Amal Vijay
Scientist-C | Decision Unit 4: Systems Biology
Amal Vijay's research focuses on understanding biomolecular recognition through multiscale modelling and computer simulations, by integrating concepts from chemistry, biology, and statistical mechanics. The focus is to advance drug discovery, biomedical research, and predictive science through evidence-based and data-driven approaches.
Specific Interests
- Exploring rare-event conformational transitions through simulations
- Development and application of enhanced-sampling molecular dynamics techniques
- Kinetics and thermodynamics prediction of molecular events
- AI/ML approaches for biomolecular recognition and modeling
The group aims to provide molecular-level insights into biochemical and biophysical problems, focusing on the interactions and dynamics of proteins, nucleic acids, and engineered molecules through computational modeling and simulations.
Selected Publications
All Citations →- 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. Vijay A, Salvadori G, Biedermann F, Rosetti G, Carloni P, Mandelli D. The Journal of Chemical Physics. 2025;163:175102.
- Unraveling the folding-assisted unbinding mechanism of TCF with its binding partner β-catenin. Vijay A, Mukherjee A. Physical Chemistry Chemical Physics. 2024;26:17481–17488.
- Targeting RdRp of SARS-CoV-2 with de novo molecule generation. Vijay A, Sai Sreyas Adury V, Mukherjee A. ACS Applied Bio Materials. 2023;7(2):609–616.
- Molecular insights into the Stereospecificity of Arginine in RNA tetraloop folding. Vijay A, Mukherjee A. Physical Chemistry Chemical Physics. 2023;25:11301–11310.
- Self-assembled anion channel formation by bis(1,3-propanediol)-linked meta-dipropynylbenzene-based small molecules. Sharma R, Vijay A, Chattopadhayay S, Mukherjee A, Talukdar P. Chemical Communications. 2023;59:3602–3605.