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Theoretical studies on the interaction between actinide species and biomolecules

Research Project

Project/Area Number 16H04635
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Nuclear engineering
Research InstitutionRikkyo University

Principal Investigator

MOCHIZUKI Yuji  立教大学, 理学部, 教授 (00434209)

Co-Investigator(Kenkyū-buntansha) 石川 岳志  長崎大学, 医歯薬学総合研究科(医学系), 准教授 (80505909)
Research Collaborator TSUSHIMA satoru  
KOMEIJI yuto  
MORI hirotoshi  
NAKANO tatsuya  
Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000)
Fiscal Year 2018: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2017: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2016: ¥8,970,000 (Direct Cost: ¥6,900,000、Indirect Cost: ¥2,070,000)
Keywords保健物理 / アクチニド / フラグメント分子軌道法 / 分子動力学法 / FMO / MD / 保険物理 / 分子動力学 / 相互作用エネルギー / タンパク質 / DNA / 環境安全 / 生物物理化学 / 量子化学計算 / 機械学習 / 生物物理 / 生体分子 / シミュレーション / バイオテクノロジー
Outline of Final Research Achievements

In this research, by combining molecular dynamics (MD) simulation and fragment molecular orbital (FMO) calculation, we have performed theoretical studies for complex systems of actinide ion species and protein/DNA in the context of health physics. Several functional enhancements were made in the FMO programs, ABINIT-MP and PAICS. In addition, we have established a protocol to handle an amount of calculated data such as matrices of interaction energies generated by the combination of MD and FMO, based on statistical analyses and machine-learning techniques. As realistic applications, we have investigated calmodulin - ion (Ca(II), Eu(III) and Cm(III)) complex, DNA-uranyl complex and so on. These results have been presented in conferences as well as papers.

Academic Significance and Societal Importance of the Research Achievements

保健物理分野で問題となるアクチニド系イオンと生体分子の結合/相互作用をFMO計算によってまるごと電子状態レベルで解析することを世界で初めて達成した点は重要だと考えています。また、FMO計算を単一構造ではなくMDシミュレーションによって生成される多数(100以上)の構造サンプル群に対して適用し、生み出される膨大な数値データを統計的・機械学習的に処理して物理化学的な描像を得るプロトコルを確立した点も学術的な意味があると思います。DNA-ウラニル系のMD-FMO連携計算はChem. Comm.誌に出版済ですが、表紙を飾る高い評価を得ました。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (39 results)

All 2019 2018 2017 2016

All Journal Article (12 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 12 results,  Open Access: 10 results) Presentation (27 results) (of which Int'l Joint Research: 3 results,  Invited: 4 results)

  • [Journal Article] Destabilization of DNA through interstrand crosslinking by UO22+2019

    • Author(s)
      A. Rossberg, T. Abe, K. Okuwaki, A. Barkleit, K. Fukuzawa, T. Nakano, Y. Mochizuki, and S. Tsushima
    • Journal Title

      Chem. Comm.

      Volume: 55 Issue: 14 Pages: 2015-2018

    • DOI

      10.1039/c8cc09329f

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A Radical Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA)2019

    • Author(s)
      中野達也, 望月祐志, 福澤薫, 沖山佳生, 渡邉千鶴
    • Journal Title

      Journal of Computer Aided Chemistry

      Volume: 20 Issue: 0 Pages: 1-6

    • DOI

      10.2751/jcac.20.1

    • NAID

      130007605302

    • ISSN
      1345-8647
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] <b>Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method</b><b> </b>2018

    • Author(s)
      T. Nakano, K. Fukuzawa, Y. Okiyama, C. Watanabe, Y. Komeiji, and Y. Mochizuki
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 18 Issue: 0 Pages: 119-122

    • DOI

      10.1273/cbij.18.119

    • NAID

      130007496283

    • ISSN
      1347-0442, 1347-6297
    • Year and Date
      2018-10-05
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] <b>A portable code for dissipative particle dynamics (DPD) simulations with additional specific interactions</b>2018

    • Author(s)
      H. Doi, S. Saitou, K. Okuwaki, T. Naitou, and Y. Mochizuki
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 18 Issue: 0 Pages: 70-85

    • DOI

      10.1273/cbij.18.70

    • NAID

      130007386454

    • ISSN
      1347-0442, 1347-6297
    • Year and Date
      2018-06-30
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] RI-MP3 calculations of biomolecules based on the fragment molecular orbital method2018

    • Author(s)
      Ishikawa Takeshi、Sakakura Kota、Mochizuki Yuji
    • Journal Title

      Journal of Computational Chemistry

      Volume: 39 Issue: 24 Pages: 1970-1978

    • DOI

      10.1002/jcc.25368

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of Educational Scratch Programs for the First-year Students in Chemistry Course of University2018

    • Author(s)
      満野仁美, 中川知樹, 土居英男, 望月祐志
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 17 Issue: 3 Pages: 111-112

    • DOI

      10.2477/jccj.2018-0022

    • NAID

      130007496290

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development and Application of FMO Calculation − DPD Simulation Conbination Scheme2018

    • Author(s)
      奥脇弘次, 土居英男, 望月祐志, 小沢拓, 泰岡顕治, 福澤薫
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 17 Issue: 3 Pages: 144-146

    • DOI

      10.2477/jccj.2018-0020

    • NAID

      130007501035

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deeper Level Parallelization and Performance Evaluation ofFMO Program ABINIT-MP on Oakforest-PACS2018

    • Author(s)
      渡邊啓正, 佐藤伸哉, 坂倉耕太, 齊藤天菜, 望月祐志
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 17 Issue: 3 Pages: 147-149

    • DOI

      10.2477/jccj.2018-0023

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] <b>Application of TensorFlow to recognition of visualized results of fragment molecular orbital (FMO) calculations</b>2018

    • Author(s)
      S. Saitou, J. Iijima, M. Fujimoto, Y. Mochizuki, K. Okuwaki, H. Doi, and Y. Komeiji
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 18 Issue: 0 Pages: 58-69

    • DOI

      10.1273/cbij.18.58

    • NAID

      130006619328

    • ISSN
      1347-0442, 1347-6297
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of the Fragment Molecular Orbital Method for Calculating Non-local Excitations in Large Molecular Systems2018

    • Author(s)
      T. Fujita, and Y. Mochizuki
    • Journal Title

      J. Phys. Chem. A

      Volume: 122 Issue: 15 Pages: 3886-3898

    • DOI

      10.1021/acs.jpca.8b00446

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Preliminary Study of Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA)2017

    • Author(s)
      中野達也, 望月祐志, 福澤薫, 沖山佳生, 渡邉千鶴
    • Journal Title

      Journal of Computer Aided Chemistry

      Volume: 18 Issue: 0 Pages: 143-148

    • DOI

      10.2751/jcac.18.143

    • NAID

      130006172777

    • ISSN
      1345-8647
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Current Status of ABINIT-MP as a FMO Program and Related Works with Machine Learning2017

    • Author(s)
      望月祐志, 坂倉耕太, 秋永宜伸, 加藤幸一郎, 渡邊啓正, 沖山佳生, 中野達也, 古明地勇人,奥沢明, 福澤薫, 田中成典
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 16 Issue: 5 Pages: 119-122

    • DOI

      10.2477/jccj.2017-0051

    • NAID

      130006322245

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Fragment molecular orbital based interaction analyses for peptides solid surface systems2019

    • Author(s)
      K. Kato, K. Fukuzawa, Y. Mochizuki
    • Organizer
      The Second International Workshop by the 174th Committee on Coexistence of Biology and Nanodevices
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] FMO-DPD手法の開発と脂質・タンパク質への応用2019

    • Author(s)
      望月祐志, 奥脇弘次, 土居英男, 小沢拓, 泰岡顕治, 福澤薫
    • Organizer
      応用物理学会春期年会2019
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 脂質ベシクル、タンパク質の非経験的粗視化シミュレーション2019

    • Author(s)
      奥脇弘次, 新庄英治, 土居英男, 望月祐志, 福澤薫, 米持悦生
    • Organizer
      応用物理学会春期年会2019
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 天然ゴム中タンパク質とイソプレン鎖末端部との相互作用解析2019

    • Author(s)
      阿部鷹也, 奥脇弘次, 望月祐志, 福澤薫, 佐藤弘一
    • Organizer
      応用物理学会春期年会2019
    • Related Report
      2018 Annual Research Report
  • [Presentation] DNA-ウラニル系のFMO計算に基づく相互作用解析2018

    • Author(s)
      津島悟, 阿部鷹也, 奥脇弘次, 望月祐志, 古明地勇人, 福澤薫, 中野達也, 沖山佳生, 三好永作
    • Organizer
      日本コンピュータ化学会2018年春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 大学初年度向け化学教育のためのScratchプログラムの開発2018

    • Author(s)
      中川知樹, 土居英男, 満野仁美, 望月祐志
    • Organizer
      日本コンピュータ化学会2018年春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Kerasを使った転移学習の応用事例2018

    • Author(s)
      伊藤雅仁, 伊藤隆登, 齊藤天菜, 土居英男, 望月祐志
    • Organizer
      日本コンピュータ化学会2018年春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] フラグメント分子軌道(FMO)法のナノバイオ系への応用事例2018

    • Author(s)
      望月祐志, 加藤幸一郎, 福澤薫
    • Organizer
      日本生物工学会大会シンポジウム
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 3Dプリント、および複合現実感(MR)による分子モデルの表現2018

    • Author(s)
      望月祐志,中村昇太,牧村健,藤本賢志,奥脇弘次,福澤薫,工藤光子
    • Organizer
      応用物理学会秋期年会2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] 脂質ベシクル、タンパク質の非経験的粗視化シミュレーション2018

    • Author(s)
      奥脇弘次, 新庄英治, 土居英男, 望月祐志, 福澤薫, 米持悦生
    • Organizer
      応用物理学会秋期年会2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] FMO法を用いたカルサイト結晶表面とペプチドの相互作用解析2018

    • Author(s)
      望月祐志, 加藤幸一郎, 福澤薫
    • Organizer
      応用物理学会秋期年会2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] Development status of ABINIT-MP program in 20182018

    • Author(s)
      Y. Mochizuki, K. Sakakura, Y. Akinaga, H. Watanabe, K. Kato, K. Fukuzawa,T. Nakano
    • Organizer
      CBI conference 2018 (国内会議)
    • Related Report
      2018 Annual Research Report
  • [Presentation] RI-MP3 calculations of biomolecules based on the fragment molecular orbital method with PAICS2018

    • Author(s)
      T. Ishikawa, K. Sakakura, Y. Mochizuki
    • Organizer
      CBI conference 2018(国内会議)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Non-empirical Coarse-grained Simulations for Lipid Bilayer and Protein2018

    • Author(s)
      K. Okuwaki, E. Shinsho, H. Doi, Y. Mochizuki, K. Fukuzawa, E. Yonemochi
    • Organizer
      CBI conference 2018(国内会議)
    • Related Report
      2018 Annual Research Report
  • [Presentation] FMO-based interaction analyses on uranyl(VI)-bound model DNA2018

    • Author(s)
      T. Abe, K. Okuwaki, S. Tsushima, Y. Mochizuki, Y. Komeiji, K. Fukuzawa, T. Nakano, K. Okiyama, E. Miyoshi
    • Organizer
      ATAS 2018 Workshop(国際、仏国ニースで開催)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] FMOとDPDを連携したマルチスケールシミュレーション手法(FMO-DPD)の開発と先導的応用2018

    • Author(s)
      奥脇弘次, 土居英男, 望月祐志, 小沢拓, 泰岡顕治, 福澤薫
    • Organizer
      分子シミュレーション討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] タイヤゴム素材に関する計算化学的研究の事例紹介2018

    • Author(s)
      石川雄太郎, 阿部鷹也, 奥脇弘次, 土居英男, 望月祐志, 福澤薫, 佐藤弘一
    • Organizer
      高分子基礎物性研究会・高分子計算機科学研究会・高分子ナノテクノロジー研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Xeon Phi KNL環境でのMO計算プログラムの性能評価2017

    • Author(s)
      齊藤天菜, 望月祐志, 石村和也, 渡邊啓正, 坂倉耕太, 佐藤伸哉
    • Organizer
      日本コンピュータ化学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Site-specific binding affinity of Eu(III) towards Ca-binding protein calmodulin: A combined spectroscopic and theoretical study2017

    • Author(s)
      S. Tsushima, S. Samsonov, B. Drobot, J. Raff, Y. Komeiji, Y. Mochizuki
    • Organizer
      Actinides 2017 Conf.
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Ca(II)およびEu(III)が結合したカルモデュリンの動的挙動の理論的解析2017

    • Author(s)
      津島悟, 望月祐志, 古明地勇人, 阿部鷹也, 奥脇弘次, 森寛敏, 田中成典
    • Organizer
      応用物理学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] FMO計算結果の機械学習による解析2017

    • Author(s)
      望月祐志, 古明地勇人,齊藤天菜,藤本真悠,飯島潤,阿部鷹也, 奥脇弘次, 土居英男,奥沢明,牧村健,中西貴哉,福澤薫,田中成典
    • Organizer
      日本コンピュータ化学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Xeon Phi KNL環境でのMO計算プログラムの性能評価-その22017

    • Author(s)
      齊藤天菜, 望月祐志, 石村和也, 渡邊啓正, 坂倉耕太, 佐藤伸哉, 土居英男
    • Organizer
      日本コンピュータ化学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ウラニルイオンとDNAの相互作用2017

    • Author(s)
      津島悟, 望月祐志, Andre Rossberg, 古明地勇人
    • Organizer
      極限環境生物学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] MD-FMO連携計算によるDNA-ウラニル系の相互作用解析2017

    • Author(s)
      津島悟, 阿部鷹也, 奥脇弘次, 望月祐志, 古明地勇人, 福澤薫, 中野達也, 沖山佳生, 三好永作
    • Organizer
      応用物理学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] FMO計算に基づくマルチスケールシミュレーションのナノバイオ系への応用2017

    • Author(s)
      奥脇弘次, 土居英男, 望月祐志, 小沢拓, 泰岡顕治, 福澤薫
    • Organizer
      応用物理学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] フラグメント分子軌道法(FMO法)による一本鎖DNAと結合タンパク質の相互作用解析2017

    • Author(s)
      古明地勇人, 沖山佳生, 望月祐志, 福澤薫
    • Organizer
      応用物理学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Fragment Molecular Orbital (FMO) for studying actinide interaction with proteins2016

    • Author(s)
      S.Tsushima*, T.Ishikawa, S.Tanaka, H.Mori, M.Saeki, T.Nakano, Y.Komeiji, Y.Mochizuki
    • Organizer
      3rd International Workshop on Advanced Techniques in Actinide Spectroscopy (ATAS 2016)
    • Place of Presentation
      EMSL Richland, Washington, USA
    • Year and Date
      2016-11-07
    • Related Report
      2016 Annual Research Report

URL: 

Published: 2016-04-21   Modified: 2020-03-30  

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