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Markov models of molecular conformation dynamics: simulation, analysis and experiments
(Freie Universität Berlin, DFG center Matheon)
Obtaining a mechanistic understanding of complex macromolecular rearrangements such as protein folding and transitions between different functional conformations is notoriously difficult for both simulation and experimental approaches. Molecular dynamics simulations are subject to sampling problems and are difficult to link to experimental data. Experiments cannot monitor structure and dynamics in detail simultaneously. In the recent years, we and others have developed the conformation dynamics approach which is a simulation and modeling framework, designed to overcome the aforementioned limitations. I will introduce the approach and cover the following topics:
•How can we efficiently explore state space using atomistic models and calculate free energy differences between states without knowing relevant reaction coordinates a priori?
•How can we calculate conformational transitions and associated rates or timescales on the milliseconds timescale if we can only afford nano to microseconds simulation lengths?
•How can we efficiently simulate on petascale computers without running into the scaling limits of MD simulations?
•How can we reconcile simulation data with kinetic ensemble experiments (e.g. T-jump, FCS, dynamical neutron scattering) and single-molecule experiments (single molecule FRET and pulling)?
We will illustrate the approach on macromolecular folding processes, conformational changes and ab initio dynamics of small molecules with high barriers.