生命科学研究部門

生命機能情報分野

名前 所属 職名
重田 育照 教授/部門主任
原田 隆平 准教授
庄司 光男 助教
西澤 宏晃 助教
堀 優太 助教
鬼頭(西岡) 宏任 研究員
満田 祐樹 研究員
Kowit Hengphasatporn 研究員
広川 貴次 医学医療系 教授(共同研究員)
吉野 龍ノ介 医学医療系 助教(共同研究員)

分子進化分野

名前 所属 職名
稲垣 祐司 教授/分野リーダー
石谷 佳之 研究員
橋本 哲男 生命環境系 生物科学専攻長(後期)/教授(共同研究員)

生命機能情報分野

氏名 重田 育照
Name Shigeta Yasuteru
所属
所属研究科/学類 数理物質科学研究科/理工学群 物理学類
職名 教授/部門主任
研究テーマ ナノ-バイオ系の計算シミュレーション
関連リンク
Email shigetaccs.tsukuba.ac.jp
  • 研究キーワード
  • 経歴
    2019年04月
    -
    量子科学技術研究開発機構 高崎量子応用研究所 客員研究員
    2018年04月
    -
    宇宙航空研究開発機構 宇宙科学研究所 学際科学研究系 客員教授
    2016年04月
    -
    2018年03月
    分子科学研究所 客員教授
    2014年05月
    -
    大阪大学 大学院基礎工学研究科 招聘教授
    2014年03月
    -
    筑波大学 大学院数理物質科学研究科物理学系 教授
    2011年08月
    -
    2013年07月
    文部科学省 研究振興局学術助成課 学術調査官(兼任)
    2010年08月
    -
    2014年03月
    大阪大学 大学院基礎工学研究科物質創成専攻 准教授
    2008年05月
    -
    2010年07月
    兵庫県立大学 大学院生命理学研究科ピコバイオロジー研究所 特任准教授
    2007年02月
    -
    2008年05月
    筑波大学 大学院数理物質科学研究科物理学専攻 講師
    2003年12月
    -
    2007年01月
    東京大学 大学院工学系研究科応用化学専攻 助手
    2001年04月
    -
    2003年12月
    東京大学 大学院総合文化研究科相関科学専攻 学術振興会博士特別研究員(DC2)
    2000年04月
    -
    2001年03月
    大阪大学 大学院理学研究科化学専攻 日本学術振興会特別研究員(PD)
    1999年01月
    -
    2000年03月
    大阪大学 大学院理学研究科化学専攻 学術振興会博士特別研究員(DC2)
  • 論文
    Local Structures and Dynamics of Imidazole Molecules in Poly(vinylphosphonic acid)–Imidazole Composite Investigated by Molecular Dynamics
    Hori, Yuta, Suetake, Toshiya, Shiota, Yoshihito, Yoshizawa, Kazunari, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, Motohiro
    ACS Applied Polymer Materials 2020年02月[査読有り]
    Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography
    Shoji, Mitsuo, Isobe, Hiroshi, Shen, Jian-Ren, Suga, Michihiro, Akita, Fusamichi, Miyagawa, Koichi, Shigeta, Yasuteru, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 730 2019年09月[査読有り]
    Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency
    Harada, Ryuhei, Shigeta, Yasuteru
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 59 (9) 2019年09月[査読有り]
    Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein Dynamics
    Harada, Ryuhei, Sladek, Vladimir, Shigeta, Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (9) 2019年09月[査読有り]
    Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water-Air Interface
    Ohto, Tatsuhiko, Dodia, Mayank, Xu, Jianhang, Imoto, Sho, Tang, Fujie, Zysk, Frederik, Kühne, Thomas D, Shigeta, Yasuteru, Bonn, Mischa, Wu, Xifan, Nagata, Yuki
    The journal of physical chemistry letters 10 (17) 2019年08月[査読有り]
    Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
    Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
    Journal of molecular graphics & modelling 92 2019年07月[査読有り]
    Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
    Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
    Journal of molecular graphics & modelling 92 2019年07月[査読有り]
    First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface
    Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Kamiya, Katsumasa, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    The journal of physical chemistry. A 123 (26) 2019年07月[査読有り]
    Pyrrole-Based π-System-Pt Complexes: Chiroptical Properties and Excited-State Dynamics with Microsecond Triplet Lifetimes
    Hirata, Goki, Kobayashi, Yoichi, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
    Chemistry (Weinheim an der Bergstrasse, Germany) 25 (37) 2019年07月[査読有り]
    Reaction mechanism of non-enzymatic stereoselective formation of wine lactone
    Kyan, Akane, Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 725 2019年06月[査読有り]
    Numerical investigation of the nano-scale solutal Marangoni convections
    Imai, Y, Yamamoto, T, Sekimoto, A, Okano, Y, Sato, R, Shigeta, Y
    JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS 98 (SI) 2019年05月[査読有り]
    In silico strcutral modelling and analysis of elongation factor 1alpha and elongation factor-like proteins.
    Kotaro, Sakamoto, Megumi, Kayanuma, Inagaki, Yuji, Tetsuo, Hashimoto, Yasuteru, Shigeta
    ACS Omega 4 (4) 2019年04月[査読有り]
    Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-order Molecular Dynamics Simulation
    Aida, Hayato, Harada, Ryuhei, Shigeta, Yasuteru
    CHEMISTRY LETTERS 48 (4) 2019年04月[査読有り]
    Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical Insight
    Xu, Tianlv, Li, Jia Hui, Momen, Roya, Huang, Wei Jie, Kirk, Steven Robert, Shigeta, Yasuteru, Jenkins, Samantha
    Journal of the American Chemical Society 141 (13) 2019年04月[査読有り]
    Photosubstitution Reaction of cis-[Ru(bpy)(2)(CH3CN)(2)](2+) and cis-[Ru(bpy)(2)(NH3)(2)](2+) in Aqueous Solution via Monoaqua Intermediate
    Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
    The journal of physical chemistry. A 123 (13) 2019年03月[査読有り]
    Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
    Kimatsuka, Masato, Sato, Ryuma, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMISTRY LETTERS 48 (3) 2019年03月[査読有り]
    分子動力学シミュレーションによる不凍タンパク質RiAFPの氷の結晶成長に及ぼす影響の解析
    木間塚政人, 佐藤竜馬, 原田隆平, 庄司, 光男, 重田, 育照
    Journal of Computer Chemistry Japan 17 (5) 2019年03月[査読有り]
    First-principle study of ammonia decomposition and nitrogen incorporation on the GaN surface in metal organic vapor phase epitaxy
    Bui, Kieu My, Iwata, Jun-Ichi, Kangawa, Yoshihiro, Shiraishi, Kenji, Shigeta, Yasuteru, Oshiyama, Atsushi
    JOURNAL OF CRYSTAL GROWTH 507 2019年02月[査読有り]
    Quadruply N-methylated octaphyrin: a helical macrocycle exhibiting chiroptical properties and dynamic conformation changes correlated with helical and inner N-methyl orientations
    Naito, Wakana, Urakawa, Kazuki, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
    ORGANIC & BIOMOLECULAR CHEMISTRY 17 (5) 2019年02月[査読有り]
    Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins
    Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
    Journal of computational chemistry 40 (15) 2019年02月[査読有り]
    Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
    Harada, Ryuhei, Shigeta, Yasuteru
    Advances in Quantum Chemistry (78) 2019年02月[査読有り]
    Theoretical study of the photodissociation reaction of methanol
    Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 714 2019年01月[査読有り]
    New Assay Method Based on Raman Spectroscopy for Enzymes Reacting with Gaseous Substrates
    Kawahara-Nakagawa, Yuka, Nishikawa, Koji, Nakashima, Satoru, Inoue, Shota, Ohta, Takehiro, Ogura, Takashi, Shigeta, Yasuteru, Fukutani, Katsuyuki, Yagi, Tatsuhiko, Higuchi, Yoshiki
    Protein science : a publication of the Protein Society 28 (3) 2019年01月[査読有り]
    Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction
    Tokiwa, Takaki, Shoji, Mitsuo, Sladek, Vladimir, Shibata, Naoki, Higuchi, Yoshiki, Kataoka, Kunishige, Sakurai, Takeshi, Shigeta, Yasuteru, Misaizu, Fuminori
    Molecules (Basel, Switzerland) 24 (1) 2019年01月[査読有り]
    Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations
    Harada, Ryuhei, Shigeta, Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (1) 2019年01月[査読有り]
    Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations
    Tokiwa, Takaki, Nakano, Shogo, Yamamoto, Yuta, Ishikawa, Takeshi, Ito, Sohei, Sladek, Vladimir, Fukuzawa, Kaori, Mochizuki, Yuji, Tokiwa, Hiroaki, Misaizu, Fuminori, Shigeta, Yasuteru
    Journal of chemical information and modeling 59 (1) 2019年01月[査読有り]
    High- performance Na ion cathodes based on the ubiquitous and reversible O redox reaction
    Assadi, M. Hussein N, Fronzi, Marco, Ford, Mike, Shigeta, Yasuteru
    JOURNAL OF MATERIALS CHEMISTRY A 6 (47) 2018年12月[査読有り]
    Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion
    Sato, Ryuma, Kitoh-Nishioka, Hirotaka, Kamada, Kenji, Mizokuro, Toshiko, Kobayashi, Kenji, Shigeta, Yasuteru
    The journal of physical chemistry letters 9 (22) 2018年11月[査読有り]
    In Silico Structural Analysis of Elongation Factor-1 Alpha and Elongation Factor-Like
    Sakamoto, Kotaro, Kayanuma, Megumi, Shigeta, Yasuteru
    PROTEIN SCIENCE 27 (1:SI) 2018年11月[査読有り]
    Reaction Pathway of Surface-Catalyzed Ammonia Decomposition and Nitrogen Incorporation in Epitaxial Growth of Gallium Nitride
    Bui, Kieu My, Iwata, Jun-Ichi, Kangawa, Yoshihiro, Shiraishi, Kenji, Shigeta, Yasuteru, Oshiyama, Atsushi
    JOURNAL OF PHYSICAL CHEMISTRY C 122 (43) 2018年11月[査読有り]
    Protein Residue Networks from Energetic and Geometric Data: Are They Identical?
    Sladek, Vladimir, Tokiwa, Hiroaki, Shimano, Hitoshi, Shigeta, Yasuteru
    Journal of chemical theory and computation 14 (12) 2018年11月[査読有り]
    How Does Friction Coefficient Affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?
    Harada, Ryuhei, Shigeta, Yasuteru
    CHEMISTRY LETTERS 47 (9) 2018年09月[査読有り]
    Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiency
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of molecular graphics & modelling 85 2018年09月[査読有り]
    A Theoretical Study on Redox Potential and pK(a) of [2Fe-25] Cluster Model from Iron-Sulfur Proteins
    Kurniawan, Isman, Kawaguehi, Kazutomo, Shoji, Mitsuo, Matsui, Toru, Shigeta, Yasuteru, Nagao, Hidemi
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 91 (9) 2018年09月[査読有り]
    Computational electrochemistry of a novel ferrocene derivative
    Ghiami-Shomami, Ali, Ghalami-Choobar, Bahram, Shigeta, Yasuteru
    Journal of molecular graphics & modelling 85 2018年08月[査読有り]
    A computational scheme of pK values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme
    Fujiki, Ryo, Kasai, Yukako, Seno, Yuki, Matsui, Toru, Shigeta, Yasuteru, Yoshida, Norio, Nakano, Haruyuki
    Physical chemistry chemical physics : PCCP 20 (43) 2018年08月[査読有り]
    Redox potential-dependent formation of an unusual His-Trp bond in bilirubin oxidase
    Akter, Mahfuza, Tokiwa, Takaki, Shoji, Mitsuo, Nishikawa, Koji, Shigeta, Yasuteru, Sakurai, Takeshi, Higuchi, Yoshiki, Kataoka, Kunishige, Shibata, Naoki
    Chemistry (Weinheim an der Bergstrasse, Germany) 24 (68) 2018年08月[査読有り]
    Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of chemical information and modeling 58 (7) 2018年07月[査読有り]
    A Practical Approach for Searching Stable Molecular Structures by Introducing Repulsive Interactions among Walkers
    Shoji, Mitsuo, Kayanuma, Megumi, Shigeta, Yasuteru
    Bulletin of the Chemical Society of Japan 91 (10) 2018年07月[査読有り]
    Dominant role of orbital splitting in determining cathode potential in O3 NaTMO2 compounds
    Hussein, M, Assadi, N, Shigeta, Yasuteru
    JOURNAL OF POWER SOURCES 388 2018年06月[査読有り]
    How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations
    Harada, Ryuhei, Shigeta, Yasuteru
    Physical chemistry chemical physics : PCCP 20 (26) 2018年06月[査読有り]
    Concerted Mechanism of Water Insertion and O Release during the S to S Transition of the Oxygen-Evolving Complex in Photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
    The journal of physical chemistry. B 122 (25) 2018年06月[査読有り]
    Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities
    Terai, Yuma, Sato, Ryuma, Yumiba, Takahiro, Harada, Ryuhei, Shimizu, Kohei, Toga, Tatsuya, Ishikawa-Fujiwara, Tomoko, Todo, Takeshi, Iwai, Shigenori, Shigeta, Yasuteru, Yamamoto, Junpei
    Nucleic acids research Epub 2018年05月[査読有り]
    On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of chemical theory and computation 14 (6) 2018年05月[査読有り]
    光合成における酸素発生の反応機構
    庄司, 光男, 磯部, 寛, 重田, 育照, 中嶋, 隆人, 山口, 兆
    生物物理 58 (3) 2018年05月[査読有り]
    Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals
    Hada, Masaki, Saito, Shohei, Sato, Ryuma, Miyata, Kiyoshi, Hayashi, Yasuhiko, Shigeta, Yasuteru, Onda, Ken
    Journal of visualized experiments : JoVE (135) 2018年05月[査読有り]
    Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
    Yamamoto, Yuta, Takei, Kenta, Arulmozhiraja, Sundaram, Sladek, Vladimir, Matsuo, Naoya, Han, Song-Iee, Matsuzaka, Takashi, Sekiya, Motohiro, Tokiwa, Takaki, Shoji, Mitsuo, Shigeta, Yasuteru, Nakagawa, Yoshimi, Tokiwa, Hiroaki, Shimano, Hitoshi
    Biochemical and biophysical research communications 2018年05月[査読有り]
    Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 698 2018年04月[査読有り]
    Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals
    Hada, Masaki, Saito, Shohei, Sato, Ryuma, Miyata, Kiyoshi, Hayashi, Yasuhiko, Shigeta, Yasuteru, Onda, Ken
    Journal of visualized experiments : JoVE (135) 2018年04月[査読有り]
    First-principles study of the formation of glycine-producing radicals from common interstellar species
    Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    Molecular Astrophysics 10 2018年03月[査読有り]
    First-principles study of the formation of glycine-producing radicals from common interstellar species
    Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    Molecular Astrophysics 10 2018年03月[査読有り]
    The effect of octahedral distortions on the electronic properties and magnetic interactions in O3 NaTMO2 compounds (TM = Ti-Ni & Zr-Pd)
    Assadi, M. Hussein N, Shigeta, Yasuteru
    RSC ADVANCES 8 (25) 2018年[査読有り]
    The Formation of Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics
    Harada, Ryuhei, Aida, Hayato, Shigeta, Yasuteru
    Chemistry Letters 47 (10) 2018年[査読有り]
    光応答カラムナー液晶の超高速構造解析
    齊藤,尚平, 羽田,真毅, 重田,育照, 恩田,健
    日本液晶学会討論会講演予稿集 2018 2018年[査読有り]
    研究室だより「筑波大学計算科学研究センター 生命科学研究部門 重田研究室」
    重田,育照
    アンサンブル 20 (1) 2018年[査読有り]
    生物学的レアイベントを再現予測するタンパク質構造サンプリング手法の開発
    原田, 隆平, 重田, 育照
    日本物理学会講演概要集 73 2018年[査読有り]
    A theoretical study of the formation of glycine via hydantoin intermediate in outer space environment
    Megumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki Umemura
    CHEMICAL PHYSICS LETTERS 687 2017年11月[査読有り]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 (44) 2017年10月[査読有り]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 (44) 2017年10月[査読有り]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 2017年10月[査読有り]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 (44) 2017年10月[査読有り]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 2017年10月[査読有り]
    Assessment of Methodology and Chemical Group Dependences in the Calculation of the pK(a) for Several Chemical Groups
    Matsui, Toru, Shigeta, Yasuteru, Morihashi, Kenji
    Journal of chemical theory and computation 13 (10) 2017年09月[査読有り]
    Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of computational chemistry 38 (31) 2017年08月[査読有り]
    Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior
    Yotsuji, Hajime, Higashiguchi, Kenji, Sato, Ryuma, Shigeta, Yasuteru, Matsuda, Kenji
    Chemistry (Weinheim an der Bergstrasse, Germany) 23 (60) 2017年07月[査読有り]
    Large-scale QM/MM calculations of the CaMn4O5 cluster in the S-3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures
    Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi
    FARADAY DISCUSSIONS 198 2017年06月[査読有り]
    Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
    Ujiie, Yuzuru, Tanaka, Wataru, Hanaoka, Kyohei, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo, Murakawa, Takeshi, Ishida, Toyokazu, Shigeta, Yasuteru, Hayashi, Hideyuki
    The journal of physical chemistry. B 121 (22) 2017年05月[査読有り]
    Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of computational chemistry 38 (22) 2017年05月[査読有り]
    Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
    Fujita, Junso, Harada, Ryuhei, Maeda, Yoko, Saito, Yuki, Mizohata, Eiichi, Inoue, Tsuyoshi, Shigeta, Yasuteru, Matsumura, Hiroyoshi
    Journal of structural biology 198 (2) 2017年04月[査読有り]
    Direct Observation of the Ultrafast Evolution of Open-Shell Biradical in Photochromic Radical Dimer
    Kobayashi, Yoichi, Okajima, Hajime, Sotome, Hikaru, Yanai, Takeshi, Mutoh, Katsuya, Yoneda, Yusuke, Shigeta, Yasuteru, Sakamoto, Akira, Miyasaka, Hiroshi, Abe, Jiro
    Journal of the American Chemical Society 139 (18) 2017年04月[査読有り]
    Cooperatively Interlocked [2+1]-Type π-System-Anion Complexes
    Yamakado, Ryohei, Ashida, Yukina, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
    Chemistry (Weinheim an der Bergstrasse, Germany) 23 (17) 2017年03月[査読有り]
    Sparsity-Weighted Outlier FLOODing (OFLOOD) Method: Efficient Rare Event Sampling Method Using Sparsity of Distribution
    Harada, Ryuhei, Nakamura, Tomotake, Shigeta, Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 37 (8) 2016年03月[査読有り]
    Solvent effects on excited-state electron-transfer rate of pyrene-labeled deoxyuridine: A theoretical study
    Maekawa, Shintaro, Sato, Ryuma, Hirao, Kimihiko, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 644 2016年01月[査読有り]
    Theoretical analyses on a flipping mechanism of UV-induced DNA damage
    Sato, Ryuma, Harada, Ryuhei, Shigeta, Yasuteru
    Biophysics and Physicobiology 13 2016年[査読有り]
    プロトンの水和自由エネルギー: 酸解離定数および標準水素電極電位の高精度計算
    松井, 亨, 喜屋武, 茜, 庄司, 光男, 重田, 育照
    Journal of Computer Chemistry, Japan 15 (5) 2016年[査読有り]
    Molecular dynamics study on the key catalytic intermediates of threonine synthase
    Shoji, Mitsuo, Ujiie, Yuzuru, Harada, Ryuhei, Kayanuma, Megumi, Shigeta, Yasuteru, Murakawa, Takeshi, Hayashi, Hideyuki
    PROTEIN SCIENCE 24 (1:SI) 2015年10月[査読有り]
    Automatic detection of hidden dimensions to obtain appropriate reaction coordinates in the Outlier FLOODing (OFLOOD) method
    Harada, Ryuhei, Nakamura, Tomotake, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 639 2015年10月[査読有り]
    Performance of the divide-and-conquer approach used as an initial guess
    Shoji,Mitsuo, Meguchi,Kayanuma, Hiroaki,Umeda, Yasuteru,Shigeta
    CHEMICAL PHYSICS LETTERS 634 2015年08月[査読有り]
    Efficient conformational sampling of proteins based on a multi-dimensional TaBoo SeArch algorithm: An application to folding of chignolin in explicit solvent
    Harada, Ryuhei, Takano, Yu, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 630 2015年06月[査読有り]
    Enhanced Conformational Sampling Method for Proteins Based on the TaBoo SeArch Algorithm: Application to the Folding of a Mini-Protein, Chignolin
    Harada, Ryuhei, Takano, Yu, Shigeta, Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (10) 2015年04月[査読有り]
    Theoretical Study on Reaction Mechanisms of Nitrite Reduction by Copper Nitrite Complexes: Toward Understanding and Controlling Possible Mechanisms of Copper Nitrite Reductase
    Maekawa, Shintaro, Matsui, Tom, Hirao, Kimihiko, Shigeta, Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY B 119 (17) 2015年04月[査読有り]
    酵素による人工物質の分解反応シミュレーション
    神谷克政, 重田,育照
    シミュレーション 34 (1) 2015年03月[査読有り]
    第一原理計算によるタンパク質のpK_aと構造機能相関
    重田,育照, 松井,亨
    日本物理学会講演概要集 70 (1) 2015年03月[査読有り]
    液体の積分方程式を用いたタンパク質中アミノ酸のpKa予測手法の開発
    笠井, 友佳子, 吉田, 紀生, 松井, 亨, 重田, 育照, 中野, 晴之
    日本物理学会講演概要集 70 (1) 2015年03月[査読有り]
    A QM/MM study of the initial steps of catalytic mechanism of nitrile hydratase
    Kayanuma, Megumi, Hanaoka, Kyohei, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 623 2015年03月[査読有り]
    Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body Systems
    Shigeta, Yasuteru, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5:::SI) 2015年03月[査読有り]
    Substitution effects on optical properties of iminonitroxide- substituted iminonitroxide diradical
    Nakamura, Ryota, Shigeta, Yasuteru, Okuno, Katsuki, Hasegawa, Miki, Fukushima, Mayuko, Suzuki, Shuichi, Kozaki, Masatoshi, Okada, Keiji, Nakano, Masayoshi
    MOLECULAR PHYSICS 113 (3-4:::SI) 2015年02月[査読有り]
    Protein folding pathways extracted by Outlier FLOODing method (OFLOOD)
    Ryuhei,Harada, Tomotake,Nakamura, Yu,Takano, Shigeta,Yasuteru
    Journal of Computational Chemistry 2015年01月[査読有り]
    Accurate Standard Hydrogen Electrode Potential and Applications to the Redox Potentials of Vitamin C and NAD/NADH
    Matsui, Toru, Kitagawa, Yasutaka, Okumura, Mitsutaka, Shigeta, Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 119 (2) 2015年01月[査読有り]
    Protein Folding Pathways Extracted by OFLOOD: Outlier FLOODing Method
    Harada, Ryuhei, Nakamura, Tomotake, Takano, Yu, Shigeta, Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (2) 2015年01月[査読有り]
    Simple, yet powerful methodologies for conformational sampling of proteins
    Harada, Ryuhei, Takano, Yu, Baba, Takeshi, Shigeta, Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (9) 2015年[査読有り]
    Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes
    Baba, Takeshi, Boero, Mauro, Kamiya, Katsumasa, Ando, Hiroyuki, Negoro, Seiji, Nakano, Masayoshi, Shigeta, Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (6) 2015年[査読有り]
    Theoretical design of solvatochromism switching by photochromic reactions using donor-acceptor disubstituted diarylethene derivatives with oxidized thiophene rings
    Okuno, Katsuki, Shigeta, Yasuteru, Kishi, Ryohei, Nakano, Masayoshi
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (9) 2015年[査読有り]
    GPGPUクラスタ上でのFMO計算の性能評価
    梅田, 宏明, 塙, 敏博, 庄司, 光男, 朴, 泰祐, 重田, 育照
    Journal of Computer Chemistry, Japan 13 (6) 2015年[査読有り]
    OpenFMOにおける4中心クーロン相互作用項計算のGPGPU化の試み
    梅田, 宏明, 塙, 敏博, 庄司, 光男, 朴, 泰祐, 重田, 育照
    Journal of Computer Chemistry, Japan 14 (3) 2015年[査読有り]
    A density functional study on pKa of small polyprotic molecules
    T.,Baba, T.,Matusui, K.,Kamiya, M.,Nakano, 重田,育照
    International Journal of Quantum Chemistry 114 (17) 2014年09月[査読有り]
    Open-Shell Character and Second Hyperpolarizabilities of One-Dimensional Chromium(II) Chains: Size Dependence and Bond-Length Alternation Effect
    H.,Fukui, S.,Takamuku, T.,Yamada, K.,Fukuda, T.,Takebayashi, Shigeta,Yasuteru, R.,Kishi, M.,Nakano
    Inorganic Chemistry 53 2014年08月[査読有り]
    タンパク質レアイベントを抽出する効率的構造サンプリング法(蛋白質: 構造機能相関,ポスター,第52回日本生物物理学会年会(2014年度))
    Ryuhei,Harada, Yu,Takano, Yasuteru,Shigeta
    生物物理 54 (1) 2014年08月[査読有り]
    Hydration effects on enzyme–substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method
    Hiroyuki Ando, Yasuteru Shigeta, Takeshi Baba, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Masayoshi Nakano
    Molecular Physics 113 (3-4) 2014年08月[査読有り]
    On the induced-fit mechanism of substrate-enzyme binding structures of Nylon-oligomer hydrolase
    T.,Baba, R.,Harada, M.,Nakano, 重田,育照
    Journal of Computational Chemistry 35 (16) 2014年06月[査読有り]
    A Nylon-oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 5 (7) 2014年03月[査読有り]
    Fluctuation Flooding Method (FFM)for accelerating conformational transitions of proteins
    Ryuhei,Harada, Yu,Takano, 重田,育照
    JOURNAL OF CHEMICAL PHYSICS 140 (12) 2014年03月[査読有り]
    A new type of organic-inorganic hybrid NLO-phore with large off-diagonal first hyperpolarizability tensors: a two-dimensional approach
    Shigeta,Yasuteru
    Dalton Transactions 42 (42) 2013年11月[査読有り]
    Non-empirical tuning of CAM-B3LYP functional in time-dependent density functional theory for excitation energies of diarylethene derivatives
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 585 (1-3) 2013年10月[査読有り]
    Binding of a positron to nucleic-acid base molecules and their pairs
    Shigeta,Yasuteru
    ChemPhysChem 14 (15) 2013年10月[査読有り]
    Finite-Field Method with Unbiased Polarizable Continuum Model for Evaluation of the Second Hyperpolarizability of an Open-Shell Singlet Molecule in Solvents
    Shigeta,Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (27) 2013年10月[査読有り]
    Photochromic Switching of Diradical Character: Design of Efficient Nonlinear Optical Switches
    重田,育照
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 4 (15) 2013年07月[査読有り]
    量子化学工学における光機能性物質設計
    重田,育照
    特集「化学工学に展開する量子化学計算」 化学工学会誌 77 2013年06月[査読有り]
    A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion: General Theory and Applications
    Shigeta,Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 9 (5) 2013年05月[査読有り]
    第一原理計算による生体内酵素反応の理論解析
    重田,育照
    豊田研究報告 66 2013年05月[査読有り]
    Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 4 (10) 2013年04月[査読有り]
    Diradicalology in Third-Order Nonlinear Optical Systems: Second Hyperpolarizabilities of Acetylene-Linked Phenalenyl Based Superpolyenes
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (4) 2013年02月[査読有り]
    Comparative Study of Diradical Characters and Third-Order Nonlinear Optical Properties of Linear/Cyclic Acenes versus Phenylenes
    重田,育照
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (4) 2013年02月[査読有り]
    Antidot Effects on the Open-Shell Characters and Second Hyperpolarizabilities of Rectangular Graphene Nanoflakes
    重田,育照
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (4) 2013年02月[査読有り]
    Qantal Cumulant Mechanics and Dynamics for Multi-Dimensional Quantum Many-Body Clusters
    重田,育照
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (3) 2013年02月[査読有り]
    Consistent Scheme for Computing Standard Hydrogen Electrode and Redox Potentials
    Shigeta,Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (1) 2013年01月[査読有り]
    Interplay between the Diradical Character and Third-Order Nonlinear Optical Properties in Fullerene Systems
    Shigeta,Yasuteru
    CHEMISTRY A EUROPEAN JOURNAL 19 (4) 2013年01月[査読有り]
    Previous Article Next Article Table of Contents Synthesis and Characterization of Quarteranthene: Elucidating the Characteristics of the Edge State of Graphene Nanoribbons at the Molecular Level
    Shigeta,Yasuteru
    Journal of the American Chemistry Society 135 (4) 2013年01月[査読有り]
    Cumulant mechanics : An explicit treatment for fluctuation on dynamics
    重田,育照
    Molecular Science 7 (1) 2013年01月[査読有り]
    Density functional studies of the structural variety of the Cu2S2 core of the CuA site
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 (24) 2012年12月[査読有り]
    DFT Analysis of Low-Frequency Heme Vibrations in Soluble Guanylate Cyclase: Raman Mode Enhancement by Propionate-Protein Interactions
    Shigeta,Yasuteru
    Chemistry Letters 41 (9) 2012年09月[査読有り]
    Impact of Antidot Structure on the Multiradical Characters, Aromaticities, and Third-Order Nonlinear Optical Properties of Hexagonal Graphene Nanoflakes
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY C 116 (33) 2012年08月[査読有り]
    Microscopic Mechanisms of Initial Oxidation of Si (100): Reaction Pathways and Free-Energy Barriers
    Shigeta,Yasuteru
    PHYSICAL REVIEW B 85 (20) 2012年05月[査読有り]
    Development of Calculation and Analysis Methods for the Dynamic First Hyperpolarizability Based on the ab initio Molecular Orbital - Quantum Master Equation Method
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 116 (17) 2012年05月[査読有り]
    Enhancement of the Third-Order Nonlinear Optical Properties in Open-Shell Singlet Transition-Metal Dinuclear Systems: Effects of the Group, of the Period, and of the Charge of the Metal Atom
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 116 (22) 2012年05月[査読有り]
    Tuned CAM-B3LYP Functional in the Time-Dependent Density Functional Theory Scheme for Excitation Energies and Properties of Diarylethene Derivatives
    Shigeta,Yasuteru
    Journal of photochemistry and Photobiology A:Chemistry 235 (1) 2012年05月[査読有り]
    Coordination Effects on the Electronic Structure of the CuA Site of Cytochrome c Oxidase
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 531 2012年04月[査読有り]
    Temperature-Independent Stereoselectivity in Intramolecular Cycloaddition of Ketene Generated from Diazoester in Solution and in Vapor Phase: How Entropy Term Governs the Selectivity
    Shigeta,Yasuteru
    Bulletin of the Chemical Society of Japan 85 (4) 2012年04月[査読有り]
    An Accurate Density Functional Theory Based Estimation of pKa Values of Polar Residues Combined with Experimental Data: From Amino Acids to Minimal Proteins
    Shigeta,Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 14 2012年03月[査読有り]
    heoretical Insight into Stereoselective Reaction Mechanisms of 2,4-Pentanediol-Tethered Ketene-Olefin [2+2] Cycloaddition
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 116 (4) 2012年02月[査読有り]
    Halide Ion Complexes of Decaborane (B10H14) and Their Derivatives: Noncovalent Charge Transfer Effect on Second-Order Nonlinear Optical Properties
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 116 (5) 2012年02月[査読有り]
    Possible Mechanisms of Water Splitting Reaction Based on Proton and Electron Release Pathways Revealed for CaMn4O5 Cluster of PSII Refined to 1.9 Å X-Ray Resolution1
    Saito,T, Yamanaka,S, Kanda,K, Isobe,H, Takano,Y, Shigeta,Yasuteru, Umena,Y, Kawakami,K, Shen,J-R, Kamiya,N, Okumura,M, Shoji,M, Yoshioka,Y, Yamaguchi,K
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 (2) 2012年01月[査読有り]
    Tuned Long-Range Corrected Density Functional Theory Method for Evaluating the Second Hyperpolarizabilities of Open-Shell Singlet Metal-metal Bonded Systems
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 523 2012年01月[査読有り]
    Full Configuration Interaction Calculations of the Second Hyperpolarizabilities of the H4 Model Compound: Summation-over-states Analysis and Interplay with Diradical Characters
    Shigeta,Yasuteru
    JOURNAL OF CHEMICAL PHYSICS 136 (2) 2012年01月[査読有り]
    (Hyper)polarizability Density Analysis for Open-Shell Molecular Systems Based on Natural Orbitals and Occupation Numbers
    Shigeta,Yasuteru
    THEORETICAL CHEMISTRY ACCOUNTS 130 (4-6) 2011年12月[査読有り]
    Self-diffusion in Crystalline Silicon: A Car-Parrinello Molecular Dynamics Study
    Shigeta,Yasuteru
    Physicla Review B 84 (20) 2011年11月[査読有り]
    First-principles Molecular Dynamics Studies on the Atomistic Behavior of His503 in Bovine Cytochrome c Oxidase
    Shigeta,Yasuteru
    Biochim Biophys Acta 1807 (10) 2011年10月[査読有り]
    Electronic Structures of the Cu2S2 Core of the CuA Site in Cytochrome c Oxidase and Nitronous Oxide Reductase
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 (2) 2011年09月[査読有り]
    Origin of the Enhancement of the Second Hyperpolarizabilities in Open-Shell Singlet Transition-Metal Systems with Metal–Metal Multiple Bonds
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2 (2) 2011年07月[査読有り]
    A Theoretical Study on Reaction Scheme of Silver (I) Containing 5-Substituted Uracils Bridge Formation
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 115 2011年06月[査読有り]
    Open-Shell Characters and Second Hyperpolarizabilities of One-Dimensional Graphene Nanoflakes Composed of Trigonal Graphene Units
    Shigeta,Yasuteru
    ChemPhysChem 12 (9) 2011年05月[査読有り]
    Giant Enhancement of the Second Hyperpolarizabilities of Open-Shell Singlet Polyaromatic Diphenalenyl Diradicaloids by an External Electric Field and Donor-Acceptor Substitution
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2 (9) 2011年04月[査読有り]
    Molecular Dynamics Studies on the Mutational Structures of a Nylon-6 Byproduct-Degrading Enzyme
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 507 (1) 2011年04月[査読有り]
    Electron Conductivity in Modified Models of Artificial Meta-DNA Using Green's Function-Based Elastic Scattering Theory
    Shigeta,Yasuteru
    Bulletin of the Chemical Society of Japan 84 (3) 2011年03月[査読有り]
    Enhancement of Second Hyperpolarizabilities in Open-Shell Singlet Slipped-Stack Dimers Composed of Square Planar Nickel Complexes Involving o-Semiquinonato Type Ligands
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 115 (6) 2011年02月[査読有り]
    A Simple Scheme for Estimating the pKa Values of 5-Substituted Uracils
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 502 (4-6) 2011年01月[査読有り]
    Approximate Spin-Projected Spin-Unrestricted Density Functional Theory Method: Application to the Diradical Character Dependences of the (Hyper) Polarizabilities in p-Quinodimethane Models
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 501 (1-3) 2010年12月[査読有り]
    Sequence-Dependent Proton-Transfer Reaction in Stacked GC Pair III: The Influence of Proton Transfer to Conductivity
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 110 (12) 2010年10月[査読有り]
    Energy Compensation Mechanism for Charge-Separated Protonation States in Aspartate-Histidine Amino Acid Residue Pairs
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY B 114 (19) 2010年05月[査読有り]
    Effects of Mercury (II) on Structural Properties, Electronic Structure and UV Absorption Spectra of Thymine-Mercury (II)-Thymine Nucleobase Pair Containing Duplex
    Shigeta,Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12 (4) 2010年01月[査読有り]
    Molecular Theory Including Quantum Effects and Thermal Fluctuations
    Shigeta,Yasuteru
    Bulletin of the Chemical Society of Japan 82 (11) 2009年11月[査読有り]
    Theoretical Studies on Sulfur and Metal Cation (Cu(II), Ni(II), Pd(II), and Pt(II))-Containing Artificial DNA
    重田,育照
    JOURNAL OF PHYSICAL CHEMISTRY B 113 (38) 2009年09月[査読有り]
    Sequence-Dependent Proton-Transfer Reaction in Stacked GC Pair II: The Origin of Stabilities of Proton-Transfer Products
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 478 (4-6) 2009年08月[査読有り]
    Theoretical Studies on Magnetic Interactions between Cu(II) Ions in Salen Nucleobases
    Shigeta,Yasuteru
    polyhedron 28 (9-10) 2009年06月[査読有り]
    Theoretical Studies on Magnetic Interactions Between Cu(II) Ions in Hydroxypyridone Nucleobases
    Shigeta,Yasuteru
    polyhedron 28 (9-10) 2009年06月[査読有り]
    Sequence Dependent Proton-Transfer Reaction in Stacked GC Pair I: The Possibility of Proton-Transfer Reactions
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 109 (10) 2009年03月[査読有り]
    Structural Origin of Copper Ion Containing Artificial DNA: A Density Functional Study
    Shigeta,Yasuteru
    Journal of Physical Chemistry B 112 (51) 2008年12月[査読有り]
    Correlation functions in quantized Hamilton dynamics and quantal cumulant dynamics
    Pereverzev, Yuriy V, Pereverzev, Andrey, Shigeta, Yasuteru, Prezhdo, Oleg V
    JOURNAL OF CHEMICAL PHYSICS 129 (14) 2008年10月[査読有り]
    Dynamic Quantum Isotope Effects on Multiple Proton-Transfer Reactions
    Shigeta, Yasuteru, Miyachi, Hideaki, Matsui, Toru, Hirao, Kimihiko
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 81 (10) 2008年10月[査読有り]
    Quantal cumulant dynamics III: A quantum confinement under a magnetic field
    Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 461 (4-6) 2008年08月[査読有り]
    分子磁性の理論 (その7) 遺伝的アルゴリズムのモンテカルロ法への導入
    重田,育照
    固体物理 40 (3) 2005年03月[査読有り]
  • 受賞
    2019年02月
    筑波大学 ベストファカルティーアワード2018 業績による評価
    2017年10月
    22nd QSCP Promising Scientist Award of CMOA Research Award
    2017年03月
    Royal Chemical Society Outstanding Reviewers for Physical Chemistry Chemical Physics in 2016 論文査読
    2013年05月
    大阪大学 第2回大阪大学総長奨励賞・研究部門 研究業績
    2012年09月
    分子科学会 第5回分子科学会奨励賞 研究業績
    2010年04月
    文部科学省 平成23年文部科学大臣表彰若手科学者賞 研究業績
    2009年03月
    日本化学会 第58回日本化学会進歩賞 研究業績
    2007年03月
    Royal Chemical Society PCCP Prize for the Outstanding Achievement of Young Scientists in Physical Chemistry and Chemical Physics Research Award
    2006年03月
    日本化学会 第86回日本化学会年会優秀講演賞 研究業績
  • 書籍等出版物
    Advances in Quantum Chemistry
    Shigeta,Yasuteru (担当:分担執筆, Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules)
    Quantum Systems in Physics, Chemistry, and Biology: Advances in Concepts and Applications
    Baba, Takeshi, Kamiya, Katsumasa, Shigeta, Yasuteru (担当:分担執筆, Integrated Computational Studies on Mutational Effects of A Nylon-degrading Enzyme)
    Reference modules in Materials Science and Engineering 2016
    Harada, Ryuhei, Inagaki, Yuji, Shigeta, Yasuteru (担当:分担執筆, Protein Folding and Evolution)
    金属錯体の量子・計算化学
    重田,育照, 北河康隆 (担当:分担執筆, 第4-1章 錯体の伝導性)
    Quantum mechanics Chap. 17
    Shigeta,Yasuteru (担当:分担執筆, Quantal Cumulant Mechanics as Extended Ehrenfest Theorem)
    Conceptual and Computational Advances in Quantum Chemistry, Chap. 25
    Shigeta,Yasuteru (担当:分担執筆, Theoretical Studies on Metal-Containing Artificial DNA Bases”, Advances in the Theory of Atomic and Molecular Systems)
    Advances in the Theory of Atomic and Molecular Systems, Conceptual and Computational Advances in Quantum Chemistry, Chap. 21
    Shigeta,Yasuteru (担当:分担執筆, Quantum Theory in Terms of Cumulant Variables)
    ADVANCES IN THE THEORY OF ATOMIC AND MOLECULAR SYSTEMS: DYNAMICS, SPECTROSCOPY, CLUSTERS, AND NANOSTRUCTURES
    Shigeta, Yasuteru, Miyachi, Hideaki, Matsui, Toru, Yokoyama, Norisuke, Hirao, Kimihiko (担当:分担執筆, Quantum Theory in Terms of Cumulant Variables)
    Challenges and Advances in Computational Chemistry and Physics, Chap. 2
    Shigeta,Yasuteru (担当:分担執筆, Single-Reference Methods for Excited States in Molecules and Polymers)
    物性量子化学入門
    重田,育照 (担当:分担執筆, 第13、14章)
  • 競争的資金等の研究課題
    生体ハイドロジェノミクスの理論解析
    新学術領域研究(研究領域提案型)
    研究期間: 2019年04月 -
    立体構造を基盤とする中分子創薬の合理的設計
    次世代治療・診断実現のための創薬基盤技術開発事業:革新的中分子創薬技術の開発
    研究期間: 2018年06月 -
    ポスト「京」重点課題 (7)「次世代の産業を支える新機能デバイス・高性能材料 の創成」サブ課題A 「高機能半導体デバイス」
    研究期間: 2016年04月 - 2019年03月
    理論と実験の協奏的アプローチによる多重スピン励起子変換制御
    新学術領域研究(研究領域提案型)
    研究期間: 2014年06月 - 2019年03月
    高次複合光応答分子システムの開拓と学理の構築
    科研費新学術領域研究(研究領域提案型)
    研究期間: 2014年06月 - 2019年03月
    メゾスケール空間内移動速度論創成のための挑戦的研究
    科学研究費補助金 挑戦的萌芽研究
    研究期間: 2015年04月 - 2017年03月
    キュミュラント粗視化動力学によるタンパク質動的秩序形成過程の理論研究
    新学術領域研究(研究領域提案型)
    研究期間: 2014年04月 - 2014年06月
    Siナノドットの非線形光学特性変化に対する動力学的解析
    新学術領域研究(研究領域提案型)
    研究期間: 2013年04月 - 2014年06月
    タンパク内で起こる協同的プロトン・電子移動反応の量子論的解析
    科学研究費補助金 若手研究(A)
    研究期間: 2010年04月 - 2014年03月
    第一原理計算による生体内酵素反応の理論解析
    フェロー
    研究期間: 2011年04月 - 2012年03月
    電子ダイナミクスによる電子集団運動の解析
    特定領域研究
    研究期間: 2008年 - 2009年
    プロトン結合電子移動反応の実時間解析:量子キュミュラント動力学法
    若手研究(B)
    研究期間: 2008年 - 2009年
harada 氏名 原田 隆平
Name Harada Ryuhei
所属
所属研究科/学類 生命環境科学研究科/生命環境学群 生物学類
職名 准教授
研究テーマ タンパク質の分子動力学シミュレーション
関連リンク
Email ryuheiccs.tsukuba.ac.jp
  • 研究キーワード
  • 経歴
    2019年02月
    -
    筑波大学 計算科学研究センター 准教授
    2018年04月
    -
    2019年01月
    筑波大学 計算科学研究センター 助教
    2015年04月
    -
    2018年03月
    日本学術振興会 特別研究員 (PD)
    2014年04月
    -
    2015年03月
    筑波大学 計算科学研究センター 研究員
    2011年04月
    -
    2014年03月
    理化学研究所 計算科学研究機構 特別研究員
  • 論文
    Distribution of Counter Ions in Negatively-charged Lipid/Water/Air Interface: Molecular Dynamics Study
    Takahashi Teruyuki, Harada Ryuhei, Shigeta Yasuteru
    CHEMISTRY LETTERS 49 (4) 2020年04月[査読有り]
    Protein Dynamics and the Folding Degree
    Sladek Vladimir, Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 60 (3) 2020年03月[査読有り]
    学術賞受賞寄稿「タンパク質の機能発現に重要なレアイベントを抽出するサンプリング手法の開発」
    原田隆平
    アンサンブル 22 2020年01月[査読有り]
    Rare Event Sampling of Biomolecules Based on Distributed Computing
    Harada Ryuhei
    BUTSURI 75 (1) 2020年01月[査読有り]
    Developments of Rare Event Sampling Methods for Proteins
    Harada Ryuhei, Sladek Vladimir, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY JAPAN 18 (5) 2019年12月[査読有り]
    Non-targeted Parallel Cascade Selection Molecular Dynamics Based on a Non-Redundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
    Harada Ryuhei, Sladek Vladimir, Shigeta Yasuteru
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 59 (12) 2019年11月[査読有り]
    Selection Rules for Outliers in Outlier Flooding Method (OFLOOD) Regulate its Conformational Sampling Efficiency
    Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 59 (9) 2019年09月[査読有り]
    Non-targeted Parallel Cascade Selection Molecular Dynamics Using Time-localised Prediction of Conformational Transitions in Protein Dynamics
    Harada Ryuhei, Sladek Vladimir, Shigeta Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (9) 2019年09月[査読有り]
    カスケード選択型分子動力学シミュレーションに基づく低解像度タンパク質構造の精密化
    原田隆平
    スーパーコンピューティングニュース特集号 21 (1) 2019年08月[査読有り]
    Parallel Cascade Selection Molecular Dynamics Simulation (PaCS-MD) Screens for Protein Complexes Generated by Rigid Docking
    Harada Ryuhei, Yoshino Ryunosuke, Nishizawa Hiroaki, Shigeta Yasuteru
    JOURNAL OF MOLECULAR GRAPHICS AND MODELING 92 2019年07月[査読有り]
    Temperature-Pressure Shuffling Outlier Flooding Method Enhances the Conformational Sampling of Proteins
    Harada Ryuhei, Yoshino Ryunosuke, Nishizawa Hiroaki, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 40 (15) 2019年04月[査読有り]
    Molecular Dynamics Studies on the Effects of Antifreezing Protein from Rhagium Inquisitor (RiAFP) onIce Growth
    Kimatsuka Masato, Sato Ryuma, Harada Ryuhei, Shoji Mitsuo, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY JAPAN 17 (5) 2019年03月[査読有り]
    Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-Order Molecular Dynamics Simulation
    Aida Hayato, Harada Ryuhei, Shigeta Yasuteru
    CHEMISTRY LETTERS 48 (4) 2019年03月[査読有り]
    Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
    Harada Ryuhei, Shigeta Yasuteru
    ADVANCES IN QUANTUM CHEMISTRY 78 2019年02月[査読有り]
    Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
    Kimatsuka Masato, Sato Ryuma, Harada Ryuhei, Shoji Mitsuo, Shigeta Yasuteru
    CHEMISTRY LETTERS 48 (3) 2019年02月[査読有り]
    Studies of Molecular Crowding by Simulations and Development of Parallel Cascade Selection Molecular Dynamics
    Harada Ryuhei
    ASSOCIATION OF ASIA PACIFIC PHYSICAL SOCIETIES (AAPPS BULLETIN), 29 (1) 2019年02月[査読有り]
    Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations
    Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (1) 2019年01月[査読有り]
    Studies of Molecular Crowding by Simulations and Development of Parallel Cascade Selection Molecular Dynamics
    Harada Ryuhei
    BUTSURI 73 (12) 2018年12月[査読有り]
    カスケード選択型分子動力学シミュレーションの開発とタンパク質構造変化予測への適用
    原田隆平
    平成29年度・京都大学スーパーコンピュータ共同研究制度広報 17 (1) 2018年12月[査読有り]
    The Formation of Central Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics
    Harada Ryuhei, Aida Hayato, Shigeta Yasuteru
    CHEMISTRY LETTERS 47 2018年09月[査読有り]
    Selection Rules on Initial Structures in Parallel Cascade Selection Molecular Dynamics Affect Conformational Sampling Efficiency
    Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF MOLECULAR GRAPHICS AND MODELING 85 2018年09月[査読有り]
    Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins
    Harada Ryuhei
    BULLETIN CHEMICAL SOCIETY OF JAPAN 91 (9) 2018年09月[査読有り]
    How does Friction Constant affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?
    Harada Ryuhei, Shigeta Yasuteru
    CHEMISTRY LETTERS 47 2018年08月[査読有り]
    Temperature Shuffled Structural Dissimilarity Sampling Based on a Root-Mean Square Deviation
    Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 58 (7) 2018年08月[査読有り]
    カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発とFtsZ細胞分裂ダイナミクスへの適用
    原田隆平
    スーパーコンピューティングニュース特集号 20 (2) 2018年08月[査読有り]
    How Low-Resolution Structural Data Predict the Conformational Changes of a Protein: A Study on Data-Driven Molecular Dynamics Simulations
    Harada Ryuhei, Shigeta Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 20 2018年07月[査読有り]
    Developments of Innovative Molecular Simulation Methods for Understanding the Biological Functions
    Harada Ryuhei
    CHEMICAL INDUSTRY 69 (7) 2018年07月[査読有り]
    Coulomb and CH–π Interactions in (6–4) Photolyase–DNA Complex Dominate DNA Binding and Repair Ability
    Terai Yuma, Sato Ryuma, Yumiba Takahiro, Harada Ryuhei, Shimizu Kohei, Toga Tatsuya, Ishikawa Tomoko, Todo Takeshi, Iwai Shigenori, Shigeta Yasuteru, Yamamoto Junpei
    NUCLEIC AICD RESEARCH 46 (13) 2018年07月[査読有り]
    On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate the Conformational Transitions of Proteins
    Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 14 (6) 2018年06月[査読有り]
    Recent Extensions and Applications of Parallel Cascade Selection Molecular Dynamics Simulations
    Harada Ryuhei, Shigeta Yasuteru
    ACTIVITY REPORT 2017 / SUPERCOMPUTER CENTER, INSTITUTE FOR SOLID STATE PHYSICS, THE UNIVERSITY OF TOKYO (INVITED ARTICLE) 2018年05月[査読有り]
    Programed Dynamics Ordering in the Self-Organization Processes of a Nanocube: A Molecular Dynamics Study
    Harada Ryuhei, Mashiko Takako, Tachikawa Masanori, Hiraoka Shuichi, Shigeta Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 20 2018年04月[査読有り]
    Development of Molecular Crowding and Cascade-Type Massive Parallel Simulation Methods for Biological Functions of Proteins
    Harada Ryuhei
    CHEMISTRY AND CHEMICAL INDUSTRY 71 (3) 2018年03月[査読有り]
    Analyses on Dynamic Ordering of Protein Functions by means of Cascade Selection Molecular Dynamics
    Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF COMPUTER CHEMISTRY JAPAN 17 (1) 2018年03月[査読有り]
    The Binding Structure and Affinity of Photodamaged Duplex DNA with Members of the Photolyase/Cryptochrome Family: A Computational Study
    Sato Ryuma, Harada Ryuhei, Shigeta Yasuteru
    BIOPHYSICS AND PHYSICOBIOLOGY 15 2018年01月[査読有り]
    An Assessment of Optimal Time Scale of Conformational Resampling for Parallel Cascade Selection Molecular Dynamics
    Harada Ryuhei, Shigeta Yasuteru
    MOLECULAR SIMULATION 44 (3) 2018年01月[査読有り]
    Temperature-Shuffled Parallel Cascade Selection Molecular Dynamics Accelerates the Structural Transitions of Proteins
    Ryuhei Harada, Yasuteru Shigeta
    JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (31) 2017年12月[査読有り]
    Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches
    Ryuhei Harada, Yasuteru Shigeta
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 57 (12) 2017年12月[査読有り]
    Dynamic Specification of Initial Structures in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Efficiently Promotes Biologically Relevant Rare Events
    Ryuhei Harada, Yasuteru Shigeta
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 90 (11) 2017年11月[査読有り]
    Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection
    Ryuhei Harada, Yasuteru Shigeta
    JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (22) 2017年08月[査読有り]
    Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
    Yuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki Hayashi
    JOURNAL OF PHYSICAL CHEMISTRY B 121 (22) 2017年06月[査読有り]
    How Does the Number of Initial Structures Affect the Conformational Sampling Efficiency and Quality in Parallel Cascade Selection Molecular Dynamics (PaCS-MD)?
    Ryuhei Harada, Yasuteru Shigeta
    CHEMISTRY LETTERS 46 (6) 2017年06月[査読有り]
    Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
    Junso Fujita, Ryuhei Harada, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi Matsumura
    JOURNAL OF STRUCTURAL BIOLOGY 198 (2) 2017年05月[査読有り]
    Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
    Junso Fujita, Ryuhei Harada, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi Matsumura
    JOURNAL OF STRUCTURAL BIOLOGY 198 (2) 2017年05月[査読有り]
    Common Folding Processes of Mini-Proteins: Partial Formations of Secondary Structures Initiate the Immediate Protein Folding
    Ryuhei Harada, Yu Takano, Yasuteru Shigeta
    JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (11) 2017年04月[査読有り]
    Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins
    Ryuhei Harada, Yasuteru Shigeta
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13 (3) 2017年03月[査読有り]
    Classical cumulant dynamics for statistical chemical physics
    Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, Thi Kieu My Bui, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma, Mitsuo Shoji
    MOLECULAR SIMULATION 43 (13-16) 2017年[査読有り]
    Theoretical Analyses on a Flipping Mechanism of UV-induced DNA Damage
    Sato Ryuma, Harada Ryuhei, Shigeta Yasuteru
    BIOPHYSICS AND PHYSICOBIOLOGY 13 2016年11月[査読有り]
    A Fast Convergent Simulated Annealing Algorithm for Protein-Folding: Simulated Annealing Outlier FLOODing (SA-OFLOOD) Method
    Harada Ryuhei, Nakamura Tomotake, Shigeta Yasuteru
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 89 (11) 2016年11月[査読有り]
    Biomolecular Interactions Modulate Macromolecular Structure and Dynamics in Atomistic Model of a Bacterial Cytoplasm
    Yu Isseki, Mori Takaharu, Ando Tadashi, Harada Ryuhei, Jung Jaewoon, Sugita Yuji, Feig Michael
    ELIFE 5 2016年11月[査読有り]
    Molecular Mechanisms of Substrate Specificities of Uridine-Cytidine Kinase
    Tanaka Wataru, Shoji Mitsuo, Tomoike Fumiaki, Ujiie Yuzuru, Hanaoka Kyohei, Harada Ryuhei, Kayanuma Megumi, Kamiya Katsumasa, Ishida Toyokazu, Masui Ryoji, Kuramitsu Seiki, Shigeta Yasuteru
    BIOPHYSICS AND PHYSICOBIOLOGY 13 2016年06月[査読有り]
    最近の研究から「カスケード型超並列シミュレーションに基づく遷移経路探索法」
    原田隆平
    アンサンブル 18 (3) 2016年06月[査読有り]
    TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins
    Harada Ryuhei, Takano Yu, Shigeta Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12 (5) 2016年05月[査読有り]
    Sparsity-Weighted Outlier FLOODing (OFLOOD) Method: Efficient Rare Event Sampling Method Using Sparsity of Distribution
    Harada Ryuhei, Nakamura Tomotake, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 37 (8) 2016年03月[査読有り]
    Parallel Cascade Selection Molecular Dynamics for Efficient Conformational Sampling and Free Energy Calculation of Proteins
    Kitao Akio, Harada Ryuhei, Nishihara Yasutaka, Duy Phuoc Tran
    PROCEEDINGS OF THE INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2016 (ICCMS-2016) 1790 2016年[査読有り]
    Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins
    Harada Ryuhei, Kitao Akio
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11 (11) 2015年11月[査読有り]
    Automatic Detection of Hidden Dimensions to Obtain Appropriate Reaction Coordinates in the Outlier FLOODing (OFLOOD) Method
    Harada Ryuhei, Nakamura Tomotake, Shigeta Yasuteru
    CHEMICAL PHYSICS LETTERS 639 2015年10月[査読有り]
    Protein Folding and Evolution
    Harada Ryuhei, Inagaki Yuji, Shigeta Yasuteru
    In book: Reference Module in Materials Science and Materials Engineering DOI: 10.1016/B978 2015年08月[査読有り]
    Efficient Conformational Sampling of Proteins Based on a Multi-dimensional TaBoo SeArch Algorithm: An Application to Folding of Chignolin in Explicit Solvent
    Harada Ryuhei, Takano Yu, Shigeta Yasuteru
    CHEMICAL PHYSICS LETTERS 630 2015年06月[査読有り]
    Complete Atomistic Model of a Bacterial Cytoplasm for Integrating Physics, Biochemistry, and Systems Biology
    Feig Michael, Harada Ryuhei, Mori Takaharu, Yu Isseki, Takahashi Koichi, Sugita Yuji
    JOURNAL OF MOLECULAR GRAPHICS & MODELLING 58 2015年05月[査読有り]
    Enhanced Conformational Sampling Method for Proteins Based on the TaBoo SeArch Algorithm: Application to the Folding of a Mini-Protein, Chignolin
    Harada Ryuhei, Takano Yu, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (10) 2015年04月[査読有り]
    Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body Systems
    Shigeta Yasuteru, Harada Ryuhei, Kayanuma Megumi, Shoji Mitsuo
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5) 2015年03月[査読有り]
    Protein Folding Pathways Extracted by OFLOOD: Outlier FLOODing Method
    Harada Ryuhei, Nakamura Tomotake, Takano Yu, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (2) 2015年01月[査読有り]
    Simple, yet Powerful Methodologies for Conformational Sampling of Proteins
    Harada Ryuhei, Takano Yu, Baba Takeshi, Shigeta Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (9) 2015年[査読有り]
    Cascade-type Massive Parallel Simulation for Protein Conformation Transition Pathway Search
    Nishihara Yasutaka, Harada Ryuhei, Kitao Akio
    PROCEEDINGS OF THE INSTITUTE OF STATISTICAL MATHEMATICS 62 (2) 2014年12月[査読有り]
    On the Induced-Fit Mechanism of Substrate-Enzyme Binding Structures of Nylon-Oligomer Hydrolase
    Baba Takeshi, Harada Ryuhei, Nakano Masayoshi, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 35 (16) 2014年06月[査読有り]
    Molecular Simulation Methods to Enhance Soft Protein Motions
    Harada Ryuhei, Kitao Akio
    SEIBUTSU BUTSURI 54 (3) 2014年03月[査読有り]
    Hydration and Protein Stability under Molecular Crowding Environments
    Harada Ryuhei
    BUSEEI KENKYU 53 2014年03月[査読有り]
    Fluctuation Flooding Method (FFM) for Accelerating Conformational Transitions of Proteins
    Harada Ryuhei, Takano Yu, Shigeta Yasuteru
    THE JOURNAL OF CHEMICAL PHYSICS 140 (12) 2014年03月[査読有り]
    Conformational Transition Pathway and Free Energy Analyses of Proteins by Parallel Cascade Selection Molecular Dynamics (PaCS-MD)
    Harada Ryuhei, Nishihara Yasutaka, Wakai Nobuhiko, Kitao Akio
    PROCEEDINGS OF THE INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2014 (ICCMS-2014) 1618 2014年[査読有り]
    Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to Generate Conformational Transition Pathway
    Harada Ryuhei, Kitao Akio
    THE JOURNAL OF CHEMICAL PHYSICS 139 (3) 2013年07月[査読有り]
    Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions
    Harada Ryuhei, Tochio Naoya, Kigawa Takanori, Sugita Yuji, Feig Michael
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135 (9) 2013年03月[査読有り]
    Hydration and Protein Stability under Cellular Environments
    Harada Ryuhei
    SEIBUTSU BUTSURI 53 (4) 2013年02月[査読有り]
    博士論文紹介「超並列マルチスケールシミュレーションMSFEL法で探る生体分子の生体分子の自由エネルギー地形」
    原田隆平
    アンサンブル 15 (1) 2013年01月[査読有り]
    Understanding Proteins in Packed Places
    Harada Ryuhei, Sugita Yuji, Feig Michael
    RIKEN RESEARCH 7 (3) 2012年07月[査読有り]
    Protein Crowding Affects Hydration Structure and Dynamics
    Harada Ryuhei, Sugita Yuji, Feig Michael
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 (10) 2012年03月[査読有り]
    The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing
    Harada Ryuhei, Kitao Akio
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8 (1) 2012年01月[査読有り]
    Exploring the Folding Free Energy Landscape of a beta-Hairpin Miniprotein, Chignolin, Using Multiscale Free Energy Landscape Calculation Method
    Harada Ryuhei, Kitao Akio
    THE JOURNAL OF PHYSICAL CHEMISTRY B 115 (27) 2011年07月[査読有り]
    Multi-Scale Free Energy Landscape Calculation Method by Combination of Coarse-Grained and All-atom Models
    Harada Ryuhei, Kitao Akio
    CHEMICAL PHYSICS LETTERS 503 (1-3) 2011年02月[査読有り]
  • 受賞
    2019年12月
    2019年度 分子シミュレーション学会 学術賞
    2019年03月
    日本物理学会 第13回 若手奨励賞 (領域12)
    2019年02月
    Royal Society of Chemistry 2018 PCCP Hot Article Collection
    2018年03月
    日本化学会 第67回 進歩賞
    2017年09月
    The 4th BIOPHYSICS Editors' Choice Award
    2016年11月
    BCSJ Selected Paper (日本化学会 優秀論文)
    2016年11月
    第54回 日本生物物理学会年会 若手招待講演賞
    2012年09月
    第50回 日本生物物理学会年会 若手招待講演証
    2010年11月
    第24回 分子シミュレーション討論会 学生優秀発表賞
  • 書籍等出版物
  • 競争的資金等の研究課題
    中分子環状ペプチドの膜透過性を評価する分子シミュレーション技術の創出
    筑波大学研究基盤支援プログラム (Aタイプ)
    研究期間: 2019年08月 - 2020年03月
    筑波大学研究支援プログラム(Cタイプ)
    研究期間: 2019年07月 - 2020年03月
    カスケード選択型分子動力学シミュレーションで実現する環状ペプチド の膜透過シミュレーション
    2019年度学際共同利用
    研究期間: 2019年04月 - 2020年03月
    PaCS-MDで実現する環状ペプチドの膜透過シミュレーション
    平成31年度 TSUBAME若手・女性利用者支援制度度
    研究期間: 2019年04月 - 2020年03月
    カスケード選択型分子動力学シミュレーションで実現する環状ペプチドの膜透過シミュレーション
    若手・女性利用者推薦 2019年度 (前期)
    研究期間: 2019年04月 - 2019年09月
    カスケード選択型分子動力学シミュレーションに基づく低解像度タンパク質構造の精密化
    平成30年度スーパーコンピューター若手・女性利用者推薦制度選択課題 (後期)
    研究期間: 2018年10月 - 2019年03月
    筑波大学研究基盤支援プログラム(Cタイプ)
    研究期間: 2018年07月 - 2019年03月
    カスケード型分子動力学シミュレーションに基づくフレキシブルドッキング法の開発
    平成30年度 TSUBAME若手・女性利用者支援制度度
    研究期間: 2018年04月 - 2019年03月
    Gタンパク質共役受容体におけるシグナル伝達機構の解明
    若手研究(A) 課題番号:16H06164
    研究期間: 2016年04月 - 2019年03月
    カスケード型分子動力学シミュレーションに基づくタンパク質構造精密化アルゴリズムの開発と応用
    平成30年度 スーパーコンピューター若手・女性利用者推薦 (前期)
    研究期間: 2018年04月 - 2018年09月
    カスケード型超並列シミュレーションで探るFtsZ の細胞分裂ダイナミクス
    平成29年度 スーパーコンピューター若手・女性利用者推薦採択課題 (後期)
    研究期間: 2017年10月 - 2018年03月
    教師あり機械学習に基づく超並列カスケード型シミュレーションの定式化とタンパク質構造変化予測への適用
    平成29年度 若手・女性研究者奨励枠
    研究期間: 2017年04月 - 2018年03月
    カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発
    平成29年度 TSUBAME若手・女性利用者支援制度
    研究期間: 2017年04月 - 2018年03月
    分子動力学シミュレーションで探る細胞環境におけるタンパク質フォールディング機構
    特別研究奨励費 課題番号:15J03797
    研究期間: 2015年04月 - 2018年03月
    カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発
    平成29年度 スーパーコンピューター若手・女性利用者推薦課題 (前期)
    研究期間: 2017年04月 - 2017年09月
    タンパク質構造揺らぎに基づく構造変化予測法の構築
    若手研究(B) 課題番号:26840056
    研究期間: 2014年04月 - 2016年03月
氏名 庄司 光男
Name Shoji Mitsuo
所属
所属研究科/学類 数理物質科学研究科/理工学群 物理学類
職名 助教
研究テーマ 生体酵素反応の理論解析
関連リンク
Email mshojiccs.tsukuba.ac.jp
  • 研究キーワード
  • 経歴
  • 論文
    Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography
    Shoji, Mitsuo, Isobe, Hiroshi, Shen, Jian-Ren, Suga, Michihiro, Akita, Fusamichi, Miyagawa, Koichi, Shigeta, Yasuteru, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 730 2019年09月[査読有り]
    First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface
    Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Kamiya, Katsumasa, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    The journal of physical chemistry. A 123 (26) 2019年07月[査読有り]
    Reaction mechanism of non-enzymatic stereoselective formation of wine lactone
    Kyan, Akane, Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 725 2019年06月[査読有り]
    Spin, Valence, and Structural Isomerism in the S State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity
    Isobe, Hiroshi, Shoji, Mitsuo, Suzuki, Takayoshi, Shen, Jian-Ren, Yamaguchi, Kizashi
    Journal of chemical theory and computation 15 (4) 2019年04月[査読有り]
    Photosubstitution Reaction of cis-[Ru(bpy)(2)(CH3CN)(2)](2+) and cis-[Ru(bpy)(2)(NH3)(2)](2+) in Aqueous Solution via Monoaqua Intermediate
    Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
    The journal of physical chemistry. A 123 (13) 2019年03月[査読有り]
    Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn O (X=5, 6) cluster in the Kok cycle S (i=0-3) of oxygen evolving complex of photosystem II
    Yamaguchi, Kizashi, Yamanaka, Shusuke, Isobe, Hiroshi, Shoji, Mitsuo, Miyagawa, Kouichi, Nakajima, Takahito, Kawakami, Takashi, Okumura, Mitsutaka
    Physiologia plantarum 166 (1:::SI) 2019年03月[査読有り]
    Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
    Kimatsuka, Masato, Sato, Ryuma, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMISTRY LETTERS 48 (3) 2019年03月[査読有り]
    分子動力学シミュレーションによる不凍タンパク質RiAFPの氷の結晶成長に及ぼす影響の解析
    木間塚政人, 佐藤竜馬, 原田隆平, 庄司, 光男, 重田, 育照
    Journal of Computer Chemistry Japan 17 (5) 2019年03月[査読有り]
    Possibility of the right-opened Mn-oxo intermediate (R-oxo(4444)) among all nine intermediates in the S-3 state of the oxygen-evolving complex of photosystem II revealed by large-scale QM/MM calculations
    Shoji, Mitsuo, Isobe, Hiroshi, Miyagawa, Koichi, Yamaguchi, Kizashi
    CHEMICAL PHYSICS 518 2019年02月[査読有り]
    Theoretical study of the photodissociation reaction of methanol
    Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 714 2019年01月[査読有り]
    Concerted bond switching mechanism coupled with one-electron transfer for the oxygen-oxygen bond formation in the oxygen-evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 714 2019年01月[査読有り]
    Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction
    Tokiwa, Takaki, Shoji, Mitsuo, Sladek, Vladimir, Shibata, Naoki, Higuchi, Yoshiki, Kataoka, Kunishige, Sakurai, Takeshi, Shigeta, Yasuteru, Misaizu, Fuminori
    Molecules (Basel, Switzerland) 24 (1) 2019年01月[査読有り]
    Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II
    Yamaguchi, Kizashi, Shoji, Mitsuo, Isobe, Hiroshi, Yamanaka, Shusuke, Kawakami, Takashi, Yamada, Satoru, Katouda, Michio, Nakajima, Takahito
    MOLECULAR PHYSICS 2018年12月[査読有り]
    UNO DMRG CAS CI calculations of binuclear manganese complex Mn(IV)(2)O-2(NHCHCO2)(4): Scope and applicability of Heisenberg model
    Kawakami, Takashi, Miyagawa, Koichi, Sharma, Sandeep, Saito, Toru, Shoji, Mitsuo, Yamada, Satoru, Yamanaka, Shusuke, Okumura, Mitsutaka, Nakajima, Takahito, Yamaguchi, Kizashi
    Journal of computational chemistry 40 (2:::SI) 2018年10月[査読有り]
    光化学系II酸素発生中心の反応機構
    庄司, 光男
    アンサンブル : 分子シミュレーション研究会会誌 40 (4) 2018年10月[査読有り]
    特集光化学系II酸素発生中心にあたって
    庄司, 光男
    アンサンブル : 分子シミュレーション研究会会誌 40 (4) 2018年10月[査読有り]
    A Theoretical Study on Redox Potential and pK(a) of [2Fe-25] Cluster Model from Iron-Sulfur Proteins
    Kurniawan, Isman, Kawaguehi, Kazutomo, Shoji, Mitsuo, Matsui, Toru, Shigeta, Yasuteru, Nagao, Hidemi
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 91 (9) 2018年09月[査読有り]
    Redox potential-dependent formation of an unusual His-Trp bond in bilirubin oxidase
    Akter, Mahfuza, Tokiwa, Takaki, Shoji, Mitsuo, Nishikawa, Koji, Shigeta, Yasuteru, Sakurai, Takeshi, Higuchi, Yoshiki, Kataoka, Kunishige, Shibata, Naoki
    Chemistry (Weinheim an der Bergstrasse, Germany) 24 (68) 2018年08月[査読有り]
    A Practical Approach for Searching Stable Molecular Structures by Introducing Repulsive Interactions among Walkers
    Shoji, Mitsuo, Kayanuma, Megumi, Shigeta, Yasuteru
    Bulletin of the Chemical Society of Japan 91 (10) 2018年07月[査読有り]
    Concerted Mechanism of Water Insertion and O Release during the S to S Transition of the Oxygen-Evolving Complex in Photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
    The journal of physical chemistry. B 122 (25) 2018年06月[査読有り]
    光合成における酸素発生の反応機構
    庄司, 光男, 磯部, 寛, 重田, 育照, 中嶋, 隆人, 山口, 兆
    生物物理 58 (3) 2018年05月[査読有り]
    Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
    Yamamoto, Yuta, Takei, Kenta, Arulmozhiraja, Sundaram, Sladek, Vladimir, Matsuo, Naoya, Han, Song-Iee, Matsuzaka, Takashi, Sekiya, Motohiro, Tokiwa, Takaki, Shoji, Mitsuo, Shigeta, Yasuteru, Nakagawa, Yoshimi, Tokiwa, Hiroaki, Shimano, Hitoshi
    Biochemical and biophysical research communications 2018年05月[査読有り]
    Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 698 2018年04月[査読有り]
    First-principles study of the formation of glycine-producing radicals from common interstellar species
    Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    Molecular Astrophysics 10 2018年03月[査読有り]
    Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II
    Yamaguchi, Kizashi, Mitsuo, Shoji, Isobe, Hiroshi, Yamanaka, Shusuke, Kawakami, Takashi, Yamada, Satoru, Katouda, Michio, Nakajima, Takahito
    Molecular Physics 116 (5-6) 2018年03月[査読有り]
    First-principles study of the formation of glycine-producing radicals from common interstellar species
    Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    Molecular Astrophysics 10 2018年03月[査読有り]
    Understanding Two Different Structures in the Dark Stable State of the Oxygen‐Evolving Complex of Photosystem II: Applicability of the Jahn–Teller Deformation Formula
    Shoji,Mitsuo
    ChemPhotoChem 116 (5-6) 2017年11月[査読有り]
    Ab initio computations of zero-field splitting parameters and effective exchange integrals for single-molecule magnets (Mn-12- and Mn11Cr-acetate clusters)
    Shinsuke Sano, Takashi Kawakami, Shohei Yoshimura, Mitsuo Shoji, Shusuke Yamanaka, Mitsutaka Okumura, Takahito Nakajima, Kizashi Yamaguchi
    POLYHEDRON 136 (4) 2017年11月[査読有り]
    A theoretical study of the formation of glycine via hydantoin intermediate in outer space environment
    Megumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki Umemura
    CHEMICAL PHYSICS LETTERS 687 2017年11月[査読有り]
    Large-scale QM/MM calculations of the CaMn4O5 cluster in the S-3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures
    Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi
    FARADAY DISCUSSIONS 198 2017年06月[査読有り]
    Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
    Ujiie, Yuzuru, Tanaka, Wataru, Hanaoka, Kyohei, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo, Murakawa, Takeshi, Ishida, Toyokazu, Shigeta, Yasuteru, Hayashi, Hideyuki
    The journal of physical chemistry. B 121 (22) 2017年05月[査読有り]
    The reaction mechanism of sarcosine oxidase elucidated using FMO and QM/MM methods
    Abe, Yukihiro, Shoji, Mitsuo, Nishiya, Yoshiaki, Aiba, Hiroshi, Kishimoto, Takahide, Kitaura, Kazuo
    Physical chemistry chemical physics : PCCP 19 (15) 2017年03月[査読有り]
    On the guiding principles for understanding of geometrical structures of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Proposal of estimation formula of structural deformations via the Jahn-Teller effects
    K. Yamaguchi, M. Shoji, H. Isobe, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya
    MOLECULAR PHYSICS 115 (5) 2017年[査読有り]
    UNO DMRG CASCI calculations of effective exchange integrals for m-phenylene-bis-methylene spin clusters
    Takashi Kawakami, Shinsuke Sano, Toru Saito, Sandeep Sharma, Mitsuo Shoji, Satoru Yamada, Yu Takano, Shusuke Yamanaka, Mitsutaka Okumura, Takahito Nakajima, Kizashi Yamaguchi
    MOLECULAR PHYSICS 115 (17-18) 2017年[査読有り]
    プロトンの水和自由エネルギー: 酸解離定数および標準水素電極電位の高精度計算
    松井, 亨, 喜屋武, 茜, 庄司, 光男, 重田, 育照
    Journal of Computer Chemistry, Japan 15 (5) 2016年[査読有り]
    Molecular dynamics study on the key catalytic intermediates of threonine synthase
    Shoji, Mitsuo, Ujiie, Yuzuru, Harada, Ryuhei, Kayanuma, Megumi, Shigeta, Yasuteru, Murakawa, Takeshi, Hayashi, Hideyuki
    PROTEIN SCIENCE 24 (1:SI) 2015年10月[査読有り]
    Performance of the divide-and-conquer approach used as an initial guess
    Shoji,Mitsuo, Meguchi,Kayanuma, Hiroaki,Umeda, Yasuteru,Shigeta
    CHEMICAL PHYSICS LETTERS 634 2015年08月[査読有り]
    A QM/MM study of the 5 '-AMP DNA hydrolysis of aprataxin
    Hanaoka, Kyohei, Tanaka, Wataru, Kayanuma, Megumi, Shoji, Mitsuo
    CHEMICAL PHYSICS LETTERS 631 2015年07月[査読有り]
    On the guiding principles for lucid understanding of the damage-free S-1 structure of the CaMn4O5 cluster in the oxygen evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Yamanaka, Shusuke, Suga, Michihiro, Akita, Fusamichi, Shen, Jian-Ren, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 627 2015年05月[査読有り]
    Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body Systems
    Shigeta, Yasuteru, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5:::SI) 2015年03月[査読有り]
    Theoretical studies of the damage- free S-1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Yamanaka, Shusuke, Suga, Michihiro, Akita, Fusamichi, Shen, Jian-Ren, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 623 2015年03月[査読有り]
    A QM/MM study of the initial steps of catalytic mechanism of nitrile hydratase
    Kayanuma, Megumi, Hanaoka, Kyohei, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 623 2015年03月[査読有り]
    トレオニン合成酵素の触媒反応前半部分の反応機構解析(第438回研究協議会研究発表要旨,ビタミンB研究委員会)
    林, 秀行, 村川, 武志, 庄司, 光男
    ビタミン 89 (3) 2015年03月[査読有り]
    Involvement of Propionate Side Chains of the Heme in Circular Dichroism of Myoglobin: Experimental and Theoretical Analyses
    Nagai, Masako, Kobayashi, Chika, Nagai, Yukifumi, Imai, Kiyohiro, Mizusawa, Naoki, Sakurai, Hiroshi, Neya, Saburo, Kayanuma, Megumi, Shoji, Mitsuo, Nagatomo, Shigenori
    JOURNAL OF PHYSICAL CHEMISTRY B 119 (4) 2015年01月[査読有り]
    GPGPUクラスタ上でのFMO計算の性能評価
    梅田, 宏明, 塙, 敏博, 庄司, 光男, 朴, 泰祐, 重田, 育照
    Journal of Computer Chemistry, Japan 13 (6) 2015年[査読有り]
    OpenFMOにおける4中心クーロン相互作用項計算のGPGPU化の試み
    梅田, 宏明, 塙, 敏博, 庄司, 光男, 朴, 泰祐, 重田, 育照
    Journal of Computer Chemistry, Japan 14 (3) 2015年[査読有り]
    An Efficient Initial Guess Formation of Broken-Symmetry Solutions by using Localized Natural Orbitals
    庄司,光男, Yoshioka,Yasunori, Yamaguchi,Kizashi
    Chemical Physics Letters 608 2014年07月[査読有り]
    A QM/MM study of nitric oxide reductase-catalyzed N2O formation
    Shoji,Mitsuo, Hanaoka,Kyohei, Kondo,Daiki, Sato,Akimasa, Umeda,Hiroaki, Kamiya,Katsumasa, Shiraishi,Kenji
    Molecular Physics 112 (3-4) 2014年02月[査読有り]
    フラグメント分子軌道法に現れるFock行列計算のGPGPU化
    梅田, 宏明, 塙, 敏博, 庄司, 光男, 朴, 泰祐, 稲富, 雄一
    情報処理学会論文誌. コンピューティングシステム 6 (4) 2013年10月[査読有り]
    3. トレオニン合成酵素における生成物リン酸イオンの触媒作用のQM/MMによる解析(第433回研究協議会研究発表要旨,ビタミンB研究委員会)
    林, 秀行, 村川, 武志, 庄司, 光男, 氏家, 謙
    ビタミン 87 (10) 2013年10月[査読有り]
    Calculation of the electron transfer coupling matrix element in diabatic reactions
    Shoji, Mitsuo, Hanaoka, Kyohei, Sato, Akimasa, Kondo, Daiki, Yang, Moon Young, Kamiya, Katsumasa, Shiraishi, Kenji
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (3:::SI) 2013年02月[査読有り]
    分子軌道計算のGPGPU化に向けた行列加算手法の提案
    梅田, 宏明, 塙, 敏博, 庄司, 光男, 朴, 泰祐
    情報処理学会研究報告. [ハイパフォーマンスコンピューティング] 2013-HPC-138 (19) 2013年02月[査読有り]
    演算加速装置に基づく超並列クラスタHA-PACSによる大規模計算科学
    朴, 泰祐, 佐藤, 三久, 塙, 敏博, 児玉, 祐悦, 高橋, 大介, 建部, 修見, 多田野, 寛人, 藏増, 嘉伸, 吉川, 耕司, 庄司, 光男
    情報処理学会研究報告. [ハイパフォーマンスコンピューティング] 2011 (21) 2011年07月[査読有り]
  • 受賞
  • 書籍等出版物
  • 競争的資金等の研究課題
    酵素反応機構の解明、生物無機化学、分子動力学、分子磁性、多核金属錯体、可視化プログラム(Makiko)
氏名 西澤 宏晃
Name Nishizawa Hiroaki
所属
所属研究科/学類 数理物質科学研究科/理工学群 物理学類
職名 助教
研究テーマ 中分子創薬に対する量子・古典混合分子動力学シミュレーション
関連リンク
Email nisizawaccs.tsukuba.ac.jp
氏名 堀 優太
Name Hori Yuta
所属
所属研究科/学類 数理物質科学研究科/理工学群 物理学類
職名 助教
研究テーマ プロトン・電子・ヒドリド移動に関する理論的研究、酵素触媒反応の理論解析、星間有機分子の理論的研究
関連リンク
Email horiccs.tsukuba.ac.jp
  • 研究キーワード
  • 経歴
    2019年04月
    -
    筑波大学 計算科学研究センター 助教
    2018年04月
    -
    2019年03月
    九州大学 先導物質化学研究所 特任助教
    2017年04月
    -
    2018年03月
    九州大学 先導物質化学研究所 学術研究員
  • 論文
    Local Structures and Dynamics of Imidazole Molecules in Poly(vinylphosphonic acid)–Imidazole Composite Investigated by Molecular Dynamics
    Hori, Yuta, Suetake, Toshiya, Shiota, Yoshihito, Yoshizawa, Kazunari, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, Motohiro
    ACS Applied Polymer Materials 2020年02月[査読有り]
    Revisiting Formic Acid Decomposition by a Graph-Theoretical Approach
    Ida, Tomonori, Nishida, Manami, Hori, Yuta
    The Journal of Physical Chemistry A 123 (44) 2019年10月[査読有り]
    Mechanistic Insights into Methane Oxidation by Molecular Oxygen under Photoirradiation: Controlled Radical Chain Reactions
    Hori, Yuta, Abe, Tsukasa, Shiota, Yoshihito, Yoshizawa, Kazunari
    Bulletin of the Chemical Society of Japan 92 (11) 2019年08月[査読有り]
    Observation of Proton Transfer Coupled Spin Transition and Trapping of Photoinduced Metastable Proton Transfer State in an Fe(II) Complex
    Nakanishi, Takumi, Hori, Yuta, Sato, Hiroyasu, Wu, Shuqi, Okazawa, Atsushi, Kojima, Norimichi, Yamamoto, Takashi, Einaga, Yasuaki, Hayami, Shinya, Horie, Yusuke, Okajima, Hajime, Sakamoto, Akira, Shiota, Yoshihito, Yoshizawa, Kazunari, Osamu, Sato
    Journal of the American Chemical Society 141 (36) 2019年08月[査読有り]
    Role of Amino-Acid Residues for Dioxygen Activation in the Second Coordination Sphere of the Dicopper Site of pMMO
    Miyanishi, Mayuko, Abe, Tsukasa, Hori, Yuta, Shiota, Yoshihito, Yoshizawa, Kazunari
    Inorganic Chemistry 58 (18) 2019年08月[査読有り]
    Dual Catalytic Cycle of H2 and H2O Oxidations by A Half-Sandwich Iridium Complex: A Theoretical Study
    Ikeda, Kei, Hori, Yuta, Mahyuddin, Muhammad Haris, Shiota, Yoshihito, Staykov, Aleksandar, Matsumoto, Takahiro, Yoshizawa, Kazunari, Ogo, Seiji
    Inorganic Chemistry 58 (11) 2019年05月[査読有り]
    Local structures and electronic properties of In atoms in In-doped ZnO
    Hori, Yuta, Shiota, Yoshihito, Ida, Tomonori, Yoshizawa, Kazunari, Mizuno, Motohiro
    Thin Solid Films 685 (1) 2019年05月[査読有り]
    Cupric-superoxide complex that induces a catalytic aldol reaction-type C–C bond formation
    Abe, T, Hori, Y, Shiota, Y, Ohta, T, Morimoto, Y, Sugimoto, H, Ogura, T, Yoshizawa, K, Itoh, S
    Communications Chemistry 2 (1) 2019年02月[査読有り]
    Redox behaviour of the β-dihydroporphycene cobalt complex: study on the effect of hydrogenation of the ligand
    K, Hashimoto, T, Koide, T, Okawara, H, Shimakoshi, Y, Hori, Y, Shiota, K, Yoshizawa, Y., Hisaeda
    Dalton Transactions 48 (3) 2019年01月[査読有り]
    Ground-State Copper(III) Stabilized by N-Confused/N-Linked Corroles: Synthesis, Characterization, and Redox Reactivity
    Yogesh Kumar Maurya, Katsuya Noda, Kazuhisa Yamasumi, Shigeki Mori, Tomoki Uchiyama, Kazutaka Kamitani, Tomoyasu Hirai, Kakeru Ninomiya, Maiko Nishibori, Yuta Hori, Yoshihito Shiota, Kazunari Yoshizawa, Masatoshi Ishida, Hiroyuki Furuta
    Journal of the American Chemical Society 140 (22) 2018年06月[査読有り]
    Construction of a Potential Energy Surface Based on a Diabatic Model for Proton Transfer in Molecular Pairs
    Hori, Yuta, Ida, Tomonori, Mizuno, Motohiro
    Concepts, Methods and Applications of Quantum Systems in Chemistry and Physics 2018年01月[査読有り]
    Catalytic Performance of a Dicopper-Oxo Complex for Methane Hydroxylation
    Y, Hori, Y, Shiota, T, Tsuji, M, Kodera, K., Yoshizawa
    Inorganic Chemistry 57 (1) 2018年01月[査読有り]
    Local structure and hydrogen bond characteristics of imidazole molecules for proton conduction in acid and base proton-conducting composite materials
    Y, Hori, T, Chikai, T, Ida, M., Mizuno
    Physical Chemistry Chemical Physics 20 (15) 2018年01月[査読有り]
    A novel approach to Bohmian mechanics using an uncompressed particle method
    Sugisawa, Hiroki, Hori, Yuta, Ida, Tomonori, Mizuno, Motohiro
    Physica E: Low-Dimensional Systems and Nanostructures 104 2018年01月[査読有り]
    Potential energy construction in the diabatic picture for quantum mechanical rate constants of intermolecular proton transfer
    Yuta Hori, Tomonori Ida, Motohiro Mizuno
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 19 (25) 2017年07月[査読有り]
    Optimization of the spin-component-scaled factor for electron propagator method
    Fang-Han Lim, Manami Nishida, Yuta Hori, Tomonori Ida, Motohiro Mizuno
    CHEMICAL PHYSICS LETTERS 678 2017年06月[査読有り]
    Complete spin contamination-free MP2 method
    Manami Nishida, Fang-Han Lim, Yuta Hori, Tomonori Ida, Motohiro Mizuno
    CHEMICAL PHYSICS LETTERS 669 2017年02月[査読有り]
    A comparative theoretical study of the hydride transfer mechanisms during LiAlH4 and LiBH4 reductions
    Y, Hori, T, Ida, M., Mizuno
    Computational and Theoretical Chemistry 1076 2016年01月[査読有り]
    Simulation of molecular Auger spectra using a two-electron Dyson propagator
    Y, Hori, M, Nishida, F.H, Lim, T, Ida, M., Mizuno
    Journal of Electron Spectroscopy and Related Phenomena 207 2016年01月[査読有り]
  • 受賞
    2017年03月
    金沢大学 金沢大学大学院自然科学研究科長賞
    2012年03月
    金沢大学 金沢大学理工学域長賞
  • 書籍等出版物
  • 競争的資金等の研究課題
    理論計算に基づく酸塩基複合体中のプロトン伝導機構の解明
    若手研究
    研究期間: 2019年04月 -
    理論的解析を軸とした新規プロトン移動型スピン制御材料の開発
    融合創発研究
    研究期間: 2018年04月 - 2019年03月
    プロトン共役電子移動反応における理論的解析手法の開発
    研究活動スタート支援
    研究期間: 2017年08月 - 2019年03月
氏名 鬼頭(西岡) 宏任
Name Kitoh-Nishioka Hirotaka
所属
所属研究科/学類
職名 研究員
研究テーマ 生体系と有機半導体における励起移動と電荷移動の理論とシミュレーション、フラグメント分子軌道法のGPU加速コンピューティング
関連リンク
Email hkitoccs.tsukuba.ac.jp
  • 研究キーワード
  • 経歴
    2019年04月
    -
    筑波大学 計算科学研究センター 研究員
    2017年10月
    -
    科学技術振興機構 戦略研究推進部 さきがけ専任研究者
    2016年04月
    -
    2017年09月
    筑波大学 計算科学研究センター 研究員
    2013年04月
    -
    2016年03月
    名古屋大学 大学院理学研究科物質理学専攻 博士研究員
    2009年04月
    -
    2013年03月
    京都大学 大学院理学研究科 特定研究員
    2006年04月
    -
    2009年03月
    名城大学 大学院総合学術研究科 博士研究員
  • 論文
    Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem I
    Kitoh-Nishioka Hirotaka, Shigeta Yasuteru, Itoh Shigeru, Kimura Akihiro
    The Journal of Physical Chemistry B 124 (2) 2020年[査読有り]
    Calculation of Charge-Transfer Electronic Coupling with Nonempirically Tuned Range-Separated Density Functional
    Kitoh-Nishioka Hirotaka, Ando Koji
    The Journal of Physical Chemistry C 123 (18) 2019年[査読有り]
    Does Inactive Alkyl Chain Enhance Triplet–Triplet Annihilation of 9,10-Diphenylanthracene Derivatives?
    Ryuma Sato, Hirotaka Kitoh-Nishioka, Kenji Kamada, Toshiko Mizokuro, Kenji Kobayashi, Yasuteru Shigeta
    The Journal of Physical Chemistry C 122 (10) 2018年02月[査読有り]
    Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited
    Sato Ryuma, Kitoh-Nishioka Hirotaka, Ando Koji, Yamato Takahisa
    The Journal of Physical Chemistry B 122 (27) 2018年[査読有り]
    Near infrared two-photon-excited and -emissive dyes based on a strapped excited-state intramolecular proton-transfer (ESIPT) scaffold
    Naoya Suzuki, Kayo Suda, Daisuke Yokogawa, Hirotaka Kitoh-Nishioka, Stephan Irle, Akihiro Ando, Luis M, G. Abeg{~{a } }o, Kenji Kamada, Aiko Fukazawa, Shigehiro Yamaguchi
    Chemical Science 9 (10) 2018年[査読有り]
    Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion
    Sato Ryuma, Kitoh-Nishioka Hirotaka, Kamada Kenji, Mizokuro Toshiko, Kobayashi Kenji, Shigeta Yasuteru
    The Journal of Physical Chemistry Letters 9 (22) 2018年[査読有り]
    Multiscale Simulations on Charge Transport in Covalent Organic Frameworks Including Dynamics of Transfer Integrals from the FMO-DFTB/LCMO Approach
    Hirotaka Kitoh-Nishioka, Kai Welke, Yoshio Nishimoto, Dmitri G. Fedorov, Stephan Irle
    JOURNAL OF PHYSICAL CHEMISTRY C 121 (33) 2017年08月[査読有り]
    Theoretical Analyses of Triplet-Triplet Annihilation Process of 9,10-Diphenylanthracene in Solution
    Ryuma Sato, Hirotaka Kitoh-Nishioka, Takeshi Yanai, Yasuteru Shigeta
    CHEMISTRY LETTERS 46 (6) 2017年06月[査読有り]
    Forster Resonance Energy Transfer between Fluorescent Proteins: Efficient Transition Charge-Based Study
    Hirotaka Kitoh-Nishioka, Daisuke Yokogawa, Stephan Irle
    JOURNAL OF PHYSICAL CHEMISTRY C 121 (8) 2017年03月[査読有り]
    Classical cumulant dynamics for statistical chemical physics
    Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, Thi Kieu My Bui, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma, Mitsuo Shoji
    MOLECULAR SIMULATION 43 (13-16) 2017年[査読有り]
    FMO3-LCMO study of electron transfer coupling matrix element and pathway: Application to hole transfer between two tryptophans through cis- and trans-polyproline-linker systems
    Kitoh-Nishioka Hirotaka, Ando Koji
    JOURNAL OF CHEMICAL PHYSICS 145 (11) 2016年09月[査読有り]
    Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors
    Sato Ryuma, Kitoh-Nishioka Hirotaka, Ando Koji, Yamato Takahisa
    CHEMICAL PHYSICS LETTERS 633 2015年07月[査読有り]
    Charge-transfer matrix elements by FMO-LCMO approach: Hole transfer in DNA with parameter tuned range-separated DFT
    Kitoh-Nishioka Hirotaka, Ando Koji
    CHEMICAL PHYSICS LETTERS 621 2015年02月[査読有り]
    Electron Transfer Pathway Analysis in Bacterial Photosynthetic Reaction Center
    Kitoh-Nishioka Hirotaka, Ando Koji
    2015年[査読有り]
    Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors
    Ryuma Sato, Hirotaka Kitoh-Nishioka, Koji Ando, Takahisa Yamato
    Chemical Physics Letters 633 2015年[査読有り]
    Charge-transfer matrix elements by FMO-LCMO approach: Hole transfer in DNA with parameter tuned range-separated DFT
    Hirotaka Kitoh-Nishioka, Koji Ando
    Chemical Physics Letters 621 2015年[査読有り]
    A Strap Strategy for Construction of an Excited-State Intramolecular Proton Transfer (ESIPT) System with Dual Fluorescence
    Suzuki Naoya, Fukazawa Aiko, Nagura Kazuhiko, Saito Shohei, Kitoh-Nishioka Hirotaka, Yokogawa Daisuke, Irle Stephan, Yamaguchi Shigehiro
    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 53 (31) 2014年07月[査読有り]
    A Strap Strategy for Construction of an Excited-State Intramolecular Proton Transfer (ESIPT) System with Dual Fluorescence
    Naoya Suzuki, Aiko Fukazawa, Kazuhiko Nagura, Shohei Saito, Hirotaka Kitoh-Nishioka, Daisuke Yokogawa, Stephan Irle, Shigehiro Yamaguchi
    Angew. Chem. 126 (31) 2014年06月[査読有り]
    A Computational Study on the Role of a Methionine at a Discriminator Site of Cyclobutane-Pyrimidine-Dimer Photolyase
    Sato Ryuma, Kitoh-Nishioka Hirotaka, Kawatsu Tsutomu, Yura Kei, Ando Koji, Yamato Takahisa
    BIOPHYSICAL JOURNAL 106 (2) 2014年01月[査読有り]
    A Computational Study on the Role of a Methionine at a Discriminator Site of Cyclobutane-Pyrimidine-Dimer Photolyase
    Ryuma Sato, Hirotaka Kitoh-Nishioka, Tsutomu Kawatsu, Kei Yura, Koji Ando, Takahisa Yamato
    Biophysical Journal 106 (2) 2014年01月[査読有り]
    Fragment Molecular Orbital Study on Electron Tunneling Mechanisms in Bacterial Photosynthetic Reaction Center
    Kitoh-Nishioka Hirotaka, Ando Koji
    JOURNAL OF PHYSICAL CHEMISTRY B 116 (43) 2012年11月[査読有り]
    Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO-LCMO approach
    Nishioka Hirotaka, Ando Koji
    JOURNAL OF CHEMICAL PHYSICS 134 (20) 2011年05月[査読有り]
    Pathway analysis of super-exchange electronic couplings in electron transfer reactions using a multi-configuration self-consistent field method
    Nishioka Hirotaka, Ando Koji
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13 (15) 2011年[査読有り]
    Identification of Functional Residues of DNA Photolyase by Biophysical Computation and Bioinformatics
    Takahisa YAMATO, Hirotaka NISHIOKA, Kei YURA
    Seibutsu Butsuri 49 (4) 2009年[査読有り]
    Average electron tunneling route of the electron transfer in protein media
    Nishioka Hirotaka, Kakitani Toshiaki
    JOURNAL OF PHYSICAL CHEMISTRY B 112 (32) 2008年08月[査読有り]
    Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue
    Miyazawa Yuji, Nishioka Hirotaka, Yura Kei, Yamato Takahisa
    BIOPHYSICAL JOURNAL 94 (6) 2008年03月[査読有り]
    Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media
    Hirotaka Nishioka, Nobuharu Ueda, Toshiaki Kakitani
    BIOPHYSICS 4 2008年[査読有り]
    Non-condon theory for the energy gap dependence of electron transfer rate
    Nishioka Hirotaka, Kimura Akihiro, Yamato Takahisa, Kakitani Toshiaki
    FRONTIERS OF COMPUTATIONAL SCIENCE 2007年[査読有り]
    Temperature dependence of the inelastic electron tunneling
    Nishioka H, Yamato T, Kakitani T
    Molecular Simulation 32 (9) 2006年[査読有り]
    Interference, Fluctuation, and Alternation of Electron Tunneling in Protein Media. 2. Non-Condon Theory for the Energy Gap Dependence of Electron Transfer Rate
    Nishioka Hirotaka, Kimura Akihiro, Yamato Takahisa, Kawatsu Tsutomu, Kakitani Toshiaki
    The Journal of Physical Chemistry B 109 (32) 2005年[査読有り]
    Interference, Fluctuation, and Alternation of Electron Tunneling in Protein Media. 1. Two Tunneling Routes in Photosynthetic Reaction Center Alternate Due to Thermal Fluctuation of Protein Conformation
    Nishioka Hirotaka, Kimura Akihiro, Yamato Takahisa, Kawatsu Tsutomu, Kakitani Toshiaki
    The Journal of Physical Chemistry B 109 (5) 2005年[査読有り]
  • 受賞
  • 書籍等出版物
    Chemical Science of π-Electron Systems
    Hirotaka Kitoh-Nishioka, Koji Ando (担当:分担執筆, Chapter 39 "Electron Transfer Pathway Analysis in Bacterial Photosynthetic Reaction Center" (pp. 658-673))
    高次π空間の創発と機能開発
    鬼頭-西岡 宏任, 安藤 耕司 (担当:分担執筆, 第4章1節 “光合成反応中心における長距離電子移動の経路解析”)
  • 競争的資金等の研究課題
    量子シミュレーション技術による未知の生体電子移動/機能発現の探索
    戦略的創造研究推進事業 さきがけ
    研究期間: 2017年10月 -
    有機半導体のエキシトン/キャリア輸送現象の理論解析
    萌芽共同研究課題
    研究期間: 2016年06月 - 2017年03月
    生体分子内の電荷移動現象の理論解析
    若手研究者奨励枠
    研究期間: 2014年06月 - 2016年03月
氏名 満田 祐樹
Name Mitsuta Yuki
所属
所属研究科/学類
職名 研究員
研究テーマ 分子シミュレーションを用いた自由エネルギー反応経路探索法の開発
関連リンク
Email mitsutayccs.tsukuba.ac.jp
氏名
Name Kowit Hengphasatporn
所属
所属研究科/学類
職名 研究員
研究テーマ
関連リンク
Email kowithccs.tsukuba.ac.jp
氏名 広川 貴次
Name Hirokawa Takatsugu
所属 医学医療系
所属研究科/学類
職名 教授(共同研究員)
研究テーマ
関連リンク
Email
氏名 吉野 龍ノ介
Name Yoshino Ryunosuke
所属 医学医療系
所属研究科/学類
職名 助教(共同研究員)
研究テーマ 分子シミュレーションを用いた薬理活性化合物の探索、及び構造最適化
関連リンク
Email

分子進化分野

氏名 稲垣 祐司
Name Inagaki Yuji
所属
所属研究科/学類 生命環境科学研究科/生命環境学群 生物学類
職名 教授/分野リーダー
研究テーマ 真核生物の分子系統解析・生物種間での遺伝子水平移動・立体構造と分子進化情報を組み合わせたタンパク質の機能解析・分子系統解析における各種アーティファクトの解析
関連リンク
Email yujiccs.tsukuba.ac.jp
  • 研究キーワード
  • 経歴
    2016年04月
    -
    筑波大学 計算科学研究センター 教授
  • 論文
    Inventory and evolution of mitochondrion-localized family A DNA polymerases in Euglenozoa.
    Ryo Harada, Yoshihisa Hirakawa, Akinori Yabuki, Yuichiro Kashiyama, Moe Maruyama, Ryo Onuma, Petr Soukal, Shinya Miyagishima, Vladimir Hampl, Goro Tanifuji, Yuji Inagaki
    Pathogens 2020年04月[査読有り]
    Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis.
    Chihiro Sarai, Goro Tanifuji, Takuro Nakayama, Ryoma Kamikawa, Kazuya Takahashi, Euki Yazaki, Eriko Matsuo, Hideaki Miyashita, Ken-ichro Ishida, Mitsunori Iwataki, Yuji Inagaki
    Proceedings of the National Academy of Sciences of the United States of America 117 (10) 2020年03月[査読有り]
    Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis.
    Tanifuji, Goro, Kamikawa, Ryoma, Moore, Christa E, Mills, Tyler, Onodera, Naoko T, Kashiyama, Yuichiro, Archibald, John M, Inagaki, Yuji, Hashimoto, Tetsuo
    Genome Biology and Evolution 12 (2) 2020年02月[査読有り]
    Barthelonids represent a deep-branching Matamonada clade with mitochondrion-related organelles generating no ATP.
    Euki, Yazaki, Kume, Keitaro, Takashi, Shiratori, Yana, Edlit, Goro, Tanifuji, Ryo, Harada, Alastair, Simpson, Ken-ichiro, Ishida, Tetsuo, Hashimoto, Inagaki, Yuji
    bioRχiv 2019年10月[査読有り]
    Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote
    Matsuo, Mitsuhiro, Katahata, Atsushi, Tchikawa, Makoto, Minakuchi, Yohei, Noguchi, Hideki, Toyoda, Atsushi, Fujiyama, Asao, Suzuki, Yutaka, Hata, Takayuki, Satoh, Soichirou, Nakayama, Takuro, Kamkawa, Ryoma, Nomura, Mami, Inagaki, Yuji, Ishida, Ken-ichiro, Obokata, Junichi
    bioRχiv 2019年10月[査読有り]
    Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host
    Takuro, Nakayama, Mami, Nomura, Yoshihito, Takano, Tanifuji, Goro, Kogiku, Shiba, Kazuo, Inaba, Inagaki, Yuji, Masakado, Kawata
    Proceedings of the National Academy of Science of the United States of America 116 (32) 2019年06月[査読有り]
    In silico strcutral modelling and analysis of elongation factor 1alpha and elongation factor-like proteins.
    Kotaro, Sakamoto, Megumi, Kayanuma, Inagaki, Yuji, Tetsuo, Hashimoto, Yasuteru, Shigeta
    ACS Omega 4 (4) 2019年04月[査読有り]
    Horizontally-acquired genetic elements in the mitochondrial genome of a centrohelid Marophrys sp. SRT127.
    Yuki, Nishimura, Takashi, Shiratori, Kenichro, Ishida, Tetsuo, Hashimoto, Moriya, Ohkuma, Inagaki, Yuji
    Scientific Reports 9 2019年03月[査読有り]
    Fates of evolutionarily distinct, plastid-type glyceraldehyde 3-phosphate dehydrogenase genes in kareniacean dinoflagellates.
    Ryoma, Kamikawa, Euki, Yazaki, Michiru, Tahara, Takaya, Sakura, Matsuo, Eriko, Kisaburo, Nagamune, Tetsuo, Hashimoto, Inagaki, Yuji
    Journal of Eukaryotic Microbiology 65 (6) 2018年09月[査読有り]
    Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates.
    Eriko, Matsuo, Inagaki, Yuji
    PeerJ 6 2018年07月[査読有り]
    Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer.
    Matsuo, Mitsuhiro, Katahata, Atsushi, Satoh, Soichirou, Matsuzaki, Motomichi, Nomura, Mami, Ken-ichiro, Ishita, Inagaki, Yuji, Obokata, Junichi
    PLOS ONE 13 (7) 2018年07月[査読有り]
    The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites.
    Tanifuji, Goro, Takabayashi, Shun, Kume, Keitaro, Takagi, Mizue, Nakayama, Takuro, Kamikawa, Ryoma, Inagaki, Yuji, Hashimoto, Tetsuo
    PLOS ONE 13 (3) 2018年03月[査読有り]
    Extensive molecular tinkering in the evolution of the membrane attachment mechanisms of the Rheb GTPase.
    Záhonová, Kristína, Petrželková, Romana, Valach, Matúš, Yazaki, Euki, Tikhonenkov, Denis V, Butenko, Anzhelika, Janouškovec, Jan, Hrdá, Štěpánka, Klimeš, Vladimír, Burger, Gertraud, Inagaki, Yuji, Keeling, Patrick J, Hampl, Vladimír, Flegontov, Pavel, Yurchenko, Vyacheslav, Eliáš, Marek
    Scientific Reports 8 2018年03月[査読有り]
    Phylogenomics places orpha protistan lineages in a novel candidate supergroup.
    Brown, Matthew R, Heiss, Aaron A, Kamikawa, Ryoma, Inagaki, Yuji, Yabuki, Akinori, Alexander, Tice T, Shiratori, Takashi, Ishida, Ken-ichiro, Hashimoto, Tetsuo, Simpson, Alastair GB, J, Roger Andrew
    Genome Biology and Evolution 10 (2) 2018年01月[査読有り]
    Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms
    Takuro Nakayama, Yuji Inagaki
    SCIENTIFIC REPORTS 7 2017年10月[査読有り]
    Global Kinetoplastea phylogeny inferred from a large-scale multigene alignment including prarasitic species for better understanding transitions from a free-living to a parasitic lifestyle.
    Yazaki, Euki, Ishikawa, Sohta, Kume, Keitaro, Kumagai, Akira, Kamaishi, Takashi, Tanifuji, Goro, Hashimoto, Tetsuo, Inagaki, Yuji
    Genes & Genetic Systems 92 (1) 2017年09月[査読有り]
    Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis
    Goro Tanifuji, Ugo Cenci, Daniel Moog, Samuel Dean, Takuro Nakayama, Vojtech David, Ivan Fiala, Bruce A. Curtis, Shannon J. Sibbald, Naoko T. Onodera, Morgan Colp, Pavel Flegontov, Jessica Johnson-MacKinnon, Michael McPhee, Yuji Inagaki, Tetsuo Hashimoto, Steven Kelly, Keith Gull, Julius Lukes, John M. Archibald
    SCIENTIFIC REPORTS 7 2017年09月[査読有り]
    A Non-photosynthetic Diatom Reveals Early Steps of Reductive Evolution in Plastids
    Ryoma Kamikawa, Daniel Moog, Stefan Zauner, Goro Tanifuji, Ken-Ichiro Ishida, Hideaki Miyashita, Shigeki Mayama, Tetsuo Hashimoto, Uwe G. Maier, John M. Archibald, Yuji Inagaki
    MOLECULAR BIOLOGY AND EVOLUTION 34 (9) 2017年09月[査読有り]
    Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes
    Michelle M. Leger, Martin Kolisko, Ryoma Kamikawa, Courtney W. Stairs, Keitaro Kume, Ivan Cepicka, Jeffrey D. Silberman, Jan O. Andersson, Feifei Xu, Akinori Yabuki, Laura Eme, Qianqian Zhang, Kiyotaka Takishita, Yuji Inagaki, Alastair G. B. Simpson, Tetsuo Hashimoto, Andrew J. Roger
    NATURE ECOLOGY & EVOLUTION 1 (4) 2017年04月[査読有り]
    Mitochondria genome of Palpitomonas bilix: Derived genome structure and ancestral system for cytochrome c maturation.
    Yuki,Nishimura, Goro,Tanifuji, Ryoma,Kamikawa, Akinori,Yabuki, Tetsuo,Hashimoto, Inagaki,Yuji
    Genome Biology and Evolution 8 (10) 2016年10月[査読有り]
    Protein folding and evolution
    Harada,Ryuhei, Inagaki,Yuji, Yasuteru,Shigeta
    Reference Module in Materials Science and Materials Engineering 2016年06月[査読有り]
    Ungulate malaria parasites
    Tomas,K. Templeton, Masahito,Asada, Montakan,Jiratanh, Sohta,A. Ishikawa, Sonthaya,Tiawsirusup, Thillaiampalam,Sivakumar, Boniface,Namangala, Mika,Takeda, Mohkaew,Supawan, Supawan,Ngamjituea, Noboru,Inoue, Chihiro,Sugimoto, Inagaki,Yuji, Yasuhiko,Suzuki, Naoaki,Yokoyama, Morakot,Kaewthamasorn, Osamu,Kaneko
    Scientific Reports 6 2016年03月[査読有り]
    共生体由来オルガネラにまつわるエトセトラ.
    稲垣,祐司
    生物の科学 遺伝 70 (2) 2016年03月[査読有り]
    シアノバクテリアと真核藻類の細胞統合―「窒素固定オルガネラ」へ続く道?
    中山卓郎, 稲垣,祐司
    生物の科学 遺伝 70 (2) 2016年03月[査読有り]
    Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes (vol 32, pg 2598, 2015)
    Kamikawa Ryoma, Tanifuji Goro, Ishikawa Sohta A, Ishii Ken-Ichiro, Matsuno Yusei, Onodera Naoko T, Ishida Ken-Ichiro, Hashimoto Tetsuo, Miyashita Hideaki, Mayama Shigeki, Inagaki Yuji
    MOLECULAR BIOLOGY AND EVOLUTION 33 (1) 2016年01月[査読有り]
    Metabolic capacity of mitochondrion-related organelle in the free-living anaerobic stramenopile Cantina marsuplialis.
    Noguchi,Fumiya, Shimamura,Shigeru, Nakayama,Takuro, Yazaki,Euki, Akinori,Yabuki, Hashimoto,Tetsuo, Inagaki,Yuji, Fujikura,Katsunori, Kiyotaka,Takishita
    Protist 166 (5) 2015年11月[査読有り]
    Proposal of a Twin-arginine translocator system-mediated constraint against loss of ATP synthase genes from nonphotosynthetic plastid genomes.
    Ryoma,Kamikawa, Goro,Tanifuji, Sohta,A Ishikawa, Ken-ichiro,Ishii, Yusei,Matsuno, Naoko,T Onodera, Ken-ichiro,Ishida, Tetsuo,Hashimoto, Hideaki,Miyashita, Shigeki,Mayama, Inagaki,Yuji
    Molecular Biology and Evolution 32 (10) 2015年10月[査読有り]
    Multiple conversion between the genes encoding bacterial class-I release factors
    Sohta,Ishikawa, Ryoma,Kamikawa, Inagaki,Yuji
    Scientific Reports 5 2015年08月[査読有り]
    Morphological identities of two different marine stramenopile environmental sequence clades: Bicosoeca kenaiensis (Hilliard 1971) and Cantina marsuplialis (Larson and Patterson, 1990) gen. nov., comb. nov.
    Naoji,Yubuki, Tomáš,Pánek, Akinori,Yabuki, Ivan,Čepička, Kiyotaka,Takishita, Inagaki,Yuji, Brian,S Leander
    Journal of Eukaryotic Microbiology 62 (4) 2015年07月[査読有り]
    The mitochondrial genomes of Kudoa species are extremely divergent among metazoa.
    Fumiya,Takeuchi, Tsuyoshi,Sekizuka, Yumiko,Ogasawara, Hiroshi,Yokoyama, Ryoma,Kamikawa, Inagaki,Yuji, Tomoyoshi,Nozaki, Yoshiko,Sugita-Konishi, Takahiro,Ohnishi, Makoto,Kuroda
    PLOS One 10 (7) 2015年07月[査読有り]
    Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum.
    Ryoma,Kamikawa, Goro,Tanifuji, Masanobu,Kawachi, Hideaki,Miyashita, Tetsuo,Hashimoto, Inagaki,Yuji
    Genome Biology and Evolution 7 (4) 2015年04月[査読有り]
    Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae)
    Ryoma Kamikawa, Naoji Yubuki, Masaki Yoshida, Misaka Taira, Noriaki Nakamura, Ken-ichiro Ishida, Brian S. Leander, Hideaki Miyashita, Tetsuo Hashimoto, Shigeki Mayama, Yuji Inagaki
    PHYCOLOGICAL RESEARCH 63 (1) 2015年01月[査読有り]
    Genome evolution triggered by acquisition of an endosymbiotic partner
    Inagaki, Yuji
    GENES & GENETIC SYSTEMS 89 (6) 2014年12月[査読有り]
    Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle
    Takuro Nakayama, Ryoma Kamikawa, Goro Tanifuji, Yuichiro Kashiyama, Naohiko Ohkouchi, John M. Archibald, Yuji Inagaki
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 (31) 2014年08月[査読有り]
    Secondary loss of a cis-spliced intron after the diversification of Giardia intestinalis assemblages.
    Ryoma Kamikawa, Yuji Inagaki, Tetsuo Hashimoto
    BMC Research Notes 7 2014年07月[査読有り]
    An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333.
    Yuki Nishimura, Ryoma Kamikawa, Tetsuo Hashimoto, Yuji Inagaki
    Mobile Genetic Elements 4 (1) 2014年05月[査読有り]
    Gene content evolution in discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa.
    Kamikawa,Ryoma, Kolisko,Martin, Nishimura,Yuki, Yabuki,Akinori, Brown,Matthew W, Ishikawa,Sohta, Ishida,Ken-ichiro, Roger,Andrew J, Hashimoto,Tetsuo, Inagaki,Yuji
    Genome Biology and Evolution 6 (2) 2014年01月[査読有り]
    Identificatio of a bacteria-like ferrochelatase gene in Strongyloides venezuelensis, an animal parasitic nematode.
    Nagayasu, E, Ishikawa, S, Taketani, S, Ooka, T, Chakraborty, G, Yoshida, A, Inagaki, Y, Hayashi, T, Maruyama, H
    PLoS One 8 (3) 2013年[査読有り]
    Prasinoxanthin is absent in the green-colored dinoflagellate Lepidodinium chlorophorum strain NIES-1868: Pigment composition and 18S rRNA phylogeny.
    Matsumoto, T, Kawachi, M, Miyashita, H, Inagaki, Y
    Journal of Plant Research 125 (6) 2012年11月[査読有り]
    Evolution of Elongation Factor-Like (EFL) Protein in Rhizaria is Revised by Radiolarian EFL Gene Sequences
    Ishitani, Yoshiyuki, Kamikawa, Ryoma, Yabuki, Akinori, Tsuchiya, Masashi, Inagaki, Yuji, Takishita, Kiyotaka
    JOURNAL OF EUKARYOTIC MICROBIOLOGY 59 (4) 2012年07月[査読有り]
    RY-coding and non-homogeneous models can ameliorate the maximum-likelihood inferences from nucleotide sequence data with parallel compositional heterogeneity
    Ishikawa, Sohta A, Inagaki, Yuji, Hashimoto, Tetsuo
    EVOLUTIONARY BIOINFORMATICS 8 2012年06月[査読有り]
    Separate Origins of Group I Introns in Two Mitochondrial Genes of the Katablepharid Leucocryptos marina
    Nishimura, Yuki, Kamikawa, Ryoma, Hashimoto, Tetsuo, Inagaki, Yuji
    PLOS ONE 7 (5) 2012年05月[査読有り]
    Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochndriate' diplomonads and retortamonads
    Takishita,K, Kolisko,M, Komatsuzaki,H, Yabuki,A, Inagaki,Y, Cepicka,I, Smejkalova,P, Silberman,JD, Hashimoto,T, Roger,AJ, Simpson,AGB【*Join, authors】
    Protist 16 (3) 2012年02月[査読有り]
    An asynchronous parallel genetic algorithm for the maximum likelihood phylogenetic tree search.
    Tsuji,M, Sato,M, Tanabe,AS, Inagaki,Y, Hashimoto,T
    Proceedings of 2012 IEEE Congress on Evolutionary Computation (CEC) 2012 2012年01月[査読有り]
    Multigene phylogenetic analyses including diverse radiolarian species support the "Retaria" hypothesis - The sister relationship of Radiolaria and Foraminifera
    Ishitani, Yoshiyuki, Ishikawa, Sohta A, Inagaki, Yuji, Tsuchiya, Masashi, Takahashi, Kozo, Takishita, Kiyotaka
    MARINE MICROPALEONTOLOGY 81 (1-2) 2011年11月[査読有り]
    Tsukubamonas globosa n. gen., n. sp., a novel excavate flagellate possibly holding a key for the early evolution in "Discoba"
    Yabuki, Akinori, Nakayama, Takeshi, Yubuki, Naoji, Hashimoto, Tetsuo, Ishida, Ken-Ichiro, Inagaki, Yuji
    JOURNAL OF EUKARYOTIC MICROBIOLOGY 58 (4) 2011年07月[査読有り]
    A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum
    Matsumoto, Takuya, Ishikawa, Sohta A, Hashimoto, Tetsuo, Inagaki, Yuji
    MOLECULAR PHYLOGENETICS AND EVOLUTION 60 (1) 2011年07月[査読有り]
    Splintrons in Giardia intestinalis: Spliceosomal introns in a split form
    Kamikawa, R, Inagaki, Y, Roger, AJ, Hashimoto, T
    Communicative and Integrative Biology 4 (4) 2011年04月[査読有り]
    Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin
    Matsumoto, Takuya, Shinozaki, Fumihiko, Chikuni, Tomoko, Yabuki, Akinori, Takishita, Kiyotaka, Kawachi, Masanobu, Nakayama, Takeshi, Inoue, Isao, Hashimoto, Tetsuo, Inagaki, Yuji
    PROTIST 162 (2) 2011年04月[査読有り]
    Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing
    Kamikawa, Ryoma, Inagaki, Yuji, Tokoro, Masaharu, Roger, Andrew J, Hashimoto, Tetsuo
    CURRENT BIOLOGY 21 (4) 2011年02月[査読有り]
    Tsukubamonas globosa gen. et sp. nov.; a novel excavate flagellate possibly hold a key for the early evolution in “Discoba”.
    Yabuki, A, Nakayama, T, Yubuki, N, Hashimoto, T, Ishida, K, Inagaki, Y
    J. Euk. Microbiol. 58 (2) 2011年01月[査読有り]
    A novel spliceosome-mediated trans-splicing can change our view on genome complexity of the divergent eukaryote Giardia intestinalis
    Kamikawa, R, Inagaki, Y, Hashimoto, T
    Biophysical Reviews 3 (4) 2011年01月[査読有り]
    Cercozoa comprises both EF-1 alpha-containing and EFL-containing members
    Kamikawa, Ryoma, Yabuki, Akinori, Nakayama, Takuro, Ishida, Ken-ichiro, Hashimoto, Tetsuo, Inagaki, Yuji
    EUROPEAN JOURNAL OF PROTISTOLOGY 47 (1) 2011年01月[査読有り]
    Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacterium
    Nakayama, Takuro, Ikegami, Yuko, Nakayama, Takeshi, Ishida, Ken-ichiro, Inagaki, Yuji, Inouye, Isao
    JOURNAL OF PLANT RESEARCH 124 (1) 2011年01月[査読有り]
    Mitochondrial genomes from two red tide forming raphidophycean algae Heterosigma akashiwo and Chattonella marina var. marina
    Masuda, Isao, Kamikawa, Ryoma, Ueda, Manabu, Oyama, Kenichi, Yoshimatsu, Sadaaki, Inagaki, Yuji, Sako, Yoshihiko
    HARMFUL ALGAE 10 (2) 2011年01月[査読有り]
    Comprehensive SSU rRNA phylogeny of Eukaryota.
    Ishida, K, Inagaki, Y, Sakaguchi, M, Oiwa, A, Kai, Atsushi, Suzuki, M, Nakayama, T, Chikuni, T, Yabuki, A, Yamaguchi, H, Yubuki, N, Yoshida, M, Nakayama, T, Inouye, I, Hashimoto, T
    Journal of Endocytobiosis and Cell Research 20 2010年12月[査読有り]
    Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. gen. et sp., as inferred from SSU rDNA sequences.
    Yubuki, N, za, V, Cepicka I, Yabuki A, Inagaki Y, Nakayama T, Inouye I, Leander BS, 稲垣, 祐司
    Journal of Eukaryotic Microbiology 57 (6) 2010年11月[査読有り]
    Palpitomonas bilix gen. et sp. nov: A novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia.
    Yabuki, A, Inagaki, Y, Ishida, K
    Protist 210 (4) 2010年10月[査読有り]
    A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats.
    Kolisko, M, Silberman, JD, Cepicka, I, Yubuki, N, Takishita, K, Yabuki, A, Leander, BS, Inouye, I, Inagaki, Y, Roger, AJ, Simpson, AG, 井上, 勲
    Environmental Microbiology 12 2010年10月[査読有り]
    Rooting for the root of elongation factor-like protein phylogeny
    Kamikawa, Ryoma, Sakaguchi, Miako, Matsumoto, Takuya, Hashimoto, Tetsuo, Inagaki, Yuji
    MOLECULAR PHYLOGENETICS AND EVOLUTION 56 (3) 2010年09月[査読有り]
    A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum
    Minge, Marianne A, Shalchian-Tabrizi, Kamran, Torresen, Ole K, Takishita, Kiyotaka, Probert, Ian, Inagaki, Yuji, Klaveness, Dag, Jakobsen, Kjetill S
    BMC EVOLUTIONARY BIOLOGY 10 2010年06月[査読有り]
    Phylogeny of Asian primate malaria parasites inferred from apicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile
    Mitsui, Hideya, Arisue, Nobuko, Sakihama, Naoko, Inagaki, Yuji, Horii, Toshihiro, Hasegawa, Masami, Tanabe, Kazuyuki, Hashimoto, Tetsuo
    GENE 450 (1-2) 2010年01月[査読有り]
    Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes
    Kamikawa, Ryoma, Sanchez-Perez, Gabino F, Sako, Yoshihiko, Roger, Andrew J, Inagaki, Yuji
    MOLECULAR PHYLOGENETICS AND EVOLUTION 53 (2) 2009年11月[査読有り]
    Eukaryotic origin of glyceraldehyde-3-phosphate dehydrogenase genes in Clostridium thermocellum and Clostridium cellulolyticum genomes and putative fates of the exogenous gene in the subsequent genome evolution
    Takishita, Kiyotaka, Inagaki, Yuji
    GENE 441 (1-2:::Sp. Iss. SI) 2009年07月[査読有り]
    Tracing back EFL gene evolution in the cryptomonads-haptophytes assemblage: Separate origins of EFL genes in haptophytes, photosynthetic cryptomonads, and goniomonads
    Sakaguchi, Miako, Takishita, Kiyotaka, Matsumoto, Takuya, Hashimoto, Tetsuo, Inagaki, Yuji
    GENE 441 (1-2:::Sp. Iss. SI) 2009年07月[査読有り]
    Gene sampling can bias multi-gene phylogenetic inferences: The relationship between red algae and green plants as a case study
    Inagaki, Yuji, Nakajima, Yoshihiro, Sato, Mitsuhisa, Sakaguchi, Miako, Hashimoto, Tetsuo
    MOLECULAR BIOLOGY AND EVOLUTION 26 (5) 2009年05月[査読有り]
    A hypothesis for the evolution of nuclear-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase genes in "chromalveolate" members.
    Takishita, K, Yamaguchi, H, Maruyama, T, Inagaki, Y
    PLoS ONE 4 (3) 2009年03月[査読有り]
    Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates
    Burki, Fabien, Inagaki, Yuji, Brate, Jon, Archibald, John M, Keeling, Patrick J, Cavalier-Smith, Thomas, Sakaguchi, Miako, Hashimoto, Tetsuo, Horak, Ales, Kumar, Surendra, Klaveness, Dag, Jakobsen, Kjetill S, Pawlowski, Jan, Shalchian-Tabrizi, Kamran
    GENOME BIOLOGY AND EVOLUTION 1 2009年01月[査読有り]
    Direct phylogenetic evidence for lateral transfer of elongation factor-like gene
    Kamikawa, Ryoma, Inagaki, Yuji, Sako, Yoshihiko
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 105 (19) 2008年05月[査読有り]
    Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum
    Takishita, Kiyotaka, Kawachi, Masanobu, Noel, Mary-Helene, Matsumoto, Takuya, Kakizoe, Natsuki, Watanabe, Makoto M, Inouye, Isao, Ishida, Ken-Ichiro, Hashimoto, Tetsuo, Inagaki, Yuji
    GENE 410 (1) 2008年02月[査読有り]
    Evolving genetic codes.
    Ohama, T, Inagaki, Y, Bessho, Y, Osawa, S
    Proceedings of the Japan Academy, Ser. B 84 (2) 2008年01月[査読有り]
    複数遺伝子の結合データに基づく分子系統樹の推測 ―真核生物の大系統の解析を例として―
    橋本哲男, 有末伸子, 坂口美亜子, 稲垣祐司
    統計数理 56 (1) 2008年01月[査読有り]
    Centrohelida is still searching for a phylogenetic home: Analyses of seven Raphidiophrys contractilis genes
    Sakaguchi, Miako, Inagaki, Yuji, Hashimoto, Tetsuo
    GENE 405 (1-2) 2007年12月[査読有り]
    Assessing the monophyly of chlorophyll-c containing plastids by multi-gene phylogenies under the unlinked model conditions.
    Iida, K, Takishita, K, Ohshima, K, Inagaki, Y
    Molecular Phylogenetics and Evolution 45 (1) 2007年10月[査読有り]
    Proposal of Pseudochattonella verruculosa gen. nov., comb. nov. (Dictyochophyceae) for a former raphidophycean Chattonella verruculosa, based on 18S rDNA phylogeny and ultrastructural characteristics.
    Hosoi-Tanabe, S, Honda, D, Fukaya, S, Otake, I, Inagaki, Y, Sako, Y
    Phycological Research 55 (3) 2007年09月[査読有り]
    ロングブランチの誘惑-分子系統解析のダークサイド
    稲垣, 祐司
    藻類 55 (2) 2007年07月[査読有り]
    Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures
    Takishita, Kiyotaka, Yubuki, Naoji, Kakizoe, Natsuki, Inagaki, Yuji, Maruyama, Tadashi
    EXTREMOPHILES 11 (4) 2007年07月[査読有り]
    Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages
    Patron, Nicola J, Inagaki, Yuji, Keeling, Patrick J
    CURRENT BIOLOGY 17 (10) 2007年05月[査読有り]
    Fragmentation of mitochondrial large subuint rRNA in a dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria.
    Kamikawa, R, Inagaki, Y, Sako, Y
    Protist 158 (2) 2007年04月[査読有り]
    Ultrastructure and ribosomal RNA phylogeny of the free-living heterotrophic flagellate Dysnectes brevis n. gen., n. sp., a new member of the fornicata
    Yubuki, Naoji, Inagaki, Yuji, Nakayama, Takeshi, Inoue, Isao
    JOURNAL OF EUKARYOTIC MICROBIOLOGY 54 (2) 2007年03月[査読有り]
    Plasticity of the domain structure in FlgJ, a bacterial protein involved in flagellar rod formation
    Nambu, Takayuki, Inagaki, Yuji, Kutsukake, Kazuhiro
    GENES & GENETIC SYSTEMS 81 (6) 2006年12月[査読有り]
    Phylogenetic estimation under codon models can be biased by codon usage heterogeneity
    Inagaki, Yuji, Roger, Andrew
    MOLECULAR PHYLOGENETICS AND EVOLUTION 40 (2) 2006年08月[査読有り]
    Recombination between elongation factor 1 alpha genes from distantly related archaeal lineages
    Inagaki, Y, Susko, E, Roger, AJ
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (12) 2006年03月[査読有り]
    Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes
    Simpson, AGB, Inagaki, Y, Roger, AJ
    MOLECULAR BIOLOGY AND EVOLUTION 23 (3) 2006年03月[査読有り]
    A close relationship between Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acid sequences of three cytoskeletal proteins (actin, alpha-tubulin, and beta-tubulin)
    Takishita,K, Inagaki,Y, Tsuchiya,M, Sakaguchi,M, Maruyama,T
    GENE 362 2005年12月[査読有り]
    The evolutionary relationships amongst excavates: a concatenated protein analysis.
    Simpson, AGB, Inagaki, Y, Roger, AJ
    Journal of Eukaryotic Microbiology 52 2005年01月[査読有り]
    Capsaspora owczarzaki is an independent opisthokont lineage.
    Ruiz-Trillo, I, Inagaki, Y, Davis, LA, Sperstad, S, Landfald, B, Roger, AJ
    Current Biology 14 (22) 2004年11月[査読有り]
    A class of eukaryotic GTPase with a punctuate distribution suggesting multiple functional replacements of translation elongation factor 1α.
    Keeling, PJ, Inagaki, Y
    Proceedings of the National Academy of Sciences USA 101 (43) 2004年10月[査読有り]
    On inconsistency of the neighbor-joining, least-squares, and minimum evolution estimation when substitution processes are incorrectly modeled.
    Susko, E, Inagaki, Y, Roger, AJ
    Molecular Biology and Evolution 21 (9) 2004年09月[査読有り]
    Phylogenetic artifacts can be caused by leucine, serine and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study.
    Inagaki, Y, Simpson, AGB, Dacks, JB, Roger, AJ
    Systematic Biology 53 (4) 2004年08月[査読有り]
    Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1α phylogenies.
    Inagaki, Y, Susko, E, Fast, NM, Roger, AJ
    Molecular Biology and Evolution 21 (7) 2004年07月[査読有り]
    Assessing functional divergence in EF-1α and its paralogs in eukaryotes and archaebacteria.
    Inagaki, Y, Blouin, C, Susko, E, Roger, AJ
    Nucleic Acids Research 31 (14) 2003年07月[査読有り]
    Testing for differences in rates-across-sites distributions in phylogenetic subtrees.
    Susko, E, Inagaki, Y, Field, C, Holder, ME, Roger, AJ
    Molecular Biology and Evolution 19 (9) 2002年09月[査読有り]
    Lateral transfer of an EF-1α gene: origin and evolution of the large subunit of ATP sulfurylase in Eubacteria.
    Inagaki, Y, Doolittle, WF, Baldauf, SL, Roger, AJ
    Current Biology 12 (9) 2002年04月[査読有り]
    Convergence and constraint in eukaryotic release factor 1 domain 1: the evolution of stop codon specificity.
    Inagaki, Y, Blouin, C, Doolittle, WF, Roger, AJ
    Nucleic Acids Research 30 (2) 2002年01月[査読有り]
    Class I release factors in ciliates with variant genetic codes.
    Inagaki, Y, Doolittle, WF
    Nucleic Acids Research 29 (4) 2001年02月[査読有り]
    Evolutionary relationship between dinoflagellates bearing obligate diatom endosymbionts: insight into tertiary endosymbiosis.
    Inagaki, Y, Dacks, JB, Doolittle, WF, Watanabe, KI, Ohama, T
    International Journal of Systematics and Evolutionary Microbiology 50 (6) 2000年11月[査読有り]
    Evolution of the eukaryotic translation termination system: origins of release factors.
    Inagaki, Y, Doolittle, WF
    Molecular Biology and Evolution 17 (6) 2000年06月[査読有り]
    Phylogenetic analysis of diatom coxI genes and implications of a fluctuating GC content on mitochondrial genetic code evolution.
    Ehara, M, Inagaki, Y, Watanabe, KI, Ohama, T
    Current Genetics 37 (1) 2000年01月[査読有り]
    Comprehensive molecular phylogenetic analysis of a heterokont alga (NIES 548) using genes from all three cellular compartments.
    Ehara, M, Kitayama, T, Watanabe, KI, Inagaki, Y, Hayashi-Ishimaru, Y, Ohama, T
    Phycological Research 47 (3) 1999年09月[査読有り]
    Distribution of the mitochondrial deviant genetic code, AUA for methionine, in heterokont algae.
    Ehara, M, Watanabe, KI, Kawai, H, Inagaki, Y, Hayashi-Ishimaru, Y, Ohama, T
    Journal of Phycology 34 (6) 1998年12月[査読有り]
    Directionally evolving genetic code: the UGA codon from stop to tryptophan in mitochondria.
    Inagaki, Y, Ehara, M, Watanabe, KI, Hayashi-Ishimaru, Y, Ohama, T
    Journal of Molecular Evolution 47 (4) 1998年10月[査読有り]
    Distinctive origins of group I introns found in the COXI genes of three green algae.
    Watanabe, KI, Ehara, M, Inagaki, Y, Ohama, T
    Gene 213 (1-2) 1998年06月[査読有り]
    A deviant mitochondrial genetic code in prymnesiophytes (yellow-algae): UGA codon for tryptophan.
    Hayashi-Ishimaru, Y, Ehara, M, Inagaki, Y, Ohama, T
    Current Genetics 32 (4) 1997年10月[査読有り]
    Algae or protozoa: phylogenetic position of euglenophytes and dinoflagellates as inferred from mitochondrial sequences.
    Inagaki, Y, Hayashi-Ishimaru, Y, Ehara, M, Igarashi, I, Ohama, T
    Journal of Molecular Evolution 45 (3) 1997年09月[査読有り]
    Use of a deviant mitochondrial genetic code in yellow-green algae as a landmark for segregating members within the phylum.
    Ehara, M, Hayashi-Ishimaru, Y, Inagaki, Y, Ohama, T
    Journal of Molecular Evolution 45 (2) 1997年08月[査読有り]
    Cloning of the Mycoplasma capricolum gene encoding peptide-chain release factor.
    Inagaki, Y, Bessho, Y, Hori, H, Osawa, S
    Gene 169 (1) 1996年02月[査読有り]
    Translation of synonymous codons in family boxes by Mycoplasma capricolum tRNAs with unmodified uridine or adenosine at the first anticodon position.
    Inagaki, Y, Kojima, A, Bessho, Y, Hori, H, Ohama, T, Osawa, S
    Journal of Molecular Biology 251 (4) 1995年08月[査読有り]
    Lack of peptide-release activity responding to codon UGA in Mycoplasma capricolum.
    Inagaki, Y, Bessho, Y, Osawa, S
    Nucleic Acids Research 21 (6) 1993年03月[査読有り]
  • 受賞
    2008年08月
    日本進化学会 日本進化学会研究奨励賞
    2007年04月
    文部科学省 科学技術分野の文部科学大臣表彰若手科学者賞
    1993年04月
    公益信託森安大学院生奨学基金
  • 書籍等出版物
    共生微生物
    稲垣,祐司, 中山卓郎 (担当:分担執筆, 第17章 現在も続く細胞内共生細菌のオルガネラ化.)
    Reference modules in Materials Science and Engineering 2016
    Harada, Ryuhei, Inagaki, Yuji, Shigeta, Yasuteru (担当:分担執筆, Protein Folding and Evolution)
    ロングブランチの誘惑--分子系統解析のダークサイド
    稲垣祐司 (担当:監修)
    アピコンプレクサ類の退化葉緑体は緑藻起源か?
    稲垣祐司 (担当:監修)
  • 競争的資金等の研究課題
    ミトコンドリアDNAポリメラーゼの多様性と進化の全容解明
    科学研究費基盤研究(B)
    研究期間: 2019年 -
    海洋原生生物に共生する細菌多様性の実態解明
    度国際共同研究加速基金(国際共同研究強化(B))
    研究期間: 2018年 -
    非光合成生物の光適応進化の全容解明
    科学研究費補助金 基盤研究(B)
    研究期間: 2017年 - 2020年
    海洋バクテリアの長期炭素隔離機能に対する海洋酸性化の影響評価
    科学研究費補助金 基盤研究(B)
    研究期間: 2016年 - 2019年
氏名 石谷 佳之
Name Ishitani Yoshiyuki
所属
所属研究科/学類
職名 研究員
研究テーマ 大規模分子データに基づく主要真核生物系統の分岐年代推定
関連リンク
Email ishitaniccs.tsukuba.ac.jp
  • 研究キーワード
  • 経歴
    2017年04月
    -
    筑波大学 計算科学研究センター 特任研究員
    2015年05月
    -
    2017年03月
    東京大学 大気海洋研究所 特任研究員
    2013年09月
    -
    2015年04月
    グラスゴー大学 地球科学科 日本学術振興会海外特別研究員
    2013年04月
    -
    2013年08月
    独立行政法人海洋研究開発機構 海洋・極限環境生物圏領域 研究支援パート(兼務)
    2013年04月
    -
    2013年08月
    東京大学 理学系研究科 特任研究員(兼務)
    2010年04月
    -
    2013年03月
    独立行政法人海洋研究開発機構 海洋・極限環境生物圏領域 日本学術振興会ポスドク研究員
  • 論文
    Nanoparticle-Biological Interactions in a Marine Benthic Foraminifer.
    Ciacci, C, Grimmelpont, M. V, Corsi, I, Bergami, E, Curzi, D, Burini, D, Bouchet, V. M. P, Ambrogini, P, Gobbi, P, Ujiié, Y, Ishitani, Y, Coccioni, R, Bernhard, J. M, Frontalini, F
    Scientific Reports 19 (9) 2019年12月[査読有り]
    Evolution of a planktonic foraminifer during environmental changes in the tropical oceans
    Yurika Ujiié, Yoshiyuki Ishitani
    PloS one 11 (2) 2016年[査読有り]
    Molecular evidence for wide vertical distribution of the marine planktonic protist Larcopyle buetschlii (Radiolaria) in a semi-enclosed marginal sea
    Ishitani Y, Takishita K
    Journal of Plankton Research 37 2015年07月[査読有り]
    有孔虫と放散虫を姉妹群とする「レタリア仮説」
    石谷 佳之, 瀧下 清貴
    化石 (97) 2015年03月[査読有り]
    Uncovering sibling species in Radiolaria: evidence for ecological partitioning in a marine planktonic protist.
    Ishitani Y, Ujiié Y, Takishita K
    Molecular phylogenetics and evolution 78 2014年09月[査読有り]
    Evolution of elongation factor-like (EFL) protein in Rhizaria is revised by radiolarian EFL gene sequences.
    Ishitani Y, Kamikawa R, Yabuki A, Tsuchiya M, Inagaki Y, Takishita K
    The Journal of eukaryotic microbiology 59 (4) 2012年07月[査読有り]
    Longitudinal differentiation among pelagic populations in a planktic foraminifer.
    Ujiié Y, Asami T, de Garidel-Thoron T, Liu H, Ishitani Y, de Vargas C
    Ecology and evolution 2 (7) 2012年07月[査読有り]
    Two distinct lineages in the radiolarian Order Spumellaria having different ecological niches
    Ishitani Y, Ujiié Y, De Vargas C, Not F, Takahashi K
    Deep-Sea Research II 61-64 2012年[査読有り]
    Phylogenetic relationships and evolutionary patterns of the order Collodaria (Radiolaria).
    Ishitani Y, Ujiié Y, de Vargas C, Not F, Takahashi K
    PloS one 7 (5) 2012年[査読有り]
    Multigene phylogenetic analyses including diverse radiolarian species support the “Retaria” hypothesis – the sister relationship of Radiolaria and foraminifera
    Ishitani Y, Ishikawa S, Inagaki Y, Tsuchiya M, Takahashi K, Takishita K
    Marine Micropaleontology 81 2011年[査読有り]
    北西太平洋西部亜寒帯循環内Station K2におけるレディオラリア(放散虫類)・フラックスの季節変動
    池上 隆仁, 高橋 孝三, 石谷 佳之, 田中 聖二
    海の研究 19 (4) 2010年07月[査読有り]
    Vertical and geographic distribution of selected radiolarian species in the North Pacific
    Ishitani Y, Takahashi K, Okazaki Y, Tanaka S
    Micropaleontology 54 (1) 2008年[査読有り]
    The vertical distribution of Radiolaria in the waters surrounding Japan
    Ishitani Y, Takahashi K
    Marine Micropaleontology 65 2007年[査読有り]
  • 受賞
    2011年10月
    放散虫研究集会 学術賞 第11回放散虫研究集会
    2010年07月
    ISEP young scientist award ISEP XVIII
  • 書籍等出版物
    アメーバのはなし
    石谷 佳之, 土屋正史 (担当:分担執筆, 海の中にいるヒトに感染しない原生生物)
    Radiolaria
    Yoshiyuki Ishitani, Colette Febvre-Chevalier, Jean Febvre (担当:共著)
    Distribution and geochemical properties of hydrothermal plumes in the Rodriguez Triple Junction
    Noguchi T, Fukuba T, Okamura K, Ijiri A, Yanagawa K, Ishitani Y, Fujii R, Sunamura M (担当:共著)
  • 競争的資金等の研究課題
    海洋原生生物に共生する細菌多様性の実態解明
    国際共同研究強化B【研究分担者】
    研究期間: 2018年10月 -
    ミトコンドリアDNAポリメラーゼの多様性と進化の全容解明
    基盤研究(B)【研究分担者】
    研究期間: 2019年04月 -
    大規模分岐年代推定ー真核生物の誕生と進化を解き明かす!!ー
    基盤研究(C)【研究代表者】
    研究期間: 2018年04月 -
    有孔虫における殻形成機構の解明ー石灰化のブラックボックスを開くー
    基盤研究(B)【研究分担者】
    研究期間: 2017年04月 - 2020年03月
    原核藻類と原生生物の光共生に関する研究
    基盤研究(C)【研究分担者】
    研究期間: 2016年04月 - 2019年03月
    浮遊性有孔虫の新規環境指標の確立:遺伝子・安定同位体・形態の複合解析から
    基盤研究(C)【研究協力者】
    研究期間: 2014年04月 - 2017年03月
    放散虫のバイオミネラリゼーションと殻形態進化:化石の分子生物学への応用に向けて
    海外特別研究員
    研究期間: 2013年09月 - 2015年04月
    浮遊性有孔虫の生物多様性と炭素循環の関係の解明
    若手研究(B)【研究協力者】
    研究期間: 2011年04月 - 2014年03月
    環境変遷に基づく放散虫の進化と多様性,古海洋環境指標としての新展望
    特別研究員
    研究期間: 2010年04月 - 2013年03月
    生物学に基づく古海洋学の新展開~放散虫・環境指標としての有用性・可能性の追求~
    日仏二国間交流事業【企画/立案/協力】
    研究期間: 2009年11月
氏名 橋本 哲男
Name Hashimoto Tetsuo
所属 生命環境系
所属研究科/学類
職名 生物科学専攻長(後期)/教授(共同研究員)
研究テーマ 真核生物の起源と初期進化に関する分子進化学的解析
関連リンク
Email