Division of Life Sciences

Biological Function and Information Group

Name Faculty Position
Shigeta Yasuteru Professor/Cheif
Harada Ryuhei Associate Professor
Shoji Mitsuo Assistant Professor
Nishizawa Hiroaki Assistant Professor
Hori Yuta Assistant Professor
Kitoh-Nishioka Hirotaka Researcher
Mitsuta Yuki Researcher
Kowit Hengphasatporn Researcher
Hirokawa Takatsugu Faculty of Medicine Professor (Collaborative Fellow)
Yoshino Ryunosuke Faculty of Medicine Assistant Professor (Collaborative Fellow)

Biological Science Group

Name Faculty Position
Inagaki Yuji Professor/Group Leader
Ishitani Yoshiyuki Researcher
Hashimoto Tetsuo Faculty of Life and Enviromental Sciences Professor (Collaborative Fellow)

Biological Function and Information Group

氏名 重田 育照
Name Shigeta Yasuteru
Faculty
Section
Position Professor/Cheif
Theme Computational analyses on nano- and bio-systems
Related Links
Email shigetaccs.tsukuba.ac.jp
  • Research Interests
  • Academic & Professional Experience
    Apr 2019
    -
    National Institutes for Quantum and Radiological Science and Technology Takasaki Advanced Radiation Research Institute Visiting Researcher
    Apr 2018
    -
    Sojo University Faculty of Engineering, Department of Aerospace Systems Engineering
    Apr 2016
    -
    Mar 2018
    Institute of Molecular Sciences Visiting professor
    May 2014
    -
    Osaka University Graduate School of Engineering Sciences Visiting Professor
    Mar 2014
    -
    University of Tsukuba
    Aug 2011
    -
    Jul 2013
    Ministry of Education,Culture,Sports,Science and Technology
    Aug 2010
    -
    Mar 2014
    Osaka University Graduate School of Engineering Science, Department of Materials Engineering Science Division of Materials Physics
    May 2008
    -
    Jul 2010
    University of Hyogo of Life Science, Graduate School
    Feb 2007
    -
    May 2008
    University of Tsukuba
    Dec 2003
    -
    Jan 2007
    The University of Tokyo The Graduate School of Engineering, Department of Applied Chemistry
    Apr 2001
    -
    Dec 2003
    The University of Tokyo Graduate School of Arts and Sciences
    Apr 2000
    -
    Mar 2001
    Osaka University Graduate School of Science, Department of Chemistry
    Jan 1999
    -
    Mar 2000
    Osaka University Graduate School of Science, Department of Chemistry
  • Published Papers
    Local Structures and Dynamics of Imidazole Molecules in Poly(vinylphosphonic acid)–Imidazole Composite Investigated by Molecular Dynamics
    Hori, Yuta, Suetake, Toshiya, Shiota, Yoshihito, Yoshizawa, Kazunari, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, Motohiro
    ACS Applied Polymer Materials Feb 2020[Refereed]
    Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography
    Shoji, Mitsuo, Isobe, Hiroshi, Shen, Jian-Ren, Suga, Michihiro, Akita, Fusamichi, Miyagawa, Koichi, Shigeta, Yasuteru, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 730 Sep 2019[Refereed]
    Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency
    Harada, Ryuhei, Shigeta, Yasuteru
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 59 (9) Sep 2019[Refereed]
    Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein Dynamics
    Harada, Ryuhei, Sladek, Vladimir, Shigeta, Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (9) Sep 2019[Refereed]
    Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water-Air Interface
    Ohto, Tatsuhiko, Dodia, Mayank, Xu, Jianhang, Imoto, Sho, Tang, Fujie, Zysk, Frederik, Kühne, Thomas D, Shigeta, Yasuteru, Bonn, Mischa, Wu, Xifan, Nagata, Yuki
    The journal of physical chemistry letters 10 (17) Aug 2019[Refereed]
    Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
    Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
    Journal of molecular graphics & modelling 92 Jul 2019[Refereed]
    Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
    Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
    Journal of molecular graphics & modelling 92 Jul 2019[Refereed]
    First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface
    Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Kamiya, Katsumasa, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    The journal of physical chemistry. A 123 (26) Jul 2019[Refereed]
    Pyrrole-Based π-System-Pt Complexes: Chiroptical Properties and Excited-State Dynamics with Microsecond Triplet Lifetimes
    Hirata, Goki, Kobayashi, Yoichi, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
    Chemistry (Weinheim an der Bergstrasse, Germany) 25 (37) Jul 2019[Refereed]
    Reaction mechanism of non-enzymatic stereoselective formation of wine lactone
    Kyan, Akane, Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 725 Jun 2019[Refereed]
    Numerical investigation of the nano-scale solutal Marangoni convections
    Imai, Y, Yamamoto, T, Sekimoto, A, Okano, Y, Sato, R, Shigeta, Y
    JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS 98 (SI) May 2019[Refereed]
    In silico strcutral modelling and analysis of elongation factor 1alpha and elongation factor-like proteins.
    Kotaro, Sakamoto, Megumi, Kayanuma, Inagaki, Yuji, Tetsuo, Hashimoto, Yasuteru, Shigeta
    ACS Omega 4 (4) Apr 2019[Refereed]
    Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-order Molecular Dynamics Simulation
    Aida, Hayato, Harada, Ryuhei, Shigeta, Yasuteru
    Chemistry Letters 48 (4) Apr 2019[Refereed]
    Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical Insight
    Xu, Tianlv, Li, Jia Hui, Momen, Roya, Huang, Wei Jie, Kirk, Steven Robert, Shigeta, Yasuteru, Jenkins, Samantha
    Journal of the American Chemical Society 141 (13) Apr 2019[Refereed]
    Photosubstitution Reaction of cis-[Ru(bpy)(2)(CH3CN)(2)](2+) and cis-[Ru(bpy)(2)(NH3)(2)](2+) in Aqueous Solution via Monoaqua Intermediate
    Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
    The journal of physical chemistry. A 123 (13) Mar 2019[Refereed]
    Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
    Kimatsuka, Masato, Sato, Ryuma, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru
    Chemistry Letters 48 (3) Mar 2019[Refereed]
    Molecular Dynamics studies on the effects of Antifreezing Protein from Rhagium inquisitor (RiAFP) on Ice Growth
    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) Mar 2019[Refereed]
    First-principle study of ammonia decomposition and nitrogen incorporation on the GaN surface in metal organic vapor phase epitaxy
    Bui, Kieu My, Iwata, Jun-Ichi, Kangawa, Yoshihiro, Shiraishi, Kenji, Shigeta, Yasuteru, Oshiyama, Atsushi
    JOURNAL OF CRYSTAL GROWTH 507 Feb 2019[Refereed]
    Quadruply N-methylated octaphyrin: a helical macrocycle exhibiting chiroptical properties and dynamic conformation changes correlated with helical and inner N-methyl orientations
    Naito, Wakana, Urakawa, Kazuki, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
    ORGANIC & BIOMOLECULAR CHEMISTRY 17 (5) Feb 2019[Refereed]
    Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins
    Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
    Journal of computational chemistry 40 (15) Feb 2019[Refereed]
    Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
    Harada, Ryuhei, Shigeta, Yasuteru
    Advances in Quantum Chemistry (78) Feb 2019[Refereed]
    Theoretical study of the photodissociation reaction of methanol
    Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 714 Jan 2019[Refereed]
    New Assay Method Based on Raman Spectroscopy for Enzymes Reacting with Gaseous Substrates
    Kawahara-Nakagawa, Yuka, Nishikawa, Koji, Nakashima, Satoru, Inoue, Shota, Ohta, Takehiro, Ogura, Takashi, Shigeta, Yasuteru, Fukutani, Katsuyuki, Yagi, Tatsuhiko, Higuchi, Yoshiki
    Protein science : a publication of the Protein Society 28 (3) Jan 2019[Refereed]
    Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction
    Tokiwa, Takaki, Shoji, Mitsuo, Sladek, Vladimir, Shibata, Naoki, Higuchi, Yoshiki, Kataoka, Kunishige, Sakurai, Takeshi, Shigeta, Yasuteru, Misaizu, Fuminori
    Molecules (Basel, Switzerland) 24 (1) Jan 2019[Refereed]
    Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations
    Harada, Ryuhei, Shigeta, Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (1) Jan 2019[Refereed]
    Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations
    Tokiwa, Takaki, Nakano, Shogo, Yamamoto, Yuta, Ishikawa, Takeshi, Ito, Sohei, Sladek, Vladimir, Fukuzawa, Kaori, Mochizuki, Yuji, Tokiwa, Hiroaki, Misaizu, Fuminori, Shigeta, Yasuteru
    Journal of chemical information and modeling 59 (1) Jan 2019[Refereed]
    High- performance Na ion cathodes based on the ubiquitous and reversible O redox reaction
    Assadi, M. Hussein N, Fronzi, Marco, Ford, Mike, Shigeta, Yasuteru
    JOURNAL OF MATERIALS CHEMISTRY A 6 (47) Dec 2018[Refereed]
    Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion
    Sato, Ryuma, Kitoh-Nishioka, Hirotaka, Kamada, Kenji, Mizokuro, Toshiko, Kobayashi, Kenji, Shigeta, Yasuteru
    The journal of physical chemistry letters 9 (22) Nov 2018[Refereed]
    In Silico Structural Analysis of Elongation Factor-1 Alpha and Elongation Factor-Like
    Sakamoto, Kotaro, Kayanuma, Megumi, Shigeta, Yasuteru
    PROTEIN SCIENCE 27 (1:SI) Nov 2018[Refereed]
    Reaction Pathway of Surface-Catalyzed Ammonia Decomposition and Nitrogen Incorporation in Epitaxial Growth of Gallium Nitride
    Bui, Kieu My, Iwata, Jun-Ichi, Kangawa, Yoshihiro, Shiraishi, Kenji, Shigeta, Yasuteru, Oshiyama, Atsushi
    JOURNAL OF PHYSICAL CHEMISTRY C 122 (43) Nov 2018[Refereed]
    Protein Residue Networks from Energetic and Geometric Data: Are They Identical?
    Sladek, Vladimir, Tokiwa, Hiroaki, Shimano, Hitoshi, Shigeta, Yasuteru
    Journal of chemical theory and computation 14 (12) Nov 2018[Refereed]
    How Does Friction Coefficient Affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?
    Harada, Ryuhei, Shigeta, Yasuteru
    Chemistry Letters 47 (9) Sep 2018[Refereed]
    Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiency
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of molecular graphics & modelling 85 Sep 2018[Refereed]
    A Theoretical Study on Redox Potential and pKa of [2Fe-2S] Cluster Model from Iron-Sulfur Proteins
    Kurniawan, Isman, Kawaguehi, Kazutomo, Shoji, Mitsuo, Matsui, Toru, Shigeta, Yasuteru, Nagao, Hidemi
    Bulletin of the Chemical Society of Japan 91 (9) Sep 2018[Refereed]
    Computational electrochemistry of a novel ferrocene derivative
    Ghiami-Shomami, Ali, Ghalami-Choobar, Bahram, Shigeta, Yasuteru
    Journal of molecular graphics & modelling 85 Aug 2018[Refereed]
    A computational scheme of pK values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme
    Fujiki, Ryo, Kasai, Yukako, Seno, Yuki, Matsui, Toru, Shigeta, Yasuteru, Yoshida, Norio, Nakano, Haruyuki
    Physical chemistry chemical physics : PCCP 20 (43) Aug 2018[Refereed]
    Redox potential-dependent formation of an unusual His-Trp bond in bilirubin oxidase
    Akter, Mahfuza, Tokiwa, Takaki, Shoji, Mitsuo, Nishikawa, Koji, Shigeta, Yasuteru, Sakurai, Takeshi, Higuchi, Yoshiki, Kataoka, Kunishige, Shibata, Naoki
    Chemistry (Weinheim an der Bergstrasse, Germany) 24 (68) Aug 2018[Refereed]
    Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of chemical information and modeling 58 (7) Jul 2018[Refereed]
    A Practical Approach for Searching Stable Molecular Structures by Introducing Repulsive Interactions among Walkers
    Shoji,Mitsuo, Kayanuma,Megumi, Shigeta,Yasuteru
    Bulletin of the Chemical Society of Japan 91 (10) Jul 2018[Refereed]
    Dominant role of orbital splitting in determining cathode potential in O3 NaTMO2 compounds
    Hussein, M, Assadi, N, Shigeta, Yasuteru
    JOURNAL OF POWER SOURCES 388 Jun 2018[Refereed]
    How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations
    Harada, Ryuhei, Shigeta, Yasuteru
    Physical chemistry chemical physics : PCCP 20 (26) Jun 2018[Refereed]
    Concerted Mechanism of Water Insertion and O Release during the S to S Transition of the Oxygen-Evolving Complex in Photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
    The journal of physical chemistry. B 122 (25) Jun 2018[Refereed]
    Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities
    Terai, Yuma, Sato, Ryuma, Yumiba, Takahiro, Harada, Ryuhei, Shimizu, Kohei, Toga, Tatsuya, Ishikawa-Fujiwara, Tomoko, Todo, Takeshi, Iwai, Shigenori, Shigeta, Yasuteru, Yamamoto, Junpei
    Nucleic acids research Epub May 2018[Refereed]
    On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of chemical theory and computation 14 (6) May 2018[Refereed]
    The Reaction Mechanisms of O2 Formation in Photosynthesis
    SHOJI,Mitsuo, ISOBE,Hiroshi, SHIGETA,Yasuteru, NAKAJIMA,Takahito, YAMAGUCHI,Kizashi
    Seibutsu Butsuri 58 (3) May 2018[Refereed]
    Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals
    Hada, Masaki, Saito, Shohei, Sato, Ryuma, Miyata, Kiyoshi, Hayashi, Yasuhiko, Shigeta, Yasuteru, Onda, Ken
    Journal of visualized experiments : JoVE (135) May 2018[Refereed]
    Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
    Yamamoto, Yuta, Takei, Kenta, Arulmozhiraja, Sundaram, Sladek, Vladimir, Matsuo, Naoya, Han, Song-Iee, Matsuzaka, Takashi, Sekiya, Motohiro, Tokiwa, Takaki, Shoji, Mitsuo, Shigeta, Yasuteru, Nakagawa, Yoshimi, Tokiwa, Hiroaki, Shimano, Hitoshi
    Biochemical and biophysical research communications May 2018[Refereed]
    Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 698 Apr 2018[Refereed]
    Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals
    Hada, Masaki, Saito, Shohei, Sato, Ryuma, Miyata, Kiyoshi, Hayashi, Yasuhiko, Shigeta, Yasuteru, Onda, Ken
    Journal of visualized experiments : JoVE (135) Apr 2018[Refereed]
    First-principles study of the formation of glycine-producing radicals from common interstellar species
    Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    Molecular Astrophysics 10 Mar 2018[Refereed]
    First-principles study of the formation of glycine-producing radicals from common interstellar species
    Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    Molecular Astrophysics 10 Mar 2018[Refereed]
    The effect of octahedral distortions on the electronic properties and magnetic interactions in O3 NaTMO2 compounds (TM = Ti-Ni & Zr-Pd)
    Assadi, M. Hussein N, Shigeta, Yasuteru
    RSC ADVANCES 8 (25) 2018[Refereed]
    The Formation of Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics
    Harada,Ryuhei, Aida,Hayato, Shigeta,Yasuteru
    Chemistry Letters 47 (10) 2018[Refereed]
    Ultrafast Structural Analysis of Photoresponsive Columnar Liquid Crystals
    Saito,Shohei, Hada,Masaki, Shigeta,Yasuteru, Onda,Ken
    Proceedings of Japanese Liquid Crystal Society Annual meeting 2018 2018[Refereed]
    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
    Ensemble 20 (1) 2018[Refereed]
    Developments of Efficient Conformational Sampling Methods for Reproducing and Predicting Biologically Relevant Rare Events of Proteins
    Harada,Ryuhei, Shigeta,Yasuteru
    Meeting Abstracts of the Physical Society of Japan 73 2018[Refereed]
    A theoretical study of the formation of glycine via hydantoin intermediate in outer space environment
    Megumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki Umemura
    CHEMICAL PHYSICS LETTERS 687 Nov 2017[Refereed]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 (44) Oct 2017[Refereed]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 (44) Oct 2017[Refereed]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 Oct 2017[Refereed]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 (44) Oct 2017[Refereed]
    Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
    Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
    Journal of the American Chemical Society 139 Oct 2017[Refereed]
    Assessment of Methodology and Chemical Group Dependences in the Calculation of the pK(a) for Several Chemical Groups
    Matsui, Toru, Shigeta, Yasuteru, Morihashi, Kenji
    Journal of chemical theory and computation 13 (10) Sep 2017[Refereed]
    Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of computational chemistry 38 (31) Aug 2017[Refereed]
    Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior
    Yotsuji, Hajime, Higashiguchi, Kenji, Sato, Ryuma, Shigeta, Yasuteru, Matsuda, Kenji
    Chemistry (Weinheim an der Bergstrasse, Germany) 23 (60) Jul 2017[Refereed]
    Large-scale QM/MM calculations of the CaMn4O5 cluster in the S-3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures
    Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi
    FARADAY DISCUSSIONS 198 Jun 2017[Refereed]
    Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
    Ujiie, Yuzuru, Tanaka, Wataru, Hanaoka, Kyohei, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo, Murakawa, Takeshi, Ishida, Toyokazu, Shigeta, Yasuteru, Hayashi, Hideyuki
    The journal of physical chemistry. B 121 (22) May 2017[Refereed]
    Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection
    Harada, Ryuhei, Shigeta, Yasuteru
    Journal of computational chemistry 38 (22) May 2017[Refereed]
    Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
    Fujita, Junso, Harada, Ryuhei, Maeda, Yoko, Saito, Yuki, Mizohata, Eiichi, Inoue, Tsuyoshi, Shigeta, Yasuteru, Matsumura, Hiroyoshi
    Journal of structural biology 198 (2) Apr 2017[Refereed]
    Direct Observation of the Ultrafast Evolution of Open-Shell Biradical in Photochromic Radical Dimer
    Kobayashi, Yoichi, Okajima, Hajime, Sotome, Hikaru, Yanai, Takeshi, Mutoh, Katsuya, Yoneda, Yusuke, Shigeta, Yasuteru, Sakamoto, Akira, Miyasaka, Hiroshi, Abe, Jiro
    Journal of the American Chemical Society 139 (18) Apr 2017[Refereed]
    Cooperatively Interlocked [2+1]-Type π-System-Anion Complexes
    Yamakado, Ryohei, Ashida, Yukina, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
    Chemistry (Weinheim an der Bergstrasse, Germany) 23 (17) Mar 2017[Refereed]
    Sparsity-Weighted Outlier FLOODing (OFLOOD) Method: Efficient Rare Event Sampling Method Using Sparsity of Distribution
    Harada, Ryuhei, Nakamura, Tomotake, Shigeta, Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 37 (8) Mar 2016[Refereed]
    Solvent effects on excited-state electron-transfer rate of pyrene-labeled deoxyuridine: A theoretical study
    Maekawa, Shintaro, Sato, Ryuma, Hirao, Kimihiko, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 644 Jan 2016[Refereed]
    Theoretical analyses on a flipping mechanism of UV-induced DNA damage
    Sato,Ryuma, Harada,Ryuhei, Shigeta,Yasuteru
    Biophysics and Physicobiology 13 2016[Refereed]
    Solvation Energy of Proton: a Consistent Calculation Schemefor Acid Dissociation Constantsand Standard Hydrogen Electrode Potentials
    MATSUI,Toru, KIYAN,Akane, SHOJI,Mitsuo, SHIGETA,Yasuteru
    Journal of Computer Chemistry, Japan 15 (5) 2016[Refereed]
    Molecular dynamics study on the key catalytic intermediates of threonine synthase
    Shoji, Mitsuo, Ujiie, Yuzuru, Harada, Ryuhei, Kayanuma, Megumi, Shigeta, Yasuteru, Murakawa, Takeshi, Hayashi, Hideyuki
    PROTEIN SCIENCE 24 (1:SI) Oct 2015[Refereed]
    Automatic detection of hidden dimensions to obtain appropriate reaction coordinates in the Outlier FLOODing (OFLOOD) method
    Harada, Ryuhei, Nakamura, Tomotake, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 639 Oct 2015[Refereed]
    Performance of the divide-and-conquer approach used as an initial guess
    Shoji,Mitsuo, Meguchi,Kayanuma, Hiroaki,Umeda, Yasuteru,Shigeta
    Chemical Physics Letters 634 Aug 2015[Refereed]
    Efficient conformational sampling of proteins based on a multi-dimensional TaBoo SeArch algorithm: An application to folding of chignolin in explicit solvent
    Harada, Ryuhei, Takano, Yu, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 630 Jun 2015[Refereed]
    Enhanced Conformational Sampling Method for Proteins Based on the TaBoo SeArch Algorithm: Application to the Folding of a Mini-Protein, Chignolin
    Harada, Ryuhei, Takano, Yu, Shigeta, Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (10) Apr 2015[Refereed]
    Theoretical Study on Reaction Mechanisms of Nitrite Reduction by Copper Nitrite Complexes: Toward Understanding and Controlling Possible Mechanisms of Copper Nitrite Reductase
    Maekawa, Shintaro, Matsui, Tom, Hirao, Kimihiko, Shigeta, Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY B 119 (17) Apr 2015[Refereed]
    Molecular Simulation of Enzymatic Cleavage Reaction for Artificial Compounds
    神谷克政, 重田,育照
    Journal of the Japan Society for Simulation Technology 34 (1) Mar 2015[Refereed]
    第一原理計算によるタンパク質のpK_aと構造機能相関
    Shigeta,Y, Matsui,Toru
    日本物理学会講演概要集 70 (1) Mar 2015[Refereed]
    21aAF-5 Theoretical prediction of pKa values of amino acids using 3D-RISM-SCF
    Kasai,Y, Yoshida,N, Matsui,T, Shigeta,Y, Nakano,H
    日本物理学会講演概要集 70 (1) Mar 2015[Refereed]
    A QM/MM study of the initial steps of catalytic mechanism of nitrile hydratase
    Kayanuma, Megumi, Hanaoka, Kyohei, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 623 Mar 2015[Refereed]
    Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body Systems
    Shigeta, Yasuteru, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5:::SI) Mar 2015[Refereed]
    Substitution effects on optical properties of iminonitroxide- substituted iminonitroxide diradical
    Nakamura, Ryota, Shigeta, Yasuteru, Okuno, Katsuki, Hasegawa, Miki, Fukushima, Mayuko, Suzuki, Shuichi, Kozaki, Masatoshi, Okada, Keiji, Nakano, Masayoshi
    MOLECULAR PHYSICS 113 (3-4:::SI) Feb 2015[Refereed]
    Protein folding pathways extracted by Outlier FLOODing method (OFLOOD)
    Ryuhei,Harada, Tomotake,Nakamura, Yu,Takano, Shigeta,Yasuteru
    Journal of Computational Chemistry Jan 2015[Refereed]
    Accurate Standard Hydrogen Electrode Potential and Applications to the Redox Potentials of Vitamin C and NAD/NADH
    Matsui, Toru, Kitagawa, Yasutaka, Okumura, Mitsutaka, Shigeta, Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 119 (2) Jan 2015[Refereed]
    Protein Folding Pathways Extracted by OFLOOD: Outlier FLOODing Method
    Harada, Ryuhei, Nakamura, Tomotake, Takano, Yu, Shigeta, Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (2) Jan 2015[Refereed]
    Simple, yet powerful methodologies for conformational sampling of proteins
    Harada, Ryuhei, Takano, Yu, Baba, Takeshi, Shigeta, Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (9) 2015[Refereed]
    Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes
    Baba, Takeshi, Boero, Mauro, Kamiya, Katsumasa, Ando, Hiroyuki, Negoro, Seiji, Nakano, Masayoshi, Shigeta, Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (6) 2015[Refereed]
    Theoretical design of solvatochromism switching by photochromic reactions using donor-acceptor disubstituted diarylethene derivatives with oxidized thiophene rings
    Okuno, Katsuki, Shigeta, Yasuteru, Kishi, Ryohei, Nakano, Masayoshi
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (9) 2015[Refereed]
    Performance Benchmark of FMO Calculation with GPU-Accelerated Fock Matrix Preparation Routine
    UMEDA,Hiroaki, HANAWA,Toshihiro, SHOJI,Mitsuo, BOKU,Taisuke, SHIGETA,Yasuteru
    Journal of Chemical Software 13 (6) 2015[Refereed]
    GPU-accelerated FMO Calculation with OpenFMO: Four-Center Inter-Fragment Coulomb Interaction
    UMEDA,Hiroaki, HANAWA,Toshihiro, SHOJI,Mitsuo, BOKU,Taisuke, SHIGETA,Yasuteru
    Journal of Chemical Software 14 (3) 2015[Refereed]
    A density functional study on pKa of small polyprotic molecules
    T.,Baba, T.,Matusui, K.,Kamiya, M.,Nakano, 重田,育照
    International Journal of Quantum Chemistry 114 (17) Sep 2014[Refereed]
    Open-Shell Character and Second Hyperpolarizabilities of One-Dimensional Chromium(II) Chains: Size Dependence and Bond-Length Alternation Effect
    H.,Fukui, S.,Takamuku, T.,Yamada, K.,Fukuda, T.,Takebayashi, Shigeta,Yasuteru, R.,Kishi, M.,Nakano
    Inorganic Chemistry 53 Aug 2014[Refereed]
    Enhanced conformational sampling methods for extracting biological rare events of proteins(Protein: Structure & Function,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))
    Ryuhei,Harada, Yu,Takano, Yasuteru,Shigeta
    Biophysics 54 (1) Aug 2014[Refereed]
    Hydration effects on enzyme–substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method
    Hiroyuki Ando, Yasuteru Shigeta, Takeshi Baba, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Masayoshi Nakano
    Molecular Physics 113 (3-4) Aug 2014[Refereed]
    On the induced-fit mechanism of substrate-enzyme binding structures of Nylon-oligomer hydrolase
    T.,Baba, R.,Harada, M.,Nakano, 重田,育照
    Journal of Computational Chemistry 35 (16) Jun 2014[Refereed]
    A Nylon-oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 5 (7) Mar 2014[Refereed]
    Fluctuation Flooding Method (FFM)for accelerating conformational transitions of proteins
    Ryuhei,Harada, Yu,Takano, 重田,育照
    Journal of Chemical Physics 140 (12) Mar 2014[Refereed]
    A new type of organic-inorganic hybrid NLO-phore with large off-diagonal first hyperpolarizability tensors: a two-dimensional approach
    Shigeta,Yasuteru
    Dalton Transactions 42 (42) Nov 2013[Refereed]
    Non-empirical tuning of CAM-B3LYP functional in time-dependent density functional theory for excitation energies of diarylethene derivatives
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 585 (1-3) Oct 2013[Refereed]
    Binding of a positron to nucleic-acid base molecules and their pairs
    Shigeta,Yasuteru
    ChemPhysChem 14 (15) Oct 2013[Refereed]
    Finite-Field Method with Unbiased Polarizable Continuum Model for Evaluation of the Second Hyperpolarizability of an Open-Shell Singlet Molecule in Solvents
    Shigeta,Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (27) Oct 2013[Refereed]
    Photochromic Switching of Diradical Character: Design of Efficient Nonlinear Optical Switches
    重田,育照
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 4 (15) Jul 2013[Refereed]
    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 Jun 2013[Refereed]
    A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion: General Theory and Applications
    Shigeta,Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 9 (5) May 2013[Refereed]
    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 May 2013[Refereed]
    Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 4 (10) Apr 2013[Refereed]
    Diradicalology in Third-Order Nonlinear Optical Systems: Second Hyperpolarizabilities of Acetylene-Linked Phenalenyl Based Superpolyenes
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (4) Feb 2013[Refereed]
    Comparative Study of Diradical Characters and Third-Order Nonlinear Optical Properties of Linear/Cyclic Acenes versus Phenylenes
    重田,育照
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (4) Feb 2013[Refereed]
    Antidot Effects on the Open-Shell Characters and Second Hyperpolarizabilities of Rectangular Graphene Nanoflakes
    重田,育照
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (4) Feb 2013[Refereed]
    Qantal Cumulant Mechanics and Dynamics for Multi-Dimensional Quantum Many-Body Clusters
    重田,育照
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (3) Feb 2013[Refereed]
    Consistent Scheme for Computing Standard Hydrogen Electrode and Redox Potentials
    Shigeta,Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (1) Jan 2013[Refereed]
    Interplay between the Diradical Character and Third-Order Nonlinear Optical Properties in Fullerene Systems
    Shigeta,Yasuteru
    CHEMISTRY A EUROPEAN JOURNAL 19 (4) Jan 2013[Refereed]
    Previous Article Next Article Table of Contents Synthesis and Characterization of Quarteranthene: Elucidating the Characteristics of the Edge State of Graphene Nanoribbons at the Molecular Level
    Shigeta,Yasuteru
    Journal of the American Chemistry Society 135 (4) Jan 2013[Refereed]
    Cumulant mechanics : An explicit treatment for fluctuation on dynamics
    重田,育照
    Molecular Science 7 (1) Jan 2013[Refereed]
    Density functional studies of the structural variety of the Cu2S2 core of the CuA site
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 (24) Dec 2012[Refereed]
    DFT Analysis of Low-Frequency Heme Vibrations in Soluble Guanylate Cyclase: Raman Mode Enhancement by Propionate-Protein Interactions
    Shigeta,Yasuteru
    Chemistry Letters 41 (9) Sep 2012[Refereed]
    Impact of Antidot Structure on the Multiradical Characters, Aromaticities, and Third-Order Nonlinear Optical Properties of Hexagonal Graphene Nanoflakes
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY C 116 (33) Aug 2012[Refereed]
    Microscopic Mechanisms of Initial Oxidation of Si (100): Reaction Pathways and Free-Energy Barriers
    Shigeta,Yasuteru
    PHYSICAL REVIEW B 85 (20) May 2012[Refereed]
    Development of Calculation and Analysis Methods for the Dynamic First Hyperpolarizability Based on the ab initio Molecular Orbital - Quantum Master Equation Method
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 116 (17) May 2012[Refereed]
    Enhancement of the Third-Order Nonlinear Optical Properties in Open-Shell Singlet Transition-Metal Dinuclear Systems: Effects of the Group, of the Period, and of the Charge of the Metal Atom
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 116 (22) May 2012[Refereed]
    Tuned CAM-B3LYP Functional in the Time-Dependent Density Functional Theory Scheme for Excitation Energies and Properties of Diarylethene Derivatives
    Shigeta,Yasuteru
    Journal of photochemistry and Photobiology A:Chemistry 235 (1) May 2012[Refereed]
    Coordination Effects on the Electronic Structure of the CuA Site of Cytochrome c Oxidase
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 531 Apr 2012[Refereed]
    Temperature-Independent Stereoselectivity in Intramolecular Cycloaddition of Ketene Generated from Diazoester in Solution and in Vapor Phase: How Entropy Term Governs the Selectivity
    Shigeta,Yasuteru
    Bulletin of the Chemical Society of Japan 85 (4) Apr 2012[Refereed]
    An Accurate Density Functional Theory Based Estimation of pKa Values of Polar Residues Combined with Experimental Data: From Amino Acids to Minimal Proteins
    Shigeta,Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 14 Mar 2012[Refereed]
    heoretical Insight into Stereoselective Reaction Mechanisms of 2,4-Pentanediol-Tethered Ketene-Olefin [2+2] Cycloaddition
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 116 (4) Feb 2012[Refereed]
    Halide Ion Complexes of Decaborane (B10H14) and Their Derivatives: Noncovalent Charge Transfer Effect on Second-Order Nonlinear Optical Properties
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 116 (5) Feb 2012[Refereed]
    Possible Mechanisms of Water Splitting Reaction Based on Proton and Electron Release Pathways Revealed for CaMn4O5 Cluster of PSII Refined to 1.9 Å X-Ray Resolution1
    Saito,T, Yamanaka,S, Kanda,K, Isobe,H, Takano,Y, Shigeta,Yasuteru, Umena,Y, Kawakami,K, Shen,J-R, Kamiya,N, Okumura,M, Shoji,M, Yoshioka,Y, Yamaguchi,K
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 (2) Jan 2012[Refereed]
    Tuned Long-Range Corrected Density Functional Theory Method for Evaluating the Second Hyperpolarizabilities of Open-Shell Singlet Metal-metal Bonded Systems
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 523 Jan 2012[Refereed]
    Full Configuration Interaction Calculations of the Second Hyperpolarizabilities of the H4 Model Compound: Summation-over-states Analysis and Interplay with Diradical Characters
    Shigeta,Yasuteru
    JOURNAL OF CHEMICAL PHYSICS 136 (2) Jan 2012[Refereed]
    (Hyper)polarizability Density Analysis for Open-Shell Molecular Systems Based on Natural Orbitals and Occupation Numbers
    Shigeta,Yasuteru
    THEORETICAL CHEMISTRY ACCOUNTS 130 (4-6) Dec 2011[Refereed]
    Self-diffusion in Crystalline Silicon: A Car-Parrinello Molecular Dynamics Study
    Shigeta,Yasuteru
    Physicla Review B 84 (20) Nov 2011[Refereed]
    First-principles Molecular Dynamics Studies on the Atomistic Behavior of His503 in Bovine Cytochrome c Oxidase
    Shigeta,Yasuteru
    Biochim Biophys Acta 1807 (10) Oct 2011[Refereed]
    Electronic Structures of the Cu2S2 Core of the CuA Site in Cytochrome c Oxidase and Nitronous Oxide Reductase
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 (2) Sep 2011[Refereed]
    Origin of the Enhancement of the Second Hyperpolarizabilities in Open-Shell Singlet Transition-Metal Systems with Metal–Metal Multiple Bonds
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2 (2) Jul 2011[Refereed]
    A Theoretical Study on Reaction Scheme of Silver (I) Containing 5-Substituted Uracils Bridge Formation
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 115 Jun 2011[Refereed]
    Open-Shell Characters and Second Hyperpolarizabilities of One-Dimensional Graphene Nanoflakes Composed of Trigonal Graphene Units
    Shigeta,Yasuteru
    ChemPhysChem 12 (9) May 2011[Refereed]
    Giant Enhancement of the Second Hyperpolarizabilities of Open-Shell Singlet Polyaromatic Diphenalenyl Diradicaloids by an External Electric Field and Donor-Acceptor Substitution
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2 (9) Apr 2011[Refereed]
    Molecular Dynamics Studies on the Mutational Structures of a Nylon-6 Byproduct-Degrading Enzyme
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 507 (1) Apr 2011[Refereed]
    Electron Conductivity in Modified Models of Artificial Meta-DNA Using Green's Function-Based Elastic Scattering Theory
    Shigeta,Yasuteru
    Bulletin of the Chemical Society of Japan 84 (3) Mar 2011[Refereed]
    Enhancement of Second Hyperpolarizabilities in Open-Shell Singlet Slipped-Stack Dimers Composed of Square Planar Nickel Complexes Involving o-Semiquinonato Type Ligands
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY A 115 (6) Feb 2011[Refereed]
    A Simple Scheme for Estimating the pKa Values of 5-Substituted Uracils
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 502 (4-6) Jan 2011[Refereed]
    Approximate Spin-Projected Spin-Unrestricted Density Functional Theory Method: Application to the Diradical Character Dependences of the (Hyper) Polarizabilities in p-Quinodimethane Models
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 501 (1-3) Dec 2010[Refereed]
    Sequence-Dependent Proton-Transfer Reaction in Stacked GC Pair III: The Influence of Proton Transfer to Conductivity
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 110 (12) Oct 2010[Refereed]
    Energy Compensation Mechanism for Charge-Separated Protonation States in Aspartate-Histidine Amino Acid Residue Pairs
    Shigeta,Yasuteru
    JOURNAL OF PHYSICAL CHEMISTRY B 114 (19) May 2010[Refereed]
    Effects of Mercury (II) on Structural Properties, Electronic Structure and UV Absorption Spectra of Thymine-Mercury (II)-Thymine Nucleobase Pair Containing Duplex
    Shigeta,Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12 (4) Jan 2010[Refereed]
    Molecular Theory Including Quantum Effects and Thermal Fluctuations
    Shigeta,Yasuteru
    Bulletin of the Chemical Society of Japan 82 (11) Nov 2009[Refereed]
    Theoretical Studies on Sulfur and Metal Cation (Cu(II), Ni(II), Pd(II), and Pt(II))-Containing Artificial DNA
    重田,育照
    JOURNAL OF PHYSICAL CHEMISTRY B 113 (38) Sep 2009[Refereed]
    Sequence-Dependent Proton-Transfer Reaction in Stacked GC Pair II: The Origin of Stabilities of Proton-Transfer Products
    Shigeta,Yasuteru
    CHEMICAL PHYSICS LETTERS 478 (4-6) Aug 2009[Refereed]
    Theoretical Studies on Magnetic Interactions between Cu(II) Ions in Salen Nucleobases
    Shigeta,Yasuteru
    polyhedron 28 (9-10) Jun 2009[Refereed]
    Theoretical Studies on Magnetic Interactions Between Cu(II) Ions in Hydroxypyridone Nucleobases
    Shigeta,Yasuteru
    polyhedron 28 (9-10) Jun 2009[Refereed]
    Sequence Dependent Proton-Transfer Reaction in Stacked GC Pair I: The Possibility of Proton-Transfer Reactions
    Shigeta,Yasuteru
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 109 (10) Mar 2009[Refereed]
    Structural Origin of Copper Ion Containing Artificial DNA: A Density Functional Study
    Shigeta,Yasuteru
    Journal of Physical Chemistry B 112 (51) Dec 2008[Refereed]
    Correlation functions in quantized Hamilton dynamics and quantal cumulant dynamics
    Pereverzev, Yuriy V, Pereverzev, Andrey, Shigeta, Yasuteru, Prezhdo, Oleg V
    JOURNAL OF CHEMICAL PHYSICS 129 (14) Oct 2008[Refereed]
    Dynamic Quantum Isotope Effects on Multiple Proton-Transfer Reactions
    Shigeta, Yasuteru, Miyachi, Hideaki, Matsui, Toru, Hirao, Kimihiko
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 81 (10) Oct 2008[Refereed]
    Quantal cumulant dynamics III: A quantum confinement under a magnetic field
    Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 461 (4-6) Aug 2008[Refereed]
    分子磁性の理論 (その7) 遺伝的アルゴリズムのモンテカルロ法への導入
    重田,育照
    固体物理 40 (3) Mar 2005[Refereed]
  • Awards & Honors
    Feb 2019
    Best Faculty Awards 2018
    Oct 2017
    22nd QSCP Promising Scientist Award of CMOA Research Award
    Mar 2017
    Royal Chemical Society Outstanding Reviewers for Physical Chemistry Chemical Physics in 2016 論文査読
    May 2013
    大阪大学 第2回大阪大学総長奨励賞・研究部門 研究業績
    Sep 2012
    分子科学会 第5回分子科学会奨励賞 研究業績
    Apr 2010
    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
    Mar 2009
    日本化学会 第58回日本化学会進歩賞 研究業績
    Mar 2007
    Royal Chemical Society PCCP Prize for the Outstanding Achievement of Young Scientists in Physical Chemistry and Chemical Physics Research Award
    Mar 2006
    日本化学会 第86回日本化学会年会優秀講演賞 研究業績
  • Books etc
    Advances in Quantum Chemistry
    Shigeta,Yasuteru (Part:分担執筆, Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules)
    Quantum Systems in Physics, Chemistry, and Biology: Advances in Concepts and Applications
    Baba, Takeshi, Kamiya, Katsumasa, Shigeta, Yasuteru (Part:分担執筆, Integrated Computational Studies on Mutational Effects of A Nylon-degrading Enzyme)
    Reference modules in Materials Science and Engineering 2016
    Harada, Ryuhei, Inagaki, Yuji, Shigeta, Yasuteru (Part:分担執筆, Protein Folding and Evolution)
    金属錯体の量子・計算化学
    重田,育照, 北河康隆 (Part:分担執筆, 第4-1章 錯体の伝導性)
    Quantum mechanics Chap. 17
    Shigeta,Yasuteru (Part:分担執筆, Quantal Cumulant Mechanics as Extended Ehrenfest Theorem)
    Conceptual and Computational Advances in Quantum Chemistry, Chap. 25
    Shigeta,Yasuteru (Part:分担執筆, Theoretical Studies on Metal-Containing Artificial DNA Bases”, Advances in the Theory of Atomic and Molecular Systems)
    Advances in the Theory of Atomic and Molecular Systems, Conceptual and Computational Advances in Quantum Chemistry, Chap. 21
    Shigeta,Yasuteru (Part:分担執筆, Quantum Theory in Terms of Cumulant Variables)
    ADVANCES IN THE THEORY OF ATOMIC AND MOLECULAR SYSTEMS: DYNAMICS, SPECTROSCOPY, CLUSTERS, AND NANOSTRUCTURES
    Shigeta, Yasuteru, Miyachi, Hideaki, Matsui, Toru, Yokoyama, Norisuke, Hirao, Kimihiko (Part:分担執筆, Quantum Theory in Terms of Cumulant Variables)
    Challenges and Advances in Computational Chemistry and Physics, Chap. 2
    Shigeta,Yasuteru (Part:分担執筆, Single-Reference Methods for Excited States in Molecules and Polymers)
    物性量子化学入門
    重田,育照 (Part:分担執筆, 第13、14章)
  • Research Grants & Projects
    生体ハイドロジェノミクスの理論解析
    新学術領域研究(研究領域提案型)
    Research period: Apr 2019 -
    Structure-based design of middle molecules for drug discovery
    Research period: Jun 2018 -
    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」
    Research period: Apr 2016 - Mar 2019
    理論と実験の協奏的アプローチによる多重スピン励起子変換制御
    新学術領域研究(研究領域提案型)
    Research period: Jun 2014 - Mar 2019
    高次複合光応答分子システムの開拓と学理の構築
    科研費新学術領域研究(研究領域提案型)
    Research period: Jun 2014 - Mar 2019
    メゾスケール空間内移動速度論創成のための挑戦的研究
    科学研究費補助金 挑戦的萌芽研究
    Research period: Apr 2015 - Mar 2017
    キュミュラント粗視化動力学によるタンパク質動的秩序形成過程の理論研究
    新学術領域研究(研究領域提案型)
    Research period: Apr 2014 - Jun 2014
    Siナノドットの非線形光学特性変化に対する動力学的解析
    新学術領域研究(研究領域提案型)
    Research period: Apr 2013 - Jun 2014
    タンパク内で起こる協同的プロトン・電子移動反応の量子論的解析
    科学研究費補助金 若手研究(A)
    Research period: Apr 2010 - Mar 2014
    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
    Research period: Apr 2011 - Mar 2012
    電子ダイナミクスによる電子集団運動の解析
    特定領域研究
    Research period: 2008 - 2009
    プロトン結合電子移動反応の実時間解析:量子キュミュラント動力学法
    若手研究(B)
    Research period: 2008 - 2009
harada 氏名 原田 隆平
Name Harada Ryuhei
Faculty
Section
Position Associate Professor
Theme
Related Links
Email ryuheiccs.tsukuba.ac.jp
  • Research Interests
  • Academic & Professional Experience
    Feb 2019
    -
    University of Tsukuba Center for Computational Sciences
    Apr 2018
    -
    Jan 2019
    University of Tsukuba Center for Computational Sciences
    Apr 2015
    -
    Mar 2018
    日本学術振興会 特別研究員 (PD)
    Apr 2014
    -
    Mar 2015
    University of Tsukuba Center for Computational Sciences
    Apr 2011
    -
    Mar 2014
    理化学研究所 計算科学研究機構 特別研究員
  • Published Papers
    Distribution of Counter Ions in Negatively-charged Lipid/Water/Air Interface: Molecular Dynamics Study
    Takahashi Teruyuki, Harada Ryuhei, Shigeta Yasuteru
    CHEMISTRY LETTERS 49 (4) Apr 2020[Refereed]
    Protein Dynamics and the Folding Degree
    Sladek Vladimir, Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 60 (3) Mar 2020[Refereed]
    学術賞受賞寄稿「タンパク質の機能発現に重要なレアイベントを抽出するサンプリング手法の開発」
    原田隆平
    アンサンブル 22 Jan 2020[Refereed]
    Rare Event Sampling of Biomolecules Based on Distributed Computing
    Harada Ryuhei
    BUTSURI 75 (1) Jan 2020[Refereed]
    Developments of Rare Event Sampling Methods for Proteins
    Harada Ryuhei, Sladek Vladimir, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY JAPAN 18 (5) Dec 2019[Refereed]
    Non-targeted Parallel Cascade Selection Molecular Dynamics Based on a Non-Redundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
    Harada Ryuhei, Sladek Vladimir, Shigeta Yasuteru
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 59 (12) Nov 2019[Refereed]
    Selection Rules for Outliers in Outlier Flooding Method (OFLOOD) Regulate its Conformational Sampling Efficiency
    Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 59 (9) Sep 2019[Refereed]
    Non-targeted Parallel Cascade Selection Molecular Dynamics Using Time-localised Prediction of Conformational Transitions in Protein Dynamics
    Harada Ryuhei, Sladek Vladimir, Shigeta Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (9) Sep 2019[Refereed]
    Supercomputing News
    Ryuhei Harada
    Supercomputing News 21 (1) Aug 2019[Refereed]
    Parallel Cascade Selection Molecular Dynamics Simulation (PaCS-MD) Screens for Protein Complexes Generated by Rigid Docking
    Harada Ryuhei, Yoshino Ryunosuke, Nishizawa Hiroaki, Shigeta Yasuteru
    JOURNAL OF MOLECULAR GRAPHICS AND MODELING 92 Jul 2019[Refereed]
    Temperature-Pressure Shuffling Outlier Flooding Method Enhances the Conformational Sampling of Proteins
    Harada Ryuhei, Yoshino Ryunosuke, Nishizawa Hiroaki, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 40 (15) Apr 2019[Refereed]
    Molecular Dynamics Studies on the Effects of Antifreezing Protein from Rhagium Inquisitor (RiAFP) onIce Growth
    Kimatsuka Masato, Sato Ryuma, Harada Ryuhei, Shoji Mitsuo, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY JAPAN 17 (5) Mar 2019[Refereed]
    Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-Order Molecular Dynamics Simulation
    Aida Hayato, Harada Ryuhei, Shigeta Yasuteru
    CHEMISTRY LETTERS 48 (4) Mar 2019[Refereed]
    Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
    Harada Ryuhei, Shigeta Yasuteru
    ADVANCES IN QUANTUM CHEMISTRY 78 Feb 2019[Refereed]
    Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
    Kimatsuka Masato, Sato Ryuma, Harada Ryuhei, Shoji Mitsuo, Shigeta Yasuteru
    CHEMISTRY LETTERS 48 (3) Feb 2019[Refereed]
    Studies of Molecular Crowding by Simulations and Development of Parallel Cascade Selection Molecular Dynamics
    Harada Ryuhei
    ASSOCIATION OF ASIA PACIFIC PHYSICAL SOCIETIES (AAPPS BULLETIN), 29 (1) Feb 2019[Refereed]
    Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations
    Harada Ryuhei, Shigeta Yasuteru
    15 (1) Jan 2019[Refereed]
    Studies of Molecular Crowding by Simulations and Development of Parallel Cascade Selection Molecular Dynamics
    Harada Ryuhei
    BUTSURI 73 (12) Dec 2018[Refereed]
    カスケード選択型分子動力学シミュレーションの開発とタンパク質構造変化予測への適用
    原田隆平
    平成29年度・京都大学スーパーコンピュータ共同研究制度広報 17 (1) Dec 2018[Refereed]
    The Formation of Central Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics
    Harada Ryuhei, Aida Hayato, Shigeta Yasuteru
    47 Sep 2018[Refereed]
    Effect of Initial Structures Rules in Parallel Cascade Selection Molecular Dynamics Affect Conformational Sampling Efficiency
    Shigeta Yasuteru
    85 Sep 2018[Refereed]
    Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins
    Harada Ryuhei
    BULLETIN CHEMICAL SOCIETY OF JAPAN, in press 91 (9) Sep 2018[Refereed]
    How does Friction Constant affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?
    Harada Ryuhei, Shigeta Yasuteru
    CHEMISTRY LETTERS 47 Aug 2018[Refereed]
    Temperature Shuffled Structural Dissimilarity Sampling Based on a Root-Mean Square Deviation
    Harada Ryuhei, Shigeta Yasuteru
    58 (7) Aug 2018[Refereed]
    カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発とFtsZ細胞分裂ダイナミクスへの適用
    原田隆平
    スーパーコンピューティングニュース特集号 20 (2) Aug 2018[Refereed]
    How Low-Resolution Structural Data Predict the Conformational Changes of a Protein: A Study on Data-Driven Molecular Dynamics Simulations
    Harada Ryuhei, Shigeta Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 20 Jul 2018[Refereed]
    Developments of Innovative Molecular Simulation Methods for Understanding the Biological Functions
    CHEMICAL INDUSTRY 69 (7) Jul 2018[Refereed]
    Coulomb and CH–π Interactions in (6–4) Photolyase–DNA Complex Dominate DNA Binding and Repair Ability
    Terai Yuma, Sato Ryuma, Yumiba Takahiro, Harada Ryuhei, Shimizu Kohei, Toga Tatsuya, Ishikawa Tomoko, Todo Takeshi, Iwai Shigenori, Shigeta Yasuteru, Yamamoto Junpei
    NUCLEIC AICD RESEARCH, accepted 46 (13) Jul 2018[Refereed]
    On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate the Conformational Transitions of Proteins
    Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 14 (6) Jun 2018[Refereed]
    Recent Extensions and Applications of Parallel Cascade Selection Molecular Dynamics Simulations
    Harada Ryuhei, Shigeta Yasuteru
    May 2018[Refereed]
    Programed Dynamics Ordering in the Self-Organization Processes of a Nanocube: A Molecular Dynamics Study
    Harada Ryuhei, Mashiko Takako, Tachikawa Masanori, Hiraoka Shuichi, Shigeta Yasuteru
    20 Apr 2018[Refereed]
    Development of Molecular Crowding and Cascade-Type Massive Parallel Simulation Methods for Biological Functions of Proteins
    Harada Ryuhei
    CHEMISTRY AND CHEMICAL INDUSTRY 71 (3) Mar 2018[Refereed]
    Analyses on Dynamic Ordering of Protein Functions by means of Cascade Selection Molecular Dynamics
    Harada Ryuhei, Shigeta Yasuteru
    JOURNAL OF COMPUTER CHEMISTRY JAPAN, in press 17 (1) Mar 2018[Refereed]
    The Binding Structure and Affinity of Photodamaged Duplex DNA with Members of the Photolyase/Cryptochrome Family: A Computational Study
    BIOPHYSICS AND, PHYSICOBIOLOGY
    15 Jan 2018[Refereed]
    An assessment of optimal time scale of conformational resampling for parallel cascade selection molecular dynamics
    Harada Ryuhei, Shigeta Yasuteru
    MOLECULAR SIMULATION 44 (3) Jan 2018[Refereed]
    Temperature-Shuffled Parallel Cascade Selection Molecular Dynamics Accelerates the Structural Transitions of Proteins
    Ryuhei Harada, Yasuteru Shigeta
    JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (31) Dec 2017[Refereed]
    Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches
    Ryuhei Harada, Yasuteru Shigeta
    JOURNAL OF CHEMICAL INFORMATION AND MODELING 57 (12) Dec 2017[Refereed]
    Dynamic Specification of Initial Structures in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Efficiently Promotes Biologically Relevant Rare Events
    Ryuhei Harada, Yasuteru Shigeta
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 90 (11) Nov 2017[Refereed]
    Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection
    Ryuhei Harada, Yasuteru Shigeta
    JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (22) Aug 2017[Refereed]
    Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
    Yuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki Hayashi
    JOURNAL OF PHYSICAL CHEMISTRY B 121 (22) Jun 2017[Refereed]
    How Does the Number of Initial Structures Affect the Conformational Sampling Efficiency and Quality in Parallel Cascade Selection Molecular Dynamics (PaCS-MD)?
    Ryuhei Harada, Yasuteru Shigeta
    CHEMISTRY LETTERS 46 (6) Jun 2017[Refereed]
    Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
    Junso Fujita, Ryuhei Harada, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi Matsumura
    JOURNAL OF STRUCTURAL BIOLOGY 198 (2) May 2017[Refereed]
    Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
    Junso Fujita, Ryuhei Harada, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi Matsumura
    JOURNAL OF STRUCTURAL BIOLOGY 198 (2) May 2017[Refereed]
    Common Folding Processes of Mini-Proteins: Partial Formations of Secondary Structures Initiate the Immediate Protein Folding
    Ryuhei Harada, Yu Takano, Yasuteru Shigeta
    JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (11) Apr 2017[Refereed]
    Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins
    Ryuhei Harada, Yasuteru Shigeta
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13 (3) Mar 2017[Refereed]
    Classical cumulant dynamics for statistical chemical physics
    Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, Thi Kieu My Bui, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma, Mitsuo Shoji
    MOLECULAR SIMULATION 43 (13-16) 2017[Refereed]
    Theoretical Analyses on a Flipping Mechanism of UV-induced DNA Damage
    BIOPHYSICS AND PHYSICOBIOLOGY 13 Nov 2016[Refereed]
    A Fast Convergent Simulated Annealing Algorithm for Protein-Folding: Simulated Annealing Outlier FLOODing (SA-OFLOOD) Method
    Harada Ryuhei, Nakamura Tomotake, Shigeta Yasuteru
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 89 (11) Nov 2016[Refereed]
    Biomolecular Interactions Modulate Macromolecular Structure and Dynamics in Atomistic Model of a Bacterial Cytoplasm
    Yu Isseki, Mori Takaharu, Ando Tadashi, Harada Ryuhei, Jung Jaewoon, Sugita Yuji, Feig Michael
    ELIFE 5 Nov 2016[Refereed]
    Molecular Mechanisms of Substrate Specificities of Uridine-Cytidine Kinase
    Tanaka Wataru, Shoji Mitsuo, Tomoike Fumiaki, Ujiie Yuzuru, Hanaoka Kyohei, Harada Ryuhei, Kayanuma Megumi, Kamiya Katsumasa, Ishida Toyokazu, Masui Ryoji, Kuramitsu Seiki, Shigeta Yasuteru
    BIOPHYSICS AND PHYSICOBIOLOGY 13 Jun 2016[Refereed]
    最近の研究から「カスケード型超並列シミュレーションに基づく遷移経路探索法」
    原田隆平
    アンサンブル 18 (3) Jun 2016[Refereed]
    TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins
    Harada Ryuhei, Takano Yu, Shigeta Yasuteru
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12 (5) May 2016[Refereed]
    Sparsity-Weighted Outlier FLOODing (OFLOOD) Method: Efficient Rare Event Sampling Method Using Sparsity of Distribution
    Harada Ryuhei, Nakamura Tomotake, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 37 (8) Mar 2016[Refereed]
    Parallel Cascade Selection Molecular Dynamics for Efficient Conformational Sampling and Free Energy Calculation of Proteins
    Kitao Akio, Harada Ryuhei, Nishihara Yasutaka, Duy Phuoc Tran
    PROCEEDINGS OF THE INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2016 (ICCMS-2016) 1790 2016[Refereed]
    Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins
    Harada Ryuhei, Kitao Akio
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11 (11) Nov 2015[Refereed]
    Automatic Detection of Hidden Dimensions to Obtain Appropriate Reaction Coordinates in the Outlier FLOODing (OFLOOD) Method
    Harada Ryuhei, Nakamura Tomotake, Shigeta Yasuteru
    CHEMICAL PHYSICS LETTERS 639 Oct 2015[Refereed]
    Protein Folding and Evolution
    Harada Ryuhei, Inagaki Yuji, Shigeta Yasuteru
    In book: Reference Module in Materials Science and Materials Engineering DOI: 10.1016/B978 Aug 2015[Refereed]
    Efficient Conformational Sampling of Proteins Based on a Multi-dimensional TaBoo SeArch Algorithm: An Application to Folding of Chignolin in Explicit Solvent
    Harada Ryuhei, Takano Yu, Shigeta Yasuteru
    CHEMICAL PHYSICS LETTERS 630 Jun 2015[Refereed]
    Complete Atomistic Model of a Bacterial Cytoplasm for Integrating Physics, Biochemistry, and Systems Biology
    Feig Michael, Harada Ryuhei, Mori Takaharu, Yu Isseki, Takahashi Koichi, Sugita Yuji
    JOURNAL OF MOLECULAR GRAPHICS & MODELLING 58 May 2015[Refereed]
    Enhanced Conformational Sampling Method for Proteins Based on the TaBoo SeArch Algorithm: Application to the Folding of a Mini-Protein, Chignolin
    Harada Ryuhei, Takano Yu, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (10) Apr 2015[Refereed]
    Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body Systems
    Shigeta Yasuteru, Harada Ryuhei, Kayanuma Megumi, Shoji Mitsuo
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5) Mar 2015[Refereed]
    Protein Folding Pathways Extracted by OFLOOD: Outlier FLOODing Method
    Harada Ryuhei, Nakamura Tomotake, Takano Yu, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (2) Jan 2015[Refereed]
    Simple, yet Powerful Methodologies for Conformational Sampling of Proteins
    Harada Ryuhei, Takano Yu, Baba Takeshi, Shigeta Yasuteru
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (9) 2015[Refereed]
    Cascade-type Massive Parallel Simulation for Protein Conformation Transition Pathway Search
    Nishihara Yasutaka, Harada Ryuhei, Kitao Akio
    PROCEEDINGS OF THE INSTITUTE OF STATISTICAL MATHEMATICS 62 (2) Dec 2014[Refereed]
    On the Induced-Fit Mechanism of Substrate-Enzyme Binding Structures of Nylon-Oligomer Hydrolase
    Baba Takeshi, Harada Ryuhei, Nakano Masayoshi, Shigeta Yasuteru
    JOURNAL OF COMPUTATIONAL CHEMISTRY 35 (16) Jun 2014[Refereed]
    Molecular Simulation Methods to Enhance Soft Protein Motions
    Harada Ryuhei, Kitao Akio
    54 (3) Mar 2014[Refereed]
    Hydration and Protein Stability under Molecular Crowding Environments
    Harada Ryuhei
    BUSEEI KENKYU 53 Mar 2014[Refereed]
    Fluctuation Flooding Method (FFM) for Accelerating Conformational Transitions of Proteins
    Harada Ryuhei, Takano Yu, Shigeta Yasuteru
    JOURNAL OF CHEMICAL PHYSICS 140 (12) Mar 2014[Refereed]
    Conformational Transition Pathway and Free Energy Analyses of Proteins by Parallel Cascade Selection Molecular Dynamics (PaCS-MD)
    Harada Ryuhei, Nishihara Yasutaka, Wakai Nobuhiko, Kitao Akio
    PROCEEDINGS OF THE INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2014 (ICCMS-201 1618 2014[Refereed]
    Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to Generate Conformational Transitions of Proteins
    Harada Ryuhei, Kitao Akio
    JOURNAL OF CHEMICAL PHYSICS 139 (3) Jul 2013[Refereed]
    Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions
    Harada Ryuhei, Tochio Naoya, Kigawa Takanori, Sugita Yuji, Feig Michael
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135 (9) Mar 2013[Refereed]
    Hydration and Protein Stability under Cellular Environments
    Harada Ryuhei
    SEIBUTSU BUTSURI 53 (4) Feb 2013[Refereed]
    博士論文紹介「超並列マルチスケールシミュレーションMSFEL法で探る生体分子の生体分子の自由エネルギー地形」
    原田隆平
    アンサンブル 15 (1) Jan 2013[Refereed]
    Understanding Proteins in Packed Places
    Harada Ryuhei, Sugita Yuji, Feig Michael
    RIKEN RESEARCH 7 (3) Jul 2012[Refereed]
    Protein Crowding Affects Hydration Structure and Dynamics
    Harada Ryuhei, Sugita Yuji, Feig Michael
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 (10) Mar 2012[Refereed]
    The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing
    Harada Ryuhei, Kitao Akio
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8 (1) Jan 2012[Refereed]
    Exploring the Folding Free Energy Landscape of a beta-Hairpin Miniprotein, Chignolin, Using Multiscale Free Energy Landscape Calculation Method
    Harada Ryuhei, Kitao Akio
    JOURNAL OF PHYSICAL CHEMISTRY B 115 (27) Jul 2011[Refereed]
    Multi-Scale Free Energy Landscape Calculation Method by Combination of Coarse-Grained and All-atom Models
    Harada Ryuhei, Kitao Akio
    CHEMICAL PHYSICS LETTERS 503 (1-3) Feb 2011[Refereed]
  • Awards & Honors
    Dec 2019
    2019年度 分子シミュレーション学会 学術賞
    Mar 2019
    日本物理学会 第13回 若手奨励賞 (領域12)
    Feb 2019
    Royal Society of Chemistry 2018 PCCP Hot Article Collection
    Mar 2018
    日本化学会 第67回 進歩賞
    Sep 2017
    The 4th BIOPHYSICS Editors' Choice Award
    Nov 2016
    BCSJ Selected Paper (日本化学会 優秀論文)
    Nov 2016
    第54回 日本生物物理学会年会 若手招待講演賞
    Sep 2012
    第50回 日本生物物理学会年会 若手招待講演証
    Nov 2010
    第24回 分子シミュレーション討論会 学生優秀発表賞
  • Books etc
  • Research Grants & Projects
    中分子環状ペプチドの膜透過性を評価する分子シミュレーション技術の創出
    筑波大学研究基盤支援プログラム (Aタイプ)
    Research period: Aug 2019 - Mar 2020
    筑波大学研究支援プログラム(Cタイプ)
    Research period: Jul 2019 - Mar 2020
    カスケード選択型分子動力学シミュレーションで実現する環状ペプチド の膜透過シミュレーション
    2019年度学際共同利用
    Research period: Apr 2019 - Mar 2020
    PaCS-MDで実現する環状ペプチドの膜透過シミュレーション
    平成31年度 TSUBAME若手・女性利用者支援制度度
    Research period: Apr 2019 - Mar 2020
    カスケード選択型分子動力学シミュレーションで実現する環状ペプチドの膜透過シミュレーション
    若手・女性利用者推薦 2019年度 (前期)
    Research period: Apr 2019 - Sep 2019
    カスケード選択型分子動力学シミュレーションに基づく低解像度タンパク質構造の精密化
    平成30年度スーパーコンピューター若手・女性利用者推薦制度選択課題 (後期)
    Research period: Oct 2018 - Mar 2019
    筑波大学研究基盤支援プログラム(Cタイプ)
    Research period: Jul 2018 - Mar 2019
    カスケード型分子動力学シミュレーションに基づくフレキシブルドッキング法の開発
    平成30年度 TSUBAME若手・女性利用者支援制度度
    Research period: Apr 2018 - Mar 2019
    Gタンパク質共役受容体におけるシグナル伝達機構の解明
    若手研究(A) 課題番号:16H06164
    Research period: Apr 2016 - Mar 2019
    カスケード型分子動力学シミュレーションに基づくタンパク質構造精密化アルゴリズムの開発と応用
    平成30年度 スーパーコンピューター若手・女性利用者推薦 (前期)
    Research period: Apr 2018 - Sep 2018
    カスケード型超並列シミュレーションで探るFtsZ の細胞分裂ダイナミクス
    平成29年度 スーパーコンピューター若手・女性利用者推薦採択課題 (後期)
    Research period: Oct 2017 - Mar 2018
    教師あり機械学習に基づく超並列カスケード型シミュレーションの定式化とタンパク質構造変化予測への適用
    平成29年度 若手・女性研究者奨励枠
    Research period: Apr 2017 - Mar 2018
    カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発
    平成29年度 TSUBAME若手・女性利用者支援制度
    Research period: Apr 2017 - Mar 2018
    分子動力学シミュレーションで探る細胞環境におけるタンパク質フォールディング機構
    特別研究奨励費 課題番号:15J03797
    Research period: Apr 2015 - Mar 2018
    カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発
    平成29年度 スーパーコンピューター若手・女性利用者推薦課題 (前期)
    Research period: Apr 2017 - Sep 2017
    タンパク質構造揺らぎに基づく構造変化予測法の構築
    若手研究(B) 課題番号:26840056
    Research period: Apr 2014 - Mar 2016
氏名 庄司 光男
Name Shoji Mitsuo
Faculty
Section
Position Assistant Professor
Theme Theoretical investigation on the reaction mechanisms of enzymes
Related Links
Email mshojiccs.tsukuba.ac.jp
  • Research Interests
  • Academic & Professional Experience
  • Published Papers
    Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography
    Shoji, Mitsuo, Isobe, Hiroshi, Shen, Jian-Ren, Suga, Michihiro, Akita, Fusamichi, Miyagawa, Koichi, Shigeta, Yasuteru, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 730 Sep 2019[Refereed]
    First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface
    Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Kamiya, Katsumasa, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    The journal of physical chemistry. A 123 (26) Jul 2019[Refereed]
    Reaction mechanism of non-enzymatic stereoselective formation of wine lactone
    Kyan, Akane, Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 725 Jun 2019[Refereed]
    Spin, Valence, and Structural Isomerism in the S State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity
    Isobe, Hiroshi, Shoji, Mitsuo, Suzuki, Takayoshi, Shen, Jian-Ren, Yamaguchi, Kizashi
    Journal of chemical theory and computation 15 (4) Apr 2019[Refereed]
    Photosubstitution Reaction of cis-[Ru(bpy)(2)(CH3CN)(2)](2+) and cis-[Ru(bpy)(2)(NH3)(2)](2+) in Aqueous Solution via Monoaqua Intermediate
    Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
    The journal of physical chemistry. A 123 (13) Mar 2019[Refereed]
    Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn O (X=5, 6) cluster in the Kok cycle S (i=0-3) of oxygen evolving complex of photosystem II
    Yamaguchi, Kizashi, Yamanaka, Shusuke, Isobe, Hiroshi, Shoji, Mitsuo, Miyagawa, Kouichi, Nakajima, Takahito, Kawakami, Takashi, Okumura, Mitsutaka
    Physiologia plantarum 166 (1:::SI) Mar 2019[Refereed]
    Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
    Kimatsuka, Masato, Sato, Ryuma, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru
    Chemistry Letters 48 (3) Mar 2019[Refereed]
    Molecular Dynamics studies on the effects of Antifreezing Protein from Rhagium inquisitor (RiAFP) on Ice Growth
    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) Mar 2019[Refereed]
    Possibility of the right-opened Mn-oxo intermediate (R-oxo(4444)) among all nine intermediates in the S-3 state of the oxygen-evolving complex of photosystem II revealed by large-scale QM/MM calculations
    Shoji, Mitsuo, Isobe, Hiroshi, Miyagawa, Koichi, Yamaguchi, Kizashi
    CHEMICAL PHYSICS 518 Feb 2019[Refereed]
    Theoretical study of the photodissociation reaction of methanol
    Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 714 Jan 2019[Refereed]
    Concerted bond switching mechanism coupled with one-electron transfer for the oxygen-oxygen bond formation in the oxygen-evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 714 Jan 2019[Refereed]
    Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction
    Tokiwa, Takaki, Shoji, Mitsuo, Sladek, Vladimir, Shibata, Naoki, Higuchi, Yoshiki, Kataoka, Kunishige, Sakurai, Takeshi, Shigeta, Yasuteru, Misaizu, Fuminori
    Molecules (Basel, Switzerland) 24 (1) Jan 2019[Refereed]
    Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II
    Yamaguchi, Kizashi, Shoji, Mitsuo, Isobe, Hiroshi, Yamanaka, Shusuke, Kawakami, Takashi, Yamada, Satoru, Katouda, Michio, Nakajima, Takahito
    MOLECULAR PHYSICS Dec 2018[Refereed]
    UNO DMRG CAS CI calculations of binuclear manganese complex Mn(IV)(2)O-2(NHCHCO2)(4): Scope and applicability of Heisenberg model
    Kawakami, Takashi, Miyagawa, Koichi, Sharma, Sandeep, Saito, Toru, Shoji, Mitsuo, Yamada, Satoru, Yamanaka, Shusuke, Okumura, Mitsutaka, Nakajima, Takahito, Yamaguchi, Kizashi
    Journal of computational chemistry 40 (2:::SI) Oct 2018[Refereed]
    光化学系II酸素発生中心の反応機構
    庄司, 光男
    アンサンブル : 分子シミュレーション研究会会誌 40 (4) Oct 2018[Refereed]
    特集光化学系II酸素発生中心にあたって
    庄司, 光男
    アンサンブル : 分子シミュレーション研究会会誌 40 (4) Oct 2018[Refereed]
    A Theoretical Study on Redox Potential and pKa of [2Fe-2S] Cluster Model from Iron-Sulfur Proteins
    Kurniawan, Isman, Kawaguehi, Kazutomo, Shoji, Mitsuo, Matsui, Toru, Shigeta, Yasuteru, Nagao, Hidemi
    Bulletin of the Chemical Society of Japan 91 (9) Sep 2018[Refereed]
    Redox potential-dependent formation of an unusual His-Trp bond in bilirubin oxidase
    Akter, Mahfuza, Tokiwa, Takaki, Shoji, Mitsuo, Nishikawa, Koji, Shigeta, Yasuteru, Sakurai, Takeshi, Higuchi, Yoshiki, Kataoka, Kunishige, Shibata, Naoki
    Chemistry (Weinheim an der Bergstrasse, Germany) 24 (68) Aug 2018[Refereed]
    A Practical Approach for Searching Stable Molecular Structures by Introducing Repulsive Interactions among Walkers
    Shoji,Mitsuo, Kayanuma,Megumi, Shigeta,Yasuteru
    Bulletin of the Chemical Society of Japan 91 (10) Jul 2018[Refereed]
    Concerted Mechanism of Water Insertion and O Release during the S to S Transition of the Oxygen-Evolving Complex in Photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
    The journal of physical chemistry. B 122 (25) Jun 2018[Refereed]
    The Reaction Mechanisms of O2 Formation in Photosynthesis
    SHOJI,Mitsuo, ISOBE,Hiroshi, SHIGETA,Yasuteru, NAKAJIMA,Takahito, YAMAGUCHI,Kizashi
    Seibutsu Butsuri 58 (3) May 2018[Refereed]
    Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
    Yamamoto, Yuta, Takei, Kenta, Arulmozhiraja, Sundaram, Sladek, Vladimir, Matsuo, Naoya, Han, Song-Iee, Matsuzaka, Takashi, Sekiya, Motohiro, Tokiwa, Takaki, Shoji, Mitsuo, Shigeta, Yasuteru, Nakagawa, Yoshimi, Tokiwa, Hiroaki, Shimano, Hitoshi
    Biochemical and biophysical research communications May 2018[Refereed]
    Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 698 Apr 2018[Refereed]
    First-principles study of the formation of glycine-producing radicals from common interstellar species
    Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    Molecular Astrophysics 10 Mar 2018[Refereed]
    Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II
    Yamaguchi, Kizashi, Mitsuo, Shoji, Isobe, Hiroshi, Yamanaka, Shusuke, Kawakami, Takashi, Yamada, Satoru, Katouda, Michio, Nakajima, Takahito
    Molecular Physics 116 (5-6) Mar 2018[Refereed]
    First-principles study of the formation of glycine-producing radicals from common interstellar species
    Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
    Molecular Astrophysics 10 Mar 2018[Refereed]
    Understanding Two Different Structures in the Dark Stable State of the Oxygen‐Evolving Complex of Photosystem II: Applicability of the Jahn–Teller Deformation Formula
    Shoji,Mitsuo
    ChemPhotoChem 116 (5-6) Nov 2017[Refereed]
    Ab initio computations of zero-field splitting parameters and effective exchange integrals for single-molecule magnets (Mn-12- and Mn11Cr-acetate clusters)
    Shinsuke Sano, Takashi Kawakami, Shohei Yoshimura, Mitsuo Shoji, Shusuke Yamanaka, Mitsutaka Okumura, Takahito Nakajima, Kizashi Yamaguchi
    POLYHEDRON 136 (4) Nov 2017[Refereed]
    A theoretical study of the formation of glycine via hydantoin intermediate in outer space environment
    Megumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki Umemura
    CHEMICAL PHYSICS LETTERS 687 Nov 2017[Refereed]
    Large-scale QM/MM calculations of the CaMn4O5 cluster in the S-3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures
    Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi
    FARADAY DISCUSSIONS 198 Jun 2017[Refereed]
    Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
    Ujiie, Yuzuru, Tanaka, Wataru, Hanaoka, Kyohei, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo, Murakawa, Takeshi, Ishida, Toyokazu, Shigeta, Yasuteru, Hayashi, Hideyuki
    The journal of physical chemistry. B 121 (22) May 2017[Refereed]
    The reaction mechanism of sarcosine oxidase elucidated using FMO and QM/MM methods
    Abe, Yukihiro, Shoji, Mitsuo, Nishiya, Yoshiaki, Aiba, Hiroshi, Kishimoto, Takahide, Kitaura, Kazuo
    Physical chemistry chemical physics : PCCP 19 (15) Mar 2017[Refereed]
    On the guiding principles for understanding of geometrical structures of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Proposal of estimation formula of structural deformations via the Jahn-Teller effects
    K. Yamaguchi, M. Shoji, H. Isobe, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya
    MOLECULAR PHYSICS 115 (5) 2017[Refereed]
    UNO DMRG CASCI calculations of effective exchange integrals for m-phenylene-bis-methylene spin clusters
    Takashi Kawakami, Shinsuke Sano, Toru Saito, Sandeep Sharma, Mitsuo Shoji, Satoru Yamada, Yu Takano, Shusuke Yamanaka, Mitsutaka Okumura, Takahito Nakajima, Kizashi Yamaguchi
    MOLECULAR PHYSICS 115 (17-18) 2017[Refereed]
    Solvation Energy of Proton: a Consistent Calculation Schemefor Acid Dissociation Constantsand Standard Hydrogen Electrode Potentials
    MATSUI,Toru, KIYAN,Akane, SHOJI,Mitsuo, SHIGETA,Yasuteru
    Journal of Computer Chemistry, Japan 15 (5) 2016[Refereed]
    Molecular dynamics study on the key catalytic intermediates of threonine synthase
    Shoji, Mitsuo, Ujiie, Yuzuru, Harada, Ryuhei, Kayanuma, Megumi, Shigeta, Yasuteru, Murakawa, Takeshi, Hayashi, Hideyuki
    PROTEIN SCIENCE 24 (1:SI) Oct 2015[Refereed]
    Performance of the divide-and-conquer approach used as an initial guess
    Shoji,Mitsuo, Meguchi,Kayanuma, Hiroaki,Umeda, Yasuteru,Shigeta
    Chemical Physics Letters 634 Aug 2015[Refereed]
    A QM/MM study of the 5 '-AMP DNA hydrolysis of aprataxin
    Hanaoka, Kyohei, Tanaka, Wataru, Kayanuma, Megumi, Shoji, Mitsuo
    CHEMICAL PHYSICS LETTERS 631 Jul 2015[Refereed]
    On the guiding principles for lucid understanding of the damage-free S-1 structure of the CaMn4O5 cluster in the oxygen evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Yamanaka, Shusuke, Suga, Michihiro, Akita, Fusamichi, Shen, Jian-Ren, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 627 May 2015[Refereed]
    Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body Systems
    Shigeta, Yasuteru, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5:::SI) Mar 2015[Refereed]
    Theoretical studies of the damage- free S-1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II
    Shoji, Mitsuo, Isobe, Hiroshi, Yamanaka, Shusuke, Suga, Michihiro, Akita, Fusamichi, Shen, Jian-Ren, Yamaguchi, Kizashi
    CHEMICAL PHYSICS LETTERS 623 Mar 2015[Refereed]
    A QM/MM study of the initial steps of catalytic mechanism of nitrile hydratase
    Kayanuma, Megumi, Hanaoka, Kyohei, Shoji, Mitsuo, Shigeta, Yasuteru
    CHEMICAL PHYSICS LETTERS 623 Mar 2015[Refereed]
    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
    Vitamins 89 (3) Mar 2015[Refereed]
    Involvement of Propionate Side Chains of the Heme in Circular Dichroism of Myoglobin: Experimental and Theoretical Analyses
    Nagai, Masako, Kobayashi, Chika, Nagai, Yukifumi, Imai, Kiyohiro, Mizusawa, Naoki, Sakurai, Hiroshi, Neya, Saburo, Kayanuma, Megumi, Shoji, Mitsuo, Nagatomo, Shigenori
    JOURNAL OF PHYSICAL CHEMISTRY B 119 (4) Jan 2015[Refereed]
    Performance Benchmark of FMO Calculation with GPU-Accelerated Fock Matrix Preparation Routine
    UMEDA,Hiroaki, HANAWA,Toshihiro, SHOJI,Mitsuo, BOKU,Taisuke, SHIGETA,Yasuteru
    Journal of Chemical Software 13 (6) 2015[Refereed]
    GPU-accelerated FMO Calculation with OpenFMO: Four-Center Inter-Fragment Coulomb Interaction
    UMEDA,Hiroaki, HANAWA,Toshihiro, SHOJI,Mitsuo, BOKU,Taisuke, SHIGETA,Yasuteru
    Journal of Chemical Software 14 (3) 2015[Refereed]
    An Efficient Initial Guess Formation of Broken-Symmetry Solutions by using Localized Natural Orbitals
    庄司,光男, Yoshioka,Yasunori, Yamaguchi,Kizashi
    Chemical Physics Letters 608 Jul 2014[Refereed]
    A QM/MM study of nitric oxide reductase-catalyzed N2O formation
    Shoji,Mitsuo, Hanaoka,Kyohei, Kondo,Daiki, Sato,Akimasa, Umeda,Hiroaki, Kamiya,Katsumasa, Shiraishi,Kenji
    Molecular Physics 112 (3-4) Feb 2014[Refereed]
    Fock Matrix Preparation in Fragment Molecular Orbital Method with GPGPU
    Hiroaki,Umeda, Toshihiro,Hanawa, Mitsuo,Shoji, Taisuke,Boku, Yuichi,Inadomi
    情報処理学会論文誌. コンピューティングシステム 6 (4) Oct 2013[Refereed]
    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
    Vitamins 87 (10) Oct 2013[Refereed]
    Calculation of the electron transfer coupling matrix element in diabatic reactions
    Shoji, Mitsuo, Hanaoka, Kyohei, Sato, Akimasa, Kondo, Daiki, Yang, Moon Young, Kamiya, Katsumasa, Shiraishi, Kenji
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (3:::SI) Feb 2013[Refereed]
    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
    IPSJ SIG Notes 2013-HPC-138 (19) Feb 2013[Refereed]
    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
    IPSJ SIG Notes 2011 (21) Jul 2011[Refereed]
  • Awards & Honors
  • Books etc
  • Research Grants & Projects
    酵素反応機構の解明、生物無機化学、分子動力学、分子磁性、多核金属錯体、可視化プログラム(Makiko)
氏名 西澤 宏晃
Name Nishizawa Hiroaki
Faculty
Section
Position Assistant Professor
Theme QM/MM molecular dynamics for middle molecular drug discovery
Related Links
Email nisizawaccs.tsukuba.ac.jp
氏名 堀 優太
Name Hori Yuta
Faculty
Section
Position Assistant Professor
Theme Theoretical studies for proton, electron, and hydride transfer reactions; Theoretical analysis for enzymatic and catalytic reactions; Theoretical studies on organic molecules in interstellar space
Related Links
Email horiccs.tsukuba.ac.jp
  • Research Interests
  • Academic & Professional Experience
    Apr 2019
    -
    University of Tsukuba Center for Computational Sciences
    Apr 2018
    -
    Mar 2019
    Kyushu University Institute for Materials Chemistry and Engineering
    Apr 2017
    -
    Mar 2018
    Kyushu University Institute for Materials Chemistry and Engineering
  • Published Papers
    Local Structures and Dynamics of Imidazole Molecules in Poly(vinylphosphonic acid)–Imidazole Composite Investigated by Molecular Dynamics
    Hori, Yuta, Suetake, Toshiya, Shiota, Yoshihito, Yoshizawa, Kazunari, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, Motohiro
    ACS Applied Polymer Materials Feb 2020[Refereed]
    Revisiting Formic Acid Decomposition by a Graph-Theoretical Approach
    Ida, Tomonori, Nishida, Manami, Hori, Yuta
    The Journal of Physical Chemistry A 123 (44) Oct 2019[Refereed]
    Mechanistic Insights into Methane Oxidation by Molecular Oxygen under Photoirradiation: Controlled Radical Chain Reactions
    Hori, Yuta, Abe, Tsukasa, Shiota, Yoshihito, Yoshizawa, Kazunari
    Bulletin of the Chemical Society of Japan 92 (11) Aug 2019[Refereed]
    Observation of Proton Transfer Coupled Spin Transition and Trapping of Photoinduced Metastable Proton Transfer State in an Fe(II) Complex
    Nakanishi, Takumi, Hori, Yuta, Sato, Hiroyasu, Wu, Shuqi, Okazawa, Atsushi, Kojima, Norimichi, Yamamoto, Takashi, Einaga, Yasuaki, Hayami, Shinya, Horie, Yusuke, Okajima, Hajime, Sakamoto, Akira, Shiota, Yoshihito, Yoshizawa, Kazunari, Osamu, Sato
    Journal of the American Chemical Society 141 (36) Aug 2019[Refereed]
    Role of Amino-Acid Residues for Dioxygen Activation in the Second Coordination Sphere of the Dicopper Site of pMMO
    Miyanishi, Mayuko, Abe, Tsukasa, Hori, Yuta, Shiota, Yoshihito, Yoshizawa, Kazunari
    Inorganic Chemistry 58 (18) Aug 2019[Refereed]
    Dual Catalytic Cycle of H2 and H2O Oxidations by A Half-Sandwich Iridium Complex: A Theoretical Study
    Ikeda, Kei, Hori, Yuta, Mahyuddin, Muhammad Haris, Shiota, Yoshihito, Staykov, Aleksandar, Matsumoto, Takahiro, Yoshizawa, Kazunari, Ogo, Seiji
    Inorganic Chemistry 58 (11) May 2019[Refereed]
    Local structures and electronic properties of In atoms in In-doped ZnO
    Hori, Yuta, Shiota, Yoshihito, Ida, Tomonori, Yoshizawa, Kazunari, Mizuno, Motohiro
    Thin Solid Films 685 (1) May 2019[Refereed]
    Cupric-superoxide complex that induces a catalytic aldol reaction-type C–C bond formation
    Abe, T, Hori, Y, Shiota, Y, Ohta, T, Morimoto, Y, Sugimoto, H, Ogura, T, Yoshizawa, K, Itoh, S
    Communications Chemistry 2 (1) Feb 2019[Refereed]
    Redox behaviour of the β-dihydroporphycene cobalt complex: study on the effect of hydrogenation of the ligand
    Hashimoto K, Koide T, Okawara T, Shimakoshi H, Hori Y, Shiota Y, Yoshizawa K, Hisaeda Y
    Dalton Transactions 48 (3) Jan 2019[Refereed]
    Ground-State Copper(III) Stabilized by N-Confused/N-Linked Corroles: Synthesis, Characterization, and Redox Reactivity
    Yogesh Kumar Maurya, Katsuya Noda, Kazuhisa Yamasumi, Shigeki Mori, Tomoki Uchiyama, Kazutaka Kamitani, Tomoyasu Hirai, Kakeru Ninomiya, Maiko Nishibori, Yuta Hori, Yoshihito Shiota, Kazunari Yoshizawa, Masatoshi Ishida, Hiroyuki Furuta
    Journal of the American Chemical Society 140 (22) Jun 2018[Refereed]
    Construction of a Potential Energy Surface Based on a Diabatic Model for Proton Transfer in Molecular Pairs
    Hori Yuta, Ida Tomonori, Mizuno Motohiro
    Concepts, Methods and Applications of Quantum Systems in Chemistry and Physics Jan 2018[Refereed]
    Catalytic Performance of a Dicopper-Oxo Complex for Methane Hydroxylation
    Hori Y, Shiota Y, Tsuji T, Kodera M, Yoshizawa K
    Inorganic Chemistry 57 (1) Jan 2018[Refereed]
    Local structure and hydrogen bond characteristics of imidazole molecules for proton conduction in acid and base proton-conducting composite materials
    Hori Y, Chikai T, Ida T, Mizuno M
    Physical Chemistry Chemical Physics 20 (15) Jan 2018[Refereed]
    A novel approach to Bohmian mechanics using an uncompressed particle method
    Sugisawa H, Hori Y, Ida T, Mizuno M
    Physica E: Low-Dimensional Systems and Nanostructures 104 Jan 2018[Refereed]
    Potential energy construction in the diabatic picture for quantum mechanical rate constants of intermolecular proton transfer
    Yuta Hori, Tomonori Ida, Motohiro Mizuno
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 19 (25) Jul 2017[Refereed]
    Optimization of the spin-component-scaled factor for electron propagator method
    Fang-Han Lim, Manami Nishida, Yuta Hori, Tomonori Ida, Motohiro Mizuno
    CHEMICAL PHYSICS LETTERS 678 Jun 2017[Refereed]
    Complete spin contamination-free MP2 method
    Manami Nishida, Fang-Han Lim, Yuta Hori, Tomonori Ida, Motohiro Mizuno
    CHEMICAL PHYSICS LETTERS 669 Feb 2017[Refereed]
    A comparative theoretical study of the hydride transfer mechanisms during LiAlH4 and LiBH4 reductions
    Hori Y, Ida T, Mizuno M
    Computational and Theoretical Chemistry 1076 Jan 2016[Refereed]
    Simulation of molecular Auger spectra using a two-electron Dyson propagator
    Hori Y, Nishida M, Lim F.H, Ida T, Mizuno M
    Journal of Electron Spectroscopy and Related Phenomena 207 Jan 2016[Refereed]
  • Awards & Honors
    Mar 2017
    金沢大学 金沢大学大学院自然科学研究科長賞
    Mar 2012
    金沢大学 金沢大学理工学域長賞
  • Books etc
  • Research Grants & Projects
    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
    Research period: Apr 2019 -
    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
    Research period: Apr 2018 - Mar 2019
    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
    Research period: Aug 2017 - Mar 2019
氏名 鬼頭(西岡) 宏任
Name Kitoh-Nishioka Hirotaka
Faculty
Section
Position Researcher
Theme Theory and Simulation of Excitation and Charge Transfers in Bio-System and Organic Semiconductor; GPU Acceleration of Fragment Molecular Orbital Method
Related Links
Email hkitoccs.tsukuba.ac.jp
  • Research Interests
  • Academic & Professional Experience
    Apr 2019
    -
    University of Tsukuba Center for Computational Sciences Researcher
    Oct 2017
    -
    科学技術振興機構 戦略研究推進部 さきがけ専任研究者
    Apr 2016
    -
    Sep 2017
    University of Tsukuba Center for Computational Sciences
    Apr 2013
    -
    Mar 2016
    Nagoya University Graduate School of Science, Division of Material Science
    Apr 2009
    -
    Mar 2013
    Kyoto University Graduate School of Science
    Apr 2006
    -
    Mar 2009
    Meijo University Graduate School of Environmental and Human Sciences
  • Published Papers
    Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem I
    Kitoh-Nishioka Hirotaka, Shigeta Yasuteru, Itoh Shigeru, Kimura Akihiro
    The Journal of Physical Chemistry B 124 (2) 2020[Refereed]
    Calculation of Charge-Transfer Electronic Coupling with Nonempirically Tuned Range-Separated Density Functional
    Kitoh-Nishioka Hirotaka, Ando Koji
    The Journal of Physical Chemistry C 123 (18) 2019[Refereed]
    Does Inactive Alkyl Chain Enhance Triplet–Triplet Annihilation of 9,10-Diphenylanthracene Derivatives?
    Ryuma Sato, Hirotaka Kitoh-Nishioka, Kenji Kamada, Toshiko Mizokuro, Kenji Kobayashi, Yasuteru Shigeta
    The Journal of Physical Chemistry C 122 (10) Feb 2018[Refereed]
    Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited
    Sato Ryuma, Kitoh-Nishioka Hirotaka, Ando Koji, Yamato Takahisa
    The Journal of Physical Chemistry B 122 (27) 2018[Refereed]
    Near infrared two-photon-excited and -emissive dyes based on a strapped excited-state intramolecular proton-transfer (ESIPT) scaffold
    Naoya Suzuki, Kayo Suda, Daisuke Yokogawa, Hirotaka Kitoh-Nishioka, Stephan Irle, Akihiro Ando, Luis M, G. Abeg{~{a } }o, Kenji Kamada, Aiko Fukazawa, Shigehiro Yamaguchi
    Chemical Science 9 (10) 2018[Refereed]
    Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion
    Sato Ryuma, Kitoh-Nishioka Hirotaka, Kamada Kenji, Mizokuro Toshiko, Kobayashi Kenji, Shigeta Yasuteru
    The Journal of Physical Chemistry Letters 9 (22) 2018[Refereed]
    Multiscale Simulations on Charge Transport in Covalent Organic Frameworks Including Dynamics of Transfer Integrals from the FMO-DFTB/LCMO Approach
    Hirotaka Kitoh-Nishioka, Kai Welke, Yoshio Nishimoto, Dmitri G. Fedorov, Stephan Irle
    JOURNAL OF PHYSICAL CHEMISTRY C 121 (33) Aug 2017[Refereed]
    Theoretical Analyses of Triplet-Triplet Annihilation Process of 9,10-Diphenylanthracene in Solution
    Ryuma Sato, Hirotaka Kitoh-Nishioka, Takeshi Yanai, Yasuteru Shigeta
    CHEMISTRY LETTERS 46 (6) Jun 2017[Refereed]
    Forster Resonance Energy Transfer between Fluorescent Proteins: Efficient Transition Charge-Based Study
    Hirotaka Kitoh-Nishioka, Daisuke Yokogawa, Stephan Irle
    JOURNAL OF PHYSICAL CHEMISTRY C 121 (8) Mar 2017[Refereed]
    Classical cumulant dynamics for statistical chemical physics
    Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, Thi Kieu My Bui, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma, Mitsuo Shoji
    MOLECULAR SIMULATION 43 (13-16) 2017[Refereed]
    FMO3-LCMO study of electron transfer coupling matrix element and pathway: Application to hole transfer between two tryptophans through cis- and trans-polyproline-linker systems
    Kitoh-Nishioka Hirotaka, Ando Koji
    JOURNAL OF CHEMICAL PHYSICS 145 (11) Sep 2016[Refereed]
    Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors
    Sato Ryuma, Kitoh-Nishioka Hirotaka, Ando Koji, Yamato Takahisa
    CHEMICAL PHYSICS LETTERS 633 Jul 2015[Refereed]
    Charge-transfer matrix elements by FMO-LCMO approach: Hole transfer in DNA with parameter tuned range-separated DFT
    Kitoh-Nishioka Hirotaka, Ando Koji
    CHEMICAL PHYSICS LETTERS 621 Feb 2015[Refereed]
    Electron Transfer Pathway Analysis in Bacterial Photosynthetic Reaction Center
    Kitoh-Nishioka Hirotaka, Ando Koji
    2015[Refereed]
    Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors
    Ryuma Sato, Hirotaka Kitoh-Nishioka, Koji Ando, Takahisa Yamato
    Chemical Physics Letters 633 2015[Refereed]
    Charge-transfer matrix elements by FMO-LCMO approach: Hole transfer in DNA with parameter tuned range-separated DFT
    Hirotaka Kitoh-Nishioka, Koji Ando
    Chemical Physics Letters 621 2015[Refereed]
    A Strap Strategy for Construction of an Excited-State Intramolecular Proton Transfer (ESIPT) System with Dual Fluorescence
    Suzuki Naoya, Fukazawa Aiko, Nagura Kazuhiko, Saito Shohei, Kitoh-Nishioka Hirotaka, Yokogawa Daisuke, Irle Stephan, Yamaguchi Shigehiro
    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 53 (31) Jul 2014[Refereed]
    A Strap Strategy for Construction of an Excited-State Intramolecular Proton Transfer (ESIPT) System with Dual Fluorescence
    Naoya Suzuki, Aiko Fukazawa, Kazuhiko Nagura, Shohei Saito, Hirotaka Kitoh-Nishioka, Daisuke Yokogawa, Stephan Irle, Shigehiro Yamaguchi
    Angew. Chem. 126 (31) Jun 2014[Refereed]
    A Computational Study on the Role of a Methionine at a Discriminator Site of Cyclobutane-Pyrimidine-Dimer Photolyase
    Sato Ryuma, Kitoh-Nishioka Hirotaka, Kawatsu Tsutomu, Yura Kei, Ando Koji, Yamato Takahisa
    BIOPHYSICAL JOURNAL 106 (2) Jan 2014[Refereed]
    A Computational Study on the Role of a Methionine at a Discriminator Site of Cyclobutane-Pyrimidine-Dimer Photolyase
    Ryuma Sato, Hirotaka Kitoh-Nishioka, Tsutomu Kawatsu, Kei Yura, Koji Ando, Takahisa Yamato
    Biophysical Journal 106 (2) Jan 2014[Refereed]
    Fragment Molecular Orbital Study on Electron Tunneling Mechanisms in Bacterial Photosynthetic Reaction Center
    Kitoh-Nishioka Hirotaka, Ando Koji
    JOURNAL OF PHYSICAL CHEMISTRY B 116 (43) Nov 2012[Refereed]
    Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO-LCMO approach
    Nishioka Hirotaka, Ando Koji
    JOURNAL OF CHEMICAL PHYSICS 134 (20) May 2011[Refereed]
    Pathway analysis of super-exchange electronic couplings in electron transfer reactions using a multi-configuration self-consistent field method
    Nishioka Hirotaka, Ando Koji
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13 (15) 2011[Refereed]
    Identification of Functional Residues of DNA Photolyase by Biophysical Computation and Bioinformatics
    Takahisa YAMATO, Hirotaka NISHIOKA, Kei YURA
    Seibutsu Butsuri 49 (4) 2009[Refereed]
    Average electron tunneling route of the electron transfer in protein media
    Nishioka Hirotaka, Kakitani Toshiaki
    JOURNAL OF PHYSICAL CHEMISTRY B 112 (32) Aug 2008[Refereed]
    Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue
    Miyazawa Yuji, Nishioka Hirotaka, Yura Kei, Yamato Takahisa
    BIOPHYSICAL JOURNAL 94 (6) Mar 2008[Refereed]
    Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media
    Hirotaka Nishioka, Nobuharu Ueda, Toshiaki Kakitani
    BIOPHYSICS 4 2008[Refereed]
    Non-condon theory for the energy gap dependence of electron transfer rate
    Nishioka Hirotaka, Kimura Akihiro, Yamato Takahisa, Kakitani Toshiaki
    FRONTIERS OF COMPUTATIONAL SCIENCE 2007[Refereed]
    Temperature dependence of the inelastic electron tunneling
    Nishioka H, Yamato T, Kakitani T
    Molecular Simulation 32 (9) 2006[Refereed]
    Interference, Fluctuation, and Alternation of Electron Tunneling in Protein Media. 2. Non-Condon Theory for the Energy Gap Dependence of Electron Transfer Rate
    Nishioka Hirotaka, Kimura Akihiro, Yamato Takahisa, Kawatsu Tsutomu, Kakitani Toshiaki
    The Journal of Physical Chemistry B 109 (32) 2005[Refereed]
    Interference, Fluctuation, and Alternation of Electron Tunneling in Protein Media. 1. Two Tunneling Routes in Photosynthetic Reaction Center Alternate Due to Thermal Fluctuation of Protein Conformation
    Nishioka Hirotaka, Kimura Akihiro, Yamato Takahisa, Kawatsu Tsutomu, Kakitani Toshiaki
    The Journal of Physical Chemistry B 109 (5) 2005[Refereed]
  • Awards & Honors
  • Books etc
    Chemical Science of π-Electron Systems
    Hirotaka Kitoh-Nishioka, Koji Ando (Part:分担執筆, Chapter 39 "Electron Transfer Pathway Analysis in Bacterial Photosynthetic Reaction Center" (pp. 658-673))
    高次π空間の創発と機能開発
    鬼頭-西岡 宏任, 安藤 耕司 (Part:分担執筆, 第4章1節 “光合成反応中心における長距離電子移動の経路解析”)
  • Research Grants & Projects
    Explorations of Unknown Biological Electron Transfers and Their Roles in Biological Functions Using Quantum Simulation Techniques
    PRESTO
    Research period: Oct 2017 -
    有機半導体のエキシトン/キャリア輸送現象の理論解析
    萌芽共同研究課題
    Research period: Jun 2016 - Mar 2017
    生体分子内の電荷移動現象の理論解析
    若手研究者奨励枠
    Research period: Jun 2014 - Mar 2016
氏名 満田 祐樹
Name Mitsuta Yuki
Faculty
Section
Position Researcher
Theme The development of free-energy reaction root mapping method by using molecular dynamics simulation
Related Links
Email mitsutayccs.tsukuba.ac.jp
氏名
Name Kowit Hengphasatporn
Faculty
Section
Position Researcher
Theme Molecular modeling and Structure-based virtual screening on the biological systems
Related Links
Email kowithccs.tsukuba.ac.jp
氏名 広川 貴次
Name Hirokawa Takatsugu
Faculty Faculty of Medicine
Section
Position Professor (Collaborative Fellow)
Theme
Related Links
Email
氏名 吉野 龍ノ介
Name Yoshino Ryunosuke
Faculty Faculty of Medicine
Section
Position Assistant Professor (Collaborative Fellow)
Theme Drug discovery and structural optimization using molecular simulation techniques
Related Links
Email

Biological Science Group

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