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Pathways for the formation of ice polymorphs from water predicted by a metadynamics method
The mechanism of how ice crystal form has been extensively studied by many researchers but remains an open question. Molecular dynamics (MD) simulations are a useful tool for investigating the molecular-scale mechanism of crystal formation. However, the timescale of phenomena that can be analyzed by...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069948/ https://www.ncbi.nlm.nih.gov/pubmed/32170179 http://dx.doi.org/10.1038/s41598-020-61773-x |
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author | Nada, Hiroki |
author_facet | Nada, Hiroki |
author_sort | Nada, Hiroki |
collection | PubMed |
description | The mechanism of how ice crystal form has been extensively studied by many researchers but remains an open question. Molecular dynamics (MD) simulations are a useful tool for investigating the molecular-scale mechanism of crystal formation. However, the timescale of phenomena that can be analyzed by MD simulations is typically restricted to microseconds or less, which is far too short to explore ice crystal formation that occurs in real systems. In this study, a metadynamics (MTD) method was adopted to overcome this timescale limitation of MD simulations. An MD simulation combined with the MTD method, in which two discrete oxygen–oxygen radial distribution functions represented by Gaussian window functions were used as collective variables, successfully reproduced the formation of several different ice crystals when the Gaussian window functions were set at appropriate oxygen–oxygen distances: cubic ice, stacking disordered ice consisting of cubic ice and hexagonal ice, high-pressure ice VII, layered ice with an ice VII structure, and layered ice with an unknown structure. The free-energy landscape generated by the MTD method suggests that the formation of each ice crystal occurred via high-density water with a similar structure to the formed ice crystal. The present method can be used not only to study the mechanism of crystal formation but also to search for new crystals in real systems. |
format | Online Article Text |
id | pubmed-7069948 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-70699482020-03-22 Pathways for the formation of ice polymorphs from water predicted by a metadynamics method Nada, Hiroki Sci Rep Article The mechanism of how ice crystal form has been extensively studied by many researchers but remains an open question. Molecular dynamics (MD) simulations are a useful tool for investigating the molecular-scale mechanism of crystal formation. However, the timescale of phenomena that can be analyzed by MD simulations is typically restricted to microseconds or less, which is far too short to explore ice crystal formation that occurs in real systems. In this study, a metadynamics (MTD) method was adopted to overcome this timescale limitation of MD simulations. An MD simulation combined with the MTD method, in which two discrete oxygen–oxygen radial distribution functions represented by Gaussian window functions were used as collective variables, successfully reproduced the formation of several different ice crystals when the Gaussian window functions were set at appropriate oxygen–oxygen distances: cubic ice, stacking disordered ice consisting of cubic ice and hexagonal ice, high-pressure ice VII, layered ice with an ice VII structure, and layered ice with an unknown structure. The free-energy landscape generated by the MTD method suggests that the formation of each ice crystal occurred via high-density water with a similar structure to the formed ice crystal. The present method can be used not only to study the mechanism of crystal formation but also to search for new crystals in real systems. Nature Publishing Group UK 2020-03-13 /pmc/articles/PMC7069948/ /pubmed/32170179 http://dx.doi.org/10.1038/s41598-020-61773-x Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Nada, Hiroki Pathways for the formation of ice polymorphs from water predicted by a metadynamics method |
title | Pathways for the formation of ice polymorphs from water predicted by a metadynamics method |
title_full | Pathways for the formation of ice polymorphs from water predicted by a metadynamics method |
title_fullStr | Pathways for the formation of ice polymorphs from water predicted by a metadynamics method |
title_full_unstemmed | Pathways for the formation of ice polymorphs from water predicted by a metadynamics method |
title_short | Pathways for the formation of ice polymorphs from water predicted by a metadynamics method |
title_sort | pathways for the formation of ice polymorphs from water predicted by a metadynamics method |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069948/ https://www.ncbi.nlm.nih.gov/pubmed/32170179 http://dx.doi.org/10.1038/s41598-020-61773-x |
work_keys_str_mv | AT nadahiroki pathwaysfortheformationoficepolymorphsfromwaterpredictedbyametadynamicsmethod |