Kiyoshi Yagi

University of Tsukuba — Japan

Physics and Astronomy · Physical Sciences

33h-index3.0kcitations106works4.22yr avg
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Research Topics

Advanced Chemical Physics Studies(53), Spectroscopy and Quantum Chemical Studies(42), Quantum, superfluid, helium dynamics(13), Protein Structure and Dynamics(12), Spectroscopy and Laser Applications(10)

Publications106 total

Effect of Nucleating Agent on Crystallization of Poly[( <i>R</i> )-3-hydroxybutyrate- <i>co</i> -( <i>R</i> )-3-hydroxyhexanoate]
ACS Omega·2026Open Access
Molecular dynamics–quantum mechanical/molecular mechanical simulation of amide I infrared spectra to identify protein conformational ensembles: a case study of chignolin
Bulletin of the Chemical Society of Japan·2026
MD–QM/MM Simulation of Amide I Infrared Spectra to Identify Protein Conformational Ensembles: A Case Study of Chignolin
2025Open Access
Ion Transport Analysis of Anion-Exchange Membranes in Various Hydration States: Combining Experiments with Molecular Dynamics Simulation
ACS Applied Polymer Materials·2025
Toward understanding whole enzymatic reaction cycles using multi-scale molecular simulations
Current Opinion in Structural Biology·2025· 3 citedOpen Access
Hyper-Raman Spectra in Solution Based on the Reference Interaction Site Model Self-Consistent Field Method Coupled with the Constrained Spatial Electron Density Distribution and Vibrational Quasi-Degenerate Perturbation Theory
The Journal of Physical Chemistry Letters·2025· 1 cited
Hyper-Raman Spectra in Solution based on theReference Interaction Site Model Self-ConsistentField Method Coupled with Constrained SpatialElectron Density Distribution and VibrationalQuasi-Degenerate Perturbation Theory
2025Open Access
Hyper-Raman Spectra in Solution based on theReference Interaction Site Model Self-ConsistentField Method Coupled with Constrained SpatialElectron Density Distribution and VibrationalQuasi-Degenerate Perturbation Theory
2025Open Access
High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM
Journal of Chemical Theory and Computation·2025· 6 citedOpen Access
Fermi resonance in the radiative vibrational cooling dynamics of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mrow><mml:mi mathvariant="normal">N</mml:mi></mml:mrow><mml:mn>2</mml:mn></mml:msub><mml:msup><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mo>+</mml:mo></mml:msup></mml:math>
Physical review. A/Physical review, A·2025· 1 cited
Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning
Journal of Chemical Theory and Computation·2025· 5 citedOpen Access
Enzymes can activate and mobilize the cytoplasmic environment across scales
2025· 6 citedOpen Access
Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning
2024Open Access
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models
The Journal of Physical Chemistry B·2024· 32 citedOpen Access
Learning QM/MM potential using equivariant multiscale model
The Journal of Chemical Physics·2024· 17 citedOpen Access
Learning QM/MM Potential using Equivariant Multiscale Model
2024· 1 citedOpen Access
Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins
Physical Chemistry Chemical Physics·2024Open Access
Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins
2023Open Access
Dataset for: Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins
Zenodo (CERN European Organization for Nuclear Research)·2023Open Access
Dataset for: Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins
Zenodo (CERN European Organization for Nuclear Research)·2023Open Access
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Frequent Co-authors

Kimihiko Hirao(19), So Hirata(15), Tetsuya Taketsugu(11), Yuji Sugita(10), Murat Keçeli(6), Bo Thomsen(5), Mark S. Gordon(3), Gennady Mil’nikov(3), Hiroki Nakamura(3), Ove Christiansen(3), Olaseni Sode(3), Valerie Rodriguez‐Garcia(2), Chikako Oyanagi(2), Chigusa Kobayashi(2), Koichiro Shirota(2), Pai‐Chi Li(2), Toshihide Kobayashi(2), Hiroshi Fujisaki(2), John E. Straub(2), Shingo Ito(2)