Berlin 2015 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 3: Statistical Physics of Biological Systems I (joint DY/BP/CPP)

BP 3.8: Vortrag

Montag, 16. März 2015, 11:45–12:00, BH-N 243

Variational approach to molecular dynamics — •Bettina Keller — Freie Universität Berlin, Institut für Chemie und Biochemie, Takustraße 3, 14195 Berlin

The eigenvalues and eigenfunctions of the classical molecular dynamics propagator contain the essential information about the molecular thermodynamics and kinetics. A matrix representation of the propagator can be constructed by partitioning the conformational space into discrete states and estimating the state-to-state transition probabilities from molecular dynamics simulations, yielding a so-called Markov state model (MSM). The precision of an MSM depends sensitively on on how well the discretization reproduces the shape of the dominant eigenfunctions. The difficulty to find a suitable discretization has limited the routine use of MSMs. Moreover, most discretizations are data-driven, impairing the comparison between MSMs and the interpretation of the eigenvectors in terms of structural transitions.

Using a recently published variational approach, it is possible to construct a matrix representation of the propagator using an arbitrary basis set, allowing to use basis functions with gentle slopes. This reduces the discretization error. More importantly, the user can define basis sets which have a chemical meaning and can be used for entire classes of molecules, thereby allowing for direct comparison of the kinetic models. I will give an overview of the variational principle for the classical molecular dynamics propagator and propose a basis set for peptide dynamics which is based on the dominant eigenfunctions of individual amino acids