--- trunk/chrisDissertation/dissertation.tex	2006/09/22 13:45:24	3019
+++ trunk/chrisDissertation/dissertation.tex	2006/10/11 14:33:13	3042
@@ -1,4 +1,4 @@
-\documentclass[12pt]{ndthesis}
+\documentclass[nosummary]{ndthesis}
 
 % some packages for things like equations and graphics
 \usepackage[tbtags]{amsmath}
@@ -11,13 +11,15 @@
 \usepackage{cite}
 \usepackage{enumitem}
 \renewcommand{\appendixname}{APPENDIX}
+\clubpenalty=10000
+\widowpenalty=10000
 
 \begin{document}
 
 \frontmatter
 
-\title{APPLICATION AND DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE 
-STUDY OF WATER AND OTHER BIOCHEMICAL SYSTEMS}     
+\title{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE 
+STUDY OF WATER AND BIOCHEMICAL SYSTEMS}     
 \author{Christopher Joseph Fennell} 
 \work{Dissertation}
 \degprior{B.Sc.}
@@ -29,34 +31,49 @@ STUDY OF WATER AND OTHER BIOCHEMICAL SYSTEMS}     
 
 \begin{abstract}
 
-The following dissertation lays out research that I have performed
-over the last several years. All of the work relies on the technique of
-molecular dynamics, and in this dissertation I start by outlining many
-of the considerations that go into molecular dynamics
-simulations. This is followed by an introduction to {\sc oopse}, the
-object oriented parallel simulation engine, which is a program for
-performing molecular simulations developed and maintained in our
-lab. Most of the research was performed either using {\sc oopse} or
-earlier code that predated {\sc oopse}.
+This dissertation comprises a body of research in the field of
+classical molecular simulations, with particular emphasis placed on
+the proper depiction of water. It is arranged such that the techniques
+and models are first developed and tested before being applied and
+compared with experimental results. Accordingly, the first chapter
+starts by introducing the technique of molecular dynamics and
+discussing technical considerations needed to correctly perform
+molecular simulations.
 
-This introduction is followed by three chapters that discuss in detail
-the primary research projects for which I am responsible. The first
-project discusses my work on electrostatic interaction correction
-techniques, with applications to water and biologically relevant
-molecular systems. This leads into work on improving the depiction of
-water in molecular simulations by refining simple and highly
-computationally efficient single point water models. The final project
-discussed in this body of research involves free energy calculations
-of ice polymorphs, and includes investigations of a new ice polymorph
-that we discovered while performing simulations involving the single
-point water models.
+The second chapter builds on these consideration aspects by discussing
+correction techniques for handling long-ranged electrostatic
+interactions. Particular focus is placed on the damped shifted force
+({\sc sf}) technique, and it is shown to be nearly equivalent to the
+Ewald summation in simulations of condensed phases. Since the {\sc sf}
+technique is pairwise, it scales as $\mathcal{O}(N)$ and lacks
+periodicity artifacts. This technique is extended to include
+point-multipoles, and optimal damping parameters are determined to
+ensure proper depiction of the dielectric behavior of molecular
+systems.
 
-I end this dissertation with some concluding remarks and
-appendices. The conclusion simply sums up the previous sections and
-comments on the research findings.  The appendices include supporting
-information and a more detailed look at systems that were treated in a
-more general form in the earlier sections.
+The third chapter applies the above techniques and focuses on water
+model development, specifically the single-point soft sticky dipole
+(SSD) model. In order to better depict water with SSD in computer
+simulations, it needed to be reparametrized, resulting in SSD/RF and
+SSD/E, new variants optimized for simulations with and without a
+reaction field correction. These new single-point models are more
+efficient than the more common multi-point models and better capture
+the dynamic properties of water. SSD/RF can be used with damped {\sc
+sf} through the multipolar extension described in the previous
+chapter.
 
+The final chapter deals with a unique polymorph of ice that was
+discovered while performing simulations with the SSD models.  This
+form of ice, called ``imaginary ice'' (Ice-$i$), has a low-density
+structure which is different from any previously known ice
+polymorph. The free energy analysis discussed here shows that it is
+the thermodynamically preferred form of ice for both the single-point
+and commonly used multi-point water models.  Including electrostatic
+corrections is necessary to obtain more realistic results; however,
+the free energies of the studied polymorphs are typically so similar
+that system properties, like the volume in $NVT$ simulations, can
+directly influence the ice polymorph expressed.
+
 \end{abstract}
 
 \begin{dedication}
@@ -71,16 +88,15 @@ teacher and helped fuel my desire to learn. I would al
 I would to thank my advisor, J. Daniel Gezelter, for the guidance,
 perspective, and direction he provided during this work. He is a great
 teacher and helped fuel my desire to learn. I would also like to thank
-my fellow group members - Dr.~Matthew A.~Meineke, Dr.~Teng Lin,
-Charles F.~Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle
-S.~Haygarth, Patrick Conforti, Megan Sprague, and Dan Combest for
-helpful comments and suggestions along the way. I would also like to
-thank Christopher Harrison and Dr. Steven Corcelli for additional
-discussions and comments. Finally, I would like to thank my parents,
-Edward P.~Fennell and Rosalie M.~Fennell, for providing the
-opprotunities and encouragement that allowed me to pursue my
-interests, and I would like to thank my wife, Kelley, for her
-unwaivering support.
+my fellow group members - Dr.~Matthew Meineke, Dr.~Teng Lin, Charles
+Vardeman~II, Kyle Daily, Xiuquan Sun, Yang Zheng, Kyle Haygarth,
+Patrick Conforti, Megan Sprague, and Dan Combest for helpful comments
+and suggestions along the way. I would also like to thank Christopher
+Harrison and Dr.~Steven Corcelli for additional discussions and
+comments. Finally, I would like to thank my parents, Edward and
+Rosalie Fennell, for providing the opportunities and encouragement
+that allowed me to pursue my interests, and I would like to thank my
+wife, Kelley, for her unwavering support.
 \end{acknowledge}
 
 \mainmatter