| 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{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE |
| 22 |
< |
STUDY OF WATER AND OTHER BIOCHEMICAL SYSTEMS} |
| 22 |
> |
STUDY OF WATER AND BIOCHEMICAL SYSTEMS} |
| 23 |
|
\author{Christopher Joseph Fennell} |
| 24 |
|
\work{Dissertation} |
| 25 |
|
\degprior{B.Sc.} |
| 33 |
|
|
| 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. This work is arranged such that the |
| 37 |
< |
techniques and models used within are first developed and tested |
| 38 |
< |
before being applied and compared with experimental results. With this |
| 39 |
< |
organization in mind, it is appropriate that the first chapter deals |
| 40 |
< |
primarily the technique of molecular dynamics and technical |
| 41 |
< |
considerations needed to correctly perform molecular simulations. |
| 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 |
< |
Building on this framework, the second chapter discusses correction |
| 44 |
< |
techniques for handling the long-ranged electrostatic interactions |
| 45 |
< |
common in molecular simulations. Particular focus is placed on a |
| 46 |
< |
shifted-force ({\sc sf}) modification of the damped shifted Coulombic |
| 47 |
< |
summation method. In this work, {\sc sf} is shown to be nearly |
| 48 |
< |
equivalent to the more commonly utilized Ewald summation in |
| 49 |
< |
simulations of condensed phases. Since the {\sc sf} technique is |
| 50 |
< |
pairwise, it scales as $\mathcal{O}(N)$ and lacks periodicity |
| 51 |
< |
artifacts introduced through heavy reliance on the reciprocal-space |
| 52 |
< |
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. |
| 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 |
|
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. This work results in the |
| 58 |
< |
development of SSD/RF and SSD/E, new variants of the SSD model |
| 59 |
< |
optimized for simulations with and without a reaction field |
| 60 |
< |
correction. These new single-point models are more efficient than the |
| 61 |
< |
common multi-point partial charge models and better capture the |
| 62 |
< |
dynamic properties of water. SSD/RF can be successfully used with |
| 63 |
< |
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). |
| 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 |
< |
Continuing in the direction of model applications, the final chapter |
| 66 |
< |
deals with a unique polymorph of ice that was discovered while |
| 67 |
< |
performing water simulations with the fast simple water models |
| 68 |
< |
discussed in the previous chapter. This form of ice, called |
| 69 |
< |
``imaginary ice'' (Ice-$i$), has a low-density structure which is |
| 70 |
< |
different from any known polymorph observed in either experiment or |
| 71 |
< |
computer simulation studies. The free energy analysis discussed here |
| 72 |
< |
shows that this structure is in fact the thermodynamically preferred |
| 73 |
< |
form of ice for both the single-point and commonly used multi-point |
| 74 |
< |
water models under the chosen simulation conditions. It is shown that |
| 75 |
< |
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. |
| 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 |
|
|
| 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 |
< |
opportunities and encouragement that allowed me to pursue my |
| 99 |
< |
interests, and I would like to thank my wife, Kelley, for her |
| 118 |
< |
unwavering 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 |
