Abstract
Single molecule experiments that can track individual trajectories of biomolecular processes provide a challenge for understanding how these stochastic trajectories relate to the global energy landscape. Using trajectories from a native structure based simulation, we use order parameters that accurately distinguish between protein folding mechanisms that involve a simple, single set of pathways versus a complex one with multiple sets of competing pathways. We show how the folding dynamics can be analyzed with replica correlation functions in a way that is compatible with single molecule experiments.
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