Rchr
J-GLOBAL ID：201801008794694205   Update date: Oct. 04, 2024

Yuto Komeiji

コメイジ ユウト | Yuto Komeiji
Affiliation and department：
National Institute of Advanced Industrial Science and Technology

About National Institute of Advanced Industrial Science and Technology


Other affiliations (3)：
  • Rikkyo University  Guest Professor
  • Saitama University  Department of Applied Chemistry, Faculty of Engineering   Part-time lecuture
  • Osaka University
Homepage URL  (1)： https://staff.aist.go.jp/y-komeiji
Research field  (3)： Software ,  Molecular biochemistry ,  Computational science
Research keywords  (9)： solvation ,  Polynucleotide ,  Protein ,  Quantum Chemistry ,  Biophysics ,  FMO-MD ,  FMO ,  MD ,  Molecular simulation
Research theme for competitive and other funds  (4)：
  • 2019 - 2022 Development of Periodic boundary FMO-MD via multipole expansion of environmental electrostatic potential
  • 2016 - 2019 Theoretical studies on the interaction between actinide species and biomolecules
  • 2010 - 2014 Microscopic Analysis of Dynamics-Controlled Organic Reactions
  • 2002 - 2003 Electronic structure calculations on K^+ ion channel protein
Papers (77)：
  • Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka, Takayuki Furuishi, Etsuo Yonemochi, Teruki Honma, et al. Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations. The Journal of Physical Chemistry B. 2024
  • Tatsuya NAKANO, Yoshio OKIYAMA, Katsunori SEGAWA, Yoshiro SAITO, Yuji MOCHIZUKI, Yuto KOMEIJI. Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD) Simulation. Journal of Computer Chemistry, Japan -International Edition. 2024. 10. n/a-n/a
  • Shigenori Tanaka, Yuto Komeiji. Thermal and Quantum Fluctuations of Harmonic Oscillator. JOURNAL OF PHYSICS AND CHEMISTRY RESEARCH. 2022. 4. 3. 1-2
  • Koji Okuwaki, Kazuki Akisawa, Ryo Hatada, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka. Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method. Applied Physics Express. 2022. 15. 1. 017001-017001
  • Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Shun Kitahara, YusukeF Tachino, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka. Fragment molecular orbital based interaction analyses on complexes between SARS-CoV-2 RBD variants and ACE2. JAPANESE JOURNAL OF APPLIED PHYSICS. 2021. 60. 9
ｍore...
MISC (3)：
  • 丸山 正, 嶋根 康弘, 岩沢 美佐子, 秦田 勇二, 吉田 尊雄, 高木 善弘, 大石 和恵, 田中 成典, 渡邉 博文, 徐 逢祺, et al. Analysis of Biological Interaction by Fragment Molecular Orbital (FMO) Method : Analyses of the interactions between measles virus hemagglutinin and their receptors. Annual report of the earth simulator. 2016. 251-257
  • T. Maruyama, Y. Shimane, K. Ohishi, M. Iwasawa, Y. Hatada, Y. Takaki, T. Yoshida, TANAKA SHIGENORI, S. Anzaki, Y. Komeiji, et al. Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method: Analyses of the Interactions between Virus Hamagglutinins and Their Receptors. Annual Report of the Earth Simulator Center. 2015. April 2014 - March 2015. 131-135
  • Komeiji Yuto, Nakano Tatsuya, Mochizuki Yuji. FMO-MD : ab initio Fragment Molecular Orbital-based Molecular Dynamics Simulation. Journal of the Japan Society for Simulation Technology. 2010. 29. 1. 2-9
Books (9)：
  • Fundamentals of molecular dynamics simulation
    CBI Society 2023 ISBN:9784910628066
  • Recent Advances of the Fragment Molecular Orbital Method (Y. Mochizuki et al., eds)
    Springer 2021
  • Quantum Mechanics in Drug Discovery (A Heifetz, ed.)
    Humana Press, New York, NY. 2020
  • Molecular Dynamics - Theoretical Developments and Applications in Nanotechnology and Energy
    InTech 2012
  • レアメタル・希少金属リサイクル技術の最先端 -ナノ・有機・メタラジーが広げるリサイクル技術-
    フロンティア出版 2011
ｍore...
Education (2)：
  • - 1992 Graduate school, Univ. Tokyo Science Botany
  • - 1987 University of Tokyo Agriculture Agricultural Biology
Professional career (1)：
  • 博士(理学) (東京大学)
Work history (8)：
  • 2024/04 - 現在 National Institute of Advanced Industrial Science and Technology carrier expert
  • 2023/04 - 現在 Osaka University
  • 2022/04 - 現在 Saitama University
  • 2019/12 - 2024/03 RIKEN Center for Biosystems Dynamics Research Guest researcher
  • 2011/04 - 現在 Rikkyo University
Show all
Association Membership(s) (5)：
JAPANESE SOCIETY FOR EXTREMOPHILES ,  Kyudo branch, Japanese academy of Budo ,  CHEM-BIO INFORMATICS SOCIETY ,  THE MOLECULAR SIMULATION SOCIETY OF JAPAN ,  Biophysical society
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