by lenov on 2007-09-26 09:04:40 as ** along with 8 people and 4 groups jberro balabu jiyu roland_ewald mattis23 dagmar csanford arjunan Projet_ENSIMAG dIEMoSIRIS MoSi-Rostock compneur
  • Efficient step size selection for the tau-leaping simulation method
    The Journal of Chemical Physics, Vol. 124, No. 4. (2006)
    by Yang Cao, Daniel T Gillespie, Linda R Petzold
    posted to gillespie leap simulation stochastic tau by jporternj on 2008-06-11 17:12:05 as *** along with 1 person RamuAnandakrishnan
  • Adaptive explicit-implicit tau-leaping method with automatic tau selection
    The Journal of Chemical Physics, Vol. 126, No. 22. (2007)
    by Yang Cao, Daniel T Gillespie, Linda R Petzold
    posted to gillespie simulation_algorithms by dagmar to the group compneur on 2007-10-11 14:50:44 as ** along with 1 person khachsar
  • The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
    Computational Biology and Chemistry, Vol. 30, No. 1. (February 2006), pp. 39-49.
    by James M Mccollum, Gregory D Peterson, Chris D Cox, Michael L Simpson, Nagiza F Samatova
    posted to gillespie simulation_algorithms by dagmar to the group compneur on 2007-10-11 13:55:16 as **
  • Improved leap-size selection for accelerated stochastic simulation
    J. Chem. Phys., Vol. 119 (October 2003), pp. 8229-8234.
    by DT Gillespie, LR Petzold
    posted to gillespie simulation_algorithms tau by dagmar to the group compneur on 2007-10-19 14:44:44 as **
  • Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics
    The Journal of Chemical Physics, Vol. 127, No. 10. (2007)
    by Tatiana, Kevin Burrage
    posted to gillespie simulation_algorithms tau by dagmar to the group compneur on 2007-10-16 17:23:00 as **
  • Avoiding negative populations in explicit Poisson tau-leaping
    J. Chem. Phys., Vol. 123 (August 2005), 4104.
    by Y Cao, DT Gillespie, LR Petzold
    posted to gillespie kisao simulation_algorithms tau by dagmar to the group compneur on 2007-10-22 16:14:37 as **
  • Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method
    The Journal of Chemical Physics, Vol. 119, No. 24. (2003), pp. 12784-12794.
    by Muruhan Rathinam, Linda R Petzold, Yang Cao, Daniel T Gillespie
    posted to gillespie simulation_algorithms stochastic by dagmar to the group compneur on 2007-10-11 14:43:41 as **
  • The slow-scale stochastic simulation algorithm.
    J Chem Phys, Vol. 122, No. 1. (1 January 2005)
    by Y Cao, DT Gillespie, LR Petzold
    posted to gillespie simulation_algorithms by dagmar to the group compneur on 2007-10-10 13:15:56 as ** along with 1 person and 2 groups roland_ewald dIEMoSIRIS MoSi-Rostock
  • The chemical Langevin equation
    The Journal of Chemical Physics, Vol. 113, No. 1. (2000), pp. 297-306.
    by Daniel T Gillespie
    posted to gillespie langevinequation ppi stochasticity by dylanwalker on 2008-06-20 03:53:14 as read along with 2 people jstajic rjoy
  • Approximate accelerated stochastic simulation of chemically reacting systems
    The Journal of Chemical Physics, Vol. 115, No. 4. (2001), pp. 1716-1733.
    by Daniel T Gillespie
    posted to gillespie simulation_algorithms tau by dagmar on 2007-10-16 17:59:52 as ** along with 1 person matthewhflamm
  • Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels
    J. Phys. Chem. A, Vol. 104, No. 9. (9 March 2000), pp. 1876-1889.
    by MA Gibson, J Bruck
    posted to gillespie by arjunan on 2008-08-04 09:28:10 as ** along with 6 people and 1 group jstajic jberro petermilner matthewhflamm rcaze jjray Projet_ENSIMAG
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