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Interactions among biological molecular assembly and among artificial molecular assembly and large-scale structural transformations

Planned Research

Project AreaDynamical ordering of biomolecular systems for creation of integrated functions
Project/Area Number 25102009
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionNagoya University

Principal Investigator

OKAMOTO Yuko  名古屋大学, 理学研究科, 教授 (70185487)

Project Period (FY) 2013-06-28 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥96,590,000 (Direct Cost: ¥74,300,000、Indirect Cost: ¥22,290,000)
Fiscal Year 2017: ¥10,790,000 (Direct Cost: ¥8,300,000、Indirect Cost: ¥2,490,000)
Fiscal Year 2016: ¥10,790,000 (Direct Cost: ¥8,300,000、Indirect Cost: ¥2,490,000)
Fiscal Year 2015: ¥20,020,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥4,620,000)
Fiscal Year 2014: ¥24,570,000 (Direct Cost: ¥18,900,000、Indirect Cost: ¥5,670,000)
Fiscal Year 2013: ¥30,420,000 (Direct Cost: ¥23,400,000、Indirect Cost: ¥7,020,000)
Keywords生体分子系 / 人工分子系 / 分子シミュレーション / 拡張アンサンブル法 / 自由エネルギー計算 / 生体系 / 蛋白質
Outline of Final Research Achievements

We have applied the generalized-ensemble algorithms that we developed by ourselves to various bimolecular and artificial molecular systems and showed their effectiveness. For instance, we applied the Replica-Exchange Molecular Dynamics Method to the development of the method for predicting membrane protein structures, analyses of three-dimensional structures of glycans attached to a protein, and the prediction of the three-dimensional structures of a supra molecule that consists of ligands and metals. We applied the Replica-Exchange Umbrella Sampling to the development of binding free energy calculation method for protein-ligand system and the calculation of isozyme selectivity of histon deacetylate. We applied the pressure simulated tempering to the chemical shift calculations of a protein under high pressure.

Report

(6 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (94 results)

All 2018 2017 2016 2015 2014 2013 Other

All Journal Article (26 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 25 results,  Open Access: 2 results,  Acknowledgement Compliant: 4 results) Presentation (59 results) (of which Int'l Joint Research: 24 results,  Invited: 52 results) Book (8 results) Remarks (1 results)

  • [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

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [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

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [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

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [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

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [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
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [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

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [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

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [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
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [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

    • Related Report
      2015 Annual Research Report
  • [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

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [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

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [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

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [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
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Biomolecular simulations in generalized ensemble Frontier Bioorganization2017

    • Author(s)
      Yuko OKAMOTO
    • Organizer
      Forum 2017: Dynamical Ordering and Integrated Functions of Biomolecular Systems
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [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)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Energy landscape of biomolecular systems studied by generalized-ensemble simulations2017

    • Author(s)
      Yuko OKAMOTO
    • Organizer
      Energy Landscapes 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Generalized-ensemble algorithms for advanced materials simulations2017

    • Author(s)
      Yuko OKAMOTO
    • Organizer
      IUMRS-ICAM 2017, The 15th International Conference on Advanced Materials
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Generalized-ensemble algorithms for materials and biomolecular simulations [Keynote Talk]2017

    • Author(s)
      Yuko OKAMOTO
    • Organizer
      Molecular Simulation Studies in Material
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Classical and quantum molecular simulations in generalized ensemble2017

    • Author(s)
      Yuko OKAMOTO
    • Organizer
      International Workshop on Molecular Simulations
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [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」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [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
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [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
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Invitation to serve as a Discussion Leader and present the following talk:“Generalized-ensemble algorithms for simulations of spin and bimolecular systems”2015

    • 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
    • Related Report
      2014 Annual Research Report
  • [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
    • Related Report
      2014 Annual Research Report
  • [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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Interactions among biological molecular assembly and among artificial molecular assebly and large-scale structural transformations2015

    • 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
    • Related Report
      2014 Annual Research Report
  • [Presentation] Lecture 1: An introduction to replica-exchange molecular dynamics simulation Lecture 2: Generalized-ensemble algorithms2015

    • 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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Protein folding and ligand binding simulations by generaized-ensemble algorithms2014

    • 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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [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
    • Related Report
      2014 Annual Research Report
  • [Presentation] 拡張アンサンブル法による生体分子の立体構造予測2014

    • 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
    • Related Report
      2014 Annual Research Report
  • [Presentation] 分子シミュレーションにおける拡張アンサンブル法2014

    • 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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Protein folding and unfolding simulations by generalized-ensemble algorithms2014

    • 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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Drug design by generalized-ensemble simulations2014

    • 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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Computer simulations of protein folding, ligand binding, and proton transfer2014

    • 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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Enhanced configurational sampling methods for spin systems and biomolecular systems2014

    • 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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [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2014

    • 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
    • Related Report
      2014 Annual Research Report
  • [Presentation] Enhanced sampling techniques for spin and biological systems2014

    • 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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 生体分子集団の相互作用と自由エネルギー計算2014

    • 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
    • Related Report
      2014 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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
    • Related Report
      2015 Annual Research Report
  • [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
    • Related Report
      2014 Annual Research Report
  • [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
    • Related Report
      2014 Annual Research Report
  • [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
    • Related Report
      2013 Annual Research Report
  • [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
    • Related Report
      2013 Annual Research Report
  • [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
    • Related Report
      2013 Annual Research Report
  • [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
    • Related Report
      2013 Annual Research Report
  • [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
    • Related Report
      2013 Annual Research Report
  • [Remarks]

    • URL

      http://www.tb.phys.nagoya-u.ac.jp/~okamoto/index.shtml

    • Related Report
      2017 Annual Research Report

URL: 

Published: 2013-07-10   Modified: 2023-03-16  

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