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Environment-dependent force fields for complex biological systems based on very large-scale first-principles calculations

Research Project

Project/Area Number 26610120
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Mathematical physics/Fundamental condensed matter physics
Research InstitutionNational Institute for Materials Science

Principal Investigator

Miyazaki Tsuyoshi  国立研究開発法人物質・材料研究機構, 理論計算科学ユニット, グループリーダー (50354147)

Co-Investigator(Renkei-kenkyūsha) SHINODA Wataru  名古屋大学, 大学院工学研究科, 准教授 (70357193)
OTSUKA Takao  理化学研究所, 生命システム研究センター, 研究員 (30465968)
Project Period (FY) 2014-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2014: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Keywords大規模第一原理計算 / プログラム開発 / 第一原理分子動力学 / 生物物理 / 計算物理 / 計算手法、プログラム開発 / イオンチャネル
Outline of Final Research Achievements

In this research project, using a large-scale first-principles calculation code we have been developing, we have succeeded to employ the self-consistent first-principles calculations for several snapshot structures of a complex biological system, an ion channel gramicidin A system embedded in lipid bilayers sandwiched by bulk water regions. By comparing the results with those by classical force fields, which are used in most theoretical studies of biological systems, we have clarified the accuracy and the problems of the classical force fields. We also developed a calculation method, which enables us to realize the molecular dynamics of complex biological systems containing several tens of thousands of atoms, based on the accurate first-principles calculations.

Report

(3 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • Research Products

    (16 results)

All 2016 2015 2014 Other

All Int'l Joint Research (1 results) Journal Article (4 results) (of which Peer Reviewed: 4 results,  Acknowledgement Compliant: 4 results) Presentation (10 results) (of which Int'l Joint Research: 3 results,  Invited: 5 results) Remarks (1 results)

  • [Int'l Joint Research] University College London(英国)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Optimized multi-site local orbitals in the large-scale DFT program CONQUEST2015

    • Author(s)
      A. Nakata, D. R. Bowler and T. Miyazaki
    • Journal Title

      Phys. Chem. Chem. Phys., published online

      Volume: - Issue: 47 Pages: 31427-31433

    • DOI

      10.1039/c5cp00934k

    • Related Report
      2015 Annual Research Report 2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Large-scale DFT simulations with a linear-scaling DFT code CONQUEST on K-computer2014

    • Author(s)
      M. Arita, S. Arapan, D. R. Bowler and T. Miyazaki
    • Journal Title

      Journal of Advanced Simulation in Science and Engineering

      Volume: 1 Issue: 1 Pages: 87-97

    • DOI

      10.15748/jasse.1.87

    • NAID

      130004709207

    • ISSN
      2188-5303
    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Efficient Calculations with Multisite Local Orbitals in a Large-Scale DFT Code CONQUEST2014

    • Author(s)
      A. Nakata, D. R. Bowler and T. Miyazaki
    • Journal Title

      J. Chem. Theory Comput.

      Volume: 10 Issue: 11 Pages: 4813-4822

    • DOI

      10.1021/ct5004934

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10000+ Atoms2014

    • Author(s)
      M. Arita, D. R. Bowler and T. Miyazaki
    • Journal Title

      J. Chem. Theory Comput

      Volume: 10 Issue: 12 Pages: 5419-5425

    • DOI

      10.1021/ct500847y

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Million-atom DFT calculations with the CONQUEST code2016

    • Author(s)
      Tsuyoshi Miyazaki
    • Organizer
      APCTCC7 (The 7th Asia-Pacific Conference of Theoretical and Computational Chemistry)
    • Place of Presentation
      Kaohsiung (Taiwan)
    • Year and Date
      2016-01-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Linear scaling first-principles molecular dynamics for very large systems with the CONQUEST code2015

    • Author(s)
      Tsuyoshi Miyazaki
    • Organizer
      250th American Chemical Society National Meeting & Exposition
    • Place of Presentation
      Boston (USA)
    • Year and Date
      2015-08-16
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Large-scale first-principles molecular dynamics study on Si/Ge core-shell nanowires using a linear-scaling technique.2015

    • Author(s)
      Tsuyoshi Miyazaki
    • Organizer
      CECAM WS: Next generation quantum based molecular dynamics
    • Place of Presentation
      Bremen (Germany)
    • Year and Date
      2015-07-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] O(N)-DFT計算プログラムCONQUESTと櫻井杉浦法による大規模系の一電子波動関数解析2015

    • Author(s)
      中田彩子, 二村保徳, 櫻井鉄也, DavidBOWLER, 宮崎剛
    • Organizer
      日本物理学会第70回年次大会
    • Place of Presentation
      早稲田大学(新宿区、東京)
    • Year and Date
      2015-03-21 – 2015-03-24
    • Related Report
      2014 Research-status Report
  • [Presentation] Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10000+ atoms2015

    • Author(s)
      T. Miyazaki, M. Arita, D. Bowler
    • Organizer
      Int. Workshop on Comp. Phys. and Materials Science: Total Energy and Force Methods
    • Place of Presentation
      ICTP (Trieste, Italy)
    • Year and Date
      2015-01-15 – 2015-01-17
    • Related Report
      2014 Research-status Report
  • [Presentation] Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10000+ atoms2014

    • Author(s)
      T. Miyazaki, M. Arita, D. Bowler
    • Organizer
      Int. Sympo. on Computics: Quantum Simulation and Design (ISC-QSD2014)
    • Place of Presentation
      東京大学(文京区、東京)
    • Year and Date
      2014-12-01 – 2014-12-03
    • Related Report
      2014 Research-status Report
  • [Presentation] Development and applications of a linear-scaling DFT code CONQUEST2014

    • Author(s)
      T. Miyazaki
    • Organizer
      4th Int. WS on Massively Parallel Programming Now in Quantum Chemistry
    • Place of Presentation
      東京大学(文京区、東京)
    • Year and Date
      2014-11-23 – 2014-11-24
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10000+ atoms2014

    • Author(s)
      M. Arita, D. Bowler, T. Miyazaki
    • Organizer
      International Symposium on Extended Molecular Dynamics (NOSE30)
    • Place of Presentation
      慶応大学(港区、東京)
    • Year and Date
      2014-11-10 – 2014-11-11
    • Related Report
      2014 Research-status Report
  • [Presentation] オーダーN法DFT計算プログラムCONQUESTにおける局在軌道の最適化と応用計算2014

    • Author(s)
      中田彩子, DavidBOWLER, 宮崎剛
    • Organizer
      第8回分子科学討論会
    • Place of Presentation
      広島大学(東広島、広島)
    • Year and Date
      2014-09-21 – 2014-09-24
    • Related Report
      2014 Research-status Report
  • [Presentation] Large-scale DFT simulations on nano structured materials using a linear-scaling technique2014

    • Author(s)
      T. Miyazaki
    • Organizer
      CC3DMR 2014
    • Place of Presentation
      Songdo Convensia (Incheon, Korea)
    • Year and Date
      2014-06-23 – 2014-06-27
    • Related Report
      2014 Research-status Report
    • Invited
  • [Remarks] 巨大分子の第一原理シミュレーションの実現

    • URL

      http://www.nims.go.jp/news/press/2014/12/201412080.html

    • Related Report
      2014 Research-status Report

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Published: 2014-04-04   Modified: 2022-01-31  

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