Updated on 2024/04/08

写真a

 
Mitsuta Yuki
 
Organization
Graduate School of Science Department of Chemistry Assistant Professor
School of Science Department of Chemistry
Title
Assistant Professor
Affiliation
Institute of Science

Position

  • Graduate School of Science Department of Chemistry 

    Assistant Professor  2022.04 - Now

  • School of Science Department of Chemistry 

    Assistant Professor  2022.04 - Now

Degree

  • 理学博士 （ Osaka University ）

  • 理学修士 （ Osaka University ）

  • 理学学士 （ Osaka University ）

Research Areas

  • Nanotechnology/Materials / Bio chemistry

  • Nanotechnology/Materials / Fundamental physical chemistry

  • Natural Science / Biophysics, chemical physics and soft matter physics

Research Interests

  • 計算生命化学

  • 分子動力学計算

  • Computational Chemistry

  • Molecular Dynamics Simulation

Research subject summary

  • 分子動力学計算による自由エネルギー反応経路探索法の開発

Professional Memberships

  • 日本化学会

  • 分子科学会

  • 分子シミュレーション学会

Awards

  • 分子科学会優秀講演賞

    2017.10   第11回分子科学討論会(仙台)2017  

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    Country：Japan

Job Career (off-campus)

  • Osaka Metropolitan University   Graduate School of Science Department of Chemistry

    2022.04 - Now

  • Osaka Prefecture University   Graduate School of Science Department of Chemistry

    2021.04 - 2022.03

  • University of Tsukuba   Center for Computational Sciences

    2019.04 - 2021.03

Papers

  • Nudged elastic stiffness band method: A method to solve kinks problems of reaction paths

    Mitsuta Y.

    Journal of Computational Chemistry   44 ( 23 )   1884 - 1897   2023.09（ ISSN:01928651 ）

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  • Computational Approach for Molecular Design of Small Organic Molecules with High Hole Mobilities in Amorphous Phase Using Random Forest Technique and Computer Simulation Method

    Nakaguro K.

    Bulletin of the Chemical Society of Japan   96 ( 10 )   1099 - 1107   2023（ ISSN:00092673 ）

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  • Curvature-weighted nudged elastic band method using the Riemann curvature Reviewed

    Yuki Mitsuta, Toshio Asada

    Journal of Computational Chemistry   44 ( 5 )   662 - 669   2022.11（ ISSN:01928651 ）

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/jcc.27030

    PubMed

    Other URL： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.27030

  • Calculation of the permeability coefficients of small molecules through lipid bilayers by free-energy reaction network analysis following the explicit treatment of the internal conformation of the solute Invited Reviewed

    Yuki Mitsuta, Toshio Asada, Yasuteru Shigeta

    Physical Chemistry Chemical Physics   24   26070 - 26082   2022.10

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   International / domestic magazine：International journal  

    We propose a molecular dynamics simulation method for estimating the permeation through lipid bilayers based on the free-energy reaction network analysis, which include the conformational changes in the rotational bonds of the solute molecules.

    DOI： 10.1039/d2cp03678a

  • Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics Calculations

    Koki Yanagi, Yuki Mitsuta, Kenta Takaoka, Teruyuki Takahashi, Kowit Hengphasatporn, Ryuhei Harada, Yasuteru Shigeta

    Chemistry Letters   50 ( 12 )   1964 - 1967   2021.12（ ISSN:0366-7022 ）

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    Publishing type：Research paper (scientific journal)  

    Using both quantum chemical and molecular dynamics calculations, free energy profiles during membrane permeable processes of Ala-containing cyclic dipeptides were evaluated with moderate computational costs. Since the balance between hydrophobicity and hydrophilicity is a key factor in the membrane permeation processes, Ala-Ala and Ala-Pro might be permeable, but Ala-Asn is not owing to the high free energy barrier at the membrane center. This protocol is useful to roughly distinguish whether a given compound has high permeability or not.

    DOI： 10.1246/cl.210488

  • Analytical Method Using a Scaled Hypersphere Search for High-Dimensional Metadynamics Simulations Reviewed

    Yuki Mitsuta, Yasuteru Shigeta

    Journal of Chemical Theory and Computation   16 ( 6 )   3869 - 3878   2020.06（ ISSN:1549-9626 ）

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)  

    Metadynamics (MTD) is one of the most effective methods for calculating the free energy surface and finding rare events. Nevertheless, numerous studies using MTD have been carried out using 3D or lower dimensional collective variables (CVs), as higher dimensional CVs require costly computational resources and the obtained results are too complex to understand the important events. The latter issue can be conveniently solved by utilizing the free energy reaction network (FERN), which is a graph structure consisting of edges of minimum free energy paths (MFEPs), nodes of equation (EQ) points, and transition state (TS) points. In the present article, a new method for exploring FERNs on high-dimensional CVs using MTD and the scaled hypersphere search (SHS) method is described. A test calculation based on the MTDSHS simulation of met-enkephalin in explicit water with 7 CVs was conducted. As a result, 889 EQpoints and 1805 TS points were found. The MTD-SHS approach can find MFEPs exhaustively; therefore, the FERNs can be estimated without any a priori knowledge of the EQ and TS points.

    DOI： 10.1021/acs.jctc.0c00010

  • Free energy reaction root mapping of alanine tripeptide in water Reviewed International coauthorship

    Yuki Mitsuta, Johannes Kästner , Shusuke Yamanaka , Takashi Kawakami, Mitsutaka Okumura

    Molecular Physics   117 ( 17 )   2284 - 2292   2019.09（ ISSN:1362-3028 ）

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)  

    DOI： 10.1080/00268976.2018.1537525

  • Linear Response Functions of Densities and Spin Densities for Systematic Modeling of the QM/MM Approach for Mono- and Poly-Nuclear Transition Metal Systems Reviewed

    Kitakawa Colin K, Maruyama Tomohiro, Oonari Jinta, Mitsuta Yuki, Kawakami Takashi, Okumura Mitsutaka, Yamaguchi Kizashi, Yamanaka Shusuke

    MOLECULES   24 ( 4 )   2019.02（ ISSN:1420-3049 ）

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    Publishing type：Research paper (scientific journal)  

    DOI： 10.3390/molecules24040821

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Presentations

  • 自由エネルギー反応経路ネットワーク計算から見た生体分子の振る舞い Invited Domestic conference

    満田祐樹

    研究会「凝縮系の理論化学」  2024.03 

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    Presentation type：Oral presentation (invited, special)  

    Venue：沖縄県市町村自治会館  

  • Nudged Elastic Band法を改良するために剛性の力を加えたNudged Elastic Stiffness Band法の開発 Domestic conference

    満田祐樹、麻田俊雄

    日本化学会 第104春季年会（2024）  2024.03 

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    Presentation type：Oral presentation (general)  

    Venue：日本大学  

  • アンブレラ積分法を利用した多次元アンブレラサンプリングのパラメーター自動最適化手法の開発 Domestic conference

    満田祐樹、麻田俊雄

    第 37 回分子シミュレーション討論会  2023.12 

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    Presentation type：Oral presentation (general)  

    Venue：福井県県民ホール  

  • Predicting the Biomembranes Permeability of Fentanyl and Its Analogues by Free Energy Reaction Route Network International conference

    Yuki Mitsuta, Toshio Asada

    The 6th International Conference on Molecular Simulation  2023.10 

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    Presentation type：Poster presentation  

    Venue：National Taiwan University  

  • Nudged Elastic Stiffness Band法：反応経路のkink問題を解決する手法の開発 Domestic conference

    満田祐樹、麻田俊雄

    第17回分子科学討論会  2023.09 

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    Presentation type：Oral presentation (general)  

    Venue：大阪大学  

  • 反応経路ネットワーク解析を利用した Fentanyl とその類似体の膜透過シミュレーション Domestic conference

    満田祐樹、麻田俊雄

    第36回分子シミュレーション討論会  2022.12 

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    Presentation type：Oral presentation (general)  

    Venue：東京工業大学  

  • Development of a Curvature Weighted Nudged Elastic Band Method Domestic conference

    2022.09 

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    Presentation type：Oral presentation (general)  

  • Free Energy Reaction Route Network of Biomolecules Using Molecular Dynamics Simulation Invited Domestic conference

    2022.09 

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    Presentation type：Oral presentation (invited, special)  

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Grant-in-Aid for Scientific Research

  • 自由エネルギー反応経路探索法を利用した薬剤分子の膜透過シミュレーション手法の開発

    Grant-in-Aid for Early-Career Scientists  2023

  • メゾヒエラルキー理論

    Grant-in-Aid for Transformative Research Areas  2023

Number of instructed thesis, researches

  • 2023

    Number of instructed the graduation thesis：1 

    [Number of instructed the Master's Program] (previous term)：1 

  • 2022

    Number of instructed the graduation thesis：1 

Social Activities

  • 大手前高校SSHサイエンス探求の中間発表での研究指導

    Role(s)： Consultant

    2024.02

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    Type：Research consultation