Biological Function and Information Group
| Name | Faculty | Position |
|---|---|---|
| SHIGETA Yasuteru | Professor/Director of CCS/Leader | |
| SHOJI Mitsuo | Professor | |
| TANI Kazutoshi | Professor | |
| HARADA Ryuhei | Associate Professor | |
| Kowit Hengphasatporn | Assistant Professor | |
| IVONINA MARIIA | Assistant Professor | |
| DUAN LIAN | Assistant Professor | |
| SAITO Kazuya | Researcher | |
| Manussada Ratanasak | Researcher | |
| HIROKAWA Takatsugu | Faculty of Medicine | Professor (Collaborative Fellow) |
| YOSHINO Ryunosuke | Faculty of Medicine | Assistant Professor (Collaborative Fellow) |
| YAGI Kiyoshi | Department of Chemistry, Institute of Pure and Applied Sciences | Professor (Collaborative Fellow) |
| MATSUI Toru | Associate Professor (Collaborative Fellow) | |
| OKAZAWA Kazuki | Institute of Pure and Applied Sciences | Assistant Professor (Collaborative) |
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/Director of CCS/Leader | |
| Theme | Computational analyses on nano- and bio-systems | |
| Related Links | ||
shigeta ccs.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Apr 2025-PresentCenter for Computational Sciences, University of Tsukuba DirectorApr 2019-PresentNational Institutes for Quantum and Radiological Science and Technology Takasaki Advanced Radiation Research Institute Visiting ResearcherApr 2016-PresentCenter for Computational Sciences, University of Tsukuba Division of Life Science ProfessorMay 2014-PresentOsaka University Graduate School of Engineering Sciences Visiting ProfessorApr 2023-Mar 2025University of Tsukuba Headquarter Vice president and Executive director for ResearchApr 2018-Mar 2020宇宙航空研究開発機構Apr 2016-Mar 2018Institute of Molecular Sciences Visiting professorMar 2014-Mar 2016筑波大学Aug 2010-Mar 2014Osaka University Graduate School of Engineering Science, Department of Materials Engineering Science Division of Materials PhysicsAug 2011-Jul 2013Ministry of Education,Culture,Sports,Science and TechnologyMay 2008-Jul 2010University of Hyogo of Life Science, Graduate SchoolFeb 2007-May 2008筑波大学Dec 2003-Jan 2007The University of Tokyo The Graduate School of Engineering, Department of Applied ChemistryApr 2001-Dec 2003The University of Tokyo Graduate School of Arts and SciencesApr 2000-Mar 2001Osaka University Graduate School of Science, Department of ChemistryJan 1999-Mar 2000Osaka University Graduate School of Science, Department of ChemistryPublished Papers
Journal of Agricultural and Food Chemistry 74 (25) Jun 2026[Refereed]ACS APPLIED MATERIALS & INTERFACES 18 (17) May 2026[Refereed]Organic & biomolecular chemistry Apr 2026Nature chemistry Apr 2026The Journal of Chemical Physics 164 (14) Apr 2026NATURAL PRODUCTS AND BIOPROSPECTING 16 (1) Mar 2026[Refereed]CARBON ENERGY Mar 2026[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 28 (14) Mar 2026[Refereed]JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Mar 2026[Refereed]SEPARATION AND PURIFICATION TECHNOLOGY 382 (3) Feb 2026[Refereed]JOURNAL OF CHEMICAL INFORMATION AND MODELING Feb 2026[Refereed]ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Feb 2026[Refereed]The journal of physical chemistry. B 130 (3) Jan 2026SCIENTIFIC REPORTS 16 (1) Jan 2026[Refereed]International Journal of Molecular Sciences Dec 2025The Journal of Physical Chemistry A Dec 2025PROTEIN SCIENCE 35 (1) Dec 2025[Refereed]Emerging microbes & infections 14 (1) Dec 2025MABS 17 (1) Dec 2025[Refereed]Awards & Honors
Sep 2023International Academic Award of the Society for Molecular Science Contribution to the theoretical analysis of triplet-triplet annihilation upconversion mechanisms in solutions and solidsSep 2023Japan Society for Molecular Science 8th Japan Society for Molecular Science International Investigator AwardsFeb 2019Best Faculty Awards 2018Oct 201722nd QSCP Promising Scientist Award of CMOA Research AwardMar 2017Royal 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 2007Royal Chemical Society PCCP Prize for the Outstanding Achievement of Young Scientists in Physical Chemistry and Chemical Physics Research AwardMar 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
Iron in Biology: Molecular Structures, Cellular Processes and Living Systems( Computational chemistry studies on iron-containing proteins toward understanding underlaying mechanism)Quantum Systems in Physics, Chemistry, and Biology: Advances in Concepts and Applications, Progress in Theoretical Chemistry and Physics (Springer)( Integrated In-Silico Drug Modeling for Viral Proteins)Hydrogenomics: The Science of Fully Utilizing Hydrogen( Biological Enzymes and Hydrogenases)Recent advances of the fragment molecular orbital method Subtitle: Enhanced performance and applicability(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(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(Role:Contributor, Integrated Computational Studies on Mutational Effects of A Nylon-degrading Enzyme)Reference modules in Materials Science and Engineering 2016(Role:Contributor, Protein Folding and Evolution)金属錯体の量子・計算化学(Role:Contributor, 第4-1章 錯体の伝導性)Quantum mechanics Chap. 17(Role:Contributor, Quantal Cumulant Mechanics as Extended Ehrenfest Theorem)Conceptual and Computational Advances in Quantum Chemistry, Chap. 25(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(Role:Contributor, Quantum Theory in Terms of Cumulant Variables)ADVANCES IN THE THEORY OF ATOMIC AND MOLECULAR SYSTEMS: DYNAMICS, SPECTROSCOPY, CLUSTERS, AND NANOSTRUCTURES(Role:Contributor, Quantum Theory in Terms of Cumulant Variables)Challenges and Advances in Computational Chemistry and Physics, Chap. 2(Role:Contributor, Single-Reference Methods for Excited States in Molecules and Polymers)物性量子化学入門(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 2030Science of Meso-HierarchyGrants-in-Aid for Scientific ResearchResearch period: Apr 2023 - Mar 2028Theory of mesohierarchyGrants-in-Aid for Scientific ResearchResearch 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 2026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 20263D 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 2026Novel drug development for the treatment of mitochondrial diseases by activation of cytochrome c oxidaseResearch grant on rare and intractable diseases ProgramResearch period: Apr 2021 - Mar 2024Theoretical study on dynamics of metalloproteins from mitochondrial DNA in aging hypothesisGrants-in-Aid for Scientific ResearchResearch period: Apr 2022 - Mar 2023Quantum Bioenergetics for Exploring Dynamics of Metals in ProteinGrant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)Research period: Apr 2020 - Mar 2022Theoretical analysis of biohydrogenomicsGrants-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 2021Structure-based design of middle molecules for drug discoveryResearch period: Jun 2018 - Mar 2021Advancement and network formation of the project Photosynergetics by international collaborationGrants-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 2019Elucidation of Structure-Function Relationship of Biological Active Sites and New Material Design by Molecular SimulationGrants-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 2019Control of multiple spin exciton states by synergetic studies of theory and experimentGrants-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 2019Application of Cooperative Excitation into Innovative Molecular Systems with High-Order PhotofunctionsGrants-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 2019Molecular design of nylon hydrolase and industrial application of the enzymeGrants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)Research period: Apr 2014 - Mar 2019Sub-issue A, Priority Issue 7, Post-K Supercomputer ProjectNew-functionality and high-performance semiconductor devicesResearch period: Apr 2016 - Mar 2019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 2019Development of materials imaging technique based on flexible fluorophoresGrants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (A)Research period: Apr 2015 - Mar 2018A Challenging Study for Development of Theory of Transport Phenomena in Mesoscale SpaceGrants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory ResearchResearch period: Apr 2015 - Mar 2017キュミュラント粗視化動力学によるタンパク質動的秩序形成過程の理論研究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 2015Si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 2015Density-Functional Approach to Atomic and Electronic Structures and their Dynamics in Nano-StructuresGrants-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 2015Molecular design of nylon oligomer degradation enzyme and its application to bioproductionGrants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)Research period: Apr 2010 - Mar 2014Quantum chemical studies on a cooperative proton and electron transfer reaction in proteinGrants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (A)Research period: Apr 2010 - Mar 2014第一原理計算による生体内酵素反応の理論解析フェローResearch period: Apr 2011 - Mar 2012電子ダイナミクスによる電子集団運動の解析科学研究費助成事業 特定領域研究Research period: 2008 - 2009Real-time analyses of proton-coupled electron transfer reactions : Quantal cumulant dynamicsGrants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)Research period: 2008 - 2009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 - 2008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 - 2008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 - 2007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 - 2003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 - 2000
|
氏名 | 庄司 光男 |
| Name | SHOJI Mitsuo | |
| Faculty | ||
| Section | ||
| Position | Professor | |
| Theme | Theoretical investigation on the reaction mechanisms of enzymes | |
| Related Links | ||
mshoji ccs.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Oct 2019-Mar 2023JSTPublished Papers
ACS APPLIED MATERIALS & INTERFACES 18 (17) May 2026[Refereed]The Journal of Chemical Physics 164 (14) Apr 2026RSC ADVANCES 15 (55) Nov 2025CHEMISTRY LETTERS 54 (11) Nov 2025Monthly Notices of the Royal Astronomical Society 544 (4) Nov 2025[Refereed]Physical Chemistry Chemical Physics 27 (1) Nov 2025[Refereed]ACS OMEGA 10 (17) Apr 2025CHEMISTRY-SWITZERLAND 7 (2) Mar 2025PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES Epub (12) Nov 2024[Refereed]Journal of Computational Chemistry 45 (32) Sep 2024The Journal of Physical Chemistry Part B 128 (29) Jul 2024[Refereed]Nature Communications 15 (1) Jun 2024SUSTAINABLE ENERGY & FUELS 8 (5) Jan 2024[Refereed]BIOORGANIC & MEDICINAL CHEMISTRY 98 Jan 2024[Refereed]PHOTOSYNTHESIS RESEARCH Epub (2-3) Nov 2023[Refereed]MOLECULES 28 (20) Oct 2023[Refereed]ASTROBIOLOGY 23 (10) Oct 2023[Refereed]ACS Catalysis 13 (18) Sep 2023PHYSICAL CHEMISTRY CHEMICAL PHYSICS 25 (21) May 2023[Refereed]The Journal of Physical Chemistry Letters 14 (13) Apr 2023CHIRALITY 35 (9) Apr 2023[Refereed]BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 96 (4) Apr 2023[Refereed]Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]2023Physical Chemistry Chemical Physics 25 (4) 2023Chem. Phys. Lett. 806 Sep 2022[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B Epub Sep 2022[Refereed]CHEMICAL SCIENCE 13 (36) Sep 2022Astrobiology 22 (9) Sep 2022[Refereed]Astrobiology 22 (11) Sep 2022[Refereed]Biophysical Journal 121 (14) Jun 2022[Refereed]Chem. Phys. Lett. 793 Feb 2022[Refereed]Chemical Physics Letters 790 Jan 2022[Refereed]Mechanism of Water Oxidation in Photosynthesis Elucidated by Interplay Between Experiment and TheoryAdvances in Photosynthesis and Respiration 47 Sep 2021[Refereed]PLOS ONE 16 (7) Jul 2021[Refereed]Advances in Quantum Chemistry 84 Apr 2021[Refereed]Biophysics and physicobiology 18 2021[Refereed]JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 405 Jan 2021[Refereed]JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 405 Jan 2021[Refereed]Bulletin of the Chemical Society of Japan 93 (12) Dec 2020[Refereed]Biochimica et Biophysica Acta (BBA) - Bioenergetics 1862 (4) Dec 2020[Refereed]Physical Chemistry Chemical Physics 46 (22) Oct 2020[Refereed]RSC Advances 10 (63) Oct 2020[Refereed]Journal of Photochemistry and Photobiology A: Chemistry 405 Sep 2020[Refereed]J. Photochem. Photobiol. A 402 (112791) Jul 2020[Refereed]Proceedings of the National Academy of Sciences of the United States of America 117 (20) May 2020[Refereed]Molecular Physics 118 (21-22) May 2020[Refereed]Chemical Physics Letters 746 May 2020[Refereed]Physical Chemistry Chemical Physics 22 (29) May 2020[Refereed]Journal of biochemistry 167 (4) Apr 2020[Refereed]Mol. Phys. - Feb 2020[Refereed]Chemical Physics Letters 734 Nov 2019[Refereed]Journal of biochemistry 167 (4) Nov 2019[Refereed]Chemical Physics Letters 732 Oct 2019[Refereed]Molecular Physics Sep 2019[Refereed]CHEMICAL PHYSICS LETTERS 730 Sep 2019[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 123 (26) Jul 2019[Refereed]CHEMICAL PHYSICS LETTERS 725 Jun 2019[Refereed]The Journal of Physical Chemistry A 123 (26) Jun 2019[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 123 (13) Apr 2019[Refereed]Journal of chemical theory and computation 15 (4) Apr 2019[Refereed]The journal of physical chemistry. A 123 (13) Mar 2019[Refereed]Physiologia plantarum 166 (1:::SI) Mar 2019[Refereed]Chemistry Letters 48 (3) Mar 2019[Refereed]Journal of Computer Chemistry, Japan 17 (5) Mar 2019[Refereed]CHEMICAL PHYSICS 518 Feb 2019[Refereed]JOURNAL OF COMPUTATIONAL CHEMISTRY 40 (2) Jan 2019[Refereed]Molecules 24 (76) Jan 2019[Refereed]CHEMICAL PHYSICS LETTERS 714 Jan 2019[Refereed]CHEMICAL PHYSICS LETTERS 714 Jan 2019[Refereed]Molecules (Basel, Switzerland) 24 (1) Dec 2018[Refereed]Chemistry (Weinheim an der Bergstrasse, Germany) 24 (68) Dec 2018[Refereed]MOLECULAR PHYSICS Dec 2018[Refereed]Journal of computational chemistry 40 (2:::SI) Oct 2018[Refereed]Ensemble 20 (4) Oct 2018[Refereed]Ensemble 20 (4) Oct 2018Bulletin of the Chemical Society of Japan 91 (9) Sep 2018[Refereed]Chemistry (Weinheim an der Bergstrasse, Germany) 24 (68) Aug 2018[Refereed]Bulletin of the Chemical Society of Japan 91 (10) Jul 2018[Refereed]Journal of Physical Chemistry B 122 (25) Jun 2018[Refereed]Biochemical and Biophysical Research Communications 499 (2) May 2018Chemical Physics Letters 705 May 2018[Refereed]Seibutsu Butsuri 58 (3) May 2018[Refereed]Chemical Physics Letters 698 Apr 2018[Refereed]Molecular Physics 116 (5-6) Mar 2018[Refereed]Molecular Astrophysics 10 Mar 2018[Refereed]ChemPhotoChem 2 (3) Dec 2017[Refereed]POLYHEDRON 136 (4) Nov 2017[Refereed]CHEMICAL PHYSICS LETTERS 687 Nov 2017[Refereed]The journal of physical chemistry. B 121 (22) Jun 2017[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 121 (22) Jun 2017[Refereed]FARADAY DISCUSSIONS 198 Jun 2017[Refereed]アスパラギン酸アミノトランスフェラーゼのアルジミン転移過程の量子化学的解析ビタミン 91 (4) Apr 2017Physical chemistry chemical physics : PCCP 19 (15) Mar 2017[Refereed]MOLECULAR PHYSICS 115 (5) 2017[Refereed]MOLECULAR PHYSICS 115 (17-18) 2017[Refereed]CHEMICAL PHYSICS LETTERS 658 Aug 2016[Refereed]BIOPHYSICS AND PHYSICOBIOLOGY 13 Jun 2016[Refereed]Journal of Computer Chemistry, Japan 15 (5) 2016CHEMICAL PHYSICS LETTERS 640 Nov 2015[Refereed]Molecular dynamics study on the key catalytic intermediates of threonine synthasePROTEIN SCIENCE 24 (1:SI) Oct 2015[Refereed]GPGPU化OpenFMOによるFMO計算の性能評価情報処理学会研究報告(Web) 2015 (HPC-151) Sep 2015CHEMICAL PHYSICS LETTERS 636 Sep 2015[Refereed]CHEMICAL PHYSICS LETTERS 631 Jul 2015CHEMICAL PHYSICS LETTERS 627 May 2015INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5) Mar 2015[Refereed]CHEMICAL PHYSICS LETTERS 623 Mar 2015CHEMICAL PHYSICS LETTERS 623 Mar 2015[Refereed]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化の試み日本コンピュータ化学会年会講演予稿集 2015 2015OpenFMOプログラムのGPGPU化分子科学討論会講演プログラム&要旨(Web) 9th 2015JOURNAL OF PHYSICAL CHEMISTRY B 119 (4) Jan 2015[Refereed]Performance Benchmark of FMO Calculation with GPU-Accelerated Fock Matrix Preparation RoutineJournal of Chemical Software 13 (6) 2015[Refereed]GPU-accelerated FMO Calculation with OpenFMO: Four-Center Inter-Fragment Coulomb InteractionJournal of Chemical Software 14 (3) 2015[Refereed]Journal of Biomolecular Structure and Dynamics 32 (11) Nov 2014[Refereed]CHEMICAL PHYSICS LETTERS 608 Jul 2014[Refereed]J. Am. Chem. Soc. 136 (12) Mar 2014[Refereed]MOLECULAR PHYSICS 112 (3-4) Feb 2014[Refereed]Seibutsu Butsuri 54 (1) 2014Seibutsu Butsuri 54 (1) 2014Seibutsu Butsuri 54 (1) 2014GPGPU化Fock行列計算ルーチンのOpenFMOへの組み込み分子科学討論会講演プログラム&要旨(Web) 8th 2014GPGPUクラスタ上でのFMO計算の性能評価日本コンピュータ化学会年会講演予稿集 2014 2014GPGPU化したFock行列計算ルーチンのOpenFMOへの組み込み日本コンピュータ化学会年会講演予稿集 2014 2014Fock Matrix Preparation in Fragment Molecular Orbital Method with GPGPU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 2013Fock Matrix Preparation in Fragment Molecular Orbital Method with GPGPU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]Vitamins 87 (10) Oct 2013[Refereed]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IPSJ SIG Notes 2013-HPC-138 (19) Feb 2013Ha-pacs: A highly accelerated parallel advanced system for computational sciencesContemporary High Performance Computing: From Petascale toward Exascale Jan 2013Seibutsu Butsuri 53 (1) 2013Seibutsu Butsuri 53 (1) 2013OpenFMOにおけるFock行列計算ルーチンのGPGPU化分子科学討論会講演プログラム&要旨(Web) 7th 2013OpenFMOにおけるFock行列計算のGPGPUによる高速化への取り組み日本コンピュータ化学会年会講演予稿集 2013 2013OpenFMOにおけるFock行列計算ルーチンのGPGPU化について日本コンピュータ化学会年会講演予稿集 2013 2013Seibutsu Butsuri 52 2012International 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IPSJ SIG Notes 2011 (21) Jul 2011International Journal of Quantum Chemistry 111 (3) Mar 2011[Refereed]Seibutsu Butsuri 51 2011Seibutsu Butsuri 51 2011International Journal of Quantum Chemistry 110 (15) 2010[Refereed]International Journal of Quantum Chemistry 110 (15) 2010[Refereed]Journal of Chemical Software 8 (1) Dec 2009POLYHEDRON 28 (9-10) Oct 2009[Refereed]Journal of Physical Chemistry A 113 (52) Oct 2009[Refereed]POLYHEDRON 28 (9-10) Jun 2009[Refereed]Polyhedron 28 (9-10) 2009[Refereed]International Journal of Quantum Chemistry 109 (15) 2009[Refereed]International Journal of Quantum Chemistry 109 (15) 2009[Refereed]International Journal of Quantum Chemistry 109 (15) 2009[Refereed]Chemical Physics Letters 456 (1-3) Oct 2008[Refereed]International Journal of Quantum Chemistry 108 (15) Oct 2008[Refereed]International Journal of Quantum Chemistry 108 (15) 2008[Refereed]International Journal of Quantum Chemistry 108 (4) 2008[Refereed]International Journal of Quantum Chemistry 108 (15) 2008[Refereed]Journal of Physical Chemistry a 112 (17) 2008[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 107 (15) Dec 2007POLYHEDRON 26 (9-11) Jun 2007[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 107 (6) May 2007[Refereed]JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS 310 (2) Mar 2007[Refereed]International Journal of Quantum Chemistry 107 (15) 2007[Refereed]Polyhedron 26 (9-11) 2007[Refereed]International Journal of Quantum Chemistry 107 (15) 2007[Refereed]Chemical Physics Letters 446 (1-3) 2007[Refereed]Polyhedron 26 (9-11) 2007[Refereed]International Journal of Quantum Chemistry 106 (15) Dec 2006European Physical Journal D 38 (1) Apr 2006JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 178 (2-3) Mar 2006[Refereed]Theoretical study on the electronic structure of [4Fe-4S] clusterRECENT 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 speciesRECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND 7B 7A-B 2006[Refereed]International Journal of Quantum Chemistry 105 (6) Dec 2005[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 105 (6) Dec 2005[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 105 (6) Dec 2005[Refereed]Polyhedron, 2005, 40, 2701-2707 24 (16-17) Nov 2005[Refereed]Polyhedron, 2005, 24, 2751-2757 24 (16-17) Nov 2005[Refereed]Polyhedron, 2005, 24, 2778-2783 24 (16-17) Nov 2005[Refereed]Polyhedron, 2005, 24, 2720-2725 24 (16-17) Nov 2005[Refereed]Polyhedron, 2005, 24, 2745-2750 24 (16-17) Nov 2005[Refereed]POLYHEDRON 24 (16-17) Nov 2005[Refereed]POLYHEDRON 24 (16-17) Nov 2005[Refereed]POLYHEDRON 24 (16-17) Nov 2005[Refereed]POLYHEDRON 24 (16-17) Nov 2005[Refereed]Int. J. Quant. Chem., 2005, 105, 628-644 105 (6) Oct 2005[Refereed]Synthetic Metals 154 (1-3) Oct 2005[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 100 (6) Nov 2004Int. J. Quant. Chem., 2004, 100, 927-936 100 (6) Oct 2004[Refereed]Int. J. Quant. Chem., 2004, 100, 943-956 100 (6) Oct 2004[Refereed]POLYHEDRON 22 (14-17) Jul 2003Awards & 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 2022Best PresentationSep 2021Best PresentationDec 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
生体の科学( 銅含有アミン酸化酵素における動的酵素反応機構)分子シミュレーション学会会誌アンサンブル( 量子分子特性からアミノ酸ホモキラリティ起源に挑む)フロンティア( 第26回理論化学討論会のご案内)フロンティア( 第26回理論化学討論会のご案内)フロンティア( 第26回理論化学討論会のご案内)ADVANCES IN QUANTUM CHEMISTRY, VOL 84( 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(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(Role:Sole author, 45-49)Gaussian16で始める量子化学超入門(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(Role:Sole author)Research Grants & Projects
Elucidation of the mechanisms for light-induced water-splitting and light energy utilization in photosynthesisGrants-in-Aid for Scientific ResearchResearch period: Apr 2022 - Mar 2027光化学系II酸素発生中心を創る学術変革領域研究(A)Research period: Apr 2025 - Mar 2027Verification of the contribution ofandchains involved in the formation of hemoglobin hinge and switch region structureGrants-in-Aid for Scientific ResearchResearch period: Apr 2023 - Mar 2026XFEL-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 2026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 2024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 2024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-PRESTOResearch period: Oct 2019 - Mar 2023Elucidation of the various water splitting mechanism used for natural, semiconductors and molecular catalysesGrants-in-Aid for Scientific ResearchResearch period: Apr 2020 - Mar 2022生体内量子多体系における特異的化学反応の機構解明Research period: 2019 - 2022Theoretical elucidation of the reactivation mechanism of the oxygen-evolving complex in photosystem IIGrants-in-Aid for Scientific ResearchResearch period: Apr 2018 - Mar 2020Elucidation of the complete reaction pathways of the water decomposition reactions in the oxygen-evolving complex of photosystem IIGrants-in-Aid for Scientific ResearchResearch period: Apr 2017 - Mar 2020Elucidation of enzyme catalytic mechanism regulating transition state by linking conformational change and fluctuations of the active siteGrants-in-Aid for Scientific ResearchResearch period: Jul 2016 - Mar 2020Theoretical Challenge in Astrobiology by Computational ScienceGrants-in-Aid for Scientific ResearchResearch period: Apr 2016 - Mar 2019Concerted proton/electron transfer mechanism in cofactor-dependent enzymeGrants-in-Aid for Scientific ResearchResearch period: Apr 2015 - Mar 2019Theoretical elucidation on the full reaction mechanisms of threonine synthaseGrants-in-Aid for Scientific ResearchResearch period: Apr 2014 - Mar 2017Elucidation of the mechanism of water-splitting in photosystem IIGrants-in-Aid for Scientific ResearchResearch period: 2012 - 2017Reaction specificity of pyridoxal enzymesGrants-in-Aid for Scientific ResearchResearch period: Apr 2012 - Mar 2016Theoretical elucidations of the reactions and the reaction-control mechanisms in enzymesGrants-in-Aid for Scientific ResearchResearch period: Apr 2012 - Mar 2014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)
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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 | ||
ktani ccs.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Dec 2023-PresentUniversity of Tsukuba Center for Computational Sciences ProfessorApr 2019-Nov 2023Mie University Graduate School of MedicineApr 2015-Mar 2019Nagoya University Cellular and Structural Physiology Institute Division Designated professorApr 2012-Mar 2015Nagoya University Cellular and Structural Physiology Institute Division Designated associate professorJan 2009-Mar 2012京都大学Apr 2002-Dec 2008日本電子(株)Mar 2002-Mar 2002京都大学Sep 1999-Feb 2002理化学研究所Published Papers
Microbial Biotechnology 19 (4) Apr 2026[Refereed]Communications Biology Mar 2026[Refereed]Biochemistry 64 (14) Jul 2025[Refereed]Nature Communications 16 (1) Feb 2025[Refereed]Communications Biology 8 (1) Jan 2025[Refereed]Biochemistry 64 Dec 2024[Refereed]Communications Biology 7 Oct 2024[Refereed]Communications Biology 7 (1) Feb 2024[Refereed]Nature communications 14 (1) Feb 2023[Refereed]The Journal of Physical Chemistry B Jan 2023[Refereed]Communications Biology 5 (1) Nov 2022[Refereed]The Journal of biological chemistry 298 (6) Apr 2022[Refereed]Nature communications 13 (1) Apr 2022[Refereed]Science signaling 15 (720) Feb 2022[Refereed]Nature Communications 12 (1) Nov 2021[Refereed]Biochemistry 62 Jul 2021[Refereed]Journal of structural biology 213 (3) May 2021[Refereed]Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides.Nature communications 11 (1) Oct 2020[Refereed]Biochemistry 59 (18) May 2020[Refereed]Biophysical Reviews 12 Mar 2020[Refereed]Science Advances 6 Feb 2020[Refereed]Journal of Structural Biology 205 (1) Jan 2019[Refereed]NATURE STRUCTURAL & MOLECULAR BIOLOGY 24 (9) Sep 2017[Refereed]SCIENTIFIC REPORTS 7 (1) Jul 2017[Refereed]ANNALS OF THE NEW YORK ACADEMY OF SCIENCES 1397 (1) Jun 2017[Refereed]NATURE COMMUNICATIONS 7 Dec 2016[Refereed]NATURE 537 (7620) Sep 2016[Refereed]JOURNAL OF MOLECULAR BIOLOGY 428 (11) Jun 2016[Refereed]MICROSCOPY 65 (3) Jun 2016[Refereed]Structure and inhibitor of water channel in brainWater: The Forgotten Biological Molecule Apr 2016MICROSCOPY 65 (2) Apr 2016[Refereed]MOLECULAR AND CELLULAR BIOLOGY 36 (6) Mar 2016[Refereed]JOURNAL OF MOLECULAR BIOLOGY 428 (6) Mar 2016[Refereed]BIOPHYSICAL JOURNAL 110 (3) Feb 2016[Refereed]ELIFE 4 (4) Mar 2015[Refereed]SCIENCE 347 (6223) Feb 2015[Refereed]JOURNAL OF MOLECULAR BIOLOGY 427 (2) Jan 2015[Refereed]JOURNAL OF BIOLOGICAL CHEMISTRY 289 (44) Oct 2014[Refereed]Biochimica et Biophysica Acta - General Subjects 1840 (5) May 2014[Refereed]SCIENCE 344 (6181) Apr 2014[Refereed]MICROSCOPY 63 (2) Apr 2014[Refereed]ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 69 (12) Dec 2013[Refereed]MICROSCOPY 62 (6) Dec 2013[Refereed]Journal of Molecular Biology 425 (22) Nov 2013[Refereed]MICROSCOPY 62 (4) Aug 2013[Refereed]Nature communications 4 2013[Refereed]Nat. Commun 4 2013[Refereed]PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 109 (45) Nov 2012[Refereed]JOURNAL OF STRUCTURAL BIOLOGY 174 (2) May 2011[Refereed]JOURNAL OF MOLECULAR BIOLOGY 405 (3) Jan 2011[Refereed]NATURE COMMUNICATIONS 2 Jan 2011[Refereed]JOURNAL OF MOLECULAR BIOLOGY 402 (4) Oct 2010[Refereed]JOURNAL OF STRUCTURAL BIOLOGY 170 (1) Apr 2010[Refereed]YAKUGAKU ZASSHI-JOURNAL OF THE PHARMACEUTICAL SOCIETY OF JAPAN 130 (2) Feb 2010[Refereed]Water: The Forgotten Biological Molecule 2010EMBO JOURNAL 28 (11) Jun 2009[Refereed]JOURNAL OF MOLECULAR BIOLOGY 389 (4) Jun 2009[Refereed]JOURNAL OF STRUCTURAL BIOLOGY 162 (2) May 2008[Refereed]Cell communication & adhesion 15 (1) May 2008[Refereed]PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104 (51) Dec 2007[Refereed]PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104 (24) Jun 2007[Refereed]Microscopy and Microanalysis 12 (2) Aug 2006[Refereed]JOURNAL OF STRUCTURAL BIOLOGY 153 (2) Feb 2006[Refereed]JOURNAL OF MOLECULAR BIOLOGY 355 (4) Jan 2006[Refereed]JOURNAL OF STRUCTURAL BIOLOGY 146 (3) Jun 2004[Refereed]JOURNAL OF BIOLOGICAL CHEMISTRY 279 (13) Mar 2004[Refereed]Inositol 1,4,5-trisphosphate receptor contains multiple cavities and L-shaped ligand-binding domainsJOURNAL OF MOLECULAR BIOLOGY 336 (1) Feb 2004[Refereed]PROTEIN SCIENCE 13 (2) Feb 2004[Refereed]Selection and prioritization of targets for protein structure determination蛋白質核酸酵素 47 (8 Suppl) 2002Automated search of natively folded protein fragments for high-throughput structure determination in structural genomicsPROTEIN SCIENCE 9 (12) Dec 2000[Refereed]ULTRAMICROSCOPY 65 (1-2) Sep 1996[Refereed]Awards & Honors
Feb 2026筑波大学 2025年度Best Faculty Member賞 クライオ電子顕微鏡を用いた膜タンパク質複合体の構造機能研究Mar 2023令和4年度 三重大学優秀論文賞May 2015日本顕微鏡学会 第30回日本顕微鏡学会論文賞(応用研究生物学部門)Feb 2014公益財団法人風戸研究奨励会 第7回 風戸賞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(Role:Joint author)STRUCTURE AND INHIBITOR OF WATER CHANNEL IN BRAIN(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 2028Structural study of photo energy conversion system of light harvesting complex from photobacteriumGrants-in-Aid for Scientific ResearchResearch 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 2024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 2022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 2022Electron crystallographic analysis of tomographic volumes of 2D crystals of membrane proteinsGrants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Exploratory)Research period: Jun 2017 - Mar 2020Studies in structural physiology of channelsGrants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (S)Research period: May 2015 - Mar 2020Structural and functional relationship of aqauporin-4 in brainGrants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)Research period: Apr 2014 - Mar 2017Electron crystallographic analysis of two dimensional crystals of membrane proteins maintaining proton gradientGrants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)Research period: Apr 2010 - Mar 2014
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氏名 | 原田 隆平 |
| Name | HARADA Ryuhei | |
| Faculty | ||
| Section | ||
| Position | Associate Professor | |
| Theme | ||
| Related Links | ||
ryuhei ccs.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Feb 2019-PresentUniversity of Tsukuba Center for Computational SciencesApr 2018-Jan 2019University of Tsukuba Center for Computational SciencesApr 2015-Mar 2018日本学術振興会Apr 2014-Mar 2015University of Tsukuba Center for Computational SciencesApr 2011-Mar 2014理化学研究所 計算科学研究機構Published Papers
Langmuir 42 (41) Oct 2026[Refereed]The Journal of Physical Chemistry B, XXXX, XXX, XXX−XXX Oct 2026[Refereed]Aromatic Fluorination Enhances Hydrophobicity and Antimicrobial Activity of Magainin 2ACS Applied Materials & Interfaces 18 (31) Jul 2026[Refereed]Journal of Chemical Information Modeling 66 (15) Jun 2026[Refereed]The Journal of Chemical Physics 164 (14) Apr 2026[Refereed]Physical Chemistry Chemical Physics 28 Apr 2026[Refereed]The Journal of Physical Chemistry Letters 17 (12) Mar 2026[Refereed]Journal of Medicinal Chemistry 69 (6) Feb 2026[Refereed]Journal of Chemical Information and Modeling 66 (4) Feb 2026[Refereed]The Journal of Physical Chemistry B 130 (2) Jan 2026[Refereed]Investigation of Chemical Properties within Chaperonins in 2 Stabilizing Substrate Protein Conformations Using Biomolecular 3 Environment-Mimicking ModelThe Journal of Physical Chemistry Letter, 16 (25) Jun 2025[Refereed]Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational SearchJournal of Chemical Information and Modeling 65 (13) Jun 2025[Refereed]Rational Designed and Engineered Antimicrobial Peptides with High Selectivity and Efficiency Against Phytopathogenic Ralstonia SolanecearumScience of the Total Environment 976 May 2025[Refereed]In-Silico Analysis of Inhibitor Intrusion into the AQP7 Channel for Efficient Drug DesignChemistry Letters 54 (4) Apr 2025[Refereed]Reaction Mechanism Path Sampling Based on Parallel Cascade Selection QM/MM Molecular Dynamics Simulation: PaCS-QJournal of Chemical Theory and Computation, 21 (8) Mar 2025[Refereed]Characterization of Delta-7 Alkenone Desaturase in Haptophytes Emiliania Huxleyi Through the Heterologous Expression in Tisochrysis LuteaMarine Biotechnology 27 (1) 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 AssayScientific Report 15 (1) Feb 2025[Refereed]BEMM-GEN: A Tool for Generating a Biomolecular Environment Mimicking Model for Molecular Dynamics SimulationJournal of Chemical Information and Modeling 64 (19) Oct 2024[Refereed]Structural Fluctuation in Homodimeric Aminoacyl-tRNA Synthetases Induces Half-of-the-sites ActivityThe 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 ValidationComputational Biology and Chemistry, 112 Oct 2024[Refereed]CommunicationMachine Learning-Based QSAR and LB-PaCS-MD Guided Design of SARS-CoV-2 Main Protease InhibitorsBioorganic & Medicinal Chemistry Letters 110 Sep 2024[Refereed]Journal of Chemical Information and Modeling 64 (16) Aug 2024[Refereed]Structural Generation by Inverse Transformation Using Principal Component Analysis Enhances Conformational Sampling of ProteinBulletin 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 ProteaseHeliyon 10 (11) Jun 2024[Refereed]Prediction of the Binding Mechanism of a Selective DNA Methyltransferase 3A Inhibitor by Molecular SimulationScientific Report 14 Jun 2024[Refereed]Development of Membrane Permeability Coefficient by Means of Novel Molecular Dynamics MethodsYAKUGAKU ZASSHI 144 (5) May 2024[Refereed]Preferential Door for Ligand Binding and Unbinding Pathways in Inhibited Human AcetylcholinesteraseThe Journal of Physical Chemistry Letters 15 (21) May 2024[Refereed]Drug-discovery Simulation for Membrane ProteinsSEIBUTSU BUTURI 64 (1) Feb 2024[Refereed]Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP)Nucleic Acids Research 52 (3) Dec 2023[Refereed]RSC Advances 13 Nov 2023[Refereed]Latrunculin Resistance Mechanism of Non-Conventional Actin NAP1 Uncovered by Molecular Dynamics SimulationsCytoskeleton 81 Oct 2023[Refereed]Bulletin of the Chemical Society of Japan 96 (7) Jul 2023[Refereed]Chemistry Letters, 52 (5) Jun 2023[Refereed]Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy AnalysesJournal of Agricultural and Food Chemistry 71 (24) Jun 2023[Refereed]Efficient Screening of Protein-Ligand Complexes in Lipid Bilayers Using LoCoMock ScoreJournal of Computer-Aided Molecular Design, 37 Mar 2023[Refereed]Journal Chemical Information and Modeling 63 (1) Jan 2023[Refereed]Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational SubspaceJournal of Chemical Information and Modeling 62 (23) Dec 2022[Refereed]Identifying Antibiotics based on Structural Differences in the Conserved Allostery from Mitochondrial Heme-copper OxidasesNature Communications 13 Dec 2022[Refereed]Scientific Reports 12 (1) Oct 2022[Refereed]Autism-Associated Mutation in Hevin Induces Endoplasmic Reticulum Stress Through Structural InstabilityScientific Report 12 Jul 2022[Refereed]The Structural Validation by G-factor Regulates Boost Potentials Employed in Conformational Sampling of ProteinsJournal of Chemical Information and Modeling 62 (14) Jul 2022[Refereed]The Role of ATP in Solubilizing RNA-binding Protein Fused in SarcomaProteins: Structure, Function, and Bioinformatics 90 (8) Jul 2022[Refereed]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)Chemistry Letters 51 Jan 2022[Refereed]Journal of Molecular Biology 434 (2) Jan 2022[Refereed]Proteins: Structure, Function, and Bioinformatics 90 (2) Jan 2022[Refereed]International Journal of Molecular Sciences 22 (23) Dec 2021[Refereed]Chemistry Letters 50 (12) Dec 2021[Refereed]The Journal of Physical Chemistry B 125 (46) Nov 2021[Refereed]Chemical Physics Letters 782 Aug 2021[Refereed]Independent Non-targeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of ProteinsJournal of Chemical Theory and Computation 17 Aug 2021[Refereed]Physical Chemistry Chemical Physics 23 (36) Aug 2021[Refereed]Structure 29 Jul 2021[Refereed]PLoS ONE 16 (7) Jul 2021[Refereed]Journal of Structural Biology 213 (2) Apr 2021[Refereed]Membrane Permeability Evaluated from Solvation Free Energy Calculation of Cyclic DipeptideJournal of Computer Chemistry Japan 19 (4) Mar 2021[Refereed]Rare Event Sampling of Proteins Based on Distributed Molecular Dynamics SimulationsJapan Society of Theoretical Chemistry 3 (1) Jan 2021[Refereed]Chemistry Letters 50 (1) Jan 2021[Refereed]Bulletin of the Chemical Society of Japan 94 (1) Jan 2021[Refereed]Journal of Chemical Theory and Computation 16 (10) Oct 2020[Refereed]The Journal of Physical Chemistry B 124 (39) Oct 2020[Refereed]Journal of Chemical Information and Modeling 60 (8) Aug 2020[Refereed]CHEMISTRY LETTERS 49 (7) Jul 2020[Refereed]CHEMISTRY LETTERS 49 (7) Jul 2020[Refereed]Chemistry Letters 49 (4) Apr 2020[Refereed]Journal of Chemical Information and Modeling 60 (3) Mar 2020[Refereed]Rare Event Sampling of Biomolecules Based on Distributed ComputingBUTSURI 75 (1) Jan 2020[Refereed]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 ProteinsJournal of Chemical Information and Modeling 59 (12) Nov 2019[Refereed]Journal of Chemical Information and Modeling 59 (9) Sep 2019[Refereed]JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (9) Sep 2019[Refereed]Parallel Cascade Selection Molecular Dynamics Simulation to Screen for Protein Complexes Generated by Rigid DockingJournal of Molecular Graphics and Modeling 92 Jul 2019[Refereed]Temperature-Pressure Shuffling Outlier Flooding Method Enhances the Conformational Sampling of ProteinsJournal of Computational Chemistry 40 (15) Apr 2019[Refereed]Molecular Dynamics Studies on the Effects of Antifreezing Protein from Rhagium Inquisitor (RiAFP) onIce GrowthJournal of Computational Chemistry Japan 17 (5) Mar 2019[Refereed]Chemistry Letters 48 (4) Mar 2019[Refereed]Chemistry Letters 48 (3) Feb 2019[Refereed]JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 (1) Jan 2019[Refereed]Chemistry Letters 47 (10) Sep 2018[Refereed]Effect of Initial Structures Rules in Parallel Cascade Selection Molecular Dynamics Affect Conformational Sampling EfficiencyJournal of Molecular Graph and Modeling 85 Sep 2018[Refereed]Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of ProteinsBulletin of the Chemical Society of Japan 91 (9) Sep 2018[Refereed]Chemistry Letters 47 (9) Aug 2018[Refereed]Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square DeviationJournal of Chemical Information and Modeling 58 (7) Aug 2018[Refereed]Physical Chemistry Chemical Physics 20 (26) Jul 2018[Refereed]Developments of Innovative Molecular Simulation Methods for Understanding the Biological FunctionsChemical Industry 69 (7) Jul 2018Nucleic Acid Research 46 (13) Jul 2018[Refereed]Journal of Chemical Theory and Computation 14 (6) Jun 2018[Refereed]JOURNAL OF COMPUTER CHEMISTRY-JAPAN 17 (1) Mar 2018[Refereed]Advances in Quantum Chemistry 78 2018[Refereed]Physical Chemistry Chemical Physics 20 (14) 2018[Refereed]BIOPHYSICS AND PHYSICOBIOLOGY 15 Jan 2018[Refereed]Molecular Simulation 44 (3) 2018[Refereed]Journal of Computational Chemistry 38 (31) Dec 2017[Refereed]Journal of Chemical Information and Modeling 57 (12) Dec 2017[Refereed]Bulletin of the Chemical Society of Japan 90 (11) Nov 2017[Refereed]Journal of Computational Chemistry 38 (22) Aug 2017[Refereed]The Journal of Physical Chemistry B 121 (22) Jun 2017[Refereed]Chemistry Letters 46 (6) Jun 2017[Refereed]Journal of Structural Biology 198 (2) May 2017Journal of Computational Chemistry 38 (11) Apr 2017[Refereed]Journal of Chemical Theory and Computation 13 (3) Mar 2017[Refereed]Molecular Simulation 43 (13-16) 2017[Refereed]Biophysics and Physicobiology 13 Nov 2016[Refereed]Bulletin of the Chemical Society of Japan 89 (11) Nov 2016[Refereed]eLife 5 Nov 2016[Refereed]Biophysics and Physicobiology 13 Jun 2016[Refereed]Journal of Chemical Theory and Computation 12 (5) May 2016[Refereed]Journal of Computational Chemistry 37 (8) Mar 2016[Refereed]Proceedings of the International Conference of Computational Methods in Sciences and Engineering 2016 (ICCMSE-2016) 1790 2016[Refereed]Journal of Chemical Theory and Computation 11 (11) Nov 2015[Refereed]Chemical Physics Letters 639 Oct 2015[Refereed]Protein Folding and EvolutionIn book: Reference Module in Materials Science and Materials Engineering DOI: 10.1016/B978 Aug 2015[Refereed]Chemical Physics Letters 630 Jun 2015[Refereed]Journal of Molecular Graphics and Modeling 58 May 2015[Refereed]Journal of Computational Chemistry 36 (10) Apr 2015[Refereed]International Journal of Quantum Chemistry 115 (5) Mar 2015[Refereed]Journal of Computational Chemistry 36 (2) Jan 2015[Refereed]Physical Chemistry Chemical Physics 17 (9) 2015[Refereed]Cascade-type Massive Parallel Simulation for Protein Conformation Transition Pathway SearchProceedings of the Institute of Statistical Mathematics 62 (2) Dec 2014[Refereed]Journal of Computational Chemistry 35 (16) Jun 2014[Refereed]SEIBUTSU BUTSURI 54 (3) Mar 2014[Refereed]Hydration and Protein Stability under Molecular Crowding EnvironmentsBUSEEI KENKYU 53 Mar 2014[Refereed]The Journal of Chemical Physics 140 (12) Mar 2014[Refereed]International Conference of Computational Methods in Sciences and Engineering 2014 1618 2014[Refereed]The Journal of Chemical Physics 139 (3) Jul 2013[Refereed]Journal of the American Chemical Society 135 (9) Mar 2013[Refereed]SEIBUTSU BUTSURI 53 (4) Feb 2013[Refereed]Journal of the American Chemical Society 134 (10) Mar 2012[Refereed]The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed ComputingJournal of Chemical Theory and Computation 8 (1) Jan 2012[Refereed]The Journal of Physical Chemistry B 115 (27) Jul 2011[Refereed]Chemical Physics Letters 503 Feb 2011[Refereed]Awards & Honors
Jul 2026武田科学振興財団(ライフサイエンス研究助成)Jun 2026池谷科学技術振興財団 助成事業Oct 2025住友電工グループ 社会貢献基金Apr 2025豊田理化学研究所 豊田理研スカラー(Phase1)Oct 2024MOLSIS-CCG GRANTJun 2024UBE学術振興財団 援助金Jun 2024UBE学術振興財団 学術奨励賞Apr 2024G-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 2023Bulletin 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 2019Royal Society of Chemistry Physical Chemistry Chemical Physics Hot Article CollectionMar 2018日本化学会 進歩賞Sep 2017The 4th BIOPHYSICS Editors' Choice AwardNov 2016Bulletin 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
「異常アミノ酸配列」の探索・蓄積・学習により疾患予測を実現する革新的なAIモデルの開発ライフサイエンス研究助成 [代表] 原田 隆平 直接経費: 2,000千円Research period: Jul 2026 - Mar 2031生体分子内環境を模倣する計算モデルの開発と分子シミュレーションへの適用挑戦的研究(萌芽)[代表] 原田 隆平 直接経費: 5,000千円 間接経費: 1,500千円 課題番号: 26K23899Research period: Jul 2026 - Mar 2029ZIPタンパク質が駆動する亜鉛輸送メカニズムの解明令和8年度・JST次世代研究者挑戦的研究プログラム [代表] 小幡 昂諒 [直接経費] 1,500千円 [受入教員] 原田 隆平Research period: Apr 2026 - Mar 2029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 間接経費: 4,320千円 課題番号: 25K03214Research period: Apr 2025 - Mar 2029環状ペプチドの膜透過性を向上させる設計指針を提供する計算システムの開発池谷科学技術振興財団 助成事業 [代表] 原田 隆平 直接経費: 2,700千円 間接経費: 300千円Research period: Apr 2026 - Mar 2028PaCS-MD/OFLOOD等を用いた構造サンプリングResearch period: Oct 2026 - Sep 2027生体内環境におけるタンパク質の構造形成・修復メカニズムを解明する計算モデルの開発住友電工グループ 社会貢献基金 [代表] 原田 隆平 直接経費: 1,290千円Research period: Oct 2025 - Mar 2027In 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] 1,500千円 [受入教員] 原田 隆平Research period: Aug 2024 - Mar 2027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 2026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: 3,000千円 間接経費: 900千円Research period: Aug 2023 - Sep 2026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] 篠原 秀文, 原田 隆平 直接経費: 2,000千円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 2026Rubisco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, 深山 浩 直接経費: 4,900千円 間接経費: 1,470千円 課題番号: 23K18033Research 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] 森田 健太, 原田 隆平 直接経費: 2,000千円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: 21K06094Research 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 2020G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: 16H06164Research 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: 15J03797Research 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: 26840056Research period: Apr 2014 - Mar 2016
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氏名 | |
| Name | Kowit Hengphasatporn | |
| Faculty | ||
| Section | ||
| Position | Assistant Professor | |
| Theme | Molecular modeling and Structure-based virtual screening on the biological systems | |
| Related Links | ||
kowith ccs.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Apr 2022-PresentCenter for Computational Sciences, University of TsukubaSep 2019-Mar 2022Center for Computational Sciences, University of TsukubaPublished Papers
Journal of Molecular Structure Dec 2026[Refereed]Dual-target inhibitors against α-amylase and α-glucosidase: novel anacardic acid depside derivativesBioorganic Chemistry Oct 2026[Refereed]Journal of Cheminformatics Sep 2026[Refereed]ACS Omega Sep 2026[Refereed]Journal of Chemical Information and Modeling Aug 2026[Refereed]Journal of Pharmacological and Toxicological Methods Aug 2026[Refereed]Journal of the American Chemical Society Jun 2026[Refereed]Journal of Agricultural and Food Chemistry Jun 2026[Refereed]Nature Chemistry Apr 2026[Refereed]Physical Chemistry Chemical Physics Apr 2026[Refereed]Carbon Energy Mar 2026[Refereed]Nature Communications Mar 2026[Refereed]Journal of Chemical Information and Modeling Feb 2026[Refereed]The Journal of Physical Chemistry B Jan 2026[Refereed]Scientific Reports Jan 2026[Refereed]Protein Science Jan 2026[Refereed]International Journal of Molecular Sciences Dec 2025[Refereed]Emerging microbes & infections 14 (1) Dec 2025[Refereed]mAbs 17 (1) Dec 2025[Refereed]Scientific Reports Nov 2025[Refereed]ACS Omega Nov 2025[Refereed]Computational and Structural Biotechnology Journal Nov 2025[Refereed]Protein Science Nov 2025[Refereed]Pharmaceuticals Oct 2025[Refereed]Separation and Purification Technology Oct 2025[Refereed]Journal of proteome research Sep 2025[Refereed]Proceedings of the National Academy of Sciences 122 (36) Sep 2025[Refereed]iScience Aug 2025[Refereed]Journal of Chemical Information and Modeling Jul 2025[Refereed]The Journal of Physical Chemistry Letters Jun 2025[Refereed]Science of The Total Environment 976 May 2025[Refereed]The journal of physical chemistry. B May 2025[Refereed]Scientific reports 15 (1) Apr 2025[Refereed]Proceedings of the National Academy of Sciences of the United States of America 122 (16) Apr 2025[Refereed]Journal of Chemical Theory and Computation Apr 2025[Refereed]Computational Biology and Chemistry Apr 2025[Refereed]Scientific reports 15 (1) Feb 2025[Refereed]ACS Omega Feb 2025[Refereed]Nature Communications Jan 2025[Refereed]Journal of Computer Chemistry, Japan 24 (1) 2025Phytomedicine Plus Jan 2025[Refereed]International Journal of Biological Macromolecules Jan 2025[Refereed]Journal of Medicinal Chemistry Dec 2024[Refereed]Cancer Science Nov 2024[Refereed]ACS Bio & Med Chem Au Oct 2024[Refereed]Computational Biology and Chemistry Oct 2024[Refereed]The Journal of Physical Chemistry B Sep 2024[Refereed]Bioorganic & Medicinal Chemistry Letters Sep 2024[Refereed]Heliyon Jun 2024[Refereed]The Journal of Physical Chemistry Letters May 2024[Refereed]ChemistrySelect Mar 2024[Refereed]Scientific reports 14 (1) Feb 2024[Refereed]Journal of Computational Chemistry Jan 2024[Refereed]Bioorganic chemistry 143 Dec 2023[Refereed]Emerging Microbes & Infections Dec 2023[Refereed]Nature communications 14 (1) Dec 2023[Refereed]Antiviral research 220 Dec 2023[Refereed]RSC Advances 13 (46) Nov 2023[Refereed]Scientific reports 13 (1) Nov 2023[Refereed]Journal of Chemical Information and Modeling Aug 2023[Refereed]Bulletin of the Chemical Society of Japan 96 (7) Jul 2023[Refereed]ACS Omega 8 (29) Jul 2023[Refereed]Journal of Agricultural and Food Chemistry 71 (24) Jun 2023[Refereed]ACS Omega Jun 2023[Refereed]PeerJ 11 Apr 2023[Refereed]Scientific Reports 13 (1) Apr 2023[Refereed]Journal of Computer Chemistry, Japan 21 (4) Mar 2023[Refereed]FEBS Journal Feb 2023[Refereed]Molecules 28 (3) Feb 2023[Refereed]Molecules 28 (3) Feb 2023[Refereed]Scientific Reports 12 (1) Dec 2022[Refereed]Scientific Reports 12 (1) Dec 2022[Refereed]ACS Omega 7 (37) Sep 2022[Refereed]Chemical Communications 58 (67) Jul 2022[Refereed]Molecules 27 (9) May 2022[Refereed]Journal of Chemical Information and Modeling 62 (6) Mar 2022[Refereed]Journal of Computer Chemistry, Japan 21 (4) 2022[Refereed]Communications Chemistry 4 (1) Dec 2021[Refereed]Chemistry Letters 50 (12) Dec 2021[Refereed]Alkyne-tagged apigenin, a chemical tool to navigate potential targets of flavonoid anti-dengue leadsMolecules 26 (22) Nov 2021[Refereed]Bulletin of the Chemical Society of Japan 94 (7) Jul 2021[Refereed]Computational and Structural Biotechnology Journal 19 Jan 2021[Refereed]Journal of Physical Chemistry B 124 (51) Dec 2020[Refereed]Molecules 25 (18) Sep 2020[Refereed]Biochemistry 59 (18) May 2020[Refereed]Molecules 25 (8) Apr 2020[Refereed]Scientia Pharmaceutica 88 (1) Mar 2020[Refereed]Chemistry Letters 49 (3) 2020[Refereed]Journal of Molecular Liquids 274 Jan 2019[Refereed]Scientific Reports 8 (1) Dec 2018[Refereed]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 2028FMO/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 2027Novel signal regulation by G protein supersulfidation and its physiological roleGrants-in-Aid for Scientific ResearchResearch period: Sep 2021 - Mar 2026
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氏名 | IVONINA MARIIA |
| Name | IVONINA MARIIA | |
| Faculty | ||
| Section | ||
| Position | Assistant Professor | |
| Theme | Molecular dynamics and quantum chemistry simulations of biomolecules | |
| Related Links | ||
ivonina.mariia.gp u.tsukuba.ac.jp |
|
氏名 | 段 練 |
| Name | DUAN LIAN | |
| Faculty | ||
| Section | ||
| Position | Assistant Professor | |
| Theme | ||
| Related Links | ||
duanlian ccs.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Published Papers
ACS Applied Materials & Interfaces in press May 2026[Refereed]Carbon Energy Mar 2026[Refereed]Nature Communications Mar 2026[Refereed]JOURNAL OF CHEMICAL INFORMATION AND MODELING Feb 2026[Refereed]Journal of Chemical Information and Modeling Jul 2025[Refereed]Science of The Total Environment 976 May 2025[Refereed]Journal of Chemical Theory and Computation Apr 2025[Refereed]Scientific Reports 15 (1) Feb 2025[Refereed]ACS Omega 10 (7) Feb 2025[Refereed]Journal of Medicinal Chemistry 67 (24) Dec 2024[Refereed]Journal of Physical Chemistry B 128 (38) Sep 2024[Refereed]Bioorganic and Medicinal Chemistry Letters 110 Sep 2024[Refereed]Nature Communications 14 (1) Dec 2023[Refereed]Chemistry Letters 51 (7) Jul 2022[Refereed]Journal of Computer Chemistry, Japan 21 (4) 2022JOURNAL OF COMPUTER CHEMISTRY-JAPAN 20 (4) Mar 2021[Refereed]Smart Materials and Structures Oct 2019[Refereed]Awards & Honors
Books etc
Research Grants & Projects
|
氏名 | 齋藤 一弥 |
| Name | SAITO Kazuya | |
| Faculty | ||
| Section | ||
| Position | Researcher | |
| Theme | ||
| Related Links | ||
kazuya chem.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Apr 2024-PresentUniversity of Tsukuba Center for Computational Sciences ResearcherApr 2024-PresentUniversity of TsukubaApr 2025National Institute for Materials Science STAM/STAM Methods Editorial Office Publishing DirectorApr 2024-Mar 2025National Institute for Materials Science STAM office Editorial CoordinatorApr 2004-Mar 2024University of Tsukuba Graduate School of Pure and Applied Sciences ProfessorDec 1995-Mar 2004Osaka University Faculty of Science & Graduate School of Science Associate ProfessorJan 1987-Nov 1995Tokyo Metropolitan University Faculty of Science Research AssociateApr 1986-Dec 1986Research Laboratory of Enginearing Materials Tokyo Institute of Technology Technical AssistantPublished Papers
Europhysics Letters 155 (3) Jul 2026[Refereed]Langmuir Mar 2026[Refereed]The Journal of Chemical Physics 162 (21) Jun 2025[Refereed]Journal of Molecular Liquids 428 Jun 2025[Refereed]Physical Chemistry Chemical Physics 2025[Refereed]Physical Chemistry Chemical Physics 25 (26) Jun 2023[Refereed]Bulletin of the Chemical Society of Japan 96 (7) May 2023[Refereed]JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 92 (5) Apr 2023[Refereed]Journal of Solution Chemistry 53 (1) Feb 2023[Refereed]SOFT MATTER 19 (6) Jan 2023[Refereed]Spontaneous Formation of Cubic Phases: A Molecular Dynamics Study for Soft Repulsive SpherocylindersLiquid Crystals Jan 2023[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 25 (1) Dec 2022[Refereed]JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 91 (10) Oct 2022[Refereed]JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 91 (7) Jul 2022[Refereed]JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 90 (12) Dec 2021[Refereed]ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 60 (42) Oct 2021[Refereed]CHEMISTRY-A EUROPEAN JOURNAL 27 (40) Jul 2021[Refereed]CRYSTAL GROWTH & DESIGN 21 (5) May 2021[Refereed]Angewandte Chemie (International ed. in English) 60 (28) Mar 2021[Refereed]Langmuir 36 (48) Dec 2020[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 22 (42) Nov 2020[Refereed]MOLECULAR CRYSTALS AND LIQUID CRYSTALS 702 (1) May 2020Crystals 10 (5) Apr 2020[Refereed]Phys. Chem. Chem. Phys. 22 (10) Feb 2020[Refereed]MEMBRANE 45 (5) 2020Physical 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JOURNAL OF JAPANESE SCIENTISTS 54 (3) Mar 2019[Refereed]JOURNAL OF CHEMICAL PHYSICS 150 (6) Feb 2019[Refereed]Physical Chemistry Chemical Physics 21 (42) 2019Proceedings of Japanese Liquid Crystal Society Annual meeting 2019 2019Proceedings of Japanese Liquid Crystal Society Annual meeting 2019 2019Proceedings of Japanese Liquid Crystal Society Annual meeting 2019 2019J. Chem. Thermodyn. 131 Dec 2018[Refereed]Bulletin of the Chemical Society of Japan 91 (11) Nov 2018[Refereed]Chemistry Letters 47 (12) Nov 2018[Refereed]Proceedings of Japanese Liquid Crystal Society Annual meeting 2017 Jun 2018Proceedings of Japanese Liquid Crystal Society Annual meeting 2017 Jun 2018Journal of Polymer Science, Part A: Polymer Chemistry 56 (10) May 2018[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 20 (8) Feb 2018[Refereed]Bulletin of the Chemical Society of Japan 91 (4) 2018[Refereed]Bulletin of the Chemical Society of Japan 91 (11) 2018Proceedings of Japanese Liquid Crystal Society Annual meeting 2018 2018Meeting Abstracts of the Physical Society of Japan 73 2018Meeting Abstracts of the Physical Society of Japan 73 2018Physical chemistry chemical physics : PCCP 19 (37) Sep 2017[Refereed]Physical chemistry chemical physics : PCCP 19 (37) Sep 2017[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 19 (29) Aug 2017[Refereed]JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 86 (8) Aug 2017[Refereed]JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 86 (8) Aug 2017[Refereed]Physical chemistry chemical physics : PCCP 19 (29) Jul 2017[Refereed]CHEMICAL PHYSICS LETTERS 673 Apr 2017[Refereed]Biochemistry 56 (9) Mar 2017[Refereed]Journal of Physical Chemistry B 121 (6) Feb 2017[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 121 (6) Feb 2017[Refereed]Meeting Abstracts of the Physical Society of Japan 72 2017Meeting Abstracts of the Physical Society of Japan 72 2017Meeting Abstracts of the Physical Society of Japan 72 2017Meeting Abstracts of the Physical Society of Japan 72 2017Meeting Abstracts of the Physical Society of Japan 72 2017Proceedings of Japanese Liquid Crystal Society Annual meeting 2017 2017Proceedings of Japanese Liquid Crystal Society Annual meeting 2017 2017ACS APPLIED MATERIALS & INTERFACES 8 (43) Nov 2016[Refereed]JOURNAL OF SOLUTION CHEMISTRY 45 (11) Nov 2016[Refereed]LANGMUIR 32 (30) Aug 2016[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18 (26) Jul 2016[Refereed]LANGMUIR 32 (23) Jun 2016[Refereed]Physical Chemistry Chemical Physics 18 (13) Apr 2016[Refereed]JOURNAL OF CHEMICAL PHYSICS 144 (4) Jan 2016[Refereed]Physical Chemistry Chemical Physics 18 (4) Jan 2016[Refereed]Proceedings of Japanese Liquid Crystal Society Annual meeting 2016 2016Proceedings of Japanese Liquid Crystal Society Annual meeting 2016 2016Proceedings of Japanese Liquid Crystal Society Annual meeting 2016 2016Proceedings of Japanese Liquid Crystal Society Annual meeting 2016 2016Meeting Abstracts of the Physical Society of Japan 71 2016PA58 Molecular diffusion in SmE phase studied by fluorescence recovery after photobreachingProceedings of Japanese Liquid Crystal Society Annual meeting (2015) Sep 2015BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 88 (7) Jul 2015Journal of Chemical Physics 142 (17) May 2015CHEMISTRY AND PHYSICS OF LIPIDS 188 May 201522pPSA-8 Possible effect of entropy gain by ions on aggregation of charged phospholipid membranesMeeting Abstracts of the Physical Society of Japan 70 (1) Mar 2015JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 84 (3) Mar 2015LIQUID CRYSTALS 42 (2) Feb 2015[Refereed]Proceedings of Japanese Liquid Crystal Society Annual meeting 2015 2015Proceedings of Japanese Liquid Crystal Society Annual meeting 2015 2015Proceedings of Japanese Liquid Crystal Society Annual meeting 2015 2015Proceedings of Japanese Liquid Crystal Society Annual meeting 2015 2015Meeting Abstracts of the Physical Society of Japan 70 2015Meeting Abstracts of the Physical Society of Japan 70 2015SOFT MATTER 11 (43) 2015[Refereed]JOURNAL OF PHYSICAL CHEMISTRY C 118 (48) Dec 2014[Refereed]熱量測定のこれからにむけて熱測定 41 (4) Nov 2014[Refereed]LANGMUIR 30 (35) Sep 2014Calorimetric Studies on Quasi-One-Dimensional MMX Complexes, M2(RCS2)4ICurr. Inorg. Chem. 4 (2) Sep 2014[Refereed]CHEMISTRY LETTERS 43 (8) Aug 2014[Refereed]THERMOCHIMICA ACTA 590 Aug 201410aAM-5 Nonlinear Force Acting on Defect and Director Field near Air-Liquid Crystal InterfaceMeeting abstracts of the Physical Society of Japan 69 (2) Aug 20148pPSB-13 Effect of n-alkane on the gel/liquid-crystalline phase transition of lipid bilayersMeeting abstracts of the Physical Society of Japan 69 (2) Aug 2014LIQUID CRYSTALS 41 (7) Jul 2014[Refereed]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液晶 18 (2) Apr 2014[Refereed]JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 83 (4) Apr 2014[Refereed]30pAC-7 Effects of monovalent salts on interactions between neutrally charged lipid membranesMeeting abstracts of the Physical Society of Japan 69 (1) Mar 2014Proceedings of Japanese Liquid Crystal Society Annual meeting 2014 2014Proceedings of Japanese Liquid Crystal Society Annual meeting 2014 2014Proceedings of Japanese Liquid Crystal Society Annual meeting 2014 2014Dynamics and Phase Transitions of 4-Bromobenzylidene-4 '-pentyloxyaniline and 4-Bromobenzylidene-4 '-hexyloxyaniline as Studied by Dielectric SpectroscopyACTA PHYSICA POLONICA A 124 (6) Dec 2013[Refereed]AMERICAN MINERALOGIST 98 (10) Oct 2013On Aggregation Structure of Smectic Phases日本液晶学会討論会講演予稿集 (2013) Sep 2013BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 86 (9) Sep 2013CHEMISTRY LETTERS 42 (9) Sep 2013JOURNAL OF CHEMICAL PHYSICS 139 (11) Sep 2013日本液晶学会討論会講演予稿集 2013 (2013) Sep 2013日本液晶学会討論会講演予稿集 2013 (2013) Sep 2013Effects of monovalent ions on interactions between neutral lipid membranesMeeting abstracts of the Physical Society of Japan 68 (2) Aug 2013JOURNAL 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Netsu Sokutei 40 (3) Jul 2013[Refereed]Anisotropic josephson-vortex dynamics in layered organic superconductor with d-wave pairing symmetryJournal of the Physical Society of Japan 82 (6) Jun 2013Bulletin of the Chemical Society of Japan 86 (5) 2013Report of the Discussion Meeting on "Blue Phase"液晶 : 日本液晶学会誌 = Ekisho 16 (4) Oct 2012JOURNAL 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)Biophysics 52 (1) Aug 2012Awards & Honors
May 2023Institute of Nuclear Physics, Polish Academy of Sciences Honorary ProfessorSep 2016The Japanese Liquid Crystal Society Award for excellent work Clarification of LC structure through thermodynamic studyAug 2012The Japan Society of Calorimetry and Thermal Analysis The Japan Society of Calorimetry and Thermal Analysis AwardJun 2011The Calorimetry Conference James J. Christensen Memorial AwardBooks etc
Instrumental Analysis of Coordination Compounds: Volume 1(Role:Contributor, Chapter 5 Calorimetry and Thermal Analysis)Gibbs Energy and Helmholtz Energy Liquids, Solution and Vapours( Stability of Real Liquid Crystals)化学便覧 基礎編 改訂6版Chemical Physics of Molecular Condensed Matter(Role:Sole author)現代化学序説(Role:Sole author)日本の結晶学(II) -輝かしき発展-(Role:Contributor, 結晶中の分子運動の相関)熱分析(Role:Contributor, 熱分析)熱量測定・熱分析ハンドブック 第2版(Role:Edit)Comprehensive Handbook of Calorimetry and Thermal Analysis(Role:Edit)Research Grants & Projects
3D-Order Formation Involving Meso-Hierarchy Brought by EntropyGrants-in-Aid for Scientific ResearchResearch period: Apr 2024 - Mar 2026Molecular Mechanism of Gyroid Formation by Small Mesogenic MoleculesGrants-in-Aid for Scientific ResearchResearch 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 2023Study of dynamic and molecular basis of gyroid formationGrants-in-Aid for Scientific ResearchResearch period: Apr 2020 - Mar 2022Crystallization and glass transition of liquid crystalsGrants-in-Aid for Scientific ResearchResearch period: Apr 2020 - Mar 2021Crystallization and glass transition of liquid crystals under negative to high pressureGrants-in-Aid for Scientific ResearchResearch period: Nov 2018 - Mar 2020Molecular Design for Low Molecular Mass Bicontinuous Cubic Liquid CrystalsGrants-in-Aid for Scientific ResearchResearch period: Apr 2016 - Mar 2019Structure and Glass Transition of Liquids of Globular AggregatesGrants-in-Aid for Scientific ResearchResearch period: Apr 2016 - Mar 2018Study of Structure and Dynamics of Thermotropics Based on Quasi-Binary PictureGrants-in-Aid for Scientific ResearchResearch period: Apr 2014 - Mar 2017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 2016Precision measurement of dependence of two-phase coexistence temperature on non-equilibriumness aiming at assessment of a possible steady-state thermodynamicsGrants-in-Aid for Scientific ResearchResearch period: Apr 2012 - Mar 2015Towards Unified Understanding of Thermotropic and Lyotropic Liquid CrystalsGrants-in-Aid for Scientific ResearchResearch period: 2010 - 2012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 - 2009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 - 2008異方性固体の反応速度論科学研究費助成事業Research period: 2006 - 2007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 - 2006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 - 2005Formation Mechanism of Triply Periodic Minimal Surface as a Thermodynamic Equilibrium StructureGrants-in-Aid for Scientific ResearchResearch period: 2003 - 2005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 - 2002Thermal properties of optically isotropic liquid crystalsGrants-in-Aid for Scientific ResearchResearch period: 1999 - 2002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 - 2000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 - 1999Impurity Effect on a Structural Phase Transition Intermediate between the Order-Disorder and Displacive Types.Grants-in-Aid for Scientific ResearchResearch period: 1997 - 1998Aggregation mechanism and higher-order structures in soft matterResearch 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 - 1991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 - 1989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 - 1988THE INFRARED AND FAR-INFRARED POLARIZED REFLECTANCE SPECTRA OF ORGANIC CONDUCTORS. MICROSPECTOROPHOTOMETORIC STUDYGrants-in-Aid for Scientific ResearchResearch period: 1986 - 1988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 - 1987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 - 1987Properties of organic/Low-dimensional conductorsResearch period: Jan 1987Molecular dynamics in crystal and phase transitionResearch period: Apr 1986
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氏名 | Manussada Ratanasak |
| Name | Manussada Ratanasak | |
| Faculty | ||
| Section | ||
| Position | Researcher | |
| Theme | Catalyst Design, QSAR/QSPR, DFT Calcula2ons, QM/MM, Reac2on Mechanism | |
| Related Links | ||
manussada ccs.tsukuba.ac.jp |
Academic & Professional Experience
Mar 2016Ph.D. Program in Nanoscience and Technology (Interna2onal Program), Graduate School, Chulalongkorn University, Bangkok, ThailandApr 2016-Apr 2024Hasegawa Group, Ins2tute for Catalysis, Hokkaido University, Japan Postdoctoral ResearcherPublished Papers
J. Org. Chem. doi: 10.1021/acs.joc.2c01576 [Refereed]New Journal of Chemistry
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氏名 | 広川 貴次 |
| Name | HIROKAWA Takatsugu | |
| Faculty | Faculty of Medicine | |
| Section | ||
| Position | Professor (Collaborative Fellow) | |
| Theme | ||
| Related Links | ||
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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 | ||
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氏名 | 八木 清 |
| Name | YAGI Kiyoshi | |
| Faculty | Department of Chemistry, Institute of Pure and Applied Sciences | |
| Section | ||
| Position | Professor (Collaborative Fellow) | |
| Theme | Molecular Vibrational Theory, QM/MM calculations | |
| Related Links | ||
kiyoshi.yagi chem.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Aug 2024-PresentUniversity of Tsukuba Department of Chemistry, Institute of Pure and Applied Sciences ProfessorApr 2015-Jul 2024RIKEN Theoretical Molecular Science Laboratory Senior Research ScientistDec 2012-Mar 2015RIKEN Theoretical Molecular Science Laboratory Research ScientistApr 2011-Nov 2012University of Illinois at Urbana-Champaign Department of Chemistry Visiting Research Assistant ProfessorApr 2009-Apr 2011University of Yamanashi Fuel Cell Nanomaterials Center LecturerMar 2005-Mar 2009Univeristy of Tokyo School of Engineering, Department of Applied Chemistry Assistant ProfessorApr 2004-Feb 2005JSPS Postdoctoral Research Associate Department of Basic Science, The University of TokyoPublished Papers
The Journal of Physical Chemistry B 130 (22) May 2026[Refereed]Journal of Chemical Theory and Computation 21 (8) Apr 2025[Refereed]Journal of Chemical Theory and Computation 21 (5) Mar 2025[Refereed]The Journal of Physical Chemistry B 128 (25) Jun 2024[Refereed]Journal of the American Chemical Society 144 (43) Oct 2022[Refereed]Nature Communications 12 Oct 2021[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 125 (18) May 2021[Refereed]JOURNAL OF MEMBRANE SCIENCE 596 Feb 2020[Refereed]Journal of Chemical Theory and Computation 15 (3) Mar 2019[Refereed]JOURNAL OF CHEMICAL PHYSICS 140 (8) Feb 2014[Refereed]JOURNAL OF CHEMICAL PHYSICS 137 (20) Nov 2012[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 10 (13) 2008[Refereed]THEORETICAL CHEMISTRY ACCOUNTS 118 (3) Sep 2007[Refereed]JOURNAL OF CHEMICAL PHYSICS 121 (3) Jul 2004[Refereed]JOURNAL OF CHEMICAL PHYSICS 113 (3) Jul 2000[Refereed]The Journal of Chemical Physics 160 Jun 2024[Refereed]Physical Chemistry Chemical Physics 26 (13) 2024[Refereed]JOURNAL OF CHEMICAL PHYSICS 158 (11) Mar 2023[Refereed]Journal of the American Chemical Society 144 (43) Oct 2022[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 126 (17) May 2022[Refereed]量子化学と分子動力学の融合が拓く高分子の分子機能解析溶液化学研究会誌 Apr 2022[Refereed]非調和振動計算プログラムSINDOの紹介分子シミュレーション学会誌 「アンサンブル」 24 Apr 2022[Refereed]CURRENT OPINION IN STRUCTURAL BIOLOGY 72 Feb 2022[Refereed]複雑分子系の振動計算:現状と展望日本分光学会会誌「分光研究」トピックス 2022[Refereed]FRONTIERS IN MOLECULAR BIOSCIENCES 8 Dec 2021[Refereed]Nature Communications 12 Oct 2021[Refereed]Journal of Chemical Theory and Computation 17 (8) Jul 2021[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 125 (18) May 2021[Refereed]JOURNAL OF MEMBRANE SCIENCE 596 Feb 2020[Refereed]Weight Averaged Anharmonic Vibrational Calculations: Applications to Polypeptide, Lipid Bilayers, and Polymer MaterialsMolecular Spectroscopy: A Quantum Chemistry Approach 1 Sep 2019[Refereed]Journal of Chemical Theory and Computation 15 (3) Mar 2019[Refereed]Physical Chemistry Chemical Physics 20 (5) Feb 2018[Refereed]Fragmentation: Toward Accurate Calculations on Complex Molecular Systems 1 Sep 2017[Refereed]PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 (37) Sep 2017[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 121 (24) Jun 2017[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 121 (12) Mar 2017[Refereed]CHEMICAL PHYSICS 482 Jan 2017[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 120 (39) Oct 2016[Refereed]BIOPHYSICAL JOURNAL 111 (5) Sep 2016[Refereed]Molecular Science 10 (1) 2016[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (43) 2015[Refereed]CHEMICAL PHYSICS LETTERS 610 Aug 2014[Refereed]JOURNAL OF CHEMICAL PHYSICS 140 (15) Apr 2014[Refereed]JOURNAL OF CHEMICAL PHYSICS 140 (8) Feb 2014[Refereed]Seibutsu Butsuri 54 (1) 2014Seibutsu Butsuri 54 (1) 2014CHEMICAL PHYSICS 419 Jun 2013[Refereed]CHEMICAL PHYSICS 419 Jun 2013[Refereed]JOURNAL OF CHEMICAL PHYSICS 138 (7) Feb 2013[Refereed]JOURNAL OF PHYSICAL CHEMISTRY C 117 (8) Feb 2013[Refereed]JOURNAL OF PHYSICAL CHEMISTRY LETTERS 3 (23) Dec 2012[Refereed]JOURNAL OF CHEMICAL PHYSICS 137 (20) Nov 2012[Refereed]“Progress in Theoretical Chemistry and Physics" Quantum Systems in Chemistry and Physics 26 Oct 2012[Refereed]ASTROPHYSICAL JOURNAL 758 (1) Oct 2012[Refereed]非調和性を考慮した赤外・近赤外スペクトルの第1原理計算分光研究 61 2012[Refereed]量子化学計算に基づく分子振動スペクトルの第一原理計算分子シミュレーション研究会会誌“アンサンブル 14 (1) 2012[Refereed]ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 63 63 2012[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 114 (34) Sep 2010[Refereed]JOURNAL OF CHEMICAL PHYSICS 133 (3) Jul 2010[Refereed]JOURNAL OF CHEMICAL PHYSICS 133 (3) Jul 2010[Refereed]RECENT ADVANCES IN SPECTROSCOPY: THEORETICAL, ASTROPHYSICAL AND EXPERIMENTAL PERSPECTIVES 2010[Refereed]CHEMICAL PHYSICS LETTERS 483 (1-3) Nov 2009[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 113 (45) Nov 2009[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 109 (9) Aug 2009[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 109 (10) Aug 2009[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 109 (10) Aug 2009[Refereed]CHEMPHYSCHEM 10 (9-10) Jul 2009[Refereed]MOLECULAR PHYSICS 107 (8-12) 2009[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 112 (40) Oct 2008[Refereed]CHEMICAL PHYSICS LETTERS 464 (4-6) Oct 2008[Refereed]JOURNAL OF CHEMICAL PHYSICS 128 (21) Jun 2008[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 10 (13) 2008[Refereed]THEORETICAL CHEMISTRY ACCOUNTS 118 (3) Sep 2007[Refereed]CHEMICAL PHYSICS LETTERS 443 (1-3) Jul 2007[Refereed]JOURNAL OF CHEMICAL PHYSICS 127 (3) Jul 2007[Refereed]JOURNAL OF CHEMICAL PHYSICS 126 (12) Mar 2007[Refereed]CHEMICAL PHYSICS LETTERS 436 (1-3) Feb 2007[Refereed]JOURNAL OF CHEMICAL PHYSICS 125 (1) Jul 2006[Refereed]JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 128 (21) May 2006[Refereed]JOURNAL OF CHEMICAL PHYSICS 124 (6) Feb 2006[Refereed]JOURNAL OF CHEMICAL PHYSICS 123 (22) Dec 2005[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 104 (5) Sep 2005[Refereed]CHEMICAL PHYSICS LETTERS 397 (4-6) Oct 2004[Refereed]JOURNAL OF CHEMICAL PHYSICS 121 (3) Jul 2004[Refereed]JOURNAL OF CHEMICAL PHYSICS 120 (22) Jun 2004[Refereed]JOURNAL OF CHEMICAL PHYSICS 120 (11) Mar 2004[Refereed]JOURNAL OF CHEMICAL PHYSICS 119 (1) Jul 2003[Refereed]JOURNAL OF CHEMICAL PHYSICS 118 (4) Jan 2003[Refereed]JOURNAL OF CHEMICAL PHYSICS 116 (10) Mar 2002[Refereed]JOURNAL OF CHEMICAL PHYSICS 115 (23) Dec 2001[Refereed]JOURNAL OF CHEMICAL PHYSICS 113 (3) Jul 2000[Refereed]Awards & Honors
Mar 2022RIKEN RIKEN Eiho AwardSep 2015Japan Society for Molecular Science Young Scientists Award Development of Molecular Vibrational Structure Theory with an Explicit Account of AnharmonicityBooks etc
Research Grants & Projects
高速QM/MM自由エネルギー計算法の開発と新規蛍光プローブの分子設計科学研究費助成事業Research period: Apr 2024 - Mar 2027Reaction dynamics of light-driven proteins studied by non-adiabatic QM/MM molecular dynamicsGrants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)Research period: Apr 2022 - Mar 2024Novel molecular design of flourophores by QM/MM molecular dynamics simulationsGrants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)Research period: Apr 2020 - Mar 2023Molecular Science of NO Dyanmics in Biological SystemGrants-in-Aid for Scientific ResearchResearch period: May 2014 - Mar 2019生体分子系に対する振動状態理論の開発と応用新学術領域研究(研究領域提案型)Research period: Apr 2016 - Mar 2018非調和振動理論の新しい展開-水素結合クラスターへの応用特定領域研究 (公募班)Research period: Apr 2010 - Apr 2010水クラスターアニオンの生成機構に対する理論的研究若手研究(B)Research period: Apr 2009 - Apr 2010振動ダイナミクスの新しい理論と水素結合系への応用特定領域研究 (公募班)Research period: Apr 2008 - Mar 2010第一原理に基づく電子・原子系の反応過程に対する理論開発と応用科学研究費助成事業Research period: 2004 - 2006第一原理に基づくポテンシャル曲面生成とダイナミックス科学研究費助成事業Research period: 2001 - 2003
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氏名 | 松井 亨 |
| Name | MATSUI Toru | |
| Faculty | ||
| Section | ||
| Position | Associate Professor (Collaborative Fellow) | |
| Theme | ||
| Related Links | ||
matsui chem.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Published Papers
Chemical Physics Letters 898 Nov 2026Journal of Chemical Theory and Computation 22 (16) Aug 2026JOURNAL OF PHYSICAL CHEMISTRY A 130 Apr 2026[Refereed]ACS OMEGA 11 (2) Jan 2026[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 130 Apr 2026[Refereed]ACS OMEGA 11 (2) Jan 2026[Refereed]Growth inhibitory factor/metallothionein-3 is a sulfane sulfur-binding proteineLife 12 May 2025[Refereed]The Journal of University Admissions Research 35 Mar 2025[Refereed]Gold (I)-catalyzed [2+ 2] and [3+ 2] cycloadditions of 1, 1-difluoroallenes with aldehydes: Switchable syntheses of fluorinated oxetanes and furansOrganic Letters 27 (15) Jan 2025[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 26 (28) Jun 2024[Refereed]高等学校における観点別学習状況の評価と高大接続 ―先進県と茨城県内高等学校への聞き取り調査から―国立大学入学者選抜研究連絡協議会 大学入試研究ジャーナル (34) Mar 2024[Refereed]MENDELEEV COMMUNICATIONS 34 (1) Jan 2024[Refereed]Chemistry Letters 53 (1) Dec 2023Journal of Chemical Theory and Computation 19 (19) Sep 2023BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 96 (3) Mar 2023[Refereed]JOURNAL OF COMPUTATIONAL CHEMISTRY 43 (22) Aug 2022[Refereed]J 4 (4) Dec 2021Bulletin of the Chemical Society of Japan 94 (7) Jul 2021ACS Omega 6 (20) May 2021Journal of Computer Chemistry, Japan 18 (5) Mar 2020[Refereed]BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 93 (5) 2020[Refereed]Chemistry Letters 49 (3) 2020Molecules (Basel, Switzerland) 24 (4) Feb 2019[Refereed]Journal of Computer Chemistry, Japan 18 (5) 2019A Theoretical Study on Redox Potential and pK(a) of [2Fe-25] Cluster Model from Iron-Sulfur ProteinsBULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 91 (9) Sep 2018[Refereed]Physical chemistry chemical physics : PCCP 20 (43) Aug 2018[Refereed]Physical chemistry chemical physics : PCCP 20 (43) Aug 2018[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 122 (29) Jul 2018[Refereed]大学入学者選抜実施要項とその変遷に関する考察―新制大学発足時から大学共通第1次学力試験導入までを中心に―大学入試研究ジャーナル (28) Mar 2018[Refereed]Chemical Physics Letters 693 Feb 2018[Refereed]POLYHEDRON 136 Nov 2017[Refereed]JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13 (10) Oct 2017[Refereed]Journal of chemical theory and computation 13 (10) Sep 2017[Refereed]BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 90 (2) Feb 2017[Refereed]CHEMISTRY & EDUCATION 65 (7) 2017CHEMISTRY LETTERS 45 (6) Jun 2016[Refereed]Journal of Computer Chemistry, Japan 15 (5) 2016Journal of Physical Chemistry B 119 (17) Apr 2015[Refereed]第一原理計算によるタンパク質のpK_aと構造機能相関日本物理学会講演概要集 70 (1) Mar 201521aAF-5 Theoretical prediction of pKa values of amino acids using 3D-RISM-SCF日本物理学会講演概要集 70 (1) Mar 2015JOURNAL OF PHYSICAL CHEMISTRY A 119 (2) Jan 2015[Refereed]INORGANIC CHEMISTRY FRONTIERS 2 (8) 2015[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 114 (17) Sep 2014[Refereed]JOURNAL OF PHYSICAL CHEMISTRY LETTERS 5 (7) Apr 2014[Refereed]POLYHEDRON 66 Dec 2013[Refereed]Seibutsu Butsuri 53 (1) 2013International Journal of Quantum Chemistry 113 (3) 2013[Refereed]JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (1) Jan 2013[Refereed]DALTON TRANSACTIONS 42 (45) 2013[Refereed]Progress in Theoretical Chemistry and Physics 26 Oct 2012[Refereed]BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 85 (4) Apr 2012[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 116 (4) Feb 2012[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 14 (12) 2012[Refereed]ADVANCES IN THE THEORY OF QUANTUM SYSTEMS IN CHEMISTRY AND PHYSICS 22 2012[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 115 (30) Aug 2011[Refereed]CHEMICAL PHYSICS LETTERS 507 (1-3) Apr 2011[Refereed]BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 84 (4) Apr 2011[Refereed]Seibutsu Butsuri 51 (supplement) 2011CHEMICAL PHYSICS LETTERS 502 (4-6) Jan 2011[Refereed]BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 83 (12) Dec 2010[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 110 (12) Oct 2010[Refereed]JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 954 (1-3) Aug 2010[Refereed]CHEMICAL PHYSICS LETTERS 495 (1-3) Jul 2010[Refereed]CHEMICAL PHYSICS 368 (1-2) Feb 2010[Refereed]International Journal of Quantum Chemistry 110 (15) 2010[Refereed]PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12 (4) 2010[Refereed]Estimation of Effective Exchange Integral Value of Polyradical Systems Based on the Band CalculationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 109 (15) Dec 2009[Refereed]Theoretical Studies on Chemical Bonding Between Cu(II) and Oxygen Molecule in Type 3 Copper ProteinsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 109 (15) Dec 2009[Refereed]JOURNAL OF PHYSICAL CHEMISTRY A 113 (52) Dec 2009[Refereed]Chemical Physics Letters 483 (1-3) Oct 2009[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 113 (38) Sep 2009[Refereed]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 109 (10) Aug 2009[Refereed]CHEMICAL PHYSICS LETTERS 478 (4-6) Aug 2009[Refereed]Polyhedron 28 (9-10) 2009[Refereed]Polyhedron 28 (9-10) 2009[Refereed]Electronic structure and UV absorption spectra of metal-mediate DNA: an approach from theoretical chemistry.Nucleic acids symposium series (2004) (53) 2009[Refereed]ADVANCES IN THE THEORY OF ATOMIC AND MOLECULAR SYSTEMS: DYNAMICS, SPECTROSCOPY, CLUSTERS, AND NANOSTRUCTURES 20 2009[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 112 (51) Dec 2008[Refereed]BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 81 (10) Oct 2008[Refereed]JOURNAL OF PHYSICAL CHEMISTRY B 111 (5) Feb 2007[Refereed]Nucleic acids symposium series (2004) (51) 2007CHEMICAL PHYSICS LETTERS 423 (4-6) Jun 2006[Refereed]Awards & Honors
Books etc
Research Grants & Projects
Development of pKa estimation scheme for polar amino acids considering protein conformational fluctuationGrant-in-Aid for Scientific Research (C)Research period: Apr 2023 - Mar 2026A theoretical study for the improvement of solvation model by machine learningGrants-in-Aid for Scientific ResearchResearch period: Apr 2019 - Mar 2023Development of pKa estimation scheme for polar amino acids considering protein conformational fluctuationGrant-in-Aid for Scientific Research (C)Research period: Apr 2023 - Mar 2026A theoretical study for the improvement of solvation model by machine learningGrants-in-Aid for Scientific ResearchResearch period: Apr 2019 - Mar 2023Integrated Theoretical and Experimental Studies on Characteristic Photo-induced Properties of Novel Naphthalimide DerivativesGrants-in-Aid for Scientific ResearchResearch period: Apr 2017 - Mar 2021A Computational study on the correlation between out-of-plane mode of heme and redox potentialGrants-in-Aid for Scientific ResearchResearch period: Apr 2014 - Mar 2017人工核酸塩基を基盤としたナノマテリアルの理論設計科学研究費助成事業Research period: 2011 - 2013高精度電子移動理論による電気伝導性DNAの分子モデリング設計科学研究費助成事業Research period: 2008 - 2009
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氏名 | 岡澤 一樹 |
| Name | OKAZAWA Kazuki | |
| Faculty | Institute of Pure and Applied Sciences | |
| Section | ||
| Position | Assistant Professor (Collaborative) | |
| Theme | Theoretical studies on electron transports of π-conjugated molecules; Theoretical studies on self-assembly processes | |
| Related Links | ||
okazawa ccs.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Apr 2025-PresentUniversity of Tsukuba Faculty of Pure and Applied Sciences Assistant ProfessorApr 2024-Mar 2025University of Tsukuba Center for Computational Sciences Assistant ProfessorApr 2023-Mar 2024Japan Society for the Promotion of Science Research FellowApr 2022-Mar 2024Kyushu University Faculty of Engineering Sciences Research AssistantApr 2021-Mar 2023Kyushu UniversityPublished Papers
Chemical Science 17 (36) Aug 2026[Refereed]Monthly Notices of the Royal Astronomical Society 544 (4) Nov 2025[Refereed]npj Computational Materials 11 (1) Jul 2025[Refereed]Bulletin of Chemical Society of Japan 98 (5) May 2025[Refereed]The Journal of Organic Chemistry 90 (10) Mar 2025[Refereed]JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Epub Oct 2024[Refereed]Journal of the American Chemical Society Jul 2024Chemistry (Weinheim an der Bergstrasse, Germany) 29 (70) Dec 2023[Refereed]The Journal of Organic Chemistry Nov 2023ACS Omega 8 (33) Aug 2023The Journal of Physical Chemistry A Jun 2023Langmuir 39 (15) Apr 2023Reaction Chemistry & Engineering 8 (6) Mar 2023Small 19 (11) Jan 2023ACS Omega 7 (49) Nov 2022The Journal of Chemical Physics 156 (9) Mar 2022The Journal of Physical Chemistry C Feb 2022Journal of Physical Chemistry C 125 (7) 2021Journal of Physical Chemistry C 124 (5) 2020Journal of Photochemistry and Photobiology A: Chemistry 389 2020Journal of Physical Chemistry C 124 (42) 2020Journal of Physical Chemistry B 123 (40) 2019Awards & Honors
Jun 2025Chemical Society of Japan BCSJ Award Understanding the transition from reversed to conventional conductance decay in single-molecule wires from the effective Hamiltonian and frontier orbital perspectiveNov 2022日本化学会ケモインフォマティクス部会 第45回ケモインフォマティクス討論会 優秀ポスター賞Feb 2021九州大学工学府物質創造工学専攻 令和二年度修士課程最終試問会優秀発表賞 ヘテロ原子を含んだ単分子接合の伝導挙動に関するグラフ理論的研究Books etc
Research Grants & Projects
Creation of Heavier-Main-Group-Element Cyclic pi-Systems and Unraveling Their Electronic States to Transform Functional Molecular DesignGrants-in-Aid for Scientific ResearchResearch period: Apr 2026 - Mar 2031Theoretical Study on the Quantum Interference for Single-Molecule Junctions with the Stacked AromaticityGrants-in-Aid for Scientific ResearchResearch period: Apr 2025 - Mar 2028Theory of mesohierarchyGrants-in-Aid for Scientific ResearchResearch period: Apr 2023 - Mar 2028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 2025Theoretical study on the change of conduction properties of single-molecule junctions by oriented external electromagnetic fieldAcademic ChallengeResearch period: Apr 2021 - Mar 2022
Biological Science Group
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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 | ||
yuji ccs.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Apr 2016-PresentUniversity of Tsukuba Center for Computational SciencesPublished Papers
Evolution of form I-related RuBisCOs revisited: Uncertainties and diversity encompassing Bacteria and Archaea.bioRχiv Sep 2026Recent plastid replacement in Karlodinium ballantinum (Kareniaceae, Dinoflagellata) challenges the paradigms of endosymbiotic gene transfer.MOLECULAR BIOLOGY AND EVOLUTION 43 (7) Jul 2026[Refereed]The Journal of eukaryotic microbiology 73 (5) Apr 2026Morphology, ultrastructure, and classification of barthelonids (Metamonada incertae sedis): with description of Microbarthelona gen. nov., and Parabarthelona gen. nov.Journal of Eukaryotic Micobiology 73 (3) Apr 2026[Refereed]Colponemidia questions the ancestry of an ATG10-lacking ATG8$2013ATG12 conjugation system in Alveolata.Journal of Protistology 57 Apr 2026[Refereed]SSRN 181 Feb 2026A deeply branching lineage in Heterolobosea (Discoba) with multiflagellated and multigrooved life stages.Journal of Eukaryotic Micobiology 72 (5) Aug 2025[Refereed]Microorganisms 13 (8) Aug 2025[Refereed]Microbes and Environments 40 (2) Jun 2025[Refereed]Open Biology 15 (6) Jun 2025[Refereed]A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome.bioRχiv May 2025bioRχiv 72 (3) Mar 2025An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group.Molecular Phylogenetics and Evolution 204 Mar 2025[Refereed]bioRχiv Jan 2025IPSJ 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.月刊アグリバイオ 8 (12) Oct 2024Protist 175 (6) Oct 2024[Refereed]Is rdxPolA a piece of the ancient system for DNA maintenance in mitochondria?The Japanese Journal of Phycology (Sôrui) 72 (2) Jul 2024[Refereed]Scientific Reports 14 (1) Jun 2024[Refereed]PROTIST 174 (6) Dec 2023[Refereed]MICROBIOLOGY RESOURCE ANNOUNCEMENTS 12 (11) Nov 2023[Refereed]Molecular Biology and Evolution 41 (2) Aug 2023[Refereed]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月刊 細胞 55 (6) Apr 2023ENVIRONMENTAL POLLUTION 330 Apr 2023[Refereed]Microbiology Resource Announcements 12 (2) Feb 2023[Refereed]Frontiers in Ecology and Evolution 10 Dec 2022[Refereed]Frontiers in Microbiology 13 Aug 2022[Refereed]FRONTIERS IN PLANT SCIENCE 13 Jul 2022[Refereed]OPEN BIOLOGY 12 (4) Apr 2022[Refereed]Genome Biology and Evolution 13 (12) Dec 2021[Refereed]bioRχiv Aug 2021Parasitology International 83 Aug 2021[Refereed]Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids.Genome Biology and Evolution Jan 2021[Refereed]Frontiers in Marine Science 7 Oct 2020[Refereed]Proceedings of the Royal Society B 287 (1934) Sep 2020[Refereed]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.Frontiers in Ecology and Evolution May 2020[Refereed]Inventory and evolution of mitochondrion-localized family A DNA polymerases in Euglenozoa.Pathogens Apr 2020[Refereed]Proceedings of the National Academy of Sciences of the United States of America 117 (10) Mar 2020[Refereed]Genome Biology and Evolution 12 (2) Feb 2020[Refereed]bioRχiv Oct 2019Proceedings of the National Academy of Science of the United States of America 116 (32) Jun 2019[Refereed]ACS Omega 4 (4) Apr 2019[Refereed]Scientific Reports 9 Mar 2019[Refereed]Scientific Reports 8 (1) Dec 2018[Refereed]Journal of Eukaryotic Microbiology 65 (6) Sep 2018[Refereed]PeerJ 6 Jul 2018[Refereed]PLOS ONE 13 (7) Jul 2018[Refereed]PLoS ONE 13 (3) Mar 2018[Refereed]Genome Biology and Evolution 10 (2) Feb 2018[Refereed]SCIENTIFIC REPORTS 7 Oct 2017[Refereed]SCIENTIFIC REPORTS 7 Sep 2017[Refereed]MOLECULAR BIOLOGY AND EVOLUTION 34 (9) Sep 2017[Refereed]NATURE ECOLOGY & EVOLUTION 1 (4) Apr 2017[Refereed]GENES & GENETIC SYSTEMS 92 (1) Feb 2017[Refereed]Genes and Genetic Systems 92 (1) 2017[Refereed]GENOME BIOLOGY AND EVOLUTION 8 (10) Oct 2016[Refereed]Reference Module in Materials Science and Materials Engineering Jun 2016[Refereed]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.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?生物の科学 遺伝 70 (2) Mar 2016MOLECULAR BIOLOGY AND EVOLUTION 33 (1) Jan 2016[Refereed]PROCEEDINGS OF 2016 10TH INTERNATIONAL CONFERENCE ON COMPLEX, INTELLIGENT, AND SOFTWARE INTENSIVE SYSTEMS (CISIS) 2016[Refereed]PROTIST 166 (5) Nov 2015[Refereed]MOLECULAR BIOLOGY AND EVOLUTION 32 (10) Oct 2015[Refereed]SCIENTIFIC REPORTS 5 Aug 2015[Refereed]JOURNAL OF EUKARYOTIC MICROBIOLOGY 62 (4) Jul 2015[Refereed]PLOS ONE 10 (7) Jul 2015[Refereed]GENOME BIOLOGY AND EVOLUTION 7 (4) Apr 2015[Refereed]PHYCOLOGICAL RESEARCH 63 (1) Jan 2015[Refereed]Genome evolution triggered by acquisition of an endosymbiotic partnerGENES & GENETIC SYSTEMS 89 (6) Dec 2014PROCEEDINGS 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.BMC Research Notes 7 Jul 2014[Refereed]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.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.Mobile genetic elements 4 2014GENOME BIOLOGY AND EVOLUTION 6 (2) 2014[Refereed]BMC EVOLUTIONARY BIOLOGY 13 Jun 2013[Refereed]PLoS One 8 (3) 2013[Refereed]JOURNAL OF PLANT RESEARCH 125 (6) Nov 2012[Refereed]JOURNAL OF EUKARYOTIC MICROBIOLOGY 59 (4) Jul 2012[Refereed]Protist 163 (3) May 2012[Refereed]PLOS ONE 7 (5) May 2012[Refereed]EVOLUTIONARY BIOINFORMATICS 8 2012[Refereed]An Asynchronous Parallel Genetic Algorithm for the Maximum Likelihood Phylogenetic Tree Search2012 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION (CEC) 2012 2012[Refereed]MARINE MICROPALEONTOLOGY 81 (1-2) Nov 2011[Refereed]JOURNAL OF EUKARYOTIC MICROBIOLOGY 58 (4) Jul 2011[Refereed]MOLECULAR PHYLOGENETICS AND EVOLUTION 60 (1) Jul 2011[Refereed]Splintrons in Giardia intestinalis: Spliceosomal introns in a split formCommunicative and Integrative Biology 4 (4) Apr 2011[Refereed]PROTIST 162 (2) Apr 2011[Refereed]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”.J. Euk. Microbiol. 58 (2) Jan 2011[Refereed]Biophysical Reviews 3 (4) 2011[Refereed]EUROPEAN JOURNAL OF PROTISTOLOGY 47 (1) Jan 2011[Refereed]JOURNAL OF PLANT RESEARCH 124 (1) Jan 2011[Refereed]HARMFUL ALGAE 10 (2) Jan 2011[Refereed]Comprehensive SSU rRNA phylogeny of Eukaryota.Journal of Endocytobiosis and Cell Research 20 Dec 2010[Refereed]JOURNAL OF EUKARYOTIC MICROBIOLOGY 57 (6) Nov 2010[Refereed]PROTIST 161 (4) Oct 2010[Refereed]ENVIRONMENTAL MICROBIOLOGY 12 (10) Oct 2010[Refereed]MOLECULAR PHYLOGENETICS AND EVOLUTION 56 (3) Sep 2010[Refereed]BMC EVOLUTIONARY BIOLOGY 10 Jun 2010[Refereed]GENE 450 (1-2) Jan 2010[Refereed]MOLECULAR PHYLOGENETICS AND EVOLUTION 53 (2) Nov 2009[Refereed]GENE 441 (1-2) Jul 2009[Refereed]GENE 441 (1-2) Jul 2009[Refereed]MOLECULAR BIOLOGY AND EVOLUTION 26 (5) May 2009[Refereed]PLOS ONE 4 (3) Mar 2009[Refereed]GENOME BIOLOGY AND EVOLUTION 1 2009[Refereed]PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 105 (19) May 2008[Refereed]GENE 410 (1) Feb 2008[Refereed]Phylogenetic inference based on combined analysis of multiple genes: Illustrative data analysis of higher-order phylogeny of Eukaryota統計数理 56 (1) Jan 2008[Refereed]Proceedings of the Japan Academy Series B: Physical and Biological Sciences 84 (2) 2008[Refereed]GENE 405 (1-2) Dec 2007[Refereed]MOLECULAR PHYLOGENETICS AND EVOLUTION 45 (1) Oct 2007[Refereed]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The Japanese journal of phycology 55 (2) Jul 2007EXTREMOPHILES 11 (4) Jul 2007[Refereed]CURRENT BIOLOGY 17 (10) May 2007[Refereed]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.Protist 158 (2) Apr 2007[Refereed]JOURNAL OF EUKARYOTIC MICROBIOLOGY 54 (2) Mar 2007[Refereed]Plasticity of the domain structure in FlgJ, a bacterial protein involved in flagellar rod formationGENES & GENETIC SYSTEMS 81 (6) Dec 2006[Refereed]MOLECULAR PHYLOGENETICS AND EVOLUTION 40 (2) Aug 2006[Refereed]PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (12) Mar 2006[Refereed]MOLECULAR BIOLOGY AND EVOLUTION 23 (3) Mar 2006[Refereed]GENE 362 Dec 2005[Refereed]The evolutionary relationships amongst excavates: a concatenated protein analysis.Journal of Eukaryotic Microbiology 52 Jan 2005Capsaspora owczarzaki is an independent opisthokont lineageCURRENT BIOLOGY 14 (22) Nov 2004[Refereed]PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (43) Oct 2004[Refereed]MOLECULAR BIOLOGY AND EVOLUTION 21 (9) Sep 2004[Refereed]SYSTEMATIC BIOLOGY 53 (4) Aug 2004[Refereed]MOLECULAR BIOLOGY AND EVOLUTION 21 (7) Jul 2004[Refereed]NUCLEIC ACIDS RESEARCH 31 (14) Jul 2003[Refereed]Testing for differences in rates-across-sites distributions in phylogenetic subtreesMOLECULAR 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 eubacteriaCURRENT BIOLOGY 12 (9) Apr 2002[Refereed]Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificityNUCLEIC ACIDS RESEARCH 30 (2) Jan 2002[Refereed]Class I release factors in ciliates with variant genetic codesNUCLEIC ACIDS RESEARCH 29 (4) Feb 2001[Refereed]Evolutionary relationship between dinoflagellates bearing obligate diatom endosymbionts: insight into tertiary endosymbiosisINTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 50 (6) Nov 2000[Refereed]Evolution of the eukaryotic translation termination system: Origins of release factorsMOLECULAR 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 evolutionCURRENT GENETICS 37 (1) Jan 2000[Refereed]Phycological Research 47 (3) 1999[Refereed]Distribution of the mitochondrial deviant genetic code AUA for methionine in heterokont algaeJOURNAL OF PHYCOLOGY 34 (6) Dec 1998[Refereed]Directionally evolving genetic code: The UGA codon from stop to tryptophan in mitochondriaJOURNAL OF MOLECULAR EVOLUTION 47 (4) Oct 1998[Refereed]Distinctive origins of group I introns found in the COXI genes of three green algaeGENE 213 (1-2) Jun 1998[Refereed]A deviant mitochondrial genetic code in prymnesiophytes (yellow-algae): UGA codon for tryptophanCURRENT GENETICS 32 (4) Oct 1997[Refereed]Algae or protozoa: Phylogenetic position of euglenophytes and dinoflagellates as inferred from mitochondrial sequencesJOURNAL 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 phylumJOURNAL OF MOLECULAR EVOLUTION 45 (2) Aug 1997[Refereed]Cloning of the Mycoplasma capricolum gene encoding peptide-chain release factorGENE 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 POSITIONJOURNAL OF MOLECULAR BIOLOGY 251 (4) Aug 1995[Refereed]LACK OF PEPTIDE-RELEASE ACTIVITY RESPONDING TO CODON UGA IN MYCOPLASMA-CAPRICOLUMNUCLEIC 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(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(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(Role:Supervisor)アピコンプレクサ類の退化葉緑体は緑藻起源か?(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 - 2023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 - 2022Elucidation of evolutionary process of light adaptation in a course of loss of photosynthesis.Grants-in-Aid for Scientific ResearchResearch period: 2017 - 2020Study on the residual green alga-derived nucleomorphs in dinoflagellatesGrants-in-Aid for Scientific ResearchResearch period: Apr 2016 - Mar 2019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 - 2019Diversity and evolution of anaerobic/microaerophilic eukaryotic microorganismsGrants-in-Aid for Scientific ResearchResearch period: Apr 2015 - Mar 2018Splicing mechanism of novel introns in a split form and their evolutionary diversityGrants-in-Aid for Scientific ResearchResearch period: Apr 2015 - Mar 2018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 2017Investigation on the evolutionary process integrating an endosymbiotic cyanobacterium into the host cellular systemGrants-in-Aid for Scientific ResearchResearch period: Apr 2011 - Mar 2016Matryoshka-type evolutionGrants-in-Aid for Scientific ResearchResearch period: Apr 2011 - Mar 2016Splicing mechanisms of a novel split intron and evolution of the mRNA maturation process in eukaryotesGrants-in-Aid for Scientific ResearchResearch period: Apr 2011 - Mar 2015Diversity and evolution of a canonical mitochondrion-lacking protist group, FornicataGrants-in-Aid for Scientific ResearchResearch period: Apr 2011 - Mar 2014Studies on a novel eukaryotic assemblage containing haptophytes and cryptophytes: Possible impact on the Chromalveolata hypothesis.Grants-in-Aid for Scientific ResearchResearch period: 2009 - 2012Basal construction studies for the diversity of algae-protist complexesGrants-in-Aid for Scientific ResearchResearch period: 2009 - 2012Novel biflagellate TKB055 as a possible early-branch in the global eukaryotic phylogeny : studies on its morphology, transcriptome, and mitochondrial genomeGrants-in-Aid for Scientific ResearchResearch period: 2010 - 2011Molecular Phylogeny of FornicataGrants-in-Aid for Scientific ResearchResearch period: 2008 - 2010Testing the Chromist monophyly based on multi-gene phylogenetic analyses considering the sequence data from katablepharids.Grants-in-Aid for Scientific ResearchResearch period: 2006 - 2007Early evolution of eukaryotes inferred by combined phylogeny of multiple genesGrants-in-Aid for Scientific ResearchResearch period: 2005 - 2006
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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 | ||
ntakuro ccs.tsukuba.ac.jp |
Research Interests
Academic & Professional Experience
Apr 2021-PresentUniversity of Tsukuba Center for Computational SciencesNov 2016-Mar 2021Tohoku UniversityNov 2016-Mar 2021Tohoku UniversityJun 2013-Oct 2016University of Tsukuba Center for Computational SciencesJun 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 DC1Published Papers
Proceedings of the National Academy of Sciences 117 (10) Mar 2020[Refereed]Proceedings of the National Academy of Sciences 116 (32) Aug 2019[Refereed]SCIENTIFIC REPORTS 7 Oct 2017[Refereed]PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 (31) Aug 2014[Refereed]NATURE 492 (7427) Dec 2012[Refereed]BMC BIOLOGY 10 Apr 2012[Refereed]CURRENT BIOLOGY 19 (7) Apr 2009[Refereed]bioRχiv May 2025bioRχiv Jan 2025ECOLOGY AND EVOLUTION 14 (3) Mar 2024[Refereed]Scientific Reports 14 (1) Jan 2024[Refereed]Briefings in Bioinformatics 24 (6) Sep 2023[Refereed]Frontiers in Cell and Developmental Biology 11 Sep 2023[Refereed]IPSJ Transactions on Bioinformatics 16 Jul 2023[Refereed]FRONTIERS IN MICROBIOLOGY 13 Aug 2022[Refereed]Frontiers in Plant Science 13 Jul 2022[Refereed]Science Advances 8 (17) Apr 2022[Refereed]Current biology : CB 31 (11) Jun 2021[Refereed]Parasitology international 83 Apr 2021[Refereed]Ecology and Evolution 11 (4) Feb 2021[Refereed]Communicative & Integrative Biology 13 (1) Jun 2020[Refereed]Proceedings of the National Academy of Sciences 117 (10) Mar 2020[Refereed]bioRχiv Oct 2019Proceedings of the National Academy of Sciences 116 (32) Aug 2019[Refereed]PLoS ONE 13 (3) Mar 2018[Refereed]SCIENTIFIC REPORTS 7 Oct 2017[Refereed]SCIENTIFIC REPORTS 7 Sep 2017[Refereed]PROTIST 168 (2) Apr 2017[Refereed]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?生物の科学 遺伝 70 (2) Mar 2016PROTIST 166 (5) Nov 2015[Refereed]PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 (31) Aug 2014[Refereed]JOURNAL OF EUKARYOTIC MICROBIOLOGY 61 (3) May 2014[Refereed]PHYCOLOGICAL RESEARCH 62 (2) Apr 2014[Refereed]ACTA SOCIETATIS BOTANICORUM POLONIAE 83 (4) 2014[Refereed]NATURE 492 (7427) Dec 2012[Refereed]PLOS ONE 7 (12) Dec 2012[Refereed]BMC BIOLOGY 10 Apr 2012[Refereed]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”.J. Euk. Microbiol. 58 (2) Jan 2011[Refereed]EUROPEAN JOURNAL OF PROTISTOLOGY 47 (1) Jan 2011[Refereed]JOURNAL OF PLANT RESEARCH 124 (1) Jan 2011[Refereed]MOLECULAR BIOLOGY AND EVOLUTION 27 (7) Jul 2010[Refereed]PHYLOGENETIC POSITION OF SYMBIOTIC CHLORELLA (TREBOUXIOPHYCEAE, CHLOROPHYTA) OF MAYORELLA VIRIDIS (AMOEBOZOA) AND ITS SYMBIOTIC MANNERPHYCOLOGIA 48 (4) Jul 2009BMC EVOLUTIONARY BIOLOGY 9 May 2009[Refereed]CURRENT BIOLOGY 19 (7) Apr 2009[Refereed]Japanese Journal of Protozoology 41 (1) 2008Awards & 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( 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
真核生物ゲノムデータに混入している原核共生体ゲノムの体系的探索科学研究費助成事業Research period: Apr 2023 - Mar 2027極小ゲノムを持つ新奇古細菌系統の実態解明一般研究助成Research period: Apr 2025 - Mar 2027二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 2027The overlooked diversity of the marine microbiome - Exploring the prokaryotic microbiome within eukaryotic microorganismsGrants-in-Aid for Scientific ResearchResearch 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 2024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 2023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 2020Fundamental studies on "mitochondrial glycolytic pathway" in cercozoan organisimsGrants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)Research period: Apr 2014 - Mar 2017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-upResearch period: 2010 - 2011Paulinella chromatophoraのシアネレに関する研究Grants-in-Aid for Scientific Research Grant-in-Aid for JSPS FellowsResearch period: 2007 - 2009
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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 | ||

ccs.tsukuba.ac.jp