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Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning
[Image: see text] Molecular dynamics simulation is an indispensable tool for understanding the collective behavior of atoms and molecules and the phases they form. Statistical mechanics provides accurate routes for predicting macroscopic properties as time-averages over visited molecular configurati...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10302466/ https://www.ncbi.nlm.nih.gov/pubmed/37307434 http://dx.doi.org/10.1021/acs.jcim.3c00472 |
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author | Li, Chunhui Gilbert, Benjamin Farrell, Steven Zarzycki, Piotr |
author_facet | Li, Chunhui Gilbert, Benjamin Farrell, Steven Zarzycki, Piotr |
author_sort | Li, Chunhui |
collection | PubMed |
description | [Image: see text] Molecular dynamics simulation is an indispensable tool for understanding the collective behavior of atoms and molecules and the phases they form. Statistical mechanics provides accurate routes for predicting macroscopic properties as time-averages over visited molecular configurations - microstates. However, to obtain convergence, we need a sufficiently long record of visited microstates, which translates to the high-computational cost of the molecular simulations. In this work, we show how to use a point cloud-based deep learning strategy to rapidly predict the structural properties of liquids from a single molecular configuration. We tested our approach using three homogeneous liquids with progressively more complex entities and interactions: Ar, NO, and H(2)O under varying pressure and temperature conditions within the liquid state domain. Our deep neural network architecture allows rapid insight into the liquid structure, here probed by the radial distribution function, and can be used with molecular/atomistic configurations generated by either simulation, first-principle, or experimental methods. |
format | Online Article Text |
id | pubmed-10302466 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-103024662023-06-29 Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning Li, Chunhui Gilbert, Benjamin Farrell, Steven Zarzycki, Piotr J Chem Inf Model [Image: see text] Molecular dynamics simulation is an indispensable tool for understanding the collective behavior of atoms and molecules and the phases they form. Statistical mechanics provides accurate routes for predicting macroscopic properties as time-averages over visited molecular configurations - microstates. However, to obtain convergence, we need a sufficiently long record of visited microstates, which translates to the high-computational cost of the molecular simulations. In this work, we show how to use a point cloud-based deep learning strategy to rapidly predict the structural properties of liquids from a single molecular configuration. We tested our approach using three homogeneous liquids with progressively more complex entities and interactions: Ar, NO, and H(2)O under varying pressure and temperature conditions within the liquid state domain. Our deep neural network architecture allows rapid insight into the liquid structure, here probed by the radial distribution function, and can be used with molecular/atomistic configurations generated by either simulation, first-principle, or experimental methods. American Chemical Society 2023-06-12 /pmc/articles/PMC10302466/ /pubmed/37307434 http://dx.doi.org/10.1021/acs.jcim.3c00472 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Li, Chunhui Gilbert, Benjamin Farrell, Steven Zarzycki, Piotr Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning |
title | Rapid Prediction
of a Liquid Structure from a Single
Molecular Configuration Using Deep Learning |
title_full | Rapid Prediction
of a Liquid Structure from a Single
Molecular Configuration Using Deep Learning |
title_fullStr | Rapid Prediction
of a Liquid Structure from a Single
Molecular Configuration Using Deep Learning |
title_full_unstemmed | Rapid Prediction
of a Liquid Structure from a Single
Molecular Configuration Using Deep Learning |
title_short | Rapid Prediction
of a Liquid Structure from a Single
Molecular Configuration Using Deep Learning |
title_sort | rapid prediction
of a liquid structure from a single
molecular configuration using deep learning |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10302466/ https://www.ncbi.nlm.nih.gov/pubmed/37307434 http://dx.doi.org/10.1021/acs.jcim.3c00472 |
work_keys_str_mv | AT lichunhui rapidpredictionofaliquidstructurefromasinglemolecularconfigurationusingdeeplearning AT gilbertbenjamin rapidpredictionofaliquidstructurefromasinglemolecularconfigurationusingdeeplearning AT farrellsteven rapidpredictionofaliquidstructurefromasinglemolecularconfigurationusingdeeplearning AT zarzyckipiotr rapidpredictionofaliquidstructurefromasinglemolecularconfigurationusingdeeplearning |