Updated on 2020/04/06

写真a

 
YOSHII Noriyuki
 
Organization
Graduate School of Engineering Center for Computational Science Designated associate professor
Title
Designated associate professor
Contact information
メールアドレス

Degree 1

  1. Doctor (Science) ( 1999.3   Tokyo Institute of Technology ) 

Research Interests 2

  1. 超並列計算

  2. 分子動力学シミュレーション

Current Research Project and SDGs 2

  1. Molecular Dynamics Study of Assembly of Amphiphilic Molecules such as Lipid Membrane and Micelle

  2. 高並列汎用分子動力学計算用のアルゴリズム開発

Research History 6

  1. Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Associate Professor

    2007.4 - 2011.7

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    Country:Japan

  2. National Institutes of Natural Sciences, Institute for Molecular Science, Asistant Professor

    2007.2 - 2007.3

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    Country:Japan

  3. National Institutes of Natural Sciences, Institute for Molecular Science, Researcher

    2004.4 - 2007.1

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    Country:Japan

  4. Okazaki National Research Institutes, Research Center for Computational Science

    2003.9 - 2004.3

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    Country:Japan

  5. Central Research Institute of Electric Power Industry, Research Scientist

    2000.4 - 2003.8

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    Country:Japan

  6. Japan Society for the Promotion of Science, Research Fellowship for Young Scientists (Tokyo Institute of Technology)

    1998.4 - 2000.3

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    Country:Japan

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Education 2

  1. Tokyo Institute of Technology   Graduate School, Division of Integrated Science and Engineering   Department of Electronic Chemistry

    1996.4 - 1999.3

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    Country: Japan

  2. Tokyo Institute of Technology   Graduate School, Division of Integrated Science and Engineering   Department of Electronic Chemistry

    1994.4 - 1996.3

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    Country: Japan

Professional Memberships 6

  1. 分子科学会   会員

  2. The Chemical Society of Japan

  3. 日本膜学会   会員

  4. 分子シミュレーション研究会   会員、編集委員、幹事

  5. 溶液化学研究会   会員

  6. 日本薬学会   会員

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Awards 3

  1. オレオサイエンス賞

    2012.4   日本油化学会  

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    Award type:Award from Japanese society, conference, symposium, etc.  Country:Japan

  2. 研究奨励賞

    2010   日本膜学会  

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    Country:Japan

  3. Helmholtz Award

    2008   The International Association for the Properties of Water and Steam (IAPWS)  

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    Country:Germany

 

Papers 25

  1. Pressure tensor for electrostatic interaction calculated by fast multipole method with periodic boundary condition

    Yoshii Noriyuki, Andoh Yoshimichi, Okazaki Susumu

    JOURNAL OF COMPUTATIONAL CHEMISTRY   Vol. 39 ( 19 ) page: 1192-1199   2018.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/jcc.25179

    Web of Science

  2. A thread-level parallelization of pairwise additive potential and force calculations suitable for current many-core architectures

    Andoh Yoshimichi, Suzuki Soichiro, Ohshima Satoshi, Sakashita Tatsuya, Ogino Masao, Katagiri Takahiro, Yoshii Noriyuki, Okazaki Susumu

    JOURNAL OF SUPERCOMPUTING   Vol. 74 ( 6 ) page: 2449-2469   2018.6

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1007/s11227-018-2272-2

    Web of Science

  3. Free Energy Change of Micelle Formation for Sodium Dodecyl Sulfate from a Dispersed State in Solution to Complete Micelles along Its Aggregation Pathways Evaluated by Chemical Species Model Combined with Molecular Dynamics Calculations

    Yoshii Noriyuki, Komori Mika, Kawada Shinji, Takabayashi Hiroaki, Fujimoto Kazushi, Okazaki Susumu

    ACTA PHYSICO-CHIMICA SINICA   Vol. 34 ( 10 ) page: 1163-1170   2018

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.3866/PKU.WHXB201802271

    Web of Science

  4. Molecular dynamics study of the potential of mean force of SDS aggregates

    Kawada Shinji, Fujimoto Kazushi, Yoshii Noriyuki, Okazaki Susumu

    JOURNAL OF CHEMICAL PHYSICS   Vol. 147 ( 8 )   2017.8

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1063/1.4998549

    Web of Science

  5. Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study

    Yoshii Noriyuki, Nimura Yuki, Fujimoto Kazushi, Okazaki Susumu

    JOURNAL OF CHEMICAL PHYSICS   Vol. 147 ( 3 )   2017.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1063/1.4994698

    Web of Science

  6. Evaluation of Atomic Pressure in the Multiple Time-Step Integration Algorithm

    Andoh Yoshimichi, Yoshii Noriyuki, Yamada Atsushi, Okazaki Susumu

    JOURNAL OF COMPUTATIONAL CHEMISTRY   Vol. 38 ( 10 ) page: 704-713   2017.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/jcc.24731

    Web of Science

  7. Molecular dynamics study of the aggregation rate for zwitterionic dodecyldimethylamine oxide and cationic dodecyltrimethylammonium chloride micelles

    Fujimoto Kazushi, Kubo Yousuke, Kawada Shinji, Yoshii Noriyuki, Okazaki Susumu

    MOLECULAR SIMULATION   Vol. 43 ( 13-16 ) page: 1331-1337   2017

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1080/08927022.2017.1328557

    Web of Science

  8. A molecular dynamics study of the breathing and deforming modes of thespherical ionic SDS and nonionic C12E8 micelles Reviewed

      Vol. 144   page: 034903   2016

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

  9. Molecular dynamics study of the structure of anionic SDS, cationic DTAC, zwitterionic DDAO, and nonionic C12E8 spherical micelles in solution Reviewed

    N. Yoshii, K. Fujimoto, S. Okazaki

    Journal of Molecular Liquids   Vol. 217   page: 99-102   2016

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

  10. Molecular dynamics study of the formation mechanisms of ionic SDS andnonionic C12E8 micelles and n-dodecane droplets Reviewed

    S. Kawada, M. Komori, K. Fujimoto, N. Yoshii, S. Okazaki

      Vol. 646   page: 34-40   2016

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    Language:English   Publishing type:Research paper (scientific journal)  

  11. A molecular dynamics study of local pressures and interfacial tensions of SDS micelles and dodecane droplets in water Reviewed

    M. Kitabata, K. Fujimoto, N. Yoshii, S. Okazaki

    Journal of Chemical Physics   Vol. 144   page: 224701   2016

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    Language:English   Publishing type:Research paper (scientific journal)  

  12. Molecular dynamics study of the structure of anionic SDS, cationic DTAC, zwitterionic DDAO, and nonionic C12E8 spherical micelles in solution Reviewed

    N. Yoshii, K. Fujimoto, S. Okazaki

    Journal of Molecular Liquids   Vol. 217   page: 99-102   2016

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    Language:English   Publishing type:Research paper (scientific journal)  

  13. MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program Reviewed

    N. Yoshii, Y. Andoh, K. Fujimoto, H. Kojima, A. Yamada, S. Okazaki

    International Journal of Quantum Chemistry   Vol. 115   page: 342–348   2015

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    Language:English  

  14. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution Reviewed

    Y. Andoh, N. Yoshii, A. Yamada, K. Fujimoto, H. Kojima, K. Mizutani, A. Nakagawa, A. Nomoto and S. Okazaki

    J. Chem. Phys.   Vol. 141   page: 165101   2014

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1063/1.4897557

  15. MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms Reviewed

    Yoshimichi Andoh, Noriyuki Yoshii, Kazushi Fujimoto, Keisuke Mizutani, Hidekazu Kojima, Atsushi Yamada, Susumu Okazaki, Kazutomo Kawaguchi, Hidemi Nagao, Kensuke Iwahashi, Fumiyasu Mizutani, Kazuo Minami, Shin-ichi Ichikawa, Hidemi Komatsu, Shigeru Ishizuki, Yasuhiro Takeda, and Masao Fukushima

    J. Chem. Theory Comput.   Vol. 9   page: 3201-3209   2013

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/ct400203a

  16. 2. Lateral diffusion of lipids separated from rotational and translational diffusion of a fluid Large unilamellar vesicle Reviewed

    N. Yoshii, T. Emoto, E. Okamura

    Colloid Surf. B-Biointerfaces   Vol. 106   page: 22-27   2013

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 22-27

  17. Enthalpy and entropy of transfer of alkanes from water phase to the micelle core Reviewed

    K. Fujimoto, N. Yoshii, and S. Okazaki

    Molecular Simulation   Vol. 38 ( 5 ) page: 342-345   2012.4

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    Language:English   Publishing type:Research paper (scientific journal)  

  18. Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations Reviewed

    K. Fujimoto, N. Yoshii, and S. Okazaki

    Journal of Chemical Physics   Vol. 136   page: 014511(9pages)   2012.1

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    Language:English   Publishing type:Research paper (scientific journal)  

  19. Molecular dynamics study of free energy of transfer of alcohol and amine from water phase to the micelle by thermodynamic integration method Reviewed

    K. Fujimoto, N. Yoshii, and S. Okazaki

    Journal of Chemical Physics   Vol. 137   page: 094902(6pages)   2012

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1063/1.4747491

  20. Binding of hydrophobic fluorinated bisphenol A to large unilamellar vesicles of egg phosphatidylcholine Reviewed

    N. Yoshii, and E. Okamura

    Journal of Physical Chemistry   Vol. B115   page: 11074-11800   2011

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    Language:English   Publishing type:Research paper (scientific journal)  

  21. Kinetics of binding and diffusivity of leucine-enkephaline in large unilamellar vesicle by pulsed-field-gradient 1H NMR in situ Reviewed

    N. Yoshii, T. Emoto, and E. Okamura

    Biophysics   Vol. 7   page: 105-111   2011

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    Language:English   Publishing type:Research paper (scientific journal)  

  22. Molecular dynamics study of solubilization of immiscible solutes by a micelle. Free energy of transfer of alkanes from water to the micelle core by thermodynamic integration method Reviewed

    K. Fujimoto, N. Yoshii, and S. Okazaki

    Journal of Chemical Physics   Vol. 133   page: 074511 (6pages)   2010

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    Language:English   Publishing type:Research paper (scientific journal)  

  23. Kinetics of membrane binding and dissociation of 5-fluorouracil by pulsed field gradient 19F NMR Reviewed

    N. Yoshii and E. Okamura

    Chemical Physics Letters   Vol. 474   page: 357-361   2009

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    Language:English   Publishing type:Research paper (scientific journal)  

  24. All-atom molecular dynamics study of a spherical micelle composed of N-acetylated poly(ethylene glycol)-poly(gamma-benzyl L-glutamate) block copolymers: A potential carrier of drug delivery systems for cancer Reviewed

    H. Kuramochi, Y. Andoh, N. Yoshii, S. Okazaki

    Journal of Physical Chemistry   Vol. B113   page: 15181-15188   2009

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    Language:English   Publishing type:Research paper (scientific journal)  

  25. Drug binding and mobility relating to the thermal fluctuation in fluid lipid membranes Reviewed

    E. Okamura and N. Yoshii

    Journal of Chemical Physics   Vol. 129   page: 215102 (8pages)   2008

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    Language:English   Publishing type:Research paper (scientific journal)  

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Books 4

  1. 計算科学のためのHPC技術1

    下司雅章編( Role: Joint author)

    大阪大学出版会  2017.4  ( ISBN:4872595866

  2. 製剤への物理化学

    斉藤博幸, 田中秀治編, 吉井範行他( Role: Joint author)

    廣川書店  2012.2 

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    Language:Japanese

  3. コンピュータシミュレーションの基礎(第二版)

    岡崎進、吉井範行( Role: Joint author)

    化学同人  2011.7  ( ISBN:978-4-7598-1475-0

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    Language:Japanese

    分子動力学シミュレーションの基礎となる力学、解析力学、統計力学の復習から、各種シミュレーション手法の詳細、さらには応用例までを一冊の本にまとめた。

  4. CBT対策と演習 物理化学

    薬学教育研究会編( Role: Sole author)

    廣川書店  2009.10 

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    Language:Japanese

KAKENHI (Grants-in-Aid for Scientific Research) 3

  1. 脂質膜とミセルからなる複合コロイド分散系における大域分子輸送の分子機構の解明

    2017.4 - 2020.3

    科学研究費補助金  基盤研究(C)

    吉井範行

  2. ミセルの脂質膜への結合・融合過程の分子論的機構

    2014.4 - 2017.3

    科学研究費補助金  基盤研究(C)

    吉井範行

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    Authorship:Principal investigator 

  3. モンテカルロ計算とNMR計測による脂質ベシクル表面の分子の制限拡散

    2011.4 - 2014.3

    科学研究費補助金  基盤研究(C)

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    Authorship:Principal investigator 

    球状ベシクルを担体としたときの分子の制限拡散に関する新規のモンテカルロ(MC)計算手法を開発する。これにより、注目する分子についてのパルス磁場勾配NMRのシグナルを予測する手法を確立する。細胞膜のモデルである脂質ベシクルを対象に、膜透過によりベシクルと結合・解離を繰り返す分子の運動を解析する。さらに、ベシクル表面に拘束されつつ運動する脂質分子についての真の側方拡散を明らかにする。
     具体的には、新規のMC計算の手法を開発し、球としてのベシクルに対する薬物分子の結合・解離運動とベシクル表面上における脂質分子の側方拡散運動に焦点を絞った解析を行う。はじめに(1)膜透過によりベシクルと結合・解離を繰り返す薬物の運動の解析として、(1A)ベシクルと結合・解離を繰り返す抗がん剤5-フルオロウラシル(5FU)の物理モデルを構築する。次に(1B)結合・解離過程のMC計算アルゴリズムの開発を行う。(1C)実際にMC計算を行い、得られた軌跡を用いてNMRシグナルの予測を行う。さらに(2)ベシクル表面上を側方拡散する脂質分子の運動の解析として、(2A)ベシクル表面上で側方拡散する脂質分子の物理モデルを構築する。(2B)ベシクル表面上の脂質分子の拡散過程を再現するMC計算アルゴリズムを構築する。(2C)実際にMC計算を実行することにより分子の軌跡を得る。この分子の軌跡を用いてNMRシグナルの予測を行う。(3)並行してNMR測定をおこない、得られたシグナルを脂質分子のベシクル上での側方拡散係数とベシクル自体の並進・回転拡散係数とに分離し、球面上の脂質分子の真の側方拡散係数を明らかにする。

 

Teaching Experience (On-campus) 7

  1. 理論・計算化学特論

    2018

  2. 基礎セミナー

    2017

  3. Advanced Physical Chemistry(APC)

    2014

  4. 分子物理化学特論

    2012

  5. 熱力学

    2012

  6. 大規模並列数値計算特論

    2012

  7. 計算科学フロンティア連続講義

    2011

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