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You searched for +publisher:"University of Southern California" +contributor:("Vernier, Paul Thomas"). Showing records 1 – 2 of 2 total matches.

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University of Southern California

1. Ho, Ming-Chak. Molecular simulations of water and monovalent ion dynamics in the electroporation of phospholipid bilayers.

Degree: PhD, Physics, 2014, University of Southern California

Electroporation provides a controllable method to introduce foreign substances into living cells. It is widely used by researchers in cell biology and the medical field to manipulate biological systems at the cellular level. For decades, electroporation has been studied extensively through experiments and theoretical models, and electroporation‐based technologies have been improved substantially with these efforts. One of the issues in utilizing electroporation is the lack of understanding in the phenomenon’s molecular mechanism and the microscopic details, mainly due to the difficulty in the direct experimental observation of the nanosecond‐scale electropore formation process and the nanometer‐sized electropore structure. To overcome this issue, Molecular Dynamics (MD) simulation has become one of the major tools to study electroporation at the microscopic level. ❧ Recent advancements of high performance computing, such as the increase in processing power, developments in algorithms and parallelization, have improved the efficiency of MD simulation substantially. Due to these advancements, MD simulation has become a popular tool for studying systems that are composed of biomolecules. For nearly a decade of effort, MD simulation revealed many different aspects of electroporation and it provided a molecular description of the process. Using MD simulation, we are able to observe the events during the electropore formation and annihilation, as well as the transport processes of molecules through the electropore. In addition, MD simulation provides a platform to study the molecular structure of electropore, and the associated energetic. ❧ My dissertation is organized as the follows: Chapter 1 provides the motivation of this research by discussing the applications of electroporation‐based technology, electroporation experiments, and the existing continuum model that describes electroporation. Chapter 2 introduces the MD formalism, models, and various algorithms used in our MD simulation. I will also discuss some of the previous MD studies of electroporation and their significances at the end of Chapter 2. In Chapter 3, we will examine the dynamics of water bridge during different stages of electroporation, and delineate the role of water molecules in electroporation by comparing the lipid bilayer system with an artificial water‐vacuum‐water system. In Chapter 4, we will examine the steady state of an electropore in lipid bilayer and evaluate the pore conductance of ions. The pore conductance values obtained from the simulations can be compared with those obtained by experiments. In Chapter 5, we will examine the effects that monovalent ions impose on lipid bilayer and electropore formation. We will also examine the pore conductance of ions under various ion concentrations, and the PS translocation process. At the end, I will summarize the findings in our research and provide a short outlook on MD simulation in the study of electroporation. Advisors/Committee Members: Gundersen, Martin A. (Committee Chair), Vernier, Paul Thomas (Committee Member), Däppen, Werner (Committee Member), Dappen, Werner (Committee Member), Daeppen, Werner (Committee Member), Haas, Stephan W. (Committee Member), Malmstadt, Noah (Committee Member).

Subjects/Keywords: molecular dynamics; electropermeabilization; monovalent salt; cell membrane; electropore

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Ho, M. (2014). Molecular simulations of water and monovalent ion dynamics in the electroporation of phospholipid bilayers. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/376394/rec/4198

Chicago Manual of Style (16th Edition):

Ho, Ming-Chak. “Molecular simulations of water and monovalent ion dynamics in the electroporation of phospholipid bilayers.” 2014. Doctoral Dissertation, University of Southern California. Accessed April 26, 2019. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/376394/rec/4198.

MLA Handbook (7th Edition):

Ho, Ming-Chak. “Molecular simulations of water and monovalent ion dynamics in the electroporation of phospholipid bilayers.” 2014. Web. 26 Apr 2019.

Vancouver:

Ho M. Molecular simulations of water and monovalent ion dynamics in the electroporation of phospholipid bilayers. [Internet] [Doctoral dissertation]. University of Southern California; 2014. [cited 2019 Apr 26]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/376394/rec/4198.

Council of Science Editors:

Ho M. Molecular simulations of water and monovalent ion dynamics in the electroporation of phospholipid bilayers. [Doctoral Dissertation]. University of Southern California; 2014. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/376394/rec/4198


University of Southern California

2. Levine, Zachary Alan. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations.

Degree: PhD, Physics, 2013, University of Southern California

Computer 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,… Advisors/Committee Members: El-Naggar, Mohamed Y. (Committee Chair), Vernier, Paul Thomas (Committee Member), Nakano, Aiichiro (Committee Member), Haas, Stephan W. (Committee Member), Malmstadt, Noah (Committee Member).

Subjects/Keywords: electroporation; electropermeabilization; electroperturbation; electrochemotherapy; lipid bilayer; lipid; phospholipid; molecular dynamics; simulation; biophysics; physics; membrane; membrane biology; membrane biophysics; DNA transfection; electrogenetherapy; pulsed power

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Levine, Z. A. (2013). Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/280283/rec/7419

Chicago Manual of Style (16th Edition):

Levine, Zachary Alan. “Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations.” 2013. Doctoral Dissertation, University of Southern California. Accessed April 26, 2019. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/280283/rec/7419.

MLA Handbook (7th Edition):

Levine, Zachary Alan. “Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations.” 2013. Web. 26 Apr 2019.

Vancouver:

Levine ZA. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations. [Internet] [Doctoral dissertation]. University of Southern California; 2013. [cited 2019 Apr 26]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/280283/rec/7419.

Council of Science Editors:

Levine ZA. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations. [Doctoral Dissertation]. University of Southern California; 2013. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/280283/rec/7419

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