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Theoretical Study on Conjugated Dynamics of Protein and Solvent

Planned Research

Project AreaMolecular Science of Fluctuations toward Biological Functions
Project/Area Number 20107008
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 InstitutionRitsumeikan University (2012)
Institute for Molecular Science (2008-2011)

Principal Investigator

HIRATA Fumio  立命館大学, 生命科学部, 教授 (90218785)

Co-Investigator(Kenkyū-buntansha) YOSHIDA Norio  九州大学, 理学(系)研究科(院), 准教授 (10390650)
Project Period (FY) 2008 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥72,020,000 (Direct Cost: ¥55,400,000、Indirect Cost: ¥16,620,000)
Fiscal Year 2012: ¥16,510,000 (Direct Cost: ¥12,700,000、Indirect Cost: ¥3,810,000)
Fiscal Year 2011: ¥15,080,000 (Direct Cost: ¥11,600,000、Indirect Cost: ¥3,480,000)
Fiscal Year 2010: ¥15,990,000 (Direct Cost: ¥12,300,000、Indirect Cost: ¥3,690,000)
Fiscal Year 2009: ¥14,560,000 (Direct Cost: ¥11,200,000、Indirect Cost: ¥3,360,000)
Fiscal Year 2008: ¥9,880,000 (Direct Cost: ¥7,600,000、Indirect Cost: ¥2,280,000)
Keywords3D-RISM/RISM / 蛋白質構造揺らき / 分子認識 / 自由エネルギー / 一般化ランジェヴァン理論 / 分散・共分散行列 / 知的創薬 / 化合物スクリーニンク / 蛋白質構造揺らぎ / 化合物スクリーニング / 3D-RISM / タンパク質の揺らぎ / ダイナミクス / 創薬 / アスピリン / Phospholipase A2 / 蛋白質の揺らぎ / 自由エネルギー計算 / 構造揺らぎ / 3D-RISM理論 / オーダーパラメタ / 熱力学積分法 / 薬剤設計 / 蛋白質 / 鳥インフルエンザウイルス / M2チャネル / プロトン透過 / 生体機能 / 揺らぎ
Research Abstract

The research program which aims to construct a theory to describe the molecular recognition process correlated with the structural fluctuation of protein was carried out along the four subjects listed below, and the goal of the research program was successfully achieved.
1. Statistical mechanics theory of molecular recognition (Equilibrium theory)
2. Application of the statistical mechanics of molecular recognition to "drug design"
3. Quasi dynamics of protein in solution based on the 3D-RISM and the molecular dynamics simulation
4. A new theory for structural fluctuation of protein, created by combining the 3D-RISM/RISM with the generalized Langevin theories

Report

(7 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report   Self-evaluation Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (168 results)

All 2013 2012 2011 2010 2009 2008 Other

All Journal Article (60 results) (of which Peer Reviewed: 60 results) Presentation (92 results) (of which Invited: 8 results) Book (13 results) Patent(Industrial Property Rights) (3 results) (of which Overseas: 3 results)

  • [Journal Article]2012

    • Author(s)
      Bongsoo Kim and Fumio Hirata
    • Journal Title

      J. Chem. Phys

      Volume: 138

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2012

    • Author(s)
      Maruyama, Yutaka; Hirata, Fumio
    • Journal Title

      J. Chem. Theory Comput

      Volume: 8 Pages: 3015-3021

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2012

    • Author(s)
      Hong, Jooyeon; Yoshida, Norio; Chong, Song-Ho; Lee, Chewook; Ham, Sihyun; Hirata, Fumio
    • Journal Title

      J. Chem. Theory Comput

      Volume: 8 Pages: 2239-2246

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2012

    • Author(s)
      Sindhikara, Daniel; Yoshida, Norio; Hirata, Fumio
    • Journal Title

      J. Comp. Chem

      Volume: 33 Pages: 1536-1543

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Modified Anderson Method for Acceleating 3D-RISM Calculations Using Graphics Processor Unit2012

    • Author(s)
      Maruyama, Yutaka; Hirata, Fumio
    • Journal Title

      J. Chem. Theory Comput

      Volume: 8 Issue: 9 Pages: 3015-3015

    • DOI

      10.1021/ct300355r

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural fluctuation of protein in water around its native state: A new statistical mechanics formulation2012

    • Author(s)
      Bongsoo Kim and Fumio Hirata
    • Journal Title

      J J. Chem. Phys

      Volume: 138 Issue: 5 Pages: 541-541

    • DOI

      10.1063/1.4776655

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Placevent : An Algorithm for Predicting of Explicit Solvent Atom Distribution - Application to HIV-1 Protease and F-ATP Synthase2012

    • Author(s)
      Sindhikara, Daniel; Yoshida, Norio; Hirata, Fumio
    • Journal Title

      J. Comp. Chem

      Volume: 33 Issue: 18 Pages: 1536-1536

    • DOI

      10.1002/jcc.22984

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Elucidating the Molecular Origin of Hydrolysis Energy of Pyrophosphate in Water2012

    • Author(s)
      Hong, Jooyeon; Yoshida, Norio; Chong, Song-Ho; Lee, Chewook; Ham, Sihyun; Hirata, Fumio
    • Journal Title

      J. Chem. Theory Comput

      Volume: 8 Issue: 7 Pages: 2239-2239

    • DOI

      10.1021/ct300099e

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solvent Effects on Electronic Structures of Coumarin 153 : Parallel Studies by Means of Spectroscopy and RISM-SCF Calculations2012

    • Author(s)
      Katsura Nishiyama, Norio Yoshida, Fumio Hirata
    • Journal Title

      Journal of the Physical Society of Japan

      Volume: (掲載確定)(未定)

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article]2011

    • Author(s)
      Y. Kiyota, N. Yoshida, and F. Hirata
    • Journal Title

      J. Chem. Theor. Comp

      Volume: 7 Pages: 3803-3815

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2011

    • Author(s)
      Danniel J. Sindhikara, Norio Yoshida, Mikio Kataoka, Fumio Hirata
    • Journal Title

      J. Mol. Liq

      Volume: 164 Pages: 120-122

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2011

    • Author(s)
      Imai, Takashi; Miyashita, Naoyuki; Sugita, Yuji; Kovalenko, Andriy; Hirata, Fumio; Kidera, Akinori
    • Journal Title

      J. Phys. Chem. B

      Volume: 115 Pages: 8288-8295

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2011

    • Author(s)
      Tatsuhiko Miyata, Yasuhiro Ikuta, and Fumio Hirata
    • Journal Title

      J. Chem. Phys

      Volume: 134 Pages: 44127-44144

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2011

    • Author(s)
      Yutaka Maruyama, Taku Matsushita, Ryuichi Ueoka, and Fumio Hirata
    • Journal Title

      J. Phys. Chem. B

      Volume: 115 Pages: 2408-2416

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Solvent penetration in photoactive yellow protein R52Q mutant : a theoretical study2011

    • Author(s)
      Daniel, J.Sindhikara
    • Journal Title

      J.Mol.Liq.

      Volume: 164 Issue: 1-2 Pages: 120-122

    • DOI

      10.1016/j.molliq.2011.04.007

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reply to "Comment on 'Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory"2011

    • Author(s)
      Saree Phongphanphanee, Norio Yoshida, Fumio Hirata
    • Journal Title

      Journal of Physical Chemistry B

      Volume: 115 Issue: 25 Pages: 8367-8369

    • DOI

      10.1021/jp203661z

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new approach for investigating the molecular recognition of protein : Toward structure-based drug-design based on the 3D-RISM theory2011

    • Author(s)
      Yasuomi Kiyota, Norio Yoshida, Fumio Hirata
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 7 Issue: 11 Pages: 3803-3815

    • DOI

      10.1021/ct200358h

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The electronic-structure theory of a large-molecular system in solution : Application to the intercalation of proflavine with solvated DNA2011

    • Author(s)
      Norio Yoshida, Yasuomi Kiyota, Fumio Hirata
    • Journal Title

      J.Mole.Liq.

      Volume: 159 Issue: 1 Pages: 83-92

    • DOI

      10.1016/j.molliq.2010.04.019

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Affinity of Small Ligands to Myoglobin Studied by the 3D-RISM Theory2011

    • Author(s)
      Yasuomi Kiyota, Norio Yoshida, Fumio Hirata
    • Journal Title

      J.Mole.Liq.

      Volume: 159 Issue: 1 Pages: 93-98

    • DOI

      10.1016/j.molliq.2010.07.016

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Statistical Mechanics Theory of Molecular Recognition and Pharmaceutical Design2011

    • Author(s)
      Norio Yoshida, Yasuomi Kiyota, Saree Phongphanphanee, Yutaka Maruyama, Takashi Imai, Fumio Hirata
    • Journal Title

      International Review in Physical Chemistry

      Volume: 30 Issue: 4 Pages: 445-478

    • DOI

      10.1007/s12539-011-0104-7

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solvent and Salt Effects on Structural Stability of Human Telomere2011

    • Author(s)
      Y. Maruyama, T. Matsushita, R. Ueoka, F. Hirata
    • Journal Title

      J. Phys. Chem. B

      Volume: 115 Issue: 10 Pages: 2408-2416

    • DOI

      10.1021/jp1096019

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Free energy calculation using molecular dynamics simulation combined with three dimensional reference interaction site model (3D-RISM) theory.II.Thermodynamic integration along reaction coordinates2011

    • Author(s)
      Tatsuhiko Miyata, Yasuhiro Ikuta, Fumio Hirata
    • Journal Title

      J.Chem.Phys.

      Volume: 134 Issue: 4 Pages: 44127-44144

    • DOI

      10.1063/1.3532078

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Functionality Mapping on Internal Surfaces of Multidrug Transporter AcrB Based on Molecular Theory of Solvation : Implications for Drug Efflux Pathway2011

    • Author(s)
      Takashi Imai, Naoyuki Miyashita, Yuji Sugita, Andriy Kovalenko, Fumio Hirata, Akinori Kidera
    • Journal Title

      J.Phys.Chem.B

      Volume: 115 Issue: 25 Pages: 8288-8295

    • DOI

      10.1021/jp2015758

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 分子認識の統計力学と生体機能2011

    • Author(s)
      吉田紀生、丸山豊、Saree Phongphanphanee、清田泰臣、平田文男
    • Journal Title

      生物物理

      Volume: 51 Pages: 222-225

    • NAID

      10029482473

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Recognition Explored by a Statistical-Mechanics Theory of Liquids2011

    • Author(s)
      Saree Phongphanphanee, Norio Yoshida, Fumio Hirata
    • Journal Title

      Current Pharmaceutical Design

      Volume: 17 Issue: 17 Pages: 1740-1757

    • DOI

      10.2174/138161211796355100

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Affinity of Small Ligands to Myoglobin Studied by the 3D-RISM Theory2011

    • Author(s)
      Yasuomi Kiyota, Norio Yoshida, Fumio Hirata
    • Journal Title

      Journal of Molecular Liquids

      Volume: Vol.159 Pages: 93-98

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The electronic-structure theory of a large-molecular system in solution : Application to the intercalation of proflavine with solvated DNA2011

    • Author(s)
      Norio Yoshida, Yasuomi Kiyota, Fumio Hirata
    • Journal Title

      Journal of Molecular Liquids

      Volume: Vol.159 Pages: 83-92

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solvent and Salt Effects on Structural Stability of Human Telomere2011

    • Author(s)
      Yutaka Maruyama, Taku Matsushita, Ryuichi Ueoka, Fumio Hirata
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: Vol.115 Pages: 2408-2416

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Free energy calculation using molecular dynamics simulation combined with the three dimensional reference interaction site model theory. II. Thermodynamic integration along a spatial reaction coordinate2011

    • Author(s)
      Tatsuhiko Miyata, Yasuhiro Ikuta, Fumio Hirata
    • Journal Title

      Journal of Chemical Physics

      Volume: Vol.134

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article]2010

    • Author(s)
      Tatsuhiko Miyata, Yasuhiro Ikuta, and Fumio Hirata
    • Journal Title

      J. Chem. Phys

      Volume: 113 Pages: 44114-44114

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2010

    • Author(s)
      Saree Phongphonphanee, Thanyada Rungromongkol, Norio Yoshida, Supot Hannongbua, and Fumio Hirata
    • Journal Title

      J. Am. Chem. Soc

      Volume: 132 Pages: 9782-9788

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2010

    • Author(s)
      Saree Phongphonphanee, Norio Yoshida, and Fumio Hirata
    • Journal Title

      J. Phys. Chem. B

      Volume: 114 Pages: 7967-7967

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2010

    • Author(s)
      Yutaka Maruyama, Norio Yoshida, and Fumio Hirata
    • Journal Title

      J. Phys. Chem. B

      Volume: 114 Pages: 6464-6471

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Free energy calculation using molecular dynamics simulation combined with three dimensional reference interaction site model (3D-RISM) theory.I.Free energy perturbation and thermodynamic integration along coupling parameter2010

    • Author(s)
      Tatsuhiko Miyata, Yasuhiro Ikuta, Fumio Hirata
    • Journal Title

      J.Chem.Phys. 113

      Pages: 44114-44129

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Proton Transport through the Influenza A M2 Channel : 3D-RISM Study2010

    • Author(s)
      Saree Phongphonphanee, Thanyada Rungromongkol, Norio Yoshida, Supot Hannongbua, Fumio Hirata
    • Journal Title

      J.Am.Chem.Soc. 132

      Pages: 9782-9788

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Free energy calculation using molecular dynamics simulation combined with the three dimensional reference interaction site model theory. I. Free energy perturbation and thermodynamic integration along a coupling parameter2010

    • Author(s)
      Tatsuhiko Miyata, Yasuhiro Ikuta, Fumio Hirata
    • Journal Title

      Journal of Chemical Physics

      Volume: Vol.133

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Proton transport through the Influenza A M2 channel : 3D-RISM Study2010

    • Author(s)
      Saree Phongphanphanee, Thanyada Rungrotmongkol, Norio Yoshida, Supot Hannongbua, Fumio Hirata
    • Journal Title

      Journal of the American Chemical Society

      Volume: Vol.132 Pages: 9782-9788

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory2010

    • Author(s)
      Saree Phongphanphanee, Norio Yoshida, Fumio Hirata
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: Vol.114 Pages: 7967-7973

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Revisiting the Salt-Induced Conformational Change of DNA with 3D-RISM Theory2010

    • Author(s)
      Yutaka Maruyama, Norio Yoshida, Fumio Hirata
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: Vol.114 Pages: 6464-6471

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article]2009

    • Author(s)
      Yui, Toshifumi; Shiiba, Hirohide; Tsutsumi, Yuya; Hayashi, Sachio; Miyata, Tatsuhiko; Hirata, Fumio
    • Journal Title

      J. Phys. Chem. B

      Volume: 114 Pages: 49-58

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2009

    • Author(s)
      Takashi Imai, Koji Oda, Andriy Kovalenko, Fumio Hirata, and Akinori Kidera
    • Journal Title

      J. Am. Chem. Soc

      Volume: 131 Pages: 12430-12440

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2009

    • Author(s)
      Takashi Imai, Andriy Kovalenko, Fumio Hirata, and Akinori Kidera
    • Journal Title

      Interdiscip. Sci. Comput. Life Sic

      Volume: 1 Pages: 156-160

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2009

    • Author(s)
      Yasuomi Kiyota, Ryusuke Hiraoka, Norio Yoshida, Yutaka Maruyama, Takashi Imai, and Fumio Hirata
    • Journal Title

      J. Am. Chem. Soc

      Volume: 131 Pages: 3852-3853

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2009

    • Author(s)
      Norio Yoshida, Takashi Imai, Saree Phongphanphanee, Andriy Kovalenko, and Fumio Hirata
    • Journal Title

      J. Phys. Chem. B

      Volume: 113 Pages: 873-886

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2009

    • Author(s)
      Katusra Nishiyama, Tsuyoshi Yamaguchi, and Fumio Hirata
    • Journal Title

      J. Phys. Chem. B

      Volume: 113 Pages: 2800-2804

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical Study of CO escaping pathway in Myoglobin with the 3D-RISM Theory2009

    • Author(s)
      Yasuomi Kiyota, Ryusuke Hiraoka, Norio Yoshida, Yutaka Maruyama, Takashi Imai, Fumio Hirata
    • Journal Title

      J.Am.Chem.Soc. 131

      Pages: 3852-3853

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Molecular Recognition in Biomolecules Studied by Statistical-Mechanical Integral- Equation Theory of Liquids2009

    • Author(s)
      Norio Yoshida, Takashi Imai, Saree Phongphanphanee, Andriy Kovalenko, Fumio Hirata
    • Journal Title

      J.Phys.Chem.(Feature article) 113

      Pages: 873-886

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Molecular Thermodynamics of Trifluoroethanol-Induced Helix Formation : Analysis of the Solvation Structure and Free Energy by the 3D-RISM Theory2009

    • Author(s)
      Takashi Imai, Andriy Kovalenko, Fumio Hirata, Akinori Kidera
    • Journal Title

      Interdisciplinary Sciences : Computational Life Sciences 1

      Pages: 156-160

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ligand Mapping on Protein Surfaces by the 3D-RISM Theory ; Toward Computational Fragment-Based Drug Design2009

    • Author(s)
      Takashi Imai, Koji Oda, Andriy Kovalenko, Fumio Hirata, Akinori Kidera
    • Journal Title

      Journal of the American Chemical Society 131

      Pages: 12430-12440

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical study of CO escaping pathway in Myoglobin with 3D-RISM Theory2009

    • Author(s)
      Y. Kiyota, R. Hiraoka, N. Yoshida, Y. Maruyama, T. Imai, F. Hirata
    • Journal Title

      Journal of the American Chemical Society 131

      Pages: 3852-3853

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Recognition in Biomolecules Studied by Statistical-Mechanical Integral-Equation Theory of Liquids2009

    • Author(s)
      N. Yoshida, T. Imai, S. Phongphanphanee, A. Kovalenko, F. Hirata
    • Journal Title

      Journal of Physical Chemistry B 113

      Pages: 873-886

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solvation Dynamics in Polar Solvents Studied by Means of RISM / Mode-Coupling Theory2009

    • Author(s)
      K. Nishiyama, T. Yamaguchi, F. Hirata
    • Journal Title

      Journal of Physical Chemistry B 113

      Pages: 2800-2804

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article]2008

    • Author(s)
      Yoshiteru Yonetani, Yutaka Maruyama, Fumio Hirata, and Hidetoshi Kono
    • Journal Title

      J. Chem. Phys

      Volume: 128

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2008

    • Author(s)
      Y. Ikuta, S. Karita, Y. Kitago, N. Watanabe, and F. Hirata
    • Journal Title

      Chem. Phys. Lett

      Volume: 465 Pages: 279-284

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article]2008

    • Author(s)
      N. Yoshida, T. Ishida, and F. Hirata
    • Journal Title

      J. Phys. Chem

      Volume: 112 Pages: 433-440

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] On the proton exclusion of aquaporins : A statistical mechanics study2008

    • Author(s)
      Saree Phongphonphanee, Norio Yoshida, Fumio Hirata
    • Journal Title

      J.Am.Chem.Soc. 130

      Pages: 1540-1541

    • Related Report
      2010 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] An intergral equation theory for inhomogeneous molecular fluids : The reference interaction site model approach2008

    • Author(s)
      R. Ishizuka, S.-H. Chong, F. Hirata
    • Journal Title

      Journal of Chemical Physics 128

      Pages: 34504-34513

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Detecting Reaction Intermediate in Enzymatic Reaction of Ce144A, GH family 44 endoalucanase with 3D-RISM Theory2008

    • Author(s)
      Y. Ikuta, S. Karita, Y. Kitago, N. Watanabe, F. Hirata
    • Journal Title

      Chemical Physics Letters 465

      Pages: 279-284

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An attempt toward the generalized Langevin dynamics simulation2008

    • Author(s)
      B. Kim, S-H. Chong, R. Ishizuka, F. Hirata
    • Journal Title

      Condensed Matter Physics 11

      Pages: 179-190

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory2008

    • Author(s)
      Y. Yonetani, Y. Maruyama, F. Hirata, H. Kono
    • Journal Title

      Journal of Chemical Physics 128

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] 3D-RISM/RISM Theory: Present and Future2013

    • Author(s)
      Fumio Hirata
    • Organizer
      2013 Workshop on 3D-RISM/RISM: Present and Future
    • Place of Presentation
      立命館大学BKCエポック立命21、滋賀県
    • Year and Date
      2013-03-26
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Protein, Fluctuation, Molecular Recognition, and Water2013

    • Author(s)
      Fumio Hirata
    • Organizer
      International Symposium on Protein Folding and its Biological Significance,
    • Place of Presentation
      岡崎市、岡崎コンファレンスセンター、愛知県
    • Year and Date
      2013-03-06
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Structural Fluctuation of Proetin in Water around Its Native State: A New Statistical Mechanics Formulation2013

    • Author(s)
      Fumio Hirata
    • Organizer
      Fifth Korea-Japan Seminars on Biomolecular Sciences - Experiments and Simulations
    • Place of Presentation
      Gohan, Korea
    • Year and Date
      2013-02-26
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] 水は生命の神様である2013

    • Author(s)
      平田文男
    • Organizer
      シンポジウム「生命進化と水」
    • Place of Presentation
      立命館大学BKCエポック立命21、滋賀県草津市
    • Year and Date
      2013-01-28
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Ligand Binding by Protein Probed with the 3D-RISM Microscope2013

    • Author(s)
      平田文男
    • Organizer
      「次世代の物質科学・ナノサイエンスを探る」研究会
    • Place of Presentation
      北海道大学百年記念会館、北海道
    • Year and Date
      2013-01-11
    • Related Report
      2012 Final Research Report
  • [Presentation] Ligand Binding by Protein Probed with the 3D-RISM Microscope2013

    • Author(s)
      平田文男
    • Organizer
      次世代の物質科学・ナノサイエンスを探る
    • Place of Presentation
      北海道大学百年記念会館、北海道
    • Year and Date
      2013-01-11
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] The molecular mechanism of the pressure denaturation of protein clarified by the 3D-RISM theory2012

    • Author(s)
      Fumio Hirata
    • Organizer
      7th International Conference on High Pressure Bioscience and Biotechnology
    • Place of Presentation
      ピアザ淡海、滋賀県
    • Year and Date
      2012-10-29
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Exploring life phenomena with a theory featuring chemical 'specificity' and physical 'universality'2012

    • Author(s)
      Fumio Hirata
    • Organizer
      "Israel -Japan Joint Symposium on Biophysics: Protein Dynamics: From single molecules to whole cell" in Biophysics Society meeting in Japan
    • Place of Presentation
      兵庫県立大学(兵庫県)
    • Year and Date
      2012-09-16
    • Related Report
      2012 Final Research Report
  • [Presentation] Ligand Binding by Protein Probed with the 3D-RISM Microscope2012

    • Author(s)
      Fumio Hirata
    • Organizer
      The ACS Symposium on "Continuum Solvation Modeling in Biological Systems
    • Place of Presentation
      Philadelphia, USA
    • Year and Date
      2012-08-20
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] Ligand Binding by Protein Probed with 3D-RISM Microscope2012

    • Author(s)
      Fumio Hirata
    • Organizer
      Foundation of Molecular Modeling and Simulation(FOMMS)
    • Place of Presentation
      Mt. Hood, Oregon, USA
    • Year and Date
      2012-07-25
    • Related Report
      2012 Final Research Report
  • [Presentation] Ligand Binding by Protein Probed with 3D-RISM Microscop2012

    • Author(s)
      Fumio Hirata
    • Organizer
      Foundation of Molecular Modeling and Simulation(FOMMS)
    • Place of Presentation
      Mt. Hood, USA
    • Year and Date
      2012-07-25
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Exploring life phenomena with a Theory Featuring Chemical Specificity and Physical Universality2012

    • Author(s)
      Fumio Hirata
    • Organizer
      International Conference on Pure and Applied Chemistry: The key for our Future
    • Place of Presentation
      Flic-en-Flac, Mauritius
    • Year and Date
      2012-07-04
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] 分子認識の統計力学(3D-RISM/RISM)と構造生物学2012

    • Author(s)
      平田文男
    • Organizer
      第12回蛋白質科学シンポジウム「YouTube 時代の構造生物学」
    • Place of Presentation
      名古屋国際会議場(愛知県)
    • Year and Date
      2012-06-22
    • Related Report
      2012 Final Research Report
  • [Presentation] 分子認識の統計力学(3D-RISM/RISM)と構造生物学2012

    • Author(s)
      平田文男
    • Organizer
      第12回蛋白質科学シンポジウム「YouTube時代の構造生物学」
    • Place of Presentation
      名古屋国際会議場、愛知県
    • Year and Date
      2012-06-22
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Theory of Molecular Recognition and Its Application to Pharmaceutical Design2012

    • Author(s)
      Fumio Hirata
    • Organizer
      12^<th> Eurasia Conference on Chemical Sciences EuAsC2S-12
    • Place of Presentation
      Corfu, Greece
    • Year and Date
      2012-04-20
    • Related Report
      2012 Final Research Report
  • [Presentation] Theory of Molecular Recognition and Its Application to Pharmaceutical Design2012

    • Author(s)
      Fumio Hirata
    • Organizer
      12th Eurasia Conference on Chemical Sciences EuAsC2S-12
    • Place of Presentation
      Corfu, Greece
    • Year and Date
      2012-04-20
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 酵素反応解析へ向けた、3D-RISM理論による分子認識解析2012

    • Author(s)
      吉田紀生
    • Organizer
      文部科学省「革新的ハイパフォーマンス・コンピューティング・インフラ(HPCI)の構築」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6回公開シンポジウム
    • Place of Presentation
      ニチイ学館,神戸市(兵庫県)
    • Year and Date
      2012-03-06
    • Related Report
      2011 Annual Research Report
  • [Presentation] バイオマス利用に向けた酵素反応解析2012

    • Author(s)
      吉田紀生
    • Organizer
      第2回CMSI研究会
    • Place of Presentation
      東北大学金属材料研究所,仙台市(宮城県)
    • Year and Date
      2012-01-31
    • Related Report
      2011 Annual Research Report
  • [Presentation] RISM理論による生体分子の分子認識と化学反応へ向けた研究2012

    • Author(s)
      吉田紀生
    • Organizer
      スーパーコンピュータワークショップ2012
    • Place of Presentation
      岡崎コンファレンスセンター,岡崎市(愛知県)
    • Year and Date
      2012-01-25
    • Related Report
      2011 Annual Research Report
  • [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution2012

    • Author(s)
      Fumio Hirata
    • Organizer
      Asian Core symposium on "The 4^<th> Japan-Korea Seminar on Biomolecular Sciences: Experiment and Simulation
    • Place of Presentation
      国際会議場(奈良県)
    • Related Report
      2012 Final Research Report
  • [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution2012

    • Author(s)
      Fumio Hirata
    • Organizer
      The 71^<st> Okazaki International Conference: New perspectives on molecular science of glycoconjugate
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県)
    • Related Report
      2012 Final Research Report
  • [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution2012

    • Author(s)
      Fumio Hirata
    • Organizer
      Asian Core symposium on "The 4^<th> Japan-Korea Seminar on Biomolecular Sciences : Experiment and Simulation,"
    • Place of Presentation
      Nara, Nara
    • Related Report
      2011 Annual Research Report
  • [Presentation] 液体の積分方程式理論に基づく溶液内生体分子の電子状態理論2011

    • Author(s)
      吉田紀生
    • Organizer
      液体・溶液の微視的構造からダイナミクスまで~最近の研究結果から見えてくるもの~
    • Place of Presentation
      愛媛大学,松山市(愛媛県)
    • Year and Date
      2011-11-28
    • Related Report
      2011 Annual Research Report
  • [Presentation] 液体の積分方程式理論を用いた溶液内化学過程に関する研究2011

    • Author(s)
      吉田紀生
    • Organizer
      第34回溶液化学シンポジウム
    • Place of Presentation
      名古屋大学,名古屋市(愛知県)
    • Year and Date
      2011-11-16
    • Related Report
      2011 Annual Research Report
  • [Presentation] QM/MM/3D-RISM理論の開発とプログラムの高速化2011

    • Author(s)
      吉田紀生
    • Organizer
      第3回HPCI戦略プログラム合同研究交流会
    • Place of Presentation
      計算科学研究機構,神戸市(兵庫県)
    • Year and Date
      2011-10-03
    • Related Report
      2011 Annual Research Report
  • [Presentation] Solvent Effects on Electronic Structures of Coumarin 153 : RISM-SCF Analysis2011

    • Author(s)
      吉田紀生, 西山桂, 平田文男
    • Organizer
      分子科学討論会2011
    • Place of Presentation
      札幌コンベンションセンター,札幌市(北海道)
    • Year and Date
      2011-09-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] Molecular Ornstein-Zernike self-consistent-field approach to hydrated electron2011

    • Author(s)
      Norio Yoshida
    • Organizer
      8th Liquid Matter Conference
    • Place of Presentation
      University of Vienna, Vienna, Austria
    • Year and Date
      2011-09-06
    • Related Report
      2011 Annual Research Report
  • [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution2011

    • Author(s)
      Fumio Hirata
    • Organizer
      32th International Conference on Solution Chemistry
    • Place of Presentation
      La Grande Motte, France
    • Year and Date
      2011-08-28
    • Related Report
      2012 Final Research Report
  • [Presentation] 3D-RISMプログラムの開発と応用2011

    • Author(s)
      吉田紀生、清田泰臣、Daniel J.Sindhikara、平田文男
    • Organizer
      計算物質科学イニシアティブ・計算分子科学研究拠点第2回研究会
    • Place of Presentation
      計算科学研究機構,神戸市(兵庫県)
    • Year and Date
      2011-08-11
    • Related Report
      2011 Annual Research Report
  • [Presentation] 液体の統計力学と量子力学に基づくATP加水分解の自由エネルギー解析2011

    • Author(s)
      吉田紀生
    • Organizer
      「水を主役としたATPエネルギー変換」後期第一回研究会議
    • Place of Presentation
      大阪ガーデンパレス,大阪市(大阪府)
    • Year and Date
      2011-08-11
    • Related Report
      2011 Annual Research Report
  • [Presentation] Statistical Mechanics Theory of Molecular Recognition and its Application to Pharmaceutical Design2011

    • Author(s)
      Fumio Hirata
    • Organizer
      Telluride Wrokshop on Free Energy Simulation
    • Place of Presentation
      Telluride, Colorado, USA
    • Year and Date
      2011-07-03
    • Related Report
      2012 Final Research Report
  • [Presentation] Collaboration between computer and computational scientists make high performance computing on the K-computer a reality2011

    • Author(s)
      Fumio Hirata
    • Organizer
      ISC'11 HPC in Asia Workshop
    • Place of Presentation
      Hamburg, Germany
    • Year and Date
      2011-06-18
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Presentation] Exploring life phenomena with a theory featuring chemical 'specificity' and physical 'universality'2011

    • Author(s)
      Fumio Hirata
    • Organizer
      Statistical Mechanics Approaches to Biomolecular Applications
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2011-06-13
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Presentation] Development of the QM/MM/RISM theory : Application to the intercalation of proflavine with solvated DNA2011

    • Author(s)
      Norio Yoshida
    • Organizer
      Statistical Mechanics Approaches to Nano/Bio-Sciences
    • Place of Presentation
      Sookmyung Women's University, Soeul, Korea
    • Year and Date
      2011-06-13
    • Related Report
      2011 Annual Research Report
  • [Presentation] Theory of Molecular Recognition and its Application to Drug Design2011

    • Author(s)
      Fumio Hirata
    • Organizer
      International Conference on Computer Science (ICCS) 2011
    • Place of Presentation
      Singapore
    • Year and Date
      2011-06-02
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular Ornstein-Zernike self-consistent-field approach to hydrated electron2011

    • Author(s)
      Norio Yoshida
    • Organizer
      International Congress on Computational Science 2011
    • Place of Presentation
      Nanyang Technological University, Singapore
    • Year and Date
      2011-06-02
    • Related Report
      2011 Annual Research Report
  • [Presentation] Statistical Mechanics of Molecular Liquids Reveals Elementary Processes in Life Phenomena2011

    • Author(s)
      Fumio Hirata
    • Organizer
      Third Korea-Japan Seminars on Biomolecular Sciences-Experiments and Simulations
    • Place of Presentation
      Lotte hotel, Jeju, Korea
    • Year and Date
      2011-02-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] 分子認識の統計力学と生体機能2011

    • Author(s)
      平田文男
    • Organizer
      自然科学研究機構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
      岡崎コンファレンスセンター(愛知県)
    • Year and Date
      2011-02-12
    • Related Report
      2012 Final Research Report
  • [Presentation] Statistical Mechanics of Molecular Liquids Reveals Elementary Processes in Life Phenomena2011

    • Author(s)
      Fumio Hirata
    • Organizer
      Third Korea-Japan Seminars on Biomolecular Sciences: - Experiments and Simulations
    • Place of Presentation
      Jeju, Korea
    • Related Report
      2012 Final Research Report
  • [Presentation] Theory of Molecular Recognition and its Application to Drug Design2011

    • Author(s)
      Fumio Hirata
    • Organizer
      ICCS2011
    • Place of Presentation
      Singapore
    • Related Report
      2011 Annual Research Report
  • [Presentation] Statistical Mechanics Theory of Molecular Recognition and its Applic ation to Pharmaceutical Design2011

    • Author(s)
      Fumio Hirata
    • Organizer
      Telluride Wrokshop on Free Energy Simulation
    • Place of Presentation
      Telluride, USA
    • Related Report
      2011 Annual Research Report
  • [Presentation] 高速3D-RISMの開発について2011

    • Author(s)
      平田文男
    • Organizer
      CMSI・計算分子科学研究拠点、第2回研究会
    • Place of Presentation
      神戸市(兵庫県)
    • Related Report
      2011 Annual Research Report
  • [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution," "32th International Conference on Solution Chemistry2011

    • Author(s)
      Fumio Hirata
    • Organizer
      32th International Conference on Solution Chemistry
    • Place of Presentation
      La Grande Motte, France
    • Related Report
      2011 Annual Research Report
  • [Presentation] Exploring life phenomena with a theory featuring chemical 'specificity' and physical 'universality'2011

    • Author(s)
      Fumio Hirata
    • Organizer
      Israel-Japan Joint Symposium on Biophysics : Protein Dynamics : From single molecules to whole cell in Biophysics Society meeting in Japan
    • Place of Presentation
      Himeji, Hyogo
    • Related Report
      2011 Annual Research Report
  • [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution2011

    • Author(s)
      Fumio Hirata
    • Organizer
      The 71^<st> Okazaki International Conference : New perspectives on molecular science of glycoconjugate
    • Place of Presentation
      Okazaki, Aichi
    • Related Report
      2011 Annual Research Report
  • [Presentation] Exploring life phenomena with a Statistical Mechanics of Molecular Solution2011

    • Author(s)
      平田文男
    • Organizer
      液体溶液の微視的構造からダイナミクスまで~最近の研究結果から見えてくるもの
    • Place of Presentation
      松山市(愛媛県)
    • Related Report
      2011 Annual Research Report
  • [Presentation] Solvent Effects on Electronic Structures of Coumarin 153.I.RISM-SCF Analysis of the Solvent Distribution and Electronic Properties2011

    • Author(s)
      Norio Yoshida, Katsura Nishiyama, Fumio Hirata
    • Organizer
      EMLG/JMLG Annual Meeting 2011
    • Place of Presentation
      University of Warsaw, Warsaw, Poland
    • Related Report
      2011 Annual Research Report
  • [Presentation] Electronic structure theory of biomolecule in solution2011

    • Author(s)
      Norio Yoshida, Fumio Hirata
    • Organizer
      Ninth Triennial Congress of the World Association of Theoretical and Computational Chemists
    • Place of Presentation
      University of Santiago, Santiago de compostela, Spain
    • Related Report
      2011 Annual Research Report
  • [Presentation] Ligand binding and escaping pathway in myoglobin studied by the 3D-RISM theory2010

    • Author(s)
      Fumio Hirata
    • Organizer
      Dynamics and Mechanisms of Photochemical Reactions of Biological Proteins, Pacifichem 2010
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2010-12-15
    • Related Report
      2010 Annual Research Report
  • [Presentation] Molecular Recognition in Biological Functions Revealed by Statistical mechanics of Molecular Liquids2010

    • Author(s)
      Fumio Hirata
    • Organizer
      4th International symposium on "Molecular Science of Fluctuations toward Biological Functions
    • Place of Presentation
      ピアザ淡海(滋賀県)
    • Year and Date
      2010-12-01
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular Recognition in Biological Functions Revealed by Statistical mechanics of Molecular Liquids2010

    • Author(s)
      Fumio Hirata
    • Organizer
      4th International symposium on "Molecular Science of Fluctuations toward Biological Functions
    • Place of Presentation
      ピアザ淡海、滋賀
    • Year and Date
      2010-12-01
    • Related Report
      2010 Annual Research Report
  • [Presentation] Statistical Mechanics of Molecular Liquids Reveals Elementary Processes in Life Phenomena2010

    • Author(s)
      Fumio Hirata
    • Organizer
      The Overseas Sokendai Lecture in Bankok : The Inaugural CU-IMS Joint Symposium
    • Place of Presentation
      Bankok, Thailand
    • Year and Date
      2010-10-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Statistical Mechanics of Molecular Liquids Reveals Elementary Processes in Life Phenomena2010

    • Author(s)
      Fumio Hirata
    • Organizer
      EMLG-JMLG joint meeting 2010
    • Place of Presentation
      Ivan Franko National University, Lviv, Ukraine
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Statistical Mechanics of Molecular Liquids Reveals Elementary Processes in Life Phenomena2010

    • Author(s)
      Fumio Hirata
    • Organizer
      EMLG-JMLG joint meeting 2010
    • Place of Presentation
      Lviv, Ukraine
    • Year and Date
      2010-09-07
    • Related Report
      2012 Final Research Report
  • [Presentation] On the origin of energy produced by the hydrolysis reaction of ATP:3D-RISM-SCF study2010

    • Author(s)
      Fumio Hirata
    • Organizer
      ICPOC-20: 20th International Conference on Physical Organic Chemistry
    • Place of Presentation
      Busan, Republic of Korea
    • Year and Date
      2010-08-25
    • Related Report
      2012 Final Research Report
  • [Presentation] On the origin of energy produced by the hydrolysis reaction of ATP : 3D-RISM-SCF study2010

    • Author(s)
      Fumio Hirata
    • Organizer
      ICPOC-20 : 20th International Conference on Physical Organic Chemistry
    • Place of Presentation
      Busan, Republic of Korea
    • Year and Date
      2010-08-22
    • Related Report
      2010 Annual Research Report
  • [Presentation] RISM-SCF理論の開発と発展~RISM-SCF理論誕生秘話~2010

    • Author(s)
      平田文男
    • Organizer
      加藤重樹教授記念シンポジウム「化学反応のポテンシャル曲面とダイナミックス」
    • Place of Presentation
      京都大学 理学研究科セミナーハウス、京都布
    • Year and Date
      2010-06-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] ナノ分野における「グランドチャレンジ」課題への挑戦と計算科学2010

    • Author(s)
      平田文男
    • Organizer
      第一回「学際計算科学による新たな知の発見・統合・創出」シンポジウム
    • Place of Presentation
      筑波大学計算科学研究センター、つくば市
    • Year and Date
      2010-05-06
    • Related Report
      2010 Annual Research Report
  • [Presentation] Ligand binding and escaping pathway in myoglobin studied by the 3D-RISM theory2010

    • Author(s)
      Fumio Hirata
    • Organizer
      Dynamics and Mechanisms of Photochemical Reactions of Biological Proteins, Pacifichem 2010
    • Place of Presentation
      Honolulu, USA
    • Related Report
      2012 Final Research Report
  • [Presentation] Statistical Mechanics of Molecular Liquids Revelas Elementary Processes in Life Phenomena2010

    • Author(s)
      Fumio Hirata
    • Organizer
      EMLG/JMLG Annual Meeting "Complex Liquids "
    • Place of Presentation
      Lviv, Ukraine(招待講演)
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids2010

    • Author(s)
      Fumio Hirata
    • Organizer
      EMLG/JMLG Annual Meeting "Intermolecular Interactions and Liquid Structure, "
    • Place of Presentation
      Salzburg(招待講演)
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] A Statistical Mechanics Study of Molecular Recognition and Drug Design2009

    • Author(s)
      Fumio Hirata
    • Organizer
      2^<nd> Japan-Korea Seminar on Biomolecular Science - Experiments and Simulations
    • Place of Presentation
      名古屋大学(愛知県)
    • Year and Date
      2009-12-23
    • Related Report
      2012 Final Research Report
  • [Presentation] Biomolecules in water and water in biomolecules on the Physics, Chemistry, and Biology of Water 20092009

    • Author(s)
      Hirata
    • Organizer
      the Fourth Annual Conference
    • Place of Presentation
      Snow Mountain, USA
    • Year and Date
      2009-10-22
    • Related Report
      2012 Final Research Report
  • [Presentation] Model Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids2009

    • Author(s)
      Fumio Hirata
    • Organizer
      International Workshop on "Continuum Modeling of Biomolecules
    • Place of Presentation
      Beijin, China
    • Year and Date
      2009-09-14
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids2009

    • Author(s)
      Fumio, Hirata
    • Organizer
      EMLG/JMLG Annual Meeting "Intermolecular Interactions and Liquid Structure,"
    • Place of Presentation
      Salzburg, Austlia
    • Year and Date
      2009-09-11
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids2009

    • Author(s)
      Fumio Hirata
    • Organizer
      6^<th> International Discussion Meeting on Relaxations in Complex Systems
    • Place of Presentation
      Roma, Italy
    • Year and Date
      2009-09-03
    • Related Report
      2012 Final Research Report
  • [Presentation] Statistical mechanics reached at the point where it can explain elementary processes in life phenomena2009

    • Author(s)
      Fumio Hirata
    • Organizer
      Statistical Physics: Modern Trends and Applications dedicated to the 100-th anniversary of Prof. M.M.Bogolyubov
    • Place of Presentation
      Lviv, Ukraine
    • Year and Date
      2009-06-24
    • Related Report
      2012 Final Research Report
  • [Presentation] 蛋白質一溶液界面と分子認識 : 統計力学的研究2009

    • Author(s)
      平田文男
    • Organizer
      特定領域研究「高次系分子科学」・SFG研究会合同シンポジウム「表面・界面を観る非線形分光の新しい展開」
    • Place of Presentation
      埼玉県和光市理化学研究所
    • Year and Date
      2009-03-23
    • Related Report
      2008 Annual Research Report
  • [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids2009

    • Author(s)
      Fumio Hirata
    • Organizer
      The 6^<th> Open Workshop on "Water and Biomolecules," and The 2^<nd> Open Workshop on "Fluctuation and Function,"
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県)
    • Year and Date
      2009-03-16
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids2009

    • Author(s)
      F. Hirata
    • Organizer
      The 6th Open Workshop on "Water and Biomolec ules" and the 2nd Open Symposium on "Fluctuati on and Biological Functions"
    • Place of Presentation
      愛知県岡崎市岡崎コンファレンスセンター
    • Year and Date
      2009-03-16
    • Related Report
      2008 Annual Research Report
  • [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids2009

    • Author(s)
      F. Hirata
    • Organizer
      Asian Core Symposium "First Korea-Japan Semin ars on Biomolecular Sciences Experiments and Si mulations"
    • Place of Presentation
      KIAS in Seoul, Korea
    • Year and Date
      2009-03-01
    • Related Report
      2008 Annual Research Report
  • [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids2009

    • Author(s)
      Fumio Hirata
    • Organizer
      Asian Core symposium "First Korea-Japan Seminars on Biomolecular Sciences - Experiments and Simulations"
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2009-02-28
    • Related Report
      2012 Final Research Report
  • [Presentation] 生体分子および溶媒の構造揺らぎと共役した機能発現過程の理論的解明2009

    • Author(s)
      平田文男
    • Organizer
      新学術領域「揺らぎと生体機能」第一回公開シンポジウム
    • Place of Presentation
      京都テルサ(京都府)
    • Year and Date
      2009-01-06
    • Related Report
      2012 Final Research Report
  • [Presentation] 生体分子および溶媒の構造揺らぎと共役した機能発現過程の理論的解明2009

    • Author(s)
      平田文男
    • Organizer
      新学術領域「揺らぎと生体機能」第一回公開シンポジウム
    • Place of Presentation
      京都府京都市京都テルサ
    • Year and Date
      2009-01-06
    • Related Report
      2008 Annual Research Report
  • [Presentation] Statistical mechanics reached at the point where it can explain elementary processes in life phenomena2009

    • Author(s)
      Fumio Hirata
    • Organizer
      Statistical Physics : Modern Trends and Applications dedicated to the 100-th anniversary of Prof.M.M.Bogolyubov
    • Place of Presentation
      Lviv, Ukraine(招待講演)
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] Possibility of Parallelization of the 3D-RISM Program on the Next-generation Supercomputer2009

    • Author(s)
      平田文男
    • Organizer
      3^<rd> French-Japanese Workshop on "Petascale Applications, Algorithms and Programing(PAAP)
    • Place of Presentation
      京都市 芝欄館
    • Related Report
      2009 Annual Research Report
  • [Presentation] An attempt toward the generalized Langevin dynamics simulation2009

    • Author(s)
      平田文男
    • Organizer
      KIAS meeting on "Recent Progress in Computer Simulations in Molecular Sciences
    • Place of Presentation
      Seoul(Korea)
    • Related Report
      2009 Annual Research Report
  • [Presentation] Statistical mechanics reached at the point where it can explain elementary processes in life phenomena2009

    • Author(s)
      平田文男
    • Organizer
      Statistical Physics : Modem Trends and Applications dedicated to the 100-th anniversary of□Prof.M.M.Bogolyubov
    • Place of Presentation
      Lviv(Ukraine)
    • Related Report
      2009 Annual Research Report
  • [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids2009

    • Author(s)
      平田文男
    • Organizer
      6^<th> International Discussion Meeting on Relaxations in Complex Systems
    • Place of Presentation
      Roma(Italy)
    • Related Report
      2009 Annual Research Report
  • [Presentation] Molecular Recognition, Fluctuation, and Function of Protein Studied by a Statistical Mechanics of Liquids2009

    • Author(s)
      平田文男
    • Organizer
      EMLG/JMLG Annual Meeting "Intermolecular Interactions and Liquid Structure
    • Place of Presentation
      Salzburg(Austria)
    • Related Report
      2009 Annual Research Report
  • [Presentation] Model Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids2009

    • Author(s)
      平田文男
    • Organizer
      International Workshop on "Continuum Modeling of Biomolecules
    • Place of Presentation
      Beijin(China)
    • Related Report
      2009 Annual Research Report
  • [Presentation] Biomolecules in water and water in biomolecules2009

    • Author(s)
      平田文男
    • Organizer
      the Fourth Annual Conference on the Physics, Chemistry, and Biology of Water 2009
    • Place of Presentation
      Vermont(U.S.A.)
    • Related Report
      2009 Annual Research Report
  • [Presentation] 「生命階層と物質階層の境界 : 分子認識」、自然科学研究機構「自然科学における階層と全体」2008

    • Author(s)
      平田文男
    • Organizer
      自然科学研究機構「自然科学における階層と全体」シンポジウム
    • Place of Presentation
      愛知県蒲郡市
    • Year and Date
      2008-12-17
    • Related Report
      2008 Annual Research Report
  • [Presentation] Molecular Recognition in Life Phenomena Probed with the Statistical Mechanics of Liauids2008

    • Author(s)
      F. Hirata
    • Organizer
      IMA Annual Program Year Workshop "Solvation"
    • Place of Presentation
      University of Minesota, Minneapolis, USA
    • Year and Date
      2008-12-11
    • Related Report
      2008 Annual Research Report
  • [Presentation] Molecular Recognition in Life Phenomena Probed with the Statistical Mechanics of Liquids2008

    • Author(s)
      F. Hirata
    • Organizer
      IMA Annual Program Tear Workshop "Solvation,"
    • Place of Presentation
      Minneapolis, USA
    • Year and Date
      2008-12-10
    • Related Report
      2012 Final Research Report
  • [Presentation] Statistical-mechanics theory of molecular recognition: water and other molecules recognized by protein2008

    • Author(s)
      F. Hirata
    • Organizer
      Water in Biological System, A French-Japanese Workshop
    • Place of Presentation
      京都大学(京都府)
    • Year and Date
      2008-11-26
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular Recognition in Life Phenomena Probed with the Statistical Mechanics of Liquids2008

    • Author(s)
      F. Hirata
    • Organizer
      The 8^<th> KIAS-Yonsei Conference on Protein Structure and Function
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2008-10-10
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular Recognition Realized by the Statistical Mechanics Theory of Liquids2008

    • Author(s)
      F. Hirata
    • Organizer
      Theory and Applications of Computational Chemistry (TACC)
    • Place of Presentation
      Shanghai, China
    • Year and Date
      2008-09-25
    • Related Report
      2012 Final Research Report
  • [Presentation] Theory of molecular recognition and it's application to the enzymatic reaction2008

    • Author(s)
      F. Hirata
    • Organizer
      The grand challenge to Next Generation Integrated Nano-science
    • Place of Presentation
      未来科学館(東京都)
    • Year and Date
      2008-06-04
    • Related Report
      2012 Final Research Report
  • [Presentation] Statistical theory of molecular recognition, and it's application to aquaporin2008

    • Author(s)
      F. Hirata
    • Organizer
      The 5^<th> Open Workshop on "Chemistry of Biological Processes Created by Water and Biomolecules
    • Place of Presentation
      能楽堂(奈良県)
    • Year and Date
      2008-01-24
    • Related Report
      2012 Final Research Report
  • [Presentation] A Statistical Mechanics Study of Molecular Recognition and Anesthesia

    • Author(s)
      Fumio Hirata
    • Organizer
      第47回生物物理学会シンポジウム"麻酔作用の分子機構:生物物理から明らかにされる生体分子と麻酔 薬の相互作用
    • Place of Presentation
      文理大学(徳島県)
    • Related Report
      2012 Final Research Report
  • [Presentation] An attempt toward the generalized Langevin dynamics simulation

    • Author(s)
      Fumio Hirata
    • Organizer
      KIAS meeting on "Recent Progress in Computer Simulations in Molecular Sciences,"
    • Place of Presentation
      Seoul, Korea
    • Related Report
      2012 Final Research Report
  • [Book] 「水と生体分子のハーモニー」。日本化学会編「巨大分子系の計算科学」第15章2012

    • Author(s)
      吉田紀生、丸山豊、清田泰臣、平田文男、今井隆志
    • Publisher
      化学同人
    • Related Report
      2012 Final Research Report
  • [Book] 「新しい分子統計力学・統計的動力学記述法」、日本化学会編「巨大分子系の計算科学」第7章2012

    • Author(s)
      平田文男
    • Publisher
      化学同人
    • Related Report
      2012 Final Research Report
  • [Book] 巨大分子系の統計力学2012

    • Author(s)
      平田文男
    • Total Pages
      12
    • Publisher
      化学同人
    • Related Report
      2012 Annual Research Report
  • [Book] 巨大分子系の統計力学2012

    • Author(s)
      吉田紀生
    • Total Pages
      12
    • Publisher
      化学同人
    • Related Report
      2012 Annual Research Report
  • [Book] Chapter 4 in Bihan and Fukuyama(Ed.) : "Water, the forgotten biological molecule."2011

    • Author(s)
      Norio Yoshida, Yasuomi Kiyota, Thanyada Rungrotmongkol, Saree Phongphanphanee, Takashi Imai, Fumio Hirata
    • Total Pages
      24
    • Publisher
      Pan Stanford Publishing
    • Related Report
      2010 Annual Research Report
  • [Book] Statistical-mechanics theory of molecular recognition: water and other molecules recognized by protein, in Bihan and Fukuyama(Ed.): "Water, the forgotten biological molecule."2010

    • Author(s)
      Norio Yoshida, Yasuomi Kiyota, Saree Phongphanphanee, Takashi Imai and Fumio Hirata
    • Publisher
      Pan Stanford Publishing, Singapore
    • Related Report
      2012 Final Research Report
  • [Book] 揺らぎと生体機能(別冊・メディカルバイオ)(Statistical Mechanics theory of molecular recognition and ion channels)2010

    • Author(s)
      平田文男, 吉田紀生
    • Publisher
      Saree Phonphanphanee
    • Related Report
      2010 Self-evaluation Report
  • [Book] Water, theforgottenbiologicalmolecule(Statistical-mechanics theory of molecular recognition : water and other molecules recognized by protein)(in Bihan and Fukuyama(Ed.))(Chapter 4)2010

    • Author(s)
      Norio Yoshida, Yasuomi Kiyota, Saree Phongphanphanee, Takashi Imai, Fumio Hirata
    • Publisher
      Pan Stanford Publishing
    • Related Report
      2010 Self-evaluation Report
  • [Book] "分子認識とイオンチャネルの統計力学理論",Medical Bio 10月別冊 揺らぎと生体機能、寺嶋正秀 監修2010

    • Author(s)
      平田文男、吉田紀生、Saree Phongphanphanee
    • Total Pages
      6
    • Publisher
      オーム社
    • Related Report
      2010 Annual Research Report
  • [Book] Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids, in Feig(Ed.) : "Modeling Solvent Environ ments."2010

    • Author(s)
      Norio Yoshida, Yasuomi Kiyota, Yasuhiro Ikuta, Takashi Imai, Ffumio Hirata
    • Total Pages
      24
    • Publisher
      Willy-VCH
    • Related Report
      2009 Annual Research Report
  • [Book] "Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids," in "Modeling Solvent Environment," Ed. M. Feig2009

    • Author(s)
      N. Yoshida, Y. Kiyota, Y. Ikuta, T. Imai, and F. Hirata
    • Publisher
      Wiley-VCH
    • Related Report
      2012 Final Research Report
  • [Book] "A Statistical Mechanics Theory of Molecular Recognition," in "Water and Biomolecules," Eds, K. Kuwajima, Y. Goto, F. Hirata, M. Kataoka, and M, Terazima2009

    • Author(s)
      T. Imai, N. Yoshida, A. Kovalenko, and F. Hirata
    • Publisher
      Springer
    • Related Report
      2012 Final Research Report
  • [Book] A Statistical Mechanics Theory of Molecular Recognition, Chapter 10, in Water and Biomolecules - Physical Chemistry of Life Phenomena.2009

    • Author(s)
      Takashi Imai, Norio Yoshida, Andriy Kovalenko, Fumio Hirata
    • Total Pages
      24
    • Publisher
      Springer Science
    • Related Report
      2009 Annual Research Report
  • [Patent(Industrial Property Rights)] 溶液中の生体高分子の構造揺らぎとダイナミクスを 記述する方程式2013

    • Inventor(s)
      平田文男;Kim,Bongsoo
    • Industrial Property Rights Holder
      平田文男; Kim Bongsoo
    • Filing Date
      2013-01-23
    • Related Report
      2012 Final Research Report
    • Overseas
  • [Patent(Industrial Property Rights)] Analysis of Biomolecular Solvation site by the 3D-RISM Theory2013

    • Inventor(s)
      Hirata, Fumio; Sindhikara, Daniel, Jon
    • Industrial Property Rights Holder
      Hirata, Fumio; Sindhikara, Daniel, Jon
    • Filing Date
      2013-04-05
    • Related Report
      2012 Final Research Report
    • Overseas
  • [Patent(Industrial Property Rights)] 溶液中の生体高分子の構造揺らぎとダイナミクスを記述する方程式2013

    • Inventor(s)
      平田文男
    • Industrial Property Rights Holder
      平田文男
    • Industrial Property Rights Type
      特許
    • Filing Date
      2013-01-23
    • Related Report
      2012 Annual Research Report
    • Overseas

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Published: 2008-04-01   Modified: 2018-03-28  

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