New Applications of Boxed Molecular Dynamics: Efficient Simulation of Rare Events

This work presents Boxed Molecular Dynamics (BXD), an efficient simulation tool for studying long time scale processes which are inaccessible to conventional methods of simulation. Boxed Molecular Dynamics is explained and introduced in the context of modelling the dynamics of proteins and peptides. Two major applications of Boxed Molecular Dynamics are reported. 1) - The mechanical unfolding of proteins induced by Atomic Force Microscopy methods is investigated. For the first time, experimental data is reproduced and unfolding pathways are investigated without the use of high artificial pulling forces which makes the simulation less realistic. 2) - A cheap and accurate in silico screening tool is developed to aid with the discovery and production of medicinal cyclic peptides. Enzymatic peptide cyclization is investigated by BXD and the ability of amino acid sequences to cyclize is predicted with an accuracy of 76 %.