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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.

Protein-drug binding free energy and kinetics calculations


Biophysics of protein-protein interactions


RNA small molecule interactions
RNA tetraloop folding-unfolding dynamics
Specefic ion channel permeation throgh synthetic channels

"RNA Breathing" in protein-RNA complexes


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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