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 probe2024-04 -- 2027-03Kiyoshi YagiJSPS/Grant-in-Aid for Scientific Research (B)18,590,000Yen
Reaction dynamics of light-driven protein based on non-adiabatic QM/MM molecular dynamics simulations2022-04 -- 2024-03Kiyoshi YagiJSPS/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 simulations2020-04 -- 2023-03Kiyoshi YagiJSPS/Grant-in-Aid for Scientific Research (B)17,680,000Yen
Development and applications of vibrational theory for biomolecules2016-04 -- 2018-03Kiyoshi YagiJSPS/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 clusters2010-04 -- 2011-03Kiyoshi YagiJSPS/Grant-in-Aid for Scientific Research on Priority Areas4,000,000Yen
Theoretical studies on the mechanism of water cluster anions2009-04 -- 2011-03Kiyoshi YagiJSPS/Grant-in-Aid for Young Scientists (B)4,550,000Yen
Novel theory on vibrational dynamics and applications to hydrogen-bonded systems2008-04 -- 2010-03Kiyoshi YagiJSPS/Grant-in-Aid for Scientific Research on Priority Areas3,200,000Yen
Career history
2005-04 -- 2009-03University of Tokyo,School of Engineering, Department of Applied Chemistry,Assistant Professor
2009-04 -- 2011-04University of Yamanashi,Fuel Cell Nanomaterial Research Center,Lecturer
2011-04 -- 2012-11University of Illinois at Urbana-Champaign,Department of Chemistry,Research Assistant Professor
2012-12 -- 2024-07RIKEN,Cluster for Pioneering Research, Theoretical Molecular Science Laboratory,Senior Research Scientist
Academic background
1995-04 -- 1999-03Univerisity of Tokyo, Faculty of Engineering, Department of Applied Chemistry
1999-04 -- 2001-03Univerisity of Tokyo, School of Engineering, Department of Applied Chemistry
2001-04 -- 2004-03Univerisity of Tokyo, School of Engineering, Department of Applied Chemistry
Degree
2004-03PhDUniversity 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
2021-03RIKEN Eiho PrizeDevelopment and Release of GENESIS Optimized for "FUGAKU" and MD Simulations of a Spike Protein of SARS-Cov-2
Articles
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
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
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)