trunk/tengDissertation/phdPreamble.tex

\documentclass[nosummary,dvips,noindentfirst]{ndthesis}
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\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 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, the 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 proposed 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:	2907
Committed:	Thu Jun 29 16:57:37 2006 UTC (18 years ago) by tim
Content type:	application/x-tex
File size:	4824 byte(s)
Log Message:	more corrections
#	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	tim	2907	\title{MOLECULAR DYNAMICS METHODOLOGY AND SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS}
40	tim	2685	\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	2907	As a rapidly expanding interdisciplinary science bridging physics,
51			chemistry and biology, the study of soft condensed matter involves
52			the kinetics, dynamics and geometric structures of complex materials
53			like membrane, liquid crystal and polymers. These soft condensed
54			materials are distinguished by the unique physical properties on the
55			mesoscopic scale which can provide useful insights to understand the
56			basic physical principles linking the microscopic structure to the
57			macroscopic properties. Knowledge of the underlying physics is of
58			benefit to a wide range areas, such as the processing of
59			biocompatible materials and development of LCD display technologies.
60			Although the separation of the length scales allows statistical
61			mechanics to be applied, the interesting behavior of these systems
62			usually happens on time scale well beyond current computing power.
63			In order to simulate large soft condensed systems for long times
64			within a reasonable amount of computational time, some new
65			coarse-grained models are presented in this dissertation to describe
66			phospholipids and banana-shaped liquid crystals. Although these
67			models can be described using a small number of physical parameters,
68			it is not trivial to introduce rigid constraints between different
69			molecular fragments correctly and efficiently. Working with
70			colleagues, I developed a new molecular dynamics framework capable
71			of performing simulation on systems with orientational degrees of
72			freedom in a variety of ensembles. Using this new package, I studied
73			the structure, the dynamics and transport properties of the
74			biological membranes as well as the the phase behavior of banana
75			shaped liquid crystals. A new Langevin dynamics algorithm for
76			arbitrary rigid particles is proposed to mimic solvent effects which
77			may eventually expand the time scale of the simulation.
78	tim	2878
79	tim	2685	\end{abstract}
80
81			\begin{dedication}
82
83	tim	2880	To my family.
84	tim	2685
85			\end{dedication}
86			\tableofcontents
87			\listoffigures % If you don't have any figures or tables, comment
88			\listoftables % out these two lines.
89			\lstlistoflistings
90
91			\begin{acknowledge} % acknowledgments go here
92
93			\noindent I would like to thank my advisor, Dr. Gezelter for his inspiring and encouraging way
94	tim	2878	to guide me to a deeper understanding of molecular modeling. Without his encouragement and constant
95	tim	2685	guidance, I could not have finished this dissertation. I am also grateful to my colleagues
96			Charles F.~Vardeman II, Christopher J.~Fennell, Xiuquan Sun, Yang Zheng, Kyle Daily,
97			Kyle S.~Haygarth, Matthew A.~Meineke, Dan Combest, Pat Conforti, and Megan Sprague,
98			who were always here for technical help and moral support. Last, but not least,
99	tim	2867	I thank my family: my fater, Zongzan Lin, and my mother, Rongying Chen,
100			for unconditional support and encouragement to pursue my dreams,
101			even when they went beyond boundaries of language and
102	tim	2690	geography. My wife, Xi, for her understanding and love during the past few years. Her support and
103	tim	2685	encouragement was in the end what made this dissertation possible.
104
105			\end{acknowledge}
106
107			\mainmatter
108	tim	2690	%\include{Introduction}
109			%\include{Methodology}
110			%\include{Lipid}
111			%\include{LiquidCrystal}
112			%\include{Conclusion}
113			%\include{Appendix}
114			%\include{phdBib}