Abhishek Singharoy, Assistant Professor, Center for Applied Structural Discovery, Biodesign Institute at Arizona State University.

Computing Free-Energy Landscapes from Molecular Dynamics Simulations

The most probable pathways of structural transition in biomolecular complexes follow minimum free-energy pathways. Employing an implicit scheme for solving the Langevin dynamics equation, called the string method, these pathways are determined for structural transitions in molecular motors. The underlying multidimensional thermodynamic landscape is probed to determine experimentally measurable quantities such as, binding affinity, turnover rates, and energy conversion efficiencies.