| Recent advances in computing technology have facilitated the application of simulations to studying biological systems at the atomic level. In particular atomistic molecular dynamics provide an opportunity to model systems that are unobservable through conventional experimental methods as well as supplement understanding of observations. In this thesis molecular dynamics were applied to study biological cell membranes, specifically lipid bilayers, the primary constituent of the cell membrane, in electric fields, and to understand the mechanism and events associated with electroporation. Electroporation is a widely used experimental and commercial technique for introducing normally excluded compounds such as DNA, RNA, ions, drugs, and other chemicals into cells. Traditional electroporation utilizes kilovolt-per-meter electric fields applied on the order of microseconds that disrupt and scramble the cell membrane and allow diffusive entry, however, ultra-short nanosecond pulses at megavolt-per-meter fields produce different effects in cells which remain largely uncharacterized. One such effect, the migration of the negatively charged lipid phosphatidylserine from the inner to outer leaflet of the cell, is of particular biological interest because of its association with cell apoptosis, or programmable cell death. Control of such an event could be useful in developing a targeted treatment for removing unwanted cells such as tumors or melanoma.;In this thesis I begin by introducing electroporation and its history and explain how molecular dynamics and its techniques can help advance our understanding of the field. In the following chapters, consisting of peer reviewed and submitted journal articles loosely tied together, I explore the mechanism of phosphatidylserine translocation induced by nanosecond pulses in megavolt-per-meter electric fields, and correlate experimental data and anecdotal evidence of phosphatidylserine translocation in vitro with a detailed molecular mechanism provided by simulations. Upon developing this relationship, I further explore the more generic mechanism of electroporation by simulating the behavior of lipids of differing composition and introduce the concept of a minimum porating electric field to aid comparison. Next I probe into the detailed structure of an electropore, focusing specifically on the alignment of both the lipid headgroups and water dipoles along the pore walls and unperturbed sections of the bilayer. I conclude by studying the lipid structural changes caused by the introduction of calcium ions to the system, as well as the kinetics of calcium binding to lipid bilayers. |
