YAGI Kiyoshi
- Affiliation
- Institute of Pure and Applied Sciences
- Official title
- Professor
- ORCID
- 0000-0003-1120-9355
- Sex
- Male
- Birth date
- 1976-05
- URL
- Office
- Chemical Computation & Information
- Phone
- 029-853-6521
- Research fields
Basic chemistry - Research keywords
Computational Chemistry, QM/MM, Biomolecules, Polymers - Research projects
Acceleration QM/MM free-energy simlations and molecular design of novel fluorogenic probe 2024-04 -- 2027-03 Kiyoshi Yagi JSPS/Grant-in-Aid for Scientific Research (B) 18,590,000Yen Reaction dynamics of light-driven protein based on non-adiabatic QM/MM molecular dynamics simulations 2022-04 -- 2024-03 Kiyoshi Yagi JSPS/Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) 6,630,000Yen Molecular design of novel fluorogenic probes based on QM/MM molecular dynamics simulations 2020-04 -- 2023-03 Kiyoshi Yagi JSPS/Grant-in-Aid for Scientific Research (B) 17,680,000Yen Development and applications of vibrational theory for biomolecules 2016-04 -- 2018-03 Kiyoshi Yagi JSPS/Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) 6,760,000Yen Novel development of anharmonic vibrational theories - Applications to hydrogen-bonded clusters 2010-04 -- 2011-03 Kiyoshi Yagi JSPS/Grant-in-Aid for Scientific Research on Priority Areas 4,000,000Yen Theoretical studies on the mechanism of water cluster anions 2009-04 -- 2011-03 Kiyoshi Yagi JSPS/Grant-in-Aid for Young Scientists (B) 4,550,000Yen Novel theory on vibrational dynamics and applications to hydrogen-bonded systems 2008-04 -- 2010-03 Kiyoshi Yagi JSPS/Grant-in-Aid for Scientific Research on Priority Areas 3,200,000Yen - Career history
2005-04 -- 2009-03 University of Tokyo,School of Engineering, Department of Applied Chemistry,Assistant Professor 2009-04 -- 2011-04 University of Yamanashi,Fuel Cell Nanomaterial Research Center,Lecturer 2011-04 -- 2012-11 University of Illinois at Urbana-Champaign,Department of Chemistry,Research Assistant Professor 2012-12 -- 2024-07 RIKEN,Cluster for Pioneering Research, Theoretical Molecular Science Laboratory,Senior Research Scientist - Academic background
1995-04 -- 1999-03 Univerisity of Tokyo, Faculty of Engineering, Department of Applied Chemistry 1999-04 -- 2001-03 Univerisity of Tokyo, School of Engineering, Department of Applied Chemistry 2001-04 -- 2004-03 Univerisity of Tokyo, School of Engineering, Department of Applied Chemistry - Degree
2004-03 PhD University of Tokyo - Academic societies
1997-06 -- (current) The Chemical Society of Japan 2006-10 -- (current) JAPAN SOCIETY FOR MOLECULAR SCIENCE 2014-12 -- (current) American Chemical Society 2017-03 -- (current) PROTEIN SCIENCE SOCIETY OF JAPAN 2018-05 -- (current) THE SPECTROSCOPICAL SOCIETY OF JAPAN 2019-07 -- (current) Japan Society of Theoretical Chemistry 2019-10 -- (current) THE BIOPHYSICAL SOCIETY OF JAPAN - Honors & Awards
2015-09 分子科学会奨励賞 Development of Molecular Vibrational Structure Theory with an Explicit Account of Anharmonicity 2021-03 RIKEN Eiho Prize Development and Release of GENESIS Optimized for "FUGAKU" and MD Simulations of a Spike Protein of SARS-Cov-2 - Articles
- High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM
Kiyoshi Yagi; Klaas Gunst; Toru Shiozaki; Yuji Sugita
Journal of Chemical Theory and Computation/21(8)/pp.4016-4029, 2025-04 - Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning
Lei Yao-Kun; YAGI Kiyoshi; Sugita Yuji
Journal of Chemical Theory and Computation/21(5)/pp.2695-2711, 2025-03 - Fermi resonance in the radiative vibrational cooling dynamics of N2O+
Harayama S.; Kuma S.; Kimura N.; Chartkunchand K. C.; ...
PHYSICAL REVIEW A/111(3)/p.032803, 2025-03-05
- High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM
- Conference, etc.
- Development of QM/MM Methods in GENESIS and Applications to Biomolecular Reactions and Spectroscopy
YAGI Kiyoshi
Asia Pacific Association of Theoretical and Computational Chemistry (APATCC) 11/2025-04-21--2025-04-25 - 非調和振動解析による複雑分子の 機能解明と制御
八木 清
高分子イオニクスシンポジウム/2025-03-18 - Development of High-Performance QM/MM Methods and Applications to Spectroscopy and Reactions of Biomolecules
八木 清
2025 Chemistry National Meeting/2025-03-07 - Vibrational Calculations of Complex Systems Using Localized Vibrational Modes
八木 清
2025 Spring Workshop on Physical and Computational Chemistry/2025-03-06 - Excited state QM/MM molecular dynamics simulations reveal the protein-molecule interaction of fluorogenic probes
八木 清
Chemistry Seminar/2025-03-05 - QM/MM計算に基づく自由エネルギー摂動法 の開発と創薬応用
八木 清
計算メディカルサイエンス事業部公開シンポジウム2024/2024-12-23 - QM/MM計算と非調和振動解析による 複雑分子の機能解明と制御
八木 清
武次徹也教授還暦記念シンポジウム/2024-11-30--2024-11-30 - QM/MM計算と非調和振動解析による 複雑分子の機能解明と制御
八木 清
計算・分光・情報・合成が拓く分子設計の最前線/2024-11-14--2024-11-14 - QM/MM計算に基づく生体分子の スペクトル解析
八木 清
化学系学協会東北大会/2024-09-14--2024-09-15
- Development of QM/MM Methods in GENESIS and Applications to Biomolecular Reactions and Spectroscopy
- Teaching
2024-09 -- 2025-02 物理化学I 理工学群化学類 - Talks
- Excited state QM/MM molecular dynamics simulations reveal the protein-molecule interaction of fluorogenic probes
八木 清
Chemistry Seminar/2025-03-05
- Excited state QM/MM molecular dynamics simulations reveal the protein-molecule interaction of fluorogenic probes
- Professional activities
2023-09 -- (current) Japan Society for Theoretical Chemistry 理論化学会幹事会/幹事
(Last updated: 2025-05-10)