News from Mar 08, 2014
Our paper "Variational Approach to Molecular Kinetics" has appeared online in JCTC. (http://pubs.acs.org/doi/abs/10.1021/ct4009156)
We use linear variational principle to estimate the eigenvectors and eigenvalues of the transfer operator and use this information to construct models of the conformational dynamics. The variational principle allows us to get away from the crisp discretizations used in Markov state models and develop basis sets which are more suited to represent the conformational changes in a molecule.
The method is quite analogous to the variational approach used in quantum chemistry to estimate the eigenstates of the Hamilton operator. However, in contrast to quantum mechanical methods, we do not calculate the matrix elements but rather estimate them from MD simulations.