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2007 Fiscal Year Annual Research Report

ナノ・バイオ物質における形状と機能の量子デザイン

Research Project

Project/Area Number 17064002
Research InstitutionUniversity of Tsukuba

Principal Investigator

押山 淳  University of Tsukuba, 大学院・数理物質科学研究科, 教授 (80143361)

Co-Investigator(Kenkyū-buntansha) 白石 賢二  筑波大学, 大学院・数理物質科学研究科, 教授 (20334039)
BOERO Mauro  筑波大学, 大学数理物質科学研究科, 准教授 (40361315)
岡田 晋  筑波大学, 大学数理物質科学研究科, 准教授 (70302388)
岩田 潤一  筑波大学, 計算科学研究センター, 研究員 (70400695)
山内 淳  慶應義塾大学, 理工学部, 専任講師 (90383984)
Keywordsナノ物質 / バイオ物質 / 量子論 / 電子状態 / 密度汎関数理論
Research Abstract

ナノ・バイオ物質における原子構造・ナノ形状・電子物性・機能発現の4者の相関を解明すべく、量子論に立脚した計算科学的手法による研究が進められた。手法開発の側面では、密度汎関数理論に基づいた全エネルギー・電子構造計算を、実空間格子上で実行する計算コード(RSDFT)が開発され、並列計算機上でのチューニングが行われた。またナノ秒を超える時間スケールでの、イオンと電子のダイナミクスを調べる、メタ・ダイナミクス手法をCar-Parrinello分子動力学計算コードにインプリメントし(CPMD-MeD)、各種の生体分子の反応に適用された。そうした計算手法め開発に加速され、以下のようなナノサイエンス、バイオサイエンスにおける研究成果が得られた。
1. RSDFTにより1000原子系の安定構造探索が可能になり、シリコン中の原子空孔周囲の緩和構造が高精度で決定された。
2. RSDFTにより、10,000原子系の電子状態計算が可能となり、シリコンクラスターの励起エネルギーが計算された。
3. CPMD-MeDにより、シトクローム酸化酵素中でのプロトン輸送機構の原子スケールの機構が解明された。
4.歪半導体薄膜での有効質量の膜圧、歪依存性が明らかになり、歪テクノロジーへの基礎が作られた。

  • Research Products

    (24 results)

All 2008 2007

All Journal Article (21 results) (of which Peer Reviewed: 21 results) Presentation (3 results)

  • [Journal Article] Effective Mass Anomalies in Strained Si Thin Films and Crystals2008

    • Author(s)
      J. Yamauchi
    • Journal Title

      IEEE Electron Device Letters 29

      Pages: 186-188

    • Peer Reviewed
  • [Journal Article] Ge Vacancies at Ge/Si Interfacee: Stress Enhanced Pairing Distrotion2008

    • Author(s)
      K. Takai, K. Shiraishi and A. Oshiyama
    • Journal Title

      Physics Beview B77

      Pages: 045308

    • Peer Reviewed
  • [Journal Article] Large-scale density-functional calculations on silicon divacancies.2008

    • Author(s)
      J. Iwata, K. Shiraishi and A. Oshiyama
    • Journal Title

      Physics Beview B77

      Pages: 115280

    • Peer Reviewed
  • [Journal Article] Energetics of nanoscale graphene ribbons: Edge geometries and electronic structures2008

    • Author(s)
      S. Okada
    • Journal Title

      Physical Review B77

      Pages: 041408(R)

    • Peer Reviewed
  • [Journal Article] Electronic transport properties of strained Si thin films: Effective mass anomalies2007

    • Author(s)
      J. Yamauchi
    • Journal Title

      Conference Porceedings 893, Physics of Semi conductors, 28^<th> International Conference

      Pages: 1405-1406

    • Peer Reviewed
  • [Journal Article] Effective-Mass Anomalies of Strained Silicon Thin Films: Surface and Confinement Effects2007

    • Author(s)
      J. Yamauchi and S. Matsuno
    • Journal Title

      Japanese Journal of Applied Physics 46

      Pages: 3273-3276

    • Peer Reviewed
  • [Journal Article] Role of Nitrogen Atoms in Reduction of Electron Charge Traps in Hf-based High-k Dielectrics2007

    • Author(s)
      N. Umezawa, K. Shiraishi, K. Torii, M. Boero, T. Chikyow, H. Watanabe, K. Yamabe, T. Ohno, K. Yamaba, and Y. Nara
    • Journal Title

      IEEE Electron Device Letters 28

      Pages: 363-365

    • Peer Reviewed
  • [Journal Article] Possible Mechanism of Proton Transfer through Peptide Groups in the H-pathway of the Bovine Cytochrome c Oxidase2007

    • Author(s)
      K. Kamiya, M. Boero, M. Tateno, K. Shiraishi and A. Oshiyama
    • Journal Title

      Journal of the American Chemical Society 129

      Pages: 9663-9673

    • Peer Reviewed
  • [Journal Article] Hydration properties of magnesium and calcium ions from constrained first principles molecular dynamics2007

    • Author(s)
      T. Ikeda, M. Boero and K. Terakura
    • Journal Title

      Journal of Chemical Physics 127

      Pages: 074503

    • Peer Reviewed
  • [Journal Article] First Principles Molecular Dynamics Study of Catalytic Reactions of Biological Systems: Toward Analyses with QM/MM Hybrid Molecular Simulations2007

    • Author(s)
      M. Boero, J. Park, Y. Hagiwara and M. Tateno
    • Journal Title

      Journal of Physics: Condensed Matter 129

      Pages: 365217

    • Peer Reviewed
  • [Journal Article] Novel Mechanism for Proton Transfer in Bovine Cytochrome c Oxidase2007

    • Author(s)
      K. Kamiya, M. Boero, M. Tateno, K. Shiraishi and A. Oshiyama
    • Journal Title

      Journal of Physics: Condensed Matter 19

      Pages: 365220

    • Peer Reviewed
  • [Journal Article] Excess electron in water at different thermodynamic conditions2007

    • Author(s)
      M. Boero
    • Journal Title

      Journal of Physical Chemistry A111

      Pages: 12248-1226

    • Peer Reviewed
  • [Journal Article] Formation of titanium-carbide in a nanospace of C782007

    • Author(s)
      M. Otani, S. Okada and A. Oshiyama
    • Journal Title

      Chemical Physics Letters 438

      Pages: 274

    • Peer Reviewed
  • [Journal Article] Quantum Effects in Cylindrical Carbon-Nanotube Capacitor2007

    • Author(s)
      K. Uchida, S. Okada, K. Shiraishi and A. Oshiyama
    • Journal Title

      Journal of Physics: Condensed Matter 19

      Pages: 365218

    • Peer Reviewed
  • [Journal Article] Energetics of Ice Nanotubes and their Encapsulation in Carbon. Nanotubes from Density-Functional Theory2007

    • Author(s)
      T. Kurita, S. Okada, A. Oshiyama
    • Journal Title

      Physics Review B75

      Pages: 205424

    • Peer Reviewed
  • [Journal Article] Quantum Effects in Double-Walled Carbon Nanotube Capacitor2007

    • Author(s)
      K. Uchida, S. Okada, K. Shiraishi and A. Oshiyama
    • Journal Title

      Physics Beview B76

      Pages: 155436

    • Peer Reviewed
  • [Journal Article] Orientaiton. Dependence of Magnetic Moment of Carbon Nanotubes with Topological Line Defects2007

    • Author(s)
      S. Okada, K. Nakada, and T. Kawai
    • Journal Title

      Applied Physics Letters 90

      Pages: 103120

    • Peer Reviewed
  • [Journal Article] Electronic structures of finite-length carbon nanotubes: Crossover from fullerenes to nanotubes2007

    • Author(s)
      S. Okada
    • Journal Title

      NANO 2

      Pages: 51-57

    • Peer Reviewed
  • [Journal Article] Radial-breathing mode frequencies for nanotubes encapsulating fullerenes2007

    • Author(s)
      S. Okada
    • Journal Title

      Chemical Physics Letters 438

      Pages: 59

    • Peer Reviewed
  • [Journal Article] Energetics and Electronic Structure of Armchair Nanotubes with Topological Line Defect2007

    • Author(s)
      S. Okada, K. Nakada, and T. Kawai
    • Journal Title

      Energetics and Electronic Structure of Armchair Nanotubes with Topological Line Defect 19

      Pages: 465231

    • Peer Reviewed
  • [Journal Article] Energetics and Electronic Structures of Carbon Nanotubes with Adatom-Vacancy Defects2007

    • Author(s)
      S. Okada
    • Journal Title

      Chemical Physics Letters 447

      Pages: 263

    • Peer Reviewed
  • [Presentation] 王又毛霧テ編素数質の雪子状薦:ネタみクー夕と暦層薄造2007

    • Author(s)
      岡田晋
    • Organizer
      本物理学会第62回年次大会、若手奨励賞引賞記念講演.
    • Place of Presentation
      北海道大学
    • Year and Date
      2007-09-22
  • [Presentation] Density-Functional Approach to Nano-and Bio-Materials2007

    • Author(s)
      A, Oshiyama
    • Organizer
      ICYS(NIMS)-ICMR(UC Santa Barbara)Summer School on Nanomaterials
    • Place of Presentation
      NIMS,Tsukuba
    • Year and Date
      2007-07-27
  • [Presentation] Proton Transfer in Cytochrome c Oxidase using CPMD+Metadynamics2007

    • Author(s)
      A, Oshiyama
    • Organizer
      Roberto Car 60th Birthday Symposium
    • Place of Presentation
      ICTP,Trieste,Italy
    • Year and Date
      2007-06-21

URL: 

Published: 2010-02-04   Modified: 2016-04-21  

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