trunk/tengDissertation/phdPreamble.tex

\documentclass[nosummary,dvips,noindentfirst]{ndthesis}
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\usepackage{listings}
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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 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:	2938
Committed:	Mon Jul 17 15:28:44 2006 UTC (19 years, 4 months ago) by tim
Content type:	application/x-tex
File size:	4792 byte(s)
Log Message:	corrections from steve
#	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 from oopseDoc.tex
9	\usepackage{times}
10	\usepackage{setspace}
11	\usepackage{tabularx}
12	\usepackage{longtable}
13	\lstset{language=C++,frame=TB,basicstyle=\small\ttfamily, %
14	xleftmargin=0in, xrightmargin=0in, %captionpos=b,% breaklines=true, %
15	abovecaptionskip=0.5cm, belowcaptionskip=0.5cm}
16	\renewcommand{\lstlistingname}{Scheme}
17	\includeonly{preview}
18
19	\begin{document}
20
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	\newcolumntype{F}{p{1.5in}}
28	\newcolumntype{G}{p{3.25in}}
29
30	\newcolumntype{H}{p{0.75in}}
31	\newcolumntype{I}{p{5in}}
32
33	\renewcommand{\lstlistlistingname}{SCHEMES}
34	\renewcommand{\lstlistingname}{Scheme}
35	\frontmatter
36	\work{Dissertation} % Change to ``Thesis'' for Master's thesis
37	\title{MOLECULAR DYNAMICS METHODOLOGY AND SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS}
38	\author{Teng Lin}
39	\degprior{B.S., B.E.} % All previously earned degrees
40	\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	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 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	the structure, dynamics and transport properties of the biological
72	membranes as well as the the phase behavior of 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
77	\end{abstract}
78
79	\begin{dedication}
80
81	To my family.
82
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	to guide me to a deeper understanding of molecular modeling. Without his encouragement and constant
93	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	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	geography. My wife, Xi, for her understanding and love during the past few years. Her support and
101	encouragement was in the end what made this dissertation possible.
102
103	\end{acknowledge}
104
105	\mainmatter
106	%\include{Introduction}
107	%\include{Methodology}
108	%\include{Lipid}
109	%\include{LiquidCrystal}
110	%\include{Conclusion}
111	%\include{Appendix}
112	%\include{phdBib}