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Simulation of inclusion complex formation and molecular recognition of cyclodextrin

Research Project

Project/Area Number 19740261
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Biophysics/Chemical physics
Research InstitutionYamaguchi University

Principal Investigator

URAKAMI Naohito  Yamaguchi University, 大学院・理工学研究科, 講師 (50314795)

Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥2,920,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥420,000)
Fiscal Year 2009: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2008: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2007: ¥1,100,000 (Direct Cost: ¥1,100,000)
Keywords計算物理 / 超分子化学 / 自己組織化 / 分子認識 / ナノ材料 / 計算物理学
Research Abstract

I developed coarse grained models of cyclodextrin and polymer chain to investigate the inclusion complex process. By carrying out Brownian dynamics simulation using the models, the formation of the inclusion complex was reproduced, and the mechanism of pseudopolyrotaxane formation was revealed. Moreover, I observed two kinds of motions-oscillating motion and shifting motion, after the formation of pseudopolyrotaxane. These two kinds of motions result in random walk of cyclodextrin along polymer chain. I also reproduced the chain length recognition observed in formation of inclusion complex. My simulation results indicated that the difference in the inclusion time between the cyclodextrins and the polymer chains controls chain length recognition.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (37 results)

All 2010 2009 2008 2007 Other

All Journal Article (10 results) (of which Peer Reviewed: 10 results) Presentation (26 results) Remarks (1 results)

  • [Journal Article] Simulation of pseudopolyrotaxane formation and orientational order between pseudopolyrotaxanes2010

    • Author(s)
      N. Urakami, J. Imada, T. Yamamoto
    • Journal Title

      J. Chem. Phys. 132

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Simulation of pseudopolyrotaxane formation and orientational order between pseudopolyrotaxanes2010

    • Author(s)
      浦上直人, 他
    • Journal Title

      The Journal of Chemical Physics 132

      Pages: 1-7

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] シクロデキストリンの包接化合物形成と分子認識-粗視化モデルを用いたシミュレーション-2010

    • Author(s)
      浦上直人
    • Journal Title

      分子シミュレーション研究会会誌 (掲載予定)

      Pages: 1-4

    • NAID

      130004566675

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nano-meter-sized domain formation in lipid membranes observed by small angle neutron scattering2008

    • Author(s)
      Tomomi Masui, 他
    • Journal Title

      The European Physical Journal E 27

      Pages: 378-389

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics of Nano-Meter-Sized Domains on a Vesicle2008

    • Author(s)
      Yuka Sakuma, 他
    • Journal Title

      American Institute of Physics Conference Proceedings 982

      Pages: 717-720

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structures of Multilayered Thin Films of Long-Chain Molecules : X-ray Scattering Study2008

    • Author(s)
      Ken Tanaka, 他
    • Journal Title

      Polymer Journal 40

      Pages: 1017-1024

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Lamellar to micelle transition of nonionic surfactant assemblies induced by addition of colloidal particles2008

    • Author(s)
      Yukiko Suganuma, 他
    • Journal Title

      The Journal of Chemical Physics 129(134903)

      Pages: 1-10

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] シクロデキストリンと高分子鎖の包接化合物形成シミュレーション2007

    • Author(s)
      浦上 直人
    • Journal Title

      高分子論文集 64

      Pages: 280-285

    • NAID

      10019929747

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Simulation of Chain Length Recognition Observed in Formation of Inclusion Complex

    • Author(s)
      N. Urakami, J. Imada, T. Yamamoto
    • Journal Title

      Comput. Phys. Comm. (accepted)(in print)

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] シクロデキストリンの包接化合物形成と分子認識-粗視化モデルを用いたシミュレーション-

    • Author(s)
      浦上直人
    • Journal Title

      分子シミュレーション研究会会誌 (掲載決定)

    • NAID

      130004566675

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Presentation] Simulation of Chain Length Recognition in the Formation of Inclusion Complex2009

    • Author(s)
      N. Urakami, J. Imada, T. Yamamoto
    • Organizer
      Conference on Computational Physics
    • Place of Presentation
      Kaohsiung(Taiwan)
    • Year and Date
      2009-12-18
    • Related Report
      2009 Final Research Report
  • [Presentation] Simulation of Chain Length Recognition in the Formation of Inclusion Complex2009

    • Author(s)
      浦上直人, 他
    • Organizer
      Conference on Computational Physics
    • Place of Presentation
      高雄(台湾)
    • Year and Date
      2009-12-18
    • Related Report
      2009 Annual Research Report
  • [Presentation] 擬ポリロタキサンの形成と鎖長認識シミュレーション2009

    • Author(s)
      浦上直人、今田絢子、山本隆
    • Organizer
      第58回高分子学会討論会
    • Place of Presentation
      熊本
    • Year and Date
      2009-09-18
    • Related Report
      2009 Final Research Report
  • [Presentation] 擬ポリロタキサンの形成と鎖長認識シミュレーション2009

    • Author(s)
      浦上直人, 他
    • Organizer
      第58回 高分子学会討論会
    • Place of Presentation
      熊本
    • Year and Date
      2009-09-18
    • Related Report
      2009 Annual Research Report
  • [Presentation] 環状分子による鎖長認識メカニズムの解析2009

    • Author(s)
      浦上直人、今田絢子、山本隆
    • Organizer
      第58回高分子学会年次大会
    • Place of Presentation
      神戸
    • Year and Date
      2009-05-28
    • Related Report
      2009 Final Research Report
  • [Presentation] 環状分子による鎖長認識メカニズムの解析2009

    • Author(s)
      浦上直人, 他
    • Organizer
      第58回 高分子学会年次大会
    • Place of Presentation
      神戸
    • Year and Date
      2009-05-28
    • Related Report
      2009 Annual Research Report
  • [Presentation] 生体膜上における脂質ドメインの融合・分裂ダイナミクス2008

    • Author(s)
      緒方祐介, 他
    • Organizer
      分子シミュレーション討論会
    • Place of Presentation
      岡山
    • Year and Date
      2008-11-19
    • Related Report
      2008 Annual Research Report
  • [Presentation] 包接化合物形成における鎖長認識メカニズム2008

    • Author(s)
      今田絢子, 他
    • Organizer
      分子シミュレーション討論会
    • Place of Presentation
      岡山
    • Year and Date
      2008-11-19
    • Related Report
      2008 Annual Research Report
  • [Presentation] 包接化合物形成における鎖長認識メカニズム2008

    • Author(s)
      今田絢子、浦上直人、山本隆
    • Organizer
      第22回分子シミュレーション討論会
    • Place of Presentation
      岡山
    • Year and Date
      2008-11-17
    • Related Report
      2009 Final Research Report
  • [Presentation] シクロデキストリンの鎖長認識メカニズムの解析2008

    • Author(s)
      今田絢子, 他
    • Organizer
      中国四国地区高分子若手研究会
    • Place of Presentation
      松山
    • Year and Date
      2008-11-06
    • Related Report
      2008 Annual Research Report
  • [Presentation] ナノサイズベシクルにおける脂質ドメインの融合と分裂過程2008

    • Author(s)
      緒方祐介, 他
    • Organizer
      高分子学会
    • Place of Presentation
      大阪
    • Year and Date
      2008-09-24
    • Related Report
      2008 Annual Research Report
  • [Presentation] Simulation of the formation of inclusion complex and the molecular recognition2008

    • Author(s)
      N. Urakami, J. Imada, T. Yamamoto
    • Organizer
      The 2008 Conference on Computational Physics
    • Place of Presentation
      Ouro Preto (Brazil)
    • Year and Date
      2008-08-08
    • Related Report
      2009 Final Research Report
  • [Presentation] Simulation of the formation of inclusion complex and the molecular recognition2008

    • Author(s)
      浦上直人, 他
    • Organizer
      The 2008 Conference on Computational Physics
    • Place of Presentation
      オーロプレット・ブラジル
    • Year and Date
      2008-08-08
    • Related Report
      2008 Annual Research Report
  • [Presentation] 包接化合物形成における分子認識シミュレーション2008

    • Author(s)
      浦上直人、今田絢子、山本隆
    • Organizer
      第57回高分子学会年次大会
    • Place of Presentation
      横浜
    • Year and Date
      2008-05-28
    • Related Report
      2009 Final Research Report
  • [Presentation] 包接化合物形成における分子認識シミュレーション2008

    • Author(s)
      浦上直人, 他
    • Organizer
      高分子学会
    • Place of Presentation
      横浜
    • Year and Date
      2008-05-28
    • Related Report
      2008 Annual Research Report
  • [Presentation] ナノサイズベシクルにおける脂質ドメインの形成とダイナミクス2008

    • Author(s)
      緒方祐介, 他
    • Organizer
      高分子学会
    • Place of Presentation
      横浜
    • Year and Date
      2008-05-28
    • Related Report
      2008 Annual Research Report
  • [Presentation] 擬ポリロタキサン形成における鎖長認識シミュレーション2008

    • Author(s)
      今田絢子
    • Organizer
      日本物理学会 第63回年次大会
    • Place of Presentation
      大阪
    • Year and Date
      2008-03-25
    • Related Report
      2007 Annual Research Report
  • [Presentation] シクロデキストリンの分子認識シミュレーション2007

    • Author(s)
      今田絢子、浦上直人、山本隆
    • Organizer
      第21回分子シミュレーション討論会
    • Place of Presentation
      金沢
    • Year and Date
      2007-11-27
    • Related Report
      2009 Final Research Report 2007 Annual Research Report
  • [Presentation] ナノサイズベシクルにおける脂質ドメイン形成シミュレーション2007

    • Author(s)
      緒方祐介
    • Organizer
      第21回分子シミュレーション討論会
    • Place of Presentation
      金沢
    • Year and Date
      2007-11-27
    • Related Report
      2007 Annual Research Report
  • [Presentation] 包接化合物の安定性による鎖長認識メカニズムの解明2007

    • Author(s)
      浦上直人、今田絢子、山本隆
    • Organizer
      日本物理学会第62回年次大会
    • Place of Presentation
      札幌
    • Year and Date
      2007-09-23
    • Related Report
      2009 Final Research Report
  • [Presentation] 包接化合物の安定性による鎖長認識メカニズムの解明2007

    • Author(s)
      浦上直人
    • Organizer
      日本物理学会 第62回年次大会
    • Place of Presentation
      札幌
    • Year and Date
      2007-09-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] 環状分子と高分子鎖における包接・解離シミュレーション2007

    • Author(s)
      今田絢子
    • Organizer
      第12回高分子計算機科学討論会
    • Place of Presentation
      京都
    • Year and Date
      2007-08-09
    • Related Report
      2007 Annual Research Report
  • [Presentation] The Molecular Dynamics Simulation of Inclusion Complex Formation2007

    • Author(s)
      N. Urakami, J. Imada, T. Yamamoto
    • Organizer
      YITP Workshop 2007 New Frontiers in Colloidal Physics: A Bridge between Micro- and Macroscopic Concepts in Soft Matter
    • Place of Presentation
      京都
    • Year and Date
      2007-07-26
    • Related Report
      2009 Final Research Report
  • [Presentation] The Molecular Dynamics Simulation of Inclusion Complex Formation2007

    • Author(s)
      浦上直人
    • Organizer
      YITP Softmatter 2007
    • Place of Presentation
      京都
    • Year and Date
      2007-07-26
    • Related Report
      2007 Annual Research Report
  • [Presentation] 環状分子と高分子鎖における包接・解離シミュレーション2007

    • Author(s)
      今田絢子、浦上直人、山本隆
    • Organizer
      第56回高分子学会年次大会
    • Place of Presentation
      京都
    • Year and Date
      2007-05-29
    • Related Report
      2009 Final Research Report
  • [Presentation] 環状分子と高分子鎖における包接・解離シミュレーション2007

    • Author(s)
      今田絢子
    • Organizer
      第56回高分子年次大会
    • Place of Presentation
      京都
    • Year and Date
      2007-05-29
    • Related Report
      2007 Annual Research Report
  • [Remarks]

    • URL

      http://www.mms.sci.yamaguchi-u.ac.jp/~urakami/index.html

    • Related Report
      2009 Final Research Report

URL: 

Published: 2007-04-01   Modified: 2016-04-21  

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