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
Morita Rikuri		Researcher
Mitsuta Yuki		Researcher
Kowit Hengphasatporn		Researcher
Hirokawa Takatsugu	Faculty of Medicine	Professor (Collaborative Fellow)
Yoshino Ryunosuke	Faculty of Medicine	Assistant Professor (Collaborative Fellow)

Biological Science Group

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

Biological Function and Information Group

	氏名	重田育照
	Name	Shigeta Yasuteru
	Faculty
	Section
	Position	Professor/Cheif
	Theme	Computational analyses on nano- and bio-systems
	Related Links	TRIOS researchmap
	Email	shigetaccs.tsukuba.ac.jp

Research Interests
分子動力学
第一原理計算
Academic & Professional Experience
Apr 2019
-
Present
National Institutes for Quantum and Radiological Science and Technology Takasaki Advanced Radiation Research Institute Visiting Researcher
May 2014
-
Present
Osaka University Graduate School of Engineering Sciences Visiting Professor
Mar 2014
-
Present
University of Tsukuba
Apr 2018
-
Mar 2020
Sojo University Faculty of Engineering, Department of Aerospace Systems Engineering
Apr 2016
-
Mar 2018
Institute of Molecular Sciences Visiting professor
Aug 2010
-
Mar 2014
Osaka University Graduate School of Engineering Science, Department of Materials Engineering Science Division of Materials Physics
Aug 2011
-
Jul 2013
Ministry of Education,Culture,Sports,Science and Technology
May 2008
-
Jul 2010
University of Hyogo of Life Science, Graduate School
Feb 2007
-
May 2008
University of Tsukuba
Dec 2003
-
Jan 2007
The University of Tokyo The Graduate School of Engineering, Department of Applied Chemistry
Apr 2001
-
Dec 2003
The University of Tokyo Graduate School of Arts and Sciences
Apr 2000
-
Mar 2001
Osaka University Graduate School of Science, Department of Chemistry
Jan 1999
-
Mar 2000
Osaka University Graduate School of Science, Department of Chemistry
Published Papers
▼▲
Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.
Takeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Chie Shibazaki, Tomoko Sunami, Taro Tamada, Naomine Yano, Taro Yamada, Katsuhiro Kusaka, Mamoru Suzuki, Yasuteru Shigeta, Ryota Kuroki, Hideyuki Hayashi, Takato Yano, Katsuyuki Tanizawa, Motoyasu Adachi, Toshihide Okajima
Proceedings of the National Academy of Sciences of the United States of America 117 (20) May 2020[Refereed]
Reaction Mechanism of Monomeric Sarcosine Oxidase with N-Cyclopropylglycine
Shoji, Mitsuo, Abe, Y, Boero, M, Shigeta, Y, Y., Nishida
Physical Chemistry Chemical Physics May 2020[Refereed]
Understanding the Detection Mechanisms and Ability of Molecular Hydrogen on Three-Dimensional Bicontinuous Nanoporous Reduced Graphene Oxide
Ito, Yoshikazu, Kayanuma, Megumi, Shigeta, Yasuteru, Fujita, Jun-ichi, Tanabe, Yoichi
Materials 13 (10) May 2020[Refereed]
Distribution of Counter Ions in Negatively-charged Lipid/Water/Air Interface: Molecular Dynamics Study
Takahashi, Teruyuki, Harada, Ryuhei, Shigeta, Yasuteru
CHEMISTRY LETTERS 49 (4) Apr 2020[Refereed]
Target Identification using Homopharma and Network-based Method for Predicting Compounds against Dengue Virus-Infected Cell
Hengphasatporn, K, Plaimas, K, Suratanee, A, Wongsriphisant, P, Yang, J.-M, Shigeta, Yasuteru, Chavasiri, W, Boonyasuppayakorn, S, Rungrotmongkol, T
Molecules (25) Apr 2020[Refereed]
Local Structures and Dynamics of Imidazole Molecules in Poly(vinylphosphonic acid)–Imidazole Composite Investigated by Molecular Dynamics
Hori, Yuta, Suetake, Toshiya, Shiota, Yoshihito, Yoshizawa, Kazunari, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, Motohiro
ACS Applied Polymer Materials 2 (4) Apr 2020[Refereed]
Estimation of Acid Dissociation Constants (pKa) of N-containing Heterocycles in DMSO and Transferability of Gibbs Free Energy in Different Solvent Conditions
Hengphasatporn, K, Matsui, T, Shigeta, Yasuteru
Chemistry Letters 49 (3) Mar 2020[Refereed]
Intramolecular Mode Coupling of the Isotopomers of Water: A Non-Scalar Charge Density-Derived Perspective
Tian, T, Xu, T, Kirk, S, Rongde, I.T, Tan, Y.B, Manzhos, S, Shigeta, Yasuteru, Jenkins, S
Physical Chemistry Chemical Physics 22 (4) Jan 2020[Refereed]
Multiple Virtual Screening Strategies for the Discovery of Novel Compounds Active Against Dengue Virus: A Hit Identification Study
Hengphasatporn, K, Garon, A, Wolschann, P, Langer, T, Shigeta, Yasuteru, Huynh, T, Nguyen Thanh, Chavasiri, W, Saelee, T, Boonyasuppayakorn, S, Rungrotmongkol, T
Scientia Pharmaceutica 88 (1) Jan 2020[Refereed]
Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: Implications into the proton transfer at the active site
Machida, Yasuhiro, Murakawa, Takeshi, Sakai, Akiko, Shoji, Mitsuo, Shigeta, Yasuteru, Hayashi, Hideyuki
Journal of biochemistry 167 (4) Nov 2019
Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography
Shoji, Mitsuo, Isobe, Hiroshi, Shen, Jian-Ren, Suga, Michihiro, Akita, Fusamichi, Miyagawa, Koichi, Shigeta, Yasuteru, Yamaguchi, Kizashi
CHEMICAL PHYSICS LETTERS 730 Sep 2019[Refereed]
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency
Harada, Ryuhei, Shigeta, Yasuteru
JOURNAL OF CHEMICAL INFORMATION AND MODELING 59 (9) Sep 2019[Refereed]
Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein Dynamics
Harada, Ryuhei, Sladek, Vladimir, Shigeta, Yasuteru
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (9) Sep 2019[Refereed]
Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water-Air Interface
Ohto, Tatsuhiko, Dodia, Mayank, Xu, Jianhang, Imoto, Sho, Tang, Fujie, Zysk, Frederik, Kühne, Thomas D, Shigeta, Yasuteru, Bonn, Mischa, Wu, Xifan, Nagata, Yuki
The journal of physical chemistry letters 10 (17) Aug 2019[Refereed]
Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
Journal of molecular graphics & modelling 92 Jul 2019
Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
Journal of molecular graphics & modelling 92 Jul 2019
Pyrrole-Based π-System-Pt Complexes: Chiroptical Properties and Excited-State Dynamics with Microsecond Triplet Lifetimes
Hirata, Goki, Kobayashi, Yoichi, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
Chemistry (Weinheim an der Bergstrasse, Germany) 25 (37) Jul 2019[Refereed]
Reaction mechanism of non-enzymatic stereoselective formation of wine lactone
Kyan, Akane, Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
CHEMICAL PHYSICS LETTERS 725 Jun 2019[Refereed]
First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface
Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Kamiya, Katsumasa, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
The Journal of Physical Chemistry A 123 (26) Jun 2019[Refereed]
Numerical investigation of the nano-scale solutal Marangoni convections
Imai, Y, Yamamoto, T, Sekimoto, A, Okano, Y, Sato, R, Shigeta, Y
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS 98 (SI) May 2019[Refereed]
In silico strcutral modelling and analysis of elongation factor 1alpha and elongation factor-like proteins.
Kotaro, Sakamoto, Megumi, Kayanuma, Inagaki, Yuji, Tetsuo, Hashimoto, Yasuteru, Shigeta
ACS Omega 4 (4) Apr 2019[Refereed]
Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-order Molecular Dynamics Simulation
Aida, Hayato, Harada, Ryuhei, Shigeta, Yasuteru
Chemistry Letters 48 (4) Apr 2019[Refereed]
Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical Insight
Xu, Tianlv, Li, Jia Hui, Momen, Roya, Huang, Wei Jie, Kirk, Steven Robert, Shigeta, Yasuteru, Jenkins, Samantha
Journal of the American Chemical Society 141 (13) Apr 2019[Refereed]
Photosubstitution Reaction of cis-[Ru(bpy)(2)(CH3CN)(2)](2+) and cis-[Ru(bpy)(2)(NH3)(2)](2+) in Aqueous Solution via Monoaqua Intermediate
Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
The journal of physical chemistry. A 123 (13) Mar 2019[Refereed]
Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
Kimatsuka, Masato, Sato, Ryuma, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru
Chemistry Letters 48 (3) Mar 2019[Refereed]
Molecular Dynamics studies on the effects of Antifreezing Protein from Rhagium inquisitor (RiAFP) on Ice Growth
木間塚政人, 佐藤竜馬, 原田隆平, 庄司, 光男, 重田, 育照
Journal of Computer Chemistry, Japan 17 (5) Mar 2019[Refereed]
First-principle study of ammonia decomposition and nitrogen incorporation on the GaN surface in metal organic vapor phase epitaxy
Bui, Kieu My, Iwata, Jun-Ichi, Kangawa, Yoshihiro, Shiraishi, Kenji, Shigeta, Yasuteru, Oshiyama, Atsushi
JOURNAL OF CRYSTAL GROWTH 507 Feb 2019[Refereed]
Quadruply N-methylated octaphyrin: a helical macrocycle exhibiting chiroptical properties and dynamic conformation changes correlated with helical and inner N-methyl orientations
Naito, Wakana, Urakawa, Kazuki, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
ORGANIC & BIOMOLECULAR CHEMISTRY 17 (5) Feb 2019[Refereed]
Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins
Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
Journal of computational chemistry 40 (15) Feb 2019[Refereed]
Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
Harada, Ryuhei, Shigeta, Yasuteru
Advances in Quantum Chemistry (78) Feb 2019[Refereed]
The Study of the Octanol-Water Partition Coefficient by the Computational Chemistry Method
KODAMA,Koichi, SYAH,Arwan, KAWAGUCHI,Kazutomo, MATSUI,Toru, NAGAO,Hidemi, SHIGETA,Yasuteru
Journal of Computer Chemistry, Japan 18 (5) 2019
Theoretical study of the photodissociation reaction of methanol
Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
CHEMICAL PHYSICS LETTERS 714 Jan 2019[Refereed]
New Assay Method Based on Raman Spectroscopy for Enzymes Reacting with Gaseous Substrates
Kawahara-Nakagawa, Yuka, Nishikawa, Koji, Nakashima, Satoru, Inoue, Shota, Ohta, Takehiro, Ogura, Takashi, Shigeta, Yasuteru, Fukutani, Katsuyuki, Yagi, Tatsuhiko, Higuchi, Yoshiki
Protein science : a publication of the Protein Society 28 (3) Jan 2019[Refereed]
Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations
Harada, Ryuhei, Shigeta, Yasuteru
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (1) Jan 2019[Refereed]
Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations
Tokiwa, Takaki, Nakano, Shogo, Yamamoto, Yuta, Ishikawa, Takeshi, Ito, Sohei, Sladek, Vladimir, Fukuzawa, Kaori, Mochizuki, Yuji, Tokiwa, Hiroaki, Misaizu, Fuminori, Shigeta, Yasuteru
Journal of chemical information and modeling 59 (1) Jan 2019[Refereed]
Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction.
Takaki Tokiwa, Mitsuo Shoji, Vladimir Sladek, Naoki Shibata, Yoshiki Higuchi, Kunishige Kataoka, Takeshi Sakurai, Yasuteru Shigeta, Fuminori Misaizu
Molecules (Basel, Switzerland) 24 (1) Dec 2018[Refereed]
High- performance Na ion cathodes based on the ubiquitous and reversible O redox reaction
Assadi, M. Hussein N, Fronzi, Marco, Ford, Mike, Shigeta, Yasuteru
JOURNAL OF MATERIALS CHEMISTRY A 6 (47) Dec 2018[Refereed]
Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion
Sato, Ryuma, Kitoh-Nishioka, Hirotaka, Kamada, Kenji, Mizokuro, Toshiko, Kobayashi, Kenji, Shigeta, Yasuteru
The journal of physical chemistry letters 9 (22) Nov 2018[Refereed]
In Silico Structural Analysis of Elongation Factor-1 Alpha and Elongation Factor-Like
Sakamoto, Kotaro, Kayanuma, Megumi, Shigeta, Yasuteru
PROTEIN SCIENCE 27 (1:SI) Nov 2018
Reaction Pathway of Surface-Catalyzed Ammonia Decomposition and Nitrogen Incorporation in Epitaxial Growth of Gallium Nitride
Bui, Kieu My, Iwata, Jun-Ichi, Kangawa, Yoshihiro, Shiraishi, Kenji, Shigeta, Yasuteru, Oshiyama, Atsushi
JOURNAL OF PHYSICAL CHEMISTRY C 122 (43) Nov 2018[Refereed]
Protein Residue Networks from Energetic and Geometric Data: Are They Identical?
Sladek, Vladimir, Tokiwa, Hiroaki, Shimano, Hitoshi, Shigeta, Yasuteru
Journal of chemical theory and computation 14 (12) Nov 2018
How Does Friction Coefficient Affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?
Harada, Ryuhei, Shigeta, Yasuteru
Chemistry Letters 47 (9) Sep 2018[Refereed]
Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiency
Harada, Ryuhei, Shigeta, Yasuteru
Journal of molecular graphics & modelling 85 Sep 2018[Refereed]
A Theoretical Study on Redox Potential and 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]
Computational electrochemistry of a novel ferrocene derivative
Ghiami-Shomami, Ali, Ghalami-Choobar, Bahram, Shigeta, Yasuteru
Journal of molecular graphics & modelling 85 Aug 2018[Refereed]
A computational scheme of pK values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme
Fujiki, Ryo, Kasai, Yukako, Seno, Yuki, Matsui, Toru, Shigeta, Yasuteru, Yoshida, Norio, Nakano, Haruyuki
Physical chemistry chemical physics : PCCP 20 (43) Aug 2018[Refereed]
Redox potential-dependent formation of an unusual His-Trp bond in bilirubin oxidase
Akter, Mahfuza, Tokiwa, Takaki, Shoji, Mitsuo, Nishikawa, Koji, Shigeta, Yasuteru, Sakurai, Takeshi, Higuchi, Yoshiki, Kataoka, Kunishige, Shibata, Naoki
Chemistry (Weinheim an der Bergstrasse, Germany) 24 (68) Aug 2018[Refereed]
Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation
Harada, Ryuhei, Shigeta, Yasuteru
Journal of chemical information and modeling 58 (7) Jul 2018[Refereed]
A Practical Approach for Searching Stable Molecular Structures by Introducing Repulsive Interactions among Walkers
Shoji,Mitsuo, Kayanuma,Megumi, Shigeta,Yasuteru
Bulletin of the Chemical Society of Japan 91 (10) Jul 2018[Refereed]
Dominant role of orbital splitting in determining cathode potential in O3 NaTMO2 compounds
Hussein, M, Assadi, N, Shigeta, Yasuteru
JOURNAL OF POWER SOURCES 388 Jun 2018[Refereed]
How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations
Harada, Ryuhei, Shigeta, Yasuteru
Physical chemistry chemical physics : PCCP 20 (26) Jun 2018[Refereed]
Concerted Mechanism of Water Insertion and O Release during the S to S Transition of the Oxygen-Evolving Complex in Photosystem II
Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
The journal of physical chemistry. B 122 (25) Jun 2018[Refereed]
Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities
Terai, Yuma, Sato, Ryuma, Yumiba, Takahiro, Harada, Ryuhei, Shimizu, Kohei, Toga, Tatsuya, Ishikawa-Fujiwara, Tomoko, Todo, Takeshi, Iwai, Shigenori, Shigeta, Yasuteru, Yamamoto, Junpei
Nucleic acids research Epub May 2018[Refereed]
On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins
Harada, Ryuhei, Shigeta, Yasuteru
Journal of chemical theory and computation 14 (6) May 2018[Refereed]
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]
The Reaction Mechanisms of O₂ Formation in Photosynthesis
SHOJI,Mitsuo, ISOBE,Hiroshi, SHIGETA,Yasuteru, NAKAJIMA,Takahito, YAMAGUCHI,Kizashi
Seibutsu Butsuri 58 (3) May 2018
Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
Yamamoto, Yuta, Takei, Kenta, Arulmozhiraja, Sundaram, Sladek, Vladimir, Matsuo, Naoya, Han, Song-Iee, Matsuzaka, Takashi, Sekiya, Motohiro, Tokiwa, Takaki, Shoji, Mitsuo, Shigeta, Yasuteru, Nakagawa, Yoshimi, Tokiwa, Hiroaki, Shimano, Hitoshi
Biochemical and biophysical research communications May 2018
Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II
Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
CHEMICAL PHYSICS LETTERS 698 Apr 2018[Refereed]
Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals
Hada, Masaki, Saito, Shohei, Sato, Ryuma, Miyata, Kiyoshi, Hayashi, Yasuhiko, Shigeta, Yasuteru, Onda, Ken
Journal of visualized experiments : JoVE (135) Apr 2018[Refereed]
First-principles study of the formation of glycine-producing radicals from common interstellar species
Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
Molecular Astrophysics 10 Mar 2018[Refereed]
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
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 Formation of Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics
Harada,Ryuhei, Aida,Hayato, Shigeta,Yasuteru
Chemistry Letters 47 (10) 2018[Refereed]
Ultrafast Structural Analysis of Photoresponsive Columnar Liquid Crystals
Saito,Shohei, Hada,Masaki, Shigeta,Yasuteru, Onda,Ken
Proceedings of Japanese Liquid Crystal Society Annual meeting 2018 2018
研究室だより「筑波大学計算科学研究センター生命科学研究部門重田研究室」
重田,育照
Ensemble 20 (1) 2018
Developments of Efficient Conformational Sampling Methods for Reproducing and Predicting Biologically Relevant Rare Events of Proteins
Harada,Ryuhei, Shigeta,Yasuteru
Meeting Abstracts of the Physical Society of Japan 73 2018
A theoretical study of the formation of glycine via hydantoin intermediate in outer space environment
Megumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki Umemura
CHEMICAL PHYSICS LETTERS 687 Nov 2017[Refereed]
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
Journal of the American Chemical Society 139 (44) Oct 2017[Refereed]
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
Journal of the American Chemical Society 139 (44) Oct 2017[Refereed]
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
Journal of the American Chemical Society 139 Oct 2017[Refereed]
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
Journal of the American Chemical Society 139 (44) Oct 2017[Refereed]
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
Hada, Masaki, Saito, Shohei, Tanaka, Sei'ichi, Sato, Ryuma, Yoshimura, Masahiko, Mouri, Kazuhiro, Matsuo, Kyohei, Yamaguchi, Shigehiro, Hara, Mitsuo, Hayashi, Yasuhiko, Röhricht, Fynn, Herges, Rainer, Shigeta, Yasuteru, Onda, Ken, Miller, R J Dwayne
Journal of the American Chemical Society 139 (44) Oct 2017[Refereed]
Assessment of Methodology and Chemical Group Dependences in the Calculation of the pK(a) for Several Chemical Groups
Matsui, Toru, Shigeta, Yasuteru, Morihashi, Kenji
Journal of chemical theory and computation 13 (10) Sep 2017[Refereed]
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins
Harada, Ryuhei, Shigeta, Yasuteru
Journal of computational chemistry 38 (31) Aug 2017[Refereed]
Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior
Yotsuji, Hajime, Higashiguchi, Kenji, Sato, Ryuma, Shigeta, Yasuteru, Matsuda, Kenji
Chemistry (Weinheim an der Bergstrasse, Germany) 23 (60) Jul 2017[Refereed]
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations.
Yuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki Hayashi
The journal of physical chemistry. B 121 (22) Jun 2017[Refereed]
Large-scale QM/MM calculations of the CaMn4O5 cluster in the S-3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures
Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi
FARADAY DISCUSSIONS 198 Jun 2017[Refereed]
Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection
Harada, Ryuhei, Shigeta, Yasuteru
Journal of computational chemistry 38 (22) May 2017[Refereed]
Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
Fujita, Junso, Harada, Ryuhei, Maeda, Yoko, Saito, Yuki, Mizohata, Eiichi, Inoue, Tsuyoshi, Shigeta, Yasuteru, Matsumura, Hiroyoshi
Journal of structural biology 198 (2) Apr 2017[Refereed]
Direct Observation of the Ultrafast Evolution of Open-Shell Biradical in Photochromic Radical Dimer
Kobayashi, Yoichi, Okajima, Hajime, Sotome, Hikaru, Yanai, Takeshi, Mutoh, Katsuya, Yoneda, Yusuke, Shigeta, Yasuteru, Sakamoto, Akira, Miyasaka, Hiroshi, Abe, Jiro
Journal of the American Chemical Society 139 (18) Apr 2017[Refereed]
Cooperatively Interlocked [2+1]-Type π-System-Anion Complexes
Yamakado, Ryohei, Ashida, Yukina, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
Chemistry (Weinheim an der Bergstrasse, Germany) 23 (17) Mar 2017[Refereed]
Sparsity-Weighted Outlier FLOODing (OFLOOD) Method: Efficient Rare Event Sampling Method Using Sparsity of Distribution
Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
JOURNAL OF COMPUTATIONAL CHEMISTRY 37 (8) Mar 2016[Refereed]
Solvent effects on excited-state electron-transfer rate of pyrene-labeled deoxyuridine: A theoretical study
Shintaro Maekawa, Ryuma Sato, Kimihiko Hirao, Yasuteru Shigeta
CHEMICAL PHYSICS LETTERS 644 Jan 2016[Refereed]
Theoretical analyses on a flipping mechanism of UV-induced DNA damage
Sato,Ryuma, Harada,Ryuhei, Shigeta,Yasuteru
Biophysics and Physicobiology 13 2016[Refereed]
Solvation Energy of Proton: a Consistent Calculation Schemefor Acid Dissociation Constantsand Standard Hydrogen Electrode Potentials
MATSUI,Toru, KIYAN,Akane, SHOJI,Mitsuo, SHIGETA,Yasuteru
Journal of Computer Chemistry, Japan 15 (5) 2016
Molecular dynamics study on the key catalytic intermediates of threonine synthase
Mitsuo Shoji, Yuzuru Ujiie, Ryuhei Harada, Megumi Kayanuma, Yasuteru Shigeta, Takeshi Murakawa, Hideyuki Hayashi
PROTEIN SCIENCE 24 (1:SI) Oct 2015[Refereed]
Automatic detection of hidden dimensions to obtain appropriate reaction coordinates in the Outlier FLOODing (OFLOOD) method
Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
CHEMICAL PHYSICS LETTERS 639 Oct 2015[Refereed]
Performance of the divide-and-conquer approach used as an initial guess
Mitsuo Shoji, Megumi 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
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
CHEMICAL PHYSICS LETTERS 630 Jun 2015[Refereed]
Enhanced Conformational Sampling Method for Proteins Based on the TaBoo SeArch Algorithm: Application to the Folding of a Mini-Protein, Chignolin
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (10) Apr 2015[Refereed]
Theoretical Study on Reaction Mechanisms of Nitrite Reduction by Copper Nitrite Complexes: Toward Understanding and Controlling Possible Mechanisms of Copper Nitrite Reductase
Shintaro Maekawa, Tom Matsui, Kimihiko Hirao, Yasuteru Shigeta
JOURNAL OF PHYSICAL CHEMISTRY B 119 (17) Apr 2015[Refereed]
Molecular Simulation of Enzymatic Cleavage Reaction for Artificial Compounds
神谷克政, 重田,育照
Journal of the Japan Society for Simulation Technology 34 (1) Mar 2015[Refereed]
第一原理計算によるタンパク質のpK_aと構造機能相関
Shigeta,Y, Matsui,Toru
日本物理学会講演概要集 70 (1) Mar 2015
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
A QM/MM study of the initial steps of catalytic mechanism of nitrile hydratase
Megumi Kayanuma, Kyohei Hanaoka, Mitsuo Shoji, Yasuteru Shigeta
CHEMICAL PHYSICS LETTERS 623 Mar 2015[Refereed]
Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body Systems
Yasuteru Shigeta, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5) Mar 2015[Refereed]
Substitution effects on optical properties of iminonitroxide- substituted iminonitroxide diradical
Ryota Nakamura, Yasuteru Shigeta, Katsuki Okuno, Miki Hasegawa, Mayuko Fukushima, Shuichi Suzuki, Masatoshi Kozaki, Keiji Okada, Masayoshi Nakano
MOLECULAR PHYSICS 113 (3-4) Feb 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]
Accurate Standard Hydrogen Electrode Potential and Applications to the Redox Potentials of Vitamin C and NAD/NADH
Toru Matsui, Yasutaka Kitagawa, Mitsutaka Okumura, Yasuteru Shigeta
JOURNAL OF PHYSICAL CHEMISTRY A 119 (2) Jan 2015
Protein Folding Pathways Extracted by OFLOOD: Outlier FLOODing Method
Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta
JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (2) Jan 2015[Refereed]
Simple, yet powerful methodologies for conformational sampling of proteins
Ryuhei Harada, Yu Takano, Takeshi Baba, Yasuteru Shigeta
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
Takeshi Baba, Mauro Boero, Katsumasa Kamiya, Hiroyuki Ando, Seiji Negoro, Masayoshi Nakano, Yasuteru Shigeta
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (6) 2015[Refereed]
Theoretical design of solvatochromism switching by photochromic reactions using donor-acceptor disubstituted diarylethene derivatives with oxidized thiophene rings
Katsuki Okuno, Yasuteru Shigeta, Ryohei Kishi, Masayoshi Nakano
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (9) 2015[Refereed]
Performance Benchmark of FMO Calculation with GPU-Accelerated Fock Matrix Preparation Routine
UMEDA,Hiroaki, HANAWA,Toshihiro, SHOJI,Mitsuo, BOKU,Taisuke, SHIGETA,Yasuteru
Journal of Chemical Software 13 (6) 2015[Refereed]
GPU-accelerated FMO Calculation with OpenFMO: Four-Center Inter-Fragment Coulomb Interaction
UMEDA,Hiroaki, HANAWA,Toshihiro, SHOJI,Mitsuo, BOKU,Taisuke, SHIGETA,Yasuteru
Journal of Chemical Software 14 (3) 2015[Refereed]
A density functional study on pKa of small polyprotic molecules
T.,Baba, T.,Matusui, K.,Kamiya, M.,Nakano, 重田,育照
International Journal of Quantum Chemistry 114 (17) Sep 2014[Refereed]
Open-Shell Character and Second Hyperpolarizabilities of One-Dimensional Chromium(II) Chains: Size Dependence and Bond-Length Alternation Effect
Hitoshi Fukui, Shota Takamuku, Taishi Yamada, Kotaro Fukuda, Taku Takebayashi, Yasuteru Shigeta, Ryohei Kishi, Benoit Champagne, Masayoshi Nakano
INORGANIC CHEMISTRY 53 (16) Aug 2014[Refereed]
Enhanced conformational sampling methods for extracting biological rare events of proteins(Protein: Structure & Function,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))
Ryuhei,Harada, Yu,Takano, Yasuteru,Shigeta
Biophysics 54 (1) Aug 2014
Hydration effects on enzyme–substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method
Hiroyuki Ando, Yasuteru Shigeta, Takeshi Baba, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Masayoshi Nakano
Molecular Physics 113 (3-4) Aug 2014
On the Induced- Fit Mechanism of Substrate- Enzyme Binding Structures of Nylon- Oligomer Hydrolase
Takeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru Shigeta
JOURNAL OF COMPUTATIONAL CHEMISTRY 35 (16) Jun 2014[Refereed]
A Nylon-oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds
Shigeta,Yasuteru
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 5 (7) Mar 2014[Refereed]
Fluctuation Flooding Method (FFM)for accelerating conformational transitions of proteins
Ryuhei,Harada, Yu,Takano, 重田,育照
Journal of Chemical Physics 140 (12) Mar 2014[Refereed]
Non-empirical tuning of CAM-B3LYP functional in time-dependent density functional theory for excitation energies of diarylethene derivatives
Shigeta,Yasuteru
CHEMICAL PHYSICS LETTERS 585 (1-3) Oct 2013[Refereed]
Binding of a positron to nucleic-acid base molecules and their pairs
Shigeta,Yasuteru
ChemPhysChem 14 (15) Oct 2013[Refereed]
Finite-Field Method with Unbiased Polarizable Continuum Model for Evaluation of the Second Hyperpolarizability of an Open-Shell Singlet Molecule in Solvents
Tomoya Inui, Yasuteru Shigeta, Katsuki Okuno, Takeshi Baba, Ryohei Kishi, Masayoshi Nakano
JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (27) Oct 2013[Refereed]
Photochromic Switching of Diradical Character: Design of Efficient Nonlinear Optical Switches
重田,育照
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 4 (15) Jul 2013
量子化学工学における光機能性物質設計
重田,育照
特集「化学工学に展開する量子化学計算」化学工学会誌 77 Jun 2013[Refereed]
A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion: General Theory and Applications
Shigeta,Yasuteru
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 9 (5) May 2013[Refereed]
第一原理計算による生体内酵素反応の理論解析
重田,育照
豊田研究報告 66 May 2013[Refereed]
Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene
Shigeta,Yasuteru
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 4 (10) Apr 2013[Refereed]
Diradicalology in third-order nonlinear optical systems: Second hyperpolarizabilities of acetylene-linked phenalenyl-based superpolyenes
Masayoshi Nakano, Ryohei Kishi, Hitoshi Fukui, Takuya Minami, Kyohei Yoneda, Shu Minamide, Yudai Inoue, Taishi Yamada, Soichi Ito, Shabbir Muhammad, Yasuteru Shigeta, Takashi Kubo, Benoit Champagne
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (4) Feb 2013[Refereed]
Comparative Study of Diradical Characters and Third-Order Nonlinear Optical Properties of Linear/Cyclic Acenes versus Phenylenes
重田,育照
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (4) Feb 2013
Antidot effects on the open-shell characters and second hyperpolarizabilities of rectangular graphene nanoflakes
Kyohei Yoneda, Shu Minamide, Taishi Yamada, Soichi Ito, Takuya Minami, Ryohei Kishi, Yasuteru Shigeta, Masayoshi Nakano
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (4) Feb 2013
Quantal cumulant mechanics and dynamics for multidimensional quantum many-body clusters
Yasuteru Shigeta, Tomoya Inui, Takeshi Baba, Katsuki Okuno, Hiroyuki Kuwabara, Ryohei Kishi, Masayoshi Nakano
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (3) Feb 2013
Consistent scheme for computing standard hydrogen electrode and redox potentials
Toru Matsui, Yasutaka Kitagawa, Mitsutaka Okumura, Yasuteru Shigeta, Shigeyoshi Sakaki
JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (1) Jan 2013[Refereed]
Interplay between the Diradical Character and Third-Order Nonlinear Optical Properties in Fullerene Systems
Shigeta,Yasuteru
CHEMISTRY A EUROPEAN JOURNAL 19 (4) Jan 2013[Refereed]
Previous Article Next Article Table of Contents Synthesis and Characterization of Quarteranthene: Elucidating the Characteristics of the Edge State of Graphene Nanoribbons at the Molecular Level
Shigeta,Yasuteru
Journal of the American Chemistry Society 135 (4) Jan 2013[Refereed]
Cumulant mechanics : An explicit treatment for fluctuation on dynamics
重田,育照
Molecular Science 7 (1) Jan 2013[Refereed]
A new type of organic-inorganic hybrid NLO-phore with large off-diagonal first hyperpolarizability tensors: a two-dimensional approach
Shabbir Muhammad, Hongliang Xu, Zhongmin Su, Kotaro Fukuda, Ryohei Kishi, Yasuteru Shigeta, Masayoshi Nakano
DALTON TRANSACTIONS 42 (42) 2013[Refereed]
Density functional studies of the structural variety of the Cu2S2 core of the Cu-A site
Yu Takano, Orio Okuyama, Yasuteru Shigeta, Haruki Nakamura
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
Minoru Kubo, Orio Okuyama, Teizo Kitagawa, Yasuteru Shigeta
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
Kyohei Yoneda, Masayoshi Nakano, Yudai Inoue, Tomoya Inui, Kotaro Fukuda, Yasuteru Shigeta
JOURNAL OF PHYSICAL CHEMISTRY C 116 (33) Aug 2012[Refereed]
Microscopic Mechanisms of Initial Oxidation of Si (100): Reaction Pathways and Free-Energy Barriers
Shigeta,Yasuteru
PHYSICAL REVIEW B 85 (20) May 2012[Refereed]
Development of Calculation and Analysis Methods for the Dynamic First Hyperpolarizability Based on the Ab Initio Molecular Orbital - Quantum Master Equation Method
Ryohei Kishi, Hiroaki Fujii, Shingo Kishimoto, Yusuke Murata, Soichi Ito, Katsuki Okuno, Yasuteru Shigeta, Masayoshi Nakano
JOURNAL OF PHYSICAL CHEMISTRY A 116 (17) May 2012[Refereed]
Enhancement of the Third-Order Nonlinear Optical Properties in Open-Shell Singlet Transition-Metal Dinuclear Systems: Effects of the Group, of the Period, and of the Charge of the Metal Atom
Shigeta,Yasuteru
JOURNAL OF PHYSICAL CHEMISTRY A 116 (22) May 2012[Refereed]
Tuned CAM-B3LYP functional in the time-dependent density functional theory scheme for excitation energies and properties of diarylethene derivatives
Katsuki Okuno, Yasuteru Shigeta, Ryohei Kishi, Hiroshi Miyasaka, Masayoshi Nakano
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 235 (1) May 2012[Refereed]
Coordination effects on the electronic structure of the Cu-A site of cytochrome c oxidase
Kenichi Koizumi, Yasuteru Shigeta, Orio Okuyama, Haruki Nakamura, Yu Takano
CHEMICAL PHYSICS LETTERS 531 Apr 2012[Refereed]
Temperature-Independent Stereoselectivity in Intramolecular Cycloaddition of Ketene Generated from Diazoester in Solution and in Vapor Phase: How Entropy Term Governs the Selectivity
Takashi Sugimura, Eigo Mitani, Takahiro Tei, Tadashi Okuyama, Katsumasa Kamiya, Toru Matsui, Yasuteru Shigeta
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 85 (4) Apr 2012[Refereed]
heoretical Insight into Stereoselective Reaction Mechanisms of 2,4-Pentanediol-Tethered Ketene-Olefin [2+2] Cycloaddition
Shigeta,Yasuteru
JOURNAL OF PHYSICAL CHEMISTRY A 116 (4) Feb 2012[Refereed]
Halide Ion Complexes of Decaborane (B10H14) and Their Derivatives: Noncovalent Charge Transfer Effect on Second-Order Nonlinear Optical Properties
Shabbir Muhammad, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Ryohei Kishi, Yasuteru Shigeta, Masayoshi Nakano
JOURNAL OF PHYSICAL CHEMISTRY A 116 (5) Feb 2012[Refereed]
Possible Mechanisms of Water Splitting Reaction Based on Proton and Electron Release Pathways Revealed for CaMn4O5 Cluster of PSII Refined to 1.9 Å X-Ray Resolution1
Saito,T, Yamanaka,S, Kanda,K, Isobe,H, Takano,Y, Shigeta,Yasuteru, Umena,Y, Kawakami,K, Shen,J-R, Kamiya,N, Okumura,M, Shoji,M, Yoshioka,Y, Yamaguchi,K
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 (2) Jan 2012[Refereed]
Tuned long-range corrected density functional theory method for evaluating the second hyperpolarizabilities of open-shell singlet metal-metal bonded systems
Hitoshi Fukui, Yudai Inoue, Ryohei Kishi, Yasuteru Shigeta, Benoit Champagne, Masayoshi Nakano
CHEMICAL PHYSICS LETTERS 523 Jan 2012[Refereed]
Full Configuration Interaction Calculations of the Second Hyperpolarizabilities of the H4 Model Compound: Summation-over-states Analysis and Interplay with Diradical Characters
Shigeta,Yasuteru
JOURNAL OF CHEMICAL PHYSICS 136 (2) Jan 2012[Refereed]
An accurate density functional theory based estimation of pK(a) values of polar residues combined with experimental data: from amino acids to minimal proteins
Toru Matsui, Takeshi Baba, Katsumasa Kamiya, Yasuteru Shigeta
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 14 (12) 2012[Refereed]
(Hyper)polarizability density analysis for open-shell molecular systems based on natural orbitals and occupation numbers
Masayoshi Nakano, Hitoshi Fukui, Takuya Minami, Kyohei Yoneda, Yasuteru Shigeta, Ryohei Kishi, Benoit Champagne, Edith Botek, Takashi Kubo, Koji Ohta, Kenji Kamada
THEORETICAL CHEMISTRY ACCOUNTS 130 (4-6) Dec 2011[Refereed]
Self-diffusion in Crystalline Silicon: A Car-Parrinello Molecular Dynamics Study
Shigeta,Yasuteru
Physicla Review B 84 (20) Nov 2011[Refereed]
First-principles Molecular Dynamics Studies on the Atomistic Behavior of His503 in Bovine Cytochrome c Oxidase
Shigeta,Yasuteru
Biochim Biophys Acta 1807 (10) Oct 2011[Refereed]
Electronic Structures of the Cu2S2 Core of the CuA Site in Cytochrome c Oxidase and Nitronous Oxide Reductase
Shigeta,Yasuteru
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 (2) Sep 2011[Refereed]
Origin of the Enhancement of the Second Hyperpolarizabilities in Open-Shell Singlet Transition-Metal Systems with Metal–Metal Multiple Bonds
Shigeta,Yasuteru
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2 (2) Jul 2011[Refereed]
A Theoretical Study on Reaction Scheme of Silver (I) Containing 5-Substituted Uracils Bridge Formation
Shigeta,Yasuteru
JOURNAL OF PHYSICAL CHEMISTRY A 115 Jun 2011[Refereed]
Open-Shell Characters and Second Hyperpolarizabilities of One-Dimensional Graphene Nanoflakes Composed of Trigonal Graphene Units
Shigeta,Yasuteru
ChemPhysChem 12 (9) May 2011[Refereed]
Giant Enhancement of the Second Hyperpolarizabilities of Open-Shell Singlet Polyaromatic Diphenalenyl Diradicaloids by an External Electric Field and Donor-Acceptor Substitution
Shigeta,Yasuteru
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2 (9) Apr 2011[Refereed]
Molecular dynamics studies on the mutational structures of a nylon-6 byproduct-degrading enzyme
Takeshi Baba, Katsumasa Kamiya, Toru Matsui, Naoki Shibata, Yoshiki Higuchi, Tatsuya Kobayashi, Seiji Negoro, Yasuteru Shigeta
CHEMICAL PHYSICS LETTERS 507 (1-3) 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
Hitoshi Fukui, Yasuteru Shigeta, Masayoshi Nakano, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek
JOURNAL OF PHYSICAL CHEMISTRY A 115 (6) Feb 2011[Refereed]
A Simple scheme for estimating the pK(a) values of 5-substituted uracils
Toru Matsui, Atsushi Oshiyama, Yasuteru Shigeta
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
Masayoshi Nakano, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Yasuteru Shigeta, Ryohei Kishi, Benoit Champagne, Edith Botek
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
Yasuyuki Nakanishi, Toru Matsui, Yasuteru Shigeta, Yasutaka Kitagawa, Toru Saito, Yusuke Kataoka, Takashi Kawakami, Mitsutaka Okumura, Kizashi Yamaguchi
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
Katsumasa Kamiya, Mauro Boero, Kenji Shiraishi, Atsushi Oshiyama, Yasuteru Shigeta
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
Yasuteru Shigeta
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
Toru Matsui, Takeshi Sato, Yasuteru Shigeta, Kimihiko Hirao
CHEMICAL PHYSICS LETTERS 478 (4-6) Aug 2009[Refereed]
Theoretical studies on magnetic interactions between Cu(II) ions in salen nucleobases
Y. Nakanishi, Y. Kitagawa, Y. Shigeta, T. Saito, T. Matsui, H. Miyachi, T. Kawakami, M. Okumura, K. Yamaguchi
POLYHEDRON 28 (9-10) Jun 2009[Refereed]
Theoretical studies on magnetic interactions between Cu(II) ions in hydroxypyridone nucleobases
Y. Nakanishi, Y. Kitagawa, Y. Shigeta, T. Saito, T. Matsui, H. Miyachi, T. Kawakami, M. Okumura, K. Yamaguchi
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
Toru Matsui, Hideaki Miyachi, Takeshi Sato, Yasuteru Shigeta, Kimihiko Hirao
JOURNAL OF PHYSICAL CHEMISTRY B 112 (51) Dec 2008[Refereed]
Correlation functions in quantized Hamilton dynamics and quantal cumulant dynamics
Yuriy V. Pereverzev, Andrey Pereverzev, Yasuteru Shigeta, Oleg V. Prezhdo
JOURNAL OF CHEMICAL PHYSICS 129 (14) Oct 2008
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
Quantal cumulant dynamics III: A quantum confinement under a magnetic field
Yasuteru Shigeta
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
▼▲
Feb 2019
Best Faculty Awards 2018
Oct 2017
22nd QSCP Promising Scientist Award of CMOA Research Award
Mar 2017
Royal Chemical Society Outstanding Reviewers for Physical Chemistry Chemical Physics in 2016 論文査読
May 2013
大阪大学第2回大阪大学総長奨励賞・研究部門研究業績
Sep 2012
分子科学会第5回分子科学会奨励賞研究業績
Apr 2010
文部科学省平成23年文部科学大臣表彰若手科学者賞研究業績
Mar 2009
日本化学会第58回日本化学会進歩賞研究業績
Mar 2007
Royal Chemical Society PCCP Prize for the Outstanding Achievement of Young Scientists in Physical Chemistry and Chemical Physics Research Award
Mar 2006
日本化学会第86回日本化学会年会優秀講演賞研究業績
Books etc
▼▲
Advances in Quantum Chemistry
Shigeta, Yasuteru, Harada, Ryuhei (Role:Contributor, Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules)
Quantum Systems in Physics, Chemistry, and Biology: Advances in Concepts and Applications
Baba, Takeshi, Kamiya, Katsumasa, Shigeta, Yasuteru (Role:Contributor, Integrated Computational Studies on Mutational Effects of A Nylon-degrading Enzyme)
Reference modules in Materials Science and Engineering 2016
Harada, Ryuhei, Inagaki, Yuji, Shigeta, Yasuteru (Role:Contributor, Protein Folding and Evolution)
金属錯体の量子・計算化学
重田,育照, 北河康隆 (Role:Contributor, 第4-1章錯体の伝導性)
Quantum mechanics Chap. 17
Shigeta,Yasuteru (Role:Contributor, Quantal Cumulant Mechanics as Extended Ehrenfest Theorem)
Conceptual and Computational Advances in Quantum Chemistry, Chap. 25
Shigeta,Yasuteru (Role:Contributor, Theoretical Studies on Metal-Containing Artificial DNA Bases”, Advances in the Theory of Atomic and Molecular Systems)
Advances in the Theory of Atomic and Molecular Systems, Conceptual and Computational Advances in Quantum Chemistry, Chap. 21
Shigeta,Yasuteru (Role:Contributor, Quantum Theory in Terms of Cumulant Variables)
ADVANCES IN THE THEORY OF ATOMIC AND MOLECULAR SYSTEMS: DYNAMICS, SPECTROSCOPY, CLUSTERS, AND NANOSTRUCTURES
Shigeta, Yasuteru, Miyachi, Hideaki, Matsui, Toru, Yokoyama, Norisuke, Hirao, Kimihiko (Role:Contributor, Quantum Theory in Terms of Cumulant Variables)
Challenges and Advances in Computational Chemistry and Physics, Chap. 2
Shigeta,Yasuteru (Role:Contributor, Single-Reference Methods for Excited States in Molecules and Polymers)
物性量子化学入門
重田,育照 (Role:Contributor, 第１３、１４章)
Research Grants & Projects
▼▲
生命金属動体解明のための量子生体エネルギー論
新学術領域研究(研究領域提案型)
Research period: Apr 2020 - Mar 2022Representative: 重田育照
生体ハイドロジェノミクスの理論解析
新学術領域研究(研究領域提案型)
Research period: Apr 2019 - Mar 2021Representative: 重田育照
Structure-based design of middle molecules for drug discovery
Research period: Jun 2018 - Mar 2021Representative: Katsumi Maenaka
ポスト「京」重点課題 (7)「次世代の産業を支える新機能デバイス・高性能材料の創成」サブ課題A 「高機能半導体デバイス」
Research period: Apr 2016 - Mar 2019Representative: 押山淳
理論と実験の協奏的アプローチによる多重スピン励起子変換制御
新学術領域研究（研究領域提案型）
Research period: Jun 2014 - Mar 2019Representative: 重田育照
高次複合光応答分子システムの開拓と学理の構築
科研費新学術領域研究(研究領域提案型)
Research period: Jun 2014 - Mar 2019Representative: 宮坂博
メゾスケール空間内移動速度論創成のための挑戦的研究
科学研究費補助金挑戦的萌芽研究
Research period: Apr 2015 - Mar 2017Representative: 岡野泰則
キュミュラント粗視化動力学によるタンパク質動的秩序形成過程の理論研究
新学術領域研究(研究領域提案型)
Research period: Apr 2014 - Jun 2014Representative: 重田育照
Siナノドットの非線形光学特性変化に対する動力学的解析
新学術領域研究(研究領域提案型)
Research period: Apr 2013 - Jun 2014Representative: 重田育照
タンパク内で起こる協同的プロトン・電子移動反応の量子論的解析
科学研究費補助金若手研究（A)
Research period: Apr 2010 - Mar 2014Representative: 重田育照
第一原理計算による生体内酵素反応の理論解析
フェロー
Research period: Apr 2011 - Mar 2012Representative: 重田育照
電子ダイナミクスによる電子集団運動の解析
特定領域研究
Research period: 2008 - 2009Representative: 重田育照
プロトン結合電子移動反応の実時間解析：量子キュミュラント動力学法
若手研究(B)
Research period: 2008 - 2009Representative: 重田育照

	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
▼▲
化学物理
物理化学
計算化学
理論化学
生物物理学
Academic & Professional Experience
Feb 2019
-
Present
University of Tsukuba Center for Computational Sciences
Apr 2018
-
Jan 2019
University of Tsukuba Center for Computational Sciences
Apr 2015
-
Mar 2018
日本学術振興会特別研究員 PD
Apr 2014
-
Mar 2015
University of Tsukuba Center for Computational Sciences
Apr 2011
-
Mar 2014
理化学研究所計算科学研究機構
Published Papers
▼▲
The Dynamics of S-adenosyl-methionine and S-adenosyl-homo-cysteine in Mouse Dnmt1 is Driven from their Structural Flexibilities
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
Chemistry Letters 49 (7) Jul 2020[Refereed]
Regenerations of Initial Velocities in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Enhance the Conformational Transitions of Proteins
Hayato Aida, Yasuteru Shigeta, Ryuhei Harada
Chemistry Letters 49 (7) Jul 2020[Refereed]
Independent Non-targeted Parallel Cascade Selection Molecular Dynamics for Enhancing Conformational Transitions of Proteins
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling, in preparation Jun 2020[Refereed]
Comprehensive Predictions of Secondary Structures on Proteins of Various Organisms
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Molecular Biology, in preparation Jun 2020[Refereed]
Protein Folding Pathways Elucidated by Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Computational Chemistry, in preparation Jun 2020[Refereed]
Enhanced Conformational Sampling Method Based on Anomaly Detection Parallel Cascade Selection Molecular Dynamics: ad-PaCS-MD
Ryuhei Harada, Kota Yamaguchi, Yasuteru Shigeta
Journal of Chemical Theory and Computation, in preparation Jun 2020[Refereed]
Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Bulletin Chemical Society of Japan, under review (Manuscript No.: BCSJ-2020-0174) Jun 2020[Refereed]
The Molecular Mechanism on the Actin-Binding Domain of the Alpha-Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis Experiments
Rikuri Morita, Kentaro Nakano, Yasuteru Shigeta, Ryuhei Harada
The Journal of Physical Chemistry B, in revision (Manuscript ID: jp-2020-046237) Jun 2020[Refereed]
Taste Recognition Mechanism of Medaka Fish Taste Receptor Type 1 upon the Ligand Binding Studied by All-atom Molecular Dynamics Simulations
Hayato Aida, Yasuteru Shigeta, Ryuhei Harada
Physical Chemistry Chemical Physics, in preparation May 2020[Refereed]
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis Based Parallel Cascade Selection Molecular Dynamics
Takanori Yasuda, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling, under review (Manuscript ID: ci-2020-00580k) May 2020[Refereed]
Distribution of Counter Ions in Negatively-charged Lipid/Water/Air Interface: Molecular Dynamics Study
Teruyuki Takahashi, Ryuhei Harada, Yasuteru Shigeta
Chemistry Letters 49 (4) Apr 2020[Refereed]
Protein Dynamics and the Folding Degree
Vladimir Sladek, Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Information and Modeling 60 (3) Mar 2020[Refereed]
学術賞受賞寄稿「タンパク質の機能発現に重要なレアイベントを抽出するサンプリング手法の開発」
原田隆平
アンサンブル 22 Jan 2020[Refereed]
Rare Event Sampling of Biomolecules Based on Distributed Computing
Ryuhei Harada
BUTSURI 75 (1) Jan 2020[Refereed]
Developments of Rare Event Sampling Methods for Proteins
Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
Journal of Computational Chemistry Japan 18 (5) Dec 2019[Refereed]
Non-targeted Parallel Cascade Selection Molecular Dynamics Based on a Non-Redundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
Journal of Chemical Information and Modeling 59 (12) Nov 2019[Refereed]
Selection Rules for Outliers in Outlier Flooding Method (OFLOOD) Regulate its Conformational Sampling Efficiency
Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
Journal of Chemical Information and Modeling 59 (9) Sep 2019[Refereed]
Non-targeted Parallel Cascade Selection Molecular Dynamics Using Time-localised Prediction of Conformational Transitions in Protein Dynamics
Ryuhei Harada, Vladimir Sladek Yasuteru Shigeta
Journal of Chemical Theory and Computation 15 (9) Sep 2019[Refereed]
Supercomputing News
Ryuhei Harada
Supercomputing News 21 (1) Aug 2019
Parallel Cascade Selection Molecular Dynamics Simulation (PaCS-MD) Screens for Protein Complexes Generated by Rigid Docking
Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
Journal of Molecular Graphics and Modeling 92 Jul 2019[Refereed]
Temperature-Pressure Shuffling Outlier Flooding Method Enhances the Conformational Sampling of Proteins
Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
Journal of Computational Chemistry 40 (15) Apr 2019[Refereed]
Molecular Dynamics Studies on the Effects of Antifreezing Protein from Rhagium Inquisitor (RiAFP) onIce Growth
Masato Kimatsuka, Ryuma Sato, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta
Journal of Computational Chemistry Japan 17 (5) Mar 2019[Refereed]
Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-Order Molecular Dynamics Simulation
Hayato Aida, Ryuhei Harada, Yasuteru Shigeta
Chemistry Letters 48 (4) Mar 2019[Refereed]
Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
Ryuhei Harada, Yasuteru Shigeta
Advances in Quantum Chemistry 78 Feb 2019[Refereed]
Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
Masato Kimatsuka, Ryuma Sato, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta
Chemistry Letters 48 (3) Feb 2019[Refereed]
Studies of Molecular Crowding by Simulations and Development of Parallel Cascade Selection Molecular Dynamics
Ryuhei Harada
Association of Asia Pacific Physical Society 29 (1) Feb 2019
Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations
Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Theory and Computation 15 (1) Jan 2019[Refereed]
Studies of Molecular Crowding by Simulations and Development of Parallel Cascade Selection Molecular Dynamics
Ryuhei Harada
BUTSURI 73 (12) Dec 2018[Refereed]
カスケード選択型分子動力学シミュレーションの開発とタンパク質構造変化予測への適用
原田隆平
平成29年度・京都大学スーパーコンピュータ共同研究制度広報 17 (1) Dec 2018
The Formation of Central Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics
Ryuhei Harada, Hayato Aida, Yasuteru Shigeta
Chemistry Letters 47 Sep 2018[Refereed]
Effect of Initial Structures Rules in Parallel Cascade Selection Molecular Dynamics Affect Conformational Sampling Efficiency
Ryuhei Harada, Yasuteru Shigeta
Journal of Molecular Graph and Modeling 85 Sep 2018[Refereed]
Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins
Ryuhei Harada
Bulletin Chemical Society of Japan 91 (9) Sep 2018[Refereed]
How does Friction Constant affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?
Ryuhei Harada, Yasuteru Shigeta
Chemistry Letters 47 Aug 2018[Refereed]
Temperature Shuffled Structural Dissimilarity Sampling Based on a Root-Mean Square Deviation
Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Information and Modeling 58 (7) Aug 2018[Refereed]
カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発とFtsZ細胞分裂ダイナミクスへの適用
原田隆平
スーパーコンピューティングニュース特集号 20 (2) Aug 2018
How Low-Resolution Structural Data Predict the Conformational Changes of a Protein: A Study on Data-Driven Molecular Dynamics Simulations
Ryuhei Harada, Yasuteru Shigeta
Physical Chemistry Chemical Physics 20 Jul 2018[Refereed]
Developments of Innovative Molecular Simulation Methods for Understanding the Biological Functions
Ryuhei Harada
Chemical Industry 69 (7) Jul 2018
Coulomb and CH–π Interactions in (6–4) Photolyase–DNA Complex Dominate DNA Binding and Repair Ability
Yuma Terai, Ryuma Sato, Takako Yumiba, Ryuhei Harada, Kohei Shimizu, Tatsuya Toga, Tomoko Ishikawa, Takashi Todo, Shigenori Iwai, Yasuteru Shigeta, Junpei Yamamoto
Nucleic Acid Research 46 (13) Jul 2018[Refereed]
On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate the Conformational Transitions of Proteins
Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Theory and Computation 14 (6) Jun 2018[Refereed]
Recent Extensions and Applications of Parallel Cascade Selection Molecular Dynamics Simulations
Ryuhei Harada, Yasuteru Shigeta
Activity Report 2017 / Supercomputer Center, Institute for Solid State Physics (The University of Tokyo) May 2018
Programed Dynamics Ordering in the Self-Organization Processes of a Nanocube: A Molecular Dynamics Study
Ryuhei Harada, Takako Mashiko,, Masanori Tachikawa,, Shuichi Hiraoka, Yasuteru Shigeta
Physical Chemistry Chemical Physics 20 Apr 2018[Refereed]
Development of Molecular Crowding and Cascade-Type Massive Parallel Simulation Methods for Biological Functions of Proteins
Ryuhei Harada
Chemistry and Chemical Industry 71 (3) Mar 2018
Analyses on Dynamic Ordering of Protein Functions by means of Cascade Selection Molecular Dynamics
Ryuhei Harada, Yasuteru Shigeta
Journal of Computer Chemistry Japan 17 (1) Mar 2018[Refereed]
The Binding Structure and Affinity of Photodamaged Duplex DNA with Members of the Photolyase/Cryptochrome Family: A Computational Study
Ryuma Sato, Ryuhei Harada, Yasuteru Shigeta
Biophysics and Physicobiology 15 Jan 2018[Refereed]
An Assessment of Optimal Time Scale of Conformational Resampling for Parallel Cascade Selection Molecular Dynamics
Ryuhei Harada, Yasuteru Shigeta
Molecular Simulation 44 (3) 2018[Refereed]
Temperature-shuffled Parallel Cascade Selection Molecular Dynamics Accelerates the Structural Transitions of Proteins
Ryuhei Harada, Yasuteru Shigeta
Journal of Computational Chemistry 38 (31) Dec 2017[Refereed]
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches
Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Information and Modeling 57 (12) Dec 2017[Refereed]
Dynamic Specification of Initial Structures in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Efficiently Promotes Biologically Relevant Rare Events
Ryuhei Harada, Yasuteru Shigeta
Bulletin of Chemical Society of Japan 90 (11) Nov 2017[Refereed]
Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection
Ryuhei Harada, Yasuteru Shigeta
Journal of Computational Chemistry 38 (22) Aug 2017[Refereed]
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
Yuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki Hayashi
The Journal of Physical Chemistry B 121 (22) Jun 2017[Refereed]
How Does the Number of Initial Structures Affect the Conformational Sampling Efficiency and Quality in Parallel Cascade Selection Molecular Dynamics (PaCS-MD)?
Ryuhei Harada, Yasuteru Shigeta
Chemistry Letters 46 (6) Jun 2017[Refereed]
Identification of the Key Interactions in Structural Transition Pathway of FtsZ from Staphylococcus Aureus
Junso Fujita*, Ryuhei Harada*, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi Matsumura (*Equally Contributed)
Journal of Structural Biology 198 (2) May 2017
Common Folding Processes of Mini-Proteins: Partial Formations of Secondary Structures Initiate the Immediate Protein Folding
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
Journal of Computational Chemistry 38 (11) Apr 2017[Refereed]
Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins
Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Theory and Computation 13 (3) Mar 2017[Refereed]
Classical cumulant dynamics for statistical chemical physics
Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, Thi Kieu My Bui, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma, Mitsuo Shoji
Molecular Simulation 43 (13-16) 2017[Refereed]
Theoretical Analyses on a Flipping Mechanism of UV-induced DNA Damage
Ryuma Sato, Ryuhei Harada, Yasuteru Shigeta
BIOPHYSICS AND PHYSICOBIOLOGY 13 Nov 2016[Refereed]
A Fast Convergent Simulated Annealing Algorithm for Protein-Folding: Simulated Annealing Outlier FLOODing (SA-OFLOOD) Method
Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
Bulletin of Chemical Society of Japan 89 (11) Nov 2016[Refereed]
Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael Feig
eLife 5 Nov 2016[Refereed]
Molecular Mechanisms of Substrate Specificities of Uridine-Cytidine Kinase
Wataru Tanaka, Mitsuo Shoji, Fumiaki Tomoike, Yuzuru Ujiie, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Katsumasa Kamiya, Toyokazu Ishida, Ryoji Masui, Seiki Kuramitsu, Yasuteru Shigeta
Biophysics and Physicobiology 13 Jun 2016[Refereed]
最近の研究から「カスケード型超並列シミュレーションに基づく遷移経路探索法」
原田隆平
アンサンブル 18 (3) Jun 2016[Refereed]
TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
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
Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
Journal of Computational Chemistry 37 (8) Mar 2016[Refereed]
Parallel Cascade Selection Molecular Dynamics for Efficient Conformational Sampling and Free Energy Calculation of Proteins
Akio Kitao, Ryuhei Harada, Yasutaka Nishihara, Duy Phuoc Tran
Proceedings of the International Conference of Computational Methods in Sciences and Engineering 2016 (ICCMSE-2016) 1790 2016[Refereed]
Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins
Ryuhei Harada, Akio Kitao
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
Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
CHEMICAL PHYSICS LETTERS 639 Oct 2015[Refereed]
Protein Folding and Evolution
Ryuhei Harada, Yuji Inagaki, Yasuteru Shigeta
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
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
CHEMICAL PHYSICS LETTERS 630 Jun 2015[Refereed]
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
Michael Feig, Ryuhei Harada, Takaharu Mori, Isseki Yu, Koichi Takahashi, Yuji Sugita
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
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (10) Apr 2015[Refereed]
Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body Systems
Yasuteru Shigeta, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5) Mar 2015[Refereed]
Protein Folding Pathways Extracted by OFLOOD: Outlier FLOODing Method
Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta
JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (2) Jan 2015[Refereed]
Simple, yet powerful methodologies for conformational sampling of proteins
Ryuhei Harada, Yu Takano, Takeshi Baba, Yasuteru Shigeta
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (9) 2015[Refereed]
Cascade-type Massive Parallel Simulation for Protein Conformation Transition Pathway Search
Yasutaka Nishihara, Ryuhei Harada, Akio Kitao
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
Takeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru Shigeta
Journal of Computational Chemistry 35 (16) Jun 2014[Refereed]
Molecular Simulation Methods to Enhance Soft Protein Motions
Ryuhei Harada, Akio Kitao
SEIBUTSU BUTSURI 54 (3) Mar 2014[Refereed]
Hydration and Protein Stability under Molecular Crowding Environments
Ryuhei Harada
BUSEEI KENKYU 53 Mar 2014[Refereed]
Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
The Journal of Chemical Physics 140 (12) Mar 2014[Refereed]
Conformational Transition Pathway and Free Energy Analyses of Proteins by Parallel Cascade Selection Molecular Dynamics (PaCS-MD)
Ryuhei Harada, Yasutaka Nishihara, Nobuhiko Wakai, Akio Kitao
International Conference of Computational Methods in Sciences and Engineering 2014 1618 2014[Refereed]
Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to Generate Conformational Transitions of Proteins
Ryuhei Harada, Akio Kitao
The Journal of Chemical Physics 139 (3) Jul 2013[Refereed]
Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions
Ryuhei Harada, Naoya Tochio, Takanori Kigawa, Yuji Sugita, Michael Feig
Journal of the American Chemical Society 135 (9) Mar 2013[Refereed]
Hydration and Protein Stability under Cellular Environments
Ryuhei Harada
SEIBUTSU BUTSURI 53 (4) Feb 2013[Refereed]
博士論文紹介「超並列マルチスケールシミュレーションMSFEL法で探る生体分子の生体分子の自由エネルギー地形」
原田隆平
アンサンブル 15 (1) Jan 2013[Refereed]
Understanding Proteins in Packed Places
Ryuhei Harada, Yuji Sugita, Michael Feig
RIKEN RESEARCH 7 (3) Jul 2012
Protein Crowding Affects Hydration Structure and Dynamics
Ryuhei Harada, Yuji Sugita, Michael Feig
Journal of the American Chemical Society 134 (10) Mar 2012[Refereed]
The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing
Ryuhei Harada, Akio Kitao
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
Ryuhei Harada, Akio Kitao
The 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
Ryuhei Harada, Akio Kitao
Chemical Physics Letters 503 (1-3) Feb 2011[Refereed]
Awards & Honors
▼▲
Dec 2019
2019年度分子シミュレーション学会学術賞
Mar 2019
日本物理学会第13回若手奨励賞 (領域12)
Feb 2019
Royal Society of Chemistry 2018 PCCP Hot Article Collection
Mar 2018
日本化学会第67回進歩賞
Sep 2017
The 4th BIOPHYSICS Editors' Choice Award
Nov 2016
BCSJ Selected Paper (日本化学会優秀論文)
Nov 2016
第54回日本生物物理学会年会若手招待講演賞
Apr 2015
日本学術振興会特別研究員 PD (化学)
Sep 2012
第50回日本生物物理学会年会若手招待講演証
Nov 2010
第24回分子シミュレーション討論会学生優秀発表賞
Books etc
Research Grants & Projects
▼▲
中分子環状ペプチドの膜透過性を評価する分子シミュレーション技術の創出
筑波大学研究基盤支援プログラム (Aタイプ)
Research period: Aug 2019 - Mar 2020Representative: 原田隆平
筑波大学研究支援プログラム(Cタイプ)
Research period: Jul 2019 - Mar 2020Representative: 原田隆平
カスケード選択型分子動力学シミュレーションで実現する環状ペプチドの膜透過シミュレーション
2019年度学際共同利用
Research period: Apr 2019 - Mar 2020Representative: 原田隆平
PaCS-MDで実現する環状ペプチドの膜透過シミュレーション
平成31年度 TSUBAME若手・女性利用者支援制度度
Research period: Apr 2019 - Mar 2020Representative: 原田隆平
カスケード選択型分子動力学シミュレーションで実現する環状ペプチドの膜透過シミュレーション
若手・女性利用者推薦 2019年度 (前期)
Research period: Apr 2019 - Sep 2019Representative: 原田隆平
カスケード選択型分子動力学シミュレーションに基づく低解像度タンパク質構造の精密化
平成30年度スーパーコンピューター若手・女性利用者推薦制度選択課題 (後期)
Research period: Oct 2018 - Mar 2019Representative: 原田隆平
筑波大学研究基盤支援プログラム(Ｃタイプ）
Research period: Jul 2018 - Mar 2019Representative: 原田隆平
カスケード型分子動力学シミュレーションに基づくフレキシブルドッキング法の開発
平成30年度 TSUBAME若手・女性利用者支援制度度
Research period: Apr 2018 - Mar 2019Representative: 原田隆平
Gタンパク質共役受容体におけるシグナル伝達機構の解明
若手研究(A) 課題番号:16H06164
Research period: Apr 2016 - Mar 2019Representative: 原田隆平
カスケード型分子動力学シミュレーションに基づくタンパク質構造精密化アルゴリズムの開発と応用
平成30年度スーパーコンピューター若手・女性利用者推薦 (前期)
Research period: Apr 2018 - Sep 2018Representative: 原田隆平
カスケード型超並列シミュレーションで探るFtsZ の細胞分裂ダイナミクス
平成29年度スーパーコンピューター若手・女性利用者推薦採択課題 (後期)
Research period: Oct 2017 - Mar 2018Representative: 原田隆平
教師あり機械学習に基づく超並列カスケード型シミュレーションの定式化とタンパク質構造変化予測への適用
平成29年度若手・女性研究者奨励枠
Research period: Apr 2017 - Mar 2018Representative: 原田隆平
カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発
平成29年度 TSUBAME若手・女性利用者支援制度
Research period: Apr 2017 - Mar 2018Representative: 原田隆平
分子動力学シミュレーションで探る細胞環境におけるタンパク質フォールディング機構
特別研究奨励費課題番号:15J03797
Research period: Apr 2015 - Mar 2018Representative: 原田隆平
カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発
平成29年度スーパーコンピューター若手・女性利用者推薦課題 (前期)
Research period: Apr 2017 - Sep 2017Representative: 原田隆平
タンパク質構造揺らぎに基づく構造変化予測法の構築
若手研究(B) 課題番号:26840056
Research period: Apr 2014 - Mar 2016Representative: 原田隆平

	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
▼▲
分子磁性
多核金属錯体
生物無機化学
反応機構の理論解明
酵素反応
Academic & Professional Experience
Published Papers
▼▲
Reaction Mechanism of Monomeric Sarcosine Oxidase with N-Cyclopropylglycine
Shoji, Mitsuo, Abe, Y, Boero, M, Shigeta, Y, Y., Nishida
Physical Chemistry Chemical Physics May 2020[Refereed]
Domain-based local pair natural orbital CCSD(T) calculations of fourteen different S2 intermediates for water oxidation in the Kok cycle of OEC of PSII. Re-visit to one LS-two HS model for the S2 state
K. Miyagawa, H. Isobe, T. Kawakami, M. Shoji, S. Yamanaka, M. Okumura, T. Nakajima, K. Yamaguchi
Chemical Physics Letters 734 Nov 2019[Refereed]
Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: Implications into the proton transfer at the active site
Machida, Yasuhiro, Murakawa, Takeshi, Sakai, Akiko, Shoji, Mitsuo, Shigeta, Yasuteru, Hayashi, Hideyuki
Journal of biochemistry 167 (4) Nov 2019[Refereed]
Domain-based local pair natural orbital CCSD (T) calculations of six different S1 structures of oxygen evolving complex of photosystem II. Proposal of multi-intermediate models for the S1 state
Shoji, Mitsuo
Chemical Physics Letters 732 Oct 2019[Refereed]
Domain-based local pair natural orbital CCSD (T) calculations of strongly correlated electron systems: Examination of dynamic equilibrium models based on multiple intermediates in S1 state of photosystem II
庄司,光男
Molecular Physics Sep 2019[Refereed]
Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography
Shoji, Mitsuo, Isobe, Hiroshi, Shen, Jian-Ren, Suga, Michihiro, Akita, Fusamichi, Miyagawa, Koichi, Shigeta, Yasuteru, Yamaguchi, Kizashi
CHEMICAL PHYSICS LETTERS 730 Sep 2019
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]
First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface
Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Kamiya, Katsumasa, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
The Journal of Physical Chemistry A 123 (26) Jun 2019[Refereed]
Spin, Valence, and Structural Isomerism in the S State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity
Isobe, Hiroshi, Shoji, Mitsuo, Suzuki, Takayoshi, Shen, Jian-Ren, Yamaguchi, Kizashi
Journal of chemical theory and computation 15 (4) Apr 2019[Refereed]
Photosubstitution Reaction of cis-[Ru(bpy)(2)(CH3CN)(2)](2+) and cis-[Ru(bpy)(2)(NH3)(2)](2+) in Aqueous Solution via Monoaqua Intermediate
Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
The journal of physical chemistry. A 123 (13) Mar 2019[Refereed]
Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn O (X=5, 6) cluster in the Kok cycle S (i=0-3) of oxygen evolving complex of photosystem II
Yamaguchi, Kizashi, Yamanaka, Shusuke, Isobe, Hiroshi, Shoji, Mitsuo, Miyagawa, Kouichi, Nakajima, Takahito, Kawakami, Takashi, Okumura, Mitsutaka
Physiologia plantarum 166 (1:::SI) Mar 2019[Refereed]
Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
Kimatsuka, Masato, Sato, Ryuma, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru
Chemistry Letters 48 (3) Mar 2019[Refereed]
Molecular Dynamics studies on the effects of Antifreezing Protein from Rhagium inquisitor (RiAFP) on Ice Growth
木間塚政人, 佐藤竜馬, 原田隆平, 庄司, 光男, 重田, 育照
Journal of Computer Chemistry, Japan 17 (5) Mar 2019[Refereed]
Possibility of the right-opened Mn-oxo intermediate (R-oxo(4444)) among all nine intermediates in the S-3 state of the oxygen-evolving complex of photosystem II revealed by large-scale QM/MM calculations
Shoji, Mitsuo, Isobe, Hiroshi, Miyagawa, Koichi, Yamaguchi, Kizashi
CHEMICAL PHYSICS 518 Feb 2019[Refereed]
Theoretical study of the photodissociation reaction of methanol
Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
CHEMICAL PHYSICS LETTERS 714 Jan 2019[Refereed]
Concerted bond switching mechanism coupled with one-electron transfer for the oxygen-oxygen bond formation in the oxygen-evolving complex of photosystem II
Shoji, Mitsuo, Isobe, Hiroshi, Yamaguchi, Kizashi
CHEMICAL PHYSICS LETTERS 714 Jan 2019[Refereed]
Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction.
Takaki Tokiwa, Mitsuo Shoji, Vladimir Sladek, Naoki Shibata, Yoshiki Higuchi, Kunishige Kataoka, Takeshi Sakurai, Yasuteru Shigeta, Fuminori Misaizu
Molecules (Basel, Switzerland) 24 (1) Dec 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 CAS CI calculations of binuclear manganese complex Mn(IV)(2)O-2(NHCHCO2)(4): Scope and applicability of Heisenberg model
Kawakami, Takashi, Miyagawa, Koichi, Sharma, Sandeep, Saito, Toru, Shoji, Mitsuo, Yamada, Satoru, Yamanaka, Shusuke, Okumura, Mitsutaka, Nakajima, Takahito, Yamaguchi, Kizashi
Journal of computational chemistry 40 (2:::SI) Oct 2018[Refereed]
光化学系ＩＩ酸素発生中心の反応機構
庄司, 光男
アンサンブル : 分子シミュレーション研究会会誌 40 (4) Oct 2018[Refereed]
特集光化学系II酸素発生中心にあたって
庄司, 光男
アンサンブル : 分子シミュレーション研究会会誌 40 (4) Oct 2018
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 Practical Approach for Searching Stable Molecular Structures by Introducing Repulsive Interactions among Walkers
Shoji,Mitsuo, Kayanuma,Megumi, Shigeta,Yasuteru
Bulletin of the Chemical Society of Japan 91 (10) Jul 2018[Refereed]
Concerted Mechanism of Water Insertion and O Release during the S to S Transition of the Oxygen-Evolving Complex in Photosystem II
Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
The journal of physical chemistry. B 122 (25) Jun 2018[Refereed]
The Reaction Mechanisms of O₂ Formation in Photosynthesis
SHOJI,Mitsuo, ISOBE,Hiroshi, SHIGETA,Yasuteru, NAKAJIMA,Takahito, YAMAGUCHI,Kizashi
Seibutsu Butsuri 58 (3) May 2018[Refereed]
Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
Yamamoto, Yuta, Takei, Kenta, Arulmozhiraja, Sundaram, Sladek, Vladimir, Matsuo, Naoya, Han, Song-Iee, Matsuzaka, Takashi, Sekiya, Motohiro, Tokiwa, Takaki, Shoji, Mitsuo, Shigeta, Yasuteru, Nakagawa, Yoshimi, Tokiwa, Hiroaki, Shimano, Hitoshi
Biochemical and biophysical research communications May 2018
Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II
Shoji, Mitsuo, Isobe, Hiroshi, Shigeta, Yasuteru, Nakajima, Takahito, Yamaguchi, Kizashi
CHEMICAL PHYSICS LETTERS 698 Apr 2018[Refereed]
First-principles study of the formation of glycine-producing radicals from common interstellar species
Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
Molecular Astrophysics 10 Mar 2018[Refereed]
Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II
Yamaguchi, Kizashi, Mitsuo, Shoji, Isobe, Hiroshi, Yamanaka, Shusuke, Kawakami, Takashi, Yamada, Satoru, Katouda, Michio, Nakajima, Takahito
Molecular Physics 116 (5-6) Mar 2018[Refereed]
First-principles study of the formation of glycine-producing radicals from common interstellar species
Sato, Akimasa, Kitazawa, Yuya, Ochi, Toshiro, Shoji, Mitsuo, Komatsu, Yu, Kayanuma, Megumi, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
Molecular Astrophysics 10 Mar 2018[Refereed]
Understanding Two Different Structures in the Dark Stable State of the Oxygen‐Evolving Complex of Photosystem II: Applicability of the Jahn–Teller Deformation Formula
Shoji,Mitsuo
ChemPhotoChem 116 (5-6) Nov 2017[Refereed]
Ab initio computations of zero-field splitting parameters and effective exchange integrals for single-molecule magnets (Mn-12- and Mn11Cr-acetate clusters)
Shinsuke Sano, Takashi Kawakami, Shohei Yoshimura, Mitsuo Shoji, Shusuke Yamanaka, Mitsutaka Okumura, Takahito Nakajima, Kizashi Yamaguchi
POLYHEDRON 136 (4) Nov 2017[Refereed]
A theoretical study of the formation of glycine via hydantoin intermediate in outer space environment
Megumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki Umemura
CHEMICAL PHYSICS LETTERS 687 Nov 2017[Refereed]
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations.
Yuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki Hayashi
The journal of physical chemistry. B 121 (22) Jun 2017[Refereed]
Large-scale QM/MM calculations of the CaMn4O5 cluster in the S-3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures
Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi
FARADAY DISCUSSIONS 198 Jun 2017[Refereed]
The reaction mechanism of sarcosine oxidase elucidated using FMO and QM/MM methods
Abe, Yukihiro, Shoji, Mitsuo, Nishiya, Yoshiaki, Aiba, Hiroshi, Kishimoto, Takahide, Kitaura, Kazuo
Physical chemistry chemical physics : PCCP 19 (15) Mar 2017[Refereed]
On the guiding principles for understanding of geometrical structures of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Proposal of estimation formula of structural deformations via the Jahn-Teller effects
K. Yamaguchi, M. Shoji, H. Isobe, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya
MOLECULAR PHYSICS 115 (5) 2017[Refereed]
UNO DMRG CASCI calculations of effective exchange integrals for m-phenylene-bis-methylene spin clusters
Takashi Kawakami, Shinsuke Sano, Toru Saito, Sandeep Sharma, Mitsuo Shoji, Satoru Yamada, Yu Takano, Shusuke Yamanaka, Mitsutaka Okumura, Takahito Nakajima, Kizashi Yamaguchi
MOLECULAR PHYSICS 115 (17-18) 2017[Refereed]
Solvation Energy of Proton: a Consistent Calculation Schemefor Acid Dissociation Constantsand Standard Hydrogen Electrode Potentials
MATSUI,Toru, KIYAN,Akane, SHOJI,Mitsuo, SHIGETA,Yasuteru
Journal of Computer Chemistry, Japan 15 (5) 2016
Molecular dynamics study on the key catalytic intermediates of threonine synthase
Mitsuo Shoji, Yuzuru Ujiie, Ryuhei Harada, Megumi Kayanuma, Yasuteru Shigeta, Takeshi Murakawa, Hideyuki Hayashi
PROTEIN SCIENCE 24 (1:SI) Oct 2015[Refereed]
Performance of the divide-and-conquer approach used as an initial guess
Mitsuo Shoji, Megumi Kayanuma, Hiroaki Umeda, Yasuteru Shigeta
CHEMICAL PHYSICS LETTERS 634 Aug 2015[Refereed]
A QM/MM study of the 5 '-AMP DNA hydrolysis of aprataxin
Kyohei Hanaoka, Wataru Tanaka, Megumi Kayanuma, Mitsuo Shoji
CHEMICAL PHYSICS LETTERS 631 Jul 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
Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi
CHEMICAL PHYSICS LETTERS 627 May 2015
Quantal Cumulant Dynamics for Real-Time Simulations of Quantum Many-Body Systems
Yasuteru Shigeta, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5) Mar 2015[Refereed]
Theoretical studies of the damage- free S-1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II
Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi
CHEMICAL PHYSICS LETTERS 623 Mar 2015
A QM/MM study of the initial steps of catalytic mechanism of nitrile hydratase
Megumi Kayanuma, Kyohei Hanaoka, Mitsuo Shoji, Yasuteru Shigeta
CHEMICAL PHYSICS LETTERS 623 Mar 2015[Refereed]
トレオニン合成酵素の触媒反応前半部分の反応機構解析(第438回研究協議会研究発表要旨,ビタミンB研究委員会)
林, 秀行, 村川, 武志, 庄司, 光男
Vitamins 89 (3) Mar 2015[Refereed]
Involvement of Propionate Side Chains of the Heme in Circular Dichroism of Myoglobin: Experimental and Theoretical Analyses
Masako Nagai, Chika Kobayashi, Yukifumi Nagai, Kiyohiro Imai, Naoki Mizusawa, Hiroshi Sakurai, Saburo Neya, Megumi Kayanuma, Mitsuo Shoji, Shigenori Nagatomo
JOURNAL OF PHYSICAL CHEMISTRY B 119 (4) Jan 2015[Refereed]
Performance Benchmark of FMO Calculation with GPU-Accelerated Fock Matrix Preparation Routine
UMEDA,Hiroaki, HANAWA,Toshihiro, SHOJI,Mitsuo, BOKU,Taisuke, SHIGETA,Yasuteru
Journal of Chemical Software 13 (6) 2015[Refereed]
GPU-accelerated FMO Calculation with OpenFMO: Four-Center Inter-Fragment Coulomb Interaction
UMEDA,Hiroaki, HANAWA,Toshihiro, SHOJI,Mitsuo, BOKU,Taisuke, SHIGETA,Yasuteru
Journal of Chemical Software 14 (3) 2015[Refereed]
An efficient initial guess formation of broken-symmetry solutions by using localized natural orbitals
Mitsuo Shoji, Yasunori Yoshioka, Kizashi Yamaguchi
CHEMICAL PHYSICS LETTERS 608 Jul 2014[Refereed]
A QM/MM study of nitric oxide reductase-catalysed N2O formation
Mitsuo Shoji, Kyohei Hanaoka, Daiki Kondo, Akimasa Sato, Hiroaki Umeda, Katsumasa Kamiya, Kenji Shiraishi
MOLECULAR PHYSICS 112 (3-4) Feb 2014[Refereed]
Fock Matrix Preparation in Fragment Molecular Orbital Method with GPGPU
Hiroaki,Umeda, Toshihiro,Hanawa, Mitsuo,Shoji, Taisuke,Boku, Yuichi,Inadomi
情報処理学会論文誌. コンピューティングシステム 6 (4) Oct 2013[Refereed]
3. トレオニン合成酵素における生成物リン酸イオンの触媒作用のQM/MMによる解析(第433回研究協議会研究発表要旨,ビタミンB研究委員会)
林, 秀行, 村川, 武志, 庄司, 光男, 氏家, 謙
Vitamins 87 (10) Oct 2013[Refereed]
Calculation of the electron transfer coupling matrix element in diabatic reactions
Mitsuo Shoji, Kyohei Hanaoka, Akimasa Sato, Daiki Kondo, Moon Young Yang, Katsumasa Kamiya, Kenji Shiraishi
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (3) Feb 2013[Refereed]
分子軌道計算のGPGPU化に向けた行列加算手法の提案
梅田, 宏明, 塙, 敏博, 庄司, 光男, 朴, 泰祐
IPSJ SIG Notes 2013-HPC-138 (19) Feb 2013
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
フリーソフトで始める分子モデリング
庄司, 光男 (Role:Sole author)
Gaussian16で始める量子化学超入門
庄司,光男 (Role:Sole author)
Research Grants & Projects
生体内量子多体系における特異的化学反応の機構解明
JST-PRESTO
Research period: Oct 2019 - Mar 2023Representative: 庄司光男
自然・半導体・分子触媒で利用可能な多様な水分解反応機構の解明
新学術領域研究(研究領域提案型)
Research period: Apr 2020 - Mar 2022Representative: 庄司光男
酵素反応機構の解明、生物無機化学、分子動力学、分子磁性、多核金属錯体、可視化プログラム(Makiko)

	氏名	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
理論化学
量子化学
Academic & Professional Experience
Apr 2019
-
Present
University of Tsukuba Center for Computational Sciences
Apr 2018
-
Mar 2019
Kyushu University Institute for Materials Chemistry and Engineering
Apr 2017
-
Mar 2018
Kyushu University Institute for Materials Chemistry and Engineering
Published Papers
▼▲
Three-step Spin State Transition and Hysteretic Proton Transfer in the Crystal of an Iron(II) Hydrazone Complex
Nakanishi, Takumi, Hori, Yuta, Wu, Shuqi, Sato, Hiroyasu, Okazawa, Atsushi, Kojima, Norimichi, Horie, Yusuke, Okajima, Hajime, Sakamoto, Akira, Shiota, Yoshihito, Yoshizawa, Kazunari, Osamu, Sato
Angewandte Chemie International Edition Jun 2020[Refereed]
Local Structures and Dynamics of Imidazole Molecules in Poly(vinylphosphonic acid)–Imidazole Composite Investigated by Molecular Dynamics
Hori, Yuta, Suetake, Toshiya, Shiota, Yoshihito, Yoshizawa, Kazunari, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, Motohiro
ACS Applied Polymer Materials 2 (4) Apr 2020[Refereed]
Revisiting Formic Acid Decomposition by a Graph-Theoretical Approach
Ida, Tomonori, Nishida, Manami, Hori, Yuta
The Journal of Physical Chemistry A 123 (44) Oct 2019[Refereed]
Observation of Proton Transfer Coupled Spin Transition and Trapping of Photoinduced Metastable Proton Transfer State in an Fe(II) Complex.
Takumi Nakanishi, Yuta Hori, Hiroyasu Sato, Shu-Qi Wu, Atsushi Okazawa, Norimichi Kojima, Takashi Yamamoto, Yasuaki Einaga, Shinya Hayami, Yusuke Horie, Hajime Okajima, Akira Sakamoto, Yoshihito Shiota, Kazunari Yoshizawa, Osamu Sato
Journal of the American Chemical Society 141 (36) Sep 2019[Refereed]
Mechanistic Insights into Methane Oxidation by Molecular Oxygen under Photoirradiation: Controlled Radical Chain Reactions
Hori, Yuta, Abe, Tsukasa, Shiota, Yoshihito, Yoshizawa, Kazunari
Bulletin of the Chemical Society of Japan 92 (11) Aug 2019[Refereed]
Role of Amino-Acid Residues for Dioxygen Activation in the Second Coordination Sphere of the Dicopper Site of pMMO
Miyanishi, Mayuko, Abe, Tsukasa, Hori, Yuta, Shiota, Yoshihito, Yoshizawa, Kazunari
Inorganic Chemistry 58 (18) Aug 2019[Refereed]
Dual Catalytic Cycle of H₂ and H₂O Oxidations by A Half-Sandwich Iridium Complex: A Theoretical Study
Ikeda, Kei, Hori, Yuta, Mahyuddin, Muhammad Haris, Shiota, Yoshihito, Staykov, Aleksandar, Matsumoto, Takahiro, Yoshizawa, Kazunari, Ogo, Seiji
Inorganic Chemistry 58 (11) May 2019[Refereed]
Local structures and electronic properties of In atoms in In-doped ZnO
Hori, Yuta, Shiota, Yoshihito, Ida, Tomonori, Yoshizawa, Kazunari, Mizuno, Motohiro
Thin Solid Films 685 (1) May 2019[Refereed]
Cupric-superoxide complex that induces a catalytic aldol reaction-type C–C bond formation
Abe, T, Hori, Y, Shiota, Y, Ohta, T, Morimoto, Y, Sugimoto, H, Ogura, T, Yoshizawa, K, Itoh, S
Communications Chemistry 2 (1) Feb 2019[Refereed]
Redox behaviour of the β-dihydroporphycene cobalt complex: study on the effect of hydrogenation of the ligand
Hashimoto K, Koide T, Okawara T, Shimakoshi H, Hori Y, Shiota Y, Yoshizawa K, Hisaeda Y
Dalton Transactions 48 (3) Jan 2019[Refereed]
Ground-State Copper(III) Stabilized by N-Confused/N-Linked Corroles: Synthesis, Characterization, and Redox Reactivity
Yogesh Kumar Maurya, Katsuya Noda, Kazuhisa Yamasumi, Shigeki Mori, Tomoki Uchiyama, Kazutaka Kamitani, Tomoyasu Hirai, Kakeru Ninomiya, Maiko Nishibori, Yuta Hori, Yoshihito Shiota, Kazunari Yoshizawa, Masatoshi Ishida, Hiroyuki Furuta
Journal of the American Chemical Society 140 (22) Jun 2018[Refereed]
Construction of a Potential Energy Surface Based on a Diabatic Model for Proton Transfer in Molecular Pairs
Hori Yuta, Ida Tomonori, Mizuno Motohiro
Concepts, Methods and Applications of Quantum Systems in Chemistry and Physics Jan 2018[Refereed]
Catalytic Performance of a Dicopper-Oxo Complex for Methane Hydroxylation
Hori Y, Shiota Y, Tsuji T, Kodera M, Yoshizawa K
Inorganic Chemistry 57 (1) Jan 2018[Refereed]
Local structure and hydrogen bond characteristics of imidazole molecules for proton conduction in acid and base proton-conducting composite materials
Hori Y, Chikai T, Ida T, Mizuno M
Physical Chemistry Chemical Physics 20 (15) Jan 2018[Refereed]
A novel approach to Bohmian mechanics using an uncompressed particle method
Sugisawa H, Hori Y, Ida T, Mizuno M
Physica E: Low-Dimensional Systems and Nanostructures 104 Jan 2018[Refereed]
Potential energy construction in the diabatic picture for quantum mechanical rate constants of intermolecular proton transfer
Yuta Hori, Tomonori Ida, Motohiro Mizuno
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 19 (25) Jul 2017[Refereed]
Optimization of the spin-component-scaled factor for electron propagator method
Fang-Han Lim, Manami Nishida, Yuta Hori, Tomonori Ida, Motohiro Mizuno
CHEMICAL PHYSICS LETTERS 678 Jun 2017[Refereed]
Complete spin contamination-free MP2 method
Manami Nishida, Fang-Han Lim, Yuta Hori, Tomonori Ida, Motohiro Mizuno
CHEMICAL PHYSICS LETTERS 669 Feb 2017[Refereed]
Simulation of molecular Auger spectra using a two-electron Dyson propagator
Y. Hori, M. Nishida, F. H. Lim, T. Ida, M. Mizuno
JOURNAL OF ELECTRON SPECTROSCOPY AND RELATED PHENOMENA 207 Feb 2016[Refereed]
A comparative theoretical study of the hydride transfer mechanisms during LiAlH4 and LiBH4 reductions
Yuta Hori, Tomonori Ida, Motohiro Mizuno
COMPUTATIONAL AND THEORETICAL CHEMISTRY 1076 Jan 2016[Refereed]
Awards & Honors
Mar 2017
金沢大学金沢大学大学院自然科学研究科長賞
Mar 2012
金沢大学金沢大学理工学域長賞
Books etc
高機能性金属錯体が拓く触媒科学:革新的分子変換反応の創出をめざして
堀, 優太, 塩田, 淑仁, 吉澤, 一成 (Role:Contributor, 計算化学が先導する酵素触媒反応の設計)
Research Grants & Projects
▼▲
理論計算に基づく酸塩基複合体中のプロトン伝導機構の解明
若手研究
Research period: Apr 2019 - Mar 2022Representative: 堀優太
プロトン移動共役型スピン転移反応の理論的解析
基盤共同研究課題
Research period: Apr 2020 - Mar 2021Representative: 堀優太
理論的解析を軸とした新規プロトン移動型スピン制御材料の開発
融合創発研究
Research period: Apr 2018 - Mar 2019Representative: 堀優太
プロトン共役電子移動反応における理論的解析手法の開発
研究活動スタート支援
Research period: Aug 2017 - Mar 2019Representative: 堀優太

	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
▼▲
一重項分裂
有機半導体
光合成
量子生物学
励起エネルギー移動
電子移動
Academic & Professional Experience
Apr 2019
-
Present
University of Tsukuba Center for Computational Sciences Researcher
Oct 2017
-
Present
科学技術振興機構
Apr 2016
-
Sep 2017
University of Tsukuba Center for Computational Sciences
Apr 2013
-
Mar 2016
Nagoya University Graduate School of Science, Division of Material Science
Apr 2009
-
Mar 2013
Kyoto University Graduate School of Science
Apr 2006
-
Mar 2009
Meijo University Graduate School of Environmental and Human Sciences
Published Papers
▼▲
Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem I
Kitoh-Nishioka Hirotaka, Shigeta Yasuteru, Itoh Shigeru, Kimura Akihiro
The Journal of Physical Chemistry B 124 (2) 2020[Refereed]
Calculation of Charge-Transfer Electronic Coupling with Nonempirically Tuned Range-Separated Density Functional
Kitoh-Nishioka Hirotaka, Ando Koji
The Journal of Physical Chemistry C 123 (18) 2019[Refereed]
Does Inactive Alkyl Chain Enhance Triplet–Triplet Annihilation of 9,10-Diphenylanthracene Derivatives?
Ryuma Sato, Hirotaka Kitoh-Nishioka, Kenji Kamada, Toshiko Mizokuro, Kenji Kobayashi, Yasuteru Shigeta
The Journal of Physical Chemistry C 122 (10) Feb 2018[Refereed]
Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited
Sato Ryuma, Kitoh-Nishioka Hirotaka, Ando Koji, Yamato Takahisa
The Journal of Physical Chemistry B 122 (27) 2018[Refereed]
Near infrared two-photon-excited and -emissive dyes based on a strapped excited-state intramolecular proton-transfer (ESIPT) scaffold
Naoya Suzuki, Kayo Suda, Daisuke Yokogawa, Hirotaka Kitoh-Nishioka, Stephan Irle, Akihiro Ando, Luis M, G. Abeg{~{a } }o, Kenji Kamada, Aiko Fukazawa, Shigehiro Yamaguchi
Chemical Science 9 (10) 2018[Refereed]
Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion
Sato Ryuma, Kitoh-Nishioka Hirotaka, Kamada Kenji, Mizokuro Toshiko, Kobayashi Kenji, Shigeta Yasuteru
The Journal of Physical Chemistry Letters 9 (22) 2018[Refereed]
Multiscale Simulations on Charge Transport in Covalent Organic Frameworks Including Dynamics of Transfer Integrals from the FMO-DFTB/LCMO Approach
Hirotaka Kitoh-Nishioka, Kai Welke, Yoshio Nishimoto, Dmitri G. Fedorov, Stephan Irle
JOURNAL OF PHYSICAL CHEMISTRY C 121 (33) Aug 2017[Refereed]
Theoretical Analyses of Triplet-Triplet Annihilation Process of 9,10-Diphenylanthracene in Solution
Ryuma Sato, Hirotaka Kitoh-Nishioka, Takeshi Yanai, Yasuteru Shigeta
CHEMISTRY LETTERS 46 (6) Jun 2017[Refereed]
Forster Resonance Energy Transfer between Fluorescent Proteins: Efficient Transition Charge-Based Study
Hirotaka Kitoh-Nishioka, Daisuke Yokogawa, Stephan Irle
JOURNAL OF PHYSICAL CHEMISTRY C 121 (8) Mar 2017[Refereed]
Classical cumulant dynamics for statistical chemical physics
Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, Thi Kieu My Bui, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma, Mitsuo Shoji
MOLECULAR SIMULATION 43 (13-16) 2017[Refereed]
FMO3-LCMO study of electron transfer coupling matrix element and pathway: Application to hole transfer between two tryptophans through cis- and trans-polyproline-linker systems
Hirotaka Kitoh-Nishioka, Koji Ando
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
Ryuma Sato, Hirotaka Kitoh-Nishioka, Koji Ando, Takahisa Yamato
CHEMICAL PHYSICS LETTERS 633 Jul 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 Jul 2015[Refereed]
Charge-transfer matrix elements by FMO-LCMO approach: Hole transfer in DNA with parameter tuned range-separated DFT
Hirotaka Kitoh-Nishioka, Koji Ando
CHEMICAL PHYSICS LETTERS 621 Feb 2015[Refereed]
Charge-transfer matrix elements by FMO-LCMO approach: Hole transfer in DNA with parameter tuned range-separated DFT
Hirotaka Kitoh-Nishioka, Koji Ando
CHEMICAL PHYSICS LETTERS 621 Feb 2015[Refereed]
Electron Transfer Pathway Analysis in Bacterial Photosynthetic Reaction Center
Kitoh-Nishioka Hirotaka, Ando Koji
2015[Refereed]
A Strap Strategy for Construction of an Excited-State Intramolecular Proton Transfer (ESIPT) System with Dual Fluorescence
Naoya Suzuki, Aiko Fukazawa, Kazuhiko Nagura, Shohei Saito, Hirotaka Kitoh-Nishioka, Daisuke Yokogawa, Stephan Irle, Shigehiro Yamaguchi
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 53 (31) Jul 2014[Refereed]
A Strap Strategy for Construction of an Excited-State Intramolecular Proton Transfer (ESIPT) System with Dual Fluorescence
Naoya Suzuki, Aiko Fukazawa, Kazuhiko Nagura, Shohei Saito, Hirotaka Kitoh-Nishioka, Daisuke Yokogawa, Stephan Irle, Shigehiro Yamaguchi
Angew. Chem. 126 (31) Jun 2014[Refereed]
A Computational Study on the Role of a Methionine at a Discriminator Site of Cyclobutane-Pyrimidine-Dimer Photolyase
Ryuma Sato, Hirotaka Kitoh-Nishioka, Tsutomu Kawatsu, Kei Yura, Koji Ando, Takahisa Yamato
BIOPHYSICAL JOURNAL 106 (2) Jan 2014[Refereed]
A Computational Study on the Role of a Methionine at a Discriminator Site of Cyclobutane-Pyrimidine-Dimer Photolyase
Ryuma Sato, Hirotaka Kitoh-Nishioka, Tsutomu Kawatsu, Kei Yura, Koji Ando, Takahisa Yamato
BIOPHYSICAL JOURNAL 106 (2) Jan 2014[Refereed]
Fragment Molecular Orbital Study on Electron Tunneling Mechanisms in Bacterial Photosynthetic Reaction Center
Hirotaka Kitoh-Nishioka, Koji Ando
JOURNAL OF PHYSICAL CHEMISTRY B 116 (43) Nov 2012[Refereed]
Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO-LCMO approach
Hirotaka Nishioka, Koji Ando
JOURNAL OF CHEMICAL PHYSICS 134 (20) May 2011[Refereed]
Pathway analysis of super-exchange electronic couplings in electron transfer reactions using a multi-configuration self-consistent field method
Hirotaka Nishioka, Koji Ando
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13 (15) 2011[Refereed]
Identification of Functional Residues of DNA Photolyase by Biophysical Computation and Bioinformatics
Takahisa YAMATO, Hirotaka NISHIOKA, Kei YURA
Seibutsu Butsuri 49 (4) 2009[Refereed]
Average electron tunneling route of the electron transfer in protein media
Hirotaka Nishioka, Toshiaki Kakitani
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
Yuji Miyazawa, Hirotaka Nishioka, Kei Yura, Takahisa Yamato
BIOPHYSICAL JOURNAL 94 (6) Mar 2008[Refereed]
Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media
Hirotaka Nishioka, Nobuharu Ueda, Toshiaki Kakitani
BIOPHYSICS 4 2008[Refereed]
Non-condon theory for the energy gap dependence of electron transfer rate
Hirotaka Nishioka, Akihiro Kimura, Takahisa Yamato, Toshiaki Kakitani
FRONTIERS OF COMPUTATIONAL SCIENCE 2007[Refereed]
Temperature dependence of the inelastic electron tunneling
H. Nishioka, T. Yamato, T. Kakitani
MOLECULAR SIMULATION 32 (9) Aug 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
H Nishioka, A Kimura, T Yamato, T Kawatsu, T Kakitani
JOURNAL OF PHYSICAL CHEMISTRY B 109 (32) Aug 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
H Nishioka, A Kimura, T Yamato, T Kawatsu, T Kakitani
JOURNAL OF PHYSICAL CHEMISTRY B 109 (5) Feb 2005[Refereed]
Awards & Honors
Books etc
Chemical Science of π-Electron Systems
Hirotaka Kitoh-Nishioka, Koji Ando (Role:Contributor, Chapter 39 "Electron Transfer Pathway Analysis in Bacterial Photosynthetic Reaction Center" (pp. 658-673))
高次π空間の創発と機能開発
鬼頭-西岡宏任, 安藤耕司 (Role:Contributor, 第４章１節 “光合成反応中心における長距離電子移動の経路解析”)
Research Grants & Projects
▼▲
多様な光合成反応中心の光捕集と電子移動と進化の理論的解析
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
Research period: Apr 2020 - Mar 2023Representative: 木村明洋
Explorations of Unknown Biological Electron Transfers and Their Roles in Biological Functions Using Quantum Simulation Techniques
PRESTO
Research period: Oct 2017 - Mar 2021Representative: Hirotaka Kitoh
有機半導体のエキシトン/キャリア輸送現象の理論解析
萌芽共同研究課題
Research period: Jun 2016 - Mar 2017Representative: 鬼頭宏任
生体分子内の電荷移動現象の理論解析
若手研究者奨励枠
Research period: Jun 2014 - Mar 2016Representative: 鬼頭宏任

	氏名	森田陸離
	Name	Morita Rikuri
	Faculty
	Section
	Position	Researcher
	Theme
	Related Links	researchmap
	Email	moritaccs.tsukuba.ac.jp

Research Interests
細胞生物学
分子動力学
Academic & Professional Experience
Apr 2020
-
Present
University of Tsukuba Center for Computational Sciences
Published Papers
Molecular dissection of the actin-binding ability of the fission yeast alpha-actinin, Ain1, in vitro and in vivo
Rikuri Morita, Masak Takaine, Osamu Numata, Kentaro Nakano
JOURNAL OF BIOCHEMISTRY 162 (2) Aug 2017[Refereed]
Awards & Honors
▼▲
Jun 2019
第４６回生体分子科学討論会優秀ポスター賞
Jan 2018
International Congress of Cell Biology 2018 The Raman Trust Award
Mar 2017
筑波大学生命環境科学研究科生物科学専攻専攻長表彰
Mar 2017
筑波大学生命環境科学研究科研究科長表彰
Books etc
Research Grants & Projects

	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	researchmap
	Email	mitsutayccs.tsukuba.ac.jp

Research Interests
Molecular Dynamics Simulation
Computational Chemistry
Academic & Professional Experience
Published Papers
Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
Y. Mitsuta, T. Kawakami, M. Okumura, S. Yamanaka
International Journal of Molecular Science 19 (4) 2018[Refereed]
Automated Search of Minimum Free-Energy Path by Umbrella Integration
Y. Mitsuta, S. Yamanaka, T. Kawakami, M. Okumura
Journal of Computational Chemistry 39 (23) 2018[Refereed]
Free energy reaction root mapping of alanine tripeptide in water
Y. Mitsuta, J. K ̈astner, S. Yamanaka, T. Kawakami, M. Okumura
Molecular Physics 2018[Refereed]
Awards & Honors
Books etc
Research Grants & Projects

	氏名
	Name	Kowit Hengphasatporn
	Faculty
	Section
	Position	Researcher
	Theme	Molecular modeling and Structure-based virtual screening on the biological systems
	Related Links
	Email	kowithccs.tsukuba.ac.jp

Published Papers
▼▲
Multiple Virtual Screening Strategies for the Discovery of Novel Compounds Active Against Dengue Virus: A Hit Identification Study
K. Hengphasatporn, A. Garon, P. Wolschann, T. Langer, W. Chavasiri, T. Saelee, S. Yasuteru, S. Boonyasuppayakorn, T. Rungrotmongkol*
ACS Omega
Binding Pattern and Susceptibility of Epigallocatechin Gallate Against Envelope Protein Homodimer of Zika Virus: A Molecular Dynamics Study.
K. Hengphasatporn, N. Kungwan, T. Rungrotmongkol*
Journal of Molecular Liquids 274 Jan 2019
Cardol triene inhibits dengue infectivity by targeting kl loops and preventing envelope fusion
P. Kanyaboon, T. Saelee, A. Suroengrit, K. Hengphasatporn, T. Rungrotmongkol, W. Chavasiri, and S Boonyasuppayakorn*
Scientific Reports 16643 (8) Nov 2018
A novel flavanone derivative inhibits dengue virus fusion and infectivity.
P. Srivarangkul, W. Yuttithamnon, A. Suroengrit, S. Pankaew, K. Hengphasatporn, T. Rungrotmongkol, P. Phuwapraisirisane, K. Ruxrungtham, S. Boonyasuppayakorn*
Antiviral Research 151 Jan 2018

	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
Apr 2016
-
Present
University of Tsukuba Center for Computational Sciences
Published Papers
▼▲
Mitochondrial genomes of Hemiarma marina and Leucocryptos marina revised the evolution of cytochrome c maturation in Cryptista.
Yuki Nishimura, Keitaro Kume, Keito Sonehara, Goro Tanifuji, Takashi Shiratori, Ken-ichiro Ishida, Tetsuo Hashimoto, Yuji Inagaki, Moriya Ohkuma
Frontiers in Ecology and Evolution May 2020[Refereed]
Inventory and evolution of mitochondrion-localized family A DNA polymerases in Euglenozoa.
Ryo Harada, Yoshihisa Hirakawa, Akinori Yabuki, Yuichiro Kashiyama, Moe Maruyama, Ryo Onuma, Petr Soukal, Shinya Miyagishima, Vladimir Hampl, Goro Tanifuji, Yuji Inagaki
Pathogens Apr 2020[Refereed]
Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis.
Chihiro Sarai, Goro Tanifuji, Takuro Nakayama, Ryoma Kamikawa, Kazuya Takahashi, Euki Yazaki, Eriko Matsuo, Hideaki Miyashita, Ken-ichro Ishida, Mitsunori Iwataki, Yuji Inagaki
Proceedings of the National Academy of Sciences of the United States of America 117 (10) Mar 2020[Refereed]
Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis.
Tanifuji, Goro, Kamikawa, Ryoma, Moore, Christa E, Mills, Tyler, Onodera, Naoko T, Kashiyama, Yuichiro, Archibald, John M, Inagaki, Yuji, Hashimoto, Tetsuo
Genome Biology and Evolution 12 (2) Feb 2020[Refereed]
Barthelonids represent a deep-branching Matamonada clade with mitochondrion-related organelles generating no ATP.
Euki, Yazaki, Kume, Keitaro, Takashi, Shiratori, Yana, Edlit, Goro, Tanifuji, Ryo, Harada, Alastair, Simpson, Ken-ichiro, Ishida, Tetsuo, Hashimoto, Inagaki, Yuji
bioRχiv Oct 2019
Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote
Matsuo, Mitsuhiro, Katahata, Atsushi, Tchikawa, Makoto, Minakuchi, Yohei, Noguchi, Hideki, Toyoda, Atsushi, Fujiyama, Asao, Suzuki, Yutaka, Hata, Takayuki, Satoh, Soichirou, Nakayama, Takuro, Kamkawa, Ryoma, Nomura, Mami, Inagaki, Yuji, Ishida, Ken-ichiro, Obokata, Junichi
bioRχiv Oct 2019
Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host
Takuro, Nakayama, Mami, Nomura, Yoshihito, Takano, Tanifuji, Goro, Kogiku, Shiba, Kazuo, Inaba, Inagaki, Yuji, Masakado, Kawata
Proceedings of the National Academy of Science of the United States of America 116 (32) Jun 2019[Refereed]
In silico strcutral modelling and analysis of elongation factor 1alpha and elongation factor-like proteins.
Kotaro, Sakamoto, Megumi, Kayanuma, Inagaki, Yuji, Tetsuo, Hashimoto, Yasuteru, Shigeta
ACS Omega 4 (4) Apr 2019[Refereed]
Horizontally-acquired genetic elements in the mitochondrial genome of a centrohelid Marophrys sp. SRT127.
Yuki, Nishimura, Takashi, Shiratori, Kenichro, Ishida, Tetsuo, Hashimoto, Moriya, Ohkuma, Inagaki, Yuji
Scientific Reports 9 Mar 2019[Refereed]
Fates of evolutionarily distinct, plastid-type glyceraldehyde 3-phosphate dehydrogenase genes in kareniacean dinoflagellates.
Ryoma, Kamikawa, Euki, Yazaki, Michiru, Tahara, Takaya, Sakura, Matsuo, Eriko, Kisaburo, Nagamune, Tetsuo, Hashimoto, Inagaki, Yuji
Journal of Eukaryotic Microbiology 65 (6) Sep 2018[Refereed]
Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates.
Eriko, Matsuo, Inagaki, Yuji
PeerJ 6 Jul 2018[Refereed]
Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer.
Matsuo, Mitsuhiro, Katahata, Atsushi, Satoh, Soichirou, Matsuzaki, Motomichi, Nomura, Mami, Ken-ichiro, Ishita, Inagaki, Yuji, Obokata, Junichi
PLOS ONE 13 (7) Jul 2018[Refereed]
The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites.
Tanifuji, Goro, Takabayashi, Shun, Kume, Keitaro, Takagi, Mizue, Nakayama, Takuro, Kamikawa, Ryoma, Inagaki, Yuji, Hashimoto, Tetsuo
PLOS ONE 13 (3) Mar 2018[Refereed]
Extensive molecular tinkering in the evolution of the membrane attachment mechanisms of the Rheb GTPase.
Záhonová, Kristína, Petrželková, Romana, Valach, Matúš, Yazaki, Euki, Tikhonenkov, Denis V, Butenko, Anzhelika, Janouškovec, Jan, Hrdá, Štěpánka, Klimeš, Vladimír, Burger, Gertraud, Inagaki, Yuji, Keeling, Patrick J, Hampl, Vladimír, Flegontov, Pavel, Yurchenko, Vyacheslav, Eliáš, Marek
Scientific Reports 8 Mar 2018[Refereed]
Phylogenomics places orpha protistan lineages in a novel candidate supergroup.
Brown, Matthew R, Heiss, Aaron A, Kamikawa, Ryoma, Inagaki, Yuji, Yabuki, Akinori, Alexander, Tice T, Shiratori, Takashi, Ishida, Ken-ichiro, Hashimoto, Tetsuo, Simpson, Alastair GB, J, Roger Andrew
Genome Biology and Evolution 10 (2) Jan 2018[Refereed]
Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms
Takuro Nakayama, Yuji Inagaki
SCIENTIFIC REPORTS 7 Oct 2017[Refereed]
Global Kinetoplastea phylogeny inferred from a large-scale multigene alignment including prarasitic species for better understanding transitions from a free-living to a parasitic lifestyle.
Yazaki, Euki, Ishikawa, Sohta, Kume, Keitaro, Kumagai, Akira, Kamaishi, Takashi, Tanifuji, Goro, Hashimoto, Tetsuo, Inagaki, Yuji
Genes & Genetic Systems 92 (1) Sep 2017[Refereed]
Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis
Goro Tanifuji, Ugo Cenci, Daniel Moog, Samuel Dean, Takuro Nakayama, Vojtech David, Ivan Fiala, Bruce A. Curtis, Shannon J. Sibbald, Naoko T. Onodera, Morgan Colp, Pavel Flegontov, Jessica Johnson-MacKinnon, Michael McPhee, Yuji Inagaki, Tetsuo Hashimoto, Steven Kelly, Keith Gull, Julius Lukes, John M. Archibald
SCIENTIFIC REPORTS 7 Sep 2017[Refereed]
A Non-photosynthetic Diatom Reveals Early Steps of Reductive Evolution in Plastids
Ryoma Kamikawa, Daniel Moog, Stefan Zauner, Goro Tanifuji, Ken-Ichiro Ishida, Hideaki Miyashita, Shigeki Mayama, Tetsuo Hashimoto, Uwe G. Maier, John M. Archibald, Yuji Inagaki
MOLECULAR BIOLOGY AND EVOLUTION 34 (9) Sep 2017[Refereed]
Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes
Michelle M. Leger, Martin Kolisko, Ryoma Kamikawa, Courtney W. Stairs, Keitaro Kume, Ivan Cepicka, Jeffrey D. Silberman, Jan O. Andersson, Feifei Xu, Akinori Yabuki, Laura Eme, Qianqian Zhang, Kiyotaka Takishita, Yuji Inagaki, Alastair G. B. Simpson, Tetsuo Hashimoto, Andrew J. Roger
NATURE ECOLOGY & EVOLUTION 1 (4) Apr 2017[Refereed]
Global Kinetoplastea phylogeny inferred from a large-scale multigene alignment including parasitic species for better understanding transitions from a free-living to a parasitic lifestyle
Euki Yazaki, Sohta A. Ishikawa, Keitaro Kume, Akira Kumagai, Takashi Kamaishi, Goro Tanifuji, Tetsuo Hashimoto, Yuji Inagaki
GENES & GENETIC SYSTEMS 92 (1) Feb 2017[Refereed]
Mitochondrial Genome of Palpitomonas bilix: Derived Genome Structure and Ancestral System for Cytochrome c Maturation
Yuki Nishimura, Goro Tanifuji, Ryoma Kamikawa, Akinori Yabuki, Tetsuo Hashimoto, Yuji Inagaki
GENOME BIOLOGY AND EVOLUTION 8 (10) Oct 2016[Refereed]
Protein folding and evolution
Harada,Ryuhei, Inagaki,Yuji, Yasuteru,Shigeta
Reference Module in Materials Science and Materials Engineering Jun 2016[Refereed]
Ungulate malaria parasites
Thomas J. Templeton, Masahito Asada, Montakan Jiratanh, Sohta A. Ishikawa, Sonthaya Tiawsirisup, Thillaiampalam Sivakumar, Boniface Namangala, Mika Takeda, Kingdao Mohkaew, Supawan Ngamjituea, Noboru Inoue, Chihiro Sugimoto, Yuji Inagaki, Yasuhiko Suzuki, Naoaki Yokoyama, Morakot Kaewthamasorn, Osamu Kaneko
SCIENTIFIC REPORTS 6 Mar 2016[Refereed]
共生体由来オルガネラにまつわるエトセトラ．
稲垣,祐司
生物の科学遺伝 70 (2) Mar 2016
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
Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes (vol 32, pg 2598, 2015)
Ryoma Kamikawa, Goro Tanifuji, Sohta A. Ishikawa, Ken-Ichiro Ishii, Yusei Matsuno, Naoko T. Onodera, Ken-Ichiro Ishida, Tetsuo Hashimoto, Hideaki Miyashita, Shigeki Mayama, Yuji Inagaki
MOLECULAR BIOLOGY AND EVOLUTION 33 (1) Jan 2016[Refereed]
Metabolic Capacity of Mitochondrion-related Organelles in the Free-living Anaerobic Stramenopile Cantina marsupialis
Fumiya Noguchi, Shigeru Shimamura, Takuro Nakayama, Euki Yazaki, Akinori Yabuki, Tetsuo Hashimoto, Yuji Inagaki, Katsunori Fujikura, Kiyotaka Takishita
PROTIST 166 (5) Nov 2015[Refereed]
Proposal of a Twin Aarginine 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, Yuji Inagaki
MOLECULAR BIOLOGY AND EVOLUTION 32 (10) Oct 2015[Refereed]
Multiple conversion between the genes encoding bacterial class-I release factors
Sohta A. Ishikawa, Ryoma Kamikawa, Yuji Inagaki
SCIENTIFIC REPORTS 5 Aug 2015[Refereed]
Morphological Identities of Two Different Marine Stramenopile Environmental Sequence Clades: Bicosoeca kenaiensis (Hilliard, 1971) and Cantina marsupialis (Larsen and Patterson, 1990) gen. nov., comb. nov.
Naoji Yubuki, Tomas Panek, Akinori Yabuki, Ivan Cepicka, Kiyotaka Takishita, Yuji Inagaki, Brian S. Leander
JOURNAL OF EUKARYOTIC MICROBIOLOGY 62 (4) Jul 2015[Refereed]
The mitochondrial genomes of Kudoa species are extremely divergent among metazoa.
Fumiya,Takeuchi, Tsuyoshi,Sekizuka, Yumiko,Ogasawara, Hiroshi,Yokoyama, Ryoma,Kamikawa, Inagaki,Yuji, Tomoyoshi,Nozaki, Yoshiko,Sugita-Konishi, Takahiro,Ohnishi, Makoto,Kuroda
PLOS One 10 (7) Jul 2015[Refereed]
Plastid Genome-Based Phylogeny Pinpointed the Origin of the Green-Colored Plastid in the Dinoflagellate Lepidodinium chlorophorum
Ryoma Kamikawa, Goro Tanifuji, Masanobu Kawachi, Hideaki Miyashita, Tetsuo Hashimoto, Yuji Inagaki
GENOME BIOLOGY AND EVOLUTION 7 (4) Apr 2015[Refereed]
Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae)
Ryoma Kamikawa, Naoji Yubuki, Masaki Yoshida, Misaka Taira, Noriaki Nakamura, Ken-ichiro Ishida, Brian S. Leander, Hideaki Miyashita, Tetsuo Hashimoto, Shigeki Mayama, Yuji Inagaki
PHYCOLOGICAL RESEARCH 63 (1) Jan 2015[Refereed]
Genome evolution triggered by acquisition of an endosymbiotic partner
Yuji Inagaki
GENES & GENETIC SYSTEMS 89 (6) Dec 2014
Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle
Takuro Nakayama, Ryoma Kamikawa, Goro Tanifuji, Yuichiro Kashiyama, Naohiko Ohkouchi, John M. Archibald, Yuji Inagaki
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 (31) Aug 2014[Refereed]
Secondary loss of a cis-spliced intron after the diversification of Giardia intestinalis assemblages.
Ryoma Kamikawa, Yuji Inagaki, Tetsuo Hashimoto
BMC Research Notes 7 Jul 2014[Refereed]
An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333.
Yuki Nishimura, Ryoma Kamikawa, Tetsuo Hashimoto, Yuji Inagaki
Mobile Genetic Elements 4 (1) May 2014[Refereed]
Gene Content Evolution in Discobid Mitochondria Deduced from the Phylogenetic Position and Complete Mitochondrial Genome of Tsukubamonas globosa
Ryoma Kamikawa, Martin Kolisko, Yuki Nishimura, Akinori Yabuki, Matthew W. Brown, Sohta A. Ishikawa, Ken-ichiro Ishida, Andrew J. Roger, Tetsuo Hashimoto, Yuji Inagaki
GENOME BIOLOGY AND EVOLUTION 6 (2) 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
Takuya Matsumoto, Masanobu Kawachi, Hideaki Miyashita, Yuji Inagaki
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
Yoshiyuki Ishitani, Ryoma Kamikawa, Akinori Yabuki, Masashi Tsuchiya, Yuji Inagaki, Kiyotaka Takishita
JOURNAL OF EUKARYOTIC MICROBIOLOGY 59 (4) Jul 2012[Refereed]
Separate Origins of Group I Introns in Two Mitochondrial Genes of the Katablepharid Leucocryptos marina
Yuki Nishimura, Ryoma Kamikawa, Tetsuo Hashimoto, Yuji Inagaki
PLOS ONE 7 (5) May 2012[Refereed]
Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochndriate' diplomonads and retortamonads
Takishita,K, Kolisko,M, Komatsuzaki,H, Yabuki,A, Inagaki,Y, Cepicka,I, Smejkalova,P, Silberman,JD, Hashimoto,T, Roger,AJ, Simpson,AGB【*Join, authors】
Protist 16 (3) Feb 2012[Refereed]
RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity
Sohta A. Ishikawa, Yuji Inagaki, Tetsuo Hashimoto
EVOLUTIONARY BIOINFORMATICS 8 2012[Refereed]
An asynchronous parallel genetic algorithm for the maximum likelihood phylogenetic tree search.
Tsuji,M, Sato,M, Tanabe,AS, Inagaki,Y, Hashimoto,T
Proceedings of 2012 IEEE Congress on Evolutionary Computation (CEC) 2012 Jan 2012[Refereed]
Multigene phylogenetic analyses including diverse radiolarian species support the "Retaria" hypothesis - The sister relationship of Radiolaria and Foraminifera
Yoshiyuki Ishitani, Sohta A. Ishikawa, Yuji Inagaki, Masashi Tsuchiya, Kozo Takahashi, Kiyotaka Takishita
MARINE MICROPALEONTOLOGY 81 (1-2) Nov 2011[Refereed]
Tsukubamonas globosa n. gen., n. sp., a Novel Excavate Flagellate Possibly Holding a Key for the Early Evolution in "Discoba"
Akinori Yabuki, Takeshi Nakayama, Naoji Yubuki, Tetsuo Hashimoto, Ken-Ichiro Ishida, Yuji Inagaki
JOURNAL OF EUKARYOTIC MICROBIOLOGY 58 (4) Jul 2011[Refereed]
A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum
Takuya Matsumoto, Sohta A. Ishikawa, Tetsuo Hashimoto, Yuji Inagaki
MOLECULAR PHYLOGENETICS AND EVOLUTION 60 (1) Jul 2011[Refereed]
Splintrons in Giardia intestinalis: Spliceosomal introns in a split form
Kamikawa, R, Inagaki, Y, Roger, AJ, Hashimoto, T
Communicative and Integrative Biology 4 (4) Apr 2011[Refereed]
Green-colored Plastids in the Dinoflagellate Genus Lepidodinium are of Core Chlorophyte Origin
Takuya Matsumoto, Fumihiko Shinozaki, Tomoko Chikuni, Akinori Yabuki, Kiyotaka Takishita, Masanobu Kawachi, Takeshi Nakayama, Isao Inouye, Tetsuo Hashimoto, Yuji Inagaki
PROTIST 162 (2) Apr 2011[Refereed]
Split Introns in the Genome of Giardia intestinalis Are Excised by Spliceosome-Mediated trans-Splicing
Ryoma Kamikawa, Yuji Inagaki, Masaharu Tokoro, Andrew J. Roger, Tetsuo Hashimoto
CURRENT BIOLOGY 21 (4) Feb 2011[Refereed]
Tsukubamonas globosa gen. et sp. nov.; a novel excavate flagellate possibly hold a key for the early evolution in “Discoba”.
Yabuki, A, Nakayama, T, Yubuki, N, Hashimoto, T, Ishida, K, Inagaki, Y
J. Euk. Microbiol. 58 (2) Jan 2011[Refereed]
A novel spliceosome-mediated trans-splicing can change our view on genome complexity of the divergent eukaryote Giardia intestinalis
Kamikawa, R, Inagaki, Y, Hashimoto, T
Biophysical Reviews 3 (4) Jan 2011[Refereed]
Cercozoa comprises both EF-1 alpha-containing and EFL-containing members
Ryoma Kamikawa, Akinori Yabuki, Takuro Nakayama, Ken-ichiro Ishida, Tetsuo Hashimoto, Yuji Inagaki
EUROPEAN JOURNAL OF PROTISTOLOGY 47 (1) Jan 2011[Refereed]
Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacterium
Takuro Nakayama, Yuko Ikegami, Takeshi Nakayama, Ken-ichiro Ishida, Yuji Inagaki, Isao Inouye
JOURNAL OF PLANT RESEARCH 124 (1) Jan 2011[Refereed]
Mitochondrial genomes from two red tide forming raphidophycean algae Heterosigma akashiwo and Chattonella marina var. marina
Isao Masuda, Ryoma Kamikawa, Manabu Ueda, Kenichi Oyama, Sadaaki Yoshimatsu, Yuji Inagaki, Yoshihiko Sako
HARMFUL ALGAE 10 (2) Jan 2011[Refereed]
Comprehensive SSU rRNA phylogeny of Eukaryota.
Ishida, K, Inagaki, Y, Sakaguchi, M, Oiwa, A, Kai, Atsushi, Suzuki, M, Nakayama, T, Chikuni, T, Yabuki, A, Yamaguchi, H, Yubuki, N, Yoshida, M, Nakayama, T, Inouye, I, Hashimoto, T
Journal of Endocytobiosis and Cell Research 20 Dec 2010[Refereed]
Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. gen. et sp., as inferred from SSU rDNA sequences.
Yubuki, N, za, V, Cepicka I, Yabuki A, Inagaki Y, Nakayama T, Inouye I, Leander BS, 稲垣, 祐司
Journal of Eukaryotic Microbiology 57 (6) Nov 2010[Refereed]
Palpitomonas bilix gen. et sp. nov: A novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia.
Yabuki, A, Inagaki, Y, Ishida, K
Protist 210 (4) Oct 2010[Refereed]
A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats
Martin Kolisko, Jeffrey D. Silberman, Ivan Cepicka, Naoji Yubuki, Kiyotaka Takishita, Akinori Yabuki, Brian S. Leander, Isao Inouye, Yuji Inagaki, Andrew J. Roger, Alastair G. B. Simpson
ENVIRONMENTAL MICROBIOLOGY 12 (10) Oct 2010[Refereed]
Rooting for the root of elongation factor-like protein phylogeny
Ryoma Kamikawa, Miako Sakaguchi, Takuya Matsumoto, Tetsuo Hashimoto, Yuji Inagaki
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
Marianne A. Minge, Kamran Shalchian-Tabrizi, Ole K. Torresen, Kiyotaka Takishita, Ian Probert, Yuji Inagaki, Dag Klaveness, Kjetill S. Jakobsen
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
Hideya Mitsui, Nobuko Arisue, Naoko Sakihama, Yuji Inagaki, Toshihiro Horii, Masami Hasegawa, Kazuyuki Tanabe, Tetsuo Hashimoto
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
Ryoma Kamikawa, Gabino F. Sanchez-Perez, Yoshihiko Sako, Andrew J. Roger, Yuji Inagaki
MOLECULAR PHYLOGENETICS AND EVOLUTION 53 (2) Nov 2009[Refereed]
Eukaryotic origin of glyceraldehyde-3-phosphate dehydrogenase genes in Clostridium thermocellum and Clostridium cellulolyticum genomes and putative fates of the exogenous gene in the subsequent genome evolution
Kiyotaka Takishita, Yuji Inagaki
GENE 441 (1-2) Jul 2009[Refereed]
Tracing back EFL gene evolution in the cryptomonads-haptophytes assemblage: Separate origins of EFL genes in haptophytes, photosynthetic cryptomonads, and goniomonads
Miako Sakaguchi, Kiyotaka Takishita, Takuya Matsumoto, Tetsuo Hashimoto, Yuji Inagaki
GENE 441 (1-2) Jul 2009[Refereed]
Gene Sampling Can Bias Multi-Gene Phylogenetic Inferences: The Relationship between Red Algae and Green Plants as a Case Study
Yuji Inagaki, Yoshihiro Nakajima, Mitsuhisa Sato, Miako Sakaguchi, Tetsuo Hashimoto
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
Fabien Burki, Yuji Inagaki, Jon Brate, John M. Archibald, Patrick J. Keeling, Thomas Cavalier-Smith, Miako Sakaguchi, Tetsuo Hashimoto, Ales Horak, Surendra Kumar, Dag Klaveness, Kjetill S. Jakobsen, Jan Pawlowski, Kamran Shalchian-Tabrizi
GENOME BIOLOGY AND EVOLUTION 1 2009[Refereed]
Direct phylogenetic evidence for lateral transfer of elongation factor-like gene
Ryoma Kamikawa, Yuji Inagaki, Yoshihiko Sako
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
Kiyotaka Takishita, Masanobu Kawachi, Mary-Helene Noel, Takuya Matsumoto, Natsuki Kakizoe, Makoto M. Watanabe, Isao Inouye, Ken-Ichiro Ishida, Tetsuo Hashimoto, Yuji Inagaki
GENE 410 (1) Feb 2008[Refereed]
Evolving genetic codes.
Ohama, T, Inagaki, Y, Bessho, Y, Osawa, S
Proceedings of the Japan Academy, Ser. B 84 (2) Jan 2008[Refereed]
Phylogenetic inference based on combined analysis of multiple genes: Illustrative data analysis of higher-order phylogeny of Eukaryota
Hashimoto ; T, Arisue, N
統計数理 56 (1) Jan 2008[Refereed]
Centrohelida is still searching for a phylogenetic home: Analyses of seven Raphidiophrys contractilis genes
Miako Sakaguchi, Yuji Inagaki, Tetsuo Hashimoto
GENE 405 (1-2) Dec 2007[Refereed]
Assessing the monophyly of chlorophyll-c containing plastids by multi-gene phylogenies under the unlinked model conditions
Kei Iida, Kiyotaka Takishita, Kazuhiko Ohshima, Yuji Inagaki
MOLECULAR PHYLOGENETICS AND EVOLUTION 45 (1) Oct 2007[Refereed]
Proposal of Pseudochattonella verruculosa gen. nov., comb. nov. (Dictyochophyceae) for a former raphidophycean Chattonella verruculosa, based on 18S rDNA phylogeny and ultrastructural characteristics.
Hosoi-Tanabe, S, Honda, D, Fukaya, S, Otake, I, Inagaki, Y, Sako, Y
Phycological Research 55 (3) Sep 2007[Refereed]
ロングブランチの誘惑-分子系統解析のダークサイド
稲垣, 祐司
The Japanese journal of phycology 55 (2) Jul 2007
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
Kiyotaka Takishita, Naoji Yubuki, Natsuki Kakizoe, Yuji Inagaki, Tadashi Maruyama
EXTREMOPHILES 11 (4) Jul 2007[Refereed]
Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages
Nicola J. Patron, Yuji Inagaki, Patrick J. Keeling
CURRENT BIOLOGY 17 (10) May 2007[Refereed]
Fragmentation of mitochondrial large subunit rRNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria
Ryoma Kamikawa, Yuji Inagaki, Yoshihiko Sako
PROTIST 158 (2) Apr 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
Naoji Yubuki, Yuji Inagaki, Takeshi Nakayama, Isao Inouye
JOURNAL OF EUKARYOTIC MICROBIOLOGY 54 (2) Mar 2007[Refereed]
Plasticity of the domain structure in FlgJ, a bacterial protein involved in flagellar rod formation
Takayuki Nambu, Yuji Inagaki, Kazuhiro Kutsukake
GENES & GENETIC SYSTEMS 81 (6) Dec 2006[Refereed]
Phylogenetic estimation under codon models can be biased by codon usage heterogeneity
Yuji Inagaki, Andrew J. Roger
MOLECULAR PHYLOGENETICS AND EVOLUTION 40 (2) Aug 2006[Refereed]
Recombination between elongation factor 1 alpha genes from distantly related archaeal lineages
Y Inagaki, E Susko, AJ Roger
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (12) Mar 2006[Refereed]
Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes
AGB Simpson, Y Inagaki, AJ Roger
MOLECULAR BIOLOGY AND EVOLUTION 23 (3) Mar 2006[Refereed]
A close relationship between Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acid sequences of three cytoskeletal proteins (actin, alpha-tubulin, and beta-tubulin)
K Takishita, Y Inagaki, M Tsuchiya, M Sakaguchi, T Maruyama
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
Aug 2008
日本進化学会日本進化学会研究奨励賞
Apr 2007
文部科学省科学技術分野の文部科学大臣表彰若手科学者賞
Apr 1993
公益信託森安大学院生奨学基金
Books etc
▼▲
共生微生物
稲垣,祐司, 中山卓郎 (Role:Contributor, 第17章現在も続く細胞内共生細菌のオルガネラ化．)
Reference modules in Materials Science and Engineering 2016
Harada, Ryuhei, Inagaki, Yuji, Shigeta, Yasuteru (Role:Contributor, Protein Folding and Evolution)
ロングブランチの誘惑--分子系統解析のダークサイド
稲垣祐司 (Role:Supervisor)
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 (Role:Supervisor)
Research Grants & Projects
▼▲
ミトコンドリアDNAポリメラーゼの多様性と進化の全容解明
科学研究費基盤研究(B)
Research period: 2019 - 2023Representative: 稲垣祐司
海洋原生生物に共生する細菌多様性の実態解明
度国際共同研究加速基金（国際共同研究強化(B)）
Research period: 2018 - 2022Representative: 稲垣祐司
非光合成生物の光適応進化の全容解明
科学研究費補助金基盤研究（B)
Research period: 2017 - 2020Representative: 谷藤吾朗
海洋バクテリアの長期炭素隔離機能に対する海洋酸性化の影響評価
科学研究費補助金基盤研究(B)
Research period: 2016 - 2019Representative: 濱健夫

	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
-
Present
Tsukuba University Center for computer science Postdoc
May 2015
-
Mar 2017
The University of Tokyo Atmosphere and Ocean Research Institute Project Researcher
Sep 2013
-
Apr 2015
University of Glasgow School of Geographical & Earth Sciences Post-doc scientist
Apr 2013
-
Aug 2013
Japan Agency for Marine-Earth Science and Technology
Apr 2013
-
Aug 2013
The University of Tokyo Graduate School of Science Project Researcher
Apr 2010
-
Mar 2013
JAMSTEC Biogeoscience Visiting Researcher
Published Papers
▼▲
Nanoparticle-Biological Interactions in a Marine Benthic Foraminifer.
Ciacci, C, Grimmelpont, M. V, Corsi, I, Bergami, E, Curzi, D, Burini, D, Bouchet, V. M. P, Ambrogini, P, Gobbi, P, Ujiié, Y, Ishitani, Y, Coccioni, R, Bernhard, J. M, Frontalini, F
Scientific Reports 19 (9) Dec 2019[Refereed]
Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans
Yurika Ujiie, Yoshiyuki Ishitani
PLOS ONE 11 (2) Feb 2016[Refereed]
Molecular evidence for wide vertical distribution of the marine planktonic protist Larcopyle buetschlii (Radiolaria) in a semi-enclosed marginal sea
Yoshiyuki Ishitani, Kiyotaka Takishita
JOURNAL OF PLANKTON RESEARCH 37 (5) Sep 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
Yoshiyui Ishitani, Yurika Ujiie, Kiyotaka Takishita
MOLECULAR PHYLOGENETICS AND EVOLUTION 78 Sep 2014[Refereed]
Evolution of Elongation Factor-Like (EFL) Protein in Rhizaria is Revised by Radiolarian EFL Gene Sequences
Yoshiyuki Ishitani, Ryoma Kamikawa, Akinori Yabuki, Masashi Tsuchiya, Yuji Inagaki, Kiyotaka Takishita
JOURNAL OF EUKARYOTIC MICROBIOLOGY 59 (4) Jul 2012[Refereed]
Longitudinal differentiation among pelagic populations in a planktic foraminifer
Yurika Ujiie, Takahiro Asami, Thibault de Garidel-Thoron, Hui Liu, Yoshiyuki Ishitani, Colomban de Vargas
ECOLOGY AND EVOLUTION 2 (7) Jul 2012[Refereed]
Phylogenetic Relationships and Evolutionary Patterns of the Order Collodaria (Radiolaria)
Yoshiyuki Ishitani, Yurika Ujiie, Colomban de Vargas, Fabrice Not, Kozo Takahashi
PLOS ONE 7 (5) May 2012[Refereed]
Two distinct lineages in the radiolarian Order Spumellaria having different ecological preferences
Yoshiyuki Ishitani, Yurika Ujiie, Colomban de Vargas, Fabrice Not, Kozo Takahashi
DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY 61-64 Feb 2012[Refereed]
Multigene phylogenetic analyses including diverse radiolarian species support the "Retaria" hypothesis - The sister relationship of Radiolaria and Foraminifera
Yoshiyuki Ishitani, Sohta A. Ishikawa, Yuji Inagaki, Masashi Tsuchiya, Kozo Takahashi, Kiyotaka Takishita
MARINE MICROPALEONTOLOGY 81 (1-2) Nov 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
Yoshiyuki Ishitani, Kozo Takahashi, Yusuke Okazaki, Seiji Tanaka
MICROPALEONTOLOGY 54 (1) 2008[Refereed]
The vertical distribution of Radiolaria in the waters surrounding Japan
Yoshiyuki Ishitani, Kozo Takahashi
MARINE MICROPALEONTOLOGY 65 (3-4) Dec 2007[Refereed]
Awards & Honors
Oct 2011
放散虫研究集会学術賞第11回放散虫研究集会
Jul 2010
ISEP young scientist award
Books etc
アメーバのはなし
石谷佳之, 土屋正史 (Role:Contributor, 海の中にいるヒトに感染しない原生生物)
Radiolaria
Yoshiyuki Ishitani, Colette Febvre-Chevalier, Jean Febvre (Role:Joint author)
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 (Role:Joint author)
Research Grants & Projects
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海洋原生生物に共生する細菌多様性の実態解明
国際共同研究強化B【研究分担者】
Research period: Oct 2018 - Mar 2023Representative: 稲垣祐司
ミトコンドリアDNAポリメラーゼの多様性と進化の全容解明
基盤研究(B)【研究分担者】
Research period: Apr 2019 - Mar 2022Representative: 稲垣祐司
大規模分岐年代推定ー真核生物の誕生と進化を解き明かす!!ー
基盤研究(C)【研究代表者】
Research period: Apr 2018 - Mar 2021Representative: 石谷佳之
有孔虫における殻形成機構の解明ー石灰化のブラックボックスを開くー
基盤研究(B)【研究分担者】
Research period: Apr 2017 - Mar 2020Representative: 氏家由利香
原核藻類と原生生物の光共生に関する研究
基盤研究(C)【研究分担者】
Research period: Apr 2016 - Mar 2019Representative: 藤木撤一
浮遊性有孔虫の新規環境指標の確立：遺伝子・安定同位体・形態の複合解析から
基盤研究（C）【研究協力者】
Research period: Apr 2014 - Mar 2017Representative: 氏家由利香
放散虫のバイオミネラリゼーションと殻形態進化：化石の分子生物学への応用に向けて
海外特別研究員
Research period: Sep 2013 - Apr 2015Representative: 石谷佳之
浮遊性有孔虫の生物多様性と炭素循環の関係の解明
若手研究（B）【研究協力者】
Research period: Apr 2011 - Mar 2014Representative: 氏家由利香
環境変遷に基づく放散虫の進化と多様性,古海洋環境指標としての新展望
特別研究員
Research period: Apr 2010 - Mar 2013Representative: 石谷佳之
生物学に基づく古海洋学の新展開~放散虫・環境指標としての有用性・可能性の追求~
日仏二国間交流事業【企画/立案/協力】
Research period: Nov 2009Representative: 高橋孝三

	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
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