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Revision 3001 by chrisfen, Thu Sep 7 20:42:27 2006 UTC vs.
Revision 3042 by chrisfen, Wed Oct 11 14:33:13 2006 UTC

# Line 1 | Line 1
1 < \documentclass[12pt]{ndthesis}
1 > \documentclass[nosummary]{ndthesis}
2  
3   % some packages for things like equations and graphics
4   \usepackage[tbtags]{amsmath}
# Line 11 | Line 11
11   \usepackage{cite}
12   \usepackage{enumitem}
13   \renewcommand{\appendixname}{APPENDIX}
14 + \clubpenalty=10000
15 + \widowpenalty=10000
16  
17   \begin{document}
18  
19   \frontmatter
20  
21 < \title{APPLICATION AND DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE
22 < STUDY OF WATER}    
21 > \title{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE
22 > STUDY OF WATER AND BIOCHEMICAL SYSTEMS}    
23   \author{Christopher Joseph Fennell}
24   \work{Dissertation}
25   \degprior{B.Sc.}
# Line 28 | Line 30 | STUDY OF WATER}    
30   \maketitle
31  
32   \begin{abstract}
33 +
34 + This dissertation comprises a body of research in the field of
35 + classical molecular simulations, with particular emphasis placed on
36 + 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 +
43 + 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 +
54 + 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 + 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 +
65 + 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 +
77   \end{abstract}
78  
79   \begin{dedication}
# Line 42 | Line 88 | teacher and helped fuel my desire to learn. I would al
88   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 < my fellow group members - Dr.~Matthew A.~Meineke, Dr.~Teng Lin,
92 < Charles F.~Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle
93 < S.~Haygarth, Patrick Conforti, Megan Sprague, and Dan Combest for
94 < helpful comments and suggestions along the way. I would also like to
95 < thank Christopher Harrison and Dr. Steven Corcelli for additional
96 < discussions and comments. Finally, I would like to thank my parents,
97 < Edward P.~Fennell and Rosalie M.~Fennell, for providing the
98 < opprotunities and encouragement that allowed me to pursue my
99 < interests, and I would like to thank my wife, Kelley, for her
54 < unwaivering support.
91 > 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   \end{acknowledge}
101  
102   \mainmatter
# Line 70 | Line 115 | unwaivering support.
115  
116   \input{IndividualSystems}
117  
118 < \input{SHAMS}
118 > %\input{SHAMS}
119  
120   \backmatter
121  

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