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 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 |
the structure, the dynamics and transport properties of the |
72 |
biological membranes as well as the the phase behavior of banana |
73 |
shaped liquid crystals. A new Langevin dynamics algorithm for |
74 |
arbitrary rigid particles is proposed to mimic solvent effects which |
75 |
may 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} |