From single molecule experiments to models of
Since a few years, experiments exist that allow the thermal fluctuations of single macromolecules to be probed. Examples are optical tweezers and atomic force microscopes that hold single molecules between an attachment point and a force sensor that detects the fluctuations of the intervening molecule. Another example is a single molecule FRET experiment where either immobilized or freely diffusing molecules are equipped with optical sensors that report on the distance between two chemical groups. These experiments deliver experimental "trajectories" of the molecule motion which allow important questions to be addressed: How many metastable states does the molecule have? What are their probabilities? What are the transition rates between them? What are their molecular structures? The challenge is to derive this information from trajectories where the high-dimensional molecular dynamics has been projected onto one or a few observable dimensions - a difficult inverse problem.
- Wu, H. and Noé, F. (2010) Probability Distance Based Compression of Hidden Markov Models. Multiscale Model. Simul., 8 . pp. 1838-1861.