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 (18 years, 7 months ago) by chrisfen
Content type:	application/x-tex
File size:	5769 byte(s)
Log Message:	Refinements. Just a little proof checking left...
#	Content
1	\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{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE
20	STUDY OF WATER AND OTHER BIOCHEMICAL SYSTEMS}
21	\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
32	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
41	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
59	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
79	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	\end{abstract}
96
97	\begin{dedication}
98	To my wife, for her understanding and support throughout this work.
99	\end{dedication}
100
101	\tableofcontents
102	\listoffigures
103	\listoftables
104
105	\begin{acknowledge}
106	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	opportunities and encouragement that allowed me to pursue my
117	interests, and I would like to thank my wife, Kelley, for her
118	unwavering support.
119	\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	%\input{SHAMS}
138
139	\backmatter
140
141	\bibliographystyle{ndthesis}
142	\bibliography{dissertation}
143
144	\end{document}
145
146
147	\endinput