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Theoretical studies on possibility of the entrainment in molecular systems

Research Project

Project/Area Number 23655101
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Polymer chemistry
Research InstitutionKanazawa University

Principal Investigator

NAGAO Hidemi  金沢大学, 数物科学系, 数物科学系 (30291892)

Co-Investigator(Renkei-kenkyūsha) NAGAYAMA Masaharu  北海道大学, 電子科学研究所, 教授 (20314289)
IWASAKI Hiroshi  金沢大学, 数物科学系, 准教授 (30242514)
SAITO Hiroaki  金沢大学, 数物科学系, 助教 (40506820)
KAWAGUCHI Kazutomo  金沢大学, 数物科学系, 助教 (90402429)
Project Period (FY) 2011 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2012: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2011: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywords引き込み現象 / 分子動力学シミュレーション / 自己組織化 / 高分子 / 脂質ミセル / 脂質 / ミセル
Research Abstract

We have discussed the dynamics of molecular systems by using some molecular models in relation to the frequency entrainment. We have found that the frequency entrainment in molecules is not observed in the solvent with lower density. On the other hand, in the case of higher density of the solvent, we have observed the frequency entrainment between molecules explicitly.

Report

(3 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Research-status Report
  • Research Products

    (34 results)

All 2013 2012 2011 Other

All Journal Article (13 results) (of which Peer Reviewed: 13 results) Presentation (20 results) (of which Invited: 4 results) Remarks (1 results)

  • [Journal Article] Theoretical Study on Entrainment Phenomenon in Model Molecular Systems2013

    • Author(s)
      H. Nagao, S. Kawamoto, M. Rusmerryani, A. Purqon, K. Kawaguchi, H. Saito
    • Journal Title

      AIP Conference Proceedings

      Volume: 1518 Pages: 729-732

    • DOI

      10.1063/1.4794669

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study on Binding Free Energy of Azurin-Cytochrome c551 Complex2012

    • Author(s)
      H. Saito, M. Iwayama, T. Mizukami, J. Kang, M.Tateno, H. Nagao
    • Journal Title

      Chemical Physics Letters

      Volume: 556 Pages: 297-302

    • DOI

      10.1016/j.cplett.2012.12.016

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Analyses of the Dissociation Process of ADP from Hsp902012

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, M.Nishimura, T. Miyakawa, H. Saito, M. Takasu, H.Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 24 Pages: 3791-3795

    • DOI

      10.1002/qua.24229

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Nanoscale Superconductivity2012

    • Author(s)
      Sergei P. Kruchinin, Hidemi Nagao
    • Journal Title

      International Journal Modern Physics

      Volume: 26 Issue: 26 Pages: 12300013-12300013

    • DOI

      10.1142/s0217979212300137

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Studies of Lipid Bilayer with Gramicidin A: Effects of Gramicidin A on Membrane Structure and Hydrophobic Match2012

    • Author(s)
      Hiroaki Saito, Taku Mizukami, Shuhei Kawamoto, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 1 Pages: 161-170

    • DOI

      10.1002/qua.23252

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cell-Penetrating Peptide Induces Various Deformations of Lipid Bilayer Membrane: Inverted Micelle,Double Bilayer, and Transmembrane2012

    • Author(s)
      Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Shiroh Futaki, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 1 Pages: 178-183

    • DOI

      10.1002/qua.23177

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Solvation Effect on the Structural Change of Globular Protein: A Molecular Dynamics Study2012

    • Author(s)
      Taku Mizukami, Hiroaki Saito, Shuhei Kawamoto,Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 1 Pages: 344-350

    • DOI

      10.1002/qua.23251

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Binding of Tat peptides on DOPC and DOPG lipid bilayer membrane studied by molecular dynamicssimulations2012

    • Author(s)
      Shuhei Kawamoto, Masako Takasu, Takeshi Miyakawa, Ryota Morikawa, Tatsuki Oda, Shiroh Futaki, Hidemi Nagao
    • Journal Title

      Molecular Simulation

      Volume: 38 Issue: 5 Pages: 366-368

    • DOI

      10.1080/08927022.2010.536546

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Structure and Lateral Pressure Profile2012

    • Author(s)
      H. Saito, M. Iwayama, H. Takagi, M. Nishimura, T. Miyakawa, K. Kawaguchi, M. Takasu, T. Mizukami, H. Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 24 Pages: 3834-3839

    • DOI

      10.1002/qua.24248

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics studies of lipid bilayer with gramicidin A: effects of gramicidin A on membrane structure and hydrophobic match2012

    • Author(s)
      Hiroaki Saito, Taku Mizukami, Shuhei Kawamoto, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Pages: 161-170

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Solvation effect on the structural change of globular protein: a molecular dynamics study2012

    • Author(s)
      Taku Mizukami, Hiroaki Saito, Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Pages: 344-350

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Cell penetrating peptide induces various deformations of lipid bilayer membrane: inverted micelle, double bilayer and trans-membrane2012

    • Author(s)
      Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Hiroaki Saito, Shiroh Futaki, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Pages: 178-183

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Inverted Micelle Formation of Cell-Penetrating Peptide Studied by Coase-grained Simulation: Importance of Attractive Force between Cell-Penetrating Peptides and Lipid Head Group2011

    • Author(s)
      Shuhei Kawamoto, Masako Takasu, Takeshi Miyakawa, Ryota Morikawa, Tatsuki Oda, Shiroh Futaki, Hidemi Nagao
    • Journal Title

      Journal of Chemical Physics

      Volume: 134

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Presentation] Hras-GTP内におけるGTP周辺にある水分子の分子動力学法による研究2013

    • Author(s)
      宮川毅, 森河良太, 高須昌子, 杉森公一, 川口一朋, 齋藤大明, 長尾秀実
    • Organizer
      第68回 日本物理学会 春季大会
    • Place of Presentation
      広島
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] Molecular dynamics analyses of dissociation process of ADP from Hsp902013

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, H. Saito, H. Nagao
    • Organizer
      International Symposium On Computational Science 2013(招待講演
    • Place of Presentation
      Kanazawa
    • Related Report
      2012 Final Research Report
  • [Presentation] Theoretical studies on oxidation of molecules by combining MD and QM/MM calculations2013

    • Author(s)
      Masashi Iwayama, Isman Kurniawan, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      The 53rd Sanibel Symposium
    • Place of Presentation
      Florida, USA
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] Molecular dynamics analyses of dissociation process of ADP from Hsp902013

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, H. Saito, H. Nagao
    • Organizer
      International Symposium On Computational Science 2013
    • Place of Presentation
      Kanazawa
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Theoretical study on entrainment phenomenon in model molecular systems2012

    • Author(s)
      Hidemi Nagao, Michke Rusmerryani, Acep Pruqon, Kazutomo Kawaguchi, Hiroaki Saito
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Final Research Report
  • [Presentation] Free energy profile of Hsp90-ADP binding by molecular dynamics simulations2012

    • Author(s)
      K. Kawaguchi, H. Saito, Hidemi Nagao
    • Organizer
      Conference on Computational Physics (CCP2012)
    • Place of Presentation
      Kobe
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] Binding Free Energy of Azurin-Cytochrome c551 Complex by all-atom Molecular DynamicsSimulation2012

    • Author(s)
      H. Saito, M. Iwayama, T. Mizukami, K.Kawaguchi, Hidemi Nagao
    • Organizer
      Conference on Computational Physics (CCP2012)
    • Place of Presentation
      Kobe
    • Related Report
      2012 Final Research Report
  • [Presentation] Structure and lateral pressure profile of lipid bilayer containing gramicidin A by molecular dynamicssimulation2012

    • Author(s)
      H. Saito, M. Iwayama, M. Nishimura, H. Takagi,K. Kawaguchi, H. Nagao
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Final Research Report
  • [Presentation] THEORETICAL STADIES ON SUPERCONDUCTIVITY IN ULTRASMALL GRAIN2012

    • Author(s)
      H.Nagao
    • Organizer
      9th International Conference on New Theories, Discoveries,and Applications of Superconductors and Related Materials
    • Place of Presentation
      Rome, Italy
    • Related Report
      2012 Final Research Report
  • [Presentation] Free energy profile for binding of ADP to Hsp90 by molecular dynamics simulation2012

    • Author(s)
      Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Hiroaki Saito, and Hidemi Nagao
    • Organizer
      The 5th International Symposium on Computational Sciences(ISCS) 2012(招待講演)
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular dynamics study of gramicidin A in lipid bilayer: structure and lateral pressure profile2012

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi,Kazutomo Kawaguchi, and Hidemi Nagao
    • Organizer
      The 5th International Symposium on Computational Sciences(ISCS) 2012(招待講演
    • Related Report
      2012 Final Research Report
  • [Presentation] Molecular dynamics study of gramicidin A in lipid bilayer: structure and lateral pressure profile2012

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Kazutomo Kawaguchi, and Hidemi Nagao
    • Organizer
      The 5th International Symposium on Computational Sciences (ISCS) 2012
    • Place of Presentation
      Yogyakarta, Indonesia
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Free energy profile for binding of ADP to Hsp90 by molecular dynamics simulation2012

    • Author(s)
      Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Hiroaki Saito, and Hidemi Nagao
    • Organizer
      The 5th International Symposium on Computational Sciences (ISCS) 2012
    • Place of Presentation
      Yogyakarta, Indonesia
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] THEORETICAL STADIES ON SUPERCONDUCTIVITY IN ULTRASMALL GRAIN2012

    • Author(s)
      H.Nagao
    • Organizer
      9th International Conference on New Theories, Discoveries, and Applications of Superconductors and Related Materials
    • Place of Presentation
      Rome, Italy
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Free energy profile for binding of ADP to Hsp90 with molecular dynamics simulation2012

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, M. Nishimura, H. Saito, Hidemi Nagao
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] Structure and lateral pressure profile of lipid bilayer containing gramicidin A by molecular dynamics simulation2012

    • Author(s)
      H. Saito, M. Iwayama, M. Nishimura, H. Takagi, K. Kawaguchi, H. Nagao
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] Binding Free Energy of Azurin-Cytochrome c551 Complex by all-atom Molecular Dynamics Simulation2012

    • Author(s)
      H. Saito, M. Iwayama, T. Mizukami, K. Kawaguchi, Hidemi Nagao
    • Organizer
      Conference on Computational Physics (CCP2012)
    • Place of Presentation
      Kobe
    • Related Report
      2012 Annual Research Report
  • [Presentation] Theoretical study on entrainment phenomenon in model molecular systems2012

    • Author(s)
      Hidemi Nagao, Michke Rusmerryani, Acep Pruqon, Kazutomo Kawaguchi, Hiroaki Saito
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      Sendai
    • Related Report
      2012 Annual Research Report
  • [Presentation] Binding free energy of oxidized Azurin - reduced Cytochrome c551 Complex2011

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Taku Mizukami, Hidemi Nagao
    • Organizer
      The Seventh Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII)
    • Place of Presentation
      Waseda University (JAPAN)
    • Related Report
      2011 Research-status Report
  • [Presentation] 膜透過ペプチドによる脂質二重膜の4種類の変形

    • Author(s)
      川本周平, 高須昌子, 宮川毅, 森河良太, 小田竜樹, 齋藤大明, 二木史朗, 長尾秀実
    • Organizer
      物理学会秋年会
    • Place of Presentation
      富山大学(富山県)
    • Related Report
      2011 Research-status Report
  • [Remarks]

    • URL

      http://hal.s.kanazawa-u.ac.jp/

    • Related Report
      2012 Final Research Report

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

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