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Revision 2987 by chrisfen, Wed Aug 30 22:36:06 2006 UTC vs.
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# Line 16 | Line 16
16  
17   \frontmatter
18  
19 < \title{APPLICATION AND DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE
20 < STUDY OF WATER}    
19 > \title{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE
20 > STUDY OF WATER AND BIOCHEMICAL SYSTEMS}    
21   \author{Christopher Joseph Fennell}
22   \work{Dissertation}
23   \degprior{B.Sc.}
# Line 28 | Line 28 | STUDY OF WATER}    
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
# Line 38 | Line 103 | STUDY OF WATER}    
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
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134  
135   \input{IndividualSystems}
136  
137 < \input{SHAMS}
137 > %\input{SHAMS}
138  
139   \backmatter
140  

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