--- trunk/tengDissertation/phdPreamble.tex	2006/04/24 18:49:32	2730
+++ trunk/tengDissertation/phdPreamble.tex	2006/07/17 20:01:05	2941
@@ -5,22 +5,39 @@
 \usepackage{amssymb}
 \usepackage{color}
 \usepackage{listings}
+\usepackage{cite}
 %\usepackage from oopseDoc.tex
 \usepackage{times}
 \usepackage{setspace}
 \usepackage{tabularx}
 \usepackage{longtable}
-
+\lstset{language=C++,frame=TB,basicstyle=\small\ttfamily, %
+        xleftmargin=0in, xrightmargin=0in, %captionpos=b,% breaklines=true, %
+        abovecaptionskip=0.5cm, belowcaptionskip=0.5cm}
+\renewcommand{\lstlistingname}{Scheme}
 \includeonly{preview}
 
 \begin{document}
+
+\newcolumntype{A}{p{1.5in}}
+\newcolumntype{B}{p{0.75in}}
+\newcolumntype{C}{p{1.5in}}
+\newcolumntype{D}{p{2in}}
+
+\newcolumntype{E}{p{0.5in}}
+\newcolumntype{F}{p{1.5in}}
+\newcolumntype{G}{p{3.25in}}
+
+\newcolumntype{H}{p{0.75in}}
+\newcolumntype{I}{p{5in}}
+
 \renewcommand{\lstlistlistingname}{SCHEMES}
 \renewcommand{\lstlistingname}{Scheme}
 \frontmatter
 \work{Dissertation}  % Change to ``Thesis'' for Master's thesis
-\title{MOLECULAR DYNAMICS SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS}
+\title{MOLECULAR DYNAMICS METHODOLOGY AND SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS}
 \author{Teng Lin}
-\degprior{B.Sc.}                 % All previously earned degrees
+\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)
@@ -29,14 +46,40 @@ I present a dissertation utilizing an open source mole
 %% \copypage              % Uncomment if you want a copyright page
 \begin{abstract}
 
-I present a dissertation utilizing an open source molecular dynamics
-simulation package {\sc oopse}.
+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}
 
-I would like to dedicate this dissertation to my wife, who has
-helped and supported me throughout all of this work.
+To my family.
 
 \end{dedication}
 \tableofcontents
@@ -47,14 +90,14 @@ helped and supported me throughout all of this work.
 \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 knowledge work. Without his encouragement and constant
+    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 parents, Zongzan Lin, and Rongying Chen,
-    for unconditional support and encouragement to pursue my interests,
-    even when the interests went beyond boundaries of language and
+    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.