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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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STUDY OF WATER AND OTHER 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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The following dissertation lays out research that I have performed |
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over the last several years. All of the work relies on the technique of |
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molecular dynamics, and in this dissertation I start by outlining many |
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of the considerations that go into molecular dynamics |
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simulations. This is followed by an introduction to {\sc oopse}, the |
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object oriented parallel simulation engine, which is a program for |
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performing molecular simulations developed and maintained in our |
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lab. Most of the research was performed either using {\sc oopse} or |
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earlier code that predated {\sc oopse}. |
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This introduction is followed by three chapters that discuss in detail |
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the primary research projects for which I am responsible. The first |
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project discusses my work on electrostatic interaction correction |
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techniques, with applications to water and biologically relevant |
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molecular systems. This leads into work on improving the depiction of |
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water in molecular simulations by refining simple and highly |
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computationally efficient single point water models. The final project |
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discussed in this body of research involves free energy calculations |
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of ice polymorphs, and includes investigations of a new ice polymorph |
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that we discovered while performing simulations involving the single |
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point water models. |
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I end this dissertation with some concluding remarks and |
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appendices. The conclusion simply sums up the previous sections and |
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comments on the research findings. The appendices include supporting |
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information and a more detailed look at systems that were treated in a |
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more general form in the earlier sections. |
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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 A.~Meineke, Dr.~Teng Lin, |
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Charles F.~Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle |
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S.~Haygarth, Patrick Conforti, Megan Sprague, and Dan Combest for |
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helpful comments and suggestions along the way. I would also like to |
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thank Christopher Harrison and Dr. Steven Corcelli for additional |
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discussions and comments. Finally, I would like to thank my parents, |
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Edward P.~Fennell and Rosalie M.~Fennell, for providing the |
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opprotunities and encouragement that allowed me to pursue my |
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interests, and I would like to thank my wife, Kelley, for her |
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unwaivering 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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