MOLECULAR DYNAMICS SIMULATIONS IN THE STUDY OF BIOLOGICAL LIPID MEMBRANES

Abstract

Molecular dynamics simulations solve Newton’s equations of motion for a system of interactingatoms using the energy gradient calculated from a potential function which describes the system of atoms. Subsequently, the trajectories generated from the classical mechanical calculations are used to gain molecular-level insight into varying problems of biological interest. More specifically, we may link important macroscopic properties of proteins or membranes (composition, organization, folding, etc.) derived from experiments to properties at the molecular level arising from interactions between individual amino acids or lipids. The simulations in this thesis investigate the dynamics of lipid monolayers involved in the tear film lipid layer (eyes), where a new class of lipid is under investigation, and in pulmonary sufactant (lungs), which has been hypothesized to be inhibited by the presence of organic compounds in the vapors of electronic cigarettes. A preliminary analysis of a novel iso-area phase transition is also provided. In addition, α-synuclein, thought to be the primary purveyor of Parkinson’s disease is investigated and its mechanism of binding is elucidated.