trunk/chrisDissertation/dissertation.tex

\documentclass[nosummary]{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}
\clubpenalty=10000
\widowpenalty=10000

\begin{document}

\frontmatter

\title{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE 
STUDY OF WATER AND 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}

This dissertation comprises a body of research in the field of
classical molecular simulations, with particular emphasis placed on
the proper depiction of water. It is arranged such that the techniques
and models are first developed and tested before being applied and
compared with experimental results. Accordingly, the first chapter
starts by introducing the technique of molecular dynamics and
discussing technical considerations needed to correctly perform
molecular simulations.

The second chapter builds on these consideration aspects by discussing
correction techniques for handling long-ranged electrostatic
interactions. Particular focus is placed on the damped shifted force
({\sc sf}) technique, and it is shown to be nearly equivalent to the
Ewald summation in simulations of condensed phases. Since the {\sc sf}
technique is pairwise, it scales as $\mathcal{O}(N)$ and lacks
periodicity artifacts. This technique is extended to include
point-multipoles, and optimal damping parameters are determined to
ensure proper depiction of the dielectric behavior of molecular
systems.

The third chapter applies the above techniques and focuses on water
model development, specifically the single-point soft sticky dipole
(SSD) model. In order to better depict water with SSD in computer
simulations, it needed to be reparametrized, resulting in SSD/RF and
SSD/E, new variants optimized for simulations with and without a
reaction field correction. These new single-point models are more
efficient than the more common multi-point models and better capture
the dynamic properties of water. SSD/RF can be used with damped {\sc
sf} through the multipolar extension described in the previous
chapter.

The final chapter deals with a unique polymorph of ice that was
discovered while performing simulations with the SSD models.  This
form of ice, called ``imaginary ice'' (Ice-$i$), has a low-density
structure which is different from any previously known ice
polymorph. The free energy analysis discussed here shows that it is
the thermodynamically preferred form of ice for both the single-point
and commonly used multi-point water models.  Including electrostatic
corrections is necessary to obtain more realistic results; however,
the free energies of the studied polymorphs are typically so similar
that system properties, like the volume in $NVT$ simulations, can
directly influence the ice polymorph expressed.

\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 Meineke, Dr.~Teng Lin, Charles
Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle 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 and
Rosalie Fennell, for providing the opportunities and encouragement
that allowed me to pursue my interests, and I would like to thank my
wife, Kelley, for her unwavering 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:	3042
Committed:	Wed Oct 11 14:33:13 2006 UTC (17 years, 11 months ago) by chrisfen
Content type:	application/x-tex
File size:	4396 byte(s)
Log Message:	Ridding the world of widowed and orphaned lines and abstracts greater than 350 words
#	User	Rev	Content
1	chrisfen	3042	\documentclass[nosummary]{ndthesis}
2	chrisfen	2987
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	chrisfen	3042	\clubpenalty=10000
15			\widowpenalty=10000
16	chrisfen	2987
17			\begin{document}
18
19			\frontmatter
20
21	chrisfen	3023	\title{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE
22	chrisfen	3029	STUDY OF WATER AND BIOCHEMICAL SYSTEMS}
23	chrisfen	2987	\author{Christopher Joseph Fennell}
24			\work{Dissertation}
25			\degprior{B.Sc.}
26			\degaward{Doctor of Philosophy}
27			\advisor{J. Daniel Gezelter}
28			\department{Chemistry and Biochemistry}
29
30			\maketitle
31
32			\begin{abstract}
33	chrisfen	3019
34	chrisfen	3023	This dissertation comprises a body of research in the field of
35			classical molecular simulations, with particular emphasis placed on
36	chrisfen	3042	the proper depiction of water. It is arranged such that the techniques
37			and models are first developed and tested before being applied and
38			compared with experimental results. Accordingly, the first chapter
39			starts by introducing the technique of molecular dynamics and
40			discussing technical considerations needed to correctly perform
41			molecular simulations.
42	chrisfen	3019
43	chrisfen	3042	The second chapter builds on these consideration aspects by discussing
44			correction techniques for handling long-ranged electrostatic
45			interactions. Particular focus is placed on the damped shifted force
46			({\sc sf}) technique, and it is shown to be nearly equivalent to the
47			Ewald summation in simulations of condensed phases. Since the {\sc sf}
48			technique is pairwise, it scales as $\mathcal{O}(N)$ and lacks
49			periodicity artifacts. This technique is extended to include
50			point-multipoles, and optimal damping parameters are determined to
51			ensure proper depiction of the dielectric behavior of molecular
52			systems.
53	chrisfen	3019
54	chrisfen	3023	The third chapter applies the above techniques and focuses on water
55			model development, specifically the single-point soft sticky dipole
56			(SSD) model. In order to better depict water with SSD in computer
57	chrisfen	3042	simulations, it needed to be reparametrized, resulting in SSD/RF and
58			SSD/E, new variants optimized for simulations with and without a
59			reaction field correction. These new single-point models are more
60			efficient than the more common multi-point models and better capture
61			the dynamic properties of water. SSD/RF can be used with damped {\sc
62			sf} through the multipolar extension described in the previous
63			chapter.
64	chrisfen	3019
65	chrisfen	3042	The final chapter deals with a unique polymorph of ice that was
66			discovered while performing simulations with the SSD models. This
67			form of ice, called ``imaginary ice'' (Ice-$i$), has a low-density
68			structure which is different from any previously known ice
69			polymorph. The free energy analysis discussed here shows that it is
70			the thermodynamically preferred form of ice for both the single-point
71			and commonly used multi-point water models. Including electrostatic
72			corrections is necessary to obtain more realistic results; however,
73			the free energies of the studied polymorphs are typically so similar
74			that system properties, like the volume in $NVT$ simulations, can
75			directly influence the ice polymorph expressed.
76	chrisfen	3023
77	chrisfen	2987	\end{abstract}
78
79			\begin{dedication}
80	chrisfen	3001	To my wife, for her understanding and support throughout this work.
81	chrisfen	2987	\end{dedication}
82
83			\tableofcontents
84			\listoffigures
85			\listoftables
86
87			\begin{acknowledge}
88	chrisfen	3001	I would to thank my advisor, J. Daniel Gezelter, for the guidance,
89			perspective, and direction he provided during this work. He is a great
90			teacher and helped fuel my desire to learn. I would also like to thank
91	chrisfen	3042	my fellow group members - Dr.~Matthew Meineke, Dr.~Teng Lin, Charles
92			Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle Haygarth,
93			Patrick Conforti, Megan Sprague, and Dan Combest for helpful comments
94			and suggestions along the way. I would also like to thank Christopher
95			Harrison and Dr.~Steven Corcelli for additional discussions and
96			comments. Finally, I would like to thank my parents, Edward and
97			Rosalie Fennell, for providing the opportunities and encouragement
98			that allowed me to pursue my interests, and I would like to thank my
99			wife, Kelley, for her unwavering support.
100	chrisfen	2987	\end{acknowledge}
101
102			\mainmatter
103
104			\input{Introduction}
105
106			\input{Electrostatics}
107
108			\input{Water}
109
110			\input{Ice}
111
112			\input{Conclusion}
113
114			\appendix
115
116			\input{IndividualSystems}
117
118	chrisfen	3016	%\input{SHAMS}
119	chrisfen	2987
120			\backmatter
121
122			\bibliographystyle{ndthesis}
123			\bibliography{dissertation}
124
125			\end{document}
126
127
128			\endinput