Kiyoshi Yagi

Professor

University of Tsukuba

Japan

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Professor Kiyoshi Yagi is a faculty member at the University of Tsukuba in Japan. His research focuses on multi-scale molecular simulations, quantum mechanics/molecular mechanics (QM/MM) methods, and the analysis of vibrational spectra in chemical and enzymatic reactions. Recent publications include studies on enzymatic reaction cycles, neural network potentials, and allosteric regulation in biochemical processes.

Articles (14)

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2025

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2025

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2025

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2025

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2025

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2024

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2024

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2024

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2023

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2022

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2022

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2021

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JAPAN

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Shinya Tahara

Assistant Professor

Tohoku University

JAPAN

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Hiroki Otaki

Nagasaki University

JAPAN

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Naoki Kimura

National Institute for Fusion Science

JAPAN

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Kiyoshi Yagi

Research Interests

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About

Articles (14)

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

Toward understanding whole enzymatic reaction cycles using multi-scale molecular simulations

High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM

Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning

Fermi resonance in the radiative vibrational cooling dynamics of N2O+

Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins

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

Learning QM/MM potential using equivariant multiscale model

Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding

General Design Strategy to Precisely Control the Emission of Fluorophores via a Twisted Intramolecular Charge Transfer (TICT) Process

Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between α/β-Ligand Binding and Distal Domain Closure

Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H2O)21

Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin

Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations

Collaborators (10)

Eita Sasaki

Masaaki Fujii

Tatsuhiro Murakami

Tasuku Ueno

Takayasu Mikuni

Kayo Suda

Takayuki Yamaguchi

Shinya Tahara

Hiroki Otaki

Naoki Kimura

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