Gillespie algorithm

Method for stochastic equation systems

In probability theory, the Gillespie algorithm generates a statistically correct trajectory of a stochastic equation system for which the reaction rates are known. It was created by Joseph L. Doob and others, presented by Dan Gillespie in 1976, and popularized in 1977 in a paper where he uses it to simulate chemical or biochemical systems of reactions efficiently and accurately using limited computational power. As computers have become faster, the algorithm has been used to simulate increasingly complex systems. The algorithm is particularly useful for simulating reactions within cells, where the number of reagents is low and keeping track of every single reaction is computationally feasible. Mathematically, it is a variant of a dynamic Monte Carlo method and similar to the kinetic Monte Carlo methods. It is used heavily in computational systems biology.

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