DUY TRAN PHUOC

チャンズイフ | DUY TRAN PHUOC

Affiliation and department：

Research field (5)： Computational science , Molecular biochemistry , Biomaterials , Biomedical engineering , Bio-, chemical, and soft-matter physics

Research keywords (3)： Protein structure prediction , Protein functional design , Computational biophysics

Research theme for competitive and other funds (7)：

2022 - 2023 How viral protein interfere the interactions of p53 protein with DNA
2019 - 2021 Atomistic mechanism of the oligomerization of p53 protein in DNA scanning
2014 - 2017 Association and dissociation simulations of bio-molecular complex using parallel cascade selection molecular dynamics
2013 - 2015 Study of structural and phase transition in free surface and confined geometry system using computer simulation
2012 - 2013 Molecular basis of odorant ligands recognition: a computational study

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Papers (25)：

Mariko Kojima, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Kunio Hirata, Keitaro Yamashita, Yuki Hishikawa, Akio Kitao, Takafumi Ueno. Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein. Biomaterials Science. 2023
Tatsuro Nishikino, Norihiro Takekawa, Duy Phuoc Tran, Jun-ichi Kishikawa, Mika Hirose, Sakura Onoe, Seiji Kojima, Michio Homma, Akio Kitao, Takayuki Kato, et al. Structure of MotA, a flagellar stator protein, from hyperthermophile. Biochemical and Biophysical Research Communications. 2022. 631. 78-85
Duy Phuoc Tran, Yuta Taira, Takumi Ogawa, Ryoga Misu, Yoshiki Miyazawa, Akio Kitao. Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer. Scientific Reports. 2022. 12. 1
Hiroaki Hata, Duy Phuoc Tran, Mohamed Marzouk Sobeh, Akio Kitao. Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model. Biophysics and Physicobiology. 2021. 18. 305-316
Duy Phuoc Tran, Seiichi Tada, Akiko Yumoto, Akio Kitao, Yoshihiro Ito, Takanori Uzawa, Koji Tsuda. Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides. Scientific Reports. 2021. 11. 1

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Lectures and oral presentations (26)：

DNA bending enhances the dissociation of tetrameric p53's core domains
(The 59th Annual Meeting of the Biophysical Society of Japan 2021)
Atomic mechanism of the complete association of intrinsically disordered peptide to protein
(The 33rd IUPAP Annual Conference on Computational Physics 2021)
Predicting the complex conformations of Protein/Peptide using a/dPaCS-MD
(The 35th Annual Symposium of The Protein Society 2021)
When computer simulations meet machine learning: unveiling the dynamics of biomolecular complexes
(the 9th Tokyo Tech International Symposium on Life Science and Technology: Visualization and Engineering of Biomolecules 2021)
Biomolecular Functional Design: an Introduction to Recent Advances
(the Annual Meeting of the Biophysical Society of Japan 2020)

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Education (3)：

2014 - 2017 The University of Tokyo Graduate School of Frontier Sciences Computational Biology and Medical Sciences
2012 - 2013 Hochiminh City University of Technology Faculty of Applied Sciences Biomedical Engineering
2006 - 2011 Hochiminh City University of Technology Faculty of Applied Science Biomedical Engineering

Work history (4)：

2019/04 - 現在 Tokyo Institute of Technology School of Life Science and Technology Assistant professor
2018/10 - 2019/03 The University of Tokyo Graduate School of Frontier Sciences Postdoctoral Researcher
2017/10 - 2018/09 Tokyo Institute of Technology School of Life Science and Technology Researcher
2011/06 - 2014/09 Hochiminh City University of Technology Faculty of Applied Science Researcher (Lecturer)

Awards (7)：

2023/10 - Research Organization for Information Science and Technology HPCI Excellent Achievement Award How viral protein interfere the interactions of p53 protein with DNA
2020/05 - Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures TSUBAME Support System for Young and Female Users Understanding the Hachimoji DNA as Functional Biomaterials: Molecular Dynamics Simulation Study
2019 - The Biophysical Society of Japan Early Career Presentation Award
2016 - Biophysical Society of Japan Student Presentation Award
2014 - Hitachi Global Foundation Hitachi Scholarship

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Association Membership(s) (4)：

VIetnam Theoretical Physics Society , Biophysical Society , PROTEIN SCIENCE SOCIETY OF JAPAN , THE BIOPHYSICAL SOCIETY OF JAPAN

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