XSEDE Scholars Program

Scholar Jorge Alarcon Ochoa

Jorge Alarcon Ochoa (Rensselaer Polytechnic University; undergraduate student; physics)

Project Title: Molecular Dynamics Simulations of Cosolvent Effects on Protein Stability

Research Advisor: Angel Garcia, Department of Physics, Rensselaer Polytechnic University


One of the main issues in molecular modeling is the inability of force fields to properly reproduce experimentally determined thermodynamics and conformations of biomolecules. For example, current force fields fail to reproduce the radius of gyration of proteins in their unfolded states, showing more compact states. This may be the result of overestimation of protein-protein interactions. We can remedy this discrepancy by modifying the interactions between amino acid cosolvents and proteins.

Through Molecular Dynamics simulations we will study cosolvent-protein interactions, and parameterize the force fields utilized for this work by matching extensive experimental data, including osmotic pressure and preferential interaction coefficients.