Updated on 2026/07/22

写真a

 
tran duy phuoc
 
Organization
School of Life Science and Technology Assistant Professor
Title
Assistant Professor
External link

News & Topics

Research Interests

  • Computational Biophysics, Protein Functional Design, Protein Structure Prediction

  • Protein functional design

  • Computational biophysics

  • Biomaterial design

Research Areas

  • Informatics / Computational science

  • Nanotechnology/Materials / Chemistry and chemical methodology of biomolecules

  • Life Science / Biomaterials

  • Life Science / Biomedical engineering

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

Research History

  • Nagoya University   Specially Appointed Assistant Professor

    2026.7

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    Country:Japan

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  • Institute of Science Tokyo   School of Life Science and Technology   Assistant professor (tenure-track)

    2024.10

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    Country:Japan

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  • Tokyo Institute of Technology   School of Life Science and Technology   Assistant Professor

    2019.4 - 2024.9

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Professional Memberships

Papers

  • Mechanistic insight into signal bias by the agonist-dependent conformational dynamics of GPR84 Reviewed

    Shota Suzuki, Duy Phuoc Tran, Kouki Nishikawa, Akio Kitao, Yoshinori Fujiyoshi

    Nature Communications   2026.7

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    Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1038/s41467-026-75728-9

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  • DRD1-driven infantile dystonia: towards a mechanism-informed framework for GPCR receptoropathies Reviewed

    Gülsüm Kayhan, Ryosuke Tany, Reza Maroofian, Esra Serdaroğlu, Eon Kurumiya, Duy Phuoc Tran, Hideko Wakasugi-Masuho, Mirja Thomsen, Kamran Salayev, Rauan Kaiyrzhanov, Saadat Badalova, Ulviyya Guliyeva, Adel Kareem, Peter Bauer, Giovanni Zifarelli, Henry Houlden, Katja Lohmann, Akio Kitao, M Fatih Mulayim, Ikuo Masuho

    Brain   2026.4

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    Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Despite remarkable advances in human genomics, most rare disorders remain undiagnosed, mechanistically obscure, and without effective treatments. In this study, we establish DRD1, encoding the dopamine D1 receptor (D1R), as a monogenic cause of an infantile-onset dystonia syndrome, for which pharmacological responsiveness may vary depending on the underlying molecular mechanism. Across three unrelated families, eight affected individuals exhibited generalised dystonia, axial hypotonia, and cognitive impairment and carried homozygous pathogenic missense DRD1 variants.

    Live-cell biosensor assays revealed that patient-derived DRD1 variants disrupt receptor integrity through mechanistically diverse failures, such as trafficking deficits and impaired agonist-induced activation—ultimately converging on a collapse of D1R-mediated signalling. In line with standard clinical practice and informed by these mechanistic insights, we initiated a trial of levodopa/carbidopa in two individuals in the index family with a partial-loss-of-function variant, which was associated with improvement in voluntary motor function and cognitive engagement. Moreover, in live-cell assays, we demonstrated that Mevidalen—a selective DRD1-positive allosteric modulator currently in clinical development—substantially improved signaling in patient-derived mutants in vitro, supporting a potential future mechanism-aligned therapeutic avenue.

    To broaden the clinical implications of our findings, we performed a structural interpretation of DRD1 variation in 807,162 individuals and identified 29 rare predicted deleterious missense variants in heterozygous carriers. These variants clustered within evolutionarily conserved transmembrane domains and signaling motifs, providing a basis for pathogenicity assignment and variant prioritization in clinical and research settings.

    Building on these insights, we developed a structure-informed pharmacological experimental framework that stratifies DRD1 variants according to molecular dysfunction and matches them with mechanistically aligned therapeutic strategies—namely, orthosteric agonists, pharmacological chaperones, allosteric modulators, and readthrough compounds. This in vitro approach enabled functional rescue of otherwise intractable variants, suggesting a potentially actionable molecular architecture across diverse genotypes, which remains to be tested clinically.

    Together, these findings identify biallelic DRD1 variants as a cause of infantile dystonia and support the potential for mechanism-informed therapeutic exploration, while emphasizing that clinical responsiveness may vary across individuals. More broadly, our integrated genomics-structure-pharmacology framework provides a proof-of-concept approach to functionally stratify G protein-coupled receptor (GPCR) variants, exemplified here by DRD1, and prioritise testable, mechanism-based therapeutic hypotheses for future evaluation.

    DOI: 10.1093/brain/awag128

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  • In Vitro Evolution of the Adenosine A 2A Receptor Based on an Antagonist Binding Using a Ribosome Display Reviewed

    Genki Fukasawa, Yuma Matsuoka, Duy Phuoc Tran, Haruka Nishigaki, Keisuke Fukunaga, Takayoshi Watanabe, Tomohiro Doura, Naohiro Terasaka, Ako Kagawa, Takeshi Murata, Akio Kitao, Shigeki Kiyonaka, Tomoaki Matsuura

    Journal of the American Chemical Society   148 ( 10 )   11415 - 11423   2026.3

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    DOI: 10.1021/jacs.6c02372

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  • The role of the tryptophan-rich allosteric network and sodium egress in GPCR activation Reviewed

    Zhenzhou Qi, Duy Phuoc Tran, Andrejs Tučs, Roopan Thiara, Louis-Philippe Picard, Koji Tsuda, Aditya Pandey, Adnan Sljoka, Akio Kitao, Robert Scott Prosser

    Proceedings of the National Academy of Sciences   123 ( 10 )   2026.3

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Proceedings of the National Academy of Sciences  

    The human adenosine A 2A receptor (A 2A R) is a prototypical member of the class A family of G Protein–Coupled Receptors (GPCRs), which are engaged by over one-third of FDA-approved drugs. Here, we used 19 F NMR to simultaneously evaluate functional states from the perspective of a CF 3 -tag on transmembrane helix-6 (TM6) and all 5-fluorotryptophan reporters. Whereas spectra from the TM6 tag reveal a dynamic conformational ensemble, the tryptophan spectra exhibit more discrete ligand-dependent states. These ligand-dependent signatures provide insights into microswitches including a universal toggle switch which interfaces with a sodium binding pocket. Over 560 GPCRs share this toggle switch — sodium pocket cluster, implying a fundamental role in activation. Computational rigidity-theory reveals tryptophan reporters reside along prominent allosteric activation pathways, underscoring their roles in mechanical signal propagation and corroborating NMR observations. Among them, W246 6.48 , associated with the toggle switch, plays a critical role in regulation of allosteric networks spanning the orthosteric pocket and extending via tryptophan-rich pathways through the receptor to the A 2A R-Gβ interface and the nucleotide pocket in G s α. While higher sodium concentrations (~100 mM) predictably stabilize the inactive conformation of the receptor, lower concentrations (below 40 mM) greatly enhanced the presence of the activation ensemble and in particular, the precoupled state, suggesting that the release of sodium from the conserved pocket—either through basal conditions for the apo receptor, or upon binding of the agonist—enables sampling of a precoupled state, ultimately needed to initiate activation and coupling.

    DOI: 10.1073/pnas.2525502123

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  • Revisiting Vacuum Simulations Using Modern Classical Protein Force Fields Reviewed

    Vi Toan Lam, Duy Phuoc Tran

    ACS Omega   11 ( 5 )   7464 - 7474   2026.1

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    DOI: 10.1021/acsomega.5c08560

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  • Single layer graphene flake transformation from flat to convex Reviewed

    Phuc Vu Le, Phi Minh Nguyen, Hoa Van Nguyen, Vi Toan Lam, Hanh Thi-Thu Tran, Duy Phuoc Tran

    Discover Materials   6   56   2025.12

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1007/s43939-025-00496-0

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  • Tandem Allosteric Effects of Reactant and Product that Promote Deacetylation Cycles in Sir2 Reviewed

    Zhen Bai, Duy Phuoc Tran, Akio Kitao

    Journal of Chemical Information and Modeling   65 ( 20 )   11326 - 11341   2025.10

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    Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jcim.5c01755

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  • Shear-induced fibronectin fibrillogenesis: Differential mechanisms under high and low shear stress conditions Reviewed

    Quang Phuc Le, Hoang Huy Mai, Thao Nghi Nguyen Hoang, Hanh Thu Thi Tran, Duy Phuoc Tran, Khon Huynh

    Archives of Biochemistry and Biophysics   771   110518 - 110518   2025.9

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    Authorship:Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.abb.2025.110518

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  • Correction to: Balancing G protein selectivity and efficacy in the adenosine A2A receptor (Nature Chemical Biology, (2025), 21, 1, (71-79), 10.1038/s41589-024-01682-6) Reviewed

    Picard, L.-P., Orazietti, A., Tran, D.P., Tucs, A., Hagimoto, S., Qi, Z., Huang, S.K., Tsuda, K., Kitao, A., Sljoka, A., Prosser, R.S.

    Nature Chemical Biology   21 ( 1 )   155 - 155   2025

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    Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41589-024-01732-z

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  • Balancing G protein selectivity and efficacy in the adenosine A2A receptor. Reviewed International journal

    Louis-Philippe Picard, Alexander Orazietti, Duy Phuoc Tran, Andrejs Tucs, Sari Hagimoto, Zhenzhou Qi, Shuya Kate Huang, Koji Tsuda, Akio Kitao, Adnan Sljoka, R Scott Prosser

    Nature chemical biology   21 ( 1 )   81 - 79   2024.7

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

    DOI: 10.1038/s41589-024-01682-6

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  • PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses Reviewed International journal

    Shinji Ikizawa, Tatsuki Hori, Tegar Nurwahyu Wijaya, Hiroshi Kono, Zhen Bai, Tatsuhiro Kimizono, Wenbo Lu, Duy Phuoc Tran, Akio Kitao

    Journal of Physical Chemistry B   128 ( 15 )   3631 - 3642   2024.4

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

    DOI: 10.1021/acs.jpcb.4c01271

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MISC

  • GPR84のバイアス作動の解明

    鈴木翔大, TRAN Phuoc Duy, 西川幸希, 北尾彰朗, 藤吉好則

    日本蛋白質科学会年会(Web)   25th   2025

  • Molecular Dynamics Simulation on Amyloid β (1-40) Heterodimerization

    KIMIZONO Tatsuhiro, KITAO Akio, TRAN Phuoc Duy

    日本蛋白質科学会年会(Web)   24th   2024

  • 芳香族環相互作用に注目した変異型アデノシンA2A受容体とリガンドの結合と解離の分子動力学計算

    堀立樹, DUY Tran Phuoc, 松岡佑真, 堂浦智裕, 荒谷剛史, 浅田秀基, 岩田想, 清中茂樹, 北尾彰朗

    分子シミュレーション討論会講演要旨集   38th   2024

Presentations

  • Insight of the signal transduction in Adenosine A2A receptor by MD simulations

    Duy Phuoc Tran, Akio Kitao

    IUPAP Conference on Computational Physics 2025  2025.11 

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    Event date: 2025.11

    Language:English   Presentation type:Oral presentation (general)  

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  • In Silico Design of Inhibitors Targeting SARS-CoV-2 Non-Structural Proteins Invited

    Duy Tran, Akio Kitao

    The 63rd Annual Meeting of the Biophysical Society of Japan  2025.9 

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    Event date: 2025.9

    Language:English   Presentation type:Oral presentation (invited, special)  

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  • Ions Permeation through the Stators of Bacterial Flagellar Motors

    Duy Phuoc Tran, Akio Kitao

    NanoBioCoM2024  2024.3 

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    Presentation type:Oral presentation (invited, special)  

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  • Simulating ion permeation through the flagellar motor stator MotA/B protein complexes

    Duy Tran, Tatsuro Nishikino, Norihiro Takekawa, Seiji Kojima, Katsumi Imada, Michio Homma, Akio Kitao

    Flagellar Meeting 2023  2024.3 

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    Presentation type:Oral presentation (general)  

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  • p53タンパク質のC末端ドメインとDNAの結合過程の解明

    Non-domain biology Symposium 

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  • Identification of sodium ion penetration pathways through the PomAB stator using SMD

    Duy Tran, Tatsuro Nishikino, Norihiro Takekawa, Seiji Kojima, Katsumi Imada, Michio Homma, Akio Kitao

    Flagellar meeting 2024  2025.3 

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  • Signal Transduction in Class A GPCRs

    Duy Phuoc Tran, Akio Kitao

    The 2nd Area “Generative Design to Unlock the Potential of Protein Function” Meeting  2024.12 

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  • Leveraging Biomolecular Simulations for Sustainable Development: from understanding to design

    Duy Phuoc Tran, Akio Kitao

    VANJ conference 2024  2024.12 

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  • Signal Transduction in G-protein Coupled Receptors Class A and Class C Invited

    Duy Phuoc Tran, Akio Kitao

    THE 4TH KEYLAB INTERNATIONAL CONFERENCE EXPERIMENTAL AND COMPUTATIONAL APPROACHES IN MOLECULAR MEDICINE  2024.10 

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    Presentation type:Oral presentation (invited, special)  

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  • In silico design of the activity-aware ligand coupled to the Adenosine A2A receptor

    Duy Phuoc Tran, Akio Kitao

    The 3rd Meeting of the Area "Protein Design" Symposium  2025.6 

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    Presentation type:Poster presentation  

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  • Understanding the G protein activation pathway through the Adenosine A2A receptor using PaCS-MD/MSM

    Duy Phuoc Tran, Akio Kitao

    The 11th Asia Pacific Association of Theoretical and Computational Chemistry  2025.4 

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    Presentation type:Oral presentation (invited, special)  

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  • Leveraging Biomolecular Simulations for Sustainable Development: from understanding to design

    Duy Phuoc Tran

    INTERNATIONAL CONFERENCE ON ENGINEERING AND TECHNOLOGIES FOR SUSTAINABLE DEVELOPMENT ICETSD 2024  2024.8 

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    Presentation type:Oral presentation (keynote)  

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  • Decoupling processes of the Adenosine A2A receptor from G- proteins through the lens of dPaCS-MD simulations

    Duy Phuoc Tran, Akio Kitao

    IUPAB 2024  2024.6 

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    Presentation type:Poster presentation  

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  • Understanding the amino acid recognition by Medaka taste receptor T1R2a/T1R3

    Duy Phuoc Tran, Vi Toan Lam, Atsuko Yamashita, Akio Kitao

    KAKENHI Scientific Transformation (A) 'Material Symbiosis' area conference  2024.6 

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  • Molecular mechanism in ion permeation of bacterial flagellar motor stators

    Duy Phuoc Tran, Akio Kitao

    Bacterial Flagella and BioMachineries joint with Annual Flagella Meeting  2026.3 

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    Language:English   Presentation type:Oral presentation (general)  

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  • Ion permeation and rotation mechanisms in bacterial flagellar motor stators Invited

    Duy Phuoc Tran, Akio Kitao

    The 12th HPCI System Research Project Report Meeting, The 8th HPCI Consortium Symposium  2025.10 

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    Language:English   Presentation type:Poster presentation  

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Research Projects

  • Development of A2A Receptor–Targeting Binders through AI-Driven Polymer Design

    Grant number:26H01458  2026.4 - 2028.3

    Ministry of Education, Culture, Sports, Science and Technology (MEXT)  FY2026 Grant-in-Aid for Transformative Research Areas (A) Public Offered Research: Creation of Next-Generation Pharmaceuticals through Data-Driven and Evolutionary Engineering of Precision Polymers 

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    Authorship:Principal investigator 

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  • Development of Next-Generation Bio-Semiconductors Based on Natural Biomaterials: Japan-ASEAN Integration of Computational Science and Tissue Engineering

    Grant number:Y2025L1015058  2026.1 - 2026.12

    Japan Science and Technology Agency  Japan-ASEAN Science, Technology, and Innovation Collaborative Partnership Program Young Talent Exchange Program Fiscal Year 2025 

    TRAN PHUOC DUY, Akio Kitao

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    Authorship:Principal investigator 

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  • AI framework for cell-penetrating peptide design to control its dynamics

    Grant number:JPMJBY25D1  2026 - 2030

    Japan Science and Technology Agency  BOOST: Broadening Opportunities for Outstanding young researchers and doctoral students in STrategic areas Fostering Researchers in Emerging AI Program (Support for Young Researchers) 

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    Authorship:Principal investigator 

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  • Understanding the internalization process of the G Protein Coupled Receptors class A

    Grant number:hp250049  2025.4 - 2026.3

    HPCI System Research Project  Fugaku Junior Researchers: FY2025 (Period A) 

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    Authorship:Principal investigator 

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  • In silico searching for the malfunctioning states of the SARS-CoV-2 Non-structural proteins

    Grant number:hp240024  2024.4 - 2025.3

    HPCI System Research Project  Fugaku Junior Researchers: FY2024 (Period A) 

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    Authorship:Principal investigator 

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  • Investigating molecular interactions of p53 regulated by post translation modifications and intrinsically disordered regions with advanced simulation

    Grant number:23K27138  2023.4 - 2027.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Grant amount:\18850000 ( Direct Cost: \14500000 、 Indirect Cost:\4350000 )

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  • Simulation- and AI-driven next-generation medicine and drug discovery based on "Fugaku"

    Grant number:JPMXP1020230120  2023.4 - 2026.3

    Ministry of Education, Culture, Sports, Science and Technology  Kyoto University 

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    Authorship:Coinvestigator(s) 

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  • Ion permeation and rotation mechanisms in bacterial flagellar motor stators

    Grant number:23K14154  2023.4 - 2025.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research, Grant-in-Aid for Early-Career Scientists 

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    Grant amount:\4680000 ( Direct Cost: \3600000 、 Indirect Cost:\1080000 )

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  • Ion permeation and rotation mechanisms in bacterial flagellar motor stators

    Grant number:hp230077  2023.4 - 2024.3

    HPCI System Research Project  Fugaku Junior Researchers: FY2023 (Period A) 

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    Authorship:Principal investigator 

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  • In silico study of phase transition mechanism of monatomic system

    Vietnam National University Hochiminh  Foundation for Science and Technology 

    Vo Van Hoang, Tran Phuoc Duy

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    Grant type:Competitive

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Teaching Experience

  • Informatics for Engineering Physics

    2024.10 Institution:Hochiminh City University of Technology

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  • Special Lecture in Life Science and Technology 1

    2024.10 Institution:Institute of Science Tokyo

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  • Fundamentals of Life Science and Technology: Laboratory and Practice I

    2024.10 Institution:Institute of Science Tokyo

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  • General Physics 1

    2019.10 Institution:Hochiminh City University of Technology

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  • LST Basic Laboratory and Exercise I

    2019.4 - 2024.10 Institution:Tokyo Institute of Technology

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  • LST Seminar 1

    2019.4 - 2024.10 Institution:Tokyo Institute of Technology

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  • Exercises in Fundamentals of Data Science

    2019.4 - 2024.10 Institution:Tokyo Institute of Technology

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