trunk/chrisDissertation/Conclusion.tex

\chapter{\label{chap:conclusion}CONCLUSION}

The preceding chapters and included appendices discuss the primary
aspects of the research I have performed and been involved with over
the last several years. Rather than presenting the topics in a
chronological fashion, they were arranged to form a series where the
later topics apply and extend the findings of the former topics. This
layout is more instructive and provides a more cohesive progression of
research efforts.

The first chapter laid out the foundation from which the research in
the later chapters is built upon, primarily the technique of molecular
dynamics. This chapter also introduces {\sc oopse}, the object
oriented parallel simulation engine, the unified code-base developed in
our lab for performing molecular simulations. Starting out as a
collection of separate programs written by different group members,
{\sc oopse} has developed into one of the few parallel molecular
dynamics packages capable of accurately integrating rigid bodies,
point multipoles, and metallic potentials.\cite{Meineke05}

The second chapter discussed correction techniques for handling the
long-ranged electrostatic interactions common in molecular
simulations, in particular our shifted-force ({\sc sf}) modification
of the damped shifted Coulombic summation method developed by Wolf
{\it et al.}\cite{Wolf99} In the work outlined here, we showed {\sc
sf} to be nearly equivalent to the more prevalent Ewald summation in
simulations of condensed phases, and since it is pairwise, it scales
as $\mathcal{O}(N)$ and lacks periodicity artifacts introduced through
heavy reliance on the reciprocal-space portion of the Ewald sum. We
extended the electrostatic damping technique used with {\sc sf} beyond
simple charge-charge interactions to include point-multipoles, and we
also identified optimal damping parameter settings to ensure proper
depiction of the dielectric behavior of molecular systems. Presenting
this technique early enables us to apply it in the systems discussed
in the later chapters and show how it can improve the quality of
various molecular simulations.

The third chapter focused on simple water models, specifically the
single-point soft sticky dipole (SSD) model for water. We implemented
this model and realized that we need to reparametrize it in order to
use it in our simulations. This lead to the development of SSD/RF and
SSD/E, new variants of the SSD model optimized for simulations with
and without a reaction field correction. These new single-point models
are more efficient than the common multi-point partial charge models
and better capture the dynamic properties of water. We also showed
that SSD/RF can be successfully used with damped {\sc sf} through our
multipolar extension of the technique. For the sake of completeness,
we also developed the two-point tetrahedrally restructured elongated
dipole (TRED) water model, which is optimized for use with the damped
{\sc sf} technique. Though there remain some algorithmic complexities
that need to be addressed (logic for neglecting charge-quadrupole
interactions between other TRED molecules) to use this model in
general simulations, it is approximately twice as efficient as the
commonly used three-point charge water models (i.e. TIP3P and
SPC/E). This work succeeds in extending the limits of the
computational efficiency of water models that can capture the
thermodynamic and dynamic properties of liquid water.

The final chapter deals with a unique polymorph of ice that we
discovered while performing water simulations with the fast simple
water models discussed in chapter~\ref{chap:water}. This form of ice,
which we called ``imaginary ice'' (Ice-$i$), has a low-density
structure which is different from any known polymorph from either
experiment or other simulations. The free energy analysis performed
here shows that this structure is in fact the thermodynamically
preferred form of ice for both the single-point and commonly used
multi-point water models under the chosen simulation conditions. We
then showed that inclusion of electrostatic corrections is necessary
to obtain more realistic results; however, the free energies of the
various polymorphs (both imaginary and real) in many of these models
was shown to be so similar that choice of system properties, like the
volume in $NVT$ simulations, will directly influence the expressed ice
polymorph. This work shows that researchers ought to be wary of using
these simplistic water models in the study of complex phase behavior
where the choice of a water model that includes many-body effects,
such as polarizability, might be more appropriate.

The work presented in this dissertation includes advancements in
simulation techniques, improved molecular models, and applications of
both in simulations of novel molecular systems. In addition to
answering interesting questions related to these topics, this work
opens up new routes which other researchers can utilize to extend and
improve their own work. Though specific in focus, through pathways
such as these, this work can gain wider utility and expand our
understanding of natural physical and chemical processes.
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#	User	Rev	Content
1	chrisfen	2987	\chapter{\label{chap:conclusion}CONCLUSION}
2
3	chrisfen	3001	The preceding chapters and included appendices discuss the primary
4			aspects of the research I have performed and been involved with over
5			the last several years. Rather than presenting the topics in a
6			chronological fashion, they were arranged to form a series where the
7			later topics apply and extend the findings of the former topics. This
8			layout is more instructive and provides a more cohesive progression of
9			research efforts.
10
11			The first chapter laid out the foundation from which the research in
12			the later chapters is built upon, primarily the technique of molecular
13			dynamics. This chapter also introduces {\sc oopse}, the object
14			oriented parallel simulation engine, the unified code-base developed in
15			our lab for performing molecular simulations. Starting out as a
16			collection of separate programs written by different group members,
17			{\sc oopse} has developed into one of the few parallel molecular
18			dynamics packages capable of accurately integrating rigid bodies,
19			point multipoles, and metallic potentials.\cite{Meineke05}
20
21			The second chapter discussed correction techniques for handling the
22			long-ranged electrostatic interactions common in molecular
23			simulations, in particular our shifted-force ({\sc sf}) modification
24			of the damped shifted Coulombic summation method developed by Wolf
25			{\it et al.}\cite{Wolf99} In the work outlined here, we showed {\sc
26	chrisfen	3023	sf} to be nearly equivalent to the more prevalent Ewald summation in
27	chrisfen	3001	simulations of condensed phases, and since it is pairwise, it scales
28			as $\mathcal{O}(N)$ and lacks periodicity artifacts introduced through
29			heavy reliance on the reciprocal-space portion of the Ewald sum. We
30			extended the electrostatic damping technique used with {\sc sf} beyond
31			simple charge-charge interactions to include point-multipoles, and we
32			also identified optimal damping parameter settings to ensure proper
33			depiction of the dielectric behavior of molecular systems. Presenting
34			this technique early enables us to apply it in the systems discussed
35			in the later chapters and show how it can improve the quality of
36			various molecular simulations.
37
38			The third chapter focused on simple water models, specifically the
39			single-point soft sticky dipole (SSD) model for water. We implemented
40			this model and realized that we need to reparametrize it in order to
41			use it in our simulations. This lead to the development of SSD/RF and
42			SSD/E, new variants of the SSD model optimized for simulations with
43			and without a reaction field correction. These new single-point models
44			are more efficient than the common multi-point partial charge models
45			and better capture the dynamic properties of water. We also showed
46			that SSD/RF can be successfully used with damped {\sc sf} through our
47			multipolar extension of the technique. For the sake of completeness,
48			we also developed the two-point tetrahedrally restructured elongated
49			dipole (TRED) water model, which is optimized for use with the damped
50			{\sc sf} technique. Though there remain some algorithmic complexities
51			that need to be addressed (logic for neglecting charge-quadrupole
52			interactions between other TRED molecules) to use this model in
53			general simulations, it is approximately twice as efficient as the
54			commonly used three-point charge water models (i.e. TIP3P and
55			SPC/E). This work succeeds in extending the limits of the
56			computational efficiency of water models that can capture the
57			thermodynamic and dynamic properties of liquid water.
58
59			The final chapter deals with a unique polymorph of ice that we
60			discovered while performing water simulations with the fast simple
61	chrisfen	3042	water models discussed in chapter~\ref{chap:water}. This form of ice,
62	chrisfen	3001	which we called ``imaginary ice'' (Ice-$i$), has a low-density
63			structure which is different from any known polymorph from either
64			experiment or other simulations. The free energy analysis performed
65			here shows that this structure is in fact the thermodynamically
66			preferred form of ice for both the single-point and commonly used
67			multi-point water models under the chosen simulation conditions. We
68			then showed that inclusion of electrostatic corrections is necessary
69			to obtain more realistic results; however, the free energies of the
70			various polymorphs (both imaginary and real) in many of these models
71			was shown to be so similar that choice of system properties, like the
72			volume in $NVT$ simulations, will directly influence the expressed ice
73			polymorph. This work shows that researchers ought to be wary of using
74			these simplistic water models in the study of complex phase behavior
75			where the choice of a water model that includes many-body effects,
76			such as polarizability, might be more appropriate.
77
78			The work presented in this dissertation includes advancements in
79			simulation techniques, improved molecular models, and applications of
80			both in simulations of novel molecular systems. In addition to
81			answering interesting questions related to these topics, this work
82			opens up new routes which other researchers can utilize to extend and
83			improve their own work. Though specific in focus, through pathways
84			such as these, this work can gain wider utility and expand our
85			understanding of natural physical and chemical processes.