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We introduce a rigorous method to microscopically compute the observableswhich characterize the thermodynamics and kinetics of rare macromoleculartransitions for which it is possible to identify a priori a slow reactioncoordinate. In order to sample the ensemble of statistically significantreaction pathways, we define a biased molecular dynamics (MD) in whichbarrier-crossing transitions are accelerated without introducing any unphysicalexternal force. In contrast to other biased MD methods, in the present approachthe systematic errors which are generated in order to accelerate the transitioncan be analytically calculated and therefore can be corrected for. This allowsfor a computationally efficient reconstruction of the free-energy profile as afunction of the reaction coordinate and for the calculation of thecorresponding diffusion coefficient. The transition path time can then bereadily evaluated within the Dominant Reaction Pathways (DRP) approach. Weillustrate and test this method by characterizing a thermally activatedtransition on a two-dimensional energy surface and the folding of a smallprotein fragment within a coarse-grained model.

Microscopically Computing Free-energy Profiles and Transition Path Time of Rare Macromolecular Transitions