Parallelization of Gillespie algorithm based on binary words

David Lacoste; Michele Castellana

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arXiv · 2412.16613

Parallelization of Gillespie algorithm based on binary words

David Lacoste·Michele Castellana

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Abstract

We present an improvement of the Gillespie Exact Stochastic Simulation Algorithm, which leverages a bitwise representation of variables to perform independent simulations in parallel. We show that the subsequent gain in computational yield is significant, and it may allow to perform simulations of non-well mixed chemical systems. We illustrate this idea with simulations of Frank model, originally introduced to explain the emergence of homochirality in prebiotic systems.

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David Lacoste, Michele Castellana. 2024-12-21. Parallelization of Gillespie algorithm based on binary words. https://arxiv.org/abs/2412.16613

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