Computational Molecular Biology Group, Institute of Mathematics and Computer Science, Free University of Berlin
The leading eigenvalues and corresponding eigenfunctions of the transfer operator are essential for the analysis of Molecular Dynamics simulations. As the transfer operator is a self-adjoint linear map, they satisfy a variational principle and can be approximated by the method of linear variation similar to the one used in quantum chemistry. In this talk, I will explain this approach and present some first applications to small peptide systems. I will also explain that Markov State Models are a special case for a specific choice of basis functions, but that more general basis sets may potentially provide better results. Finally, I will discuss what needs to be done in the future to make use of the method when the system size grows.
Jun 12, 2014 | 02:15 PM