--- trunk/chrisDissertation/dissertation.tex	2006/09/26 03:07:59	3023
+++ 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{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE 
-STUDY OF WATER AND OTHER BIOCHEMICAL SYSTEMS}     
+STUDY OF WATER AND BIOCHEMICAL SYSTEMS}     
 \author{Christopher Joseph Fennell} 
 \work{Dissertation}
 \degprior{B.Sc.}
@@ -31,66 +33,46 @@ classical molecular simulations, with particular empha
 
 This dissertation comprises a body of research in the field of
 classical molecular simulations, with particular emphasis placed on
-the proper depiction of water. This work is arranged such that the
-techniques and models used within are first developed and tested
-before being applied and compared with experimental results. With this
-organization in mind, it is appropriate that the first chapter deals
-primarily the technique of molecular dynamics and technical
-considerations needed to correctly perform molecular simulations.
+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.
 
-Building on this framework, the second chapter discusses correction
-techniques for handling the long-ranged electrostatic interactions
-common in molecular simulations. Particular focus is placed on a
-shifted-force ({\sc sf}) modification of the damped shifted Coulombic
-summation method. In this work, {\sc sf} is shown to be nearly
-equivalent to the more commonly utilized Ewald summation in
-simulations of condensed phases. Since the {\sc sf} technique 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. The electrostatic damping technique used
-with {\sc sf} is then extended beyond simple charge-charge
-interactions to include point-multipoles. Optimal damping parameter
-settings are also determined to ensure proper depiction of the
-dielectric behavior of molecular systems. Presenting this technique
-early enables its application in the systems discussed in the later
-chapters and shows how it can improve the quality of various molecular
-simulations.
+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.
 
 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. This work results in 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. SSD/RF can be successfully used with
-damped {\sc sf} through the multipolar extension of the technique
-described in the previous chapter. Discussion on the development of
-the two-point tetrahedrally restructured elongated dipole (TRED) water
-model is also presented, and this model 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 water models (i.e. TIP3P
-and SPC/E).
+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.
 
-Continuing in the direction of model applications, the final chapter
-deals with a unique polymorph of ice that was discovered while
-performing water simulations with the fast simple water models
-discussed in the previous chapter. This form of ice, called
-``imaginary ice'' (Ice-$i$), has a low-density structure which is
-different from any known polymorph observed in either experiment or
-computer simulation studies. The free energy analysis discussed 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. It is shown 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 is shown
-to be so similar that choice of system properties, like the volume in
-$NVT$ simulations, can directly influence the ice polymorph expressed.
+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}
 
@@ -106,16 +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
-opportunities and encouragement that allowed me to pursue my
-interests, and I would like to thank my wife, Kelley, for her
-unwavering 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