Decomposition of Friction Coefficients to Analyze Hydration Effects on a C$_{60}$(OH)$_{\rm n}$
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arXiv
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| Autori principali: | , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866916410965360640 |
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| author | Iwashita, Tomoya Uematsu, Yuki Terazima, Masahide Akiyama, Ryo |
| author_facet | Iwashita, Tomoya Uematsu, Yuki Terazima, Masahide Akiyama, Ryo |
| contents | To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the molecular friction coefficient into the contributions for each site on the macromolecule. The method was applied to several fullerenols in ambient water. The friction coefficients for the hydrophilic part, such as the OH group, were larger than those for the hydrophobic part, such as the C. The hydration effect did not depend only on the kind of functional group but also on surface roughness. This approach would be useful in explaining the experimentally observed large changes in diffusion coefficients of proteins that were accompanied by conformation changes. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2409_17028 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Decomposition of Friction Coefficients to Analyze Hydration Effects on a C$_{60}$(OH)$_{\rm n}$ Iwashita, Tomoya Uematsu, Yuki Terazima, Masahide Akiyama, Ryo Biological Physics To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the molecular friction coefficient into the contributions for each site on the macromolecule. The method was applied to several fullerenols in ambient water. The friction coefficients for the hydrophilic part, such as the OH group, were larger than those for the hydrophobic part, such as the C. The hydration effect did not depend only on the kind of functional group but also on surface roughness. This approach would be useful in explaining the experimentally observed large changes in diffusion coefficients of proteins that were accompanied by conformation changes. |
| title | Decomposition of Friction Coefficients to Analyze Hydration Effects on a C$_{60}$(OH)$_{\rm n}$ |
| topic | Biological Physics |
| url | https://arxiv.org/abs/2409.17028 |