--- trunk/mattDisertation/Conclusion.tex	2004/03/05 22:16:34	1087
+++ trunk/mattDisertation/Conclusion.tex	2004/03/08 22:15:54	1089
@@ -1,42 +1,50 @@
 
 \chapter{\label{chapt:conclusion}CONCLUSION}
 
-This dissertation has presented the work and research I have
-accomplished in the past five years. Chapt.~\ref{chapt:RSA}
-illustrates one of the first problems I had applied myself to. Given a
-relatively simple model, could we account for the differences seen in
-experiment? By using the methods described in Monte Carlo modeling, I
-was able to write several simulations that provided a clear
-explanation for the majority of the experimental evidence.
+This dissertation has presented the work and research accomplished
+over the course of the past five years. Chapt.~\ref{chapt:RSA}
+illustrated the application of statistical mechanical principles to
+the solution of an experimental problem. Given a relatively simple
+model, could the differences in experimental coverage be accounted
+for? By utilizing Monte Carlo modeling methods, I wrote several
+simulations that provided a clear explanation for the majority of the
+experimental evidence. Namely, that overlapping, or interdigitating
+molecules were responsible for the high surface coverage of the
+``umbrella'' silicon phthalocyanines, while the ``octopus'' molecules,
+which do not overlap, have a much lower coverage.
 
-Later in Chapt.~\ref{chapt:oopse} I present the work I had to do in
-order to solve more complex research problems. It became clear, after
-the work on the RSA simulations, that even simple simulations can take
-a great deal of programming. If I were to simulate the bilayer
-simulations I wanted to investigate, a sophisticated molecular
-modeling package was needed. After examining the options available at
-the time, writing an advanced simulation suite was the best method
-of accomplishing my goals.
+Chapt.~\ref{chapt:oopse} presented the work necessary to the solution
+of more complex research problems. It became clear, after the work on
+the RSA simulations, that even simple simulations can take a great
+deal of programming. If I were to simulate the bilayer systems using a
+coarse-grained model, a sophisticated molecular modeling program was
+required. After examining the options available at the time, writing
+an advanced simulation program was the only realistic solution.
 
-Working with my colleagues we have developed {\sc oopse} to the point
-where it is capable of many unique simulation features. It properly
-integrates rigid body dynamics. It has the capabilities to model
-dipoles rather than point charges only. It can use the MPI interface
-to calculate the long range forces across multiple processors. And
-lastly, it is open source, so that other scientists may use the code,
-and contribute back to the project to enhance the package.
+Working with my lab-mates, I have developed our simulation program
+({\sc oopse}) to the point where it is capable carrying out many
+unique simulations. It properly integrates rigid body dynamics. It has
+the capability to model dipoles rather than point charges only; and is
+therefore able to integrate larger systems for longer times than any
+other current modeling package. It can use the MPI interface to
+calculate the long range forces across multiple processors. And
+lastly, it is open source, so that other scientists may use the code
+and contribute back to the project and enhance the program.
 
-Lastly Chapt.~\ref{chapt:lipid} presents the research for which I
-originally set about the development of {\sc oopse}. The lipid model
-was under continual development while {\sc oopse} was being
-designed. In fact many of the integration ensembles in {\sc oopse}
-were specifically written to continue development of the lipid
-model. The set of simulations presented in the chapter proved that the
-model was capable of spontaneously forming bilayers. It also explored
-the properties of the bilayers formed over a range of
-temperatures. Further extensions to the model will likely include
-exploration of dipole strength on the head as well as varying chain
-configurations (one chain versus two chains, etc.). However, at this
-point there are many questions that can now be explored with this model
-such as the inclusion molecules to diffuse through the bilayer, or
-perhaps exploration of special phases such as the ripple phase.
+Lastly Chapt.~\ref{chapt:lipid} presented the research that became the
+main design goal of {\sc oopse}. The lipid model was under continual
+development while {\sc oopse} was being written. In fact many of the
+integration ensembles in {\sc oopse} were specifically written to
+continue development of the lipid model. The set of simulations
+presented in the chapter have shown that the model is capable of
+spontaneously forming bilayers. It also explored the properties of the
+bilayers over a range of temperatures. Further extensions to the model
+will likely include exploration of how head group dipole strength and
+varying chain configurations (one chain versus two chains, etc.)
+affect the structure and dynamics of the lipid bilayer. However, at
+this point there are many questions that can now be explored with this
+model such as how do small molecules include themselves, and diffuse
+through the bilayer? Or what are the characteristic events that lead
+to the formation of special lipid phases (i.e.~the ripple phase)? It
+is my hope that my contributions to this research will make it
+possible to answer these important questions and many others.