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A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow
Many properties of water, such as turbulent flow, are closely related to water clusters, whereas how water clusters form and transform in bulk water remains unclear. A hierarchical clustering method is introduced to search out water clusters in hydrogen bonded network based on modified Louvain algor...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8100111/ https://www.ncbi.nlm.nih.gov/pubmed/33953246 http://dx.doi.org/10.1038/s41598-021-88810-7 |
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author | Gao, Yitian Fang, Hongwei Ni, Ke |
author_facet | Gao, Yitian Fang, Hongwei Ni, Ke |
author_sort | Gao, Yitian |
collection | PubMed |
description | Many properties of water, such as turbulent flow, are closely related to water clusters, whereas how water clusters form and transform in bulk water remains unclear. A hierarchical clustering method is introduced to search out water clusters in hydrogen bonded network based on modified Louvain algorithm of graph community. Hydrogen bonds, rings and fragments are considered as 1st-, 2nd-, and 3rd-level structures, respectively. The distribution, dynamics and structural characteristics of 4th- and 5th-level clusters undergoing non-shear- and shear-driven flow are also analyzed at various temperatures. At low temperatures, nearly 50% of water molecules are included in clusters. Over 60% of clusters remain unchanged between neighboring configurations. Obvious collective translational motion of clusters is observed. The topological difference for clusters is elucidated between the inner layer, which favors 6-membered rings, and the external surface layer, which contains more 5-membered rings. Temperature and shearing can not only accelerate the transformation or destruction of clusters at all levels but also change cluster structures. The assembly of large clusters can be used to discretize continuous liquid water to elucidate the properties of liquid water. |
format | Online Article Text |
id | pubmed-8100111 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-81001112021-05-07 A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow Gao, Yitian Fang, Hongwei Ni, Ke Sci Rep Article Many properties of water, such as turbulent flow, are closely related to water clusters, whereas how water clusters form and transform in bulk water remains unclear. A hierarchical clustering method is introduced to search out water clusters in hydrogen bonded network based on modified Louvain algorithm of graph community. Hydrogen bonds, rings and fragments are considered as 1st-, 2nd-, and 3rd-level structures, respectively. The distribution, dynamics and structural characteristics of 4th- and 5th-level clusters undergoing non-shear- and shear-driven flow are also analyzed at various temperatures. At low temperatures, nearly 50% of water molecules are included in clusters. Over 60% of clusters remain unchanged between neighboring configurations. Obvious collective translational motion of clusters is observed. The topological difference for clusters is elucidated between the inner layer, which favors 6-membered rings, and the external surface layer, which contains more 5-membered rings. Temperature and shearing can not only accelerate the transformation or destruction of clusters at all levels but also change cluster structures. The assembly of large clusters can be used to discretize continuous liquid water to elucidate the properties of liquid water. Nature Publishing Group UK 2021-05-05 /pmc/articles/PMC8100111/ /pubmed/33953246 http://dx.doi.org/10.1038/s41598-021-88810-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Gao, Yitian Fang, Hongwei Ni, Ke A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow |
title | A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow |
title_full | A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow |
title_fullStr | A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow |
title_full_unstemmed | A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow |
title_short | A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow |
title_sort | hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8100111/ https://www.ncbi.nlm.nih.gov/pubmed/33953246 http://dx.doi.org/10.1038/s41598-021-88810-7 |
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