Amal Vijay
Research Quest
My research interests are to understand how biomolecules recognize, respond, and transform within complex biological environments, and to translate this knowledge into therapeutic insight. Working at the interface of Computational Biomolecular Medicine and Quantum Biophysics, I aim to uncover the physical rules that govern molecular decisions—how an RNA folds, how a ligand binds, and how quantum-level effects shape biological outcomes.
A major part of my work integrates data-driven approaches with advanced molecular dynamics simulations. I utilize enhanced-sampling techniques with quantum biophysics tools to reveal energy landscapes of biological relevance and to predict the underlying mechanisms to predict & compliment the experimental observations.
My research is driven by a desire to make molecular modeling more predictive, interpretable, and impactful for biomedicine. By uniting physics-based simulations with data-guided learning, I strive to push computation toward actionable insights that can shape the next generation of therapeutic strategies.
Academic Bio
Amal completed his B.Sc. in Chemistry from Loyola College, Chennai, followed by his M.Sc. in Chemistry from the University of Hyderabad. He then earned his Ph.D. in Computational Biophysics from IISER Pune with Prof. Arnab Mukherjee, where he specialized in free-energy methods for biomolecular recognition. During his doctoral research, he received the Fulbright Fellowship, which enabled him to conduct research at UC Irvine with Prof. Ioan Andricioaei. He later completed his postdoctoral research in Computational Biomedicine at the Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich, Germany, under Prof. Paolo Carloni.
Educational Qualification
• Postdoctoral Researcher (2024-2025): Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich, Germany Advisor: Prof. Paolo Carloni • Fulbright Research Fellow: (2022-2023) University of California, Irvine (UC Irvine), USA Advisor: Prof. Ioan Andricioaei • Ph.D. Computational Biophysics (2019–2023): IISER Pune, Advisor: Prof. Arnab Mukherjee • M.Sc. Chemistry (2018): University of Hyderabad • B.Sc. Chemistry (2015): Loyola College, ChennaiPublications
- Vijay, A., Vijay, A., Salvadori, G., Biedermann, F., Rosetti, G., Carloni, P., Mandelli, D. (2025). Fine tuning of long-range interactions to describe the binding of adamantane and diamantane derivatives to a Cucurbit[7]uril-based synthetic receptor: Insights from metadynamics simulations based on a new force field. J. Chem. Phys. 163, 175102.
- Vijay, A., Mukherjee, A. (2024). Unraveling the folding-assisted unbinding mechanism of TCF with its binding partner β-catenin. Phys. Chem. Chem. Phys. 26 (25), 17481–17488.
- Vijay, A., Sreyas Adury, V. S., Mukherjee, A. (2023). Targeting RdRp of SARS-CoV-2 with De Novo Molecule Generation. ACS Applied Bio Materials, 27 (2), 609–616.
- Vijay, A., Mukherjee, A. (2023). Molecular insights into the stereospecificity of arginine in RNA tetraloop folding. Phys. Chem. Chem. Phys. 25 (16), 11301–11310.
- Sharma, R., Vijay, A., Chattopadhayay, S., Mukherjee, A., Talukdar, P. (2023). Self-assembled anion channel formation by bis(1,3-propanediol)-linked meta-dipropynylbenzene-based small molecules. Chem. Commun. 59, 3602–3605.
- Sharma, R., Vijay, A., Mukherjee, A., Talukdar, P. (2022). Bis(cholyl)-based chloride channels with oxalamide and hydrazide selectivity filters. Org. Biomol. Chem. 20, 2054–2058.
- Chowdhury, R., Sai Sreyas Adury, V., Vijay, A., Singh, R. K., Mukherjee, A. (2021). Atomistic de-novo inhibitor generation-guided drug repurposing for SARS-CoV-2 spike protein with free-energy validation by well-tempered metadynamics. Chemistry – An Asian Journal, 16, 1634–1642.
- Malla, J. A., Umesh, R. M., Vijay, A., Mukherjee, A., Lahiri, M., Talukdar, P. (2020). Apoptosis-inducing activity of a fluorescent barrel-rosette M⁺/Cl⁻ channel. Chemical Science, 11, 2420–2428.
Projects
- Selected for Fulbright – Nehru Doctoral Research Fellowship for research at the University of California, Irvine, for the year 2022–2023.
- Recipient, DBT-CTEP Travel grant, Ministry of Science and Technology, Government of India (June 2022)
- Recipient, CSIR Travel Grant, Ministry of Science and Technology, Government of India (May 2022)
- Recipient, Infosys Foundation Travel award, IISER Pune (March 2022)
- Qualified CSIR NET-JRF with All India rank-57
- Qualified GATE 2018 in Chemical Sciences with a 96.55 percentile score
- Gold Medalist in Physical Chemistry during Bachelor degree, Loyola College Chennai (August 2015)
- Rashtrapati Scout Award – An award presented by the President of India for extracurricular achievement in scouting. (March 2010)