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 March 13, 2014 | 13:00 | Seminar Room 424/8

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The potential energy surface (PES) of large molecules can be described as a 3n dimensional surface, where n describes the number of atoms; n can vary from 1000 to 10000. Thus such PES contains more than 10^100 minima. This huge number can not be sampled by any computational method. However it is known that proteins at natural environment adopt the global minima structure. This lecture will describe three methods to reveal the global minima of proteins: (1) the usages of the RRKM/MD hybrid simulations for exploring PES and dynamics of small molecules; (2) usage of MD simulations for prediction of mass spectrometry dynamics; and (3) usage of smoothing surface methods and simulated annealing for prediction of final structures at mass spectrometry experiments, and the usage of PES in behavioral studies.