Free energy simulations

By and large, microscopic processes such as ion permeation, macromolecular conformational changes, ligand binding specificity, and protein-protein association are driven thermodynamically by the free energy (or potential of mean force) in diverse and complex environments such as bulk aqueous solution, the active site of an enzyme, the interior of an ion channel, or a bilayer membrane. A quantitative determination of free energies is thus a problem of central importance in theoretical biophysics. We are currently developing and extending current methodologies to allow precise and computationally inexpensive free energy calculations (see Pomes et al, 1999, Shobana et al, 2000, Wang et al, 2006, Deng and Roux, 2009).