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\documentclass[nosummary]{ndthesis} |
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% some packages for things like equations and graphics |
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\usepackage[tbtags]{amsmath} |
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\usepackage{cite} |
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\usepackage{enumitem} |
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\renewcommand{\appendixname}{APPENDIX} |
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\clubpenalty=10000 |
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\begin{document} |
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\frontmatter |
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\title{APPLICATION AND DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE |
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STUDY OF WATER} |
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\title{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE |
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STUDY OF WATER AND BIOCHEMICAL SYSTEMS} |
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\author{Christopher Joseph Fennell} |
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\work{Dissertation} |
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\degprior{B.Sc.} |
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\maketitle |
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\begin{abstract} |
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This dissertation comprises a body of research in the field of |
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classical molecular simulations, with particular emphasis placed on |
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the proper depiction of water. It is arranged such that the techniques |
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and models are first developed and tested before being applied and |
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compared with experimental results. Accordingly, the first chapter |
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starts by introducing the technique of molecular dynamics and |
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discussing technical considerations needed to correctly perform |
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molecular simulations. |
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The second chapter builds on these consideration aspects by discussing |
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correction techniques for handling long-ranged electrostatic |
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interactions. Particular focus is placed on the damped shifted force |
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({\sc sf}) technique, and it is shown to be nearly equivalent to the |
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Ewald summation in simulations of condensed phases. Since the {\sc sf} |
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technique is pairwise, it scales as $\mathcal{O}(N)$ and lacks |
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periodicity artifacts. This technique is extended to include |
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point-multipoles, and optimal damping parameters are determined to |
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ensure proper depiction of the dielectric behavior of molecular |
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systems. |
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The third chapter applies the above techniques and focuses on water |
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model development, specifically the single-point soft sticky dipole |
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(SSD) model. In order to better depict water with SSD in computer |
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simulations, it needed to be reparametrized, resulting in SSD/RF and |
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SSD/E, new variants optimized for simulations with and without a |
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reaction field correction. These new single-point models are more |
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efficient than the more common multi-point models and better capture |
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the dynamic properties of water. SSD/RF can be used with damped {\sc |
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sf} through the multipolar extension described in the previous |
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chapter. |
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The final chapter deals with a unique polymorph of ice that was |
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discovered while performing simulations with the SSD models. This |
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form of ice, called ``imaginary ice'' (Ice-$i$), has a low-density |
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structure which is different from any previously known ice |
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polymorph. The free energy analysis discussed here shows that it is |
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the thermodynamically preferred form of ice for both the single-point |
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and commonly used multi-point water models. Including electrostatic |
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corrections is necessary to obtain more realistic results; however, |
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the free energies of the studied polymorphs are typically so similar |
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that system properties, like the volume in $NVT$ simulations, can |
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directly influence the ice polymorph expressed. |
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\end{abstract} |
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\begin{dedication} |
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To my wife, for her understanding and support throughout this work. |
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\end{dedication} |
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\tableofcontents |
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\listoftables |
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\begin{acknowledge} |
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I would to thank my advisor, J. Daniel Gezelter, for the guidance, |
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perspective, and direction he provided during this work. He is a great |
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teacher and helped fuel my desire to learn. I would also like to thank |
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my fellow group members - Dr.~Matthew Meineke, Dr.~Teng Lin, Charles |
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Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle Haygarth, |
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Patrick Conforti, Megan Sprague, and Dan Combest for helpful comments |
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and suggestions along the way. I would also like to thank Christopher |
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Harrison and Dr.~Steven Corcelli for additional discussions and |
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comments. Finally, I would like to thank my parents, Edward and |
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Rosalie Fennell, for providing the opportunities and encouragement |
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that allowed me to pursue my interests, and I would like to thank my |
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wife, Kelley, for her unwavering support. |
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\end{acknowledge} |
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\mainmatter |
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\input{IndividualSystems} |
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\input{SHAMS} |
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%\input{SHAMS} |
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\backmatter |
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