trunk/mattDisertation/Conclusion.tex


\chapter{\label{chapt:conclusion}CONCLUSION}

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.
Revision:	1089
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#	User	Rev	Content
1	mmeineke	1020
2			\chapter{\label{chapt:conclusion}CONCLUSION}
3
4	mmeineke	1089	This dissertation has presented the work and research accomplished
5			over the course of the past five years. Chapt.~\ref{chapt:RSA}
6			illustrated the application of statistical mechanical principles to
7			the solution of an experimental problem. Given a relatively simple
8			model, could the differences in experimental coverage be accounted
9			for? By utilizing Monte Carlo modeling methods, I wrote several
10			simulations that provided a clear explanation for the majority of the
11			experimental evidence. Namely, that overlapping, or interdigitating
12			molecules were responsible for the high surface coverage of the
13			``umbrella'' silicon phthalocyanines, while the ``octopus'' molecules,
14			which do not overlap, have a much lower coverage.
15	mmeineke	1087
16	mmeineke	1089	Chapt.~\ref{chapt:oopse} presented the work necessary to the solution
17			of more complex research problems. It became clear, after the work on
18			the RSA simulations, that even simple simulations can take a great
19			deal of programming. If I were to simulate the bilayer systems using a
20			coarse-grained model, a sophisticated molecular modeling program was
21			required. After examining the options available at the time, writing
22			an advanced simulation program was the only realistic solution.
23	mmeineke	1087
24	mmeineke	1089	Working with my lab-mates, I have developed our simulation program
25			({\sc oopse}) to the point where it is capable carrying out many
26			unique simulations. It properly integrates rigid body dynamics. It has
27			the capability to model dipoles rather than point charges only; and is
28			therefore able to integrate larger systems for longer times than any
29			other current modeling package. It can use the MPI interface to
30			calculate the long range forces across multiple processors. And
31			lastly, it is open source, so that other scientists may use the code
32			and contribute back to the project and enhance the program.
33	mmeineke	1087
34	mmeineke	1089	Lastly Chapt.~\ref{chapt:lipid} presented the research that became the
35			main design goal of {\sc oopse}. The lipid model was under continual
36			development while {\sc oopse} was being written. In fact many of the
37			integration ensembles in {\sc oopse} were specifically written to
38			continue development of the lipid model. The set of simulations
39			presented in the chapter have shown that the model is capable of
40			spontaneously forming bilayers. It also explored the properties of the
41			bilayers over a range of temperatures. Further extensions to the model
42			will likely include exploration of how head group dipole strength and
43			varying chain configurations (one chain versus two chains, etc.)
44			affect the structure and dynamics of the lipid bilayer. However, at
45			this point there are many questions that can now be explored with this
46			model such as how do small molecules include themselves, and diffuse
47			through the bilayer? Or what are the characteristic events that lead
48			to the formation of special lipid phases (i.e.~the ripple phase)? It
49			is my hope that my contributions to this research will make it
50			possible to answer these important questions and many others.