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MOLECULAR DYNAMICS SIMULATIONS OF LIPID BILAYERS IN MEGAVOLT
PER METER ELECTRIC FIELDS
by
Matthew James Ziegler
A Dissertation Presented to the
FACULTY OF THE GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(CHEMICAL ENGINEERING)
December 2008
Copyright 2008 Matthew James Ziegler
Object Description
| Title | Molecular dynamics simulations of lipid bilayers in megavolt per meter electric fields |
| Author | Ziegler, Matthew James |
| Author email | mjzglr@gmail.com; mjziegle@usc.edu |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Chemical Engineering |
| School | Viterbi School of Engineering |
| Date defended/completed | 2008-10-06 |
| Date submitted | 2008 |
| Restricted until | Unrestricted |
| Date published | 2008-12-12 |
| Advisor (committee chair) |
Vernier, P. Thomas Gundersen, Martin |
| Advisor (committee member) |
Shing, Katherine Warshel, Arieh |
| Abstract | 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 |
| Keyword | molecular dynamics; lipids; GROMACS; phosphatidylserine; phosphatidylcholine; electroporation; simulation; calcium binding; translocation; headgroup dipole angle; kinetics |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m1920 |
| Rights | Ziegler, Matthew James |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | http://www.usc.edu/isd/libraries/services/ask_a_librarian/email/ |
| Filename | etd-Ziegler-2481 |
| Archival file | uscthesesreloadpub_Volume23/etd-Ziegler-2481.pdf |
Description
| Title | Page 1 |
| Full text | MOLECULAR DYNAMICS SIMULATIONS OF LIPID BILAYERS IN MEGAVOLT PER METER ELECTRIC FIELDS by Matthew James Ziegler A Dissertation Presented to the FACULTY OF THE GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (CHEMICAL ENGINEERING) December 2008 Copyright 2008 Matthew James Ziegler |
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