Yasuoka, Kenji

写真a

Affiliation

Faculty of Science and Technology, Department of Mechanical Engineering (Yagami)

Position

Professor

Related Websites

External Links

Career 【 Display / hide

  • 1997.04
    -
    1998.03

    理化学研究所,基礎科学特別研究員

  • 1998.04
    -
    2000.03

    慶應義塾大学理工学部,助手

  • 1998.04
    -
    Present

    理化学研究所 ,共同研究員

  • 1999.01
    -
    1999.03

    科学技術振興事業団領域探索プログラム ,研究員

  • 2000.04
    -
    2004.03

    Assistant Professor, Keio University

display all >>

Academic Background 【 Display / hide

  • 1992.03

    Nagoya University, Faculty of Science, Department of Physics

    University, Graduated, Other

  • 1994.03

    Nagoya University, Graduate School of Engineering, Department of Applied Physics

    Graduate School, Completed, Master's course

  • 1997.03

    Nagoya University, Graduate School of Engineering, Department of Applied Physics

    Graduate School, Completed, Doctoral course

Academic Degrees 【 Display / hide

  • PhD, Nagoya University, Coursework, 1997.03

 

Papers 【 Display / hide

  • Mechanism for H<inf>2</inf>diffusion in sII hydrates by molecular dynamics simulations

    Hasegawa T., Brumby P.E., Yasuoka K., Sum A.K.

    Journal of Chemical Physics (Journal of Chemical Physics)  153 ( 5 )  2020.08

    ISSN  00219606

     View Summary

    © 2020 Author(s). Among the many different types of molecules that form clathrate hydrates, H2 is unique as it can easily diffuse into and out of clathrate cages, a process that involves the physical-chemical interactions between guest (H2) and host (water) molecules, and is unlike any other molecular system. The dynamic and nano-scale process of H2 diffusion into binary structure II hydrates, where the large cages are occupied by larger molecules, was studied using molecular dynamics simulation. As the H2 molecules diffused from one cage to another, two types of diffusion processes were observed: (i) when moving between a pair of large cages, the H2 molecules pass through the central part of the hexagonal rings; (ii) however, when the H2 molecules move from a large cage to a small one, it requires one of the pentagonal rings to partially break, as this allows the H2 molecule to pass through the widened space. While the diffusion of H2 molecules between large cages was found to occur more frequently, the presence of SF6 molecules in the large cages was found to inhibit diffusion. Therefore, in order to attain higher H2 storage capacities in binary hydrates, it is suggested that there is an optimal number of large cages that should be occupied by SF6 molecules.

  • Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application

    Pua K., Yuhara D., Ayuba S., Yasuoka K.

    PLoS ONE (PLoS ONE)  15 ( 4 )  2020.04

     View Summary

    © 2020 Pua et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The study of molecular dynamics simulations is largely facilitated by analysis and visualization toolsets. However, these toolsets are often designed for specific use cases and those only, while scripting extensions to such toolsets is often exceedingly complicated. To overcome this problem, we designed a software application called AViS which focuses on the extensibility of analysis. By utilizing the dataflow programming (DFP) paradigm, algorithms can be defined by execution graphs, and arbitrary data can be transferred between nodes using visual connectors. Extension nodes can be implemented in either Python, C++, and Fortran, and combined in the same algorithm. AViS offers a comprehensive collection of nodes for sophisticated visualization state modifications, thus greatly simplifying the rules for writing extensions. Input files can also be read from the server automatically, and data is fetched automatically to improve memory usage. In addition, the visualization system of AViS uses physically-based rendering techniques, improving the 3D perception of molecular structures for interactive visualization. By performing two case studies on complex molecular systems, we show that the DFP workflow offers a much higher level of flexibility and extensibility when compared to legacy workflows.

  • A biointerface effect on the self-assembly of ribonucleic acids: A possible mechanism of RNA polymerisation in the self-replication cycle

    Arai N., Kobayashi Y., Yasuoka K.

    Nanoscale (Nanoscale)  12 ( 12 ) 6691 - 6698 2020.03

    ISSN  20403364

     View Summary

    © 2020 The Royal Society of Chemistry. Despite decades of intensive research, many questions remain on the formation and growth of the first cells on Earth. Here, we used computer simulation to compare the self-assembly process of ribonucleic acids in two environments: Enclosed in a vesicle-cell membrane and in the bulk. The self-assembly was found to be more favoured in the former environment, and the origin of such a biointerface effect was identified. These results will contribute to a better understanding of the origin of life on the primitive Earth.

  • The acidic tail of HMGB1 regulates its secondary structure and conformational flexibility: A circular dichroism and molecular dynamics simulation study

    Anggayasti W.L., Ogino K., Yamamoto E., Helmerhorst E., Yasuoka K., Mancera R.L.

    Computational and Structural Biotechnology Journal (Computational and Structural Biotechnology Journal)  18   1160 - 1172 2020

     View Summary

    © 2020 The Author(s) High mobility group box 1 (HMGB1) is a damage-associated molecular pattern (DAMP) molecule that triggers the progression of several pro-inflammatory diseases such as diabetes, Alzheimer's disease and cancer, by inducing signals upon interaction with the receptors such as the receptor for advanced glycation end-products (RAGE) and toll-like receptors (TLRs). The acidic C-terminal tail of HMGB1 is an intrinsically disordered region of the protein which is known to determine the interaction of HMGB1 to DNA and histones. This study characterizes its structural properties using a combination of circular dichroism (CD) and molecular dynamics (MD) simulations. The full-length and tail-less forms of HMGB1 were compared to rationalise the role of the acidic tail in maintaining the stability of the entire structure of HMGB1 in atomistic detail. Consistent with experimental data, the acidic tail was predicted to adopt an extended conformation that allows it to make a range of hydrogen-bonding and electrostatic interactions with the box-like domains that stabilize the overall structure of HMGB1. Absence of the acidic tail was predicted to increase structural fluctuations of all amino acids, leading to changes in secondary structure from α-helical to more hydrophilic turns along with increased exposure of multiple amino acids to the surrounding solvent. These structural changes reveal the intrinsic conformational dynamics of HMGB1 that are likely to affect the accessibility of its receptors.

  • Crystal Engineering of Bi<inf>2</inf>WO<inf>6</inf> to Polar Aurivillius-Phase Oxyhalides

    Morita K., Park J., Kim S., Yasuoka K., Walsh A.

    Journal of Physical Chemistry C (Journal of Physical Chemistry C)  123 ( 48 ) 29155 - 29161 2019.12

    ISSN  19327447

     View Summary

    © 2019 American Chemical Society. The Aurivillius phases of complex bismuth oxides have attracted considerable attention because of their lattice polarization (ferroelectricity) and photocatalytic activity. We report a first-principles exploration of Bi2WO6 and the crystal engineering through replacing W6+ by pentavalent (Nb5+ and Ta5+) and tetravalent (Ti4+ and Sn4+) ions, with charge neutrality maintained by the formation of a mixed anion oxyhalide sublattice. We find that Bi2SnO4F2 is thermodynamically unstable, in contrast to Bi2TaO5F, Bi2NbO5F, and Bi2TiO4F2. The electric dipoles introduced by chemical substitutions in the parent compound are found to suppress the spontaneous polarization from 61.55 μC/cm2 to below 15.50 μC/cm2. Analysis of the trends in electronic structure, surface structure, and ionization potentials is reported. This family of materials can be further extended with control of layer thicknesses and choice of compensating halide species.

display all >>

Papers, etc., Registered in KOARA 【 Display / hide

display all >>

Reviews, Commentaries, etc. 【 Display / hide

  • Anomalous Diffusion of Water Molecules on Cell Membranes Investigated by Using Molecular Dynamics Simulations

    Eiji YAMAMOTO, Takuma AKIMOTO and Kenji YASUOKA

    生物物理 (一般社団法人 日本生物物理学会)   2015.10

    Article, review, commentary, editorial, etc. (scientific journal), Joint Work

Presentations 【 Display / hide

  • 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

    奥脇 弘次, 土居 英男, 望月 祐志, 小沢 拓, 泰岡 顕治, 福澤 薫

    第65回応用物理学会春期学術講演会 (東京) , 

    2018.03

    Oral presentation (general)

  • FMO計算に基づくマルチスケールシミュレーション環境の構築

    奥脇 弘次, 土居 英男, 望月 祐志, 小沢 拓, 泰岡 顕治, 福澤 薫

    2017年度 高分子基礎物性研究会・高分子計算機科学研究会 合同討論会 (東京) , 

    2018.03

    Oral presentation (general)

  • 高分子ダイナミクスの普遍性を応用した分子シミュレーションの階層間接続

    高橋和義,西村龍斗,大和伸好,泰岡顕治,増渕雄一

    第31回分子シミュレーション討論会, 

    2017.11

    Poster presentation, 石川

  • FDPS を用いた水の分子動力学シミュレーション

    野村 昴太郎 ,岩澤全規,行方大輔,野澤拓磨,泰岡顕治,牧野淳一郎

    第31回分子シミュレーション討論会 (石川) , 

    2017.11

    Poster presentation

  • FDPS を用いた水の分子動力学シミュレーション

    野村 昴太郎 ,岩澤全規,行方大輔,野澤拓磨,泰岡顕治,牧野淳一郎

    第31回分子シミュレーション討論会 (石川) , 

    2017.11

    Poster presentation

display all >>

Research Projects of Competitive Funds, etc. 【 Display / hide

  • クラスレート水和物の相平衡条件の分子論的予測手法の開発

    2015.04
    -
    2020.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (A) , Principal investigator

Awards 【 Display / hide

  • Gordon Bell Prize (Price Performance Category)

    Tsuyoshi Hamada, Kiyoshi Oguri, Rio Yokota, Keigo Nitadori, Makoto Taiji, Tetsu Narumi, Kenji Yasuoka, 2009.11, 42 TFlops Hierarchical N-body Simulations on GPUs with Applications in both Astrophysics and Turbulence

    Type of Award: International academic award (Japan or overseas)

  • 分子シミュレ―ション研究会学術賞

    YASUOKA KENJI, 2006.11, 分子シミュレ―ション研究会, 流体の界面現象・核生成現象の微視的機構の大規模分子シミュレーションによる研究

    Type of Award: Award from Japanese society, conference, symposium, etc.

  • Gordon Bell Prizes(Peak Performance Category)

    泰岡 顕治, 2000.11, 米国電気電子技術学会コンピュータ協会(IEEE Computer Society)

  • 第8回計算力学講演会(日本機械学会計算力学部門)学生優秀講演賞

    泰岡 顕治, 1995.11, 日本機械学会

 

Courses Taught 【 Display / hide

  • ENVIRONMENTAL TECHNOSCIENCE AND POLICY

    2022

  • ENVIRONMENTAL INFORMATION SYSTEM ARCHITECTURE

    2022

  • BACHELOR'S THESIS

    2022

  • ADVANCED COURSE OF MOLECULAR DYNAMICS

    2022

  • FACTORY VISITING

    2022

display all >>

 

Memberships in Academic Societies 【 Display / hide

  • 日本機械学会, 

    1998.04
    -
    Present
  • 日本伝熱学会, 

    1998.04
    -
    Present
  • 日本設計工学会, 

    1998.04
    -
    2003.03
  • 日本物理学会, 

    1994.04
    -
    Present
  • 日本熱物性学会, 

    1994.04
    -
    Present

display all >>

Committee Experiences 【 Display / hide

  • 2017.01
    -
    Present

    事務局長, 分子シミュレーション研究会

  • 2015.01
    -
    Present

    幹事, 分子シミュレーション研究会

  • 2015.01
    -
    2016.12

    編集委員会委員長, 分子シミュレーション研究会

  • 2014.11
    -
    2016.12

    実行委員, Asian Thermophysical Properties Conference 2016 (ATPC2016)

  • 2014.04
    -
    2014.12

    実行委員, International Symposium on Extended Molecular Dynamics and Enhanced Sampling:Nosé Dynamics 30 Years (NOSE30)

display all >>