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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 OTHER 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 | |
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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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