Prediction of rare events associated with biomolecules using mean force dynamics
| Project/Area Number |
17K05620
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Biological physics/Chemical physics/Soft matter physics
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| Research Institution | National Institute of Advanced Industrial Science and Technology |
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Principal Investigator |
Morishita Tetsuya 国立研究開発法人産業技術総合研究所, 材料・化学領域, 主任研究員 (10392672)
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| Co-Investigator(Kenkyū-buntansha) |
米澤 康滋 近畿大学, 先端技術総合研究所, 教授 (40248753)
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| Project Period (FY) |
2017-04-01 – 2022-03-31
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| Project Status |
Completed (Fiscal Year 2021)
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| Budget Amount *help |
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2020: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2019: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2017: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
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| Keywords | 自由エネルギー / レア・イベント / 分子動力学 / 機械学習 / 自由エネルギー計算 / レアイベント / 生体分子 / 平均力 / 位相空間 / 化学物理 / 分子動力学シミュレーション |
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| Outline of Final Research Achievements |
We have proposed an approach that incorporates time dependence in principal component analysis to identify each of step-by-step structural changes in molecular dynamics (MD) simulations (TDPCA). The time dependence allows for re-optimization of the principal components according to the structural development, which can be exploited for enhanced sampling in MD simulations. We have also developed algorithms that allow for reconstructing free-energy profiles along collective variables (CVs) by extending the logarithmic mean-force (LogMFD) dynamics. The logarithmic parallel-dynamics (LogPD) algorithm was proposed to efficiently reconstruct free-energy profiles using multiple replicas of the system based on Crooks-Jarzynski nonequilibrium work relation. Also, isokinetic dynamics was incorporated in LogMFD/PD to enable uniform sampling along the CVs. These new approaches allow for on-the-fly free-energy estimation, which can be implemented using an open-source library, PLUMED.
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| Academic Significance and Societal Importance of the Research Achievements |
本研究では、分子シミュレーションが抱える時間スケールに関する問題に取り組み、従来では実現不可能な長時間現象を、限られた時間内において実現できる手法開発を推進した。これにより、複雑な構造を有する生体分子やナノ物質の原子レベルの長時間挙動を予測することが可能となり、ナノ材料設計や分子材料設計、ひいては創薬におけるシミュレーションによる開発促進に繋がることが期待される。
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Report
(6 results)
Research Products
(33 results)
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[Journal Article] Epigenetic Protection of Vertebrate Lymphoid Progenitor Cells by Dnmt12020
Author(s)
Iwanami Norimasa、Takeshita Kohei、Lawir Divine-Fondzenyuy、Suetake Isao、Tajima Shoji、Sikora Katarzyna、Trancoso In?s、?Meara Connor、Siamishi Iliana、Takahama Yousuke、Furutani-Seiki Makoto、Kondoh Hisato、Yonezawa Yasushige、Schorpp Michael、Boehm Thomas
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Journal Title
iScience
Volume: 23
Issue: 7
Pages: 101260-101260
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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