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{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}

This dissertation comprises a body of research in the field of
classical molecular simulations, with particular emphasis placed on
the proper depiction of water. This work is arranged such that the
techniques and models used within are first developed and tested
before being applied and compared with experimental results. With this
organization in mind, it is appropriate that the first chapter deals
primarily the technique of molecular dynamics and technical
considerations needed to correctly perform molecular simulations.

Building on this framework, the second chapter discusses correction
techniques for handling the long-ranged electrostatic interactions
common in molecular simulations. Particular focus is placed on a
shifted-force ({\sc sf}) modification of the damped shifted Coulombic
summation method. In this work, {\sc sf} is shown to be nearly
equivalent to the more commonly utilized Ewald summation in
simulations of condensed phases. Since the {\sc sf} technique is
pairwise, it scales as $\mathcal{O}(N)$ and lacks periodicity
artifacts introduced through heavy reliance on the reciprocal-space
portion of the Ewald sum. The electrostatic damping technique used
with {\sc sf} is then extended beyond simple charge-charge
interactions to include point-multipoles. Optimal damping parameter
settings are also determined to ensure proper depiction of the
dielectric behavior of molecular systems. Presenting this technique
early enables its application in the systems discussed in the later
chapters and shows how it can improve the quality of various molecular
simulations.

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. This work results in the
development of SSD/RF and SSD/E, new variants of the SSD model
optimized for simulations with and without a reaction field
correction. These new single-point models are more efficient than the
common multi-point partial charge models and better capture the
dynamic properties of water. SSD/RF can be successfully used with
damped {\sc sf} through the multipolar extension of the technique
described in the previous chapter. Discussion on the development of
the two-point tetrahedrally restructured elongated dipole (TRED) water
model is also presented, and this model is optimized for use with the
damped {\sc sf} technique. Though there remain some algorithmic
complexities that need to be addressed (logic for neglecting
charge-quadrupole interactions between other TRED molecules) to use
this model in general simulations, it is approximately twice as
efficient as the commonly used three-point water models (i.e. TIP3P
and SPC/E).

Continuing in the direction of model applications, the final chapter
deals with a unique polymorph of ice that was discovered while
performing water simulations with the fast simple water models
discussed in the previous chapter. This form of ice, called
``imaginary ice'' (Ice-$i$), has a low-density structure which is
different from any known polymorph observed in either experiment or
computer simulation studies. The free energy analysis discussed here
shows that this structure is in fact the thermodynamically preferred
form of ice for both the single-point and commonly used multi-point
water models under the chosen simulation conditions. It is shown that
inclusion of electrostatic corrections is necessary to obtain more
realistic results; however, the free energies of the various
polymorphs (both imaginary and real) in many of these models is shown
to be so similar that choice of 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 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
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:	3023
Committed:	Tue Sep 26 03:07:59 2006 UTC (17 years, 11 months ago) by chrisfen
Content type:	application/x-tex
File size:	5769 byte(s)
Log Message:	Refinements. Just a little proof checking left...
#	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	chrisfen	3023	\title{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	chrisfen	3023	This dissertation comprises a body of research in the field of
33			classical molecular simulations, with particular emphasis placed on
34			the proper depiction of water. This work is arranged such that the
35			techniques and models used within are first developed and tested
36			before being applied and compared with experimental results. With this
37			organization in mind, it is appropriate that the first chapter deals
38			primarily the technique of molecular dynamics and technical
39			considerations needed to correctly perform molecular simulations.
40	chrisfen	3019
41	chrisfen	3023	Building on this framework, the second chapter discusses correction
42			techniques for handling the long-ranged electrostatic interactions
43			common in molecular simulations. Particular focus is placed on a
44			shifted-force ({\sc sf}) modification of the damped shifted Coulombic
45			summation method. In this work, {\sc sf} is shown to be nearly
46			equivalent to the more commonly utilized Ewald summation in
47			simulations of condensed phases. Since the {\sc sf} technique is
48			pairwise, it scales as $\mathcal{O}(N)$ and lacks periodicity
49			artifacts introduced through heavy reliance on the reciprocal-space
50			portion of the Ewald sum. The electrostatic damping technique used
51			with {\sc sf} is then extended beyond simple charge-charge
52			interactions to include point-multipoles. Optimal damping parameter
53			settings are also determined to ensure proper depiction of the
54			dielectric behavior of molecular systems. Presenting this technique
55			early enables its application in the systems discussed in the later
56			chapters and shows how it can improve the quality of various molecular
57			simulations.
58	chrisfen	3019
59	chrisfen	3023	The third chapter applies the above techniques and focuses on water
60			model development, specifically the single-point soft sticky dipole
61			(SSD) model. In order to better depict water with SSD in computer
62			simulations, it needed to be reparametrized. This work results in the
63			development of SSD/RF and SSD/E, new variants of the SSD model
64			optimized for simulations with and without a reaction field
65			correction. These new single-point models are more efficient than the
66			common multi-point partial charge models and better capture the
67			dynamic properties of water. SSD/RF can be successfully used with
68			damped {\sc sf} through the multipolar extension of the technique
69			described in the previous chapter. Discussion on the development of
70			the two-point tetrahedrally restructured elongated dipole (TRED) water
71			model is also presented, and this model is optimized for use with the
72			damped {\sc sf} technique. Though there remain some algorithmic
73			complexities that need to be addressed (logic for neglecting
74			charge-quadrupole interactions between other TRED molecules) to use
75			this model in general simulations, it is approximately twice as
76			efficient as the commonly used three-point water models (i.e. TIP3P
77			and SPC/E).
78	chrisfen	3019
79	chrisfen	3023	Continuing in the direction of model applications, the final chapter
80			deals with a unique polymorph of ice that was discovered while
81			performing water simulations with the fast simple water models
82			discussed in the previous chapter. This form of ice, called
83			``imaginary ice'' (Ice-$i$), has a low-density structure which is
84			different from any known polymorph observed in either experiment or
85			computer simulation studies. The free energy analysis discussed here
86			shows that this structure is in fact the thermodynamically preferred
87			form of ice for both the single-point and commonly used multi-point
88			water models under the chosen simulation conditions. It is shown that
89			inclusion of electrostatic corrections is necessary to obtain more
90			realistic results; however, the free energies of the various
91			polymorphs (both imaginary and real) in many of these models is shown
92			to be so similar that choice of system properties, like the volume in
93			$NVT$ simulations, can directly influence the ice polymorph expressed.
94
95	chrisfen	2987	\end{abstract}
96
97			\begin{dedication}
98	chrisfen	3001	To my wife, for her understanding and support throughout this work.
99	chrisfen	2987	\end{dedication}
100
101			\tableofcontents
102			\listoffigures
103			\listoftables
104
105			\begin{acknowledge}
106	chrisfen	3001	I would to thank my advisor, J. Daniel Gezelter, for the guidance,
107			perspective, and direction he provided during this work. He is a great
108			teacher and helped fuel my desire to learn. I would also like to thank
109			my fellow group members - Dr.~Matthew A.~Meineke, Dr.~Teng Lin,
110			Charles F.~Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle
111			S.~Haygarth, Patrick Conforti, Megan Sprague, and Dan Combest for
112			helpful comments and suggestions along the way. I would also like to
113			thank Christopher Harrison and Dr. Steven Corcelli for additional
114			discussions and comments. Finally, I would like to thank my parents,
115			Edward P.~Fennell and Rosalie M.~Fennell, for providing the
116	chrisfen	3023	opportunities and encouragement that allowed me to pursue my
117	chrisfen	3001	interests, and I would like to thank my wife, Kelley, for her
118	chrisfen	3023	unwavering support.
119	chrisfen	2987	\end{acknowledge}
120
121			\mainmatter
122
123			\input{Introduction}
124
125			\input{Electrostatics}
126
127			\input{Water}
128
129			\input{Ice}
130
131			\input{Conclusion}
132
133			\appendix
134
135			\input{IndividualSystems}
136
137	chrisfen	3016	%\input{SHAMS}
138	chrisfen	2987
139			\backmatter
140
141			\bibliographystyle{ndthesis}
142			\bibliography{dissertation}
143
144			\end{document}
145
146
147			\endinput