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      Perspective: Stochastic algorithms for chemical kinetics.

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          Abstract

          We outline our perspective on stochastic chemical kinetics, paying particular attention to numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose description using ordinary differential equations has served as the basis for traditional chemical kinetics for the past 150 years. For such systems, we review the physical and mathematical rationale for a discrete-stochastic approach, and for the approximations that need to be made in order to regain the traditional continuous-deterministic description. We next take note of some of the more promising strategies for dealing stochastically with stiff systems, rare events, and sensitivity analysis. Finally, we review some recent efforts to adapt and extend the discrete-stochastic approach to systems that are not well-mixed. In that currently developing area, we focus mainly on the strategy of subdividing the system into well-mixed subvolumes, and then simulating diffusional transfers of reactant molecules between adjacent subvolumes together with chemical reactions inside the subvolumes.

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          Author and article information

          Journal
          J Chem Phys
          The Journal of chemical physics
          1089-7690
          0021-9606
          May 7 2013
          : 138
          : 17
          Affiliations
          [1 ] Dan T Gillespie Consulting, 30504 Cordoba Pl., Castaic, California 91384, USA. gillespiedt@mailaps.org
          Article
          10.1063/1.4801941
          23656106
          deb88701-31cd-4b6f-8f25-e7495aaeb1f6
          History

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