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First-principles simulations of water on the basis of quantum Monte Carlo and fragment molecular orbital methods

Research Project

Project/Area Number 23540451
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Mathematical physics/Fundamental condensed matter physics
Research InstitutionKobe University

Principal Investigator

TANAKA Shigenori  神戸大学, システム情報学研究科, 教授 (10379480)

Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2013: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2012: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2011: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Keywords水 / 電子状態 / 量子モンテカルロ法 / フラグメント分子軌道法 / 経路積分法 / 積分方程式 / 核量子効果 / 第一原理計算
Research Abstract

Ab initio, first-principles simulation methods for describing the correlational and thermodynamic properties of water systems have been developed. The quantum Monte Carlo (QMC) method, the fragment molecular orbital (FMO) method, and the reference interaction site model (RISM) combined with the density functional theory were employed for the simulations. The QMC method is useful for the accurate descriptions of the electronic state and the nuclear quantum effect of molecular systems. The FMO method enables us to perform ab initio calculations of the electronic state of large molecular systems with high accuracy. The RISM method was used to carry out the statistical-mechanical description of intermolecular correlations of liquid water. Through the novel developments of these simulation methods and their combinations, we have been led to a status where it is possible to perform highly parallelized, first-principles simulations for water systems on high-performance supercomputers.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (42 results)

All 2014 2013 2012 2011 Other

All Journal Article (14 results) (of which Peer Reviewed: 13 results) Presentation (23 results) (of which Invited: 7 results) Book (2 results) Remarks (3 results)

  • [Journal Article] Electron- Correlated Fragment-Molecular-Orbital Calculations for Biomolecular and Nano Systems2014

    • Author(s)
      S. Tanaka, Y. Mochizuki, Y. Komeiji, Y. Okiyama, K. Fukuzawa
    • Journal Title

      Phys. Chem. Chem. Phys

      Volume: 16 Issue: 22 Pages: 10310-10344

    • DOI

      10.1039/c4cp00316k

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Charge Clamps of Lysines and Hydrogen Bonds Play Key Roles in the Mechanism to Fix Helix 12 in the Agonist and Antagonist Positions of Estrogen Receptor α: Intramolecular Interactions Studied by the Ab Initio Fragment Molecular Orbital Method2014

    • Author(s)
      C. Watanabe, K. Fukuzawa, S. Tanaka, and S. Aida-Hyugaji
    • Journal Title

      J. Phys. Chem

      Volume: B118 Issue: 19 Pages: 4993-5008

    • DOI

      10.1021/jp411627y

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Accuracy of the Fragment Molecular Orbital (FMO) Calculations for DNA: Total Energy, Molecular Orbital, and Inter-Fragment Interaction Energy2014

    • Author(s)
      K. Fukuzawa, C. Watanabe, I. Kurisaki, N. Taguchi, Y. Mochizuki, T. Nakano, S. Tanaka, Y. Komeiji
    • Journal Title

      Computational and Theoretical Chemistry

      Volume: 1034 Pages: 7-16

    • DOI

      10.1016/j.comptc.2014.02.002

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Classical Density Functional Calculation of Radial Distribution Functions of Liquid Water2014

    • Author(s)
      S. Tanaka and M. Nakano
    • Journal Title

      Chem. Phys

      Volume: 430 Pages: 18-22

    • DOI

      10.1016/j.chemphys.2013.12.007

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Choline Ion Interactions with DNA Atoms Explain Unique Stabilization of A-T Base Pairs in DNA Duplexes: A Microscopic View2014

    • Author(s)
      M. Nakano, H. Tateishi-Karimata, S. Tanaka, N. Sugimoto
    • Journal Title

      J. Phys. Chem. B

      Volume: 118 Issue: 2 Pages: 379-389

    • DOI

      10.1021/jp406647b

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Variational Quantum Monte Carlo with Inclusion of Orbital Correlations2013

    • Author(s)
      S. Tanaka
    • Journal Title

      J. Phys. Soc. Jpn

      Volume: 82 Issue: 7 Pages: 75001-75001

    • DOI

      10.7566/jpsj.82.075001

    • NAID

      210000132670

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Triplet Correlations and Bridge Functions in Classical Density Functional Theory for Liquid Water2013

    • Author(s)
      S. Tanaka and M. Nakano
    • Journal Title

      Chem. Phys. Lett

      Volume: 572 Pages: 38-43

    • DOI

      10.1016/j.cplett.2013.04.005

    • Related Report
      2013 Annual Research Report 2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Modeling of peptide - silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations2013

    • Author(s)
      Y. Okiyama
    • Journal Title

      Chemical Physics Letters

      Volume: 566 Pages: 25-31

    • DOI

      10.1016/j.cplett.2013.02.020

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Statistical Correction to Effective Interactions in the Fragment Molecular Orbital Method2013

    • Author(s)
      S. Tanaka, C. Watanabe, and Y. Okiyama
    • Journal Title

      Chem. Phys. Lett

      Volume: 556 Pages: 272-277

    • DOI

      10.1016/j.cplett.2012.11.085

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Three- and Four-body Corrected Fragment Molecular Orbital Calculations with a Novel Subdividing Fragmentation Method Applicable to Structure-Based Drug Design2013

    • Author(s)
      C. Watanabe, K. Fukuzawa, Y. Okiyama, T. Tsukamoto, A. Kato, S. Tanaka, Y. Mochizuki, T. Nakano
    • Journal Title

      Journal of Molecular Graphics and Modelling

      Volume: 41 Pages: 31-42

    • DOI

      10.1016/j.jmgm.2013.01.006

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Ab initio path integral Monte Carlo simulations for water trimer with electron correlation effects2012

    • Author(s)
      T. Fujita
    • Journal Title

      Computational and Theoretical Chemistry

      Volume: 997 Pages: 7-13

    • DOI

      10.1016/j.comptc.2012.07.029

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Development of the Four-Body Corrected Fragment Molecular Orbital (FMO4) Method2012

    • Author(s)
      T.Nakano, Y.Mochizuki, K.Yamashita, C.Watanabe, K.Fukuzawa, K.Segawa, Y.Okiyama, T.Tsukamoto, S.Tanaka
    • Journal Title

      Chemical Physics Letters

      Volume: 523 Pages: 128-133

    • DOI

      10.1016/j.cplett.2011.12.004

    • Related Report
      2013 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Fragment Molecular Orbital Calculations under Periodic Boundary Condition2011

    • Author(s)
      T. Fujita, T. Nakano, S. Tanaka
    • Journal Title

      Chem. Phys. Lett.

      Volume: 506 Issue: 1-3 Pages: 112-116

    • DOI

      10.1016/j.cplett.2011.02.055

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] 量子モンテカルロ法による分子系のシミュレーション2011

    • Author(s)
      田中成典
    • Journal Title

      信学技報 IEICE Technical Report

      Volume: 111, No. 255 Pages: 47-48

    • NAID

      110008900034

    • Related Report
      2011 Research-status Report
  • [Presentation] Multi-Scale Simulations for Complex Biomolecular Systems2014

    • Author(s)
      S. Tanaka
    • Organizer
      Workshop on Current Topics in Nano Simulations (CT-NanoSim2014)
    • Place of Presentation
      University of Tsukuba, Tsukuba, Japan
    • Year and Date
      2014-03-10
    • Related Report
      2013 Final Research Report
  • [Presentation] Large-Scale Biomolecular Simulations on the Basis of Fragment Molecular Orbital Method2014

    • Author(s)
      S. Tanaka
    • Organizer
      International Workshop on Eigenvalue Problems : Algorithms, Software and Applications in Petascale Computing (EPASA2014)
    • Place of Presentation
      Tsukuba International Congress Center, Tsukuba, Japan
    • Year and Date
      2014-03-08
    • Related Report
      2013 Final Research Report
  • [Presentation] Exploring Theoretical Models for Water2013

    • Author(s)
      S. Tanaka
    • Organizer
      The 5th JCS International Symposium on Theoretical Chemistry
    • Place of Presentation
      Todai-ji Culture Center, Nara, Japan
    • Year and Date
      2013-12-03
    • Related Report
      2013 Final Research Report
  • [Presentation] 大規模分子シミュレーションと創薬2013

    • Author(s)
      田中成典
    • Organizer
      VINAS Users Conference 2013
    • Place of Presentation
      東京コンファレンスセンター品川, 東京
    • Year and Date
      2013-10-11
    • Related Report
      2013 Final Research Report
  • [Presentation] 第一原理シミュレーションと創薬2013

    • Author(s)
      田中成典
    • Organizer
      HPCI ワークショップ2013
    • Place of Presentation
      産業技術総合研究所臨海副都心センター, 東京
    • Year and Date
      2013-09-11
    • Related Report
      2013 Final Research Report
  • [Presentation] 大規模シミュレーションの意義2013

    • Author(s)
      田中成典
    • Organizer
      科学基礎論学会2013年度講演会ワークショップ「High Performance Computing の哲学」
    • Place of Presentation
      大阪大学大学院人間科学研究科(吹田キャンパス), 大阪
    • Year and Date
      2013-06-16
    • Related Report
      2013 Final Research Report
  • [Presentation] 第一原理シミュレーションによる生体高分子の電子状態・ダイナミクス・輸送特性の解析2013

    • Author(s)
      田中成典
    • Organizer
      日本磁気学会第190回研究会「生体物質の物理」
    • Place of Presentation
      中央大学駿河台記念館, 東京
    • Year and Date
      2013-05-24
    • Related Report
      2013 Final Research Report
  • [Presentation] Structure-Based Drug Design with the Fragment Molecular Orbital Method2013

    • Author(s)
      S. Tanaka
    • Organizer
      Workshop on Innovation and Pioneering Technology - Recent Development in Drug Discovery Sciences (WINPTech 2012)
    • Place of Presentation
      Kobe University, Kobe, Japan
    • Year and Date
      2013-02-18
    • Related Report
      2013 Final Research Report
  • [Presentation] フラグメント分子軌道法を用いた薬剤耐性メカニズムの解析2013

    • Author(s)
      田中成典
    • Organizer
      平成24年度地球シミュレータ利用報告会
    • Place of Presentation
      海洋研究開発機構横浜研究所三好記念講堂, 横浜
    • Year and Date
      2013-01-31
    • Related Report
      2013 Final Research Report
  • [Presentation] Towards the First-Principles and Coarse-Grained Descriptions for Charge and Energy Transfers in Biomolecular Systems2012

    • Author(s)
      S. Tanaka
    • Organizer
      Joint Dresden-Japan Workshop on Molecular Scale and Organic Electronic Materials
    • Place of Presentation
      Max Planck Institute for the Physics of Complex Systems (MPIPKS), Dresden, Germany
    • Year and Date
      2012-12-13
    • Related Report
      2013 Final Research Report
  • [Presentation] Towards the First-Principles and Coarse-Grained Descriptions for Charge and Energy Transfers in Biomolecular Systems2012

    • Author(s)
      S. Tanaka
    • Organizer
      Indo-Japan Workshop on "Recent Advances in Spectroscopy and Microscopy : Fundamentals and Applications to Materials and Biology"
    • Place of Presentation
      University of Hyderabad, Hyderabad, India
    • Year and Date
      2012-11-21
    • Related Report
      2013 Final Research Report
  • [Presentation] フラグメント分子軌道(FMO)計算の現状と今後2012

    • Author(s)
      田中成典
    • Organizer
      日本機械学会第25回計算力学講演会
    • Place of Presentation
      甲南大学, 神戸
    • Year and Date
      2012-10-06
    • Related Report
      2013 Final Research Report
  • [Presentation] FMO 計算の今後2012

    • Author(s)
      田中成典
    • Organizer
      第4回「イノベーション基盤シミュレーションソフトウェアの研究開発」シンポジウム
    • Place of Presentation
      東京大学生産技術研究所, 東京
    • Year and Date
      2012-07-05
    • Related Report
      2013 Final Research Report
  • [Presentation] Charge and Energy Transfers in Biomolecular Systems2012

    • Author(s)
      S. Tanaka
    • Organizer
      NRI-TUD Joint Workshop for Organic Nanomaterials 2012
    • Place of Presentation
      AIST, Tsukuba, Japan
    • Year and Date
      2012-03-13
    • Related Report
      2013 Final Research Report
  • [Presentation] Multi-Scale Simulations for Biomolecular Functions2012

    • Author(s)
      S. Tanaka
    • Organizer
      2nd AICS International Symposium - Computer and Computational Sciences for Exascale Computing -
    • Place of Presentation
      RIKEN Advanced Institute for Computational Science, Kobe, Japan
    • Year and Date
      2012-03-01
    • Related Report
      2013 Final Research Report
  • [Presentation] フラグメント分子軌道法を用いた薬剤耐性メカニズムの解析2012

    • Author(s)
      田中成典
    • Organizer
      平成23年度地球シミュレータ利用報告会
    • Place of Presentation
      海洋研究開発機構横浜研究所三好記念講堂, 横浜
    • Year and Date
      2012-02-07
    • Related Report
      2013 Final Research Report
  • [Presentation] フラグメント分子軌道(FMO)計算の現状と今後2012

    • Author(s)
      田中成典
    • Organizer
      日本機械学会第25回計算力学講演会
    • Place of Presentation
      甲南大学
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 第一原理シミュレーションによる生体高分子の電子状態・ダイナミクス・輸送特性の解析

    • Author(s)
      田中成典
    • Organizer
      日本磁気学会第190回研究会「生体物質の物理」
    • Place of Presentation
      中央大学駿河台記念館(東京)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 大規模シミュレーションの意義

    • Author(s)
      田中成典
    • Organizer
      科学基礎論学会2013年度講演会ワークショップ「High Performance Computingの哲学」
    • Place of Presentation
      大阪大学大学院人間科学研究科(吹田キャンパス、大阪)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 第一原理シミュレーションと創薬

    • Author(s)
      田中成典
    • Organizer
      HPCIワークショップ2013
    • Place of Presentation
      産業技術総合研究所臨海副都心センター(東京)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Exploring Theoretical Models for Water

    • Author(s)
      S. Tanaka
    • Organizer
      The 5th JCS International Symposium on Theoretical Chemistry
    • Place of Presentation
      Todai-ji Culture Center (Nara)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Large-Scale Biomolecular Simulations on the Basis of Fragment Molecular Orbital Method

    • Author(s)
      S. Tanaka
    • Organizer
      International Workshop on Eigenvalue Problems: Algorithms, Software and Applications in Petascale Computing (EPASA2014)
    • Place of Presentation
      Tsukuba International Congress Center (Tsukuba)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Multi-Scale Simulations for Complex Biomolecular Systems

    • Author(s)
      S. Tanaka
    • Organizer
      Workshop on Current Topics in Nano Simulations (CT-NanoSim2014)
    • Place of Presentation
      University of Tsukuba (Tsukuba)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Book] "Advances in Quantum Monte Carlo" (ACS Symposium Series 1094)2012

    • Author(s)
      S. Tanaka, S.M. Rothstein, and W.A. Lester, Jr., ed
    • Total Pages
      230
    • Publisher
      American Chemical Society, Washington, DC
    • Related Report
      2013 Final Research Report
  • [Book] Advances in Quantum Monte Carlo2012

    • Author(s)
      S. Tanaka, S.M. Rothstein, W.A. Lester, Jr.
    • Total Pages
      230
    • Publisher
      American Chemical Society
    • Related Report
      2011 Research-status Report
  • [Remarks]

    • URL

      http://eniac.scitec.kobe-u.ac.jp/tanaka/index_en.html

    • Related Report
      2013 Final Research Report
  • [Remarks] Shigenori Tanaka's Home Page

    • URL

      http://eniac.scitec.kobe-u.ac.jp/tanaka/index_en.html

    • Related Report
      2013 Annual Research Report
  • [Remarks] 特にありません。

    • Related Report
      2011 Research-status Report

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

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