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 |
|
|
\title{MOLECULAR DYNAMICS SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS} |
40 |
|
|
\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 |
2878 |
As an rapidly expanding interdisciplinary of physics, chemistry and |
51 |
|
|
biology \emph{etc}, soft condensed matter science studies the |
52 |
|
|
kinetics, dynamics and geometric structures of complex materials |
53 |
tim |
2904 |
like membrane, liquid crystal and polymers \emph{etc}. These soft |
54 |
tim |
2878 |
condensed matters are distinguished by the unique physical |
55 |
|
|
properties on the mesoscopic scale which can provide useful insights |
56 |
|
|
to understand the basic physical principles linking the microscopic |
57 |
|
|
structure to the macroscopic properties. Knowledge of the underlying |
58 |
|
|
physics is of benefit to a wide range of applications areas, such as |
59 |
|
|
the processing of biocompatible materials and development of LCD |
60 |
|
|
display technologies. Although the separation of the length scale |
61 |
|
|
allows statistical mechanics to be applied, the interesting behavior |
62 |
|
|
of these systems usually happens on the time scale well beyond the |
63 |
|
|
current computing power. In order to simulate large soft condensed |
64 |
|
|
systems for long times within a reasonable amount of computational |
65 |
|
|
time, some new coarse-grained models were proposed in this |
66 |
tim |
2904 |
dissertation to describe phospholipids and banana-shaped liquid |
67 |
tim |
2878 |
crystals. Although these models can be described using a small |
68 |
|
|
number of physical parameter, it is not trivial to maintain the |
69 |
tim |
2880 |
introducing rigid constraints between different molecular fragments |
70 |
|
|
correctly and efficiently. Working with colleagues, I developed a |
71 |
|
|
new molecular dynamics framework capable of performing simulation on |
72 |
tim |
2878 |
systems with orientational degrees of freedom in a variety of |
73 |
|
|
ensembles. Using this new package, I study the structure, the |
74 |
|
|
dynamics and transport properties of the biological membranes as |
75 |
|
|
well as the the phase behavior of banana shaped liquid crystal. A |
76 |
|
|
new Langevin dynamics algorithm for arbitrary rigid particles is |
77 |
|
|
proposed to mimic solvent effect which may eventually expand the |
78 |
|
|
time scale of the simulation. |
79 |
|
|
|
80 |
tim |
2685 |
\end{abstract} |
81 |
|
|
|
82 |
|
|
\begin{dedication} |
83 |
|
|
|
84 |
tim |
2880 |
To my family. |
85 |
tim |
2685 |
|
86 |
|
|
\end{dedication} |
87 |
|
|
\tableofcontents |
88 |
|
|
\listoffigures % If you don't have any figures or tables, comment |
89 |
|
|
\listoftables % out these two lines. |
90 |
|
|
\lstlistoflistings |
91 |
|
|
|
92 |
|
|
\begin{acknowledge} % acknowledgments go here |
93 |
|
|
|
94 |
|
|
\noindent I would like to thank my advisor, Dr. Gezelter for his inspiring and encouraging way |
95 |
tim |
2878 |
to guide me to a deeper understanding of molecular modeling. Without his encouragement and constant |
96 |
tim |
2685 |
guidance, I could not have finished this dissertation. I am also grateful to my colleagues |
97 |
|
|
Charles F.~Vardeman II, Christopher J.~Fennell, Xiuquan Sun, Yang Zheng, Kyle Daily, |
98 |
|
|
Kyle S.~Haygarth, Matthew A.~Meineke, Dan Combest, Pat Conforti, and Megan Sprague, |
99 |
|
|
who were always here for technical help and moral support. Last, but not least, |
100 |
tim |
2867 |
I thank my family: my fater, Zongzan Lin, and my mother, Rongying Chen, |
101 |
|
|
for unconditional support and encouragement to pursue my dreams, |
102 |
|
|
even when they went beyond boundaries of language and |
103 |
tim |
2690 |
geography. My wife, Xi, for her understanding and love during the past few years. Her support and |
104 |
tim |
2685 |
encouragement was in the end what made this dissertation possible. |
105 |
|
|
|
106 |
|
|
\end{acknowledge} |
107 |
|
|
|
108 |
|
|
\mainmatter |
109 |
tim |
2690 |
%\include{Introduction} |
110 |
|
|
%\include{Methodology} |
111 |
|
|
%\include{Lipid} |
112 |
|
|
%\include{LiquidCrystal} |
113 |
|
|
%\include{Conclusion} |
114 |
|
|
%\include{Appendix} |
115 |
|
|
%\include{phdBib} |