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RESEARCH OBJECTIVES

My research focuses on multiscale modeling and molecular simulations, utilizing computational tools to address challenges in molecular recognition processes within biological and chemical systems for potential drug discovery and biomedical applications. I extensively employ all-atom molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) methods, integrated with data-driven approaches and state-of-the-art advanced enhanced sampling techniques, to provide molecular insights that complement and explain experimental observations.

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Protein-drug binding free energy and kinetics calculations

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 Biophysics of protein-protein interactions

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RNA small molecule interactions

RNA tetraloop folding-unfolding dynamics

Specefic ion channel permeation throgh synthetic channels

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"RNA Breathing" in protein-RNA complexes

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METHODS

Free energy calculations: Well-tempered Metadynamics, Parallel bias metadynamics, Funnel metadynamics, Multiple walker based approaches, OPES explore, Free energy pertubation, Umbrella Sampling, Combined sampling approaches

Kinetics calculations: Infrequent Metadynamics

PACKAGES

Classical molecular dynamics: GROMACS

Enhanced Sampling approaches: PLUMED, MLCOLVAR

QM/MM simulations: MiMiC, CPMD, CP2K

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