メンバー
Abdul Raafik Arattu Thodika
Education
| 2026 | Ph. D. (Chemistry), University of Texas at Arlington, Texas, USA |
| 2020 | BS-MS dual degree (Chemistry), Indian Institute of Science Education and Research – Pune, Maharashtra, India |
Research Experience
| 2026-present | Postdoctoral Researcher, Quantum Mathematical Science Team, RIKEN iTHEMS, Wako, Japan |
| 2026-present | Postdoctoral Researcher, Theoretical Molecular Science Laboratory, RIKEN PRI, Wako, Japan |
| 2022-2026 | Research Assistant, Kwangho Nam Group, University of Texas at Arlington, Texas, USA |
| 2021-2022 | Teaching Assistant, Dept. Of Chemistry and Biochemistry, University of Texas at Arlington, Texas, USA |
Research Projects
- Machine-Learning Potential Architectures for Free-Energy Simulations of Condensed-Phase Reactions
- QM/MM Molecular Dynamics Studies of Enzyme-Catalyzed Phosphoryl-Transfer Reactions
- QM/MM Ground-State Energy Calculations Using Quantum Computers
Relevant Publications
- Arattu Thodika, A. R.; Panda, S. K.; Pan, X.; Shao, Y.; Nam, K. Accurate and Time-Efficient Condensed-Phase Free Energy Simulations with Reaction Specific Δ-Machine Learning Potentials in CHARMM. J. Chem. Theory Comput.(2026).
https://doi.org/10.1021/acs.jctc.6c00798 - Arattu Thodika, A. R.; Pan, X.; Shao, Y.; Nam, K. Machine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions. J. Chem. Theory Comput., 21, 817-832 (2025).
https://doi.org/10.1021/acs.jctc.4c01487 - Nam, K.; Thodika, A. R. A.; Tischlik, S.; Phoeurk, C.; Nagy, T. M.; Schierholz, L.; Ådén, J.; Rogne, P.; Drescher, M.; Sauer-Eriksson, A. E.; Wolf-Watz, M. Magnesium Induced Structural Reorganization in the Active Site of Adenylate Kinase. Sci. Adv., 10, eado5504 (2024).
https://doi.org/10.1126/sciadv.ado5504 - Suh, D.; Arattu Thodika, A. R.; Kim, S.; Nam, K.; Im, W. CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. J. Chem. Theory Comput., 20, 5337–5351 (2024).
https://doi.org/10.1021/acs.jctc.4c00439 - Nam, K.; Arattu Thodika, A. R.; Grundström, C.; Sauer, U. H.; Wolf-Watz, M. Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. J. Chem. Inf. Model., 64, 150–163 (2024).
https://doi.org/10.1021/acs.jcim.3c01618
