Research Projects

Understanding folding/unfolding dynamics of peptides/proteins is extremely crucial for applications in drug delivery, bio-sensing and also to understand mechanism of protein folding and aggregation. However, simulating such dynamics is extremely challenging due to the long time scales of folding and/or presence of large free energy barriers. Metropolis Monte Carlo (MC) simulations with various biasing techniques have been traditionally used to overcome these free energy barriers. However, at temperatures near folding, the Boltzmann acceptance probability becomes negligible. Consequently, sampling of low energy folded states of the protein is very difficult resulting in inaccurate estimation of free energies and the equilibrium of the system. In the current proposal, we propose to modify an existing non-Boltzmann technique known as Wang-Landau sampling to understand the dynamics and to quantify the free energy barriers for protein folding/unfolding.

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