--- trunk/mattDisertation/Conclusion.tex	2004/02/04 20:22:16	1020
+++ trunk/mattDisertation/Conclusion.tex	2004/03/08 22:15:54	1089
@@ -1,4 +1,50 @@
 
 \chapter{\label{chapt:conclusion}CONCLUSION}
 
-The End.
+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.
+
+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 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} 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.