trunk/chrisDissertation/dissertation.tex

\documentclass[12pt]{ndthesis}

% some packages for things like equations and graphics
\usepackage[tbtags]{amsmath}
\usepackage{amsmath,bm}
\usepackage{amssymb}
\usepackage{mathrsfs}
\usepackage{tabularx}
\usepackage{graphicx}
\usepackage{booktabs}
\usepackage{cite}
\usepackage{enumitem}
\renewcommand{\appendixname}{APPENDIX}

\begin{document}

\frontmatter

\title{APPLICATION AND DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE 
STUDY OF WATER AND OTHER BIOCHEMICAL SYSTEMS}     
\author{Christopher Joseph Fennell} 
\work{Dissertation}
\degprior{B.Sc.}
\degaward{Doctor of Philosophy}
\advisor{J. Daniel Gezelter}
\department{Chemistry and Biochemistry}

\maketitle

\begin{abstract}

The following dissertation lays out research that I have performed
over the last several years. All of the work relies on the technique of
molecular dynamics, and in this dissertation I start by outlining many
of the considerations that go into molecular dynamics
simulations. This is followed by an introduction to {\sc oopse}, the
object oriented parallel simulation engine, which is a program for
performing molecular simulations developed and maintained in our
lab. Most of the research was performed either using {\sc oopse} or
earlier code that predated {\sc oopse}.

This introduction is followed by three chapters that discuss in detail
the primary research projects for which I am responsible. The first
project discusses my work on electrostatic interaction correction
techniques, with applications to water and biologically relevant
molecular systems. This leads into work on improving the depiction of
water in molecular simulations by refining simple and highly
computationally efficient single point water models. The final project
discussed in this body of research involves free energy calculations
of ice polymorphs, and includes investigations of a new ice polymorph
that we discovered while performing simulations involving the single
point water models.

I end this dissertation with some concluding remarks and
appendices. The conclusion simply sums up the previous sections and
comments on the research findings.  The appendices include supporting
information and a more detailed look at systems that were treated in a
more general form in the earlier sections.

\end{abstract}

\begin{dedication}
To my wife, for her understanding and support throughout this work.
\end{dedication}

\tableofcontents
\listoffigures
\listoftables

\begin{acknowledge}
I would to thank my advisor, J. Daniel Gezelter, for the guidance,
perspective, and direction he provided during this work. He is a great
teacher and helped fuel my desire to learn. I would also like to thank
my fellow group members - Dr.~Matthew A.~Meineke, Dr.~Teng Lin,
Charles F.~Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle
S.~Haygarth, Patrick Conforti, Megan Sprague, and Dan Combest for
helpful comments and suggestions along the way. I would also like to
thank Christopher Harrison and Dr. Steven Corcelli for additional
discussions and comments. Finally, I would like to thank my parents,
Edward P.~Fennell and Rosalie M.~Fennell, for providing the
opprotunities and encouragement that allowed me to pursue my
interests, and I would like to thank my wife, Kelley, for her
unwaivering support.
\end{acknowledge}

\mainmatter

\input{Introduction}

\input{Electrostatics}

\input{Water}

\input{Ice}

\input{Conclusion}

\appendix

\input{IndividualSystems}

%\input{SHAMS}

\backmatter
 
\bibliographystyle{ndthesis}
\bibliography{dissertation}  

\end{document}


\endinput
Revision:	3019
Committed:	Fri Sep 22 13:45:24 2006 UTC (17 years, 9 months ago) by chrisfen
Content type:	application/x-tex
File size:	3562 byte(s)
Log Message:	more changes and an abstract included
#	User	Rev	Content
1	chrisfen	2987	\documentclass[12pt]{ndthesis}
2
3			% some packages for things like equations and graphics
4			\usepackage[tbtags]{amsmath}
5			\usepackage{amsmath,bm}
6			\usepackage{amssymb}
7			\usepackage{mathrsfs}
8			\usepackage{tabularx}
9			\usepackage{graphicx}
10			\usepackage{booktabs}
11			\usepackage{cite}
12			\usepackage{enumitem}
13			\renewcommand{\appendixname}{APPENDIX}
14
15			\begin{document}
16
17			\frontmatter
18
19			\title{APPLICATION AND DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE
20	chrisfen	3019	STUDY OF WATER AND OTHER BIOCHEMICAL SYSTEMS}
21	chrisfen	2987	\author{Christopher Joseph Fennell}
22			\work{Dissertation}
23			\degprior{B.Sc.}
24			\degaward{Doctor of Philosophy}
25			\advisor{J. Daniel Gezelter}
26			\department{Chemistry and Biochemistry}
27
28			\maketitle
29
30			\begin{abstract}
31	chrisfen	3019
32			The following dissertation lays out research that I have performed
33			over the last several years. All of the work relies on the technique of
34			molecular dynamics, and in this dissertation I start by outlining many
35			of the considerations that go into molecular dynamics
36			simulations. This is followed by an introduction to {\sc oopse}, the
37			object oriented parallel simulation engine, which is a program for
38			performing molecular simulations developed and maintained in our
39			lab. Most of the research was performed either using {\sc oopse} or
40			earlier code that predated {\sc oopse}.
41
42			This introduction is followed by three chapters that discuss in detail
43			the primary research projects for which I am responsible. The first
44			project discusses my work on electrostatic interaction correction
45			techniques, with applications to water and biologically relevant
46			molecular systems. This leads into work on improving the depiction of
47			water in molecular simulations by refining simple and highly
48			computationally efficient single point water models. The final project
49			discussed in this body of research involves free energy calculations
50			of ice polymorphs, and includes investigations of a new ice polymorph
51			that we discovered while performing simulations involving the single
52			point water models.
53
54			I end this dissertation with some concluding remarks and
55			appendices. The conclusion simply sums up the previous sections and
56			comments on the research findings. The appendices include supporting
57			information and a more detailed look at systems that were treated in a
58			more general form in the earlier sections.
59
60	chrisfen	2987	\end{abstract}
61
62			\begin{dedication}
63	chrisfen	3001	To my wife, for her understanding and support throughout this work.
64	chrisfen	2987	\end{dedication}
65
66			\tableofcontents
67			\listoffigures
68			\listoftables
69
70			\begin{acknowledge}
71	chrisfen	3001	I would to thank my advisor, J. Daniel Gezelter, for the guidance,
72			perspective, and direction he provided during this work. He is a great
73			teacher and helped fuel my desire to learn. I would also like to thank
74			my fellow group members - Dr.~Matthew A.~Meineke, Dr.~Teng Lin,
75			Charles F.~Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle
76			S.~Haygarth, Patrick Conforti, Megan Sprague, and Dan Combest for
77			helpful comments and suggestions along the way. I would also like to
78			thank Christopher Harrison and Dr. Steven Corcelli for additional
79			discussions and comments. Finally, I would like to thank my parents,
80			Edward P.~Fennell and Rosalie M.~Fennell, for providing the
81			opprotunities and encouragement that allowed me to pursue my
82			interests, and I would like to thank my wife, Kelley, for her
83			unwaivering support.
84	chrisfen	2987	\end{acknowledge}
85
86			\mainmatter
87
88			\input{Introduction}
89
90			\input{Electrostatics}
91
92			\input{Water}
93
94			\input{Ice}
95
96			\input{Conclusion}
97
98			\appendix
99
100			\input{IndividualSystems}
101
102	chrisfen	3016	%\input{SHAMS}
103	chrisfen	2987
104			\backmatter
105
106			\bibliographystyle{ndthesis}
107			\bibliography{dissertation}
108
109			\end{document}
110
111
112			\endinput