Rchr
J-GLOBAL ID：201801010434644023   Update date: Jul. 02, 2024

Yamashita Takefumi

Yamashita Takefumi
Affiliation and department：
Hoshi University

About Hoshi University


Other affiliations (1)：
Research field  (6)： Bio-, chemical, and soft-matter physics ,  Structural biochemistry ,  Basic physical chemistry ,  Molecular biochemistry ,  Structural and functional materials ,  Computational science
Research keywords  (1)： molecular dynamics
Research theme for competitive and other funds  (9)：
  • 2021 - 2025 1細胞計測に基づく細胞モデルとそれに基づく形態形成の理論の開発
  • 2020 - 2023 Optimization of pretargeted alpha therapy for multiple types of cancer
  • 2018 - 2023 Dynamics of protein-protein interface: Development of analysis methods based on machine learning and MD simulation
  • 2016 - 2023 Theoretical elucidation of dynamical solvent effects in controling chemical reactions
  • 2015 - 2020 Development of Molecular Dynamics Classification Theories for Life Science and Drug Design
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Papers (59)：
  • Syeda Rubaiya Nasrin, Takefumi Yamashita, Mitsunori Ikeguchi, Takayuki Torisawa, Kazuhiro Oiwa, Kazuki Sada, Akira Kakugo. Tensile Stress on Microtubules Facilitates Dynein-Driven Cargo Transport. Nano letters. 2024
  • Senjuti Nowroz, Syeda Rubaiya Nasrin, Arif Md Rashedul Kabir, Takefumi Yamashita, Tomoichiro Kusumoto, Junichi Taira, Marie Tani, Masatoshi Ichikawa, Kazuki Sada, Akira Kakugo. Role of tubulin C-terminal tail on mechanical properties of microtubule. Biochemical and biophysical research communications. 2024. 706. 149761-149761
  • Kazuhiro Miyanabe, Takefumi Yamashita, Kouhei Tsumoto. Thermodynamic and molecular dynamic insights into how fusion influences peptide-tag recognition of an antibody. Scientific reports. 2024. 14. 1. 8685-8685
  • Takefumi Yamashita. A molecular dynamics study on the PD-1-Nivolumab interaction: Roles of the N-terminal loop and N58-glycosylation of PD-1. AIP Conference Proceedings. 2024. 3030. 1
  • Naoyuki Shoji, Takefumi Yamashita. Tensile Stress Reduction and Strain Concentration of Epoxy Resin Caused by Heterogeneity: A Multiscale Approach Combining Molecular Dynamics Simulation and Finite Element Method. The journal of physical chemistry. B. 2023. 127. 42. 9066-9073
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MISC (72)：
  • 山下雄史, 山下雄史. 医薬品開発における分子動力学シミュレーションの役割. SAR News (Web). 2023. 45
  • 小倉由未佳, 奥脇弘次, 古石誉之, 山下雄史, 米持悦生, 福澤薫. 処方設計への応用に向けた計算科学を用いたイオン性脂質ナノ粒子の構造予測. 製剤と粒子設計シンポジウム講演要旨集. 2023. 40th
  • Yamashita Takefumi. スーパーコンピューター「富岳」による創薬・医療の革新 MDシミュレーションで考える抗原-抗体界面 合理的な抗体医薬品設計に向けて(A molecular dynamics study on the antigen-antibody interface: Toward rational antibody drug design). 生物物理. 2022. 62. Suppl.1-2. S214-S214
  • 高橋和希, 山次健三, 加藤洋人, 山下雄史, 安藝翔, 巽俊文, 金子雄大, 川村猛, 川村猛, 三浦麻衣, et al. Near-infrared Phototherapy Using Modified Streptavidin-iminobiotin Drug Delivery System. 日本薬学会年会要旨集(Web). 2022. 142年会. 26T-pm01S
  • 山下雄史. MDシミュレーションで考える抗原-抗体界面における塩橋の役割:合理的な抗体設計に向けて. 日本蛋白質科学会年会プログラム・要旨集. 2022. 22nd (Web)
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Patents (5)：
Lectures and oral presentations  (85)：
  • Molecular Dynamics Simulation for Biological and Material polymers
    (International Congress on Pure & Applied Chemistry (ICPAC) 2022 2022)
  • A molecular dynamics study on the antigen-antibody interface: Toward rational antibody drug design
    (2022)
  • Properties of the Protein-Protein Interface Revealed by Molecular dynamics Simulations
    (18th International Conference of Computational Methods in Sciences and Engineering (QS symposium of ICCMSE 2022) 2022)
  • MDシミュレーションで考える抗原-抗体界面における塩橋の役割:合理的な抗体設計に向けて
    (日本蛋白質科学会学会年会 ワークショップ:「富岳」時代の計算蛋白質科学 2022)
  • 結合自由エネルギーの定量的予測と分子設計のための構造モチーフ探索
    (CBI学会第432回講演会「結合自由エネルギー計算は創薬研究戦略を変えるか」 2022)
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Education (3)：
  • 1998 - 2004 Kyoto University Graduate School of Science
  • 1996 - 1998 Kyoto University Graduate School of Science
  • 1992 - 1996 Kyoto University Faculty of Science
Professional career (1)：
  • 博士(理学) (京都大学)
Work history (7)：
  • 2023/04 - 現在 Hoshi University
  • 2011/01 - 現在 The University of Tokyo Research Center for Advanced Science and Technology
  • 2010/04 - 2010/12 シカゴ大学 化学科 G.A.Voth研究室 博士研究員
  • 2008/04 - 2010/03 ユタ大学 化学科 G.A.Voth研究室 博士研究員
  • 2007/04 - 2008/03 ユタ大学 化学科 G.A.Voth研究室 日本学術振興会特別研究員
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