trunk/tengDissertation/phdPreamble.tex

\documentclass[nosummary,dvips,noindentfirst]{ndthesis}
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\usepackage{setspace}
\usepackage{tabularx}
\usepackage{longtable}
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        captionpos=b, %
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\begin{document}

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\renewcommand{\lstlistlistingname}{SCHEMES}
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\frontmatter
\work{Dissertation}  % Change to ``Thesis'' for Master's thesis
\title{MOLECULAR DYNAMICS SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS}
\author{Teng Lin}
\degprior{B.S., B.E.}                 % All previously earned degrees
\degaward{Doctor of Philosophy}  % What this paper is for
\advisor{J. Daniel Gezelter} % supervisor/director/advisor
%% \advisorB{}            % second supervisor/director/advisor (if present)
\department{Chemistry and Biochemistry}      % Dept. granting the degree
\maketitle                % Uncomment to get the title page printed out
%% \copypage              % Uncomment if you want a copyright page
\begin{abstract}

As an rapidly expanding interdisciplinary of physics, chemistry and
biology \emph{etc}, soft condensed matter science studies the
kinetics, dynamics and geometric structures of complex materials
like membrane,liquid crystal and polymers \emph{etc}. These soft
condensed matters are distinguished by the unique physical
properties on the mesoscopic scale which can provide useful insights
to understand the basic physical principles linking the microscopic
structure to the macroscopic properties. Knowledge of the underlying
physics is of benefit to a wide range of applications areas, such as
the processing of biocompatible materials and development of LCD
display technologies. Although the separation of the length scale
allows statistical mechanics to be applied, the interesting behavior
of these systems usually happens on the time scale well beyond the
current computing power. In order to simulate large soft condensed
systems for long times within a reasonable amount of computational
time, some new coarse-grained models were proposed in this
dissertation to describe phosphlipids and banana-shaped liquid
crystals. Although these models can be described using a small
number of physical parameter, it is not trivial to maintain the
introducing rigid constraints between different molecular fragments
correctly and efficiently. Working with colleagues, I developed a
new molecular dynamics framework capable of performing simulation on
systems with orientational degrees of freedom in a variety of
ensembles. Using this new package, I study the structure, the
dynamics and transport properties of the biological membranes as
well as the the phase behavior of banana shaped liquid crystal. A
new Langevin dynamics algorithm for arbitrary rigid particles is
proposed to mimic solvent effect which may eventually expand the
time scale of the simulation.

\end{abstract}

\begin{dedication}

To my family.

\end{dedication}
\tableofcontents
\listoffigures          % If you don't have any figures or tables, comment
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\lstlistoflistings

\begin{acknowledge}    % acknowledgments go here

    \noindent I would like to thank my advisor, Dr. Gezelter for his inspiring and encouraging way
    to guide me to a deeper understanding of molecular modeling. Without his encouragement and constant
    guidance, I could not have finished this dissertation. I am also grateful to my colleagues
    Charles F.~Vardeman II, Christopher J.~Fennell, Xiuquan Sun, Yang Zheng, Kyle Daily,
    Kyle S.~Haygarth, Matthew A.~Meineke, Dan Combest, Pat Conforti, and Megan Sprague,
    who were always here for technical help and moral support. Last, but not least,
    I thank my family: my fater, Zongzan Lin, and my mother, Rongying Chen,
    for unconditional support and encouragement to pursue my dreams,
    even when they went beyond boundaries of language and
    geography. My wife, Xi, for her understanding and love during the past few years. Her support and
    encouragement was in the end what made this dissertation possible.

\end{acknowledge}

\mainmatter
%\include{Introduction}
%\include{Methodology}
%\include{Lipid}
%\include{LiquidCrystal}
%\include{Conclusion}
%\include{Appendix}
%\include{phdBib}
Revision:	2880
Committed:	Thu Jun 22 22:19:02 2006 UTC (18 years ago) by tim
Content type:	application/x-tex
File size:	4840 byte(s)
Log Message:	finish conclusion; some format checking correction
#	User	Rev	Content
1	tim	2685	\documentclass[nosummary,dvips,noindentfirst]{ndthesis}
2			\usepackage{graphicx}
3			\usepackage{psfrag}
4			\usepackage{amsmath}
5			\usepackage{amssymb}
6			\usepackage{color}
7			\usepackage{listings}
8	tim	2730	%\usepackage from oopseDoc.tex
9			\usepackage{times}
10			\usepackage{setspace}
11			\usepackage{tabularx}
12			\usepackage{longtable}
13	tim	2834	\lstset{language=C++,frame=TB,basicstyle=\footnotesize, %
14	tim	2830	captionpos=b, %
15	tim	2836	xleftmargin=0.1in,xrightmargin=0.1in,
16	tim	2834	keywordstyle=\footnotesize, breaklines=true,
17	tim	2830	abovecaptionskip=0.5cm, belowcaptionskip=0.5cm
18			}
19	tim	2685	\includeonly{preview}
20
21			\begin{document}
22	tim	2805
23			\newcolumntype{A}{p{1.5in}}
24			\newcolumntype{B}{p{0.75in}}
25			\newcolumntype{C}{p{1.5in}}
26			\newcolumntype{D}{p{2in}}
27
28			\newcolumntype{E}{p{0.5in}}
29	tim	2810	\newcolumntype{F}{p{1.5in}}
30			\newcolumntype{G}{p{3.25in}}
31	tim	2805
32			\newcolumntype{H}{p{0.75in}}
33			\newcolumntype{I}{p{5in}}
34
35	tim	2880	\renewcommand{\lstlistlistingname}{SCHEMES}
36			\renewcommand{\lstlistingname}{Scheme}
37	tim	2685	\frontmatter
38			\work{Dissertation} % Change to ``Thesis'' for Master's thesis
39			\title{MOLECULAR DYNAMICS SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS}
40			\author{Teng Lin}
41	tim	2880	\degprior{B.S., B.E.} % All previously earned degrees
42	tim	2685	\degaward{Doctor of Philosophy} % What this paper is for
43			\advisor{J. Daniel Gezelter} % supervisor/director/advisor
44			%% \advisorB{} % second supervisor/director/advisor (if present)
45			\department{Chemistry and Biochemistry} % Dept. granting the degree
46			\maketitle % Uncomment to get the title page printed out
47			%% \copypage % Uncomment if you want a copyright page
48			\begin{abstract}
49
50	tim	2878	As an rapidly expanding interdisciplinary of physics, chemistry and
51			biology \emph{etc}, soft condensed matter science studies the
52			kinetics, dynamics and geometric structures of complex materials
53			like membrane,liquid crystal and polymers \emph{etc}. These soft
54			condensed matters are distinguished by the unique physical
55			properties on the mesoscopic scale which can provide useful insights
56			to understand the basic physical principles linking the microscopic
57			structure to the macroscopic properties. Knowledge of the underlying
58			physics is of benefit to a wide range of applications areas, such as
59			the processing of biocompatible materials and development of LCD
60			display technologies. Although the separation of the length scale
61			allows statistical mechanics to be applied, the interesting behavior
62			of these systems usually happens on the time scale well beyond the
63			current computing power. In order to simulate large soft condensed
64			systems for long times within a reasonable amount of computational
65			time, some new coarse-grained models were proposed in this
66			dissertation to describe phosphlipids and banana-shaped liquid
67			crystals. Although these models can be described using a small
68			number of physical parameter, it is not trivial to maintain the
69	tim	2880	introducing rigid constraints between different molecular fragments
70			correctly and efficiently. Working with colleagues, I developed a
71			new molecular dynamics framework capable of performing simulation on
72	tim	2878	systems with orientational degrees of freedom in a variety of
73			ensembles. Using this new package, I study the structure, the
74			dynamics and transport properties of the biological membranes as
75			well as the the phase behavior of banana shaped liquid crystal. A
76			new Langevin dynamics algorithm for arbitrary rigid particles is
77			proposed to mimic solvent effect which may eventually expand the
78			time scale of the simulation.
79
80	tim	2685	\end{abstract}
81
82			\begin{dedication}
83
84	tim	2880	To my family.
85	tim	2685
86			\end{dedication}
87			\tableofcontents
88			\listoffigures % If you don't have any figures or tables, comment
89			\listoftables % out these two lines.
90			\lstlistoflistings
91
92			\begin{acknowledge} % acknowledgments go here
93
94			\noindent I would like to thank my advisor, Dr. Gezelter for his inspiring and encouraging way
95	tim	2878	to guide me to a deeper understanding of molecular modeling. Without his encouragement and constant
96	tim	2685	guidance, I could not have finished this dissertation. I am also grateful to my colleagues
97			Charles F.~Vardeman II, Christopher J.~Fennell, Xiuquan Sun, Yang Zheng, Kyle Daily,
98			Kyle S.~Haygarth, Matthew A.~Meineke, Dan Combest, Pat Conforti, and Megan Sprague,
99			who were always here for technical help and moral support. Last, but not least,
100	tim	2867	I thank my family: my fater, Zongzan Lin, and my mother, Rongying Chen,
101			for unconditional support and encouragement to pursue my dreams,
102			even when they went beyond boundaries of language and
103	tim	2690	geography. My wife, Xi, for her understanding and love during the past few years. Her support and
104	tim	2685	encouragement was in the end what made this dissertation possible.
105
106			\end{acknowledge}
107
108			\mainmatter
109	tim	2690	%\include{Introduction}
110			%\include{Methodology}
111			%\include{Lipid}
112			%\include{LiquidCrystal}
113			%\include{Conclusion}
114			%\include{Appendix}
115			%\include{phdBib}