title: Free energy profiles from single-molecule pulling experiments.
abstract: Nonequilibrium pulling experiments provide detailed information about the thermodynamic and kinetic properties of molecules. We show that unperturbed free energy profiles as a function of molecular extension can be obtained rigorously from such experiments without using work-weighted position histograms. An inverse Weierstrass transform is used to relate the system free energy obtained from the Jarzynski equality directly to the underlying molecular free energy surface. An accurate approximation for the free energy surface is obtained by using the method of steepest descent to evaluate the inverse transform. The formalism is applied to simulated data obtained from a kinetic model of RNA folding, in which the dynamics consists of jumping between linker-dominated folded and unfolded free energy surfaces.
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, MD 20892-0520, USA. gerhard.hummer@nih.gov
authors.forename: Gerhard
authors.initials: G
authors.lastname: Hummer
authors.forename: Attila
authors.initials: A
authors.lastname: Szabo
mesh_terms: D003198:Computer Simulation; D019277:Entropy; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013314:Stress, Mechanical; D013816:Thermodynamics
chemical_list: D012313:RNA