OKAMOTO Yuko 岡本祐幸

… Alternative Names

岡本祐幸オカモトユウコウ

Less

Researcher Number	70185487
Other IDs
External Links
Affiliation (Current)	2025: 名古屋大学, 情報連携推進本部, 招へい教員
Affiliation (based on the past Project Information) *help	2016 – 2018: 名古屋大学, 理学研究科, 教授 2017: 名古屋大学, 理学研究科, 特任准教授 2012 – 2015: 名古屋大学, 理学(系)研究科(研究院), 教授 2014: 名古屋大学, 大学院理学研究科, 教授 2012 – 2013: 名古屋大学, 理学研究科, 教授 … More 2007 – 2012: Nagoya University, 大学院・理学研究科, 教授 2006: 名古屋大学, 大学院理学研究科, 教授 2005: 名古屋大学, 大学院・理学研究科, 教授 2004: 分子科学研究所, 理論分子科学研究系, 助教授 2003: 岡崎国立共同研究機構, 分子科学研究所, 助教授 1995 – 1998: 岡崎国立共同研究機構, 分子科学研究所, 助教授 1993: 奈良女子大学, 理学部・物理学科, 助教授 Less
Review Section/Research Field	Principal Investigator Science and Engineering / Biophysics / Science and Engineering / Biological physics/Chemical physics/Soft matter physics / 物理学一般 Except Principal Investigator Science and Engineering
Keywords	Principal Investigator 拡張アンサンブル法 / マルチカノニカル法 / 立体構造予測 / 蛋白質 / 分子シミュレーション / 分子動力学法 / モンテカルロ法 / 自由エネルギー計算 / 生体系 / 核酸 … More / 徐冷法 / 最適化 / 徐冷モンテカルロ法 / タンパク質 / レプリカ交換法 / タンパク質の立体構造 / 最適化問題 / generalized-eusemble algorithm / murticanonieal algorithm / NMR experiment / X-ray experiment / structure determination / nudeic acid / proteiu / マルナカノニカル法 / NMR実験 / X線実験 / 立体構造決定 / Nucleic Acids / Generalized Ensemble / Multicanonical Algorithm / Simulated Annealing / Molecular Dynamics / Monte Carlo / Optimization / Protein Tertiary Structures / 創薬 / レプリカ交換溶質焼き戻し法 / レプリカ交換傘サンプル法 / ドッキング / 量子効果 / 密度汎関数法 / 分子動力学シミュレーション / 計算物理学 / 人工分子系 / 生体分子系 / 分子シュミレーション / 拡張アンサンブル / 自由エネルギー / エネルギー関数 / シミュレーション / 蛋白質折り畳み / 折り畳み / 膜タンパク質 / マルチバーリック法 / 計算機シミュレーション / タンパク質の折り畳み / タンパク質の主体構造 / 最適化アルゴリズム / タンパク質の折れたたみ / ペプチド / alpha-ヘリックス … More Except Principal Investigator 離合集散 / 高次機能 / 集合離散 / 超分子 / 生命分子 / 動的秩序 / 分子科学 / 生物物理 / 分子シミュレーション / 電子状態計算 / 蛋白質 / 計算物理 / 反応 / 機能 / 生体分子 / ダイナミクス / 揺らぎ Less

International Activity Support for Dynamical ordering of biomolecular systems for creation of integrated functions
- Principal Investigator
  
  Kato Koichi
- Project Period (FY)
  2015 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Center for Novel Science Initatives, National Institutes of Natural Sciences
  Okazaki Research Facilities, National Institutes of Natural Sciences
Management for Dynamical ordering of biomolecular systems for creation of integrated functions
- Principal Investigator
  
  Kato Koichi
- Project Period (FY)
  2013 – 2017
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Okazaki Research Facilities, National Institutes of Natural Sciences
Interactions among biological molecular assembly and among artificial molecular assembly and large-scale structural transformationsPrincipal Investigator
- Principal Investigator
  
  OKAMOTO Yuko
- Project Period (FY)
  2013 – 2017
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Nagoya University
拡張アンサンブル密度汎関数分子動力学法によるATP加水分解の研究Principal Investigator
- Principal Investigator
  
  岡本祐幸
- Project Period (FY)
  2013
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Nagoya University
Study on the mechanism of docking of small molecules to proteins by generalized-ensemble algorithmsPrincipal Investigator
- Principal Investigator
  
  OKAMOTO Yuko
- Project Period (FY)
  2013 – 2017
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  Biological physics/Chemical physics/Soft matter physics
- Research Institution
  Nagoya University
Exploration of reactions and structural space in multi-degree-of-freedom and large-scale systems
- Principal Investigator
  
  YAMATO Takahisa
- Project Period (FY)
  2010 – 2014
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Nagoya University
蛋白質系分子シミュレーションのための新規エネルギー関数の開発Principal Investigator
- Principal Investigator
  
  岡本祐幸
- Project Period (FY)
  2008
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Science and Engineering
- Research Institution
  Nagoya University
Management for Molecular Science of Fluctuations toward Biological Functions
- Principal Investigator
  
  TERAZIMA Masahide
- Project Period (FY)
  2008 – 2013
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Kyoto University
Development of molecular simulation algorithms for enhancing structural fluctuations and for accurate free -energy calculationsPrincipal Investigator
- Principal Investigator
  
  OKAMOTO Yuko
- Project Period (FY)
  2008 – 2012
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Nagoya University
拡張アンサンブル法による蛋白質折り畳み機構の研究Principal Investigator
- Principal Investigator
  
  岡本祐幸
- Project Period (FY)
  2003 – 2007
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Science and Engineering
- Research Institution
  Nagoya University
  Institute for Molecular Science
  Okazaki National Research Institutes
拡張アンサンブル法による蛋白質の立体構造予測Principal Investigator
- Principal Investigator
  
  岡本祐幸
- Project Period (FY)
  1997 – 1998
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Research Institution
  Okazaki National Research Institutes
Tertiavy structure analysis of biomolecules based on X-ray and NMR data by multicawowical algorithmPrincipal Investigator
- Principal Investigator
  
  OKAMOTO Yuko
- Project Period (FY)
  1997 – 1998
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Biophysics
- Research Institution
  OKAZAKI NATIONAL RESEARCH INSTITVTES
新最適化アルゴリズムによるタンパク質の折れたたみの研究Principal Investigator
- Principal Investigator
  
  岡本祐幸
- Project Period (FY)
  1996
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Research Institution
  Okazaki National Research Institutes
新最適化アルゴリズムによるタンパク質の折れたたみ機構の研究Principal Investigator
- Principal Investigator
  
  岡本祐幸
- Project Period (FY)
  1995
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Research Institution
  Okazaki National Research Institutes
Prediction of Protein Tertiary Structures by Monte Carlo Simulated Annealing and Multicanonical AlgorithmsPrincipal Investigator
- Principal Investigator
  
  OKAMOTO Yuko
- Project Period (FY)
  1995 – 1996
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Biophysics
- Research Institution
  OKAZAKI NATIONAL RESEARCH INSTITUTES
徐冷モンテカルロ法によるタンパク質の立体構造予測Principal Investigator
- Principal Investigator
  
  岡本祐幸
- Project Period (FY)
  1993
- Research Category
  
  Grant-in-Aid for Encouragement of Young Scientists (A)
- Research Field
  
  物理学一般
- Research Institution
  Nara Women's University

[Book] Molecular Science of Fluctuations Toward Biological Functions2016
- Author(s)
  M. Terazima, M. Kataoka, R. Ueoka, and Y. Okamoto (eds.)
- Total Pages
  270
- Publisher
  Springer
- Data Source
  KAKENHI-PLANNED-25102009
[Book] Molecular Science of Fluctuations Toward Biological Functions2016
- Author(s)
  M. Terazima, M. Kataoka, R. Ueoka, and Y. Okamoto (eds.)
- Total Pages
  270
- Publisher
  Springer
- Data Source
  KAKENHI-PROJECT-25247071
[Book] “Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation” in Advances in Experimental Medicine and Biology 842: Biochemical Roles of Eukaryotic Cell Surface Macromolecules2015
- Author(s)
  Y. Zhang, T. Yamaguchi, T. Satoh, M. Yagi-Utsumi, Y. Kamiya, Y. Sakae, Y. Okamoto, and K. Kato　(edited by A. Chakrabarti and A. Surolia)
- Publisher
  Springer
- Data Source
  KAKENHI-PLANNED-25102009
[Book] “Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation” in Advances in Experimental Medicine and Biology 842: Biochemical Roles of Eukaryotic Cell Surface Macromolecules2015
- Author(s)
  Y. Zhang, T. Yamaguchi, T. Satoh, M. Yagi-Utsumi, Y. Kamiya, Y. Sakae, Y. Okamoto, and K. Kato　(edited by A. Chakrabarti and A. Surolia)
- Publisher
  Springer
- Data Source
  KAKENHI-PROJECT-25247071
[Book] Advances in Experimental Medicine and Biology2015
- Author(s)
  Y.Zhang, T.Yamaguchi, T.Satoh, M.Yagi-Utsumi, Y.Kamiya, Y.Sakae, Y.Okamoto, and K.Kato
- Total Pages
  411
- Publisher
  Springer (Switzerland)
- Data Source
  KAKENHI-ORGANIZER-25102001
[Book] "Optimizations of protein force fields" in Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes-; from Bioinformatics to Molecular Quantum Mechanics2014
- Author(s)
  Y. Sakae and Y. Okamoto, (A. Liwo ed.)
- Total Pages
  810
- Publisher
  Springer-Verlag
- Data Source
  KAKENHI-ORGANIZER-25102001
[Book] Advances in Experimental Medicine and Biology 805: Protein Conformational Dynamics2014
- Author(s)
  T. Yoda, Y. Sugita, and Y. Okamoto (edited by K.-L. Han, Xin Zhang, and M.-J. Yang)
- Total Pages
  410
- Publisher
  Springer
- Data Source
  KAKENHI-ORGANIZER-25102001
[Book] Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes – from Bioinformatics to Molecular Quantum Mechanics2014
- Author(s)
  Yoshitake Sakae and Yuko Okamoto (edited by A. Liwo)
- Publisher
  Springer-Verlag
- Data Source
  KAKENHI-PLANNED-25102009
[Book] “Protein folding simulations by generalized-ensemble algorithms” in Advances in Experimental Medicine and Biology 805: Protein Conformational Dynamics2014
- Author(s)
  T. Yoda, Y. Sugita, and Y. Okamoto (edited by K.-L. Han, Xin Zhang, and M.-J. Yang)
- Publisher
  Springer
- Data Source
  KAKENHI-PLANNED-25102009
[Book] Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes – from Bioinformatics to Molecular Quantum Mechanics2014
- Author(s)
  Y. Sakae and Y. Okamoto (edited by A. Liwo)
- Publisher
  Springer-Verlag
- Data Source
  KAKENHI-PROJECT-25247071
[Book] “Protein folding simulations by generalized-ensemble algorithms” in Advances in Experimental Medicine and Biology 805: Protein Conformational Dynamics2014
- Author(s)
  T. Yoda, Y. Sugita, and Y. Okamoto (edited by K.-L. Han, Xin Zhang, and M.-J. Yang)
- Publisher
  Springer
- Data Source
  KAKENHI-PROJECT-25247071
[Book] 「計算科学講座」第９巻「超多自由度系の最適化」第２章「拡張アンサンブル法」2013
- Author(s)
  岡本祐幸 (古橋武、笹井理生編）
- Publisher
  共立出版
- Data Source
  KAKENHI-PROJECT-25247071
[Book] 計算科学講座第９巻「超多自由度系の最適化」第２章「拡張アンサンブル法」2013
- Author(s)
  岡本祐幸（古橋武、笹井理生編集）
- Publisher
  共立出版
- Data Source
  KAKENHI-PUBLICLY-25104715
[Book] DOJIN BIOSCIENCEシリーズ「生体分子の動きを探るー揺らぎと生体機能ー」第１２章2013
- Author(s)
  岡本祐幸（寺嶋正秀編）
- Publisher
  化学同人
- Data Source
  KAKENHI-PROJECT-25247071
[Book] 計算科学講座第９巻「超多自由度系の最適化」　第２章拡張アンサンブル法2013
- Author(s)
  岡本祐幸（古橋武、笹井理生編）
- Total Pages
  248
- Publisher
  共立出版
- Data Source
  KAKENHI-ORGANIZER-25102001
[Book] Proceedings of the 5th Japan-Russia International Workshop MSSMBS'12 "Molecular Simulations Studies in Material and Biological Sciences"2013
- Author(s)
  T. Yoda, Y. Sugita, and Y. Okamoto (edited by K. Kholmurodov)
- Publisher
  Nova Science
- Data Source
  KAKENHI-PLANNED-25102009
[Book] Proceedings of the 5th Japan-Russia International Workshop MSSMBS'12 "Molecular Simulations Studies in Material and Biological Sciences"2013
- Author(s)
  T. Yoda, Y. Sugita, and Y. Okamoto (edited by K. Kholmurodov)
- Publisher
  Nova Science
- Data Source
  KAKENHI-PROJECT-25247071
[Book] DOJIN BIOSCIENCEシリーズ「生体分子の動きを探る　―　揺らぎと生体機能　―」第12章2013
- Author(s)
  岡本祐幸（寺嶋正秀編）
- Publisher
  化学同人
- Data Source
  KAKENHI-PLANNED-25102009
[Book] "Ligand docking simulations by generalized-ensemble algorithms" in Advances in Protein Chemistry and Structural Biology, Vol. 922013
- Author(s)
  H. Kokubo, T. Tanaka, and Y. Okamoto (T. Karabencheva-Christova ed.)
- Total Pages
  357
- Publisher
  Academic Press
- Data Source
  KAKENHI-ORGANIZER-25102001
[Book] 「拡張アンサンブル法」,「計算科学講座」第9巻「超多自由度系の最適化」第2章2013
- Author(s)
  岡本祐幸
- Publisher
  古橋武、笹井理生編、共立出版
- Data Source
  KAKENHI-PLANNED-20107002
[Book] "Salt effect on folding of villin headpiece subdomain HP36 studied by generalized-ensemble simulations" in Proceedings of the 5th Japan-Russia International Workshop MSSMBS'12 "Molecular Simulations Studies in Material and Biological Sciences"2013
- Author(s)
  T. Yoda, Y. Sugita, and Y. Okamoto (K. Kholmurodov ed.)
- Total Pages
  219
- Publisher
  Nova Science
- Data Source
  KAKENHI-ORGANIZER-25102001
[Book] 「計算科学講座」第９巻「超多自由度系の最適化」第２章「拡張アンサンブル法」2013
- Author(s)
  岡本祐幸 (古橋武、笹井理生編）
- Publisher
  共立出版
- Data Source
  KAKENHI-PLANNED-25102009
[Book] 揺らぎ・ダイナミクスと生体機能2013
- Author(s)
  寺嶋正秀、加藤晃一、芳坂貴弘、佐藤啓文、岡本祐幸（寺嶋正秀編）
- Total Pages
  368
- Publisher
  化学同人
- Data Source
  KAKENHI-ORGANIZER-25102001
[Book] Advances in Protein Chemistry and Structural Biology, Vol. 922013
- Author(s)
  H. Kokubo, T. Tanaka, and Y. Okamoto (edited by T. Karabencheva-Christova)
- Publisher
  Academic Press
- Data Source
  KAKENHI-PLANNED-25102009
[Book] Advances in Protein Chemistry and Structural Biology　Vol.922013
- Author(s)
  H.Kokubo,T.Tanaka, and Y.Okamoto (edited by T.Karabencheva-Christova)
- Publisher
  Academic Press
- Data Source
  KAKENHI-PROJECT-25247071
[Book] Generalized-ensemble algorithms for simulations of complex molecular systems," in Practical Aspects of Computational Chemistry II: An Overview of the Last Two Decades and Current Trends, J. Leszczynski and M.K. Shukla (eds.)2012
- Author(s)
  H. Okumura, S.G. Itoh, and Y. Okamoto
- Publisher
  Generalized-ensemble algorithms for simulations of complex molecular systems," in Practical Aspects of Computational Chemistry II: An Overview of the Last Two Decades and Current Trends, J. Leszczynski and M.K. Shukla (eds.)
- Data Source
  KAKENHI-PLANNED-20107002
[Book] "Enhanced sampling algorithms," in Biomolecular Simulations: Methods and Protocols, L. Monticelli and E. Salonen (eds.)2012
- Author(s)
  A. Mitsutake, Y. Mori, and Y. Okamoto
- Publisher
  Humana Press, New York
- Data Source
  KAKENHI-PLANNED-20107002
[Book] Biomolecular Simulations: Methods and Protocols2012
- Author(s)
  A. Mitsutake, Y. Mori, and Y. Okamoto (edited by L. Monticelli and E. Salonen)
- Publisher
  Humana Press
- Data Source
  KAKENHI-PLANNED-20107002
[Book] Practical Aspects of Computational Chemistry II: An Overview of the Last Two Decades and Current Trends2012
- Author(s)
  H. Okumura, S.G. Itoh, and Y. Okamoto (edited by J. Leszczynski and M.K. Shukla)
- Publisher
  Springer
- Data Source
  KAKENHI-PLANNED-20107002
[Book] “Enhanced sampling algorithms’”, Biomolecular Simulations: Methods and Protocols, edited by L.Monticelli and E.Salonen, pp. 153-195.2012
- Author(s)
  A. Mitsutake, Y. Mori, and Y. Okamoto
- Total Pages
  702
- Publisher
  Humana Press, New York
- Data Source
  KAKENHI-PLANNED-22104009
[Book] Proceedings of the 4th Japan-Russia International Workshop MSSMBS'10 "Molecular Simulations Studies in Material and Biological Sciences", K.Kholmurodov (ed.), (Nova Science, Hauppauge)2011
- Author(s)
  Y Mori, A.Mitsutake, Y Okamoto
- Publisher
  Generalized-ensemble simulations in protein science
- Data Source
  KAKENHI-PLANNED-20107002
[Book] Springer-Verlag, Berlin2009
- Author(s)
  Y.Okamoto
- Publisher
  Generalized-ensemble algorithms for studying protein folding in Water and Biomolecules(K.Kuwajima, Y.Goto, F.Hirata, M.Kataoka, and M.Terazima, (eds.))
- Data Source
  KAKENHI-PLANNED-20107002
[Book] "Generalized-ensemble algorithms for studying protein folding" in Water and Biomolecules (edited by K.Kuwajima, Y.Goto, F.Hirata, M.Kataoka, and M.Terazima)2009
- Author(s)
  Y.Okamoto
- Publisher
  Springer-Verlag
- Data Source
  KAKENHI-PLANNED-20107002
[Book] Lecture Notes in Physics, Springer-Verlag2008
- Author(s)
  Y. Sugita, A. Mitsutake, & Y. Okamoto (edited by W. Janke)
- Publisher
  Lecture Notes
- Data Source
  KAKENHI-PROJECT-15076213
[Book] 分子科学者がいどむ12の謎2005
- Author(s)
  岡本祐幸(分担執筆)
- Total Pages
  235
- Publisher
  化学同人
- Data Source
  KAKENHI-PROJECT-15076213
[Book] Enhanced sampling algorithms, in biomolecular simulations : methods and protocols(edited by L.Monticelli and E.Salonen)
- Author(s)
  A.Mitsutake, Y.Mori, Y.Okamoto
- Publisher
  Humana Press, Berlin(in press)
- Data Source
  KAKENHI-PLANNED-22104009
[Journal Article] Determination of the Structural Ensemble of the Molten Globule State of a Protein by Computer Simulations2019
- Author(s)
  Shimizu Masahiro、Kajikawa Yukihito、Kuwajima Kunihiro、Dobson Christopher M.、Okamoto Yuko
- Journal Title
  
  Proteins: Structure, Function, and Bioinformatics
  
  Volume: in press Issue: 8 Pages: 635-645
- DOI
  10.1002/prot.25688
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07314, KAKENHI-INTERNATIONAL-15K21708
[Journal Article] Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations2018
- Author(s)
  Tsukamoto Shuichiro、Sakae Yoshitake、Itoh Yukihiro、Suzuki Takayoshi、Okamoto Yuko
- Journal Title
  
  The Journal of Chemical Physics
  
  Volume: 148 Issue: 12 Pages: 125102-125102
- DOI
  10.1063/1.5019209
- NAID
  120006545081
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071, KAKENHI-PROJECT-16KT0060
[Journal Article] Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation2017
- Author(s)
  Eiji Kurimoro, Tadashi Satoh, Yuri Ito, Eri Ishihara, Kenta Okamoto, Maho Yagi-Utsumi, Keiji Tanaka, and Koichi Kato
- Journal Title
  
  Protein Sci.
  
  Volume: 26 Issue: 5 Pages: 1080-1085
- DOI
  10.1002/pro.3153
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-15H02491, KAKENHI-PROJECT-15K21680, KAKENHI-PROJECT-17K15441, KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102008, KAKENHI-PROJECT-26000014
[Journal Article] Two major stable structures of amyloid-forming peptides: amorphous aggregates and amyloid fibrils2017
- Author(s)
  Nishikawa Naohiro、Sakae Yoshitake、Gouda Takuya、Tsujimura Yuichiro、Okamoto Yuko
- Journal Title
  
  Molecular Simulation
  
  Volume: 43 Issue: 13-16 Pages: 1370-1376
- DOI
  10.1080/08927022.2017.1359746
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa2017
- Author(s)
  Sakae Yoshitake、Satoh Tadashi、Yagi Hirokazu、Yanaka Saeko、Yamaguchi Takumi、Isoda Yuya、Iida Shigeru、Okamoto Yuko、Kato Koichi
- Journal Title
  
  Sci. Rep.
  
  Volume: 7 Issue: 1 Pages: 13780-13780
- DOI
  10.1038/s41598-017-13845-8
- NAID
  120006545940
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102008, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071, KAKENHI-PROJECT-15K07935
[Journal Article] Structure?function insights into direct lipid transfer between membranes by Mmm1?Mdm12 of ERMES2017
- Author(s)
  Kawano Shin、Tamura Yasushi、Kojima Rieko、Bala Siqin、Asai Eri、Michel Agn?s H.、Kornmann Beno?t、Riezman Isabelle、Riezman Howard、Sakae Yoshitake、Okamoto Yuko、Endo Toshiya
- Journal Title
  
  The Journal of Cell Biology
  
  Volume: 217 Issue: 3 Pages: 959-974
- DOI
  10.1083/jcb.201704119
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17K19338, KAKENHI-PROJECT-16K18534, KAKENHI-PLANNED-17H06414, KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071, KAKENHI-PROJECT-15H05595
[Journal Article] Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study2017
- Author(s)
  Yoshiharu Mori, Yuko Okamoto
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 38 Issue: 15 Pages: 1167-1173
- DOI
  10.1002/jcc.24767
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K18532, KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] 計算生物物理学の将来2016
- Author(s)
  岡本祐幸
- Journal Title
  
  Seibutsu Butsuri
  
  Volume: 56 Issue: 2 Pages: 075-075
- DOI
  10.2142/biophys.56.075
- NAID
  130005140938
- ISSN
  0582-4052, 1347-4219
- Language
  Japanese
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001
[Journal Article] “Modeling 15N NMR chemical shift changes in protein backbone with pressure”2016
- Author(s)
  G. La Penna, Y. Mori, R. Kitahara, K. Akasaka, and Y. Okamoto
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 145 Issue: 8 Pages: 085104-085104
- DOI
  10.1063/1.4961507
- NAID
  120006545080
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] QM/MM free energy simulations: recent progress and challenges2016
- Author(s)
  X. Lu, D. Fang, S. Ito, Y. Okamoto, V. Ovchinnikov, and Q. Cui
- Journal Title
  
  Molecular Simulation
  
  Volume: 42 Issue: 13 Pages: 1056-1078
- DOI
  10.1080/08927022.2015.1132317
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-25102008, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Molecular Simulations of Protein Systems toward Drug Discovery2016
- Author(s)
  榮慶丈，西川直宏，塚本修一朗，鈴木孝禎，岡本祐幸
- Journal Title
  
  YAKUGAKU ZASSHI
  
  Volume: 136 Issue: 1 Pages: 113-120
- DOI
  10.1248/yakushi.15-00230-4
- NAID
  130005115191
- ISSN
  0031-6903, 1347-5231
- Year and Date
  2016-01-01
- Language
  Japanese
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071, KAKENHI-ORGANIZER-25102001
[Journal Article] Implementation of replica-exchange umbrella sampling to DFTB+ simulation package2016
- Author(s)
  S. Ito, S. Irle, Y. Okamoto
- Journal Title
  
  Comp. Phys. Commun.
  
  Volume: accepted Pages: 1-10
- DOI
  10.1016/j.cpc.2016.02.010
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26410013, KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation2015
- Author(s)
  Ying Zhang
- Journal Title
  
  Adv. Exp. Med. Biol.
  
  Volume: 842 Pages: 217-230
- DOI
  10.1007/978-3-319-11280-0_14
- ISBN
  9783319112794, 9783319112800
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-25121730, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Equilibrium molecular thermodynamics from Kirkwood sampling2015
- Author(s)
  S. Somani, Y. Okamoto, A.J. Ballard, and D.J. Wales
- Journal Title
  
  J. Phys. Chem. B,
  
  Volume: 119 Issue: 20 Pages: 6155-6169
- DOI
  10.1021/acs.jpcb.5b01800
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-INTERNATIONAL-15K21708, KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Designed-walk Replica-exchange Method for Simulations of Complex Systems2015
- Author(s)
  R. Urano, Y. Okamoto
- Journal Title
  
  Comput. Phys. Commun.
  
  Volume: - Pages: 380-383
- DOI
  10.1016/j.cpc.2015.07.007
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Conformational search simulations of Trp-cage using genetic crossover2015
- Author(s)
  Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Mikic, Katsuya Ishii & Yuko Okamoto
- Journal Title
  
  Moleculer Simulation
  
  Volume: 41 Issue: 10-12 Pages: 1045-1049
- DOI
  10.1080/08927022.2015.1016937
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Predictions of Tertiary Structures of a-helical Membrane Proteins by Replica-exchange Method with Consideration of Helix Deformations2015
- Author(s)
  R. Urano, H. Kokubo, Y. Okamoto
- Journal Title
  
  J. Phys. Soc. Jpn.
  
  Volume: 84 Issue: 8 Pages: 084802-084802
- DOI
  10.7566/jpsj.84.084802
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Observation of Helix Associations for Insertion of a Retinal Molecule and Distortions of Helix Structures in Bacteriorhodopsin2015
- Author(s)
  R. Urano, Y. Okamoto
- Journal Title
  
  J. Chem. Phys.
  
  Volume: 143 Issue: 23 Pages: 235101-235101
- DOI
  10.1063/1.4935964
- NAID
  120006545079
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Conformational search simulations of Trp-cage using genetic crossover2015
- Author(s)
  Y. Sakae, T. Hiroyasu, M. Miki, K. Ishii, and Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 41 Pages: 1045-1049
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001
[Journal Article] New Implementations of Replica-exchange Method for Simulations of Complex Systems: Dsigned-walk and Deterministic Replica-exchange Methods2015
- Author(s)
  R. Urano, Y. Okamoto
- Journal Title
  
  Phys. Procedia.
  
  Volume: 68 Pages: 100-104
- DOI
  10.1016/j.phpro.2015.07.116
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001
[Journal Article] Molecular dynamics simulations to clarify the concentration dependency of protein aggregation2015
- Author(s)
  N. Nishikawa, Y. Sakae, and Y. Okamoto
- Journal Title
  
  JPS Conference Proceedings
  
  Volume: 5
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001
[Journal Article] Editorial: ICMS2013 in Special Issue Special Issue: Proceedings of the 3rd International Conference on Molecular Simulation2015
- Author(s)
  Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 41 Issue: 10-12 Pages: 779-779
- DOI
  10.1080/08927022.2015.1048075
- Data Source
  KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation2015
- Author(s)
  N. Nishikawa, P.H. Nguyen, P. Derreumaux, and Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 41 Issue: 10-12 Pages: 1041-1044
- DOI
  10.1080/08927022.2014.938445
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Deterministic Replica-exchange Method without Pseudo Random Numbers for Simulations of Complex Systems2015
- Author(s)
  R. Urano, Y. Okamoto
- Journal Title
  
  Comput. Phys. Commun.
  
  Volume: 197 Pages: 128-135
- DOI
  10.1016/j.cpc.2015.08.020
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Molecular dynamics simulations to clarify the concentration dependency of protein aggregation2015
- Author(s)
  N. Nishikawa, Y. Sakae, and Y. Okamoto
- Journal Title
  
  JPS Conference Proceedings: Proceedings of Computational Science Workshop 2014 (CSW2014)
  
  Volume: * Pages: 011020-011020
- DOI
  10.7566/jpscp.5.011020
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] A conformational search method for protein systems using genetic crossover and metropolis criterion2014
- Author(s)
  Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Katsuya Ishii, Yuko Okamoto
- Journal Title
  
  J. Phys.: Conf. Ser.
  
  Volume: 487 Pages: 12003-12003
- DOI
  10.1088/1742-6596/487/1/012003
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001
[Journal Article] A conformational search method for protein systems using genetic crossover and metropolis criterion2014
- Author(s)
  Y. Sakae, T. Hiroyasu, M. Miki, K. Ishii, and Y. Okamoto
- Journal Title
  
  Journal of Physics: Conference Series
  
  Volume: 487
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-25102009
[Journal Article] Prediction of ligand binding affinity by the combination of replica-exchange method and double-decoupling method2014
- Author(s)
  Y. Okamoto, H. Kokubo, and T. Tanaka
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 10 Issue: 8 Pages: 3563-3569
- DOI
  10.1021/ct500539u
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Exploration of conformational spaces of high-mannose-type oligosaccharides by an NMR-validated simulation2014
- Author(s)
  T.Yamaguchi, Y.Sakae, Y.Zhang, S.Yamamoto, Y.Okamoto, and K.Kato
- Journal Title
  
  Angew. Chem. Int. Ed.
  
  Volume: 53 Issue: 41 Pages: 10941-10944
- DOI
  10.1002/ange.201406145
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-24249002, KAKENHI-PROJECT-24750170, KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102008, KAKENHI-PROJECT-26560451
[Journal Article] A conformational search method for protein systems using genetic crossover and Metropolis criterion2014
- Author(s)
  Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Katsuya Ishii, and Yuko Okamoto
- Journal Title
  
  Journal of Physics: Conference Series
  
  Volume: 487
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-25247071
[Journal Article] Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations2014
- Author(s)
  T. Yoda, Y. Sugita, and Y. Okamoto
- Journal Title
  
  Proteins: Structure, Function, and Bioinformatics
  
  Volume: 82 Issue: 6 Pages: 933-943
- DOI
  10.1002/prot.24467
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071, KAKENHI-PROJECT-25330355
[Journal Article] Exploration of conformational spaces of high-mannose-type oligosaccharides by an NMR-validated simulation2014
- Author(s)
  T. Yamaguchi, Y. Sakae, Y. Zhang, S. Yamamoto, Y. Okamoto, and K. Kato
- Journal Title
  
  Angewandte Chemie International Edition
  
  Volume: 53 Issue: 41 Pages: 10941-10944
- DOI
  10.1002/anie.201406145
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Simulated tempering with fast on-the-fly weight determination2013
- Author(s)
  P.H. Nguyen, Y. Okamoto, and P. Derreumaux
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 138
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Amino-acid-dependent main-chain torsion-energy terms for protein systems2013
- Author(s)
  Y. Sakae and Y. Okamoto
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 138 Issue: 6
- DOI
  10.1063/1.4774159
- NAID
  120006545077
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Improvement of the backbone-torsion-energy term in the force field for protein systems by double Fourier series expansion2013
- Author(s)
  Y. Sakae and Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 39 Issue: 2 Pages: 85-93
- DOI
  10.1080/08927022.2012.705432
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Simulated tempering with fast on-the-fly weight determination2013
- Author(s)
  P.H. Nguyen, Y. Okamoto, and P. Derreumaux
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 138 Issue: 6
- DOI
  10.1063/1.4792046
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Free-energy analyses of a proton transfer reaction by simulated-temperingumbrella sampling and first-principles molecular dynamics simulations2013
- Author(s)
  Yoshiharu Mori, Yuko Okamoto
- Journal Title
  
  Physical Review E
  
  Volume: Volume 87 Issue: 2
- DOI
  10.1103/physreve.87.023301
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-11J05693, KAKENHI-PLANNED-20107002
[Journal Article] Application of simulated tempering and magnetizing to a two-dimensional Potts model2013
- Author(s)
  T. Nagai, Y. Okamoto, and W. Janke
- Journal Title
  
  Journal of Statistical Mechanics: Theory and Experiment 2013
  
  Volume: P02039 Pages: 21-21
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Improvement of the backbone-torsion-energy term in the force field for protein systems by the double Fourier series expansion2013
- Author(s)
  Y. Sakae and Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 39 Pages: 85-93
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations2013
- Author(s)
  Y. Mori and Y. Okamoto
- Journal Title
  
  Physical Review E
  
  Volume: 87
- NAID
  120006545928
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Application of simulated tempering and magnetizing to a two-dimensional Potss model2013
- Author(s)
  T. Nagai, Y. Okamoto, and W. Janke
- Journal Title
  
  Journal of Statistical Mechanics: Theory and Experiment
  
  Volume: 2013 Issue: 02 Pages: P02039-P02039
- DOI
  10.1088/1742-5468/2013/02/p02039
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Amino-aciddependent main-chain torsion-energy terms for protein systems2013
- Author(s)
  Y. Sakae and Y. Okamoto
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 138
- NAID
  120006545077
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Crossover scaling in the two-dimensional three-state Potts model2013
- Author(s)
  Tetsuro Nagai, Yuko Okamoto, and Wolfhard Janke
- Journal Title
  
  Condensed Matter Physics
  
  Volume: 16 Issue: 2 Pages: 23605-23605
- DOI
  10.5488/cmp.16.23605
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Two-dimensional replica-exchange method for predicting protein-ligand binding structures2013
- Author(s)
  Hironori Kokubo1, Toshimasa Tanaka, Yuko Okamoto
- Journal Title
  
  J. Comput. Chem.
  
  Volume: 34 Issue: 30 Pages: 2601-2614
- DOI
  10.1002/jcc.23427
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations: application to kinase systems2013
- Author(s)
  Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto
- Journal Title
  
  J. Chem. Theory Comput.
  
  Volume: 9 Issue: 10 Pages: 4660-4671
- DOI
  10.1021/ct4004383
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071
[Journal Article] Molecular simulations in generalized ensemble2012
- Author(s)
  Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 38 Issue: 14-15 Pages: 1282-1296
- DOI
  10.1080/08927022.2012.690878
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] タンパク質分子シミュレーションのための力場関数2012
- Author(s)
  榮慶丈、依田隆夫、杉田有治、岡本祐幸
- Journal Title
  
  日本物理学会誌
  
  Volume: 67 Pages: 343-349
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Simulated tempering and magnetizing simulations of the Ising model2012
- Author(s)
  T. Nagai and Y. Okamoto
- Journal Title
  
  Physics Procedia
  
  Volume: 34 Pages: 100-104
- DOI
  10.1016/j.phpro.2012.05.016
- NAID
  120006545937
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Phase behavior of a lipid bilayer system studied by a replica-exchange molecular dynamics simulation2012
- Author(s)
  T.Nagai, R.Ueoka, Y.Okamoto
- Journal Title
  
  Journal of the Physical Society of Japan
  
  Volume: 81 Issue: 2 Pages: 24002-24010
- DOI
  10.1143/jpsj.81.024002
- NAID
  40019151203
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002, KAKENHI-PROJECT-24656509, KAKENHI-PLANNED-20107007
[Journal Article] タンパク質系分子シミュレーションのための力場関数2012
- Author(s)
  榮慶丈,依田隆夫,杉田有治,岡本祐幸
- Journal Title
  
  日本物理学会誌
  
  Volume: 67巻 Pages: 343-349
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] 疎水コアとα-ヘリックスを含む小蛋白質のフォールディングシミュレーション2012
- Author(s)
  依田隆夫、杉田有治、岡本祐幸
- Journal Title
  
  生物物理(日本生物物理学会誌)
  
  Volume: 52 Pages: 22-23
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Simulated tempering and magnetizing: Application of two-dimensional simulated tempering to the two-dimensional Ising model and its crossover2012
- Author(s)
  T. Nagai and Y. Okamoto
- Journal Title
  
  Physical Review E
  
  Volume: 86 Issue: 5
- DOI
  10.1103/physreve.86.056705
- NAID
  120006545927
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Residual entropy of ordinary ice calculated from multicanonical Monte Carlo simulations2012
- Author(s)
  B. A. Berg
- Journal Title
  
  Molecular Simulation
  
  Volume: 38 Issue: 11 Pages: 856-860
- DOI
  10.1080/08927022.2011.651140
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-20107001, KAKENHI-PLANNED-20107002
[Journal Article] Generalized-ensemble algorithms for protein folding and unfolding2012
- Author(s)
  Y.Okamoto
- Journal Title
  
  Current Physical Chemistry
  
  Volume: 2 Pages: 92-106
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] temperature and pressure dependence of complex systems2012
- Author(s)
  Generalized-ensemble algorithms for studying Y. Mori, Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 38 Issue: 5 Pages: 452-457
- DOI
  10.1080/08927022.2011.651139
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-20107001
[Journal Article] Phase behavior of a lipid bilayer system studied by a replica-exchange molecular dynamics simulation2012
- Author(s)
  T. Nagai, R. Ueoka, and Y. Okamoto
- Journal Title
  
  Journal of the Physical Society of Japan
  
  Volume: 81
- NAID
  40019151203
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Ab initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations2011
- Author(s)
  H. Kokubo, T. Tanaka, and Y. Okamoto
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 32 Pages: 2810-2821
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Dynamic structure of the polytheonamide B channel studied by normal mode analysis2011
- Author(s)
  T. Mori, H. Kokubo, S. Oiki, and Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 37 Pages: 975-985
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Drug design by generalized-ensemble simulations2011
- Author(s)
  Y. Okamoto
- Journal Title
  
  Current Pharmaceutical Design
  
  Volume: 17 Pages: 1758-1772
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Generalized-ensemble simulations in protein science2011
- Author(s)
  Y.Mori, A.Mitsutake, Y.Okamoto
- Journal Title
  
  Proceedings of the 4th Japan-Russia International Workshop MSSMBS'10 "Molecular Simulations Studies in Material and Biological Sciences"
  
  Pages: 46-60
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] New conformational search method using genetic algorithm and knot theory for proteins2011
- Author(s)
  Y.Sakae, T.Hiroyasu, M.Miki, Y.Okamoto
- Journal Title
  
  Pacific Symposium on Biocomputing
  
  Volume: 16 Pages: 217-228
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover2011
- Author(s)
  Y. Sakae, T. Hiroyasu, M. Miki, and Y. Okamoto
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 32 Pages: 1353-1360
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Determination method of the balance of the secondary-structure-forming tendencies of force fields2010
- Author(s)
  Y.Sakae, Y.Okamoto
- Journal Title
  
  Molecular Simulation 36
  
  Pages: 159-165
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Controlling the secondary-structure-forming tendencies of proteins by a backbone torsion-energy term2010
- Author(s)
  Y.Sakae, Y.Okamoto
- Journal Title
  
  Molecular Simulation 36
  
  Pages: 138-158
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] 計算機シミュレーションによるアミロイド病発現原理の追求2010
- Author(s)
  岡本祐幸
- Journal Title
  
  Medical Bio(10月別冊、特集「揺らぎと生体機能」)
  
  Pages: 17-20
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] 『拡張アンサンブル法』の特集にあたって2010
- Author(s)
  岡本祐幸
- Journal Title
  
  分子シミュレーション研究会会誌"アンナンブル"
  
  Volume: 12 Pages: 6-7
- NAID
  130004566668
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] マルチカノニカルレプリカ交換分子動力学法による小蛋白質の折れ畳みシミュレーション2010
- Author(s)
  依田隆夫、杉田有治、岡本祐幸
- Journal Title
  
  分子シミュレーション研究会会誌"アンサンブル"
  
  Volume: 12 Pages: 15-18
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations2010
- Author(s)
  T.Yoda, Y.Sugita, Y.Okamoto
- Journal Title
  
  Biophysical Journal 99
  
  Pages: 1637-1644
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Replica-exchange molecular dynamics simulations for various constant temperature algorithms2010
- Author(s)
  Y.Mori, Y.Okamoto
- Journal Title
  
  Journal of the Physical Society of Japan
  
  Volume: 79
- NAID
  40017205438
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations2010
- Author(s)
  T. Yoda, Y. Sugita, and Y. Okamoto
- Journal Title
  
  Biophysical Journal
  
  Volume: 99 Pages: 1637-1644
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Generalized-ensemble algorithms for the isobaric-isothermal ensemble.2010
- Author(s)
  Y.Mori , Y.Okamoto
- Journal Title
  
  Journal of the Physical Society of Japan 79
- NAID
  40017205440
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Generalized-ensemble algorithms for the isobaric-isothermal ensemble2010
- Author(s)
  Y. Mori and Y. Okamoto
- Journal Title
  
  Journal of the Physical Society of Japan
  
  Volume: 79
- NAID
  40017205440
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Multi-dimensional multicanonical algorithm, simulated tempering, replica-exchange method, and all that2010
- Author(s)
  A.Mitsutake, Y.Mori, Y.Okamoto
- Journal Title
  
  Physics Procedia
  
  Volume: 4 Pages: 89-105
- NAID
  120006545938
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Helix-hairpin transitions of a designed peptide studied by a generalized-ensemble simulations2010
- Author(s)
  S.G.Itoh, A.Tamura, Y.Okamoto
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 6 Pages: 979-983
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Helix-hairpin transitions of a designed peptide studied by a generalized-ensemble simulation2010
- Author(s)
  S.G. Itoh, A. Tamura, and Y. Okamoto
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 6 Pages: 979-983
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Folding simulations of three proteins having all alpha-helix, all beta-stand and alpha/beta structures2010
- Author(s)
  Y. Sakae and Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 36 Pages: 302-310
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Generalized-ensemble algorithms for the isobaric-isothermal ensembles2010
- Author(s)
  Y.Mori, Y.Okamoto
- Journal Title
  
  Journal of the Physical Society of Japan
  
  Volume: 79
- NAID
  40017205440
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Optimisation of OPLS-UA force-field parameters for protein systems using protein data bank2010
- Author(s)
  Y.Sakae, Y.Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 36 Pages: 1147-1155
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Hydrophobic core formation and dehydration in protein folding studied by generalized ensemble simulations2010
- Author(s)
  T.Yoda, Y.Sugita, Y.Okamoto
- Journal Title
  
  Biophysical Journal
  
  Volume: 99 Pages: 1637-1644
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Replica-exchange method in van der Waals radius space : overcoming steric restrictions for biomolecules2010
- Author(s)
  S.G.Itoh, H.Okumura, Y.Okamoto
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 132
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Replica-exchange method in van der Waals radius space: overcoming steric resctirctions for biomolecules2010
- Author(s)
  S.G. Itoh, H. Okumura, and Y. Okamoto
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 132
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Optimisation of OPLS-UA force-field parameters for protein systems using protein data bank2010
- Author(s)
  Y. Sakae and Y. Okamoto
- Journal Title
  
  Molecular Simulation
  
  Volume: 36 Pages: 1148-1156
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Dependency of ligand free energy landscapes on charge parameters and solvent models2010
- Author(s)
  Y. Okamoto, T. Tanaka, and H. Kokubo
- Journal Title
  
  Journal of Computer-Aided Molecular Design
  
  Volume: 24 Pages: 699-712
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Replica-exchange molecular dynamics simulations for various constant temperature algorithms2010
- Author(s)
  Y. Mori and Y. Okamoto
- Journal Title
  
  Journal of the Physical Society of Japan
  
  Volume: 79
- NAID
  40017205438
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] タンパク質系のポテンシャル関数の比較と改良2009
- Author(s)
  榮慶丈、依田隆夫、杉田有治、岡本祐幸
- Journal Title
  
  アンサンブル 11
  
  Pages: 8-12
- NAID
  130004566636
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Multidimensional generalized-ensemble algorithms for complex systems2009
- Author(s)
  A. Mitsutake and Y. Okamoto
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 130
- NAID
  120001804816
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Folding simulations of gramicidin A into the β -helix conformations: simulated annealing molecular dynamics study2009
- Author(s)
  T. Mori and Y. Okamoto
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 131
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Generalized-ensemble algorithms for protein structure predictions2009
- Author(s)
  Y.Sakae, Y.Okamoto
- Journal Title
  
  Proceedings of International Conference on Computational & Experimental Engineering (Tech Science Press, Norcross) and Sciences 2009 (ICCES'09)
  
  Pages: 791-801
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering2009
- Author(s)
  A. Mitsutake and Y. Okamoto
- Journal Title
  
  Physical Review E
  
  Volume: 79
- NAID
  120006545926
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Multidimensional generalized-ensemble algorithms for complex systems2009
- Author(s)
  A.Mitsutake, Y.Okamoto
- Journal Title
  
  Journal of Chemical Physics 130
- NAID
  120001804816
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Multidimensional generalized- ensemble algorithms for complex systems.2009
- Author(s)
  A.Mitsutake , Y.Okamoto
- Journal Title
  
  Journal of Chemical Physics 130
- NAID
  120001804816
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering2009
- Author(s)
  A.Mitsutake, Y.Okamoto
- Journal Title
  
  Physical Review E 79
- NAID
  120006545926
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Analysis of helix-helix interactions of bacteriorhodopsin by replica-exchange simulations2009
- Author(s)
  H. Kokubo, Y. Okamoto
- Journal Title
  
  Biophysical Journal 96(in press)
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20038025
[Journal Article] Folding simulations of gramicidin A into the β-helix conformations : simulated annealing molecular dynamics study2009
- Author(s)
  T.Mori, Y.Okamoto
- Journal Title
  
  Journal of Chemical Physics 131
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-20107002
[Journal Article] Thermodynamics of two lattice ice models in three dimensions2008
- Author(s)
  C. muguruma, Y. Okamoto, B.A. Berg
- Journal Title
  
  Physical Review E 78
- NAID
  120006545924
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20038025
[Journal Article] Temperuature and pressure dependence of alanine dipeptide studied by multibaric-multithermal molecular dynamics simulations2008
- Author(s)
  H. Okumura, Y. Okamoto
- Journal Title
  
  Journal of Physical Chemistry B 112
  
  Pages: 12038-12049
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20038025
[Journal Article] Multibaric-multithermal molecular dynamics simulation of alanine dipe ptide in explicit water2007
- Author(s)
  H. Okumura & Y. Okamoto
- Journal Title
  
  Bulletin of the Chemical Society of Japan 80
  
  Pages: 1114-1123
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] A new generalized-ensemble algorithm : multicanonical-multioverlap algorithm2007
- Author(s)
  S.G.Itoh, Y.Okamoto
- Journal Title
  
  Molecular Simulation 33
  
  Pages: 83-90
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Generalized-ensemble algorithms for molecular dynamics simulations2007
- Author(s)
  S.G.Itoh, H.Okumura, Y.Okamoto
- Journal Title
  
  Molecular Simulation 33
  
  Pages: 47-56
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Replica-exchange moleculr dynamics simulation of diffracted X-ray tracking2007
- Author(s)
  Y.Kawashima, Y.C.Sasaki, Y.Sugita, T.Yoda, Y.Okamoto
- Journal Title
  
  Molecular Simulation 33
  
  Pages: 97-102
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation2007
- Author(s)
  T.Yoda, Y.Sugita, Y Okamoto
- Journal Title
  
  PROTEINS : Structure, Function, and Bioinformatics 66
  
  Pages: 846-859
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Multibaric-multithermal molecular dynamics simulation : generalized Nose-Poincare-Andersen method2007
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Molecular Simulation 33
  
  Pages: 91-96
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Residual entropy of ordinary ice from multicanonical simulations2007
- Author(s)
  B.A.Berg, C.Muguruma, Y.Okamoto
- Journal Title
  
  Physical Review B 75
- NAID
  120006545083
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm2007
- Author(s)
  S.G. Itoh & Y. Okamoto
- Journal Title
  
  Physical Review E 76
  
  Pages: 2670510-2670510
- NAID
  120006545922
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles2007
- Author(s)
  H.Okumura, S.G.Itoh, Y.Okamoto
- Journal Title
  
  Journal of Chemical Physics 126
- NAID
  120006545076
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Replica-exchange methods and predictions of helix configuration of membrane proteins2006
- Author(s)
  H.Kokubo, Y.Okamoto
- Journal Title
  
  Molecular Simulation 32
  
  Pages: 791-801
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Theoretical studies of transition states by the multioverlap molecular dynamics methods2006
- Author(s)
  S.G.Itoh, Y.Okamoto
- Journal Title
  
  Journal of Chemical Physics 124
- NAID
  120000975328
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Secondary-structure design of proteins by a backbone torsion energy2006
- Author(s)
  Y.Sakae, Y.Okamoto
- Journal Title
  
  Journal of Physical Society of Japan 75
- NAID
  110004702343
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] 拡張アンサンブル法による膜タンパク質の立体構造予測2006
- Author(s)
  小久保裕功, 岡本祐幸
- Journal Title
  
  統計数理 54
  
  Pages: 211-222
- NAID
  120006019067
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] 生体系における大規模分子シミュレーション2006
- Author(s)
  岡本祐幸
- Journal Title
  
  応用数理 16
  
  Pages: 15-19
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Multibaric-multithermal ensemble molecular dynamics simulations2006
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Journal of Computational Chemistry 27
  
  Pages: 379-395
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Structures of a peptide fragment of β2-microglobulin studied by replica-exchange molecular dynamics simulations - towards the understanding of the mechanism of amyloid formation2005
- Author(s)
  M.Nishino, Y.Sugita, T.Yoda, Y.Okamoto
- Journal Title
  
  FEBS Letters 579
  
  Pages: 5425-5429
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Molecular simulations in the multibaric-multithermal ensembles2005
- Author(s)
  H.Okurnura, Y.Okamoto
- Journal Title
  
  Computer Physics Communications 169
  
  Pages: 317-321
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] PDBデータベースを用いたタンパク質力場パラメータの最適化2005
- Author(s)
  榮慶丈, 岡本祐幸
- Journal Title
  
  生物物理 45
  
  Pages: 145-148
- NAID
  110001801950
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] マルチバーリック・マルチサーマルアンサンブルにおけるレナード・ジョーンズ流体のシミュレーション2005
- Author(s)
  奥村久士, 岡本祐幸
- Journal Title
  
  物性研究 85
  
  Pages: 341-346
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Multibaric-multithermal ensemble simulations for fluid systems2005
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Physica A 350
  
  Pages: 150-158
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. II. Free energy analysis2005
- Author(s)
  Murata, Y.Sugita, Y.Okamoto
- Journal Title
  
  Journal of Theoretical & Computational Chemistry 4
  
  Pages: 433-448
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Effects of the fixed end in single-molecule imaging techniques : A replica-exchange molecular dynamics study2005
- Author(s)
  Y.Kawashima, Y.Sugita, T.Yoda, Y.Okamoto
- Journal Title
  
  Chemical Physics Letters 414
  
  Pages: 449-455
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Replica-exchange molecular dynamics simulation of small peptide in water and in ethanol2005
- Author(s)
  K.Yoshida, T.Yamaguchi, Y.Okamoto
- Journal Title
  
  Chemical Physics Letters 412
  
  Pages: 280-284
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent2005
- Author(s)
  Y.Sugita, Y.Okamoto
- Journal Title
  
  Biophysical Journal 88
  
  Pages: 3180-3190
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. I. Test of sampling efficiency2005
- Author(s)
  K.Murata, Y.Sugita, Y.Okamoto
- Journal Title
  
  Journal of Theoretical & Computational Chemistry 4
  
  Pages: 411-432
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] タンパク質のフォールディングシミュレーションから立体構造予測問題に迫る2005
- Author(s)
  岡本祐幸, 高田彰二
- Journal Title
  
  現代化学 408
  
  Pages: 47-53
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Generalized-ensemble algorithms : enhanced sampling techniques for Monte Carlo and molecular dynamics simulations2004
- Author(s)
  Y.Okamoto
- Journal Title
  
  J.Mol.Graphics Modell. 22
  
  Pages: 425-439
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Prediction of membrane protein structures by replica-exchange Monte Carlo simulations : case of two helices2004
- Author(s)
  H.Kokubo, Y.Okamoto
- Journal Title
  
  J.Chem.Phys. 120
  
  Pages: 10837-10847
- NAID
  120006545074
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Multi-overlap molecular dynamics methods for biomolecular systems2004
- Author(s)
  S.G.Itoh, Y.Okamoto
- Journal Title
  
  Chem.Phys.Lett. 400
  
  Pages: 308-313
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Replica-exchange extensions of simulated tempering method2004
- Author(s)
  A.Mitsutake, Y.Okamoto
- Journal Title
  
  J.Chem.Phys. 121
  
  Pages: 2491-2504
- NAID
  120006545075
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Protein force-field parameters optimized with the Protein Data Bank. II.Comparisons of force fields by folding simulations of short peptides2004
- Author(s)
  Y.Sakae, Y.Okamoto
- Journal Title
  
  J.Theor.Comput.Chem. 3
  
  Pages: 359-378
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Comparisons of force fields for proteins by generalized-ensemble simulations2004
- Author(s)
  T.Yoda, Y.Sugita, Y.Okamoto
- Journal Title
  
  Chem.Phys.Lett. 386
  
  Pages: 460-467
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations2004
- Author(s)
  T.Yoda, Y.Sugita, Y.Okamoto
- Journal Title
  
  Chem.Phys. 307
  
  Pages: 269-283
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Monte Carlo simulations in new generalized isobaric-isothermal ensemble2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Trans.MRS-J. 29
  
  Pages: 3783-3786
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Monte Carlo simulations in generalized isobaric-isothermal ensembles2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Phys.Rev.E 70
  
  Pages: 26702-26702
- NAID
  120006545921
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Multibaric-multithermal ensemble simulation for simple liquids2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Mol.Sim. 30
  
  Pages: 847-852
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] New approach to the first-order phase transition of Lennard-Jones fluids2004
- Author(s)
  C.Muguruma, Y.Okamoto, M.Mikami
- Journal Title
  
  J.Chem.Phys. 120
  
  Pages: 7557-7563
- NAID
  120006545073
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Classification and prediction of low-energy membrane protein helix configurations by replica-exchange Monte Carlo method2004
- Author(s)
  H.Kokubo, Y.Okamoto
- Journal Title
  
  J.Phys.Soc.Jpn. 73
  
  Pages: 2571-2585
- NAID
  110001955018
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Liquid-gas phase transitions studied by multibaric-multithermal Monte Carlo simulations2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  J.Phys.Soc.Jpn. 73
  
  Pages: 3304-3311
- NAID
  110001979299
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange simulation2004
- Author(s)
  H.Kokubo, Y.Okamoto
- Journal Title
  
  Chem.Phys.Lett. 392
  
  Pages: 168-175
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Combination of the replica-exchange Monte Carlo method and the reference interaction site model theory for simulating a peptide molecule in aqueous solution2004
- Author(s)
  A.Mitsutake, M.Kinoshita, Y.Okamoto, F.Hirata
- Journal Title
  
  J.Phys.Chem.B 108
  
  Pages: 19002-19012
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Molecular dynamics simulations in multibaric-multithermal ensemble2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Chem.Phys.Lett. 383
  
  Pages: 403-408
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Protein force-field parameters optimized with the Protein Data Bank. I.Force-filed optimizations2004
- Author(s)
  Y.Sakae, Y.Okamoto
- Journal Title
  
  J.Theor.Comput.Chem. 3
  
  Pages: 339-358
- Data Source
  KAKENHI-PROJECT-15076213
[Presentation] Generalized-ensemble simulations of biological molecular assembly and artificial molecular assembly2018
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 6th International Symposium on Dynamical Ordering of Biological Systems for Creation of Integrated Functions
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble simulations of biological molecular assembly and artificial molecular assembly2018
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 6th International Symposium on Dynamical Ordering of Biological Systems for Creation of Integrated Functions
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Energy landscape of biomolecular systems studied by generalized-ensemble simulations2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  Energy Landscapes 2017
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Conformational analysis of high mannose-type oligosaccharides by self-guided langevin dynamics simulation2017
- Author(s)
  Yoshitake Sakae, Takumi Yamaguchi, Xiongwu Wu, Bernard R. Brooks, Koichi Kato, and Yuko Okamoto
- Organizer
  The 5th International Symposium on Dynamical Ordering of Biomolecular Systems
- Place of Presentation
  東京大学駒場キャンパス（東京都目黒区）
- Year and Date
  2017-01-21
- Int'l Joint Research
- Data Source
  KAKENHI-INTERNATIONAL-15K21708
[Presentation] Efficient sampling methods for classical and quantum simulations2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  TSRC Workshop on the Chemistry and Dynamics in Complex Environments (CHEM-DiCE)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Biomolecular simulations in generalized ensemble　Frontier Bioorganization2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  Forum 2017: Dynamical Ordering and Integrated　Functions of Biomolecular Systems
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Biomolecular simulations in generalized ensemble　Frontier Bioorganization2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  Forum 2017: Dynamical Ordering and Integrated　Functions of Biomolecular Systems
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble algorithms: enhanced conformational sampling methods2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 16th KIAS Protein Folding Winter School
- Place of Presentation
  High 1 Resort, Korea
- Year and Date
  2017-01-16
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Classical and quantum molecular simulations in generalized ensemble2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  International Workshop on Molecular Simulations
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Energy landscape of biomolecular systems studied by generalized-ensemble simulations2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  Energy Landscapes 2017
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble algorithms for advanced materials simulations2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  IUMRS-ICAM 2017, The 15th International Conference on Advanced Materials
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Classical and quantum molecular simulations in generalized ensemble2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  International Workshop on Molecular Simulations
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms: enhanced conformational sampling methods2017
- Author(s)
  Yuko Okamoto
- Organizer
  The 16th KIAS Protein Folding Winter School
- Place of Presentation
  High 1 Resort,seoul, Korea
- Year and Date
  2017-01-16
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for materials and biomolecular simulations [Keynote Talk]2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  Molecular Simulation Studies in Material
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 蛋白質高圧変性の分子シミュレーション2017
- Author(s)
  岡本　祐幸
- Organizer
  第58回高圧討論会「生物関連高圧シンポジウム：高圧力と生命・生体分子」
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Biomolecular simulations in generalized ensemble2017
- Author(s)
  Yuko Okamoto
- Organizer
  Frontier Bioorganization Forum 2017: Dynamical ordering and integrated functions of biomolecular systems
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-INTERNATIONAL-15K21708
[Presentation] Generalized-ensemble algorithms for advanced materials simulations2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  IUMRS-ICAM 2017, The 15th International Conference on Advanced Materials
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Efficient sampling methods for classical and quantum simulations2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  TSRC Workshop on the Chemistry and Dynamics in Complex Environments (CHEM-DiCE)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble algorithms for materials and biomolecular simulations [Keynote Talk]2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  Molecular Simulation Studies in Material
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Conformational analysis of high mannose-type oligosaccharides by self-guided langevin dynamics simulation2017
- Author(s)
  Yoshitake Sakae, Takumi Yamaguchi, Xiongwu Wu, Bernard R. Brooks, Koichi Kato, and Yuko Okamoto
- Organizer
  The 5th International Symposium on Dynamical Ordering of Biomolecular Systems
- Place of Presentation
  東京大学駒場キャンパス（東京都目黒区）
- Year and Date
  2017-01-21
- Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] 蛋白質高圧変性の分子シミュレーション2017
- Author(s)
  岡本　祐幸
- Organizer
  第58回高圧討論会「生物関連高圧シンポジウム：高圧力と生命・生体分子」
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms: enhanced conformational sampling methods2017
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 16th KIAS Protein Folding Winter School
- Place of Presentation
  High 1 Resort, Korea
- Year and Date
  2017-01-16
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル法による複雑系の計算機シミュレーション2016
- Author(s)
  岡本祐幸
- Organizer
  国際高等研究所　研究プロジェクト「分子基盤に基づく生体機能ネットワークとダイナミクスの解明」第５回研究会
- Place of Presentation
  木津川市、日本
- Year and Date
  2016-02-18
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Protein dynamics studied by generalized-ensemble simulations2016
- Author(s)
  Yuko Okamoto
- Organizer
  The 251st American Chemical Society National Meeting
- Place of Presentation
  San Diego, U.S.A
- Year and Date
  2016-03-13
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble simulations of complex systems2016
- Author(s)
  Yuko Okamoto
- Organizer
  2016 NCTS March Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Hsinchu, Taiwan
- Year and Date
  2016-03-28
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Introduction to Generalized-Ensemble MD　Simulations Including the Replica-Exchange　Umbrella Sampling (REUS) Method2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  2-Day Mini Workshop: Approximate DFT Methods for Extended Systems
- Place of Presentation
  Nagoya, Japan
- Year and Date
  2016-06-20
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Enhanced sampling methods for classical and quantum molecular simulations2016
- Author(s)
  Yuko Okamoto
- Organizer
  The 9th Korea-Japan Seminars on Biomolecular Sciences: Experiments and Simulations
- Place of Presentation
  Gyeongju, Korea
- Year and Date
  2016-11-14
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Introduction to Generalized-Ensemble MD　Simulations Including the Replica-Exchange　Umbrella Sampling (REUS) Method2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  2-Day Mini Workshop: Approximate DFT Methods for Extended Systems
- Place of Presentation
  Nagoya, Japan
- Year and Date
  2016-06-20
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] レプリカ交換分子動力学シミュレーションによる抗体及びFc受容体内の糖鎖分子の解析2016
- Author(s)
  榮　慶丈，山口拓実，佐藤匡史，谷中冴子，加藤晃一，岡本祐幸
- Organizer
  第43回生体分子科学討論会
- Place of Presentation
  名古屋大学大学院理学研究科（愛知県名古屋市）
- Year and Date
  2016-06-25
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Enhanced sampling methods for classical and quantum molecular simulations2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 9th Korea-Japan Seminars on Biomolecular Sciences: Experiments and Simulations
- Place of Presentation
  Gyeongju, Korea
- Year and Date
  2016-11-14
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Energy landscape explored by generalized-ensemble algorithms2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  Energy Landscapes: Theory and Applications (ELAND 2016)
- Place of Presentation
  Porquerolles, France
- Year and Date
  2016-06-27
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms and free energy calculations2016
- Author(s)
  Yuko Okamoto
- Organizer
  Symposium “Free Energy Landscape of Protein Folding and Dynamics by Simulations Based on Enhanced Conformational Sampling Algorithms”
- Place of Presentation
  Nagoya Univ.(Nagoya,Aichi, Japan)
- Year and Date
  2016-08-06
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for classical and quantum molecular simulations (Plenary talk)2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 4th International Conference on Molecular Simulation (ICMS2016)
- Place of Presentation
  Shanghai, China
- Year and Date
  2016-10-23
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble algorithms for classical and quantum molecular simulations (Plenary talk)2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 4th International Conference on Molecular Simulation (ICMS2016)
- Place of Presentation
  Shanghai, China
- Year and Date
  2016-10-23
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble simulations of complex systems2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  2016 NCTS March Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Hsinchu, Taiwan
- Year and Date
  2016-03-28
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル法による複雑系の計算機シミュレーション2016
- Author(s)
  岡本祐幸
- Organizer
  国際高等研究所　研究プロジェクト「分子基盤に基づく生体機能ネットワークとダイナミクスの解明」第５回研究会
- Place of Presentation
  木津川市、日本
- Year and Date
  2016-02-18
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble algorithms and free energy calculations2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  Symposium “Free Energy Landscape of Protein Folding and Dynamics by Simulations Based on Enhanced Conformational Sampling Algorithms”
- Place of Presentation
  Nagoya, Japan
- Year and Date
  2016-08-06
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms and free energy calculations2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  Symposium “Free Energy Landscape of Protein Folding and Dynamics by Simulations Based on Enhanced Conformational Sampling Algorithms”
- Place of Presentation
  Nagoya, Japan
- Year and Date
  2016-08-06
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble simulations of complex systems2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  2016 NCTS March Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Hsinchu, Taiwan
- Year and Date
  2016-03-28
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Protein dynamics studied by generalized-ensemble simulations2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 251st American Chemical Society National Meeting Symposium under the Computers in Chemistry (COMP) Division “30 Years of Protein Dynamics in Silico”
- Place of Presentation
  San Diego, California, U.S.A.
- Year and Date
  2016-03-13
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Protein dynamics studied by generalized-ensemble simulations2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 251st American Chemical Society National Meeting Symposium under the Computers in Chemistry (COMP) Division “30 Years of Protein Dynamics in Silico”
- Place of Presentation
  San Diego, California, U.S.A.
- Year and Date
  2016-03-13
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Energy landscape explored by generalized-ensemble algorithms2016
- Author(s)
  Yuko Okamoto
- Organizer
  Energy landscape explored by generalized-ensemble algorithms
- Place of Presentation
  Porquerolles, France
- Year and Date
  2016-06-27
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Enhanced sampling methods for classical and quantum molecular simulations2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 9th Korea-Japan Seminars on Biomolecular Sciences: Experiments and Simulations
- Place of Presentation
  Gyeongju, Korea
- Year and Date
  2016-11-14
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Energy landscape explored by generalized-ensemble algorithms2016
- Author(s)
  Yuko OKAMOTO
- Organizer
  Energy Landscapes: Theory and Applications (ELAND 2016)
- Place of Presentation
  Porquerolles, France
- Year and Date
  2016-06-27
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Introduction to Generalized-Ensemble MD Simulations Including the Replica-Exchange Umbrella Sampling (REUS) Method2016
- Author(s)
  Yuko Okamoto
- Organizer
  2-Day Mini Workshop: Approximate DFT Methods for Extended Systems
- Place of Presentation
  Nagoya Univ.(Nagoya,Aichi, Japan)
- Year and Date
  2016-06-20
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for calculations of ligand binding affinity2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  BIRS Workshop: Free-Energy Calculations. A Mathematical Perspective
- Place of Presentation
  Oaxaca, Mexico
- Year and Date
  2015-07-19
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 古典系および量子系の拡張アンサンブルシミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  スーパーコンピュータワークショップ
- Place of Presentation
  岡崎市、日本
- Year and Date
  2015-09-07
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] 拡張アンサンブル法による生体分子系のシミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  リトリート分子科学研究所研修「分子科学の新世界：理論と実験のハーモニー」
- Place of Presentation
  岡崎市、愛知県、日本
- Year and Date
  2015-01-24
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble simulations of classical and quantum molecular systems2015
- Author(s)
  Yuko Okamoto
- Organizer
  The 6th Japan-Czech-Slovak International Symposium for Theoretical Chemistry
- Place of Presentation
  Smolenice, Slovakia
- Year and Date
  2015-10-11
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble simulations of classical and quantum molecular systems2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 6th Japan-Czech-Slovak International Symposium for Theoretical Chemistry
- Place of Presentation
  Smolenice, Slovakia
- Year and Date
  2015-10-11
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble simulations of classical and quantum molecular systems2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 6th Japan-Czech-Slovak International Symposium for Theoretical Chemistry
- Place of Presentation
  Smolenice, Slovakia
- Year and Date
  2015-10-11
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Efficient sampling methods for complex systems2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 19th International Annual Symposium on Computational Science and Engineering (ANSCSE19)
- Place of Presentation
  Ubon Ratchathani, Thailand
- Year and Date
  2015-06-17
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル法による量子化学シミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  分子研研究会「理論計算分子科学ワークショップ」
- Place of Presentation
  岡崎市、日本
- Year and Date
  2015-10-22
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble simulations of complex systems2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  2015 NCTS International Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Hsinchu, Taiwan
- Year and Date
  2015-08-15
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] 拡張アンサンブル法による量子化学シミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  分子研研究会「理論計算分子科学ワークショップ」
- Place of Presentation
  岡崎市、日本
- Year and Date
  2015-10-22
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble simulations2015
- Author(s)
  Yuko Okamoto
- Organizer
  Hands-on Workshop on Computational Biophysics at Okazaki
- Place of Presentation
  岡崎コンファレンスセンター（愛知県岡崎市）
- Year and Date
  2015-09-09
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble simulations of complex systems2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  2015 NCTS International Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Hsinchu, Taiwan
- Year and Date
  2015-08-15
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms for enhanced sampling and free energy calculations2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  Summer Snowmass Biophysics Workshop Free Energy Calculations: Three Decades of Adventure in Chemistry and Biophysics
- Place of Presentation
  Snowmass, Colorado, U.S.A.
- Year and Date
  2015-07-05
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] 拡張アンサンブル法による生体分子シミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  バイオスーパーコンピューティング名古屋2015
- Place of Presentation
  名古屋市、愛知県、日本
- Year and Date
  2015-01-22
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル法による生体分子系のシミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  リトリート分子科学研究所研修「分子科学の新世界：理論と実験のハーモニー」
- Place of Presentation
  岡崎市、愛知県、日本
- Year and Date
  2015-01-24
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms for calculations of ligand binding affinity2015
- Author(s)
  Yuko Okamoto
- Organizer
  BIRS Workshop: Free-Energy Calculations. A Mathematical Perspective
- Place of Presentation
  Oaxaca, Mexico
- Year and Date
  2015-07-19
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Efficient sampling methods for identifying transition states2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  TSRC Workshop on the Chemistry and Dynamics in Complex Environments (CHEM-DiCE)
- Place of Presentation
  Telluride, Colorado, U.S.A.
- Year and Date
  2015-06-23
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] 古典系および量子系の拡張アンサンブルシミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  スーパーコンピュータワークショップ
- Place of Presentation
  岡崎コンファレンスセンター（愛知県岡崎市）
- Year and Date
  2015-09-07
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for enhanced sampling and free energy calculations2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  Summer Snowmass Biophysics Workshop Free Energy Calculations: Three Decades of Adventure in Chemistry and Biophysics
- Place of Presentation
  Snowmass, Colorado, U.S.A.
- Year and Date
  2015-07-05
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms for enhanced configurational sampling2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  Algorithms in Structural Bioinformatics: Sampling in Biomacromolecular Systems (AlgoSB Winter School - 2015)
- Place of Presentation
  Cargese, Corsica, France
- Year and Date
  2015-11-29
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms for enhanced configurational sampling2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  Algorithms in Structural Bioinformatics: Sampling in Biomacromolecular Systems (AlgoSB Winter School - 2015)
- Place of Presentation
  Cargese, Corsica, France
- Year and Date
  2015-11-29
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] 拡張アンサンブル法による量子化学シミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  分子研研究会「理論計算分子科学ワークショップ」
- Place of Presentation
  岡崎コンファレンスセンター（愛知県岡崎市）
- Year and Date
  2015-10-22
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for enhanced configurational sampling　Algorithms in Structural Bioinformatics: Sampling in Biomacromolecular Systems2015
- Author(s)
  Yuko Okamoto
- Organizer
  AlgoSB Winter School - 2015
- Place of Presentation
  Corsica, France
- Year and Date
  2015-11-29
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble simulations of complex systems2015
- Author(s)
  Yuko Okamoto
- Organizer
  2015 NCTS International Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Hsinchu, Taiwan
- Year and Date
  2015-08-15
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Efficient sampling methods for identifying transition states2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  TSRC Workshop on the Chemistry and Dynamics in Complex Environments (CHEM-DiCE)
- Place of Presentation
  Telluride, Colorado, U.S.A.
- Year and Date
  2015-06-23
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble simulations2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  Hands-on Workshop on Computational Biophysics at Okazaki
- Place of Presentation
  Okazaki, Japan
- Year and Date
  2015-09-09
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル法による生体分子シミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  バイオスーパーコンピューティング名古屋2015
- Place of Presentation
  名古屋市、愛知県、日本
- Year and Date
  2015-01-22
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Efficient sampling methods for complex systems2015
- Author(s)
  Yuko Okamoto
- Organizer
  The 19th International Annual Symposium on Computational Science and　Engineering (ANSCSE19)
- Place of Presentation
  Ubon Ratchathani, Thailand
- Year and Date
  2015-06-17
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] 古典系および量子系の拡張アンサンブルシミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  スーパーコンピュータワークショップ
- Place of Presentation
  岡崎市、日本
- Year and Date
  2015-09-07
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms for calculations of ligand binding affinity2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  BIRS Workshop: Free-Energy Calculations. A Mathematical Perspective
- Place of Presentation
  Oaxaca, Mexico
- Year and Date
  2015-07-19
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Enhanced sampling methods for exascale computational chemistry2015
- Author(s)
  Yuko Okamoto
- Organizer
  PACIFICHEM 2015
- Place of Presentation
  Honolulu, U.S.A.
- Year and Date
  2015-12-15
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] 拡張アンサンブル法による生体分子シミュレーション2015
- Author(s)
  岡本祐幸
- Organizer
  バイオスーパーコンピューティング名古屋2015
- Place of Presentation
  名古屋工業大学（愛知県名古屋市）
- Year and Date
  2015-01-22
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Enhanced sampling methods for exascale computational chemistry2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 2015 International Chemical Congress of Pacific Basin Societies (PACIFICHEM2015)
- Place of Presentation
  Honolulu, Hawaii, U.S.A.
- Year and Date
  2015-12-15
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Efficient sampling methods for complex systems2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 19th International Annual Symposium on Computational Science and Engineering (ANSCSE19)
- Place of Presentation
  Ubon Ratchathani, Thailand
- Year and Date
  2015-06-17
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble algorithms for enhanced sampling and free energy calculations2015
- Author(s)
  Yuko Okamoto
- Organizer
  Summer Snowmass Biophysics Workshop Free Energy Calculations: Three Decades of Adventure in Chemistry and Biophysics
- Place of Presentation
  Colorado U.S.A
- Year and Date
  2015-07-05
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble simulations2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  Hands-on Workshop on Computational Biophysics at Okazaki
- Place of Presentation
  Okazaki, Japan
- Year and Date
  2015-09-09
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Enhanced sampling methods for exascale computational chemistry2015
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 2015 International Chemical Congress of Pacific Basin Societies (PACIFICHEM2015)
- Place of Presentation
  Honolulu, Hawaii, U.S.A.
- Year and Date
  2015-12-15
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Efficient sampling methods for identifying transition states2015
- Author(s)
  Yuko Okamoto
- Organizer
  TSRC Workshop on the Chemistry and Dynamics in Complex Environments (CHEM-DiCE)
- Place of Presentation
  Colorado U.S.A
- Year and Date
  2015-06-23
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Reweighting techniques for Monte Carlo and molecular dynamics simulations2014
- Author(s)
  岡本祐幸
- Organizer
  The 13th KIAS Protein Folding Winter School
- Place of Presentation
  High1Resort, Korea
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Enhanced sampling algorithms for biomolecular simulations2014
- Author(s)
  岡本祐幸
- Organizer
  International Workshop on Computational Biomolecular
- Place of Presentation
  長野、日本
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Reweighting techniques for Monte Carlo and molecular dynamics simulations2014
- Author(s)
  Yuko Okamoto
- Organizer
  The 13th KIAS Protein Folding Winter School
- Place of Presentation
  High 1 Resort, Korea
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Enhanced Sampling Techniques for Spin and Biomolecular Simulations2014
- Author(s)
  岡本祐幸
- Organizer
  RIKEN Theoretical Science Colloquium
- Place of Presentation
  和光市、埼玉県、日本
- Year and Date
  2014-09-16
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble simulations of biological molecular assembly and artificial molecular assembly2014
- Author(s)
  Yuko Okamoto
- Organizer
  The 2nd International Symposium "Dynamical ordering of biomolecular systems for creation of integrated functions
- Place of Presentation
  キャンパスプラザ京都(京都府）
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Enhanced sampling algorithms for biomolecular simulations2014
- Author(s)
  岡本祐幸
- Organizer
  International Workshop on Computational Biomolecular
- Place of Presentation
  おんたけ休暇村（長野県）
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Enhanced Sampling Techniques for Spin and Biomolecular Simulations2014
- Author(s)
  岡本祐幸
- Organizer
  RIKEN Theoretical Science Colloquium
- Place of Presentation
  和光市、埼玉県、日本
- Year and Date
  2014-09-16
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] レプリカ交換法によるタンパク質の立体構造2014
- Author(s)
  岡本祐幸
- Organizer
  HPCI第1回成果報告会
- Place of Presentation
  東京、日本
- Year and Date
  2014-10-31
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Enhanced Sampling Techniques for Spin and Biomolecular Simulations2014
- Author(s)
  岡本祐幸
- Organizer
  RIKEN Theoretical Science Colloquium
- Place of Presentation
  理化学研究所（埼玉県和光市）
- Year and Date
  2014-09-16
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble simulations of biological molecular assembly and artificial molecular aseembly2014
- Author(s)
  岡本祐幸
- Organizer
  The 2nd International Symposium on Dynamical Ordering of Biological Systems for Creation of Integrated Functions
- Place of Presentation
  京都、日本
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] レプリカ交換法によるタンパク質の立体構造2014
- Author(s)
  岡本祐幸
- Organizer
  HPCI第1回成果報告会
- Place of Presentation
  東京、日本
- Year and Date
  2014-10-31
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル法による分子シミュレーション2014
- Author(s)
  岡本祐幸
- Organizer
  第3回産学連携シンポジウム「HPCの利用と成果と人材」
- Place of Presentation
  名古屋、日本
- Year and Date
  2014-01-31
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Enhanced-sampling simulations of spin and biological systems2013
- Author(s)
  岡本祐幸
- Organizer
  West-Lake International Workshop on Statistical Physics and Complex Systems
- Place of Presentation
  Hangzhou, China
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Replica-exchange, simulated tempering, and multicanonical algorithms for simulations of complex systems2013
- Author(s)
  Y. Okamoto
- Organizer
  The 5th Korea-Japan Seminars on Biomolecular Sciences - Experiments and Simulations
- Place of Presentation
  High 1 Resort, Korea
- Year and Date
  2013-02-24
- Invited
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Computer modeling of complex systems by generalized-ensemble simulations2013
- Author(s)
  Yuko Okamoto
- Organizer
  The 2013 Hong Kong Workshop in Computer Modeling of Complex Processes
- Place of Presentation
  Hong Kong、China
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Computer modeling of complex systems by generalized-ensemble simulations2013
- Author(s)
  岡本祐幸
- Organizer
  The 2013 Hong Kong Workshop in Computer Modeling of Complex Processes
- Place of Presentation
  Hong Kong
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble algorithms for molecular simulations2013
- Author(s)
  Yuko Okamoto
- Organizer
  The 3rd International Conference on Molecular Simulation (ICMS 2013)
- Place of Presentation
  Kobe, Japan
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for first-principles electronic structure calculations2013
- Author(s)
  岡本祐幸
- Organizer
  16th Asian Workshop on First-Principles Electronic Structure Calculations (ASIAN-16)
- Place of Presentation
  Beijing, China
- Invited
- Data Source
  KAKENHI-PUBLICLY-25104715
[Presentation] Generalized-ensemble algorithms for free energy calculations Free Energy Calculations2013
- Author(s)
  Yuko Okamoto
- Organizer
  Three Decades of Adventure in Chemistry and Biophysics
- Place of Presentation
  Snowmass, Colorado, USA
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for free energy calculations2013
- Author(s)
  岡本祐幸
- Organizer
  Free Energy Calculations: Three Decades of Adventure in Chemistry and Biophysics
- Place of Presentation
  Snowmass, Colorado, USA
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble simulations of spin and biological systems2013
- Author(s)
  岡本祐幸
- Organizer
  The 1st International Symposium on Computational Materials and Biological Sciences
- Place of Presentation
  Tokyo, Japan
- Invited
- Data Source
  KAKENHI-PUBLICLY-25104715
[Presentation] Generalized-ensemble simulations for biological and spin systems2013
- Author(s)
  岡本祐幸
- Organizer
  Kavli Institute of Theoretical Physics Special Program on Advanced Molecular Simulation Methods in the Physical Sciences
- Place of Presentation
  Beinjing, China
- Invited
- Data Source
  KAKENHI-PUBLICLY-25104715
[Presentation] 拡張アンサンブル法による生体分子の高次構造と機能の解明2013
- Author(s)
  岡本祐幸
- Organizer
  物性研スパコン共同利用・CMSI合同研究会（第４回CMSI研究会）
- Place of Presentation
  東京大学柏キャンパス(千葉県）
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for molecular simulations2013
- Author(s)
  岡本祐幸
- Organizer
  The 3rd International Conference on Molecular Simulation (ICMS 2013)
- Place of Presentation
  神戸、日本
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Simulational physics in generalized ensemble2013
- Author(s)
  岡本祐幸
- Organizer
  VII Brazilian Meeting on Simulational Physics
- Place of Presentation
  Joao Pessoa, Brazil
- Invited
- Data Source
  KAKENHI-PUBLICLY-25104715
[Presentation] Enhanced-sampling simulations of spin and biological systems2013
- Author(s)
  Yuko Okamoto
- Organizer
  West-Lake International Workshop on Statistical Physics and Complex Systems
- Place of Presentation
  Hangzhou, China
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for free energy calculations2013
- Author(s)
  岡本祐幸
- Organizer
  Free Energy Calculations: Three Decades of Adventure in Chemistry and Biophysics
- Place of Presentation
  Snowmass, Colorado, USA
- Invited
- Data Source
  KAKENHI-PUBLICLY-25104715
[Presentation] Generalized-ensemble algorithms for first-principles electronic structure calculations2013
- Author(s)
  岡本祐幸
- Organizer
  16th Asian Workshop on First-Principles Electronic Structure Calculations(ASIAN-16)
- Place of Presentation
  Beijing, China
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] 拡張アンサンブル密度汎関数分子動力学法によるＡＴＰ加水分解の研究2013
- Author(s)
  岡本祐幸
- Organizer
  新学術領域研究「コンピューティクスによる物質デザイン：複合相関と非平衡ダイナミクス」平成25年度第１回研究会
- Place of Presentation
  東京、日本
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble simulations of spin and biological systems2013
- Author(s)
  岡本祐幸
- Organizer
  The 1st International Symposium on Computational Materials and Biological Sciences
- Place of Presentation
  東京、日本
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Multidimensional generalized-ensemble simulations of biological systems2013
- Author(s)
  Y. Okamoto
- Organizer
  International Symposium on Protein Folding and Its Biological Significance
- Place of Presentation
  Okazaki, Japan
- Year and Date
  2013-03-04
- Invited
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of spin and biological systems2013
- Author(s)
  Yuko Okamoto
- Organizer
  The 1st International Symposium on Computational Materials and Biological Sciences
- Place of Presentation
  早稲田大学（東京都新宿区）
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for molecular simulations2013
- Author(s)
  岡本祐幸
- Organizer
  The 3rd International Conference on Molecular Simulation (ICMS 2013)
- Place of Presentation
  Kobe, Japan
- Invited
- Data Source
  KAKENHI-PUBLICLY-25104715
[Presentation] 生体分子集団および人工分子集団の相互作用と大規模構造転換2013
- Author(s)
  岡本祐幸
- Organizer
  新学術領域研究「動的秩序と機能」第1回公開シンポジウム
- Place of Presentation
  岡崎、日本
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Simulational physics in generalized ensemble2013
- Author(s)
  岡本祐幸
- Organizer
  VII Brazilian Meeting on Simulational Physics
- Place of Presentation
  Joao Pessoa, Brazil
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Simulational physics in generalized ensemble2013
- Author(s)
  Yuko Okamoto
- Organizer
  VII Brazilian Meeting on Simulational Physics
- Place of Presentation
  Joao Pessoa, Brazil
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] 生体分子集団および人工分子集団の相互作用と大規模構造転換2013
- Author(s)
  岡本祐幸
- Organizer
  新学術領域研究「動的秩序と機能」第1回公開シンポジウム
- Place of Presentation
  岡崎、日本
- Year and Date
  2013-10-02
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms for first-principles electronic structure calculations2013
- Author(s)
  Yuko Okamoto
- Organizer
  16th Asian Workshop on First-Principles Electronic Structure Calculations (ASIAN-16)
- Place of Presentation
  Beijing, China
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] 拡張アンサンブル法による生体分子の高次構造と機能の解明2013
- Author(s)
  岡本祐幸
- Organizer
  物性研スパコン共同利用・CMSI合同研究会（第4回CMSI研究会）
- Place of Presentation
  柏市、日本
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Replica-exchange, simulated tempering, and multicanonical algorithms for simulations of complex systems2013
- Author(s)
  Y. Okamoto
- Organizer
  The 5th Korea-Japan Seminars on Biomolecular Sciences
- Place of Presentation
  Experiments and Simulations, High 1 Resort, Korea
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for classical and quantum simulations2012
- Author(s)
  Y. Okamoto
- Organizer
  International Workshop on Recent Advances in Computational and Theoretical Chemistry
- Place of Presentation
  Nagoya, Japan
- Invited
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Multidimensional simulated tempering simulations of spin systems2012
- Author(s)
  岡本祐幸
- Organizer
  The 24th Annual Workshop of the Center of Simulational Physics : Recent Developments in Computer Simulation Studies in Condensed Matter Physics
- Place of Presentation
  Athens, Georgia (USA)(招待講演)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for classical and quantum simulations2012
- Author(s)
  Y. Okamoto
- Organizer
  International Workshop on Recent Advances in Computational and Theoretical Chemistry
- Place of Presentation
  Nagoya, Japan
- Year and Date
  2012-11-09
- Data Source
  KAKENHI-ORGANIZER-20107001
[Presentation] Generalized-ensemble simulations in materials and biological sciences [plenary talk]2012
- Author(s)
  Y. Okamoto
- Organizer
  The 5th Japan-Russia International Workshop on Molecular Simulation Studies in Material and Biological Sciences (MSSMBS'12)
- Place of Presentation
  Dubna-Moscow, Russia
- Year and Date
  2012-09-09
- Invited
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations in materials and biological sciences2012
- Author(s)
  Y. Okamoto
- Organizer
  [Plenary Talk] The 5th Japan-Russia International Workshop on Molecular Simulation Studies in Material and Biological Sciences (MSSMBS'12)
- Place of Presentation
  Dubna-Moscow, Russia
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Development of Molecular Simulation Methods that Enhance Conformational Fluctuations of Biomolecules2012
- Author(s)
  岡本祐幸
- Organizer
  5th International Symposium on Molecular Science of Fluctuations toward Biological Functions
- Place of Presentation
  奈良(日本)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Greneralized-ensemble simulations for protein folding, unfolding, and ligand binding2012
- Author(s)
  岡本祐幸
- Organizer
  The 4th Japan-Korea Seminar on Biomolecular Sciences-Experiments and Simulations
- Place of Presentation
  奈良(日本)(招待講演)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for simulations of bionanomaterials2012
- Author(s)
  Y. Okamoto
- Organizer
  The 1st International Conference on Emerging Advanced Nanomaterials (ICEAN 2012)
- Place of Presentation
  Brisbane, Australia
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Computational biophysics by generalized-ensemble algorithms2012
- Author(s)
  Y. Okamoto
- Organizer
  The 17th Biophysics Conference
- Place of Presentation
  Taipei, Taiwan
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Molecular simulations in generalized ensemble2012
- Author(s)
  Y. Okamoto
- Organizer
  Professor N. Quirke 60th Birthday Symposium
- Place of Presentation
  London, United Kingdom
- Invited
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Structural fluctuations of proteins in folding, unfolding, and ligand docking studied by generalized-ensemble simulations2012
- Author(s)
  Y. Okamoto
- Organizer
  The 6th International Symposium on Molecular Science of Fluctuations toward Biological Functions
- Place of Presentation
  Kyoto, Japan
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 付加機能ソフト:REM(レプリカ交換法)2012
- Author(s)
  岡本祐幸
- Organizer
  文部科学省「最先端・高性能スーパーコンピュータの開発利用」プロジェクト次世代ナノ統合シミュレーションソフトウェアの研究開発第2回次世代ナノ統合シミュレーションソフトウェア説明会
- Place of Presentation
  東京(日本)
- Year and Date
  2012-01-26
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 特別支援課題:拡張アンサンブル法による生体分子の高次構造と機能の解明2012
- Author(s)
  岡本祐幸
- Organizer
  第2回CMSI研究会「新物質・エネルギー創成を目指して」
- Place of Presentation
  仙台(日本)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] US-Japan Workshops on Computational Physics-International Liaison Activities2011
- Author(s)
  Y.Okamoto
- Organizer
  American Physical Society March Meeting 2011
- Place of Presentation
  Dallas, Texas, USA
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Multidimensional generalized-ensemble algorithms for biomolecular simulations2011
- Author(s)
  Y. Okamoto
- Organizer
  The 3rd Korea-Japan Seminar on Biomolecular Sciences
- Place of Presentation
  Experiments and Simulations, Jeju, Korea
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 185-Frypan sampling, a simple, knowledge-based improvement from umbrella sampling : Application to peptide folding2011
- Author(s)
  Daniel J Sindhikara, Y.Okamoto
- Organizer
  Fall 2011 National Meeting & Exposition
- Place of Presentation
  Denver, Colorado, USA
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] レプリカ交換法を実現する付加機能ソフトREM2011
- Author(s)
  岡本祐幸
- Organizer
  文部科学省「最先端・高性能スーパーコンピュータの開発利用」プロジェクト次世代ナノ統合シミュレーションソフトウェアの研究開発第5回公開シンポジウム
- Place of Presentation
  神戸
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Quest for global minimizations : generalized-ensemble approach From Computational Biophysics to Systems Biology (CBSB11)2011
- Author(s)
  岡本祐幸
- Organizer
  Celebrating Harold Scheraga's Forthcoming 90th Birthday
- Place of Presentation
  Juelich (Germany)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Computer simulations of biomolecular systems2011
- Author(s)
  Y. Okamoto
- Organizer
  The 7th Asian Biophysics Association (ABA) Symposium
- Place of Presentation
  New Delhi, India
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for protein aggregation and ligand binding2011
- Author(s)
  Y. Okamoto
- Organizer
  [Plenary Lecture] The 7th International Conference: Structure and Stability of Biomacromolecules (SSB2011)
- Place of Presentation
  Kosice, Slovakia
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Computer simulations of biomolecular system2011
- Author(s)
  Y.Okamoto
- Organizer
  The 7th Asian Biophysics Association (ABA) Symposium
- Place of Presentation
  New Delhi, India(招待)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Multidimensional generalized-ensemble algorithms for biomolecular simulations2011
- Author(s)
  Y.Okamoto
- Organizer
  The 3rd Korea-Japan Seminar on Biomolecular Sciences-Experiments and Simulations
- Place of Presentation
  Jeju, Korea(招待)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] New coformational search method using genetic algorithm and knot theory for proteins2011
- Author(s)
  Y.Sakae, T.Hiroyasu, M.Miki, Y.Okamoto
- Organizer
  Pacific Symposium on Biocomputing 2011 (PSB2011), The Big Island of Hawaii, USA
- Place of Presentation
  The Big Island of Hawaii, USA
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for protein aggregation and ligand binding [Plenary Lecture]2011
- Author(s)
  岡本祐幸
- Organizer
  The 7th International Conference : Structure and Stability of Biomacromolecules (SSB 2011)
- Place of Presentation
  Kosice (Slovakia)(招待講演)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms : powerful conformational sampling techniques for biomolecular simulations2011
- Author(s)
  Y.Okamoto
- Organizer
  Jawaharlal Nehru University International Conference, Biomolecular Simulation : Algorithm and Application
- Place of Presentation
  New Delhi, India(招待)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 計算機シミュレーションによる生体分子科学研究2011
- Author(s)
  岡本祐幸
- Organizer
  岡崎統合バイオサイエンスセンター「10周年記念シンポジウム」
- Place of Presentation
  岡崎(招待)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 構造ゆらぎを促進する分子シミュレーション手法の開発と自由エネルギー計算2011
- Author(s)
  岡本祐幸
- Organizer
  科研費新学術領域研究「揺らぎと生体機能」平成23年度合同班会議
- Place of Presentation
  夕張(日本)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of spin models and biomolecular systems2011
- Author(s)
  岡本祐幸
- Organizer
  12th International NTZ-Workshop on New Developments in Computational Physics (CompPhys11)
- Place of Presentation
  Leipzig (Germany)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms: powerful conformational sampling techniques for biomolecular simulations2011
- Author(s)
  Y. Okamoto
- Organizer
  Jawaharlal Nehru University International Conference, Biomolecular Simulation: Algorithm and Application
- Place of Presentation
  New Delhi, India
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Efficient conformational sampling techniques for biomolecular simulations2011
- Author(s)
  Y.Okamoto
- Organizer
  G-COE Symposium in Nagoya on Biochemistry and Biotechnology
- Place of Presentation
  Nagoya, Japan(招待)
- Year and Date
  2011-01-12
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] レプリカ交換法プログラム:REM2011
- Author(s)
  岡本祐幸
- Organizer
  スーパーコンピュータワークショップ2011「分子科学プログラムライブラリの充実にむけて」
- Place of Presentation
  岡崎(招待)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations in protein science2010
- Author(s)
  Y.Okamoto
- Organizer
  The 4th Japan-Russia International Workshop on Molecular Simulation Studies in Material and Biological Sciences (MSSMBS'10)
- Place of Presentation
  Dubna-Moscow, Russia(招待 Keynote Talk)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 分子シミュレーションによる分子内運動の計測2010
- Author(s)
  岡本祐幸
- Organizer
  真空・表面科学合同講演会
- Place of Presentation
  吹田(招待)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of protein folding2010
- Author(s)
  Y.Okamoto
- Organizer
  The 23rd Annual Workshop of the Center of Simulational Physics : Recent Developments in Computer Simulation Studies in Condensed Matter Physics, Athens
- Place of Presentation
  Georgia, USA[Invited Talk]
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Folding and misfolding simulations of biomolecules2010
- Author(s)
  Y. Okamoto
- Organizer
  The 10th Taiwan International Symposium on Statistical Physics (StatPhys-Taiwan-2010)
- Place of Presentation
  Taipei, Taiwan
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations in protein science2010
- Author(s)
  Y. Okamoto
- Organizer
  [Keynote Talk] The 4th Japan-Russia International Workshop on Molecular Simulation Studies in Material and Biological Sciences (MSSMBS'10)
- Place of Presentation
  Dubna-Moscow, Russia
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for multiscale biomolecular simulations2010
- Author(s)
  Y.Okamoto
- Organizer
  BioScience2010 Workshop on Expanding the Frontiers of Biomolecular Science
- Place of Presentation
  Juelich, Germany(招待)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Nagoya University and Biophysics Research2010
- Author(s)
  Y.Okamoto
- Organizer
  International Symposium : Fifty Years of Biophysics Research at Nagoya University
- Place of Presentation
  名古屋大学
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Molecular dynamics methods in generalized ensemble2010
- Author(s)
  Y. Okamoto
- Organizer
  The 239th American Chemical Society National Meeting
- Place of Presentation
  San Francisco, California, U.S.A.
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] レプリカ交換法による膜蛋白質の立体構造予測2010
- Author(s)
  岡本祐幸
- Organizer
  次世代スパコンプロジェクト連続研究会「イオンチャネル(No.2)」
- Place of Presentation
  福井
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of protein folding (invited)2010
- Author(s)
  Y.Okamoto
- Organizer
  The 23rd Annual Workshop of the Center for Simulational Physics : Recent Developments in Computer Simulation Studies in Condensed Matter Physics
- Place of Presentation
  Athens, Georgia, USA
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 構造揺らぎを促進する分子シミュレーション手法の開発と自由エネルギー計算2010
- Author(s)
  岡本祐幸
- Organizer
  新学術領域研究「揺らぎと生体機能」平成22年度合同班会議
- Place of Presentation
  片山津
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Computer simulations of protein folding and misfolding2010
- Author(s)
  岡本祐幸
- Organizer
  第10回日本蛋白質科学会年会
- Place of Presentation
  札幌(招待)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of protein folding2010
- Author(s)
  Y. Okamoto
- Organizer
  The 23rd Annual Workshop of the Center of Simulational Physics: Recent Developments in Computer Simulations Studies in Condensed Matter Physics
- Place of Presentation
  Athens, Georgia, U.S.A.
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Molecular dynamics methods in generalized ensemble (invited)2010
- Author(s)
  Y.Okamoto
- Organizer
  The 239th American Chemical Society National Meeting
- Place of Presentation
  San Francisco, California, USA
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generallized-ensemble algorithms for modeling of biological macromolecules2010
- Author(s)
  Y.Okamoto
- Organizer
  The Pacific Symposium on Biocomputing 2010
- Place of Presentation
  Big Island of Hawaii, USA
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations in protein science2010
- Author(s)
  Y.Okamoto
- Organizer
  The 4th Japan-Russia International Workshop on Molecular Simulation Studies in Material and Biological Sciences (MSSMBS'10)
- Place of Presentation
  Dubna-Moscow, Russia[Invited Keynote Talk]
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Folding and misfolding simulations of biomolecules2010
- Author(s)
  Y.Okamoto
- Organizer
  The 10th Taiwan International Symposium on Statistical Physics (StatPhys-Taiwan-2010)
- Place of Presentation
  Taipei, Taiwan(招待)
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for multiscale biomolecular simulations2010
- Author(s)
  Y. Okamoto
- Organizer
  BioScience2010: Workshop on Expanding the Frontiers of Biomolecular Science
- Place of Presentation
  Juelich, Germany
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Residual entropy of ordinary ice calculated from multicanonical Monte Carlo simulations2010
- Author(s)
  Y.Okamoto, C.Muguruma, B.A.Berg
- Organizer
  21st IUPAC International Conference on Chemical Thermodynamics ICCT-2010
- Place of Presentation
  Tsukuba Japan
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Protein structure predictions by generalized-ensemble simulations2009
- Author(s)
  Y. Okamoto
- Organizer
  Zing Conference on Nanobiophysics, Nanochemistry, Nanomedicine and Nanotoxicology
- Place of Presentation
  Antigua
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 揺らぎを誘起する拡張アンサンブル法によるタンパク質の折畳みシミュレーション(招待講演)2009
- Author(s)
  岡本祐幸
- Organizer
  第9回日本蛋白質科学会
- Place of Presentation
  熊本
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 計算機シミュレーションによる蛋白質分子の立体構造予測(招待講演)2009
- Author(s)
  岡本祐幸
- Organizer
  分子研シンポジウム
- Place of Presentation
  岡崎
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Protein folding simulations and optimization of potential energy functions for protein systems (invited)2009
- Author(s)
  Y.Okamoto
- Organizer
  第2回Road to Ab Initio Design of Materials and Bio-Artifacts研究会
- Place of Presentation
  東京
- Year and Date
  2009-06-25
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 拡張アンサンブル法によるナノシミュレーション～蛋白質分子の立体構造予測～(招待講演)2009
- Author(s)
  岡本祐幸
- Organizer
  日本材料学会分子動力学部門委員会・北陸信越支部合同研究会「ナノスケール現象のその場観察～顕微鏡と原子シミュレーションの役割～」
- Place of Presentation
  金沢大学
- Year and Date
  2009-07-03
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of water and biomolecules (invited)2009
- Author(s)
  Y. Okamoto
- Organizer
  The 6^<th> Open Workshop of the Scientific Reseach in Priority Areas : Water and Biomolecules
- Place of Presentation
  Okazaki, Japan
- Year and Date
  2009-03-16
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of bionanostructures (invited)2009
- Author(s)
  Y.Okamoto
- Organizer
  The 238th American Chemical Society National Meeting
- Place of Presentation
  Washington, D.C., USA
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of biomolecular systems (invited)2009
- Author(s)
  Y Okamoto
- Organizer
  Korea-Japan Seminars on Biomolecular Sciences-Experiments and Simulations
- Place of Presentation
  Seoul, Korea
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for protein structure predictions [Keynote Talk] (invited)2009
- Author(s)
  Y.SaKae, Y.Okamoto
- Organizer
  2009 International Conference on Computational & Experimental Engineering and Sciences
- Place of Presentation
  Phuket, Thailand
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations in biomolecular science (invited)2009
- Author(s)
  Y.Okamoto
- Organizer
  The 2nd Japan-Korea Seminars on Biomolecular Sciences-Experiments and Simulations
- Place of Presentation
  名古屋
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for protein structure predictions2009
- Author(s)
  Y.Okamoto
- Organizer
  2009 International Conference on Computational, &, Experimental Engineering and Sciences, ICCES'09
- Place of Presentation
  Phuket, Thailand[Invited Keynote Talk]
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of biomolecular systems2009
- Author(s)
  Y. Okamoto
- Organizer
  Korea-Japan Seminars on Biomolecular Sciences. Experiments and Simulations
- Place of Presentation
  Seoul, Korea
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble algorithms for protein structure predictions2009
- Author(s)
  Y. Okamoto
- Organizer
  [Keynote Talk] 2009 International Conference on Computational & Experimental Engineering and Sciences, ICCES'09
- Place of Presentation
  Phuket, Thailand
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 拡張アンサンブル法で探るタンパク質のフォールディングとミスフォールディング(招待講演)2009
- Author(s)
  伊藤暁、岡本祐幸
- Organizer
  大阪大学蛋白質研究所セミナー「蛋白質立体構造を基盤とするプリオン現象の解明と制御」
- Place of Presentation
  大阪大学、吹田
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Protein structure predictions by generalized-ensemble simulations (invited)2009
- Author(s)
  Y. Okamoto
- Organizer
  Zing Conference on Nanobiophysics, Nanochemistry, Nanomedicine and Nanotoxicology
- Place of Presentation
  Antigua
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Generalized-ensemble simulations of bionanostructures2009
- Author(s)
  Y. Okamoto
- Organizer
  The 238th American Chemical Society National Meeting
- Place of Presentation
  Washington, D.C., U.S.A.
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] 拡張アンサンブル法:状態空間の効率的なサンプリング(招待講演)2009
- Author(s)
  岡本祐幸
- Organizer
  分野横断型研究会「アルゴリズムによる計算科学の融合と発展」
- Place of Presentation
  筑波大学計算科学研究センター、つくば
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Molecular Simulations by Generalized-Ensemble Algorithms2009
- Author(s)
  Y.Okamoto
- Organizer
  International Symposiumm on "Reaction Dynamics of Many-Body Chemical Systems" (RDMCS2009)
- Place of Presentation
  京都大学
- Data Source
  KAKENHI-PLANNED-20107002
[Presentation] Computer simulationsof spin systems arid biomolecular systems in Geberalized ensembles2008
- Author(s)
  Y. Okamoto
- Organizer
  The 9^<th> Taiwan Inter. Symp. on Statistical Physics (Statphys-Taiwan-2008)
- Place of Presentation
  Taipei, Taiwan(invited)
- Data Source
  KAKENHI-PROJECT-20038025
[Presentation] Generalized-ensemble algorithms for protein folding and misfolding2008
- Author(s)
  Y. Okamoto
- Organizer
  The 8th KIAS-Yonsei Conf. on Protein Structure and Function
- Place of Presentation
  Seoul, Korea(invited)
- Data Source
  KAKENHI-PROJECT-20038025
[Presentation] Replica-exchange method and its generalizations2008
- Author(s)
  Y. Okamoto
- Organizer
  The 235^<th> American Chem. Soc Nat. Meeting Symp. Under the Computers in Chemistry
- Place of Presentation
  New Orleans, Luisiana, U.S.A(COMP) (invited)
- Data Source
  KAKENHI-PROJECT-20038025
[Presentation] Generalized-ensemble algorithms for simulations in molecular Nanoscience2008
- Author(s)
  Y. Okamoto
- Organizer
  The 1^<st> Inter. Conf. of The Grand Challenge to Next-Generation Integrated nanscience
- Place of Presentation
  Tokyo, Japan(invited)
- Data Source
  KAKENHI-PROJECT-20038025
[Presentation] Protein folding simulations in generalized ensembles2007
- Author(s)
  Y. Okamoto(招待講演)
- Organizer
  Mainz Materials Simulation Days 2007 (MMSD 2007)
- Place of Presentation
  Mainz, Germany
- Data Source
  KAKENHI-PROJECT-15076213
[Presentation] Enhanced configurational sampling methods for spin systems and biomolecular systems
- Author(s)
  Yuko OKAMOTO
- Organizer
  XXVI IUPAP Conference on Computational Physics, CCP2014
- Place of Presentation
  Boston, Massachusetts, USA
- Year and Date
  2014-08-11 – 2014-08-14
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] 拡張アンサンブル法による分子シミュレーション
- Author(s)
  岡本祐幸
- Organizer
  第3回産学連携シンポジウム「HPCの利用と成果と人材」
- Place of Presentation
  名古屋大学（愛知県）
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Simulational physics in generalized ensemble
- Author(s)
  岡本祐幸
- Organizer
  VII Brazilian Meeting on Simulational Physics
- Place of Presentation
  Joao Pessoa, Brazil
- Year and Date
  2013-08-06 – 2013-08-10
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 分子シミュレーションにおける拡張アンサンブル法
- Author(s)
  岡本祐幸
- Organizer
  第８回分子シミュレーションスクール　－基礎から応用までー
- Place of Presentation
  岡崎コンファレンスセンター(愛知県岡崎市）
- Year and Date
  2014-10-14 – 2014-10-17
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Computer simulations of protein folding, ligand binding, and proton transfer
- Author(s)
  Yuko OKAMOTO
- Organizer
  2nd International Conference on Computational Science and Engineering (2nd ICCSE 2014)
- Place of Presentation
  Ho Chi Minh City, Vietnam
- Year and Date
  2014-08-21 – 2014-08-23
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] 生体分子集団および人工分子集団の相互作用と大規模構造転換
- Author(s)
  岡本祐幸
- Organizer
  生命システムにおける動的秩序形成と高次機能発現　第1回公開シンポジウム
- Place of Presentation
  岡崎コンファレンスセンター(愛知県）
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Computer modeling of complex systems by generalized-ensemble simulations
- Author(s)
  岡本祐幸
- Organizer
  The 2013 Hong Kong Workshop in Computer Modeling of Complex Processes
- Place of Presentation
  Hong Kong
- Year and Date
  2013-12-17 – 2013-12-20
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Drug design by generalized-ensemble simulations
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 6th Japan-Russia International Workshop onMolecular Simulation Studies in Material and Biological Sciences (MSSMBS-2014)
- Place of Presentation
  Moscow, Russia
- Year and Date
  2014-09-21 – 2014-09-22
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Enhanced sampling techniques for spin and biological systems
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 10th AIMS Conference on Dynamical Systems, Differential Equations and Applications
- Place of Presentation
  Madrid, Spain
- Year and Date
  2014-07-07 – 2014-07-11
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] 拡張アンサンブル法による生体分子の立体構造予測
- Author(s)
  岡本祐幸
- Organizer
  TCCI第5回研究会
- Place of Presentation
  岡崎市、愛知県、日本
- Year and Date
  2014-10-17 – 2014-10-18
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble simulations of biological molecular assembly and artificial molecular aseembly
- Author(s)
  岡本祐幸
- Organizer
  The 2nd International Symposium on Dynamical Ordering of Biological Systems for Creation of Integrated Functions
- Place of Presentation
  京都、日本
- Year and Date
  2014-01-11 – 2014-01-12
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Interactions among biological molecular assembly and among artificial molecular assebly and large-scale structural transformations
- Author(s)
  岡本祐幸
- Organizer
  The 3rd International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
- Place of Presentation
  合歓の郷、志摩市、三重県、日本
- Year and Date
  2015-01-10 – 2015-01-11
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 生体分子集団の相互作用と自由エネルギー計算
- Author(s)
  岡本祐幸
- Organizer
  第14回日本蛋白質科学会年会
- Place of Presentation
  横浜市、神奈川県、日本
- Year and Date
  2014-06-25 – 2014-06-27
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル密度汎関数分子動力学法によるＡＴＰ加水分解の研究
- Author(s)
  岡本祐幸
- Organizer
  新学術領域研究「コンピューティクスによる物質デザイン：複合相関と非平衡ダイナミクス」平成25年度第１回研究会
- Place of Presentation
  東京、日本
- Year and Date
  2013-07-08 – 2013-07-09
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Reweighting techniques for Monte Carlo and molecular dynamics simulations
- Author(s)
  岡本祐幸
- Organizer
  The 13th KIAS Protein Folding Winter School
- Place of Presentation
  High1Resort, Korea
- Year and Date
  2014-01-19 – 2014-01-24
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Generalized-ensemble algorithms for free energy calculations
- Author(s)
  岡本祐幸
- Organizer
  Free Energy Calculations: Three Decades of Adventure in Chemistry and Biophysics
- Place of Presentation
  Snowmass, Colorado, USA
- Year and Date
  2013-07-15 – 2013-07-19
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Drug design by generalized-ensemble simulations
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 6th Japan-Russia International Workshop onMolecular Simulation Studies in Material and Biological Sciences (MSSMBS-2014)
- Place of Presentation
  Moscow, Russia
- Year and Date
  2014-09-21 – 2014-09-22
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Protein folding and ligand binding simulations by generaized-ensemble algorithms [Invited Talk]
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 7th Korea-Japan Seminars on Biomolecular Sciences: Experiments and Simulations
- Place of Presentation
  Seoul 、Korea
- Year and Date
  2014-11-26 – 2014-11-28
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble simulations of spin and biological systems
- Author(s)
  岡本祐幸
- Organizer
  The 1st International Symposium on Computational Materials and Biological Sciences
- Place of Presentation
  東京、日本
- Year and Date
  2013-09-10 – 2013-09-12
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Enhanced-sampling simulations of spin and biological systems
- Author(s)
  岡本祐幸
- Organizer
  West-Lake International Workshop on Statistical Physics and Complex Systems
- Place of Presentation
  Hangzhou, China
- Year and Date
  2013-11-08 – 2013-11-10
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Computer simulations of protein folding, ligand binding, and proton transfer
- Author(s)
  Yuko OKAMOTO
- Organizer
  2nd International Conference on Computational Science and Engineering (2nd ICCSE 2014)
- Place of Presentation
  Ho Chi Minh City, Vietnam
- Year and Date
  2014-08-21 – 2014-08-23
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Enhanced sampling techniques for spin and biological systems
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 10th AIMS Conference on Dynamical Systems, Differential Equations and Applications Special Session “Enhanced Sampling Techniques in Simulation of Complex Systems”
- Place of Presentation
  Madrid, Spain
- Year and Date
  2014-07-07 – 2014-07-11
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 生体分子集団および人工分子集団の相互作用と大規模構造転換
- Author(s)
  岡本祐幸
- Organizer
  新学術領域研究「動的秩序と機能」全体班会議
- Place of Presentation
  小松市、石川県、日本
- Year and Date
  2014-08-04 – 2014-08-07
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Protein folding and ligand binding simulations by generaized-ensemble algorithms
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 7th Korea-Japan Seminars on Biomolecular Sciences – Experiments and Simulations
- Place of Presentation
  Seoul, Korea
- Year and Date
  2014-11-26 – 2014-11-28
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Lecture 1: An introduction to replica-exchange molecular dynamics simulation Lecture 2: Generalized-ensemble algorithms
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 11th Thai Summer School of Computational Chemistry 2015 Workshop: Replica Exchange Molecular Dynamics Simulation
- Place of Presentation
  Nan, Thailand
- Year and Date
  2015-01-04 – 2015-01-07
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル法による生体分子の立体構造予測
- Author(s)
  岡本祐幸
- Organizer
  TCCI第5回研究会
- Place of Presentation
  岡崎市、愛知県、日本
- Year and Date
  2014-10-17 – 2014-10-18
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Protein folding and ligand binding simulations by generaized-ensemble algorithms
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 7th Korea-Japan Seminars on Biomolecular Sciences – Experiments and Simulations
- Place of Presentation
  Seoul, Korea
- Year and Date
  2014-11-26 – 2014-11-28
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Enhanced sampling techniques for spin and biological systems
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 10th AIMS Conference on Dynamical Systems, Differential Equations and Applications Special Session “Enhanced Sampling Techniques in Simulation of Complex Systems”
- Place of Presentation
  Madrid, Spain
- Year and Date
  2014-07-07 – 2014-07-11
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] 分子シミュレーションにおける拡張アンサンブル法
- Author(s)
  岡本祐幸
- Organizer
  第８回分子シミュレーションスクール　－基礎から応用までー
- Place of Presentation
  岡崎市、愛知県、日本
- Year and Date
  2014-10-14 – 2014-10-17
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] 分子シミュレーションにおける拡張アンサンブル法
- Author(s)
  岡本祐幸
- Organizer
  第８回分子シミュレーションスクール　－基礎から応用までー
- Place of Presentation
  岡崎市、愛知県、日本
- Year and Date
  2014-10-14 – 2014-10-17
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] An introduction to replica-exchange molecular dynamics simulation
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 11th Thai Summer School of Computational Chemistry 2015 Workshop: Replica Exchange Molecular Dynamics Simulation
- Place of Presentation
  Nan, Thailand
- Year and Date
  2015-01-04 – 2015-01-07
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Enhanced sampling algorithms for biomolecular simulations
- Author(s)
  岡本祐幸
- Organizer
  International Workshop on Computational Biomolecular
- Place of Presentation
  長野、日本
- Year and Date
  2014-03-31 – 2014-04-01
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 生体分子集団の相互作用と自由エネルギー計算
- Author(s)
  岡本祐幸
- Organizer
  第14回日本蛋白質科学会年会
- Place of Presentation
  横浜市、神奈川県、日本
- Year and Date
  2014-06-25 – 2014-06-27
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble algorithms for molecular simulations
- Author(s)
  岡本祐幸
- Organizer
  The 3rd International Conference on Molecular Simulation (ICMS 2013)
- Place of Presentation
  神戸市、日本
- Year and Date
  2013-11-18 – 2013-11-20
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Enhanced configurational sampling methods for spin systems and biomolecular systems
- Author(s)
  Yuko OKAMOTO
- Organizer
  XXVI IUPAP Conference on Computational Physics, CCP2014
- Place of Presentation
  Boston, Massachusetts, USA
- Year and Date
  2014-08-11 – 2014-08-14
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Generalized-ensemble algorithms for first-principles electronic structure calculations
- Author(s)
  岡本祐幸
- Organizer
  16th Asian Workshop on First-Principles Electronic Structure Calculations (ASIAN-16)
- Place of Presentation
  Beijing, China
- Year and Date
  2013-10-27 – 2013-10-30
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル法による生体分子の高次構造と機能の解明
- Author(s)
  岡本祐幸
- Organizer
  物性研スパコン共同利用・CMSI合同研究会（第4回CMSI研究会）
- Place of Presentation
  柏市、日本
- Year and Date
  2013-12-11 – 2013-12-13
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Invitation to serve as a Discussion Leader and present the following talk:“Generalized-ensemble algorithms for simulations of spin and bimolecular systems”
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 28th Annual Workshop of the Center of Simulational Physics: Recent Developments in Computer Simulation Studies in Condensed Matter Physics
- Place of Presentation
  Athens, Georgia, U.S.A.
- Year and Date
  2015-02-23 – 2015-02-27
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Computer simulations of protein folding, ligand binding, and proton transfer
- Author(s)
  Yuko OKAMOTO
- Organizer
  2nd International Conference on Computational Science and Engineering (2nd ICCSE 2014)
- Place of Presentation
  Ho Chi Minh City, Vietnam
- Year and Date
  2014-08-21 – 2014-08-23
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Protein folding and unfolding simulations by generalized-ensemble algorithms
- Author(s)
  Yuko OKAMOTO
- Organizer
  Dushanbe Symposium on Computational Materials and Biological Sciences (DSCMBS-2014)
- Place of Presentation
  Dushanbe, Tajikistan
- Year and Date
  2014-09-23 – 2014-09-28
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Generalized-ensemble algorithms for simulations of spin and bimolecular systems
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 28th Annual Workshop of the Center of Simulational Physics: Recent Developments in Computer Simulation Studies in Condensed Matter Physics
- Place of Presentation
  Athens, Georgia, U.S.A.
- Year and Date
  2015-02-23 – 2015-02-27
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 生体分子集団および人工分子集団の相互作用と大規模構造転換
- Author(s)
  岡本祐幸
- Organizer
  新学術領域研究「動的秩序と機能」全体班会議
- Place of Presentation
  小松市、石川県、日本
- Year and Date
  2014-08-04 – 2014-08-07
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Enhanced configurational sampling methods for spin systems and biomolecular systems
- Author(s)
  Yuko OKAMOTO
- Organizer
  XXVI IUPAP Conference on Computational Physics, CCP2014
- Place of Presentation
  Boston, Massachusetts, USA
- Year and Date
  2014-08-11 – 2014-08-14
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] 拡張アンサンブル法による分子シミュレーション
- Author(s)
  岡本祐幸
- Organizer
  第3回産学連携シンポジウム「HPCの利用と成果と人材」
- Place of Presentation
  名古屋、日本
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Drug design by generalized-ensemble simulations
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 6th Japan-Russia International Workshop onMolecular Simulation Studies in Material and Biological Sciences (MSSMBS-2014)
- Place of Presentation
  Moscow, Russia
- Year and Date
  2014-09-21 – 2014-09-22
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001
[Presentation] Protein folding and unfolding simulations by generalized-ensemble algorithms
- Author(s)
  Yuko OKAMOTO
- Organizer
  Dushanbe Symposium on Computational Materials and Biological Sciences (DSCMBS-2014)
- Place of Presentation
  Dushanbe, Tajikistan
- Year and Date
  2014-09-23 – 2014-09-28
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Interactions among biological molecular assembly and among artificial molecular assebly and large-scale structural transformations
- Author(s)
  岡本祐幸
- Organizer
  The 3rd International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
- Place of Presentation
  合歓の郷、志摩市、三重県、日本
- Year and Date
  2015-01-10 – 2015-01-11
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] Protein folding and unfolding simulations by generalized-ensemble algorithms
- Author(s)
  Yuko OKAMOTO
- Organizer
  Dushanbe Symposium on Computational Materials and Biological Sciences (DSCMBS-2014)
- Place of Presentation
  Dushanbe, Tajikistan
- Year and Date
  2014-09-23 – 2014-09-28
- Invited
- Data Source
  KAKENHI-PROJECT-25247071
[Presentation] Lecture 1: An introduction to replica-exchange molecular dynamics simulation Lecture 2: Generalized-ensemble algorithms
- Author(s)
  Yuko OKAMOTO
- Organizer
  The 11th Thai Summer School of Computational Chemistry 2015 Workshop: Replica Exchange Molecular Dynamics Simulation
- Place of Presentation
  Nan, Thailand
- Year and Date
  2015-01-04 – 2015-01-07
- Invited
- Data Source
  KAKENHI-PLANNED-25102009
[Presentation] 生体分子集団の相互作用と自由エネルギー計算
- Author(s)
  岡本祐幸
- Organizer
  第14回日本蛋白質科学会年会
- Place of Presentation
  ワークピア横浜(神奈川県横浜市）
- Year and Date
  2014-06-25 – 2014-06-27
- Invited
- Data Source
  KAKENHI-ORGANIZER-25102001

1. TERAZIMA Masahide (00188674)

# of Collaborated Projects: 3 results

# of Collaborated Products: 1 results
2. KATO Koichi (20211849)

# of Collaborated Projects: 3 results

# of Collaborated Products: 8 results
3. HOHSAKA Takahiro (30263619)

# of Collaborated Projects: 3 results

# of Collaborated Products: 1 results
4. 中沢隆 (30175492)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
5. 平岡秀一 (10322538)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
6. 稲垣直之 (20223216)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
7. 上久保裕生 (20311128)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
8. 佐藤宗太 (40401129)

# of Collaborated Projects: 2 results

# of Collaborated Products: 4 results
9. 佐藤啓文 (70290905)

# of Collaborated Projects: 2 results

# of Collaborated Products: 4 results
10. KATAOKA Mikio (30150254)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. UEOKA Ryuichi (70099076)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
12. HIRATA Fumio (90218785)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. KUWAJIMA Kunihiro (70091444)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
14. YAMATO Takahisa (90251587)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
15. MITSUTAKE Ayori (00338253)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
16. ADACHI Shinichi (60260220)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
17. 奥村久士 (80360337)

# of Collaborated Projects: 1 results

# of Collaborated Products: 12 results
18. YAMAGUCHI Takumi

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
19. SATO Tadashi

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
20. YAGI Hirokazu

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
21. YAGI Maho

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
22. 田村康

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
23. IRLE Stephan

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
24. 森義治

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

OKAMOTO Yuko 岡本 祐幸

岡本 祐幸 オカモト ユウコウ

Research Projects

Research Products

Co-Researchers

International Activity Support for Dynamical ordering of biomolecular systems for creation of integrated functions

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Management for Dynamical ordering of biomolecular systems for creation of integrated functions

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Interactions among biological molecular assembly and among artificial molecular assembly and large-scale structural transformationsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

拡張アンサンブル密度汎関数分子動力学法によるATP加水分解の研究Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Study on the mechanism of docking of small molecules to proteins by generalized-ensemble algorithmsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Exploration of reactions and structural space in multi-degree-of-freedom and large-scale systems

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

蛋白質系分子シミュレーションのための新規エネルギー関数の開発Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Management for Molecular Science of Fluctuations toward Biological Functions

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Development of molecular simulation algorithms for enhancing structural fluctuations and for accurate free -energy calculationsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

拡張アンサンブル法による蛋白質折り畳み機構の研究Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

拡張アンサンブル法による蛋白質の立体構造予測Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Institution

Tertiavy structure analysis of biomolecules based on X-ray and NMR data by multicawowical algorithmPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

新最適化アルゴリズムによるタンパク質の折れたたみの研究Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

OKAMOTO Yuko 岡本祐幸

岡本祐幸オカモトユウコウ

[Book] 「計算科学講座」第９巻「超多自由度系の最適化」第２章「拡張アンサンブル法」2013