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