32 |
|
\newcolumntype{H}{p{0.75in}} |
33 |
|
\newcolumntype{I}{p{5in}} |
34 |
|
|
35 |
< |
\renewcommand{\lstlistlistingname}{LISTS} |
36 |
< |
\renewcommand{\lstlistingname}{List} |
35 |
> |
\renewcommand{\lstlistlistingname}{SCHEMES} |
36 |
> |
\renewcommand{\lstlistingname}{Scheme} |
37 |
|
\frontmatter |
38 |
|
\work{Dissertation} % Change to ``Thesis'' for Master's thesis |
39 |
< |
\title{MOLECULAR DYNAMICS SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS} |
39 |
> |
\title{MOLECULAR DYNAMICS METHODOLOGY AND SIMULATIONS OF PHOSPHOLIPID BILAYERS AND LIQUID CRYSTALS} |
40 |
|
\author{Teng Lin} |
41 |
< |
\degprior{B.Sc., B.E.} % All previously earned degrees |
41 |
> |
\degprior{B.S., B.E.} % All previously earned degrees |
42 |
|
\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) |
47 |
|
%% \copypage % Uncomment if you want a copyright page |
48 |
|
\begin{abstract} |
49 |
|
|
50 |
< |
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 |
< |
like membrane,liquid crystal and polymers \emph{etc}. These soft |
54 |
< |
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 |
< |
dissertation to describe phosphlipids and banana-shaped liquid |
67 |
< |
crystals. Although these models can be described using a small |
68 |
< |
number of physical parameter, it is not trivial to maintain the |
69 |
< |
rigid constraints between different molecular fragments correctly |
70 |
< |
and efficiently. Working with colleagues, I developed a new |
71 |
< |
molecular dynamics framework capable of performing simulation on |
72 |
< |
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. |
50 |
> |
As a rapidly expanding interdisciplinary science bridging physics, |
51 |
> |
chemistry and biology, the study of soft condensed matter involves |
52 |
> |
the kinetics, dynamics and geometric structures of complex materials |
53 |
> |
like membrane, liquid crystal and polymers. These soft condensed |
54 |
> |
materials are distinguished by the unique physical properties on the |
55 |
> |
mesoscopic scale which can provide useful insights to understand the |
56 |
> |
basic physical principles linking the microscopic structure to the |
57 |
> |
macroscopic properties. Knowledge of the underlying physics is of |
58 |
> |
benefit to a wide range areas, such as the processing of |
59 |
> |
biocompatible materials and development of LCD display technologies. |
60 |
> |
Although the separation of the length scales allows statistical |
61 |
> |
mechanics to be applied, the interesting behavior of these systems |
62 |
> |
usually happens on time scale well beyond current computing power. |
63 |
> |
In order to simulate large soft condensed systems for long times |
64 |
> |
within a reasonable amount of computational time, some new |
65 |
> |
coarse-grained models are presented in this dissertation to describe |
66 |
> |
phospholipids and banana-shaped liquid crystals. Although these |
67 |
> |
models can be described using a small number of physical parameters, |
68 |
> |
it is not trivial to introduce rigid constraints between different |
69 |
> |
molecular fragments correctly and efficiently. Working with |
70 |
> |
colleagues, I developed a new molecular dynamics framework capable |
71 |
> |
of performing simulation on systems with orientational degrees of |
72 |
> |
freedom in a variety of ensembles. Using this new package, I studied |
73 |
> |
the structure, the dynamics and transport properties of the |
74 |
> |
biological membranes as well as the the phase behavior of banana |
75 |
> |
shaped liquid crystals. A new Langevin dynamics algorithm for |
76 |
> |
arbitrary rigid particles is proposed to mimic solvent effects which |
77 |
> |
may eventually expand the time scale of the simulation. |
78 |
|
|
79 |
|
\end{abstract} |
80 |
|
|
81 |
|
\begin{dedication} |
82 |
|
|
83 |
< |
I would like to dedicate this dissertation to my wife, who has |
85 |
< |
helped and supported me throughout all of this work. |
83 |
> |
To my family. |
84 |
|
|
85 |
|
\end{dedication} |
86 |
|
\tableofcontents |