Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations

2013-06-26Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. ❧ Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. ❧ In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant system where lipids can become damaged or severely impacted from interacting with reactive oxygen species, and these events become more frequent with age. The results are then compared to experiments where we show agreement between our simulations, theoretical models, and experiments with peroxidized cells in our lab. In Chapter 3 I outline a set of unique metrics which can be used to quantitatively measure the life cycle of a discrete electropore for the first time, across multiple lipid species, and I compare these results to analytical models where we find good agreement with theory. In Chapter 4 I use the life cycle of an electropore as a tool to measure the effects of electrolyte and lipid headgroup charge on electroporation compared to electrolyte-free and zwitterionic systems, in addition to presenting ion binding isotherms to determine the validity of our simulated electrolyte models. Chapters 5 and 6 focus on the roles of water and lipid respectively on electroporation using simplified water:vacuum systems, osmotic swelling simulations, systems at varying temperature, and systems where we successfully modulated the electropore radius using customized time-dependent electric fields. I conclude this dissertation with a brief summary of these studies followed by a short outlook on the future of electroporation simulations as a whole