http://www.syndicatemizzou.org Fri, 09 Jan 2009 22:44:12 GMT en-us 40 Center for eResearch Connecting you with the University of Missouri’s innovative research and creative activity http://www.syndicatemizzou.org/images/logo.png 384 80 http://syndicatemizzou.org/resources/urm2006/ipod/URM-Forney.m4v Education http://syndicatemizzou.org/resources/urm2006/ipod/URM-Forney.m4v ####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. 3 Mon, 13 Nov 2006 16:15:56 GMT