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\begin{document} |
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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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\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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I present a dissertation utilizing an open source molecular dynamics |
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simulation package {\sc oopse}. |
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As an rapidly expanding interdisciplinary of physics, chemistry and |
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biology \emph{etc}, soft condensed matter science studies the |
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kinetics, dynamics and geometric structures of complex materials |
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like membrane, liquid crystal and polymers \emph{etc}. These soft |
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condensed matters are distinguished by the unique physical |
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properties on the mesoscopic scale which can provide useful insights |
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to understand the basic physical principles linking the microscopic |
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structure to the macroscopic properties. Knowledge of the underlying |
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physics is of benefit to a wide range of applications areas, such as |
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the processing of biocompatible materials and development of LCD |
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display technologies. Although the separation of the length scale |
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allows statistical mechanics to be applied, the interesting behavior |
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of these systems usually happens on the time scale well beyond the |
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current computing power. In order to simulate large soft condensed |
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systems for long times within a reasonable amount of computational |
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time, some new coarse-grained models were proposed in this |
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dissertation to describe phospholipids and banana-shaped liquid |
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crystals. Although these models can be described using a small |
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number of physical parameter, it is not trivial to maintain the |
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introducing rigid constraints between different molecular fragments |
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correctly and efficiently. Working with colleagues, I developed a |
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new molecular dynamics framework capable of performing simulation on |
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systems with orientational degrees of freedom in a variety of |
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ensembles. Using this new package, I study the structure, the |
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dynamics and transport properties of the biological membranes as |
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well as the the phase behavior of banana shaped liquid crystal. A |
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new Langevin dynamics algorithm for arbitrary rigid particles is |
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proposed to mimic solvent effect which may eventually expand the |
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time scale of the simulation. |
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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, |
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who were always here for technical help and moral support. Last, but not least, |
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I thank my family: my parents, Zongzan Lin, and Rongying Chen, |
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for unconditional support and encouragement to pursue my interests, |
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even when the interests went beyond boundaries of language and |
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I thank my family: my fater, Zongzan Lin, and my mother, Rongying Chen, |
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for unconditional support and encouragement to pursue my dreams, |
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even when they went beyond boundaries of language and |
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geography. My wife, Xi, for her understanding and love during the past few years. Her support and |
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encouragement was in the end what made this dissertation possible. |
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