In single-molecule experiments forces can be exerted directly on individual molecules and their response can be followed as a function of time. These experiments reveal fundamentally novel and unique information on the structure, dynamics, and interactions of individual biomolecules. Theory of single molecule force spectroscopy. In collaboration with Dr. Szabo (NIDDK, NIH), we have continued our development of formalisms to extract accurate kinetic and thermodynamic information from single-molecule force spectroscopy experiments. In such molecular pulling experiments, one can transform the measured force-extension curves into Helmholtz free energies of the entire system with the help of the Jarzynski identity. We could show how these free energies can be transformed into the underlying molecular free energy surface, which is the quantity of interest. A paper resulting from this work is currently under review. Controlled molecular dynamics. We developed a reverse integration approach for the exploration of low-dimensional free energy landscapes (Frewen et al., J. Chem. Phys. 2010). We show that coarse reverse integration enables efficient navigation on the landscape terrain: Escape from local effective potential wells, detection of saddle points, and identification of significant transition paths between wells. While derived originally for simulations, single-molecule manipulation devices, and in particular optical tweezers, make it possible to use the same methodology also in experiment.
| Mittal, Jeetain; Hummer, Gerhard (2012) Pair diffusion, hydrodynamic interactions, and available volume in dense fluids. J Chem Phys 137:034110 |
| Best, Robert B; Hummer, Gerhard (2011) Diffusion models of protein folding. Phys Chem Chem Phys 13:16902-11 |
| Hummer, Gerhard (2010) Catching a protein in the act. Proc Natl Acad Sci U S A 107:2381-2 |
| Hummer, Gerhard; Szabo, Attila (2010) Free energy profiles from single-molecule pulling experiments. Proc Natl Acad Sci U S A 107:21441-6 |
| Frewen, Thomas A; Hummer, Gerhard; Kevrekidis, Ioannis G (2009) Exploration of effective potential landscapes using coarse reverse integration. J Chem Phys 131:134104 |
| Berezhkovskii, Alexander; Hummer, Gerhard; Szabo, Attila (2009) Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J Chem Phys 130:205102 |
| Best, Robert B; Hummer, Gerhard (2009) Biochemistry. Unfolding the secrets of calmodulin. Science 323:593-4 |
| Dudko, Olga K; Hummer, Gerhard; Szabo, Attila (2008) Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proc Natl Acad Sci U S A 105:15755-60 |
