Division of Life Sciences

Biological Function and Information Group

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

Biological Science Group

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

Biological Function and Information Group

氏名 重田 育照
Name Shigeta Yasuteru
Faculty
Section
Position Professor/Cheif
Theme Computational analyses on nano- and bio-systems
Related Links
Email shigetaccs.tsukuba.ac.jp
harada 氏名 原田 隆平
Name Harada Ryuhei
Faculty
Section
Position Associate Professor
Theme
Related Links
Email ryuheiccs.tsukuba.ac.jp
  • Research Interests
  • Academic & Professional Experience
    Feb 2019
    -
    Present
    University of Tsukuba Center for Computational Sciences
    Apr 2018
    -
    Jan 2019
    University of Tsukuba Center for Computational Sciences
    Apr 2015
    -
    Mar 2018
    日本学術振興会 特別研究員 PD
    Apr 2014
    -
    Mar 2015
    University of Tsukuba Center for Computational Sciences
    Apr 2011
    -
    Mar 2014
    理化学研究所 計算科学研究機構
  • Published Papers
    Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
    Chemistry Letters 49 (7) Jul 2020[Refereed]
    Independent Non-targeted Parallel Cascade Selection Molecular Dynamics for Enhancing Conformational Transitions of Proteins
    Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
    Journal of Chemical Information and Modeling, in preparation Jun 2020[Refereed]
    Comprehensive Predictions of Secondary Structures on Proteins of Various Organisms
    Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
    Journal of Molecular Biology, in preparation Jun 2020[Refereed]
    Protein Folding Pathways Elucidated by Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics
    Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
    Journal of Computational Chemistry, in preparation Jun 2020[Refereed]
    Enhanced Conformational Sampling Method Based on Anomaly Detection Parallel Cascade Selection Molecular Dynamics: ad-PaCS-MD
    Ryuhei Harada, Kota Yamaguchi, Yasuteru Shigeta
    Journal of Chemical Theory and Computation, in preparation Jun 2020[Refereed]
    Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations
    Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
    Bulletin Chemical Society of Japan, under review (Manuscript No.: BCSJ-2020-0174) Jun 2020[Refereed]
    The Molecular Mechanism on the Actin-Binding Domain of the Alpha-Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis Experiments
    Rikuri Morita, Kentaro Nakano, Yasuteru Shigeta, Ryuhei Harada
    The Journal of Physical Chemistry B, in revision (Manuscript ID: jp-2020-046237) Jun 2020[Refereed]
    Taste Recognition Mechanism of Medaka Fish Taste Receptor Type 1 upon the Ligand Binding Studied by All-atom Molecular Dynamics Simulations
    Hayato Aida, Yasuteru Shigeta, Ryuhei Harada
    Physical Chemistry Chemical Physics, in preparation May 2020[Refereed]
    Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis Based Parallel Cascade Selection Molecular Dynamics
    Takanori Yasuda, Yasuteru Shigeta, Ryuhei Harada
    Journal of Chemical Information and Modeling, under review (Manuscript ID: ci-2020-00580k) May 2020[Refereed]
    Teruyuki Takahashi, Ryuhei Harada, Yasuteru Shigeta
    Chemistry Letters 49 (4) Apr 2020[Refereed]
    Protein Dynamics and the Folding Degree
    Vladimir Sladek, Ryuhei Harada, Yasuteru Shigeta
    Journal of Chemical Information and Modeling 60 (3) Mar 2020[Refereed]
    学術賞受賞寄稿「タンパク質の機能発現に重要なレアイベントを抽出するサンプリング手法の開発」
    原田隆平
    アンサンブル 22 Jan 2020[Refereed]
    Rare Event Sampling of Biomolecules Based on Distributed Computing
    Ryuhei Harada
    BUTSURI 75 (1) Jan 2020[Refereed]
    Developments of Rare Event Sampling Methods for Proteins
    Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
    Journal of Computational Chemistry Japan 18 (5) Dec 2019[Refereed]
    Non-targeted Parallel Cascade Selection Molecular Dynamics Based on a Non-Redundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
    Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
    Journal of Chemical Information and Modeling 59 (12) Nov 2019[Refereed]
    Selection Rules for Outliers in Outlier Flooding Method (OFLOOD) Regulate its Conformational Sampling Efficiency
    Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
    Journal of Chemical Information and Modeling 59 (9) Sep 2019[Refereed]
    Non-targeted Parallel Cascade Selection Molecular Dynamics Using Time-localised Prediction of Conformational Transitions in Protein Dynamics
    Ryuhei Harada, Vladimir Sladek Yasuteru Shigeta
    Journal of Chemical Theory and Computation 15 (9) Sep 2019[Refereed]
    Supercomputing News
    Ryuhei Harada
    Supercomputing News 21 (1) Aug 2019
    Parallel Cascade Selection Molecular Dynamics Simulation (PaCS-MD) Screens for Protein Complexes Generated by Rigid Docking
    Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
    Journal of Molecular Graphics and Modeling 92 Jul 2019[Refereed]
    Temperature-Pressure Shuffling Outlier Flooding Method Enhances the Conformational Sampling of Proteins
    Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
    Journal of Computational Chemistry 40 (15) Apr 2019[Refereed]
    Molecular Dynamics Studies on the Effects of Antifreezing Protein from Rhagium Inquisitor (RiAFP) onIce Growth
    Masato Kimatsuka, Ryuma Sato, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta
    Journal of Computational Chemistry Japan 17 (5) Mar 2019[Refereed]
    Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-Order Molecular Dynamics Simulation
    Hayato Aida, Ryuhei Harada, Yasuteru Shigeta
    Chemistry Letters 48 (4) Mar 2019[Refereed]
    Ryuhei Harada, Yasuteru Shigeta
    Advances in Quantum Chemistry 78 Feb 2019[Refereed]
    Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
    Masato Kimatsuka, Ryuma Sato, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta
    Chemistry Letters 48 (3) Feb 2019[Refereed]
    Studies of Molecular Crowding by Simulations and Development of Parallel Cascade Selection Molecular Dynamics
    Ryuhei Harada
    Association of Asia Pacific Physical Society 29 (1) Feb 2019
    Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations
    Ryuhei Harada, Yasuteru Shigeta
    Journal of Chemical Theory and Computation 15 (1) Jan 2019[Refereed]
    Studies of Molecular Crowding by Simulations and Development of Parallel Cascade Selection Molecular Dynamics
    Ryuhei Harada
    BUTSURI 73 (12) Dec 2018[Refereed]
    カスケード選択型分子動力学シミュレーションの開発とタンパク質構造変化予測への適用
    原田隆平
    平成29年度・京都大学スーパーコンピュータ共同研究制度広報 17 (1) Dec 2018
    The Formation of Central Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics
    Ryuhei Harada, Hayato Aida, Yasuteru Shigeta
    Chemistry Letters 47 Sep 2018[Refereed]
    Effect of Initial Structures Rules in Parallel Cascade Selection Molecular Dynamics Affect Conformational Sampling Efficiency
    Ryuhei Harada, Yasuteru Shigeta
    Journal of Molecular Graph and Modeling 85 Sep 2018[Refereed]
    Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins
    Ryuhei Harada
    Bulletin Chemical Society of Japan 91 (9) Sep 2018[Refereed]
    How does Friction Constant affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?
    Ryuhei Harada, Yasuteru Shigeta
    Chemistry Letters 47 Aug 2018[Refereed]
    Temperature Shuffled Structural Dissimilarity Sampling Based on a Root-Mean Square Deviation
    Ryuhei Harada, Yasuteru Shigeta
    Journal of Chemical Information and Modeling 58 (7) Aug 2018[Refereed]
    カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発とFtsZ細胞分裂ダイナミクスへの適用
    原田隆平
    スーパーコンピューティングニュース特集号 20 (2) Aug 2018
    How Low-Resolution Structural Data Predict the Conformational Changes of a Protein: A Study on Data-Driven Molecular Dynamics Simulations
    Ryuhei Harada, Yasuteru Shigeta
    Physical Chemistry Chemical Physics 20 Jul 2018[Refereed]
    Developments of Innovative Molecular Simulation Methods for Understanding the Biological Functions
    Ryuhei Harada
    Chemical Industry 69 (7) Jul 2018
    Yuma Terai, Ryuma Sato, Takako Yumiba, Ryuhei Harada, Kohei Shimizu, Tatsuya Toga, Tomoko Ishikawa, Takashi Todo, Shigenori Iwai, Yasuteru Shigeta, Junpei Yamamoto
    Nucleic Acid Research 46 (13) Jul 2018[Refereed]
    On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate the Conformational Transitions of Proteins
    Ryuhei Harada, Yasuteru Shigeta
    Journal of Chemical Theory and Computation 14 (6) Jun 2018[Refereed]
    Recent Extensions and Applications of Parallel Cascade Selection Molecular Dynamics Simulations
    Ryuhei Harada, Yasuteru Shigeta
    Activity Report 2017 / Supercomputer Center, Institute for Solid State Physics (The University of Tokyo) May 2018
    Ryuhei Harada, Takako Mashiko,, Masanori Tachikawa,, Shuichi Hiraoka, Yasuteru Shigeta
    Physical Chemistry Chemical Physics 20 Apr 2018[Refereed]
    Development of Molecular Crowding and Cascade-Type Massive Parallel Simulation Methods for Biological Functions of Proteins
    Ryuhei Harada
    Chemistry and Chemical Industry 71 (3) Mar 2018
    Ryuhei Harada, Yasuteru Shigeta
    Journal of Computer Chemistry Japan 17 (1) Mar 2018[Refereed]
    The Binding Structure and Affinity of Photodamaged Duplex DNA with Members of the Photolyase/Cryptochrome Family: A Computational Study
    Ryuma Sato, Ryuhei Harada, Yasuteru Shigeta
    Biophysics and Physicobiology 15 Jan 2018[Refereed]
    Ryuhei Harada, Yasuteru Shigeta
    Journal of Computational Chemistry 38 (31) Dec 2017[Refereed]
    Ryuhei Harada, Yasuteru Shigeta
    Journal of Chemical Information and Modeling 57 (12) Dec 2017[Refereed]
    Ryuhei Harada, Yasuteru Shigeta
    Journal of Computational Chemistry 38 (22) Aug 2017[Refereed]
    Yuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki Hayashi
    The Journal of Physical Chemistry B 121 (22) Jun 2017[Refereed]
    Junso Fujita*, Ryuhei Harada*, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi Matsumura (*Equally Contributed)
    Journal of Structural Biology 198 (2) May 2017
    Ryuhei Harada, Yu Takano, Yasuteru Shigeta
    Journal of Computational Chemistry 38 (11) Apr 2017[Refereed]
    Ryuhei Harada, Yasuteru Shigeta
    Journal of Chemical Theory and Computation 13 (3) Mar 2017[Refereed]
    Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, Thi Kieu My Bui, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma, Mitsuo Shoji
    Molecular Simulation 43 (13-16) 2017[Refereed]
    Theoretical Analyses on a Flipping Mechanism of UV-induced DNA Damage
    Ryuma Sato, Ryuhei Harada, Yasuteru Shigeta
    BIOPHYSICS AND PHYSICOBIOLOGY 13 Nov 2016[Refereed]
    Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
    Bulletin of Chemical Society of Japan 89 (11) Nov 2016[Refereed]
    Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael Feig
    eLife 5 Nov 2016[Refereed]
    Molecular Mechanisms of Substrate Specificities of Uridine-Cytidine Kinase
    Wataru Tanaka, Mitsuo Shoji, Fumiaki Tomoike, Yuzuru Ujiie, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Katsumasa Kamiya, Toyokazu Ishida, Ryoji Masui, Seiki Kuramitsu, Yasuteru Shigeta
    Biophysics and Physicobiology 13 Jun 2016[Refereed]
    最近の研究から「カスケード型超並列シミュレーションに基づく遷移経路探索法」
    原田隆平
    アンサンブル 18 (3) Jun 2016[Refereed]
    Ryuhei Harada, Yu Takano, Yasuteru Shigeta
    Journal of Chemical Theory and Computation 12 (5) May 2016[Refereed]
    Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
    Journal of Computational Chemistry 37 (8) Mar 2016[Refereed]
    Akio Kitao, Ryuhei Harada, Yasutaka Nishihara, Duy Phuoc Tran
    Proceedings of the International Conference of Computational Methods in Sciences and Engineering 2016 (ICCMSE-2016) 1790 2016[Refereed]
    Ryuhei Harada, Akio Kitao
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11 (11) Nov 2015[Refereed]
    Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
    CHEMICAL PHYSICS LETTERS 639 Oct 2015[Refereed]
    Protein Folding and Evolution
    Ryuhei Harada, Yuji Inagaki, Yasuteru Shigeta
    In book: Reference Module in Materials Science and Materials Engineering DOI: 10.1016/B978 Aug 2015[Refereed]
    Michael Feig, Ryuhei Harada, Takaharu Mori, Isseki Yu, Koichi Takahashi, Yuji Sugita
    JOURNAL OF MOLECULAR GRAPHICS & MODELLING 58 May 2015[Refereed]
    Ryuhei Harada, Yu Takano, Yasuteru Shigeta
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (10) Apr 2015[Refereed]
    Yasuteru Shigeta, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 115 (5) Mar 2015[Refereed]
    Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta
    JOURNAL OF COMPUTATIONAL CHEMISTRY 36 (2) Jan 2015[Refereed]
    Ryuhei Harada, Yu Takano, Takeshi Baba, Yasuteru Shigeta
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17 (9) 2015[Refereed]
    Cascade-type Massive Parallel Simulation for Protein Conformation Transition Pathway Search
    Yasutaka Nishihara, Ryuhei Harada, Akio Kitao
    Proceedings of the Institute of Statistical Mathematics 62 (2) Dec 2014[Refereed]
    Takeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru Shigeta
    Journal of Computational Chemistry 35 (16) Jun 2014[Refereed]
    Ryuhei Harada, Akio Kitao
    SEIBUTSU BUTSURI 54 (3) Mar 2014[Refereed]
    Hydration and Protein Stability under Molecular Crowding Environments
    Ryuhei Harada
    BUSEEI KENKYU 53 Mar 2014[Refereed]
    Ryuhei Harada, Yu Takano, Yasuteru Shigeta
    The Journal of Chemical Physics 140 (12) Mar 2014[Refereed]
    Ryuhei Harada, Yasutaka Nishihara, Nobuhiko Wakai, Akio Kitao
    International Conference of Computational Methods in Sciences and Engineering 2014 1618 2014[Refereed]
    Ryuhei Harada, Akio Kitao
    The Journal of Chemical Physics 139 (3) Jul 2013[Refereed]
    Ryuhei Harada, Naoya Tochio, Takanori Kigawa, Yuji Sugita, Michael Feig
    Journal of the American Chemical Society 135 (9) Mar 2013[Refereed]
    Ryuhei Harada
    SEIBUTSU BUTSURI 53 (4) Feb 2013[Refereed]
    博士論文紹介「超並列マルチスケールシミュレーションMSFEL法で探る生体分子の生体分子の自由エネルギー地形」
    原田隆平
    アンサンブル 15 (1) Jan 2013[Refereed]
    Understanding Proteins in Packed Places
    Ryuhei Harada, Yuji Sugita, Michael Feig
    RIKEN RESEARCH 7 (3) Jul 2012
    Ryuhei Harada, Yuji Sugita, Michael Feig
    Journal of the American Chemical Society 134 (10) Mar 2012[Refereed]
    Ryuhei Harada, Akio Kitao
    Journal of Chemical Theory and Computation 8 (1) Jan 2012[Refereed]
    Ryuhei Harada, Akio Kitao
    Chemical Physics Letters 503 (1-3) Feb 2011[Refereed]
  • Awards & Honors
    Dec 2019
    2019年度 分子シミュレーション学会 学術賞
    Mar 2019
    日本物理学会 第13回 若手奨励賞 (領域12)
    Feb 2019
    Royal Society of Chemistry 2018 PCCP Hot Article Collection
    Mar 2018
    日本化学会 第67回 進歩賞
    Sep 2017
    The 4th BIOPHYSICS Editors' Choice Award
    Nov 2016
    BCSJ Selected Paper (日本化学会 優秀論文)
    Nov 2016
    第54回 日本生物物理学会年会 若手招待講演賞
    Apr 2015
    日本学術振興会特別研究員 PD (化学)
    Sep 2012
    第50回 日本生物物理学会年会 若手招待講演証
    Nov 2010
    第24回 分子シミュレーション討論会 学生優秀発表賞
  • Books etc
  • Research Grants & Projects
    中分子環状ペプチドの膜透過性を評価する分子シミュレーション技術の創出
    筑波大学研究基盤支援プログラム (Aタイプ)
    Research period: Aug 2019 - Mar 2020Representative: 原田隆平
    筑波大学研究支援プログラム(Cタイプ)
    Research period: Jul 2019 - Mar 2020Representative: 原田隆平
    カスケード選択型分子動力学シミュレーションで実現する環状ペプチド の膜透過シミュレーション
    2019年度学際共同利用
    Research period: Apr 2019 - Mar 2020Representative: 原田隆平
    PaCS-MDで実現する環状ペプチドの膜透過シミュレーション
    平成31年度 TSUBAME若手・女性利用者支援制度度
    Research period: Apr 2019 - Mar 2020Representative: 原田隆平
    カスケード選択型分子動力学シミュレーションで実現する環状ペプチドの膜透過シミュレーション
    若手・女性利用者推薦 2019年度 (前期)
    Research period: Apr 2019 - Sep 2019Representative: 原田隆平
    カスケード選択型分子動力学シミュレーションに基づく低解像度タンパク質構造の精密化
    平成30年度スーパーコンピューター若手・女性利用者推薦制度選択課題 (後期)
    Research period: Oct 2018 - Mar 2019Representative: 原田隆平
    筑波大学研究基盤支援プログラム(Cタイプ)
    Research period: Jul 2018 - Mar 2019Representative: 原田隆平
    カスケード型分子動力学シミュレーションに基づくフレキシブルドッキング法の開発
    平成30年度 TSUBAME若手・女性利用者支援制度度
    Research period: Apr 2018 - Mar 2019Representative: 原田隆平
    Gタンパク質共役受容体におけるシグナル伝達機構の解明
    若手研究(A) 課題番号:16H06164
    Research period: Apr 2016 - Mar 2019Representative: 原田隆平
    カスケード型分子動力学シミュレーションに基づくタンパク質構造精密化アルゴリズムの開発と応用
    平成30年度 スーパーコンピューター若手・女性利用者推薦 (前期)
    Research period: Apr 2018 - Sep 2018Representative: 原田隆平
    カスケード型超並列シミュレーションで探るFtsZ の細胞分裂ダイナミクス
    平成29年度 スーパーコンピューター若手・女性利用者推薦採択課題 (後期)
    Research period: Oct 2017 - Mar 2018Representative: 原田隆平
    教師あり機械学習に基づく超並列カスケード型シミュレーションの定式化とタンパク質構造変化予測への適用
    平成29年度 若手・女性研究者奨励枠
    Research period: Apr 2017 - Mar 2018Representative: 原田隆平
    カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発
    平成29年度 TSUBAME若手・女性利用者支援制度
    Research period: Apr 2017 - Mar 2018Representative: 原田隆平
    分子動力学シミュレーションで探る細胞環境におけるタンパク質フォールディング機構
    特別研究奨励費 課題番号:15J03797
    Research period: Apr 2015 - Mar 2018Representative: 原田隆平
    カスケード型超並列シミュレーションに立脚した遷移経路探索法の開発
    平成29年度 スーパーコンピューター若手・女性利用者推薦課題 (前期)
    Research period: Apr 2017 - Sep 2017Representative: 原田隆平
    タンパク質構造揺らぎに基づく構造変化予測法の構築
    若手研究(B) 課題番号:26840056
    Research period: Apr 2014 - Mar 2016Representative: 原田隆平
氏名 庄司 光男
Name Shoji Mitsuo
Faculty
Section
Position Assistant Professor
Theme Theoretical investigation on the reaction mechanisms of enzymes
Related Links
Email mshojiccs.tsukuba.ac.jp
氏名 西澤 宏晃
Name Nishizawa Hiroaki
Faculty
Section
Position Assistant Professor
Theme QM/MM molecular dynamics for middle molecular drug discovery
Related Links
Email nisizawaccs.tsukuba.ac.jp
氏名 堀 優太
Name Hori Yuta
Faculty
Section
Position Assistant Professor
Theme Theoretical studies for proton, electron, and hydride transfer reactions; Theoretical analysis for enzymatic and catalytic reactions; Theoretical studies on organic molecules in interstellar space
Related Links
Email horiccs.tsukuba.ac.jp
氏名 鬼頭(西岡) 宏任
Name Kitoh-Nishioka Hirotaka
Faculty
Section
Position Researcher
Theme Theory and Simulation of Excitation and Charge Transfers in Bio-System and Organic Semiconductor; GPU Acceleration of Fragment Molecular Orbital Method
Related Links
Email hkitoccs.tsukuba.ac.jp
氏名 森田 陸離
Name Morita Rikuri
Faculty
Section
Position Researcher
Theme
Related Links
Email moritaccs.tsukuba.ac.jp
  • Research Interests
  • Academic & Professional Experience
    Apr 2020
    -
    Present
    University of Tsukuba Center for Computational Sciences
  • Published Papers
    Rikuri Morita, Masak Takaine, Osamu Numata, Kentaro Nakano
    JOURNAL OF BIOCHEMISTRY 162 (2) Aug 2017[Refereed]
  • Awards & Honors
    Jun 2019
    第46回生体分子科学討論会 優秀ポスター賞
    Jan 2018
    International Congress of Cell Biology 2018 The Raman Trust Award
    Mar 2017
    筑波大学 生命環境科学研究科 生物科学専攻 専攻長表彰
    Mar 2017
    筑波大学 生命環境科学研究科 研究科長表彰
  • Books etc
  • Research Grants & Projects
氏名 満田 祐樹
Name Mitsuta Yuki
Faculty
Section
Position Researcher
Theme The development of free-energy reaction root mapping method by using molecular dynamics simulation
Related Links
Email mitsutayccs.tsukuba.ac.jp
氏名
Name Kowit Hengphasatporn
Faculty
Section
Position Researcher
Theme Molecular modeling and Structure-based virtual screening on the biological systems
Related Links
Email kowithccs.tsukuba.ac.jp
氏名 広川 貴次
Name Hirokawa Takatsugu
Faculty Faculty of Medicine
Section
Position Professor (Collaborative Fellow)
Theme
Related Links
Email
氏名 吉野 龍ノ介
Name Yoshino Ryunosuke
Faculty Faculty of Medicine
Section
Position Assistant Professor (Collaborative Fellow)
Theme Drug discovery and structural optimization using molecular simulation techniques
Related Links
Email

Biological Science Group

氏名 稲垣 祐司
Name Inagaki Yuji
Faculty
Section
Position Professor/Group Leader
Theme Molecular phylogeny of eukaryotes Investigation of lateral genetransfers at the whole-gene and sub-gene levels Estimation of protein functions by combining structural and evolutionary parameters Artifacts in molecular dataanalyses
Related Links
Email yujiccs.tsukuba.ac.jp
氏名 石谷 佳之
Name Ishitani Yoshiyuki
Faculty
Section
Position Researcher
Theme Divergence time estimation of major eukaryotes based on multi genes analysis
Related Links
Email ishitaniccs.tsukuba.ac.jp
  • Research Interests
  • Academic & Professional Experience
    Apr 2017
    -
    Present
    Tsukuba University Center for computer science Postdoc
    May 2015
    -
    Mar 2017
    The University of Tokyo Atmosphere and Ocean Research Institute Project Researcher
    Sep 2013
    -
    Apr 2015
    University of Glasgow School of Geographical & Earth Sciences Post-doc scientist
    Apr 2013
    -
    Aug 2013
    Japan Agency for Marine-Earth Science and Technology
    Apr 2013
    -
    Aug 2013
    The University of Tokyo Graduate School of Science Project Researcher
    Apr 2010
    -
    Mar 2013
    JAMSTEC Biogeoscience Visiting Researcher
  • Published Papers
    Ciacci, C, Grimmelpont, M. V, Corsi, I, Bergami, E, Curzi, D, Burini, D, Bouchet, V. M. P, Ambrogini, P, Gobbi, P, Ujiié, Y, Ishitani, Y, Coccioni, R, Bernhard, J. M, Frontalini, F
    Scientific Reports 19 (9) Dec 2019[Refereed]
    Yurika Ujiie, Yoshiyuki Ishitani
    PLOS ONE 11 (2) Feb 2016[Refereed]
    "Retaria" hypothesis, a sister relationship between Foraminifera and Radiolaria
    Ishitani Yoshiyuki, Takishita Kiyotaka
    化石 (97) Mar 2015[Refereed]
    Yoshiyui Ishitani, Yurika Ujiie, Kiyotaka Takishita
    MOLECULAR PHYLOGENETICS AND EVOLUTION 78 Sep 2014[Refereed]
    Yoshiyuki Ishitani, Ryoma Kamikawa, Akinori Yabuki, Masashi Tsuchiya, Yuji Inagaki, Kiyotaka Takishita
    JOURNAL OF EUKARYOTIC MICROBIOLOGY 59 (4) Jul 2012[Refereed]
    Yurika Ujiie, Takahiro Asami, Thibault de Garidel-Thoron, Hui Liu, Yoshiyuki Ishitani, Colomban de Vargas
    ECOLOGY AND EVOLUTION 2 (7) Jul 2012[Refereed]
    Yoshiyuki Ishitani, Yurika Ujiie, Colomban de Vargas, Fabrice Not, Kozo Takahashi
    PLOS ONE 7 (5) May 2012[Refereed]
    Yoshiyuki Ishitani, Yurika Ujiie, Colomban de Vargas, Fabrice Not, Kozo Takahashi
    DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY 61-64 Feb 2012[Refereed]
    Yoshiyuki Ishitani, Sohta A. Ishikawa, Yuji Inagaki, Masashi Tsuchiya, Kozo Takahashi, Kiyotaka Takishita
    MARINE MICROPALEONTOLOGY 81 (1-2) Nov 2011[Refereed]
    Seasonal flux changes of radiolarians at Station K2 in the Western Subarctic Gyre
    Ikenoue Takahito, Takahashi Kozo, Ishitani Yoshiyuki, Tanaka Seiji
    Umi no Kenkyu (Oceanography in Japan) 19 (4) Jul 2010[Refereed]
    Vertical and geographic distribution of selected radiolarian species in the North Pacific
    Yoshiyuki Ishitani, Kozo Takahashi, Yusuke Okazaki, Seiji Tanaka
    MICROPALEONTOLOGY 54 (1) 2008[Refereed]
    Yoshiyuki Ishitani, Kozo Takahashi
    MARINE MICROPALEONTOLOGY 65 (3-4) Dec 2007[Refereed]
  • Awards & Honors
    Oct 2011
    放散虫研究集会 学術賞 第11回放散虫研究集会
    Jul 2010
    ISEP young scientist award
  • Books etc
    アメーバのはなし
    石谷 佳之, 土屋正史 (Role:Contributor, 海の中にいるヒトに感染しない原生生物)
    Radiolaria
    Yoshiyuki Ishitani, Colette Febvre-Chevalier, Jean Febvre (Role:Joint author)
    Distribution and geochemical properties of hydrothermal plumes in the Rodriguez Triple Junction
    Noguchi T, Fukuba T, Okamura K, Ijiri A, Yanagawa K, Ishitani Y, Fujii R, Sunamura M (Role:Joint author)
  • Research Grants & Projects
    海洋原生生物に共生する細菌多様性の実態解明
    国際共同研究強化B【研究分担者】
    Research period: Oct 2018 - Mar 2023Representative: 稲垣 祐司
    ミトコンドリアDNAポリメラーゼの多様性と進化の全容解明
    基盤研究(B)【研究分担者】
    Research period: Apr 2019 - Mar 2022Representative: 稲垣 祐司
    大規模分岐年代推定ー真核生物の誕生と進化を解き明かす!!ー
    基盤研究(C)【研究代表者】
    Research period: Apr 2018 - Mar 2021Representative: 石谷 佳之
    有孔虫における殻形成機構の解明ー石灰化のブラックボックスを開くー
    基盤研究(B)【研究分担者】
    Research period: Apr 2017 - Mar 2020Representative: 氏家 由利香
    原核藻類と原生生物の光共生に関する研究
    基盤研究(C)【研究分担者】
    Research period: Apr 2016 - Mar 2019Representative: 藤木 撤一
    浮遊性有孔虫の新規環境指標の確立:遺伝子・安定同位体・形態の複合解析から
    基盤研究(C)【研究協力者】
    Research period: Apr 2014 - Mar 2017Representative: 氏家 由利香
    放散虫のバイオミネラリゼーションと殻形態進化:化石の分子生物学への応用に向けて
    海外特別研究員
    Research period: Sep 2013 - Apr 2015Representative: 石谷 佳之
    浮遊性有孔虫の生物多様性と炭素循環の関係の解明
    若手研究(B)【研究協力者】
    Research period: Apr 2011 - Mar 2014Representative: 氏家 由利香
    環境変遷に基づく放散虫の進化と多様性,古海洋環境指標としての新展望
    特別研究員
    Research period: Apr 2010 - Mar 2013Representative: 石谷 佳之
    生物学に基づく古海洋学の新展開~放散虫・環境指標としての有用性・可能性の追求~
    日仏二国間交流事業【企画/立案/協力】
    Research period: Nov 2009Representative: 高橋 孝三
氏名 橋本 哲男
Name Hashimoto Tetsuo
Faculty Faculty of Life and Enviromental Sciences
Section
Position Professor (Collaborative Fellow)
Theme Molecular evolutionary studies on the origin and early evolution of eukaryotes
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