| 1 |
< |
\documentclass[12pt]{ndthesis} |
| 1 |
> |
\documentclass[nosummary]{ndthesis} |
| 2 |
|
|
| 3 |
|
% some packages for things like equations and graphics |
| 4 |
|
\usepackage[tbtags]{amsmath} |
| 11 |
|
\usepackage{cite} |
| 12 |
|
\usepackage{enumitem} |
| 13 |
|
\renewcommand{\appendixname}{APPENDIX} |
| 14 |
+ |
\clubpenalty=10000 |
| 15 |
+ |
\widowpenalty=10000 |
| 16 |
|
|
| 17 |
|
\begin{document} |
| 18 |
|
|
| 19 |
|
\frontmatter |
| 20 |
|
|
| 21 |
< |
\title{APPLICATION AND DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE |
| 22 |
< |
STUDY OF WATER AND OTHER BIOCHEMICAL SYSTEMS} |
| 21 |
> |
\title{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE |
| 22 |
> |
STUDY OF WATER AND BIOCHEMICAL SYSTEMS} |
| 23 |
|
\author{Christopher Joseph Fennell} |
| 24 |
|
\work{Dissertation} |
| 25 |
|
\degprior{B.Sc.} |
| 31 |
|
|
| 32 |
|
\begin{abstract} |
| 33 |
|
|
| 34 |
< |
The following dissertation lays out research that I have performed |
| 35 |
< |
over the last several years. All of the work relies on the technique of |
| 36 |
< |
molecular dynamics, and in this dissertation I start by outlining many |
| 37 |
< |
of the considerations that go into molecular dynamics |
| 38 |
< |
simulations. This is followed by an introduction to {\sc oopse}, the |
| 39 |
< |
object oriented parallel simulation engine, which is a program for |
| 40 |
< |
performing molecular simulations developed and maintained in our |
| 41 |
< |
lab. Most of the research was performed either using {\sc oopse} or |
| 40 |
< |
earlier code that predated {\sc oopse}. |
| 34 |
> |
This dissertation comprises a body of research in the field of |
| 35 |
> |
classical molecular simulations, with particular emphasis placed on |
| 36 |
> |
the proper depiction of water. It is arranged such that the techniques |
| 37 |
> |
and models are first developed and tested before being applied and |
| 38 |
> |
compared with experimental results. Accordingly, the first chapter |
| 39 |
> |
starts by introducing the technique of molecular dynamics and |
| 40 |
> |
discussing technical considerations needed to correctly perform |
| 41 |
> |
molecular simulations. |
| 42 |
|
|
| 43 |
< |
This introduction is followed by three chapters that discuss in detail |
| 44 |
< |
the primary research projects for which I am responsible. The first |
| 45 |
< |
project discusses my work on electrostatic interaction correction |
| 46 |
< |
techniques, with applications to water and biologically relevant |
| 47 |
< |
molecular systems. This leads into work on improving the depiction of |
| 48 |
< |
water in molecular simulations by refining simple and highly |
| 49 |
< |
computationally efficient single point water models. The final project |
| 50 |
< |
discussed in this body of research involves free energy calculations |
| 51 |
< |
of ice polymorphs, and includes investigations of a new ice polymorph |
| 52 |
< |
that we discovered while performing simulations involving the single |
| 52 |
< |
point water models. |
| 43 |
> |
The second chapter builds on these consideration aspects by discussing |
| 44 |
> |
correction techniques for handling long-ranged electrostatic |
| 45 |
> |
interactions. Particular focus is placed on the damped shifted force |
| 46 |
> |
({\sc sf}) technique, and it is shown to be nearly equivalent to the |
| 47 |
> |
Ewald summation in simulations of condensed phases. Since the {\sc sf} |
| 48 |
> |
technique is pairwise, it scales as $\mathcal{O}(N)$ and lacks |
| 49 |
> |
periodicity artifacts. This technique is extended to include |
| 50 |
> |
point-multipoles, and optimal damping parameters are determined to |
| 51 |
> |
ensure proper depiction of the dielectric behavior of molecular |
| 52 |
> |
systems. |
| 53 |
|
|
| 54 |
< |
I end this dissertation with some concluding remarks and |
| 55 |
< |
appendices. The conclusion simply sums up the previous sections and |
| 56 |
< |
comments on the research findings. The appendices include supporting |
| 57 |
< |
information and a more detailed look at systems that were treated in a |
| 58 |
< |
more general form in the earlier sections. |
| 54 |
> |
The third chapter applies the above techniques and focuses on water |
| 55 |
> |
model development, specifically the single-point soft sticky dipole |
| 56 |
> |
(SSD) model. In order to better depict water with SSD in computer |
| 57 |
> |
simulations, it needed to be reparametrized, resulting in SSD/RF and |
| 58 |
> |
SSD/E, new variants optimized for simulations with and without a |
| 59 |
> |
reaction field correction. These new single-point models are more |
| 60 |
> |
efficient than the more common multi-point models and better capture |
| 61 |
> |
the dynamic properties of water. SSD/RF can be used with damped {\sc |
| 62 |
> |
sf} through the multipolar extension described in the previous |
| 63 |
> |
chapter. |
| 64 |
|
|
| 65 |
+ |
The final chapter deals with a unique polymorph of ice that was |
| 66 |
+ |
discovered while performing simulations with the SSD models. This |
| 67 |
+ |
form of ice, called ``imaginary ice'' (Ice-$i$), has a low-density |
| 68 |
+ |
structure which is different from any previously known ice |
| 69 |
+ |
polymorph. The free energy analysis discussed here shows that it is |
| 70 |
+ |
the thermodynamically preferred form of ice for both the single-point |
| 71 |
+ |
and commonly used multi-point water models. Including electrostatic |
| 72 |
+ |
corrections is necessary to obtain more realistic results; however, |
| 73 |
+ |
the free energies of the studied polymorphs are typically so similar |
| 74 |
+ |
that system properties, like the volume in $NVT$ simulations, can |
| 75 |
+ |
directly influence the ice polymorph expressed. |
| 76 |
+ |
|
| 77 |
|
\end{abstract} |
| 78 |
|
|
| 79 |
|
\begin{dedication} |
| 88 |
|
I would to thank my advisor, J. Daniel Gezelter, for the guidance, |
| 89 |
|
perspective, and direction he provided during this work. He is a great |
| 90 |
|
teacher and helped fuel my desire to learn. I would also like to thank |
| 91 |
< |
my fellow group members - Dr.~Matthew A.~Meineke, Dr.~Teng Lin, |
| 92 |
< |
Charles F.~Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle |
| 93 |
< |
S.~Haygarth, Patrick Conforti, Megan Sprague, and Dan Combest for |
| 94 |
< |
helpful comments and suggestions along the way. I would also like to |
| 95 |
< |
thank Christopher Harrison and Dr. Steven Corcelli for additional |
| 96 |
< |
discussions and comments. Finally, I would like to thank my parents, |
| 97 |
< |
Edward P.~Fennell and Rosalie M.~Fennell, for providing the |
| 98 |
< |
opprotunities and encouragement that allowed me to pursue my |
| 99 |
< |
interests, and I would like to thank my wife, Kelley, for her |
| 83 |
< |
unwaivering support. |
| 91 |
> |
my fellow group members - Dr.~Matthew Meineke, Dr.~Teng Lin, Charles |
| 92 |
> |
Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle Haygarth, |
| 93 |
> |
Patrick Conforti, Megan Sprague, and Dan Combest for helpful comments |
| 94 |
> |
and suggestions along the way. I would also like to thank Christopher |
| 95 |
> |
Harrison and Dr.~Steven Corcelli for additional discussions and |
| 96 |
> |
comments. Finally, I would like to thank my parents, Edward and |
| 97 |
> |
Rosalie Fennell, for providing the opportunities and encouragement |
| 98 |
> |
that allowed me to pursue my interests, and I would like to thank my |
| 99 |
> |
wife, Kelley, for her unwavering support. |
| 100 |
|
\end{acknowledge} |
| 101 |
|
|
| 102 |
|
\mainmatter |
