ホーム > 八木 清/ YAGI, Kiyoshi
八木 清
YAGI, Kiyoshi
数理物質系化学域 , 教授 Department of Chemistry, Institute of Pure Science , Professor
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1.
Deciphering Infrared Difference Spectra of Bovine Rhodopsin in the Amide I Region by Localized Anharmonic Vibrational Calculations
Nao Matsuyama; Kota Katayama; Kiyoshi Yagi
The Journal of Physical Chemistry B (2026)
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2.
Computational Analysis of Structural and Photophysical Properties of a 1,8-Naphthalimide Derivative in Aqueous Solution
Natsumi Watanabe; Masato Sumita; Hironori Izawa; Kiyoshi YagiToru Matsui
The Journal of Physical Chemistry A (2026) Semantic Scholar
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3.
Effect of Nucleating Agent on Crystallization of Poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate]
Masahiro Fujita; Noboru Ohta; Kiyoshi Yagi; Hideki Abe
ACS Omega (2026) Semantic Scholar
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4.
Molecular dynamics–quantum mechanical/molecular mechanical simulation of amide I infrared spectra to identify protein conformational ensembles: a case study of chignolin
Hiraku Oshima; Shogo Fukatsu; Wataru Sato; Kiyoshi YagiMinoru Kubo
Bulletin of the Chemical Society of Japan 99: (2026) Semantic Scholar
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5.
Toward understanding whole enzymatic reaction cycles using multi-scale molecular simulations
Shingo Ito; Chigusa Kobayashi; Kiyoshi Yagi; Yuji Sugita
Current Opinion in Structural Biology (2025) Semantic Scholar
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6.
MD–QM/MM Simulation of Amide I Infrared Spectra to Identify Protein Conformational Ensembles: A Case Study of Chignolin
Hiraku Oshima; Shogo Fukatsu; Wataru Sato; Kiyoshi YagiMinoru Kubo
(2025)
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7.
Ion Transport Analysis of Anion-Exchange Membranes in Various Hydration States: Combining Experiments with Molecular Dynamics Simulation
Yuri Nara; Kento Kasahara; Kiyoshi Yagi; Kang Kim (+2 著者) Manabu Tanaka
ACS Applied Polymer Materials (2025) Semantic Scholar
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8.
Hyper-Raman Spectra in Solution based on the Reference Interaction Site Model Self-Consistent Field Method Coupled with Constrained Spatial Electron Density Distribution and Vibrational Quasi-Degenerate Perturbation Theory
Kayo Suda; Kiyoshi Yagi; Daisuke Yokogawa
The Journal of Physical Chemistry Letters (2025)
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9.
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: 4016 (2025) Semantic Scholar
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10.
Fermi resonance in the radiative vibrational cooling dynamics of N2O+
S. Harayama; S. Kuma; N. Kimura; K. C. Chartkunchand (+6 著者) T. Azuma
Physical Review A (2025) Semantic Scholar
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11.
Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning
Yao-Kun Lei; Kiyoshi Yagi; Yuji Sugita
Journal of Chemical Theory and Computation 21: 2695 (2025) Semantic Scholar
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12.
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
Jaewoon Jung; Kiyoshi Yagi; Cheng Tan; Hiraku Oshima (+6 著者) Yuji Sugita
The Journal of Physical Chemistry B 128: 6028 (2024) Semantic Scholar
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13.
Learning QM/MM potential using equivariant multiscale model
Yao-Kun Lei; Kiyoshi Yagi; Yuji Sugita
The Journal of Chemical Physics (2024) Semantic Scholar
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14.
Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins
Hiroki Otaki; Shun-ichi Ishiuchi; Masaaki Fujii; Yuji SugitaKiyoshi Yagi
Physical Chemistry Chemical Physics 26: 9906 (2024) Semantic Scholar
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15.
Allosteric regulation of beta-reaction stage I in tryptophan synthase upon the alpha-ligand binding
Shingo Ito; Kiyoshi Yagi; Yuji Sugita
JOURNAL OF CHEMICAL PHYSICS 158: (2023) Semantic Scholar
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16.
General Design Strategy to Precisely Control the Emission of Fluorophores via a Twisted Intramolecular Charge Transfer (TICT) Process.
Kenjiro Hanaoka; Shimpei Iwaki; Kiyoshi Yagi; Takuya Myochin (+13 著者) Yasuteru Urano
Journal of the American Chemical Society 144: 19778 (2022) Semantic Scholar
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17.
Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between alpha/beta-Ligand Binding and Distal Domain Closure
Shingo Ito; Kiyoshi Yagi; Yuji Sugita
JOURNAL OF PHYSICAL CHEMISTRY B 126: 3300 (2022) Semantic Scholar
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18.
非調和振動計算プログラムSINDOの紹介
八木清
分子シミュレーション学会誌 「アンサンブル」 24: 125 (2022)
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19.
量子化学と分子動力学の融合が拓く高分子の分子機能解析
八木清
溶液化学研究会誌 (2022)
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20.
Weight average approaches for predicting dynamical properties of biomolecules
Kiyoshi Yagi; Suyong Re; Takaharu Mori; Yuji Sugita
CURRENT OPINION IN STRUCTURAL BIOLOGY 72: 88 (2022) Semantic Scholar
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