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\documentclass[12pt]{ndthesis} |
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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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\begin{document} |
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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. This work is arranged such that the |
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techniques and models used within are first developed and tested |
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before being applied and compared with experimental results. With this |
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organization in mind, it is appropriate that the first chapter deals |
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primarily the technique of molecular dynamics and technical |
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considerations needed to correctly perform molecular simulations. |
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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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Building on this framework, the second chapter discusses correction |
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techniques for handling the long-ranged electrostatic interactions |
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common in molecular simulations. Particular focus is placed on a |
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shifted-force ({\sc sf}) modification of the damped shifted Coulombic |
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summation method. In this work, {\sc sf} is shown to be nearly |
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equivalent to the more commonly utilized Ewald summation in |
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simulations of condensed phases. Since the {\sc sf} technique is |
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pairwise, it scales as $\mathcal{O}(N)$ and lacks periodicity |
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artifacts introduced through heavy reliance on the reciprocal-space |
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portion of the Ewald sum. The electrostatic damping technique used |
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with {\sc sf} is then extended beyond simple charge-charge |
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interactions to include point-multipoles. Optimal damping parameter |
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settings are also determined to ensure proper depiction of the |
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dielectric behavior of molecular systems. Presenting this technique |
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early enables its application in the systems discussed in the later |
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chapters and shows how it can improve the quality of various molecular |
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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. This work results in the |
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development of SSD/RF and SSD/E, new variants of the SSD model |
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optimized for simulations with and without a reaction field |
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correction. These new single-point models are more efficient than the |
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common multi-point partial charge models and better capture the |
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dynamic properties of water. SSD/RF can be successfully used with |
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damped {\sc sf} through the multipolar extension of the technique |
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described in the previous chapter. Discussion on the development of |
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the two-point tetrahedrally restructured elongated dipole (TRED) water |
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model is also presented, and this model is optimized for use with the |
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damped {\sc sf} technique. Though there remain some algorithmic |
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complexities that need to be addressed (logic for neglecting |
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charge-quadrupole interactions between other TRED molecules) to use |
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this model in general simulations, it is approximately twice as |
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efficient as the commonly used three-point water models (i.e. TIP3P |
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and SPC/E). |
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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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Continuing in the direction of model applications, the final chapter |
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deals with a unique polymorph of ice that was discovered while |
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performing water simulations with the fast simple water models |
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discussed in the previous chapter. This form of ice, called |
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``imaginary ice'' (Ice-$i$), has a low-density structure which is |
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different from any known polymorph observed in either experiment or |
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computer simulation studies. The free energy analysis discussed here |
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shows that this structure is in fact the thermodynamically preferred |
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form of ice for both the single-point and commonly used multi-point |
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water models under the chosen simulation conditions. It is shown that |
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inclusion of electrostatic corrections is necessary to obtain more |
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realistic results; however, the free energies of the various |
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polymorphs (both imaginary and real) in many of these models is shown |
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to be so similar that choice of system properties, like the volume in |
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$NVT$ simulations, can directly influence the ice polymorph expressed. |
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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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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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opportunities 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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unwavering support. |
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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 |
