Generating and Validating Transition Path Ensembles of Protein Folding

This thesis proposes to provide a unified and systematic strategy to overcome the second timescale in protein folding, by exploiting qualities and drawbacks of the Bias Functional Method and proposing new theoretical approaches to overcome its limitations. The first half of the thesis is dedicated to the development of theoretical solutions to the dependence of the Bias Functional Method on an a-priori defined collective coordinate and microscopic non-reversibility of the dynamics. The second part of the manuscript is devoted to applications of the BF method on two different proteins: Canine milk lysozyme and alpha1-antitrypsin (A1AT).