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\usepackage{amssymb} |
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\usepackage{color} |
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\usepackage{listings} |
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\usepackage{cite} |
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%\usepackage from oopseDoc.tex |
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\usepackage{times} |
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\usepackage{setspace} |
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\usepackage{tabularx} |
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\usepackage{longtable} |
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\lstset{language=C++,frame=TB,basicstyle=\footnotesize, % |
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captionpos=b, % |
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xleftmargin=0.1in,xrightmargin=0.1in, |
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keywordstyle=\footnotesize, breaklines=true, |
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abovecaptionskip=0.5cm, belowcaptionskip=0.5cm |
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} |
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\lstset{language=C++,frame=TB,basicstyle=\small\ttfamily, % |
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xleftmargin=0in, xrightmargin=0in, %captionpos=b,% breaklines=true, % |
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abovecaptionskip=0.5cm, belowcaptionskip=0.5cm} |
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\renewcommand{\lstlistingname}{Scheme} |
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\includeonly{preview} |
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\begin{document} |
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\newcolumntype{H}{p{0.75in}} |
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\newcolumntype{I}{p{5in}} |
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\renewcommand{\lstlistlistingname}{LISTS} |
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\renewcommand{\lstlistingname}{List} |
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\renewcommand{\lstlistlistingname}{SCHEMES} |
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\renewcommand{\lstlistingname}{Scheme} |
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\frontmatter |
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\work{Dissertation} % Change to ``Thesis'' for Master's thesis |
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\title{MOLECULAR DYNAMICS SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS} |
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\title{MOLECULAR DYNAMICS METHODOLOGY AND SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS} |
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\author{Teng Lin} |
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\degprior{B.Sc.} % All previously earned degrees |
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\degprior{B.S., B.E.} % All previously earned degrees |
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\degaward{Doctor of Philosophy} % What this paper is for |
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\advisor{J. Daniel Gezelter} % supervisor/director/advisor |
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%% \advisorB{} % second supervisor/director/advisor (if present) |
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%% \copypage % Uncomment if you want a copyright page |
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\begin{abstract} |
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|
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I present a dissertation utilizing an open source molecular dynamics |
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simulation package {\sc oopse}. |
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As a rapidly expanding interdisciplinary science bridging physics, |
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chemistry and biology, the study of soft condensed matter involves |
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the kinetics, dynamics and geometric structures of complex materials |
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like membrane, liquid crystal and polymers. These soft condensed |
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materials are distinguished by the unique physical properties on the |
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mesoscopic scale which can provide useful insights to understand the |
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basic physical principles linking the microscopic structure to the |
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macroscopic properties. Knowledge of the underlying physics is of |
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benefit to a wide range areas, such as the processing of |
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biocompatible materials and development of LCD display technologies. |
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Although the separation of the length scales allows statistical |
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mechanics to be applied, the interesting behavior of these systems |
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usually happens on time scale well beyond current computing power. |
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In order to simulate large soft condensed systems for long times |
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within a reasonable amount of computational time, some new |
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coarse-grained models are presented in this dissertation to describe |
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phospholipids and liquid crystals. Although these |
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models can be described using a small number of physical parameters, |
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it is not trivial to introduce rigid constraints between different |
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molecular fragments correctly and efficiently. Working with |
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colleagues, I developed a new molecular dynamics framework capable |
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of performing simulation on systems with orientational degrees of |
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freedom in a variety of ensembles. Using this new package, I studied |
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the structure, dynamics and transport properties of the biological |
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membranes as well as the the phase behavior of liquid |
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crystals. A new Langevin dynamics algorithm for arbitrary rigid |
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particles is also presented to mimic solvent effects which may |
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eventually expand the time scale of the simulation. |
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|
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\end{abstract} |
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\begin{dedication} |
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I would like to dedicate this dissertation to my wife, who has |
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helped and supported me throughout all of this work. |
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To my family. |
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\end{dedication} |
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\tableofcontents |
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\begin{acknowledge} % acknowledgments go here |
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\noindent I would like to thank my advisor, Dr. Gezelter for his inspiring and encouraging way |
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to guide me to a deeper understanding of knowledge work. Without his encouragement and constant |
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to guide me to a deeper understanding of molecular modeling. Without his encouragement and constant |
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guidance, I could not have finished this dissertation. I am also grateful to my colleagues |
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Charles F.~Vardeman II, Christopher J.~Fennell, Xiuquan Sun, Yang Zheng, Kyle Daily, |
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Kyle S.~Haygarth, Matthew A.~Meineke, Dan Combest, Pat Conforti, and Megan Sprague, |
