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
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	TRIOS researchmap
	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 2016
-
Mar 2018
Institute of Molecular Sciences Visiting professor
May 2014

Osaka University Graduate School of Engineering Sciences Visiting Professor
Published Papers
▼▲
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 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 Oct 2017[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 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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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
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]
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
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]
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]
A Practical Approach for Searching Stable Molecular Structures by Introducing Repulsive Interactions among Walkers
Shoji,Mitsuo;Kayanuma,Megumi;Shigeta,Yasuteru
Bulletin of the Chemical Society of Japan 91 (10) 2018[Refereed]
A Theoretical Study on Redox Potential and pK_a 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 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]
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]
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]
A theoretical study of the formation of glycine via hydantoin intermediate in outer space environment
Kayanuma, Megumi;Kidachi, Kaori;Shoji, Mitsuo;Komatsu, Yu;Sato, Akimasa;Shigeta, Yasuteru;Aikawa, Yuri;Umemura, Masayuki
Chem Phys Lett 687 Nov 2017[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 Reaction Mechanisms of O₂ Formation in Photosynthesis
SHOJI,Mitsuo;ISOBE,Hiroshi;SHIGETA,Yasuteru;NAKAJIMA,Takahito;YAMAGUCHI,Kizashi
Seibutsu Butsuri 58 (3) May 2018
Computational electrochemistry of a novel ferrocene derivative
Ghiami-Shomami, Ali; Ghalami-Choobar, Bahram; Shigeta, Yasuteru
Journal of molecular graphics & modelling 85 Aug 2018[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]
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]
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]
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]
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]
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 Jan 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
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]
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]
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]
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]
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]
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]
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]
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]
Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection
Harada, Ryuhei; Shigeta, Yasuteru
Journal of computational chemistry 38 (22) May 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]
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]
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]
Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures
Shoji, Mitsuo; Isobe, Hiroshi; Nakajima, Takahito; Shigeta, Yasuteru; Suga, Michihiro; Akita, Fusamichi; Shen, Jian-Ren; Yamaguchi, Kizashi
Faraday discussions 198 Mar 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]
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
Theoretical analyses on a flipping mechanism of UV-induced DNA damage
Sato,Ryuma;Harada,Ryuhei;Shigeta,Yasuteru
Biophysics and Physicobiology 13 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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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
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
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]
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
Hydration effects on enzyme-substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method
Ando, Hiroyuki; Shigeta, Yasuteru; Baba, Takeshi; Watanabe, Chiduru; Okiyama, Yoshio; Mochizuki, Yuji; Nakano, Masayoshi
MOLECULAR PHYSICS 113 (3-4:::SI) Feb 2015
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]
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
Protein folding pathways extracted by Outlier FLOODing method (OFLOOD)
Ryuhei,Harada;Tomotake,Nakamura;Yu,Takano;Shigeta,Yasuteru
Journal of Computational Chemistry Jan 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]
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
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]
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]
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 Nylon-oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds
Shigeta,Yasuteru
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 5 (7) 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]
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]
Binding of a positron to nucleic-acid base molecules and their pairs
Shigeta,Yasuteru
ChemPhysChem 14 (15) Oct 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]
Photochromic Switching of Diradical Character: Design of Efficient Nonlinear Optical Switches
重田,育照
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 4 (15) Jul 2013
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]
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]
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]
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]
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
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
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
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]
Cumulant mechanics : An explicit treatment for fluctuation on dynamics
重田,育照
Molecular Science 7 (1) 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]
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]
Consistent Scheme for Computing Standard Hydrogen Electrode and Redox Potentials
Shigeta,Yasuteru
JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (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]
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]
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]
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]
Microscopic Mechanisms of Initial Oxidation of Si (100): Reaction Pathways and Free-Energy Barriers
Shigeta,Yasuteru
PHYSICAL REVIEW B 85 (20) May 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]
Coordination Effects on the Electronic Structure of the CuA Site of Cytochrome c Oxidase
Shigeta,Yasuteru
CHEMICAL PHYSICS LETTERS 531 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]
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]
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]
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]
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]
(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]
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]
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]
Molecular Dynamics Studies on the Mutational Structures of a Nylon-6 Byproduct-Degrading Enzyme
Shigeta,Yasuteru
CHEMICAL PHYSICS LETTERS 507 (1) Apr 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]
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
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 Hydroxypyridone Nucleobases
Shigeta,Yasuteru
polyhedron 28 (9-10) Jun 2009[Refereed]
Theoretical Studies on Magnetic Interactions between Cu(II) Ions in Salen 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]
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
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
Quantal cumulant dynamics III: A quantum confinement under a magnetic field
Shigeta, Yasuteru
CHEMICAL PHYSICS LETTERS 461 (4-6) Aug 2008
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
▼▲
Mar 2007
Royal Chemical Society PCCP Prize for the Outstanding Achievement of Young Scientists in Physical Chemistry and Chemical Physics Research Award
Mar 2017
Royal Chemical Society Outstanding Reviewers for Physical Chemistry Chemical Physics in 2016 論文査読
Oct 2017
22nd QSCP Promising Scientist Award of CMOA Research Award
Feb 2019
Best Faculty Awards 2018
Books etc
▼▲
Reference modules in Materials Science and Engineering 2016
Harada, Ryuhei;Inagaki, Yuji;Shigeta, Yasuteru (Part:Contributor, Protein Folding and Evolution)
Quantum Systems in Physics, Chemistry, and Biology: Advances in Concepts and Applications
Baba, Takeshi;Kamiya, Katsumasa;Shigeta, Yasuteru (Part:Contributor, Integrated Computational Studies on Mutational Effects of A Nylon-degrading Enzyme)
Advances in Quantum Chemistry
Shigeta,Yasuteru (Part:Contributor, Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules)
金属錯体の量子・計算化学
重田,育照;北河康隆 (Part:Contributor, 第4-1章錯体の伝導性)
物性量子化学入門
重田,育照 (Part:Contributor, 第１３、１４章)
Challenges and Advances in Computational Chemistry and Physics, Chap. 2
Shigeta,Yasuteru (Part:Contributor, Single-Reference Methods for Excited States in Molecules and Polymers)
Advances in the Theory of Atomic and Molecular Systems, Conceptual and Computational Advances in Quantum Chemistry, Chap. 21
Shigeta,Yasuteru (Part:Contributor, Quantum Theory in Terms of Cumulant Variables)
Conceptual and Computational Advances in Quantum Chemistry, Chap. 25
Shigeta,Yasuteru (Part:Contributor, Theoretical Studies on Metal-Containing Artificial DNA Bases”, Advances in the Theory of Atomic and Molecular Systems)
Quantum mechanics Chap. 17
Shigeta,Yasuteru (Part:Contributor, Quantal Cumulant Mechanics as Extended Ehrenfest Theorem)
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:Contributor, Quantum Theory in Terms of Cumulant Variables)
Research Grants & Projects
Structure-based design of middle molecules for drug discovery
Research period: Jun 2018 - Representative: Katsumi Maenaka

	氏名	原田隆平
	Name	Harada Ryuhei
	Faculty
	Section
	Position	Associate Professor
	Theme
	Related Links	TRIOS researchmap
	Email	ryuheiccs.tsukuba.ac.jp

Research Interests
Academic & Professional Experience
Published Papers
▼▲
Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
Harada Ryuhei, Shigeta Yasuteru
ADVANCES IN QUANTUM CHEMISTRY 78 Feb 2019[Refereed]
Cascade-Type Molecular Dynamics Combined with Markov State Model Efficiently Calculates Free Energy Landscapes of Proteins
Harada Ryuhei, Shigeta Yasuteru
15 (1) Jan 2019[Refereed]
Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Relevant Rare Events of Proteins (The Chemical Society of Japan Award for Young Chemist 2017)
Harada Ryuhei
BULLETIN CHEMICAL SOCIETY OF JAPAN, in press 91 (9) Sep 2018[Refereed]
Effect of Initial Structures Rules in Parallel Cascade Selection Molecular Dynamics Affect Conformational Sampling Efficiency
, Shigeta Yasuteru
85 Sep 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]
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]
Developments of Innovative Molecular Simulation Methods for Understanding the Biological Functions
CHEMICAL INDUSTRY 69 (7) Jul 2018
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]
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
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]
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]
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
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
Harada Ryuhei, Shigeta Yasuteru
JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (31) Dec 2017[Refereed]
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches
Harada Ryuhei, Shigeta Yasuteru
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
Harada Ryuhei, Shigeta Yasuteru
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 90 (11) Nov 2017[Refereed]
Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection
Harada Ryuhei, Shigeta Yasuteru
JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (22) Aug 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
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)?
Harada Ryuhei, Shigeta Yasuteru
CHEMISTRY LETTERS 46 (6) Jun 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) May 2017[Refereed]
Common Folding Processes of Mini-Proteins: Partial Formations of Secondary Structures Initiate the Immediate Protein Folding
Harada Ryuhei, Takano Yu, Shigeta Yasuteru
JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (11) Apr 2017[Refereed]
Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins
Harada Ryuhei, Shigeta Yasuteru
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13 (3) Mar 2017[Refereed]
Classical Cumulant Dynamics for Statistical Chemical Physics
Shigeta Yasuteru, Harada Ryuhei, Sato Ryuma, Kitoh-Nishioka Hirotaka, Bui Thi Kieu My, Sato Akimasa, Tokiwa Takaki, Kyan Akane, Ishii Yuki, Kimatsuka Masato, Yamasaki Sotaro, Kayanuma Megumi, Shoji Mitsuo
MOLECULAR SIMULATION 43 (13-16) 2017[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]
Theoretical Analyses on a Flipping Mechanism of UV-induced DNA Damage
BIOPHYSICS AND PHYSICOBIOLOGY 13 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]
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]
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]
Hydration and Protein Stability under Molecular Crowding Environments
Harada Ryuhei
BUSEEI KENKYU 53 Mar 2014[Refereed]
Molecular Simulation Methods to Enhance Soft Protein Motions
Harada Ryuhei, Kitao Akio
54 (3) 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]
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
Books etc
Research Grants & Projects

	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	TRIOS researchmap
	Email	mshojiccs.tsukuba.ac.jp

Research Interests
Academic & Professional Experience
Published Papers
▼▲
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]
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]
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]
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]
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]
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]
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]
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]
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]
A Practical Approach for Searching Stable Molecular Structures by Introducing Repulsive Interactions among Walkers
Shoji,Mitsuo;Kayanuma,Megumi;Shigeta,Yasuteru
Bulletin of the Chemical Society of Japan 91 (10) 2018[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]
A Theoretical Study on Redox Potential and pK_a 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 theoretical study of the formation of glycine via hydantoin intermediate in outer space environment
Kayanuma, Megumi;Kidachi, Kaori;Shoji, Mitsuo;Komatsu, Yu;Sato, Akimasa;Shigeta, Yasuteru;Aikawa, Yuri;Umemura, Masayuki
Chem Phys Lett 687 Nov 2017[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 Reaction Mechanisms of O₂ Formation in Photosynthesis
SHOJI,Mitsuo;ISOBE,Hiroshi;SHIGETA,Yasuteru;NAKAJIMA,Takahito;YAMAGUCHI,Kizashi
Seibutsu Butsuri 58 (3) May 2018
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]
Ab initio computations of zero-field splitting parameters and effective exchange integrals for single-molecule magnets (Mn12- and Mn11Cr-acetate clusters
Sano, Shinsuke;Kawakami, Takashi;Yoshimura, Shohei;Shoji, Mitsuo;Yamanaka, Shusuke;Okumura, Mitsutaka;Nakajima, Takahito;Yamaguchi, Kizashi
Polyhedron 136 (4) Nov 2017[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]
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 Jan 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]
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 CASCI calculations of effective exchange integrals for m-phenylene-bis-methylene spin clusters
Kawakami, Takashi; Sano, Shinsuke; Saito, Toru; Sharma, Sandeep; Shoji, Mitsuo; Yamada, Satoru; Takano, Yu; Yamanaka, Shusuke; Okumura, Mitsutaka; Nakajima, Takahito; Yamaguchi, Kizashi
MOLECULAR PHYSICS 115 (17-18) Mar 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]
Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures
Shoji, Mitsuo; Isobe, Hiroshi; Nakajima, Takahito; Shigeta, Yasuteru; Suga, Michihiro; Akita, Fusamichi; Shen, Jian-Ren; Yamaguchi, Kizashi
Faraday discussions 198 Mar 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
Yamaguchi, K.;Shoji, M.;Isobe, H.;Yamanaka, S.;Umena, Y.;Kawakami, K.;Kamiya, N.
MOLECULAR PHYSICS 115 (5:::SI) Feb 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
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]
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]
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]
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
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]
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]
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]
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
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
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]
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]
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]
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]
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
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]
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
Awards & Honors
Books etc
Advances in Quantum Chemistry
Shoji, Mitsuo;Isobe, Hiroshi;Yamanaka, Shusuke;Umena, Yasufumi;Kawakami, Keisuke;Kamiya, Nobuo;Yamaguchi, Kizashi (Part:Contributor, Theoretical Elucidation of Geometrical Structures of the CaMn4O5 Cluster in Oxygen Evolving Complex of Photosystem II Scope and Applicability of Estimation Formulae of Structural Deformations via the Mixed-Valence and Jahn–Teller Effects)
Chemical Physics Letters
Shoji,Mitsuo (Part:Contributor, Relative stability between the manganese hydroxide- and oxo-models for water oxidation by CCSD, DMRG CASCI, CASSCF, CASPT2 and CASDFT methods; Importance of static and dynamical electron correlation effects for OEC of PSII)
Research Grants & Projects

	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	TRIOS
	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	TRIOS researchmap
	Email	horiccs.tsukuba.ac.jp

Research Interests
Academic & Professional Experience
Published Papers
▼▲
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]
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]
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]
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]
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]
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]
Construction of a Potential Energy Surface Based on a Diabatic Model for Proton Transfer in Molecular Pairs
Hori Yutaand Ida Tomonoriand Mizuno Motohiro
Concepts, Methods and Applications of Quantum Systems in Chemistry and Physics Jan 2018[Refereed]
Ground-State Copper(III) Stabilized by N-Confused/N-Linked Corroles: Synthesis, Characterization, and Redox Reactivity
Maurya Y.K, Noda K, Yamasumi K, Mori S, Uchiyama T, Kamitani K, Hirai T, Ninomiya K, Nishibori M, Hori Y, Shiota Y, Yoshizawa K, Ishida M, Furuta H.
Journal of the American Chemical Society 140 (22) Jan 2018[Refereed]
Potential energy construction in the diabatic picture for quantum mechanical rate constants of intermolecular proton transfer
Hori Y, Ida T, Mizuno M.
Physical Chemistry Chemical Physics 19 (25) Jan 2017[Refereed]
Optimization of the spin-component-scaled factor for electron propagator method
Lim F.-H, Nishida M, Hori Y, Ida T, Mizuno M.
Chemical Physics Letters 678 Jan 2017[Refereed]
Complete spin contamination-free MP2 method
Nishida M, Lim F.-H, Hori Y, Ida T, Mizuno M.
Chemical Physics Letters 669 Jan 2017[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]
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]
Awards & Honors
Books etc
Research Grants & Projects

	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	researchmap
	Email	hkitoccs.tsukuba.ac.jp

Research Interests
Academic & Professional Experience
Apr 2019
-
University of Tsukuba Center for Computational Sciences Researcher
Published Papers
▼▲
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]
Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion
Sato Ryuma, Kitoh-Nishioka Hirotaka, Kamada Kenjiand Mizokuro Toshiko, Kobayashi Kenji, Shigeta Yasuteru
The Journal of Physical Chemistry Letters 9 (22) 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]
Multiscale Simulations on Charge Transport in Covalent Organic Frameworks Including Dynamics of Transfer Integrals from the FMO-DFTB/LCMO Approach
Kitoh-Nishioka Hirotaka, Welke Kai, Nishimoto Yoshio, Fedorov Dmitri G., Irle Stephan
JOURNAL OF PHYSICAL CHEMISTRY C 121 (33) Aug 2017[Refereed]
Theoretical Analyses of Triplet-Triplet Annihilation Process of 9,10-Diphenylanthracene in Solution
Sato Ryuma, Kitoh-Nishioka Hirotaka, Yanai Takeshi, Shigeta Yasuteru
CHEMISTRY LETTERS 46 (6) Jun 2017[Refereed]
Forster Resonance Energy Transfer between Fluorescent Proteins: Efficient Transition Charge-Based Study
Kitoh-Nishioka Hirotaka, Yokogawa Daisuke, Irle Stephan
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]
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]
Electron Transfer Pathway Analysis in Bacterial Photosynthetic Reaction Center
Kitoh-Nishioka Hirotakaand 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]
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]
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]
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]
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]
Identification of Functional Residues of DNA Photolyase by Biophysical Computation and Bioinformatics
Takahisa YAMATO, Hirotaka NISHIOKA, Kei YURA
Seibutsu Butsuri 49 (4) 2009[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]
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]
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]
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]
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 and Koji Ando (Part:Contributor, Chapter 39 "Electron Transfer Pathway Analysis in Bacterial Photosynthetic Reaction Center" (pp. 658-673))
Research Grants & Projects
Explorations of Unknown Biological Electron Transfers and Their Roles in Biological Functions Using Quantum Simulation Techniques
PRESTO
Research period: Oct 2017 - Representative: Hirotaka Kitoh

	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	mutsutayccs.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	TRIOS researchmap
	Email	yujiccs.tsukuba.ac.jp

Research Interests
Academic & Professional Experience
Published Papers
▼▲
Dinoflagellates with relic endosymbiont nuclei as novel models for elucidating organellogenesis.
Sarai, Chihiro;Tanifuji, Goro;Nakayama, Takuro;Kamikawa, Ryoma;Takahashi, Kazuya;Miyashita, Hideaki;Ken-ichro, Ishida;Iwataki, Mitsunori;Inagaki, Yuji
bioRxiv Jul 2019
Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host
Takuro, Nakayama;Mami, Nomura;Yoshihito, Takano;Kogiku, Shiba;Kazuo, Inaba;Inagaki, Yuji;Masakado, Kawata
Proceedings of the National Academy of Science of the United States of America Jun 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]
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]
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]
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]
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]
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]
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]
Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms.
Takuro, Nakayama;Inagaki, Yuji
Scientific Reports 7 Oct 2017[Refereed]
Protein folding and evolution
Harada,Ryuhei;Inagaki,Yuji;Yasuteru,Shigeta
Reference Module in Materials Science and Materials Engineering Jun 2016[Refereed]
A non-photosynthetic diatom revelas early steps of reductive evolution in plastids.
Kamikawa, Ryoma;Moog, Daniel;Zauner, Stefan;Tanifuji, Goro;Ishida, Ken-ichiro;Miyashita, Hideaki;Mayama, Shigeki;Hashimoto, Tetsuo;Maier, Uwe G;Archibald, John A;Inagaki, Yuji
Molecular Biology and Evolution 34 (9) Sep 2017[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]
Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis.
Tanifuji,Goro;Cenci,Ugo;Mood,Daniel;Dean,Samuel;Nakayama,Takuro;David,Vojtěch;Fiala,Ivan;Curtis,Bruce A;Sibald,Shannon;Onodera,Naoko T;Colp,Morgan;Flegontov,Pavel;Johnson-MacKinnon,Jessica;McPhee,Michael;Inagaki,Yuji;Hashimoto,Tetsuo;Kelly,Steven;Gull,Keith;Lukeš,Julius;Archibald,John M.
Scientific Reports 7 Oct 2017[Refereed]
Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes.
Leger, Michelle M;Kolisko, Martin;Kamikawa, Ryoma;Stairs, Courtney W;Kume, Keitaro;Čepička, Ivan;Silberman, Jeffrey D;Andersson, Jan O;Xu, Feifei;Yabuki, Akinori;Eme, Laura;Zhan, Qianqian;Takishita, Kiyotaka;Inagaki, Yuji;Simpson, Alastair GB;Hashimoto, Tetsuo;Roger, Andrew J.
Nature Ecology & Evolution 1 (4) Feb 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]
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]
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
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
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]
Genome evolution triggered by acquisition of an endosymbiotic partner
Inagaki, Yuji
GENES & GENETIC SYSTEMS 89 (6) Dec 2014
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]
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]
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]
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]
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
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【*Joint 1st 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]
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,Y*;Kamikawa,R*;Hashimoto,T;Inagaki,Y
PLoS One 7 (5) 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
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]
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]
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]
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
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]
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
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]
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]
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]
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, Céza, 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]
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]
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]
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]
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]
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]
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]
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]
Evolving genetic codes.
Ohama, T;Inagaki, Y;Bessho, Y;Osawa, S.
Proceedings of the Japan Academy, Ser. B 84 (2) 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, Kei;Takishita, Kiyotaka;Ohshima, Kazuhiko;Inagaki, Yuji
MOLECULAR PHYLOGENETICS AND EVOLUTION 45 (1) Oct 2007
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]
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]
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
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]
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]
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]
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
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
Books etc
▼▲
Reference modules in Materials Science and Engineering 2016
Harada, Ryuhei;Inagaki, Yuji;Shigeta, Yasuteru (Part:Contributor, Protein Folding and Evolution)
共生微生物
稲垣,祐司;中山卓郎 (Part:Contributor, 第17章現在も続く細胞内共生細菌のオルガネラ化．)
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:Supervisor)
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:Supervisor)
Research Grants & Projects

	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	researchmap
	Email	ishitaniccs.tsukuba.ac.jp

Research Interests
Phylogeography
Foraminifera
Radiolaria
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
The University of Tokyo Graduate School of Science Project Researcher
Apr 2010
-
Mar 2013
JAMSTEC Biogeoscience Visiting Researcher
Published Papers
▼▲
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]
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]
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]
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]
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]
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
Jul 2010
ISEP young scientist award
Books etc
Radiolaria
Yoshiyuki Ishitani, Colette Febvre-Chevalier, Jean Febvre (Part:Joint Work)
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:Joint Work)
Research Grants & Projects

	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

Division of Life Sciences

Biological Function and Information Group

Biological Science Group

Biological Function and Information Group

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Biological Science Group

Research Interests

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Published Papers

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Research Grants & Projects

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects