--- trunk/chrisDissertation/dissertation.tex	2006/09/22 13:45:24	3019
+++ trunk/chrisDissertation/dissertation.tex	2006/09/26 03:07:59	3023
@@ -16,7 +16,7 @@
 
 \frontmatter
 
-\title{APPLICATION AND DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE 
+\title{DEVELOPMENT OF MOLECULAR DYNAMICS TECHNIQUES FOR THE 
 STUDY OF WATER AND OTHER BIOCHEMICAL SYSTEMS}     
 \author{Christopher Joseph Fennell} 
 \work{Dissertation}
@@ -29,34 +29,69 @@ 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. 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.
 
-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.
+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.
 
-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. 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).
 
+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.
+
 \end{abstract}
 
 \begin{dedication}
@@ -78,9 +113,9 @@ Edward P.~Fennell and Rosalie M.~Fennell, for providin
 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
+opportunities and encouragement that allowed me to pursue my
 interests, and I would like to thank my wife, Kelley, for her
-unwaivering support.
+unwavering support.
 \end{acknowledge}
 
 \mainmatter