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Spatio-temporal hierarchy in the dynamics of a minimalist protein model
| Title: | Spatio-temporal hierarchy in the dynamics of a minimalist protein model |
| Authors: | Matsunaga, Yasuhiro Browse this author | | Baba, Akinori Browse this author | | Li, Chun-Biu Browse this author | | Straub, John E. Browse this author | | Toda, Mikito Browse this author →KAKEN DB | | Komatsuzaki, Tamiki Browse this author →KAKEN DB | | Berry, R. Stephen Browse this author |
| Issue Date: | 7-Dec-2013 |
| Publisher: | American Institute of Physics |
| Journal Title: | Journal of chemical physics |
| Volume: | 139 |
| Issue: | 21 |
| Start Page: | 215101-1 |
| End Page: | 215101-13 |
| Publisher DOI: | 10.1063/1.4834415 |
| Abstract: | A method for time series analysis of molecular dynamics simulation of a protein is presented. In this approach, wavelet analysis and principal component analysis are combined to decompose the spatio-temporal protein dynamics into contributions from a hierarchy of different time and space scales. Unlike the conventional Fourier-based approaches, the time-localized wavelet basis captures the vibrational energy transfers among the collective motions of proteins. As an illustrative vehicle, we have applied our method to a coarse-grained minimalist protein model. During the folding and unfolding transitions of the protein, vibrational energy transfers between the fast and slow time scales were observed among the large-amplitude collective coordinates while the other small-amplitude motions are regarded as thermal noise. Analysis employing a Gaussian-based measure revealed that the time scales of the energy redistribution in the subspace spanned by such large-amplitude collective coordinates are slow compared to the other small-amplitude coordinates. Future prospects of the method are discussed in detail. |
| Rights: | Copyright 2013 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in Journal of Chemical Physics 139, 215101 (2013) and may be found at http://scitation.aip.org/content/aip/journal/jcp/139/21/10.1063/1.4834415. |
| Type: | article |
| URI: | http://hdl.handle.net/2115/54747 |
| Appears in Collections: | 電子科学研究所 (Research Institute for Electronic Science) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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Submitter: 小松崎 民樹
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