A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks.

@article{Ramaswamy2009ANC,
  title={A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks.},
  author={Rajesh Ramaswamy and N{\'e}lido Gonz{\'a}lez-Segredo and Ivo F. Sbalzarini},
  journal={The Journal of chemical physics},
  year={2009},
  volume={130 24},
  pages={244104}
}
We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) for sampling trajectories of the chemical master equation for a well-stirred system of coupled chemical reactions. Our formulation is based on factored-out, partial reaction propensities. This novel exact SSA, called the partial-propensity direct method (PDM), is highly efficient and has a computational cost that scales at most linearly with the number of chemical species, irrespective of the degree of… CONTINUE READING

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Memory requirement The memory requirement of PDM is given by the total size of the data structures

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