Division of Life Sciences

Biological Function and Information Group

Name	Faculty	Position
SHIGETA Yasuteru		Professor/Group Leader
SHOJI Mitsuo		Professor
TANI Kazutoshi		Professor
HARADA Ryuhei		Associate Professor
HORI Yuta		Assistant Professor
Kowit Hengphasatporn		Assistant Professor
OKAZAWA Kazuki		Assistant Professor
SAITO Kazuya		Researcher
Manussada Ratanasak		Researcher
MIYAGAWA Koichi		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 / Chief
NAKAYAMA Takuro		Assistant Professor
HASHIMOTO Tetsuo	Faculty of Life and Enviromental Sciences	Honorary Professor (Collaborative Fellow)

Biological Function and Information Group

	氏名	重田育照
	Name	SHIGETA Yasuteru
	Faculty
	Section
	Position	Professor/Group Leader
	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 2023
-
Present
University of Tsukuba Headquarter Vice president and Executive director for Research
Apr 2019
-
Present
National Institutes for Quantum and Radiological Science and Technology Takasaki Advanced Radiation Research Institute Visiting Researcher
Apr 2016
-
Present
Center for Computational Sciences, University of Tsukuba Division of Life Science Professor
May 2014
-
Present
Osaka University Graduate School of Engineering Sciences Visiting Professor
Apr 2018
-
Mar 2020
宇宙航空研究開発機構
Apr 2016
-
Mar 2018
Institute of Molecular Sciences Visiting professor
Mar 2014
-
Mar 2016
筑波大学
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
筑波大学
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
▼▲
Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method
Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Koji Ando
The Journal of chemical physics 153 (10) Sep 2020[Refereed]
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling 60 (8) Aug 2020[Refereed]
Analytical Method Using a Scaled Hypersphere Search for High-Dimensional Metadynamics Simulations
Yuki Mitsuta, Yasuteru Shigeta
Journal of Chemical Theory and Computation 16 (6) 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 16 (10) Jun 2020[Refereed]
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 of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active site
Yasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki Hayashi
JOURNAL OF BIOCHEMISTRY 167 (4) Apr 2020[Refereed]
Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active site
Yasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki Hayashi
Journal of biochemistry 167 (4) Apr 2020[Refereed]
Split Conformation of Chaetomium Thermophilum Hsp104 Disaggregase
Inoue Yosuke, Hanazono Yuya, Noi Kentaro, Kawamoto Akihiro, Kimatsuka Masato, Harada Ryuhei, Takeda Kazuki, Iwamasa Natsuki, Noguchi Keiichi, Shigeta Yasuteru, Namba Keiichi, Ogura Teru, Miki Kunio, Shinohara Kyosuke, Yohda Masafumi
Science Advances 29 (7) 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]
Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem i
Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru Itoh, Akihiro Kimura
Journal of Physical Chemistry B 124 (2) Jan 2020[Refereed]
Why are lopinavir and ritonavir effective against the newly emerged coronavirus 2019? Atomistic insights into the inhibitory mechanisms
Bodee Nutho, Panupong Mahalapbutr, Kowit Hengphasatporn, Nawanwat Chainuwong Pattaranggoon, Nattapon Simanon, Yasuteru Shigeta, Supot Hannongbua, Thanyada Rungrotmongkol
Biochemistry 59 (18) 2020[Refereed]
Intramolecular mode coupling of the isotopomers of water: A non-scalar charge density-derived perspective
Tian Tian, Tianlv Xu, Steven R. Kirk, Ian Tay Rongde, Yong Boon Tan, Sergei Manzhos, Yasuteru Shigeta, Samantha Jenkins
Physical Chemistry Chemical Physics 22 (4) 2020[Refereed]
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
Journal of Chemical Information and Modeling 59 (12) Dec 2019[Refereed]
Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
Journal of Molecular Graphics and Modelling 92 Nov 2019[Refereed]
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency
Ryuhei Harada, Yasuteru Shigeta
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
Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
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
Tatsuhiko Ohto, Mayank Dodia, Jianhang Xu, Sho Imoto, Fujie Tang, Frederik Zysk, Thomas D. Kühne, Yasuteru Shigeta, Mischa Bonn, Xifan Wu, Yuki Nagata
Journal of Physical Chemistry Letters 10 (17) Sep 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) Jun 2019[Refereed]
Numerical investigation of the nano-scale solutal Marangoni convections
Y. Imai, T. Yamamoto, A. Sekimoto, Y. Okano, R. Sato, Y. Shigeta
Journal of the Taiwan Institute of Chemical Engineers 98 (SI) May 2019[Refereed]
Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical Insight
Tianlv Xu, Jia Hui Li, Roya Momen, Wei Jie Huang, Steven Robert Kirk, Yasuteru Shigeta, Samantha Jenkins
Journal of the American Chemical Society 141 (13) 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]
New assay method based on Raman spectroscopy for enzymes reacting with gaseous substrates
Yuka Kawahara-Nakagawa, Koji Nishikawa, Satoru Nakashima, Shota Inoue, Takehiro Ohta, Takashi Ogura, Yasuteru Shigeta, Katsuyuki Fukutani, Tatsuhiko Yagi, Yoshiki Higuchi
Protein Science 28 (3) Mar 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]
Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
Ryuhei Harada, Yasuteru Shigeta
Advances in Quantum Chemistry 78 (78) 2019[Refereed]
Protein Residue Networks from Energetic and Geometric Data: Are They Identical?
Vladimir Sladek, Hiroaki Tokiwa, Hitoshi Shimano, Yasuteru Shigeta
Journal of Chemical Theory and Computation 14 (12) Dec 2018[Refereed]
Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion
Ryuma Sato, Hirotaka Kitoh-Nishioka, Kenji Kamada, Toshiko Mizokuro, Kenji Kobayashi, Yasuteru Shigeta
Journal of Physical Chemistry Letters 9 (22) 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
Concerted Mechanism of Water Insertion and O2 Release during the S4 to S0 Transition of the Oxygen-Evolving Complex in Photosystem II
Mitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Kizashi Yamaguchi
Journal of Physical Chemistry B 122 (25) Jun 2018[Refereed]
On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins
Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Theory and Computation 14 (6) 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]
Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
Yuta Yamamoto, Kenta Takei, Sundaram Arulmozhiraja, Vladimir Sladek, Naoya Matsuo, Song iee Han, Takashi Matsuzaka, Motohiro Sekiya, Takaki Tokiwa, Mitsuo Shoji, Yasuteru Shigeta, Yoshimi Nakagawa, Hiroaki Tokiwa, Hitoshi Shimano
Biochemical and Biophysical Research Communications 499 (2) May 2018[Refereed]
Molecular association model of PPAR alpha and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARM alpha
Yuta Yamamoto, Kenta Takei, Sundaram Arulmozhiraja, Vladimir Sladek, Naoya Matsuo, Song-iee Han, Takashi Matsuzaka, Motohiro Sekiya, Takaki Tokiwa, Mitsuo Shoji, Yasuteru Shigeta, Yoshimi Nakagawa, Hiroaki Tokiwa, Hitoshi Shimano
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 499 (2) May 2018[Refereed]
Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study
Harada, Ryuhei, Mashiko, Takako, Tachikawa, Masanori, Hiraoka, Shuichi, Shigeta, Yasuteru
Physical chemistry chemical physics : PCCP 20 (14) Apr 2018[Refereed]
Nonadiabatic one-electron transfer mechanism for the O–O bond formation in the oxygen-evolving complex of photosystem II
Mitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Kizashi Yamaguchi
Chemical Physics Letters 698 Apr 2018[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
Journal of Physical Chemistry C 122 (10) Mar 2018[Refereed]
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 (26) 2018[Refereed]
Coulomb and CH-φ interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities
Yuma Terai, Ryuma Sato, Takahiro Yumiba, Ryuhei Harada, Kohei Shimizu, Tatsuya Toga, Tomoko Ishikawa-Fujiwara, Takeshi Todo, Shigenori Iwai, Yasuteru Shigeta, Junpei Yamamoto
Nucleic Acids Research 46 (13) 2018[Refereed]
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
Masaki Hada, Shohei Saito, Sei'Ichi Tanaka, Ryuma Sato, Masahiko Yoshimura, Kazuhiro Mouri, Kyohei Matsuo, Shigehiro Yamaguchi, Mitsuo Hara, Yasuhiko Hayashi, Fynn Röhricht, Rainer Herges, Yasuteru Shigeta, Ken Onda, R. J. Dwayne Miller
Journal of the American Chemical Society 139 (44) Nov 2017[Refereed]
Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior
Hajime Yotsuji, Kenji Higashiguchi, Ryuma Sato, Yasuteru Shigeta, Kenji Matsuda
Chemistry - A European Journal 23 (60) Oct 2017[Refereed]
Combining AI-based Modeling and Flexible Docking for Efficient Refinement of Protein-RNA Complexes using PaCS-MD
Hengphasatporn, Kowi, Nitchakan, Darai, Harada, Ryuhei, Shigeta, Yasuteru
PROTEIN SCIENCE 32 (12) Dec 2023
The 8-bromobaicalein alleviated chikungunya-induced musculoskeletal inflammation and reduced the viral load in healthy adult mice
Cao, Van, Loeanurit, Napha, Hengphasatporn, Kowi, Hairani, Rita, Wacharachaisurapol, Noppadol, Prompila, Nantaporn, Wittayalertpanya, Supeecha, Shigeta, Yasuteru, Khotavivattana, Tanatorn, Chavasiri, Warinthorn, Boonyasuppayakorn, Siwaporn
EMERGING MICROBES & INFECTIONS 12 (2) Dec 2023[Refereed]
A sulfonamide chalcone inhibited dengue virus with a potential target at the SAM-binding site of viral methyltransferase.
Van Cao, I Putu Sukanadi, Naphat Loeanurit, Aphinya Suroengrit, Wattamon Paunrat, Vipanee Vibulakhaopan, Kowit Hengphasatporn, Yasuteru Shigeta, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn
Antiviral research 220 Dec 2023
The 8-bromobaicalein inhibited the replication of dengue, and Zika viruses and targeted the dengue polymerase
Siwaporn Boonyasuppayakorn, Thanaphon Saelee, Thao Nguyen Thanh Huynh, Rita Hairani, Kowit Hengphasatporn, Naphat Loeanurit, Van Cao, Vipanee Vibulakhaophan, Panattida Siripitakpong, Parveen Kaur, Justin Jang Hann Chu, Chairat Tunghirun, Opas Choksupmanee, Sarin Chimnaronk, Yasuteru Shigeta, Thanyada Rungrotmongkol, Warinthorn Chavasiri
Scientific Reports 13 (1) Dec 2023
Deciphering the Potential of Multidimensional Carbon Materials for Surface-Enhanced Raman Spectroscopy through Density Functional Theory
Xuke Tang, Naoki Kishimoto, Yasutaka Kitahama, Ting-Ting You, Motoyasu Adachi, Yasuteru Shigeta, Shigenori Tanaka, Ting-Hui Xiao, Keisuke Goda
The Journal of Physical Chemistry Letters Nov 2023
Structure-yeast α-glucosidase inhibitory activity relationship of 9-O-berberrubine carboxylates.
Duy Vu Nguyen, Kowit Hengphasatporn, Ade Danova, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Ryo Fujiki, Yasuteru Shigeta, Thanyada Rungrotmongkol, Warinthorn Chavasiri
Scientific reports 13 (1) Nov 2023
Latrunculin resistance mechanism of non-conventional actin NAP1 uncovered by molecular dynamics simulations
Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei
CYTOSKELETON Epub Oct 2023[Refereed]
Origin of Homochirality in Amino Acids Induced by Lyman-α Irradiation in the Early Stage of the Milky Way
Sato, Akimasa, Shoji, Mitsuo, Watanabe, Natsuki, Boero, Mauro, Shigeta, Yasuteru, Umemura, Masayuki
ASTROBIOLOGY 23 (10) Oct 2023[Refereed]
Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor
Takeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Naomine Yano, Katsuhiro Kusaka, Yoshiaki Kawano, Mamoru Suzuki, Yasuteru Shigeta, Takato Yano, Motoyasu Adachi, Katsuyuki Tanizawa, Toshihide Okajima
ACS Catalysis Sep 2023
Development of an Iron(II) Complex Exhibiting Thermal- and Photoinduced Double Proton-Transfer-Coupled Spin Transition in a Short Hydrogen Bond
Takumi Nakanishi, Yuta Hori, Yasuteru Shigeta, Hiroyasu Sato, Ryoji Kiyanagi, Koji Munakata, Takashi Ohhara, Atsushi Okazawa, Rintaro Shimada, Akira Sakamoto, Osamu Sato
Journal of the American Chemical Society Aug 2023
Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CL^pro through Structure-Based Virtual Screening and Experimental Approaches
Pojtanadithee, Piyatida, Hengphasatporn, Kowi, Suroengrit, Aphinya, Boonyasuppayakorn, Siwaporn, Wilasluck, Patcharin, Deetanya, Peerapon, Wangkanont, Kittikhun, Sukanadi, I Putu, Chavasiri, Warinthorn, Wolschann, Peter, Langer, Thierry, Shigeta, Yasuteru, Maitarad, Phornphimon, Sanachai, Kamonpan, Rungrotmongkol, Thanyada
JOURNAL OF CHEMICAL INFORMATION AND MODELING Epub Aug 2023
A Structural Refinement Technique for Protein-RNA Complexes Based on a Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein
Nitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
Bulletin of the Chemical Society of Japan 96 (7) Jul 2023
Designing Potent α-Glucosidase Inhibitors: A Synthesis and QSAR Modeling Approach for Biscoumarin Derivatives
Thi-Hong-Truc Phan, Kowit Hengphasatporn, Yasuteru Shigeta, Wanting Xie, Phornphimon Maitarad, Thanyada Rungrotmongkol, Warinthorn Chavasiri
ACS Omega 8 (29) Jul 2023
Finite temperature effects on the structural stability of Si-doped HfO₂ using first-principles calculations
Harashima, Y, Koga, H, Ni, Z, Yonehara, T, Katouda, M, Notake, A, Matsui, H, Moriya, T, Si, M. K, Hasunuma, R, Uedono, A, Shigeta, Y
APPLIED PHYSICS LETTERS 122 (26) Jun 2023[Refereed]
A Variety of Initial Velocities in Restarting Molecular Dynamics Simulations Promotes Protein Transitions
Yohei Munei, Yasuteru Shigeta, Ryuhei Harada
Chemistry Letters, 52 (5) Jun 2023[Refereed]
Sulfonylated Indeno[1,2-c]quinoline Derivatives as Potent EGFR Tyrosine Kinase Inhibitors
Hengphasatporn, Kowi, Aiebchun, Thitinan, Mahalapbutr, Panupong, Auepattanapong, Atima, Khaikate, Onnicha, Choowongkomon, Kiattawee, Kuhakarn, Chutima, Meesin, Jatuporn, Shigeta, Yasuteru, Rungrotmongkol, Thanyada
ACS omega 8 (22) Jun 2023
1T/1H-SnS₂ Sheets for Electrochemical CO₂ Reduction to Formate
Kawabe, Yusuke, Ito, Yoshikazu, Hori, Yuta, Kukunuri, Suresh, Shiokawa, Fumiya, Nishiuchi, Tomohiko, Jeong, Samuel, Katagiri, Kosuke, Xi, Zeyu, Li, Zhikai, Shigeta, Yasuteru, Takahashi, Yasufumi
ACS nano 17 (12) Jun 2023
Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses
Munei, Yohei, Hengphasatporn, Kowi, Hori, Yuta, Harada, Ryuhei, Shigeta, Yasuteru
Journal of agricultural and food chemistry 71 (24) Jun 2023
Enantioselective Amino Acid interactions in Solution
Watanabe, Natsuki, Shoji, Mitsuo, Miyagawa, Koichi, Hori, Yuta, Boero, Mauro, Umemura, Masayuki, Shigeta, Yasuteru
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 25 (21) May 2023[Refereed]
Helical Organic and Inorganic Polymers
So Hirata, Yasuteru Shigeta, Sotiris S. Xantheas, Rodney J. Bartlett
The Journal of Physical Chemistry B Apr 2023
Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino Acids
Mitsuo Shoji, Yuya Kitazawa, Akimasa Sato, Natsuki Watanabe, Mauro Boero, Yasuteru Shigeta, Masayuki Umemura
The Journal of Physical Chemistry Letters Apr 2023
Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres
Kudo, Genki, Hirao, Takumi, Yoshino, Ryunosuke, Shigeta, Yasuteru, Hirokawa, Takatsugu
BIOINFORMATICS 39 (4) Apr 2023[Refereed]
Organocatalytic-racemization reaction elucidation of aspartic acid by density functional theory
Watanabe, Natsuki, Hori, Yuta, Shoji, Mitsuo, Boero, Mauro, Shigeta, Yasuteru
CHIRALITY 35 (9) Apr 2023[Refereed]
In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease
Boonthaworn, Kanpong, Hengphasatporn, Kowi, Shigeta, Yasuteru, Chavasiri, Warinthorn, Rungrotmongkol, Thanyada, Ounjai, Puey
PEERJ 11 Apr 2023[Refereed]
Biological advantage of the arrangements of C-phycocyanin chromophores in phycobilisome from the electronic energy transfer viewpoint
Mishima, Kenji, Shoji, Mitsuo, Umena, Yasufumi, Shigeta, Yasuteru
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 96 (4) Apr 2023[Refereed]
Observation of proton-transfer-coupled spin transition by single-crystal neutron-diffraction measurement
Nakanishi, Takumi, Hori, Yuta, Shigeta, Yasuteru, Sato, Hiroyasu, Wu, Shuqi, Kiyanagi, Ryoji, Munakata, Koji, Ohhara, Takashi, Osamu, Sato
Physical Chemistry Chemical Physics 25 (17) Apr 2023[Refereed]
Deprotonation-Induced and Ion-Pairing-Modulated Diradical Properties of Partially Conjugated Pyrrole–Quinone Conjunction
Shinya Sugiura, Takashi Kubo, Yohei Haketa, Yuta Hori, Yasuteru Shigeta, Hayato Sakai, Taku Hasobe, Hiromitsu Maeda
Journal of the American Chemical Society 145 (14) Mar 2023[Refereed]
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score.
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of computer-aided molecular design Mar 2023
シトクロムcの複合体形成過程の再現シミュレーション
下山紘充, 重田, 育照
Journal of Computer Chemistry Japan 21 (4) Mar 2023[Refereed]
Theoretical Characterization of the Electronic and Spin Structures for Iron–Sulfur Cubane in Reduced High-Potential Iron–Sulfur Proteins Using Density Functional Theory
Hori, Yuta, Sato, Ayaka, Yasuteru, Shigeta
Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]
4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価
宗井, 陽平, 堀, 優太, Kowit, Hengphasatporn, 原田, 隆平, 重田, 育照
Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]
有機分子触媒を用いたアミノ酸ラセミ化反応の理論的研究
渡辺, 七都稀, 堀, 優太, 庄司, 光男, 重田, 育照
Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]
X‐ray crystallographic and mutational analysis of the NylC precursor: Catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolase
Seiji Negoro, Naoki Shibata, Dai‐ichiro Kato, Yusuke Tanaka, Kengo Yasuhira, Keisuke Nagai, Shohei Oshima, Yoko Furuno, Risa Yokoyama, Kaito Miyazaki, Masahiro Takeo, Kowit Hengphasatporn, Yasuteru Shigeta, Young‐Ho Lee, Yoshiki Higuchi
The FEBS Journal Feb 2023
Theoretical Study on the Regulating Mechanism of the Transition Between the Open-closed State of hCtBP2: A Combined Molecular Dynamics and Quantum Mechanical Interaction Analysis
Yamamoto, Yuta, Shigeta, Yasuteru
CHEMISTRY LETTERS 52 (3) Feb 2023[Refereed]
Design of electron-donating group substituted 2-PAM analogs as antidotes for organophosphate insecticide poisoning
Nalinee Kongkaew, Kowit Hengphasatporn, Yuwanda Injongkol, Pitchayathida Mee-udorn, Liyi Shi, Panupong Mahalapbutr, Phornphimon Maitarad, Ryuhei Harada, Yasuteru Shigeta, Thanyada Rungrotmongkol, Alisa S. Vangnai
RSC Advances 13 (46) 2023
New insights into the oxidation process from neutron and X-ray crystal structures of an O₂-sensitive [NiFe]-hydrogenase
Takeshi Hiromoto, Koji Nishikawa, Seiya Inoue, Hideaki Ogata, Yuta Hori, Katsuhiro Kusaka, Yu Hirano, Kazuo Kurihara, Yasuteru Shigeta, Taro Tamada, Yoshiki Higuchi
Chemical Science 2023
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods
Harada, R., Morita, R., Shigeta, Y.
Journal of Chemical Information and Modeling 63 (1) 2023
Specific zinc binding to heliorhodopsin
Masanori Hashimoto, Koichi Miyagawa, Manish Singh, Kota Katayama, Mitsuo Shoji, Yuji Furutani, Yasuteru Shigeta, Hideki Kandori
Physical Chemistry Chemical Physics 25 (4) 2023
Lichen-Derived Diffractaic Acid Inhibited Dengue Virus Replication in a Cell-Based System
Naphat Loeanurit, Truong Lam Tuong, Van-Kieu Nguyen, Vipanee Vibulakhaophan, Kowit Hengphasatporn, Yasuteru Shigeta, Si Xian Ho, Justin Jang Hann Chu, Thanyada Rungrotmongkol, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn
Molecules 28 (3) Jan 2023
N-Containing α-Mangostin Analogs via Smiles Rearrangement as the Promising Cytotoxic, Antitrypanosomal, and SARS-CoV-2 Main Protease Inhibitory Agents
Nan Yadanar Lin Pyae, Arnatchai Maiuthed, Wongsakorn Phongsopitanun, Bongkot Ouengwanarat, Warongrit Sukma, Nitipol Srimongkolpithak, Jutharat Pengon, Roonglawan Rattanajak, Sumalee Kamchonwongpaisan, Zin Zin Ei, Preedakorn Chunhacha, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Supakarn Chamni
Molecules 28 (3) Jan 2023
Characterization of the Geometrical and Electronic Structures of the Active Site and Its Effects on the Surrounding Environment in Reduced High-Potential Iron–Sulfur Proteins Investigated by the Density Functional Theory Approach
Sato, Ayaka, Hori, Yuta, Yasuteru, Shigeta
Inorganic Chemistry 62 (5) Jan 2023[Refereed]
Dynamical interaction analysis of proteins by a random forest-fragment molecular orbital (RF-FMO) method and application to Src tyrosine kinase
Yuta Yamamoto, Shogo Nakano, Yasuteru Shigeta
Bulletin of the Chemical Society of Japan 96 (1) Dec 2022
Systematic Search for Stabilizing Dopants in ZrO₂ and HfO₂ Using First-Principles Calculations
Yosuke Harashima, Hiroaki Koga, Zeyuan Ni, Takehiro Yonehara, Michio Katouda, Akira Notake, Hidefumi Matsui, Tsuyoshi Moriya, Mrinal Kanti Si, Ryu Hasunuma, Akira Uedono, Yasuteru Shigeta
2022 International Symposium on Semiconductor Manufacturing (ISSM) Dec 2022
Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases
Yuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Chai Gopalasingam, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Yoshikazu Ishii, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori Shintani
Nature Communications 13 (1) Dec 2022
Autism-associated mutation in Hevin/Sparcl1 induces endoplasmic reticulum stress through structural instability
Takumi Taketomi, Takunori Yasuda, Rikuri Morita, Jaehyun Kim, Yasuteru Shigeta, Cagla Eroglu, Ryuhei Harada, Fuminori Tsuruta
Scientific Reports 12 (1) Dec 2022
Reaction Mechanism of Ancestral l-Lys α-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis
Tomoharu Motoyama, Yuta Yamamoto, Chiharu Ishida, Fumihito Hasebe, Yui Kawamura, Yasuteru Shigeta, Sohei Ito, Shogo Nakano
ACS Omega 7 (48) Nov 2022
Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO
Hengphasatporn, Kowi, Harada, Ryuhei, Wilasluck, Patcharin, Deetanya, Peerapon, Sukandar, Edwin R, Chavasiri, Warinthorn, Suroengrit, Aphinya, Boonyasuppayakorn, Siwaporn, Rungrotmongkol, Thanyada, Wangkanont, Kittikhun, Shigeta, Yasuteru
Scientific reports 12 (1) Oct 2022
Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase
Mitsuo Shoji, Takeshi Murakawa, Shota Nakanishi, Mauro Boero, Yasuteru Shigeta, Hideyuki Hayashi, Toshihide Okajima
CHEMICAL SCIENCE 13 (36) Sep 2022
Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic Syntheses
Mitsuo, Shoji, Natsuki, Watanabe, Hori, Yuta, Kenji, Furuya, Masayuki, Umemura, Mauro, Boero, Yasuteru, Shigeta
Astrobiology 22 (9) Sep 2022[Refereed]
Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in Space
Hori, Yuta, Nakamura, Honami, Sakawa, Takahide, Natsuki, Watanabe, Kayanuma, Megumi, Mitsuo, Shoji, Masayuki, Umemura, Yasuteru, Shigeta
Astrobiology 22 (11) Sep 2022[Refereed]
The role of ATP in solubilizing RNA-binding protein fused in sarcoma
Aida, Hayato, Shigeta, Yasuteru, Harada, Ryuhei
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 90 (8) Aug 2022[Refereed]
Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling 62 (14) Jul 2022
Heme-bound tyrosine vibrations in hemoglobin M: Resonance Raman, crystallography, and DFT calculation
Nagatomo, Shigenori, Shoji, Mitsuo, Terada, Takuto, Nakatani, Kiyoharu, Shigeta, Yasuteru, Hirota, Shun, Yanagisawa, Sachiko, Kubo, Minoru, Kitagawa, Teizo, Nagai, Masako, Ohki, Mio, Park, Sam-Yong, Shibayama, Naoya
BIOPHYSICAL JOURNAL 121 (14) Jun 2022[Refereed]
Semi-Synthesis of N-Aryl Amide Analogs of Piperine from Piper nigrum and Evaluation of Their Antitrypanosomal, Antimalarial, and Anti-SARS-CoV-2 Main Protease Activities
Rattanaporn Wansri, Aye Chan Khine Lin, Jutharat Pengon, Sumalee Kamchonwongpaisan, Nitipol Srimongkolpithak, Roonglawan Rattanajak, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Kowit Hengphasatporn, Yasuteru Shigeta, Jatupol Liangsakul, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Taksina Chuanasa, Wanchai De-eknamkul, Supot Hannongbua, Thanyada Rungrotmongkol, Supakarn Chamni
Molecules 27 (9) Apr 2022
Halogenated baicalein as a promising antiviral agent toward SARS-CoV-2 main protease
Hengphasatporn, Kowi, Wilasluck, P, Deetanya, P, Wangkanont, K, Chavasiri, W, Visitchanakun, P, Leelahavanichkul, A, Paunrat, W, Boonyasuppayakorn, S, Rungrotmongkol, T, Hannongbua, S, Shigeta, Yasuteru
JOURNAL OF CHEMICAL INFORMATION AND MODELING 62 (6) Mar 2022[Refereed]
Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD
Aida, Hayato, Shigeta, Yasuteru, Harada, Ryuhei
Materials 15 (4) Feb 2022[Refereed]
Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1
Yasuda, Takunori, Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei
Journal of molecular biology 434 (2) Jan 2022
Theoretical Analysis of Structure of Antibody Light Chain Tetramer
LIAN Duan, HENGPHASATPORN Kowi, SHIGETA Y
Journal of Computer Chemistry, Japan 21 (4) 2022
Investigation of Computational Methods for Membrane Permeability of Middle-Sized Molecules
TAKAHASHI T, HENGPHASATPORN K, HARADA R, SHIGETA Y
Journal of Computer Chemistry, Japan 21 (4) 2022
Corrigendum to: Chirality without Stereoisomers: Insight from the Helical Response of Bond Electrons (ChemPhysChem, (2021), 22, 19, (1989-1995), 10.1002/cphc.202100397)
Xu, T., Nie, X., Li, S., Yang, Y., Fr{"u}chtl, H., van Mourik, T., Kirk, S.R., Paterson, M.J., Shigeta, Y., Jenkins, S.
ChemPhysChem 23 (5) 2022
Evaluation of an Appropriate Standard Hydrogen Electrode Potential for Computing Redox Potentials of Catechins with Density Functional Theory
Duan, L., Takano, Y., Shigeta, Y.
Chemistry Letters 51 (7) 2022
Design, synthesis, in vitro, in silico, and SAR studies of flavone analogs towards anti-dengue activity
Patigo, A., Hengphasatporn, K., Cao, V., Paunrat, W., Vijara, N., Chokmahasarn, T., Maitarad, P., Rungrotmongkol, T., Shigeta, Y., Boonyasuppayakorn, S., Khotavivattana, T.
Scientific Reports 12 (1) 2022
Pharmacophore-Based Virtual Screening and Experimental Validation of Pyrazolone-Derived Inhibitors toward Janus Kinases
Sanachai, K., Mahalapbutr, P., Hengphasatporn, K., Shigeta, Y., Seetaha, S., Tabtimmai, L., Langer, T., Wolschann, P., Kittikool, T., Yotphan, S., Choowongkomon, K., Rungrotmongkol, T.
ACS Omega 7 (37) 2022
Vacancy-type defects in TiN/ZrO₂/TiN capacitors probed by monoenergetic positron beams
Uedono, A., Takahashi, N., Hasunuma, R., Harashima, Y., Shigeta, Y., Ni, Z., Matsui, H., Notake, A., Kubo, A., Moriya, T., Michishio, K., Oshima, N., Ishibashi, S.
Thin Solid Films 762 2022
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace
Yasuda, T., Morita, R., Shigeta, Y., Harada, R.
Journal of Chemical Information and Modeling 62 (23) 2022
Calculation of the permeability coefficients of small molecules through lipid bilayers by free-energy reaction network analysis following the explicit treatment of the internal conformation of the solute
Yuki Mitsuta, Toshio Asada, Yasuteru Shigeta
Physical Chemistry Chemical Physics 2022
Supramolecular polymerization of thiobarbituric acid naphthalene dye
Takumi Aizawa, Maika Kawaura, Takashi Kajitani, Kowit Hengphasatporn, Yasuteru Shigeta, Shiki Yagai
Chemical Communications 58 (67) 2022
Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiation
Li, Zi, Yang, Yong, Xu, Tianlv, Fruchtl, Herber, van Mourik, Tanja, Paterson, Martin J, Shigeta, Yasuteru, Kirk, Steven R, Jenkins, Samantha
JOURNAL OF COMPUTATIONAL CHEMISTRY 43 (3) Jan 2022[Refereed]
Residue Folding Degree-Relationship to Secondary Structure Categories and Use as Collective Variable
Sladek, Vladimir, Harada, Ryuhei, Shigeta, Yasuteru
International Journal of Molecular Sciences 22 (23) Dec 2021[Refereed]
Recent developments of computational methods for pKa pre-diction based on electronic structure theory with solvation models
Fujiki, R, Matsui, T, Shigeta, Yasuteru, Nakano, H, Yoshida, N
Multidisciplinary Scientific Journal 4 (4) Dec 2021[Refereed]
A Free Energy Landscape Analysis of Calmodulin Obtained from an NMR-data Utilized Multi-scale Divide-and-conquer Molecular Dynamics Simulation
Shimoyama, Hiromitsu, Shigeta, Yasuteru
LIFE-BASEL 11 (11) Dec 2021[Refereed]
Effects of mechanical grinding on the phase behavior and anhydrous proton conductivity of imidazolium hydrogen succinate
Dekura, Shun, Sunairi, Yoshiya, Okamoto, Kei, Takeiri, Fumitaka, Kobayashi, Genki, Hori, Yuta, Shigeta, Yasuteru, Mori, Hatsumi
Solid State Ionics 372 Dec 2021[Refereed]
Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations
Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei
The journal of physical chemistry. B 125 (46) Nov 2021
Control of chirality, bond flexing and anharmonicity in an electric field
Li, Zi, Nie, Xing, Xu, Tianlv, Li, Shuman, Yang, Yong, Fruchtl, Herber, van Mourik, Tanja, Kirk, Steven R, Paterson, Martin J, Shigeta, Yasuteru, Jenkins, Samantha
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 121 (22) Nov 2021[Refereed]
A post-process to estimate an approximated minimal free energy path based on local centroids
Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei
CHEMICAL PHYSICS LETTERS 782 Nov 2021[Refereed]
Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region
Xie, Cheng, Shimoyama, Hiromitsu, Yamanaka, Masaru, Nagao, Satoshi, Komori, Hirofumi, Shibata, Naoki, Higuchi, Yoshiki, Shigeta, Yasuteru, Hirota, Shun
RSC ADVANCES 11 (59) Nov 2021[Refereed]
Alkyne-Tagged Apigenin, a Chemical Tool to Navigate Potential Targets of Flavonoid Anti-Dengue Leads
Hengphasatporn, Kowi, Kaewmalai, Benyapa, Jansongsaeng, Somruedee, Badavath, Vishnu Nayak, Saelee, Thanaphon, Chokmahasarn, Thamonwan, Khotavivattana, Tanatorn, Shigeta, Yasuteru, Rungrotmongkol, Thanyada, Boonyasuppayakorn, Siwaporn
MOLECULES 26 (22) Nov 2021[Refereed]
Chirality without Stereoisomers: Insight from the Helical Response of Bond Electrons
Xu, Tianlv, Nie, Xing, Li, Shuman, Yang, Yong, Fruchtl, Herber, van Mourik, Tanja, Kirk, Steven R, Paterson, Martin J, Shigeta, Yasuteru, Jenkins, Samantha
CHEMPHYSCHEM 22 (19) Oct 2021[Refereed]
Integrate in silico studies on the role of nicotinamide adenine dinucleotide (NADH) binding in activating C-terminal binding protein 2 (CtBP2)
Tsukasa, Aoyagi, Yoshino, Ryunosuke, Yuki, Mitsuta, Rikuri, Morita, Ryuhei, Harada, Yasuteru, Shigeta
Chemistry Letters 51 (1) Oct 2021[Refereed]
Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics Calculations
Yanagi, Koki, Mitsuta, Yuki, Takaoka, Kenta, Takahashi, Teruyuki, Hengphasatporn, Kowi, Harada, Ryuhei, Shigeta, Yasuteru
Chemistry Letters 50 (12) Sep 2021[Refereed]
Phosphorylation in the accessory domain of yeast histone chaperone protein 1 exposes the nuclear export signal sequence
Ashida, Sho, Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Epub (2) Sep 2021[Refereed]
Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins
Yasuda, Takunori, Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 17 (9) Sep 2021[Refereed]
On-Demand Chirality Transfer of Human Serum Albumin to Bis(thiophen-2-yl)hexafluorocyclopentenes through Their Photochromic Ring Closure
Saeki, Yuri, Kayanuma, Megumi, Nitta, Aki, Shigeta, Yasuteru, Kawamura, Izuru, Nakagawa, Tetsuya, Ubukata, Takashi, Yokoyama, Yasushi
JOURNAL OF ORGANIC CHEMISTRY 86 (18) Sep 2021[Refereed]
Solvophobicity-directed assembly of microporous molecular crystals
Yamagishi, Hiroshi, Tsunoda, Monika, Iwai, Kohei, Hengphasatporn, Kowi, Shigeta, Yasuteru, Sato, Hiroyasu, Yamamoto, Yohei
COMMUNICATIONS CHEMISTRY 4 (1) Aug 2021
Could London Dispersion Force Control Regioselective (2 + 2) Cyclodimerizations of Benzynes? YES: Application to the Synthesis of Helical Biphenylenes
Takashi Ikawa, Yuta Yamamoto, Akito Heguri, Yutaka Fukumoto, Tomonari Murakami, Akira Takagi, Yuto Masuda, Kenzo Yahata, Hiroshi Aoyama, Yasuteru Shigeta, Hiroaki Tokiwa, Shuji Akai
Journal of the American Chemical Society 143 (29) Jul 2021
pyProGA-A PyMOL plugin for protein residue network analysis
Sladek, Vladimir, Yamamoto, Yuta, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru, Sladek, Vladimir
PLOS ONE 16 (7) Jul 2021[Refereed]
A Practical Prediction of LogP(o/w) through Semiempirical Electronic Structure Calculations with Dielectric Continuum Model
Takahashi, Teruyuki, Matsui, Toru, Hengphasatporn, Kowi, Shigeta, Yasuteru
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 94 (7) Jul 2021
Ion-pairing pi-electronic systems: ordered arrangement and noncovalent interactions of negatively charged porphyrins
Yoshifumi Sasano, Hiroki Tanaka, Yohei Haketa, Yoichi Kobayashi, Yukihide Ishibashi, Tatsuki Morimoto, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Tsuyoshi Asahi, Hiromitsu Maeda
CHEMICAL SCIENCE 12 (28) Jul 2021
Proton Conduction Mechanism for Anhydrous Imidazolium Hydrogen Succinate Based on Local Structures and Molecular Dynamics
Hori, Yuta, Dekura, Shun, Sunairi, Yoshiya, Ida, Tomonori, Mizuno, Motohiro, Mori, Hatsumi, Shigeta, Yasuteru
The Journal of Physical Chemistry Letters 12 (22) Jun 2021[Refereed]
Comparison between the Light-Harvesting Mechanisms of Type-I Photosynthetic Reaction Centers of Heliobacteria and Photosystem I: Pigment Site Energy Distribution and Exciton State.
Akihiro Kimura, Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru Itoh
The journal of physical chemistry. B 125 (15) Apr 2021
Comprehensive Predictions of Secondary Structures for Comparative Analysis in Different Species
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Structural Biology 213 (2) Apr 2021
Structural and functional characterization of nylon hydrolases
Negoro, Seiji, Kato, Dai-Ichiro, Ohki, Taku, Yasuhira, Kengo, Kawashima, Yasuyuki, Nagai, Keisuke, Takeo, Masahiro, Shibata, Naoki, Kamiya, Katsumasa, Shigeta, Yasuteru
Methods in enzymology 648 Apr 2021[Refereed]
Structure, solubility, and permeability relationships in a diverse middle molecule library
Miyachi, Hiroyuki, Kanamitsu, Kayoko, Ishii, Mayumi, Watanabe, Eri, Katsuyama, Akira, Otsuguro, Satoko, Yakushiji, Fumika, Watanabe, Mizuki, Matsui, Kouhei, Sato, Yukina, Shuto, Satoshi, Tadokoro, Takashi, Kita, Shunsuke, Matsumaru, Takanori, Matsuda, Akira, Hirose, Tomoyasu, Iwatsuki, Masato, Shigeta, Yasuteru, Nagano, Tetsuo, Kojima, Hirotatsu, Ichikawa, Satoshi, Sunazuka, Toshiaki, Maenaka, Katsumi
Bioorganic & medicinal chemistry letters 37 Apr 2021[Refereed]
Weak O2 binding and strong H2O2 binding at the non-heme diiron center of trypanosome alternative oxidase
Yamasaki, Sotaro, Shoji, Mitsuo, Kayanuma, Megumi, Sladek, Vladimir, Inaoka, Daniel Ken, Matsuo, Yuichi, Shiba, Tomoo, Young, Luke, Moore, Anthony L, Kita, Kiyoshi, Shigeta, Yasuteru
Biochimica et biophysica acta. Bioenergetics 1862 (4) Apr 2021[Refereed]
Theoretical Prediction of the Redox Potential of Catechins with First Principle Calculation
Duan, Lian, Takano, Yu, Shigeta, Yasuteru
JOURNAL OF COMPUTER CHEMISTRY-JAPAN 20 (4) Mar 2021[Refereed]
環状ペプチドの膜透過における溶媒和自由エネルギー計算
栁, 昂輝, 原田, 隆平, 満田, 祐樹, 重田育照
Journal of Computational Chemistry Japan 19 (4) Mar 2021[Refereed]
Comprehensive Analysis of Intrinsically Disordered Regions to Elucidate Their Physical Properties using a Modified Parameter
Aida, Hayato, Harada, Ryuhei, Shigeta, Yasuteru, Tomii, Kentaro
BIOPHYSICAL JOURNAL 120 (3::1) Feb 2021[Refereed]
Computational Analysis Reveals a Critical Point Mutation in the -Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Virus
Yamamoto, Yuta, Nakano, Shogo, Seki, Fumio, Shigeta, Yasuteru, Ito, Sohei, Tokiwa, Hiroaki, Takeda, Makoto
Molecules (Basel, Switzerland) 26 (5) Feb 2021[Refereed]
Proton conduction mechanism in proton-conducting PVPA-xIm composites investigated by theoretical approaches
Hori, Yuta, Suetake, Toshiya, Ida, Tomonori, Mizuno, Motohiro, Shigeta, Yasuteru
The Journal of Computer Chemistry, Japan 19 (4) Feb 2021[Refereed]
Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification
Deetanya, Peerapon, Hengphasatporn, Kowi, Wilasluck, Patcharin, Shigeta, Yasuteru, Rungrotmongkol, Thanyada, Wangkanont, Kittikhun
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 19 2021[Refereed]
Estimation of the relative contributions to the electronic energy transfer rates based on Forster theory: The case of C-phycocyanin chromophores
Mishima, Kenji, Shoji, Mitsuo, Umena, Yasufumi, Boero, Mauro, Shigeta, Yasuteru
Biophysics and physicobiology 18 2021[Refereed]
In Silico Mutational Analyses Reveal Different Ligand-Binding Abilities of Double Pockets of Medaka Fish Taste Receptor Type 1 Essential for Efficient Taste Recognitions
Hayato Aida, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Physical Chemistry Chemical Physics 23 (36) 2021
AnalysisFMO Toolkit: A PyMOL Plugin for 3D-Visualization of Interaction Energies in Proteins (3D-VIEP) Calculated by the FMO Method
Takaki Tokiwa, Shogo Nakano, Hiroaki Tokiwa, Yasuteru Shigeta
Recent Advances of the Fragment Molecular Orbital Method 2021
Linear Combination of Molecular Orbitals of Fragments (FMO-LCMO) Method: Its Application to Charge Transfer Studies
Hirotaka Kitoh-Nishioka, Ryuma Sato, Yasuteru Shigeta, Koji Ando
Recent Advances of the Fragment Molecular Orbital Method 2021
Open-Architecture Program of Fragment Molecular Orbital Method for Massive Parallel Computing (OpenFMO) with GPU Acceleration
Hirotaka Kitoh-Nishioka, Hiroaki Umeda, Yasuteru Shigeta
Recent Advances of the Fragment Molecular Orbital Method 2021
Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins
Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei
Bulletin of the Chemical Society of Japan 94 (1) Jan 2021[Refereed]
The Folding of Trp-cage is Regulated by Stochastic Flip of the Side Chain of Tryptophan
Yasuda, Takunori, Shigeta, Yasuteru, Harada, Ryuhei
CHEMISTRY LETTERS 50 (1) Jan 2021[Refereed]
Conformation-Changeable π-Electronic Systems with Metastable Bent-Core Conformations and Liquid-Crystalline-State Electric-Field-Responsive Properties
Nakamura, Kazuto, Sugiura, Shinya, Araoka, Fumito, Aya, Satoshi, Takanishi, Yoichi, Watanabe, Go, Sato, Ryuma, Shigeta, Yasuteru, Maeda, Hiromitsu
Organic letters 23 (2) Jan 2021[Refereed]
Agonist and Antagonist-Diverted Twisting Motions of a Single TRPV1 Channel
Fujimura, Shoko, Mio, Kazuhiro, Kuramochi, Masahiro, Sekiguchi, Hiroshi, Ikezaki, Keigo, Mio, Muneyo, Hengphasatporn, Kowit, Shigeta, Yasuteru, Kubo, Tai, Sasaki, Yuji C
JOURNAL OF PHYSICAL CHEMISTRY B 124 (51) Dec 2020[Refereed]
Molecular Mechanism for the Actin-Binding Domain of alpha-Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis Experiments
Morita, Rikuri, Nakano, Kentaro, Shigeta, Yasuteru, Harada, Ryuhei
JOURNAL OF PHYSICAL CHEMISTRY B 124 (39) Oct 2020[Refereed]
Unique protonation states of aspartate and topaquinone in the active site of copper amine oxidase
Shoji, Mitsuo, Murakawa, Takeshi, Boero, Mauro, Shigeta, Yasuteru, Hayashi, Hideyuki, Okajima, Toshihide
RSC ADVANCES 10 (63) Oct 2020[Refereed]
Molecular Motions of Imidazole in Poly(vinylphosphonic acid)-imidazole Composites Investigated by Molecular Dynamics Simulations
Hori, Yuta, Suetake, Toshiya, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, Motohiro
Chemistry Letters 50 (1) Oct 2020[Refereed]
Molecular Motions of Imidazole in Poly(vinylphosphonic acid)-imidazole Composites Investigated by Molecular Dynamics Simulations
Hori, Yuta, Suetake, Toshiya, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, Motohiro
Chemistry Letters 50 (1) Oct 2020[Refereed]
Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method
Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Koji Ando
The Journal of chemical physics 153 (10) Sep 2020[Refereed]
Dibromopinocembrin and Dibromopinostrobin Are Potential Anti-Dengue Leads with Mild Animal Toxicity
Siwaporn Boonyasuppayakorn, Thanaphon Saelee, Peerapat Visitchanakun, Asada Leelahavanichkul, Kowit Hengphasatporn, Yasuteru Shigeta, Thao Nguyen Thanh Huynh, Justin Jang Hann Chu, Thanyada Rungrotmongkol, Warinthorn Chavasiri
Molecules 25 (18) Sep 2020[Refereed]
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling 60 (8) Aug 2020[Refereed]
Reaction mechanism of: N-cyclopropylglycine oxidation by monomeric sarcosine oxidase
Mitsuo Shoji, Yukihiro Abe, Mauro Boero, Yasuteru Shigeta, Yoshiaki Nishiya
Physical Chemistry Chemical Physics 22 (29) Aug 2020[Refereed]
Self-Associating Curved π-Electronic Systems with Electron-Donating and Hydrogen-Bonding Properties
Haketa, Yohei, Miyasue, Mika, Kobayashi, Yoichi, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Tamai, Naoto, Maeda, Hiromitsu
Journal of the American Chemical Society 142 (38) Aug 2020[Refereed]
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics
Yasuda, Takunori, Shigeta, Yasuteru, Harada, Ryuhei
Journal of chemical information and modeling 60 (8) Aug 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]
The dynamics of S-adenosyl-methionine and S-adenosyl-homocysteine in Mouse Dnmt1 is driven by their structural flexibilities
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
Chemistry Letters 49 (7) Jul 2020[Refereed]
Analytical Method Using a Scaled Hypersphere Search for High-Dimensional Metadynamics Simulations
Yuki Mitsuta, Yasuteru Shigeta
Journal of Chemical Theory and Computation 16 (6) 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]
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 16 (10) Jun 2020[Refereed]
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]
Understanding the detection mechanisms and ability of molecular hydrogen on three-dimensional bicontinuous nanoporous reduced graphene oxide
Yoshikazu Ito, Megumi Kayanuma, Yasuteru Shigeta, Jun Ichi Fujita, Yoichi Tanabe
Materials 13 (10) May 2020[Refereed]
Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active site
Yasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki Hayashi
JOURNAL OF BIOCHEMISTRY 167 (4) Apr 2020[Refereed]
Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active site
Yasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki Hayashi
Journal of biochemistry 167 (4) Apr 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]
Target identification using homopharma and network-based methods for predicting compounds against dengue virus-infected cells
Kowit Hengphasatporn, Kitiporn Plaimas, Apichat Suratanee, Peemapat Wongsriphisant, Jinn Moon Yang, Yasuteru Shigeta, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol
Molecules 25 (8) Apr 2020[Refereed]
Split Conformation of Chaetomium Thermophilum Hsp104 Disaggregase
Inoue Yosuke, Hanazono Yuya, Noi Kentaro, Kawamoto Akihiro, Kimatsuka Masato, Harada Ryuhei, Takeda Kazuki, Iwamasa Natsuki, Noguchi Keiichi, Shigeta Yasuteru, Namba Keiichi, Ogura Teru, Miki Kunio, Shinohara Kyosuke, Yohda Masafumi
Science Advances 29 (7) Apr 2020[Refereed]
Local Structures and Dynamics of Imidazole Molecules in Poly(vinylphosphonic acid)-Imidazole Composite Investigated by Molecular Dynamics
Yuta Hori, Toshiya Suetake, Yoshihito Shiota, Kazunari Yoshizawa, Yasuteru Shigeta, Tomonori Ida, Motohiro Mizuno
ACS APPLIED POLYMER MATERIALS 2 (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]
Multiple Virtual Screening Strategies for the Discovery of Novel Compounds Active Against Dengue Virus: A Hit Identification Study
Kowit Hengphasatporn, Arthur Garon, Peter Wolschann, Thierry Langer, Shigeta Yasuteru, Thao N. T. Huynh, Warinthorn Chavasiri, Thanaphon Saelee, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol
SCIENTIA PHARMACEUTICA 88 (1) Mar 2020[Refereed]
Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem i
Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru Itoh, Akihiro Kimura
Journal of Physical Chemistry B 124 (2) Jan 2020[Refereed]
Photosynergetic Effects on Triplet–Triplet Annihilation Upconversion Processes in Solid Studied by Theory and Experiments
Kenji Kamada, Ryuma Sato, Toshiko Mizokuro, Hirotaka Kito-Nishioka, Yasuteru Shigeta
Photosynergetic Responses in Molecules and Molecular Aggregates 2020
Role of the Propionic Acid Side-Chain of C-Phycocyanin Chromophores in the Excited States for the Photosynthesis Process
Mishima,Kenji, Shoji,Mitsuo, Umena,Yasufumi, Boero,Mauro, Shigeta,Yasuteru
Bulletin of the Chemical Society of Japan 93 (12) 2020[Refereed]
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) Jan 2020[Refereed]
Why are lopinavir and ritonavir effective against the newly emerged coronavirus 2019? Atomistic insights into the inhibitory mechanisms
Bodee Nutho, Panupong Mahalapbutr, Kowit Hengphasatporn, Nawanwat Chainuwong Pattaranggoon, Nattapon Simanon, Yasuteru Shigeta, Supot Hannongbua, Thanyada Rungrotmongkol
Biochemistry 59 (18) 2020[Refereed]
Estimation of acid dissociation constants (PKA) of N-containing heterocycles in DMSO and transferability of Gibbs free energy in different solvent conditions
Kowit Hengphasatporn, Toru Matsui, Yasuteru Shigeta
Chemistry Letters 49 (3) 2020[Refereed]
Intramolecular mode coupling of the isotopomers of water: A non-scalar charge density-derived perspective
Tian Tian, Tianlv Xu, Steven R. Kirk, Ian Tay Rongde, Yong Boon Tan, Sergei Manzhos, Yasuteru Shigeta, Samantha Jenkins
Physical Chemistry Chemical Physics 22 (4) 2020[Refereed]
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
Journal of Chemical Information and Modeling 59 (12) Dec 2019[Refereed]
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
Harada, Ryuhei, Sladek, Vladimir, Shigeta, Yasuteru
Journal of chemical information and modeling 59 (12) Dec 2019[Refereed]
Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
Journal of Molecular Graphics and Modelling 92 Nov 2019[Refereed]
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency
Ryuhei Harada, Yasuteru Shigeta
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
Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
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
Tatsuhiko Ohto, Mayank Dodia, Jianhang Xu, Sho Imoto, Fujie Tang, Frederik Zysk, Thomas D. Kühne, Yasuteru Shigeta, Mischa Bonn, Xifan Wu, Yuki Nagata
Journal of Physical Chemistry Letters 10 (17) 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
Mitsuo Shoji, Hiroshi Isobe, Jian Ren Shen, Michihiro Suga, Fusamichi Akita, Koichi Miyagawa, Yasuteru Shigeta, Kizashi Yamaguchi
Chemical Physics Letters 730 Sep 2019[Refereed]
First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface
Megumi Kayanuma, Mitsuo Shoji, Kenji Furuya, Katsumasa Kamiya, Yuri Aikawa, Masayuki Umemura, Yasuteru Shigeta
Journal of Physical Chemistry A 123 (26) Jul 2019[Refereed]
Pyrrole-Based π-System–Pt^II Complexes: Chiroptical Properties and Excited-State Dynamics with Microsecond Triplet Lifetimes
Goki Hirata, Yoichi Kobayashi, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Hiromitsu Maeda
Chemistry - A European Journal 25 (37) Jul 2019[Refereed]
Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
Journal of molecular graphics & modelling 92 Jul 2019[Refereed]
First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface
Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Kamiya, Katsumasa, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
The journal of physical chemistry. A 123 (26) Jul 2019[Refereed]
Pyrrole-Based π-System-Pt Complexes: Chiroptical Properties and Excited-State Dynamics with Microsecond Triplet Lifetimes
Hirata, Goki, Kobayashi, Yoichi, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
Chemistry (Weinheim an der Bergstrasse, Germany) 25 (37) Jul 2019[Refereed]
Reaction mechanism of non-enzymatic stereoselective formation of wine lactone
Akane Kyan, Megumi Kayanuma, Mitsuo Shoji, Yasuteru Shigeta
Chemical Physics Letters 725 Jun 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) Jun 2019[Refereed]
Numerical investigation of the nano-scale solutal Marangoni convections
Y. Imai, T. Yamamoto, A. Sekimoto, Y. Okano, R. Sato, Y. Shigeta
Journal of the Taiwan Institute of Chemical Engineers 98 (SI) May 2019[Refereed]
Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical Insight
Tianlv Xu, Jia Hui Li, Roya Momen, Wei Jie Huang, Steven Robert Kirk, Yasuteru Shigeta, Samantha Jenkins
Journal of the American Chemical Society 141 (13) Apr 2019[Refereed]
Photosubstitution Reaction of cis-[Ru(bpy) 2 (CH 3 CN) 2 ] ²⁺ and cis-[Ru(bpy) 2 (NH 3 ) 2 ] ²⁺ in Aqueous Solution via Monoaqua Intermediate
Megumi Kayanuma, Mitsuo Shoji, Yasuteru Shigeta
Journal of Physical Chemistry A 123 (13) Apr 2019[Refereed]
In Silico Structural Modeling and Analysis of Elongation Factor-1 Alpha and Elongation Factor-like Protein
Kotaro Sakamoto, Megumi Kayanuma, Yuji Inagaki, Tetsuo Hashimoto, Yasuteru Shigeta
ACS Omega 4 (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]
New assay method based on Raman spectroscopy for enzymes reacting with gaseous substrates
Yuka Kawahara-Nakagawa, Koji Nishikawa, Satoru Nakashima, Shota Inoue, Takehiro Ohta, Takashi Ogura, Yasuteru Shigeta, Katsuyuki Fukutani, Tatsuhiko Yagi, Yoshiki Higuchi
Protein Science 28 (3) Mar 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]
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
Kieu My Bui, Jun Ichi Iwata, Yoshihiro Kangawa, Kenji Shiraishi, Yasuteru Shigeta, Atsushi Oshiyama
Journal of Crystal Growth 507 Feb 2019[Refereed]
Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations
Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta
Journal of Chemical Information and Modeling 59 (1) Jan 2019[Refereed]
Theoretical study of the photodissociation reaction of methanol
Megumi Kayanuma, Mitsuo Shoji, Kenji Furuya, Yuri Aikawa, Masayuki Umemura, Yasuteru Shigeta
Chemical Physics Letters 714 Jan 2019[Refereed]
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]
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[Refereed]
Structural Changes in the Trinuclear Copper Center upon the Reduction of Bilirubin Oxidase (BOD)
T. Tokiwa, M. Shoji, V. Sladek, N. Shibata, Y. Higuchi, K. Kataoka, Y. Shigeta, F Misaizu
Molecules 24 (76) Jan 2019[Refereed]
Developments of Rare Event Sampling Methods for Proteins
Ryuhei Harada, Sladek Vladimir, Yasuteru Shigeta
JOURNAL OF COMPUTER CHEMISTRY-JAPAN 18 (5) 2019[Refereed]
New Assay Method Based on Raman Spectroscopy for Enzymes Reacting with Gaseous Substrates
Kawahara-Nakagawa, Yuka, Nishikawa, Koji, Nakashima, Satoru, Inoue, Shota, Ohta, Takehiro, Ogura, Takashi, Shigeta, Yasuteru, Fukutani, Katsuyuki, Yagi, Tatsuhiko, Higuchi, Yoshiki
Protein science : a publication of the Protein Society 28 (3) Jan 2019[Refereed]
Structural changes of the trinuclear copper center in bilirubin oxidase upon reduction
Takaki Tokiwa, Mitsuo Shoji, Vladimir Sladek, Naoki Shibata, Yoshiki Higuchi, Kunishige Kataoka, Takeshi Sakurai, Yasuteru Shigeta, Fuminori Misaizu
Molecules 24 (1) 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]
Quadruply: N -methylated octaphyrin: A helical macrocycle exhibiting chiroptical properties and dynamic conformation changes correlated with helical and inner N -methyl orientations
Wakana Naito, Kazuki Urakawa, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Hiromitsu Maeda
Organic and Biomolecular Chemistry 17 (5) 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) 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) 2019[Refereed]
Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
Ryuhei Harada, Yasuteru Shigeta
Advances in Quantum Chemistry 78 (78) 2019[Refereed]
Protein Residue Networks from Energetic and Geometric Data: Are They Identical?
Vladimir Sladek, Hiroaki Tokiwa, Hitoshi Shimano, Yasuteru Shigeta
Journal of Chemical Theory and Computation 14 (12) Dec 2018[Refereed]
Redox Potential-Dependent Formation of an Unusual His–Trp Bond in Bilirubin Oxidase
Mahfuza Akter, Takaki Tokiwa, Mitsuo Shoji, Koji Nishikawa, Yasuteru Shigeta, Takeshi Sakurai, Yoshiki Higuchi, Kunishige Kataoka, Naoki Shibata
Chemistry - A European Journal 24 (68) Dec 2018[Refereed]
Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion
Ryuma Sato, Hirotaka Kitoh-Nishioka, Kenji Kamada, Toshiko Mizokuro, Kenji Kobayashi, Yasuteru Shigeta
Journal of Physical Chemistry Letters 9 (22) Nov 2018[Refereed]
In Silico Structural Analysis of Elongation Factor-1 Alpha and Elongation Factor-Like
Kotaro Sakamoto, Megumi Kayanuma, Yasuteru Shigeta
PROTEIN SCIENCE 27 (1:SI) Nov 2018[Refereed]
Reaction Pathway of Surface-Catalyzed Ammonia Decomposition and Nitrogen Incorporation in Epitaxial Growth of Gallium Nitride
Kieu My Bui, Jun Ichi Iwata, Yoshihiro Kangawa, Kenji Shiraishi, Yasuteru Shigeta, Atsushi Oshiyama
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
Computational electrochemistry of a novel ferrocene derivative
Ali Ghiami-Shomami, Bahram Ghalami-Choobar, Yasuteru Shigeta
Journal of Molecular Graphics and Modelling 85 Oct 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]
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
Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Information and Modeling 58 (7) Jul 2018[Refereed]
Concerted Mechanism of Water Insertion and O2 Release during the S4 to S0 Transition of the Oxygen-Evolving Complex in Photosystem II
Mitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Kizashi Yamaguchi
Journal of Physical Chemistry B 122 (25) Jun 2018[Refereed]
On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins
Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Theory and Computation 14 (6) 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]
Dominant role of orbital splitting in determining cathode potential in O3 NaTMO2 compounds
M. Hussein N. Assadi, Yasuteru Shigeta
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]
Novel techniques for observing structural dynamics of photoresponsive liquid crystals
Masaki Hada, Shohei Saito, Ryuma Sato, Kiyoshi Miyata, Yasuhiko Hayashi, Yasuteru Shigeta, Ken Onda
Journal of Visualized Experiments 2018 (135) May 2018[Refereed]
Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
Yuta Yamamoto, Kenta Takei, Sundaram Arulmozhiraja, Vladimir Sladek, Naoya Matsuo, Song iee Han, Takashi Matsuzaka, Motohiro Sekiya, Takaki Tokiwa, Mitsuo Shoji, Yasuteru Shigeta, Yoshimi Nakagawa, Hiroaki Tokiwa, Hitoshi Shimano
Biochemical and Biophysical Research Communications 499 (2) 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]
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 499 (2) May 2018
Recent Extensions and Applications of Parallel Cascade Selection Molecular Dynamics Simulations
Harada Ryuhei, Shigeta Yasuteru
ACTIVITY REPORT 2017 / SUPERCOMPUTER CENTER, INSTITUTE FOR SOLID STATE PHYSICS, THE UNIVERSITY OF TOKYO (INVITED ARTICLE) May 2018
Molecular association model of PPAR alpha and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARM alpha
Yuta Yamamoto, Kenta Takei, Sundaram Arulmozhiraja, Vladimir Sladek, Naoya Matsuo, Song-iee Han, Takashi Matsuzaka, Motohiro Sekiya, Takaki Tokiwa, Mitsuo Shoji, Yasuteru Shigeta, Yoshimi Nakagawa, Hiroaki Tokiwa, Hitoshi Shimano
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 499 (2) May 2018[Refereed]
Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities
Terai, Yuma, Sato, Ryuma, Yumiba, Takahiro, Harada, Ryuhei, Shimizu, Kohei, Toga, Tatsuya, Ishikawa-Fujiwara, Tomoko, Todo, Takeshi, Iwai, Shigenori, Shigeta, Yasuteru, Yamamoto, Junpei
Nucleic acids research Epub May 2018[Refereed]
The Reaction Mechanisms of O₂ Formation in Photosynthesis
SHOJI,Mitsuo, ISOBE,Hiroshi, SHIGETA,Yasuteru, NAKAJIMA,Takahito, YAMAGUCHI,Kizashi
Seibutsu Butsuri 58 (3) May 2018
Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals
Masaki Hada, Shohei Saito, Ryuma Sato, Kiyoshi Miyata, Yasuhiko Hayashi, Yasuteru Shigeta, Ken Onda
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (135) May 2018[Refereed]
Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study
Harada, Ryuhei, Mashiko, Takako, Tachikawa, Masanori, Hiraoka, Shuichi, Shigeta, Yasuteru
Physical chemistry chemical physics : PCCP 20 (14) Apr 2018[Refereed]
Nonadiabatic one-electron transfer mechanism for the O–O bond formation in the oxygen-evolving complex of photosystem II
Mitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Kizashi Yamaguchi
Chemical Physics Letters 698 Apr 2018[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
Journal of Physical Chemistry C 122 (10) Mar 2018[Refereed]
First-principles study of the formation of glycine-producing radicals from common interstellar species
Akimasa Sato, Yuya Kitazawa, Toshiro Ochi, Mitsuo Shoji, Yu Komatsu, Megumi Kayanuma, Yuri Aikawa, Masayuki Umemura, Yasuteru Shigeta
Molecular Astrophysics 10 Mar 2018[Refereed]
First-principles study of the formation of glycine-producing radicals from common interstellar species
Akimasa Sato, Yuya Kitazawa, Toshiro Ochi, Mitsuo Shoji, Yu Komatsu, Megumi Kayanuma, Yuri Aikawa, Masayuki Umemura, Yasuteru Shigeta
MOLECULAR ASTROPHYSICS 10 Mar 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) Feb 2018[Refereed]
Free energy calculation method based on the parallel cascade selection molecular dynamics simulation combined with Markov state model
Harada,Ryuhei, Shigeta,Yasuteru
Meeting Abstracts of the Physical Society of Japan 73 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 (26) 2018[Refereed]
Analyses on Dynamical Ordering of Protein Functions by Means of Cascade Selection Molecular Dynamics
Ryuhei Harada, Yasuteru Shigeta
JOURNAL OF COMPUTER CHEMISTRY-JAPAN 17 (1) 2018[Refereed]
Coulomb and CH-φ interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities
Yuma Terai, Ryuma Sato, Takahiro Yumiba, Ryuhei Harada, Kohei Shimizu, Tatsuya Toga, Tomoko Ishikawa-Fujiwara, Takeshi Todo, Shigenori Iwai, Yasuteru Shigeta, Junpei Yamamoto
Nucleic Acids Research 46 (13) 2018[Refereed]
Programed dynamical ordering in 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 (14) 2018[Refereed]
A computational scheme of p: K a values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme
Ryo Fujiki, Yukako Kasai, Yuki Seno, Toru Matsui, Yasuteru Shigeta, Norio Yoshida, Haruyuki Nakano
Physical Chemistry Chemical Physics 20 (43) 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 2018[Refereed]
Analyses on Dynamical Ordering of Protein Functions by Means of Cascade Selection Molecular Dynamics
HARADA,Ryuhei, SHIGETA,Yasuteru
Journal of Computer Chemistry, Japan 17 (1) 2018[Refereed]
The effect of octahedral distortions on the electronic properties and magnetic interactions in O3 NaTMO2 compounds (TM = Ti-Ni & Zr-Pd)
M. Hussein N. Assadi, Yasuteru Shigeta
RSC Advances 8 (25) 2018[Refereed]
How does friction coefficient affect the conformational sampling efficiency of parallel cascade selection molecular dynamics?
Ryuhei Harada, Yasuteru Shigeta
Chemistry Letters 47 (9) 2018[Refereed]
A theoretical study on redox potential and pKa of [2Fe-2S] cluster model from iron-sulfur proteins
Isman Kurniawan, Kazutomo Kawaguchi, Mitsuo Shoji, Toru Matsui, Yasuteru Shigeta, Hidemi Nagao
Bulletin of the Chemical Society of Japan 91 (9) 2018[Refereed]
A practical approach for searching stable molecular structures by introducing repulsive interactions among walkers
Mitsuo Shoji, Megumi Kayanuma, Yasuteru Shigeta
Bulletin of the Chemical Society of Japan 91 (10) 2018
The formation of hydrophobic core regulates the protein folding of villin elucidated with parallel cascade selection molecular dynamics
Ryuhei Harada, Hayato Aida, Yasuteru Shigeta
Chemistry Letters 47 (10) 2018[Refereed]
High-performance Na ion cathodes based on the ubiquitous and reversible O redox reaction
M. Hussein N. Assadi, Marco Fronzi, Mike Ford, Yasuteru Shigeta
Journal of Materials Chemistry A 6 (47) 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
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]
Temperature-Shuffled Parallel Cascade Selection Molecular Dynamics Accelerates the Structural Transitions of Proteins
Harada Ryuhei, Shigeta Yasuteru
JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (31) Dec 2017[Refereed]
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]
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
Masaki Hada, Shohei Saito, Sei'Ichi Tanaka, Ryuma Sato, Masahiko Yoshimura, Kazuhiro Mouri, Kyohei Matsuo, Shigehiro Yamaguchi, Mitsuo Hara, Yasuhiko Hayashi, Fynn Röhricht, Rainer Herges, Yasuteru Shigeta, Ken Onda, R. J. Dwayne Miller
Journal of the American Chemical Society 139 (44) Nov 2017[Refereed]
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase
Masaki Hada, Shohei Saito, Sei'Ichi Tanaka, Ryuma Sato, Masahiko Yoshimura, Kazuhiro Mouri, Kyohei Matsuo, Shigehiro Yamaguchi, Mitsuo Hara, Yasuhiko Hayashi, Fynn Röhricht, Rainer Herges, Yasuteru Shigeta, Ken Onda, R. J.Dwayne Miller
Journal of the American Chemical Society 139 (44) Nov 2017[Refereed]
Theoretical study on relationship between spin structure and electron conductivity of one-dimensional tri-nickel(II) complex
Yasutaka Kitagawa, Mizuki Asaoka, Yoshiki Natori, Koji Miyagi, Rena Teramoto, Toru Matsui, Yasuteru Shigeta, Mitsutaka Okumura, Masayoshi Nakano
Polyhedron 136 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]
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches
Harada, Ryuhei, Shigeta, Yasuteru
Journal of chemical information and modeling 57 (12) Nov 2017[Refereed]
Cover Feature: Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior (Chem. Eur. J. 60/2017)
Hajime Yotsuji, Kenji Higashiguchi, Ryuma Sato, Yasuteru Shigeta, Kenji Matsuda
Chemistry - A European Journal 23 (60) Oct 2017
Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior
Hajime Yotsuji, Kenji Higashiguchi, Ryuma Sato, Yasuteru Shigeta, Kenji Matsuda
Chemistry - A European Journal 23 (60) Oct 2017[Refereed]
Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior
Hajime Yotsuji, Kenji Higashiguchi, Ryuma Sato, Yasuteru Shigeta, Kenji Matsuda
Chemistry - A European Journal 23 (60) Oct 2017[Refereed]
Mechanistic Insight into Weak Base-Catalyzed Generation of Carbon Monoxide from Phenyl Formate and Its Application to Catalytic Carbonylation at Room Temperature without Use of External Carbon Monoxide Gas
Hideyuki Konishi, Mika Matsubara, Keisuke Mori, Takaki Tokiwa, Sundaram Arulmozhiraja, Yuta Yamamoto, Yoshinobu Ishikawa, Hiroshi Hashimoto, Yasuteru Shigeta, Hiroaki Tokiwa, Kei Manabe
Advanced Synthesis and Catalysis 359 (20) Oct 2017[Refereed]
H-Aggregated π-Systems Based on Disulfide-Linked Dimers of Dipyrrolyldiketone Boron Complexes
Yoshifumi Sasano, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Hiromitsu Maeda
Journal of Organic Chemistry 82 (20) Oct 2017[Refereed]
H-Aggregated π-Systems Based on Disulfide-Linked Dimers of Dipyrrolyldiketone Boron Complexes
Yoshifumi Sasano, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Hiromitsu Maeda
Journal of Organic Chemistry 82 (20) Oct 2017[Refereed]
Assessment of Methodology and Chemical Group Dependences in the Calculation of the pKa for Several Chemical Groups
Toru Matsui, Yasuteru Shigeta, Kenji Morihashi
Journal of Chemical Theory and Computation 13 (10) Oct 2017[Refereed]
Assessment of Methodology and Chemical Group Dependences in the Calculation of the pKa for Several Chemical Groups
Toru Matsui, Yasuteru Shigeta, Kenji Morihashi
Journal of Chemical Theory and Computation 13 (10) 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 Dissimilarity Sampling with Dynamically Self-Guiding Selection
Harada Ryuhei, Shigeta Yasuteru
JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (22) Aug 2017[Refereed]
Structural dissimilarity sampling with dynamically self-guiding selection
Ryuhei Harada, Yasuteru Shigeta
Journal of Computational Chemistry 38 (22) Aug 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]
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
Yuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki Hayashi
Journal of Physical Chemistry B 121 (22) Jun 2017[Refereed]
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
Ujiie Yuzuru, Tanaka Wataru, Hanaoka Kyohei, Harada Ryuhei, Kayanuma Megumi, Shoji Mitsuo, Murakawa Takeshi, Ishida Toyokazu, Shigeta Yasuteru, Hayashi Hideyuki
JOURNAL OF PHYSICAL CHEMISTRY B 121 (22) Jun 2017[Refereed]
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) May 2017[Refereed]
Direct Observation of the Ultrafast Evolution of Open-Shell Biradical in Photochromic Radical Dimer
Yoichi Kobayashi, Hajime Okajima, Hikaru Sotome, Takeshi Yanai, Katsuya Mutoh, Yusuke Yoneda, Yasuteru Shigeta, Akira Sakamoto, Hiroshi Miyasaka, Jiro Abe
Journal of the American Chemical Society 139 (18) May 2017[Refereed]
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
Ujiie, Yuzuru, Tanaka, Wataru, Hanaoka, Kyohei, Harada, Ryuhei, Kayanuma, Megumi, Shoji, Mitsuo, Murakawa, Takeshi, Ishida, Toyokazu, Shigeta, Yasuteru, Hayashi, Hideyuki
The journal of physical chemistry. B 121 (22) May 2017[Refereed]
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) May 2017[Refereed]
Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
Junso Fujita, Ryuhei Harada, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi Matsumura
Journal of Structural Biology 198 (2) May 2017[Refereed]
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]
Common Folding Processes of Mini-Proteins: Partial Formations of Secondary Structures Initiate the Immediate Protein Folding
Harada Ryuhei, Takano Yu, Shigeta Yasuteru
JOURNAL OF COMPUTATIONAL CHEMISTRY 38 (11) Apr 2017[Refereed]
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]
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]
Cooperatively Interlocked [2+1]-Type pi-System-Anion Complexes
Yamakado, Ryohei, Ashida, Yukina, Sato, Ryuma, Shigeta, Yasuteru, Yasuda, Nobuhiro, Maeda, Hiromitsu
CHEMISTRY-A EUROPEAN JOURNAL 23 (17) Mar 2017[Refereed]
Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins
Harada Ryuhei, Shigeta Yasuteru
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13 (3) Mar 2017[Refereed]
Outstanding Reviewers for Physical Chemistry Chemical Physics in 2016
Katsuhiko Ariga, Leonardo Bernasconi, Antonio Cammarata, Ayan Datta, Sergei Manzhos, Aurelien Perera, Jose Plata, Yasuteru Shigeta, Leonidas Tsetseris, Lijun Xu
Physical Chemistry Chemical Physics 19 (12) 2017[Refereed]
Molecular dynamics simulation of the nanoscale solutal marangoni convection
Yosuke Imai, Takuya Yamamoto, Yasunori Okano, Ryuma Sato, Yasuteru Shigeta
ASEAN Journal of Chemical Engineering 17 (1) 2017[Refereed]
Cooperatively Interlocked [2+1]-Type π-System–Anion Complexes
Ryohei Yamakado, Yukina Ashida, Ryuma Sato, Yasuteru Shigeta, Nobuhiro Yasuda, Hiromitsu Maeda
Chemistry - A European Journal 23 (17) 2017[Refereed]
Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures
Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian Ren Shen, Kizashi Yamaguchi
Faraday Discussions 198 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) 2017[Refereed]
Theoretical analyses of triplettriplet annihilation process of 9,10-diphenylanthracene in solution
Ryuma Sato, Hirotaka Kitoh-Nishioka, Takeshi Yanai, Yasuteru Shigeta
Chemistry Letters 46 (6) 2017[Refereed]
Dynamic specification of initial structures in parallel cascade selection molecular dynamics (PaCS-MD) efficiently promotes biologically relevant rare events
Ryuhei Harada, Yasuteru Shigeta
Bulletin of the Chemical Society of Japan 90 (11) 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]
A theoretical study of the formation of glycine via hydantoin intermediate in outer space environment
Megumi Kayanuma, Kaori Kidachi, Mitsuo Shoji, Yu Komatsu, Akimasa Sato, Yasuteru Shigeta, Yuri Aikawa, Masayuki Umemura
Chemical Physics Letters 687 2017[Refereed]
Refractive indices of organo-metallic and -metalloid compounds: A long-range corrected DFT study
Shintaro Maekawa, Krzysztof Moorthi, Yasuteru Shigeta
Journal of Computational Chemistry 37 (32) Dec 2016[Refereed]
Molecular dynamics simulation of atomic-scale solutal Marangoni convection
Y. Imai, T. Yamamoto, Y. Okano, R. Sato, Y. Shigeta
Proceedings of 23th Regional Symposium on Chemical Engineering Oct 2016
Ion-Pairing Crystal Polymorphs of Interlocked [2 + 1]-Type Receptor-Anion Complexes
Ryohei Yamakado, Ryuma Sato, Yasuteru Shigeta, Hiromitsu Maeda
Journal of Organic Chemistry 81 (18) Sep 2016[Refereed]
Mutations affecting the internal equilibrium of the reaction catalyzed by 6-aminohexanoate-dimer hydrolase
Seiji Negoro, Yasuyuki Kawashima, Naoki Shibata, Tatsuya Kobayashi, Takeshi Baba, Young Ho Lee, Katsumasa Kamiya, Yasuteru Shigeta, Keisuke Nagai, Ikki Takehara, Dai ichiro Kato, Masahiro Takeo, Yoshiki Higuchi
FEBS Letters 590 (18) Sep 2016
Ultrafast snapshots of the molecules twisting in liquid crystal state
Masaki Hada, Shohei Saito, Sei'ichi Tanaka, Ryuma Sato, Kyohei Matsuo, Mitsuo Hara, Yasuhiko Hayashi, Kazuhiro Mouri, Masahiko Yoshimura, Yasuteru Shigeta, Shigehiro Yamaguchi, Ken Onda, R. J.Dwayne Miller
Optics InfoBase Conference Papers Jul 2016[Refereed]
Doubly N-Methylated Porphyrinoids
Wakana Naito, Nobuhiro Yasuda, Tatsuki Morimoto, Yasuteru Shigeta, Hikaru Takaya, Ichiro Hisaki, Hiromitsu Maeda
Organic Letters 18 (12) Jun 2016[Refereed]
Protein folding and evolution
Harada,Ryuhei, Inagaki,Yuji, Yasuteru,Shigeta
Reference Module in Materials Science and Materials Engineering 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]
Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study
Megumi Kayanuma, Mitsuo Shoji, Masafumi Yohda, Masafumi Odaka, Yasuteru Shigeta
Journal of Physical Chemistry B 120 (13) Apr 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]
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]
A fast convergent simulated annealing algorithm for protein-folding: Simulated annealing outlier flooding (sa-oflood) method
Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
Bulletin of the Chemical Society of Japan 89 (11) 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 2016[Refereed]
Theoretical analyses on a flipping mechanism of UV-induced DNA damage
Ryuma Sato, Ryuhei Harada, Yasuteru Shigeta
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
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]
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]
GPGPU化OpenFMOによるFMO計算の性能評価
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
情報処理学会研究報告(Web) 2015 (HPC-151) Sep 2015
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]
Performance of the divide-and-conquer approach used as an initial guess
Mitsuo Shoji, Megumi Kayanuma, Hiroaki Umeda, Yasuteru Shigeta
Chemical Physics Letters 634 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, Toru Matsui, Kimihiko Hirao, Yasuteru Shigeta
Journal of Physical Chemistry B 119 (17) Apr 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 Apr 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) Mar 2015
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) Mar 2015[Refereed]
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]
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
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) Feb 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[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) Feb 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) Feb 2015
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[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]
Static electric field effect on third-order nonlinear optical (NLO) properties of singlet diradical molecules: Toward the realization of an electric field induced open-shell NLO switch
Masayoshi Nakano, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Yasuteru Shigeta, Benoît Champagne, Edith Botek, Koji Ohta, Kenji Kamada, Takashi Kubo
AIP Conference Proceedings 1642 2015[Refereed]
OpenFMOにおける4中心クーロン相互作用項計算のGPGPU化の試み
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
日本コンピュータ化学会年会講演予稿集 2015 2015
OpenFMOプログラムのGPGPU化
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
分子科学討論会講演プログラム&要旨(Web) 9th 2015
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]
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 the pKa of small polyprotic molecules
Takeshi Baba, Toru Matsui, Katsumasa Kamiya, Masayoshi Nakano, Yasuteru Shigeta
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, Benoît 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
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]
Nylon-oligomer hydrolase promoting cleavage reactions in unnatural amide compounds
Katsumasa Kamiya, Takeshi Baba, Mauro Boero, Toru Matsui, Seiji Negoro, Yasuteru Shigeta
Journal of Physical Chemistry Letters 5 (7) Apr 2014[Refereed]
Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
Journal of Chemical Physics 140 (12) Mar 2014[Refereed]
第一原理 Meta-Dynamics 法，Blue Moon Ensemble 法を用いた反応経路解析
馬場剛史, 安東寛之, 重田育照
アンサンブル 16 (1) 2014
3P077 A theoretical study on the substrate bindings in uridine-cytidine kinase(01D. Protein: Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
Tanaka Wataru, Ujiie Yuzuru, Tomoike Fumiaki, Shoji Mitsuo, Kayanuma Megumi, Masui Ryoji, Kuramitsu Seiki, Shigeta Yasuteru
Seibutsu Butsuri 54 (1) 2014
3P076 Molecular dynamics study on the reaction control mechanism of threonine synthase: evaluating the free energies of the intermediate states(01D. Protein: Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
Ujiie Yuzuru, Tanaka Wataru, Shoji Mitsuo, Kayanuma Megumi, Shigeta Yasuteru, Machida Yasuhiro, Murakawa Takeshi, Hayashi Hideyuki
Seibutsu Butsuri 54 (1) 2014
1P074 A QM/MM study of amide formation reaction of Nitrile Hydratase(01D. Protein : Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
Kayanuma Megumi, Shoji Mitsuo, Shigeta Yasuteru
Seibutsu Butsuri 54 (1) 2014
GPGPU化Fock行列計算ルーチンのOpenFMOへの組み込み
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
分子科学討論会講演プログラム&要旨(Web) 8th 2014
GPGPUクラスタ上でのFMO計算の性能評価
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
日本コンピュータ化学会年会講演予稿集 2014 2014
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) Nov 2013[Refereed]
Binding of a positron to nucleic base molecules and their Pairs
Katsuhiko Koyanagi, Yukiumi Kita, Yasuteru Shigeta, Masanori Tachikawa
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
Katsuki Okuno, Yasuteru Shigeta, Ryohei Kishi, Masayoshi Nakano
Journal of Physical Chemistry Letters 4 (15) Aug 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
Toru Matsui, Yasutaka Kitagawa, Yasuteru Shigeta, Mitsutaka Okumura
Journal of Chemical Theory and Computation 9 (7) Jul 2013[Refereed]
量子化学工学における光機能性物質設計
重田,育照
特集「化学工学に展開する量子化学計算」化学工学会誌 77 Jun 2013[Refereed]
イミノニトロキシドジラジカルからランタニドへのエネルギー移動
福嶋真由子, 竹内利明, 鈴木修一, 小嵜正敏, 岡田惠次, 重田育照, 長谷川美貴
希土類 = Rare earths (62) May 2013[Refereed]
Atom-scale reaction pathways and free-energy landscapes in oxygen plasma etching of graphene
Kenichi Koizumi, Mauro Boero, Yasuteru Shigeta, Atsushi Oshiyama
Journal of Physical Chemistry Letters 4 (10) 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]
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, Benoît 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
Shabbir Muhammad, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Shu Minamide, Ryohei Kishi, Yasuteru Shigeta, Masayoshi Nakano
International Journal of Quantum Chemistry 113 (4) Feb 2013[Refereed]
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[Refereed]
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[Refereed]
Synthesis and characterization of quarteranthene: Elucidating the characteristics of the edge state of graphene nanoribbons at the molecular level
Akihito Konishi, Yasukazu Hirao, Kouzou Matsumoto, Hiroyuki Kurata, Ryohei Kishi, Yasuteru Shigeta, Masayoshi Nakano, Kazuya Tokunaga, Kenji Kamada, Takashi Kubo
Journal of the American Chemical Society 135 (4) Jan 2013[Refereed]
Interplay between the diradical character and third-order nonlinear optical properties in fullerene systems
Shabbir Muhammad, Kotaro Fukuda, Takuya Minami, Ryohei Kishi, Yasuteru Shigeta, Masayoshi Nakano
Chemistry - A European Journal 19 (5) Jan 2013[Refereed]
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]
3P048 Computational studies of mutational effects on nylon degrading enzyme(01A. Protein: Structure,Poster)
Baba Takeshi, Kamiya Katsumasa, Matsui Toru, Nakano Masayoshi, Negoro Seiji, Mauro Boero, Shigeta Yasuteru
Seibutsu Butsuri 53 (1) 2013
Energy Transfer from iminonitroxide diradicals to a series of lanthanide ion
Mayuko Fukushima, Toshiaki Takeuchi, Shuichi Suzuki, Masatoshi Kozaki, Keiji Okada, Yasuteru Shigeta, Miki Hasegawa
Kidorui 62 2013[Refereed]
Cumulant mechanics : An explicit treatment for fluctuation on dynamics
重田,育照
Molecular Science 7 (1) Jan 2013[Refereed]
Non-empirical tuning of CAM-B3LYP functional in time-dependent density functional theory for excitation energies of diarylethene derivatives
Katsuki Okuno, Yasuteru Shigeta, Ryohei Kishi, Masayoshi Nakano
Chemical Physics Letters 585 (1-3) 2013[Refereed]
Density functional studies of the structural variety of the Cu 2S 2 core of the Cu A site
Yu Takano, Orio Okuyama, Yasuteru Shigeta, Haruki Nakamura
International Journal of Quantum Chemistry 112 (24) Dec 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, Takashi Kubo, Benoît Champagne
Journal of Physical Chemistry C 116 (33) Aug 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
Hitoshi Fukui, Yudai Inoue, Taishi Yamada, Soichi Ito, Yasuteru Shigeta, Ryohei Kishi, Benoît Champagne, Masayoshi Nakano
Journal of Physical Chemistry A 116 (22) Jun 2012[Refereed]
Microscopic mechanisms of initial oxidation of Si(100): Reaction pathways and free-energy barriers
Kenichi Koizumi, Mauro Boero, Yasuteru Shigeta, Atsushi Oshiyama
Physical Review B - Condensed Matter and Materials Physics 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]
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]
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) Mar 2012[Refereed]
Halide ion complexes of decaborane (B 10H 14) 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]
Theoretical insight into stereoselective reaction mechanisms of 2,4-pentanediol-tethered ketene-olefin [2 + 2] cycloaddition
Katsumasa Kamiya, Toru Matsui, Takashi Sugimura, Yasuteru Shigeta
Journal of Physical Chemistry A 116 (4) Feb 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, Benoît Champagne, Masayoshi Nakano
Chemical Physics Letters 523 Jan 2012[Refereed]
Full configuration interaction calculations of the second hyperpolarizabilities of the H 4 model compound: Summation-over-states analysis and interplay with diradical characters
Masayoshi Nakano, Takuya Minami, Hitoshi Fukui, Ryohei Kishi, Yasuteru Shigeta, Benot Champagne
Journal of Chemical Physics 136 (2) Jan 2012[Refereed]
Computational study toward micro electronics engineering
K. Shiraishi, K. Yamaguchi, M. Yang, S. G. Park, K. Kamiya, Y. Shigeta, B. Magyari-Kope, M. Niwa, Y. Nishi
2012 28th International Conference on Microelectronics - Proceedings, MIEL 2012 2012[Refereed]
Theoretical Studies on Metal-Containing Artificial DNA Bases
Toru Matsui, Hideaki Miyachi, Yasuteru Shigeta
ADVANCES IN THE THEORY OF QUANTUM SYSTEMS IN CHEMISTRY AND PHYSICS 22 2012[Refereed]
Electronic structures of the Cu2S2 core of the CuA site in cytochrome c oxidase and nitrous oxide reductase
Yu Takano, Yasuteru Shigeta, Kenichi Koizumi, Haruki Nakamura
International Journal of Quantum Chemistry 112 (1) Jan 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 resolution
T. Saito, S. Yamanaka, K. Kanda, H. Isobe, Y. Takano, Y. Shigeta, Y. Umena, K. Kawakami, J. R. Shen, N. Kamiya, M. Okumura, M. Shoji, Y. Yoshioka, K. Yamaguchi
International Journal of Quantum Chemistry 112 (1) Jan 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) 2012[Refereed]
DFT analysis of low-frequency heme vibrations in soluble guanylate cyclase: Raman mode enhancement by propionateprotein interactions
Minoru Kubo, Orio Okuyama, Teizo Kitagawa, Yasuteru Shigeta
Chemistry Letters 41 (9) 2012[Refereed]
Erratum to: (Hyper)polarizability density analysis for open-shell molecular systems based on natural orbitals and occupation numbers (Theor Chem Acc, DOI 10.1007/s00214-010-0871-y)
Masayoshi Nakano, Hitoshi Fukui, Takuya Minami, Kyohei Yoneda, Yasuteru Shigeta, Ryohei Kishi, Benoît Champagne, Edith Botek, Takashi Kubo, Koji Ohta, Kenji Kamada
Theoretical Chemistry Accounts 130 (4-6) Dec 2011[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, Benoît 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
Kenichi Koizumi, Mauro Boero, Yasuteru Shigeta, Atsushi Oshiyama
Physical Review B - Condensed Matter and Materials Physics 84 (20) Nov 2011[Refereed]
First-principles molecular dynamics study on the atomistic behavior of His503 in bovine cytochrome c oxidase
Katsumasa Kamiya, Yasuteru Shigeta
Biochimica et Biophysica Acta - Bioenergetics 1807 (10) Oct 2011[Refereed]
Origin of the enhancement of the second hyperpolarizabilities in open-shell singlet transition-metal systems with metal-metal multiple bonds
Hitoshi Fukui, Masayoshi Nakano, Yasuteru Shigeta, Benoît Champagne
Journal of Physical Chemistry Letters 2 (16) Aug 2011[Refereed]
Third-order nonlinear optical properties of open-shell supermolecular systems composed of acetylene linked phenalenyl radicals
Masayoshi Nakano, Ryohei Kishi, Kyohei Yoneda, Yudai Inoue, Tomoya Inui, Yasuteru Shigeta, Takashi Kubo, Benot Champagne
Journal of Physical Chemistry A 115 (31) Aug 2011[Refereed]
Theoretical study on reaction scheme of silver(I) containing 5-substituted uracils bridge formation
Toru Matsui, Hideaki Miyachi, Takeshi Baba, Yasuteru Shigeta
Journal of Physical Chemistry A 115 (30) Aug 2011[Refereed]
Open-shell characters and second hyperpolarizabilities of one-dimensional graphene nanoflakes composed of trigonal graphene units
Kyohei Yoneda, Masayoshi Nakano, Hitoshi Fukui, Takuya Minami, Yasuteru Shigeta, Takashi Kubo, Edith Botek, Benoët Champagne
ChemPhysChem 12 (9) Jun 2011[Refereed]
Giant enhancement of the second hyperpolarizabilities of open-shell singlet polyaromatic diphenalenyl diradicaloids by an external electric field and donor-acceptor substitution
Masayoshi Nakano, Takuya Minami, Kyohei Yoneda, Shabbir Muhammad, Ryohei Kishi, Yasuteru Shigeta, Takashi Kubo, Léa Rougier, Benoiit Champagne, Kenji Kamada, Koji Ohta
Journal of Physical Chemistry Letters 2 (9) May 2011[Refereed]
Study on collective electron motion in Si-nano dot floating gate MOS capacitor
Masakazu Muraguchi, Yoko Sakurai, Yukihiro Takada, Shintaro Nomura, Kenji Shiraishi, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi Miyazaki, Yasuteru Shigeta, Tetsuo Endoh
IEICE Transactions on Electronics E94-C (5) May 2011[Refereed]
An atomistic study on hydrogenation effects toward quality improvement of program/erase cycle of MONOS-type memory
Akira Otake, Keita Yamaguchi, Katsumasa Kamiya, Yasuteru Shigeta, Kenji Shiraishi
IEICE Transactions on Electronics E94-C (5) May 2011[Refereed]
Collective tunneling model in charge-trap-type nonvolatile memory cell
Masakazu Muraguchi, Yoko Sakurai, Yukihiro Takada, Yasuteru Shigeta, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi Miyazaki, Shintaro Nomura, Kenji Shiraishi, Tetsuo Endoh
Japanese Journal of Applied Physics 50 (4 PART 2) Apr 2011[Refereed]
Atomistic design of guiding principles for high quality metal-oxide-nitride-oxide-semiconductor memories: First principles study of H and O incorporation effects for N vacancies in SiN charge trap layers
Keita Yamguchi, Akira Otake, Katsumasa Kamiya, Yasuteru Shigeta, Kenji Shiraishi
Japanese Journal of Applied Physics 50 (4 PART 2) 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]
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, Benoît Champagne, Edith Botek
Journal of Physical Chemistry A 115 (6) Feb 2011[Refereed]
A Simple scheme for estimating the pKa values of 5-substituted uracils
Toru Matsui, Atsushi Oshiyama, Yasuteru Shigeta
Chemical Physics Letters 502 (4-6) Jan 2011[Refereed]
3N0912 Experimental and computational studies on mutational effects on nylon-6 byproducts-degrading enzyme(Protein : Measurement & Analysis, Origin of life & Evolution,The 49th Annual Meeting of the Biophysical Society of Japan)
Baba Takeshi, Kamiya Katsumasa, Matsui Toru, Shibata Naoki, Higuchi Yoshiki, Negoro Seiji, Shigeta Yasuteru
Seibutsu Butsuri 51 2011
First principle study of the stability of H atoms in SiN layers on MONOS-type memories during program/erase operations
Keita Yamaguchi, Akira Otake, Katsumasa Kamiya, Kenji Shiraishi, Yasuteru Shigeta
International Conference on Simulation of Semiconductor Processes and Devices, SISPAD 2011[Refereed]
Collective tunneling model between two-dimensional electron gas to Si-Nano Dot
M. Muraguchi, Y. Sakurai, Y. Takada, S. Nomura, K. Shiraishi, K. Makihara, M. Ikeda, S. Miyazaki, Y. Shigeta, T. Endoh
AIP Conference Proceedings 1399 2011[Refereed]
Efficient guiding principle of highly scalable MONOS-type memories
K. Kamiya, K. Yamaguchi, A. Otake, Y. Shigeta, K. Shiraishi
ECS Transactions 41 (7) 2011[Refereed]
Collective electron tunneling model in Si-Nano dot floating gate MOS structure
Masakazu Muraguchi, Yoko Sakurai, Yukihiro Takada, Yasuteru Shigeta, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi Miyazaki, Shintaro Nomura, Kenji Shiraishi, Tetsuo Endoh
Key Engineering Materials 470 2011[Refereed]
Electron conductivity in modified models of artificial metal-DNA using green's function-based elastic scattering theory
Yasuyuki Nakanishi, Toru Matsui, Yasutaka Kitagawa, Yasuteru Shigeta, Toru Saito, Yusuke Kataoka, Takashi Kawakami, Mitsutaka Okumura, Kizashi Yamaguchi
Bulletin of the Chemical Society of Japan 84 (4) 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, Benoît 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]
Importance of electronic state of two-dimensional electron gas for electron injection process in nano-electronic devices
M. Muraguchi, T. Endoh, Y. Takada, Y. Sakurai, S. Nomura, K. Shiraishi, M. Ikeda, K. Makihara, S. Miyazaki, Y. Shigeta
Physica E: Low-Dimensional Systems and Nanostructures 42 (10) Sep 2010[Refereed]
Possibility of multi-conformational structure of mismatch DNA nucleobase in the presence of silver(I) ions
Hideaki Miyachi, Toru Matsui, Yasuteru Shigeta, Koichi Yamashita, Kimihiko Hirao
Chemical Physics Letters 495 (1-3) Jul 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]
Anomalous temperature dependence of electron tunneling between a two-dimensional electron gas and Si dots
Y. Sakurai, S. Nomura, Y. Takada, J. Iwata, K. Shiraishi, M. Muraguchi, T. Endoh, Y. Shigeta, M. Ikeda, K. Makihara, S. Miyazaki
Physica E: Low-Dimensional Systems and Nanostructures 42 (4) Feb 2010[Refereed]
1P042 Molecular dynamics studies on Mutational structures of a Nylon-6 Byproduct-degrading Enzyme(Protein:Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)
Baba Takeshi, Kamiya Katsumasa, Shigeta yasuteru, Negoro Seiji
Seibutsu Butsuri 50 (2) 2010
3P034 First-principles Studies of Relationship between Proton Behaviour and Physiological Environments in Proteins(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)
Kamiya Katsumasa, Shigeta Yasuteru
Seibutsu Butsuri 50 (2) 2010
Electron tunneling between Si quantum dots and tow dimensional electron gas under optical excitation at low temperatures
Y. Sakurai, Y. Takada, J. I. Iwata, K. Shiraishi, S. Nomura, M. Muraguchi, T. Endoh, Y. Shigeta, M. Ikeda, K. Makihara, S. Miyazaki
ECS Transactions 28 (1) 2010[Refereed]
Guiding principles for charge trap memories - A theoretical approach
Kenji Shiraishi, Keita Yamaguchi, Akira Otake, Katsumasa Kamiya, Yasuteru Shigeta
ICSICT-2010 - 2010 10th IEEE International Conference on Solid-State and Integrated Circuit Technology, Proceedings 2010[Refereed]
Universal guiding principle for the fabrication of highly scalable MONOS-type memory - Atomistic recipes based on designing interface oxygen chemical potential
K. Yamaguchi, A. Otake, K. Kamiya, Y. Shigeta, K. Shiraishi
Technical Digest - International Electron Devices Meeting, IEDM 2010[Refereed]
Temperature dependence of electron tunneling between two dimensional electron gas and Si quantum dots
Yoko Sakurai, Jun Ichi Iwata, Masakazu Muraguchi, Yasuteru Shigeta, Yukihiro Takada, Shintaro Nomura, Tetsuo Endoh, Shin Ichi Saito, Kenji Shiraishi, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi Miyazaki
Japanese Journal of Applied Physics 49 (1 Part 1) 2010[Refereed]
Effects of mercury(ii) on structural properties, electronic structure and UV absorption spectra of a duplex containing thymine-mercury(ii)-thymine nucleobase pairs
Hideaki Miyachi, Toru Matsui, Yasuteru Shigeta, Kimihiko Hirao
Physical Chemistry Chemical Physics 12 (4) 2010[Refereed]
Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNA
Toru Matsui, Hideaki Miyachi, Yasuyuki Nakanishi, Yasuteru Shigeta, Takeshi Sato, Yasutaka Kitagawa, Mitsutaka Okumura, Kimihiko Hirao
Journal of Physical Chemistry B 113 (38) Sep 2009[Refereed]
Sequence-dependent proton-transfer reaction in stacked GC pair II: The origin of stabilities of proton-transfer products
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]
Physics of nano-contact between Si quantum dots and inversion layer
Y. Sakurai, S. Nomura, Y. Takada, J. Iwata, K. Shiraishi, M. Muraguchi, T. Endoh, Y. Shigeta, M. Ikeda, K. Makihara, S. Miyazaki
ECS Transactions 25 (7) 2009[Refereed]
Effects of Hydrogen-Bonding Environments on Protonation States around the Entrance of Proton Transfer Pathways in Cytochrome c Oxidase
Katsumasa Kamiya, Yasuteru Shigeta, Atsushi Oshiyama
AIP Conference Proceedings 1102 2009[Refereed]
Quantum Theory in Terms of Cumulant Variables
Yasuteru Shigeta, Hideaki Miyachi, Toru Matsui, Norisuke Yokoyama, Kimihiko Hirao
ADVANCES IN THE THEORY OF ATOMIC AND MOLECULAR SYSTEMS: DYNAMICS, SPECTROSCOPY, CLUSTERS, AND NANOSTRUCTURES 20 2009[Refereed]
Electronic structure and UV absorption spectra of metal-mediate DNA: an approach from theoretical chemistry.
Toru Matsui, Hideaki Miyachi, Yasuyuki Nakanishi, Yasuteru Shigeta, Yasutaka Kitagawa, Mitsutaka Okumura, Kimihiko Hirao
Nucleic acids symposium series (2004) (53) 2009[Refereed]
Sequence dependent proton-transfer reaction in stacked gc pair I: The possibility of proton-transfer reactions
Toru Matsui, Takeshi Sato, Yasuteru Shigeta
International Journal of Quantum Chemistry 109 (10) 2009[Refereed]
Molecular theory including quantum effects and thermal fluctuations
Yasuteru Shigeta
Bulletin of the Chemical Society of Japan 82 (11) 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]
Dynamic quantum isotope effects on multiple proton-transfer reactions
Yasuteru Shigeta, Hideaki Miyachi, Toru Matsui, Kimihiko Hirao
Bulletin of the Chemical Society of Japan 81 (10) Oct 2008[Refereed]
Quantal cumulant dynamics III: A quantum confinement under a magnetic field
Yasuteru Shigeta
Chemical Physics Letters 461 (4-6) Aug 2008[Refereed]
2P-065 Theoretical proposal of a new pKa concept applicable in protein environment by the first principles calculations(The 46th Annual Meeting of the Biophysical Society of Japan)
Tanaka Tomonori, Kamiya Katsumasa, Shigeta Yasuteru, Shiraishi Kenji
Seibutsu Butsuri 48 2008
Single-Reference Methods for Excited States in Molecules and Polymers
So Hirata, Peng Dong Fan, Toru Shiozaki, Yasuteru Shigeta
Challenges and Advances in Computational Chemistry and Physics 5 2008[Refereed]
Distribution function in quantal cumulant dynamics
Yasuteru Shigeta
Journal of Chemical Physics 128 (16) 2008[Refereed]
Quantal cumulant dynamics for dissipative systems
Yasuteru Shigeta
AIP Conference Proceedings 1046 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) 2008[Refereed]
Quantal cumulant dynamics II: An efficient time-reversible integrator
Yasuteru Shigeta, Hideaki Miyachi, Kimihiko Hirao
Chemical Physics Letters 443 (4-6) Aug 2007[Refereed]
Multiple proton-transfer reactions in DNA base pairs by coordination of Pt complex
Toru Matsui, Yasuteru Shigeta, Kimihiko Hirao
Journal of Physical Chemistry B 111 (5) Feb 2007[Refereed]
Metal-assisted proton transfer reaction in base pairs.
Toru Matsui, Yasuteru Shigeta, Kimihiko Hirao
Nucleic acids symposium series (2004) (51) 2007[Refereed]
Quantal cumulant dynamics for dissipative systems
Yasuteru Shigeta
AIP Conference Proceedings 963 (2) 2007[Refereed]
Real time mixed quantum-classical dynamics with ab initio quartic force field: Application to molecular vibrational frequency analysis
Hideaki Miyachi, Yasuteru Shigeta, Kimihiko Hirao
Chemical Physics Letters 432 (4-6) Dec 2006[Refereed]
Influence of Pt complex binding on the guanine-cytosine pair: A theoretical study
Toru Matsui, Yasuteru Shigeta, Kimihiko Hirao
Chemical Physics Letters 423 (4-6) Jun 2006[Refereed]
Unidirectional electronic ring current driven by a few cycle circularly polarized laser pulse: Quantum model simulations for Mg-porphyrin
Ingo Barth, Jörn Manz, Yasuteru Shigeta, Kiyoshi Yagi
Journal of the American Chemical Society 128 (21) May 2006[Refereed]
Exact-exchange time-dependent density-functional theory with the frequency-dependent kernel
Yasuteru Shigeta, Kimihiko Hirao, So Hirata
Physical Review A - Atomic, Molecular, and Optical Physics 73 (1) 2006[Refereed]
Quantal cumulant dynamics: General theory
Yasuteru Shigeta, Hideaki Miyachi, Kimihiko Hirao
Journal of Chemical Physics 125 (24) 2006[Refereed]
Search for the ground states of ising spin clusters by using the genetic algorithms
Akifumi Oda, Hidemi Nagao, Yasutaka Kitagawa, Yasuteru Shigeta, Mitsuo Shoji, Hiroya Nitta, Mitsutaka Okumura, Kizashi Yamaguchi
International Journal of Quantum Chemistry 105 (6) Dec 2005[Refereed]
Theoretical study of the mechanism of hydrogenation of side-on coordinated dinitrogen activated by Zr binuclear complexes ([(η5-C 5Me4H)2Zr]2(μ2, η²,η²η²-N2))
Hideaki Miyachi, Yasuteru Shigeta, Kimihiko Hirao
Journal of Physical Chemistry A 109 (39) Oct 2005[Refereed]
Dynamic charge fluctuation of endohedral fullerene with coencapsulated Be atom and H 2
Yasuteru Shigeta, Kazuo Takatsuka
Journal of Chemical Physics 123 (13) Oct 2005[Refereed]
分子磁性の理論 (その7) 遺伝的アルゴリズムのモンテカルロ法への導入
重田,育照
固体物理 40 (3) Mar 2005[Refereed]
Optimized Effective Potential Method at Finite Temperature: An Application to Superconductivity
Yasuteru Shigeta
International Journal of Quantum Chemistry 101 (6) Feb 2005[Refereed]
Internal motion of confined molecules in fullerene
Yasuteru Shigeta
AIP Conference Proceedings 708 Apr 2004[Refereed]
Hybrid QM/MM Studies on Energetics of Malonaldehyde in Condensed Phase
Yasuteru Shigeta
International Journal of Quantum Chemistry 96 (1) Jan 2004[Refereed]
Spin and pseudo spins in theoretical chemistry. A unified view for superposed and entangled quantum systems
K. Yamaguchi, M. Nakano, H. Nagao, M. Okumura, S. Yamanaka, T. Kawakami, D. Yamaki, M. Nishino, Y. Shigeta, Y. Kitagawa, Y. Takano, M. Takahata, R. Takeda
Bulletin of the Korean Chemical Society 24 (6) Jun 2003[Refereed]
A QM/MM molecular dynamics study of a dynamical change in effective charge on Be atom in (Be+nH2)@C60
Y. Shigeta, H. Saito
Synthetic Metals 135-136 Apr 2003[Refereed]
Models for double proton and electron transfer reactions: Analyses by means of quantum dynamics
Y. Shigeta, H. Ushiyama, K. Takatsuka
Journal of Molecular Structure 615 (1-3) Sep 2002[Refereed]
Electron propagator calculations with Kohn-Sham reference states
Y. Shigeta, A. M. Ferreira, V. G. Zakrzewski, J. V. Ortiz
International Journal of Quantum Chemistry 85 (4-5) Nov 2001[Refereed]
Noncollinear spin density functional theory for spin-frustrated and spin-degenerate systems
S. Yamanaka, D. Yamaki, Y. Shigeta, H. Nagao, K. Yamaguchi
International Journal of Quantum Chemistry 84 (6) Sep 2001[Refereed]
Electronic structure calculation by Monte Carlo diagonalization method
Y. Shigeta, H. Nagao, K. Yamaguchi
International Journal of Quantum Chemistry 84 (5) Sep 2001[Refereed]
Generalized spin orbital calculations of spin-frustrated molecules
D. Yamaki, Y. Shigeta, S. Yamanaka, H. Nagao, K. Yamaguchi
International Journal of Quantum Chemistry 84 (5) Sep 2001[Refereed]
Generalized spin density functional theory for noncollinear molecular magnetism
S. Yamanaka, D. Yamaki, Y. Shigeta, H. Nagao, Y. Yoshioka, N. Suzuki, K. Yamaguchi
International Journal of Quantum Chemistry 80 (4-5) Sep 2001[Refereed]
Non-Born-Oppenheimer density functional theory for excited states by using Green's function techniques
T. Yoshimoto, Y. Ohta, J. Maki, Y. Shigeta, H. Nagao, K. Nishikawa
International Journal of Quantum Chemistry 84 (3) Aug 2001[Refereed]
Generalized spin orbital GW theory for spin-frustrated and spin-degenerate systems
S. Yamanaka, Y. Shigeta, Y. Ohta, D. Yamaki, H. Nagao, K. Yamaguchi
International Journal of Quantum Chemistry 84 (3) Aug 2001[Refereed]
Calculation of quasiparticle energy of molecular systems by the GW method
Y. Ohta, J. Maki, T. Yoshimoto, Y. Shigeta, H. Nagao, K. Nishikawa
International Journal of Quantum Chemistry 84 (3) Aug 2001[Refereed]
A theoretical study on conductivity of model polymer including DNA base pairs
Y. Shigeta, H. Nagao, Y. Yoshioka, J. Toyoda, Y. Morita, K. Nakasuji, K. Yamaguchi
Synthetic Metals 119 (1-3) Mar 2001[Refereed]
Theoretical study on triplet superconducting phase and other phases in hole-doped ferromagnetic systems
H. Nagao, Y. Shigeta, K. Yamaguchi, K. Nishikawa
Synthetic Metals 121 (1-3) Mar 2001[Refereed]
Theoretical studies on the proton and electron transfer (PET) in a pseudo one-dimensional hydrogen bonded network system
Y. Shigeta, Y. Kitagawa, H. Nagao, Y. Yoshioka, J. Toyoda, K. Nakasuji, K. Yamaguchi
Journal of Molecular Liquids 90 (1-3) Feb 2001[Refereed]
Quantum spin dynamics in solution applicable to quantum computing
H. Nagao, K. Kinugawa, Y. Shigeta, K. Ohta, K. Yamaguchi
Journal of Molecular Liquids 90 (1-3) Feb 2001[Refereed]
Theoretical studies on anomalous phases of photodoped systems in two-band model
Hidemi Nagao, Masamichi Nishino, Yasuteru Shigeta, Yasunori Yoshioka, Kizashi Yamaguchi
Journal of Chemical Physics 113 (24) Dec 2000[Refereed]
Theoretical study on dependency of conductivity on structure of the proton- and electron-coupled system
Y. Shigeta, H. Nagao, J. Toyoda, Y. Morita, K. Nakasuji, Y. Yoshioka, K. Yamaguchi
International Journal of Quantum Chemistry 80 (4-5) Oct 2000[Refereed]
MP2, Tamm-Dancoff, and RPA methods based on the generalized HF solution
D. Yamaki, Y. Shigeta, S. Yamanaka, H. Nagao, K. Yamaguchi
International Journal of Quantum Chemistry 80 (4-5) Oct 2000[Refereed]
Theoretical studies on superconducting and other phases: Triplet superconductivity, ferromagnetism, and ferromagnetic metal
Hidemi Nagao, Masamichi Nishino, Yasuteru Shigeta, Yasunori Yoshioka, Kizashi Yamaguchi
International Journal of Quantum Chemistry 80 (4-5) Oct 2000[Refereed]
Theoretical studies on magnetic behavior in clusters by the genetic algorithms
Akifumi Oda, Hidemi Nagao, Yasutaka Kitagawa, Yasuteru Shigeta, Kizashi Yamaguchi
International Journal of Quantum Chemistry 80 (4-5) Oct 2000[Refereed]
Ab initio computations of effective exchange integrals for H-H, H-He-H and Mn 2 O 2 complex: Comparison of broken-symmetry approaches
T. Soda, Y. Kitagawa, T. Onishi, Y. Takano, Y. Shigeta, H. Nagao, Y. Yoshioka, K. Yamaguchi
Chemical Physics Letters 319 (3-4) Mar 2000[Refereed]
Generalized spin-density functional calculation for the spin frustrated systems
S Yamanaka, D Yamaki, Y Shigeta, H Nagao, Y Yoshioka, K Yamaguchi, N Suzuki
MOLECULAR CRYSTALS AND LIQUID CRYSTALS 343 2000
Generalized spin-density functional calculation for the spin frustrated systems
S. Yamanaka, D. Yamaki, Y. Shigeta, H. Nagao, Y. Yoshioka, K. Yamaguchi, N. Suzuki
Molecular Crystals and Liquid Crystals Science and Technology Section A: Molecular Crystals and Liquid Crystals 343 2000[Refereed]
Exciton condensate in model dendrimers
Hidemi Nagao, Masayoshi Nakano, Koji Ohta, Yasuteru Shigeta, Shinji Kiribayashi, Yasunori Yoshioka, Kizashi Yamaguchi
Molecular Crystals and Liquid Crystals Science and Technology Section A: Molecular Crystals and Liquid Crystals 342 2000[Refereed]
Quantum spin dynamics by path integral centroid molecular dynamics method
Yasuteru Shigeta, Kenichi Kinugawa, Hidemi Nagao, Koji Ohta, Kizashi Yamaguchi
Progress of Theoretical Physics Supplement (138) 2000[Refereed]
Theoretical studies on effective spin interactions, spin alignments and macroscopic spin tunneling in polynuclear manganese and related complexes and their mesoscopic clusters
H. Nagao, M. Nishino, Y. Shigeta, T. Soda, Y. Kitagawa, T. Onishi, Y. Yoshioka, K. Yamaguchi
Coordination Chemistry Reviews 198 (1) 2000
Theoretical studies on quantum tunneling of spins in cluster of clusters
Yasuteru Shigeta, Hidemi Nagao, Yasunori Yoshioka, Kizashi Yamaguchi
Molecular Crystals and Liquid Crystals Science and Technology Section A: Molecular Crystals and Liquid Crystals 342 2000[Refereed]
A theoretical study of spin level crossing induced by an external magnetic field of ring molecule magnet models
Y. Shigeta, T. Kawakami, H. Nagao, K. Yamaguchi
Chemical Physics Letters 315 (5-6) Dec 1999[Refereed]
A formulation and numerical approach to molecular systems by the Green function method without the Born-Oppenheimer approximation
Yasuteru Shigeta, Hidemi Nagao, Kiyoshi Nishikawa, Kizashi Yamaguchi
Journal of Chemical Physics 111 (14) Oct 1999[Refereed]
Theoretical studies on anomalous phases in model plane systems of LiBeH3
H. Nagao, H. Kawabe, Y. Shigeta, M. Nishino, M. Mitani, K. Yamaguchi
Synthetic Metals 103 (1-3) Jun 1999[Refereed]
Theoretical studies of magnetization by ab initio path integral method
Y. Shigeta, T. Kawakami, H. Nagao, K. Yamaguchi
Synthetic Metals 103 (1-3) Jun 1999[Refereed]
Theoretical study on polarizability of ethylene by path integral method
Y. Shigeta, S. Yamada, H. Nagao, M. Nakano, K. Ohta, K. Yamaguchi
Synthetic Metals 101 (1) May 1999[Refereed]
Quantum phase dynamics of interaction between photon field and magnetic system: Effects of magnetic quantum tunnelling
Hidemi Nagao, Masayoshi Nakano, Yasuteru Shigeta, Kizashi Yamaguchi
Optical Review 6 (3) 1999[Refereed]
Theoretical Studies on Anomalous Phases in Molecular Systems with External Field: Possibility of Photo-Induced Superconductivity
Hidemi Nagao, Masaki Mitani, Masamichi Nishino, Yasuteru Shigeta, Yasunori Yoshioka, Kizashi Yamaguchi
International Journal of Quantum Chemistry 75 (4-5) 1999[Refereed]
Density functional theory without the born-oppenheimer approximation. II. Green function techniques
Y. Shigeta, H. Nagao, K. Nishikawa, K. Yamaguchi
International Journal of Quantum Chemistry 75 (4-5) 1999[Refereed]
Nonadiabatic molecular theory and its application. II. Water molecule
Y. Shigeta, Y. Ozaki, K. Kodama, H. Nagao, H. Kawabe, K. Nishikawa
International Journal of Quantum Chemistry 69 (5) 1998[Refereed]
Possibility of charge-mediated superconductors in the intermediate region of metal-insulator transitions
Hidemi Nagao, Masaki Mitani, Masamichi Nishino, Yasuteru Shigeta, Yasunori Yoshioka, Kizashi Yamaguchi
International Journal of Quantum Chemistry 70 (4-5) 1998[Refereed]
Density functional theory without the Born-Oppenheimer approximation and its application
Y. Shigeta, H. Takahashi, S. Yamanaka, M. Mitani, H. Nagao, K. Yamaguchi
International Journal of Quantum Chemistry 70 (4-5) 1998[Refereed]
Path integral method by means of generalized coherent states and its numerical approach to molecular systems .1. Ensemble average of total energy
H Nagao, Y Shigeta, H Kawabe, T Kawakami, K Nishikawa, K Yamaguchi
JOURNAL OF CHEMICAL PHYSICS 107 (16) Oct 1997[Refereed]
Many-electron-wavepackets method
H. Nagao, M. Nakano, S. Yamanaka, S. Yamada, D. Yamaki, I. Shigemoto, S. Kiribayashi, K. Yamaguchi, Y. Shigeta
International Journal of Quantum Chemistry 60 (7) Dec 1996[Refereed]
Nonadiabatic treatment of molecular systems by the wavepackets method
H. Nagao, K. Kodama, Y. Shigeta, K. Nishikawa, H. Kawabe, M. Nakano, K. Yamaguchi
International Journal of Quantum Chemistry 60 (7) Dec 1996[Refereed]
Awards & Honors
▼▲
Sep 2023
International Academic Award of the Society for Molecular Science Contribution to the theoretical analysis of triplet-triplet annihilation upconversion mechanisms in solutions and solids
Sep 2023
Japan Society for Molecular Science 8th Japan Society for Molecular Science International Investigator Awards
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
▼▲
Hydrogenomics: The Science of Fully Utilizing Hydrogen
Hori, Yuta, Nishikawa, Koji, Shigeta, Yasuteru, Higuchi, Yoshiki ( Biological Enzymes and Hydrogenases)
Recent advances of the fragment molecular orbital method Subtitle: Enhanced performance and applicability
Shigeta, Yasuteru (Role:Contributor, AnalysisFMO toolkit: PyMOL plugin module to 3D-visualize interaction energies in protein (3D-VIEP) generated by fragment molecular orbital calculation)
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
▼▲
量子生命技術の創製と医学・生命科学の革新
光・量子飛躍フラッグシッププログラム (分担者)
Research period: Sep 2020 - Mar 2030Representative: 馬場嘉信
Science of Meso-Hierarchy
Grants-in-Aid for Scientific Research
Research period: Apr 2023 - Mar 2028
Theory of mesohierarchy
Grants-in-Aid for Scientific Research
Research period: Apr 2023 - Mar 2028
クライオ電顕による１分子構造解析に基づいた蛋白質構造の連続的なダイナミクスの解析
科学研究費助成事業
Research period: Apr 2023 - Mar 2026Representative: 守屋俊夫, 重田育照, 村田武士
3D ドメインスワッピングを利用したタンパク質の自在配列と機能化
戦略的創造研究推進事業 (分担者)
Research period: Dec 2020 - Mar 2026Representative: 廣田俊
Novel drug development for the treatment of mitochondrial diseases by activation of cytochrome c oxidase
Research grant on rare and intractable diseases Program
Research period: Apr 2021 - Mar 2024Representative: Yasunori SHINTANI
Theoretical study on dynamics of metalloproteins from mitochondrial DNA in aging hypothesis
Grants-in-Aid for Scientific Research
Research period: Apr 2022 - Mar 2023
Quantum Bioenergetics for Exploring Dynamics of Metals in Protein
Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Research period: Apr 2020 - Mar 2022Representative: SHIGETA Yasuteru
Theoretical analysis of biohydrogenomics
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Research period: Apr 2019 - Mar 2021
Structure-based design of middle molecules for drug discovery
Research period: Jun 2018 - Mar 2021Representative: Katsumi MAENAKA
Advancement and network formation of the project Photosynergetics by international collaboration
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Research period: Nov 2015 - Mar 2019Representative: MIYASAKA Hiroshi
Elucidation of Structure-Function Relationship of Biological Active Sites and New Material Design by Molecular Simulation
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Research period: Jul 2014 - Mar 2019Representative: Takano Yu, SHIGETA yasuteru, KAMIYA katsumasa, SHOJI mitsuo, KONDO hiroko x.
Control of multiple spin exciton states by synergetic studies of theory and experiment
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Research period: Jul 2014 - Mar 2019Representative: Yasuteru Shigeta, NAKANO Masayoshi, MIZOKURO Toshiko, FUJIMOTO Kazuhiro
Application of Cooperative Excitation into Innovative Molecular Systems with High-Order Photofunctions
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Research period: Jul 2014 - Mar 2019Representative: Miyasaka Hiroshi
Molecular design of nylon hydrolase and industrial application of the enzyme
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
Research period: Apr 2014 - Mar 2019Representative: Negoro Seiji, HIGUCHI yoshiki, SHIBATA naoki, SHIGETA yasuteru, GOTO yuji, NAGAI keisuke, TAKEHARA ikki
Sub-issue A, Priority Issue 7, Post-K Supercomputer Project
New-functionality and high-performance semiconductor devices
Research period: Apr 2016 - Mar 2019Representative: Atsushi Oshiyama
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
Development of materials imaging technique based on flexible fluorophores
Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (A)
Research period: Apr 2015 - Mar 2018Representative: SAITO Shohei, YABU Hiroshi, MIYASAKA Hiroshi, SOTOME Hikaru, SAKAMOTO Akira, OKAJIMA Hajime, MATSUMOTO Yoshiyasu, WATANABE Kazuya, OTSUBO Kazuya, HADA Masaki, ONDA Ken, SHIGETA Yasuteru, SATO Ryuma, NOBUSUE Shunpei, SEKI Takahiro, SEKI Mitsuo
A Challenging Study for Development of Theory of Transport Phenomena in Mesoscale Space
Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
Research period: Apr 2015 - Mar 2017Representative: Yasunori Okano
キュミュラント粗視化動力学によるタンパク質動的秩序形成過程の理論研究
科学研究費助成事業新学術領域研究(研究領域提案型)
Research period: Apr 2014 - Mar 2015Representative: 重田育照
Siナノドットの非線形光学特性変化に対する動力学的解析
科学研究費助成事業新学術領域研究(研究領域提案型)
Research period: Apr 2013 - Mar 2015Representative: 重田育照
Density-Functional Approach to Atomic and Electronic Structures and their Dynamics in Nano-Structures
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Research period: Apr 2010 - Mar 2015Representative: OSHIYAMA Atsushi, MIYAZAKI Tsuyoshi, TSUCHIDA Eiji, OZAKI Taisuke, IWARA Junichi, UCHIDA Kazuyuki, SHIGETA Yasuteru
Molecular design of nylon oligomer degradation enzyme and its application to bioproduction
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
Research period: Apr 2010 - Mar 2014Representative: NEGORO Seiji, TAKEO Masahiro, KATO Dai-ichiro, HIGUCHI Yoshiki, SHIBATA Naoki, GOTO Yuji, IKEGAMI Takahisa, SHIGETA Yasuteru, KAMIYA Katsumasa
Quantum chemical studies on a cooperative proton and electron transfer reaction in protein
Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (A)
Research period: Apr 2010 - Mar 2014Representative: SHIGETA Yasuteru
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
科学研究費助成事業特定領域研究
Research period: 2008 - 2009Representative: 重田育照
Real-time analyses of proton-coupled electron transfer reactions : Quantal cumulant dynamics
Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
Research period: 2008 - 2009Representative: SHIGETA Yasuteru
量子ハイブリッド分子動力学法による生体機能の量子デザイン
科学研究費助成事業特定領域研究
Research period: 2007 - 2008Representative: 舘野賢, 濡木理, 重田育照
電子ダイナミクスに基づく生体分子触媒反応のシミュレーション
科学研究費助成事業基盤研究(B)
Research period: 2007 - 2008Representative: BOERO Mauro, 舘野賢, 重田育照
タンパク質超分子中のプロトン移動機構の電子レベルでの解明
科学研究費助成事業特定領域研究
Research period: 2006 - 2007Representative: BOERO Mauro, 白石賢二, 舘野賢, 重田育照
凝縮相および生体内における電子・水素移動の協同現象に対する理論的研究
科学研究費助成事業特別研究員奨励費
Research period: 2001 - 2003Representative: 重田育照
電子-核密度汎関数理論の構築と量子ダイナミクスへの展開
科学研究費助成事業特別研究員奨励費
Research period: 1999 - 2000Representative: 重田育照

	氏名	庄司光男
	Name	SHOJI Mitsuo
	Faculty
	Section
	Position	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
Oct 2019
-
Mar 2023
JST
Published Papers
▼▲
Enantioselective interactions of aminonitrile dimers
Natsuki Watanabe, Yu Komatsu, Koichi Miyagawa, Yuta Hori, Yasuteru Shigeta, Mitsuo Shoji
Physical Chemistry Chemical Physics Nov 2025[Refereed]
A machine learning potential construction based on radial distribution function sampling
Natsuki Watanabe, Yuta Hori, Hiroki Sugisawa, Tomonori Ida, Mitsuo Shoji, Yasuteru Shigeta
Journal of Computational Chemistry Sep 2024
Calcium binding mechanism in TAT rhodopsin
Sugimoto, Teppei, Miyagawa, Koichi, SHOJI, Mitsuo, Katayama, Kota, Shigeta, Yasuteru, Kandori, Hideki
The Journal of Physical Chemistry Part B 128 (29) Jul 2024[Refereed]
Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography
Basudev Maity, Mitsuo Shoji, Fangjia Luo, Takanori Nakane, Satoshi Abe, Shigeki Owada, Jungmin Kang, Kensuke Tono, Rie Tanaka, Thuc Toan Pham, Mariko Kojima, Yuki Hishikawa, Junko Tanaka, Jiaxin Tian, Misaki Nagama, Taiga Suzuki, Hiroki Noya, Yuto Nakasuji, Asuka Asanuma, Xinchen Yao, So Iwata, Yasuteru Shigeta, Eriko Nango, Takafumi Ueno
Nature Communications 15 (1) Jun 2024
Water oxidation utilizing a ruthenium complex featuring a phenolic moiety inspired by the oxygen-evolving centre (OEC) of photosystem II
Kumagai, Yugo, Takabe, Risa, Nakazono, Takashi, Shoji, Mitsuo, Isobe, Hiroshi, Yamaguchi, Kizashi, Misawa-Suzuki, Tomoyo, Nagao, Hirotaka, Wada, Tohru
SUSTAINABLE ENERGY & FUELS 8 (5) Jan 2024[Refereed]
A new small molecule DoNA binding to CAG repeat RNA
Chen, Qingwen, Yamada, Takeshi, Miyagawa, Koichi, Murata, Asako, Shoji, Mitsuo, Nakatani, Kazuhiko
BIOORGANIC & MEDICINAL CHEMISTRY 98 Jan 2024[Refereed]
Theoretical elucidation of the structure, bonding, and reactivity of the CaMn₄O_x clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation
Yamaguchi, Kizashi, Miyagawa, Koichi, Shoji, Mitsuo, Kawakami, Takashi, Isobe, Hiroshi, Yamanaka, Shusuke, Nakajima, Takahito
PHOTOSYNTHESIS RESEARCH Epub Nov 2023[Refereed]
The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations
Yamaguchi, Kizashi, Isobe, Hiroshi, Shoji, Mitsuo, Kawakami, Takashi, Miyagawa, Koichi
MOLECULES 28 (20) Oct 2023[Refereed]
Origin of Homochirality in Amino Acids Induced by Lyman-α Irradiation in the Early Stage of the Milky Way
Sato, Akimasa, Shoji, Mitsuo, Watanabe, Natsuki, Boero, Mauro, Shigeta, Yasuteru, Umemura, Masayuki
ASTROBIOLOGY 23 (10) Oct 2023[Refereed]
Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor
Takeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Naomine Yano, Katsuhiro Kusaka, Yoshiaki Kawano, Mamoru Suzuki, Yasuteru Shigeta, Takato Yano, Motoyasu Adachi, Katsuyuki Tanizawa, Toshihide Okajima
ACS Catalysis Sep 2023
Enantioselective Amino Acid interactions in Solution
Watanabe, Natsuki, Shoji, Mitsuo, Miyagawa, Koichi, Hori, Yuta, Boero, Mauro, Umemura, Masayuki, Shigeta, Yasuteru
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 25 (21) May 2023[Refereed]
Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino Acids
Mitsuo Shoji, Yuya Kitazawa, Akimasa Sato, Natsuki Watanabe, Mauro Boero, Yasuteru Shigeta, Masayuki Umemura
The Journal of Physical Chemistry Letters Apr 2023
Organocatalytic-racemization reaction elucidation of aspartic acid by density functional theory
Watanabe, Natsuki, Hori, Yuta, Shoji, Mitsuo, Boero, Mauro, Shigeta, Yasuteru
CHIRALITY 35 (9) Apr 2023[Refereed]
Biological advantage of the arrangements of C-phycocyanin chromophores in phycobilisome from the electronic energy transfer viewpoint
Mishima, Kenji, Shoji, Mitsuo, Umena, Yasufumi, Shigeta, Yasuteru
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 96 (4) Apr 2023[Refereed]
有機分子触媒を用いたアミノ酸ラセミ化反応の理論的研究
渡辺, 七都稀, 堀, 優太, 庄司, 光男, 重田, 育照
Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]
Specific zinc binding to heliorhodopsin
Masanori Hashimoto, Koichi Miyagawa, Manish Singh, Kota Katayama, Mitsuo Shoji, Yuji Furutani, Yasuteru Shigeta, Hideki Kandori
Physical Chemistry Chemical Physics 25 (4) 2023
Elucidation of a multiple S3 intermediates model for water oxidation in the oxygen evolving complex of photosystem II. Calcium-assisted concerted O-O bond formation
K. Yamaguchi, K. Miyagawa, M. Shoji, H. Isobe, T. Kawakami
Chem. Phys. Lett. 806 Sep 2022[Refereed]
Roles of the Flexible Primary Coordination Sphere of the Mn4CaOx Cluster: What Are the Immediate Decay Products of the S-3 State?
Isobe, Hiroshi, Shoji, Mitsuo, Suzuki, Takayoshi, Shen, Jian-Ren, Yamaguchi, Kizashi
JOURNAL OF PHYSICAL CHEMISTRY B Epub Sep 2022[Refereed]
Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase
Mitsuo Shoji, Takeshi Murakawa, Shota Nakanishi, Mauro Boero, Yasuteru Shigeta, Hideyuki Hayashi, Toshihide Okajima
CHEMICAL SCIENCE 13 (36) Sep 2022
Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic Syntheses
Mitsuo, Shoji, Natsuki, Watanabe, Hori, Yuta, Kenji, Furuya, Masayuki, Umemura, Mauro, Boero, Yasuteru, Shigeta
Astrobiology 22 (9) Sep 2022[Refereed]
Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in Space
Hori, Yuta, Nakamura, Honami, Sakawa, Takahide, Natsuki, Watanabe, Kayanuma, Megumi, Mitsuo, Shoji, Masayuki, Umemura, Yasuteru, Shigeta
Astrobiology 22 (11) Sep 2022[Refereed]
Heme-bound tyrosine vibrations in hemoglobin M: Resonance Raman, crystallography, and DFT calculation
Nagatomo, Shigenori, Shoji, Mitsuo, Terada, Takuto, Nakatani, Kiyoharu, Shigeta, Yasuteru, Hirota, Shun, Yanagisawa, Sachiko, Kubo, Minoru, Kitagawa, Teizo, Nagai, Masako, Ohki, Mio, Park, Sam-Yong, Shibayama, Naoya
Biophysical Journal 121 (14) Jun 2022[Refereed]
Relative energies among S3 intermediates in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Possible pathways of water insertion in the S2 to S3 transition
K. Miyagawa, M. Shoji, H. Isobe, T. Kawakami, T. Nakajima, K. Yamaguchi
Chem. Phys. Lett. 793 Feb 2022[Refereed]
Relative energies among proton-shifted S2 isomers in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Proton transfer coupled spin transitions of the CaMn4Ox cluster in OEC of PSII
Miyagawa, Koichi, Shoji, Mitsuo, Isobe, Hiroshi, Kawakami, Takashi, Nakajima, Takahito, Yamaguchi, Kizashi
Chemical Physics Letters 790 Jan 2022[Refereed]
Mechanism of Water Oxidation in Photosynthesis Elucidated by Interplay Between Experiment and Theory
K. Yamaguchi, S. Yamanaka, H. Isobe, M. Shoji, T. Kawakami, K. Miyagawa
Advances in Photosynthesis and Respiration 47 Sep 2021[Refereed]
pyProGA-A PyMOL plugin for protein residue network analysis
Sladek, Vladimir, Yamamoto, Yuta, Harada, Ryuhei, Shoji, Mitsuo, Shigeta, Yasuteru, Sladek, Vladimir
PLOS ONE 16 (7) Jul 2021[Refereed]
Isolobal and isospin analogy between organic and inorganic open-shell molecules Application to oxygenation reactions by active oxygen and oxy-radicals and water oxidation in the native and artificial photosynthesis
K. Yamaguchi, K. Miyagawa, H. Isobe, M. Shoji, T. Kawakami, S. Yamanaka
Advances in Quantum Chemistry 84 Apr 2021[Refereed]
Estimation of the relative contributions to the electronic energy transfer rates based on Forster theory: The case of C-phycocyanin chromophores
Mishima, Kenji, Shoji, Mitsuo, Umena, Yasufumi, Boero, Mauro, Shigeta, Yasuteru
Biophysics and physicobiology 18 2021[Refereed]
Exploring reaction pathways for the structural rearrangements of the Mn cluster induced by water binding in the S-3 state of the oxygen evolving complex of photosystem II
Isobe, Hiroshi, Shoji, Mitsuo, Suzuki, Takayoshi, Shen, Jian-Ren, Yamaguchi, Kizashi
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 405 Jan 2021[Refereed]
A three states model for hydrogen abstraction reactions with the cytochrome P450 compound I is revisited. Isolobal and isospin analogy among Fe(IV)=O, O = O and O
Miyagawa, Koichi, Isobe, Hiroshi, Shoji, Mitsuo, Kawakami, Takashi, Yamanaka, Shusuke, Yamaguchi, Kizashi
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 405 Jan 2021[Refereed]
Role of the Propionic Acid Side-Chain of C-Phycocyanin Chromophores in the Excited States for the Photosynthesis Process
Kenji Mishima, Mitsuo Shoji, Yasufumi Umena, Mauro Boero, Yasuteru Shigeta
Bulletin of the Chemical Society of Japan 93 (12) Dec 2020[Refereed]
Weak O2 binding and strong H2O2 binding at the non-heme diiron center of trypanosome alternative oxidase
Sotaro Yamasaki, Mitsuo Shoji, Megumi Kayanuma, Vladimir Sladek, Daniel Ken Inaoka, Yuichi Matsuo, Tomoo Shiba, Luke Young, Anthony L. Moore, Kiyoshi Kita, Yasuteru Shigeta
Biochimica et Biophysica Acta (BBA) - Bioenergetics 1862 (4) Dec 2020[Refereed]
Electronic and spin structures of CaMn4Ox clusters in the S0 state of the oxygen evolving complex of photosystem II. Domain-based local pair natural orbital (DLPNO) coupled-cluster (CC) calculations using optimized geometries and natural orbitals (UNO) by hybrid density functional theory (HDFT) calculations
Miyagawa, K, Yamanaka, S, Isobe, H, Shoji, Mitsuo, Kawakami, T, Taniguchi, M, Okumura, M, Yamaguchi, K
Physical Chemistry Chemical Physics 46 (22) Oct 2020[Refereed]
Unique protonation states of aspartate and topaquinone in the active site of copper amine oxidase
Mitsuo Shoji, Takeshi Murakawa, Mauro Boero, Yasuteru Shigeta, Hideyuki Hayashi, Toshihide Okajima
RSC Advances 10 (63) Oct 2020[Refereed]
Relative stability among intermediate structures in S2 state of CaMn4O5 cluster in PSII by using hybrid-DFT and DLPNO-CC methods and evaluation of magnetic interactions between Mn ions
Shoji,Mitsuo
Journal of Photochemistry and Photobiology A: Chemistry 405 Sep 2020[Refereed]
Development of broken-symmetry (BS) methods in chemical reactions. A theoretical view of water oxidation in photosystem II and related systems
Yamaguchi, Kizashi, Isobe, Hiroshi, Shoji, Mitsuo, Miyagawa, Koichi, Yamanaka, Shusuke, Kawakami, Takashi, Nakajima, Takahito
J. Photochem. Photobiol. A 402 (112791) Jul 2020[Refereed]
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]
Theory of chemical bonds in metalloenzymes XXIV electronic and spin structures of FeMoco and Fe-S clusters by classical and quantum computing
Miyagawa, K, Shoji, Mitsuo, Isobe, H, Yamanaka, S, Kawakami, T, Okumura, M, Yamaguchi, K
Molecular Physics 118 (21-22) May 2020[Refereed]
UNO(ULO) active space for multireference calculations on classical and quantum computers. Revisit to the iron-sulfur complexes
Koichi Miyagawa, Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Takashi Kawakami, Mitsutaka Okumura, Kizashi Yamaguchi
Chemical Physics Letters 746 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 22 (29) May 2020[Refereed]
Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active site.
Yasuhiro Machida, Takeshi Murakawa, Akiko Sakai, Mitsuo Shoji, Yasuteru Shigeta, Hideyuki Hayashi
Journal of biochemistry 167 (4) Apr 2020[Refereed]
Theory of chemical bonds in metalloenzymes XXIII Fundamental principles for the photo-induced water oxidation in oxygen evolving complex of photosystem II
K. Yamaguchi, S. Yamanaka, H. Isobe, M. Shoji, K. Miyagawa, T. Kawakami
Mol. Phys. - Feb 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[Refereed]
First-Principles Study of the Reaction Mechanism of CHO plus H on Graphene Surface
Kayanuma Megumi, Shoji Mitsuo, Furuya Kenji, Kamiya Katsumasa, Aikawa Yuri, Umemura Masayuki, Shigeta Yasuteru
JOURNAL OF PHYSICAL CHEMISTRY A 123 (26) Jul 2019[Refereed]
Reaction mechanism of non-enzymatic stereoselective formation of wine lactone
Kyan, Akane, Kayanuma, Megumi, Shoji, Mitsuo, Shigeta, Yasuteru
CHEMICAL PHYSICS LETTERS 725 Jun 2019[Refereed]
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]
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
JOURNAL OF PHYSICAL CHEMISTRY A 123 (13) Apr 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]
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) Jan 2019[Refereed]
Structural Changes in the Trinuclear Copper Center upon the Reduction of Bilirubin Oxidase (BOD)
T. Tokiwa, M. Shoji, V. Sladek, N. Shibata, Y. Higuchi, K. Kataoka, Y. Shigeta, F Misaizu
Molecules 24 (76) Jan 2019[Refereed]
Theoretical study of the photodissociation reaction of methanol
Kayanuma, Megumi, Shoji, Mitsuo, Furuya, Kenji, Aikawa, Yuri, Umemura, Masayuki, Shigeta, Yasuteru
CHEMICAL PHYSICS LETTERS 714 Jan 2019[Refereed]
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]
Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase.
Mahfuza Akter, Takaki Tokiwa, Mitsuo Shoji, Koji Nishikawa, Yasuteru Shigeta, Takeshi Sakurai, Yoshiki Higuchi, Kunishige Kataoka, Naoki Shibata
Chemistry (Weinheim an der Bergstrasse, Germany) 24 (68) 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
Ensemble 20 (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
Ensemble 20 (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 O2 Release during the S4 to S0 Transition of the Oxygen-Evolving Complex in Photosystem II
Mitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Kizashi Yamaguchi
Journal of Physical Chemistry B 122 (25) Jun 2018[Refereed]
Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
Yuta Yamamoto, Kenta Takei, Sundaram Arulmozhiraja, Vladimir Sladek, Naoya Matsuo, Song-iee Han, Takashi Matsuzaka, Motohiro Sekiya, Takaki Tokiwa, Mitsuo Shoji, Yasuteru Shigeta, Yoshimi Nakagawa, Hiroaki Tokiwa, Hitoshi Shimano
Biochemical and Biophysical Research Communications 499 (2) May 2018
Relative stability between the manganese hydroxide- and oxo-models for water oxidation by CCSD, DMRG CASCI, CASSCF, CASPT2 and CASDFT methods; Importance of static and dynamical electron correlation effects for OEC of PSII
T. Kawakami, K. Miyagawa, H. Isobe, M. Shoji, S. Yamanaka, M. Katouda, T. Nakajima, K. Nakatani, M. Okumura, K. Yamaguchi
Chemical Physics Letters 705 May 2018[Refereed]
The Reaction Mechanisms of O₂ Formation in Photosynthesis
SHOJI,Mitsuo, ISOBE,Hiroshi, SHIGETA,Yasuteru, NAKAJIMA,Takahito, YAMAGUCHI,Kizashi
Seibutsu Butsuri 58 (3) May 2018[Refereed]
Nonadiabatic one-electron transfer mechanism for the O–O bond formation in the oxygen-evolving complex of photosystem II
Mitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Kizashi Yamaguchi
Chemical Physics Letters 698 Apr 2018[Refereed]
Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II
Kizashi Yamaguchi, Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Takashi Kawakami, Satoru Yamada, Michio Katouda, Takahito Nakajima
Molecular Physics 116 (5-6) Mar 2018[Refereed]
First-principles study of the formation of glycine-producing radicals from common interstellar species
Akimasa Sato, Yuya Kitazawa, Toshiro Ochi, Mitsuo Shoji, Yu Komatsu, Megumi Kayanuma, Yuri Aikawa, Masayuki Umemura, Yasuteru Shigeta
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 2 (3) Dec 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]
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
Ujiie Yuzuru, Tanaka Wataru, Hanaoka Kyohei, Harada Ryuhei, Kayanuma Megumi, Shoji Mitsuo, Murakawa Takeshi, Ishida Toyokazu, Shigeta Yasuteru, Hayashi Hideyuki
JOURNAL OF PHYSICAL CHEMISTRY B 121 (22) Jun 2017[Refereed]
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]
Large-scale QM/MM calculations of the CaMn4O5 cluster in the oxygen-evolving complex of photosystem II: Comparisons with EXAFS structures
Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Kizashi Yamaguchi
CHEMICAL PHYSICS LETTERS 658 Aug 2016[Refereed]
Molecular Mechanisms of Substrate Specificities of Uridine-Cytidine Kinase
Tanaka Wataru, Shoji Mitsuo, Tomoike Fumiaki, Ujiie Yuzuru, Hanaoka Kyohei, Harada Ryuhei, Kayanuma Megumi, Kamiya Katsumasa, Ishida Toyokazu, Masui Ryoji, Kuramitsu Seiki, Shigeta Yasuteru
BIOPHYSICS AND PHYSICOBIOLOGY 13 Jun 2016[Refereed]
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
Full geometry optimizations of the CaMn4O4 model cluster for the oxygen evolving complex of photosystem II
Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Kizashi Yamaguchi
CHEMICAL PHYSICS LETTERS 640 Nov 2015[Refereed]
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]
GPGPU化OpenFMOによるFMO計算の性能評価
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
情報処理学会研究報告(Web) 2015 (HPC-151) Sep 2015
QM/MM study of the S-2 to S-3 transition reaction in the oxygen-evolving complex of photosystem II
Mitsuo Shoji, Hiroshi Isobe, Kizashi Yamaguchi
CHEMICAL PHYSICS LETTERS 636 Sep 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]
OpenFMOにおける4中心クーロン相互作用項計算のGPGPU化の試み
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
日本コンピュータ化学会年会講演予稿集 2015 2015
OpenFMOプログラムのGPGPU化
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
分子科学討論会講演プログラム&要旨(Web) 9th 2015
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]
Substrate-mediated proton relay mechanism for the religation reaction in topoisomerase II
Kyohei Hanaoka, Mitsuo Shoji, Daiki Kondo, Akimasa Sato, Moon Young Yang, Katsumasa Kamiya, Kenji Shiraishi
Journal of Biomolecular Structure and Dynamics 32 (11) Nov 2014[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 the l -Threonine Formation Reaction of Threonine Synthase: Implications into the Mechanism of the Reaction Specificity
Mitsuo Shoji, Kyohei Hanaoka, Yuzuru Ujiie, Wataru Tanaka, Daiki Kondo, Hiroaki Umeda, Yoshikazu Kamoshida, Megumi Kayanuma, Katsumasa Kamiya, Kenji Shiraishi, Yasuhiro Machida, Takeshi Murakawa, Hideyuki Hayashi
J. Am. Chem. Soc. 136 (12) Mar 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]
3P077 A theoretical study on the substrate bindings in uridine-cytidine kinase(01D. Protein: Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
Tanaka Wataru, Ujiie Yuzuru, Tomoike Fumiaki, Shoji Mitsuo, Kayanuma Megumi, Masui Ryoji, Kuramitsu Seiki, Shigeta Yasuteru
Seibutsu Butsuri 54 (1) 2014
3P076 Molecular dynamics study on the reaction control mechanism of threonine synthase: evaluating the free energies of the intermediate states(01D. Protein: Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
Ujiie Yuzuru, Tanaka Wataru, Shoji Mitsuo, Kayanuma Megumi, Shigeta Yasuteru, Machida Yasuhiro, Murakawa Takeshi, Hayashi Hideyuki
Seibutsu Butsuri 54 (1) 2014
1P074 A QM/MM study of amide formation reaction of Nitrile Hydratase(01D. Protein : Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
Kayanuma Megumi, Shoji Mitsuo, Shigeta Yasuteru
Seibutsu Butsuri 54 (1) 2014
GPGPU化Fock行列計算ルーチンのOpenFMOへの組み込み
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
分子科学討論会講演プログラム&要旨(Web) 8th 2014
GPGPUクラスタ上でのFMO計算の性能評価
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 重田育照
日本コンピュータ化学会年会講演予稿集 2014 2014
GPGPU化したFock行列計算ルーチンのOpenFMOへの組み込み
梅田宏明, 塙敏博, 庄司光男, 朴泰祐
日本コンピュータ化学会年会講演予稿集 2014 2014
Fock Matrix Preparation in Fragment Molecular Orbital Method with GPGPU
梅田宏明, 塙敏博, 庄司光男, 朴泰祐, 稲富雄一
情報処理学会論文誌トランザクションコンピューティングシステム(Web) 6 (4) Oct 2013
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
Ha-pacs: A highly accelerated parallel advanced system for computational sciences
Taisuke Boku, Toshihiro Hanawa, Yoshinobu Kuramashi, Kohji Yoshikawa, Mitsuo Shoji, Yuetsu Kodama, Mitsuhisa Sato, Masayuki Umemura
Contemporary High Performance Computing: From Petascale toward Exascale Jan 2013
1P076 Theoretical elucidation on the reaction control mechanism in Threonine Synthase(01D. Protein:Function,Poster)
Shoji Mitsuo, Hanaoka Kyohei, Ujiie Yuzuru, Tanaka Wataru, Kayanuma Megumi, Umeda Hiroaki, Machida Yasuhiro, Murakawa Takeshi, Hayashi Hideyuki
Seibutsu Butsuri 53 (1) 2013
1P074 Theoretical Study on Catalytic Mechanism of Nitrile Hydratase(01D. Protein:Function,Poster)
Kayanuma Megumi, Hanaoka Kyohei, Shoji Mitsuo
Seibutsu Butsuri 53 (1) 2013
1SAA-03 QM/MM study on the photosystem II oxygen evolving complex at the S1 state(1SAA Molecular mechanism of light-driven water oxidation : photosystem II and artificial photosynthesis,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)
Shoji Mitsuo, Isobe Hiroshi, Yamanaka Shusuke, Kamiya Nobuo, Shen Jian-Ren, Yamaguchi Kizashi
Seibutsu Butsuri 53 (1) 2013
OpenFMOにおけるFock行列計算ルーチンのGPGPU化
梅田宏明, 塙敏博, 庄司光男, 朴泰祐
分子科学討論会講演プログラム&要旨(Web) 7th 2013
OpenFMOにおけるFock行列計算のGPGPUによる高速化への取り組み
梅田宏明, 塙敏博, 庄司光男, 朴泰祐
日本コンピュータ化学会年会講演予稿集 2013 2013
OpenFMOにおけるFock行列計算ルーチンのGPGPU化について
梅田宏明, 塙敏博, 庄司光男, 朴泰祐
日本コンピュータ化学会年会講演予稿集 2013 2013
3PT222 QM/MM study on the reaction mechanism of assimilatory nitrite reductase(The 50th Annual Meeting of the Biophysical Society of Japan)
Shoji Mitsuo, Hanaoka Kyohei, Kondo Daiki, Umeda Hiroaki, Kayanuma Megumi, Kamiya Katsumasa, Shiraishi Kenji, Nakano Shogo, Katayanagi Katsuo
Seibutsu Butsuri 52 2012
Theory of Chemical Bonds in Metalloenzymes. XVII. Symmetry Breaking in Manganese Cluster Structures and Chameleonic Mechanisms for the O-O Bond Formation of Water Splitting Reaction
Saito Toru, Shoji Mitsuo, Kanda Keita, Isobe Hiroshi, Yamanaka Shusuke, Kitagawa Yasutaka, Yamada Satoru, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi Kizashi
International Journal of Quantum Chemistry 112 (1) 2012[Refereed]
演算加速装置に基づく超並列クラスタHA-PACSによる大規模計算科学
朴, 泰祐, 佐藤, 三久, 塙, 敏博, 児玉, 祐悦, 高橋, 大介, 建部, 修見, 多田野, 寛人, 藏増, 嘉伸, 吉川, 耕司, 庄司, 光男
IPSJ SIG Notes 2011 (21) Jul 2011
Theoretical studies on electronic structure and magnetic properties of mixed-valence uteroferrin active site
Kenichi Koizumi, Mitsuo Shoji, Kizashi Yamaguchi, Haruki Nakamura
International Journal of Quantum Chemistry 111 (3) Mar 2011[Refereed]
1D1336 Theoretical Investigation of Structural Stability of β-Helix Model for Amyloid Fibrils from Yeast Prion Sup35(Protein: Property 1,The 49th Annual Meeting of the Biophysical Society of Japan)
Kondo Daiki, Hanaoka Kyohei, Yang Moonyoung, Kamiya Katsumasa, Shoji Mitsuo, Kawai-Noma Shigeko, Taguchi Hideki, Shiraishi Kenji
Seibutsu Butsuri 51 2011
3C1048 Theoretical investigation on the substrate binding states of nitric oxide reductase(3C Protein: Funcrion 2,The 49th Annual Meeting of the Biophysical Society of Japan)
Shoji Mitsuo, Kondo Daiki, Hanaoka Kyouhei, Yang Moonyoung, Umeda Hiroaki, Kamiya Norimasa, Shiraishi Kenji
Seibutsu Butsuri 51 2011
Theory of Chemical Bonds in Metalloenzymes. XV. Local Singlet and Triplet Diradical Mechanisms for Radical Coupling Reactions in the Oxygen Evolution Complex
Yamaguchi Kizashi, Shoji Mitsuo, Saito Toru, Isobe Hiroshi, Nishihara Satomichi, Koizumi Kenichi, Yamada Satoru, Kawakami Takashi, Kitagawa Yasutaka, Yamanaka Shusuke, Okumura Mitsutaka
International Journal of Quantum Chemistry 110 (15) 2010[Refereed]
Theory of Chemical Bonds in Metalloenzymes. XIV. Correspondence Between Magnetic Coupling Mode and Radical Coupling Mechanism in Hydroxylations with Methane Monooxygenase and Related Species
Saito Toru, Shoji Mitsuo, Isobe Hiroshi, Yamanaka Shusuke, Kitagawa Yasutaka, Yamada Satoru, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi Kizashi
International Journal of Quantum Chemistry 110 (15) 2010[Refereed]
Development of a New Molecular Visualization Package : Makiko
SHOJI Mitsuo, SHOJI Makiko
Journal of Chemical Software 8 (1) Dec 2009
Theoretical study of magnetic interaction between C-60 anion radicals
Y. Kitagawa, Y. Nakanishi, T. Saito, K. Koizumi, M. Shoji, S. Yamada, T. Kawakami, M. Okumura, K. Yamaguchi
POLYHEDRON 28 (9-10) Oct 2009[Refereed]
Symmetry and Broken-Symmetry in Molecular Orbital Descriptions of Unstable Molecules. 3. The Nature of Chemical Bonds of Spin Frustrated Systems
T. Kawakami, R. Takeda, S. Nishihara, T. Saito, M. Shoji, S. Yamada, S. Yamanaka, Y. Kitagawa, M. Okumura, K. Yamaguchi
Journal of Physical Chemistry A 113 (52) Oct 2009[Refereed]
Quantum dynamic simulations for single molecular magnets using anisotropic spin models
T. Kawakami, H. Nitta, M. Takahata, M. Shoji, Y. Kitagawa, M. Nakano, M. Okumura, K. Yamaguchi
POLYHEDRON 28 (9-10) Jun 2009[Refereed]
Theory of chemical bonds in metalloenzymes XII: Electronic and spin structures of metallo-oxo and isoelectronic species and spin crossover phenomena in oxygenation reactions
Yamaguchi Kizashi, Shoji Mitsuo, Isobe Hiroshi, Yamanaka Syusuke, Shimada Jiro, Kitagawa Yasutaka, Okumura Mitsutaka
Polyhedron 28 (9-10) 2009[Refereed]
Theory of Chemical Bonds in Metalloenzymes XIII: Singlet and Triplet Diradical Mechanisms of Hydroxylations With Iron-Oxo Species and P450 are Revisited
Yamaguchi Kizashi, Yamanaka Syusuke, Isobe Hiroshi, Shoji Mitsuo, Saito Toru, Kitagawa Yasutaka, Okumura Mitsutaka, Shimada Jiro
International Journal of Quantum Chemistry 109 (15) 2009[Refereed]
Extended Hartree-Fock Theory of Chemical Reactions. IX. Diradical and Perepoxide Mechanisms for Oxygenations of Ethylene With Molecular Oxygen and Iron-Oxo Species Are Revisited
Yamaguchi Kizashi, Yamanaka Syusuke, Shimada Jiro, Isobe Hiroshi, Saito Toru, Shoji Mitsuo, Kitagawa Yasutaka, Okumura Mitsutaka
International Journal of Quantum Chemistry 109 (15) 2009[Refereed]
Approximately Spin-Projected Hessian for Broken Symmetry Method and Stretching Frequencies of F-2 and Singlet O-2
Kitagawa Yasutaka, Saito Toru, Nakanishi Yasuyuki, Kataoka Yusuke, Shoji Mitsuo, Koizumi Kenichi, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi Kizashi
International Journal of Quantum Chemistry 109 (15) 2009[Refereed]
Theoretical studies on the structure and effective exchange integral (J(ab)) of an active site in oxyhemocyanin (oxyHc) by using approximately spin-projected geometry optimization (AP-opt) method
T. Saito, Y. Kitagawa, M. Shoji, Y. Nakanishi, M. Ito, T. Kawakami, M. Okumura, K. Yamaguchi
Chemical Physics Letters 456 (1-3) Oct 2008[Refereed]
Theoretical Studies on Effects of Hydrogen Bonds Attaching to Cysteine Ligands on 4Fe-4S Clusters
Kitagawa, M. Shoji, T. Saito, Y. Nakanishi, K. Koizumi, T. Kawakami, M. Okumura, K. Yamaguchi
International Journal of Quantum Chemistry 108 (15) Oct 2008[Refereed]
Extended hartree-fock theory of chemical reactions. VIII. hydroxylation reactions by P450
Hiroshi Isobe, Satomichi Nishihara, Mitsuo Shoji, Shusuke Yamanaka, Jiro Shimada, Masayuki Hagiwara, Kizashi Yamaguchi
International Journal of Quantum Chemistry 108 (15) 2008[Refereed]
Theory of chemical bonds in metalloenzymes. VII. Hybrid-density functional theory studies on the electronic structures of P450
Shoji Mitsuo, Isobe Hiroshi, Saito Toru, Yabushita Hirotaka, Koizumi Kenichi, Kitagawa Yasutaka, Yamanaka Shusuke, Kawakami Takashi, Okumura Mitsutaka, Hagiwara Masayuki, Yamaguchi Kizashi
International Journal of Quantum Chemistry 108 (4) 2008[Refereed]
Theory of Chemical Bonds in Metalloenzymes XI: Full Geometry Optimization and Vibration Analysis of Porphyrin Iron-Oxo Species
Shoji Mitsuo, Isobe Hiroshi, Saito Toru, Kitagawa Yasutaka, Yamanaka Shusuke, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi Kizashi
International Journal of Quantum Chemistry 108 (15) 2008[Refereed]
Theoretical investigation of the magnetic interactions of Ni-9 complexes
Shoji Mitsuo, Kitagawa Yasutaka, Kawakami Takashi, Yamanaka Shusuke, Okumura Mitsutaka, Yamaguchi Kizashi
Journal of Physical Chemistry a 112 (17) 2008[Refereed]
Density functional study of manganese dimer
Shusuke Yamanaka, Takeshi Ukai, Kazuto Nakata, Ryo Takeda, Mitsuo Shoji, Takashi Kawakami, Toshikazu Takada, Kizashi Yamaguchi
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 107 (15) Dec 2007
Ab initio studies on the zero-field splitting parameters of manganese porphyrin complexes
Ryo Takeda, K. Koizumi, M. Shoji, H. Nitta, S. Yamanaka, M. Okumura, K. Yamaguchi
POLYHEDRON 26 (9-11) Jun 2007[Refereed]
Ab initio calculation of the Dzyaloshinskii-Moriya parameters: Spin-orbit GSO-HF, HFT, and CI approaches
R. Takeda, S. Yamanaka, M. Shoji, K. Yamaguchi
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 107 (6) May 2007[Refereed]
Quantum spin correction scheme based on spin-correlation functional for Kohn-Sham spin density functional theory
Shusuke Yamanaka, Ryo Takeda, Kazuto Nakata, Toshikazu Takada, Mitsuo Shoji, Yasutaka Kitagawa, Kizashi Yamaguchi
JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS 310 (2) Mar 2007[Refereed]
Theory of chemical bonds in metalloenzymes. IX. Theoretical study on the active site of the ribonucieotide reductase and the related species
Shoji Mitsuo, Isobe Hiroshi, Takano Yu, Kitagawa Yasutaka, Yamanaka Shusuke, Okumura Mitsutaka, Yamaguchi Kizashi
International Journal of Quantum Chemistry 107 (15) 2007[Refereed]
Theoretical studies on ferromagnetic behavior of [Cr(C-5(CH3)(5))(2)](+)[TCNE](-) and [Mn(C-5(CH3)(5))(2)](+)[TCNQ](-)
Koizumi Kenichi, Shoji Mitsuo, Kitagawa Yasutaka, Takeda Ryo, Yamanaka Shusuke, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi Kizashi
Polyhedron 26 (9-11) 2007[Refereed]
Geometry optimization method based on approximate spin projection and its application to F(2), CH(2), CH(2)OO, and active site of urease
Kitagawa Yasutaka, Saito Toru, Ito Masahide, Nakanishi Yasuyuki, Shoji Mitsuo, Koizumi Kenichi, Yamanaka Shusuke, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi Kizashi
International Journal of Quantum Chemistry 107 (15) 2007[Refereed]
Assignments of the Mossbauer spectra of an inorganic [8fe-7S] complex based on the first-principle calculations
Shoji Mitsuo, Saito Toru, Takeda Ryo, Kitagawa Yasutaka, Kawakami Takashi, Yamanaka Shusuke, Okumura Mitutaka, Yamaguchi Kizashi
Chemical Physics Letters 446 (1-3) 2007[Refereed]
A GSO-HDFT study of noncollinear spin structures of [2Fe-2S] cluster
Shoji Mitsuo, Koizumi Kenichi, Takeda Ryo, Kitagawa Yasutaka, Yamanaka Shusuke, Okumura Mitsutaka, Yamaguchi Kizashi
Polyhedron 26 (9-11) 2007[Refereed]
Theory of chemical bonds in metalloenzymes V: Hybrid-DFT studies of the inorganic [8Fe-7S] core
M. Shoji, K. Koizumi, Y. Kitagawa, S. Yamanaka, M. Okumura, K. Yamaguchi, Y. Ohki, Y. Sunada, M. Honda, K. Tatsumi
International Journal of Quantum Chemistry 106 (15) Dec 2006
The electronic structure and magnetic property of μ-hydroxo bridged manganese porphyrin dimer
K. Koizumi, M. Shoji, Y. Kitagawa, H. Ohoyama, T. Kasai, K. Yamaguchi
European Physical Journal D 38 (1) Apr 2006
Quantum dynamics of exciton recurrence motion in dendritic molecular aggregates
H Nitta, M Shoji, M Takahata, M Nakano, D Yamaki, K Yamaguchi
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 178 (2-3) Mar 2006[Refereed]
Theoretical study on the electronic structure of [4Fe-4S] cluster
M. Shoji, K. Koizumi, Y. Kitagawa, T. Kawakami, S. Yamanaka, M. Okumura, K. Yamaguchi
RECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND 7B 7A-B 2006[Refereed]
Hybrid-DFT study on the high-valent metal-oxo bonds in manganese porphyrins and related species
K. Koizumi, M. Shoji, Y. Kitagawa, H. Isobe, R. Takeda, S. Yamanaka, K. Yamaguchi
RECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND 7B 7A-B 2006[Refereed]
Search for the ground states of ising spin clusters by using the genetic algorithms
Akifumi Oda, Hidemi Nagao, Yasutaka Kitagawa, Yasuteru Shigeta, Mitsuo Shoji, Hiroya Nitta, Mitsutaka Okumura, Kizashi Yamaguchi
International Journal of Quantum Chemistry 105 (6) Dec 2005[Refereed]
Quantum spin correction scheme for ab initio spin-unrestricted solutions: Multiple bonds case
S Yamanaka, R Takeda, M Shoji, Y Kitagawa, H Honda, K Yamaguchi
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 105 (6) Dec 2005[Refereed]
Quantum dynamics in high-spin molecules, spin dendrimers, and spin lattices
M Takahata, M Shoji, H Nitta, R Takeda, S Yamanaka, M Okumura, M Nakano, K Yamaguchi
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 105 (6) Dec 2005[Refereed]
Theoretical study on the magnetic interactions of active site in hemerythrin
M. Shoji, T. Hamamoto, K. Koizumi, H. Isobe, Y. Kitagawa, Y. Takano, S. Yamanaka, M. Okumura, K. Yamaguchi
Polyhedron, 2005, 40, 2701-2707 24 (16-17) Nov 2005[Refereed]
Theoretical studies on magnetic interactions between Ni(II) ions in Urease
Y. Maruno, M. Shoji, K. Koizumi, Y. Nishiyama, Y. Kitagawa, T. Kawakami, M. Okumura, K. Yamaguchi
Polyhedron, 2005, 24, 2751-2757 24 (16-17) Nov 2005[Refereed]
Theoretical studies on magnetic interactions and charge-dope effects in one-dimensional Ni5 and Ni7 complexes
Y. Kitagawa, M. Shoji, K. Koizumi, T. Kawakami, M. Okumura, K. Yamaguchi
Polyhedron, 2005, 24, 2778-2783 24 (16-17) Nov 2005[Refereed]
Theoretical studies on ferrimagnetic behavior of TCNE and manganese porphyrin dimer
K. Koizumi, M. Shoji, Y. Kitagawa, T. Taniguchi, T. Kawakami, M. Okumura, K. Yamaguchi
Polyhedron, 2005, 24, 2720-2725 24 (16-17) Nov 2005[Refereed]
Theoretical studies on dissociation of metal-carbon bond in Cobalamin;- formulation and calculation -
Y. Nishiyama, M. Shoji, K. Koizumi, Y. Maruno, Y. Kitagawa, T. Kawakami, M. Okumura, K. Yamaguchi
Polyhedron, 2005, 24, 2745-2750 24 (16-17) Nov 2005[Refereed]
A theoretical study of zero-field splitting of organic biradicals
M Shoji, K Koizumi, T Hamamoto, T Taniguchi, R Takeda, Y Kitagawa, T Kawakami, M Okumura, S Yamanaka, K Yamaguchi
POLYHEDRON 24 (16-17) Nov 2005[Refereed]
Theoretical direct evaluation of inter-dimer J values in BETS salts
T Kawakami, T Taniguchi, M Shoji, Y Kitagawa, M Okumura, K Yamaguchi
POLYHEDRON 24 (16-17) Nov 2005[Refereed]
Ab initio GSO-DFT study of spin-frustrated transition metal systems
S Yamanaka, R Takeda, M Shoji, K Koizumi, Y Kitagawa, K Yamaguchi
POLYHEDRON 24 (16-17) Nov 2005[Refereed]
Formulation of master equation approach involving spin-phonon coupling: Toward an understanding of spin dynamics in magnetic dendrimers
M Takahata, M Shoji, S Yamanaka, M Nakano, K Yamaguchi
POLYHEDRON 24 (16-17) Nov 2005[Refereed]
Theory of chemical bonds in metalloenzymes II: Hybrid-DFT studies in iron-sulfur clusters
M. Shoji, K. Koizumi, Y. Kitagawa, S. Yamanaka, T. Kawakami, M. Okumura, K. Yamaguchi
Int. J. Quant. Chem., 2005, 105, 628-644 105 (6) Oct 2005[Refereed]
A quantum chemical study of magnetic interactions in phenazine derivatives for chemical or photo-induced organic magnets
Takeshi Taniguchi, Yuji Watazu, Mitsuo Shoji, Takashi Kawakami, Mitsutaka Okumura, Kizashi Yamaguchi
Synthetic Metals 154 (1-3) Oct 2005[Refereed]
Theory of chemical bonds in metalloenzymes I:Analytical and hybrid-DFT studies on oxo and hydroxo diiron cores
M. Shoji, Y. Nishiyama, Y. Maruno, K. Koizumi, Y. Kitagawa, S. Yamanaka, T. Kawakami, M. Okumura, K. Yamaguchi
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 100 (6) Nov 2004
Theoretical studies on effective exchange integrals by using spin correlation function analysis and magnetic effective density functional (MEDF) method
Y. Kitagawa, S. Yamanaka, R. Takeda, M. Shoji, K. Koizumi, Y. Nishiyama, Y. Maruno, T. Kawakami, M. Okumura, K. Yamaguchi
Int. J. Quant. Chem., 2004, 100, 927-936 100 (6) Oct 2004[Refereed]
The Electronic structure and magnetic propertiy of metal-oxo, porphyrin manganese-oxo and m-oxo-bridged manganese prophyrin dimmer
K. Koizumi, M. Shoji, Y. Nishiyama, Y. Maruno, Y. Kitagawa, K. Soda, S. Yamanaka, M. Okumura, K. Yamaguchi
Int. J. Quant. Chem., 2004, 100, 943-956 100 (6) Oct 2004[Refereed]
Hybrid density-functional theory studies on stable polycarbenes
M Shoji, T Taniguchi, T Kawakami, K Yamaguchi
POLYHEDRON 22 (14-17) Jul 2003
Awards & Honors
▼▲
May 2023
量子生命科学会量子生命科学会研究奨励賞量子生命科学に関連する研究において顕著な業績を挙げた
May 2022
Best Presentation
Sep 2021
Best Presentation
Dec 2020
量子生命科学会量子生命科学会第二回大会優秀発表賞 (口頭発表) 銅含有アミン酸化酵素のプロトン化状態についてのQM/MM解析
Books etc
▼▲
ADVANCES IN QUANTUM CHEMISTRY, VOL 84
Yamaguchi, Kizashi, Miyagawa, Koichi, Isobe, Hiroshi, Shoji, Mitsuo, Kawakami, Takashi, Yamanaka, Shusuke ( Isolobal and isospin analogy between organic and inorganic open-shell molecules-Application to oxygenation reactions by active oxygen and oxy-radicals and water oxidation in the native and artificial photosynthesis)
環境技術
庄司,光男 (Role:Contributor, 量子化学計算ビギナーズガイド)
量子化学計算ビギナーズガイド
庄司光男 (Role:Sole author, 45-49)
Gaussian16で始める量子化学超入門
庄司, 光男 (Role:Sole author, フリーソフトで始める分子モデリング)
フリーソフトで始める分子モデリング
庄司, 光男 (Role:Sole author)
Research Grants & Projects
▼▲
Elucidation of the mechanisms for light-induced water-splitting and light energy utilization in photosynthesis
Grants-in-Aid for Scientific Research
Research period: Apr 2022 - Mar 2027
XFEL-SFXによる化学反応解明を目指した「反応追跡結晶」の構築
科学研究費助成事業
Research period: Apr 2022 - Mar 2026Representative: 上野隆史, 庄司光男, 南後恵理子
分子シミュレーションによるタンパク質化学反応ダイナミクスの解明
科学研究費助成事業
Research period: Apr 2020 - Mar 2024Representative: 宮下治, 庄司光男, 篠田恵子
時分割実験のための多様な反応誘起システムの開発
科学研究費助成事業
Research period: Jun 2019 - Mar 2024Representative: 南後恵理子, 清水伸隆, 大和田成起, 宮下治, 庄司光男, 篠田恵子
生体内量子多体系における特異的化学反応の機構解明
JST-PRESTO
Research period: Oct 2019 - Mar 2023Representative: 庄司光男
Elucidation of the various water splitting mechanism used for natural, semiconductors and molecular catalyses
Grants-in-Aid for Scientific Research
Research period: Apr 2020 - Mar 2022
Theoretical elucidation of the reactivation mechanism of the oxygen-evolving complex in photosystem II
Grants-in-Aid for Scientific Research
Research period: Apr 2018 - Mar 2020
Elucidation of the complete reaction pathways of the water decomposition reactions in the oxygen-evolving complex of photosystem II
Grants-in-Aid for Scientific Research
Research period: Apr 2017 - Mar 2020Representative: Shoji Mitsuo
Elucidation of enzyme catalytic mechanism regulating transition state by linking conformational change and fluctuations of the active site
Grants-in-Aid for Scientific Research
Research period: Jul 2016 - Mar 2020Representative: Okajima Toshihide
Theoretical Challenge in Astrobiology by Computational Science
Grants-in-Aid for Scientific Research
Research period: Apr 2016 - Mar 2019Representative: Aikawa Yuri
Concerted proton/electron transfer mechanism in cofactor-dependent enzyme
Grants-in-Aid for Scientific Research
Research period: Apr 2015 - Mar 2019Representative: HAYASHI Hideyuki, SHOJI mitsuo
Theoretical elucidation on the full reaction mechanisms of threonine synthase
Grants-in-Aid for Scientific Research
Research period: Apr 2014 - Mar 2017Representative: SHOJI MITSUO, HAYASHI HIDEYUKI, UJIIE YUZURU, TANAKA WATARU
Elucidation of the mechanism of water-splitting in photosystem II
Grants-in-Aid for Scientific Research
Research period: 2012 - 2017Representative: SHEN Jian-Ren, NOGUCHI Takumi, YAMAGUCHI Kizashi, SHOJI Mitsuo, SUGA Michihiro, AKITA Fusamichi, MINO Hiroyuki, KATO Yuki, ISOBE Hiroshi
Reaction specificity of pyridoxal enzymes
Grants-in-Aid for Scientific Research
Research period: Apr 2012 - Mar 2016Representative: Hayashi Hideyuki, Murakawa Takeshi, Shoji Mitsuo
Theoretical elucidations of the reactions and the reaction-control mechanisms in enzymes
Grants-in-Aid for Scientific Research
Research period: Apr 2012 - Mar 2014Representative: SHOJI Mitsuo
酵素反応機構の解明、生物無機化学、分子動力学、分子磁性、多核金属錯体、可視化プログラム(Makiko)

	氏名	谷一寿
	Name	TANI Kazutoshi
	Faculty
	Section
	Position	Professor
	Theme	Structural Analysis of Protein Compelexes using cryo-electron microscopy (cryo-EM)
	Related Links	trios researchmap
	Email	ktaniccs.tsukuba.ac.jp

Research Interests
Academic & Professional Experience
Dec 2023
-
Present
University of Tsukuba Center for Computational Sciences Professor
Apr 2019
-
Nov 2023
Mie University Graduate School of Medicine
Apr 2015
-
Mar 2019
Nagoya University Cellular and Structural Physiology Institute Division Designated professor
Apr 2012
-
Mar 2015
Nagoya University Cellular and Structural Physiology Institute Division Designated associate professor
Published Papers
▼▲
A distinct double-ring LH1–LH2 photocomplex from an extremophilic phototroph
Kazutoshi Tani, Kenji V. P. Nagashima, Risa Kojima, Masaharu Kondo, Ryo Kanno, Issei Satoh, Mai Kawakami, Naho Hiwatashi, Kazuna Nakata, Sakiko Nagashima, Kazuhito Inoue, Yugo Isawa, Ryoga Morishita, Shinichi Takaichi, Endang R. Purba, Malgorzata Hall, Long-Jiang Yu, Michael T. Madigan, Akira Mizoguchi, Bruno M. Humbel, Yukihiro Kimura, Yutaka Nagasawa, Takehisa Dewa, Zheng-Yu Wang-Otomo
Nature Communications 16 (1) Feb 2025[Refereed]
A Native LH1–RC–HiPIP Supercomplex from an Extremophilic Phototroph
Kazutoshi Tani, Ryo Kanno, Kenji V. P. Nagashima, Mai Kawakami, Naho Hiwatashi, Kazuna Nakata, Sakiko Nagashima, Kazuhito Inoue, Shinichi Takaichi, Endang R. Purba, Malgorzata Hall, Long-Jiang Yu, Michael T. Madigan, Akira Mizoguchi, Bruno M. Humbel, Yukihiro Kimura, Zheng-Yu Wang-Otomo
Communications Biology 8 (1) Jan 2025[Refereed]
The Thermal-Stable LH1–RC Complex of a Hot Spring Purple Bacterium Powers Photosynthesis with Extremely Low-Energy Near-Infrared Light
Yukihiro Kimura, Ryo Kanno, Kaisei Mori, Yoshiki Matsuda, Ryuta Seto, Shinji Takenaka, Hiroyuki Mino, Tatsunari Ohkubo, Mai Honda, Yuji C. Sasaki, Jun-ichi Kishikawa, Kaoru Mitsuoka, Kazuhiro Mio, Malgorzata Hall, Endang R. Purba, Toshiaki Mochizuki, Akira Mizoguchi, Bruno M. Humbel, Michael T. Madigan, Zheng-Yu Wang-Otomo, Kazutoshi Tani
Biochemistry Dec 2024[Refereed]
Structure of endothelin ETB receptor–Gi complex in a conformation stabilized by unique NPxxL motif
Kazutoshi Tani, Saori Maki-Yonekura, Ryo Kanno, Tatsuki Negami, Tasuku Hamaguchi, Malgorzata Hall, Akira Mizoguchi, Bruno M. Humbel, Tohru Terada, Koji Yonekura, Tomoko Doi
Communications Biology 7 Oct 2024[Refereed]
High-resolution structure and biochemical properties of the LH1–RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum
Kazutoshi Tani, Ryo Kanno, Ayaka Harada, Yuki Kobayashi, Akane Minamino, Shinji Takenaka, Natsuki Nakamura, Xuan-Cheng Ji, Endang R. Purba, Malgorzata Hall, Long-Jiang Yu, Michael T. Madigan, Akira Mizoguchi, Kenji Iwasaki, Bruno M. Humbel, Yukihiro Kimura, Zheng-Yu Wang-Otomo
Communications Biology 7 (1) Feb 2024[Refereed]
Rhodobacter capsulatus forms a compact crescent-shaped LH1-RC photocomplex.
Kazutoshi Tani, Ryo Kanno, Xuan-Cheng Ji, Itsusei Satoh, Yuki Kobayashi, Malgorzata Hall, Long-Jiang Yu, Yukihiro Kimura, Akira Mizoguchi, Bruno M Humbel, Michael T Madigan, Zheng-Yu Wang-Otomo
Nature communications 14 (1) Feb 2023[Refereed]
Advances in the Spectroscopic and Structural Characterization of Core Light-Harvesting Complexes from Purple Phototrophic Bacteria
Yukihiro Kimura, Kazutoshi Tani, Michael T. Madigan, Zheng-Yu Wang-Otomo
The Journal of Physical Chemistry B Jan 2023[Refereed]
An LH1–RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteins
Kazutoshi Tani, Ryo Kanno, Keigo Kurosawa, Shinichi Takaichi, Kenji V. P. Nagashima, Malgorzata Hall, Long-Jiang Yu, Yukihiro Kimura, Michael T. Madigan, Akira Mizoguchi, Bruno M. Humbel, Zheng-Yu Wang-Otomo
Communications Biology 5 (1) Nov 2022[Refereed]
A Ca2+-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes.
Kazutoshi Tani, Kazumi Kobayashi, Naoki Hosogi, Xuan-Cheng Ji, Sakiko Nagashima, Kenji V P Nagashima, Airi Izumida, Kazuhito Inoue, Yusuke Tsukatani, Ryo Kanno, Malgorzata Hall, Long-Jiang Yu, Isamu Ishikawa, Yoshihiro Okura, Michael T Madigan, Akira Mizoguchi, Bruno M Humbel, Yukihiro Kimura, Zheng-Yu Wang-Otomo
The Journal of biological chemistry 298 (6) Apr 2022[Refereed]
Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex.
Kazutoshi Tani, Ryo Kanno, Riku Kikuchi, Saki Kawamura, Kenji V P Nagashima, Malgorzata Hall, Ai Takahashi, Long-Jiang Yu, Yukihiro Kimura, Michael T Madigan, Akira Mizoguchi, Bruno M Humbel, Zheng-Yu Wang-Otomo
Nature communications 13 (1) Apr 2022[Refereed]
Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.
Maki Kuzuya, Hidemi Hirano, Kenichi Hayashida, Masakatsu Watanabe, Kazumi Kobayashi, Tohru Terada, Md Iqbal Mahmood, Florence Tama, Kazutoshi Tani, Yoshinori Fujiyoshi, Atsunori Oshima
Science signaling 15 (720) Feb 2022[Refereed]
A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplex
Kazutoshi Tani, Kenji V. P. Nagashima, Ryo Kanno, Saki Kawamura, Riku Kikuchi, Malgorzata Hall, Long-Jiang Yu, Yukihiro Kimura, Michael T. Madigan, Akira Mizoguchi, Bruno M. Humbel, Zheng-Yu Wang-Otomo
Nature Communications 12 (1) Nov 2021[Refereed]
Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum.
Kazutoshi Tani, Ryo Kanno, Xuan-Cheng Ji, Malgorzata Hall, Long-Jiang Yu, Yukihiro Kimura, Michael T Madigan, Akira Mizoguchi, Bruno M Humbel, Zheng-Yu Wang-Otomo
Biochemistry 62 Jul 2021[Refereed]
Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.
Keito Hiragi, Kazuya Nishio, Shu Moriyama, Tasuku Hamaguchi, Akira Mizoguchi, Koji Yonekura, Kazutoshi Tani, Tsunehiro Mizushima
Journal of structural biology 213 (3) May 2021[Refereed]
Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides.
Kazutoshi Tani, Ryo Kanno, Yuki Makino, Malgorzata Hall, Mizuki Takenouchi, Michie Imanishi, Long-Jiang Yu, Jörg Overmann, Michael T Madigan, Yukihiro Kimura, Akira Mizoguchi, Bruno M Humbel, Zheng-Yu Wang-Otomo
Nature communications 11 (1) Oct 2020[Refereed]
Characterization of Critical Residues in the Extracellular and Transmembrane Domains of the Endothelin Type B Receptor for Propagation of the Endothelin-1 Signal.
Tomoko Doi, Kohei Kikuta, Kazutoshi Tani
Biochemistry 59 (18) May 2020[Refereed]
Development of a deep learning-based method to identify “good” regions of a cryo-electron microscopy grid
Yuichi Yokoyama, Tohru Terada, Kentaro Shimizu, Kouki Nishikawa, Daisuke Kozai, Atsuhiro Shimada, Akira Mizoguchi, Yoshinori Fujiyoshi, Kazutoshi Tani
Biophysical Reviews 12 Mar 2020[Refereed]
Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids
Batuujin Burendei, Ruriko Shinozaki, Masakatsu Watanabe, Tohru Terada, Kazutoshi Tani, Yoshinori Fujiyoshi, Atsunori Oshima
Science Advances 6 Feb 2020[Refereed]
Structural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopy
Hiroki Yamaguchi, Akiko Kamegawa, Kunio Nakata, Tatsuki Kashiwagi, Toshimi Mizukoshi, Yoshinori Fujiyoshi, Kazutoshi Tani
Journal of Structural Biology 205 (1) Jan 2019[Refereed]
X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog
Wataru Shihoya, Tomohiro Nishizawa, Keitaro Yamashita, Asuka Inoue, Kunio Hirata, Francois Marie Ngako Kadji, Akiko Okuta, Kazutoshi Tani, Junken Aoki, Yoshinori Fujiyoshi, Tomoko Doi, Osamu Nureki
NATURE STRUCTURAL & MOLECULAR BIOLOGY 24 (9) Sep 2017[Refereed]
The cryo-EM structure of gastric H+, K+-ATPase with bound BYK99, a high-affinity member of K+-competitive, imidazo[1,2-a]pyridine inhibitors
Kazuhiro Abe, Jun Shimokawa, Mao Naito, Keith Munson, Olga Vagin, George Sachs, Hiroshi Suzuki, Kazutoshi Tani, Yoshinori Fujiyoshi
SCIENTIFIC REPORTS 7 (1) Jul 2017[Refereed]
Crystal structures of claudins: insights into their intermolecular interactions
Hiroshi Suzuki, Kazutoshi Tani, Yoshinori Fujiyoshi
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES 1397 (1) Jun 2017[Refereed]
Atomic structure of the innexin-6 gap junction channel determined by cryo-EM
Atsunori Oshima, Kazutoshi Tani, Yoshinori Fujiyoshi
NATURE COMMUNICATIONS 7 Dec 2016[Refereed]
Activation mechanism of endothelin ETB receptor by endothelin-1
Wataru Shihoya, Tomohiro Nishizawa, Akiko Okuta, Kazutoshi Tani, Naoshi Dohmae, Yoshinori Fujiyoshi, Osamu Nureki, Tomoko Doi
NATURE 537 (7620) Sep 2016[Refereed]
Thermostabilization of the Human Endothelin Type B Receptor
Akiko Okuta, Kazutoshi Tani, Shoko Nishimura, Yoshinori Fujiyoshi, Tomoko Doi
JOURNAL OF MOLECULAR BIOLOGY 428 (11) Jun 2016[Refereed]
Two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes
Yukiho Osuda, Kyoko Shinzawa-Itoh, Kazutoshi Tani, Shintaro Maeda, Shinya Yoshikawa, Tomitake Tsukihara, Christoph Gerle
MICROSCOPY 65 (3) Jun 2016[Refereed]
Structure and inhibitor of water channel in brain
Yukihiro Tanimura, Kazutoshi Tani, Hiroshi Suzuki, Kouki Nishikawa, Akiko Kamegawa, Yoko Hiroaki, Yoshinori Fujiyoshi
Water: The Forgotten Biological Molecule Apr 2016
Two-dimensional crystal structure of aquaporin-4 bound to the inhibitor acetazolamide
Akiko Kamegawa, Yoko Hiroaki, Kazutoshi Tani, Yoshinori Fujiyoshi
MICROSCOPY 65 (2) Apr 2016[Refereed]
Claudin-21 Has a Paracellular Channel Role at Tight Junctions
Hiroo Tanaka, Yasuko Yamamoto, Hiroka Kashihara, Yuji Yamazaki, Kazutoshi Tani, Yoshinori Fujiyoshi, Katsuhiko Mineta, Kosei Takeuchi, Atsushi Tamura, Sachiko Tsukita
MOLECULAR AND CELLULAR BIOLOGY 36 (6) Mar 2016[Refereed]
Hexadecameric structure of an invertebrate gap junction channel
Oshima, Atsunori, Matsuzawa, Tomohiro, Murata, Kazuyoshi, Tani, Kazutoshi, Fujiyoshi, Yoshinori
JOURNAL OF MOLECULAR BIOLOGY 428 (6) Mar 2016[Refereed]
Three-Dimensional Structure of Innexin GAP Junction Channels Studied by Electron Crystallography
Oshima Atsunori, Matsuzawa Tomohiro, Murata Kazuyoshi, Tani Kazutoshi, Fujiyoshi Yoshinori
BIOPHYSICAL JOURNAL 110 (3) Feb 2016[Refereed]
Bovine F1Fo ATP synthase monomers bend the lipid bilayer in 2D membrane crystals
Chimari Jiko, Karen M. Davies, Kyoko Shinzawa-Itoh, Kazutoshi Tani, Shintaro Maeda, Deryck J. Mills, Tomitake Tsukihara, Yoshinori Fujiyoshi, Werner Kuehlbrandt, Christoph Gerle
ELIFE 4 (4) Mar 2015[Refereed]
Structural insight into tight junction disassembly by Clostridium perfringens enterotoxin
Yasunori Saitoh, Hiroshi Suzuki, Kazutoshi Tani, Kouki Nishikawa, Katsumasa Irie, Yuki Ogura, Atsushi Tamura, Sachiko Tsukita, Yoshinori Fujiyoshi
SCIENCE 347 (6223) Feb 2015[Refereed]
Model for the Architecture of Claudin-Based Paracellular Ion Channels through Tight Junctions
Hiroshi Suzuki, Kazutoshi Tani, Atsushi Tamura, Sachiko Tsukita, Yoshinori Fujiyoshi
JOURNAL OF MOLECULAR BIOLOGY 427 (2) Jan 2015[Refereed]
Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating
Kazuhiro Abe, Kazutoshi Tani, Yoshinori Fujiyoshi
JOURNAL OF BIOLOGICAL CHEMISTRY 289 (44) Oct 2014[Refereed]
Water channel structures analysed by electron crystallography
Tani, K., Fujiyoshi, Y.
Biochimica et Biophysica Acta - General Subjects 1840 (5) May 2014[Refereed]
Crystal Structure of a Claudin Provides Insight into the Architecture of Tight Junctions
Hiroshi Suzuki, Tomohiro Nishizawa, Kazutoshi Tani, Yuji Yamazaki, Atsushi Tamura, Ryuichiro Ishitani, Naoshi Dohmae, Sachiko Tsukita, Osamu Nureki, Yoshinori Fujiyoshi
SCIENCE 344 (6181) Apr 2014[Refereed]
Three-dimensional structure of bovine heart NADH: ubiquinone oxidoreductase (complex I) by electron microscopy of a single negatively stained two-dimensional crystal
Satoru Shimada, Kyoko Shinzawa-Itoh, Satoko Amano, Yui Akira, Atsuo Miyazawa, Tomitake Tsukihara, Kazutoshi Tani, Christoph Gerle, Shinya Yoshikawa
MICROSCOPY 63 (2) Apr 2014[Refereed]
Two-dimensional crystallization of intact F-ATP synthase isolated from bovine heart mitochondria
Shintaro Maeda, Kyoko Shinzawa-Itoh, Kaoru Mieda, Mami Yamamoto, Yumiko Nakashima, Yumi Ogasawara, Chimari Jiko, Kazutoshi Tani, Atsuo Miyazawa, Christoph Gerle, Shinya Yoshikawa
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 69 (12) Dec 2013[Refereed]
Carbon sandwich preparation preserves quality of two-dimensional crystals for cryo-electron microscopy
Fan Yang, Kazuhiro Abe, Kazutoshi Tani, Yoshinori Fujiyoshi
MICROSCOPY 62 (6) Dec 2013[Refereed]
Two alternative conformations of a voltage-gated sodium channel
Ching-Ju Tsai, Kazutoshi Tani, Katsumasa Irie, Yoko Hiroaki, Takushi Shimomura, Duncan G. McMillan, Gregory M. Cook, Gebhard F.X. Schertler, Yoshinori Fujiyoshi, Xiao-Dan Li
Journal of Molecular Biology 425 (22) Nov 2013[Refereed]
Visualization of two distinct states of disassembly in the bacterial V-ATPase from Thermus thermophilus
Kazutoshi Tani, Christopher P. Arthur, Masatada Tamakoshi, Ken Yokoyama, Kaoru Mitsuoka, Yoshinori Fujiyoshi, Christoph Gerle
MICROSCOPY 62 (4) Aug 2013[Refereed]
The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat.
Hiroshi Suzuki, Yasuyuki Ito, Yuji Yamazaki, Katsuhiko Mineta, Masami Uji, Kazuhiro Abe, Kazutoshi Tani, Yoshinori Fujiyoshi, Sachiko Tsukita
Nature communications 4 2013[Refereed]
Strand formation by a trimeric unit repeat of four-transmembrane proteins in Euglena
H. Suzuki, Y. Ito, Y. Yamazaki, K. Mineta, M. Uji, K. Abe, K. Tani, Y. Fujiyoshi, S. Tsukita
Nat. Commun 4 2013[Refereed]
Cryo-EM structure of gastric H+,K+-ATPase with a single occupied cation-binding site
Kazuhiro Abe, Kazutoshi Tani, Thomas Friedrich, Yoshinori Fujiyoshi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 109 (45) Nov 2012[Refereed]
Water permeability and characterization of aquaporin-11
Kaya Yakata, Kazutoshi Tani, Yoshinori Fujiyoshi
JOURNAL OF STRUCTURAL BIOLOGY 174 (2) May 2011[Refereed]
Asymmetric Configurations and N-terminal Rearrangements in Connexin26 Gap Junction Channels
Oshima, Atsunori, Tani, Kazutoshi, Toloue, Masoud M., Hiroaki, Yoko, Smock, Amy, Inukai, Sayaka, Cone, Angela, Nicholson, Bruce J., Sosinsky, Gina E., Fujiyoshi, Yoshinori
JOURNAL OF MOLECULAR BIOLOGY 405 (3) Jan 2011[Refereed]
Conformational rearrangement of gastric H+,K+-ATPase induced by an acid suppressant
Kazuhiro Abe, Kazutoshi Tani, Yoshinori Fujiyoshi
NATURE COMMUNICATIONS 2 Jan 2011[Refereed]
Influence of the Cytoplasmic Domains of Aquaporin-4 on Water Conduction and Array Formation
Tadanori Mitsuma, Kazutoshi Tani, Yoko Hiroaki, Akiko Kamegawa, Hiroshi Suzuki, Hiroshi Hibino, Yoshihisa Kurachi, Yoshinori Fujiyoshi
JOURNAL OF MOLECULAR BIOLOGY 402 (4) Oct 2010[Refereed]
Structural and functional characterization of H+,K+-ATPase with bound fluorinated phosphate analogs
Kazuhiro Abe, Kazutoshi Tani, Yoshinori Fujiyoshi
JOURNAL OF STRUCTURAL BIOLOGY 170 (1) Apr 2010[Refereed]
Structure and inhibitor of water channel in brain
Tanimura, Y., Tani, K., Suzuki, H., Nishikawa, K., Kamegawa, A., Hiroaki, Y., Fujiyoshi, Y.
Water: The Forgotten Biological Molecule 2010
Inter-subunit interaction of gastric H+,K+-ATPase prevents reverse reaction of the transport cycle
Kazuhiro Abe, Kazutoshi Tani, Tomohiro Nishizawa, Yoshinori Fujiyoshi
EMBO JOURNAL 28 (11) Jun 2009[Refereed]
Mechanism of Aquaporin-4's Fast and Highly Selective Water Conduction and Proton Exclusion
Kazutoshi Tani, Tadanori Mitsuma, Yoko Hiroaki, Akiko Kamegawa, Kouki Nishikawa, Yukihiro Tanimura, Yoshinori Fujiyoshi
JOURNAL OF MOLECULAR BIOLOGY 389 (4) Jun 2009[Refereed]
Structural analysis of 2D crystals of gastric H+,K+-ATPase in different states of the transport cycle
Tomohiro Nishizawa, Kazuhiro Abe, Kazutoshi Tani, Yoshinori Fujiyoshi
JOURNAL OF STRUCTURAL BIOLOGY 162 (2) May 2008[Refereed]
Projection structure of a N-terminal deletion mutant of connexin 26 channel with decreased central pore density.
Atsunori Oshima, Kazutoshi Tani, Yoko Hiroaki, Yoshinori Fujiyoshi, Gina E Sosinsky
Cell communication & adhesion 15 (1) May 2008[Refereed]
Dodecamer rotor ring defines H+/ATP ratio for ATP synthesis of prokaryotic V-ATPase from Thermus thermophilus
Masashi Toei, Christoph Gerle, Masahiro Nakano, Kazutoshi Tani, Nobuhiko Gyobu, Masatada Tamakoshi, Nobuhito Sone, Masasuke Yoshida, Yoshinori Fujiyoshi, Kaoru Mitsuoka, Ken Yokoyama
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104 (51) Dec 2007[Refereed]
Three-dimensional structure of a human connexin26 gap junction channel reveals a plug in the vestibule
Oshima, Atsunori, Tani, Kazutoshi, Hiroaki, Yoko, Fujiyoshi, Yoshinori, Sosinsky, Gina E.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104 (24) Jun 2007[Refereed]
Two dimensional crystallization and projection structure of a human connexin26
A. Oshima, K. Tani, Y. Hiroaki, Y. Fujiyoshi, G. E. Sosinsky
Microscopy and Microanalysis 12 (2) Aug 2006[Refereed]
Two-dimensional crystallization and analysis of projection images of intact Thermus thermophilus V-ATPase
C Gerle, K Tani, K Yokoyama, M Tamakoshi, M Yoshida, Y Fujiyoshi, K Mitsuoka
JOURNAL OF STRUCTURAL BIOLOGY 153 (2) Feb 2006[Refereed]
Implications of the aquaporin-4 structure on array formation and cell adhesion
Y Hiroaki, K Tani, A Kamegawa, N Gyobu, K Nishikawa, H Suzuki, T Walz, S Sasaki, K Mitsuoka, K Kimura, A Mizoguchi, Y Fujiyoshi
JOURNAL OF MOLECULAR BIOLOGY 355 (4) Jan 2006[Refereed]
Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich technique
N Gyobu, K Tani, Y Hiroaki, A Kamegawa, K Mitsuoka, Y Fujiyoshi
JOURNAL OF STRUCTURAL BIOLOGY 146 (3) Jun 2004[Refereed]
Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16)
T Maeda, M Inoue, S Koshiba, T Yabuki, M Aoki, E Nunokawa, E Seki, T Matsuda, Y Motoda, A Kobayashi, F Hiroyasu, M Shirouzu, T Terada, N Hayami, Y Ishizuka, N Shinya, A Tatsuguchi, M Yoshida, H Hirota, Y Matsuo, K Tani, T Arakawa, P Carninci, J Kawai, Y Hayashizaki, T Kigawa, S Yokoyama
JOURNAL OF BIOLOGICAL CHEMISTRY 279 (13) Mar 2004[Refereed]
Inositol 1,4,5-trisphosphate receptor contains multiple cavities and L-shaped ligand-binding domains
C Sato, K Hamada, T Ogura, A Miyazawa, K Iwasaki, Y Hiroaki, K Tani, A Terauchi, Y Fujiyoshi, K Mikoshiba
JOURNAL OF MOLECULAR BIOLOGY 336 (1) Feb 2004[Refereed]
Solution structure of a BolA-like protein from Mus musculus
T Kasai, M Inoue, S Koshiba, T Yabuki, M Aoki, E Nunokawa, E Seki, T Matsuda, N Matsuda, Y Tomo, M Shirouzu, T Terada, N Obayashi, H Hamana, N Shinya, A Tatsuguchi, S Yasuda, M Yoshida, H Hirota, Y Matsuo, K Tani, H Suzuki, T Arakawa, P Carninci, J Kawai, Y Hayashizaki, T Kigawa, S Yokoyama
PROTEIN SCIENCE 13 (2) Feb 2004[Refereed]
Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics
Y Kuroda, K Tani, Y Matsuo, S Yokoyama
PROTEIN SCIENCE 9 (12) Dec 2000[Refereed]
A set of computer programs for determining defocus and astigmatism in electron images
K Tani, H Sasabe, C Toyoshima
ULTRAMICROSCOPY 65 (1-2) Sep 1996[Refereed]
Awards & Honors
Books etc
現代生物科学入門構造機能生物学・膜タンパク質構造機能生物学
藤吉好則, 谷一寿 (Role:Joint author)
STRUCTURE AND INHIBITOR OF WATER CHANNEL IN BRAIN
Y. Tanimura, K. Tani, H. Suzuki, K. Nishikawa, A. Kamegawa, Y. Hiroaki, Y. Fujiyoshi (Role:Joint author)
Research Grants & Projects
▼▲
ユビキチンリガーゼが制御する病原菌感染と生体防御応答の構造生物学的解析
科学研究費助成事業
Research period: Apr 2024 - Mar 2028Representative: 水島恒裕, 谷一寿
Structural study of photo energy conversion system of light harvesting complex from photobacterium
Grants-in-Aid for Scientific Research
Research period: Apr 2022 - Mar 2025
病原細菌エフェクターによるNF-κB経路を標的とした感染機構の解析
科学研究費助成事業基盤研究(B)
Research period: Apr 2020 - Mar 2024Representative: 水島恒裕, 谷一寿, Kim Minsoo
クライオ電子顕微鏡を用いた膜タンパク質の高分解能動的構造解析と技術人材育成支援
創薬等ライフサイエンス研究支援基盤事業
Research period: Sep 2017 - Mar 2022Representative: 谷一寿
タンパク質の複合体構造・分子間相互作用・ダイナミクス・機能の予測と解析
創薬等ライフサイエンス研究支援基盤事業
Research period: Apr 2017 - Mar 2022Representative: 寺田透, 清水謙多郎, 森脇由隆, 谷一寿
Electron crystallographic analysis of tomographic volumes of 2D crystals of membrane proteins
Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Exploratory)
Research period: Jun 2017 - Mar 2020Representative: Tani Kazutoshi
Studies in structural physiology of channels
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (S)
Research period: May 2015 - Mar 2020Representative: FUJIYOSHI Yoshinori
Structural and functional relationship of aqauporin-4 in brain
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
Research period: Apr 2014 - Mar 2017Representative: Tani Kazutoshi, Fujiyoshi Yoshinori
Electron crystallographic analysis of two dimensional crystals of membrane proteins maintaining proton gradient
Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
Research period: Apr 2010 - Mar 2014Representative: TANI Kazutoshi, FUJIYOSHI Yoshinori, ABE Kazuhiro

	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
▼▲
生物物理学
ソフトマターの物理
非平衡物理
タンパク質・核酸
物理化学
理論化学
化学物理
自由エネルギー地形
計算化学
バイオインフォマティクス
レアイベントサンプリング
機械学習
インシリコ創薬
受容体
液-液相分離
膜透過
エピジェネティクス
核膜輸送
分散型計算
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
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
▼▲
In-Silico Analysis of Inhibitor Intrusion into the AQP7 Channel for Efficient Drug Design
Koryo Obata, Yasuteru Shigeta, Ryuhei Harada
Chemistry Letters, accepted Mar 2025[Refereed]
Reaction Mechanism Path Sampling Based on Parallel Cascade Selection QM/MM Molecular Dynamics Simulation: PaCS-Q
Lian Duan, Kowit Hengphasatporn, Ryuhei Harada, Yasuteru Shigeta
Journal of Chemical Theory and Computation, Manuscript ID: ct-2025-00169y, under revision Mar 2025[Refereed]
Chemical Diversity within Chaperonins Contributes to Stabilizing Substrate Protein Configurations
Takunori Yasuda, Yoshino Okamoto, Yasuteru Shigeta, Ryuhei Harada
The Journal of Physical Chemistry Letter, Manuscript ID: jz-2025-00092c, under revison Mar 2025[Refereed]
Rational Designed and Engineered Antimicrobial Peptides with High Selectivity and Efficiency Against Phytopathogenic Ralstonia Solanecearum
Melvalia Cristin Manik, Kikrusenuo Kiewhuo, Thanyada Rungrotmongkol, Lian Duan, Ryuhei Harada, Yasuteru Shigeta, Kowit Hengphasatporn, Nitchakan Darai, Alisa Vangnai
Communications Biology, Reference Number: COMMSBIO-24-8187-T, under review Mar 2025[Refereed]
Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search
Genki Kudo, Takumi Hirao, Ryuhei Harada, Yasuteru Shigeta, Taketsugu Hirokawa, Ryunosuke Yoshino
Journal of Chemical Information and Modeling, Manuscript ID: ci-2025-00102n, under revision Mar 2025[Refereed]
Characterization of Delta-7 Alkenone Desaturase in Haptophytes Emiliania Huxleyi Through the Heterologous Expression in Tisochrysis Lutea
Kohei Yoneda, Chinatsu Kobayashi, Hiroya Araie, Rikuri Morita, Ryuhei Harada, Yasuteru Shigeta, Hirotoshi Endo, Yoshiaki Maeda, Iwane Suzuki
Marine Biotechnology 27 (44) Feb 2025[Refereed]
Unveiling the Antiviral Inhibitory Activity of Ebselen and Ebsulfur Derivatives on SARS-CoV-2 Using Machine Learning-based QSAR, LB-PaCS-MD, and Experimental Assay
Silpsiri Sinsulpsiri, Yuji Nishii, Qing-Feng Xu-Xu, Masahiro Miura, Patcharin Wilasluck, Kanokwan Salamteh, Peerapon Deetanya, Kittikhun Wangkanon, Aphinya Suroengri, Siwaporn Boonyasuppayakorn, Lian Duan, Ryuhei Harada, Kowit Hengphasatporn, Yasuteru Shigeta, Liyi Shi, Phornphimon Maitarad, Thanyada Rungrotmongkol
Scientific Report 15 Feb 2025[Refereed]
BEMM-GEN: A Tool for Generating a Biomolecular Environment Mimicking Model for Molecular Dynamics Simulation
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling 64 (19) Oct 2024[Refereed]
Structural Fluctuation in Homodimeric Aminoacyl-tRNA Synthetases Induces Half-of-the-sites Activity
Yoshino Okamoto, Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
The Journal of Physical Chemistry B 128 (44) Oct 2024[Refereed]
Evaluating Solubility, Stability, and Inclusion Complexation of Oxyresveratrol with Various β-cyclodextrin Derivatives Using Advanced Computational Techniques and Experimental Validation
Saba Ali, Aamir Aman, Kowit Hengphasatporn, Ryo Fujiki, Ryuhei Harada, Yasuteru Shigeta, Kuakarun Krusong, Kiattawee Choowongkomon, Warinthorn Chavasiri, Peter Wolschann, Panupong Mahalapbutr, Thanyada Rungrotmongkol
Computational Biology and Chemistry, 112 Oct 2024[Refereed]
CommunicationMachine Learning-Based QSAR and LB-PaCS-MD Guided Design of SARS-CoV-2 Main Protease Inhibitors
Borwornlak Toopradab, Wanting Xie, Lian Duan, Kowit Hengphasatporn, Ryuhei Harada, Silpsiri Sinsulpsiri, Yasuteru Shigeta, Liyi Shi, Phornphimon Maitarad, Thanyada Rungrotmongkol
Bioorganic & Medicinal Chemistry Letters 110 Sep 2024[Refereed]
Ribosome Tunnel Environment Drives the Formation of α-Helix During Co-Translational Folding
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling 64 (16) Aug 2024[Refereed]
Structural Generation by Inverse Transformation Using Principal Component Analysis Enhances Conformational Sampling of Protein
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Bulletin of the Chemical Society of Japan 97 (8) Aug 2024[Refereed]
Alpha and Gamma Mangostins Inhibit Wild-type B SARS-CoV-2 More Effectively than the SARS-CoV-2 Variants and the Major Target is Unlikely a 3C-like Protease
Aphinya Suroengri, Van Cao, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanon, Kowit Hengphasatporn, Ryuhei Harada, Supakarn Chamni, Asada Leelahavanichkul, Yasuteru Shigeta, Thanyada Rungrotmongkol, Supo Hannongbua, Warinthorn Chavasiri, Supaporn Wacharapluesadee, Eakachai Prompetchara, Siwaporn Boonyasuppayakorn
Heliyon 10 (11) Jun 2024[Refereed]
Prediction of the Binding Mechanism of a Selective DNA Methyltransferase 3A Inhibitor by Molecular Simulation
Genki Kudo, Takumi Hirao, Ryuhei Harada, Takatsugu Hirokawa, Yasuteru Shigeta, Ryunosuke Yoshino
Scientific Report 14 Jun 2024[Refereed]
Development of Membrane Permeability Coefficient by Means of Novel Molecular Dynamics Methods
Ryuhei Harada, Yuki Mitsuta, Yasuteru Shigeta
YAKUGAKU ZASSHI 144 (5) May 2024[Refereed]
Preferential Door for Ligand Binding and Unbinding Pathways in Inhibited Human Acetylcholinesterase
Nalinee Kongkaew, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
The Journal of Physical Chemistry Letters 15 (21) May 2024[Refereed]
Drug-discovery Simulation for Membrane Proteins
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
SEIBUTSU BUTURI 64 (1) Feb 2024[Refereed]
Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP)
Raja Norazireen, Raja Ahmad, Long-teng Zhang, Rikuri Morita, Haruna Tani, Yong Wu, Takeshi Chujo, Akiko Ogawa, Ryuhei Harada, Yasuteru Shigeta, Kazuhito Tomizawa, Fan-Yan Wei
Nucleic Acids Research 52 (3) Dec 2023[Refereed]
Design of Electron-Donating Group Substituted 2-PAM Analogs as Antidotes for Organophosphate Insecticide Poisoning
Nalinee Kongkaew, Kowit Hengphasatporn, Yuwanda Injongkol, Pitchayathida Mee-udorn, Liyi Shi, Panupong Mahalapbutr, Phornphimon Maitarad, Ryuhei Harada, Yasuteru Shigeta, Thanyada Rungrotmongkol, Alisa S. Vangnai
RSC Advances 13 Nov 2023[Refereed]
レアイベントサンプリング法の開発とタンパク質機能解析への適用
原田隆平
日本薬学会構造活性相関部会 SAR News Cutting Edge 45 Oct 2023[Refereed]
Latrunculin Resistance Mechanism of Non-Conventional Actin NAP1 Uncovered by Molecular Dynamics Simulations
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Cytoskeleton 81 Oct 2023[Refereed]
A Structural Refinement Technique for Protein-RNA Complexes Using Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein
Nitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
Bulletin of the Chemical Society of Japan 96 (7) Jul 2023[Refereed]
A Variety of Initial Velocities in Restarting Molecular Dynamics Simulations Promotes Protein Transitions
Yohei Munei, Yasuteru Shigeta, Ryuhei Harada
Chemistry Letters, 52 (5) Jun 2023[Refereed]
中分子の膜透過性に対する計算手法の検討
高橋輝行, Kowit Hengphasatporn, 原田隆平, 重田育照
Journal of Computer Chemistry, Japan 21 (4) Jun 2023[Refereed]
Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses
Yohei Munei, Kowit Hengphasatporn, Yuta Hori, Ryuhei Harada, Yasuteru Shigeta
Journal of Agricultural and Food Chemistry 71 (24) Jun 2023[Refereed]
化合物の膜透過プロセスを紐解く自由エネルギー計算手法の開発
原田隆平, 森田陸離, 重田育照
日本薬学会構造活性相関部会 SAR News 44 Apr 2023
第一原理計算と分子動力学計算による膜透過性の評価・推定
重田育照, 高橋輝行, 満田祐樹, 原田隆平
技術情報協会「ケモインフォマティクスにおけるデータ収集の最適化と解析手法」 8 Apr 2023
4-hydroxyphenylpyruvate dioxygenase (HPPD) における金属活性中心の力場パラメータの構築とその評価
宗井陽平, 堀優太, Kowit Hengphasatporn, 原田隆平, 重田育照
Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]
Efficient Screening of Protein-Ligand Complexes in Lipid Bilayers Using LoCoMock Score
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Computer-Aided Molecular Design, 37 Mar 2023[Refereed]
Parallel Cascade Selection Molecular Dynamics (PaCS-MD) に基づくタンパク質の遷移経路探索
保田拓範, 原田隆平
分子シミュレーション学会誌「アンサンブル」 25 (1) Jan 2023[Refereed]
Free-energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
Journal Chemical Information and Modeling 63 (1) Jan 2023[Refereed]
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling 62 (23) Dec 2022[Refereed]
Identifying Antibiotics based on Structural Differences in the Conserved Allostery from Mitochondrial Heme-copper Oxidases
Yuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori Shintani
Nature Communications 13 Dec 2022[Refereed]
Promising SARS-CoV-2 Main Protease Inhibitor Ligand-Binding Modes Evaluated Using LB-PaCS-MD/FMO
Kowit Hengphasatporn, Ryuhei Harada, Patcharin Wilasluck, Peerapon Deetanya, Edwin R. Sukandar, Warinthorn Chavasiri, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol, Kittikhun Wangkanont, Yasuteru Shigeta
Scientific Reports 12 (1) Oct 2022[Refereed]
PaCS-MDと異常検知を援用したタンパク質構造遷移経路の探索
原田隆平
スーパーコンピューティングニュース特集号 24 (1) Aug 2022[Refereed]
Autism-Associated Mutation in Hevin Induces Endoplasmic Reticulum Stress Through Structural Instability
Takumi Taketomi, Takunori Yasuda, Rikuri Morita, Jaehyun Kim, Yasuteru Shigeta, Cagla Eroglu, Ryuhei Harada, Fuminori Tsuruta
Scientific Report 12 Jul 2022[Refereed]
The Structural Validation by G-factor Regulates Boost Potentials Employed in Conformational Sampling of Proteins
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling 62 (14) Jul 2022[Refereed]
The Role of ATP in Solubilizing RNA-binding Protein Fused in Sarcoma
Hayato Aida, Yasuteru Shigeta, Ryuhei Harada
Proteins: Structure, Function, and Bioinformatics 90 (8) Jul 2022[Refereed]
Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD
Hayato Aida, Yasuteru Shigeta, Ryuhei Harada
Materials 15 (4) Feb 2022[Refereed]
Integrate In Silico Studies on the Role of Nicotinamide Adenine Dinucleotide (NADH) Binding in Activating C-terminal Binding Protein 2 (CtBP2)
Tsukasa Aoyagi, Ryunosuke Yoshino, Yuki Mitsuta, Rikuri Morita, Ryuhei Harada, Yasuteru Shigeta
Chemistry Letters 51 Jan 2022[Refereed]
Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Molecular Biology 434 (2) Jan 2022[Refereed]
Phosphorylation on the Accessory Domain of Yeast Histone Chaperone yNap1 Exposes the Nuclear Export Sequence
Syo Ashida, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Proteins: Structure, Function, and Bioinformatics 90 (2) Jan 2022[Refereed]
Residue Folding Degree - Relationship to Secondary Structure Categories and use as Collective Variable
Vladimir Sladek, Ryuhei Harada, Yasuteru Shigeta
International Journal of Molecular Sciences 22 (23) Dec 2021[Refereed]
Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics Calculations
Koki Yanagki, Yuki Mitsuta, Kenta Takaoka, Teruyuki Takahashi, Kowit Hengphasatporn, Ryuhei Harada, Yasuteru Shigeta
Chemistry Letters 50 (12) Dec 2021[Refereed]
Structural Variations of Metallothionein with or without Zinc Ions Elucidated Using Molecular Dynamics Simulations
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
The Journal of Physical Chemistry B 125 (46) Nov 2021[Refereed]
PaCS-MDに基づく効率的リガンド結合経路探索法の開発
原田隆平
スーパーコンピューティングニュース特集号 23 (1) Aug 2021[Refereed]
A Post-Process to Estimate an Approximated Minimal Free Energy Path Based on Local Centroids
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Chemical Physics Letters 782 Aug 2021[Refereed]
Independent Non-targeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Theory and Computation 17 Aug 2021[Refereed]
In Silico Mutational Analyses Reveal Different Ligand-Binding Abilities of Double Pockets of Medaka Fish Taste Receptor Type 1 Essential for Efficient Taste Recognitions
Hayato Aida, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Physical Chemistry Chemical Physics 23 (36) Aug 2021[Refereed]
Split Conformation of Chaetomium Thermophilum Hsp104 Disaggregase
Yosuke Inoue, Yuya Hanazono, Kentaro Noi, Akihiro Kawamoto, Masato Kimatsuka, Ryuhei Harada, Kazuki Takeda, Ryoichi Kita, Natsuki Iwamasa, Kyoka Shibata, Keiichi Noguchi, Yasuteru Shigeta, Keiichi Namba, Teru Ogura, Kunio Miki, Kyosuke Shinohara, Masafumi Yohda
Structure 29 Jul 2021[Refereed]
pyProGA - A PyMOL Plugin for Protein Residue Network Analysis
Vladimir Sladek, Yuta Yamamoto, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta
PLoS ONE 16 (7) Jul 2021[Refereed]
Comprehensive Predictions of Secondary Structures for Comparative Analysis in Different Species
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Journal of Structural Biology 213 (2) Apr 2021[Refereed]
Membrane Permeability Evaluated from Solvation Free Energy Calculation of Cyclic Dipeptide
Koki Yanagi, Ryuhei Harada, Yuki Mitsuta, Yasuteru Shigeta
Journal of Computer Chemistry Japan 19 (4) Mar 2021[Refereed]
Rare Event Sampling of Proteins Based on Distributed Molecular Dynamics Simulations
Ryuhei Harada
Japan Society of Theoretical Chemistry 3 (1) Jan 2021[Refereed]
The Folding of Trp-cage is Regulated by Stochastic Flip of the Sidechain of Tryptophan
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
Chemistry Letters 50 (1) Jan 2021[Refereed]
Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Bulletin of the Chemical Society of Japan 94 (1) Jan 2021[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 16 (10) Oct 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 124 (39) Oct 2020[Refereed]
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
原田隆平
スーパーコンピューティングニュース特集号 22 (1) Aug 2020[Refereed]
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis Based Parallel Cascade Selection Molecular Dynamics
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
Journal of Chemical Information and Modeling 60 (8) Aug 2020[Refereed]
The Dynamics of S-adenosyl-methionine and S-adenosyl-homocysteine in Mouse Dnmt1 is Driven by 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]
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, Sladek Vladimir, Yasuteru Shigeta
JOURNAL OF COMPUTER CHEMISTRY-JAPAN 18 (5) Dec 2019[Refereed]
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant 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 Regulate its Conformational Sampling Efficiency
Ryuhei Harada, Yasuteru Shigeta
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
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 to Screen 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]
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 Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics
Ryuhei Harada, Hayato Aida, Yasuteru Shigeta
Chemistry Letters 47 (10) 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 of the Chemical Society of Japan 91 (9) Sep 2018[Refereed]
How does Friction Coefficient Affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?
Ryuhei Harada, Yasuteru Shigeta
Chemistry Letters 47 (9) 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 (26) 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, Takahiro Yumiba, Ryuhei Harada, Kohei Shimizu, Tatsuya Toga, Tomoko Ishikawa-Fujiwara, Takeshi 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 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
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]
Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules
Ryuhei Harada, Yasuteru Shigeta
Advances in Quantum Chemistry 78 2018[Refereed]
Programed Dynamical Ordering in 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 (14) 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 the Chemical Society of Japan 90 (11) Nov 2017[Refereed]
Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection
Ryuhei Harada, Yasuteru Shigeta
Journal of Computational Chemistry 38 (22) Aug 2017[Refereed]
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
Yuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki Hayashi
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 the 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 and Modeling 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 Feb 2011[Refereed]
Awards & Honors
▼▲
Apr 2025
豊田理化学研究所豊田理研スカラー（Phase1）
Oct 2024
MOLSIS-CCG GRANT
Jun 2024
UBE学術振興財団援助金
Jun 2024
UBE学術振興財団学術奨励賞
Apr 2024
G-7奨学財団令和６年度研究開発助成事業定期公募（ＩＴ）
Apr 2024
豊田理化学研究所豊田理研スカラー（Phase1）
Apr 2024
島津科学技術振興財団研究開発助成
Apr 2024
小柳財団研究開発助成
Jan 2024
カシオ科学振興財団研究助成
Jul 2023
Bulletin of the Chemical Society of Japan, Selected Paper（日本化学会欧文誌優秀論文）
Apr 2023
豊田理化学研究所豊田理研スカラー
Mar 2023
日立財団倉田奨励金
Nov 2022
筑波大学幸多き人生 100 年時代を創る『知』活用プログラム
Nov 2022
日本薬学会構造活性相関部会構造活性相関シンポジウム優秀発表賞（SAR Presentation Award）
Nov 2022
住友財団基礎科学研究助成
Sep 2022
日揮・実吉奨学会研究助成制度
Jul 2022
三島海雲記念財団学術研究奨励金
Jan 2022
American Chemical Society, Journal of Chemical Information and Modeling, Editorial Advisory Board
Apr 2021
筑波大学若手教員特別奨励賞
Apr 2021
科学技術分野の文部科学大臣表彰若手科学者賞
Oct 2020
筑波大学若手教員奨励賞
Dec 2019
分子シミュレーション学会学術賞
Mar 2019
日本物理学会若手奨励賞
Feb 2019
Royal Society of Chemistry Physical Chemistry Chemical Physics Hot Article Collection
Mar 2018
日本化学会進歩賞
Sep 2017
The 4th BIOPHYSICS Editors' Choice Award
Nov 2016
Bulletin of the Chemical Society of Japan, Selected Paper（日本化学会欧文誌優秀論文）
Nov 2016
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）特別研究奨励費
Sep 2012
日本生物物理学会年会若手招待講演証
Nov 2010
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
▼▲
薬効発揮に重要な長時間ダイナミクスを抽出・解析する分子シミュレーション手法の開発
基盤研究(B) [代表] 原田隆平直接経費: 14,400千円
Research period: Apr 2025 - Mar 2029
植物ペプチドホルモンの進化多様性を解明するドライとウェットの真の融合研究
豊田理研スカラー（Phase1） [共同代表] 原田隆平直接経費: 800千円
Research period: Apr 2025 - Mar 2026
公益財団法人 UBE学術振興財団援助金
[代表] 原田隆平直接経費: 1,000千円
Research period: Jun 2024 - Mar 2026
Rubiscoを改良する構造的要因の決定
挑戦的研究（萌芽）[代表] 松村浩由 [分担] 原田隆平直接経費: 750千円間接経費: 225千円課題番号: 23K18033
Research period: Jul 2023 - Mar 2026
タンパク質の複合体と相互作用を高精度に計測する計算技術の開発
[代表] 原田隆平直接経費: 1,000千円
Research period: Dec 2023 - Dec 2025
分子間相互作用から疾患原因を推定する異常検知システムの構築
第3回 MOLSIS-CCG GRANT [代表] 原田隆平直接経費: 500千円
Research period: Oct 2024 - Sep 2025
拡張サンプリング手法 (PaCS-MD, OFLOOD等) を用いた論理的創薬手法に関する研究
[代表] 原田隆平直接経費: 2,000千円間接経費: 600千円
Research period: Aug 2023 - Sep 2025
タンパク質と核酸の「揺らぎ」を考慮したフレキシブルドッキングに基づく複合体モデリング技術の開発
研究助成金 [代表] 原田隆平直接経費: 1,000千円
Research period: Jan 2024 - Jul 2025
In Silico Guided Therapeutic Antibody Design by Integrating Molecular Simulation and Deep Learning
令和6年度・JST次世代研究者挑戦的研究プログラム [代表] Wanda Destiarani [直接経費] 500千円 [受入教員] 原田隆平
Research period: Aug 2024 - Mar 2025Representative: Wanda Destiarani
令和6年度学術センター（量子生命情報研究センター）形成支援事業
[分担] 原田隆平直接経費: 400千円
Research period: Aug 2024 - Mar 2025Representative: 原田隆平
疾患原因につながる相互作用を特定する異常検知システムの開発
公益財団法人 G-7奨学財団令和６年度研究開発助成事業定期公募（ＩＴ）[代表] 原田隆平直接経費: 900千円間接経費: 100千円
Research period: Apr 2024 - Mar 2025
分子凝集をトリガーとする酵素阻害の現象解明と新規創薬分野への展開
豊田理研スカラー（Phase1） [共同代表] 原田隆平直接経費: 1,000千円
Research period: Apr 2024 - Mar 2025
病原菌においてヘム濃度を感知・調整するタンパク質ダイナミクスの解明
研究助成金 [代表] 原田隆平直接経費: 1,000千円
Research period: Apr 2024 - Mar 2025
分子動力学計算に基づくノンコーディングRNAの立体構造予測
日本学術振興会特別研究員奨励費 (DC1) [代表] 保田拓範直接経費: 2,500千円課題番号: 22J20084 [受入研究者] 原田隆平
Research period: Apr 2022 - Mar 2025
中分子環状ペプチドの生体膜透過プロセスを抽出・評価する計算技術の開発
基礎科学研究助成 [代表] 原田隆平直接経費: 1,300千円
Research period: Oct 2022 - Nov 2024
生物学的相分離を予測・体系化する分子シミュレーション技術の開発と応用
研究助成制度 [代表] 原田隆平直接経費: 1,800千円間接経費: 200千円
Research period: Sep 2022 - Aug 2024
令和5年度学術センター（量子生命情報研究センター）形成支援事業
[分担] 原田隆平直接経費: 1,000千円
Research period: Aug 2023 - Mar 2024
細胞表面での分子動態解析のための多角的構造解析プラットフォームの構築
TIA連携プログラム [代表] 田中良和 [分担] 原田隆平直接経費: 700千円
Research period: Jun 2023 - Mar 2024
日本曹達との共同研究（寄付金）
[代表] 原田隆平直接経費: 500千円
Research period: Apr 2023 - Mar 2024
タンパク質の基質特異性発現メカニズムを解明する分子シミュレーション手法の開発：新規基質の合理的デザイン実現にむけて
豊田理研スカラー [代表] 原田隆平直接経費: 1,000千円
Research period: Apr 2023 - Mar 2024
先端インシリコ創薬技術で実現する化合物のフレキシブルドッキングと結合ポケットのテーラーメイドデザイン
倉田奨励金 [代表] 原田隆平直接経費: 1,000千円
Research period: Mar 2023 - Mar 2024
分子動力学計算と機械学習を援用してタンパク質の構造変化を予測する
基盤研究(C) [代表] 原田隆平直接経費: 3,200千円間接経費: 960千円課題番号: 21K06094
Research period: Apr 2021 - Mar 2024
分子シミュレーションに基づくヒト由来味覚受容体の味物質認識メカニズムの解明
2022年度学術研究奨励金（自然科学部門/個人研究奨励金）[代表] 原田隆平直接経費: 1,000千円
Research period: Jul 2022 - Jun 2023
感染爆発の原因となる標的分子の阻害剤発見を加速する革新的インシリコ技術の創出
幸多き人生 100 年時代を創る『知』活用プログラム [代表] 原田隆平直接経費: 500千円（辞退）
Research period: Nov 2022 - Mar 2023
研究基盤支援プログラム（Cタイプ）
[代表] 原田隆平直接経費: 500千円
Research period: Jul 2020 - Mar 2021
中分子環状ペプチドの膜透過性を評価する分子シミュレーション技術の創出
研究基盤支援プログラム（Aタイプ）[代表] 原田隆平直接経費: 1,000千円
Research period: Aug 2019 - Mar 2020
研究基盤支援プログラム（Cタイプ）
[代表] 原田隆平直接経費: 500千円
Research period: Jul 2019 - Mar 2020
Gタンパク質共役受容体におけるシグナル伝達機構の解明
若手研究(A) [代表] 原田隆平直接経費: 15,800千円間接経費: 4,740千円課題番号: 16H06164
Research period: Apr 2016 - Mar 2019
分子動力学シミュレーションで探る細胞環境におけるタンパク質フォールディング機構
特別研究奨励費 [代表] 原田隆平直接経費: 3,400千円間接経費: 1,020千円課題番号: 15J03797
Research period: Apr 2015 - Mar 2018
タンパク質構造揺らぎに基づく構造変化予測法の構築
若手研究(B) [代表] 原田隆平直接経費: 3,200千円間接経費: 960千円課題番号: 26840056
Research period: Apr 2014 - Mar 2016

	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
Theoretical Chemistry
Quantum Chemistry
Computational Chemistry
Academic & Professional Experience
Apr 2019
-
Present
University of Tsukuba Center for Computational Sciences Assistant Professor
Jul 2024
-
Mar 2025
National Institute of Advanced Industrial Science and Technology Interdisciplinary Research Center for Catalytic Chemistry
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
▼▲
Enantioselective interactions of aminonitrile dimers
Natsuki Watanabe, Yu Komatsu, Koichi Miyagawa, Yuta Hori, Yasuteru Shigeta, Mitsuo Shoji
Physical Chemistry Chemical Physics Nov 2025[Refereed]
A machine learning potential construction based on radial distribution function sampling
Natsuki Watanabe, Yuta Hori, Hiroki Sugisawa, Tomonori Ida, Mitsuo Shoji, Yasuteru Shigeta
Journal of Computational Chemistry Sep 2024[Refereed]
Development of an Fe^II Complex Exhibiting Intermolecular Proton Shifting Coupled Spin Transition
Ji, Tianchi, Su, Shengqun, Wu, Shuqi, Hori, Yuta, Shigeta, Yasuteru, Huang, Yubo, Zheng, Wenwei, Xu, Wenhuang, Zhang, Xiaopeng, Kiyanagi, Ryoji, Munakata, Koji, Ohhara, Takashi, Nakanishi, Takumi, Sato, Osamu
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 63 (25) Jun 2024[Refereed]
Cocrystalline Matrices for Hyperpolarization at Room Temperature Using Photoexcited Electrons
Inukai, Munehiro, Sato, Haruki, Miyanishi, Koichiro, Negoro, Makoto, Kagawa, Akinori, Hori, Yuta, Shigeta, Yasuteru, Kurihara, Takuya, Nakamura, Koichi
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 146 (21) May 2024[Refereed]
Network Topology Diversification of Porous Organic Salts
Hiroi Sei, Kouki Oka, Yuta Hori, Yasuteru Shigeta, Norimitsu Tohnai
Chemical Science 15 May 2024[Refereed]
Grinding-Induced Water Solubility Exhibited by Mechanochromic Luminescent Supramolecular Fibers
Liu, Qiming, Zhang, Tianyue, Ikemoto, Yuka, Shinozaki, Yudai, Watanabe, Go, Hori, Yuta, Shigeta, Yasuteru, Midorikawa, Takemi, Harano, Koji, Sagara, Yoshimitsu
SMALL Epub Mar 2024[Refereed]
Predicting and analyzing organic reaction pathways by combining machine learning and reaction network approaches
Ida, Tomonori, Kojima, Honoka, Hori, Yuta
CHEMICAL COMMUNICATIONS 59 (83) Oct 2023[Refereed]
Development of an Iron(II) Complex Exhibiting Thermal- and Photoinduced Double Proton-Transfer-Coupled Spin Transition in a Short Hydrogen Bond
Takumi Nakanishi, Yuta Hori, Yasuteru Shigeta, Hiroyasu Sato, Ryoji Kiyanagi, Koji Munakata, Takashi Ohhara, Atsushi Okazawa, Rintaro Shimada, Akira Sakamoto, Osamu Sato
Journal of the American Chemical Society 145 (35) Aug 2023[Refereed]
1T/1H-SnS₂ Sheets for Electrochemical CO₂ Reduction to Formate
Kawabe, Yusuke, Ito, Yoshikazu, Hori, Yuta, Kukunuri, Suresh, Shiokawa, Fumiya, Nishiuchi, Tomohiko, Jeong, Samuel, Katagiri, Kosuke, Xi, Zeyu, Li, Zhikai, Shigeta, Yasuteru, Takahashi, Yasufumi
ACS nano 17 (12) Jun 2023[Refereed]
Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses
Munei, Yohei, Hengphasatporn, Kowi, Hori, Yuta, Harada, Ryuhei, Shigeta, Yasuteru
Journal of agricultural and food chemistry 71 (24) Jun 2023[Refereed]
Enantioselective Amino Acid interactions in Solution
Watanabe, Natsuki, Shoji, Mitsuo, Miyagawa, Koichi, Hori, Yuta, Boero, Mauro, Umemura, Masayuki, Shigeta, Yasuteru
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 25 (21) May 2023[Refereed]
Organocatalytic-racemization reaction elucidation of aspartic acid by density functional theory
Watanabe, Natsuki, Hori, Yuta, Shoji, Mitsuo, Boero, Mauro, Shigeta, Yasuteru
CHIRALITY 35 (9) Apr 2023[Refereed]
Observation of proton-transfer-coupled spin transition by single-crystal neutron-diffraction measurement
Nakanishi, Takumi, Hori, Yuta, Shigeta, Yasuteru, Sato, Hiroyasu, Wu, Shuqi, Kiyanagi, Ryoji, Munakata, Koji, Ohhara, Takashi, Osamu, Sato
Physical Chemistry Chemical Physics 25 (17) Apr 2023[Refereed]
Deprotonation-Induced and Ion-Pairing-Modulated Diradical Properties of Partially Conjugated Pyrrole-Quinone Conjunction
Shinya, Sugiura, Takashi, Kubo, Yohei, Haketa, Yuta, Hori, Yasuteru, Shigeta, Hayato, Sakai, Taku, Hasobe, Hiromitsu, Maeda
Journal of the American Chemical Society 145 (14) Mar 2023[Refereed]
Theoretical Characterization of the Electronic and Spin Structures for Iron–Sulfur Cubane in Reduced High-Potential Iron–Sulfur Proteins Using Density Functional Theory
Hori, Yuta, Sato, Ayaka, Yasuteru, Shigeta
Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]
4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価
宗井, 陽平, 堀, 優太, Kowit, Hengphasatporn, 原田, 隆平, 重田, 育照
Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]
Theoretical Investigation of Racemization of Amino Acid using Organic Catalysts
渡辺, 七都稀, 堀, 優太, 庄司, 光男, 重田, 育照
Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]
New insights into the oxidation process from neutron and X-ray crystal structures of an O₂-sensitive [NiFe]-hydrogenase
Takeshi Hiromoto, Koji Nishikawa, Seiya Inoue, Hideaki Ogata, Yuta Hori, Katsuhiro Kusaka, Yu Hirano, Kazuo Kurihara, Yasuteru Shigeta, Taro Tamada, Yoshiki Higuchi
Chemical Science 14 2023[Refereed]
Characterization of the Geometrical and Electronic Structures of the Active Site and Its Effects on the Surrounding Environment in Reduced High-Potential Iron–Sulfur Proteins Investigated by the Density Functional Theory Approach
Sato, Ayaka, Hori, Yuta, Yasuteru, Shigeta
Inorganic Chemistry 62 (5) Jan 2023[Refereed]
Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic Syntheses
Mitsuo, Shoji, Natsuki, Watanabe, Hori, Yuta, Kenji, Furuya, Masayuki, Umemura, Mauro, Boero, Yasuteru, Shigeta
Astrobiology 22 (9) Sep 2022[Refereed]
Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in Space
Hori, Yuta, Nakamura, Honami, Sakawa, Takahide, Natsuki, Watanabe, Kayanuma, Megumi, Mitsuo, Shoji, Masayuki, Umemura, Yasuteru, Shigeta
Astrobiology 22 (11) Sep 2022[Refereed]
Effects of mechanical grinding on the phase behavior and anhydrous proton conductivity of imidazolium hydrogen succinate
Dekura, Shun, Sunairi, Yoshiya, Okamoto, Kei, Takeiri, Fumitaka, Kobayashi, Genki, Hori, Yuta, Shigeta, Yasuteru, Mori, Hatsumi
Solid State Ionics 372 Dec 2021[Refereed]
Proton Conduction Mechanism for Anhydrous Imidazolium Hydrogen Succinate Based on Local Structures and Molecular Dynamics
Hori, Yuta, Dekura, Shun, Sunairi, Yoshiya, Ida, Tomonori, Mizuno, Motohiro, Mori, Hatsumi, Shigeta, Yasuteru
The Journal of Physical Chemistry Letters 12 (22) Jun 2021[Refereed]
Proton conduction mechanism in proton-conducting PVPA-xIm composites investigated by theoretical approaches
Hori, Yuta, Suetake, Toshiya, Ida, Tomonori, Mizuno, Motohiro, Shigeta, Yasuteru
The Journal of Computer Chemistry, Japan 19 (4) Feb 2021[Refereed]
Molecular Motions of Imidazole in Poly(vinylphosphonic acid)-imidazole Composites Investigated by Molecular Dynamics Simulations
Hori, Yuta, Suetake, Toshiya, Shigeta, Yasuteru, Ida, Tomonori, Mizuno, Motohiro
Chemistry Letters 50 (1) Oct 2020[Refereed]
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 59 (35) 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) Feb 2020[Refereed]
Revisiting Formic Acid Decomposition by a Graph-Theoretical Approach
Ida, Tomonori, Nishida, Manami, Hori, Yuta
The Journal of Physical Chemistry A 123 (44) Oct 2019[Refereed]
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 beta-dihydroporphycene cobalt complex: study on the effect of hydrogenation of the ligand
Koichi Hashimoto, Taro Koide, Toru Okawara, Hisashi Shimakoshi, Yuta Hori, Yoshihito Shiota, Kazunari Yoshizawa, Yoshio Hisaeda
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]
Catalytic Performance of a Dicopper-Oxo Complex for Methane Hydroxylation
Yuta Hori, Yoshihito Shiota, Tomokazu Tsuji, Masahito Kodera, Kazunari Yoshizawa
Inorganic Chemistry 57 (1) Jan 2018[Refereed]
Construction of a Potential Energy Surface Based on a Diabatic Model for Proton Transfer in Molecular Pairs
Hori Yuta, Ida Tomonori, Mizuno Motohiro
Concepts, Methods and Applications of Quantum Systems in Chemistry and Physics Jan 2018[Refereed]
Local structure and hydrogen bond characteristics of imidazole molecules for proton conduction in acid and base proton-conducting composite materials
Yuta Hori, Takuma Chikai, Tomonori Ida, Motohiro Mizuno
Physical Chemistry Chemical Physics 20 (15) 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
▼▲
Nov 2024
筑波大学筑波大学若手教員奨励賞
Jul 2024
University of Tsukuba TRiSTAR (Top Runners in Strategy of Transborder Advanced Researches) Fellow
May 2024
理論化学会第5回理論化学会奨励賞理論化学計算によるプロトン移動解析と材料設計への展開
May 2022
2nd International Symposium “Hydrogenomics” Best Poster Award 2022
Dec 2020
量子生命科学会量子生命科学会第二回大会優秀発表賞
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
Hydrogenomics: The Science of Fully Utilizing Hydrogen
Hori, Yuta, Nishikawa, Koji, Shigeta, Yasuteru, Higuchi, Yoshiki ( Biological Enzymes and Hydrogenases)
Direct Hydroxylation of Methane: Interplay Between Theory and Experiment
Hori, Yuta, Abe, Tsukasa (Role:Contributor, Theoretical Approach to Homogeneous Catalyst of Methane Hydroxylation: Collaboration with Computation and Experiment)
高機能性金属錯体が拓く触媒科学:革新的分子変換反応の創出をめざして
堀, 優太, 塩田, 淑仁, 吉澤, 一成 (Role:Contributor, 計算化学が先導する酵素触媒反応の設計)
Research Grants & Projects
▼▲
Amino acid homochirality formation mechanism based on elementary processes in gas and solid phases
Grant-in-Aid for Early-Career Scientists
Research period: Apr 2024 - Mar 2027Representative: Yuta HORI
理論先導型次世代クリーンエネルギーシステムの構築
世界で活躍できる研究者戦略育成事業大学×国研×企業連携によるトップランナー育成プログラム
Research period: Sep 2024 - Mar 2026Representative: 堀優太
メタン酸化触媒の設計に向けた量子化学とデータ駆動型触媒インフォマティクス
覚醒プロジェクト
Research period: Jul 2024 - Mar 2025Representative: 堀優太
有機柔粘性結晶のナノサイズ化による分子ダイナミクスの制御と機能探索
2024年度TIA連携プログラム探索推進事業「かけはし」
Research period: Jul 2024 - Mar 2025Representative: 堀優太
Exploration of precise protein engineering through the fusion of synthetic chemistry and theoretical calculation
Research period: Apr 2024 - Mar 2025Representative: Yuta Hori
無水プロトン伝導物質の伝導機構の理解に基づく物質設計
クロスオーバー共同研究
Research period: Apr 2024 - Mar 2025Representative: 堀優太
電子共役プロトン移動反応のための電子状態解析
基盤共同研究課題
Research period: Apr 2024 - Mar 2025Representative: 堀優太
Elucidation of Anhydrous Hydrogen Ion Conduction Process Mechanism by Theoretical Chemistry and Theoretical Proposal for Materials Design
Research period: Apr 2023 - Mar 2024Representative: Yuta Hori
Quantum Chemical Exploration of the Formation Process of Homochiral Amino Acids in Outer Space
Grants-in-Aid for Scientific Research
Research period: Apr 2021 - Mar 2023
Theoretical development of biohydrogenomics based on hydrogen activation and transport
Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
Research period: Apr 2021 - Mar 2023Representative: Yuta Hori
無水プロトン伝導材料設計に向けた計算化学による機能解析
第36回マツダ研究助成
Research period: Apr 2021 - Mar 2023Representative: 堀優太
プロトン移動を伴う機能性材料開発のための電子状態解析
基盤共同研究
Research period: Apr 2021 - Mar 2022Representative: 堀優太
Elucidation of proton conduction mechanism in acid-base complexes investigated by theoretical calculations
Grants-in-Aid for Scientific Research
Research period: Apr 2019 - Mar 2022Representative: Hori Yuta
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
Development of theoretical analysis method for proton coupled electron transfer reaction
Grant-in-Aid for Research Activity Start-up
Research period: Aug 2017 - Mar 2019Representative: Yuta Hori

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

Research Interests
▼▲
Bioinformatics
Structure-based virtual screening
MD simulation
Fragment molecular orbital method
Molecular modeling
Cheminformatics
Academic & Professional Experience
Apr 2022
-
Present
Center for Computational Sciences, University of Tsukuba
Sep 2019
-
Mar 2022
Center for Computational Sciences, University of Tsukuba
Published Papers
▼▲
Exploring mimosamycin as a Janus kinase 2 inhibitor: A combined computational and experimental investigation
Kamonpan Sanachai, Kowit Hengphasatporn, Supakarn Chamni, Khanit Suwanborirux, Panupong Mahalapbutr, Yasuteru Shigeta, Supaphorn Seetaha, Kiattawee Choowongkomon, Thanyada Rungrotmongkol
Computational Biology and Chemistry Apr 2025[Refereed]
Apoprotein Intermolecular Interactions and Heme Insertion for 3D Domain Swapping in Myoglobin
Gissi Novientri, Koji Takeda, Lian Duan, Kowit Hengphasatporn, Yasuteru Shigeta, Cheng Xie, Tsuyoshi Mashima, Shun Hirota
ACS Omega Feb 2025[Refereed]
Polysulfur-based bulking of dynamin-related protein 1 prevents ischemic sulfide catabolism and heart failure in mice
Akiyuki Nishimura, Seiryo Ogata, Xiaokang Tang, Kowit Hengphasatporn, Keitaro Umezawa, Makoto Sanbo, Masumi Hirabayashi, Yuri Kato, Yuko Ibuki, Yoshito Kumagai, Kenta Kobayashi, Yasunari Kanda, Yasuteru Urano, Yasuteru Shigeta, Takaaki Akaike, Motohiro Nishida
Nature Communications Jan 2025[Refereed]
Nymphaea pubescens Willd. extract and its flavonoid constituents vasodilate rat isolated pulmonary artery via NO-sGC-cGMP pathway
Teerapap Panklai, Prapapan Temkitthawon, Nungruthai Suphrom, Corine Girard, Perle Totoson, Kowit Hengphasatporn, Yasuteru Shigeta, Krongkarn Chootip, Kornkanok Ingkaninan
Phytomedicine Plus Jan 2025[Refereed]
Structure and catalytic activity of a dihydrofolate reductase-like enzyme from Leptospira interrogans
Charin Chandit, Kowit Hengphasatporn, Pattraporn Donsuy, Yasuteru Shigeta, Kittikhun Wangkanont
International Journal of Biological Macromolecules Jan 2025[Refereed]
Experimental and Computational Studies on Domain-Swapped Structure Stabilization of an Antibody Light Chain by Disulfide Bond Introduction
Wahyu Fitriana, Takahiro Sakai, Lian Duan, Kowit Hengphasatporn, Yasuteru Shigeta, Tsuyoshi Mashima, Taizo Uda, Emi Hifumi, Shun Hirota
Journal of Medicinal Chemistry Dec 2024[Refereed]
GPNMB is a novel binding partner of FGFR1 that affects tumorigenic potential through AKT phosphorylation in TNBC
Manar Ahmed Elhinnawi, Yukari Okita, Katsunobu Shigematsu, Mohammed Abdelaziz, Rie Shiratani, Kunio Kawanishi, Kowit Hengphasatporn, Thuy Linh Dang Cao, Yasuteru Shigeta, Mitsuyasu Kato
Cancer Science Nov 2024[Refereed]
Design, Synthesis, and Biological Evaluation of Darunavir Analogs as HIV-1 Protease Inhibitors
Muhammad Asad Ur Rehman, Hathaichanok Chuntakaruk, Soraat Amphan, Aphinya Suroengrit, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Kuakarun Krusong, Siwaporn Boonyasuppayakorn, Chanat Aonbangkhen, Tanatorn Khotavivattana
ACS Bio & Med Chem Au Oct 2024[Refereed]
Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation
Saba Ali, Aamir Aman, Kowit Hengphasatporn, Lipika Oopkaew, Bunyaporn Todee, Ryo Fujiki, Ryuhei Harada, Yasuteru Shigeta, Kuakarun Krusong, Kiattawee Choowongkomon, Warinthorn Chavasiri, Peter Wolschann, Panupong Mahalapbutr, Thanyada Rungrotmongkol
Computational Biology and Chemistry Oct 2024[Refereed]
Why is Dimeric 3D Domain Swapping in Antibody Light Chains Missing from the Solution? Atomistic Insights Mechanisms
Lian Duan, Kowit Hengphasatporn, Takahiro Sakai, Ryo Fujiki, Norio Yoshida, Shun Hirota, Yasuteru Shigeta
The Journal of Physical Chemistry B Sep 2024[Refereed]
Machine learning-based QSAR and LB-PaCS-MD guided design of SARS-CoV-2 main protease inhibitors
Borwornlak Toopradab, Wanting Xie, Lian Duan, Kowit Hengphasatporn, Ryuhei Harada, Silpsiri Sinsulpsiri, Yasuteru Shigeta, Liyi Shi, Phornphimon Maitarad, Thanyada Rungrotmongkol
Bioorganic & Medicinal Chemistry Letters Sep 2024[Refereed]
Alpha and gamma mangostins inhibit wild-type B SARS-CoV-2 more effectively than the SARS-CoV-2 variants and the major target is unlikely the 3C-like protease
Aphinya Suroengrit, Van Cao, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Kowit Hengphasatporn, Ryuhei Harada, Supakarn Chamni, Asada Leelahavanichkul, Yasuteru Shigeta, Thanyada Rungrotmongkol, Supot Hannongbua, Warinthorn Chavasiri, Supaporn Wacharapluesadee, Eakachai Prompetchara, Siwaporn Boonyasuppayakorn
Heliyon Jun 2024[Refereed]
Preferential Door for Ligand Binding and Unbinding Pathways in Inhibited Human Acetylcholinesterase
Nalinee Kongkaew, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
The Journal of Physical Chemistry Letters May 2024[Refereed]
Unlocking E‐arylidene Steroid Derivatives as Promising α‐Glucosidase Inhibitors
Ade Danova, Kovit Pattanapanyasat, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Elvira Hermawati, Warinthorn Chavasiri
ChemistrySelect Mar 2024[Refereed]
FMO-guided design of darunavir analogs as HIV-1 protease inhibitors.
Hathaichanok Chuntakaruk, Kowit Hengphasatporn, Yasuteru Shigeta, Chanat Aonbangkhen, Vannajan Sanghiran Lee, Tanatorn Khotavivattana, Thanyada Rungrotmongkol, Supot Hannongbua
Scientific reports 14 (1) Feb 2024[Refereed]
Machine learning‐guided design of potent darunavir analogs targeting HIV‐1 proteases: A computational approach for antiretroviral drug discovery
Hathaichanok Chuntakaruk, Kajjana Boonpalit, Jiramet Kinchagawat, Fahsai Nakarin, Tanatorn Khotavivattana, Chanat Aonbangkhen, Yasuteru Shigeta, Kowit Hengphasatporn, Sarana Nutanong, Thanyada Rungrotmongkol, Supot Hannongbua
Journal of Computational Chemistry Jan 2024[Refereed]
Integrated In-Silico Drug Modeling for Viral Proteins
Kowit Hengphasatporn, Yasuteru Shigeta
2024
Synthesis and biological evaluation of 2'-hydroxychalcone derivatives as AMPK activators.
Duy Vu Nguyen, Chatchai Muanprasat, Suchada Kaewin, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Warinthorn Chavasiri
Bioorganic chemistry 143 Dec 2023[Refereed]
The 8-bromobaicalein alleviated chikungunya-induced musculoskeletal inflammation and reduced the viral load in healthy adult mice
Van Cao, Naphat Loeanurit, Kowit Hengphasatporn, Rita Hairani, Noppadol Wacharachaisurapol, Nantaporn Prompila, Supeecha Wittayalertpanya, Yasuteru Shigeta, Tanatorn Khotavivattana, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn
Emerging Microbes & Infections Dec 2023[Refereed]
Structural and thermodynamic insights into antibody light chain tetramer formation through 3D domain swapping.
Takahiro Sakai, Tsuyoshi Mashima, Naoya Kobayashi, Hideaki Ogata, Lian Duan, Ryo Fujiki, Kowit Hengphasatporn, Taizo Uda, Yasuteru Shigeta, Emi Hifumi, Shun Hirota
Nature communications 14 (1) Dec 2023[Refereed]
A sulfonamide chalcone inhibited dengue virus with a potential target at the SAM-binding site of viral methyltransferase.
Van Cao, I Putu Sukanadi, Naphat Loeanurit, Aphinya Suroengrit, Wattamon Paunrat, Vipanee Vibulakhaopan, Kowit Hengphasatporn, Yasuteru Shigeta, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn
Antiviral research 220 Dec 2023[Refereed]
Design of electron-donating group substituted 2-PAM analogs as antidotes for organophosphate insecticide poisoning
Nalinee Kongkaew, Kowit Hengphasatporn, Yuwanda Injongkol, Pitchayathida Mee-udorn, Liyi Shi, Panupong Mahalapbutr, Phornphimon Maitarad, Ryuhei Harada, Yasuteru Shigeta, Thanyada Rungrotmongkol, Alisa S. Vangnai
RSC Advances 13 (46) Nov 2023[Refereed]
Structure-yeast α-glucosidase inhibitory activity relationship of 9-O-berberrubine carboxylates.
Duy Vu Nguyen, Kowit Hengphasatporn, Ade Danova, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Ryo Fujiki, Yasuteru Shigeta, Thanyada Rungrotmongkol, Warinthorn Chavasiri
Scientific reports 13 (1) Nov 2023[Refereed]
Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches
Piyatida Pojtanadithee, Kowit Hengphasatporn, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, I. Putu Sukanadi, Warinthorn Chavasiri, Peter Wolschann, Thierry Langer, Yasuteru Shigeta, Phornphimon Maitarad, Kamonpan Sanachai, Thanyada Rungrotmongkol
Journal of Chemical Information and Modeling Aug 2023[Refereed]
A Structural Refinement Technique for Protein-RNA Complexes Based on a Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein
Nitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
Bulletin of the Chemical Society of Japan 96 (7) Jul 2023[Refereed]
Designing Potent α-Glucosidase Inhibitors: A Synthesis and QSAR Modeling Approach for Biscoumarin Derivatives
Thi-Hong-Truc Phan, Kowit Hengphasatporn, Yasuteru Shigeta, Wanting Xie, Phornphimon Maitarad, Thanyada Rungrotmongkol, Warinthorn Chavasiri
ACS Omega 8 (29) Jul 2023[Refereed]
Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses
Yohei Munei, Kowit Hengphasatporn, Yuta Hori, Ryuhei Harada, Yasuteru Shigeta
Journal of Agricultural and Food Chemistry 71 (24) Jun 2023[Refereed]
Sulfonylated Indeno[1,2-c]quinoline Derivatives as Potent EGFR Tyrosine Kinase Inhibitors
Kowit Hengphasatporn, Thitinan Aiebchun, Panupong Mahalapbutr, Atima Auepattanapong, Onnicha Khaikate, Kiattawee Choowongkomon, Chutima Kuhakarn, Jatuporn Meesin, Yasuteru Shigeta, Thanyada Rungrotmongkol
ACS Omega Jun 2023[Refereed]
In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease
Kanpong Boonthaworn, Kowit Hengphasatporn, Yasuteru Shigeta, Warinthorn Chavasiri, Thanyada Rungrotmongkol, Puey Ounjai
PeerJ 11 Apr 2023[Refereed]
The 8-bromobaicalein inhibited the replication of dengue, and Zika viruses and targeted the dengue polymerase
Siwaporn Boonyasuppayakorn, Thanaphon Saelee, Thao Nguyen Thanh Huynh, Rita Hairani, Kowit Hengphasatporn, Naphat Loeanurit, Van Cao, Vipanee Vibulakhaophan, Panattida Siripitakpong, Parveen Kaur, Justin Jang Hann Chu, Chairat Tunghirun, Opas Choksupmanee, Sarin Chimnaronk, Yasuteru Shigeta, Thanyada Rungrotmongkol, Warinthorn Chavasiri
Scientific Reports 13 (1) Apr 2023[Refereed]
4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価
宗井, 陽平, 堀, 優太, Kowit, Hengphasatporn, 原田, 隆平, 重田, 育照
Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]
X-ray crystallographic and mutational analysis of the NylC precursor: catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolase
Seiji Negoro, Naoki Shibata, Dai ichiro Kato, Yusuke Tanaka, Kengo Yasuhira, Keisuke Nagai, Shohei Oshima, Yoko Furuno, Risa Yokoyama, Kaito Miyazaki, Masahiro Takeo, Kowit Hengphasatporn, Yasuteru Shigeta, Young Ho Lee, Yoshiki Higuchi
FEBS Journal Feb 2023[Refereed]
N-Containing α-Mangostin Analogs via Smiles Rearrangement as the Promising Cytotoxic, Antitrypanosomal, and SARS-CoV-2 Main Protease Inhibitory Agents
Nan Yadanar Lin Pyae, Arnatchai Maiuthed, Wongsakorn Phongsopitanun, Bongkot Ouengwanarat, Warongrit Sukma, Nitipol Srimongkolpithak, Jutharat Pengon, Roonglawan Rattanajak, Sumalee Kamchonwongpaisan, Zin Zin Ei, Preedakorn Chunhacha, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Supakarn Chamni
Molecules 28 (3) Feb 2023[Refereed]
Lichen-Derived Diffractaic Acid Inhibited Dengue Virus Replication in a Cell-Based System
Naphat Loeanurit, Truong Lam Tuong, Van Kieu Nguyen, Vipanee Vibulakhaophan, Kowit Hengphasatporn, Yasuteru Shigeta, Si Xian Ho, Justin Jang Hann Chu, Thanyada Rungrotmongkol, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn
Molecules 28 (3) Feb 2023[Refereed]
Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO
Kowit Hengphasatporn, Ryuhei Harada, Patcharin Wilasluck, Peerapon Deetanya, Edwin R. Sukandar, Warinthorn Chavasiri, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol, Kittikhun Wangkanont, Yasuteru Shigeta
Scientific Reports 12 (1) Dec 2022[Refereed]
Design, synthesis, in vitro, in silico, and SAR studies of flavone analogs towards anti-dengue activity
Apinya Patigo, Kowit Hengphasatporn, Van Cao, Wattamon Paunrat, Natthanan Vijara, Thamonwan Chokmahasarn, Phornphimon Maitarad, Thanyada Rungrotmongkol, Yasuteru Shigeta, Siwaporn Boonyasuppayakorn, Tanatorn Khotavivattana
Scientific Reports 12 (1) Dec 2022[Refereed]
Pharmacophore-Based Virtual Screening and Experimental Validation of Pyrazolone-Derived Inhibitors toward Janus Kinases
Kamonpan Sanachai, Panupong Mahalapbutr, Kowit Hengphasatporn, Yasuteru Shigeta, Supaphorn Seetaha, Lueacha Tabtimmai, Thierry Langer, Peter Wolschann, Tanakorn Kittikool, Sirilata Yotphan, Kiattawee Choowongkomon, Thanyada Rungrotmongkol
ACS Omega 7 (37) Sep 2022[Refereed]
Supramolecular polymerization of thiobarbituric acid naphthalene dye
Takumi Aizawa, Maika Kawaura, Takashi Kajitani, Kowit Hengphasatporn, Yasuteru Shigeta, Shiki Yagai
Chemical Communications 58 (67) Jul 2022[Refereed]
Semi-Synthesis of N-Aryl Amide Analogs of Piperine from Piper nigrum and Evaluation of Their Antitrypanosomal, Antimalarial, and Anti-SARS-CoV-2 Main Protease Activities
Rattanaporn Wansri, Aye Chan Khine Lin, Jutharat Pengon, Sumalee Kamchonwongpaisan, Nitipol Srimongkolpithak, Roonglawan Rattanajak, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Kowit Hengphasatporn, Yasuteru Shigeta, Jatupol Liangsakul, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Taksina Chuanasa, Wanchai De-Eknamkul, Supot Hannongbua, Thanyada Rungrotmongkol, Supakarn Chamni
Molecules 27 (9) May 2022[Refereed]
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease
Kowit Hengphasatporn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Warinthorn Chavasiri, Peerapat Visitchanakun, Asada Leelahavanichkul, Wattamon Paunrat, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol, Supot Hannongbua, Yasuteru Shigeta
Journal of Chemical Information and Modeling 62 (6) Mar 2022[Refereed]
Investigation of Computational Methods for Membrane Permeability of Middle-Sized Molecules
T. TAKAHASHI, K. HENGPHASATPORN, R. HARADA, Y. SHIGETA
Journal of Computer Chemistry, Japan 21 (4) 2022[Refereed]
Solvophobicity-directed assembly of microporous molecular crystals
Hiroshi Yamagishi, Monika Tsunoda, Kohei Iwai, Kowit Hengphasatporn, Yasuteru Shigeta, Hiroyasu Sato, Yohei Yamamoto
Communications Chemistry 4 (1) Dec 2021[Refereed]
Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics Calculations
Koki Yanagi, Yuki Mitsuta, Kenta Takaoka, Teruyuki Takahashi, Kowit Hengphasatporn, Ryuhei Harada, Yasuteru Shigeta
Chemistry Letters 50 (12) Dec 2021[Refereed]
Alkyne-tagged apigenin, a chemical tool to navigate potential targets of flavonoid anti-dengue leads
Kowit Hengphasatporn, Benyapa Kaewmalai, Somruedee Jansongsaeng, Vishnu Nayak Badavath, Thanaphon Saelee, Thamonwan Chokmahasarn, Tanatorn Khotavivattana, Yasuteru Shigeta, Thanyada Rungrotmongkol, Siwaporn Boonyasuppayakorn
Molecules 26 (22) Nov 2021[Refereed]
A practical prediction of LogPo/wthrough semiempirical electronic structure calculations with dielectric continuum model
Teruyuki Takahashi, Toru Matsui, Kowit Hengphasatporn, Yasuteru Shigeta
Bulletin of the Chemical Society of Japan 94 (7) Jul 2021[Refereed]
Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification
Peerapon Deetanya, Kowit Hengphasatporn, Patcharin Wilasluck, Yasuteru Shigeta, Thanyada Rungrotmongkol, Kittikhun Wangkanont
Computational and Structural Biotechnology Journal 19 Jan 2021[Refereed]
Agonist and antagonist-diverted twisting motions of a single TRPV1 channel
Shoko Fujimura, Kazuhiro Mio, Masahiro Kuramochi, Hiroshi Sekiguchi, Keigo Ikezaki, Muneyo Mio, Kowit Hengphasatporn, Yasuteru Shigeta, Tai Kubo, Yuji C. Sasaki
Journal of Physical Chemistry B 124 (51) Dec 2020[Refereed]
Dibromopinocembrin and Dibromopinostrobin Are Potential Anti-Dengue Leads with Mild Animal Toxicity
Siwaporn Boonyasuppayakorn, Thanaphon Saelee, Peerapat Visitchanakun, Asada Leelahavanichkul, Kowit Hengphasatporn, Yasuteru Shigeta, Thao Nguyen Thanh Huynh, Justin Jang Hann Chu, Thanyada Rungrotmongkol, Warinthorn Chavasiri
Molecules 25 (18) Sep 2020[Refereed]
Why are lopinavir and ritonavir effective against the newly emerged coronavirus 2019? Atomistic insights into the inhibitory mechanisms
Bodee Nutho, Panupong Mahalapbutr, Kowit Hengphasatporn, Nawanwat Chainuwong Pattaranggoon, Nattapon Simanon, Yasuteru Shigeta, Supot Hannongbua, Thanyada Rungrotmongkol
Biochemistry 59 (18) May 2020[Refereed]
Target identification using homopharma and network-based methods for predicting compounds against dengue virus-infected cells
Kowit Hengphasatporn, Kitiporn Plaimas, Apichat Suratanee, Peemapat Wongsriphisant, Jinn Moon Yang, Yasuteru Shigeta, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol
Molecules 25 (8) Apr 2020[Refereed]
Multiple virtual screening strategies for the discovery of novel compounds active against dengue virus: A hit identification study
Kowit Hengphasatporn, Arthur Garon, Peter Wolschann, Thierry Langer, Shigeta Yasuteru, Thao N.T. Huynh, Warinthorn Chavasiri, Thanaphon Saelee, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol
Scientia Pharmaceutica 88 (1) Mar 2020[Refereed]
Estimation of acid dissociation constants (PKA) of N-containing heterocycles in DMSO and transferability of Gibbs free energy in different solvent conditions
Kowit Hengphasatporn, Toru Matsui, Yasuteru Shigeta
Chemistry Letters 49 (3) 2020[Refereed]
Binding pattern and susceptibility of epigallocatechin gallate against envelope protein homodimer of Zika virus: A molecular dynamics study
Kowit Hengphasatporn, Nawee Kungwan, Thanyada Rungrotmongkol
Journal of Molecular Liquids 274 Jan 2019[Refereed]
Cardol triene inhibits dengue infectivity by targeting kl loops and preventing envelope fusion
Parichat Kanyaboon, Thanaphon Saelee, Aphinya Suroengrit, Kowit Hengphasatporn, Thanyada Rungrotmongkol, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn
Scientific Reports 8 (1) Dec 2018[Refereed]
A novel flavanone derivative inhibits dengue virus fusion and infectivity
Pimsiri Srivarangkul, Wanchalerm Yuttithamnon, Aphinya Suroengrit, Saran Pankaew, Kowit Hengphasatporn, Thanyada Rungrotmongkol, Preecha Phuwapriasirisan, Kiat Ruxrungtham, Siwaporn Boonyasuppayakorn
Antiviral Research 151 Mar 2018[Refereed]
Awards & Honors
Books etc
Advances in Methods and Applications of Quantum Systems in Chemistry, Physics, and Biology
(Role:Joint author)
Research Grants & Projects
癌細胞の代謝リプログラミング依存的な糖鎖修飾と癌微小環境応答の解明
科学研究費助成事業
Research period: Apr 2024 - Mar 2028Representative: 川西邦夫, 久野敦, HENGPHASATPORN Kowit
FMO/ML-Guided Drug Design: Accelerating Novel Inhibitor Development and Drug Discovery
科学研究費助成事業
Research period: Apr 2024 - Mar 2027Representative: HENGPHASATPORN Kowit
Novel signal regulation by G protein supersulfidation and its physiological role
Grants-in-Aid for Scientific Research
Research period: Sep 2021 - Mar 2026

	氏名	岡澤一樹
	Name	OKAZAWA Kazuki
	Faculty
	Section
	Position	Assistant Professor
	Theme	Theoretical studies on electron transports of π-conjugated molecules; Theoretical studies on self-assembly processes
	Related Links	Trios researchmap
	Email	okazawaccs.tsukuba.ac.jp

Research Interests
▼▲
Theoretical Chemistry
Quantum Chemistry
Computational Chemistry
Graph Theory
Single-molecule Device
Nonequilibrium Green`s Function
Academic & Professional Experience
Apr 2024
-
Present
Center for Computational Sciences Assistant Professor
Apr 2023
-
Mar 2024
Japan Society for the Promotion of Science Research Fellow
Apr 2022
-
Mar 2024
Kyushu University Faculty of Engineering Sciences Research Assistant
Apr 2021
-
Mar 2023
Kyushu University
Published Papers
▼▲
Pseudo[3]rotaxane and [3]Rotaxane of Per(5-carboxy-5-dehydroxymethyl)-Cyclodextrins Utilizing Carboxylic Acid Dimer as Recognition Units
Nakamura, Takashi, Kuwabara, Masamune, Zhang, Haoyang, Okazawa, Kazuki, Boero, Mauro, Shigeta, Yasuteru, Nabeshima, Tatsuya
The Journal of Organic Chemistry Mar 2025[Refereed]
Density Functional Theory Study of Adhesion Mechanism between Epoxy Resins Cured with 4,4′-Diaminodiphenyl Sulfone and 4,4′-Diaminodiphenylmethane and Carboxyl Functionalized Carbon Fiber
Amit Shrestha, Yosuke Sumiya, Kazuki Okazawa, Yuta Tsuji, Kazunari Yoshizawa
Langmuir Oct 2024
σ Interference: Through-Space and Through-Bond Dichotomy
Tsuji, Yuta, Okazawa, Kazuki, Tatsumi, Toshinobu, Yoshizawa, Kazunari
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Epub Oct 2024[Refereed]
Thiourea as a “Polar Hydrophobic” Hydrogen-Bonding Motif: Application to Highly Durable All-Underwater Adhesion
Kohei Kikkawa, Yosuke Sumiya, Kazuki Okazawa, Kazunari Yoshizawa, Yoshimitsu Itoh, Takuzo Aida
Journal of the American Chemical Society Jul 2024
Complexation-Triggered Fluctuation of π-Conjugation on an Antiaromatic Dicyanoanthracene Dianion
Imagawa, Taiki, Okazawa, Kazuki, Yoshizawa, Kazunari, Yoshida, Hiroto, Shang, Rong, Yamamoto, Yohsuke, Nakamoto, Masaaki
Chemistry (Weinheim an der Bergstrasse, Germany) 29 (70) Dec 2023[Refereed]
Hückel Molecular Orbital Analysis for Stability and Instability of Stacked Aromatic and Stacked Antiaromatic Systems
Yuta Tsuji, Kazuki Okazawa, Kazunari Yoshizawa
The Journal of Organic Chemistry Nov 2023
Exploring Metal Nanocluster Catalysts for Ammonia Synthesis Using Informatics Methods: A Concerted Effort of Bayesian Optimization, Swarm Intelligence, and First-Principles Computation
Yuta Tsuji, Yuta Yoshioka, Kazuki Okazawa, Kazunari Yoshizawa
ACS Omega 8 (33) Aug 2023
Frontier Orbital Views of Stacked Aromaticity
Kazuki Okazawa, Yuta Tsuji, Kazunari Yoshizawa
The Journal of Physical Chemistry A Jun 2023
Molecular Understanding of Adhesion of Epoxy Resin to Graphene and Graphene Oxide Surfaces in Terms of Orbital Interactions
Amit Shrestha, Yosuke Sumiya, Kazuki Okazawa, Takahiro Uwabe, Kazunari Yoshizawa
Langmuir 39 (15) Apr 2023
Mechanistic origins of accelerated hydrogenation of mixed alkylaromatics by synchronised adsorption over Rh/SiO₂
Nikolay Cherkasov, Shusaku Asano, Yuta Tsuji, Kazuki Okazawa, Kazunari Yoshizawa, Hiroyuki Miyamura, Jun-ichiro Hayashi, Alexander A. Kunitsa, Samuel Jackson
Reaction Chemistry & Engineering 8 (6) Mar 2023
Extraordinary Acceleration of an Electrophilic Reaction Driven by the Polar Surface of 2D Aluminosilicate Nanosheets
Nagy Torad, Yuta Tsuji, Azhar Alowasheeir, Masako Momotake, Kazuki Okazawa, Kazunari Yoshizawa, Michio Matsumoto, Masafumi Yamato, Yusuke Yamauchi, miharu eguchi
Small 19 (11) Jan 2023
Exploring the Optimal Alloy for Nitrogen Activation by Combining Bayesian Optimization with Density Functional Theory Calculations
Kazuki Okazawa, Yuta Tsuji, Keita Kurino, Masataka Yoshida, Yoshifumi Amamoto, Kazunari Yoshizawa
ACS Omega 7 (49) Nov 2022
Graph-theoretical exploration of the relation between conductivity and connectivity in heteroatom-containing single-molecule junctions
Kazuki Okazawa, Yuta Tsuji, Kazunari Yoshizawa
The Journal of Chemical Physics 156 (9) Mar 2022
Topology Dictates Magnetic and Conductive Properties of a π-Stacked System: Insight into Possible Coexistence of Magnetic and Conductive Systems
Yuta Tsuji, Kazuki Okazawa, Keita Kurino, Kazunari Yoshizawa
The Journal of Physical Chemistry C Feb 2022
Electronic Origin of Catalytic Activity of TiH2 for Ammonia Synthesis
Tsuji, Y., Okazawa, K., Kobayashi, Y., Kageyama, H., Yoshizawa, K.
Journal of Physical Chemistry C 125 (7) 2021
Understanding Single-Molecule Parallel Circuits on the Basis of Frontier Orbital Theory
Okazawa, K., Tsuji, Y., Yoshizawa, K.
Journal of Physical Chemistry C 124 (5) 2020
Time-resolved infrared study of photo-induced ring-closure reaction of trans-2-hydroxychalcone
Kondoh, M., Takizawa, C., Okazawa, K., Akase, D., Aida, M., Ishibashi, T.-A.
Journal of Photochemistry and Photobiology A: Chemistry 389 2020
Mechanical Control of Molecular Conductance and Diradical Character in Bond Stretching and π-Stack Compression
Tsuji, Y., Okazawa, K., Chen, B., Yoshizawa, K.
Journal of Physical Chemistry C 124 (42) 2020
Photo-Induced Ring-Opening Reaction of Flav-3-en-2-ol Monitored by Time-Resolved Infrared Spectroscopy
Kondoh, M., Sakuta, A., Okazawa, K., Akase, D., Aida, M., Ishibashi, T.-A.
Journal of Physical Chemistry B 123 (40) 2019
Awards & Honors
Nov 2022
Division of Chemoinformatics, The Chemical Society of Japan Poster Award, 45th Symposium on Chemoinformatics
Books etc
Research Grants & Projects
新規単分子圧電素子の開発に向けた積層π共役単分子接合の伝導特性に関する理論的研究
科学研究費助成事業
Research period: Apr 2023 - Mar 2025Representative: 岡澤一樹
Theoretical study on the change of conduction properties of single-molecule junctions by oriented external electromagnetic field
Academic Challenge
Research period: Apr 2021 - Mar 2022

	氏名	齋藤一弥
	Name	SAITO Kazuya
	Faculty
	Section
	Position	Researcher
	Theme
	Related Links	researchmap
	Email	kazuyachem.tsukuba.ac.jp

Research Interests
Academic & Professional Experience
Apr 2024
-
Present
University of Tsukuba Center for Computational Sciences Researcher
Apr 2024
-
Present
National Institute for Materials Science STAM office Editorial Coordinator
Apr 2024
-
Present
University of Tsukuba
Apr 2004
-
Mar 2024
University of Tsukuba Graduate School of Pure and Applied Sciences Professor
Dec 1995
-
Mar 2004
Osaka University Faculty of Science & Graduate School of Science Associate Professor
Jan 1987
-
Nov 1995
Tokyo Metropolitan University Faculty of Science Research Associate
Apr 1986
-
Dec 1986
Research Laboratory of Enginearing Materials Tokyo Institute of Technology Technical Assistant
Published Papers
▼▲
Methyl side-groups control the Ia3̄d phase in core-non-symmetric aryloyl-hydrazine-based molecules
Sota Takebe, Nachia Isobe, Taro Udagawa, Yasuhisa Yamamura, Kazuya Saito, Yohei Miwa, Kei Hashimoto, Shoichi Kutsumizu
Physical Chemistry Chemical Physics 2025
Room-temperature Ia3d phase obtained for the binary mixture containing different sizes of siloxanyl terminals
Yuki Kawase, Shoichi Kutsumizu, Taro Udagawa, Yohei Miwa, Yasuhisa Yamamura, Kazuya Saito
Physical Chemistry Chemical Physics 25 (26) Jun 2023[Refereed]
Reticular-Chemical Approach to Soft-Matter Self-Assembly: Why Are srs and noh Nets Realized in Thermotropics?
Kazuya Saito, Yasuhisa Yamamura
Bulletin of the Chemical Society of Japan 96 (7) May 2023[Refereed]
Three-Step Ordering of Classical Headless Spins Preferring Twists on Icositetrachoric Honeycomb, a Four-Dimensional Analog of the Triangular Lattice
SAITO, Kazuya, Yamamura, Yasuhisa
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 92 (5) Apr 2023[Refereed]
Anti-sigmoidal Composition Dependence of Glass Transition Temperature and Excess Heat Capacity Across It in a Binary System of Globular Alcohols
Yamamura, Yasuhisa, Nomiya, Kaoru, Hishida, Mafumi, Saito, Kazuya
Journal of Solution Chemistry 53 (1) Feb 2023[Refereed]
Aggregation Structure of Chiral Cubic Liquid Crystals Revealed by X-ray Diffraction Utilizing a New Algorithm
Oka, Toshihiko, Yamamura, Yasuhisa, Kutsumizu, Shoichi, Saito, Kazuya
SOFT MATTER 19 (6) Jan 2023[Refereed]
Spontaneous Formation of Cubic Phases: A Molecular Dynamics Study for Soft Repulsive Spherocylinders
Aoki, Keiko M, Yamamura, Yasuhisa, Kutsumizu, Shoichi, Saito, Kazuya
Liquid Crystals Jan 2023[Refereed]
Molecular dynamics and kinetics of isothermal cold crystallization with tunable dimensionality in a molecular glass former, 5’-(2,3-difluorophenyl)-2’-ethoxy-4-pentyloxy-2,3-difluorotolane
Rozwadowski, Tomasz, Noda, Hiroshi, Kolek, Łukasz, Ito, Mizuki, Yamamura, Yasuhisa, Saitoh, Hideki, Saito, Kazuya
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 25 (1) Dec 2022[Refereed]
Small Spin Clusters Mimicking a Temperature-Induced Phase Transition: Spins on Vertices of Regular Octahedron and Icositetrachoron
Saito, Kazuya, Yamamura, Yasuhisa
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 91 (10) Oct 2022[Refereed]
Headless Heisenberg Spin Models Preferring Twist on Triangular Lattice: Phase Transition under External Field
Saito, Kazuya, Yamamura, Yasuhisa
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 91 (7) Jul 2022[Refereed]
Two-Dimensional Spin Model Possibly Undergoing a Phase Transition: Heisenberg Model of Headless Spins Preferring Twist on Triangular Lattice
Saito, Kazuya, Hishida, Mafumi, Yamamura, Yasuhisa
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 90 (12) Dec 2021[Refereed]
Various Stacking Patterns of Two-Dimensional Molecular Assemblies in Hydrogen-Bonded Cocrystals: Insight into Competitive Intermolecular Interactions and Control of Stacking Patterns
Donoshita, Masaki, Yoshida, Yukihiro, Hayashi, Mikihiro, Ikeda, Ryuichi, Tanaka, Susumu, Yamamura, Yasuhisa, Saito, Kazuya, Kawaguchi, Shogo, Sugimoto, Kunihisa, Kitagawa, Hiroshi
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 60 (42) Oct 2021[Refereed]
Stabilization of Bicontinuous Cubic Phase and Its Two-Sided Nature Produced by Use of Siloxane Tails and Introduction of Molecular Nonsymmetry
Kutsumizu, Shoichi, Kawafuchi, Akane, Yamamura, Yasuhisa, Udagawa, Taro, Otaki, Takashi, Masuda, Masaki, Miwa, Yohei, Saito, Kazuya
CHEMISTRY-A EUROPEAN JOURNAL 27 (40) Jul 2021[Refereed]
Interplay between Melt and Cold Crystallization in a Smectic Liquid Crystal, 4-Pentylphenyl 4-(trans-4-Pentylcyclohexyl)benzoate
Rozwadowski, Tomasz, Yamamura, Yasuhisa, Saito, Kazuya
CRYSTAL GROWTH & DESIGN 21 (5) May 2021[Refereed]
Reversible supra-folding of user-programmed functional DNA nanostructures on fuzzy cationic substrates
Nakazawa, Koyomi, El Fakih, Farah, Jallet, Vincen, Rossi-Gendron, Caroline, Mariconti, Marina, Chocron, Léa, Hishida, Mafumi, Saito, Kazuya, Morel, Mathieu, Rudiuk, Sergii, Baigl, Damien
Angewandte Chemie (International ed. in English) 60 (28) Mar 2021[Refereed]
Phase Transition from the Interdigitated to Bilayer Membrane of a Cationic Surfactant Induced by Addition of Hydrophobic Molecules
Hishida, Mafumi, Shimokawa, Naofumi, Okubo, Yuki, Taguchi, Shun, Yamamura, Yasuhisa, Saito, Kazuya
Langmuir 36 (48) Dec 2020[Refereed]
Designing the disorder: the kinetics of nonisothermal crystallization of the orientationally disordered crystalline phase in a nematic mesogen
Rozwadowski, Tomasz, Jasiurkowska-Delaporte, Malgorzata, Massalska-Arodz, Maria, Yamamura, Yasuhisa, Saito, Kazuya
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 22 (42) Nov 2020[Refereed]
Positive definite distortion term of the extended Landau-de Gennes model
Pelka, Rober, Saito, Kazuya
MOLECULAR CRYSTALS AND LIQUID CRYSTALS 702 (1) May 2020
Ordering Phase Transition with Symmetry-Breaking from Disorder over Non-Equivalent Sites: Calorimetric and Crystallographic Study of Crystalline d-Sorbose
Iwagaki, Sakiko, Kakuta, Hiroki, Yamamura, Yasuhisa, Saitoh, Hideki, Hishida, Mafumi, Fukada, Kazuhiro, Saito, Kazuya
Crystals 10 (5) Apr 2020[Refereed]
Interleaflet coupling of n-alkane incorporated bilayers
Usuda, Hatsuho, Hishida, Mafumi, Kelley, Elizabeth G, Yamamura, Yasuhisa, Nagao, Michihiro, Saito, Kazuya
Phys. Chem. Chem. Phys. 22 (10) Feb 2020[Refereed]
Structural Thermodynamics of Real Liquid Crystals – Cause of Stability and The Beyond
Saito,Kazuya
MEMBRANE 45 (5) 2020
Molecular packing in two bicontinuous Ia(3)over-bard gyroid phases of calamitic cubic mesogens BABH(n): roles in structural stability and reentrant behavior
Yamamura, Yasuhisa, Nakazawa, Yuri, Kutsumizu, Shoichi, Saito, Kazuya
Physical chemistry chemical physics : PCCP 21 (42) Nov 2019[Refereed]
液晶の発現機構と凝集構造 − エントロピーを足がかりにした物性科学の例として
齋藤,一弥
JOURNAL OF JAPANESE SCIENTISTS 54 (3) Mar 2019[Refereed]
Phase separation of a ternary lipid vesicle including n-alkane: Rugged vesicle and bilayer flakes formed by separation between highly rigid and flexible domains"
Hishida, Mafumi, Yanagisawa, Ryuta, Yamamura, Yasuhisa, Saito, Kazuya
JOURNAL OF CHEMICAL PHYSICS 150 (6) Feb 2019[Refereed]
Molecular packing in two bicontinuous: Ia 3 d gyroid phases of calamitic cubic mesogens BABH(n): Roles in structural stability and reentrant behavior
Yasuhisa Yamamura, Yuri Nakazawa, Shoichi Kutsumizu, Kazuya Saito
Physical Chemistry Chemical Physics 21 (42) 2019
Role of alkyl-chain in cubic Ia3d phase of BABH(n)
Yamamura,Yasuhisa, Nakazawa,Yuri, Kutsumizu,Shoichi, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2019 2019
Glass transition and crystallization of ODIC phase in nematic liquid crystal
Rozwadowski,Tomasz, Jasiurkowska-Delaporte,Malgorzata, Massalska-Arodz,Maria, Hishida,Mafumi, Yamamura,Yasuhisa, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2019 2019
Phase behavior in a binary system between PHOAB and 8OCB exhibiting SmA phase
Noda,Hiroshi, Yamamura,Yasuhisa, Hishida,Mafumi, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2019 2019
Heat capacity and standard thermodynamic functions of three ketohexoses in monosaccharides including rare sugars: D-fructose, D-psicose, and D-tagatose
Yamamura, Yasuhisa, Iwagaki, Sakiko, Hishida, Mafumi, Nagatomo, Shigenori, Fukada, Kazuhiro, Saito, Kazuya
J. Chem. Thermodyn. 131 Dec 2018[Refereed]
Optical Switching between Liquid-crystalline Assemblies with Different Structural Symmetries and Molecular Orders
Aya Nagai, Hideaki Kondo, Yohei Miwa, Tomonori Kondo, Shoichi Kutsumizu, Yasuhisa Yamamura, Kazuya Saito
Bulletin of the Chemical Society of Japan 91 (11) Nov 2018[Refereed]
Common Effects of Incorporated n-Alkane Derivatives on Molecular Packing and Phase Behavior of DPPC Bilayers
Usuda, Hatsuho, Hishida, Mafumi, Yamamura, Yasuhisa, Saito, Kazuya
Chemistry Letters 47 (12) Nov 2018[Refereed]
Photochemical manipulation of the upper-critical-solution-temperature ofpolymers in photoresponsive liquid crystals
Kawata,Yuki, Yamamoto,Takahiro, Kihara,Hideyuki, Yamamura,Yasuhisa, Saito,Kazuya, Ohno,Kohji
Proceedings of Japanese Liquid Crystal Society Annual meeting 2017 Jun 2018
Reversible switching between one-dimensionally ordered smectic and three-dimensionally periodic bicontinuous cubic phases by use of photoisomerization of azobenzene derivatives
Nagai,Aya, Kondo,Hideaki, Miwa,Yohei, Kutsumizu,Shoichi, Yamamura,Yasuhisa, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2017 Jun 2018
Synthesis of PEO-based physical gels with tunable viscoelastic properties
Takuya Murakami, Takashi Kawamori, Jeffrey D. Gopez, Alaina J. McGrath, Daniel Klinger, Kazuya Saito
Journal of Polymer Science, Part A: Polymer Chemistry 56 (10) May 2018[Refereed]
Unusual photoresponses in the upper critical solution temperature of polymer solutions mediated by changes in intermolecular interactions in an azo-doped liquid crystalline solvent
Kawata Yuki, Yamamoto Takahiro, Kihara Hideyuki, Yamamura Yasuhisa, Saito Kazuya, Ohno Kohji
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 20 (8) Feb 2018[Refereed]
Insight into structural demand for cold crystallization of a small molecule. A case study for schiff base compounds that exhibit prototropic tautomerization
Katsunori Iwase, Yasuhiro Toyama, Isao Yoshikawa, Yasuhisa Yamamura, Kazuya Saito, Hirohiko Houjou
Bulletin of the Chemical Society of Japan 91 (4) 2018[Refereed]
Optical Switching between Liquid-Crystalline Assemblies with Different Structural Symmetries and Molecular Orders
Aya Nagai, Hideaki Kondo, Yohei Miwa, Tomonori Kondo, Shoichi Kutsumizu, Yasuhisa Yamamura, Kazuya Saito
Bulletin of the Chemical Society of Japan 91 (11) 2018
Packing modes of alkyl-chain in cubic Ia3d phase of BABH(n)
Yamamura,Yasuhisa, Nakazawa,Yuri, Kutsumizu,Shoichi, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2018 2018
Effect of incorporated alkanes on thickness fluctuation of lipid membranes
Usuda,Hatsuho, Hishida,Mafumi, Kelley,Elizabeth G, Saito,Kazuya, Nagao,Michihiro
Meeting Abstracts of the Physical Society of Japan 73 2018
Electric surface potential of multi-lamellar vesicle of charged lipid bilayers
Hishida,Mafumi, Akiyama,Ryo, Yamamura,Yasuhisa, Saito,Kazuya
Meeting Abstracts of the Physical Society of Japan 73 2018
Examination of molecular packing in orthogonal smectic liquid crystal phases: a guide for molecular design of functional smectic phases
Yamamura, Yasuhisa, Murakoshi, Takahito, Hishida, Mafumi, Saito, Kazuya
Physical chemistry chemical physics : PCCP 19 (37) Sep 2017[Refereed]
Examination of molecular packing in orthogonal smectic liquid crystal phases: a guide for molecular design of functional smectic phases
Yamamura, Yasuhisa, Murakoshi, Takahito, Hishida, Mafumi, Saito, Kazuya
Physical chemistry chemical physics : PCCP 19 (37) Sep 2017[Refereed]
Structure and molecular packing in smectic B-Cr and A(d) phases of Schiff base liquid crystal compounds through the analyses of layer spacing, entropy and crystal structure
Yasuhisa Yamamura, Takahito Murakoshi, Sakiko Iwagaki, Natalia Osiecka, Hideki Saitoh, Mafumi Hishida, Zbigniew Galewski, Maria Massalska-Arodz, Kazuya Saito
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 19 (29) Aug 2017[Refereed]
Orders Exhibited by Ensemble of Headless Spins Preferring Twisted Alignment: Phase Diagram of Extended Maier-Saupe Model on Simple Cubic Lattice
Kazuya Saito, Mafumi Hishida, Yasuhisa Yamamura
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 86 (8) Aug 2017[Refereed]
Dimensional Crossover and Its Interplay with In-Plane Anisotropy of Upper Critical Field in beta-(BDA-TTP)(2)SbF6
Syuma Yasuzuka, Hiroaki Koga, Yasuhisa Yamamura, Kazuya Saito, Shinya Uji, Taichi Terashima, Hiroki Akutsu, Jun-Ichi Yamada
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 86 (8) Aug 2017[Refereed]
Structure and molecular packing in smectic BCr and Ad phases of Schiff base liquid crystal compounds through the analyses of layer spacing, entropy and crystal structure
Yamamura, Yasuhisa, Murakoshi, Takahito, Iwagaki, Sakiko, Osiecka, Natalia, Saitoh, Hideki, Hishida, Mafumi, Galewski, Zbigniew, Massalska-Arodź, Maria, Saito, Kazuya
Physical chemistry chemical physics : PCCP 19 (29) Jul 2017[Refereed]
X-ray study of molecular association in alcohols having bulky substituents
Kazuya Saito, Mafumi Hishida, Kent Koike, Shigenori Nagatomo, Yasuhisa Yamamura
CHEMICAL PHYSICS LETTERS 673 Apr 2017[Refereed]
Interrelationship among Fe-His Bond Strengths, Oxygen Affinities, and Intersubunit Hydrogen Bonding Changes upon Ligand Binding in the β Subunit of Human Hemoglobin: The Alkaline Bohr Effect
Shigenori Nagatomo, Miki Okumura, Kazuya Saito, Takashi Ogura, Teizo Kitagawa, Masako Nagai
Biochemistry 56 (9) Mar 2017[Refereed]
Odd-Even Effect on Nematic SmAd Phase Boundary and SmAd Structure in Homologous Binary Systems of Cyanobiphenyl Mesogens: 4-Alkyl-4′-cyanobiphenyl (nCB) and 4-Alkoxy-4′-cyanobiphenyl (nOCB)
Yasuhisa Yamamura, Rei Tsuchiya, Shuhei Fujimura, Mafumi Hishida, Kazuya Saito
Journal of Physical Chemistry B 121 (6) Feb 2017[Refereed]
Odd Even Effect on Nematic SmAd Phase Boundary and SmAd Structure in Homologous Binary Systems of Cyanobiphenyl Mesogens: 4-Alkyl-4'-cyanobiphenyl (nCB) and 4-Alkoxy-4'cyanobiphenyl (nOCB)
Yasuhisa Yamamura, Rei Tsuchiya, Shuhei Fujimura, Mafumi Hishida, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 121 (6) Feb 2017[Refereed]
Competition of effects of added alkane and cholesterol in lipid bilayer
Yokoyama,Natsuki
Meeting Abstracts of the Physical Society of Japan 72 2017
Linear chain molecules densify molecular packing of lipid bilayers in the gel phase irrespective of molecular species
Usuda,Hatsuho, Hishida,Mafumi, Yamamura,Yasuhisa, Nagatomo,Shigenori, Saito,Kazuya
Meeting Abstracts of the Physical Society of Japan 72 2017
Change in water behavior upon the gel/liquid crystalline phase transition of a lipid bilayer
Hemmi,Yuta, Hishida,Mafumi, Yamamura,Yasuhisa, Saito,Kazuya
Meeting Abstracts of the Physical Society of Japan 72 2017
Electrostatic double-layer interaction between charged lipid bilayers discussed by co-ion valence dependence
Hishida,Mafumi, Nomura,Yoko, Akiyama,Ryo, Yamamura,Yasuhisa, Saito,Kazuya
Meeting Abstracts of the Physical Society of Japan 72 2017
Freezing point elevation of phospholipid bilayers containing linear chain molecules
Usuda,Hatsuho, Hishida,Mafumi, Yamamura,Yasuhisa, Nagatomo,Shigenori, Saito,Kazuya
Meeting Abstracts of the Physical Society of Japan 72 2017
Aggregation modes of molecules preferring twisted arrangements through computer simulation of extended Maier-Saupe model on lattice
Saito,Kazuya, Hishida,Mafumi, Yamamura,Yasuhisa
Proceedings of Japanese Liquid Crystal Society Annual meeting 2017 2017
Molecular packing modes in orthogonal smectic liquid crystal phases
Yamamura,Yasuhisa, Murakoshi,Takahito, Hishida,Mafumi, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2017 2017
Three Gel States of Colloidal Composites Consisting of Polymer-Brush-Afforded Silica Particles and a Nematic Liquid Crystal with Distinct Viscoelastic and Optical Properties
Yuki Kawata, Takahiro Yamamoto, Hideyuki Kihara, Yasuhisa Yamamura, Kazuya Saito, Kohji Ohno
ACS APPLIED MATERIALS & INTERFACES 8 (43) Nov 2016[Refereed]
Salt Effects on Lamellar Structure of Nonionic Surfactants
Mafumi Hishida, Yohei Kaneko, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF SOLUTION CHEMISTRY 45 (11) Nov 2016[Refereed]
Photoinduced Bilayer-to-Nonbilayer Phase Transition of POPE by Photoisomerization of Added Stilbene Molecules
Koyomi Nakazawa, Mafumi Hishida, Shigenori Nagatomo, Yasuhisa Yamamura, Kazuya Saito
LANGMUIR 32 (30) Aug 2016[Refereed]
Mirror symmetry breaking by mixing of equimolar amounts of two gyroid phase-forming achiral molecules
Shoichi Kutsumizu, Suguru Miisako, Yohei Miwa, Makoto Kitagawa, Yasuhisa Yamamura, Kazuya Saito
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18 (26) Jul 2016[Refereed]
Contrasting Effects of a Rigid Core and an Alkyl Chain in nCB on the Phase Behavior of Lipid Bilayers
Hatsuho Usuda, Mafumi Hishida, Yasuhisa Yamamura, Kazuya Saito
LANGMUIR 32 (23) Jun 2016[Refereed]
Stabilization of bicontinuous cubic phase in siloxane-terminated mesogens, 1,2-bis[4'-(n-(oligodimethylsiloxyl)alkoxy)benzoyl]hydrazine,
Kutsumizu Shoichi(Gifu University, Tokiwa Issei(Gifu University, Kawafuchi Akane(Gifu University, Miwa Yohei(Gifu University, Yamamura Yasuhisa, University of Tsukuba, Saito Kazuya, U, i, rsity of Tsukub
Physical Chemistry Chemical Physics 18 (13) Apr 2016[Refereed]
Communication: Rigidification of a lipid bilayer by an incorporated n-alkane
Mafumi Hishida, Ryuta Yanagisawa, Hatsuho Usuda, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF CHEMICAL PHYSICS 144 (4) Jan 2016[Refereed]
A Structural Model of the Chiral"Im3m"Cubic Phase
Saito Kazuya, i, rsity of Tsukuba, Yamamura Yasuhisa, University of Tsukuba, Miwa Yohei, Gifu University, Kutsumizu Shoichi(Gifu University
Physical Chemistry Chemical Physics 18 (4) Jan 2016[Refereed]
Effect of Chemical Structures of Constituent Molecules for Light-induced Bicontinuous Cubic Liquid Crystalline Phase Transition
Nagai,Aya, Mizutani,Mariko, Miwa,Yohei, Kutsumizu,Shoichi, Yamamura,Yasuhisa, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2016 2016
Phase Diagram of System with Intermolecular Interaction Having Both P2 and -P4 Terms
Saito,Kazuya, Hishida,Mafumi, Yamamura,Yasuhisa
Proceedings of Japanese Liquid Crystal Society Annual meeting 2016 2016
Spontaneous mirror symmetry breaking in the formation of bicontinuous cubic phases by BABH-based achiral single molecules and mixtures
Kutsumizu,Shoichi, Miwa,Yohei, Yamamura,Yasuhisa, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2016 2016
Binary systems between calamitic mesogens exhibiting smectic phases and n-alkane
Yamamura,Yasuhisa, Murakoshi,Takahito, Miyazawa,Takahito, Osiecka,Natalia, Hishida,Mafumi, Galewski,Zbigniew, Massalska-Arodz,Maria, Urban,Stanislaw, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2016 2016
20pBW-8 Aggregation of charged bilayers depends on the charges of added co-ions
Hishida,M, Nomura,Y, Yamamura,Y, Saito,K
Meeting Abstracts of the Physical Society of Japan 71 2016
PA58 Molecular diffusion in SmE phase studied by fluorescence recovery after photobreaching
Tanaka,Natsuho, Hishida,Mafumi, Yamamura,Yasuhisa, Nagatomo,Shigenori, Saito,Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting (2015) Sep 2015
Structural Isomerization and Cold Crystallization of Bis[1-(2-propyl)iminomethylnaphthalen-2-olato]nickel(II) by Thermal Analysis, X-ray Diffraction, and FT-IR
Katsunori Iwase, Isao Yoshikawa, Hirohiko Houjou, Yasuhisa Yamamura, Kazuya Saito
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 88 (7) Jul 2015
Communication: Salt-induced water orientation at a surface of non-ionic surfactant in relation to a mechanism of Hofmeister effect
Mafumi Hishida, Yohei Kaneko, Masanari Okuno, Yasuhisa Yamamura, Taka-Aki Ishibashi, Kazuya Saito
Journal of Chemical Physics 142 (17) May 2015
Effect of n-alkanes on lipid bilayers depending on headgroups
Mafumi Hishida, Asami Endo, Koyomi Nakazawa, Yasuhisa Yamamura, Kazuya Saito
CHEMISTRY AND PHYSICS OF LIPIDS 188 May 2015
22pPSA-8 Possible effect of entropy gain by ions on aggregation of charged phospholipid membranes
Nomura,Y, Hishida,M, Yamamura,Y, Nagatomo,S, Saito,K
Meeting Abstracts of the Physical Society of Japan 70 (1) Mar 2015
Ultraslow Oscillation of Nematic Disclination after Abrupt Switching of DC Voltage
Takuya Yanagimachi, Mafumi Hishida, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 84 (3) Mar 2015
Effects of the lateral substituent on the cubic phase formation of two analogous compounds, 4MODIFIER LETTER PRIME-n-hexadecyloxy-3MODIFIER LETTER PRIME-cyanobiphenyl-4-carboxylic acid (ACBC-16) and its 3MODIFIER LETTER PRIME-nitro compound (ANBC-16)
Ryoji Ogawa, Yohei Miwa, Masato Sumita, Kazuya Saito, Shoichi Kutsumizu
LIQUID CRYSTALS 42 (2) Feb 2015[Refereed]
PB06 Possible critical point for nematic phase transition in smectic liquid crystal induced by phase-separation
SAITO Kazuya, HISHIDA Mafumi, YAMAMURA Yasuhisa
Proceedings of Japanese Liquid Crystal Society Annual meeting 2015 2015
PB57 Smectic B phase in binary system of 8BBAA and n-decane
Murakoshi Takahito, Yamamura Yasuhisa, Osiecka Natalia, Hishida Mafumi, Galewski Zbigniew, Massalska-Arodz Maria, Saito Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2015 2015
2C03 Phase behavior and odd-even effect in nCB/9CB binary systems
Tsuchiya Rei, Yamamura Yasuhisa, Hishida Mafumi, Nagatomo Shigenori, Saito Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2015 2015
3A13 Lattice Periodicity "Fluctuation" of Bicontinuous Cubic Phase of Siloxane-Terminated Mesogens
Kutsumizu Shoichi, Tokiwa Issei, Miwa Yohei, Yamamura Yasuhisa, Saito Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2015 2015
17pPSB-22 Phase separation behavior of ternary phospholipid bilayer including alkane
Hishida M., Yanagisawa R., Yamamura Y., Saito K.
Meeting Abstracts of the Physical Society of Japan 70 2015
21pAQ-2 Stiffening and rupture of lipid vesicles by addition of alkane
Hishida M., Yanagisawa R., Yamamura Y., Saito K.
Meeting Abstracts of the Physical Society of Japan 70 2015
A possible critical point for nematic order on the basis of Landau free energy having dual instabilities for nano-segregated smectic liquid crystals
Kazuya Saito, Mafumi Hishida, Yasuhisa Yamamura
SOFT MATTER 11 (43) 2015[Refereed]
Cold Crystallization in Schiff-Base Nickel(II) Complexes Derived from Three Toluidine Isomers
Katsunori Iwase, Yuta Nagano, Isao Yoshikawa, Hirohiko Houjou, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY C 118 (48) Dec 2014[Refereed]
熱量測定のこれからにむけて
齋藤,一弥
熱測定 41 (4) Nov 2014[Refereed]
Salt Effects on Lamellar Repeat Distance Depending on Head Groups of Neutrally Charged Lipids
Mafumi Hishida, Yasuhisa Yamamura, Kazuya Saito
LANGMUIR 30 (35) Sep 2014
Calorimetric Studies on Quasi-One-Dimensional MMX Complexes, M2(RCS2)4I
Saito,Kazuya, Ikeuchi,Satoaki
Curr. Inorg. Chem. 4 (2) Sep 2014[Refereed]
Interplay between Phase Transition of DPPC Bilayer and Photoisomerization of Doped Stilbene Molecules
Koyomi Nakazawa, Mafumi Hishida, Shigenori Nagatomo, Yasuhisa Yamamura, Kazuya Saito
CHEMISTRY LETTERS 43 (8) Aug 2014[Refereed]
Liquid-crystallinity of cubic phase of BABH(6) through thermal analysis of solid-solid phase transitions
Mika Umeyama, Shuhei Fujimura, Yasuhisa Yamamura, Mafumi Hishida, Shoichi Kutsumizu, Kazuya Saito
THERMOCHIMICA ACTA 590 Aug 2014
10aAM-5 Nonlinear Force Acting on Defect and Director Field near Air-Liquid Crystal Interface
Yanagimachi,Takuya, Hishida,Mafumi, Yamamura,Yasuhisa, Saito,Kazuya
Meeting abstracts of the Physical Society of Japan 69 (2) Aug 2014
8pPSB-13 Effect of n-alkane on the gel/liquid-crystalline phase transition of lipid bilayers
Endo,Asami, Hishida,Mafumi, Yamamura,Yasuhisa, Nagatomo,Shigenori, Saito,Kazuya
Meeting abstracts of the Physical Society of Japan 69 (2) Aug 2014
Reentrant nematic phase in 4-alkyl-4 '-cyanobiphenyl (nCB) binary mixtures
Shuhei Fujimura, Yasuhisa Yamamura, Mafumi Hishida, Shigenori Nagatomo, Kazuya Saito
LIQUID CRYSTALS 41 (7) Jul 2014[Refereed]
Phase behaviour of a thermotropic cubic mesogen of 1,2-bis(4 '-n-hexyloxybenzoyl)hydrazine under pressure
Yoji Maeda, Yasuhisa Yamamura, Shoichi Kutsumizu, Kazuya Saito
LIQUID CRYSTALS 41 (5) May 2014[Refereed]
サーモトロピックキュービック相における分子配列とリエントラント
齋藤一弥, 山村,泰久, 沓水祥一
液晶 18 (2) Apr 2014[Refereed]
Cooperativity between Water and Lipids in Lamellar to Inverted-Hexagonal Phase Transition
Mafumi Hishida, Koichiro Tanaka, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 83 (4) Apr 2014[Refereed]
30pAC-7 Effects of monovalent salts on interactions between neutrally charged lipid membranes
Hishida,Masafumi, Yamamura,Yasuhisa, Saito,Kazuya
Meeting abstracts of the Physical Society of Japan 69 (1) Mar 2014
Phase diagram and reentrant phenomenon in 0CB/8CB binary system
Tsuchiya Rei, Yamamura Yasuhisa, Hishida Mafumi, Nagatomo Shigenori, Saito Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2014 2014
Conformational disorder of alkyl chain in crystal of 5ABCA exhibiting SmB phase
Murakoshi Takahito, Yamamura Yasuhisa, Saitoh Hideki, Hishida Mafumi, Nagatomo Shigenori, Galewski Zbigniwe, Massalska-Arodź Maria, Saito Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2014 2014
Reentrant nematic phase in nCB/8CB (n = 1 - 6) binary mixtures
Fujimura Shuhei, Yamamura Yasuhisa, Hishida Mafumi, Nagatomo Shigenori, Saito Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2014 2014
Dynamics and Phase Transitions of 4-Bromobenzylidene-4 '-pentyloxyaniline and 4-Bromobenzylidene-4 '-hexyloxyaniline as Studied by Dielectric Spectroscopy
N. Osiecka, M. Massalska-Arodz, Z. Galewski, K. Chledowska, S. Wrobel, T. Morito, Y. Yamamura, K. Saito
ACTA PHYSICA POLONICA A 124 (6) Dec 2013[Refereed]
Thermodynamic properties of saponite, nontronite, and vermiculite derived from calorimetric measurements
Helene Gailhanou, Philippe Blanc, Jacques Rogez, Georges Mikaelian, Katsuya Horiuchi, Yasuhisa Yamamura, Kazuya Saito, Hitoshi Kawaji, Fabienne Warmont, Jean-Marc Greneche, Philippe Vieillard, Claire I. Fialips, Eric Giffaut, Eric C. Gaucher
AMERICAN MINERALOGIST 98 (10) Oct 2013
On Aggregation Structure of Smectic Phases
SAITO,Kazuya, HISHIDA,Mafumi, YAMAMURA,Yasuhisa
日本液晶学会討論会講演予稿集 (2013) Sep 2013
Universality of Molten State of Alkyl Chain in Liquid-Crystalline Mesophases: Smectic E Phase of 6-Alkyl-2-phenylazulene
Takuya Adachi, Hideki Saitoh, Yasuhisa Yamamura, Mafumi Hishida, Mao Ueda, Shunji Ito, Kazuya Saito
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 86 (9) Sep 2013
Cold Crystallization in Bis[1-(3-methylphenyl)iminomethylnaphthalen-2-olato]nickel(II) Studied by Thermal Analysis and X-ray Diffraction
Katsunori Iwase, Hirohiko Houjou, Yasuhisa Yamamura, Kazuya Saito
CHEMISTRY LETTERS 42 (9) Sep 2013
Reassessment of structure of smectic phases: Nano-segregation in smectic E phase in 4-n-alkyl-4 '-isothiocyanato-1,1 '-biphenyls
Kazuya Saito, Takahito Miyazawa, Akio Fujiwara, Mafumi Hishida, Hideki Saitoh, Maria Massalska-Arodz, Yasuhisa Yamamura
JOURNAL OF CHEMICAL PHYSICS 139 (11) Sep 2013
PA04 Highly sensitive DSC measurement of 7CB-heptane binary system
Umeyama,Mika, Yamamura,Yasuhisa, Fujimura,Shuhei, Hishida,Mafumi, Saito,Kazuya
日本液晶学会討論会講演予稿集 2013 (2013) Sep 2013
3a09 Thermodynamic study of 5CBAA and 5BBAA exhibiting SmB phase
Yamamura,Yasuhisa, Morito,Takehiro, Hishida,Mafumi, Nagatomo,Shigenori, Massalska-Arodz,Maria, Saito,Kazuya
日本液晶学会討論会講演予稿集 2013 (2013) Sep 2013
Effects of monovalent ions on interactions between neutral lipid membranes
Hishida,Mafumi, Yamamura,Yasuhisa, Saito,Kazuya
Meeting abstracts of the Physical Society of Japan 68 (2) Aug 2013
Revisiting Smectic E Structure through Swollen Smectic E Phase in Binary System of 4-Nonyl-4 '-isothiocyanatobiphenyl (9TCB) and n-Nonane
Takahito Miyazawa, Yasuhisa Yamamura, Mafumi Hishida, Shigenori Nagatomo, Maria Massalska-Arodz, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 117 (27) Jul 2013[Refereed]
有機液体における水素結合による環状会合体形成
長友重紀, 山村,泰久, 齋藤一弥
Netsu Sokutei 40 (3) Jul 2013[Refereed]
Anisotropic josephson-vortex dynamics in layered organic superconductor with d-wave pairing symmetry
Syuma Yasuzuka, Kazuya Saito, Shinya Uji, Motoi Kimata, Hidetaka Satsukawa, Taichi Terashima, Jun-Ichi Yamada
Journal of the Physical Society of Japan 82 (6) Jun 2013
Identification of hydrogen-bonded oligomers in associating liquid by 1HNMR: 1-Phenyl-1-cyclohexanol
Shigenori Nagatomo, Megumi Nobuhira, Yasuhisa Yamamura, Masato Sumita, Kazuya Saito
Bulletin of the Chemical Society of Japan 86 (5) 2013
Report of the Discussion Meeting on "Blue Phase"
SAITO,Kazuya
液晶 : 日本液晶学会誌 = Ekisho 16 (4) Oct 2012
Molecular Mechanism Responsible for Reentrance to Ia3d Gyroid Phase in Cubic Mesogen BABH(n)
Yuri Nakazawa, Yasuhisa Yamamura, Shoichi Kutsumizu, Kazuya Saito
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 81 (9) Sep 2012[Refereed]
Essence in oxygen affinity regulation of human adult hemoglobin : Change of Fe-His bond length by quaternary or tertiary structure change(The 50th Annual Meeting of the Biophysical Society of Japan)
Nagatomo,Shigenori, Yamamura,Yasuhisa, Saito,Kazuya
Biophysics 52 (1) Aug 2012
Calorimetric and Spectroscopic Evidence of Chain-Melting in Smectic E and Smectic A Phases of 4-Alkyl-4 '-isothiocyanatobiphenyl (nTCB)
Yasuhisa Yamamura, Takuya Adachi, Takahito Miyazawa, Katsuya Horiuchi, Masato Sumita, Maria Massalska-Arodz, Stanislaw Urban, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 116 (30) Aug 2012[Refereed]
Real-Space Distribution of Local WO4 Ordering in Negative Thermal Expansive ZrW2O8
Yukio Sato, Yasuhisa Yamamura, Kazuya Saito, Yuichi Ikuhara
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 (34) Aug 2012[Refereed]
Cell Gap Dependence of Nematic Backflow around Annihilating Disclination Pair
Takuya Yanagimachi, Syuma Yasuzuka, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 81 (7) Jul 2012[Refereed]
Comparative Study of Imidazolium- and Pyrrolidinium-Based Ionic Liquids: Thermodynamic Properties
Yoshitaka Shimizu, Yoko Ohte, Yasuhisa Yamamura, Seiji Tsuzuki, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 116 (18) May 2012[Refereed]
Calorimetric Study of Glass Transition in Molecular Liquids Consisting of Globular Associates: Dicyclorohexylmethanol and Tricyclohexylmethanol
Yasuhisa Yamamura, Yu-ta Suzuki, Masato Sumita, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 116 (13) Apr 2012[Refereed]
Backflow-Induced Asymmetric Annihilation of Nematic Disclinations under Strong Anchoring Condition
Takuya Yanagimachi, Syuma Yasuzuka, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 81 (3) Mar 2012[Refereed]
Small Fermi Pocket in Layered Organic Superconductor beta-(BDA-TTP)(2)SbF6
Syuma Yasuzuka, Hiroaki Koga, Yasuhisa Yamamura, Kazuya Saito, Shinya Uji, Taichi Terashima, Hirohito Aizawa, Kazuhiko Kuroki, Masahisa Tsuchiizu, Hiroki Akutsu, Jun-ichi Yamada
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 81 (3) Mar 2012[Refereed]
Dynamics of Flexible Alkyl-chain in Lyotropic and Thermotropic Liquid Crystals
Yasuhisa, Yamamura, Takuya, Adachi, Shigenori, Nagatomo, Kazuya, Saito
2nd International Symposium on Creation of Functional Materials (Univ. of Tsukuba, 2012) Feb 2012
Relationship between Fe-His bond and fluctuations of helices in oxygen affinity regulation of human adult hemoglobin
Shigenori, Nagatomo, Yasuhisa, Yamamura, Kazuya, Saito
2nd International Symposium on Creation of Functional Materials (Univ. of Tsukuba, 2012) Feb 2012
ROLE OF Fe-His BOND AND FLUCTUATIONS OF HELICES IN FUNCTIONAL REGULATION OF HUMAN ADULT HEMOGLOBIN
Shigenori, Nagatomo, Yasuhisa, Yamamura, Kazuya, Saito
Molecular Science of Fluctuations toward Biological Functions, 5th International Symposium, (Nara, Japan) Jan 2012
New Organic Ferroelectrics: Cocrystal of 5,5 '-Dimethyl-2,2 '-bipyridine and Bromanilic Acid
Yasuhisa Yamamura, Erika Saito, Hideki Saitoh, Norie Hoshino, Kazuya Saito
CHEMISTRY LETTERS 41 (1) Jan 2012[Refereed]
Comprehensive characterisation of the E phase of 6-octyl-2-phenylazulene
Takuya Adachi, Yasuhisa Yamamura, Mafumi Hishida, Mao Ueda, Shunji Ito, Kazuya Saito
LIQUID CRYSTALS 39 (11) 2012[Refereed]
Association through H-bond of 3-Ethyl-3-pentanol in the Liquid Phase
Megumi, Nobuhira, Shigenori, Nagatomo, Yasuhisa, Yamamura, Kazuya, Saito
1st International Symposium on Creation of Functional Materials (Dec. 2011, Univ. of Tsukuba) Dec 2011
Effect of Cis and Trans Double Bonds on Conformational Disordering of the Hydrocarbon Chain of Lipid, Unsaturated Monoacylglycerols, in the Lamellar Phase of a Binary System with Water
Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 115 (50) Dec 2011[Refereed]
Materials with Negative Thermal Expansion in Wide Temperature Range
YAMAMURA,Yasuhisa, SAITO,Kazuya
Ceramics Japan 46 (11) Nov 2011[Refereed]
Study of Polymorphism of 4-Hexyl-4 '-isothiocyanatobiphenyl by Complementary Methods
Malgorzata Jasiurkowska, Piotr M. Zielinski, Maria Massalska-Arodz, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 115 (43) Nov 2011[Refereed]
Self-assembly of Compact Molecules Possessing Two Carboxy and One Amide Groups into Tubular Nanostructures in Liquid Crystal Phases
Keiki Kishikawa, Miyuki Isaka, Masahiro Takahashi, Kazuya Saito, Shigeo Kohmoto
CHEMISTRY LETTERS 40 (11) Nov 2011[Refereed]
Self-assembly of Compact Molecules Possessing Two Carboxy and One Amide Groups into Tubular Nanostructures in Liquid Crystal Phases
KISHIKAWA,Keiki, ISAKA,Miyuki, TAKAHASHI,Masahiro, SAITO,Kazuya, KOHMOTO,Shigeo
Chemistry letters 40 (11) Nov 2011[Refereed]
Cyanide-Bridged [Fe8M6] Clusters Displaying Single-Molecule Magnetism (M = Ni) and Electron-Transfer-Coupled Spin Transitions (M = Co)
Kiyotaka Mitsumoto, Emiko Oshiro, Hiroyuki Nishikawa, Takuya Shiga, Yasuhisa Yamamura, Kazuya Saito, Hiroki Oshio
CHEMISTRY-A EUROPEAN JOURNAL 17 (35) Aug 2011[Refereed]
Experimental assessment of quasi-binary picture of thermotropics: Induced smectic A phase in 7CB-n-heptane system
Yuuki Yamaoka, Yuki Taniguchi, Syuma Yasuzuka, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF CHEMICAL PHYSICS 135 (4) Jul 2011[Refereed]
Thermal Conductivity of YBCO Coated Conductors Reinforced by Metal Tape
Tomoyuki Naito, Hiroyuki Fujishiro, Yasuhisa Yamamura, Kazuya Saito, Hiroshi Okamoto, Hidemi Hayashi, Noboru Fujiwara, Yoshihiro Gosho, Yuh Shiohara
IEEE TRANSACTIONS ON APPLIED SUPERCONDUCTIVITY 21 (3) Jun 2011
Polarization Reversal by Intramolecular Disordering in Organic Ferroelectrics: Trichloroacetamide
Kazuya, SAITO, Yasuhisa, YAMAMURA, Naoya, KIKUCHI, Akiko, NAKAO, Syuma, YASUZUKA, Yukikuni, AKISHIGE, Youichi, MURAKAMI
CrystEngComm 13 (7) Apr 2011[Refereed]
温度上昇で収縮するセラミックス
SAITO,Kazuya, YAMAMURA,Yasuhisa
Chemical education 59 (2) Feb 2011[Refereed]
Negative thermal expansion emerging upon structural phase transition in ZrV2O7 and HfV2O7
Yasuhisa Yamamura, Aruto Horikoshi, Syuma Yasuzuka, Hideki Saitoh, Kazuya Saito
DALTON TRANSACTIONS 40 (10) 2011[Refereed]
Non-Debye Excess Heat Capacity and Boson Peak of Binary Lithium Borate Glasses
Yu, MATSUDA, Hitoshi, KAWAJI, Tooru, ATAKE, Yasuhisa, YAMAMURA, Syuma, YASUZUKA, Kazuya, SAITO, Seiji, KOJIMA
J. Non-Cryst. Solids 357 (2) Jan 2011[Refereed]
Negative thermal expansion emerging upon structural phase transition in ZrV2O7 and HfV2O7
Yamamura, Yasuhisa, Horikoshi, Aruto, Yasuzuka, Syuma, Saitoh, Hideki, Saito, Kazuya
DALTON TRANSACTIONS 40 (10) Jan 2011[Refereed]
Thermal Conductivity of YBCO Coated Conductors Reinforced by Metal Tape
Hiroyuki, FUJISHIRO, Yasuhisa, YAMAMURA, Kazuya, SAITO, Hiroshi, OKAMOTO, Hidemi, HAYASHI, Noboru, FUJIWARA, Yoshihiro, GOSHO, Yuh, SHIOHARA
IEEE Trans. Appl. Supercond. 21 (3) Jan 2011[Refereed]
Computational Study on Photo- and Thermo-Reactions between Tetra-tert-Butyl-Substituted Cyclobutadiene and Tetrahedrane
Masato, SUMITA, Kazuya, SAITO, Yoshitaka, TATEYAMA
Comp. Theor. Chem. 969 Jan 2011[Refereed]
Temperature-Jump Time-Resolved X-ray Diffraction Study of Cubic-Cubic Phase-Transition Kinetics in Thermotropic Cubic Mesogen 1,2-Bis(4 '-n-alkoxybenzoyl)hydrazines (BABH-n)
Hiroyuki Mori, Shoichi Kutsumizu, Kazuya Saito, Katsuhiro Yarnamoto, Shinichi Sakurai, Koichi Sakajiri
LANGMUIR 26 (14) Jul 2010[Refereed]
Anisotropic Josephson-vortex dynamics in layered organic superconductors
S. Yasuzuka, S. Uji, H. Satsukawa, M. Kimata, T. Terashima, H. Koga, Y. Yamamura, K. Saito, H. Akutsu, J. Yamada
PHYSICA B-CONDENSED MATTER 405 (11) Jun 2010[Refereed]
Entropic Contribution of Flexible Terminals to Mesophase Formation Revealed by Thermodynamic Analysis of 4-Alkyl-4 '-isothiocyanatobiphenyl (nTCB)
Katsuya Horiuchi, Yasuhisa Yamamura, Robert Pelka, Masato Sumita, Syuma Yasuzuka, Maria Massalska-Arodz, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 114 (14) Apr 2010[Refereed]
23pGT-6 Josephson-vortex flow resistance in layered organic superconductor β-(BDA-TTP)_2SbF_6
Yasuzuka,S, Koga,H, Yamamura,Y, Saito,K, Uji,S, Terashima,T, Satsukawa,H, Kimata,M, Akutsu,H, Yamada,J
Meeting abstracts of the Physical Society of Japan 65 (1) Mar 2010
Calorimetric Study of Correlated Ligand Dynamics in Mixed-Valence MMX Chain Complex [{Ni-2(n-BuCS2)(4)}I]
Satoaki Ikeuchi, Yasuhisa Yamamura, Yuji Yoshida, Minoru Mitsumi, Koshiro Toriumi, Kazuya Saito
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 83 (3) Mar 2010[Refereed]
Multiple Bistability and Tristability with Dual Spin-State Conversions in [Fe(dpp)(2)][Ni(mnt)(2)](2)center dot MeNO2
Masayuki Nihei, Hirotaka Tahira, Nobukazu Takahashi, Yusuke Otake, Yasuhisa Yamamura, Kazuya Saito, Hiroki Oshio
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 132 (10) Mar 2010
Tetra-radical and Ionic S₁/S₀ Conical Intersections of Cyclobutadiene
Masato, SUMITA, Kazuya, SAITO
Chem. Phys. 371 (1) Jan 2010[Refereed]
Ground State Potential Energy Surface between Cyclobutadiene and Tetrahedrane Looked Down from S₁/S₀ Conical Intersections
Masato, SUMITA, Kazuya, SAITO
Tetrahedron 66 (28) Jan 2010[Refereed]
Effects of Alkyl Length in Ligands in Mixed Valence MMX Complexes: Properties of Pt-2(n-HeXCS2)(4)I (n-Hex = n-Hexyl Group)
Satoaki Ikeuchi, Yasuhisa Yamamura, Minoru Mitsumi, Koshiro Toriumi, Hideki Saitoh, Tooru Atake, Kazuya Saito
CHEMISTRY LETTERS 38 (12) Dec 2009[Refereed]
Microphase-separated multicontinuous phase in low-molecular-mass thermotropic liquid crystals
Kazuya Saito
PURE AND APPLIED CHEMISTRY 81 (10) Oct 2009
Calorimetric Study of MMX Chain Complexes Having Alkyl Groups, Ni-2(EtCS2)(4)I and Ni-2(n-PrCS2)(4)I
Satoaki Ikeuchi, Yasuhisa Yamamura, Yuji Yoshida, Minoru Mitsumi, Koshiro Toriumi, Kazuya Saito
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 78 (9) Sep 2009[Refereed]
Neat Liquid Consisting of Hydrogen-Bonded Tetramers: Dicyclohexylmethanol
Yu-ta Suzuki, Yasuhisa Yamamura, Masato Sumita, Syuma Yasuzuka, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 113 (30) Jul 2009[Refereed]
Characteristic Phonon Spectrum of Negative Thermal Expansion Materials with Framework Structure through Calorimetric Study of Sc2M3O12 (M = W and Mo)
Yasuhisa Yamamura, Satoaki Ikeuchi, Kazuya Saito
CHEMISTRY OF MATERIALS 21 (13) Jul 2009[Refereed]
Heat Capacity of a Layered Molecule-Based Ferrimagnet [Mn-II(S-pnH)(H2O)][Mn-III(CN)(6)center dot 2H(2)O
Syuma Yasuzuka, Yasuhisa Yamamura, Wakako Kaneko, Masaaki Ohba, Susumu Kitagawa, Kazuya Saito
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 78 (6) Jun 2009[Refereed]
Infrared Spectroscopic and X-ray Studies of the 4-Propyl-4 '-isothiocyanatobiphenyl (3TCB)
Malgorzata Jasiurkowska, Jan Sciesinski, Joanna Czub, Maria Massalska-Arodz, Robert Pelka, Ewa Juszynska, Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 113 (21) May 2009[Refereed]
Structure Analyses of Highly Symmetric Superstructures Formed by Rodlike Mesogen
SAITO,Kazuya, KUTSUMIZU,Shoichi
Nihon Kessho Gakkaishi 51 (2) Apr 2009
27pVC-13 Heat Anomaly of the Supercooled Liquid of Dicyclohexylmethanol
Suzuki,Y, Yamamura,Y, Sumita,M, Yasuzuka,S, Saito,K
Meeting abstracts of the Physical Society of Japan 64 (1) Mar 2009
27aVB-2 Dynamics of Nematic Liquid Crystal Disclinations under DC Electric Field
Yanagimachi,T, Yasuzuka,S, Yamamura,Y, Saito,K
Meeting abstracts of the Physical Society of Japan 64 (1) Mar 2009
Is the liquid or the solid phase responsible for the low melting points of ionic liquids? Alkyl-chain-length dependence of thermodynamic properties of [C(n)mim][Tf2N]
Yoshitaka Shimizu, Yoko Ohte, Yasuhisa Yamamura, Kazuya Saito
CHEMICAL PHYSICS LETTERS 470 (4-6) Mar 2009[Refereed]
Is the Liquid or the Solid Phase Responsible for the Low Melting Points of Ionic Liquids? Alkyl-Chain-Length Dependence of Thermodynamic Properties of [C_nmim][Tf₂N]
Yoshitaka, SHIMIZU, Yoko, OHTE, Yasuhisa, YAMAMURA, and, Kazuya SAITO, 齋藤, 一弥
Chem. Phys. Lett. 470 Feb 2009[Refereed]
Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane motion: theoretical study on a model system of retinal protonated Schiff base
Masato Sumita, Mikhail N. Ryazantsev, Kazuya Saito
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 11 (30) 2009[Refereed]
Calorimetric and dielectric study of organic ferroelectrics, phenazine-chloranilic acid, and its bromo analog
Masakazu Amano, Yasuhisa Yamamura, Masato Sumita, Syuma Yasuzuka, Hitoshi Kawaji, Tooru Atake, Kazuya Saito
JOURNAL OF CHEMICAL PHYSICS 130 (3) Jan 2009[Refereed]
Thermodynamic Symptom of Coexistence of Two Aggregation Modes in the Im3m Cubic Phase Formed in Thermotropic Mesogen, ANBC(n)
Kazuya, SAITO, Tadahiro, NAKAMOTO, Michio, SORAI, Haruhiko, YAO, Kenji, EMA, Kunio, TAKEKOSHI, and, Shoichi KUTSUMIZU
Chem. Phys. Lett. 469 Jan 2009[Refereed]
Coexistence of two aggregation modes in exotic liquid-crystalline superstructure: Systematic maximum entropy analysis for cubic mesogen, 1,2-bis(4 '-n-alkoxybenzoyl)hydrazine [BABH(n)]
Kazurni Ozawa, Yasuhisa Yamamura, Syuma Yasuzuka, Hiroyuki Mori, Shoichi Kutspmizu, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY B 112 (39) Oct 2008[Refereed]
Possible Formation of Multicontinuous Structures by Rodlike Particles
Saito Kazuya, Yamamura Yasuhisa, Kutsumizu Shoichi
J Phys Soc Jpn 77 (9) Sep 2008
Thermodynamic relationship between structural isomers of the thermochromic compound bis(N-isopropyl-5,6-benzosalicylideneiminato)nickel(II)
Qi Wang, Akira Takeuchi, Yasuhisa Yamamura, Kazuya Saito, Wasuke Mori, Michio Sorai
JOURNAL OF PHYSICAL CHEMISTRY B 112 (35) Sep 2008[Refereed]
Possible Formation of Multicontinuous Structures by Rodlike Particles(Condensed matter: structure and thermal properties)
SAITO, Kazuya, YAMAMURA, Yasuhisa, KUTSUMIZU, Shoichi
Journal of the Physical Society of Japan 77 (9) Sep 2008[Refereed]
22aWE-1 Dynamics of alkyl chain of lipid molecules in lamellar phase of lyotropic liquid crystals
Yamamura,Y, Nakada,S, Katagiri,A, Yasuzuka,S, Saito,K
Meeting abstracts of the Physical Society of Japan 63 (2) Aug 2008
Thermodynamic Relationship between Structural Isomers of the Thermochromic Compound Bis(N-Isopropyl-5,6-benzosalicylideneiminato)nickel(II)
Qi, WANG, Akira, TAKEUCHI, Yasuhisa, YAMAMURA, Kazuya, SAITO, Wasuke, MORI, and, Michio SORAI
J. Phys. Chem. B 112 (39) Aug 2008[Refereed]
Cubic phase formation and interplay between alkyl chains and hydrogen bonds in 1,2-bis(4 '-n-alkoxybenzoyl)hydrazines (BABH-n)
Shoichi Kutsumizu, Hiroyuki Mori, Machiko Fukatami, Shigeharu Naito, Koichi Sakajiri, Kazuya Saito
CHEMISTRY OF MATERIALS 20 (11) Jun 2008[Refereed]
Deduction of channel-length distribution from isothermal thermogravimetry
Saito, Kazuya, Yamamura, Yasuhisa
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY 92 (2) May 2008[Refereed]
Calorimetric study of correlated disordering in [Hdamel](2)[Cu-II(tdpd)(2)]center dot 2THF crystal
Yasuhisa Yamamura, Hiroyasu Shimoi, Masato Sumita, Syuma Yasuzuka, Keiichi Adachi, Akira Fuyuhiro, Satoshi Kawata, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY A 112 (19) May 2008[Refereed]
25pYC-7 Anisotropic particles possibly form periodic structures with cubic symmetry
Saito,Kazuya, Ozawa,Kazumi, Yamamura,Yasuhisa, Yasuzuka,Syuma, Kutsumizu,Shoichi
Meeting abstracts of the Physical Society of Japan 63 (1) Feb 2008
26pWB-9 Fourfold Symmetry in Josephson-Vortex Flow Resistance in a Quasi-Two-Dimensional Organic Superconductor ET_2Cu(NCS)_2
Yasuzuka,S, Uji,S, Terashima,T, Konoike,T, Yamamura,Y, Saito,K, Yamada,J
Meeting abstracts of the Physical Society of Japan 63 (1) Feb 2008
Rich polymorphism in 4-propyl-4'-thiocyanato-1,1'-biphenyl (3TCB) revealed by adiabatic calorimetry
R. Pelka, Yasuhisa Yamamura, M. Jasiurkowska, M. Massalska-Arodz, Kazuya Saito
LIQUID CRYSTALS 35 (2) 2008[Refereed]
Revisiting the S-1/S-0 degeneracy space along the exocyclic methylene twist motion of fulvene through a two-step procedure
Masato Sumita, Kazuya Saito
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 4 (1) Jan 2008[Refereed]
Possible phonon density of states of high-temperature phase structure of the negative thermal expansion compound ZrW2O8
Yasuhisa Yamamura, Kazuya Saito
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 76 (12) Dec 2007[Refereed]
Effects of thermal history on thermal anomaly in solid of ionic liquid compound, [C(4)mim][Tf2N]
Yoshitaka Shimizu, Yoko Ohte, Yasuhisa Yamamura, Kazuya Saito
CHEMISTRY LETTERS 36 (12) Dec 2007[Refereed]
Structural Analysis of Im3m Phase of BABH-n by Maximum Entropy Method(Poster session 1, New Frontiers in Colloidal Physics : A Bridge between Micro- and Macroscopic Concepts in Soft Matter)
Ozawa, Kazumi, Yamamura, Yasuhisa, Yasuzuka, Syuma, Saito, Kazuya, Mori, Hiroyuki, Kutsumizu, Shoichi
Bussei Kenkyu 89 (1) Oct 2007[Refereed]
Spin Crossover Phenomenon Accompanying Order-Disorder Phase Transition in the Ligand of [Fe^II(DAPP)(abpt)](ClO₄)₂ Compound (DAPP = Bis(3-aminopropyl)(2-pyridylmethyl) amine, abpt = 4-Amino-3,5-bis(pyridin-2-yl)-1,2,4-triazole) and Its Successive Self-Grinding Effect
Yuji, MIYAZAKI, Tadahiro, NAKAMOTO, Satoaki, IKEUCHI, Kazuya, SAITO, Akira, INABA, Michio, SORAI, Takeo, TOJO, Tooru, ATAKE, Galina, S. MATOUZENKO, Samir, ZEIN, and, Serguei A. BORSHCH
J. Phys. Chem. B 111 (43) Oct 2007[Refereed]
21aRL-10 Attempt to Analyze Molecular Aggregation Mode in Im3m Cubic Phase of Thermotropic Mesogen, BABH
Saito,K, Ozawa,K, Yamamura,Y, Yasuzuka,S, Mori,H, Kutsumizu,S
Meeting abstracts of the Physical Society of Japan 62 (2) Aug 2007
X-ray Study of Self-Organized Structure Formed by BABH-n Homologues: 1. Ia3d-Gyroid Structure
Shoichi, KUTSUMIZU, Hiroyuki, MORI, Machiko, FUKATAMI, Kazuya, SAITO
J. Appl. Crystallogr. 40 Apr 2007[Refereed]
X-ray studies of the self-organized structure formed by 1,2-bis(4′-n-alkoxybenzoyl)hydrazine (BABH-n) homologues. 1. Ia3d-gyroid structure
Shoichi Kutsumizu, Hiroyuki Mori, Machiko Fukatami, Kazuya Saito
Journal of Applied Crystallography 40 (1) Apr 2007[Refereed]
X-ray studies of the self-organized structure formed by 1,2-bis(4 '-n-alkoxybenzoyl)hydrazine (BABH-n) homologues. 1. Ia3d-gyroid structure
Shoichi Kutsumizu, Hiroyuki Mori, Machiko Fukatami, Kazuya Saito
JOURNAL OF APPLIED CRYSTALLOGRAPHY 40 Apr 2007[Refereed]
One-Dimensional Correlation in the Dipolar Ising Crystal Tricyclohexylmethanol: Crystal Structure Revisited and Heat Capacity
Y., Yamamura, H., Saitoh, M., Sumita, K., Saito
J. Phys.: Condens. Matter 19 (17) Mar 2007[Refereed]
Ab initio study on one-way photoisomerization of the maleic acid and fumaric acid anion radical system as a model system of their esters
Masato Sumita, Kazuya Saito
JOURNAL OF PHYSICAL CHEMISTRY A 110 (44) Nov 2006[Refereed]
Theoretical study on hula-twist motion of penta-2,4-dieniminium on the S-1 surface under isolated condition by the complete active space self-consistent field theory
Masato Sumita, Kazuya Saito
CHEMICAL PHYSICS LETTERS 424 (4-6) Jun 2006[Refereed]
サーモトロピック液晶における双連結構造
沓水, 祥一, 齋藤, 一弥
Solid state physics 41 (6) Jun 2006
Two cubic phases of 1,2-bis(4 '-n-alkoxybenzoyl)hydrazines (BABH-n)
Hiroyuki Mori, Shoichi Kutsumizu, Takeya Ito, Machiko Fukatami, Kazuya Saito, Koichi Sakajiri, Keiichi Moriya
CHEMISTRY LETTERS 35 (4) Apr 2006[Refereed]
Low-temperature phase transitions of an organic ferroelectrics, phenazine-chloranilic acid
K Saito, M Amano, Y Yamamura, T Tojo, T Atake
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 75 (3) Mar 2006[Refereed]
Thermodynamic study on cubic phases in the monoolein/water system
Katagiri Airi, Yamamura Yasuhisa, Saito Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2006 2006
Cubic Phases Formation of BABH-n. Part 2.:Molecular Aggregation Structure.
Mori Hiroyuki, Kutsumizu Shoichi, Saito Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2006 2006
Cub Phases Formation of BABH-n. Part 1.:Dependence of Phase Transition Behaviors on the Alkyl Chain Length and Cub-Cub Phase Transitions
Mori Hiroyuki, Fukatami Machiko, Kutsumizu Shoichi, Saito Kazuya
Proceedings of Japanese Liquid Crystal Society Annual meeting 2006 2006
Heat Capacity and Phase Transitions of Phenazine-Chloranilic Acid
Amano Masakazu, Yamamura Yasuhisa, Saito Kazuya
Abstract book of Russia/CIS/Baltic/Japan Symposium on Ferroelectricity 2006 2006
Hydrogen-Bonded Porous Coordination Polymers: Structural Transformation, Sorption Properties, and Particle Size Distribution from Kinetic Studies
Kazuhiro, UEMURA, Kazuya, SAITO, Susumu, KITAGAWA, and, Hidetoshi KITA
J. Am. Chem. Soc. 128 (50) Jan 2006[Refereed]
Thermodynamic aspect of reversible structural conversion induced by guest adsorption/desorption based on infinite Co(NCS)(2)Py-4 (Py=pyridine) system
Kazuhiro Uemura, Susumu Kitagawa, Kazuya Saito, Kôichi Fukui, Kazuko Matsumoto
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY 81 (3) Aug 2005[Refereed]
27pYK-4 Heat capacity of Ni_2(n-BuCS_2)_4I
Ikeuchi,Satoaki, Yamamura,Yasuhisa, saito,Kazuya, Yoshida,Yuji, Mitsumi,Minoru, Toriumi,Koshiro
Meeting abstracts of the Physical Society of Japan 60 (1) Mar 2005
The Significance of Education on Calorimetry and Thermal Analysis and Teaching Materials for Laboratory at Universities
KOGA,Nobuyoshi, YAMAMURA,Yasuhisa, SAITO,Kazuya, NISHIMOTO,Yuko, TANAKA,Haruhiko
Calorimetry and thermal analysis. 32 (1) Jan 2005
Cooperativity of Dynamics of 18-Crown-6 Molecule Forming One-Dimensional Chain in Cs₂(18-crown-6)₃[Ni(dmit)₂]₂
Satoaki, IKEUCHI, Yuji, MIYAZAKI, Sadamu, TAKEDA, Tomoyuki, AKUTAGAWA, Sadafumi, NISHIHARA, Takayoshi, NAKAMURA, Kazuya, SAITO
J. Chem. Phys. 123 (4) Jan 2005[Refereed]
Configurational Entropy and Possible Plateau Smaller than Rln2 in Complex Crystals
Kazuya, SAITO, Yasuhisa, YAMAMURA
Thermochim. Acta 431 (1/2) Jan 2005[Refereed]
Anomalous Enhancement of Electronic Heat Capacity in Organic Conductors kappa-(BEDT-TTF)₄Hg_3-deltaX₈ (X = Br, Cl)
Akihito, NAITO, Yasuhiro, NAKAZAWA, Kazuya, SAITO, Hiromi, TANIGUCHI, Kazushi, KANODA, and, Michio SORAI
Phys. Rev. B 71 (5) Jan 2005[Refereed]
Molecular Rotor of Cs₂([18]crown-6)₃ in the Solid State Coupled with the Magnetism of [Ni(dmit)₂]
Tomoyuki, AKUTAGAWA, Kozo, SHITAGAMI, Sadafumi, NISHIHARA, Sadamu, TAKEDA, Tatsuo, HASEGAWA, Takayoshi, NAKAMURA, Yuko, HOSOKOSHI, Katsuya, INOUE, Satoaki, IKEUCHI, Yuji, MIYAZAKI, and, Kazuya SAITO, 齋藤, 一弥
J. Am. Chem. Soc. 127 (12) Jan 2005[Refereed]
Alkyl Group as Entropy Reservoir in an MMX Chain Complex, Pt₂(n-PenCS₂)₄I
Kazuya, SAITO, Satoaki, IKEUCHI, Yasuhiro, NAKAZAWA, Akane, SATO, Minoru, MITSUMI, Takami, YAMASHITA, Koshiro, TORIUMI, Michio, SORAI
J. Phys. Chem. B 109 (7) Jan 2005[Refereed]
A Contrivance for a Dynamic Porous Framework: Cooperative Guest Adsorption Based on Square Grids Connected by Amide - Amide Hydrogen Bonds
Kazuhiro Uemura, Susumu Kitagawa, Kôichi Fukui, Kazuya Saito
Journal of the American Chemical Society 126 (12) Mar 2004[Refereed]
Structure of cubic phase in ACBC-16
Kutsumizu Shoichi, Nojima Shuichi, Saito Kazuya, Sorai Michio, Galyametdinov Yuri G., Galyametdinov Irina, Eidenschink Rudolf, Hasse Wolfgang
Proceedings of Japanese Liquid Crystal Society Annual meeting 2004 2004
Structure of cubic phases of BABH-n homologues
Ito Takeya, Naito Shigeharu, Kutsumizu Shoichi, Saito Kazuya, Sorai Michio
Proceedings of Japanese Liquid Crystal Society Annual meeting 2004 2004
Calorimetric and Raman studies on negative thermal expansion materials Zr1-xHfxW2O8 solid solutions
Y., Yamamura, N., Nakajima, T., Tsuji, M., Koyano, Y., Iwasa, S., Katayama, K., Saito, and, M. Sorai
Journal of the Ceramic Society of Japan 112 Jan 2004[Refereed]
Heat capacity and order-disorder phase transition in negative thermal expansion compound ZrW2O8
Y., Yamamura, T., Tsuji, K., Saito, and, M. Sorai
Journal of Chemical Thermodynamics 36 Jan 2004[Refereed]
Calorimetric Study of a Halogen-Bridged MMX Chain Complex Having Alkyl Chains, Pt₂(n-PrCS₂)₄I (n-Pr = Propyl Group)
Satoaki, IKEUCHI, Kazuya, SAITO, Yasuhiro, NAKAZAWA, Minoru, MITSUMI, Koshiro, TORIUMI, and, Michio SORAI
J. Phys. Chem. B 108 (1) Jan 2004[Refereed]
Freezing of Crankshaft Motion of trans-Stilbene Molecule in Charge Transfer Complexes, STB－TCNQ and STB－TCNQF₄
Kazuya, SAITO, Mizuho, OKADA, Hiroki, AKUTSU, Akane, SATO, and, Michio SORAI
J. Phys. Chem. B 108 (4) Jan 2004[Refereed]
Equipments for Calorimetry
SAITO K.
Netsu Sokutei 30 (5) Dec 2003
Low-temperature heat capacity measurements of κ-(BEDT-TTF)4Hg2.89Br8
Akihito Naito, Yasuhiro Nakazawa, Kazuya Saito, Hiromi Taniguchi, Kazushi Kanoda, Michio Sorai
Physica C: Superconductivity and its Applications 388-389 May 2003[Refereed]
Chemical pressure effect on bandwidth and dimensionality of quasi-one-dimensional organic conductors: (formula presented) (formula presented) (formula presented) (formula presented) (formula presented) (formula presented) (formula presented) and SCN]
Harukazu Yoshino, Keizo Murata, Kazuya Saito, Hiroyuki Nishikawa, Koichi Kikuchi, Isao Ikemoto
Physical Review B - Condensed Matter and Materials Physics 67 (3) 2003[Refereed]
Chemical pressure effect on bandwidth and dimensionality of quasi-one-dimensional organic conductors: (DMET)(2)X [X = Au(CN)(2), AuI2, AuCl2, IBr2, I-3, AuBr2, and SCN]
H Yoshino, K Murata, K Saito, H Nishikawa, K Kikuchi, Ikemoto, I
PHYSICAL REVIEW B 67 (3) Jan 2003[Refereed]
2A05 Phase Transition Behaviour of Cubic Liquid Crystals BABH (n) under Pressure
Maeda Yoji, Ito Takeya, Kutsumizu Shoichi, Saito Kazuya, Sorai Michio
Proceedings of Japanese Liquid Crystal Society Annual meeting 2003 2003
2A06 Heat Capacities of Cubic Liquid Crystalline Phases with Different Space Groups
Saito Kazuya, Takekoshi Kunio, Yao Haruhiko, Ema Kenji, Kutsumizu Shoichi
Proceedings of Japanese Liquid Crystal Society Annual meeting 2003 2003
Alkyl chains acting as entropy reservoir in liquid crystalline materials
M Sorai, K Saito
CHEMICAL RECORD 3 (1) 2003[Refereed]
Phase Diagram of Lithium-Doped Copper Oxide, Cu_1-xLi_xO
齋藤, 一弥
Solid State Commun. 125 (1) Jan 2003[Refereed]
Thermodynamic Study of Phase Transitions in Lyotropic Systems: Adiabatic Calorimetry on Non-Ionic Surfactant C₁₆E₈－Water System
齋藤, 一弥
J. Phys. Chem. B 107 (3) Jan 2003[Refereed]
Spin-Peierls Transition of Quasi-One-Dimensional Electronic System (DMe- DCNQI)₂M (M = Li, Ag) Probed by Heat Capacity
齋藤, 一弥
Phys. Rev. B 68 (8) Jan 2003[Refereed]
Calorimetric study of the halogen-bridged mixed-valence binuclear metal chain complex Pt2(n-BuCS2)4I (Bu=butyl chain)
Satoaki Ikeuchi, Kazuya Saito, Yasuhiro Nakazawa, Akane Sato, Minoru Mitsumi, Koshiro Toriumi, Michio Sorai
Physical Review B - Condensed Matter and Materials Physics 66 (11) Sep 2002[Refereed]
Low-temperature heat capacities and Raman spectra of negative thermal expansion compounds ZrW2O8 and HfW2O8
Yasuhisa Yamamura, Noriyuki Nakajima, Toshihide Tsuji, Mikio Koyano, Yoshihiro Iwasa, Shin’ichi Katayama, Kazuya Saito, Michio Sorai
Physical Review B - Condensed Matter and Materials Physics 66 Jul 2002
Thermodynamic Investigation of the Charge-Ordered Insulating State of the Quasi-One-Dimensional Organic System [Formula presented]
Yasuhiro Nakazawa, Mitsuro Seki, Kazuya Saito, Ko-ichi Hiraki, Toshihiro Takahashi, Kazushi Kanoda, Michio Sorai
Physical Review Letters 88 (7) 2002[Refereed]
3C14 On Structures of Thermotropic Isotropic Liquid Crystals
SAITO Kazuya, SORAI Michio
Proceedings of Japanese Liquid Crystal Society Annual meeting 2002 2002
Calorimetric study of the halogen-bridged mixed-valence binuclear metal chain complex (formula presented)=butyl chain)
Satoaki Ikeuchi, Kazuya Saito, Yasuhiro Nakazawa, Akane Sato, Minoru Mitsumi, Koshiro Toriumi, Michio Sorai
Physical Review B - Condensed Matter and Materials Physics 66 (11) 2002[Refereed]
Heat capacity and Grüneisen function of negative thermal expansion compound HfW2O8
Y., Yamamura, N., Nakajima, T., Tsuji, Y., Iwasa, K., Saito, and, M. Sorai
Solid State Communications 121 Jan 2002[Refereed]
Electrical properties of organic conductors at high temperature
H., Yoshino, K., Murata, Y., Yamamura, T., Tsuji, J., Yamada, S., Nakatsuji, H., Anzai, H., Nishikawa, K., Kikuchi, I., Ikemoto, and, K. Saito
Mol. Cryst. Liq. Cryst. 380 Jan 2002[Refereed]
Thermodynamic Implication of the Dependence of Mesomorphic Transition Entropy on Chain-Length: Smectic A － Nematic Phase Transition
齋藤, 一弥
J. Therm. Anal. Calor. 70 (2) Jan 2002[Refereed]
Quasi-Binary Picture of Thermotropic Liquid Crystals and Its Application to Cubic Mesophases
齋藤, 一弥
Chem. Phys. Lett. 366 (1/2) Jan 2002[Refereed]
Degree of Disorder in Cubic Mesophases in Thermotropics: Thermodynamic Study of a Liquid Crystal Showing Two Cubic Mesophases
齋藤, 一弥
Phys. Rev. E 65 (3) Jan 2002[Refereed]
Low Temperature Heat Capacity and Raman Spectra of Negative Thermal Expansion Compounds ZrW₂O₈ and HfW₂O₈
齋藤, 一弥
Phys. Rev. B 66 (1) Jan 2002[Refereed]
Calorimetric Study of Halogen-Bridged MMX Chain Complex, Pt₂(n-BuCS₂)₄I
齋藤, 一弥
Phys. Rev. B 66 (11) Jan 2002[Refereed]
Thermodynamic Investigation on the Charge-Ordered Insulating State of Quasi-One Dimensional Organic System (DI-DCNQI)₂Ag
齋藤, 一弥
Phys. Rev. Lett. 88 (7) Jan 2002[Refereed]
Heat-capacity anomaly due to spin reorientation and thermodynamic functions of ErFeO3 and TmFeO3
K Saito, Y Yamamura, J Mayer, H Kobayashi, Y Miyazaki, J Ensling, P Gutlich, B Lesniewska, M Sorai
JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS 225 (3) Apr 2001[Refereed]
解説分子結晶の物性と分子内運動自由度
齋藤, 一弥
Solid state physics 36 (4) Apr 2001
Heat Capacity and Phase Transition of the Negative Thermal Expansion Material ZrW_2O_8
Yamamura,Y, Nakajima,N, Tsuji,T, Nakamoto,T, Saito,K, Sorai,M
Meeting abstracts of the Physical Society of Japan 56 (1) Mar 2001
Heat Capacity. 2. Lattice Vibration.
Saito Kazuya
Netsu Sokutei 28 (5) 2001
Glass Transition in k-(BEDT-TTF)2Cu[N(CN)2]X (X=Br and Cl)
A. Sato, H. Akutsu, K. Saito, M. Sorai
Synthetic Metals 120 2001[Refereed]
Thermodynamics of Thermotoropic Cubic Mesogens : Cubic Liquid Crystals as a "Binary System" between Molecular Cores and Conformationally Melted Alkyl Chains
SAITO,Kazuya, SORAI,Michio
Journal of the Japanese Liquid Crystal Society 5 (1) Jan 2001
Anomalous Lattice Heat Capacity of Orientationally Glassy Crystal of p-Chloronitrobenzene at Low Temperature
齋藤, 一弥
Solid State Commun. 118 (12) Jan 2001[Refereed]
High-Precision Detection of Heat-Capacity Anomaly Due to Spin Reorientation in TmFeO₃ and HoFeO₃
齋藤, 一弥
Solid State Commun. 120 (4) Jan 2001[Refereed]
ac Calorimetry and EPR Study on Metal-Insulator Transition and Glass Transition in an Organic Conductor with Double-Column Structure, (DIMET)₂BF₄
齋藤, 一弥
J. Phys. Soc. Jpn. 70 (6) Jan 2001[Refereed]
Thermodynamic Study of Phase Transitions in Lyotropic Liquid Crystals: Adiabatic Calorimetry on Non-Ionic Surfactant C₁₂E₆－Water System
齋藤, 一弥
J. Phys. Chem. B 105 (15) Jan 2001[Refereed]
Calorimetric study of metal-insulator transition in (DIMET)(2)I-3
K Saito, A Sato, K Kikuchi, H Nishikawa, Ikemoto, I, M Sorai
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 69 (11) Nov 2000[Refereed]
Heat Capacity of Zr_<1-x>Hf_xW_2O_8
Yamamura,Y, Nakajima,N, Tsuji,T, Iwasa,Y, Saito,K, Sorai,M
Meeting abstracts of the Physical Society of Japan 55 (2) Sep 2000
Phase Behavior of Organic Superconductors kappa-(BEDT-TTF)₂Cu[N(CN)₂]X (X = Br and Cl) Studied by ac Calorimetry
齋藤, 一弥
Phys. Rev. B. 61 (6) Jan 2000[Refereed]
Heat capacities of cubic mesogen ANBC-22 with two different cubic phases
SHINHARA Takashi, SAITO Kazuya, KUTSUMIZU Syoichi, YANO Shinichi, SORAI Michio
Proceedings of Japanese Liquid Crystal Society Annual meeting 2000 2000
Magnetic field dependent heat capacity of the molecule-based magnetic material NBu4[(FeFeIII)-Fe-II(ox)(3)] (Bu = n-C4H9+, ox = oxalate)
A Bhattacharjee, K Saito, M Sorai
SOLID STATE COMMUNICATIONS 113 (10) 2000[Refereed]
Apparent Violation of the Third Law without a Detectable Glass Transition in Simple Molecular Solids: Calorimetric Entropy of p-Bromochlorobenzene
Y., Tozuka, H., Akutsu, Y., Yamamura, K., Saito, and, M. Sorai
Bulletin of the Chemical Society of Japan 73 Jan 2000[Refereed]
Calorimetric Study on Optically Isotropic Liquid Crystals
K., Saito, A., Sato, N., Morimoto, Y., Yamamura, and, M. Sorai
Mol. Cryst. and Liq. Cryst. 347 Jan 2000[Refereed]
Twist Phase Transition in Poly(p-phenylene) Oligomers: Heat Capacity of p-Quinquephenyl
齋藤, 一弥
Bull. Chem. Soc. Jpn. 73 (12) Jan 2000[Refereed]
Can the Molecule Involved in a CT Interaction Reorient Itself in the Crystal Lattice? Phase Transition and Glass Transition in trans-Stilbene－TCNQ
齋藤, 一弥
Chem. Phys. Lett. 318 (1-3) Jan 2000[Refereed]
Phase behavior of the organic superconductors and Cl) studied by ac calorimetry
Hiroki Akutsu, Kazuya Saito, Michio Sorai
Physical Review B - Condensed Matter and Materials Physics 61 (6) 2000[Refereed]
Thermodynamic Study of a Phase Transition between the Ordered and Disordered Phases and Orientational Disorder in Crystalline p-Chloronitrobenzene
齋藤, 一弥
J. Chem. Phys. 112 (5) Jan 2000[Refereed]
Calorimetric study on the thermotropic cubic mesogen, 4 '-n-hexadecyloxy-3 '-nitrobiphenyl-4-carboxylic acid, ANBC(16)
A Sato, K Saito, M Sorai
LIQUID CRYSTALS 26 (3) Mar 1999[Refereed]
Heat Capacity of TTF-TCNQ and TSF-TCNQ
K., Saito, Y., Yamamura, H., Akutsu, M., Takeda, H., Asaoka, H., Nishikawa, I., Ikemoto, and, M. Sorai
J. Phys. Soc. Jpn. 68 (4) Jan 1999[Refereed]
Metal-Insulator, SDW and Glass Transitions in (DMET)2BF4 and (DMET)2ClO4 Studied by ac Calorimetry
H., Akutsu, K., Saito, Y., Yamamura, K., Kikuchi, H., Nishikawa, I., Ikemoto, and, M. Sorai
J. Phys. Soc. Jpn. 26 (8) Jan 1999[Refereed]
Heat Capacity of Intercalated Layered Materials FexNbS2 at Low Temperature
T., Tsuji, Y., Yamamura, H., Watanabe, K., Saito, and, M. Sorai
Journal of Thermal Analysis and Calorimetry 57 Jan 1999[Refereed]
Thermodynamic metal-insulator transition in a hydrogen-bonded organic-inorganic hybrid conductor, [Pd(H_{2-cursive Greek chi}edag)(Hedag)]·TCNQ (cursive Greek chi ≈ 1/3)
K. Saito, Y. Yamamura, H. Kitagawa, D. Yoshida, T. Mitani, M. Sorai
Journal of the Physical Society of Japan 68 (11) 1999[Refereed]
Possibility of the Isostructural Condensed States of Matter in the D Phase of ANBC and the Cubic Mesophase of BABH: Heat Capacity of 4'-n-Octadecyloxy-3'-nitrobiphenyl-4-carboxylic acid, ANBC(18)
A., Sato, Y., Yamamura, K., Saito, and, M. Sorai
Liquid Crystals 26 (8) Jan 1999[Refereed]
Glass transition in the organic superconductor with the highest T-c under ambient pressure, kappa-(ET)(2)Cu[N(CN)(2)]Br
K Saito, H Akutsu, M Sorai
SOLID STATE COMMUNICATIONS 111 (9) 1999[Refereed]
Metal－Insulator, SDW and Glass Transitions in the Organic Conductors, (DMET)₂BF₄ and (DMET)₂ClO₄, Studied by ac Calorimetry
齋藤, 一弥
J. Phys. Soc. Jpn. 68 (6) Jan 1999[Refereed]
Thermodynamic Metal－Insulator Transition in a Hydrogen-Bonded Organic-Inorganic Hybrid Conductor, [Pd(H_2-xedag)(Hedag)].TCNQ (x = 1/3)
齋藤, 一弥
J. Phys. Soc. Jpn. 68 (11) Jan 1999[Refereed]
General Purpose Cryostat Applicable to Chopped-Light ac Calorimetry with Highly Stable Thermal Condition
SAITO,Kazuya, YAMAMURA,Yasuhisa, SORAI,Michio
Calorimetry and thermal analysis. 25 (5) Dec 1998[Refereed]
Heat Capacity of Intercalation Compounds Fe_xNbS_2の低温熱容量
YAMAMURA,Y, WATANABE,H, TSUJI,T, KOYANO,M, KATAYAMA,S, SAITO,K, SORAI,M
Meeting abstracts of the Physical Society of Japan 53 (2) Sep 1998
Phase Behavior and Intramolecular Motional Degrees of Freedom in Crystals
YAMAMURA,Yasuhisa, SAITO,Kazuya
Calorimetry and thermal analysis. 25 (2) Apr 1998
Heat Capacity of the Lyotropic Liquid Crystal, Hexaoxyethylene-n-dodecyl ether / Water Binary System
NISHIZAWA Makoto, SAITO Kazuya, SORAI Michio
Proceedings of Japanese Liquid Crystal Society Annual meeting 1998 1998
Do Alkoxy Chains Behave Like a Solvent in the D Phase? DSC Study of Binary Systems, ANBC(n_C) (n_C = 8, 16 and 18) － n-Tetradecane
齋藤, 一弥
Liq. Cryst. 25 (4) Jan 1998[Refereed]
Disappearance of a Displacive Phase Transition in Crystalline Biphenyl by a Small Amount of Impurity
齋藤, 一弥
J. Phys. Soc. Jpn. 67 (5) Jan 1998[Refereed]
Distortion of Local Order Parameter Caused by Impurities in Displacive Phase Transition
齋藤, 一弥
J. Phys. Soc. Jpn. 67 (9) Jan 1998[Refereed]
Entropic Evidence of the Order-Disorder Nature of the Phase Transition in p-Terphenyl Crystal
齋藤, 一弥
J. Phys.: Condensed. Matt. 10 (15) Jan 1998[Refereed]
Heat Capacity and Thermodynamic Functions of Anhydrous 4,4'-Bipyridine
Y., Yamamura, K., Saito, and, I. Ikemoto
Netsu Sokutei 24 Jan 1997[Refereed]
In-Plane Angular Effect of Magnetoresistance of Quasi-One-Dimensional Organic Metals, (DMET)₂AuBr₂ and (TMTSF)₂ClO₄
齋藤, 一弥
J. Phys. Soc. Jpn. 66 (8) Jan 1997[Refereed]
Deuterium-induced Phase Transition of Crystalline Tolane-d10
Y., Yamamura, K., Saito, H., Matsuyama, and, I. Ikemoto
Chem. Phys. Lett. 256 Jan 1996[Refereed]
Heat Capacity and Thermodynamic Functions of Crystalline 4,4"'-Difluoro-p-quaterphenyl
Y., Yamamura, K., Saito, H., Saitoh, H., Matsuyama, K., Kikuchi, and, I. Ikemoto
Thermochim. Acta 287 Jan 1996[Refereed]
Lattice-Dynamical Study of the Abnormally Short Bond-Length in trans-Stilbene Molecules in a Crystal
齋藤, 一弥
Bull. Chem. Soc. Jpn. 69 (4) Jan 1996[Refereed]
Field-orientation Dependence of Magnetoresistance of a Double-column Organic Conductor, (DMET)₂ClO₄, and Its Temperature Dependence
齋藤, 一弥
Synth. Metals 82 Jan 1996[Refereed]
Molecular Motion and Phase Transition in Molecular Crystals
SAITO,Kazuya, ATAKE,Tooru
Nihon Kessho Gakkaishi 37 (1) Feb 1995
Heat Capacity Measurements and Phase Transition of Crystalline 4,4"-Difluoro-p-terphenyl
Y., Yamamura, K., Saito, H., Saitoh, H., Matsuyama, K., Kikuchi, and, I. Ikemoto
J. Phys. Chem. Solids 56 Jan 1995[Refereed]
Metal-Insulator Transitions in Double-Column Salts: (DMET)₂BF₄, (DMET)₂ClO₄ and (DIMET)₂BF₄
齋藤, 一弥
Synth. Metals 72 (2) Jan 1995[Refereed]
Glass Transition Due to Freezing of Intramolecular Motion: Crystalline trans-Azobenzene and trans-Stilbene
齋藤, 一弥
J. Phys. Chem. Solids 56 (6) Jan 1995[Refereed]
The Search for a Possible Twist Phase Transition in a Biphenyl Analogue: Heat Capacity of Crystalline Tolan
齋藤, 一弥
J. Phys.: Condensed. Matt. 7 (47) Jan 1995[Refereed]
Anomalous Angular Dependence of Magnetoresistance of an Organic Superconductor, (DMET)₂I₃
齋藤, 一弥
J. Phys. Soc. Jpn. 64 (7) Jan 1995[Refereed]
Heat Capacity of Solid at Low Temperatures. After the Anderson's Theory of Amorphous Solids.:After the Anderson's Theory of Amorphous Solids
Shirakami Tatsuya, Saito Kazuya, Atake Tooru
Netsu Sokutei 21 (3) 1994
Phase Transition in Crystalline p-Polyphenyls: Heat Capacity of 4,4"'-Difluoro-p-quaterphenyl
K., Saito, Y., Yamamura, H., Saitoh, H., Matsuyama, K., Kikuchi, and, I. Ikemoto
Solid State Commun. 92 (6) Jan 1994[Refereed]
Heat Capacity and an Incommensurate Phase Transition of Crystalline Bis(4-chlorophenyl)sulfone
齋藤, 一弥
J. Chem. Thermodyn. 26 (12) Jan 1994[Refereed]
X-ray Study on Structural Phase Transitions of 4,4''-Difluoro-p-terphenyl and 4,4'''-Difluoro-p-quaterphenyl
齋藤, 一弥
Solid State Commun. 91 (2) Jan 1994[Refereed]
ANOMALOUS TEMPERATURE-DEPENDENCE IN RESISTIVITY AND THERMOPOWER OF SOME RADICAL SALTS IN SDW STATE
K SAITO, H YOSHINO, K KIKUCHI, IKEMOTO, I, K KOBAYASHI
SYNTHETIC METALS 56 (2-3) Apr 1993[Refereed]
De Haas-van Alphen effect in κ-(DMET)2AuBr2
K. Kanoda, K. Kato, A. Kawamoto, K. Oshima, T. Takahashi, K. Kikuchi, K. Saito, I. Ikemoto
Synthetic Metals 56 (1) Mar 1993[Refereed]
Phase Transition Associated with Molecular Twisting in Crystalline 4,4"-Difluoro-p-terphenyl: Displacive or Order-disorder Transition?
齋藤, 一弥, Y., Yamamura, H., Saitoh, H., Matsuyama, K., Kikuchi, and, I. Ikemoto
Solid State Commun. 87 (10) Jan 1993[Refereed]
Determination of Band-Filling in Radical Salts with Plural Types of Columns from Anisotropy
齋藤, 一弥
Synth. Metals 56 (1) Jan 1993[Refereed]
Crystal Structures of the Room Temperature Phase of 4,4"-Difluoro-p-terphenyl and 4,4"'-Difluoro-p-quaterphenyl
齋藤, 一弥
Bull. Chem. Soc. Jpn. 66 (10) Jan 1993[Refereed]
Incommensurate Crystal-Instability and a Role of Internal Degrees of Freedom in Bis(4-chlorophenyl)sulfone Molecules
齋藤, 一弥
Solid State Commun. 81 (3) Jan 1992[Refereed]
Crystal Structures and Physical Properties of DIMET Triiodides
齋藤, 一弥
Synth. Metals 52 (1) Jan 1992[Refereed]
NMR Characterization of Isomers of C₇₈, C₈₂ and C₈₄
齋藤, 一弥
Nature 357 (6374) Jan 1992[Refereed]
ANTIFERROMAGNETIC TRANSITIONS IN THE ORGANIC CONDUCTORS BASED ON ASYMMETRIC DONORS
K KANODA, S OKUI, Y KOBAYASHI, T TAKAHASHI, K KIKUCHI, K SAITO, IKEMOTO, I, T INUKAI, G SAITO
SYNTHETIC METALS 42 (1-2) May 1991[Refereed]
THERMOELECTRIC-POWER OF (DMET)2X
K SAITO, H YOSHINO, K KIKUCHI, IKEMOTO, I, K KOBAYASHI
SYNTHETIC METALS 42 (3) May 1991[Refereed]
Crystal Structure of the Organic Metal (DMET)₂BF₄ with Two Columns along Two Crystallographic Axes
齋藤, 一弥
Bull. Chem. Soc. Jpn. 64 (1) Jan 1991[Refereed]
Improvement of Bertaut's Method for Calculating Electric Field Gradient
齋藤, 一弥
Z. Naturforsch. A 45 Jan 1990[Refereed]
Low Temperature Heat Capacity of Cubic Boron Nitride
齋藤, 一弥
Jpn. J. Appl. Phys., Part 2 20 (10) Jan 1990[Refereed]
Tetramerized Structure of (DMET)₂ReO₄ and Its Apparent Metallic Behavior in Resistivity
齋藤, 一弥
Bull. Chem. Soc. Jpn. 63 (7) Jan 1990[Refereed]
Thermoelectric Power and an Order-Parameter Associated with the Phase Transition at 180 K in the Organic Metal, (DMET)₂Au(CN)₂
齋藤, 一弥
J. Phys. Soc. Jpn. 58 (11) Jan 1989[Refereed]
Phase Transition of (DMET)₂Au(CN)₂ at 180 K
齋藤, 一弥
J. Phys.: Condensed. Matt. 1 (45) Jan 1989[Refereed]
Phase Relation and Dehydration Behavior of Barium Nitrite Hydrate
齋藤, 一弥
Thermochim. Acta 127 (1-4) Jan 1988[Refereed]
Incommensurate Phase Transitions and Anomalous Lattice Heat Capacities of Biphenyl
齋藤, 一弥
Bull. Chem. Soc. Jpn. 61 (3) Jan 1988[Refereed]
Thermodynamic Studies on Order-Disorder Phase Transitions of p-Terphenyl and p-Terphenyl-d₁₄
齋藤, 一弥
Bull. Chem. Soc. Jpn. 61 (7) Jan 1988[Refereed]
Stability of a Planar Molecular Conformation in a 4,4'-Difluorobiphenyl Crystal
齋藤, 一弥
Acta Crystalligr. Sect. B 43 (3) Jan 1987[Refereed]
New Organic Superconductor, (DMET)₂Au(CN)₂
齋藤, 一弥
Chem. Lett. (5) Jan 1987[Refereed]
Superconductivity and the Possibility of Semiconductor-Metal Transition in (DMET)₂AuBr₂
齋藤, 一弥
J. Phys. Soc. Jpn. 56 (8) Jan 1987[Refereed]
On Ambient-Pressure Superconductivity in Organic Conductors: Electrical Properties of (DMET)₂I₃, (DMET)₂I₂Br and (DMET)₂IBr₂
齋藤, 一弥
J. Phys. Soc. Jpn. 56 (10) Jan 1987[Refereed]
Superconductivity in (DMET)₂AuCl₂ and (DMET)₂AuI₂
齋藤, 一弥
J. Phys. Soc. Jpn. 56 (12) Jan 1987[Refereed]
Thermodynamic studies of molecular motions in p-polyphenyl crystals.
Saito Kazuya
Netsu Sokutei 13 (4) 1986
Theoretical Analysis of Heat-Flux Differential Scanning Calorimetry Based on a General Model
齋藤, 一弥
Thermochim. Acta 99 (1-4) Jan 1986[Refereed]
Baseline Drawing for the Determination of the Enthalpy of Transition in Classical DTA, Power-Compensated DSC and Heat-Flux DSC
齋藤, 一弥
Thermochim. Acta 104 (1-4) Jan 1986[Refereed]
Thermodynamic Studies of p-Polyphenyls: Heat Capacity of 4,4'-Difluorobiphenyl
齋藤, 一弥
J. Chem. Thermodyn. 18 (5) Jan 1986[Refereed]
Molar Heat Capacity and Thermodynamic Properties of p-Quaterphenyl
齋藤, 一弥
J. Chem. Thermodyn. 17 (6) Jan 1985[Refereed]
Crossover of the Low Temperature Heat Capacities of Biphenyl and p-Terphenyl
齋藤, 一弥
Chem. Lett. (4) Jan 1984[Refereed]
Low Temperature Heat Capacities of Biphenyl and Biphenyl-d₁₀
齋藤, 一弥
Chem. Lett. (4) Jan 1983[Refereed]
Awards & Honors
▼▲
May 2023
Institute of Nuclear Physics, Polish Academy of Sciences Honorary Professor
Sep 2016
The Japanese Liquid Crystal Society Award for excellent work Clarification of LC structure through thermodynamic study
Aug 2012
The Japan Society of Calorimetry and Thermal Analysis The Japan Society of Calorimetry and Thermal Analysis Award
Jun 2011
The Calorimetry Conference James J. Christensen Memorial Award
Books etc
▼▲
Instrumental Analysis of Coordination Compounds: Volume 1
Kazuya SAITO (Role:Contributor, Chapter 5 Calorimetry and Thermal Analysis)
Gibbs Energy and Helmholtz Energy Liquids, Solution and Vapours
Saito, Kazuya ( Stability of Real Liquid Crystals)
化学便覧基礎編改訂6版
齋藤, 一弥
Chemical Physics of Molecular Condensed Matter
Saito,Kazuya (Role:Sole author)
現代化学序説
齋藤,一弥 (Role:Sole author)
日本の結晶学(II) －輝かしき発展－
齋藤,一弥 (Role:Contributor, 結晶中の分子運動の相関)
熱分析
齋藤,一弥, 森川淳子 (Role:Contributor, 熱分析)
熱量測定・熱分析ハンドブック第2版
日本熱測定学会編, 編集委員長, 齋藤一弥, 齋藤, 一弥 (Role:Edit)
Comprehensive Handbook of Calorimetry and Thermal Analysis
Ed, by The Japan, Society of Calorimetry, Thermal, Analysis, Editor-in-chief, Michio SORAI, K., Saito, Executive editor, 齋藤, 一弥 (Role:Edit)
Research Grants & Projects
▼▲
Molecular Mechanism of Gyroid Formation by Small Mesogenic Molecules
Grants-in-Aid for Scientific Research
Research period: Apr 2021 - Mar 2024
熱伝導下における一次転移：新しい現象の同定と熱力学の拡張
科学研究費助成事業
Research period: Apr 2020 - Mar 2023Representative: 佐々真一, 湯川諭, 齋藤一弥, 中川尚子
Study of dynamic and molecular basis of gyroid formation
Grants-in-Aid for Scientific Research
Research period: Apr 2020 - Mar 2022
Crystallization and glass transition of liquid crystals
Grants-in-Aid for Scientific Research
Research period: Apr 2020 - Mar 2021
Crystallization and glass transition of liquid crystals under negative to high pressure
Grants-in-Aid for Scientific Research
Research period: Nov 2018 - Mar 2020
Structure and Glass Transition of Liquids of Globular Aggregates
Grants-in-Aid for Scientific Research
Research period: Apr 2016 - Mar 2018
Study of Structure and Dynamics of Thermotropics Based on Quasi-Binary Picture
Grants-in-Aid for Scientific Research
Research period: Apr 2014 - Mar 2017Representative: SAITO Kazuya
実在モデル系としての球形分子会合体からなる液体のガラス転移
科学研究費助成事業
Research period: Apr 2014 - Mar 2016Representative: 齋藤一弥
Precision measurement of dependence of two-phase coexistence temperature on non-equilibriumness aiming at assessment of a possible steady-state thermodynamics
Grants-in-Aid for Scientific Research
Research period: Apr 2012 - Mar 2015Representative: SAITO Kazuya, YAMAMURA Yasuhisa, HISHIDA Mafumi
Towards Unified Understanding of Thermotropic and Lyotropic Liquid Crystals
Grants-in-Aid for Scientific Research
Research period: 2010 - 2012Representative: SAITO Kazuya, YAMAMURA Yasuhisa, HISHIDA Mafumi
アルキル鎖のダイナミクスとイオン液体の安定性
科学研究費助成事業
Research period: 2008 - 2009Representative: 齋藤一弥, 山村泰久, 清水由隆
サーモトロピック液晶に特異的なIm3mキュービック相
科学研究費助成事業
Research period: 2007 - 2008Representative: 齋藤一弥
異方性固体の反応速度論
科学研究費助成事業
Research period: 2006 - 2007Representative: 齋藤一弥, 山村泰久
有機物質中の分子運動と相転移
科学研究費助成事業
Research period: 2005 - 2006Representative: 齋藤一弥, PELKA Robert
ナノ空間を利用したサーモクロミズムの機構解明
科学研究費助成事業
Research period: 2005 - 2005Representative: 齋藤一弥, 齋藤英樹, 高橋央宜, 山村泰久
Formation Mechanism of Triply Periodic Minimal Surface as a Thermodynamic Equilibrium Structure
Grants-in-Aid for Scientific Research
Research period: 2003 - 2005Representative: SAITO Kazuya, MIYAZAKI Yuji
ナノカロリメトリーの開発と応用
科学研究費助成事業
Research period: 2002 - 2002Representative: 徂徠道夫, 宇治進也, 齋藤一弥, 阿竹徹, 中澤康浩, 川路均
Thermal properties of optically isotropic liquid crystals
Grants-in-Aid for Scientific Research
Research period: 1999 - 2002Representative: SORAI Michio, MIYAZAKI Yuji, SAITO Kazuya
結晶中に広がった非局在電子系の物性熱力学
科学研究費助成事業
Research period: 2000 - 2000Representative: 齋藤一弥, 中澤康浩
非局在電子系分子集合体の物性熱力学
科学研究費助成事業
Research period: 1999 - 1999Representative: 齋藤一弥
Impurity Effect on a Structural Phase Transition Intermediate between the Order-Disorder and Displacive Types.
Grants-in-Aid for Scientific Research
Research period: 1997 - 1998Representative: SAITO Kazuya
Aggregation mechanism and higher-order structures in soft matter
Research period: Apr 1996
フッ素置換p-ポリフェニルの構造相転移
科学研究費助成事業
Research period: 1991 - 1991Representative: 齋藤一弥
分子性結晶BCPSのインコメンシュレート相転移の熱力学的研究
科学研究費助成事業
Research period: 1989 - 1989Representative: 齋藤一弥
有機伝導体の電気的性質に及ぼす構造相転移の影響
科学研究費助成事業
Research period: 1988 - 1988Representative: 齋藤一弥
THE INFRARED AND FAR-INFRARED POLARIZED REFLECTANCE SPECTRA OF ORGANIC CONDUCTORS. MICROSPECTOROPHOTOMETORIC STUDY
Grants-in-Aid for Scientific Research
Research period: 1986 - 1988Representative: IKEMOTO Isao, SAITO Kazuya, KIKUCHI Koichi
伝導性高分子錯体-修飾フタロシアニンー合成と物性
科学研究費助成事業
Research period: 1987 - 1987Representative: 池本勲, 齋藤一弥, 菊地耕一
高伝導性を示す有機金属化合物錯体の電子状態と物性
科学研究費助成事業
Research period: 1987 - 1987Representative: 池本勲, 齋藤一弥, 菊地耕一
Properties of organic/Low-dimensional conductors
Research period: Jan 1987
Molecular dynamics in crystal and phase transition
Research period: Apr 1986

	氏名	Manussada Ratanasak
	Name	Manussada Ratanasak
	Faculty
	Section
	Position	Researcher
	Theme	Catalyst Design, QSAR/QSPR, DFT Calcula2ons, QM/MM, Reac2on Mechanism
	Related Links
	Email	manussadaccs.tsukuba.ac.jp

Academic & Professional Experience
Mar 2016

Ph.D. Program in Nanoscience and Technology (Interna2onal Program), Graduate School, Chulalongkorn University, Bangkok, Thailand
Apr 2016
-
Apr 2024
Hasegawa Group, Ins2tute for Catalysis, Hokkaido University, Japan Postdoctoral Researcher
Published Papers
▼▲
Asymmetric Dehydrative Cyclization of Allyl Alcohol to Cyclic Ether Using Chiral Brønsted Acid/CpRu(II) Hybrid Catalysts: A DFT Study of the Origin of Enantioselectivity
Manussada Ratanasak , Shinji Tanaka , Masato Kitamura , Jun-Ya Hasegawa
J. Org. Chem. doi: 10.1021/acs.joc.2c01576 [Refereed]
Mechanism of BPh3 -Catalyzed N-Methylation of Amines with CO2 and Phenylsilane: Cooperative Activation of Hydrosilane
Manussada Ratanasak, Takumi Murata, Taishin Adachi, Jun-Ya Hasegawa, Tadashi Ema
Design and prediction of high potent ansa-zirconocene catalyst for olefin polymerizations: combined DFT calculations and QSPR approach
Manussada Ratanasak, Jun-ya Hasegawa and Vudhichai Parasuk
New Journal of Chemistry
Roles of Salicylate Donors in Enhancement of Productivity and Isotacticity of Ziegler-Natta Catalyzed Propylene Polymerization
Manussada Ratanasak,Jun-ya Hasegawa and Vudhichai Parasuk
Polymers
Aluminum porphyrins with quaternary ammonium halides as catalysts for copolymerization of cyclohexene oxide and CO2: metal–ligand cooperative catalysis
Jingyuan Deng, Manussada Ratanasak, Yuma Sako, Hideki Tokuda, Chihiro Maeda, Jun-ya Hasegawa, Kyoko Nozaki and Tadashi Ema
Chemical Science

	氏名	宮川晃一
	Name	MIYAGAWA Koichi
	Faculty
	Section
	Position	Researcher
	Theme
	Related Links	researchmap
	Email	miyakccs.tsukuba.ac.jp

Research Interests
Academic & Professional Experience
Published Papers
Awards & Honors
Books etc
Research Grants & Projects

	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 / Chief
	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
▼▲
An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group.
Pánek, Tomáš, Tice, Alexander K., Corre, Pia, Hrubá, Pavla, Žihala, David, Kamikawa, Ryoma, Yazaki, Euki, Shiratori, Takashi, Kume, Keitaro, Hashimoto, Tetsuo, Ishida, Ken-ichiro, Hradilová, Miluše, Jeffrey D. Silberman, Roger, Andrew, INAGAKI, Yuji, Eliáš, Marek, Brown, Matthew W., Čepička, Ivan
Molecular Phylogenetics and Evolution 204 Mar 2025[Refereed]
Glissandra oviformis n. sp.: a novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs.
Euki, Yazaki, Ryo, Harada, Ryu, Isogai, Kohei, Bamba, Ken-ichiro, Ishida, INAGAKI, Yuji, Shiratori, Takashi
bioRχiv Feb 2025
Drastic genome reduction driven by parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate.
Nakayama, Takuro, Harada, Ryo, Yabuki, Akinori, Nomura, Mami, Shiba, Kogiku, Inaba, Kazuo, Inagaki, Yuji
bioRχiv Jan 2025
AUTOEB: A software for systematically evaluating bipartitions in a phylogenetic tree employing an approximately unbiased test.
Kohei, Bamba, Ryo, Harada, INAGAKI, Yuji
IPSJ Transactions on Bioinformatics 17 Dec 2024[Refereed]
The diversity and evolution of DNA polymerases localized in organelles: What we have unveiled and what we are uncertain about.
稲垣, 祐司, 原田亮
月刊アグリバイオ 8 (12) Oct 2024
Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems.
Yazaki, Euki, Uehara, Tadaaki, Sakaoto, Hirokazu, Inagaki, Yuji
Protist 175 (6) Oct 2024[Refereed]
Is rdxPolA a piece of the ancient system for DNA maintenance in mitochondria?
原田亮, 稲垣, 祐司
The Japanese Journal of Phycology (Sôrui) 72 (2) Jul 2024[Refereed]
Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates
Takuro Nakayama, Mami Nomura, Akinori Yabuki, Kogiku Shiba, Kazuo Inaba, Yuji Inagaki
Scientific Reports 14 (1) Jun 2024[Refereed]
Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data
Harada, Ryo, Inagaki, Yuji
PROTIST 174 (6) Dec 2023[Refereed]
Transcriptome data sets of free-living diplomonads, Treponema sp, and Hexamita sp.
Kume, Keitaro, Tsubasa, Gen, Kazuki, Abe, Hiroshi, Komatsuzaki, Euki, Yazaki, Goro, Tanifuji, Ryoma, Kamikawa, Inagaki, Yuji, Hashimoto, Tetsuo
MICROBIOLOGY RESOURCE ANNOUNCEMENTS 12 (11) Nov 2023[Refereed]
Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of diverse bacteria including the proto-mitochodrion.
Harada, Ryo, Hirakawa, Yoshihisa, Yabuki, Akinori, Kim, Eunsoo, Yazaki, Euki, Kamikawa, Ryoma, Kentaro, Nakano, Elias, Marek, Inagaki, Yuji
Molecular Biology and Evolution 41 (2) Aug 2023[Refereed]
AtLASS: A scheme for end-to-end prediction of splice sites using attention-based bi-LSTM.
Harada, Ryo, Kume, Keitaro, Horie, Kazumasa, Nakayama, Takuro, Inagaki, Yuji, Amagasa, Toshiyuki
IPSJ Transactions on Bioinformatics 16 Jul 2023[Refereed]
遺伝子水平伝播が支配するオルガネラ局在ファミリーA DNAポリメラーゼの進化
原田亮, 稲垣, 祐司
月刊細胞 55 (6) Apr 2023
Fascinating strategies of marine organisms to cope with coming pollutant: Titanium dioxide nanoparticles.
Ishitani, Yoshiyuki, Ciacci, Caterina, Ujiié, Yurika, Tame, Akihiro, Tiboni, Mattia, Tanifuji, Goro, Inagaki, Yuji, Frontalini, Fabrizio
ENVIRONMENTAL POLLUTION 330 Apr 2023[Refereed]
Draft genome sequence of Aduncisulcus paluster, a free-living microaerophilic eukaryote belonging to Fornicata.
Ikuko, Yuyama, Kume, Keitaro, Tamura, Takumi, Inagaki, Yuji, Hashimoto, Tetsuo
Microbiology Resource Announcements 12 (2) Feb 2023[Refereed]
Microheliella maris possesses the most gene-rich mitochondrial genomes in Diaphoretickes.
Yazaki, Euki, Yabuki, Akinori, Nishimura, Yuki, Shiratori, Takashi, Inagaki, Yuji
Frontiers in Ecology and Evolution 10 Dec 2022[Refereed]
A novel structural maintenance of chromosomes (SMC)-related protein family specific to Archaea
Yoshinaga, Mari, Nakayama, Takuro, Inagaki, Yuji
Frontiers in Microbiology 13 Aug 2022[Refereed]
Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA Editing
Eriko, Matsuo, Kounosuke, Morita, Takuro, Nakayama, Yazaki, Euki, Chihiro, Sarai, Kazuya, Takahashi, Mitsunori, Iwataki, Inagaki, Yuji
FRONTIERS IN PLANT SCIENCE 13 Jul 2022[Refereed]
The closest relative of Archaeplastida is revealed by phylogenomic analyses that include Microheliella maris.
Yazaki, Euki, Yabuki, Akinori, Imaizumi, Ayaka, Kume, Keitaro, Hashimoto, Tetsuo, Inagaki, Yuji
OPEN BIOLOGY 12 (4) Apr 2022[Refereed]
Ubiquity and Origins of Structural Maintenance of Chromosomes (SMC) Proteins in Eukaryotes
Mari Yoshinaga, Yuji Inagaki
Genome Biology and Evolution 13 (12) Dec 2021[Refereed]
Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and Microheliella maris.
Yazaki, Euki, Yabuki, Akinori, Imaizumi, Ayaka, Kume, Keitaro, Hashimoto, Tetsuo, Inagaki, Yuji
bioRχiv Aug 2021
Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species
Yazaki, Euki, Miyata, Ryosuke, Chikami, Yasuhiko, Harada, Ryo, Kawakubo, Takashi, Tanifuji, Goro, Nakayama, Takuro, Yahata, Kensuke, Hashimoto, Tetsuo, Inagaki, Yuji
Parasitology International 83 Aug 2021[Refereed]
Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids.
Ryo, Harada, Inagaki, Yuji
Genome Biology and Evolution Jan 2021[Refereed]
Experimental analysis of diurnal variations in humic-like fluorescent dissolved organic matters in surface seawater.
Omori, Yuko, Saeki, AKira, Wada, Shigeki, Inagaki, Yuji, Hama, Takeo
Frontiers in Marine Science 7 Oct 2020[Refereed]
Barthelonids represent a deep-branching matamonad clade with mitochondrion-related organelles predicted to generate no ATP.
Euki, Yazaki, Kume, Keitaro, Takashi, Shiratori, Yana, Eglit, Goro, Tanifuji, Ryo, Harada, Alastair, Simpson, Ken-ichiro, Ishida, Tetsuo, Hashimoto, Inagaki, Yuji
Proceedings of the Royal Society B 287 (1934) Sep 2020[Refereed]
Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organisms
Takuro Nakayama, Kazuya Takahashi, Ryoma Kamikawa, Mitsunori Iwataki, Yuji Inagaki, Goro Tanifuji
Communicative & Integrative Biology 13 (1) Jun 2020[Refereed]
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]
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]
Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase
Kristína Záhonová, Romana Petrželková, Matus Valach, Euki Yazaki, Denis V. Tikhonenkov, Anzhelika Butenko, Jan Janouškovec, Štěpánka Hrdá, Vladimír Klimeš, Gertraud Burger, Yuji Inagaki, Patrick J. Keeling, Vladimír Hampl, Pavel Flegontov, Vyacheslav Yurchenko, Marek Eliáš
Scientific Reports 8 (1) Dec 2018[Refereed]
Fates of evolutionarily distinct, plastid-type glyceraldehyde 3-phosphate dehydrogenase genes in kareniacean dinoflagellates.
Ryoma, Kamikawa, Euki, Yazaki, Michiru, Tahara, Takaya, Sakura, Matsuo, Eriko, Kisaburo, Nagamune, Tetsuo, Hashimoto, Inagaki, Yuji
Journal of Eukaryotic Microbiology 65 (6) Sep 2018[Refereed]
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
Mitsuhiro Matsuo, Atsushi Katahata, Soichirou Satoh, Motomichi Matsuzaki, Mami Nomura, Ken-ichiro Ishida, Yuji Inagaki, Junichi Obokata
PLOS ONE 13 (7) Jul 2018[Refereed]
The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites
Goro Tanifuji, Shun Takabayashi, Keitaro Kume, Mizue Takagi, Takuro Nakayama, Ryoma Kamikawa, Yuji Inagaki, Tetsuo Hashimoto
PLoS ONE 13 (3) Mar 2018[Refereed]
Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group
Matthew W Brown, Aaron A Heiss, Ryoma Kamikawa, Yuji Inagaki, Akinori Yabuki, Alexander K Tice, Takashi Shiratori, Ken-Ichiro Ishida, Tetsuo Hashimoto, Alastair G. B. Simpson, Andrew J. Roger
Genome Biology and Evolution 10 (2) Feb 2018[Refereed]
Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms
Takuro Nakayama, Yuji Inagaki
SCIENTIFIC REPORTS 7 Oct 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]
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 and Genetic Systems 92 (1) 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]
A system for phylogenetic analyses over alignments of next generation sequence data
Yuki Nishimura, Toshiyuki Amagasa, Yuji Inagaki, Tetsuo Hashimoto, Hiroyuki Kitagawa
PROCEEDINGS OF 2016 10TH INTERNATIONAL CONFERENCE ON COMPLEX, INTELLIGENT, AND SOFTWARE INTENSIVE SYSTEMS (CISIS) 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 a Myxozoan Genus Kudoa Are Extremely Divergent in Metazoa
Fumihiko Takeuchi, Tsuyoshi Sekizuka, Yumiko Ogasawara, Hiroshi Yokoyama, Ryoma Kamikawa, Yuji Inagaki, 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]
MPI/OpenMP HYBRID Parallelization of Phylogenetic Analyses Based on Non-Homogeneous Substitution Models: Implementation and Performance Evaluation for Large-scale Computing Systems
Sohta,A.Ishikawa, Masahiro,Nakao, Yuji,Inagaki, Tetsuo,Hashimoto, Mitsuhisa,Sato
情報処理学会論文誌. コンピューティングシステム 7 (3) 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]
Secondary loss of a cis-spliced intron during the divergence of Giardia intestinalis assemblages
Ryoma Kamikawa, Yuji Inagaki, Tetsuo Hashimoto
BMC Research Notes 7 (1) Jun 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]
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 2014
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]
Parallel re-modeling of EF-1 alpha function: divergent EF-1 alpha genes co-occur with EFL genes in diverse distantly related eukaryotes
Ryoma Kamikawa, Matthew W. Brown, Yuki Nishimura, Yoshihiko Sako, Aaron A. Heiss, Naoji Yubuki, Ryan Gawryluk, Alastair G. B. Simpson, Andrew J. Roger, Tetsuo Hashimoto, Yuji Inagaki
BMC EVOLUTIONARY BIOLOGY 13 Jun 2013[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]
Multigene Phylogenies of Diverse Carpediemonas-like Organisms Identify the Closest Relatives of 'Amitochondriate' Diplomonads and Retortamonads
Kiyotaka Takishita, Martin Kolisko, Hiroshi Komatsuzaki, Akinori Yabuki, Yuji Inagaki, Ivan Cepicka, Pavla Smejkalová, Jeffrey D. Silberman, Tetsuo Hashimoto, Andrew J. Roger, Alastair G.B. Simpson
Protist 163 (3) May 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]
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
Miwako Tsuji, Mitsuhisa Sato, Akifumi S. Tanabe, Yuji Inagaki, Tetsuo Hashimoto
2012 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION (CEC) 2012 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
Ryoma Kamikawa, Yuji Inagaki, Tetsuo Hashimoto
Biophysical Reviews 3 (4) 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. g., n. sp., as Inferred from Small Subunit rDNA Sequences
Naoji Yubuki, Vit Ceza, Ivan Cepicka, Akinori Yabuki, Yuji Inagaki, Takeshi Nakayama, Isao Inouye, Brian S. Leander
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
Akinori Yabuki, Yuji Inagaki, Ken-ichiro Ishida
PROTIST 161 (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
Kiyotaka Takishita, Haruyo Yamaguchi, Tadashi Maruyama, Yuji Inagaki
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]
Phylogenetic inference based on combined analysis of multiple genes: Illustrative data analysis of higher-order phylogeny of Eukaryota
Hashimoto ; T, Arisue, N
統計数理 56 (1) Jan 2008[Refereed]
Evolving genetic code
Takeshi Ohama, Yuji Inagaki, Yoshitaka Bessho, Syozo Osawa
Proceedings of the Japan Academy Series B: Physical and Biological Sciences 84 (2) 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 formar raphidophycean alga Chattonella verruculosa, based on 18S rDNA phylogeny and ultrastructural characteristics
Shoko Hosoi-Tanabe, Daiske Honda, Sachiko Fukaya, Isamu Otake, Yuji Inagaki, Yoshihiko Sako
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, Y Inagaki, LA Davis, S Sperstad, B Landfald, AJ Roger
CURRENT BIOLOGY 14 (22) Nov 2004[Refereed]
A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1 alpha
PJ Keeling, Y Inagaki
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (43) Oct 2004[Refereed]
On inconsistency of the Neighbor-Joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled
E Susko, Y Inagaki, AJ Roger
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
Y Inagaki, AGB Simpson, JB Dacks, AJ Roger
SYSTEMATIC BIOLOGY 53 (4) Aug 2004[Refereed]
Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1 alpha phylogenies
Y Inagaki, E Susko, NM Fast, AJ Roger
MOLECULAR BIOLOGY AND EVOLUTION 21 (7) Jul 2004[Refereed]
Assessing functional divergence in EF-1 alpha and its paralogs in eukaryotes and archaebacteria
Y Inagaki, C Blouin, E Susko, AJ Roger
NUCLEIC ACIDS RESEARCH 31 (14) Jul 2003[Refereed]
Testing for differences in rates-across-sites distributions in phylogenetic subtrees
E Susko, Y Inagaki, C Field, ME Holder, AJ Roger
MOLECULAR BIOLOGY AND EVOLUTION 19 (9) Sep 2002[Refereed]
Lateral transfer of an EF-1 alpha gene: Origin and evolution of the large subunit of ATP sulfurylase in eubacteria
Y Inagaki, WF Doolittle, SL Baldauf, AJ Roger
CURRENT BIOLOGY 12 (9) Apr 2002[Refereed]
Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity
Y Inagaki, C Blouin, WF Doolittle, AJ Roger
NUCLEIC ACIDS RESEARCH 30 (2) Jan 2002[Refereed]
Class I release factors in ciliates with variant genetic codes
Y Inagaki, WF Doolittle
NUCLEIC ACIDS RESEARCH 29 (4) Feb 2001[Refereed]
Evolutionary relationship between dinoflagellates bearing obligate diatom endosymbionts: insight into tertiary endosymbiosis
Y Inagaki, JB Dacks, WF Doolittle, KI Watanabe, T Ohama
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 50 (6) Nov 2000[Refereed]
Evolution of the eukaryotic translation termination system: Origins of release factors
Y Inagaki, WF Doolittle
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
M Ehara, Y Inagaki, KI Watanabe, T Ohama
CURRENT GENETICS 37 (1) Jan 2000[Refereed]
Comprehensive molecular phylogenetic analysis of a heterokont alga (NIES 548) using genes from all three cellular compartments
Megumi Ehara, Taiju Kitayama, Kazuo I. Watanabe, Yuji Inagaki, Yasuko Hayashi-Ishimaru, Takeshi Ohama
Phycological Research 47 (3) 1999[Refereed]
Distribution of the mitochondrial deviant genetic code AUA for methionine in heterokont algae
M Ehara, KI Watanabe, H Kawai, Y Inagaki, Y Hayashi-Ishimaru, T Ohama
JOURNAL OF PHYCOLOGY 34 (6) Dec 1998[Refereed]
Directionally evolving genetic code: The UGA codon from stop to tryptophan in mitochondria
Y Inagaki, M Ehara, KI Watanabe, Y Hasashi-Ishimaru, T Ohama
JOURNAL OF MOLECULAR EVOLUTION 47 (4) Oct 1998[Refereed]
Distinctive origins of group I introns found in the COXI genes of three green algae
KI Watanabe, M Ehara, Y Inagaki, T Ohama
GENE 213 (1-2) Jun 1998[Refereed]
A deviant mitochondrial genetic code in prymnesiophytes (yellow-algae): UGA codon for tryptophan
Y HayashiIshimaru, M Ehara, Y Inagaki, T Ohama
CURRENT GENETICS 32 (4) Oct 1997[Refereed]
Algae or protozoa: Phylogenetic position of euglenophytes and dinoflagellates as inferred from mitochondrial sequences
Y Inagaki, Y HayashiIshimaru, R Ehara, Igarashi, I, T Ohama
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
M Ehara, Y HayashiIshimaru, Y Inagaki, T Ohama
JOURNAL OF MOLECULAR EVOLUTION 45 (2) Aug 1997[Refereed]
Cloning of the Mycoplasma capricolum gene encoding peptide-chain release factor
Y Inagaki, Y Bessho, H Hori, S Osawa
GENE 169 (1) Feb 1996[Refereed]
TRANSLATION OF SYNONYMOUS CODONS IN FAMILY BOXES BY MYCOPLASMA-CAPRICOLUM TRANSFER-RNAS WITH UNMODIFIED URIDINE OR ADENOSINE AT THE FIRST ANTICODON POSITION
Y INAGAKI, A KOJIMA, Y BESSHO, H HORI, T OHAMA, S OSAWA
JOURNAL OF MOLECULAR BIOLOGY 251 (4) Aug 1995[Refereed]
LACK OF PEPTIDE-RELEASE ACTIVITY RESPONDING TO CODON UGA IN MYCOPLASMA-CAPRICOLUM
Y INAGAKI, Y BESSHO, S OSAWA
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
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
Elucidation of evolutionary process of light adaptation in a course of loss of photosynthesis.
Grants-in-Aid for Scientific Research
Research period: 2017 - 2020Representative: Tanifuji Goro
Study on the residual green alga-derived nucleomorphs in dinoflagellates
Grants-in-Aid for Scientific Research
Research period: Apr 2016 - Mar 2019Representative: Inagaki Yuji
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
Diversity and evolution of anaerobic/microaerophilic eukaryotic microorganisms
Grants-in-Aid for Scientific Research
Research period: Apr 2015 - Mar 2018Representative: HASHIMOTO Tetsuo, HANZAWA Naoto
Splicing mechanism of novel introns in a split form and their evolutionary diversity
Grants-in-Aid for Scientific Research
Research period: Apr 2015 - Mar 2018Representative: HASHIMOTO Tetsuo
マトリョーシカ型進化原理の展開
科学研究費助成事業
Research period: Apr 2016 - Mar 2017Representative: 野崎智義, 守屋繁春, 山本雅裕, 松崎素道, 石田健一郎, 神川龍馬, 小保方潤一, 稲垣祐司, 木原久美子
Investigation on the evolutionary process integrating an endosymbiotic cyanobacterium into the host cellular system
Grants-in-Aid for Scientific Research
Research period: Apr 2011 - Mar 2016Representative: INAGAKI Yuji, OBOKATA Junichi, KAMIKAWA Ryoma
Matryoshka-type evolution
Grants-in-Aid for Scientific Research
Research period: Apr 2011 - Mar 2016Representative: Nozaki Tomoyoshi, SUZAKI Toshinobu, TSUBOI Takafumi, MORIYA Shigeharu, TSUKUI Kumiko, MATSUZAKI Motomichi, TACHIBANA Hiroshi, ISHIDA Kenichiro, OBOKATA Junichi, HASHIMOTO Tetsuo, KANEKO Osamu, INAGAKI Yuji, INOUE Isao, NAGAI Hiroki, KURODA Makoto, NAGAMUNE Kisaburo
Splicing mechanisms of a novel split intron and evolution of the mRNA maturation process in eukaryotes
Grants-in-Aid for Scientific Research
Research period: Apr 2011 - Mar 2015Representative: HASHIMOTO Tetsuo, INAGAKI Yuji, NARA Takeshi, IIDA Kei
Diversity and evolution of a canonical mitochondrion-lacking protist group, Fornicata
Grants-in-Aid for Scientific Research
Research period: Apr 2011 - Mar 2014Representative: HASHIMOTO Tetsuo, ISHIDA Kenichiro, INAGAKI Inagaki
Studies on a novel eukaryotic assemblage containing haptophytes and cryptophytes: Possible impact on the Chromalveolata hypothesis.
Grants-in-Aid for Scientific Research
Research period: 2009 - 2012Representative: INAGAKI Yuji, ISHIDA Ken-ichiro
Basal construction studies for the diversity of algae-protist complexes
Grants-in-Aid for Scientific Research
Research period: 2009 - 2012Representative: INOUYE Isao, WATANABE Makoto, HASHIMOTO Tetsuo, ISHIDA Kenichiro, INAGAKI Yuji, NAKAYAMA Takeshi, KIKUCHI Jun, MORIYA Shigeharu
Novel biflagellate TKB055 as a possible early-branch in the global eukaryotic phylogeny : studies on its morphology, transcriptome, and mitochondrial genome
Grants-in-Aid for Scientific Research
Research period: 2010 - 2011Representative: INAGAKI Yuji
Molecular Phylogeny of Fornicata
Grants-in-Aid for Scientific Research
Research period: 2008 - 2010Representative: HASHIMOTO Tetsuo, INAGAKI Yuji
Testing the Chromist monophyly based on multi-gene phylogenetic analyses considering the sequence data from katablepharids.
Grants-in-Aid for Scientific Research
Research period: 2006 - 2007Representative: INAGAKI Yuji
Early evolution of eukaryotes inferred by combined phylogeny of multiple genes
Grants-in-Aid for Scientific Research
Research period: 2005 - 2006Representative: HASHIMOTO Tetsuo, INOUYE Isao, NAKAYAMA Takeshi, INAGAKI Yuji

	氏名	中山卓郎
	Name	NAKAYAMA Takuro
	Faculty
	Section
	Position	Assistant Professor
	Theme	Organellogenesis through intracellular symbiosis, Diversity and ecology of eukaryotic unicellular organisms
	Related Links
	Email	ntakuroccs.tsukuba.ac.jp

Research Interests
Academic & Professional Experience
Apr 2021
-
Present
University of Tsukuba Center for Computational Sciences
Nov 2016
-
Mar 2021
Tohoku University
Nov 2016
-
Mar 2021
Tohoku University
Jun 2013
-
Oct 2016
University of Tsukuba Center for Computational Sciences
Jun 2011
-
Jun 2013
ダルハウジー大学
Apr 2010
-
Jun 2011
国立環境研究所
Apr 2007
-
Mar 2010
日本学術振興会特別研究員 DC1
Published Papers
▼▲
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) Feb 2020[Refereed]
Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host
Takuro Nakayama, Mami Nomura, Yoshihito Takano, Goro Tanifuji, Kogiku Shiba, Kazuo Inaba, Yuji Inagaki, Masakado Kawata
Proceedings of the National Academy of Sciences 116 (32) Jun 2019[Refereed]
Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms
Takuro Nakayama, Yuji Inagaki
SCIENTIFIC REPORTS 7 Oct 2017[Refereed]
Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle
Takuro Nakayama, Ryoma Kamikawa, Goro Tanifuji, Yuichiro Kashiyama, Naohiko Ohkouchi, John M. Archibald, Yuji Inagaki
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 (31) Aug 2014[Refereed]
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
Bruce A. Curtis, Goro Tanifuji, Fabien Burki, Ansgar Gruber, Manuel Irimia, Shinichiro Maruyama, Maria C. Arias, Steven G. Ball, Gillian H. Gile, Yoshihisa Hirakawa, Julia F. Hopkins, Alan Kuo, Stefan A. Rensing, Jeremy Schmutz, Aikaterini Symeonidi, Marek Elias, Robert J. M. Eveleigh, Emily K. Herman, Mary J. Klute, Takuro Nakayama, Miroslav Obornik, Adrian Reyes-Prieto, E. Virginia Armbrust, Stephen J. Aves, Robert G. Beiko, Pedro Coutinho, Joel B. Dacks, Dion G. Durnford, Naomi M. Fast, Beverley R. Green, Cameron J. Grisdale, Franziska Hempel, Bernard Henrissat, Marc P. Hoeppner, Ken-Ichiro Ishida, Eunsoo Kim, Lude. K. Koreny, Peter G. Kroth, Yuan Liu, Shehre-Banoo Malik, Uwe G. Maier, Darcy McRose, Thomas Mock, Jonathan A. D. Neilson, Naoko T. Onodera, Anthony M. Poole, Ellen J. Pritham, Thomas A. Richards, Gabrielle Rocap, Scott W. Roy, Chihiro Sarai, Sarah Schaack, Shu Shirato, Claudio H. Slamovits, David F. Spencer, Shigekatsu Suzuki, Alexandra Z. Worden, Stefan Zauner, Kerrie Barry, Callum Bell, Arvind K. Bharti, John A. Crow, Jane Grimwood, Robin Kramer, Erika Lindquist, Susan Lucas, Asaf Salamov, Geoffrey I. McFadden, Christopher E. Lane, Patrick J. Keeling, Michael W. Gray, Igor V. Grigoriev, John M. Archibald
NATURE 492 (7427) Dec 2012[Refereed]
Evolving a photosynthetic organelle
Takuro Nakayama, John M. Archibald
BMC BIOLOGY 10 Apr 2012[Refereed]
Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophora
Takuro Nakayama, Ken-ichiro Ishida
CURRENT BIOLOGY 19 (7) Apr 2009[Refereed]
Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA Editing
Eriko Matsuo, Kounosuke Morita, Takuro Nakayama, Euki Yazaki, Chihiro Sarai, Kazuya Takahashi, Mitsunori Iwataki, Yuji Inagaki
Frontiers in Plant Science 13 Jul 2022[Refereed]
Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida
Ryoma Kamikawa, Takako Mochizuki, Mika Sakamoto, Yasuhiro Tanizawa, Takuro Nakayama, Ryo Onuma, Ugo Cenci, Daniel Moog, Samuel Speak, Krisztina Sarkozi, Andrew Toseland, Cock van Oosterhout, Kaori Oyama, Misako Kato, Keitaro Kume, Motoki Kayama, Tomonori Azuma, Ken-ichiro Ishii, Hideaki Miyashita, Bernard Henrissat, Vincent Lombard, Joe Win, Sophien Kamoun, Yuichiro Kashiyama, Shigeki Mayama, Shin-ya Miyagishima, Goro Tanifuji, Thomas Mock, Yasukazu Nakamura
Science Advances 8 (17) Apr 2022[Refereed]
Rappemonads are haptophyte phytoplankton.
Masanobu Kawachi, Takuro Nakayama, Motoki Kayama, Mami Nomura, Hideaki Miyashita, Othman Bojo, Lesley Rhodes, Stuart Sym, Richard N Pienaar, Ian Probert, Isao Inouye, Ryoma Kamikawa
Current biology : CB 31 (11) Jun 2021[Refereed]
Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species.
Euki Yazaki, Ryosuke Miyata, Yasuhiko Chikami, Ryo Harada, Takashi Kawakubo, Goro Tanifuji, Takuro Nakayama, Kensuke Yahata, Tetsuo Hashimoto, Yuji Inagaki
Parasitology international 83 Apr 2021[Refereed]
Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areas
Shunsuke Kanamori, Antonio Cádiz, Luis M. Díaz, Yuu Ishii, Takuro Nakayama, Masakado Kawata
Ecology and Evolution 11 (4) Feb 2021[Refereed]
Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organisms
Takuro Nakayama, Kazuya Takahashi, Ryoma Kamikawa, Mitsunori Iwataki, Yuji Inagaki, Goro Tanifuji
Communicative & Integrative Biology 13 (1) Jun 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) Feb 2020[Refereed]
Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote
Matsuo, Mitsuhiro, Katahata, Atsushi, Tchikawa, Makoto, Minakuchi, Yohei, Noguchi, Hideki, Toyoda, Atsushi, Fujiyama, Asao, Suzuki, Yutaka, Hata, Takayuki, Satoh, Soichirou, Nakayama, Takuro, Kamkawa, Ryoma, Nomura, Mami, Inagaki, Yuji, Ishida, Ken-ichiro, Obokata, Junichi
bioRχiv Oct 2019
Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host
Takuro Nakayama, Mami Nomura, Yoshihito Takano, Goro Tanifuji, Kogiku Shiba, Kazuo Inaba, Yuji Inagaki, Masakado Kawata
Proceedings of the National Academy of Sciences 116 (32) Jun 2019[Refereed]
The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites
Goro Tanifuji, Shun Takabayashi, Keitaro Kume, Mizue Takagi, Takuro Nakayama, Ryoma Kamikawa, Yuji Inagaki, Tetsuo Hashimoto
PLoS ONE 13 (3) Mar 2018[Refereed]
Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms
Takuro Nakayama, Yuji Inagaki
SCIENTIFIC REPORTS 7 Oct 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]
Diversity of the Photosynthetic Paulinella Species, with the Description of Paulinella micropora sp nov and the Chromatophore Genome Sequence for strain KR01
Duckhyun Lhee, Eun Chan Yang, Jong Im Kim, Takuro Nakayama, Giuseppe Zuccarello, Robert A. Andersen, Hwan Su Yoon
PROTIST 168 (2) Apr 2017[Refereed]
Evolution of UhpC-type hexose-phosphate transporters in dinoflagellates
Yoshihisa Hirakawa, Takuro Nakayama, Nadine Keilert, Ken-ichiro Ishida
PHYCOLOGICAL RESEARCH 65 (2) Apr 2017[Refereed]
シアノバクテリアと真核藻類の細胞統合―「窒素固定オルガネラ」へ続く道？
中山卓郎, 稲垣,祐司
生物の科学遺伝 70 (2) Mar 2016
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]
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]
Detailed Process of Shell Construction in the Photosynthetic Testate Amoeba Paulinella chromatophora ( Euglyphid, Rhizaria)
Mami Nomura, Takuro Nakayama, Ken-ichiro Ishida
JOURNAL OF EUKARYOTIC MICROBIOLOGY 61 (3) May 2014[Refereed]
Genetic structure of Japanese Chattonella marina (Raphidophyceae) populations revealed using microsatellite markers
Mikihide Demura, Takuro Nakayama, Fumie Kasai, Masanobu Kawachi
PHYCOLOGICAL RESEARCH 62 (2) Apr 2014[Refereed]
Unique genome evolution in an intracellular N-2-fixing symbiont of a rhopalodiacean diatom
Takuro Nakayama, Yuji Inagaki
ACTA SOCIETATIS BOTANICORUM POLONIAE 83 (4) 2014[Refereed]
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
Bruce A. Curtis, Goro Tanifuji, Fabien Burki, Ansgar Gruber, Manuel Irimia, Shinichiro Maruyama, Maria C. Arias, Steven G. Ball, Gillian H. Gile, Yoshihisa Hirakawa, Julia F. Hopkins, Alan Kuo, Stefan A. Rensing, Jeremy Schmutz, Aikaterini Symeonidi, Marek Elias, Robert J. M. Eveleigh, Emily K. Herman, Mary J. Klute, Takuro Nakayama, Miroslav Obornik, Adrian Reyes-Prieto, E. Virginia Armbrust, Stephen J. Aves, Robert G. Beiko, Pedro Coutinho, Joel B. Dacks, Dion G. Durnford, Naomi M. Fast, Beverley R. Green, Cameron J. Grisdale, Franziska Hempel, Bernard Henrissat, Marc P. Hoeppner, Ken-Ichiro Ishida, Eunsoo Kim, Lude. K. Koreny, Peter G. Kroth, Yuan Liu, Shehre-Banoo Malik, Uwe G. Maier, Darcy McRose, Thomas Mock, Jonathan A. D. Neilson, Naoko T. Onodera, Anthony M. Poole, Ellen J. Pritham, Thomas A. Richards, Gabrielle Rocap, Scott W. Roy, Chihiro Sarai, Sarah Schaack, Shu Shirato, Claudio H. Slamovits, David F. Spencer, Shigekatsu Suzuki, Alexandra Z. Worden, Stefan Zauner, Kerrie Barry, Callum Bell, Arvind K. Bharti, John A. Crow, Jane Grimwood, Robin Kramer, Erika Lindquist, Susan Lucas, Asaf Salamov, Geoffrey I. McFadden, Christopher E. Lane, Patrick J. Keeling, Michael W. Gray, Igor V. Grigoriev, John M. Archibald
NATURE 492 (7427) Dec 2012[Refereed]
Broad Distribution of TPI-GAPDH Fusion Proteins among Eukaryotes: Evidence for Glycolytic Reactions in the Mitochondrion?
Takuro Nakayama, Ken-ichiro Ishida, John M. Archibald
PLOS ONE 7 (12) Dec 2012[Refereed]
Evolving a photosynthetic organelle
Takuro Nakayama, John M. Archibald
BMC BIOLOGY 10 Apr 2012[Refereed]
Succession of genetic diversity of Botryococcus braunii (Trebouxiophyceae) in two Japanese reservoirs
Mikihide Demura, Masanobu Kawachi, Hiroshi Koshikawa, Takuro Nakayama, Yusuke Mayuzumi, Makoto M. Watanabe
INNOVATIVE RESEARCHES ON ALGAL BIOMASS 15 2012[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]
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]
Differential Gene Retention in Plastids of Common Recent Origin
Adrian Reyes-Prieto, Hwan Su Yoon, Ahmed Moustafa, Eun Chan Yang, Robert A. Andersen, Sung Min Boo, Takuro Nakayama, Ken-ichiro Ishida, Debashish Bhattacharya
MOLECULAR BIOLOGY AND EVOLUTION 27 (7) Jul 2010[Refereed]
PHYLOGENETIC POSITION OF SYMBIOTIC CHLORELLA (TREBOUXIOPHYCEAE, CHLOROPHYTA) OF MAYORELLA VIRIDIS (AMOEBOZOA) AND ITS SYMBIOTIC MANNER
T. Nishimura, H. Yamaguchi, Y. Kodama, Takuro Nakayama, Takeshi Nakayama, I. Inouye
PHYCOLOGIA 48 (4) Jul 2009
A single origin of the photosynthetic organelle in different Paulinella lineages
Hwan Su Yoon, Takuro Nakayama, Adrian Reyes-Prieto, Robert A. Andersen, Sung Min Boo, Ken-ichiro Ishida, Debashish Bhattacharya
BMC EVOLUTIONARY BIOLOGY 9 May 2009[Refereed]
Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophora
Takuro Nakayama, Ken-ichiro Ishida
CURRENT BIOLOGY 19 (7) Apr 2009[Refereed]
Another primary endosymbiosis? —Paulinella chromatophora and its cyanelle—
Nakayama Takuro, Ishida Ken-ichiro
Japanese Journal of Protozoology 41 (1) 2008
Awards & Honors
▼▲
Apr 2022
科学技術分野の文部科学大臣表彰若手科学者賞
Apr 2022
筑波大学若手教員特別奨励賞
Sep 2021
日本植物学会賞奨励賞
Mar 2015
日本藻類学会日本藻類学会研究奨励賞
Books etc
原生生物学事典
中山, 卓郎 ( 2-8-3. アピコンプレクサ; 2-9-1. ケルコゾア; 3-14 共生体からオルガネラへの進化)
Research Grants & Projects
▼▲
二次共生の中間段階にある共生者ゲノムの解読
科学研究費助成事業基盤研究(c)(一般）
Research period: Apr 2024 - Mar 2027Representative: 中山卓郎
The overlooked diversity of the marine microbiome - Exploring the prokaryotic microbiome within eukaryotic microorganisms
Grants-in-Aid for Scientific Research
Research period: Apr 2020 - Mar 2024
光合成補助色素フコキサンチンの未知なる生合成系の解明とその誕生の謎を紐解く
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
Research period: Apr 2019 - Mar 2024Representative: 神川龍馬
海洋原生生物に共生する細菌多様性の実態解明
Grants-in-Aid for Scientific Research Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))
Research period: Oct 2018 - Mar 2023Representative: 稲垣祐司
渦鞭毛藻細胞に見られるシアノバクテリア共生体の機能および進化の解明
Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
Research period: Apr 2017 - Mar 2020Representative: 中山卓郎
Fundamental studies on "mitochondrial glycolytic pathway" in cercozoan organisims
Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
Research period: Apr 2014 - Mar 2017Representative: Nakayama Takuro, YABUKI Akinori, SHIRATORI Takashi
細胞内共生を通じた新奇オルガネラ獲得:珪藻細胞に見られる窒素固定構造の進化解明
Grants-in-Aid for Scientific Research Grant-in-Aid for Research Activity start-up
Research period: 2010 - 2011Representative: 中山卓郎
Paulinella chromatophoraのシアネレに関する研究
Grants-in-Aid for Scientific Research Grant-in-Aid for JSPS Fellows
Research period: 2007 - 2009Representative: 中山卓郎

	氏名	橋本哲男
	Name	HASHIMOTO Tetsuo
	Faculty	Faculty of Life and Enviromental Sciences
	Section
	Position	Honorary Professor (Collaborative Fellow)
	Theme	Molecular evolutionary studies on the origin and early evolution of eukaryotes
	Related Links
	Email

Division of Life Sciences

Biological Function and Information Group

Biological Science Group

Biological Function and Information Group

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects

Research Interests

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Published Papers

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Books etc

Research Grants & Projects

Research Interests

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Published Papers

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Books etc

Research Grants & Projects

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects

Academic & Professional Experience

Published Papers

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects

Biological Science Group

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects

Research Interests

Academic & Professional Experience

Published Papers

Awards & Honors

Books etc

Research Grants & Projects