Stochastic modelling

• Stochastic master equation (McQuarrie 1964)

  • Generally intractable

• Gillespie method (Gillespie 1976)

  • Reaction-based stochastic algorithm
    • No representation of individual particles

• StochSim 1.0 (Morton-Firth et al. 1998)

  • Molecule-based stochastic algorithm
    • Individual particles are represented as software objects

Grand probability function: P(X1,X2 …,Xi;t)

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