Michael Forney, Department of Physics and Astronomy

Ioan Kosztin, Mentor

In order to establish the structure-function relationship of nanoscopic biomolecules, one needs to follow their dynamics on a mesoscopic time scale that is beyond the reach of current all-atom molecular dynamics (MD) simulations. A viable approach to this daunting problem is a multiscale modeling approach that requires as input the detailed free energy profile (potential of mean force [PMF]) of the system. In the present study we report PMF calculations based on a recently proposed method that employs fast (~10ns long) nonequilibrium MD simulations. Our PMF calculation method, which is more efficient than previously used ones, has yielded very good results for the folding/unfolding of deca-alanine and for the potassium ions transport through the gramicidin A channel protein.