Parallelization of Gillespie algorithm based on binary words
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arXiv
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| Main Authors: | , |
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| Format: | Preprint |
| Published: |
2024
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| _version_ | 1866916538086326272 |
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| author | Lacoste, David Castellana, Michele |
| author_facet | Lacoste, David Castellana, Michele |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2412_16613 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Parallelization of Gillespie algorithm based on binary words Lacoste, David Castellana, Michele Statistical Mechanics Computational Physics 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. |
| title | Parallelization of Gillespie algorithm based on binary words |
| topic | Statistical Mechanics Computational Physics |
| url | https://arxiv.org/abs/2412.16613 |