Wolfsberg Fellows

Praveen Ranganath Prabhakar 2025-2026 

Research synopsis: 

In molecular dynamics (MD) simulations, one of the central challenges is the presence of a wide distribution of energy barriers in multiple dimensions that prevent adequate sampling of biologically relevant conformations on computationally affordable timescales. Praveen’s research in the Andricioaei group focuses on implementing enhanced/path sampling methods such as metadynamics, umbrella sampling and weighted ensemble simulations for overcoming these energetic and/or entropic bottlenecks. These techniques not only accelerate rare transitions, but also help in the computation of thermodynamic and kinetic properties. His research leverages these advanced methods to tackle problems that span the gamut from protein folding, to protein-ligand binding and to ribonucleic acid (RNA) conformational dynamics. In one example, in collaboration with the Tobias group, he employs MD simulations to model the translocation of solutes across the stratum corneum membrane, the outermost layer of the skin, and evaluate important properties such as the free energy cost of solute partitioning and position-dependent diffusion constants. Collectively, these research efforts are grounded in the framework of statistical mechanics, with the common goal of uncovering fundamental mechanisms that regulate biomolecular behavior, thereby pushing the boundaries of computational biophysics and opening avenues for novel scientific discoveries.