The dynamical response of molecular systems, when the potential energy function is perturbed at a microscopic level, is difficult to predict without a numerical or laboratory experiment.
This is due to the non-linearity and high-dimensionality of molecular systems.
An efficient investigation of such a behaviour is necessary to better understand the nature of molecules and to improve the predictability of Molecular Dynamics simulations.
In this thesis we propose a reweighting scheme for Markov State Models (MSMs), based on the Girsanov theorem, that permits to reduce the computational cost of the analysis when the potential energy function of a molecule is perturbed.
The method has been successfully extended and implemented with metadynamics, in order to build the MSM of a molecular system in a significantly shorter computational time compared to a standard unbiased MD simulation.
We also propose a new method to discretize the infinitesimal generator into a rate matrix, that could be used to efficiently study Hamiltonian perturbations as well.
XI, 155 Seiten
markov state models
500 Natural sciences and mathematics::540 Chemistry and allied sciences::541 Physical and theoretical chemistry
Reweighting methods for Molecular Dynamics
Biologie, Chemie, Pharmazie