trunk/tengDissertation/phdPreamble.tex

\documentclass[nosummary,dvips,noindentfirst]{ndthesis}
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\usepackage{tabularx}
\usepackage{longtable}
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\begin{document}

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\frontmatter
\work{Dissertation}  % Change to ``Thesis'' for Master's thesis
\title{MOLECULAR DYNAMICS METHODOLOGY AND 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 a rapidly expanding interdisciplinary science bridging physics,
chemistry and biology, the study of soft condensed matter involves
the kinetics, dynamics and geometric structures of complex materials
like membrane, liquid crystal and polymers. These soft condensed
materials 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 areas, such as the processing of
biocompatible materials and development of LCD display technologies.
Although the separation of the length scales allows statistical
mechanics to be applied, the interesting behavior of these systems
usually happens on time scale well beyond 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 are presented in this dissertation to describe
phospholipids and banana-shaped liquid crystals. Although these
models can be described using a small number of physical parameters,
it is not trivial to introduce 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 studied
the structure, dynamics and transport properties of the biological
membranes as well as the the phase behavior of banana shaped liquid
crystals. A new Langevin dynamics algorithm for arbitrary rigid
particles is also presented to mimic solvent effects 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
\listoftables        % out these two lines.
\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:	2913
Committed:	Fri Jun 30 03:19:40 2006 UTC (19 years, 4 months ago) by tim
Content type:	application/x-tex
File size:	4820 byte(s)
Log Message:	Version 0.95
#	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	2913	\lstset{language=C++,frame=TB,basicstyle=\small\ttfamily, %
14			xleftmargin=0in, xrightmargin=0in, %captionpos=b,% breaklines=true, %
15	tim	2909	abovecaptionskip=0.5cm, belowcaptionskip=0.5cm}
16			\renewcommand{\lstlistingname}{Scheme}
17	tim	2685	\includeonly{preview}
18
19			\begin{document}
20	tim	2805
21			\newcolumntype{A}{p{1.5in}}
22			\newcolumntype{B}{p{0.75in}}
23			\newcolumntype{C}{p{1.5in}}
24			\newcolumntype{D}{p{2in}}
25
26			\newcolumntype{E}{p{0.5in}}
27	tim	2810	\newcolumntype{F}{p{1.5in}}
28			\newcolumntype{G}{p{3.25in}}
29	tim	2805
30			\newcolumntype{H}{p{0.75in}}
31			\newcolumntype{I}{p{5in}}
32
33	tim	2880	\renewcommand{\lstlistlistingname}{SCHEMES}
34			\renewcommand{\lstlistingname}{Scheme}
35	tim	2685	\frontmatter
36			\work{Dissertation} % Change to ``Thesis'' for Master's thesis
37	tim	2907	\title{MOLECULAR DYNAMICS METHODOLOGY AND SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS}
38	tim	2685	\author{Teng Lin}
39	tim	2880	\degprior{B.S., B.E.} % All previously earned degrees
40	tim	2685	\degaward{Doctor of Philosophy} % What this paper is for
41			\advisor{J. Daniel Gezelter} % supervisor/director/advisor
42			%% \advisorB{} % second supervisor/director/advisor (if present)
43			\department{Chemistry and Biochemistry} % Dept. granting the degree
44			\maketitle % Uncomment to get the title page printed out
45			%% \copypage % Uncomment if you want a copyright page
46			\begin{abstract}
47
48	tim	2907	As a rapidly expanding interdisciplinary science bridging physics,
49			chemistry and biology, the study of soft condensed matter involves
50			the kinetics, dynamics and geometric structures of complex materials
51			like membrane, liquid crystal and polymers. These soft condensed
52			materials are distinguished by the unique physical properties on the
53			mesoscopic scale which can provide useful insights to understand the
54			basic physical principles linking the microscopic structure to the
55			macroscopic properties. Knowledge of the underlying physics is of
56			benefit to a wide range areas, such as the processing of
57			biocompatible materials and development of LCD display technologies.
58			Although the separation of the length scales allows statistical
59			mechanics to be applied, the interesting behavior of these systems
60			usually happens on time scale well beyond current computing power.
61			In order to simulate large soft condensed systems for long times
62			within a reasonable amount of computational time, some new
63			coarse-grained models are presented in this dissertation to describe
64			phospholipids and banana-shaped liquid crystals. Although these
65			models can be described using a small number of physical parameters,
66			it is not trivial to introduce rigid constraints between different
67			molecular fragments correctly and efficiently. Working with
68			colleagues, I developed a new molecular dynamics framework capable
69			of performing simulation on systems with orientational degrees of
70			freedom in a variety of ensembles. Using this new package, I studied
71	tim	2911	the structure, dynamics and transport properties of the biological
72			membranes as well as the the phase behavior of banana shaped liquid
73			crystals. A new Langevin dynamics algorithm for arbitrary rigid
74			particles is also presented to mimic solvent effects which may
75			eventually expand the time scale of the simulation.
76	tim	2878
77	tim	2685	\end{abstract}
78
79			\begin{dedication}
80
81	tim	2880	To my family.
82	tim	2685
83			\end{dedication}
84			\tableofcontents
85			\listoffigures % If you don't have any figures or tables, comment
86			\listoftables % out these two lines.
87			\lstlistoflistings
88
89			\begin{acknowledge} % acknowledgments go here
90
91			\noindent I would like to thank my advisor, Dr. Gezelter for his inspiring and encouraging way
92	tim	2878	to guide me to a deeper understanding of molecular modeling. Without his encouragement and constant
93	tim	2685	guidance, I could not have finished this dissertation. I am also grateful to my colleagues
94			Charles F.~Vardeman II, Christopher J.~Fennell, Xiuquan Sun, Yang Zheng, Kyle Daily,
95			Kyle S.~Haygarth, Matthew A.~Meineke, Dan Combest, Pat Conforti, and Megan Sprague,
96			who were always here for technical help and moral support. Last, but not least,
97	tim	2867	I thank my family: my fater, Zongzan Lin, and my mother, Rongying Chen,
98			for unconditional support and encouragement to pursue my dreams,
99			even when they went beyond boundaries of language and
100	tim	2690	geography. My wife, Xi, for her understanding and love during the past few years. Her support and
101	tim	2685	encouragement was in the end what made this dissertation possible.
102
103			\end{acknowledge}
104
105			\mainmatter
106	tim	2690	%\include{Introduction}
107			%\include{Methodology}
108			%\include{Lipid}
109			%\include{LiquidCrystal}
110			%\include{Conclusion}
111			%\include{Appendix}
112			%\include{phdBib}