R-leaping: accelerating the stochastic simulation algorithm by reaction leaps.

@article{Auger2006RleapingAT,
  title={R-leaping: accelerating the stochastic simulation algorithm by reaction leaps.},
  author={Anne Auger and Philippe Chatelain and Petros Koumoutsakos},
  journal={The Journal of chemical physics},
  year={2006},
  volume={125 8},
  pages={084103}
}
A novel algorithm is proposed for the acceleration of the exact stochastic simulation algorithm by a predefined number of reaction firings (R-leaping) that may occur across several reaction channels. In the present approach, the numbers of reaction firings are correlated binomial distributions and the sampling procedure is independent of any permutation of the reaction channels. This enables the algorithm to efficiently handle large systems with disparate rates, providing substantial… CONTINUE READING

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