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Center for Nonlinear Studies |
Technology has brought us today to the stage where one can investigate biomolecules at the single-molecule level in experiments or computer simulations. Fluctuations play such an important role at the nanometer scale of biomolecules that the theory of nonequilibrium statistical mechanics is indispensable for analyzing the results of these experiments and simulations. This talk will show how one can use the recently discovered nonequilibrium work relation to calculate free energy differences, or potentials of mean force, from molecular dynamics simulations of biomolecules. Related theoretical and practical issues will be discussed, along with applications to membrane channel conduction and polypeptide folding/unfolding.