trunk/tengDissertation/phdPreamble.tex

\documentclass[nosummary,dvips,noindentfirst]{ndthesis}
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\usepackage{cite}
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\usepackage{setspace}
\usepackage{tabularx}
\usepackage{longtable}
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        xleftmargin=0in, xrightmargin=0in, %captionpos=b,% breaklines=true, %
        abovecaptionskip=0.5cm, belowcaptionskip=0.5cm}
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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 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 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:	2941
Committed:	Mon Jul 17 20:01:05 2006 UTC (17 years, 11 months ago) by tim
Content type:	application/x-tex
File size:	4810 byte(s)
Log Message:	references corrections
#	Content
1	\documentclass[nosummary,dvips,noindentfirst]{ndthesis}
2	\usepackage{graphicx}
3	\usepackage{psfrag}
4	\usepackage{amsmath}
5	\usepackage{amssymb}
6	\usepackage{color}
7	\usepackage{listings}
8	\usepackage{cite}
9	%\usepackage from oopseDoc.tex
10	\usepackage{times}
11	\usepackage{setspace}
12	\usepackage{tabularx}
13	\usepackage{longtable}
14	\lstset{language=C++,frame=TB,basicstyle=\small\ttfamily, %
15	xleftmargin=0in, xrightmargin=0in, %captionpos=b,% breaklines=true, %
16	abovecaptionskip=0.5cm, belowcaptionskip=0.5cm}
17	\renewcommand{\lstlistingname}{Scheme}
18	\includeonly{preview}
19
20	\begin{document}
21
22	\newcolumntype{A}{p{1.5in}}
23	\newcolumntype{B}{p{0.75in}}
24	\newcolumntype{C}{p{1.5in}}
25	\newcolumntype{D}{p{2in}}
26
27	\newcolumntype{E}{p{0.5in}}
28	\newcolumntype{F}{p{1.5in}}
29	\newcolumntype{G}{p{3.25in}}
30
31	\newcolumntype{H}{p{0.75in}}
32	\newcolumntype{I}{p{5in}}
33
34	\renewcommand{\lstlistlistingname}{SCHEMES}
35	\renewcommand{\lstlistingname}{Scheme}
36	\frontmatter
37	\work{Dissertation} % Change to ``Thesis'' for Master's thesis
38	\title{MOLECULAR DYNAMICS METHODOLOGY AND SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS}
39	\author{Teng Lin}
40	\degprior{B.S., B.E.} % All previously earned degrees
41	\degaward{Doctor of Philosophy} % What this paper is for
42	\advisor{J. Daniel Gezelter} % supervisor/director/advisor
43	%% \advisorB{} % second supervisor/director/advisor (if present)
44	\department{Chemistry and Biochemistry} % Dept. granting the degree
45	\maketitle % Uncomment to get the title page printed out
46	%% \copypage % Uncomment if you want a copyright page
47	\begin{abstract}
48
49	As a rapidly expanding interdisciplinary science bridging physics,
50	chemistry and biology, the study of soft condensed matter involves
51	the kinetics, dynamics and geometric structures of complex materials
52	like membrane, liquid crystal and polymers. These soft condensed
53	materials are distinguished by the unique physical properties on the
54	mesoscopic scale which can provide useful insights to understand the
55	basic physical principles linking the microscopic structure to the
56	macroscopic properties. Knowledge of the underlying physics is of
57	benefit to a wide range areas, such as the processing of
58	biocompatible materials and development of LCD display technologies.
59	Although the separation of the length scales allows statistical
60	mechanics to be applied, the interesting behavior of these systems
61	usually happens on time scale well beyond current computing power.
62	In order to simulate large soft condensed systems for long times
63	within a reasonable amount of computational time, some new
64	coarse-grained models are presented in this dissertation to describe
65	phospholipids and liquid crystals. Although these
66	models can be described using a small number of physical parameters,
67	it is not trivial to introduce rigid constraints between different
68	molecular fragments correctly and efficiently. Working with
69	colleagues, I developed a new molecular dynamics framework capable
70	of performing simulation on systems with orientational degrees of
71	freedom in a variety of ensembles. Using this new package, I studied
72	the structure, dynamics and transport properties of the biological
73	membranes as well as the the phase behavior of liquid
74	crystals. A new Langevin dynamics algorithm for arbitrary rigid
75	particles is also presented to mimic solvent effects which may
76	eventually expand the time scale of the simulation.
77
78	\end{abstract}
79
80	\begin{dedication}
81
82	To my family.
83
84	\end{dedication}
85	\tableofcontents
86	\listoffigures % If you don't have any figures or tables, comment
87	\listoftables % out these two lines.
88	\lstlistoflistings
89
90	\begin{acknowledge} % acknowledgments go here
91
92	\noindent I would like to thank my advisor, Dr. Gezelter for his inspiring and encouraging way
93	to guide me to a deeper understanding of molecular modeling. Without his encouragement and constant
94	guidance, I could not have finished this dissertation. I am also grateful to my colleagues
95	Charles F.~Vardeman II, Christopher J.~Fennell, Xiuquan Sun, Yang Zheng, Kyle Daily,
96	Kyle S.~Haygarth, Matthew A.~Meineke, Dan Combest, Pat Conforti, and Megan Sprague,
97	who were always here for technical help and moral support. Last, but not least,
98	I thank my family: my fater, Zongzan Lin, and my mother, Rongying Chen,
99	for unconditional support and encouragement to pursue my dreams,
100	even when they went beyond boundaries of language and
101	geography. My wife, Xi, for her understanding and love during the past few years. Her support and
102	encouragement was in the end what made this dissertation possible.
103
104	\end{acknowledge}
105
106	\mainmatter
107	%\include{Introduction}
108	%\include{Methodology}
109	%\include{Lipid}
110	%\include{LiquidCrystal}
111	%\include{Conclusion}
112	%\include{Appendix}
113	%\include{phdBib}