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本文へ toggle navigation センター紹介 カラム1 センター長挨拶 目的 沿革 カラム2 組織 運営協議会（名簿） 運営委員会（名簿） カラム3 教員・研究員紹介 計算科学研究センターフェロー 教員・研究員 素粒子物理研究部門 宇宙物理研究部門 原子核物理研究部門 量子物性研究部門 生命科学研究部門 地球環境研究部門 高性能計算システム研究部門 計算情報学研究部門 学外共同研究員 カラム3 研究実績・評価 論文・学会発表 年次報告書 研究評価・外部評価 SC出展ポスター 「超並列計算機CP-PACS」プロジェクトを振り返る 研究開発推進 カラム1 先端計算科学推進室 次世代計算システム研究開発室 HPCI推進室 ビッグデータ・AI連携推進室 計算科学振興室 高性能計算システム運用開発室 学際計算科学連携室 計算科学社会実装推進室 広報・戦略室 計算メディカルサイエンス事業部 研究部門 カラム1 素粒子物理研究部門 宇宙物理研究部門 原子核物理研究部門 量子物性研究部門 カラム2 生命科学研究部門 生命機能情報分野 分子進化分野 地球環境研究部門 高性能計算システム研究部門 計算情報学研究部門 データ基盤分野 計算メディア分野 研究プロジェクト カラム1 提供データベース 公開コード カラム３ 筑波山プロジェクト プロジェクトの経緯 プロジェクトの目的 筑波山神社・筑波大学計算科学研究センター共同気象観測所の概要と観測項目 過去の観測データ 連絡先 カラム２ 宇宙生命計算科学連携拠点 最先端共同HPC基盤施設（外部リンク） 終了したプロジェクト スーパーコンピュータ シンポジウム・研究会 カラム1 シンポジウム ワークショップ 計算科学コロキウム 全国共同利用 カラム1 学際共同利用プログラム 学際共同利用プログラム公募 採択課題一覧 共同研究支援 謝辞の手引き 採択後の手続き カラム2 HPCI共同利用 一般利用 スーパーコンピュータ利用の手引き 広報 カラム1 見学 よくある質問 プレスリリース CCS Premium Friday 研究者に聞く パンフレット カラム2 ロゴ ギャラリー メディア掲載情報 お問い合わせ 災害時の対応 English お問い合わせ 教員等採用情報 RSS登録 交通アクセス 文字サイズ： 標準 拡大 センター紹介 カラム1 センター長挨拶 目的 沿革 カラム2 組織 運営協議会（名簿） 運営委員会（名簿） カラム3 教員・研究員紹介 計算科学研究センターフェロー 教員・研究員 素粒子物理研究部門 宇宙物理研究部門 原子核物理研究部門 量子物性研究部門 生命科学研究部門 地球環境研究部門 高性能計算システム研究部門 計算情報学研究部門 学外共同研究員 カラム3 研究実績・評価 論文・学会発表 年次報告書 研究評価・外部評価 SC出展ポスター 「超並列計算機CP-PACS」プロジェクトを振り返る 研究開発推進 カラム1 先端計算科学推進室 次世代計算システム研究開発室 HPCI推進室 ビッグデータ・AI連携推進室 計算科学振興室 高性能計算システム運用開発室 学際計算科学連携室 計算科学社会実装推進室 広報・戦略室 計算メディカルサイエンス事業部 研究部門 カラム1 素粒子物理研究部門 宇宙物理研究部門 原子核物理研究部門 量子物性研究部門 カラム2 生命科学研究部門 生命機能情報分野 分子進化分野 地球環境研究部門 高性能計算システム研究部門 計算情報学研究部門 データ基盤分野 計算メディア分野 研究プロジェクト カラム1 提供データベース 公開コード カラム３ 筑波山プロジェクト プロジェクトの経緯 プロジェクトの目的 筑波山神社・筑波大学計算科学研究センター共同気象観測所の概要と観測項目 過去の観測データ 連絡先 カラム２ 宇宙生命計算科学連携拠点 最先端共同HPC基盤施設（外部リンク） 終了したプロジェクト スーパーコンピュータ シンポジウム・研究会 カラム1 シンポジウム ワークショップ 計算科学コロキウム 全国共同利用 カラム1 学際共同利用プログラム 学際共同利用プログラム公募 採択課題一覧 共同研究支援 謝辞の手引き 採択後の手続き カラム2 HPCI共同利用 一般利用 スーパーコンピュータ利用の手引き 広報 カラム1 見学 よくある質問 プレスリリース CCS Premium Friday 研究者に聞く パンフレット カラム2 ロゴ ギャラリー メディア掲載情報 お問い合わせ 災害時の対応 生命科学研究部門 トップページ > センター紹介 > 教員・研究員紹介 > 教員・研究員 > 生命科学研究部門 センター紹介センター長挨拶 目的 沿革 組織 運営協議会（名簿） 運営委員会（名簿） 研究員会議（趣旨説明） 教員・研究員紹介 計算科学研究センターフェロー 教員・研究員 素粒子物理研究部門 宇宙物理研究部門 原子核物理研究部門 量子物性研究部門 生命科学研究部門 地球環境研究部門 高性能計算システム研究部門 計算情報学研究部門 学外共同研究員 研究実績・評価 論文・学会発表 年次報告書 研究評価・外部評価 External Review (2008-2013) External Review (2007) External Review (2014-2019) SC出展ポスター 「超並列計算機CP-PACS」プロジェクトを振り返る 生命機能情報分野 名前 所属 職名 重田 育照 教授/分野リーダー 庄司 光男 教授 谷 一寿 教授 原田 隆平 准教授 堀 優太 助教 Kowit Hengphasatporn 助教 森田 陸離 研究員 宮川 晃一 研究員 Mrinal Kanti Si 研究員 Sittiwanichai Sirin 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/部門主任 中山 卓郎 助教 橋本 哲男 生命環境系 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/分野リーダー 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 TRIOS researchmap Email shigetaccs.tsukuba.ac.jp 研究キーワード分子動力学第一原理計算経歴2023年4月 - 現在筑波大学 本部 研究担当副学長・理事 2019年4月 - 現在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 2016年4月 - 現在筑波大学計算科学研究センター 生命科学研究部門 教授 2014年5月 - 現在大阪大学 大学院基礎工学研究科 招聘教授 2018年4月 - 2020年3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4月 - 2018年3月分子科学研究所 客員教授 2014年3月 - 2016年3月筑波大学 大学院数理物質科学研究科物理学系 教授 2010年8月 - 2014年3月大阪大学 大学院基礎工学研究科物質創成専攻 准教授 2011年8月 - 2013年7月文部科学省 研究振興局学術助成課 学術調査官（兼任） 2008年5月 - 2010年7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2月 - 2008年5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1月東京大学 大学院工学系研究科応用化学専攻 助手 2001年4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4月 - 2001年3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1月 - 2000年3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▼▲Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital methodHirotaka Kitoh-Nishioka, Yasuteru Shigeta, Koji AndoThe Journal of chemical physics 153 (10) 2020年9月[査読有り] Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular DynamicsTakunori Yasuda, Yasuteru Shigeta, Ryuhei HaradaJournal of Chemical Information and Modeling 60 (8) 2020年8月[査読有り] Analytical Method Using a Scaled Hypersphere Search for High-Dimensional Metadynamics SimulationsYuki Mitsuta, Yasuteru ShigetaJournal of Chemical Theory and Computation 16 (6) 2020年6月[査読有り] Enhanced Conformational Sampling Method Based on Anomaly Detection Parallel Cascade Selection Molecular Dynamics: ad-PaCS-MDRyuhei Harada, Kota Yamaguchi, Yasuteru ShigetaJournal of Chemical Theory and Computation, in preparation 16 (10) 2020年6月[査読有り] Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharingTakeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Chie Shibazaki, Tomoko Sunami, Taro Tamada, Naomine Yano, Taro Yamada, Katsuhiro Kusaka, Mamoru Suzuki, Yasuteru Shigeta, Ryota Kuroki, Hideyuki Hayashi, Takato Yano, Katsuyuki Tanizawa, Motoyasu Adachi, Toshihide OkajimaProceedings of the National Academy of Sciences of the United States of America 117 (20) 2020年5月[査読有り] Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active siteYasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki HayashiJOURNAL OF BIOCHEMISTRY 167 (4) 2020年4月[査読有り] Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active siteYasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki HayashiJournal of biochemistry 167 (4) 2020年4月[査読有り] Split Conformation of Chaetomium Thermophilum Hsp104 DisaggregaseInoue Yosuke, Hanazono Yuya, Noi Kentaro, Kawamoto Akihiro, Kimatsuka Masato, Harada Ryuhei, Takeda Kazuki, Iwamasa Natsuki, Noguchi Keiichi, Shigeta Yasuteru, Namba Keiichi, Ogura Teru, Miki Kunio, Shinohara Kyosuke, Yohda MasafumiScience Advances, submitted 29 (7) 2020年4月[査読有り] Protein Dynamics and the Folding DegreeVladimir Sladek, Ryuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling 60 (3) 2020年3月[査読有り] Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem iHirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru Itoh, Akihiro KimuraJournal of Physical Chemistry B 124 (2) 2020年1月[査読有り] Why are lopinavir and ritonavir effective against the newly emerged coronavirus 2019? Atomistic insights into the inhibitory mechanismsBodee Nutho, Panupong Mahalapbutr, Kowit Hengphasatporn, Nawanwat Chainuwong Pattaranggoon, Nattapon Simanon, Yasuteru Shigeta, Supot Hannongbua, Thanyada RungrotmongkolBiochemistry 59 (18) 2020年[査読有り] Intramolecular mode coupling of the isotopomers of water: A non-scalar charge density-derived perspectiveTian Tian, Tianlv Xu, Steven R. Kirk, Ian Tay Rongde, Yong Boon Tan, Sergei Manzhos, Yasuteru Shigeta, Samantha JenkinsPhysical Chemistry Chemical Physics 22 (4) 2020年[査読有り] Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of ProteinsRyuhei Harada, Vladimir Sladek, Yasuteru ShigetaJournal of Chemical Information and Modeling 59 (12) 2019年12月[査読有り] Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid dockingRyuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru ShigetaJournal of Molecular Graphics and Modelling 92 2019年11月[査読有り] Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling EfficiencyRyuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling 59 (9) 2019年9月[査読有り] Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein DynamicsRyuhei Harada, Vladimir Sladek, Yasuteru ShigetaJournal of Chemical Theory and Computation 15 (9) 2019年9月[査読有り] Accessing the accuracy of density functional theory through structure and dynamics of the water-air interfaceTatsuhiko Ohto, Mayank Dodia, Jianhang Xu, Sho Imoto, Fujie Tang, Frederik Zysk, Thomas D. Kühne, Yasuteru Shigeta, Mischa Bonn, Xifan Wu, Yuki NagataJournal of Physical Chemistry Letters 10 (17) 2019年9月[査読有り] Temperature–pressure shuffling outlier flooding method enhances the conformational sampling of proteinsRyuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru ShigetaJournal of Computational Chemistry 40 (15) 2019年6月[査読有り] Numerical investigation of the nano-scale solutal Marangoni convectionsY. Imai, T. Yamamoto, A. Sekimoto, Y. Okano, R. Sato, Y. ShigetaJournal of the Taiwan Institute of Chemical Engineers 98 (SI) 2019年5月[査読有り] Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical InsightTianlv Xu, Jia Hui Li, Roya Momen, Wei Jie Huang, Steven Robert Kirk, Yasuteru Shigeta, Samantha JenkinsJournal of the American Chemical Society 141 (13) 2019年4月[査読有り] Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical InsightXu, Tianlv, Li, Jia Hui, Momen, Roya, Huang, Wei Jie, Kirk, Steven Robert, Shigeta, Yasuteru, Jenkins, SamanthaJournal of the American Chemical Society 141 (13) 2019年4月[査読有り] New assay method based on Raman spectroscopy for enzymes reacting with gaseous substratesYuka Kawahara-Nakagawa, Koji Nishikawa, Satoru Nakashima, Shota Inoue, Takehiro Ohta, Takashi Ogura, Yasuteru Shigeta, Katsuyuki Fukutani, Tatsuhiko Yagi, Yoshiki HiguchiProtein Science 28 (3) 2019年3月[査読有り] New Assay Method Based on Raman Spectroscopy for Enzymes Reacting with Gaseous SubstratesKawahara-Nakagawa, Yuka, Nishikawa, Koji, Nakashima, Satoru, Inoue, Shota, Ohta, Takehiro, Ogura, Takashi, Shigeta, Yasuteru, Fukutani, Katsuyuki, Yagi, Tatsuhiko, Higuchi, YoshikiProtein science : a publication of the Protein Society 28 (3) 2019年1月[査読有り] Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of BiomoleculesRyuhei Harada, Yasuteru ShigetaAdvances in Quantum Chemistry 78 (78) 2019年[査読有り] Protein Residue Networks from Energetic and Geometric Data: Are They Identical?Vladimir Sladek, Hiroaki Tokiwa, Hitoshi Shimano, Yasuteru ShigetaJournal of Chemical Theory and Computation 14 (12) 2018年12月[査読有り] Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon UpconversionRyuma Sato, Hirotaka Kitoh-Nishioka, Kenji Kamada, Toshiko Mizokuro, Kenji Kobayashi, Yasuteru ShigetaJournal of Physical Chemistry Letters 9 (22) 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, YasuteruJournal of chemical theory and computation 14 (12) 2018年11月Concerted Mechanism of Water Insertion and O Release during the S to S Transition of the Oxygen-Evolving Complex in Photosystem IIShoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, KizashiThe journal of physical chemistry. B 122 (25) 2018年6月[査読有り] On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of ProteinsRyuhei Harada, Yasuteru ShigetaJournal of Chemical Theory and Computation 14 (6) 2018年6月[査読有り] How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulationsHarada, Ryuhei, Shigeta, YasuteruPhysical chemistry chemical physics : PCCP 20 (26) 2018年6月[査読有り] Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMαYamamoto, 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, HitoshiBiochemical and biophysical research communications 499 (2) 2018年5月[査読有り] Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMαYamamoto, 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, HitoshiBiochemical and biophysical research communications 499 (2) 2018年5月[査読有り] Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics studyHarada, Ryuhei, Mashiko, Takako, Tachikawa, Masanori, Hiraoka, Shuichi, Shigeta, YasuteruPhysical chemistry chemical physics : PCCP 20 (14) 2018年4月[査読有り] Nonadiabatic one-electron transfer mechanism for the O–O bond formation in the oxygen-evolving complex of photosystem IIMitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Kizashi YamaguchiChemical Physics Letters 698 2018年4月[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 ShigetaJournal of Physical Chemistry C 122 (10) 2018年3月[査読有り] How low-resolution structural data predict the conformational changes of a protein: A study on data-driven molecular dynamics simulationsRyuhei Harada, Yasuteru ShigetaPhysical Chemistry Chemical Physics 20 (26) 2018年[査読有り] Coulomb and CH-φ interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilitiesYuma Terai, Ryuma Sato, Takahiro Yumiba, Ryuhei Harada, Kohei Shimizu, Tatsuya Toga, Tomoko Ishikawa-Fujiwara, Takeshi Todo, Shigenori Iwai, Yasuteru Shigeta, Junpei YamamotoNucleic Acids Research 46 (13) 2018年[査読有り] Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal PhaseMasaki Hada, Shohei Saito, Sei'Ichi Tanaka, Ryuma Sato, Masahiko Yoshimura, Kazuhiro Mouri, Kyohei Matsuo, Shigehiro Yamaguchi, Mitsuo Hara, Yasuhiko Hayashi, Fynn Röhricht, Rainer Herges, Yasuteru Shigeta, Ken Onda, R. J. Dwayne MillerJournal of the American Chemical Society 139 (44) 2017年11月[査読有り] Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature BehaviorHajime Yotsuji, Kenji Higashiguchi, Ryuma Sato, Yasuteru Shigeta, Kenji MatsudaChemistry - A European Journal 23 (60) 2017年10月[査読有り] X‐ray crystallographic and mutational analysis of the NylC precursor: Catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolaseSeiji Negoro, Naoki Shibata, Dai‐ichiro Kato, Yusuke Tanaka, Kengo Yasuhira, Keisuke Nagai, Shohei Oshima, Yoko Furuno, Risa Yokoyama, Kaito Miyazaki, Masahiro Takeo, Kowit Hengphasatporn, Yasuteru Shigeta, Young‐Ho Lee, Yoshiki HiguchiThe FEBS Journal 2023年2月Design of electron-donating group substituted 2-PAM analogs as antidotes for organophosphate insecticide poisoningNalinee Kongkaew, Kowit Hengphasatporn, Yuwanda Injongkol, Pitchayathida Mee-udorn, Liyi Shi, Panupong Mahalapbutr, Phornphimon Maitarad, Ryuhei Harada, Yasuteru Shigeta, Thanyada Rungrotmongkol, Alisa S. VangnaiRSC Advances 13 (46) 2023年New insights into the oxidation process from neutron and X-ray crystal structures of an O2-sensitive [NiFe]-hydrogenaseTakeshi Hiromoto, Koji Nishikawa, Seiya Inoue, Hideaki Ogata, Yuta Hori, Katsuhiro Kusaka, Yu Hirano, Kazuo Kurihara, Yasuteru Shigeta, Taro Tamada, Yoshiki HiguchiChemical Science 2023年Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling MethodsHarada, R., Morita, R., Shigeta, Y.Journal of Chemical Information and Modeling 63 (1) 2023年Specific zinc binding to heliorhodopsinMasanori Hashimoto, Koichi Miyagawa, Manish Singh, Kota Katayama, Mitsuo Shoji, Yuji Furutani, Yasuteru Shigeta, Hideki KandoriPhysical Chemistry Chemical Physics 25 (4) 2023年Lichen-Derived Diffractaic Acid Inhibited Dengue Virus Replication in a Cell-Based SystemNaphat Loeanurit, Truong Lam Tuong, Van-Kieu Nguyen, Vipanee Vibulakhaophan, Kowit Hengphasatporn, Yasuteru Shigeta, Si Xian Ho, Justin Jang Hann Chu, Thanyada Rungrotmongkol, Warinthorn Chavasiri, Siwaporn BoonyasuppayakornMolecules 28 (3) 2023年1月N-Containing α-Mangostin Analogs via Smiles Rearrangement as the Promising Cytotoxic, Antitrypanosomal, and SARS-CoV-2 Main Protease Inhibitory AgentsNan Yadanar Lin Pyae, Arnatchai Maiuthed, Wongsakorn Phongsopitanun, Bongkot Ouengwanarat, Warongrit Sukma, Nitipol Srimongkolpithak, Jutharat Pengon, Roonglawan Rattanajak, Sumalee Kamchonwongpaisan, Zin Zin Ei, Preedakorn Chunhacha, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Supakarn ChamniMolecules 28 (3) 2023年1月Characterization of the Geometrical and Electronic Structures of the Active Site and Its Effects on the Surrounding Environment in Reduced High-Potential Iron–Sulfur Proteins Investigated by the Density Functional Theory ApproachSato, Ayaka, Hori, Yuta, Yasuteru, ShigetaInorganic Chemistry 62 (5) 2023年1月[査読有り] Dynamical interaction analysis of proteins by a random forest-fragment molecular orbital (RF-FMO) method and application to Src tyrosine kinaseYuta Yamamoto, Shogo Nakano, Yasuteru ShigetaBulletin of the Chemical Society of Japan 96 (1) 2022年12月Systematic Search for Stabilizing Dopants in ZrO2 and HfO2 Using First-Principles CalculationsYosuke Harashima, Hiroaki Koga, Zeyuan Ni, Takehiro Yonehara, Michio Katouda, Akira Notake, Hidefumi Matsui, Tsuyoshi Moriya, Mrinal Kanti Si, Ryu Hasunuma, Akira Uedono, Yasuteru Shigeta2022 International Symposium on Semiconductor Manufacturing (ISSM) 2022年12月Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidasesYuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Chai Gopalasingam, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Yoshikazu Ishii, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori ShintaniNature Communications 13 (1) 2022年12月Autism-associated mutation in Hevin/Sparcl1 induces endoplasmic reticulum stress through structural instabilityTakumi Taketomi, Takunori Yasuda, Rikuri Morita, Jaehyun Kim, Yasuteru Shigeta, Cagla Eroglu, Ryuhei Harada, Fuminori TsurutaScientific Reports 12 (1) 2022年12月Reaction Mechanism of Ancestral l-Lys α-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational AnalysisTomoharu Motoyama, Yuta Yamamoto, Chiharu Ishida, Fumihito Hasebe, Yui Kawamura, Yasuteru Shigeta, Sohei Ito, Shogo NakanoACS Omega 7 (48) 2022年11月Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMOHengphasatporn, Kowi, Harada, Ryuhei, Wilasluck, Patcharin, Deetanya, Peerapon, Sukandar, Edwin R, Chavasiri, Warinthorn, Suroengrit, Aphinya, Boonyasuppayakorn, Siwaporn, Rungrotmongkol, Thanyada, Wangkanont, Kittikhun, Shigeta, YasuteruScientific reports 12 (1) 2022年10月Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidaseMitsuo Shoji, Takeshi Murakawa, Shota Nakanishi, Mauro Boero, Yasuteru Shigeta, Hideyuki Hayashi, Toshihide OkajimaCHEMICAL SCIENCE 13 (36) 2022年9月Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic SynthesesMitsuo, Shoji, Natsuki, Watanabe, Hori, Yuta, Kenji, Furuya, Masayuki, Umemura, Mauro, Boero, Yasuteru, ShigetaASTROBIOLOGY 22 (9) 2022年9月[査読有り] Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in SpaceHori, Yuta, Nakamura, Honami, Sakawa, Takahide, Natsuki, Watanabe, Kayanuma, Megumi, Mitsuo, Shoji, Masayuki, Umemura, Yasuteru, ShigetaASTROBIOLOGY 22 (11) 2022年9月[査読有り] The role of ATP in solubilizing RNA-binding protein fused in sarcomaAida, Hayato, Shigeta, Yasuteru, Harada, RyuheiPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 90 (8) 2022年8月[査読有り] Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of ProteinsTakunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Chemical Information and Modeling 62 (14) 2022年7月Heme-bound tyrosine vibrations in hemoglobin M: Resonance Raman, crystallography, and DFT calculationNagatomo, Shigenori, Shoji, Mitsuo, Terada, Takuto, Nakatani, Kiyoharu, Shigeta, Yasuteru, Hirota, Shun, Yanagisawa, Sachiko, Kubo, Minoru, Kitagawa, Teizo, Nagai, Masako, Ohki, Mio, Park, Sam-Yong, Shibayama, NaoyaBIOPHYSICAL JOURNAL 121 (14) 2022年6月[査読有り] Semi-Synthesis of N-Aryl Amide Analogs of Piperine from Piper nigrum and Evaluation of Their Antitrypanosomal, Antimalarial, and Anti-SARS-CoV-2 Main Protease ActivitiesRattanaporn Wansri, Aye Chan Khine Lin, Jutharat Pengon, Sumalee Kamchonwongpaisan, Nitipol Srimongkolpithak, Roonglawan Rattanajak, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Kowit Hengphasatporn, Yasuteru Shigeta, Jatupol Liangsakul, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Taksina Chuanasa, Wanchai De-eknamkul, Supot Hannongbua, Thanyada Rungrotmongkol, Supakarn ChamniMolecules 27 (9) 2022年4月Halogenated baicalein as a promising antiviral agent toward SARS-CoV-2 main proteaseHengphasatporn, Kowi, Wilasluck, P, Deetanya, P, Wangkanont, K, Chavasiri, W, Visitchanakun, P, Leelahavanichkul, A, Paunrat, W, Boonyasuppayakorn, S, Rungrotmongkol, T, Hannongbua, S, Shigeta, YasuteruJOURNAL OF CHEMICAL INFORMATION AND MODELING 62 (6) 2022年3月[査読有り] Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MDAida, Hayato, Shigeta, Yasuteru, Harada, RyuheiMaterials 15 (4) 2022年2月[査読有り] Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1Yasuda, Takunori, Morita, Rikuri, Shigeta, Yasuteru, Harada, RyuheiJournal of molecular biology 434 (2) 2022年1月抗体軽鎖四量体の立体構造の理論解析Lian Duan, Hengphasatporn Kowi, 重田 育照JCPE Journal 21 (4) 2022年中分子の膜透過性に対する計算手法の検討高橋 輝行, Hengphasatporn Kowi, 原田 隆平, 重田 育照JCPE Journal 21 (4) 2022年Corrigendum to: Chirality without Stereoisomers: Insight from the Helical Response of Bond Electrons (ChemPhysChem, (2021), 22, 19, (1989-1995), 10.1002/cphc.202100397)Xu, T., Nie, X., Li, S., Yang, Y., Fr{"u}chtl, H., van Mourik, T., Kirk, S.R., Paterson, M.J., Shigeta, Y., Jenkins, S.ChemPhysChem 23 (5) 2022年Evaluation of an Appropriate Standard Hydrogen Electrode Potential for Computing Redox Potentials of Catechins with Density Functional TheoryDuan, L., Takano, Y., Shigeta, Y.Chemistry Letters 51 (7) 2022年Design, synthesis, in vitro, in silico, and SAR studies of flavone analogs towards anti-dengue activityPatigo, A., Hengphasatporn, K., Cao, V., Paunrat, W., Vijara, N., Chokmahasarn, T., Maitarad, P., Rungrotmongkol, T., Shigeta, Y., Boonyasuppayakorn, S., Khotavivattana, T.Scientific Reports 12 (1) 2022年Pharmacophore-Based Virtual Screening and Experimental Validation of Pyrazolone-Derived Inhibitors toward Janus KinasesSanachai, K., Mahalapbutr, P., Hengphasatporn, K., Shigeta, Y., Seetaha, S., Tabtimmai, L., Langer, T., Wolschann, P., Kittikool, T., Yotphan, S., Choowongkomon, K., Rungrotmongkol, T.ACS Omega 7 (37) 2022年Vacancy-type defects in TiN/ZrO2/TiN capacitors probed by monoenergetic positron beamsUedono, A., Takahashi, N., Hasunuma, R., Harashima, Y., Shigeta, Y., Ni, Z., Matsui, H., Notake, A., Kubo, A., Moriya, T., Michishio, K., Oshima, N., Ishibashi, S.Thin Solid Films 762 2022年Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational SubspaceYasuda, T., Morita, R., Shigeta, Y., Harada, R.Journal of Chemical Information and Modeling 62 (23) 2022年Calculation of the permeability coefficients of small molecules through lipid bilayers by free-energy reaction network analysis following the explicit treatment of the internal conformation of the soluteYuki Mitsuta, Toshio Asada, Yasuteru ShigetaPhysical Chemistry Chemical Physics 2022年Supramolecular polymerization of thiobarbituric acid naphthalene dyeTakumi Aizawa, Maika Kawaura, Takashi Kajitani, Kowit Hengphasatporn, Yasuteru Shigeta, Shiki YagaiChemical Communications 58 (67) 2022年Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiationLi, Zi, Yang, Yong, Xu, Tianlv, Fruchtl, Herber, van Mourik, Tanja, Paterson, Martin J, Shigeta, Yasuteru, Kirk, Steven R, Jenkins, SamanthaJOURNAL OF COMPUTATIONAL CHEMISTRY 43 (3) 2022年1月[査読有り] Residue Folding Degree-Relationship to Secondary Structure Categories and Use as Collective VariableSladek, Vladimir, Harada, Ryuhei, Shigeta, YasuteruInternational Journal of Molecular Sciences 22 (23) 2021年12月[査読有り] Recent developments of computational methods for pKa pre-diction based on electronic structure theory with solvation modelsFujiki, R, Matsui, T, Shigeta, Yasuteru, Nakano, H, Yoshida, NMultidisciplinary Scientific Journal 4 (4) 2021年12月[査読有り] A Free Energy Landscape Analysis of Calmodulin Obtained from an NMR-data Utilized Multi-scale Divide-and-conquer Molecular Dynamics SimulationShimoyama, Hiromitsu, Shigeta, YasuteruLIFE-BASEL 11 (11) 2021年12月[査読有り] Effects of mechanical grinding on the phase behavior and anhydrous proton conductivity of imidazolium hydrogen succinateDekura, Shun, Sunairi, Yoshiya, Okamoto, Kei, Takeiri, Fumitaka, Kobayashi, Genki, Hori, Yuta, Shigeta, Yasuteru, Mori, HatsumiSolid State Ionics 372 2021年12月[査読有り] Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics SimulationsMorita, Rikuri, Shigeta, Yasuteru, Harada, RyuheiThe journal of physical chemistry. B 125 (46) 2021年11月Control of chirality, bond flexing and anharmonicity in an electric fieldLi, Zi, Nie, Xing, Xu, Tianlv, Li, Shuman, Yang, Yong, Fruchtl, Herber, van Mourik, Tanja, Kirk, Steven R, Paterson, Martin J, Shigeta, Yasuteru, Jenkins, SamanthaINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 121 (22) 2021年11月[査読有り] A post-process to estimate an approximated minimal free energy path based on local centroidsMorita, Rikuri, Shigeta, Yasuteru, Harada, RyuheiCHEMICAL PHYSICS LETTERS 782 2021年11月[査読有り] Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge regionXie, Cheng, Shimoyama, Hiromitsu, Yamanaka, Masaru, Nagao, Satoshi, Komori, Hirofumi, Shibata, Naoki, Higuchi, Yoshiki, Shigeta, Yasuteru, Hirota, ShunRSC ADVANCES 11 (59) 2021年11月[査読有り] Alkyne-Tagged Apigenin, a Chemical Tool to Navigate Potential Targets of Flavonoid Anti-Dengue LeadsHengphasatporn, Kowi, Kaewmalai, Benyapa, Jansongsaeng, Somruedee, Badavath, Vishnu Nayak, Saelee, Thanaphon, Chokmahasarn, Thamonwan, Khotavivattana, Tanatorn, Shigeta, Yasuteru, Rungrotmongkol, Thanyada, Boonyasuppayakorn, SiwapornMOLECULES 26 (22) 2021年11月[査読有り] Chirality without Stereoisomers: Insight from the Helical Response of Bond ElectronsXu, Tianlv, Nie, Xing, Li, Shuman, Yang, Yong, Fruchtl, Herber, van Mourik, Tanja, Kirk, Steven R, Paterson, Martin J, Shigeta, Yasuteru, Jenkins, SamanthaCHEMPHYSCHEM 22 (19) 2021年10月[査読有り] Integrate in silico studies on the role of nicotinamide adenine dinucleotide (NADH) binding in activating C-terminal binding protein 2 (CtBP2)Tsukasa, Aoyagi, Yoshino, Ryunosuke, Yuki, Mitsuta, Rikuri, Morita, Ryuhei, Harada, Yasuteru, ShigetaChemistry Letters 51 (1) 2021年10月[査読有り] Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics CalculationsYanagi, Koki, Mitsuta, Yuki, Takaoka, Kenta, Takahashi, Teruyuki, Hengphasatporn, Kowi, Harada, Ryuhei, Shigeta, YasuteruChemistry Letters 50 (12) 2021年9月[査読有り] Phosphorylation in the accessory domain of yeast histone chaperone protein 1 exposes the nuclear export signal sequenceAshida, Sho, Morita, Rikuri, Shigeta, Yasuteru, Harada, RyuheiPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Epub (2) 2021年9月[査読有り] Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of ProteinsYasuda, Takunori, Morita, Rikuri, Shigeta, Yasuteru, Harada, RyuheiJOURNAL OF CHEMICAL THEORY AND COMPUTATION 17 (9) 2021年9月[査読有り] On-Demand Chirality Transfer of Human Serum Albumin to Bis(thiophen-2-yl)hexafluorocyclopentenes through Their Photochromic Ring ClosureSaeki, Yuri, Kayanuma, Megumi, Nitta, Aki, Shigeta, Yasuteru, Kawamura, Izuru, Nakagawa, Tetsuya, Ubukata, Takashi, Yokoyama, YasushiJOURNAL OF ORGANIC CHEMISTRY 86 (18) 2021年9月[査読有り] Solvophobicity-directed assembly of microporous molecular crystalsYamagishi, Hiroshi, Tsunoda, Monika, Iwai, Kohei, Hengphasatporn, Kowi, Shigeta, Yasuteru, Sato, Hiroyasu, Yamamoto, YoheiCOMMUNICATIONS CHEMISTRY 4 (1) 2021年8月Could London Dispersion Force Control Regioselective (2 + 2) Cyclodimerizations of Benzynes? YES: Application to the Synthesis of Helical BiphenylenesTakashi Ikawa, Yuta Yamamoto, Akito Heguri, Yutaka Fukumoto, Tomonari Murakami, Akira Takagi, Yuto Masuda, Kenzo Yahata, Hiroshi Aoyama, Yasuteru Shigeta, Hiroaki Tokiwa, Shuji AkaiJournal of the American Chemical Society 143 (29) 2021年7月pyProGA-A PyMOL plugin for protein residue network analysisSladek, Vladimir, Yamamoto, Yuta, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru, Sladek, VladimirPLOS ONE 16 (7) 2021年7月[査読有り] A Practical Prediction of LogP(o/w) through Semiempirical Electronic Structure Calculations with Dielectric Continuum ModelTakahashi, Teruyuki, Matsui, Toru, Hengphasatporn, Kowi, Shigeta, YasuteruBULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 94 (7) 2021年7月Ion-pairing pi-electronic systems: ordered arrangement and noncovalent interactions of negatively charged porphyrinsYoshifumi Sasano, Hiroki Tanaka, Yohei Haketa, Yoichi Kobayashi, Yukihide Ishibashi, Tatsuki Morimoto, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Tsuyoshi Asahi, Hiromitsu MaedaCHEMICAL SCIENCE 12 (28) 2021年7月Proton Conduction Mechanism for Anhydrous Imidazolium Hydrogen Succinate Based on Local Structures and Molecular DynamicsHori, Yuta, Dekura, Shun, Sunairi, Yoshiya, Ida, Tomonori, Mizuno, Motohiro, Mori, Hatsumi, Shigeta, YasuteruThe Journal of Physical Chemistry Letters 12 (22) 2021年6月[査読有り] Comparison between the Light-Harvesting Mechanisms of Type-I Photosynthetic Reaction Centers of Heliobacteria and Photosystem I: Pigment Site Energy Distribution and Exciton State.Akihiro Kimura, Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru ItohThe journal of physical chemistry. B 125 (15) 2021年4月Comprehensive Predictions of Secondary Structures for Comparative Analysis in Different SpeciesRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Structural Biology 213 (2) 2021年4月Structural and functional characterization of nylon hydrolasesNegoro, Seiji, Kato, Dai-Ichiro, Ohki, Taku, Yasuhira, Kengo, Kawashima, Yasuyuki, Nagai, Keisuke, Takeo, Masahiro, Shibata, Naoki, Kamiya, Katsumasa, Shigeta, YasuteruMethods in enzymology 648 2021年4月[査読有り] Structure, solubility, and permeability relationships in a diverse middle molecule libraryMiyachi, Hiroyuki, Kanamitsu, Kayoko, Ishii, Mayumi, Watanabe, Eri, Katsuyama, Akira, Otsuguro, Satoko, Yakushiji, Fumika, Watanabe, Mizuki, Matsui, Kouhei, Sato, Yukina, Shuto, Satoshi, Tadokoro, Takashi, Kita, Shunsuke, Matsumaru, Takanori, Matsuda, Akira, Hirose, Tomoyasu, Iwatsuki, Masato, Shigeta, Yasuteru, Nagano, Tetsuo, Kojima, Hirotatsu, Ichikawa, Satoshi, Sunazuka, Toshiaki, Maenaka, KatsumiBioorganic & medicinal chemistry letters 37 2021年4月[査読有り] Weak O2 binding and strong H2O2 binding at the non-heme diiron center of trypanosome alternative oxidaseYamasaki, Sotaro, Shoji, Mitsuo, Kayanuma, Megumi, Sladek, Vladimir, Inaoka, Daniel Ken, Matsuo, Yuichi, Shiba, Tomoo, Young, Luke, Moore, Anthony L, Kita, Kiyoshi, Shigeta, YasuteruBiochimica et biophysica acta. Bioenergetics 1862 (4) 2021年4月[査読有り] Theoretical Prediction of the Redox Potential of Catechins with First Principle CalculationDuan, Lian, Takano, Yu, Shigeta, YasuteruJOURNAL OF COMPUTER CHEMISTRY-JAPAN 20 (4) 2021年3月[査読有り] 環状ペプチドの膜透過における溶媒和自由エネルギー計算栁, 昂輝, 原田, 隆平, 満田, 祐樹, 重田育照日本コンピュータ化学会 19 (4) 2021年3月[査読有り] Comprehensive Analysis of Intrinsically Disordered Regions to Elucidate Their Physical Properties using a Modified ParameterAida, Hayato, Harada, Ryuhei, Shigeta, Yasuteru, Tomii, KentaroBIOPHYSICAL JOURNAL 120 (3::1) 2021年2月[査読有り] Computational Analysis Reveals a Critical Point Mutation in the -Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper VirusYamamoto, Yuta, Nakano, Shogo, Seki, Fumio, Shigeta, Yasuteru, Ito, Sohei, Tokiwa, Hiroaki, Takeda, MakotoMolecules (Basel, Switzerland) 26 (5) 2021年2月[査読有り] プロトン伝導性PVPA-xIm複合体のプロトン伝導機構の理論的解明Hori, Yuta, Suetake, Toshiya, Ida, Tomonori, Mizuno, Motohiro, Shigeta, YasuteruThe Journal of Computer Chemistry, Japan 19 (4) 2021年2月[査読有り] Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identificationDeetanya, Peerapon, Hengphasatporn, Kowi, Wilasluck, Patcharin, Shigeta, Yasuteru, Rungrotmongkol, Thanyada, Wangkanont, KittikhunCOMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 19 2021年[査読有り] Estimation of the relative contributions to the electronic energy transfer rates based on Forster theory: The case of C-phycocyanin chromophoresMishima, Kenji, Shoji, Mitsuo, Umena, Yasufumi, Boero, Mauro, Shigeta, YasuteruBiophysics and physicobiology 18 2021年[査読有り] In Silico Mutational Analyses Reveal Different Ligand-Binding Abilities of Double Pockets of Medaka Fish Taste Receptor Type 1 Essential for Efficient Taste RecognitionsHayato Aida, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaPhysical Chemistry Chemical Physics 23 (36) 2021年AnalysisFMO Toolkit: A PyMOL Plugin for 3D-Visualization of Interaction Energies in Proteins (3D-VIEP) Calculated by the FMO MethodTakaki Tokiwa, Shogo Nakano, Hiroaki Tokiwa, Yasuteru ShigetaRecent Advances of the Fragment Molecular Orbital Method 2021年Linear Combination of Molecular Orbitals of Fragments (FMO-LCMO) Method: Its Application to Charge Transfer StudiesHirotaka Kitoh-Nishioka, Ryuma Sato, Yasuteru Shigeta, Koji AndoRecent Advances of the Fragment Molecular Orbital Method 2021年Open-Architecture Program of Fragment Molecular Orbital Method for Massive Parallel Computing (OpenFMO) with GPU AccelerationHirotaka Kitoh-Nishioka, Hiroaki Umeda, Yasuteru ShigetaRecent Advances of the Fragment Molecular Orbital Method 2021年Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of ProteinsMorita, Rikuri, Shigeta, Yasuteru, Harada, RyuheiBulletin of the Chemical Society of Japan 94 (1) 2021年1月[査読有り] The Folding of Trp-cage is Regulated by Stochastic Flip of the Side Chain of TryptophanYasuda, Takunori, Shigeta, Yasuteru, Harada, RyuheiCHEMISTRY LETTERS 50 (1) 2021年1月[査読有り] Conformation-Changeable π-Electronic Systems with Metastable Bent-Core Conformations and Liquid-Crystalline-State Electric-Field-Responsive PropertiesNakamura, Kazuto, Sugiura, Shinya, Araoka, Fumito, Aya, Satoshi, Takanishi, Yoichi, Watanabe, Go, Sato, Ryuma, Shigeta, Yasuteru, Maeda, HiromitsuOrganic letters 23 (2) 2021年1月[査読有り] Agonist and Antagonist-Diverted Twisting Motions of a Single TRPV1 ChannelFujimura, Shoko, Mio, Kazuhiro, Kuramochi, Masahiro, Sekiguchi, Hiroshi, Ikezaki, Keigo, Mio, Muneyo, Hengphasatporn, Kowit, Shigeta, Yasuteru, Kubo, Tai, Sasaki, Yuji CJOURNAL OF PHYSICAL CHEMISTRY B 124 (51) 2020年12月[査読有り] Molecular Mechanism for the Actin-Binding Domain of alpha-Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis ExperimentsMorita, Rikuri, Nakano, Kentaro, Shigeta, Yasuteru, Harada, RyuheiJOURNAL OF PHYSICAL CHEMISTRY B 124 (39) 2020年10月[査読有り] Unique protonation states of aspartate and topaquinone in the active site of copper amine oxidaseShoji, Mitsuo, Murakawa, Takeshi, Boero, Mauro, Shigeta, Yasuteru, Hayashi, Hideyuki, Okajima, ToshihideRSC ADVANCES 10 (63) 2020年10月[査読有り] Molecular Motions of Imidazole in Poly(vinylphosphonic acid)-imidazole Composites Investigated by Molecular Dynamics SimulationsHori, Yuta, Suetake, Toshiya, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, MotohiroChemistry Letters 50 (1) 2020年10月[査読有り] Molecular Motions of Imidazole in Poly(vinylphosphonic acid)-imidazole Composites Investigated by Molecular Dynamics SimulationsHori, Yuta, Suetake, Toshiya, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, MotohiroChemistry Letters 50 (1) 2020年10月[査読有り] Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital methodHirotaka Kitoh-Nishioka, Yasuteru Shigeta, Koji AndoThe Journal of chemical physics 153 (10) 2020年9月[査読有り] Dibromopinocembrin and Dibromopinostrobin Are Potential Anti-Dengue Leads with Mild Animal ToxicitySiwaporn Boonyasuppayakorn, Thanaphon Saelee, Peerapat Visitchanakun, Asada Leelahavanichkul, Kowit Hengphasatporn, Yasuteru Shigeta, Thao Nguyen Thanh Huynh, Justin Jang Hann Chu, Thanyada Rungrotmongkol, Warinthorn ChavasiriMolecules 25 (18) 2020年9月[査読有り] Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular DynamicsTakunori Yasuda, Yasuteru Shigeta, Ryuhei HaradaJournal of Chemical Information and Modeling 60 (8) 2020年8月[査読有り] Reaction mechanism of: N-cyclopropylglycine oxidation by monomeric sarcosine oxidaseMitsuo Shoji, Yukihiro Abe, Mauro Boero, Yasuteru Shigeta, Yoshiaki NishiyaPhysical Chemistry Chemical Physics 22 (29) 2020年8月[査読有り] Self-Associating Curved π-Electronic Systems with Electron-Donating and Hydrogen-Bonding PropertiesHaketa, Yohei, Miyasue, Mika, Kobayashi, Yoichi, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Tamai, Naoto, Maeda, HiromitsuJournal of the American Chemical Society 142 (38) 2020年8月[査読有り] Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular DynamicsYasuda, Takunori, Shigeta, Yasuteru, Harada, RyuheiJournal of chemical information and modeling 60 (8) 2020年8月[査読有り] Regenerations of Initial Velocities in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Enhance the Conformational Transitions of ProteinsHayato Aida, Yasuteru Shigeta, Ryuhei HaradaChemistry Letters 49 (7) 2020年7月[査読有り] The dynamics of S-adenosyl-methionine and S-adenosyl-homocysteine in Mouse Dnmt1 is driven by their structural flexibilitiesTakunori Yasuda, Yasuteru Shigeta, Ryuhei HaradaChemistry Letters 49 (7) 2020年7月[査読有り] Analytical Method Using a Scaled Hypersphere Search for High-Dimensional Metadynamics SimulationsYuki Mitsuta, Yasuteru ShigetaJournal of Chemical Theory and Computation 16 (6) 2020年6月[査読有り] Comprehensive Predictions of Secondary Structures on Proteins of Various OrganismsRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Molecular Biology, in preparation 2020年6月[査読有り] Enhanced Conformational Sampling Method Based on Anomaly Detection Parallel Cascade Selection Molecular Dynamics: ad-PaCS-MDRyuhei Harada, Kota Yamaguchi, Yasuteru ShigetaJournal of Chemical Theory and Computation, in preparation 16 (10) 2020年6月[査読有り] Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharingTakeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Chie Shibazaki, Tomoko Sunami, Taro Tamada, Naomine Yano, Taro Yamada, Katsuhiro Kusaka, Mamoru Suzuki, Yasuteru Shigeta, Ryota Kuroki, Hideyuki Hayashi, Takato Yano, Katsuyuki Tanizawa, Motoyasu Adachi, Toshihide OkajimaProceedings of the National Academy of Sciences of the United States of America 117 (20) 2020年5月[査読有り] Understanding the detection mechanisms and ability of molecular hydrogen on three-dimensional bicontinuous nanoporous reduced graphene oxideYoshikazu Ito, Megumi Kayanuma, Yasuteru Shigeta, Jun Ichi Fujita, Yoichi TanabeMaterials 13 (10) 2020年5月[査読有り] Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active siteYasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki HayashiJOURNAL OF BIOCHEMISTRY 167 (4) 2020年4月[査読有り] Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active siteYasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki HayashiJournal of biochemistry 167 (4) 2020年4月[査読有り] Distribution of counter ions in negatively-charged lipid/water/air interface: Molecular dynamics studyTeruyuki Takahashi, Ryuhei Harada, Yasuteru ShigetaChemistry Letters 49 (4) 2020年4月[査読有り] Target identification using homopharma and network-based methods for predicting compounds against dengue virus-infected cellsKowit Hengphasatporn, Kitiporn Plaimas, Apichat Suratanee, Peemapat Wongsriphisant, Jinn Moon Yang, Yasuteru Shigeta, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn, Thanyada RungrotmongkolMolecules 25 (8) 2020年4月[査読有り] Split Conformation of Chaetomium Thermophilum Hsp104 DisaggregaseInoue Yosuke, Hanazono Yuya, Noi Kentaro, Kawamoto Akihiro, Kimatsuka Masato, Harada Ryuhei, Takeda Kazuki, Iwamasa Natsuki, Noguchi Keiichi, Shigeta Yasuteru, Namba Keiichi, Ogura Teru, Miki Kunio, Shinohara Kyosuke, Yohda MasafumiScience Advances, submitted 29 (7) 2020年4月[査読有り] Local Structures and Dynamics of Imidazole Molecules in Poly(vinylphosphonic acid)–Imidazole Composite Investigated by Molecular DynamicsHori, Yuta, Suetake, Toshiya, Shiota, Yoshihito, Yoshizawa, Kazunari, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, MotohiroACS Applied Polymer Materials 2 (4) 2020年4月[査読有り] Protein Dynamics and the Folding DegreeVladimir Sladek, Ryuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling 60 (3) 2020年3月[査読有り] Multiple Virtual Screening Strategies for the Discovery of Novel Compounds Active Against Dengue Virus: A Hit Identification StudyKowit Hengphasatporn, Arthur Garon, Peter Wolschann, Thierry Langer, Shigeta Yasuteru, Thao N. T. Huynh, Warinthorn Chavasiri, Thanaphon Saelee, Siwaporn Boonyasuppayakorn, Thanyada RungrotmongkolSCIENTIA PHARMACEUTICA 88 (1) 2020年3月[査読有り] Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem iHirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru Itoh, Akihiro KimuraJournal of Physical Chemistry B 124 (2) 2020年1月[査読有り] Photosynergetic Effects on Triplet–Triplet Annihilation Upconversion Processes in Solid Studied by Theory and ExperimentsKenji Kamada, Ryuma Sato, Toshiko Mizokuro, Hirotaka Kito-Nishioka, Yasuteru ShigetaPhotosynergetic Responses in Molecules and Molecular Aggregates 2020年Role of the Propionic Acid Side-Chain of C-Phycocyanin Chromophores in the Excited States for the Photosynthesis ProcessMishima, Kenji, Shoji, Mitsuo, Umena, Yasufumi, Boero, Mauro, Shigeta, YasuteruBulletin of the Chemical Society of Japan 93 (12) 2020年[査読有り] Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem IKitoh-Nishioka, Hirotaka, Shigeta, Yasuteru, Itoh, Shigeru, Kimura, AkihiroThe journal of physical chemistry. B 124 (2) 2020年1月[査読有り] Why are lopinavir and ritonavir effective against the newly emerged coronavirus 2019? Atomistic insights into the inhibitory mechanismsBodee Nutho, Panupong Mahalapbutr, Kowit Hengphasatporn, Nawanwat Chainuwong Pattaranggoon, Nattapon Simanon, Yasuteru Shigeta, Supot Hannongbua, Thanyada RungrotmongkolBiochemistry 59 (18) 2020年[査読有り] Estimation of acid dissociation constants (PKA) of N-containing heterocycles in DMSO and transferability of Gibbs free energy in different solvent conditionsKowit Hengphasatporn, Toru Matsui, Yasuteru ShigetaChemistry Letters 49 (3) 2020年[査読有り] Intramolecular mode coupling of the isotopomers of water: A non-scalar charge density-derived perspectiveTian Tian, Tianlv Xu, Steven R. Kirk, Ian Tay Rongde, Yong Boon Tan, Sergei Manzhos, Yasuteru Shigeta, Samantha JenkinsPhysical Chemistry Chemical Physics 22 (4) 2020年[査読有り] Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of ProteinsRyuhei Harada, Vladimir Sladek, Yasuteru ShigetaJournal of Chemical Information and Modeling 59 (12) 2019年12月[査読有り] Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of ProteinsHarada, Ryuhei, Sladek, Vladimir, Shigeta, YasuteruJournal of chemical information and modeling 59 (12) 2019年12月[査読有り] Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid dockingRyuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru ShigetaJournal of Molecular Graphics and Modelling 92 2019年11月[査読有り] Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling EfficiencyRyuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling 59 (9) 2019年9月[査読有り] Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein DynamicsRyuhei Harada, Vladimir Sladek, Yasuteru ShigetaJournal of Chemical Theory and Computation 15 (9) 2019年9月[査読有り] Accessing the accuracy of density functional theory through structure and dynamics of the water-air interfaceTatsuhiko Ohto, Mayank Dodia, Jianhang Xu, Sho Imoto, Fujie Tang, Frederik Zysk, Thomas D. Kühne, Yasuteru Shigeta, Mischa Bonn, Xifan Wu, Yuki NagataJournal of Physical Chemistry Letters 10 (17) 2019年9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 crystallographyMitsuo Shoji, Hiroshi Isobe, Jian Ren Shen, Michihiro Suga, Fusamichi Akita, Koichi Miyagawa, Yasuteru Shigeta, Kizashi YamaguchiChemical Physics Letters 730 2019年9月[査読有り] First-Principles Study of the Reaction Mechanism of CHO + H on Graphene SurfaceMegumi Kayanuma, Mitsuo Shoji, Kenji Furuya, Katsumasa Kamiya, Yuri Aikawa, Masayuki Umemura, Yasuteru ShigetaJournal of Physical Chemistry A 123 (26) 2019年7月[査読有り] Pyrrole-Based π-System–PtII Complexes: Chiroptical Properties and Excited-State Dynamics with Microsecond Triplet LifetimesGoki Hirata, Yoichi Kobayashi, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Hiromitsu MaedaChemistry - A European Journal 25 (37) 2019年7月[査読有り] Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid dockingHarada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, YasuteruJournal of molecular graphics & modelling 92 2019年7月[査読有り] First-Principles Study of the Reaction Mechanism of CHO + H on Graphene SurfaceKayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Kamiya, Katsumasa, Aikawa, Yuri, Umemura, Masayuki, Shigeta, YasuteruThe journal of physical chemistry. A 123 (26) 2019年7月[査読有り] Pyrrole-Based π-System-Pt Complexes: Chiroptical Properties and Excited-State Dynamics with Microsecond Triplet LifetimesHirata, Goki, Kobayashi, Yoichi, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, HiromitsuChemistry (Weinheim an der Bergstrasse, Germany) 25 (37) 2019年7月[査読有り] Reaction mechanism of non-enzymatic stereoselective formation of wine lactoneAkane Kyan, Megumi Kayanuma, Mitsuo Shoji, Yasuteru ShigetaChemical Physics Letters 725 2019年6月[査読有り] Temperature–pressure shuffling outlier flooding method enhances the conformational sampling of proteinsRyuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru ShigetaJournal of Computational Chemistry 40 (15) 2019年6月[査読有り] Numerical investigation of the nano-scale solutal Marangoni convectionsY. Imai, T. Yamamoto, A. Sekimoto, Y. Okano, R. Sato, Y. ShigetaJournal of the Taiwan Institute of Chemical Engineers 98 (SI) 2019年5月[査読有り] Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical InsightTianlv Xu, Jia Hui Li, Roya Momen, Wei Jie Huang, Steven Robert Kirk, Yasuteru Shigeta, Samantha JenkinsJournal of the American Chemical Society 141 (13) 2019年4月[査読有り] Photosubstitution Reaction of cis-[Ru(bpy) 2 (CH 3 CN) 2 ] 2+ and cis-[Ru(bpy) 2 (NH 3 ) 2 ] 2+ in Aqueous Solution via Monoaqua IntermediateMegumi Kayanuma, Mitsuo Shoji, Yasuteru ShigetaJournal of Physical Chemistry A 123 (13) 2019年4月[査読有り] In Silico Structural Modeling and Analysis of Elongation Factor-1 Alpha and Elongation Factor-like ProteinKotaro Sakamoto, Megumi Kayanuma, Yuji Inagaki, Tetsuo Hashimoto, Yasuteru ShigetaACS Omega 4 (4) 2019年4月[査読有り] Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical InsightXu, Tianlv, Li, Jia Hui, Momen, Roya, Huang, Wei Jie, Kirk, Steven Robert, Shigeta, Yasuteru, Jenkins, SamanthaJournal of the American Chemical Society 141 (13) 2019年4月[査読有り] New assay method based on Raman spectroscopy for enzymes reacting with gaseous substratesYuka Kawahara-Nakagawa, Koji Nishikawa, Satoru Nakashima, Shota Inoue, Takehiro Ohta, Takashi Ogura, Yasuteru Shigeta, Katsuyuki Fukutani, Tatsuhiko Yagi, Yoshiki HiguchiProtein Science 28 (3) 2019年3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 IntermediateKayanuma, Megumi, Shoji, Mitsuo, Shigeta, YasuteruThe journal of physical chemistry. A 123 (13) 2019年3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3月[査読有り] First-principle study of ammonia decomposition and nitrogen incorporation on the GaN surface in metal organic vapor phase epitaxyKieu My Bui, Jun Ichi Iwata, Yoshihiro Kangawa, Kenji Shiraishi, Yasuteru Shigeta, Atsushi OshiyamaJournal of Crystal Growth 507 2019年2月[査読有り] Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital CalculationsTakaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru ShigetaJournal of Chemical Information and Modeling 59 (1) 2019年1月[査読有り] Theoretical study of the photodissociation reaction of methanolMegumi Kayanuma, Mitsuo Shoji, Kenji Furuya, Yuri Aikawa, Masayuki Umemura, Yasuteru ShigetaChemical Physics Letters 714 2019年1月[査読有り] Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy CalculationsRyuhei Harada, Yasuteru ShigetaJournal of Chemical Theory and Computation 15 (1) 2019年1月[査読有り] 計算化学的手法による水/オクタノール分配係数の研究兒玉, 浩一, Arwansyah, Muhammad Saleh, 川口, 一朋, 松井, 亨, 重田, 育照, 長尾, 秀実Journal of Computer Chemistry, Japan 18 (5) 2019年[査読有り] Structural Changes in the Trinuclear Copper Center upon the Reduction of Bilirubin Oxidase (BOD)T. Tokiwa, M. Shoji, V. Sladek, N. Shibata, Y. Higuchi, K. Kataoka, Y. Shigeta, F MisaizuMolecules 24 (76) 2019年1月[査読有り] Developments of Rare Event Sampling Methods for ProteinsRyuhei Harada, Sladek Vladimir, Yasuteru ShigetaJOURNAL OF COMPUTER CHEMISTRY-JAPAN 18 (5) 2019年[査読有り] New Assay Method Based on Raman Spectroscopy for Enzymes Reacting with Gaseous SubstratesKawahara-Nakagawa, Yuka, Nishikawa, Koji, Nakashima, Satoru, Inoue, Shota, Ohta, Takehiro, Ogura, Takashi, Shigeta, Yasuteru, Fukutani, Katsuyuki, Yagi, Tatsuhiko, Higuchi, YoshikiProtein science : a publication of the Protein Society 28 (3) 2019年1月[査読有り] Structural changes of the trinuclear copper center in bilirubin oxidase upon reductionTakaki Tokiwa, Mitsuo Shoji, Vladimir Sladek, Naoki Shibata, Yoshiki Higuchi, Kunishige Kataoka, Takeshi Sakurai, Yasuteru Shigeta, Fuminori MisaizuMolecules 24 (1) 2019年[査読有り] Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital CalculationsTokiwa, Takaki, Nakano, Shogo, Yamamoto, Yuta, Ishikawa, Takeshi, Ito, Sohei, Sladek, Vladimir, Fukuzawa, Kaori, Mochizuki, Yuji, Tokiwa, Hiroaki, Misaizu, Fuminori, Shigeta, YasuteruJournal of chemical information and modeling 59 (1) 2019年1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 orientationsWakana Naito, Kazuki Urakawa, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Hiromitsu MaedaOrganic and Biomolecular Chemistry 17 (5) 2019年[査読有り] Possible configurations of apo-form taste receptor type 1 (T1r) studied by microsecond-order molecular dynamics simulationHayato Aida, Ryuhei Harada, Yasuteru ShigetaChemistry Letters 48 (4) 2019年[査読有り] Effects of antifreezing protein from rhagium inquisitor binding on ice growth: A molecular dynamics studyMasato Kimatsuka, Ryuma Sato, Ryuhei Harada, Mitsuo Shoji, Yasuteru ShigetaChemistry Letters 48 (3) 2019年[査読有り] Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of BiomoleculesRyuhei Harada, Yasuteru ShigetaAdvances in Quantum Chemistry 78 (78) 2019年[査読有り] Protein Residue Networks from Energetic and Geometric Data: Are They Identical?Vladimir Sladek, Hiroaki Tokiwa, Hitoshi Shimano, Yasuteru ShigetaJournal of Chemical Theory and Computation 14 (12) 2018年12月[査読有り] Redox Potential-Dependent Formation of an Unusual His–Trp Bond in Bilirubin OxidaseMahfuza Akter, Takaki Tokiwa, Mitsuo Shoji, Koji Nishikawa, Yasuteru Shigeta, Takeshi Sakurai, Yoshiki Higuchi, Kunishige Kataoka, Naoki ShibataChemistry - A European Journal 24 (68) 2018年12月[査読有り] Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon UpconversionRyuma Sato, Hirotaka Kitoh-Nishioka, Kenji Kamada, Toshiko Mizokuro, Kenji Kobayashi, Yasuteru ShigetaJournal 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-LikeKotaro Sakamoto, Megumi Kayanuma, Yasuteru ShigetaPROTEIN 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 NitrideKieu My Bui, Jun Ichi Iwata, Yoshihiro Kangawa, Kenji Shiraishi, Yasuteru Shigeta, Atsushi OshiyamaJournal 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, YasuteruJournal of chemical theory and computation 14 (12) 2018年11月Computational electrochemistry of a novel ferrocene derivativeAli Ghiami-Shomami, Bahram Ghalami-Choobar, Yasuteru ShigetaJournal of Molecular Graphics and Modelling 85 2018年10月[査読有り] Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiencyHarada, Ryuhei, Shigeta, YasuteruJournal of molecular graphics & modelling 85 2018年9月[査読有り] Computational electrochemistry of a novel ferrocene derivativeGhiami-Shomami, Ali, Ghalami-Choobar, Bahram, Shigeta, YasuteruJournal of molecular graphics & modelling 85 2018年8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 schemeFujiki, Ryo, Kasai, Yukako, Seno, Yuki, Matsui, Toru, Shigeta, Yasuteru, Yoshida, Norio, Nakano, HaruyukiPhysical chemistry chemical physics : PCCP 20 (43) 2018年8月[査読有り] Redox potential-dependent formation of an unusual His-Trp bond in bilirubin oxidaseAkter, Mahfuza, Tokiwa, Takaki, Shoji, Mitsuo, Nishikawa, Koji, Shigeta, Yasuteru, Sakurai, Takeshi, Higuchi, Yoshiki, Kataoka, Kunishige, Shibata, NaokiChemistry (Weinheim an der Bergstrasse, Germany) 24 (68) 2018年8月[査読有り] Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square DeviationRyuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling 58 (7) 2018年7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 IIShoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, KizashiThe journal of physical chemistry. B 122 (25) 2018年6月[査読有り] On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of ProteinsRyuhei Harada, Yasuteru ShigetaJournal of Chemical Theory and Computation 14 (6) 2018年6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 IIShoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, KizashiThe journal of physical chemistry. B 122 (25) 2018年6月[査読有り] Dominant role of orbital splitting in determining cathode potential in O3 NaTMO2 compoundsM. Hussein N. Assadi, Yasuteru ShigetaJournal of Power Sources 388 2018年6月[査読有り] How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulationsHarada, Ryuhei, Shigeta, YasuteruPhysical chemistry chemical physics : PCCP 20 (26) 2018年6月[査読有り] Novel techniques for observing structural dynamics of photoresponsive liquid crystalsMasaki Hada, Shohei Saito, Ryuma Sato, Kiyoshi Miyata, Yasuhiko Hayashi, Yasuteru Shigeta, Ken OndaJournal of Visualized Experiments 2018 (135) 2018年5月[査読有り] Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMαYamamoto, 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, HitoshiBiochemical and biophysical research communications 499 (2) 2018年5月[査読有り] On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of ProteinsHarada, Ryuhei, Shigeta, YasuteruJournal of chemical theory and computation 14 (6) 2018年5月[査読有り] Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMαYamamoto, 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, HitoshiBiochemical and biophysical research communications 499 (2) 2018年5月Recent Extensions and Applications of Parallel Cascade Selection Molecular Dynamics SimulationsHarada Ryuhei, Shigeta YasuteruACTIVITY REPORT 2017 / SUPERCOMPUTER CENTER, INSTITUTE FOR SOLID STATE PHYSICS, THE UNIVERSITY OF TOKYO (INVITED ARTICLE) 2018年5月Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMαYamamoto, 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, HitoshiBiochemical and biophysical research communications 499 (2) 2018年5月[査読有り] Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilitiesTerai, Yuma, Sato, Ryuma, Yumiba, Takahiro, Harada, Ryuhei, Shimizu, Kohei, Toga, Tatsuya, Ishikawa-Fujiwara, Tomoko, Todo, Takeshi, Iwai, Shigenori, Shigeta, Yasuteru, Yamamoto, JunpeiNucleic acids research Epub 2018年5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5月Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid CrystalsMasaki Hada, Shohei Saito, Ryuma Sato, Kiyoshi Miyata, Yasuhiko Hayashi, Yasuteru Shigeta, Ken OndaJOVE-JOURNAL OF VISUALIZED EXPERIMENTS (135) 2018年5月[査読有り] Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics studyHarada, Ryuhei, Mashiko, Takako, Tachikawa, Masanori, Hiraoka, Shuichi, Shigeta, YasuteruPhysical chemistry chemical physics : PCCP 20 (14) 2018年4月[査読有り] Nonadiabatic one-electron transfer mechanism for the O–O bond formation in the oxygen-evolving complex of photosystem IIMitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Kizashi YamaguchiChemical Physics Letters 698 2018年4月[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 ShigetaJournal of Physical Chemistry C 122 (10) 2018年3月[査読有り] First-principles study of the formation of glycine-producing radicals from common interstellar speciesAkimasa Sato, Yuya Kitazawa, Toshiro Ochi, Mitsuo Shoji, Yu Komatsu, Megumi Kayanuma, Yuri Aikawa, Masayuki Umemura, Yasuteru ShigetaMolecular Astrophysics 10 2018年3月[査読有り] First-principles study of the formation of glycine-producing radicals from common interstellar speciesAkimasa Sato, Yuya Kitazawa, Toshiro Ochi, Mitsuo Shoji, Yu Komatsu, Megumi Kayanuma, Yuri Aikawa, Masayuki Umemura, Yasuteru ShigetaMOLECULAR ASTROPHYSICS 10 2018年3月[査読有り] An assessment of optimal time scale of conformational resampling for parallel cascade selection molecular dynamicsRyuhei Harada, Yasuteru ShigetaMolecular Simulation 44 (3) 2018年2月[査読有り] カスケード型並列分子動力学シミュレーションとマルコフ状態モデルを併用したタンパク質の自由エネルギー計算原田, 隆平, 重田, 育照日本物理学会講演概要集 73 2018年How low-resolution structural data predict the conformational changes of a protein: A study on data-driven molecular dynamics simulationsRyuhei Harada, Yasuteru ShigetaPhysical Chemistry Chemical Physics 20 (26) 2018年[査読有り] Analyses on Dynamical Ordering of Protein Functions by Means of Cascade Selection Molecular DynamicsRyuhei Harada, Yasuteru ShigetaJOURNAL OF COMPUTER CHEMISTRY-JAPAN 17 (1) 2018年[査読有り] Coulomb and CH-φ interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilitiesYuma Terai, Ryuma Sato, Takahiro Yumiba, Ryuhei Harada, Kohei Shimizu, Tatsuya Toga, Tomoko Ishikawa-Fujiwara, Takeshi Todo, Shigenori Iwai, Yasuteru Shigeta, Junpei YamamotoNucleic Acids Research 46 (13) 2018年[査読有り] Programed dynamical ordering in self-organization processes of a nanocube: A molecular dynamics studyRyuhei Harada, Takako Mashiko, Masanori Tachikawa, Shuichi Hiraoka, Yasuteru ShigetaPhysical Chemistry Chemical Physics 20 (14) 2018年[査読有り] A computational scheme of p: K a values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction schemeRyo Fujiki, Yukako Kasai, Yuki Seno, Toru Matsui, Yasuteru Shigeta, Norio Yoshida, Haruyuki NakanoPhysical Chemistry Chemical Physics 20 (43) 2018年[査読有り] The binding structure and affinity of photodamaged duplex DNA with members of the photolyase/cryptochrome family: A computational studyRyuma Sato, Ryuhei Harada, Yasuteru ShigetaBIOPHYSICS AND PHYSICOBIOLOGY 15 2018年[査読有り] カスケード選択型分子動力学法によるタンパク質機能の動的秩序解析原田, 隆平, 重田, 育照Journal of Computer Chemistry, Japan 17 (1) 2018年[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)M. Hussein N. Assadi, Yasuteru ShigetaRSC Advances 8 (25) 2018年[査読有り] How does friction coefficient affect the conformational sampling efficiency of parallel cascade selection molecular dynamics?Ryuhei Harada, Yasuteru ShigetaChemistry Letters 47 (9) 2018年[査読有り] A theoretical study on redox potential and pKa of [2Fe-2S] cluster model from iron-sulfur proteinsIsman Kurniawan, Kazutomo Kawaguchi, Mitsuo Shoji, Toru Matsui, Yasuteru Shigeta, Hidemi NagaoBulletin of the Chemical Society of Japan 91 (9) 2018年[査読有り] A practical approach for searching stable molecular structures by introducing repulsive interactions among walkersMitsuo Shoji, Megumi Kayanuma, Yasuteru ShigetaBulletin of the Chemical Society of Japan 91 (10) 2018年The formation of hydrophobic core regulates the protein folding of villin elucidated with parallel cascade selection molecular dynamicsRyuhei Harada, Hayato Aida, Yasuteru ShigetaChemistry Letters 47 (10) 2018年[査読有り] High-performance Na ion cathodes based on the ubiquitous and reversible O redox reactionM. Hussein N. Assadi, Marco Fronzi, Mike Ford, Yasuteru ShigetaJournal of Materials Chemistry A 6 (47) 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Self-Avoiding Conformational Sampling Based on Histories of Past Conformational SearchesRyuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling 57 (12) 2017年12月[査読有り] Temperature-Shuffled Parallel Cascade Selection Molecular Dynamics Accelerates the Structural Transitions of ProteinsHarada Ryuhei, Shigeta YasuteruJOURNAL OF COMPUTATIONAL CHEMISTRY 38 (31) 2017年12月[査読有り] Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteinsRyuhei Harada, Yasuteru ShigetaJournal of Computational Chemistry 38 (31) 2017年12月[査読有り] Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal PhaseMasaki Hada, Shohei Saito, Sei'Ichi Tanaka, Ryuma Sato, Masahiko Yoshimura, Kazuhiro Mouri, Kyohei Matsuo, Shigehiro Yamaguchi, Mitsuo Hara, Yasuhiko Hayashi, Fynn Röhricht, Rainer Herges, Yasuteru Shigeta, Ken Onda, R. J. Dwayne MillerJournal of the American Chemical Society 139 (44) 2017年11月[査読有り] Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal PhaseMasaki Hada, Shohei Saito, Sei'Ichi Tanaka, Ryuma Sato, Masahiko Yoshimura, Kazuhiro Mouri, Kyohei Matsuo, Shigehiro Yamaguchi, Mitsuo Hara, Yasuhiko Hayashi, Fynn Röhricht, Rainer Herges, Yasuteru Shigeta, Ken Onda, R. J.Dwayne MillerJournal of the American Chemical Society 139 (44) 2017年11月[査読有り] Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal PhaseMasaki Hada, Shohei Saito, Sei'Ichi Tanaka, Ryuma Sato, Masahiko Yoshimura, Kazuhiro Mouri, Kyohei Matsuo, Shigehiro Yamaguchi, Mitsuo Hara, Yasuhiko Hayashi, Fynn Röhricht, Rainer Herges, Yasuteru Shigeta, Ken Onda, R. J. Dwayne MillerJournal of the American Chemical Society 139 (44) 2017年11月[査読有り] Theoretical study on relationship between spin structure and electron conductivity of one-dimensional tri-nickel(II) complexYasutaka Kitagawa, Mizuki Asaoka, Yoshiki Natori, Koji Miyagi, Rena Teramoto, Toru Matsui, Yasuteru Shigeta, Mitsutaka Okumura, Masayoshi NakanoPolyhedron 136 2017年11月[査読有り] A theoretical study of the formation of glycine via hydantoin intermediate in outer space environmentMegumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki UmemuraCHEMICAL PHYSICS LETTERS 687 2017年11月[査読有り] Self-Avoiding Conformational Sampling Based on Histories of Past Conformational SearchesHarada, Ryuhei, Shigeta, YasuteruJournal of chemical information and modeling 57 (12) 2017年11月[査読有り] Cover Feature: Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior (Chem. Eur. J. 60/2017)Hajime Yotsuji, Kenji Higashiguchi, Ryuma Sato, Yasuteru Shigeta, Kenji MatsudaChemistry - A European Journal 23 (60) 2017年10月Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature BehaviorHajime Yotsuji, Kenji Higashiguchi, Ryuma Sato, Yasuteru Shigeta, Kenji MatsudaChemistry - A European Journal 23 (60) 2017年10月[査読有り] Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature BehaviorHajime Yotsuji, Kenji Higashiguchi, Ryuma Sato, Yasuteru Shigeta, Kenji MatsudaChemistry - A European Journal 23 (60) 2017年10月[査読有り] Mechanistic Insight into Weak Base-Catalyzed Generation of Carbon Monoxide from Phenyl Formate and Its Application to Catalytic Carbonylation at Room Temperature without Use of External Carbon Monoxide GasHideyuki Konishi, Mika Matsubara, Keisuke Mori, Takaki Tokiwa, Sundaram Arulmozhiraja, Yuta Yamamoto, Yoshinobu Ishikawa, Hiroshi Hashimoto, Yasuteru Shigeta, Hiroaki Tokiwa, Kei ManabeAdvanced Synthesis and Catalysis 359 (20) 2017年10月[査読有り] H-Aggregated π-Systems Based on Disulfide-Linked Dimers of Dipyrrolyldiketone Boron ComplexesYoshifumi Sasano, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Hiromitsu MaedaThe Journal of Organic Chemistry 82 (20) 2017年10月[査読有り] H-Aggregated π-Systems Based on Disulfide-Linked Dimers of Dipyrrolyldiketone Boron ComplexesSasano, Yoshifumi, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, HiromitsuThe Journal of organic chemistry 82 (20) 2017年10月[査読有り] Assessment of Methodology and Chemical Group Dependences in the Calculation of the pKa for Several Chemical GroupsToru Matsui, Yasuteru Shigeta, Kenji MorihashiJournal of Chemical Theory and Computation 13 (10) 2017年10月[査読有り] Assessment of Methodology and Chemical Group Dependences in the Calculation of the pKa for Several Chemical GroupsToru Matsui, Yasuteru Shigeta, Kenji MorihashiJournal of Chemical Theory and Computation 13 (10) 2017年10月[査読有り] Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal PhaseHada, 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 DwayneJournal of the American Chemical Society 139 2017年10月[査読有り] Structural Dissimilarity Sampling with Dynamically Self-Guiding SelectionHarada Ryuhei, Shigeta YasuteruJOURNAL OF COMPUTATIONAL CHEMISTRY 38 (22) 2017年8月[査読有り] Structural dissimilarity sampling with dynamically self-guiding selectionRyuhei Harada, Yasuteru ShigetaJournal of Computational Chemistry 38 (22) 2017年8月[査読有り] Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteinsHarada, Ryuhei, Shigeta, YasuteruJournal of computational chemistry 38 (31) 2017年8月[査読有り] Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate ConformationsYuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki HayashiJournal of Physical Chemistry B 121 (22) 2017年6月[査読有り] Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate ConformationsUjiie Yuzuru, Tanaka Wataru, Hanaoka Kyohei, Harada Ryuhei, Kayanuma Megumi, Shoji Mitsuo, Murakawa Takeshi, Ishida Toyokazu, Shigeta Yasuteru, Hayashi HideyukiTHE JOURNAL OF PHYSICAL CHEMISTRY B 121 (22) 2017年6月[査読有り] Direct Observation of the Ultrafast Evolution of Open-Shell Biradical in Photochromic Radical DimerKobayashi Yoichi, Okajima Hajime, Sotome Hikaru, Yanai Takeshi, Mutoh Katsuya, Yoneda Yusuke, Shigeta Yasuteru, Sakamoto Akira, Miyasaka Hiroshi, Abe JiroJOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139 (18) 2017年5月[査読有り] Direct Observation of the Ultrafast Evolution of Open-Shell Biradical in Photochromic Radical DimerYoichi Kobayashi, Hajime Okajima, Hikaru Sotome, Takeshi Yanai, Katsuya Mutoh, Yusuke Yoneda, Yasuteru Shigeta, Akira Sakamoto, Hiroshi Miyasaka, Jiro AbeJournal of the American Chemical Society 139 (18) 2017年5月[査読有り] Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate ConformationsUjiie, Yuzuru, Tanaka, Wataru, Hanaoka, Kyohei, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo, Murakawa, Takeshi, Ishida, Toyokazu, Shigeta, Yasuteru, Hayashi, HideyukiThe journal of physical chemistry. B 121 (22) 2017年5月[査読有り] Structural Dissimilarity Sampling with Dynamically Self-Guiding SelectionHarada, Ryuhei, Shigeta, YasuteruJournal of computational chemistry 38 (22) 2017年5月[査読有り] Identification of the Key Interactions in Structural transition Pathway of FtsZ from Staphylococcus AureusFujita Junso, Harada Ryuhei, Maeda Yoko, Saito Yuki, Mizohata Eiichi, Inoue Tsuyoshi, Shigeta Yasuteru, Matsumura HiroyoshiJOURNAL OF STRUCTURAL BIOLOGY 198 (2) 2017年5月[査読有り] Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureusJunso Fujita, Ryuhei Harada, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi MatsumuraJournal of Structural Biology 198 (2) 2017年5月[査読有り] Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureusFujita, Junso, Harada, Ryuhei, Maeda, Yoko, Saito, Yuki, Mizohata, Eiichi, Inoue, Tsuyoshi, Shigeta, Yasuteru, Matsumura, HiroyoshiJournal of structural biology 198 (2) 2017年4月[査読有り] Direct Observation of the Ultrafast Evolution of Open-Shell Biradical in Photochromic Radical DimerKobayashi, Yoichi, Okajima, Hajime, Sotome, Hikaru, Yanai, Takeshi, Mutoh, Katsuya, Yoneda, Yusuke, Shigeta, Yasuteru, Sakamoto, Akira, Miyasaka, Hiroshi, Abe, JiroJournal of the American Chemical Society 139 (18) 2017年4月[査読有り] Common Folding Processes of Mini-Proteins: Partial Formations of Secondary Structures Initiate the Immediate Protein FoldingHarada Ryuhei, Takano Yu, Shigeta YasuteruJOURNAL OF COMPUTATIONAL CHEMISTRY 38 (11) 2017年4月[査読有り] Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein foldingRyuhei Harada, Yu Takano, Yasuteru ShigetaJournal of Computational Chemistry 38 (11) 2017年4月[査読有り] Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of ProteinsRyuhei Harada, Yasuteru ShigetaJournal of Chemical Theory and Computation 13 (3) 2017年3月[査読有り] Cooperatively Interlocked [2+1]-Type π-System-Anion ComplexesYamakado, Ryohei, Ashida, Yukina, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, HiromitsuChemistry (Weinheim an der Bergstrasse, Germany) 23 (17) 2017年3月[査読有り] Cooperatively Interlocked [2+1]-Type π-System-Anion ComplexesRyohei Yamakado, Yukina Ashida, Ryuma Sato, Yasuteru Shigera, Nobuhiro Yasuda, Hiromitsu MaedaChemistry - A European Journal 23 (17) 2017年3月[査読有り] Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of ProteinsHarada Ryuhei, Shigeta YasuteruJOURNAL OF CHEMICAL THEORY AND COMPUTATION 13 (3) 2017年3月[査読有り] Outstanding Reviewers for Physical Chemistry Chemical Physics in 2016Katsuhiko Ariga, Leonardo Bernasconi, Antonio Cammarata, Ayan Datta, Sergei Manzhos, Aurelien Perera, Jose Plata, Yasuteru Shigeta, Leonidas Tsetseris, Lijun XuPhysical Chemistry Chemical Physics 19 (12) 2017年[査読有り] Molecular dynamics simulation of the nanoscale solutal marangoni convectionYosuke Imai, Takuya Yamamoto, Yasunori Okano, Ryuma Sato, Yasuteru ShigetaASEAN Journal of Chemical Engineering 17 (1) 2017年[査読有り] Cooperatively Interlocked [2+1]-Type π-System-Anion ComplexesYamakado, Ryohei, Ashida, Yukina, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, HiromitsuChemistry (Weinheim an der Bergstrasse, Germany) 23 (17) 2017年[査読有り] Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structuresMitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian Ren Shen, Kizashi YamaguchiFaraday Discussions 198 2017年[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 ShigetaChemistry Letters 46 (6) 2017年[査読有り] Theoretical analyses of triplettriplet annihilation process of 9,10-diphenylanthracene in solutionRyuma Sato, Hirotaka Kitoh-Nishioka, Takeshi Yanai, Yasuteru ShigetaChemistry Letters 46 (6) 2017年[査読有り] Dynamic specification of initial structures in parallel cascade selection molecular dynamics (PaCS-MD) efficiently promotes biologically relevant rare eventsRyuhei Harada, Yasuteru ShigetaBulletin of the Chemical Society of Japan 90 (11) 2017年[査読有り] Classical cumulant dynamics for statistical chemical physicsYasuteru 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 ShojiMolecular Simulation 43 (13-16) 2017年[査読有り] A theoretical study of the formation of glycine via hydantoin intermediate in outer space environmentMegumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki UmemuraChemical Physics Letters 687 2017年[査読有り] Refractive indices of organo-metallic and -metalloid compounds: A long-range corrected DFT studyShintaro Maekawa, Krzysztof Moorthi, Yasuteru ShigetaJournal of Computational Chemistry 37 (32) 2016年12月[査読有り] Molecular dynamics simulation of atomic-scale solutal Marangoni convectionY. Imai, T. Yamamoto, Y. Okano, R. Sato, Y. ShigetaProceedings of 23th Regional Symposium on Chemical Engineering 2016年10月Ion-Pairing Crystal Polymorphs of Interlocked [2 + 1]-Type Receptor-Anion ComplexesRyohei Yamakado, Ryuma Sato, Yasuteru Shigeta, Hiromitsu MaedaJournal of Organic Chemistry 81 (18) 2016年9月[査読有り] Mutations affecting the internal equilibrium of the reaction catalyzed by 6-aminohexanoate-dimer hydrolaseSeiji Negoro, Yasuyuki Kawashima, Naoki Shibata, Tatsuya Kobayashi, Takeshi Baba, Young Ho Lee, Katsumasa Kamiya, Yasuteru Shigeta, Keisuke Nagai, Ikki Takehara, Dai ichiro Kato, Masahiro Takeo, Yoshiki HiguchiFEBS Letters 590 (18) 2016年9月Ultrafast snapshots of the molecules twisting in liquid crystal stateMasaki Hada, Shohei Saito, Sei'ichi Tanaka, Ryuma Sato, Kyohei Matsuo, Mitsuo Hara, Yasuhiko Hayashi, Kazuhiro Mouri, Masahiko Yoshimura, Yasuteru Shigeta, Shigehiro Yamaguchi, Ken Onda, R. J.Dwayne MillerOptics InfoBase Conference Papers 2016年7月[査読有り] Doubly N-Methylated PorphyrinoidsWakana Naito, Nobuhiro Yasuda, Tatsuki Morimoto, Yasuteru Shigeta, Hikaru Takaya, Ichiro Hisaki, Hiromitsu MaedaOrganic Letters 18 (12) 2016年6月[査読有り] Protein folding and evolutionHarada,Ryuhei, Inagaki,Yuji, Yasuteru,ShigetaReference Module in Materials Science and Materials Engineering 2016年6月[査読有り] TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of ProteinsRyuhei Harada, Yu Takano, Yasuteru ShigetaJournal of Chemical Theory and Computation 12 (5) 2016年5月[査読有り] Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM StudyMegumi Kayanuma, Mitsuo Shoji, Masafumi Yohda, Masafumi Odaka, Yasuteru ShigetaJournal of Physical Chemistry B 120 (13) 2016年4月[査読有り] Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distributionRyuhei Harada, Tomotake Nakamura, Yasuteru ShigetaJournal of Computational Chemistry 37 (8) 2016年3月[査読有り] Solvent effects on excited-state electron-transfer rate of pyrene-labeled deoxyuridine: A theoretical studyShintaro Maekawa, Ryuma Sato, Kimihiko Hirao, Yasuteru ShigetaChemical Physics Letters 644 2016年1月[査読有り] A fast convergent simulated annealing algorithm for protein-folding: Simulated annealing outlier flooding (sa-oflood) methodRyuhei Harada, Tomotake Nakamura, Yasuteru ShigetaBulletin of the Chemical Society of Japan 89 (11) 2016年[査読有り] Molecular mechanisms of substrate specificities of uridine-cytidine kinaseWataru Tanaka, Mitsuo Shoji, Fumiaki Tomoike, Yuzuru Ujiie, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Katsumasa Kamiya, Toyokazu Ishida, Ryoji Masui, Seiki Kuramitsu, Yasuteru ShigetaBIOPHYSICS AND PHYSICOBIOLOGY 13 2016年[査読有り] Theoretical analyses on a flipping mechanism of UV-induced DNA damageRyuma Sato, Ryuhei Harada, Yasuteru ShigetaBIOPHYSICS 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Automatic detection of hidden dimensions to obtain appropriate reaction coordinates in the Outlier FLOODing (OFLOOD) methodRyuhei Harada, Tomotake Nakamura, Yasuteru ShigetaChemical Physics Letters 639 2015年10月[査読有り] Molecular dynamics study on the key catalytic intermediates of threonine synthaseMitsuo Shoji, Yuzuru Ujiie, Ryuhei Harada, Megumi Kayanuma, Yasuteru Shigeta, Takeshi Murakawa, Hideyuki HayashiPROTEIN SCIENCE 24 (1:SI) 2015年10月[査読有り] GPGPU化OpenFMOによるFMO計算の性能評価梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照情報処理学会研究報告(Web) 2015 (HPC-151) 2015年9月Performance of the divide-and-conquer approach used as an initial guessMitsuo,Shoji, Megumi,Kayanuma, Hiroaki,Umeda, Yasuteru,ShigetaChemical Physics Letters 634 2015年8月[査読有り] Performance of the divide-and-conquer approach used as an initial guessMitsuo Shoji, Megumi Kayanuma, Hiroaki Umeda, Yasuteru ShigetaChemical Physics Letters 634 2015年6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, chignolinRyuhei Harada, Yu Takano, Yasuteru ShigetaJournal of Computational Chemistry 36 (10) 2015年4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 ReductaseShintaro Maekawa, Toru Matsui, Kimihiko Hirao, Yasuteru ShigetaJournal of Physical Chemistry B 119 (17) 2015年4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 solventRyuhei Harada, Yu Takano, Yasuteru ShigetaChemical Physics Letters 630 2015年4月[査読有り] Simple, yet powerful methodologies for conformational sampling of proteinsRyuhei Harada, Yu Takano, Takeshi Baba, Yasuteru ShigetaPhysical Chemistry Chemical Physics 17 (9) 2015年3月Theoretical design of solvatochromism switching by photochromic reactions using donor-acceptor disubstituted diarylethene derivatives with oxidized thiophene ringsKatsuki Okuno, Yasuteru Shigeta, Ryohei Kishi, Masayoshi NakanoPhysical Chemistry Chemical Physics 17 (9) 2015年3月[査読有り] A QM/MM study of the initial steps of catalytic mechanism of nitrile hydrataseMegumi Kayanuma, Kyohei Hanaoka, Mitsuo Shoji, Yasuteru ShigetaChemical Physics Letters 623 2015年3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3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3月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3月Hydration effects on enzyme-substrate complex of nylon oligomer hydrolase: Inter-fragment interaction energy study by the fragment molecular orbital methodHiroyuki Ando, Yasuteru Shigeta, Takeshi Baba, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Masayoshi NakanoMolecular Physics 113 (3-4) 2015年2月[査読有り] Substitution effects on optical properties of iminonitroxide-substituted iminonitroxide diradicalRyota Nakamura, Yasuteru Shigeta, Katsuki Okuno, Miki Hasegawa, Mayuko Fukushima, Shuichi Suzuki, Masatoshi Kozaki, Keiji Okada, Masayoshi NakanoMolecular Physics 113 (3-4) 2015年2月[査読有り] Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: From induced-fit to acylation processesTakeshi Baba, Mauro Boero, Katsumasa Kamiya, Hiroyuki Ando, Seiji Negoro, Masayoshi Nakano, Yasuteru ShigetaPhysical Chemistry Chemical Physics 17 (6) 2015年2月[査読有り] Quantal cumulant dynamics for real-time simulations of quantum many-body systemsYasuteru Shigeta, Ryuhei Harada, Megumi Kayanuma, Mitsuo ShojiInternational Journal of Quantum Chemistry 115 (5) 2015年2月Accurate Standard Hydrogen Electrode Potential and Applications to the Redox Potentials of Vitamin C and NAD/NADHToru Matsui, Yasutaka Kitagawa, Mitsutaka Okumura, Yasuteru ShigetaJournal of Physical Chemistry A 119 (2) 2015年1月[査読有り] Protein folding pathways extracted by OFLOOD: Outlier flooding methodRyuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru ShigetaJournal of Computational Chemistry 36 (2) 2015年1月[査読有り] Static electric field effect on third-order nonlinear optical (NLO) properties of singlet diradical molecules: Toward the realization of an electric field induced open-shell NLO switchMasayoshi Nakano, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Yasuteru Shigeta, Benoît Champagne, Edith Botek, Koji Ohta, Kenji Kamada, Takashi KuboAIP Conference Proceedings 1642 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, 重田育照日本コンピュータ化学会年会講演予稿集 2015 2015年OpenFMOプログラムのGPGPU化梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照分子科学討論会講演プログラム&要旨(Web) 9th 2015年Protein Folding Pathways Extracted by OFLOOD: Outlier FLOODing MethodRyuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru ShigetaJOURNAL OF COMPUTATIONAL CHEMISTRY 36 (2) 2015年1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] A density functional study on the pKa of small polyprotic moleculesTakeshi Baba, Toru Matsui, Katsumasa Kamiya, Masayoshi Nakano, Yasuteru ShigetaInternational Journal of Quantum Chemistry 114 (17) 2014年9月[査読有り] Open-shell character and second hyperpolarizabilities of one-dimensional chromium(II) chains: Size dependence and bond-length alternation effectHitoshi Fukui, Shota Takamuku, Taishi Yamada, Kotaro Fukuda, Taku Takebayashi, Yasuteru Shigeta, Ryohei Kishi, Benoît Champagne, Masayoshi NakanoInorganic Chemistry 53 (16) 2014年8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8月On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolaseTakeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru ShigetaJournal of Computational Chemistry 35 (16) 2014年6月[査読有り] Nylon-oligomer hydrolase promoting cleavage reactions in unnatural amide compoundsKatsumasa Kamiya, Takeshi Baba, Mauro Boero, Toru Matsui, Seiji Negoro, Yasuteru ShigetaJournal of Physical Chemistry Letters 5 (7) 2014年4月[査読有り] Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteinsRyuhei Harada, Yu Takano, Yasuteru ShigetaJournal of Chemical Physics 140 (12) 2014年3月[査読有り] 第一原理 Meta-Dynamics 法，Blue Moon Ensemble 法を用いた反応経路解析馬場 剛史, 安東 寛之, 重田 育照アンサンブル 16 (1) 2014年3P077 ウリジンシチジンキナーゼの基質結合相互作用についての理論的研究(01D. 蛋白質:機能,ポスター,第52回日本生物物理学会年会(2014年度))Tanaka Wataru, Ujiie Yuzuru, Tomoike Fumiaki, Shoji Mitsuo, Kayanuma Megumi, Masui Ryoji, Kuramitsu Seiki, Shigeta Yasuteru生物物理 54 (1) 2014年3P076 トレオニン合成酵素の反応制御機構解明のための分子動力学計算 : 反応中間体間自由エネルギー評価(01D. 蛋白質:機能,ポスター,第52回日本生物物理学会年会(2014年度))Ujiie Yuzuru, Tanaka Wataru, Shoji Mitsuo, Kayanuma Megumi, Shigeta Yasuteru, Machida Yasuhiro, Murakawa Takeshi, Hayashi Hideyuki生物物理 54 (1) 2014年1P074 ニトリルヒドラターゼ(NHase)によるアミド生成機構に関する理論的研究(01D. 蛋白質 : 機能,ポスター,第52回日本生物物理学会年会(2014年度))Kayanuma Megumi, Shoji Mitsuo, Shigeta Yasuteru生物物理 54 (1) 2014年GPGPU化Fock行列計算ルーチンのOpenFMOへの組み込み梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照分子科学討論会講演プログラム&要旨(Web) 8th 2014年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, 重田育照日本コンピュータ化学会年会講演予稿集 2014 2014年A new type of organic-inorganic hybrid NLO-phore with large off-diagonal first hyperpolarizability tensors: A two-dimensional approachShabbir Muhammad, Hongliang Xu, Zhongmin Su, Kotaro Fukuda, Ryohei Kishi, Yasuteru Shigeta, Masayoshi NakanoDalton Transactions 42 (42) 2013年11月[査読有り] Binding of a positron to nucleic base molecules and their PairsKatsuhiko Koyanagi, Yukiumi Kita, Yasuteru Shigeta, Masanori TachikawaChemPhysChem 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 solventsTomoya Inui, Yasuteru Shigeta, Katsuki Okuno, Takeshi Baba, Ryohei Kishi, Masayoshi NakanoJournal of Computational Chemistry 34 (27) 2013年10月[査読有り] Photochromic switching of diradical character: Design of efficient nonlinear optical switchesKatsuki Okuno, Yasuteru Shigeta, Ryohei Kishi, Masayoshi NakanoJournal of Physical Chemistry Letters 4 (15) 2013年8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 applicationsToru Matsui, Yasutaka Kitagawa, Yasuteru Shigeta, Mitsutaka OkumuraJournal of Chemical Theory and Computation 9 (7) 2013年7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6月[査読有り] イミノニトロキシドジラジカルからランタニドへのエネルギー移動福嶋 真由子, 竹内 利明, 鈴木 修一, 小嵜 正敏, 岡田 惠次, 重田 育照, 長谷川 美貴希土類 = Rare earths (62) 2013年5月[査読有り] Atom-scale reaction pathways and free-energy landscapes in oxygen plasma etching of grapheneKenichi Koizumi, Mauro Boero, Yasuteru Shigeta, Atsushi OshiyamaJournal of Physical Chemistry Letters 4 (10) 2013年5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5月[査読有り] Diradicalology in third-order nonlinear optical systems: Second hyperpolarizabilities of acetylene-linked phenalenyl-based superpolyenesMasayoshi Nakano, Ryohei Kishi, Hitoshi Fukui, Takuya Minami, Kyohei Yoneda, Shu Minamide, Yudai Inoue, Taishi Yamada, Soichi Ito, Shabbir Muhammad, Yasuteru Shigeta, Takashi Kubo, Benoît ChampagneInternational Journal of Quantum Chemistry 113 (4) 2013年2月[査読有り] Comparative study of diradical characters and third-order nonlinear optical properties of linear/cyclic acenes versus phenylenesShabbir Muhammad, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Shu Minamide, Ryohei Kishi, Yasuteru Shigeta, Masayoshi NakanoInternational Journal of Quantum Chemistry 113 (4) 2013年2月[査読有り] Antidot effects on the open-shell characters and second hyperpolarizabilities of rectangular graphene nanoflakesKyohei Yoneda, Shu Minamide, Taishi Yamada, Soichi Ito, Takuya Minami, Ryohei Kishi, Yasuteru Shigeta, Masayoshi NakanoInternational Journal of Quantum Chemistry 113 (4) 2013年2月[査読有り] Quantal cumulant mechanics and dynamics for multidimensional quantum many-body clustersYasuteru Shigeta, Tomoya Inui, Takeshi Baba, Katsuki Okuno, Hiroyuki Kuwabara, Ryohei Kishi, Masayoshi NakanoInternational Journal of Quantum Chemistry 113 (3) 2013年2月[査読有り] Synthesis and characterization of quarteranthene: Elucidating the characteristics of the edge state of graphene nanoribbons at the molecular levelAkihito Konishi, Yasukazu Hirao, Kouzou Matsumoto, Hiroyuki Kurata, Ryohei Kishi, Yasuteru Shigeta, Masayoshi Nakano, Kazuya Tokunaga, Kenji Kamada, Takashi KuboJournal of the American Chemical Society 135 (4) 2013年1月[査読有り] Interplay between the diradical character and third-order nonlinear optical properties in fullerene systemsShabbir Muhammad, Kotaro Fukuda, Takuya Minami, Ryohei Kishi, Yasuteru Shigeta, Masayoshi NakanoChemistry - A European Journal 19 (5) 2013年1月[査読有り] Consistent scheme for computing standard hydrogen electrode and redox potentialsToru Matsui, Yasutaka Kitagawa, Mitsutaka Okumura, Yasuteru Shigeta, Shigeyoshi SakakiJournal of Computational Chemistry 34 (1) 2013年1月[査読有り] 3P048 Computational studies of mutational effects on nylon degrading enzyme(01A. Protein: Structure,Poster)Baba Takeshi, Kamiya Katsumasa, Matsui Toru, Nakano Masayoshi, Negoro Seiji, Mauro Boero, Shigeta Yasuteru生物物理 53 (1) 2013年Energy Transfer from iminonitroxide diradicals to a series of lanthanide ionMayuko Fukushima, Toshiaki Takeuchi, Shuichi Suzuki, Masatoshi Kozaki, Keiji Okada, Yasuteru Shigeta, Miki HasegawaKidorui 62 2013年[査読有り] Cumulant mechanics : An explicit treatment for fluctuation on dynamics重田,育照Molecular Science 7 (1) 2013年1月[査読有り] Non-empirical tuning of CAM-B3LYP functional in time-dependent density functional theory for excitation energies of diarylethene derivativesKatsuki Okuno, Yasuteru Shigeta, Ryohei Kishi, Masayoshi NakanoChemical Physics Letters 585 (1-3) 2013年[査読有り] Density functional studies of the structural variety of the Cu 2S 2 core of the Cu A siteYu Takano, Orio Okuyama, Yasuteru Shigeta, Haruki NakamuraInternational Journal of Quantum Chemistry 112 (24) 2012年12月[査読有り] Impact of antidot structure on the multiradical characters, aromaticities, and third-order nonlinear optical properties of hexagonal graphene nanoflakesKyohei Yoneda, Masayoshi Nakano, Yudai Inoue, Tomoya Inui, Kotaro Fukuda, Yasuteru Shigeta, Takashi Kubo, Benoît ChampagneJournal of Physical Chemistry C 116 (33) 2012年8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 atomHitoshi Fukui, Yudai Inoue, Taishi Yamada, Soichi Ito, Yasuteru Shigeta, Ryohei Kishi, Benoît Champagne, Masayoshi NakanoJournal of Physical Chemistry A 116 (22) 2012年6月[査読有り] Microscopic mechanisms of initial oxidation of Si(100): Reaction pathways and free-energy barriersKenichi Koizumi, Mauro Boero, Yasuteru Shigeta, Atsushi OshiyamaPhysical Review B - Condensed Matter and Materials Physics 85 (20) 2012年5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 methodRyohei Kishi, Hiroaki Fujii, Shingo Kishimoto, Yusuke Murata, Soichi Ito, Katsuki Okuno, Yasuteru Shigeta, Masayoshi NakanoJournal of Physical Chemistry A 116 (17) 2012年5月[査読有り] Tuned CAM-B3LYP functional in the time-dependent density functional theory scheme for excitation energies and properties of diarylethene derivativesKatsuki Okuno, Yasuteru Shigeta, Ryohei Kishi, Hiroshi Miyasaka, Masayoshi NakanoJournal of Photochemistry and Photobiology A: Chemistry 235 (1) 2012年5月[査読有り] Coordination effects on the electronic structure of the Cu A site of cytochrome c oxidaseKenichi Koizumi, Yasuteru Shigeta, Orio Okuyama, Haruki Nakamura, Yu TakanoChemical Physics Letters 531 2012年4月[査読有り] An accurate density functional theory based estimation of pK a values of polar residues combined with experimental data: From amino acids to minimal proteinsToru Matsui, Takeshi Baba, Katsumasa Kamiya, Yasuteru ShigetaPhysical Chemistry Chemical Physics 14 (12) 2012年3月[査読有り] Halide ion complexes of decaborane (B 10H 14) and their derivatives: Noncovalent charge transfer effect on second-order nonlinear optical propertiesShabbir Muhammad, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Ryohei Kishi, Yasuteru Shigeta, Masayoshi NakanoJournal of Physical Chemistry A 116 (5) 2012年2月[査読有り] Theoretical insight into stereoselective reaction mechanisms of 2,4-pentanediol-tethered ketene-olefin [2 + 2] cycloadditionKatsumasa Kamiya, Toru Matsui, Takashi Sugimura, Yasuteru ShigetaJournal of Physical Chemistry A 116 (4) 2012年2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 systemsHitoshi Fukui, Yudai Inoue, Ryohei Kishi, Yasuteru Shigeta, Benoît Champagne, Masayoshi NakanoChemical Physics Letters 523 2012年1月[査読有り] Full configuration interaction calculations of the second hyperpolarizabilities of the H 4 model compound: Summation-over-states analysis and interplay with diradical charactersMasayoshi Nakano, Takuya Minami, Hitoshi Fukui, Ryohei Kishi, Yasuteru Shigeta, Benot ChampagneJournal of Chemical Physics 136 (2) 2012年1月[査読有り] Computational study toward micro electronics engineeringK. Shiraishi, K. Yamaguchi, M. Yang, S. G. Park, K. Kamiya, Y. Shigeta, B. Magyari-Kope, M. Niwa, Y. Nishi2012 28th International Conference on Microelectronics - Proceedings, MIEL 2012 2012年[査読有り] Theoretical Studies on Metal-Containing Artificial DNA BasesToru Matsui, Hideaki Miyachi, Yasuteru ShigetaADVANCES IN THE THEORY OF QUANTUM SYSTEMS IN CHEMISTRY AND PHYSICS 22 2012年[査読有り] Electronic structures of the Cu2S2 core of the CuA site in cytochrome c oxidase and nitrous oxide reductaseYu Takano, Yasuteru Shigeta, Kenichi Koizumi, Haruki NakamuraInternational Journal of Quantum Chemistry 112 (1) 2012年1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 Resolution1Saito,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,KINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 (1) 2012年1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 selectivityTakashi Sugimura, Eigo Mitani, Takahiro Tei, Tadashi Okuyama, Katsumasa Kamiya, Toru Matsui, Yasuteru ShigetaBulletin of the Chemical Society of Japan 85 (4) 2012年[査読有り] DFT analysis of low-frequency heme vibrations in soluble guanylate cyclase: Raman mode enhancement by propionateprotein interactionsMinoru Kubo, Orio Okuyama, Teizo Kitagawa, Yasuteru ShigetaChemistry Letters 41 (9) 2012年[査読有り] Erratum to: (Hyper)polarizability density analysis for open-shell molecular systems based on natural orbitals and occupation numbers (Theor Chem Acc, DOI 10.1007/s00214-010-0871-y)Masayoshi Nakano, Hitoshi Fukui, Takuya Minami, Kyohei Yoneda, Yasuteru Shigeta, Ryohei Kishi, Benoît Champagne, Edith Botek, Takashi Kubo, Koji Ohta, Kenji KamadaTheoretical Chemistry Accounts 130 (4-6) 2011年12月[査読有り] (Hyper)polarizability density analysis for open-shell molecular systems based on natural orbitals and occupation numbersMasayoshi Nakano, Hitoshi Fukui, Takuya Minami, Kyohei Yoneda, Yasuteru Shigeta, Ryohei Kishi, Benoît Champagne, Edith Botek, Takashi Kubo, Koji Ohta, Kenji KamadaTheoretical Chemistry Accounts 130 (4-6) 2011年12月[査読有り] Self-diffusion in crystalline silicon: A Car-Parrinello molecular dynamics studyKenichi Koizumi, Mauro Boero, Yasuteru Shigeta, Atsushi OshiyamaPhysical Review B - Condensed Matter and Materials Physics 84 (20) 2011年11月[査読有り] First-principles molecular dynamics study on the atomistic behavior of His503 in bovine cytochrome c oxidaseKatsumasa Kamiya, Yasuteru ShigetaBiochimica et Biophysica Acta - Bioenergetics 1807 (10) 2011年10月[査読有り] Origin of the Enhancement of the Second Hyperpolarizabilities in Open-Shell Singlet Transition-Metal Systems with Metal–Metal Multiple BondsShigeta,YasuteruJOURNAL OF PHYSICAL CHEMISTRY LETTERS 2 (16) 2011年8月[査読有り] Third-order nonlinear optical properties of open-shell supermolecular systems composed of acetylene linked phenalenyl radicalsMasayoshi Nakano, Ryohei Kishi, Kyohei Yoneda, Yudai Inoue, Tomoya Inui, Yasuteru Shigeta, Takashi Kubo, Benot ChampagneJournal of Physical Chemistry A 115 (31) 2011年8月[査読有り] Theoretical study on reaction scheme of silver(I) containing 5-substituted uracils bridge formationToru Matsui, Hideaki Miyachi, Takeshi Baba, Yasuteru ShigetaJournal of Physical Chemistry A 115 (30) 2011年8月[査読有り] Open-shell characters and second hyperpolarizabilities of one-dimensional graphene nanoflakes composed of trigonal graphene unitsKyohei Yoneda, Masayoshi Nakano, Hitoshi Fukui, Takuya Minami, Yasuteru Shigeta, Takashi Kubo, Edith Botek, Benoët ChampagneChemPhysChem 12 (9) 2011年6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 substitutionMasayoshi Nakano, Takuya Minami, Kyohei Yoneda, Shabbir Muhammad, Ryohei Kishi, Yasuteru Shigeta, Takashi Kubo, Léa Rougier, Benoiit Champagne, Kenji Kamada, Koji OhtaJournal of Physical Chemistry Letters 2 (9) 2011年5月[査読有り] Study on collective electron motion in Si-nano dot floating gate MOS capacitorMasakazu Muraguchi, Yoko Sakurai, Yukihiro Takada, Shintaro Nomura, Kenji Shiraishi, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi Miyazaki, Yasuteru Shigeta, Tetsuo EndohIEICE Transactions on Electronics E94-C (5) 2011年5月[査読有り] An atomistic study on hydrogenation effects toward quality improvement of program/erase cycle of MONOS-type memoryAkira Otake, Keita Yamaguchi, Katsumasa Kamiya, Yasuteru Shigeta, Kenji ShiraishiIEICE Transactions on Electronics E94-C (5) 2011年5月[査読有り] Collective tunneling model in charge-trap-type nonvolatile memory cellMasakazu Muraguchi, Yoko Sakurai, Yukihiro Takada, Yasuteru Shigeta, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi Miyazaki, Shintaro Nomura, Kenji Shiraishi, Tetsuo EndohJapanese Journal of Applied Physics 50 (4 PART 2) 2011年4月[査読有り] Atomistic design of guiding principles for high quality metal-oxide-nitride-oxide-semiconductor memories: First principles study of H and O incorporation effects for N vacancies in SiN charge trap layersKeita Yamguchi, Akira Otake, Katsumasa Kamiya, Yasuteru Shigeta, Kenji ShiraishiJapanese Journal of Applied Physics 50 (4 PART 2) 2011年4月[査読有り] Molecular dynamics studies on the mutational structures of a nylon-6 byproduct-degrading enzymeTakeshi Baba, Katsumasa Kamiya, Toru Matsui, Naoki Shibata, Yoshiki Higuchi, Tatsuya Kobayashi, Seiji Negoro, Yasuteru ShigetaChemical Physics Letters 507 (1-3) 2011年4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 ligandsHitoshi Fukui, Yasuteru Shigeta, Masayoshi Nakano, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoît Champagne, Edith BotekJournal of Physical Chemistry A 115 (6) 2011年2月[査読有り] A Simple scheme for estimating the pKa values of 5-substituted uracilsToru Matsui, Atsushi Oshiyama, Yasuteru ShigetaChemical Physics Letters 502 (4-6) 2011年1月[査読有り] 3N0912 Experimental and computational studies on mutational effects on nylon-6 byproducts-degrading enzyme(Protein : Measurement & Analysis, Origin of life & Evolution,The 49th Annual Meeting of the Biophysical Society of Japan)Baba Takeshi, Kamiya Katsumasa, Matsui Toru, Shibata Naoki, Higuchi Yoshiki, Negoro Seiji, Shigeta Yasuteru生物物理 51 2011年First principle study of the stability of H atoms in SiN layers on MONOS-type memories during program/erase operationsKeita Yamaguchi, Akira Otake, Katsumasa Kamiya, Kenji Shiraishi, Yasuteru ShigetaInternational Conference on Simulation of Semiconductor Processes and Devices, SISPAD 2011年[査読有り] Collective tunneling model between two-dimensional electron gas to Si-Nano DotM. Muraguchi, Y. Sakurai, Y. Takada, S. Nomura, K. Shiraishi, K. Makihara, M. Ikeda, S. Miyazaki, Y. Shigeta, T. EndohAIP Conference Proceedings 1399 2011年[査読有り] Efficient guiding principle of highly scalable MONOS-type memoriesK. Kamiya, K. Yamaguchi, A. Otake, Y. Shigeta, K. ShiraishiECS Transactions 41 (7) 2011年[査読有り] Collective electron tunneling model in Si-Nano dot floating gate MOS structureMasakazu Muraguchi, Yoko Sakurai, Yukihiro Takada, Yasuteru Shigeta, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi Miyazaki, Shintaro Nomura, Kenji Shiraishi, Tetsuo EndohKey Engineering Materials 470 2011年[査読有り] Electron conductivity in modified models of artificial metal-DNA using green's function-based elastic scattering theoryYasuyuki Nakanishi, Toru Matsui, Yasutaka Kitagawa, Yasuteru Shigeta, Toru Saito, Yusuke Kataoka, Takashi Kawakami, Mitsutaka Okumura, Kizashi YamaguchiBulletin of the Chemical Society of Japan 84 (4) 2011年[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 modelsMasayoshi Nakano, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Yasuteru Shigeta, Ryohei Kishi, Benoît Champagne, Edith BotekChemical 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 conductivityYasuyuki Nakanishi, Toru Matsui, Yasuteru Shigeta, Yasutaka Kitagawa, Toru Saito, Yusuke Kataoka, Takashi Kawakami, Mitsutaka Okumura, Kizashi YamaguchiInternational Journal of Quantum Chemistry 110 (12) 2010年10月[査読有り] Importance of electronic state of two-dimensional electron gas for electron injection process in nano-electronic devicesM. Muraguchi, T. Endoh, Y. Takada, Y. Sakurai, S. Nomura, K. Shiraishi, M. Ikeda, K. Makihara, S. Miyazaki, Y. ShigetaPhysica E: Low-Dimensional Systems and Nanostructures 42 (10) 2010年9月[査読有り] Possibility of multi-conformational structure of mismatch DNA nucleobase in the presence of silver(I) ionsHideaki Miyachi, Toru Matsui, Yasuteru Shigeta, Koichi Yamashita, Kimihiko HiraoChemical Physics Letters 495 (1-3) 2010年7月[査読有り] Energy compensation mechanism for charge-separated protonation states in aspartate-histidine amino acid residue pairsKatsumasa Kamiya, Mauro Boero, Kenji Shiraishi, Atsushi Oshiyama, Yasuteru ShigetaJournal of Physical Chemistry B 114 (19) 2010年5月[査読有り] Anomalous temperature dependence of electron tunneling between a two-dimensional electron gas and Si dotsY. Sakurai, S. Nomura, Y. Takada, J. Iwata, K. Shiraishi, M. Muraguchi, T. Endoh, Y. Shigeta, M. Ikeda, K. Makihara, S. MiyazakiPhysica E: Low-Dimensional Systems and Nanostructures 42 (4) 2010年2月[査読有り] 1P042 Molecular dynamics studies on Mutational structures of a Nylon-6 Byproduct-degrading Enzyme(Protein:Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)Baba Takeshi, Kamiya Katsumasa, Shigeta yasuteru, Negoro Seiji生物物理 50 (2) 2010年3P034 First-principles Studies of Relationship between Proton Behaviour and Physiological Environments in Proteins(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)Kamiya Katsumasa, Shigeta Yasuteru生物物理 50 (2) 2010年Electron tunneling between Si quantum dots and tow dimensional electron gas under optical excitation at low temperaturesY. Sakurai, Y. Takada, J. I. Iwata, K. Shiraishi, S. Nomura, M. Muraguchi, T. Endoh, Y. Shigeta, M. Ikeda, K. Makihara, S. MiyazakiECS Transactions 28 (1) 2010年[査読有り] Guiding principles for charge trap memories - A theoretical approachKenji Shiraishi, Keita Yamaguchi, Akira Otake, Katsumasa Kamiya, Yasuteru ShigetaICSICT-2010 - 2010 10th IEEE International Conference on Solid-State and Integrated Circuit Technology, Proceedings 2010年[査読有り] Universal guiding principle for the fabrication of highly scalable MONOS-type memory - Atomistic recipes based on designing interface oxygen chemical potentialK. Yamaguchi, A. Otake, K. Kamiya, Y. Shigeta, K. ShiraishiTechnical Digest - International Electron Devices Meeting, IEDM 2010年[査読有り] Temperature dependence of electron tunneling between two dimensional electron gas and Si quantum dotsYoko Sakurai, Jun Ichi Iwata, Masakazu Muraguchi, Yasuteru Shigeta, Yukihiro Takada, Shintaro Nomura, Tetsuo Endoh, Shin Ichi Saito, Kenji Shiraishi, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi MiyazakiJapanese Journal of Applied Physics 49 (1 Part 1) 2010年[査読有り] Effects of mercury(ii) on structural properties, electronic structure and UV absorption spectra of a duplex containing thymine-mercury(ii)-thymine nucleobase pairsHideaki Miyachi, Toru Matsui, Yasuteru Shigeta, Kimihiko HiraoPhysical Chemistry Chemical Physics 12 (4) 2010年[査読有り] Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNAToru Matsui, Hideaki Miyachi, Yasuyuki Nakanishi, Yasuteru Shigeta, Takeshi Sato, Yasutaka Kitagawa, Mitsutaka Okumura, Kimihiko HiraoJournal of Physical Chemistry B 113 (38) 2009年9月[査読有り] Sequence-dependent proton-transfer reaction in stacked GC pair II: The origin of stabilities of proton-transfer productsToru Matsui, Takeshi Sato, Yasuteru Shigeta, Kimihiko HiraoChemical Physics Letters 478 (4-6) 2009年8月[査読有り] Theoretical studies on magnetic interactions between Cu(II) ions in salen nucleobasesY. Nakanishi, Y. Kitagawa, Y. Shigeta, T. Saito, T. Matsui, H. Miyachi, T. Kawakami, M. Okumura, K. YamaguchiPolyhedron 28 (9-10) 2009年6月[査読有り] Theoretical studies on magnetic interactions between Cu(II) ions in hydroxypyridone nucleobasesY. Nakanishi, Y. Kitagawa, Y. Shigeta, T. Saito, T. Matsui, H. Miyachi, T. Kawakami, M. Okumura, K. YamaguchiPolyhedron 28 (9-10) 2009年6月[査読有り] Physics of nano-contact between Si quantum dots and inversion layerY. Sakurai, S. Nomura, Y. Takada, J. Iwata, K. Shiraishi, M. Muraguchi, T. Endoh, Y. Shigeta, M. Ikeda, K. Makihara, S. MiyazakiECS Transactions 25 (7) 2009年[査読有り] Effects of Hydrogen-Bonding Environments on Protonation States around the Entrance of Proton Transfer Pathways in Cytochrome c OxidaseKatsumasa Kamiya, Yasuteru Shigeta, Atsushi OshiyamaAIP Conference Proceedings 1102 2009年[査読有り] Quantum Theory in Terms of Cumulant VariablesYasuteru Shigeta, Hideaki Miyachi, Toru Matsui, Norisuke Yokoyama, Kimihiko HiraoADVANCES IN THE THEORY OF ATOMIC AND MOLECULAR SYSTEMS: DYNAMICS, SPECTROSCOPY, CLUSTERS, AND NANOSTRUCTURES 20 2009年[査読有り] Electronic structure and UV absorption spectra of metal-mediate DNA: an approach from theoretical chemistry.Toru Matsui, Hideaki Miyachi, Yasuyuki Nakanishi, Yasuteru Shigeta, Yasutaka Kitagawa, Mitsutaka Okumura, Kimihiko HiraoNucleic acids symposium series (2004) (53) 2009年[査読有り] Sequence dependent proton-transfer reaction in stacked gc pair I: The possibility of proton-transfer reactionsToru Matsui, Takeshi Sato, Yasuteru ShigetaInternational Journal of Quantum Chemistry 109 (10) 2009年[査読有り] Molecular theory including quantum effects and thermal fluctuationsYasuteru ShigetaBulletin of the Chemical Society of Japan 82 (11) 2009年[査読有り] Structural origin of copper Ion containing artificial DNA: A density functional studyToru Matsui, Hideaki Miyachi, Takeshi Sato, Yasuteru Shigeta, Kimihiko HiraoJournal of Physical Chemistry B 112 (51) 2008年12月[査読有り] Dynamic quantum isotope effects on multiple proton-transfer reactionsYasuteru Shigeta, Hideaki Miyachi, Toru Matsui, Kimihiko HiraoBulletin 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 fieldYasuteru ShigetaChemical Physics Letters 461 (4-6) 2008年8月[査読有り] 2P-065 タンパク質内環境下における新しいpKaの第一原理計算による提案(蛋白質・構造機能相関(2),第46回日本生物物理学会年会)Tanaka Tomonori, Kamiya Katsumasa, Shigeta Yasuteru, Shiraishi Kenji生物物理 48 2008年Single-Reference Methods for Excited States in Molecules and PolymersSo Hirata, Peng Dong Fan, Toru Shiozaki, Yasuteru ShigetaChallenges and Advances in Computational Chemistry and Physics 5 2008年[査読有り] Distribution function in quantal cumulant dynamicsYasuteru ShigetaJournal of Chemical Physics 128 (16) 2008年[査読有り] Quantal cumulant dynamics for dissipative systemsYasuteru ShigetaAIP Conference Proceedings 1046 2008年[査読有り] Correlation functions in quantized Hamilton dynamics and quantal cumulant dynamicsYuriy V. Pereverzev, Andrey Pereverzev, Yasuteru Shigeta, Oleg V. PrezhdoJournal of Chemical Physics 129 (14) 2008年[査読有り] Quantal cumulant dynamics II: An efficient time-reversible integratorYasuteru Shigeta, Hideaki Miyachi, Kimihiko HiraoChemical Physics Letters 443 (4-6) 2007年8月[査読有り] Multiple proton-transfer reactions in DNA base pairs by coordination of Pt complexToru Matsui, Yasuteru Shigeta, Kimihiko HiraoJournal of Physical Chemistry B 111 (5) 2007年2月[査読有り] Metal-assisted proton transfer reaction in base pairs.Toru Matsui, Yasuteru Shigeta, Kimihiko HiraoNucleic acids symposium series (2004) (51) 2007年[査読有り] Quantal cumulant dynamics for dissipative systemsYasuteru ShigetaAIP Conference Proceedings 963 (2) 2007年[査読有り] Real time mixed quantum-classical dynamics with ab initio quartic force field: Application to molecular vibrational frequency analysisHideaki Miyachi, Yasuteru Shigeta, Kimihiko HiraoChemical Physics Letters 432 (4-6) 2006年12月[査読有り] Influence of Pt complex binding on the guanine-cytosine pair: A theoretical studyToru Matsui, Yasuteru Shigeta, Kimihiko HiraoChemical Physics Letters 423 (4-6) 2006年6月[査読有り] Unidirectional electronic ring current driven by a few cycle circularly polarized laser pulse: Quantum model simulations for Mg-porphyrinIngo Barth, Jörn Manz, Yasuteru Shigeta, Kiyoshi YagiJournal of the American Chemical Society 128 (21) 2006年5月[査読有り] Exact-exchange time-dependent density-functional theory with the frequency-dependent kernelYasuteru Shigeta, Kimihiko Hirao, So HirataPhysical Review A - Atomic, Molecular, and Optical Physics 73 (1) 2006年[査読有り] Quantal cumulant dynamics: General theoryYasuteru Shigeta, Hideaki Miyachi, Kimihiko HiraoJournal of Chemical Physics 125 (24) 2006年[査読有り] Search for the ground states of ising spin clusters by using the genetic algorithmsAkifumi Oda, Hidemi Nagao, Yasutaka Kitagawa, Yasuteru Shigeta, Mitsuo Shoji, Hiroya Nitta, Mitsutaka Okumura, Kizashi YamaguchiInternational Journal of Quantum Chemistry 105 (6) 2005年12月[査読有り] Theoretical study of the mechanism of hydrogenation of side-on coordinated dinitrogen activated by Zr binuclear complexes ([(η5-C 5Me4H)2Zr]2(μ2, η2,η2η2-N2))Hideaki Miyachi, Yasuteru Shigeta, Kimihiko HiraoJournal of Physical Chemistry A 109 (39) 2005年10月[査読有り] Dynamic charge fluctuation of endohedral fullerene with coencapsulated Be atom and H 2Yasuteru Shigeta, Kazuo TakatsukaJournal of Chemical Physics 123 (13) 2005年10月[査読有り] 誌上セミナー 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小田 彰史, 北河 康隆, 重田 育照固体物理 40 (3) 2005年3月[査読有り] Optimized Effective Potential Method at Finite Temperature: An Application to SuperconductivityYasuteru ShigetaInternational Journal of Quantum Chemistry 101 (6) 2005年2月[査読有り] Internal motion of confined molecules in fullereneYasuteru ShigetaAIP Conference Proceedings 708 2004年4月[査読有り] Hybrid QM/MM Studies on Energetics of Malonaldehyde in Condensed PhaseYasuteru ShigetaInternational Journal of Quantum Chemistry 96 (1) 2004年1月[査読有り] Spin and pseudo spins in theoretical chemistry. A unified view for superposed and entangled quantum systemsK. Yamaguchi, M. Nakano, H. Nagao, M. Okumura, S. Yamanaka, T. Kawakami, D. Yamaki, M. Nishino, Y. Shigeta, Y. Kitagawa, Y. Takano, M. Takahata, R. TakedaBulletin of the Korean Chemical Society 24 (6) 2003年6月[査読有り] A QM/MM molecular dynamics study of a dynamical change in effective charge on Be atom in (Be+nH2)@C60Y. Shigeta, H. SaitoSynthetic Metals 135-136 2003年4月[査読有り] Models for double proton and electron transfer reactions: Analyses by means of quantum dynamicsY. Shigeta, H. Ushiyama, K. TakatsukaJournal of Molecular Structure 615 (1-3) 2002年9月[査読有り] Electron propagator calculations with Kohn-Sham reference statesY. Shigeta, A. M. Ferreira, V. G. Zakrzewski, J. V. OrtizInternational Journal of Quantum Chemistry 85 (4-5) 2001年11月[査読有り] Noncollinear spin density functional theory for spin-frustrated and spin-degenerate systemsS. Yamanaka, D. Yamaki, Y. Shigeta, H. Nagao, K. YamaguchiInternational Journal of Quantum Chemistry 84 (6) 2001年9月[査読有り] Electronic structure calculation by Monte Carlo diagonalization methodY. Shigeta, H. Nagao, K. YamaguchiInternational Journal of Quantum Chemistry 84 (5) 2001年9月[査読有り] Generalized spin orbital calculations of spin-frustrated moleculesD. Yamaki, Y. Shigeta, S. Yamanaka, H. Nagao, K. YamaguchiInternational Journal of Quantum Chemistry 84 (5) 2001年9月[査読有り] 3.0.co;2-c" target="_blank">Generalized spin density functional theory for non-collinear molecular magnetismYAMANAKA S, YAMAKI D, SHIGETA Y, NAGAO H, YOSHIOKA Y, SUZUKI N, YAMAGUCHI KInt. J. Quantum. Chem. 80 (4-5) 2001年9月[査読有り] Non-Born-Oppenheimer density functional theory for excited states by using Green's function techniquesT. Yoshimoto, Y. Ohta, J. Maki, Y. Shigeta, H. Nagao, K. NishikawaInternational Journal of Quantum Chemistry 84 (3) 2001年8月[査読有り] Generalized spin orbital GW theory for spin-frustrated and spin-degenerate systemsS. Yamanaka, Y. Shigeta, Y. Ohta, D. Yamaki, H. Nagao, K. YamaguchiInternational Journal of Quantum Chemistry 84 (3) 2001年8月[査読有り] Calculation of quasiparticle energy of molecular systems by the GW methodY. Ohta, J. Maki, T. Yoshimoto, Y. Shigeta, H. Nagao, K. NishikawaInternational Journal of Quantum Chemistry 84 (3) 2001年8月[査読有り] A theoretical study on conductivity of model polymer including DNA base pairsY. Shigeta, H. Nagao, Y. Yoshioka, J. Toyoda, Y. Morita, K. Nakasuji, K. YamaguchiSynthetic Metals 119 (1-3) 2001年3月[査読有り] Theoretical study on triplet superconducting phase and other phases in hole-doped ferromagnetic systemsH. Nagao, Y. Shigeta, K. Yamaguchi, K. NishikawaSynthetic Metals 121 (1-3) 2001年3月[査読有り] Theoretical studies on the proton and electron transfer (PET) in a pseudo one-dimensional hydrogen bonded network systemY. Shigeta, Y. Kitagawa, H. Nagao, Y. Yoshioka, J. Toyoda, K. Nakasuji, K. YamaguchiJournal of Molecular Liquids 90 (1-3) 2001年2月[査読有り] Quantum spin dynamics in solution applicable to quantum computingH. Nagao, K. Kinugawa, Y. Shigeta, K. Ohta, K. YamaguchiJournal of Molecular Liquids 90 (1-3) 2001年2月[査読有り] Theoretical studies on anomalous phases of photodoped systems in two-band modelHidemi Nagao, Masamichi Nishino, Yasuteru Shigeta, Yasunori Yoshioka, Kizashi YamaguchiJournal of Chemical Physics 113 (24) 2000年12月[査読有り] 3.0.co;2-w" target="_blank">Theoretical study on dependency of conductivity on structure of the proton and electron coupled systemSHIGETA Y, NAGAO H, TOYODA J, MORITA Y, NAKASUJI K, YOSHIOKA Y, YAMAGUCHI KInt. J. Quantum. Chem. 80 (4-5) 2000年10月[査読有り] MP2, Tamm-Dancoff, and RPA methods based on the generalized HF solutionYamaki D, Shigeta Y, Yamanaka S, Nagao H, Yamaguchi KINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 80 (4-5) 2000年10月[査読有り] 3.0.co;2-y" target="_blank">Theoretical studies on superconducting and other phases: Triplet superconductivity, ferromagnetism, and ferromagnetic metalNagao H, Nishino M, Shigeta Y, Yoshioka Y, Yamaguchi KINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 80 (4-5) 2000年10月[査読有り] Theoretical studies on magnetic behavior in clusters by the genetic algorithmsAkifumi Oda, Hidemi Nagao, Yasutaka Kitagawa, Yasuteru Shigeta, Kizashi YamaguchiInternational Journal of Quantum Chemistry 80 (4-5) 2000年10月[査読有り] Ab initio computations of effective exchange integrals for H–H, H–He–H and Mn2O2 complex: comparison of broken-symmetry approachesTomohisa Soda, Yasutaka Kitagawa, Taku Onishi, Yu Takano, Yasuteru Shigeta, Hidemi Nagao, Yasunori Yoshioka, Kizashi YamaguchiChemical Physics Letters 319 (3-4) 2000年3月[査読有り] Generalized spin-density functional calculation for the spin frustrated systemsS Yamanaka, D Yamaki, Y Shigeta, H Nagao, Y Yoshioka, K Yamaguchi, N SuzukiMOLECULAR CRYSTALS AND LIQUID CRYSTALS 343 2000年Generalized spin-density functional calculation for the spin frustrated systemsS. Yamanaka, D. Yamaki, Y. Shigeta, H. Nagao, Y. Yoshioka, K. Yamaguchi, N. SuzukiMolecular Crystals and Liquid Crystals Science and Technology Section A: Molecular Crystals and Liquid Crystals 343 2000年[査読有り] Exciton condensate in model dendrimersHidemi Nagao, Masayoshi Nakano, Koji Ohta, Yasuteru Shigeta, Shinji Kiribayashi, Yasunori Yoshioka, Kizashi YamaguchiMolecular Crystals and Liquid Crystals Science and Technology Section A: Molecular Crystals and Liquid Crystals 342 2000年[査読有り] Quantum spin dynamics by path integral centroid molecular dynamics methodYasuteru Shigeta, Kenichi Kinugawa, Hidemi Nagao, Koji Ohta, Kizashi YamaguchiProgress of Theoretical Physics Supplement (138) 2000年[査読有り] Theoretical studies on effective spin interactions, spin alignments and macroscopic spin tunneling in polynuclear manganese and related complexes and their mesoscopic clustersH. Nagao, M. Nishino, Y. Shigeta, T. Soda, Y. Kitagawa, T. Onishi, Y. Yoshioka, K. YamaguchiCoordination Chemistry Reviews 198 (1) 2000年Theoretical studies on quantum tunneling of spins in cluster of clustersYasuteru Shigeta, Hidemi Nagao, Yasunori Yoshioka, Kizashi YamaguchiMolecular Crystals and Liquid Crystals Science and Technology Section A: Molecular Crystals and Liquid Crystals 342 2000年[査読有り] A theoretical study of spin level crossing induced by an external magnetic field of ring molecule magnet modelsY. Shigeta, T. Kawakami, H. Nagao, K. YamaguchiChemical Physics Letters 315 (5-6) 1999年12月[査読有り] A formulation and numerical approach to molecular systems by the Green function method without the Born-Oppenheimer approximationYasuteru Shigeta, Hidemi Nagao, Kiyoshi Nishikawa, Kizashi YamaguchiJournal of Chemical Physics 111 (14) 1999年10月[査読有り] Theoretical studies on anomalous phases in model plane systems of LiBeH3H. Nagao, H. Kawabe, Y. Shigeta, M. Nishino, M. Mitani, K. YamaguchiSynthetic Metals 103 (1-3) 1999年6月[査読有り] Theoretical studies of magnetization by ab initio path integral methodY. Shigeta, T. Kawakami, H. Nagao, K. YamaguchiSynthetic Metals 103 (1-3) 1999年6月[査読有り] Theoretical study on polarizability of ethylene by path integral methodY. Shigeta, S. Yamada, H. Nagao, M. Nakano, K. Ohta, K. YamaguchiSynthetic Metals 101 (1) 1999年5月[査読有り] Quantum phase dynamics of interaction between photon field and magnetic system: Effects of magnetic quantum tunnellingHidemi Nagao, Masayoshi Nakano, Yasuteru Shigeta, Kizashi YamaguchiOptical Review 6 (3) 1999年[査読有り] 3.0.CO;2-1" target="_blank">Theoretical Studies on Anomalous Phases in Molecular Systems with External Field: Possibility of Photo-Induced SuperconductivityHidemi Nagao, Masaki Mitani, Masamichi Nishino, Yasuteru Shigeta, Yasunori Yoshioka, Kizashi YamaguchiInternational Journal of Quantum Chemistry 75 (4-5) 1999年[査読有り] 3.0.CO;2-L" target="_blank">Density functional theory without the born-oppenheimer approximation. II. Green function techniquesY. Shigeta, H. Nagao, K. Nishikawa, K. YamaguchiInternational Journal of Quantum Chemistry 75 (4-5) 1999年[査読有り] 3.0.CO;2-X" target="_blank">Nonadiabatic molecular theory and its application. II. Water moleculeY. Shigeta, Y. Ozaki, K. Kodama, H. Nagao, H. Kawabe, K. NishikawaInternational Journal of Quantum Chemistry 69 (5) 1998年[査読有り] 3.0.co;2-0" target="_blank">Possibility of charge-mediated superconductors in the intermediate region of metal-insulator transitionsHidemi Nagao, Masaki Mitani, Masamichi Nishino, Yasuteru Shigeta, Yasunori Yoshioka, Kizashi YamaguchiInternational Journal of Quantum Chemistry 70 (4-5) 1998年[査読有り] 3.0.co;2-y" target="_blank">Density functional theory without the Born-Oppenheimer approximation and its applicationY. Shigeta, H. Takahashi, S. Yamanaka, M. Mitani, H. Nagao, K. YamaguchiInternational Journal of Quantum Chemistry 70 (4-5) 1998年[査読有り] Path integral method by means of generalized coherent states and its numerical approach to molecular systems .1. Ensemble average of total energyH Nagao, Y Shigeta, H Kawabe, T Kawakami, K Nishikawa, K YamaguchiJOURNAL OF CHEMICAL PHYSICS 107 (16) 1997年10月[査読有り] 3.0.CO;2-8" target="_blank">Many-electron-wavepackets methodH. Nagao, M. Nakano, S. Yamanaka, S. Yamada, D. Yamaki, I. Shigemoto, S. Kiribayashi, K. Yamaguchi, Y. ShigetaInternational Journal of Quantum Chemistry 60 (7) 1996年12月[査読有り] 3.0.CO;2-X" target="_blank">Nonadiabatic treatment of molecular systems by the wavepackets methodH. Nagao, K. Kodama, Y. Shigeta, K. Nishikawa, H. Kawabe, M. Nakano, K. YamaguchiInternational Journal of Quantum Chemistry 60 (7) 1996年12月[査読有り] 受賞▼▲2023年9月日本分子科学会 第８回分子科学国際学術賞 溶液および固体における光アップコンバージョン機構の理論解析 2019年2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3月Royal Chemical Society Outstanding Reviewers for Physical Chemistry Chemical Physics in 2016 論文査読 2013年5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9月分子科学会 第5回分子科学会奨励賞 研究業績 2010年4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3月日本化学会 第58回日本化学会進歩賞 研究業績 2007年3月Royal Chemical Society PCCP Prize for the Outstanding Achievement of Young Scientists in Physical Chemistry and Chemical Physics Research Award 2006年3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▼▲Hydrogenomics: The Science of Fully Utilizing HydrogenHori, Yuta, Nishikawa, Koji, Shigeta, Yasuteru, Higuchi, Yoshiki (範囲:Biological Enzymes and Hydrogenases)Recent advances of the fragment molecular orbital method Subtitle: Enhanced performance and applicabilityShigeta, Yasuteru (担当:分担執筆, 範囲:AnalysisFMO toolkit: PyMOL plugin module to 3D-visualize interaction energies in protein (3D-VIEP) generated by fragment molecular orbital calculation)Recent advances of the fragment molecular orbital method Subtitle: Enhanced performance and applicabilityShigeta, Yasuteru (担当:分担執筆, 範囲:AnalysisFMO toolkit: PyMOL plugin module to 3D-visualize interaction energies in protein (3D-VIEP) generated by fragment molecular orbital calculation)Advances in Quantum ChemistryShigeta, Yasuteru, Harada, Ryuhei (担当:分担執筆, 範囲:Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules)Quantum Systems in Physics, Chemistry, and Biology: Advances in Concepts and ApplicationsBaba, Takeshi, Kamiya, Katsumasa, Shigeta, Yasuteru (担当:分担執筆, 範囲:Integrated Computational Studies on Mutational Effects of A Nylon-degrading Enzyme)Reference modules in Materials Science and Engineering 2016Harada, Ryuhei, Inagaki, Yuji, Shigeta, Yasuteru (担当:分担執筆, 範囲: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, 範囲:第4-1章 錯体の伝導性)Quantum mechanics Chap. 17Shigeta,Yasuteru (担当:分担執筆, 範囲:Quantal Cumulant Mechanics as Extended Ehrenfest Theorem)Conceptual and Computational Advances in Quantum Chemistry, Chap. 25Shigeta,Yasuteru (担当:分担執筆, 範囲: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. 21Shigeta,Yasuteru (担当:分担執筆, 範囲:Quantum Theory in Terms of Cumulant Variables)ADVANCES IN THE THEORY OF ATOMIC AND MOLECULAR SYSTEMS: DYNAMICS, SPECTROSCOPY, CLUSTERS, AND NANOSTRUCTURESShigeta, Yasuteru, Miyachi, Hideaki, Matsui, Toru, Yokoyama, Norisuke, Hirao, Kimihiko (担当:分担執筆, 範囲:Quantum Theory in Terms of Cumulant Variables)Challenges and Advances in Computational Chemistry and Physics, Chap. 2Shigeta,Yasuteru (担当:分担執筆, 範囲: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, 範囲:第１３、１４章)競争的資金等の研究課題▼▲量子生命技術の創製と医学・生命科学の革新光・量子飛躍フラッグシッププログラム（Q-LEAP）研究期間: 2020年9月 - 2030年3月代表者: 馬場嘉信メゾヒエラルキーの学理構築科学研究費助成事業研究期間: 2023年4月 - 2028年3月代表者: 矢貝 史樹, 雲林院 宏, VACHA Martin, 相良 剛光, 羽會部 卓, 原野 幸治, 重田 育照メゾヒエラルキー理論科学研究費助成事業研究期間: 2023年4月 - 2028年3月代表者: 重田 育照, 藤田 貴敏, 満田 祐樹クライオ電顕による１分子構造解析に基づいた蛋白質構造の連続的なダイナミクスの解析科学研究費助成事業研究期間: 2023年4月 - 2026年3月代表者: 守屋 俊夫, 重田 育照, 村田 武士3D ドメインスワッピングを利用したタンパク質の自在配列と機能化戦略的創造研究推進事業研究期間: 2020年12月 - 2026年3月代表者: 廣田俊チトクロム C オキシダーゼを標的としたミトコンドリア病の新規治療薬開発難治性疾患実用化研究事業研究期間: 2021年4月 - 2024年3月代表者: 新谷泰範加齢ミトコンドリアDNA説における金属タンパク質動態に関する理論的研究文部科学省/新学術領域研究（研究領域提案型）研究期間: 2022年4月 - 2023年3月代表者: 重田育照生命金属動体解明のための量子生体エネルギー論新学術領域研究(研究領域提案型)研究期間: 2020年4月 - 2022年3月代表者: 重田育照生体ハイドロジェノミクスの理論解析科学研究費助成事業 新学術領域研究(研究領域提案型)研究期間: 2019年4月 - 2021年3月代表者: 重田 育照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6月 - 2021年3月代表者: 前仲勝実国際連携による高次複合光応答系の高度化とネットワーク形成科学研究費助成事業 新学術領域研究(研究領域提案型)研究期間: 2015年11月 - 2019年3月代表者: 宮坂 博, 河合 壯, 阿部 二朗, 松田 建児, 内田 欣吾, 重田 育照, 玉井 尚登, 前田 大光, 横山 泰, 朝日 剛, 井村 考平, 小畠 誠也, VACHA Martin分子シミュレーションによる生体活性サイトの構造・機能相関の解明とデザイン科学研究費助成事業 新学術領域研究(研究領域提案型)研究期間: 2014年7月 - 2019年3月代表者: 鷹野 優, 石北 央, 兼松 佑典, 米澤 康滋, 齋藤 徹, 重田 育照, 神谷 克政, 庄司 光男, 近藤 寛子理論と実験の協奏的アプローチによる複合スピン励起子変換制御科学研究費助成事業 新学術領域研究(研究領域提案型)研究期間: 2014年7月 - 2019年3月代表者: 重田 育照, 鎌田 賢司, 北河 康隆, 岸 亮平, 中野 雅由, 溝黒 登志子, 藤本 和宏高次複合光応答分子システムの開拓と学理の構築科学研究費助成事業 新学術領域研究(研究領域提案型)研究期間: 2014年7月 - 2019年3月代表者: 宮坂 博, 小畠 誠也, 朝日 剛, 河合 壯, VACHA Martin, 横山 泰, 玉井 尚登, 阿部 二朗, 内田 欣吾, 松田 建児, 井村 考平, 重田 育照, 前田 大光ナイロン加水分解酵素の分子設計と産業応用への基盤研究科学研究費助成事業 基盤研究(B)研究期間: 2014年4月 - 2019年3月代表者: 根来 誠司, 武尾 正弘, 加藤 太一郎, 樋口 芳樹, 柴田 直樹, 重田 育照, 後藤 祐児, 永井 圭介, 竹原 一起ポスト「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4月 - 2019年3月代表者: 押山淳機能性可視化剤としての柔軟な発光分子の開発とマテリアルイメージング技術の確立科学研究費助成事業 若手研究(A)研究期間: 2015年4月 - 2018年3月代表者: 齊藤 尚平, 藪 浩, 宮坂 博, 五月女 光, 坂本 章, 岡島 元, 松本 吉泰, 渡邊 一也, 大坪 主弥, 羽田 真毅, 恩田 健, 重田 育照, 佐藤 竜馬, 信末 俊平, 関 隆広, 原 光生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助成事業 挑戦的萌芽研究研究期間: 2015年4月 - 2017年3月代表者: 岡野 泰則, 清水 一憲, 重田 育照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科学研究費助成事業 新学術領域研究(研究領域提案型)研究期間: 2014年4月 - 2015年3月代表者: 重田 育照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科学研究費助成事業 新学術領域研究(研究領域提案型)研究期間: 2013年4月 - 2015年3月代表者: 重田 育照ナノ構造形成・新機能発現における電子論ダイナミクス科学研究費助成事業 新学術領域研究(研究領域提案型)研究期間: 2010年4月 - 2015年3月代表者: 押山 淳, 宮崎 剛, 土田 英二, 尾崎 泰助, 岩田 潤一, 内田 和之, 重田 育照, 岩田 潤一ナイロンオリゴマー分解酵素（ＮｙｌＡＢＣ）の分子設計と物質生産への応用科学研究費助成事業 基盤研究(B)研究期間: 2010年4月 - 2014年3月代表者: 根来 誠司, 武尾 正弘, 加藤 太一郎, 樋口 芳樹, 柴田 直樹, 後藤 祐児, 池上 貴久, 重田 育照, 神谷 克政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助成事業 若手研究(A)研究期間: 2010年4月 - 2014年3月代表者: 重田 育照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4月 - 2012年3月代表者: 重田育照電子ダイナミクスによる電子集団運動の解析科学研究費助成事業 特定領域研究研究期間: 2008年 - 2009年代表者: 重田 育照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科学研究費助成事業 若手研究(B)研究期間: 2008年 - 2009年代表者: 重田 育照量子ハイブリッド分子動力学法による生体機能の量子デザイン科学研究費助成事業 特定領域研究研究期間: 2007年 - 2008年代表者: 舘野 賢, 濡木 理, 重田 育照電子ダイナミクスに基づく生体分子触媒反応のシミュレーション科学研究費助成事業 基盤研究(B)研究期間: 2007年 - 2008年代表者: BOERO Mauro, 舘野 賢, 重田 育照タンパク質超分子中のプロトン移動機構の電子レベルでの解明科学研究費助成事業 特定領域研究研究期間: 2006年 - 2007年代表者: BOERO Mauro, 白石 賢二, 舘野 賢, 重田 育照凝縮相および生体内における電子・水素移動の協同現象に対する理論的研究科学研究費助成事業 特別研究員奨励費研究期間: 2001年 - 2003年代表者: 重田 育照電子-核密度汎関数理論の構築と量子ダイナミクスへの展開科学研究費助成事業 特別研究員奨励費研究期間: 1999年 - 2000年代表者: 重田 育照 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 教授 研究テーマ 生体酵素反応の理論解析 関連リンク TRIOS researchmap Email mshojiccs.tsukuba.ac.jp 研究キーワード▼▲分子磁性多核金属錯体生物無機化学反応機構の理論解明酵素反応経歴2019年10月 - 2023年3月JST さきがけ 研究員（兼任） 論文▼▲A new small molecule DoNA binding to CAG repeat RNAChen, Qingwen, Yamada, Takeshi, Miyagawa, Koichi, Murata, Asako, Shoji, Mitsuo, Nakatani, KazuhikoBioorganic & medicinal chemistry 98 2024年1月[査読有り] Theoretical elucidation of the structure, bonding, and reactivity of the CaMn4Ox clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formationYamaguchi, Kizashi, Miyagawa, Koichi, Shoji, Mitsuo, Kawakami, Takashi, Isobe, Hiroshi, Yamanaka, Shusuke, Nakajima, TakahitoPHOTOSYNTHESIS RESEARCH Epub 2023年11月[査読有り] The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum ComputationsYamaguchi, Kizashi, Isobe, Hiroshi, Shoji, Mitsuo, Kawakami, Takashi, Miyagawa, KoichiMOLECULES 28 (20) 2023年10月[査読有り] Origin of Homochirality in Amino Acids Induced by Lyman-&＃x3b1; Irradiation in the Early Stage of the Milky WaySato, Akimasa, Shoji, Mitsuo, Watanabe, Natsuki, Boero, Mauro, Shigeta, Yasuteru, Umemura, MasayukiAstrobiology 23 (10) 2023年10月[査読有り] Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone CofactorTakeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Naomine Yano, Katsuhiro Kusaka, Yoshiaki Kawano, Mamoru Suzuki, Yasuteru Shigeta, Takato Yano, Motoyasu Adachi, Katsuyuki Tanizawa, Toshihide OkajimaACS Catalysis 2023年9月Enantioselective Amino Acid interactions in SolutionWatanabe, Natsuki, Shoji, Mitsuo, Miyagawa, Koichi, Hori, Yuta, Boero, Mauro, Umemura, Masayuki, Shigeta, YasuteruPHYSICAL CHEMISTRY CHEMICAL PHYSICS 25 (21) 2023年5月[査読有り] Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino AcidsMitsuo Shoji, Yuya Kitazawa, Akimasa Sato, Natsuki Watanabe, Mauro Boero, Yasuteru Shigeta, Masayuki UmemuraThe Journal of Physical Chemistry Letters 2023年4月Organocatalytic-racemization reaction elucidation of aspartic acid by density functional theoryWatanabe, Natsuki, Hori, Yuta, Shoji, Mitsuo, Boero, Mauro, Shigeta, YasuteruCHIRALITY 35 (9) 2023年4月[査読有り] Biological advantage of the arrangements of C-phycocyanin chromophores in phycobilisome from the electronic energy transfer viewpointMishima, Kenji, Shoji, Mitsuo, Umena, Yasufumi, Shigeta, YasuteruBULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 96 (4) 2023年4月[査読有り] 有機分子触媒を用いたアミノ酸ラセミ化反応の理論的研究渡辺, 七都稀, 堀, 優太, 庄司, 光男, 重田, 育照The Journal of Computer Chemistry, Japan 21 (4) 2023年3月[査読有り] Specific zinc binding to heliorhodopsinMasanori Hashimoto, Koichi Miyagawa, Manish Singh, Kota Katayama, Mitsuo Shoji, Yuji Furutani, Yasuteru Shigeta, Hideki KandoriPhysical Chemistry Chemical Physics 25 (4) 2023年Elucidation of a multiple S3 intermediates model for water oxidation in the oxygen evolving complex of photosystem II. Calcium-assisted concerted O-O bond formationK. Yamaguchi, K. Miyagawa, M. Shoji, H. Isobe, T. KawakamiChem. Phys. Lett. 806 2022年9月[査読有り] Roles of the Flexible Primary Coordination Sphere of the Mn4CaOx Cluster: What Are the Immediate Decay Products of the S-3 State?Isobe, Hiroshi, Shoji, Mitsuo, Suzuki, Takayoshi, Shen, Jian-Ren, Yamaguchi, KizashiJOURNAL OF PHYSICAL CHEMISTRY B Epub 2022年9月[査読有り] Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidaseMitsuo Shoji, Takeshi Murakawa, Shota Nakanishi, Mauro Boero, Yasuteru Shigeta, Hideyuki Hayashi, Toshihide OkajimaCHEMICAL SCIENCE 13 (36) 2022年9月Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic SynthesesMitsuo, Shoji, Natsuki, Watanabe, Hori, Yuta, Kenji, Furuya, Masayuki, Umemura, Mauro, Boero, Yasuteru, ShigetaASTROBIOLOGY 22 (9) 2022年9月[査読有り] Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in SpaceHori, Yuta, Nakamura, Honami, Sakawa, Takahide, Natsuki, Watanabe, Kayanuma, Megumi, Mitsuo, Shoji, Masayuki, Umemura, Yasuteru, ShigetaASTROBIOLOGY 22 (11) 2022年9月[査読有り] Heme-bound tyrosine vibrations in hemoglobin M: Resonance Raman, crystallography, and DFT calculationNagatomo, Shigenori, Shoji, Mitsuo, Terada, Takuto, Nakatani, Kiyoharu, Shigeta, Yasuteru, Hirota, Shun, Yanagisawa, Sachiko, Kubo, Minoru, Kitagawa, Teizo, Nagai, Masako, Ohki, Mio, Park, Sam-Yong, Shibayama, NaoyaBiophysical Journal 121 (14) 2022年6月[査読有り] Relative energies among S3 intermediates in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Possible pathways of water insertion in the S2 to S3 transitionK. Miyagawa, M. Shoji, H. Isobe, T. Kawakami, T. Nakajima, K. YamaguchiChem. Phys. Lett. 793 2022年2月[査読有り] Relative energies among proton-shifted S2 isomers in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Proton transfer coupled spin transitions of the CaMn4Ox cluster in OEC of PSIIMiyagawa, Koichi, Shoji, Mitsuo, Isobe, Hiroshi, Kawakami, Takashi, Nakajima, Takahito, Yamaguchi, KizashiChemical Physics Letters 790 2022年1月[査読有り] Mechanism of Water Oxidation in Photosynthesis Elucidated by Interplay Between Experiment and TheoryK. Yamaguchi, S. Yamanaka, H. Isobe, M. Shoji, T. Kawakami, K. MiyagawaAdvances in Photosynthesis and Respiration 47 2021年9月[査読有り] pyProGA-A PyMOL plugin for protein residue network analysisSladek, Vladimir, Yamamoto, Yuta, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru, Sladek, VladimirPLOS ONE 16 (7) 2021年7月[査読有り] Isolobal and isospin analogy between organic and inorganic open-shell molecules Application to oxygenation reactions by active oxygen and oxy-radicals and water oxidation in the native and artificial photosynthesisK. Yamaguchi, K. Miyagawa, H. Isobe, M. Shoji, T. Kawakami, S. YamanakaAdvances in Quantum Chemistry 84 2021年4月[査読有り] Estimation of the relative contributions to the electronic energy transfer rates based on Forster theory: The case of C-phycocyanin chromophoresMishima, Kenji, Shoji, Mitsuo, Umena, Yasufumi, Boero, Mauro, Shigeta, YasuteruBiophysics and physicobiology 18 2021年[査読有り] Exploring reaction pathways for the structural rearrangements of the Mn cluster induced by water binding in the S-3 state of the oxygen evolving complex of photosystem IIIsobe, Hiroshi, Shoji, Mitsuo, Suzuki, Takayoshi, Shen, Jian-Ren, Yamaguchi, KizashiJOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 405 2021年1月[査読有り] A three states model for hydrogen abstraction reactions with the cytochrome P450 compound I is revisited. Isolobal and isospin analogy among Fe(IV)=O, O = O and OMiyagawa, Koichi, Isobe, Hiroshi, Shoji, Mitsuo, Kawakami, Takashi, Yamanaka, Shusuke, Yamaguchi, KizashiJOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 405 2021年1月[査読有り] Role of the Propionic Acid Side-Chain of C-Phycocyanin Chromophores in the Excited States for the Photosynthesis ProcessKenji Mishima, Mitsuo Shoji, Yasufumi Umena, Mauro Boero, Yasuteru ShigetaBulletin of the Chemical Society of Japan 93 (12) 2020年12月[査読有り] Weak O2 binding and strong H2O2 binding at the non-heme diiron center of trypanosome alternative oxidaseSotaro Yamasaki, Mitsuo Shoji, Megumi Kayanuma, Vladimir Sladek, Daniel Ken Inaoka, Yuichi Matsuo, Tomoo Shiba, Luke Young, Anthony L. Moore, Kiyoshi Kita, Yasuteru ShigetaBiochimica et Biophysica Acta (BBA) - Bioenergetics 1862 (4) 2020年12月[査読有り] Electronic and spin structures of CaMn4Ox clusters in the S0 state of the oxygen evolving complex of photosystem II. Domain-based local pair natural orbital (DLPNO) coupled-cluster (CC) calculations using optimized geometries and natural orbitals (UNO) by hybrid density functional theory (HDFT) calculationsMiyagawa, K, Yamanaka, S, Isobe, H, Shoji, Mitsuo, Kawakami, T, Taniguchi, M, Okumura, M, Yamaguchi, KPhysical Chemistry Chemical Physics 46 (22) 2020年10月[査読有り] Unique protonation states of aspartate and topaquinone in the active site of copper amine oxidaseMitsuo Shoji, Takeshi Murakawa, Mauro Boero, Yasuteru Shigeta, Hideyuki Hayashi, Toshihide OkajimaRSC Advances 10 (63) 2020年10月[査読有り] Relative stability among intermediate structures in S2 state of CaMn4O5 cluster in PSII by using hybrid-DFT and DLPNO-CC methods and evaluation of magnetic interactions between Mn ionsShoji,MitsuoJournal of Photochemistry and Photobiology A: Chemistry 405 2020年9月[査読有り] Development of broken-symmetry (BS) methods in chemical reactions. A theoretical view of water oxidation in photosystem II and related systemsYamaguchi, Kizashi, Isobe, Hiroshi, Shoji, Mitsuo, Miyagawa, Koichi, Yamanaka, Shusuke, Kawakami, Takashi, Nakajima, TakahitoJ. Photochem. Photobiol. A 402 (112791) 2020年7月[査読有り] Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.Takeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Chie Shibazaki, Tomoko Sunami, Taro Tamada, Naomine Yano, Taro Yamada, Katsuhiro Kusaka, Mamoru Suzuki, Yasuteru Shigeta, Ryota Kuroki, Hideyuki Hayashi, Takato Yano, Katsuyuki Tanizawa, Motoyasu Adachi, Toshihide OkajimaProceedings of the National Academy of Sciences of the United States of America 117 (20) 2020年5月[査読有り] Theory of chemical bonds in metalloenzymes XXIV electronic and spin structures of FeMoco and Fe-S clusters by classical and quantum computingMiyagawa, K, Shoji, Mitsuo, Isobe, H, Yamanaka, S, Kawakami, T, Okumura, M, Yamaguchi, KMolecular Physics 118 (21-22) 2020年5月[査読有り] UNO(ULO) active space for multireference calculations on classical and quantum computers. Revisit to the iron-sulfur complexesKoichi Miyagawa, Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Takashi Kawakami, Mitsutaka Okumura, Kizashi YamaguchiChemical Physics Letters 746 2020年5月[査読有り] Reaction Mechanism of Monomeric Sarcosine Oxidase with N-CyclopropylglycineShoji, Mitsuo, Abe, Y, Boero, M, Shigeta, Y, Y., NishidaPhysical Chemistry Chemical Physics 22 (29) 2020年5月[査読有り] Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active site.Yasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki HayashiJournal of biochemistry 167 (4) 2020年4月[査読有り] Theory of chemical bonds in metalloenzymes XXIII Fundamental principles for the photo-induced water oxidation in oxygen evolving complex of photosystem IIK. Yamaguchi, S. Yamanaka, H. Isobe, M. Shoji, K. Miyagawa, T. KawakamiMol. Phys. - 2020年2月[査読有り] Domain-based local pair natural orbital CCSD(T) calculations of fourteen different S2 intermediates for water oxidation in the Kok cycle of OEC of PSII. Re-visit to one LS-two HS model for the S2 stateK. Miyagawa, H. Isobe, T. Kawakami, M. Shoji, S. Yamanaka, M. Okumura, T. Nakajima, K. YamaguchiChemical Physics Letters 734 2019年11月[査読有り] Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: Implications into the proton transfer at the active siteMachida, Yasuhiro, Murakawa, Takeshi, Sakai, Akiko, Shoji, Mitsuo, Shigeta, Yasuteru, Hayashi, HideyukiJournal of biochemistry 167 (4) 2019年11月[査読有り] Domain-based local pair natural orbital CCSD (T) calculations of six different S1 structures of oxygen evolving complex of photosystem II. Proposal of multi-intermediate models for the S1 stateShoji, MitsuoChemical Physics Letters 732 2019年10月[査読有り] Domain-based local pair natural orbital CCSD (T) calculations of strongly correlated electron systems: Examination of dynamic equilibrium models based on multiple intermediates in S1 state of photosystem II庄司,光男Molecular Physics 2019年9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 crystallographyShoji, Mitsuo, Isobe, Hiroshi, Shen, Jian-Ren, Suga, Michihiro, Akita, Fusamichi, Miyagawa, Koichi, Shigeta, Yasuteru, Yamaguchi, KizashiCHEMICAL PHYSICS LETTERS 730 2019年9月[査読有り] First-Principles Study of the Reaction Mechanism of CHO plus H on Graphene SurfaceKayanuma Megumi, Shoji Mitsuo, Furuya Kenji, Kamiya Katsumasa, Aikawa Yuri, Umemura Masayuki, Shigeta YasuteruJOURNAL OF PHYSICAL CHEMISTRY A 123 (26) 2019年7月[査読有り] Reaction mechanism of non-enzymatic stereoselective formation of wine lactoneKyan, Akane, Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, YasuteruCHEMICAL PHYSICS LETTERS 725 2019年6月[査読有り] First-Principles Study of the Reaction Mechanism of CHO + H on Graphene SurfaceKayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Kamiya, Katsumasa, Aikawa, Yuri, Umemura, Masayuki, Shigeta, YasuteruThe Journal of Physical Chemistry A 123 (26) 2019年6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 IntermediateKayanuma Megumi, Shoji Mitsuo, Shigeta YasuteruJOURNAL OF PHYSICAL CHEMISTRY A 123 (13) 2019年4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 CooperativityIsobe, Hiroshi, Shoji, Mitsuo, Suzuki, Takayoshi, Shen, Jian-Ren, Yamaguchi, KizashiJournal of chemical theory and computation 15 (4) 2019年4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 IntermediateKayanuma, Megumi, Shoji, Mitsuo, Shigeta, YasuteruThe journal of physical chemistry. A 123 (13) 2019年3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 IIYamaguchi, Kizashi, Yamanaka, Shusuke, Isobe, Hiroshi, Shoji, Mitsuo, Miyagawa, Kouichi, Nakajima, Takahito, Kawakami, Takashi, Okumura, MitsutakaPhysiologia plantarum 166 (1:::SI) 2019年3月[査読有り] Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics StudyKimatsuka, Masato, Sato, Ryuma, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, YasuteruCHEMISTRY LETTERS 48 (3) 2019年3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3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 calculationsShoji, Mitsuo, Isobe, Hiroshi, Miyagawa, Koichi, Yamaguchi, KizashiCHEMICAL PHYSICS 518 2019年2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 modelKawakami Takashi, Miyagawa Koichi, Sharma Sandeep, Saito Toru, Shoji Mitsuo, Yamada Satoru, Yamanaka Shusuke, Okumura Mitsutaka, Nakajima Takahito, Yamaguchi KizashiJOURNAL OF COMPUTATIONAL CHEMISTRY 40 (2) 2019年1月[査読有り] Structural Changes in the Trinuclear Copper Center upon the Reduction of Bilirubin Oxidase (BOD)T. Tokiwa, M. Shoji, V. Sladek, N. Shibata, Y. Higuchi, K. Kataoka, Y. Shigeta, F MisaizuMolecules 24 (76) 2019年1月[査読有り] Theoretical study of the photodissociation reaction of methanolKayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Aikawa, Yuri, Umemura, Masayuki, Shigeta, YasuteruCHEMICAL PHYSICS LETTERS 714 2019年1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 IIShoji, Mitsuo, Isobe, Hiroshi, Yamaguchi, KizashiCHEMICAL PHYSICS LETTERS 714 2019年1月[査読有り] Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction.Takaki Tokiwa, Mitsuo Shoji, Vladimir Sladek, Naoki Shibata, Yoshiki Higuchi, Kunishige Kataoka, Takeshi Sakurai, Yasuteru Shigeta, Fuminori MisaizuMolecules (Basel, Switzerland) 24 (1) 2018年12月[査読有り] Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase.Mahfuza Akter, Takaki Tokiwa, Mitsuo Shoji, Koji Nishikawa, Yasuteru Shigeta, Takeshi Sakurai, Yoshiki Higuchi, Kunishige Kataoka, Naoki ShibataChemistry (Weinheim an der Bergstrasse, Germany) 24 (68) 2018年12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 IIYamaguchi, Kizashi, Shoji, Mitsuo, Isobe, Hiroshi, Yamanaka, Shusuke, Kawakami, Takashi, Yamada, Satoru, Katouda, Michio, Nakajima, TakahitoMOLECULAR 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 modelKawakami, Takashi, Miyagawa, Koichi, Sharma, Sandeep, Saito, Toru, Shoji, Mitsuo, Yamada, Satoru, Yamanaka, Shusuke, Okumura, Mitsutaka, Nakajima, Takahito, Yamaguchi, KizashiJournal 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 20 (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 20 (4) 2018年10月A Theoretical Study on Redox Potential and pK(a) of [2Fe-25] Cluster Model from Iron-Sulfur ProteinsKurniawan, Isman, Kawaguehi, Kazutomo, Shoji, Mitsuo, Matsui, Toru, Shigeta, Yasuteru, Nagao, HidemiBULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 91 (9) 2018年9月[査読有り] Redox potential-dependent formation of an unusual His-Trp bond in bilirubin oxidaseAkter, Mahfuza, Tokiwa, Takaki, Shoji, Mitsuo, Nishikawa, Koji, Shigeta, Yasuteru, Sakurai, Takeshi, Higuchi, Yoshiki, Kataoka, Kunishige, Shibata, NaokiChemistry (Weinheim an der Bergstrasse, Germany) 24 (68) 2018年8月[査読有り] A Practical Approach for Searching Stable Molecular Structures by Introducing Repulsive Interactions among WalkersShoji, Mitsuo, Kayanuma, Megumi, Shigeta, YasuteruBulletin of the Chemical Society of Japan 91 (10) 2018年7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 IIShoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, KizashiThe journal of physical chemistry. B 122 (25) 2018年6月[査読有り] Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMαYamamoto, 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, HitoshiBiochemical and biophysical research communications 499 (2) 2018年5月Relative stability between the manganese hydroxide- and oxo-models for water oxidation by CCSD, DMRG CASCI, CASSCF, CASPT2 and CASDFT methods; Importance of static and dynamical electron correlation effects for OEC of PSIIT. Kawakami, K. Miyagawa, H. Isobe, M. Shoji, S. Yamanaka, M. Katouda, T. Nakajima, K. Nakatani, M. Okumura, K. YamaguchiChemical Physics Letters 705 2018年5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5月[査読有り] Nonadiabatic one-electron transfer mechanism for the O–O bond formation in the oxygen-evolving complex of photosystem IIMitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Kizashi YamaguchiChemical Physics Letters 698 2018年4月[査読有り] Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem IIKizashi Yamaguchi, Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Takashi Kawakami, Satoru Yamada, Michio Katouda, Takahito NakajimaMolecular Physics 116 (5-6) 2018年3月[査読有り] First-principles study of the formation of glycine-producing radicals from common interstellar speciesAkimasa Sato, Yuya Kitazawa, Toshiro Ochi, Mitsuo Shoji, Yu Komatsu, Megumi Kayanuma, Yuri Aikawa, Masayuki Umemura, Yasuteru ShigetaMolecular Astrophysics 10 2018年3月[査読有り] First-principles study of the formation of glycine-producing radicals from common interstellar speciesAkimasa Sato, Yuya Kitazawa, Toshiro Ochi, Mitsuo Shoji, Yu Komatsu, Megumi Kayanuma, Yuri Aikawa, Masayuki Umemura, Yasuteru ShigetaMolecular Astrophysics 10 2018年3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 FormulaShoji,MitsuoChemPhotoChem 2 (3) 2017年12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 YamaguchiPOLYHEDRON 136 (4) 2017年11月[査読有り] A theoretical study of the formation of glycine via hydantoin intermediate in outer space environmentMegumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki UmemuraCHEMICAL PHYSICS LETTERS 687 2017年11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 HayashiThe journal of physical chemistry. B 121 (22) 2017年6月[査読有り] Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate ConformationsUjiie Yuzuru, Tanaka Wataru, Hanaoka Kyohei, Harada Ryuhei, Kayanuma Megumi, Shoji Mitsuo, Murakawa Takeshi, Ishida Toyokazu, Shigeta Yasuteru, Hayashi HideyukiTHE JOURNAL OF PHYSICAL CHEMISTRY B 121 (22) 2017年6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 structuresMitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi YamaguchiFARADAY DISCUSSIONS 198 2017年6月[査読有り] The reaction mechanism of sarcosine oxidase elucidated using FMO and QM/MM methodsAbe, Yukihiro, Shoji, Mitsuo, Nishiya, Yoshiaki, Aiba, Hiroshi, Kishimoto, Takahide, Kitaura, KazuoPhysical chemistry chemical physics : PCCP 19 (15) 2017年3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 effectsK. Yamaguchi, M. Shoji, H. Isobe, S. Yamanaka, Y. Umena, K. Kawakami, N. KamiyaMOLECULAR PHYSICS 115 (5) 2017年[査読有り] UNO DMRG CASCI calculations of effective exchange integrals for m-phenylene-bis-methylene spin clustersTakashi Kawakami, Shinsuke Sano, Toru Saito, Sandeep Sharma, Mitsuo Shoji, Satoru Yamada, Yu Takano, Shusuke Yamanaka, Mitsutaka Okumura, Takahito Nakajima, Kizashi YamaguchiMOLECULAR PHYSICS 115 (17-18) 2017年[査読有り] Large-scale QM/MM calculations of the CaMn4O5 cluster in the oxygen-evolving complex of photosystem II: Comparisons with EXAFS structuresMitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Kizashi YamaguchiCHEMICAL PHYSICS LETTERS 658 2016年8月[査読有り] Molecular Mechanisms of Substrate Specificities of Uridine-Cytidine KinaseTanaka Wataru, Shoji Mitsuo, Tomoike Fumiaki, Ujiie Yuzuru, Hanaoka Kyohei, Harada Ryuhei, Kayanuma Megumi, Kamiya Katsumasa, Ishida Toyokazu, Masui Ryoji, Kuramitsu Seiki, Shigeta YasuteruBIOPHYSICS AND PHYSICOBIOLOGY 13 2016年6月[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Full geometry optimizations of the CaMn4O4 model cluster for the oxygen evolving complex of photosystem IIMitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Kizashi YamaguchiCHEMICAL PHYSICS LETTERS 640 2015年11月[査読有り] Molecular dynamics study on the key catalytic intermediates of threonine synthaseMitsuo Shoji, Yuzuru Ujiie, Ryuhei Harada, Megumi Kayanuma, Yasuteru Shigeta, Takeshi Murakawa, Hideyuki HayashiPROTEIN SCIENCE 24 (1:SI) 2015年10月[査読有り] GPGPU化OpenFMOによるFMO計算の性能評価梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照情報処理学会研究報告(Web) 2015 (HPC-151) 2015年9月QM/MM study of the S-2 to S-3 transition reaction in the oxygen-evolving complex of photosystem IIMitsuo Shoji, Hiroshi Isobe, Kizashi YamaguchiCHEMICAL PHYSICS LETTERS 636 2015年9月[査読有り] Performance of the divide-and-conquer approach used as an initial guessMitsuo Shoji, Megumi Kayanuma, Hiroaki Umeda, Yasuteru ShigetaCHEMICAL PHYSICS LETTERS 634 2015年8月[査読有り] A QM/MM study of the 5 '-AMP DNA hydrolysis of aprataxinKyohei Hanaoka, Wataru Tanaka, Megumi Kayanuma, Mitsuo ShojiCHEMICAL PHYSICS LETTERS 631 2015年7月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 IIMitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi YamaguchiCHEMICAL PHYSICS LETTERS 627 2015年5月Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body SystemsYasuteru Shigeta, Ryuhei Harada, Megumi Kayanuma, Mitsuo ShojiINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5) 2015年3月[査読有り] Theoretical studies of the damage- free S-1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem IIMitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi YamaguchiCHEMICAL PHYSICS LETTERS 623 2015年3月A QM/MM study of the initial steps of catalytic mechanism of nitrile hydrataseMegumi Kayanuma, Kyohei Hanaoka, Mitsuo Shoji, Yasuteru ShigetaCHEMICAL PHYSICS LETTERS 623 2015年3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3月[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, 重田育照日本コンピュータ化学会年会講演予稿集 2015 2015年OpenFMOプログラムのGPGPU化梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照分子科学討論会講演プログラム&要旨(Web) 9th 2015年Involvement of Propionate Side Chains of the Heme in Circular Dichroism of Myoglobin: Experimental and Theoretical AnalysesMasako Nagai, Chika Kobayashi, Yukifumi Nagai, Kiyohiro Imai, Naoki Mizusawa, Hiroshi Sakurai, Saburo Neya, Megumi Kayanuma, Mitsuo Shoji, Shigenori NagatomoJOURNAL OF PHYSICAL CHEMISTRY B 119 (4) 2015年1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] Substrate-mediated proton relay mechanism for the religation reaction in topoisomerase IIKyohei Hanaoka, Mitsuo Shoji, Daiki Kondo, Akimasa Sato, Moon Young Yang, Katsumasa Kamiya, Kenji ShiraishiJournal of Biomolecular Structure and Dynamics 32 (11) 2014年11月[査読有り] An efficient initial guess formation of broken-symmetry solutions by using localized natural orbitalsMitsuo Shoji, Yasunori Yoshioka, Kizashi YamaguchiCHEMICAL PHYSICS LETTERS 608 2014年7月[査読有り] A QM/MM Study of the l -Threonine Formation Reaction of Threonine Synthase: Implications into the Mechanism of the Reaction SpecificityMitsuo Shoji, Kyohei Hanaoka, Yuzuru Ujiie, Wataru Tanaka, Daiki Kondo, Hiroaki Umeda, Yoshikazu Kamoshida, Megumi Kayanuma, Katsumasa Kamiya, Kenji Shiraishi, Yasuhiro Machida, Takeshi Murakawa, Hideyuki HayashiJ. Am. Chem. Soc. 136 (12) 2014年3月[査読有り] A QM/MM study of nitric oxide reductase-catalysed N2O formationMitsuo Shoji, Kyohei Hanaoka, Daiki Kondo, Akimasa Sato, Hiroaki Umeda, Katsumasa Kamiya, Kenji ShiraishiMOLECULAR PHYSICS 112 (3-4) 2014年2月[査読有り] 3P077 ウリジンシチジンキナーゼの基質結合相互作用についての理論的研究(01D. 蛋白質:機能,ポスター,第52回日本生物物理学会年会(2014年度))Tanaka Wataru, Ujiie Yuzuru, Tomoike Fumiaki, Shoji Mitsuo, Kayanuma Megumi, Masui Ryoji, Kuramitsu Seiki, Shigeta Yasuteru生物物理 54 (1) 2014年3P076 トレオニン合成酵素の反応制御機構解明のための分子動力学計算 : 反応中間体間自由エネルギー評価(01D. 蛋白質:機能,ポスター,第52回日本生物物理学会年会(2014年度))Ujiie Yuzuru, Tanaka Wataru, Shoji Mitsuo, Kayanuma Megumi, Shigeta Yasuteru, Machida Yasuhiro, Murakawa Takeshi, Hayashi Hideyuki生物物理 54 (1) 2014年1P074 ニトリルヒドラターゼ(NHase)によるアミド生成機構に関する理論的研究(01D. 蛋白質 : 機能,ポスター,第52回日本生物物理学会年会(2014年度))Kayanuma Megumi, Shoji Mitsuo, Shigeta Yasuteru生物物理 54 (1) 2014年GPGPU化Fock行列計算ルーチンのOpenFMOへの組み込み梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照分子科学討論会講演プログラム&要旨(Web) 8th 2014年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, 重田育照日本コンピュータ化学会年会講演予稿集 2014 2014年GPGPU化したFock行列計算ルーチンのOpenFMOへの組み込み梅田宏明, 塙敏博, 庄司光男, 朴泰祐日本コンピュータ化学会年会講演予稿集 2014 2014年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トランザクション コンピューティングシステム(Web) 6 (4) 2013年10月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 reactionsMitsuo Shoji, Kyohei Hanaoka, Akimasa Sato, Daiki Kondo, Moon Young Yang, Katsumasa Kamiya, Kenji ShiraishiINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (3) 2013年2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2月1P076 トレオニン合成酵素における反応制御機構の理論的解明(01D. 蛋白質:機能,ポスター,日本生物物理学会年会第51回(2013年度))Shoji Mitsuo, Hanaoka Kyohei, Ujiie Yuzuru, Tanaka Wataru, Kayanuma Megumi, Umeda Hiroaki, Machida Yasuhiro, Murakawa Takeshi, Hayashi Hideyuki生物物理 53 (1) 2013年1P074 ニトリルヒドラターゼの触媒機構に関する理論的研究(01D. 蛋白質:機能,ポスター,日本生物物理学会年会第51回(2013年度))Kayanuma Megumi, Hanaoka Kyohei, Shoji Mitsuo生物物理 53 (1) 2013年1SAA-03 QM/MM法による光合成酸素発生中心S1状態の電子状態解析(1SAA 新学術領域「人工光合成による太陽光エネルギーの物質変換 : 実用化に向けての異分野融合」共催,光駆動水分解の分子機構 : 光化学系IIと人工光合成,シンポジウム,日本生物物理学会第51回年会(2013年度))庄司 光男, 礒部 寛, 山中 秀介, 神谷 信夫, 沈 建仁, 山口 兆生物物理 53 (1) 2013年OpenFMOにおけるFock行列計算ルーチンのGPGPU化梅田宏明, 塙敏博, 庄司光男, 朴泰祐分子科学討論会講演プログラム&要旨(Web) 7th 2013年OpenFMOにおけるFock行列計算のGPGPUによる高速化への取り組み梅田宏明, 塙敏博, 庄司光男, 朴泰祐日本コンピュータ化学会年会講演予稿集 2013 2013年OpenFMOにおけるFock行列計算ルーチンのGPGPU化について梅田宏明, 塙敏博, 庄司光男, 朴泰祐日本コンピュータ化学会年会講演予稿集 2013 2013年3PT222 QM/MM法による同化型亜硝酸還元酵素の反応機構についての理論的研究(日本生物物理学会第50回年会(2012年度))Shoji Mitsuo, Hanaoka Kyohei, Kondo Daiki, Umeda Hiroaki, Kayanuma Megumi, Kamiya Katsumasa, Shiraishi Kenji, Nakano Shogo, Katayanagi Katsuo生物物理 52 2012年Theory of Chemical Bonds in Metalloenzymes. XVII. Symmetry Breaking in Manganese Cluster Structures and Chameleonic Mechanisms for the O-O Bond Formation of Water Splitting ReactionSaito Toru, Shoji Mitsuo, Kanda Keita, Isobe Hiroshi, Yamanaka Shusuke, Kitagawa Yasutaka, Yamada Satoru, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi KizashiInternational Journal of Quantum Chemistry 112 (1) 2012年[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7月Theoretical studies on electronic structure and magnetic properties of mixed-valence uteroferrin active siteKenichi Koizumi, Mitsuo Shoji, Kizashi Yamaguchi, Haruki NakamuraInternational Journal of Quantum Chemistry 111 (3) 2011年3月[査読有り] 1D1336 酵母プリオンSup35の形成するアミロイド線維のベータヘリックスモデルの安定性に関する理論的研究(蛋白質_物性1,第49回日本生物物理学会年会)Kondo Daiki, Hanaoka Kyohei, Yang Moonyoung, Kamiya Katsumasa, Shoji Mitsuo, Kawai-Noma Shigeko, Taguchi Hideki, Shiraishi Kenji生物物理 51 2011年3C1048 一酸化窒素還元酵素における基質結合状態についての理論的研究(3C 蛋白質_機能2,日本生物物理学会第49回年会)Shoji Mitsuo, Kondo Daiki, Hanaoka Kyouhei, Yang Moonyoung, Umeda Hiroaki, Kamiya Norimasa, Shiraishi Kenji生物物理 51 2011年Theory of Chemical Bonds in Metalloenzymes. XV. Local Singlet and Triplet Diradical Mechanisms for Radical Coupling Reactions in the Oxygen Evolution ComplexYamaguchi Kizashi, Shoji Mitsuo, Saito Toru, Isobe Hiroshi, Nishihara Satomichi, Koizumi Kenichi, Yamada Satoru, Kawakami Takashi, Kitagawa Yasutaka, Yamanaka Shusuke, Okumura MitsutakaInternational Journal of Quantum Chemistry 110 (15) 2010年[査読有り] Theory of Chemical Bonds in Metalloenzymes. XIV. Correspondence Between Magnetic Coupling Mode and Radical Coupling Mechanism in Hydroxylations with Methane Monooxygenase and Related SpeciesSaito Toru, Shoji Mitsuo, Isobe Hiroshi, Yamanaka Shusuke, Kitagawa Yasutaka, Yamada Satoru, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi KizashiInternational Journal of Quantum Chemistry 110 (15) 2010年[査読有り] 新規分子構造表示プログラム Makiko の開発庄司 光男, 庄司 真紀子Journal of computer chemistry, Japan 8 (1) 2009年12月Theoretical study of magnetic interaction between C-60 anion radicalsY. Kitagawa, Y. Nakanishi, T. Saito, K. Koizumi, M. Shoji, S. Yamada, T. Kawakami, M. Okumura, K. YamaguchiPOLYHEDRON 28 (9-10) 2009年10月[査読有り] Symmetry and Broken-Symmetry in Molecular Orbital Descriptions of Unstable Molecules. 3. The Nature of Chemical Bonds of Spin Frustrated SystemsT. Kawakami, R. Takeda, S. Nishihara, T. Saito, M. Shoji, S. Yamada, S. Yamanaka, Y. Kitagawa, M. Okumura, K. YamaguchiJournal of Physical Chemistry A 113 (52) 2009年10月[査読有り] Quantum dynamic simulations for single molecular magnets using anisotropic spin modelsT. Kawakami, H. Nitta, M. Takahata, M. Shoji, Y. Kitagawa, M. Nakano, M. Okumura, K. YamaguchiPOLYHEDRON 28 (9-10) 2009年6月[査読有り] Theory of chemical bonds in metalloenzymes XII: Electronic and spin structures of metallo-oxo and isoelectronic species and spin crossover phenomena in oxygenation reactionsYamaguchi Kizashi, Shoji Mitsuo, Isobe Hiroshi, Yamanaka Syusuke, Shimada Jiro, Kitagawa Yasutaka, Okumura MitsutakaPolyhedron 28 (9-10) 2009年[査読有り] Theory of Chemical Bonds in Metalloenzymes XIII: Singlet and Triplet Diradical Mechanisms of Hydroxylations With Iron-Oxo Species and P450 are RevisitedYamaguchi Kizashi, Yamanaka Syusuke, Isobe Hiroshi, Shoji Mitsuo, Saito Toru, Kitagawa Yasutaka, Okumura Mitsutaka, Shimada JiroInternational Journal of Quantum Chemistry 109 (15) 2009年[査読有り] Extended Hartree-Fock Theory of Chemical Reactions. IX. Diradical and Perepoxide Mechanisms for Oxygenations of Ethylene With Molecular Oxygen and Iron-Oxo Species Are RevisitedYamaguchi Kizashi, Yamanaka Syusuke, Shimada Jiro, Isobe Hiroshi, Saito Toru, Shoji Mitsuo, Kitagawa Yasutaka, Okumura MitsutakaInternational Journal of Quantum Chemistry 109 (15) 2009年[査読有り] Approximately Spin-Projected Hessian for Broken Symmetry Method and Stretching Frequencies of F-2 and Singlet O-2Kitagawa Yasutaka, Saito Toru, Nakanishi Yasuyuki, Kataoka Yusuke, Shoji Mitsuo, Koizumi Kenichi, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi KizashiInternational Journal of Quantum Chemistry 109 (15) 2009年[査読有り] Theoretical studies on the structure and effective exchange integral (J(ab)) of an active site in oxyhemocyanin (oxyHc) by using approximately spin-projected geometry optimization (AP-opt) methodT. Saito, Y. Kitagawa, M. Shoji, Y. Nakanishi, M. Ito, T. Kawakami, M. Okumura, K. YamaguchiChemical Physics Letters 456 (1-3) 2008年10月[査読有り] Theoretical Studies on Effects of Hydrogen Bonds Attaching to Cysteine Ligands on 4Fe-4S ClustersKitagawa, M. Shoji, T. Saito, Y. Nakanishi, K. Koizumi, T. Kawakami, M. Okumura, K. YamaguchiInternational Journal of Quantum Chemistry 108 (15) 2008年10月[査読有り] Extended hartree-fock theory of chemical reactions. VIII. hydroxylation reactions by P450Hiroshi Isobe, Satomichi Nishihara, Mitsuo Shoji, Shusuke Yamanaka, Jiro Shimada, Masayuki Hagiwara, Kizashi YamaguchiInternational Journal of Quantum Chemistry 108 (15) 2008年[査読有り] Theory of chemical bonds in metalloenzymes. VII. Hybrid-density functional theory studies on the electronic structures of P450Shoji Mitsuo, Isobe Hiroshi, Saito Toru, Yabushita Hirotaka, Koizumi Kenichi, Kitagawa Yasutaka, Yamanaka Shusuke, Kawakami Takashi, Okumura Mitsutaka, Hagiwara Masayuki, Yamaguchi KizashiInternational Journal of Quantum Chemistry 108 (4) 2008年[査読有り] Theory of Chemical Bonds in Metalloenzymes XI: Full Geometry Optimization and Vibration Analysis of Porphyrin Iron-Oxo SpeciesShoji Mitsuo, Isobe Hiroshi, Saito Toru, Kitagawa Yasutaka, Yamanaka Shusuke, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi KizashiInternational Journal of Quantum Chemistry 108 (15) 2008年[査読有り] Theoretical investigation of the magnetic interactions of Ni-9 complexesShoji Mitsuo, Kitagawa Yasutaka, Kawakami Takashi, Yamanaka Shusuke, Okumura Mitsutaka, Yamaguchi KizashiJournal of Physical Chemistry a 112 (17) 2008年[査読有り] Density functional study of manganese dimerShusuke Yamanaka, Takeshi Ukai, Kazuto Nakata, Ryo Takeda, Mitsuo Shoji, Takashi Kawakami, Toshikazu Takada, Kizashi YamaguchiINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 107 (15) 2007年12月Ab initio studies on the zero-field splitting parameters of manganese porphyrin complexesRyo Takeda, K. Koizumi, M. Shoji, H. Nitta, S. Yamanaka, M. Okumura, K. YamaguchiPOLYHEDRON 26 (9-11) 2007年6月[査読有り] Ab initio calculation of the Dzyaloshinskii-Moriya parameters: Spin-orbit GSO-HF, HFT, and CI approachesR. Takeda, S. Yamanaka, M. Shoji, K. YamaguchiINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 107 (6) 2007年5月[査読有り] Quantum spin correction scheme based on spin-correlation functional for Kohn-Sham spin density functional theoryShusuke Yamanaka, Ryo Takeda, Kazuto Nakata, Toshikazu Takada, Mitsuo Shoji, Yasutaka Kitagawa, Kizashi YamaguchiJOURNAL OF MAGNETISM AND MAGNETIC MATERIALS 310 (2) 2007年3月[査読有り] Theory of chemical bonds in metalloenzymes. IX. Theoretical study on the active site of the ribonucieotide reductase and the related speciesShoji Mitsuo, Isobe Hiroshi, Takano Yu, Kitagawa Yasutaka, Yamanaka Shusuke, Okumura Mitsutaka, Yamaguchi KizashiInternational Journal of Quantum Chemistry 107 (15) 2007年[査読有り] Theoretical studies on ferromagnetic behavior of [Cr(C-5(CH3)(5))(2)](+)[TCNE](-) and [Mn(C-5(CH3)(5))(2)](+)[TCNQ](-)Koizumi Kenichi, Shoji Mitsuo, Kitagawa Yasutaka, Takeda Ryo, Yamanaka Shusuke, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi KizashiPolyhedron 26 (9-11) 2007年[査読有り] Geometry optimization method based on approximate spin projection and its application to F(2), CH(2), CH(2)OO, and active site of ureaseKitagawa Yasutaka, Saito Toru, Ito Masahide, Nakanishi Yasuyuki, Shoji Mitsuo, Koizumi Kenichi, Yamanaka Shusuke, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi KizashiInternational Journal of Quantum Chemistry 107 (15) 2007年[査読有り] Assignments of the Mossbauer spectra of an inorganic [8fe-7S] complex based on the first-principle calculationsShoji Mitsuo, Saito Toru, Takeda Ryo, Kitagawa Yasutaka, Kawakami Takashi, Yamanaka Shusuke, Okumura Mitutaka, Yamaguchi KizashiChemical Physics Letters 446 (1-3) 2007年[査読有り] A GSO-HDFT study of noncollinear spin structures of [2Fe-2S] clusterShoji Mitsuo, Koizumi Kenichi, Takeda Ryo, Kitagawa Yasutaka, Yamanaka Shusuke, Okumura Mitsutaka, Yamaguchi KizashiPolyhedron 26 (9-11) 2007年[査読有り] Theory of chemical bonds in metalloenzymes V: Hybrid-DFT studies of the inorganic [8Fe-7S] coreM. Shoji, K. Koizumi, Y. Kitagawa, S. Yamanaka, M. Okumura, K. Yamaguchi, Y. Ohki, Y. Sunada, M. Honda, K. TatsumiInternational Journal of Quantum Chemistry 106 (15) 2006年12月The electronic structure and magnetic property of μ-hydroxo bridged manganese porphyrin dimerK. Koizumi, M. Shoji, Y. Kitagawa, H. Ohoyama, T. Kasai, K. YamaguchiEuropean Physical Journal D 38 (1) 2006年4月Quantum dynamics of exciton recurrence motion in dendritic molecular aggregatesH Nitta, M Shoji, M Takahata, M Nakano, D Yamaki, K YamaguchiJOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 178 (2-3) 2006年3月[査読有り] Theoretical study on the electronic structure of [4Fe-4S] clusterM. Shoji, K. Koizumi, Y. Kitagawa, T. Kawakami, S. Yamanaka, M. Okumura, K. YamaguchiRECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND 7B 7A-B 2006年[査読有り] Hybrid-DFT study on the high-valent metal-oxo bonds in manganese porphyrins and related speciesK. Koizumi, M. Shoji, Y. Kitagawa, H. Isobe, R. Takeda, S. Yamanaka, K. YamaguchiRECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND 7B 7A-B 2006年[査読有り] Search for the ground states of ising spin clusters by using the genetic algorithmsAkifumi Oda, Hidemi Nagao, Yasutaka Kitagawa, Yasuteru Shigeta, Mitsuo Shoji, Hiroya Nitta, Mitsutaka Okumura, Kizashi YamaguchiInternational Journal of Quantum Chemistry 105 (6) 2005年12月[査読有り] Quantum spin correction scheme for ab initio spin-unrestricted solutions: Multiple bonds caseS Yamanaka, R Takeda, M Shoji, Y Kitagawa, H Honda, K YamaguchiINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 105 (6) 2005年12月[査読有り] Quantum dynamics in high-spin molecules, spin dendrimers, and spin latticesM Takahata, M Shoji, H Nitta, R Takeda, S Yamanaka, M Okumura, M Nakano, K YamaguchiINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 105 (6) 2005年12月[査読有り] Theoretical study on the magnetic interactions of active site in hemerythrinM. Shoji, T. Hamamoto, K. Koizumi, H. Isobe, Y. Kitagawa, Y. Takano, S. Yamanaka, M. Okumura, K. YamaguchiPolyhedron, 2005, 40, 2701-2707 24 (16-17) 2005年11月[査読有り] Theoretical studies on magnetic interactions between Ni(II) ions in UreaseY. Maruno, M. Shoji, K. Koizumi, Y. Nishiyama, Y. Kitagawa, T. Kawakami, M. Okumura, K. YamaguchiPolyhedron, 2005, 24, 2751-2757 24 (16-17) 2005年11月[査読有り] Theoretical studies on magnetic interactions and charge-dope effects in one-dimensional Ni5 and Ni7 complexesY. Kitagawa, M. Shoji, K. Koizumi, T. Kawakami, M. Okumura, K. YamaguchiPolyhedron, 2005, 24, 2778-2783 24 (16-17) 2005年11月[査読有り] Theoretical studies on ferrimagnetic behavior of TCNE and manganese porphyrin dimerK. Koizumi, M. Shoji, Y. Kitagawa, T. Taniguchi, T. Kawakami, M. Okumura, K. YamaguchiPolyhedron, 2005, 24, 2720-2725 24 (16-17) 2005年11月[査読有り] Theoretical studies on dissociation of metal-carbon bond in Cobalamin;- formulation and calculation -Y. Nishiyama, M. Shoji, K. Koizumi, Y. Maruno, Y. Kitagawa, T. Kawakami, M. Okumura, K. YamaguchiPolyhedron, 2005, 24, 2745-2750 24 (16-17) 2005年11月[査読有り] A theoretical study of zero-field splitting of organic biradicalsM Shoji, K Koizumi, T Hamamoto, T Taniguchi, R Takeda, Y Kitagawa, T Kawakami, M Okumura, S Yamanaka, K YamaguchiPOLYHEDRON 24 (16-17) 2005年11月[査読有り] Theoretical direct evaluation of inter-dimer J values in BETS saltsT Kawakami, T Taniguchi, M Shoji, Y Kitagawa, M Okumura, K YamaguchiPOLYHEDRON 24 (16-17) 2005年11月[査読有り] Ab initio GSO-DFT study of spin-frustrated transition metal systemsS Yamanaka, R Takeda, M Shoji, K Koizumi, Y Kitagawa, K YamaguchiPOLYHEDRON 24 (16-17) 2005年11月[査読有り] Formulation of master equation approach involving spin-phonon coupling: Toward an understanding of spin dynamics in magnetic dendrimersM Takahata, M Shoji, S Yamanaka, M Nakano, K YamaguchiPOLYHEDRON 24 (16-17) 2005年11月[査読有り] Theory of chemical bonds in metalloenzymes II: Hybrid-DFT studies in iron-sulfur clustersM. Shoji, K. Koizumi, Y. Kitagawa, S. Yamanaka, T. Kawakami, M. Okumura, K. YamaguchiInt. J. Quant. Chem., 2005, 105, 628-644 105 (6) 2005年10月[査読有り] A quantum chemical study of magnetic interactions in phenazine derivatives for chemical or photo-induced organic magnetsTakeshi Taniguchi, Yuji Watazu, Mitsuo Shoji, Takashi Kawakami, Mitsutaka Okumura, Kizashi YamaguchiSynthetic Metals 154 (1-3) 2005年10月[査読有り] Theory of chemical bonds in metalloenzymes I:Analytical and hybrid-DFT studies on oxo and hydroxo diiron coresM. Shoji, Y. Nishiyama, Y. Maruno, K. Koizumi, Y. Kitagawa, S. Yamanaka, T. Kawakami, M. Okumura, K. YamaguchiINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 100 (6) 2004年11月Theoretical studies on effective exchange integrals by using spin correlation function analysis and magnetic effective density functional (MEDF) methodY. Kitagawa, S. Yamanaka, R. Takeda, M. Shoji, K. Koizumi, Y. Nishiyama, Y. Maruno, T. Kawakami, M. Okumura, K. YamaguchiInt. J. Quant. Chem., 2004, 100, 927-936 100 (6) 2004年10月[査読有り] The Electronic structure and magnetic propertiy of metal-oxo, porphyrin manganese-oxo and m-oxo-bridged manganese prophyrin dimmerK. Koizumi, M. Shoji, Y. Nishiyama, Y. Maruno, Y. Kitagawa, K. Soda, S. Yamanaka, M. Okumura, K. YamaguchiInt. J. Quant. Chem., 2004, 100, 943-956 100 (6) 2004年10月[査読有り] Hybrid density-functional theory studies on stable polycarbenesM Shoji, T Taniguchi, T Kawakami, K YamaguchiPOLYHEDRON 22 (14-17) 2003年7月受賞▼▲2023年5月量子生命科学会 量子生命科学会 研究奨励賞 量子生命科学に関連する研究において顕著な業績を挙げた 2022年5月量子生命学会 量子生命学会 第四回大会 優秀発表賞（口頭発表） 光合成水分解酸素発生における Mnの自然選択の理由 2021年9月量子生命科学会 量子生命科学会 第3回大会 優秀発表賞 (口頭発表） 銅含有アミン酸化酵素におけるセミキノンラジカル生成機構の理論解明 2020年12月量子生命科学会 量子生命科学会 第二回大会 優秀発表賞 (口頭発表) 銅含有アミン酸化酵素のプロトン化状態 についてのQM/MM解析 書籍等出版物▼▲ADVANCES IN QUANTUM CHEMISTRY, VOL 84Yamaguchi, Kizashi, Miyagawa, Koichi, Isobe, Hiroshi, Shoji, Mitsuo, Kawakami, Takashi, Yamanaka, Shusuke (範囲:Isolobal and isospin analogy between organic and inorganic open-shell molecules-Application to oxygenation reactions by active oxygen and oxy-radicals and water oxidation in the native and artificial photosynthesis)環境技術庄司,光男 (担当:分担執筆, 範囲:量子化学計算ビギナーズガイド)量子化学計算ビギナーズガイド庄司光男 (担当:単著, 範囲:45-49)Gaussian16で始める量子化学超入門庄司, 光男 (担当:単著, 範囲:フリーソフトで始める分子モデリング)フリーソフトで始める分子モデリング庄司, 光男 (担当:単著)競争的資金等の研究課題▼▲光合成における光誘導水分解反応機構及び光エネルギー利用機構の解明科学研究費助成事業研究期間: 2022年4月 - 2027年3月代表者: 沈 建仁, 庄司 光男, 秋田 総理, 菅 倫寛, 山口 兆XFEL-SFXによる化学反応解明を目指した「反応追跡結晶」の構築科学研究費助成事業研究期間: 2022年4月 - 2026年3月代表者: 上野 隆史, 庄司 光男, 南後 恵理子分子シミュレーションによるタンパク質化学反応ダイナミクスの解明科学研究費助成事業研究期間: 2020年4月 - 2024年3月代表者: 宮下 治, 庄司 光男, 篠田 恵子時分割実験のための多様な反応誘起システムの開発科学研究費助成事業研究期間: 2019年6月 - 2024年3月代表者: 南後 恵理子, 清水 伸隆, 大和田 成起, 宮下 治, 庄司 光男, 篠田 恵子生体内量子多体系における特異的化学反応の機構解明JST-PRESTO研究期間: 2019年10月 - 2023年3月代表者: 庄司光男自然・半導体・分子触媒で利用可能な多様な水分解反応機構の解明新学術領域研究(研究領域提案型)研究期間: 2020年4月 - 2022年3月代表者: 庄司光男光化学系II酸素発生中心における再活性化機構についての理論的解明科学研究費助成事業研究期間: 2018年4月 - 2020年3月代表者: 庄司 光男光化学系II酸素発生中心における水分解反応の全反応経路解明科学研究費助成事業研究期間: 2017年4月 - 2020年3月代表者: 庄司 光男酵素活性中心の構造変化とゆらぎにリンクする触媒反応遷移状態の制御機構科学研究費助成事業研究期間: 2016年7月 - 2020年3月代表者: 岡島 俊英, 中井 忠志, 庄司 光男, 村川 武志計算科学によるアストロバイオロジーへの理論的挑戦科学研究費助成事業研究期間: 2016年4月 - 2019年3月代表者: 相川 祐理, 庄司 光男, 古家 健次補欠分子族含有酵素におけるプロトン・電子移動の協同的制御機構の解明科学研究費助成事業研究期間: 2015年4月 - 2019年3月代表者: 林 秀行, 村川 武志, 庄司 光男トレオニン合成酵素の全反応機構の理論的解明科学研究費助成事業研究期間: 2014年4月 - 2017年3月代表者: 庄司 光男, 林 秀行, 氏家 譲, 田中 弥光合成系Ⅱにおける水分解反応の学理解明科学研究費助成事業研究期間: 2012年 - 2017年代表者: 沈 建仁, 野口 巧, 山口 兆, 庄司 光男, 菅 倫寛, 秋田 総理, 三野 広幸, 加藤 祐樹, 磯部 寛ピリドキサール酵素の反応特異性制御機構の解明科学研究費助成事業研究期間: 2012年4月 - 2016年3月代表者: 林 秀行, 村川 武志, 庄司 光男生体酵素における反応機構と反応制御機構解明のための理論的研究科学研究費助成事業研究期間: 2012年4月 - 2014年3月代表者: 庄司 光男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 谷 一寿 Name TANI Kazutoshi 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 研究テーマ クライオ電子顕微鏡を用いた蛋白質複合体立体構造解析 関連リンク Trios researchmap Email ktaniccs.tsukuba.ac.jp 研究キーワード経歴2023年12月 - 現在筑波大学 計算科学研究センター 教授 2019年4月 - 2023年11月三重大学 医学系研究科 特任教授 2015年4月 - 2019年3月名古屋大学 細胞生理学研究センター 基礎生物学研究部門 特任教授 2012年4月 - 2015年3月名古屋大学 細胞生理学研究センター 基礎生物学研究部門 特任准教授 論文▼▲High-resolution structure and biochemical properties of the LH1–RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosumKazutoshi Tani, Ryo Kanno, Ayaka Harada, Yuki Kobayashi, Akane Minamino, Shinji Takenaka, Natsuki Nakamura, Xuan-Cheng Ji, Endang R. Purba, Malgorzata Hall, Long-Jiang Yu, Michael T. Madigan, Akira Mizoguchi, Kenji Iwasaki, Bruno M. Humbel, Yukihiro Kimura, Zheng-Yu Wang-OtomoCommunications Biology 2024年2月Rhodobacter capsulatus forms a compact crescent-shaped LH1-RC photocomplex.Kazutoshi Tani, Ryo Kanno, Xuan-Cheng Ji, Itsusei Satoh, Yuki Kobayashi, Malgorzata Hall, Long-Jiang Yu, Yukihiro Kimura, Akira Mizoguchi, Bruno M Humbel, Michael T Madigan, Zheng-Yu Wang-OtomoNature communications 14 (1) 2023年2月[査読有り] Advances in the Spectroscopic and Structural Characterization of Core Light-Harvesting Complexes from Purple Phototrophic BacteriaYukihiro Kimura, Kazutoshi Tani, Michael T. Madigan, Zheng-Yu Wang-OtomoThe Journal of Physical Chemistry B 2023年1月[査読有り] An LH1–RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteinsKazutoshi Tani, Ryo Kanno, Keigo Kurosawa, Shinichi Takaichi, Kenji V. P. Nagashima, Malgorzata Hall, Long-Jiang Yu, Yukihiro Kimura, Michael T. Madigan, Akira Mizoguchi, Bruno M. Humbel, Zheng-Yu Wang-OtomoCommunications Biology 5 (1) 2022年11月[査読有り] A Ca2+-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes.Kazutoshi Tani, Kazumi Kobayashi, Naoki Hosogi, Xuan-Cheng Ji, Sakiko Nagashima, Kenji V P Nagashima, Airi Izumida, Kazuhito Inoue, Yusuke Tsukatani, Ryo Kanno, Malgorzata Hall, Long-Jiang Yu, Isamu Ishikawa, Yoshihiro Okura, Michael T Madigan, Akira Mizoguchi, Bruno M Humbel, Yukihiro Kimura, Zheng-Yu Wang-OtomoThe Journal of biological chemistry 298 (6) 2022年4月[査読有り] Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex.Kazutoshi Tani, Ryo Kanno, Riku Kikuchi, Saki Kawamura, Kenji V P Nagashima, Malgorzata Hall, Ai Takahashi, Long-Jiang Yu, Yukihiro Kimura, Michael T Madigan, Akira Mizoguchi, Bruno M Humbel, Zheng-Yu Wang-OtomoNature communications 13 (1) 2022年4月[査読有り] Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.Maki Kuzuya, Hidemi Hirano, Kenichi Hayashida, Masakatsu Watanabe, Kazumi Kobayashi, Tohru Terada, Md Iqbal Mahmood, Florence Tama, Kazutoshi Tani, Yoshinori Fujiyoshi, Atsunori OshimaScience signaling 15 (720) 2022年2月[査読有り] A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplexKazutoshi Tani, Kenji V. P. Nagashima, Ryo Kanno, Saki Kawamura, Riku Kikuchi, Malgorzata Hall, Long-Jiang Yu, Yukihiro Kimura, Michael T. Madigan, Akira Mizoguchi, Bruno M. Humbel, Zheng-Yu Wang-OtomoNature Communications 12 (1) 2021年11月[査読有り] Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum.Kazutoshi Tani, Ryo Kanno, Xuan-Cheng Ji, Malgorzata Hall, Long-Jiang Yu, Yukihiro Kimura, Michael T Madigan, Akira Mizoguchi, Bruno M Humbel, Zheng-Yu Wang-OtomoBiochemistry 62 2021年7月[査読有り] A Novel Membrane Protein in the Rhodobacter sphaeroides LH1-RC PhotocomplexK. Tani, K. V. P. Nagashima, R. Kanno, S. Kawamura, R. Kikuchi, M. Hall, L.-J. Yu, Y. Kimura, M. T. Madigan, A. Mizoguchi, B. M. Humbel, Z.-Y. Wang-Otomo2021年6月Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.Keito Hiragi, Kazuya Nishio, Shu Moriyama, Tasuku Hamaguchi, Akira Mizoguchi, Koji Yonekura, Kazutoshi Tani, Tsunehiro MizushimaJournal of structural biology 213 (3) 2021年5月[査読有り] Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides.Kazutoshi Tani, Ryo Kanno, Yuki Makino, Malgorzata Hall, Mizuki Takenouchi, Michie Imanishi, Long-Jiang Yu, Jörg Overmann, Michael T Madigan, Yukihiro Kimura, Akira Mizoguchi, Bruno M Humbel, Zheng-Yu Wang-OtomoNature communications 11 (1) 2020年10月[査読有り] Characterization of Critical Residues in the Extracellular and Transmembrane Domains of the Endothelin Type B Receptor for Propagation of the Endothelin-1 Signal.Tomoko Doi, Kohei Kikuta, Kazutoshi TaniBiochemistry 59 (18) 2020年5月[査読有り] Development of a deep learning-based method to identify “good” regions of a cryo-electron microscopy gridYuichi Yokoyama, Tohru Terada, Kentaro Shimizu, Kouki Nishikawa, Daisuke Kozai, Atsuhiro Shimada, Akira Mizoguchi, Yoshinori Fujiyoshi, Kazutoshi TaniBiophysical Reviews 12 2020年3月[査読有り] Cryo-EM structures of undocked innexin-6 hemichannels in phospholipidsBatuujin Burendei, Ruriko Shinozaki, Masakatsu Watanabe, Tohru Terada, Kazutoshi Tani, Yoshinori Fujiyoshi, Atsunori OshimaScience Advances 6 2020年2月[査読有り] Structural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopyHiroki Yamaguchi, Akiko Kamegawa, Kunio Nakata, Tatsuki Kashiwagi, Toshimi Mizukoshi, Yoshinori Fujiyoshi, Kazutoshi TaniJournal of Structural Biology 205 (1) 2019年1月[査読有り] X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analogWataru Shihoya, Tomohiro Nishizawa, Keitaro Yamashita, Asuka Inoue, Kunio Hirata, Francois Marie Ngako Kadji, Akiko Okuta, Kazutoshi Tani, Junken Aoki, Yoshinori Fujiyoshi, Tomoko Doi, Osamu NurekiNATURE STRUCTURAL & MOLECULAR BIOLOGY 24 (9) 2017年9月[査読有り] The cryo-EM structure of gastric H+, K+-ATPase with bound BYK99, a high-affinity member of K+-competitive, imidazo[1,2-a]pyridine inhibitorsKazuhiro Abe, Jun Shimokawa, Mao Naito, Keith Munson, Olga Vagin, George Sachs, Hiroshi Suzuki, Kazutoshi Tani, Yoshinori FujiyoshiSCIENTIFIC REPORTS 7 (1) 2017年7月[査読有り] Crystal structures of claudins: insights into their intermolecular interactionsHiroshi Suzuki, Kazutoshi Tani, Yoshinori FujiyoshiANNALS OF THE NEW YORK ACADEMY OF SCIENCES 1397 (1) 2017年6月[査読有り] Atomic structure of the innexin-6 gap junction channel determined by cryo-EMAtsunori Oshima, Kazutoshi Tani, Yoshinori FujiyoshiNATURE COMMUNICATIONS 7 2016年12月[査読有り] Activation mechanism of endothelin ETB receptor by endothelin-1Wataru Shihoya, Tomohiro Nishizawa, Akiko Okuta, Kazutoshi Tani, Naoshi Dohmae, Yoshinori Fujiyoshi, Osamu Nureki, Tomoko DoiNATURE 537 (7620) 2016年9月[査読有り] Thermostabilization of the Human Endothelin Type B ReceptorAkiko Okuta, Kazutoshi Tani, Shoko Nishimura, Yoshinori Fujiyoshi, Tomoko DoiJOURNAL OF MOLECULAR BIOLOGY 428 (11) 2016年6月[査読有り] Two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranesYukiho Osuda, Kyoko Shinzawa-Itoh, Kazutoshi Tani, Shintaro Maeda, Shinya Yoshikawa, Tomitake Tsukihara, Christoph GerleMICROSCOPY 65 (3) 2016年6月[査読有り] Two-dimensional crystal structure of aquaporin-4 bound to the inhibitor acetazolamideAkiko Kamegawa, Yoko Hiroaki, Kazutoshi Tani, Yoshinori FujiyoshiMICROSCOPY 65 (2) 2016年4月[査読有り] Claudin-21 Has a Paracellular Channel Role at Tight JunctionsHiroo Tanaka, Yasuko Yamamoto, Hiroka Kashihara, Yuji Yamazaki, Kazutoshi Tani, Yoshinori Fujiyoshi, Katsuhiko Mineta, Kosei Takeuchi, Atsushi Tamura, Sachiko TsukitaMOLECULAR AND CELLULAR BIOLOGY 36 (6) 2016年3月[査読有り] Hexadecameric structure of an invertebrate gap junction channelOshima, Atsunori, Matsuzawa, Tomohiro, Murata, Kazuyoshi, Tani, Kazutoshi, Fujiyoshi, YoshinoriJOURNAL OF MOLECULAR BIOLOGY 428 (6) 2016年3月[査読有り] Three-Dimensional Structure of Innexin GAP Junction Channels Studied by Electron CrystallographyAtsunori Oshima, Tomohiro Matsuzawa, Kazuyoshi Murata, Kazutoshi Tani, Yoshinori FujiyoshiBIOPHYSICAL JOURNAL 110 (3) 2016年2月[査読有り] Bovine F1Fo ATP synthase monomers bend the lipid bilayer in 2D membrane crystalsChimari Jiko, Karen M. Davies, Kyoko Shinzawa-Itoh, Kazutoshi Tani, Shintaro Maeda, Deryck J. Mills, Tomitake Tsukihara, Yoshinori Fujiyoshi, Werner Kuehlbrandt, Christoph GerleELIFE 4 (4) 2015年3月[査読有り] Structural insight into tight junction disassembly by Clostridium perfringens enterotoxinYasunori Saitoh, Hiroshi Suzuki, Kazutoshi Tani, Kouki Nishikawa, Katsumasa Irie, Yuki Ogura, Atsushi Tamura, Sachiko Tsukita, Yoshinori FujiyoshiSCIENCE 347 (6223) 2015年2月[査読有り] Model for the Architecture of Claudin-Based Paracellular Ion Channels through Tight JunctionsHiroshi Suzuki, Kazutoshi Tani, Atsushi Tamura, Sachiko Tsukita, Yoshinori FujiyoshiJOURNAL OF MOLECULAR BIOLOGY 427 (2) 2015年1月[査読有り] Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal GatingKazuhiro Abe, Kazutoshi Tani, Yoshinori FujiyoshiJOURNAL OF BIOLOGICAL CHEMISTRY 289 (44) 2014年10月[査読有り] Water channel structures analysed by electron crystallographyTani, K., Fujiyoshi, Y.Biochimica et Biophysica Acta - General Subjects 1840 (5) 2014年5月[査読有り] Crystal Structure of a Claudin Provides Insight into the Architecture of Tight JunctionsHiroshi Suzuki, Tomohiro Nishizawa, Kazutoshi Tani, Yuji Yamazaki, Atsushi Tamura, Ryuichiro Ishitani, Naoshi Dohmae, Sachiko Tsukita, Osamu Nureki, Yoshinori FujiyoshiSCIENCE 344 (6181) 2014年4月[査読有り] Three-dimensional structure of bovine heart NADH: ubiquinone oxidoreductase (complex I) by electron microscopy of a single negatively stained two-dimensional crystalSatoru Shimada, Kyoko Shinzawa-Itoh, Satoko Amano, Yui Akira, Atsuo Miyazawa, Tomitake Tsukihara, Kazutoshi Tani, Christoph Gerle, Shinya YoshikawaMICROSCOPY 63 (2) 2014年4月[査読有り] Two-dimensional crystallization of intact F-ATP synthase isolated from bovine heart mitochondriaShintaro Maeda, Kyoko Shinzawa-Itoh, Kaoru Mieda, Mami Yamamoto, Yumiko Nakashima, Yumi Ogasawara, Chimari Jiko, Kazutoshi Tani, Atsuo Miyazawa, Christoph Gerle, Shinya YoshikawaACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 69 (12) 2013年12月[査読有り] Carbon sandwich preparation preserves quality of two-dimensional crystals for cryo-electron microscopyFan Yang, Kazuhiro Abe, Kazutoshi Tani, Yoshinori FujiyoshiMICROSCOPY 62 (6) 2013年12月[査読有り] Two alternative conformations of a voltage-gated sodium channelChing-Ju Tsai, Kazutoshi Tani, Katsumasa Irie, Yoko Hiroaki, Takushi Shimomura, Duncan G. McMillan, Gregory M. Cook, Gebhard F.X. Schertler, Yoshinori Fujiyoshi, Xiao-Dan LiJournal of Molecular Biology 425 (22) 2013年11月[査読有り] Visualization of two distinct states of disassembly in the bacterial V-ATPase from Thermus thermophilusKazutoshi Tani, Christopher P. Arthur, Masatada Tamakoshi, Ken Yokoyama, Kaoru Mitsuoka, Yoshinori Fujiyoshi, Christoph GerleMICROSCOPY 62 (4) 2013年8月[査読有り] The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat.Hiroshi Suzuki, Yasuyuki Ito, Yuji Yamazaki, Katsuhiko Mineta, Masami Uji, Kazuhiro Abe, Kazutoshi Tani, Yoshinori Fujiyoshi, Sachiko TsukitaNature communications 4 2013年[査読有り] Strand formation by a trimeric unit repeat of four-transmembrane proteins in EuglenaH. Suzuki, Y. Ito, Y. Yamazaki, K. Mineta, M. Uji, K. Abe, K. Tani, Y. Fujiyoshi, S. TsukitaNat. Commun 4 2013年[査読有り] Cryo-EM structure of gastric H+,K+-ATPase with a single occupied cation-binding siteKazuhiro Abe, Kazutoshi Tani, Thomas Friedrich, Yoshinori FujiyoshiPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 109 (45) 2012年11月[査読有り] Water permeability and characterization of aquaporin-11Kaya Yakata, Kazutoshi Tani, Yoshinori FujiyoshiJOURNAL OF STRUCTURAL BIOLOGY 174 (2) 2011年5月[査読有り] Asymmetric Configurations and N-terminal Rearrangements in Connexin26 Gap Junction ChannelsOshima, Atsunori, Tani, Kazutoshi, Toloue, Masoud M., Hiroaki, Yoko, Smock, Amy, Inukai, Sayaka, Cone, Angela, Nicholson, Bruce J., Sosinsky, Gina E., Fujiyoshi, YoshinoriJOURNAL OF MOLECULAR BIOLOGY 405 (3) 2011年1月[査読有り] Conformational rearrangement of gastric H+,K+-ATPase induced by an acid suppressantKazuhiro Abe, Kazutoshi Tani, Yoshinori FujiyoshiNATURE COMMUNICATIONS 2 2011年1月[査読有り] Influence of the Cytoplasmic Domains of Aquaporin-4 on Water Conduction and Array FormationTadanori Mitsuma, Kazutoshi Tani, Yoko Hiroaki, Akiko Kamegawa, Hiroshi Suzuki, Hiroshi Hibino, Yoshihisa Kurachi, Yoshinori FujiyoshiJOURNAL OF MOLECULAR BIOLOGY 402 (4) 2010年10月[査読有り] Structural and functional characterization of H+,K+-ATPase with bound fluorinated phosphate analogsKazuhiro Abe, Kazutoshi Tani, Yoshinori FujiyoshiJOURNAL OF STRUCTURAL BIOLOGY 170 (1) 2010年4月[査読有り] A Novel Ratchet Mechanism of Gastric H+,K+-ATPase Revealed by Electron Crystallography of Two-dimensional CrystalsKazuhiro Abe, Kazutoshi Tani, Tomohiro Nishizawa, Yoshinori FujiyoshiYAKUGAKU ZASSHI-JOURNAL OF THE PHARMACEUTICAL SOCIETY OF JAPAN 130 (2) 2010年2月[査読有り] Structure and inhibitor of water channel in brainTanimura, Y., Tani, K., Suzuki, H., Nishikawa, K., Kamegawa, A., Hiroaki, Y., Fujiyoshi, Y.Water: The Forgotten Biological Molecule 2010年Inter-subunit interaction of gastric H+,K+-ATPase prevents reverse reaction of the transport cycleKazuhiro Abe, Kazutoshi Tani, Tomohiro Nishizawa, Yoshinori FujiyoshiEMBO JOURNAL 28 (11) 2009年6月[査読有り] Mechanism of Aquaporin-4's Fast and Highly Selective Water Conduction and Proton ExclusionKazutoshi Tani, Tadanori Mitsuma, Yoko Hiroaki, Akiko Kamegawa, Kouki Nishikawa, Yukihiro Tanimura, Yoshinori FujiyoshiJOURNAL OF MOLECULAR BIOLOGY 389 (4) 2009年6月[査読有り] Structural analysis of 2D crystals of gastric H+,K+-ATPase in different states of the transport cycleTomohiro Nishizawa, Kazuhiro Abe, Kazutoshi Tani, Yoshinori FujiyoshiJOURNAL OF STRUCTURAL BIOLOGY 162 (2) 2008年5月[査読有り] Projection structure of a N-terminal deletion mutant of connexin 26 channel with decreased central pore density.Atsunori Oshima, Kazutoshi Tani, Yoko Hiroaki, Yoshinori Fujiyoshi, Gina E SosinskyCell communication & adhesion 15 (1) 2008年5月[査読有り] Aquaporin-4Tani, K., Hiroaki, Y., Fujiyoshi, Y.Clinical Neurology 48 (11) 2008年Aquaporin-4Tani, K., Hiroaki, Y., Fujiyoshi, Y.Clinical Neurology 48 (11) 2008年Dodecamer rotor ring defines H+/ATP ratio for ATP synthesis of prokaryotic V-ATPase from Thermus thermophilusMasashi Toei, Christoph Gerle, Masahiro Nakano, Kazutoshi Tani, Nobuhiko Gyobu, Masatada Tamakoshi, Nobuhito Sone, Masasuke Yoshida, Yoshinori Fujiyoshi, Kaoru Mitsuoka, Ken YokoyamaPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104 (51) 2007年12月[査読有り] Three-dimensional structure of a human connexin26 gap junction channel reveals a plug in the vestibuleOshima, Atsunori, Tani, Kazutoshi, Hiroaki, Yoko, Fujiyoshi, Yoshinori, Sosinsky, Gina E.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104 (24) 2007年6月[査読有り] Two dimensional crystallization and projection structure of a human connexin26A. Oshima, K. Tani, Y. Hiroaki, Y. Fujiyoshi, G. E. SosinskyMicroscopy and Microanalysis 12 (2) 2006年8月[査読有り] Two-dimensional crystallization and analysis of projection images of intact Thermus thermophilus V-ATPaseC Gerle, K Tani, K Yokoyama, M Tamakoshi, M Yoshida, Y Fujiyoshi, K MitsuokaJOURNAL OF STRUCTURAL BIOLOGY 153 (2) 2006年2月[査読有り] Implications of the aquaporin-4 structure on array formation and cell adhesionY Hiroaki, K Tani, A Kamegawa, N Gyobu, K Nishikawa, H Suzuki, T Walz, S Sasaki, K Mitsuoka, K Kimura, A Mizoguchi, Y FujiyoshiJOURNAL OF MOLECULAR BIOLOGY 355 (4) 2006年1月[査読有り] Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich techniqueN Gyobu, K Tani, Y Hiroaki, A Kamegawa, K Mitsuoka, Y FujiyoshiJOURNAL OF STRUCTURAL BIOLOGY 146 (3) 2004年6月[査読有り] Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16)T Maeda, M Inoue, S Koshiba, T Yabuki, M Aoki, E Nunokawa, E Seki, T Matsuda, Y Motoda, A Kobayashi, F Hiroyasu, M Shirouzu, T Terada, N Hayami, Y Ishizuka, N Shinya, A Tatsuguchi, M Yoshida, H Hirota, Y Matsuo, K Tani, T Arakawa, P Carninci, J Kawai, Y Hayashizaki, T Kigawa, S YokoyamaJOURNAL OF BIOLOGICAL CHEMISTRY 279 (13) 2004年3月[査読有り] Inositol 1,4,5-trisphosphate receptor contains multiple cavities and L-shaped ligand-binding domainsC Sato, K Hamada, T Ogura, A Miyazawa, K Iwasaki, Y Hiroaki, K Tani, A Terauchi, Y Fujiyoshi, K MikoshibaJOURNAL OF MOLECULAR BIOLOGY 336 (1) 2004年2月[査読有り] Solution structure of a BolA-like protein from Mus musculusT Kasai, M Inoue, S Koshiba, T Yabuki, M Aoki, E Nunokawa, E Seki, T Matsuda, N Matsuda, Y Tomo, M Shirouzu, T Terada, N Obayashi, H Hamana, N Shinya, A Tatsuguchi, S Yasuda, M Yoshida, H Hirota, Y Matsuo, K Tani, H Suzuki, T Arakawa, P Carninci, J Kawai, Y Hayashizaki, T Kigawa, S YokoyamaPROTEIN SCIENCE 13 (2) 2004年2月[査読有り] Selection and prioritization of targets for protein structure determinationMatsuo, Y., Tani, K.Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 47 (8 Suppl) 2002年Selection and prioritization of targets for protein structure determinationMatsuo, Y., Tani, K.Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 47 (8 Suppl) 2002年Automated search of natively folded protein fragments for high-throughput structure determination in structural genomicsY Kuroda, K Tani, Y Matsuo, S YokoyamaPROTEIN SCIENCE 9 (12) 2000年12月[査読有り] A set of computer programs for determining defocus and astigmatism in electron imagesK Tani, H Sasabe, C ToyoshimaULTRAMICROSCOPY 65 (1-2) 1996年9月[査読有り] 受賞書籍等出版物現代生物科学入門 構造機能生物学・膜タンパク質構造機能生物学藤吉好則, 谷一寿 (担当:共著)STRUCTURE AND INHIBITOR OF WATER CHANNEL IN BRAINY. Tanimura, K. Tani, H. Suzuki, K. Nishikawa, A. Kamegawa, Y. Hiroaki, Y. Fujiyoshi (担当:共著)競争的資金等の研究課題▼▲クライオ電子顕微鏡を用いた膜タンパク質の高分解能動的構造解析と技術人材育成支援創薬等ライフサイエンス研究支援基盤事業研究期間: 2017年9月 - 現在代表者: 谷 一寿電子線トモグラフィーと結晶学を組み合わせた膜タンパク質の構造解析手法の確立科学研究費助成事業研究期間: 2017年6月 - 現在光合成細菌由来コア光捕集複合体の光エネルギー変換最適化の構造基盤解明科学研究費助成事業研究期間: 2022年4月 - 2025年3月代表者: 谷 一寿病原細菌エフェクターによるNF-κB経路を標的とした感染機構の解析科学研究費助成事業 基盤研究(B)研究期間: 2020年4月 - 2024年3月代表者: 水島 恒裕, 谷 一寿, Kim Minsoo電子線トモグラフィーと結晶学を組み合わせた膜タンパク質の構造解析手法の確立科学研究費助成事業 挑戦的研究(萌芽)研究期間: 2017年6月 - 2020年3月代表者: 谷 一寿チャネルを中心とした構造生理学的研究科学研究費助成事業 基盤研究(S)研究期間: 2015年5月 - 2020年3月代表者: 藤吉 好則, 大嶋 篤典, 谷 一寿, 阿部 一啓, 入江 克雅脳におけるアクアポリン４の立体構造と機能連関科学研究費助成事業 基盤研究(C)研究期間: 2014年4月 - 2017年3月代表者: 谷 一寿, 藤吉 好則プロトン濃度勾配維持に関連する膜タンパク質の電子線結晶学を用いた構造機能解析科学研究費助成事業 若手研究(B)研究期間: 2010年4月 - 2014年3月代表者: 谷 一寿, 藤吉 好則, 阿部 一啓 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 TRIOS researchmap Email ryuheiccs.tsukuba.ac.jp 研究キーワード▼▲生物物理学ソフトマターの物理非平衡物理タンパク質・核酸物理化学理論化学化学物理自由エネルギー地形計算化学バイオインフォマティクスレアイベントサンプリング機械学習インシリコ創薬受容体液-液相分離膜透過エピジェネティクス核膜輸送分散型計算経歴2019年2月 - 現在筑波大学 計算科学研究センター 准教授 2018年4月 - 2019年1月筑波大学 計算科学研究センター 助教 2015年4月 - 2018年3月日本学術振興会 特別研究員 PD 2014年4月 - 2015年3月筑波大学 計算科学研究センター 研究員 2011年4月 - 2014年3月理化学研究所 計算科学研究機構 特別研究員 論文▼▲Development of Membrane Permeability Coefficient by Means of Novel Molecular Dynamics MethodsRyuhei Harada, Yuki Mitsuta, Yasuteru ShigetaYAKUGAKU ZASSHI 144 (5) 2024年5月[査読有り] Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP)Raja Norazireen, Raja Ahmad, Long-teng Zhang, Rikuri Morita, Haruna Tani, Yong Wu, Takeshi Chujo, Akiko Ogawa, Ryuhei Harada, Yasuteru Shigeta, Kazuhito Tomizawa, Fan-Yan WeiNucleic Acids Research 52 (3) 2023年12月[査読有り] Design of Electron-Donating Group Substituted 2-PAM Analogs as Antidotes for Organophosphate Insecticide PoisoningNalinee Kongkaew, Kowit Hengphasatporn, Yuwanda Injongkol, Pitchayathida Mee-udorn, Liyi Shi, Panupong Mahalapbutr, Phornphimon Maitarad, Ryuhei Harada, Yasuteru Shigeta, Thanyada Rungrotmongkol, Alisa S. VangnaiRSC Advances 13 2023年11月[査読有り] Latrunculin Resistance Mechanism of Non-Conventional Actin NAP1 Uncovered by Molecular Dynamics SimulationsRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaCytoskeleton 81 2023年10月[査読有り] A Structural Refinement Technique for Protein-RNA Complexes Using Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 ProteinNitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei HaradaBulletin of the Chemical Society of Japan 96 (7) 2023年7月[査読有り] A Variety of Initial Velocities in Restarting Molecular Dynamics Simulations Promotes Protein TransitionsYohei Munei, Yasuteru Shigeta, Ryuhei HaradaChemistry Letters, 52 (5) 2023年6月[査読有り] Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy AnalysesYohei Munei, Kowit Hengphasatporn, Yuta Hori, Ryuhei Harada, Yasuteru ShigetaJournal of Agricultural and Food Chemistry 71 (24) 2023年6月[査読有り] Efficient Screening of Protein-Ligand Complexes in Lipid Bilayers Using LoCoMock ScoreRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Computer-Aided Molecular Design, 37 2023年3月[査読有り] Free-energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling MethodsRyuhei Harada, Rikuri Morita, Yasuteru ShigetaJournal Chemical Information and Modeling 63 (1) 2023年1月[査読有り] Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational SubspaceTakunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Chemical Information and Modeling 62 (23) 2022年12月[査読有り] Identifying Antibiotics based on Structural Differences in the Conserved Allostery from Mitochondrial Heme-copper OxidasesYuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori ShintaniNature Communications 13 2022年12月[査読有り] Promising SARS-CoV-2 Main Protease Inhibitor Ligand-Binding Modes Evaluated Using LB-PaCS-MD/FMOKowit Hengphasatporn, Ryuhei Harada, Patcharin Wilasluck, Peerapon Deetanya, Edwin R Sukandar, Warinthorn Chavasiri, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol, Kittikhun Wangkanont, Yasuteru ShigetaScientific Report 12 (1) 2022年10月[査読有り] Autism-Associated Mutation in Hevin Induces Endoplasmic Reticulum Stress Through Structural InstabilityTakumi Taketomi, Takunori Yasuda, Rikuri Morita, Jaehyun Kim, Yasuteru Shigeta, Cagla Eroglu, Ryuhei Harada, Fuminori TsurutaScientific Report 12 2022年7月[査読有り] The Structural Validation by G-factor Regulates Boost Potentials Employed in Conformational Sampling of ProteinsTakunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Chemical Information and Modeling 62 (14) 2022年7月[査読有り] The Role of ATP in Solubilizing RNA-binding Protein Fused in SarcomaHayato Aida, Yasuteru Shigeta, Ryuhei HaradaProteins: Structure, Function, and Bioinformatics 90 (8) 2022年7月[査読有り] Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MDHayato Aida, Yasuteru Shigeta, Ryuhei HaradaMaterials 15 (4) 2022年2月[査読有り] Integrate In Silico Studies on the Role of Nicotinamide Adenine Dinucleotide (NADH) Binding in Activating C-terminal Binding Protein 2 (CtBP2)Tsukasa Aoyagi, Ryunosuke Yoshino, Yuki Mitsuta, Rikuri Morita, Ryuhei Harada, Yasuteru ShigetaChemistry Letters 51 2022年1月[査読有り] Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Molecular Biology 434 (2) 2022年1月[査読有り] Phosphorylation on the Accessory Domain of Yeast Histone Chaperone yNap1 Exposes the Nuclear Export SequenceSyo Ashida, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaProteins: Structure, Function, and Bioinformatics 90 (2) 2022年1月[査読有り] Residue Folding Degree - Relationship to Secondary Structure Categories and use as Collective VariableVladimir Sladek, Ryuhei Harada, Yasuteru ShigetaInternational Journal of Molecular Sciences 22 (23) 2021年12月[査読有り] Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics CalculationsKoki Yanagki, Yuki Mitsuta, Kenta Takaoka, Teruyuki Takahashi, Kowit Hengphasatporn, Ryuhei Harada, Yasuteru ShigetaChemistry Letters 50 (12) 2021年12月[査読有り] Structural Variations of Metallothionein with or without Zinc Ions Elucidated Using Molecular Dynamics SimulationsRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaThe Journal of Physical Chemistry B 125 (46) 2021年11月[査読有り] A Post-Process to Estimate an Approximated Minimal Free Energy Path Based on Local CentroidsRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaChemical Physics Letters 782 2021年8月[査読有り] Independent Non-targeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of ProteinsTakunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Chemical Theory and Computation 17 2021年8月[査読有り] In Silico Mutational Analyses Reveal Different Ligand-Binding Abilities of Double Pockets of Medaka Fish Taste Receptor Type 1 Essential for Efficient Taste RecognitionsHayato Aida, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaPhysical Chemistry Chemical Physics 23 (36) 2021年8月[査読有り] Split Conformation of Chaetomium Thermophilum Hsp104 DisaggregaseYosuke Inoue, Yuya Hanazono, Kentaro Noi, Akihiro Kawamoto, Masato Kimatsuka, Ryuhei Harada, Kazuki Takeda, Ryoichi Kita, Natsuki Iwamasa, Kyoka Shibata, Keiichi Noguchi, Yasuteru Shigeta, Keiichi Namba, Teru Ogura, Kunio Miki, Kyosuke Shinohara, Masafumi YohdaStructure 29 2021年7月[査読有り] pyProGA - A PyMOL Plugin for Protein Residue Network AnalysisVladimir Sladek, Yuta Yamamoto, Ryuhei Harada, Mitsuo Shoji, Yasuteru ShigetaPLoS ONE 16 (7) 2021年7月[査読有り] Comprehensive Predictions of Secondary Structures for Comparative Analysis in Different SpeciesRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Structural Biology 213 (2) 2021年4月[査読有り] The Folding of Trp-cage is Regulated by Stochastic Flip of the Sidechain of TryptophanTakunori Yasuda, Yasuteru Shigeta, Ryuhei HaradaChemistry Letters 50 (1) 2021年1月[査読有り] Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural ExplorationsRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaBulletin of the Chemical Society of Japan 94 (1) 2021年1月[査読有り] Enhanced Conformational Sampling Method Based on Anomaly Detection Parallel Cascade Selection Molecular Dynamics: ad-PaCS-MDRyuhei Harada, Kota Yamaguchi, Yasuteru ShigetaJournal of Chemical Theory and Computation 16 (10) 2020年10月[査読有り] The Molecular Mechanism on the Actin-Binding Domain of the Alpha-Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis ExperimentsRikuri Morita, Kentaro Nakano, Yasuteru Shigeta, Ryuhei HaradaThe Journal of Physical Chemistry B 124 (39) 2020年10月[査読有り] Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis Based Parallel Cascade Selection Molecular DynamicsTakanori Yasuda, Yasuteru Shigeta, Ryuhei HaradaJournal of Chemical Information and Modeling 60 (8) 2020年8月[査読有り] The Dynamics of S-adenosyl-methionine and S-adenosyl-homo-cysteine in Mouse Dnmt1 is Driven from their Structural FlexibilitiesTakunori Yasuda, Yasuteru Shigeta, Ryuhei HaradaChemistry Letters 49 (7) 2020年7月[査読有り] Regenerations of Initial Velocities in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Enhance the Conformational Transitions of ProteinsHayato Aida, Yasuteru Shigeta, Ryuhei HaradaChemistry Letters 49 (7) 2020年7月[査読有り] Distribution of Counter Ions in Negatively-charged Lipid/Water/Air Interface: Molecular Dynamics StudyTeruyuki Takahashi, Ryuhei Harada, Yasuteru ShigetaChemistry Letters 49 (4) 2020年4月[査読有り] Protein Dynamics and the Folding DegreeVladimir Sladek, Ryuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling 60 (3) 2020年3月[査読有り] Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of ProteinsRyuhei Harada, Vladimir Sladek, Yasuteru ShigetaJournal of Chemical Information and Modeling 59 (12) 2019年11月[査読有り] Selection Rules for Outliers in Outlier Flooding Method Regulate its Conformational Sampling EfficiencyRyuhei Harada, Vladimir Sladek, Yasuteru ShigetaJournal of Chemical Information and Modeling 59 (9) 2019年9月[査読有り] Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-localized Prediction of Conformational Transitions in Protein DynamicsRyuhei Harada, Vladimir Sladek Yasuteru ShigetaJournal of Chemical Theory and Computation 15 (9) 2019年9月[査読有り] Parallel Cascade Selection Molecular Dynamics Simulation to Screen for Protein Complexes Generated by Rigid DockingRyuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru ShigetaJournal of Molecular Graphics and Modeling 92 2019年7月[査読有り] Temperature-Pressure Shuffling Outlier Flooding Method Enhances the Conformational Sampling of ProteinsRyuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru ShigetaJournal of Computational Chemistry 40 (15) 2019年4月[査読有り] Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-Order Molecular Dynamics SimulationHayato Aida, Ryuhei Harada, Yasuteru ShigetaChemistry Letters 48 (4) 2019年3月[査読有り] Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics StudyMasato Kimatsuka, Ryuma Sato, Ryuhei Harada, Mitsuo Shoji, Yasuteru ShigetaChemistry Letters 48 (3) 2019年2月[査読有り] Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy CalculationsRyuhei Harada, Yasuteru ShigetaJournal of Chemical Theory and Computation 15 (1) 2019年1月[査読有り] The Formation of Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular DynamicsRyuhei Harada, Hayato Aida, Yasuteru ShigetaChemistry Letters 47 (10) 2018年9月[査読有り] Selection Rules on Initial Structures in Parallel Cascade Selection Molecular Dynamics Affect Conformational Sampling EfficiencyRyuhei Harada, Yasuteru ShigetaJournal of Molecular Graph and Modeling 85 2018年9月[査読有り] Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of ProteinsRyuhei HaradaBulletin of the Chemical Society of Japan 91 (9) 2018年9月[査読有り] How does Friction Coefficient Affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?Ryuhei Harada, Yasuteru ShigetaChemistry Letters 47 (9) 2018年8月[査読有り] Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square DeviationRyuhei Harada, Yasuteru ShigetaJournal of Chemical Information and Modeling 58 (7) 2018年8月[査読有り] How Low-Resolution Structural Data Predict the Conformational Changes of a Protein: A Study on Data-Driven Molecular Dynamics SimulationsRyuhei Harada, Yasuteru ShigetaPhysical Chemistry Chemical Physics 20 (26) 2018年7月[査読有り] Developments of Innovative Molecular Simulation Methods for Understanding the Biological FunctionsRyuhei HaradaChemical Industry 69 (7) 2018年7月Coulomb and CH–π Interactions in (6–4) Photolyase–DNA Complex Dominate DNA Binding and Repair AbilityYuma Terai, Ryuma Sato, Takako Yumiba, Ryuhei Harada, Kohei Shimizu, Tatsuya Toga, Tomoko Ishikawa, Takashi Todo, Shigenori Iwai, Yasuteru Shigeta, Junpei YamamotoNucleic Acid Research 46 (13) 2018年7月[査読有り] On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of ProteinsRyuhei Harada, Yasuteru ShigetaJournal of Chemical Theory and Computation 14 (6) 2018年6月[査読有り] Programed Dynamical Ordering in Self-Organization Processes of a Nanocube: A Molecular Dynamics StudyRyuhei Harada, Takako Mashiko, Masanori Tachikawa, Shuichi Hiraoka, Yasuteru ShigetaPhysical Chemistry Chemical Physics 20 (14) 2018年[査読有り] The Binding Structure and Affinity of Photodamaged Duplex DNA with Members of the Photolyase/Cryptochrome Family: A Computational StudyRyuma Sato, Ryuhei Harada, Yasuteru ShigetaBiophysics and Physicobiology 15 2018年1月[査読有り] An Assessment of Optimal Time Scale of Conformational Resampling for Parallel Cascade Selection Molecular DynamicsRyuhei Harada, Yasuteru ShigetaMolecular Simulation 44 (3) 2018年[査読有り] Temperature-shuffled Parallel Cascade Selection Molecular Dynamics Accelerates the Structural Transitions of ProteinsRyuhei Harada, Yasuteru ShigetaJournal of Computational Chemistry 38 (31) 2017年12月[査読有り] Self-Avoiding Conformational Sampling Based on Histories of Past Conformational SearchesRyuhei Harada, Yasuteru ShigetaJournal 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 EventsRyuhei Harada, Yasuteru ShigetaBulletin of the Chemical Society of Japan 90 (11) 2017年11月[査読有り] Structural Dissimilarity Sampling with Dynamically Self-Guiding SelectionRyuhei Harada, Yasuteru ShigetaJournal of Computational Chemistry 38 (22) 2017年8月[査読有り] Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate ConformationsYuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki HayashiThe Journal of Physical Chemistry B 121 (22) 2017年6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 ShigetaChemistry Letters 46 (6) 2017年6月[査読有り] Identification of the Key Interactions in Structural Transition Pathway of FtsZ from Staphylococcus AureusJunso Fujita*, Ryuhei Harada*, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi Matsumura (*Equally Contributed)Journal of Structural Biology 198 (2) 2017年5月Common Folding Processes of Mini-Proteins: Partial Formations of Secondary Structures Initiate the Immediate Protein FoldingRyuhei Harada, Yu Takano, Yasuteru ShigetaJournal of Computational Chemistry 38 (11) 2017年4月[査読有り] Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of ProteinsRyuhei Harada, Yasuteru ShigetaJournal of Chemical Theory and Computation 13 (3) 2017年3月[査読有り] Classical Cumulant Dynamics for Statistical Chemical PhysicsYasuteru 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 ShojiMolecular Simulation 43 (13-16) 2017年[査読有り] Theoretical Analyses on a Flipping Mechanism of UV-induced DNA DamageRyuma Sato, Ryuhei Harada, Yasuteru ShigetaBiophysics 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) MethodRyuhei Harada, Tomotake Nakamura, Yasuteru ShigetaBulletin 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 CytoplasmIsseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael FeigeLife 5 2016年11月[査読有り] Molecular Mechanisms of Substrate Specificities of Uridine-Cytidine KinaseWataru Tanaka, Mitsuo Shoji, Fumiaki Tomoike, Yuzuru Ujiie, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Katsumasa Kamiya, Toyokazu Ishida, Ryoji Masui, Seiki Kuramitsu, Yasuteru ShigetaBiophysics and Physicobiology 13 2016年6月[査読有り] TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of ProteinsRyuhei Harada, Yu Takano, Yasuteru ShigetaJournal of Chemical Theory and Computation 12 (5) 2016年5月[査読有り] Sparsity-Weighted Outlier FLOODing (OFLOOD) Method: Efficient Rare Event Sampling Method Using Sparsity of DistributionRyuhei Harada, Tomotake Nakamura, Yasuteru ShigetaJournal of Computational Chemistry 37 (8) 2016年3月[査読有り] Parallel Cascade Selection Molecular Dynamics for Efficient Conformational Sampling and Free Energy Calculation of ProteinsAkio Kitao, Ryuhei Harada, Yasutaka Nishihara, Duy Phuoc TranProceedings of the International Conference of Computational Methods in Sciences and Engineering 2016 (ICCMSE-2016) 1790 2016年[査読有り] Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of ProteinsRyuhei Harada, Akio KitaoJournal 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) MethodRyuhei Harada, Tomotake Nakamura, Yasuteru ShigetaChemical Physics Letters 639 2015年10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 SolventRyuhei Harada, Yu Takano, Yasuteru ShigetaChemical Physics Letters 630 2015年6月[査読有り] Complete Atomistic Model of a Bacterial Cytoplasm for Integrating Physics, Biochemistry, and Systems BiologyMichael Feig, Ryuhei Harada, Takaharu Mori, Isseki Yu, Koichi Takahashi, Yuji SugitaJournal of Molecular Graphics and Modeling 58 2015年5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, ChignolinRyuhei Harada, Yu Takano, Yasuteru ShigetaJournal of Computational Chemistry 36 (10) 2015年4月[査読有り] Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body SystemsYasuteru Shigeta, Ryuhei Harada, Megumi Kayanuma, Mitsuo ShojiInternational Journal of Quantum Chemistry 115 (5) 2015年3月[査読有り] Protein Folding Pathways Extracted by OFLOOD: Outlier FLOODing MethodRyuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru ShigetaJournal of Computational Chemistry 36 (2) 2015年1月[査読有り] Simple, yet Powerful Methodologies for Conformational Sampling of ProteinsRyuhei Harada, Yu Takano, Takeshi Baba, Yasuteru ShigetaPhysical Chemistry Chemical Physics 17 (9) 2015年[査読有り] Cascade-type Massive Parallel Simulation for Protein Conformation Transition Pathway SearchYasutaka Nishihara, Ryuhei Harada, Akio KitaoProceedings 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 HydrolaseTakeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru ShigetaJournal of Computational Chemistry 35 (16) 2014年6月[査読有り] Fluctuation Flooding Method (FFM) for Accelerating Conformational Transitions of ProteinsRyuhei Harada, Yu Takano, Yasuteru ShigetaThe Journal of Chemical Physics 140 (12) 2014年3月[査読有り] Conformational Transition Pathway and Free Energy Analyses of Proteins by Parallel Cascade Selection Molecular Dynamics (PaCS-MD)Ryuhei Harada, Yasutaka Nishihara, Nobuhiko Wakai, Akio KitaoInternational Conference of Computational Methods in Sciences and Engineering 2014 1618 2014年[査読有り] Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to Generate Conformational Transition PathwayRyuhei Harada, Akio KitaoThe Journal of Chemical Physics 139 (3) 2013年7月[査読有り] Reduced Native State Stability in Crowded Cellular Environment due to Protein-Protein InteractionsRyuhei Harada, Naoya Tochio, Takanori Kigawa, Yuji Sugita, Michael FeigJournal of the American Chemical Society 135 (9) 2013年3月[査読有り] Protein Crowding Affects Hydration Structure and DynamicsRyuhei Harada, Yuji Sugita, Michael FeigJournal of the American Chemical Society 134 (10) 2012年3月[査読有り] The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed ComputingRyuhei Harada, Akio KitaoJournal of Chemical Theory and Computation 8 (1) 2012年1月[査読有り] Exploring the Folding Free Energy Landscape of a Beta-Hairpin Miniprotein, Chignolin, Using Multiscale Free Energy Landscape Calculation MethodRyuhei Harada, Akio KitaoThe Journal of Physical Chemistry B 115 (27) 2011年7月[査読有り] Multi-Scale Free Energy Landscape Calculation Method by Combination of Coarse-Grained and All-Atom ModelsRyuhei Harada, Akio KitaoChemical Physics Letters 503 2011年2月[査読有り] 受賞▼▲2024年6月UBE学術振興財団 援助金 2024年6月UBE学術振興財団 学術奨励賞 2024年4月G-7奨学財団 令和６年度 研究開発助成事業 定期公募（ＩＴ） 2024年4月豊田理化学研究所 豊田理研スカラー（Phase1） 2024年4月島津科学技術振興財団 研究開発助成 2024年4月小柳財団 研究開発助成 2024年1月カシオ科学振興財団 研究助成 2023年7月Bulletin of the Chemical Society of Japan, Selected Paper（日本化学会 欧文誌 優秀論文） 2023年4月豊田理化学研究所 豊田理研スカラー 2023年3月日立財団 倉田奨励金 2022年11月筑波大学 幸多き人生 100 年時代を創る『知』活用プログラム 2022年11月日本薬学会 構造活性相関部会 構造活性相関シンポジウム 優秀発表賞（SAR Presentation Award） 2022年11月住友財団 基礎科学研究助成 2022年9月日揮・実吉奨学会 研究助成制度 2022年7月三島海雲記念財団 学術研究奨励金 2022年1月American Chemical Society, Journal of Chemical Information and Modeling, Editorial Advisory Board 2021年4月筑波大学 若手教員特別奨励賞 2021年4月科学技術分野の文部科学大臣表彰 若手科学者賞 2020年10月筑波大学 若手教員奨励賞 2019年12月分子シミュレーション学会 学術賞 2019年3月日本物理学会 若手奨励賞 2019年2月Royal Society of Chemistry Physical Chemistry Chemical Physics Hot Article Collection 2018年3月日本化学会 進歩賞 2017年9月The 4th BIOPHYSICS Editors' Choice Award 2016年11月Bulletin of the Chemical Society of Japan, Selected Paper（日本化学会 欧文誌 優秀論文） 2016年11月日本生物物理学会年会 若手招待講演賞 2015年4月日本学術振興会 特別研究員（PD） 特別研究奨励費 2012年9月日本生物物理学会年会 若手招待講演証 2010年11月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▼▲Rubiscoを改良する構造的要因の決定挑戦的研究（萌芽）[代表] 松村 浩由 [分担] 原田 隆平 直接経費: 750千円 間接経費: 225千円 課題番号: 23K18033研究期間: 2023年7月 - 2026年3月公益財団法人 UBE学術振興財団 援助金[代表] 原田 隆平 直接経費: 1,000千円研究期間: 2024年6月 - 2025年3月疾患原因につながる相互作用を特定する異常検知システムの開発公益財団法人 G-7奨学財団 令和６年度研究開発助成事業定期公募（ＩＴ）[代表] 原田 隆平 直接経費: 900千円 間接経費: 100千円研究期間: 2024年4月 - 2025年3月分子凝集をトリガーとする酵素阻害の現象解明と新規創薬分野への展開豊田理研スカラー（Phase1） [共同代表] 原田 隆平 直接経費: 1,000千円研究期間: 2024年4月 - 2025年3月タンパク質の複合体と相互作用を高精度に計測する計算技術の開発[代表] 原田 隆平 直接経費: 1,000千円研究期間: 2024年4月 - 2025年3月病原菌においてヘム濃度を感知・調整するタンパク質ダイナミクスの解明研究助成金 [代表] 原田 隆平 直接経費: 1,000千円研究期間: 2024年4月 - 2025年3月タンパク質と核酸の「揺らぎ」を考慮したフレキシブルドッキングに基づく複合体モデリング技術の開発研究助成金 [代表] 原田 隆平 直接経費: 1,000千円研究期間: 2024年1月 - 2024年12月拡張サンプリング手法 (PaCS-MD, OFLOOD等) を用いた論理的創薬手法に関する研究[代表] 原田 隆平 直接経費: 1,000千円 間接経費: 300千円研究期間: 2023年10月 - 2024年9月生物学的相分離を予測・体系化する分子シミュレーション技術の開発と応用研究助成制度 [代表] 原田 隆平 直接経費: 1,800千円 間接経費: 200千円研究期間: 2022年9月 - 2024年8月令和5年度 学術センター（量子生命情報研究センター）形成支援事業[分担] 原田 隆平 直接経費: 1,000千円研究期間: 2023年8月 - 2024年3月細胞表面での分子動態解析のための多角的構造解析プラットフォームの構築TIA連携プログラム [代表] 田中 良和 [分担] 原田 隆平 直接経費: 700千円研究期間: 2023年6月 - 2024年3月日本曹達との共同研究（寄付金）[代表] 原田 隆平 直接経費: 500千円研究期間: 2023年4月 - 2024年3月タンパク質の基質特異性発現メカニズムを解明する分子シミュレーション手法の開発：新規基質の合理的デザイン実現にむけて豊田理研スカラー [代表] 原田 隆平 直接経費: 1,000千円研究期間: 2023年4月 - 2024年3月先端インシリコ創薬技術で実現する化合物のフレキシブルドッキングと結合ポケットのテーラーメイドデザイン倉田奨励金 [代表] 原田 隆平 直接経費: 1,000千円研究期間: 2023年3月 - 2024年3月分子動力学計算と機械学習を援用してタンパク質の構造変化を予測する基盤研究(C) [代表] 原田 隆平 直接経費: 3,200千円 間接経費: 960千円 課題番号: 21K06094研究期間: 2021年4月 - 2024年3月中分子環状ペプチドの生体膜透過プロセスを抽出・評価する計算技術の開発基礎科学研究助成 [代表] 原田 隆平 直接経費: 1,300千円研究期間: 2022年11月 - 2023年10月分子シミュレーションに基づくヒト由来味覚受容体の味物質認識メカニズムの解明2022年度 学術研究奨励金（自然科学部門/個人研究奨励金）[代表] 原田 隆平 直接経費: 1,000千円研究期間: 2022年7月 - 2023年6月感染爆発の原因となる標的分子の阻害剤発見を加速する革新的インシリコ技術の創出幸多き人生 100 年時代を創る『知』活用プログラム [代表] 原田 隆平 直接経費: 500千円（辞退）研究期間: 2022年11月 - 2023年3月研究基盤支援プログラム（Cタイプ）[代表] 原田 隆平 直接経費: 500千円研究期間: 2020年7月 - 2021年3月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研究基盤支援プログラム（Aタイプ）[代表] 原田 隆平 直接経費: 1,000千円研究期間: 2019年8月 - 2020年3月研究基盤支援プログラム（Cタイプ）[代表] 原田 隆平 直接経費: 500千円研究期間: 2019年7月 - 2020年3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) [代表] 原田 隆平 直接経費: 15,800千円 間接経費: 4,740千円 課題番号: 16H06164研究期間: 2016年4月 - 2019年3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 [代表] 原田 隆平 直接経費: 3,400千円 間接経費: 1,020千円 課題番号: 15J03797研究期間: 2015年4月 - 2018年3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) [代表] 原田 隆平 直接経費: 3,200千円 間接経費: 960千円 課題番号: 26840056研究期間: 2014年4月 - 2016年3月 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 TRIOS researchmap Email horiccs.tsukuba.ac.jp 研究キーワード理論化学量子化学計算化学経歴2019年4月 - 現在筑波大学 計算科学研究センター 助教 2018年4月 - 2019年3月九州大学 先導物質化学研究所 特任助教 2017年4月 - 2018年3月九州大学 先導物質化学研究所 学術研究員 論文▼▲Network Topology Diversification of Porous Organic SaltsHiroi Sei, Kouki Oka, Yuta Hori, Yasuteru Shigeta, Norimitsu TohnaiChemical Science 2024年Predicting and analyzing organic reaction pathways by combining machine learning and reaction network approachesIda, Tomonori, Kojima, Honoka, Hori, YutaCHEMICAL COMMUNICATIONS 59 (83) 2023年10月Development of an Iron(II) Complex Exhibiting Thermal- and Photoinduced Double Proton-Transfer-Coupled Spin Transition in a Short Hydrogen BondTakumi Nakanishi, Yuta Hori, Yasuteru Shigeta, Hiroyasu Sato, Ryoji Kiyanagi, Koji Munakata, Takashi Ohhara, Atsushi Okazawa, Rintaro Shimada, Akira Sakamoto, Osamu SatoJournal of the American Chemical Society 2023年8月1T/1H-SnS2 Sheets for Electrochemical CO2 Reduction to FormateKawabe, Yusuke, Ito, Yoshikazu, Hori, Yuta, Kukunuri, Suresh, Shiokawa, Fumiya, Nishiuchi, Tomohiko, Jeong, Samuel, Katagiri, Kosuke, Xi, Zeyu, Li, Zhikai, Shigeta, Yasuteru, Takahashi, YasufumiACS nano 17 (12) 2023年6月Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy AnalysesMunei, Yohei, Hengphasatporn, Kowi, Hori, Yuta, Harada, Ryuhei, Shigeta, YasuteruJournal of agricultural and food chemistry 71 (24) 2023年6月Enantioselective Amino Acid interactions in SolutionWatanabe, Natsuki, Shoji, Mitsuo, Miyagawa, Koichi, Hori, Yuta, Boero, Mauro, Umemura, Masayuki, Shigeta, YasuteruPHYSICAL CHEMISTRY CHEMICAL PHYSICS 25 (21) 2023年5月[査読有り] Organocatalytic-racemization reaction elucidation of aspartic acid by density functional theoryWatanabe, Natsuki, Hori, Yuta, Shoji, Mitsuo, Boero, Mauro, Shigeta, YasuteruCHIRALITY 35 (9) 2023年4月[査読有り] Observation of proton-transfer-coupled spin transition by single-crystal neutron-diffraction measurementNakanishi, Takumi, Hori, Yuta, Shigeta, Yasuteru, Sato, Hiroyasu, Wu, Shuqi, Kiyanagi, Ryoji, Munakata, Koji, Ohhara, Takashi, Osamu, SatoPhysical Chemistry Chemical Physics 25 (17) 2023年4月[査読有り] Deprotonation-Induced and Ion-Pairing-Modulated Diradical Properties of Partially Conjugated Pyrrole?Quinone ConjunctionShinya, Sugiura, Takashi, Kubo, Yohei, Haketa, Yuta, Hori, Yasuteru, Shigeta, Hayato, Sakai, Taku, Hasobe, Hiromitsu, MaedaJournal of the American Chemical Society 145 (14) 2023年3月Theoretical Characterization of the Electronic and Spin Structures for Iron–Sulfur Cubane in Reduced High-Potential Iron–Sulfur Proteins Using Density Functional TheoryHori, Yuta, Sato, Ayaka, Yasuteru, ShigetaThe Journal of Computer Chemistry, Japan 21 (4) 2023年3月[査読有り] 4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価宗井, 陽平, 堀, 優太, Kowit, Hengphasatporn, 原田, 隆平, 重田, 育照The Journal of Computer Chemistry, Japan 21 (4) 2023年3月[査読有り] 有機分子触媒を用いたアミノ酸ラセミ化反応の理論的研究渡辺, 七都稀, 堀, 優太, 庄司, 光男, 重田, 育照The Journal of Computer Chemistry, Japan 21 (4) 2023年3月[査読有り] New insights into the oxidation process from neutron and X-ray crystal structures of an O2-sensitive [NiFe]-hydrogenaseTakeshi Hiromoto, Koji Nishikawa, Seiya Inoue, Hideaki Ogata, Yuta Hori, Katsuhiro Kusaka, Yu Hirano, Kazuo Kurihara, Yasuteru Shigeta, Taro Tamada, Yoshiki HiguchiChemical Science 2023年Characterization of the Geometrical and Electronic Structures of the Active Site and Its Effects on the Surrounding Environment in Reduced High-Potential Iron–Sulfur Proteins Investigated by the Density Functional Theory ApproachSato, Ayaka, Hori, Yuta, Yasuteru, ShigetaInorganic Chemistry 62 (5) 2023年1月[査読有り] Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic SynthesesMitsuo, Shoji, Natsuki, Watanabe, Hori, Yuta, Kenji, Furuya, Masayuki, Umemura, Mauro, Boero, Yasuteru, ShigetaASTROBIOLOGY 22 (9) 2022年9月[査読有り] Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in SpaceHori, Yuta, Nakamura, Honami, Sakawa, Takahide, Natsuki, Watanabe, Kayanuma, Megumi, Mitsuo, Shoji, Masayuki, Umemura, Yasuteru, ShigetaASTROBIOLOGY 22 (11) 2022年9月[査読有り] Effects of mechanical grinding on the phase behavior and anhydrous proton conductivity of imidazolium hydrogen succinateDekura, Shun, Sunairi, Yoshiya, Okamoto, Kei, Takeiri, Fumitaka, Kobayashi, Genki, Hori, Yuta, Shigeta, Yasuteru, Mori, HatsumiSolid State Ionics 372 2021年12月[査読有り] Proton Conduction Mechanism for Anhydrous Imidazolium Hydrogen Succinate Based on Local Structures and Molecular DynamicsHori, Yuta, Dekura, Shun, Sunairi, Yoshiya, Ida, Tomonori, Mizuno, Motohiro, Mori, Hatsumi, Shigeta, YasuteruThe Journal of Physical Chemistry Letters 12 (22) 2021年6月[査読有り] プロトン伝導性PVPA-xIm複合体のプロトン伝導機構の理論的解明Hori, Yuta, Suetake, Toshiya, Ida, Tomonori, Mizuno, Motohiro, Shigeta, YasuteruThe Journal of Computer Chemistry, Japan 19 (4) 2021年2月[査読有り] Molecular Motions of Imidazole in Poly(vinylphosphonic acid)-imidazole Composites Investigated by Molecular Dynamics SimulationsHori, Yuta, Suetake, Toshiya, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, MotohiroChemistry Letters 50 (1) 2020年10月[査読有り] Three-step Spin State Transition and Hysteretic Proton Transfer in the Crystal of an Iron(II) Hydrazone ComplexNakanishi, Takumi, Hori, Yuta, Wu, Shuqi, Sato, Hiroyasu, Okazawa, Atsushi, Kojima, Norimichi, Horie, Yusuke, Okajima, Hajime, Sakamoto, Akira, Shiota, Yoshihito, Yoshizawa, Kazunari, Osamu, SatoAngewandte Chemie International Edition 59 (35) 2020年6月[査読有り] Local Structures and Dynamics of Imidazole Molecules in Poly(vinylphosphonic acid)–Imidazole Composite Investigated by Molecular DynamicsHori, Yuta, Suetake, Toshiya, Shiota, Yoshihito, Yoshizawa, Kazunari, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, MotohiroACS Applied Polymer Materials 2 (4) 2020年2月[査読有り] Revisiting Formic Acid Decomposition by a Graph-Theoretical ApproachIda, Tomonori, Nishida, Manami, Hori, YutaThe Journal of Physical Chemistry A 123 (44) 2019年10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.Takumi Nakanishi, Yuta Hori, Hiroyasu Sato, Shu-Qi Wu, Atsushi Okazawa, Norimichi Kojima, Takashi Yamamoto, Yasuaki Einaga, Shinya Hayami, Yusuke Horie, Hajime Okajima, Akira Sakamoto, Yoshihito Shiota, Kazunari Yoshizawa, Osamu SatoJournal of the American Chemical Society 141 (36) 2019年9月[査読有り] Mechanistic Insights into Methane Oxidation by Molecular Oxygen under Photoirradiation: Controlled Radical Chain ReactionsHori, Yuta, Abe, Tsukasa, Shiota, Yoshihito, Yoshizawa, KazunariBulletin of the Chemical Society of Japan 92 (11) 2019年8月[査読有り] Role of Amino-Acid Residues for Dioxygen Activation in the Second Coordination Sphere of the Dicopper Site of pMMOMiyanishi, Mayuko, Abe, Tsukasa, Hori, Yuta, Shiota, Yoshihito, Yoshizawa, KazunariInorganic Chemistry 58 (18) 2019年8月[査読有り] Dual Catalytic Cycle of H2 and H2O Oxidations by A Half-Sandwich Iridium Complex: A Theoretical StudyIkeda, Kei, Hori, Yuta, Mahyuddin, Muhammad Haris, Shiota, Yoshihito, Staykov, Aleksandar, Matsumoto, Takahiro, Yoshizawa, Kazunari, Ogo, SeijiInorganic Chemistry 58 (11) 2019年5月[査読有り] Local structures and electronic properties of In atoms in In-doped ZnOHori, Yuta, Shiota, Yoshihito, Ida, Tomonori, Yoshizawa, Kazunari, Mizuno, MotohiroThin Solid Films 685 (1) 2019年5月[査読有り] Cupric-superoxide complex that induces a catalytic aldol reaction-type C–C bond formationAbe, T, Hori, Y, Shiota, Y, Ohta, T, Morimoto, Y, Sugimoto, H, Ogura, T, Yoshizawa, K, Itoh, SCommunications Chemistry 2 (1) 2019年2月[査読有り] Redox behaviour of the β-dihydroporphycene cobalt complex: study on the effect of hydrogenation of the ligandK, Hashimoto, T, Koide, T, Okawara, H, Shimakoshi, Y, Hori, Y, Shiota, K, Yoshizawa, Y., HisaedaDalton Transactions 48 (3) 2019年1月[査読有り] Ground-State Copper(III) Stabilized by N-Confused/N-Linked Corroles: Synthesis, Characterization, and Redox ReactivityYogesh 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 FurutaJournal of the American Chemical Society 140 (22) 2018年6月[査読有り] Catalytic Performance of a Dicopper-Oxo Complex for Methane HydroxylationYuta Hori, Yoshihito Shiota, Tomokazu Tsuji, Masahito Kodera, Kazunari YoshizawaInorganic Chemistry 57 (1) 2018年1月[査読有り] Construction of a Potential Energy Surface Based on a Diabatic Model for Proton Transfer in Molecular PairsHori, Yuta, Ida, Tomonori, Mizuno, MotohiroConcepts, Methods and Applications of Quantum Systems in Chemistry and Physics 2018年1月[査読有り] Local structure and hydrogen bond characteristics of imidazole molecules for proton conduction in acid and base proton-conducting composite materialsYuta Hori, Takuma Chikai, Tomonori Ida, Motohiro MizunoPhysical Chemistry Chemical Physics 20 (15) 2018年[査読有り] A novel approach to Bohmian mechanics using an uncompressed particle methodSugisawa, Hiroki, Hori, Yuta, Ida, Tomonori, Mizuno, MotohiroPhysica E: Low-Dimensional Systems and Nanostructures 104 2018年1月[査読有り] Potential energy construction in the diabatic picture for quantum mechanical rate constants of intermolecular proton transferYuta Hori, Tomonori Ida, Motohiro MizunoPhysical Chemistry Chemical Physics 19 (25) 2017年7月[査読有り] Optimization of the spin-component-scaled factor for electron propagator methodFang-Han Lim, Manami Nishida, Yuta Hori, Tomonori Ida, Motohiro MizunoCHEMICAL PHYSICS LETTERS 678 2017年6月[査読有り] Complete spin contamination-free MP2 methodManami Nishida, Fang-Han Lim, Yuta Hori, Tomonori Ida, Motohiro MizunoCHEMICAL PHYSICS LETTERS 669 2017年2月[査読有り] Simulation of molecular Auger spectra using a two-electron Dyson propagatorYuta Hori, Manami Nishida, Fang-Han Lim, Tomonori Ida, Motohiro MizunoJournal of Electron Spectroscopy and Related Phenomena 207 2016年2月[査読有り] A comparative theoretical study of the hydride transfer mechanisms during LiAlH4 and LiBH4 reductionsYuta Hori, Tomonori Ida, Motohiro MizunoCOMPUTATIONAL AND THEORETICAL CHEMISTRY 1076 2016年1月[査読有り] 受賞▼▲2022年5月2nd International Symposium “Hydrogenomics” Best Poster Award 2022 2020年12月量子生命科学会 量子生命科学会 第二回大会 優秀発表賞 2017年3月金沢大学 金沢大学大学院自然科学研究科長賞 2012年3月金沢大学 金沢大学理工学域長賞 書籍等出版物Hydrogenomics: The Science of Fully Utilizing HydrogenHori, Yuta, Nishikawa, Koji, Shigeta, Yasuteru, Higuchi, Yoshiki (範囲:Biological Enzymes and Hydrogenases)Direct Hydroxylation of Methane: Interplay Between Theory and ExperimentHori, Yuta, Abe, Tsukasa (担当:分担執筆, 範囲:Theoretical Approach to Homogeneous Catalyst of Methane Hydroxylation: Collaboration with Computation and Experiment)高機能性金属錯体が拓く触媒科学:革新的分子変換反応の創出をめざして堀, 優太, 塩田, 淑仁, 吉澤, 一成 (担当:分担執筆, 範囲:計算化学が先導する酵素触媒反応の設計)競争的資金等の研究課題▼▲気相・固相の反応素過程に基づくアミノ酸ホモキラリティー生成機構の解明若手研究研究期間: 2024年4月 - 2027年3月代表者: 堀 優太合成化学と理論計算の融合を起爆剤とする精密設計タンパク質工学の開拓豊田理研スカラー共同研究 (Phase1)研究期間: 2024年4月 - 2025年3月代表者: 堀 優太無水プロトン伝導物質の伝導機構の理解に基づく物質設計クロスオーバー共同研究研究期間: 2024年4月 - 2025年3月代表者: 堀 優太電子共役プロトン移動反応のための電子状態解析基盤共同研究課題研究期間: 2024年4月 - 2025年3月代表者: 堀 優太理論化学による無水水素イオン伝導プロセス機構の解明および材料開発への理論提案豊田理研スカラー研究期間: 2023年4月 - 2024年3月代表者: 堀 優太星間空間におけるアミノ酸ホモキラリティー生成過程の量子化学的探求学術変革領域研究(A)研究期間: 2021年4月 - 2023年3月代表者: 堀 優太水素活性と輸送に立脚した生体内ハイドロジェノミクスの理論展開新学術領域研究（公募研究）研究期間: 2021年4月 - 2023年3月代表者: 堀 優太無水プロトン伝導材料設計に向けた計算化学による機能解析第36回 マツダ研究助成研究期間: 2021年4月 - 2023年3月代表者: 堀 優太プロトン移動を伴う機能性材料開発のための電子状態解析基盤共同研究研究期間: 2021年4月 - 2022年3月代表者: 堀 優太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4月 - 2022年3月代表者: 堀 優太プロトン移動共役型スピン転移反応の理論的解析基盤共同研究課題研究期間: 2020年4月 - 2021年3月代表者: 堀 優太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4月 - 2019年3月代表者: 堀 優太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8月 - 2019年3月代表者: 堀 優太 氏名 Name Kowit Hengphasatporn 所属 所属研究科/学類 職名 助教 研究テーマ 関連リンク Email kowithccs.tsukuba.ac.jp 経歴   論文▼▲Multiple Virtual Screening Strategies for the Discovery of Novel Compounds Active Against Dengue Virus: A Hit Identification StudyK. Hengphasatporn, A. Garon, P. Wolschann, T. Langer, W. Chavasiri, T. Saelee, S. Yasuteru, S. Boonyasuppayakorn, T. Rungrotmongkol*ACS Omega Binding Pattern and Susceptibility of Epigallocatechin Gallate Against Envelope Protein Homodimer of Zika Virus: A Molecular Dynamics Study.K. Hengphasatporn, N. Kungwan, T. Rungrotmongkol*Journal of Molecular Liquids 274 2019年1月Cardol triene inhibits dengue infectivity by targeting kl loops and preventing envelope fusionP. Kanyaboon, T. Saelee, A. Suroengrit, K. Hengphasatporn, T. Rungrotmongkol, W. Chavasiri, and S Boonyasuppayakorn*Scientific Reports 16643 (8) 2018年11月A novel flavanone derivative inhibits dengue virus fusion and infectivity. P. Srivarangkul, W. Yuttithamnon, A. Suroengrit, S. Pankaew, K. Hengphasatporn, T. Rungrotmongkol, P. Phuwapraisirisane, K. Ruxrungtham, S. Boonyasuppayakorn*Antiviral Research 151 2018年1月 氏名 森田 陸離 Name MORITA Rikuri 所属 所属研究科/学類 職名 研究員 研究テーマ 分子動力学を用いた中分子化合物の結合解離過程の研究 関連リンク researchmap Email moritaccs.tsukuba.ac.jp 研究キーワード細胞生物学分子動力学経歴2020年4月 - 現在筑波大学 計算科学研究センター 研究員 論文▼▲Latrunculin resistance mechanism of non‐conventional actin NAP1 uncovered by molecular dynamics simulationsRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaCytoskeleton 2024年2月[査読有り] Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP).Raja Norazireen Raja Ahmad, Long-Teng Zhang, Rikuri Morita, Haruna Tani, Yong Wu, Takeshi Chujo, Akiko Ogawa, Ryuhei Harada, Yasuteru Shigeta, Kazuhito Tomizawa, Fan-Yan WeiNucleic acids research 2023年12月Yeast PRPP amidotransferase assembles into fine granules to promotede novopurine synthesis through intermolecular substrate channelingMasak Takaine, Rikuri Morita2023年6月Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score.Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of computer-aided molecular design 2023年3月[査読有り] Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods.Ryuhei Harada, Rikuri Morita, Yasuteru ShigetaJournal of chemical information and modeling 63 (1) 2023年1月[査読有り] Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational SubspaceTakunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Chemical Information and Modeling 62 (23) 2022年12月Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidasesYuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Chai Gopalasingam, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Yoshikazu Ishii, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori ShintaniNature Communications 13 (1) 2022年12月[査読有り] Autism-associated mutation in Hevin/Sparcl1 induces endoplasmic reticulum stress through structural instabilityTakumi Taketomi, Takunori Yasuda, Rikuri Morita, Jaehyun Kim, Yasuteru Shigeta, Cagla Eroglu, Ryuhei Harada, Fuminori TsurutaScientific Reports 12 (1) 2022年12月[査読有り] Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of ProteinsTakunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of Chemical Information and Modeling 62 (14) 2022年7月Phosphorylation in the accessory domain of yeast histone chaperone protein 1 exposes the nuclear export signal sequence.Sho Ashida, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaProteins 90 (2) 2022年2月[査読有り] Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1.Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of molecular biology 434 (2) 2022年1月Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations.Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaThe journal of physical chemistry. B 125 (46) 2021年11月[査読有り] A post-process to estimate an approximated minimal free energy path based on local centroidsRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaCHEMICAL PHYSICS LETTERS 782 2021年11月[査読有り] Integrate in silico studies on the role of nicotinamide adenine dinucleotide (NADH) binding in activating C-terminal binding protein 2 (CtBP2)Tsukasa Aoyagi, Ryunosuke Yoshino, Yuki Mitsuta, Rikuri Morita, Ryuhei Harada, Yasuteru ShigetaChemistry Letters 2021年10月[査読有り] In silico mutational analyses reveal different ligand-binding abilities of double pockets of medaka fish taste receptor type 1 essential for efficient taste recognition.Hayato Aida, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaPhysical chemistry chemical physics : PCCP 23 (36) 2021年9月[査読有り] Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins.Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of chemical theory and computation 17 (9) 2021年9月[査読有り] Comprehensive predictions of secondary structures for comparative analysis in different species.Rikuri Morita, Yasuteru Shigeta, Ryuhei HaradaJournal of structural biology 213 (2) 2021年6月[査読有り] Cell cycle-dependent phosphorylation of IQGAP is involved in assembly and stability of the contractile ring in fission yeast.Rikuri Morita, Osamu Numata, Kentaro Nakano, Masak TakaineBiochemical and biophysical research communications 534 2021年1月[査読有り] Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of ProteinsRikuri Morita, Yasuteru Shigeta, Ryuhei HaradaBULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 94 (1) 2021年1月[査読有り] Molecular Mechanism for the Actin-Binding Domain of α-Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis ExperimentsRikuri Morita, Kentaro Nakano, Yasuteru Shigeta, Ryuhei HaradaThe Journal of Physical Chemistry B 124 (39) 2020年10月[査読有り] Molecular dissection of the actin-binding ability of the fission yeast alpha-actinin, Ain1, in vitro and in vivoRikuri Morita, Masak Takaine, Osamu Numata, Kentaro NakanoJOURNAL OF BIOCHEMISTRY 162 (2) 2017年8月[査読有り] 受賞▼▲2021年7月新学術領域研究「生命金属科学」領域会議 第４回地方巡業（東京） 若手優秀研究発表賞 2019年6月第４６回生体分子科学討論会 優秀ポスター賞 2018年1月国際細胞生物学会 2018 ポスター賞 2017年3月筑波大学 生命環境科学研究科 生物科学専攻 専攻長表彰 2017年3月筑波大学 生命環境科学研究科 研究科長表彰 書籍等出版物競争的資金等の研究課題▼▲アクチン細胞骨格の機能的品質と量を保障する分子機構の解明科学研究費助成事業研究期間: 2023年4月 - 2027年3月代表者: 中野 賢太郎, 松田 真弥, 森田 陸離分子動力学計算とモデル生物で導き出す減数分裂開始機構の実態科学研究費助成事業研究期間: 2023年4月 - 2026年3月代表者: 松田 真弥, 森田 陸離生体膜の両親媒効果を取り込んだドッキングシミュレーション手法の開発科学研究費助成事業研究期間: 2023年4月 - 2025年3月代表者: 森田 陸離任意のタンパク質に蛍光能を付加する分子設計第1回 MOLSIS-CCG GRANT研究期間: 2022年10月 - 2023年9月プリン生合成を制御する細胞内構造体プリノソームの形成機構と役割の解明令和4年度内分泌・代謝学共同研究拠点共同研究研究期間: 2022年4月 - 2023年3月代表者: 森田陸離, 高稲正勝プリン生合成を制御する細胞内構造体プリノソームの形成機構と役割の解明令和3年度内分泌・代謝学共同研究拠点共同研究（若手）研究期間: 2021年4月 - 2022年3月代表者: 森田陸離, 高稲正勝 氏名 宮川 晃一 Name MIYAGAWA Koichi 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 氏名 Name Mrinal Kanti Si 所属 所属研究科/学類 職名 研究員 研究テーマ 関連リンク google scholar Email mrinal.si.gfu.tsukuba.ac.jp 論文Quantitative analysis of essential metals (Magnesium, Calcium and Iron) in various Indian vegetables and fruitsMrinal Kanti Si, Shruti Shriwastri Afshin Ali, Ankush Vaidya, Sudhakar Singh, Kajal Deshmukh, Neha Bhagat, Punam Hanwat, Nandini Sahu, Pallavi Bhagat, Sakshi TilaseINTERNATIONAL JOURNAL OF ENGINEERING RESEARCH & TECHNOLOGY 10 2021年Colorimetric dual sensor for Cu (II) and tyrosine and its application as paper strips for detection in water and human saliva as real samplesGaurav Vyas, Shreya Bhatt, Mrinal Kanti Si, Sana Jindani, Eringathodi Suresh, Bishwajit Ganguly, Parimal PaulSpectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2020年Exploiting σ-hole interaction to design small uncharged ligand molecules to stabilize G-quadruplex-DNA: a computational studyMrinal Kanti Si, Anusuya Saha and Bishwajit GangulyJournal of Molecular Modeling 26 2020年 氏名 Sittiwanichai Sirin Name Sittiwanichai Sirin 所属 所属研究科/学類 職名 研究員 研究テーマ Molecular Dynamics Simulation, Protein Dynamics, Computational Biochemistry, Protein Modeling 関連リンク google scholar Email sirinsccs.tsukuba.ac.jp 論文Binding of Apo and Glycated Human Serum Albumins to an Albumin-Selective Aptamer-Bound Graphene Quantum Dot ComplexSirin Sittiwanichai, Jitti Niramitranon, Deanpen Japrung*, and Prapasiri Pongprayoon*ACS Omega 8 (24) [査読有り] Structural and Dynamic Alteration of Glycated Human Serum Albumin in Schiff Base and Amadori Adducts: A Molecular Simulation StudySirin Sittiwanichai, Deanpen Japrung, Toshifumi Mori*, and Prapasiri Pongprayoon*The Journal of Physical Chemistry B 127 (23) [査読有り] The binding of apo and glucose-bound human serum albumins to a free graphene sheet in aqueous environment: Simulation studiesSirin Sittiwanichai a, Deanpen Japrung b, Prapasiri Pongprayoon a c*Journal of Molecular Graphics and Modelling 110 [査読有り] 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/部門主任 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 TRIOS researchmap Email yujiccs.tsukuba.ac.jp 研究キーワード経歴2016年4月 - 現在筑波大学 計算科学研究センター 教授 論文▼▲Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates.Nakayama, Takuro, Yabuki, Akinori, Nomura, Mami, Shiba, Kogiku, Inaba, Kazuo, Inagaki, YujibioRχiv 2024年1月Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochodrion.Harada, Ryo, Hirakawa, Yoshihisa, Yabuki, Akinori, Kim, Eunsoo, Yazaki, Euki, Kamikawa, Ryoma, Kentaro, Nakano, Eliáš, Marek, Inagaki, YujiMolecular Biology and Evolution 41 (2) 2024年1月[査読有り] Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data.Harada, Ryo, Inagaki, YujiProtist 174 (6) 2023年12月[査読有り] Transcriptome data sets of free-living diplomonads, Treponema sp, and Hexamita sp.Kume, Keitaro, Tsubasa, Gen, Kazuki, Abe, Hiroshi, Komatsuzaki, Euki, Yazaki, Goro, Tanifuji, Ryoma, Kamikawa, Inagaki, Yuji, Hashimoto, TetsuoMICROBIOLOGY RESOURCE ANNOUNCEMENTS 12 (11) 2023年11月[査読有り] AtLASS: A scheme for end-to-end prediction of splice sites using attention-based bi-LSTM.Harada, Ryo, Kume, Keitaro, Horie, Kazumasa, Nakayama, Takuro, Inagaki, Yuji, Amagasa, ToshiyukiIPSJ Transactions on Bioinformatics 16 2023年7月[査読有り] 遺伝子水平伝播が支配するオルガネラ局在ファミリーA DNAポリメラーゼの進化原田亮, 稲垣, 祐司月刊 細胞 55 (6) 2023年4月Fascinating strategies of marine organisms to cope with coming pollutant: Titanium dioxide nanoparticles.Ishitani, Yoshiyuki, Ciacci, Caterina, Ujiié, Yurika, Tame, Akihiro, Tiboni, Mattia, Tanifuji, Goro, Inagaki, Yuji, Frontalini, FabrizioENVIRONMENTAL POLLUTION 330 2023年4月[査読有り] Draft genome sequence of Aduncisulcus paluster, a free-living microaerophilic eukaryote belonging to Fornicata.Ikuko, Yuyama, Kume, Keitaro, Tamura, Takumi, Inagaki, Yuji, Hashimoto, TetsuoMicrobiology Resource Announcements 12 (2) 2023年2月[査読有り] Microheliella maris possesses the most gene-rich mitochondrial genomes in Diaphoretickes.Yazaki, Euki, Yabuki, Akinori, Nishimura, Yuki, Shiratori, Takashi, Inagaki, YujiFrontiers in Ecology and Evolution 10 2022年12月[査読有り] A novel structural maintenance of chromosomes (SMC)-related protein family specific to ArchaeaYoshinaga, Mari, Nakayama, Takuro, Inagaki, YujiFrontiers in Microbiology 13 2022年8月[査読有り] Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA EditingEriko, Matsuo, Kounosuke, Morita, Takuro, Nakayama, Yazaki, Euki, Chihiro, Sarai, Kazuya, Takahashi, Mitsunori, Iwataki, Inagaki, YujiFRONTIERS IN PLANT SCIENCE 13 2022年7月[査読有り] The closest relative of Archaeplastida is revealed by phylogenomic analyses that include Microheliella maris.Yazaki, Euki, Yabuki, Akinori, Imaizumi, Ayaka, Kume, Keitaro, Hashimoto, Tetsuo, Inagaki, YujiOPEN BIOLOGY 12 (4) 2022年4月[査読有り] Ubiquity and origins of structural maintenance of chromosomes (SMC) proteins in eukaryotesYoshinaga, Mari, Inagaki, YujiGenome Biology and Evolution 13 (12) 2021年12月[査読有り] Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and Microheliella maris.Yazaki, Euki, Yabuki, Akinori, Imaizumi, Ayaka, Kume, Keitaro, Hashimoto, Tetsuo, Inagaki, YujibioRχiv 2021年8月Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine speciesYazaki, Euki, Miyata, Ryosuke, Chikami, Yasuhiko, Harada, Ryo, Kawakubo, Takashi, Tanifuji, Goro, Nakayama, Takuro, Yahata, Kensuke, Hashimoto, Tetsuo, Inagaki, YujiParasitology International 83 2021年8月[査読有り] Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids.Ryo, Harada, Inagaki, YujiGenome Biology and Evolution 2021年1月[査読有り] Experimental analysis of diurnal variations in humic-like fluorescent dissolved organic matters in surface seawater.Omori, Yuko, Saeki, AKira, Wada, Shigeki, Inagaki, Yuji, Hama, TakeoFrontiers in Marine Science 7 2020年10月[査読有り] Barthelonids represent a deep-branching matamonad clade with mitochondrion-related organelles predicted to generate no ATP.Euki, Yazaki, Kume, Keitaro, Takashi, Shiratori, Yana, Eglit, Goro, Tanifuji, Ryo, Harada, Alastair, Simpson, Ken-ichiro, Ishida, Tetsuo, Hashimoto, Inagaki, YujiProceedings of the Royal Society B 287 (1934) 2020年9月[査読有り] Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organismsTakuro Nakayama, Kazuya Takahashi, Ryoma Kamikawa, Mitsunori Iwataki, Yuji Inagaki, Goro TanifujiCommunicative & Integrative Biology 13 (1) 2020年6月[査読有り] Mitochondrial genomes of Hemiarma marina and Leucocryptos marina revised the evolution of cytochrome c maturation in Cryptista.Yuki Nishimura, Keitaro Kume, Keito Sonehara, Goro Tanifuji, Takashi Shiratori, Ken-ichiro Ishida, Tetsuo Hashimoto, Yuji Inagaki, Moriya OhkumaFrontiers in Ecology and Evolution 2020年5月[査読有り] 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 InagakiPathogens 2020年4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 InagakiProceedings of the National Academy of Sciences of the United States of America 117 (10) 2020年3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, TetsuoGenome Biology and Evolution 12 (2) 2020年2月[査読有り] Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryoteMatsuo, 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, JunichibioRχiv 2019年10月Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate hostTakuro, Nakayama, Mami, Nomura, Yoshihito, Takano, Tanifuji, Goro, Kogiku, Shiba, Kazuo, Inaba, Inagaki, Yuji, Masakado, KawataProceedings of the National Academy of Science of the United States of America 116 (32) 2019年6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, ShigetaACS Omega 4 (4) 2019年4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, YujiScientific Reports 9 2019年3月[査読有り] Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPaseKristína Záhonová, Romana Petrželková, Matus Valach, Euki Yazaki, Denis V. Tikhonenkov, Anzhelika Butenko, Jan Janouškovec, Štěpánka Hrdá, Vladimír Klimeš, Gertraud Burger, Yuji Inagaki, Patrick J. Keeling, Vladimír Hampl, Pavel Flegontov, Vyacheslav Yurchenko, Marek EliášScientific Reports 8 (1) 2018年12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, YujiJournal of Eukaryotic Microbiology 65 (6) 2018年9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, YujiPeerJ 6 2018年7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 transferMitsuhiro Matsuo, Atsushi Katahata, Soichirou Satoh, Motomichi Matsuzaki, Mami Nomura, Ken-ichiro Ishida, Yuji Inagaki, Junichi ObokataPLOS ONE 13 (7) 2018年7月[査読有り] The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasitesGoro Tanifuji, Shun Takabayashi, Keitaro Kume, Mizue Takagi, Takuro Nakayama, Ryoma Kamikawa, Yuji Inagaki, Tetsuo HashimotoPLoS ONE 13 (3) 2018年3月[査読有り] Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-GroupMatthew W Brown, Aaron A Heiss, Ryoma Kamikawa, Yuji Inagaki, Akinori Yabuki, Alexander K Tice, Takashi Shiratori, Ken-Ichiro Ishida, Tetsuo Hashimoto, Alastair G. B. Simpson, Andrew J. RogerGenome Biology and Evolution 10 (2) 2018年2月[査読有り] Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatomsTakuro Nakayama, Yuji InagakiSCIENTIFIC REPORTS 7 2017年10月[査読有り] Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosisGoro 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. ArchibaldSCIENTIFIC REPORTS 7 2017年9月[査読有り] A Non-photosynthetic Diatom Reveals Early Steps of Reductive Evolution in PlastidsRyoma Kamikawa, Daniel Moog, Stefan Zauner, Goro Tanifuji, Ken-Ichiro Ishida, Hideaki Miyashita, Shigeki Mayama, Tetsuo Hashimoto, Uwe G. Maier, John M. Archibald, Yuji InagakiMOLECULAR BIOLOGY AND EVOLUTION 34 (9) 2017年9月[査読有り] Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomesMichelle 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. RogerNATURE ECOLOGY & EVOLUTION 1 (4) 2017年4月[査読有り] Global Kinetoplastea phylogeny inferred from a large-scale multigene alignment including parasitic species for better understanding transitions from a free-living to a parasitic lifestyleEuki Yazaki, Sohta A. Ishikawa, Keitaro Kume, Akira Kumagai, Takashi Kamaishi, Goro Tanifuji, Tetsuo Hashimoto, Yuji InagakiGENES & GENETIC SYSTEMS 92 (1) 2017年2月[査読有り] Global kinetoplastea phylogeny inferred from a large-scale multigene alignment including parasitic species for better understanding transitions from a free-living to a parasitic lifestyleEuki Yazaki, Sohta A. Ishikawa, Keitaro Kume, Akira Kumagai, Takashi Kamaishi, Goro Tanifuji, Tetsuo Hashimoto, Yuji InagakiGenes and Genetic Systems 92 (1) 2017年[査読有り] Mitochondrial Genome of Palpitomonas bilix: Derived Genome Structure and Ancestral System for Cytochrome c MaturationYuki Nishimura, Goro Tanifuji, Ryoma Kamikawa, Akinori Yabuki, Tetsuo Hashimoto, Yuji InagakiGENOME BIOLOGY AND EVOLUTION 8 (10) 2016年10月[査読有り] Protein folding and evolutionHarada,Ryuhei, Inagaki,Yuji, Yasuteru,ShigetaReference Module in Materials Science and Materials Engineering 2016年6月[査読有り] Ungulate malaria parasitesThomas J. Templeton, Masahito Asada, Montakan Jiratanh, Sohta A. Ishikawa, Sonthaya Tiawsirisup, Thillaiampalam Sivakumar, Boniface Namangala, Mika Takeda, Kingdao Mohkaew, Supawan Ngamjituea, Noboru Inoue, Chihiro Sugimoto, Yuji Inagaki, Yasuhiko Suzuki, Naoaki Yokoyama, Morakot Kaewthamasorn, Osamu KanekoSCIENTIFIC REPORTS 6 2016年3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3月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3月Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes (vol 32, pg 2598, 2015)Ryoma Kamikawa, Goro Tanifuji, Sohta A. Ishikawa, Ken-Ichiro Ishii, Yusei Matsuno, Naoko T. Onodera, Ken-Ichiro Ishida, Tetsuo Hashimoto, Hideaki Miyashita, Shigeki Mayama, Yuji InagakiMOLECULAR BIOLOGY AND EVOLUTION 33 (1) 2016年1月[査読有り] A system for phylogenetic analyses over alignments of next generation sequence dataYuki Nishimura, Toshiyuki Amagasa, Yuji Inagaki, Tetsuo Hashimoto, Hiroyuki KitagawaPROCEEDINGS OF 2016 10TH INTERNATIONAL CONFERENCE ON COMPLEX, INTELLIGENT, AND SOFTWARE INTENSIVE SYSTEMS (CISIS) 2016年[査読有り] Metabolic Capacity of Mitochondrion-related Organelles in the Free-living Anaerobic Stramenopile Cantina marsupialisFumiya Noguchi, Shigeru Shimamura, Takuro Nakayama, Euki Yazaki, Akinori Yabuki, Tetsuo Hashimoto, Yuji Inagaki, Katsunori Fujikura, Kiyotaka TakishitaPROTIST 166 (5) 2015年11月[査読有り] Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid GenomesRyoma Kamikawa, Goro Tanifuji, Sohta A. Ishikawa, Ken-Ichiro Ishii, Yusei Matsuno, Naoko T. Onodera, Ken-Ichiro Ishida, Tetsuo Hashimoto, Hideaki Miyashita, Shigeki Mayama, Yuji InagakiMOLECULAR BIOLOGY AND EVOLUTION 32 (10) 2015年10月[査読有り] Multiple conversion between the genes encoding bacterial class-I release factorsSohta A. Ishikawa, Ryoma Kamikawa, Yuji InagakiSCIENTIFIC REPORTS 5 2015年8月[査読有り] Morphological Identities of Two Different Marine Stramenopile Environmental Sequence Clades: Bicosoeca kenaiensis (Hilliard, 1971) and Cantina marsupialis (Larsen and Patterson, 1990) gen. nov., comb. nov.Naoji Yubuki, Tomas Panek, Akinori Yabuki, Ivan Cepicka, Kiyotaka Takishita, Yuji Inagaki, Brian S. LeanderJOURNAL OF EUKARYOTIC MICROBIOLOGY 62 (4) 2015年7月[査読有り] The Mitochondrial Genomes of a Myxozoan Genus Kudoa Are Extremely Divergent in MetazoaFumihiko Takeuchi, Tsuyoshi Sekizuka, Yumiko Ogasawara, Hiroshi Yokoyama, Ryoma Kamikawa, Yuji Inagaki, Tomoyoshi Nozaki, Yoshiko Sugita-Konishi, Takahiro Ohnishi, Makoto KurodaPLOS ONE 10 (7) 2015年7月[査読有り] Plastid Genome-Based Phylogeny Pinpointed the Origin of the Green-Colored Plastid in the Dinoflagellate Lepidodinium chlorophorumRyoma Kamikawa, Goro Tanifuji, Masanobu Kawachi, Hideaki Miyashita, Tetsuo Hashimoto, Yuji InagakiGENOME BIOLOGY AND EVOLUTION 7 (4) 2015年4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 InagakiPHYCOLOGICAL RESEARCH 63 (1) 2015年1月[査読有り] Genome evolution triggered by acquisition of an endosymbiotic partnerYuji InagakiGENES & GENETIC SYSTEMS 89 (6) 2014年12月Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyleTakuro Nakayama, Ryoma Kamikawa, Goro Tanifuji, Yuichiro Kashiyama, Naohiko Ohkouchi, John M. Archibald, Yuji InagakiPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 (31) 2014年8月[査読有り] Non-Homogeneous置換モデルに基づく進化系統樹推測のMPI/OpenMP HYBRID並列化: 大規模計算システム向けプログラムの開発と性能評価石川,奏太, 中尾,昌広, 稲垣,祐司, 橋本,哲男, 佐藤,三久情報処理学会論文誌. コンピューティングシステム 7 (3) 2014年8月[査読有り] Secondary loss of a cis-spliced intron after the diversification of Giardia intestinalis assemblages.Ryoma Kamikawa, Yuji Inagaki, Tetsuo HashimotoBMC Research Notes 7 2014年7月[査読有り] Secondary loss of a cis-spliced intron during the divergence of Giardia intestinalis assemblagesRyoma Kamikawa, Yuji Inagaki, Tetsuo HashimotoBMC Research Notes 7 (1) 2014年6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 InagakiMobile Genetic Elements 4 (1) 2014年5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 InagakiMobile genetic elements 4 2014年Gene Content Evolution in Discobid Mitochondria Deduced from the Phylogenetic Position and Complete Mitochondrial Genome of Tsukubamonas globosaRyoma Kamikawa, Martin Kolisko, Yuki Nishimura, Akinori Yabuki, Matthew W. Brown, Sohta A. Ishikawa, Ken-ichiro Ishida, Andrew J. Roger, Tetsuo Hashimoto, Yuji InagakiGENOME BIOLOGY AND EVOLUTION 6 (2) 2014年[査読有り] Parallel re-modeling of EF-1α function in eukaryotic evolution: Divergent, low-expressed EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes.Ryoma,Kamikawa, Matthew,W Brown, Yuki,Nishimura, Yoshihiko,Sako, Aaron,A Heiss, Naoji,Yubuki, Ryan,Gawryluk, Alastair,GB Simpson, Andrew,J Roger, Tetsuo,Hashimoto, Yuji,InagakiBMC Evolutionary Biology 13 2013年6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, HPLoS 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 phylogenyTakuya Matsumoto, Masanobu Kawachi, Hideaki Miyashita, Yuji InagakiJOURNAL 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 SequencesYoshiyuki Ishitani, Ryoma Kamikawa, Akinori Yabuki, Masashi Tsuchiya, Yuji Inagaki, Kiyotaka TakishitaJOURNAL OF EUKARYOTIC MICROBIOLOGY 59 (4) 2012年7月[査読有り] Multigene Phylogenies of Diverse Carpediemonas-like Organisms Identify the Closest Relatives of 'Amitochondriate' Diplomonads and RetortamonadsKiyotaka Takishita, Martin Kolisko, Hiroshi Komatsuzaki, Akinori Yabuki, Yuji Inagaki, Ivan Cepicka, Pavla Smejkalová, Jeffrey D. Silberman, Tetsuo Hashimoto, Andrew J. Roger, Alastair G.B. SimpsonProtist 163 (3) 2012年5月[査読有り] Separate Origins of Group I Introns in Two Mitochondrial Genes of the Katablepharid Leucocryptos marinaYuki Nishimura, Ryoma Kamikawa, Tetsuo Hashimoto, Yuji InagakiPLOS ONE 7 (5) 2012年5月[査読有り] RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional HeterogeneitySohta A. Ishikawa, Yuji Inagaki, Tetsuo HashimotoEVOLUTIONARY BIOINFORMATICS 8 2012年[査読有り] An Asynchronous Parallel Genetic Algorithm for the Maximum Likelihood Phylogenetic Tree SearchMiwako Tsuji, Mitsuhisa Sato, Akifumi S. Tanabe, Yuji Inagaki, Tetsuo Hashimoto2012 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION (CEC) 2012 2012年[査読有り] Multigene phylogenetic analyses including diverse radiolarian species support the "Retaria" hypothesis - The sister relationship of Radiolaria and ForaminiferaYoshiyuki Ishitani, Sohta A. Ishikawa, Yuji Inagaki, Masashi Tsuchiya, Kozo Takahashi, Kiyotaka TakishitaMARINE 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"Akinori Yabuki, Takeshi Nakayama, Naoji Yubuki, Tetsuo Hashimoto, Ken-Ichiro Ishida, Yuji InagakiJOURNAL OF EUKARYOTIC MICROBIOLOGY 58 (4) 2011年7月[査読有り] A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorumTakuya Matsumoto, Sohta A. Ishikawa, Tetsuo Hashimoto, Yuji InagakiMOLECULAR PHYLOGENETICS AND EVOLUTION 60 (1) 2011年7月[査読有り] Splintrons in Giardia intestinalis: Spliceosomal introns in a split formKamikawa, R, Inagaki, Y, Roger, AJ, Hashimoto, TCommunicative and Integrative Biology 4 (4) 2011年4月[査読有り] Green-colored Plastids in the Dinoflagellate Genus Lepidodinium are of Core Chlorophyte OriginTakuya Matsumoto, Fumihiko Shinozaki, Tomoko Chikuni, Akinori Yabuki, Kiyotaka Takishita, Masanobu Kawachi, Takeshi Nakayama, Isao Inouye, Tetsuo Hashimoto, Yuji InagakiPROTIST 162 (2) 2011年4月[査読有り] Split Introns in the Genome of Giardia intestinalis Are Excised by Spliceosome-Mediated trans-SplicingRyoma Kamikawa, Yuji Inagaki, Masaharu Tokoro, Andrew J. Roger, Tetsuo HashimotoCURRENT BIOLOGY 21 (4) 2011年2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, YJ. Euk. Microbiol. 58 (2) 2011年1月[査読有り] A novel spliceosome-mediated trans-splicing can change our view on genome complexity of the divergent eukaryote Giardia intestinalisRyoma Kamikawa, Yuji Inagaki, Tetsuo HashimotoBiophysical Reviews 3 (4) 2011年[査読有り] Cercozoa comprises both EF-1 alpha-containing and EFL-containing membersRyoma Kamikawa, Akinori Yabuki, Takuro Nakayama, Ken-ichiro Ishida, Tetsuo Hashimoto, Yuji InagakiEUROPEAN JOURNAL OF PROTISTOLOGY 47 (1) 2011年1月[査読有り] Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacteriumTakuro Nakayama, Yuko Ikegami, Takeshi Nakayama, Ken-ichiro Ishida, Yuji Inagaki, Isao InouyeJOURNAL OF PLANT RESEARCH 124 (1) 2011年1月[査読有り] Mitochondrial genomes from two red tide forming raphidophycean algae Heterosigma akashiwo and Chattonella marina var. marinaIsao Masuda, Ryoma Kamikawa, Manabu Ueda, Kenichi Oyama, Sadaaki Yoshimatsu, Yuji Inagaki, Yoshihiko SakoHARMFUL ALGAE 10 (2) 2011年1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, TJournal 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. g., n. sp., as Inferred from Small Subunit rDNA SequencesNaoji Yubuki, Vit Ceza, Ivan Cepicka, Akinori Yabuki, Yuji Inagaki, Takeshi Nakayama, Isao Inouye, Brian S. LeanderJOURNAL 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 HacrobiaAkinori Yabuki, Yuji Inagaki, Ken-ichiro IshidaPROTIST 161 (4) 2010年10月[査読有り] A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitatsMartin Kolisko, Jeffrey D. Silberman, Ivan Cepicka, Naoji Yubuki, Kiyotaka Takishita, Akinori Yabuki, Brian S. Leander, Isao Inouye, Yuji Inagaki, Andrew J. Roger, Alastair G. B. SimpsonENVIRONMENTAL MICROBIOLOGY 12 (10) 2010年10月[査読有り] Rooting for the root of elongation factor-like protein phylogenyRyoma Kamikawa, Miako Sakaguchi, Takuya Matsumoto, Tetsuo Hashimoto, Yuji InagakiMOLECULAR PHYLOGENETICS AND EVOLUTION 56 (3) 2010年9月[査読有り] A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorumMarianne A. Minge, Kamran Shalchian-Tabrizi, Ole K. Torresen, Kiyotaka Takishita, Ian Probert, Yuji Inagaki, Dag Klaveness, Kjetill S. JakobsenBMC EVOLUTIONARY BIOLOGY 10 2010年6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. fragileHideya Mitsui, Nobuko Arisue, Naoko Sakihama, Yuji Inagaki, Toshihiro Horii, Masami Hasegawa, Kazuyuki Tanabe, Tetsuo HashimotoGENE 450 (1-2) 2010年1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 eukaryotesRyoma Kamikawa, Gabino F. Sanchez-Perez, Yoshihiko Sako, Andrew J. Roger, Yuji InagakiMOLECULAR 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 evolutionKiyotaka Takishita, Yuji InagakiGENE 441 (1-2) 2009年7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 goniomonadsMiako Sakaguchi, Kiyotaka Takishita, Takuya Matsumoto, Tetsuo Hashimoto, Yuji InagakiGENE 441 (1-2) 2009年7月[査読有り] Gene Sampling Can Bias Multi-Gene Phylogenetic Inferences: The Relationship between Red Algae and Green Plants as a Case StudyYuji Inagaki, Yoshihiro Nakajima, Mitsuhisa Sato, Miako Sakaguchi, Tetsuo HashimotoMOLECULAR BIOLOGY AND EVOLUTION 26 (5) 2009年5月[査読有り] A Hypothesis for the Evolution of Nuclear-Encoded, Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenase Genes in "Chromalveolate" MembersKiyotaka Takishita, Haruyo Yamaguchi, Tadashi Maruyama, Yuji InagakiPLOS ONE 4 (3) 2009年3月[査読有り] Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic ChromalveolatesFabien Burki, Yuji Inagaki, Jon Brate, John M. Archibald, Patrick J. Keeling, Thomas Cavalier-Smith, Miako Sakaguchi, Tetsuo Hashimoto, Ales Horak, Surendra Kumar, Dag Klaveness, Kjetill S. Jakobsen, Jan Pawlowski, Kamran Shalchian-TabriziGENOME BIOLOGY AND EVOLUTION 1 2009年[査読有り] Direct phylogenetic evidence for lateral transfer of elongation factor-like geneRyoma Kamikawa, Yuji Inagaki, Yoshihiko SakoPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 105 (19) 2008年5月[査読有り] Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorumKiyotaka Takishita, Masanobu Kawachi, Mary-Helene Noel, Takuya Matsumoto, Natsuki Kakizoe, Makoto M. Watanabe, Isao Inouye, Ken-Ichiro Ishida, Tetsuo Hashimoto, Yuji InagakiGENE 410 (1) 2008年2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1月[査読有り] Evolving genetic codeTakeshi Ohama, Yuji Inagaki, Yoshitaka Bessho, Syozo OsawaProceedings of the Japan Academy Series B: Physical and Biological Sciences 84 (2) 2008年[査読有り] Centrohelida is still searching for a phylogenetic home: Analyses of seven Raphidiophrys contractilis genesMiako Sakaguchi, Yuji Inagaki, Tetsuo HashimotoGENE 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 conditionsKei Iida, Kiyotaka Takishita, Kazuhiko Ohshima, Yuji InagakiMOLECULAR PHYLOGENETICS AND EVOLUTION 45 (1) 2007年10月[査読有り] Proposal of Pseudochattonella verruculosa gen. nov., comb. nov (Dictyochophyceae) for a formar raphidophycean alga Chattonella verruculosa, based on 18S rDNA phylogeny and ultrastructural characteristicsShoko Hosoi-Tanabe, Daiske Honda, Sachiko Fukaya, Isamu Otake, Yuji Inagaki, Yoshihiko SakoPHYCOLOGICAL RESEARCH 55 (3) 2007年9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7月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 culturesKiyotaka Takishita, Naoji Yubuki, Natsuki Kakizoe, Yuji Inagaki, Tadashi MaruyamaEXTREMOPHILES 11 (4) 2007年7月[査読有り] Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineagesNicola J. Patron, Yuji Inagaki, Patrick J. KeelingCURRENT BIOLOGY 17 (10) 2007年5月[査読有り] Fragmentation of mitochondrial large subunit rRNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondriaRyoma Kamikawa, Yuji Inagaki, Yoshihiko SakoPROTIST 158 (2) 2007年4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, YProtist 158 (2) 2007年4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 fornicataNaoji Yubuki, Yuji Inagaki, Takeshi Nakayama, Isao InouyeJOURNAL OF EUKARYOTIC MICROBIOLOGY 54 (2) 2007年3月[査読有り] Plasticity of the domain structure in FlgJ, a bacterial protein involved in flagellar rod formationTakayuki Nambu, Yuji Inagaki, Kazuhiro KutsukakeGENES & GENETIC SYSTEMS 81 (6) 2006年12月[査読有り] Phylogenetic estimation under codon models can be biased by codon usage heterogeneityYuji Inagaki, Andrew J. RogerMOLECULAR PHYLOGENETICS AND EVOLUTION 40 (2) 2006年8月[査読有り] Recombination between elongation factor 1 alpha genes from distantly related archaeal lineagesY Inagaki, E Susko, AJ RogerPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (12) 2006年3月[査読有り] Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotesAGB Simpson, Y Inagaki, AJ RogerMOLECULAR BIOLOGY AND EVOLUTION 23 (3) 2006年3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)K Takishita, Y Inagaki, M Tsuchiya, M Sakaguchi, T MaruyamaGENE 362 2005年12月[査読有り] The evolutionary relationships amongst excavates: a concatenated protein analysis.Simpson, AGB, Inagaki, Y, Roger, AJJournal of Eukaryotic Microbiology 52 2005年1月Capsaspora owczarzaki is an independent opisthokont lineageRuiz-Trillo, I, Y Inagaki, LA Davis, S Sperstad, B Landfald, AJ RogerCURRENT 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, YProceedings 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 modeledE Susko, Y Inagaki, AJ RogerMOLECULAR BIOLOGY AND EVOLUTION 21 (9) 2004年9月[査読有り] Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: Dinoflagellate plastid origins as a case studyY Inagaki, AGB Simpson, JB Dacks, AJ RogerSYSTEMATIC BIOLOGY 53 (4) 2004年8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, AJMolecular Biology and Evolution 21 (7) 2004年7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, AJNucleic Acids Research 31 (14) 2003年7月[査読有り] Testing for differences in rates-across-sites distributions in phylogenetic subtreesE Susko, Y Inagaki, C Field, ME Holder, AJ RogerMOLECULAR BIOLOGY AND EVOLUTION 19 (9) 2002年9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, AJCurrent Biology 12 (9) 2002年4月[査読有り] Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificityY Inagaki, C Blouin, WF Doolittle, AJ RogerNUCLEIC ACIDS RESEARCH 30 (2) 2002年1月[査読有り] Class I release factors in ciliates with variant genetic codesY Inagaki, WF DoolittleNUCLEIC ACIDS RESEARCH 29 (4) 2001年2月[査読有り] Evolutionary relationship between dinoflagellates bearing obligate diatom endosymbionts: insight into tertiary endosymbiosisY Inagaki, JB Dacks, WF Doolittle, KI Watanabe, T OhamaINTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 50 (6) 2000年11月[査読有り] Evolution of the eukaryotic translation termination system: Origins of release factorsY Inagaki, WF DoolittleMOLECULAR BIOLOGY AND EVOLUTION 17 (6) 2000年6月[査読有り] Phylogenetic analysis of diatom coxI genes and implications of a fluctuating GC content on mitochondrial genetic code evolutionM Ehara, Y Inagaki, KI Watanabe, T OhamaCURRENT GENETICS 37 (1) 2000年1月[査読有り] Comprehensive molecular phylogenetic analysis of a heterokont alga (NIES 548) using genes from all three cellular compartmentsMegumi Ehara, Taiju Kitayama, Kazuo I. Watanabe, Yuji Inagaki, Yasuko Hayashi-Ishimaru, Takeshi OhamaPhycological Research 47 (3) 1999年[査読有り] Distribution of the mitochondrial deviant genetic code AUA for methionine in heterokont algaeM Ehara, KI Watanabe, H Kawai, Y Inagaki, Y Hayashi-Ishimaru, T OhamaJOURNAL OF PHYCOLOGY 34 (6) 1998年12月[査読有り] Directionally evolving genetic code: The UGA codon from stop to tryptophan in mitochondriaY Inagaki, M Ehara, KI Watanabe, Y Hasashi-Ishimaru, T OhamaJOURNAL 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 algaeKI Watanabe, M Ehara, Y Inagaki, T OhamaGENE 213 (1-2) 1998年6月[査読有り] A deviant mitochondrial genetic code in prymnesiophytes (yellow-algae): UGA codon for tryptophanY HayashiIshimaru, M Ehara, Y Inagaki, T OhamaCURRENT GENETICS 32 (4) 1997年10月[査読有り] Algae or protozoa: Phylogenetic position of euglenophytes and dinoflagellates as inferred from mitochondrial sequencesY Inagaki, Y HayashiIshimaru, R Ehara, Igarashi, I, T OhamaJOURNAL OF MOLECULAR EVOLUTION 45 (3) 1997年9月[査読有り] Use of a deviant mitochondrial genetic code in yellow-green algae as a landmark for segregating members within the phylumM Ehara, Y HayashiIshimaru, Y Inagaki, T OhamaJOURNAL OF MOLECULAR EVOLUTION 45 (2) 1997年8月[査読有り] Cloning of the Mycoplasma capricolum gene encoding peptide-chain release factorY Inagaki, Y Bessho, H Hori, S OsawaGENE 169 (1) 1996年2月[査読有り] TRANSLATION OF SYNONYMOUS CODONS IN FAMILY BOXES BY MYCOPLASMA-CAPRICOLUM TRANSFER-RNAS WITH UNMODIFIED URIDINE OR ADENOSINE AT THE FIRST ANTICODON POSITIONY INAGAKI, A KOJIMA, Y BESSHO, H HORI, T OHAMA, S OSAWAJOURNAL OF MOLECULAR BIOLOGY 251 (4) 1995年8月[査読有り] LACK OF PEPTIDE-RELEASE ACTIVITY RESPONDING TO CODON UGA IN MYCOPLASMA-CAPRICOLUMY INAGAKI, Y BESSHO, S OSAWANUCLEIC ACIDS RESEARCH 21 (6) 1993年3月[査読有り] 受賞2008年8月日本進化学会 日本進化学会研究奨励賞 2007年4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4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, 範囲: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 2016Harada, Ryuhei, Inagaki, Yuji, Shigeta, Yasuteru (担当:分担執筆, 範囲: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 - 2023年代表者: 稲垣祐司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加速基金（国際共同研究強化(B)）研究期間: 2018年 - 2022年代表者: 稲垣祐司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年代表者: 谷藤吾朗渦鞭毛藻細胞内に発見された新たな共生体痕跡核ゲノムの解読科学研究費助成事業研究期間: 2016年4月 - 2019年3月代表者: 稲垣 祐司, 谷藤 吾朗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年代表者: 濱健夫嫌気環境に生育する真核微生物の多様性の解明科学研究費助成事業研究期間: 2015年4月 - 2018年3月代表者: 橋本 哲男, 石田 健一郎, 稲垣 祐司, 半澤 直人新型分割イントロンのスプライシング機構と進化多様性の解明科学研究費助成事業研究期間: 2015年4月 - 2018年3月代表者: 橋本 哲男, 奈良 武司, 稲垣 祐司, 谷藤 吾朗マトリョーシカ型進化原理の展開科学研究費助成事業研究期間: 2016年4月 - 2017年3月代表者: 野崎 智義, 守屋 繁春, 山本 雅裕, 松崎 素道, 石田 健一郎, 神川 龍馬, 小保方 潤一, 稲垣 祐司, 木原 久美子ミトコンドリア・色素体以外の共生オルガネラ成立過程の解明科学研究費助成事業研究期間: 2011年4月 - 2016年3月代表者: 稲垣 祐司, 小保方 潤一, 神川 龍馬マトリョーシカ型進化原理（総括班）科学研究費助成事業研究期間: 2011年4月 - 2016年3月代表者: 野崎 智義, 洲崎 敏伸, 坪井 敏文, 守屋 繁春, 津久井 久美子, 松崎 素道, 橘 裕司, 石田 健一郎, 小保方 潤一, 橋本 哲男, 金子 修, 稲垣 祐司, 井上 勲, 永井 宏樹, 黒田 誠, 永宗 喜三郎新型分割イントロンの切り出し因子同定に基づく真核生物ｍＲＮＡ成熟機構進化の解明科学研究費助成事業研究期間: 2011年4月 - 2015年3月代表者: 橋本 哲男, 稲垣 祐司, 奈良 武司, 飯田 慶ミトコンドリアをもたない真核微生物群フォルニカータの多様性の解明科学研究費助成事業研究期間: 2011年4月 - 2014年3月代表者: 橋本 哲男, 石田 健一郎, 稲垣 祐司ハプト・クリプト藻類を含む新奇巨大生物群の提唱とクロムアルベオラータ仮説の検証科学研究費助成事業研究期間: 2009年 - 2012年代表者: 稲垣 祐司, 石田 健一郎藻類・プロティスト複合系の多様性研究の基盤構築科学研究費助成事業研究期間: 2009年 - 2012年代表者: 井上 勲, 渡辺 信, 橋本 哲男, 石田 健一郎, 稲垣 祐司, 中山 剛, 菊地 淳, 守屋 繁春原始真核生物を求めて : 新奇真核微生物の形態・発現遺伝子・ミトコンドリアゲノム解析科学研究費助成事業研究期間: 2010年 - 2011年代表者: 稲垣 祐司フォルニケータ生物群の分子系統進化科学研究費助成事業研究期間: 2008年 - 2010年代表者: 橋本 哲男, 稲垣 祐司カタブレファリス類配列をふくむ連結データ系統解析によるクロミスタ仮説の検討科学研究費助成事業研究期間: 2006年 - 2007年代表者: 稲垣 祐司複数遺伝子の配列情報に基づく真核生物の初期進化の解明科学研究費助成事業研究期間: 2005年 - 2006年代表者: 橋本 哲男, 井上 勲, 中山 剛, 稲垣 祐司 氏名 中山 卓郎 Name NAKAYAMA Takuro 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 助教 研究テーマ 細胞内共生を通じたオルガネラ進化, 真核微生物の多様性および生態に関する研究 関連リンク TRIOS researchmap Email ntakuroccs.tsukuba.ac.jp 研究キーワード経歴2021年4月 - 現在筑波大学 計算科学研究センター 助教 2016年11月 - 2021年3月東北大学 データ科学国際共同大学院 助教 2016年11月 - 2021年3月東北大学 生命科学研究科 助教 2013年6月 - 2016年10月筑波大学 計算科学研究センター 研究員 2011年6月 - 2013年6月ダルハウジー大学 日本学術振興会 海外特別研究員 2010年4月 - 2011年6月国立環境研究所 NIESポスドクフェロー 2007年4月 - 2010年3月日本学術振興会 特別研究員 DC1 論文▼▲Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesisChihiro Sarai, Goro Tanifuji, Takuro Nakayama, Ryoma Kamikawa, Kazuya Takahashi, Euki Yazaki, Eriko Matsuo, Hideaki Miyashita, Ken-ichro Ishida, Mitsunori Iwataki, Yuji InagakiProceedings of the National Academy of Sciences of the United States of America 117 (10) 2020年2月[査読有り] Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate hostTakuro NakayamaProceedings of the National Academy of Sciences 116 (32) 2019年6月[査読有り] Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatomsTakuro Nakayama, Yuji InagakiSCIENTIFIC REPORTS 7 2017年10月[査読有り] Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyleTakuro Nakayama, Ryoma Kamikawa, Goro Tanifuji, Yuichiro Kashiyama, Naohiko Ohkouchi, John M. Archibald, Yuji InagakiPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 (31) 2014年8月[査読有り] Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphsBruce A. Curtis, Goro Tanifuji, Fabien Burki, Ansgar Gruber, Manuel Irimia, Shinichiro Maruyama, Maria C. Arias, Steven G. Ball, Gillian H. Gile, Yoshihisa Hirakawa, Julia F. Hopkins, Alan Kuo, Stefan A. Rensing, Jeremy Schmutz, Aikaterini Symeonidi, Marek Elias, Robert J. M. Eveleigh, Emily K. Herman, Mary J. Klute, Takuro Nakayama, Miroslav Obornik, Adrian Reyes-Prieto, E. Virginia Armbrust, Stephen J. Aves, Robert G. Beiko, Pedro Coutinho, Joel B. Dacks, Dion G. Durnford, Naomi M. Fast, Beverley R. Green, Cameron J. Grisdale, Franziska Hempel, Bernard Henrissat, Marc P. Hoeppner, Ken-Ichiro Ishida, Eunsoo Kim, Lude. K. Koreny, Peter G. Kroth, Yuan Liu, Shehre-Banoo Malik, Uwe G. Maier, Darcy McRose, Thomas Mock, Jonathan A. D. Neilson, Naoko T. Onodera, Anthony M. Poole, Ellen J. Pritham, Thomas A. Richards, Gabrielle Rocap, Scott W. Roy, Chihiro Sarai, Sarah Schaack, Shu Shirato, Claudio H. Slamovits, David F. Spencer, Shigekatsu Suzuki, Alexandra Z. Worden, Stefan Zauner, Kerrie Barry, Callum Bell, Arvind K. Bharti, John A. Crow, Jane Grimwood, Robin Kramer, Erika Lindquist, Susan Lucas, Asaf Salamov, Geoffrey I. McFadden, Christopher E. Lane, Patrick J. Keeling, Michael W. Gray, Igor V. Grigoriev, John M. ArchibaldNATURE 492 (7427) 2012年12月[査読有り] Evolving a photosynthetic organelleTakuro Nakayama, John M. ArchibaldBMC BIOLOGY 10 2012年4月[査読有り] Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophoraTakuro Nakayama, Ken-ichiro IshidaCURRENT BIOLOGY 19 (7) 2009年4月[査読有り] Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putridaRyoma Kamikawa, Takako Mochizuki, Mika Sakamoto, Yasuhiro Tanizawa, Takuro Nakayama, Ryo Onuma, Ugo Cenci, Daniel Moog, Samuel Speak, Krisztina Sarkozi, Andrew Toseland, Cock van Oosterhout, Kaori Oyama, Misako Kato, Keitaro Kume, Motoki Kayama, Tomonori Azuma, Ken-ichiro Ishii, Hideaki Miyashita, Bernard Henrissat, Vincent Lombard, Joe Win, Sophien Kamoun, Yuichiro Kashiyama, Shigeki Mayama, Shin-ya Miyagishima, Goro Tanifuji, Thomas Mock, Yasukazu NakamuraScience Advances 8 (17) 2022年4月Rappemonads are haptophyte phytoplankton.Masanobu Kawachi, Takuro Nakayama, Motoki Kayama, Mami Nomura, Hideaki Miyashita, Othman Bojo, Lesley Rhodes, Stuart Sym, Richard N Pienaar, Ian Probert, Isao Inouye, Ryoma KamikawaCurrent biology : CB 31 (11) 2021年6月Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species.Euki Yazaki, Ryosuke Miyata, Yasuhiko Chikami, Ryo Harada, Takashi Kawakubo, Goro Tanifuji, Takuro Nakayama, Kensuke Yahata, Tetsuo Hashimoto, Yuji InagakiParasitology international 83 2021年4月Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areasShunsuke Kanamori, Antonio Cádiz, Luis M. Díaz, Yuu Ishii, Takuro Nakayama, Masakado KawataEcology and Evolution 11 (4) 2021年2月Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organismsTakuro Nakayama, Kazuya Takahashi, Ryoma Kamikawa, Mitsunori Iwataki, Yuji Inagaki, Goro TanifujiCommunicative & Integrative Biology 13 (1) 2020年6月[査読有り] Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesisChihiro Sarai, Goro Tanifuji, Takuro Nakayama, Ryoma Kamikawa, Kazuya Takahashi, Euki Yazaki, Eriko Matsuo, Hideaki Miyashita, Ken-ichro Ishida, Mitsunori Iwataki, Yuji InagakiProceedings of the National Academy of Sciences of the United States of America 117 (10) 2020年2月[査読有り] Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryoteMatsuo, 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, JunichibioRχiv 2019年10月Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate hostTakuro NakayamaProceedings of the National Academy of Sciences 116 (32) 2019年6月[査読有り] The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasitesGoro Tanifuji, Shun Takabayashi, Keitaro Kume, Mizue Takagi, Takuro Nakayama, Ryoma Kamikawa, Yuji Inagaki, Tetsuo HashimotoPLoS ONE 13 (3) 2018年3月[査読有り] Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatomsTakuro Nakayama, Yuji InagakiSCIENTIFIC REPORTS 7 2017年10月[査読有り] Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosisGoro 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. ArchibaldSCIENTIFIC REPORTS 7 2017年9月[査読有り] Diversity of the Photosynthetic Paulinella Species, with the Description of Paulinella micropora sp nov and the Chromatophore Genome Sequence for strain KR01Duckhyun Lhee, Eun Chan Yang, Jong Im Kim, Takuro Nakayama, Giuseppe Zuccarello, Robert A. Andersen, Hwan Su YoonPROTIST 168 (2) 2017年4月[査読有り] Evolution of UhpC-type hexose-phosphate transporters in dinoflagellatesYoshihisa Hirakawa, Takuro Nakayama, Nadine Keilert, Ken-ichiro IshidaPHYCOLOGICAL RESEARCH 65 (2) 2017年4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3月Metabolic Capacity of Mitochondrion-related Organelles in the Free-living Anaerobic Stramenopile Cantina marsupialisFumiya Noguchi, Shigeru Shimamura, Takuro Nakayama, Euki Yazaki, Akinori Yabuki, Tetsuo Hashimoto, Yuji Inagaki, Katsunori Fujikura, Kiyotaka TakishitaPROTIST 166 (5) 2015年11月[査読有り] Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyleTakuro Nakayama, Ryoma Kamikawa, Goro Tanifuji, Yuichiro Kashiyama, Naohiko Ohkouchi, John M. Archibald, Yuji InagakiPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 (31) 2014年8月[査読有り] Detailed Process of Shell Construction in the Photosynthetic Testate Amoeba Paulinella chromatophora ( Euglyphid, Rhizaria)Mami Nomura, Takuro Nakayama, Ken-ichiro IshidaJOURNAL OF EUKARYOTIC MICROBIOLOGY 61 (3) 2014年5月[査読有り] Genetic structure of Japanese Chattonella marina (Raphidophyceae) populations revealed using microsatellite markersMikihide Demura, Takuro Nakayama, Fumie Kasai, Masanobu KawachiPHYCOLOGICAL RESEARCH 62 (2) 2014年4月[査読有り] Unique genome evolution in an intracellular N-2-fixing symbiont of a rhopalodiacean diatomTakuro Nakayama, Yuji InagakiACTA SOCIETATIS BOTANICORUM POLONIAE 83 (4) 2014年[査読有り] Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphsBruce A. Curtis, Goro Tanifuji, Fabien Burki, Ansgar Gruber, Manuel Irimia, Shinichiro Maruyama, Maria C. Arias, Steven G. Ball, Gillian H. Gile, Yoshihisa Hirakawa, Julia F. Hopkins, Alan Kuo, Stefan A. Rensing, Jeremy Schmutz, Aikaterini Symeonidi, Marek Elias, Robert J. M. Eveleigh, Emily K. Herman, Mary J. Klute, Takuro Nakayama, Miroslav Obornik, Adrian Reyes-Prieto, E. Virginia Armbrust, Stephen J. Aves, Robert G. Beiko, Pedro Coutinho, Joel B. Dacks, Dion G. Durnford, Naomi M. Fast, Beverley R. Green, Cameron J. Grisdale, Franziska Hempel, Bernard Henrissat, Marc P. Hoeppner, Ken-Ichiro Ishida, Eunsoo Kim, Lude. K. Koreny, Peter G. Kroth, Yuan Liu, Shehre-Banoo Malik, Uwe G. Maier, Darcy McRose, Thomas Mock, Jonathan A. D. Neilson, Naoko T. Onodera, Anthony M. Poole, Ellen J. Pritham, Thomas A. Richards, Gabrielle Rocap, Scott W. Roy, Chihiro Sarai, Sarah Schaack, Shu Shirato, Claudio H. Slamovits, David F. Spencer, Shigekatsu Suzuki, Alexandra Z. Worden, Stefan Zauner, Kerrie Barry, Callum Bell, Arvind K. Bharti, John A. Crow, Jane Grimwood, Robin Kramer, Erika Lindquist, Susan Lucas, Asaf Salamov, Geoffrey I. McFadden, Christopher E. Lane, Patrick J. Keeling, Michael W. Gray, Igor V. Grigoriev, John M. ArchibaldNATURE 492 (7427) 2012年12月[査読有り] Broad Distribution of TPI-GAPDH Fusion Proteins among Eukaryotes: Evidence for Glycolytic Reactions in the Mitochondrion?Takuro Nakayama, Ken-ichiro Ishida, John M. ArchibaldPLOS ONE 7 (12) 2012年12月[査読有り] Evolving a photosynthetic organelleTakuro Nakayama, John M. ArchibaldBMC BIOLOGY 10 2012年4月[査読有り] Succession of genetic diversity of Botryococcus braunii (Trebouxiophyceae) in two Japanese reservoirsMikihide Demura, Masanobu Kawachi, Hiroshi Koshikawa, Takuro Nakayama, Yusuke Mayuzumi, Makoto M. WatanabeINNOVATIVE RESEARCHES ON ALGAL BIOMASS 15 2012年[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, YJ. Euk. Microbiol. 58 (2) 2011年1月[査読有り] Cercozoa comprises both EF-1 alpha-containing and EFL-containing membersRyoma Kamikawa, Akinori Yabuki, Takuro Nakayama, Ken-ichiro Ishida, Tetsuo Hashimoto, Yuji InagakiEUROPEAN JOURNAL OF PROTISTOLOGY 47 (1) 2011年1月[査読有り] Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacteriumTakuro Nakayama, Yuko Ikegami, Takeshi Nakayama, Ken-ichiro Ishida, Yuji Inagaki, Isao InouyeJOURNAL OF PLANT RESEARCH 124 (1) 2011年1月[査読有り] Differential Gene Retention in Plastids of Common Recent OriginAdrian Reyes-Prieto, Hwan Su Yoon, Ahmed Moustafa, Eun Chan Yang, Robert A. Andersen, Sung Min Boo, Takuro Nakayama, Ken-ichiro Ishida, Debashish BhattacharyaMOLECULAR BIOLOGY AND EVOLUTION 27 (7) 2010年7月[査読有り] PHYLOGENETIC POSITION OF SYMBIOTIC CHLORELLA (TREBOUXIOPHYCEAE, CHLOROPHYTA) OF MAYORELLA VIRIDIS (AMOEBOZOA) AND ITS SYMBIOTIC MANNERT. Nishimura, H. Yamaguchi, Y. Kodama, Takuro Nakayama, Takeshi Nakayama, I. InouyePHYCOLOGIA 48 (4) 2009年7月A single origin of the photosynthetic organelle in different Paulinella lineagesHwan Su Yoon, Takuro Nakayama, Adrian Reyes-Prieto, Robert A. Andersen, Sung Min Boo, Ken-ichiro Ishida, Debashish BhattacharyaBMC EVOLUTIONARY BIOLOGY 9 2009年5月[査読有り] Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophoraTakuro Nakayama, Ken-ichiro IshidaCURRENT BIOLOGY 19 (7) 2009年4月[査読有り] もう一つの一次共生？―Paulinella chromatophora とそのシアネレ―中山 卓郎, 石田 健一郎原生動物学雑誌 41 (1) 2008年受賞▼▲2022年4月科学技術分野の文部科学大臣表彰 若手科学者賞 2022年4月筑波大学若手教員特別奨励賞 2021年9月日本植物学会賞奨励賞 2015年3月日本藻類学会 日本藻類学会研究奨励賞 書籍等出版物原生生物学事典中山, 卓郎 (範囲:2-8-3. アピコンプレクサ; 2-9-1. ケルコゾア; 3-14 共生体からオルガネラへの進化)競争的資金等の研究課題▼▲二次共生の中間段階にある共生者ゲノムの解読科学研究費助成事業 基盤研究(c)(一般）研究期間: 2024年4月 - 2027年3月代表者: 中山 卓郎海洋微生物多様性の盲点―真核微生物に潜在する原核微生物叢の実態を探る科学研究費助成事業 基盤研究(B)研究期間: 2020年4月 - 2024年3月代表者: 中山 卓郎光合成補助色素フコキサンチンの未知なる生合成系の解明とその誕生の謎を紐解く科学研究費助成事業 基盤研究(B)研究期間: 2019年4月 - 2024年3月代表者: 神川 龍馬海洋原生生物に共生する細菌多様性の実態解明科学研究費助成事業 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10月 - 2023年3月代表者: 稲垣 祐司渦鞭毛藻細胞に見られるシアノバクテリア共生体の機能および進化の解明科学研究費助成事業 若手研究(B)研究期間: 2017年4月 - 2020年3月代表者: 中山 卓郎ケルコゾア生物における“ミトコンドリア型解糖系”の理解に向けた基礎的研究科学研究費助成事業 若手研究(B)研究期間: 2014年4月 - 2017年3月代表者: 中山 卓郎, 矢吹 彬憲, 白鳥 峻志細胞内共生を通じた新奇オルガネラ獲得:珪藻細胞に見られる窒素固定構造の進化解明科学研究費助成事業 研究活動スタート支援研究期間: 2010年 - 2011年代表者: 中山 卓郎Paulinella chromatophoraのシアネレに関する研究科学研究費助成事業 特別研究員奨励費研究期間: 2007年 - 2009年代表者: 中山 卓郎 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 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 センター紹介「超並列計算機CP-PACS」プロジェクトを振り返る 研究実績・評価 SC出展ポスター 研究評価・外部評価 External Review (2014-2019) External Review (2008-2013) Parallel Tracks for Divisions External Review Photo Gallery External Review (2007) 年次報告書 論文・学会発表 教員・研究員紹介 学外共同研究員 教員・研究員 計算情報学研究部門 高性能計算システム研究部門 地球環境研究部門 生命科学研究部門 量子物性研究部門 原子核物理研究部門 宇宙物理研究部門 素粒子物理研究部門 計算科学研究センターフェロー 組織 研究員会議（趣旨説明） 運営委員会（名簿） 運営協議会（名簿） 沿革 目的 センター長挨拶 研究開発推進計算メディカルサイエンス事業部 計算科学社会実装推進室 広報・戦略室 学際計算科学連携室 高性能計算システム運用開発室 ビッグデータ・AI連携推進室 計算科学振興室 HPCI推進室 次世代計算システム研究開発室 先端計算科学推進室 研究部門計算情報学研究部門 計算メディア分野 データ基盤分野 高性能計算システム研究部門 地球環境研究部門 生命科学研究部門 分子進化分野 生命機能情報分野 量子物性研究部門 原子核物理研究部門 宇宙物理研究部門 素粒子物理研究部門 スーパーコンピュータ シンポジウム・研究会計算科学コロキウム ワークショップ シンポジウム 研究プロジェクトHA-PACS HA-PACS ロゴマーク PACS/PAXの歴史 進捗と成果 HA-PACSベースクラスタ 次世代計算システム開発 先端計算科学推進 組織およびメンバー プロジェクトの目的 筑波山プロジェクト 連絡先 メンバー リンク メディア取材などの記録 プロジェクトの成果 過去の観測データ 筑波山神社・筑波大学計算科学研究センター共同気象観測所の概要と観測項目 プロジェクトの目的 プロジェクトの経緯 最先端共同HPC基盤施設（JCAHPC） 宇宙生命計算科学連携拠点 公開コード 提供データベース 全国共同利用スーパーコンピュータ利用の手引き システム利用に関するQ&A 一般利用 採択後の手続き（一般利用） 一般利用に関する情報 HPCI共同利用 学際共同利用プログラム 採択後の手続き 謝辞の手引き 共同研究支援 採択課題一覧 学際共同利用プログラム公募 広報災害時の対応 「東北地方太平洋沖地震」特設ページ お問い合わせ メディア掲載情報 ロゴ パンフレット ギャラリー CCS Premium Friday 研究者に聞く プレスリリース よくある質問 見学 過去の見学 著作権について サイトポリシー リンク 計算科学研究センター〒305-8577 茨城県つくば市天王台1-1-1　TEL 029-853-6487（センター事務室） © 2016 Center for Computational Sciences, University of Tsukuba.