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The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function
The tiny encryption algorithm (TEA) is widely used when performing dissipative particle dynamics (DPD) calculations in parallel, usually on distributed memory systems. In this research, we reduced the computational cost of the TEA hash function and investigated the influence of the quality of the ra...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8078758/ https://www.ncbi.nlm.nih.gov/pubmed/33905444 http://dx.doi.org/10.1371/journal.pone.0250593 |
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author | Okada, Kiyoshiro Brumby, Paul E. Yasuoka, Kenji |
author_facet | Okada, Kiyoshiro Brumby, Paul E. Yasuoka, Kenji |
author_sort | Okada, Kiyoshiro |
collection | PubMed |
description | The tiny encryption algorithm (TEA) is widely used when performing dissipative particle dynamics (DPD) calculations in parallel, usually on distributed memory systems. In this research, we reduced the computational cost of the TEA hash function and investigated the influence of the quality of the random numbers generated on the results of DPD calculations. It has already been established that the randomness, or quality, of the random numbers depend on the number of processes from internal functions such as SHIFT, XOR and ADD, which are commonly referred to as “rounds”. Surprisingly, if we choose seed numbers from high entropy sources, with a minimum number of rounds, the quality of the random numbers generated is sufficient to successfully perform accurate DPD simulations. Although it is well known that using a minimal number of rounds is insufficient for generating high-quality random numbers, the combination of selecting good seed numbers and the robustness of DPD simulations means that we can reduce the random number generation cost without reducing the accuracy of the simulation results. |
format | Online Article Text |
id | pubmed-8078758 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-80787582021-05-05 The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function Okada, Kiyoshiro Brumby, Paul E. Yasuoka, Kenji PLoS One Research Article The tiny encryption algorithm (TEA) is widely used when performing dissipative particle dynamics (DPD) calculations in parallel, usually on distributed memory systems. In this research, we reduced the computational cost of the TEA hash function and investigated the influence of the quality of the random numbers generated on the results of DPD calculations. It has already been established that the randomness, or quality, of the random numbers depend on the number of processes from internal functions such as SHIFT, XOR and ADD, which are commonly referred to as “rounds”. Surprisingly, if we choose seed numbers from high entropy sources, with a minimum number of rounds, the quality of the random numbers generated is sufficient to successfully perform accurate DPD simulations. Although it is well known that using a minimal number of rounds is insufficient for generating high-quality random numbers, the combination of selecting good seed numbers and the robustness of DPD simulations means that we can reduce the random number generation cost without reducing the accuracy of the simulation results. Public Library of Science 2021-04-27 /pmc/articles/PMC8078758/ /pubmed/33905444 http://dx.doi.org/10.1371/journal.pone.0250593 Text en © 2021 Okada et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Okada, Kiyoshiro Brumby, Paul E. Yasuoka, Kenji The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function |
title | The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function |
title_full | The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function |
title_fullStr | The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function |
title_full_unstemmed | The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function |
title_short | The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function |
title_sort | influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8078758/ https://www.ncbi.nlm.nih.gov/pubmed/33905444 http://dx.doi.org/10.1371/journal.pone.0250593 |
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