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Analysis of the dynamics of supercooled water in carbon materials using reactive molecular dynamics simulations

Research Project

Project/Area Number 19K05209
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 28030:Nanomaterials-related
Research InstitutionKyoto Institute of Technology

Principal Investigator

Mizuguchi Tomoko  京都工芸繊維大学, 材料化学系, 准教授 (90758963)

Project Period (FY) 2019-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2021: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2020: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2019: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywordsカーボンナノチューブ / 反応力場 / 分子動力学シミュレーション / OHラジカル / 脂質膜 / 水の透過 / 膜透過 / 過冷却液体 / 局所構造 / 反応分子動力学法 / 動的反応力場 / 炭素構造体 / ナノ空間 / 閉じ込め系 / 過冷却水
Outline of Research at the Start

疎水性細孔中における過冷却水の構造およびダイナミクスを、化学反応を取り入れた分子動力学シミュレーションで解析する。親水性のシリカ細孔における結果と比較することで、界面の性質が過冷却水の物性に及ぼす影響を、原子レベルで明らかにする。シミュレーションの結果を実験へとフィードバックすることで、細孔内実験で得られた結果のより正確な解釈を可能とし、今後の細孔材料の開発に役立てることを目指す。界面の影響を考慮した上で低温の水の性質を調べることにより、細孔内実験で観測される過冷却水の異常な振る舞いのメカニズム解明に繋げる。

Outline of Final Research Achievements

To investigate the behavior of water within a carbon nanotube (CNT), molecular dynamics simulations using the reactive force field, ReaxFF, were carried out. First, four different parameter sets of ReaxFF were evaluated, revealing significant variations in the rate of water penetration into the CNT depending on the chosen parameter set. One particular parameter set precluded any water penetration into the CNT. Subsequently, simulations were conducted to examine the permeation of water and OH radicals through the CNT vertically penetrating a lipid membrane. The findings indicated that the CNT, featuring hydrogen terminations at its ends, allow water to pass through, but not OH radicals. For comparison, additional permeation simulations were performed with aquaporin incorporated into the lipid membrane. Intriguingly, it was observed that a small amount of OH radicals managed to traverse the aquaporin channel by forming hydrogen bonds with water.

Academic Significance and Societal Importance of the Research Achievements

CNTを用いた膜透過の研究は、CNTの末端修飾により選択的な分子透過システムを実現する可能性を秘めている。OHラジカルをガン細胞に選択的に透過させることができれば、ガン細胞を狙い撃ちした治療システムの構築に繋がる。アクアポリンを透過させるシミュレーションでは、入り口付近にエネルギー障壁があることが分かったので、CNTの末端修飾により入り口の障壁を下げてやれば、水との複合体として透過が可能かもしれない。ラジカルのような反応性が高い種を扱うときには、反応力場を用いたシミュレーションが力を発揮するので、そのパラメータ調整を含めて計算を進めていくことが重要である。

Report

(5 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • Research Products

    (32 results)

All 2023 2022 2021 2020 2019

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 4 results) Presentation (26 results) (of which Int'l Joint Research: 14 results,  Invited: 2 results)

  • [Journal Article] Determination of cooperatively rearranging regions in a binary glass former2023

    • Author(s)
      Mizuguchi Tomoko、Odagaki T
    • Journal Title

      Journal of Physics: Condensed Matter

      Volume: - Issue: 33 Pages: 334003-334003

    • DOI

      10.1088/1361-648x/acd50c

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The study on the stability of DNA structure by steered molecular dynamics simulations2022

    • Author(s)
      Mizuguchi Tomoko、Fukushima Naoto、Aoki Takashi、Fujiwara Susumu、Hashimoto Masato
    • Journal Title

      Journal of Advanced Simulation in Science and Engineering

      Volume: 9 Issue: 1 Pages: 160-169

    • DOI

      10.15748/jasse.9.160

    • ISSN
      2188-5303
    • Related Report
      2022 Annual Research Report 2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Icosahedral order in liquid and glassy phases of cyclohexane2020

    • Author(s)
      T. Mizuguchi, S. Tatsumi, and S. Fujiwara
    • Journal Title

      Molecular Simulation

      Volume: 46 Issue: 10 Pages: 721-726

    • DOI

      10.1080/08927022.2020.1757092

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural change of damaged polyethylene by beta-decay of substituted tritium using reactive force field2020

    • Author(s)
      Li Haolun、Fujiwara Susumu、Nakamura Hiroaki、Mizuguchi Tomoko、Nakata Ayako、Miyazaki Tsuyoshi、Saito Shinji
    • Journal Title

      Japanese Journal of Applied Physics

      Volume: 60 Issue: SA Pages: SAAB06-SAAB06

    • DOI

      10.35848/1347-4065/abbdc8

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Hydrogen bond analysis of confined water in mesoporous silica using the reactive force field2019

    • Author(s)
      Mizuguchi Tomoko、Hagita Katsumi、Fujiwara Susumu、Yamada Takeshi
    • Journal Title

      Molecular Simulation

      Volume: 45 Issue: 17 Pages: 1437-1446

    • DOI

      10.1080/08927022.2019.1652740

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics study on DNA damage by tritium disintegration2019

    • Author(s)
      Nakamura Hiroaki、Miyanishi Hisanori、Yasunaga Takuo、Fujiwara Susumu、Mizuguchi Tomoko、Nakata Ayako、Miyazaki Tsuyoshi、Otsuka Takao、Kenmotsu Takahiro、Hatano Yuji、Saito Shinji
    • Journal Title

      Japanese Journal of Applied Physics

      Volume: 59 Issue: SA Pages: SAAE01-SAAE01

    • DOI

      10.7567/1347-4065/ab460d

    • NAID

      210000157157

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Reactive molecular dynamics study on intermolecular structural changes of hydrogen-abstracted polyethylene chains2022

    • Author(s)
      Haolun Li, Susumu Fujiwara, Hiroaki Nakamura, Tomoko Mizuguchi, Shinji Saito and Wataru Sakai
    • Organizer
      The 41st JSST Annual International Conference on Simulation TechnologyJSST2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Molecular dynamics study of microscopic mechanism of OH radical-induced DNA damage2022

    • Author(s)
      Ryuta Kawanami, Susumu Fujiwara, Tomoko Mizuguchi, Yoshiteru Yonetani and Hiroaki Nakamura
    • Organizer
      The 41st JSST Annual International Conference on Simulation TechnologyJSST2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The role of DNA sequence in the stability of double-stranded structure2022

    • Author(s)
      Tomoko Mizuguchi, Takashi Aoki, Naoto Fukushima, Masato Hashimoto, and Susumu Fujiwara
    • Organizer
      AROB-ISBC-SWARM 2022
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] 真空中における損傷炭化水素の構造安定化に関する反応分子動力学シミュレーション2021

    • Author(s)
      LI HAOLUN・藤原 進・中村 浩章・水口 朋子・中田 彩子・宮崎 剛・斉藤 真司・坂井 亙
    • Organizer
      第70回高分子学会年次大会
    • Related Report
      2021 Research-status Report
  • [Presentation] The study on the stability of DNA structure by steered molecular dynamics simulations2021

    • Author(s)
      Tomoko Mizuguchi, Naoto Fukushima, Takashi Aoki, Masato Hashimoto and Susumu Fujiwara
    • Organizer
      The 40th JSST Annual International Conference on Simulation Technology
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Reactive molecular dynamics study on damaged polyethylene after hydrogen abstraction by radiation2021

    • Author(s)
      Haolun Li, Susumu Fujiwara, Hiroaki Nakamura, Tomoko Mizuguchi, Ayako Nakata, Tsuyoshi Miyazaki, Shinji Saito and Wataru Sakai
    • Organizer
      The 40th JSST Annual International Conference on Simulation Technology
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Effect of tritium beta decay in deoxy-D-ribose on double helix structure of telomeric DNA2021

    • Author(s)
      Kento Ishiguro, Hiroaki Nakamura, Takuo Yasunaga, Susumu Fujiwara and Tomoko Mizuguchi
    • Organizer
      The 40th JSST Annual International Conference on Simulation Technology
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Tritium-induced damage on polymers and biopolymers: Molecular dynamics simulations and theoretical calculations2021

    • Author(s)
      Susumu Fujiwara, Haolun Li, Ryuta Kawanami, Kazushi Terakawa, Tomoko Mizuguchi, Hiroaki Nakamura, Yoshiteru Yonetani, Kazumi Omata, Seiki Saito, Takuo Yasunaga, Ayako Nakata, Tsuyoshi Miyazaki, Takao Otsuka, Takahiro Kenmotsu, Yuji Hatano and Shinji Saito
    • Organizer
      The 40th JSST Annual International Conference on Simulation Technology
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] 真空中における損傷炭化水素の構造変化に関する反応分子動力学シミュレーション2021

    • Author(s)
      Li Haolun・藤原 進・中村 浩章・水口 朋子・中田 彩子・宮崎 剛・斉藤 真司・坂井 亙
    • Organizer
      第70回高分子討論会
    • Related Report
      2021 Research-status Report
  • [Presentation] Reactive Molecular Dynamics Simulations on Polyethylene Damaged by Tritium Disintegration2021

    • Author(s)
      Haolun Li, Susumu Fujiwara, Hiroaki Nakamura, Tomoko Mizuguchi, Ayako Nakata, Tsuyoshi Miyazaki, Shinji Saito
    • Organizer
      ISPlasma2021/IC-PLANTS2021
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] 高分子・生体分子への置換トリチウムの壊変効果に関する分子動力学シミュレーション2021

    • Author(s)
      藤原 進, 中村 浩章, 水口 朋子, 米谷 佳晃, 尾又 一実, 安永 卓生, 大谷 寛明, 齋藤 誠紀, 中田 彩子, 宮崎 剛, 大塚 教雄, 剣持 貴弘, 波多野 雄治, 斉藤 真司
    • Organizer
      置換トリチウムのヘリウム 3 への壊変による DNA 構造変化に関する研究会
    • Related Report
      2020 Research-status Report
  • [Presentation] 真空中における損傷ポリエチレン一本鎖の構造安定化に関する反応分子動 力学シミュレーション2021

    • Author(s)
      LI HAOLUN, 藤原 進, 中村 浩章, 水口 朋子, 中田 彩子, 宮崎 剛, 斉藤 真司
    • Organizer
      置換トリチウムのヘリウム 3 への壊変による DNA 構造変化に関する研究会
    • Related Report
      2020 Research-status Report
  • [Presentation] クラスタ―DNA 損傷の分子動力学シミュレーション2021

    • Author(s)
      寺川 和志, 川波 竜太, LI HAOLUN, 藤原 進, 水口 朋子, 米谷 佳晃, 中村 浩章
    • Organizer
      置換トリチウムのヘリウム 3 への壊変による DNA 構造変化に関する研究会
    • Related Report
      2020 Research-status Report
  • [Presentation] DNAシミュレーションに適用する反応力場 ReaxFFの比較2021

    • Author(s)
      石黒 健人, 中村 浩章, 藤原 進, 水 口 朋子, LI HAOLUN, 米谷 佳晃, 安永 卓生, 齋藤 誠紀, 中田 彩子, 宮崎 剛, 大塚 教雄, 剣持 貴弘, 波多野 雄治, 斉藤 真司
    • Organizer
      置換トリチウムのヘリウム 3 への壊変による DNA 構造変化に関する研究会
    • Related Report
      2020 Research-status Report
  • [Presentation] Evaluation of Reactive Force Field on Simulating Damaged Polyethylene Chain by Substituted Tritium2020

    • Author(s)
      Haolun Li, Susumu Fujiwara, Hiroaki Nakamura, Tomoko Mizuguchi, Ayako Nakata, Tsuyoshi Miyazaki, Wataru Sakai, Shinji Saito
    • Organizer
      The 29th International Toki Conference on Plasma and Fusion Research (ITC-29)
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] DNAテロメア中デオキシDリボースのトリチウムβ崩壊による構造変化のMD解析2020

    • Author(s)
      中村浩章, 石黒健人, 藤原進, 水口朋子, 米谷佳晃, 安永卓生, 中田彩子, 宮崎剛, 大塚教雄, 剣持貴弘, 波多野雄治, 斉藤真司
    • Organizer
      第37回プラズマ・核融合学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] A Molecular Dynamics Study on Structural Change of Damaged Polyethylene by Beta-Decay of Substituted Tritium using Reactive Force Field2020

    • Author(s)
      Haolun Li・Susumu Fujiwara・Hiroaki Nakamura・Tomoko Mizuguchi・Ayako Nakata・Tsuyoshi Miyazaki・Shinji Saito
    • Organizer
      高分子学会第69回高分子討論会
    • Related Report
      2020 Research-status Report
  • [Presentation] 置換トリチウムのベータ崩壊による損傷ポリエチレンの構造変化に関する反応力場分子動力学研究2020

    • Author(s)
      LI HAOLUN・藤原 進、中村 浩章、水口 朋子、中田 彩子・宮崎 剛、斉藤 真司
    • Organizer
      2020年度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 合同討論会
    • Related Report
      2020 Research-status Report
  • [Presentation] 反応力場を用いた置換トリチウムの崩壊による損傷ポリエチレンの構造変化に関する分子動力学研究2020

    • Author(s)
      LI HAOLUN・藤原 進・中村 浩章・水口 朋子・中田 彩子・宮崎 剛・斉藤 真司
    • Organizer
      高分子学会第29回ポリマー材料フォーラム
    • Related Report
      2020 Research-status Report
  • [Presentation] 細孔中に拘束されたシクロヘキサンのダイナミクス2020

    • Author(s)
      辰巳創一, 水口朋子, 野田泰斗, Zach Evenson, 藤原進
    • Organizer
      日本物理学会2020年秋季大会
    • Related Report
      2020 Research-status Report
  • [Presentation] Icosahedral order in liquid and glassy phases of cyclohexane2019

    • Author(s)
      Tomoko Mizuguchi, Soichi Tatsumi, and Susumu Fujiwara
    • Organizer
      The 5th International Conference on Molecular Simulation
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Hydrogen bond analysis of confined water in mesoporous silica using the reactive force field2019

    • Author(s)
      Tomoko Mizuguchi, Katsumi Hagita and Susumu Fujiwara
    • Organizer
      The 5th International Conference on Molecular Simulation
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Icosahedral order in liquid and glassy phases of cyclohexane2019

    • Author(s)
      Tomoko Mizuguchi, Soichi Tatsumi and Susumu Fujiwara
    • Organizer
      2019 International Workshop on Glass Physics in Beijing
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] メソポーラスシリカ中の水に関する反応分子動力学計算2019

    • Author(s)
      水口朋子、萩田克美、藤原進
    • Organizer
      プラズマシミュレータシンポジウム2019
    • Related Report
      2019 Research-status Report
  • [Presentation] Hydrogen bond analysis of confined water in nanoporoussilica using molecular dynamics simulations2019

    • Author(s)
      Tomoko Mizuguchi, Katsumi Hagita and Susumu Fujiwara
    • Organizer
      APSMR 2019 Annual Meeting
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Hydrogen bond analysis of confined water in nanoporous silica using the reactive force field2019

    • Author(s)
      Tomoko Mizuguchi, Katsumi Hagita, Susumu Fujiwara and Takeshi Yamada
    • Organizer
      XXVI Sitges Conference on Statistical Mechanics
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research

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Published: 2019-04-18   Modified: 2024-01-30  

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