titlepg.sty

% 
%       All the information in the fields below should be changed for the thesis/dissertation 
%       The fields here are used with fake information only as a guide.  You may add or delete
%       fields as needed.  The Advisory Committee varies in size, so add members as needed. 
%
\newcommand{\thesistitle}{A Model for the Evolution of Nucleotide Polymerase Directionality}
\newcommand{\thesisyear}{2011}
\newcommand{\thesisname}{Joshua Ballanco}
\newcommand{\thesischairadvisor}{Marc Mansfield}    % this name prints on the title page as chairman and the abstract page as advisor
\newcommand{\committeenameA}{Philip Leopold}
\newcommand{\committeenameB}{A. K. Ganguly}
\newcommand{\committeenameC}{Nicholas Murgolo}
\newcommand{\committeenameD}{Knut Stamnes}
\newcommand{\thesisdepartment}{Chemistry, Chemical Biology, and Biomedical Engineering}
\newcommand{\thesisdate}{May 9th, 2011}
\newcommand{\thesistype}{dissertation}
\newcommand{\thesisdegree}{Doctor of Philosophy}
\newcommand{\thesissigline}[1]{%
  \leftline{\hbox to 2.5in{}\hrulefill}
  \endgraf
  \vspace*{-18pt}
  \leftline{\hbox to 2.5in{}{#1}}}

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% 
%     Thesis / Dissertation title page
%
%     This template is set up initially for dissertations.  The title page will have
%     some modifications to it for a master thesis.  Please read the comments 
%     below
%
%
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\newcommand{\thesistitlepage}{
    \thispagestyle{empty}
    \begin{center}
    \begin{spacing}{2}
      \MakeUppercase {\thesistitle} \\
       by \\
       \thesisname \\
       A \MakeUppercase {\thesistype} \\[3mm]
     \end{spacing}
     \begin{spacing}{1}
       Submitted to the Faculty of the Stevens Institute of Technology \\ 
      in partial fulfillment of the requirements for the degree of \\[3mm]
      \end{spacing}
      \begin{spacing}{2}
    \MakeUppercase {\thesisdegree} \\
    \vspace{20mm}
     \end{spacing}
       \strut \vfill
  \mbox{ }  \hfill \begin{minipage}{80mm}
                       \begin{spacing}{1}
                   

\noindent \rule{3.1in}{0.1mm}
\thesisname, Candidate\\[3mm]
\underline{ADVISORY COMMITTEE}\\[3mm]
\noindent \rule{3.1in}{0.1mm}\\[-1.3mm]
% for master thesis, change Chairman to Advisor
{\thesischairadvisor}, Chairman  \hfill{Date}\\[2mm]
{\noindent \rule{3.1in}{0.1mm}}\\[-1.3mm]
% for master thesis, add Reader after committeenameA
%
{\committeenameA}        \hfill{Date}\\[2mm]
%
%  for master thesis, remove / comment out the following six lines
{\noindent \rule{3.1in}{0.1mm}}\\[-1.3mm]
{\committeenameB}  \hfill{Date}\\[2mm]
{\noindent \rule{3.1in}{0.1mm}}\\[-1.3mm]
{\committeenameC}  \hfill{Date}\\[2mm]
{\noindent \rule{3.1in}{0.1mm}}\\[-1.3mm]
{\committeenameD}  \hfill{Date}\\[2mm]
                 	\end{spacing}
				   \end{minipage}
     \vfill \strut
  \begin{spacing}{1}
   \MakeUppercase {Stevens Institute of Technology}\\
   Castle Point on Hudson \\
  Hoboken, NJ 07030 \\
   \thesisyear
  \end{spacing}
    \end{center}
%   \vfill \strut
    \newpage}

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% 
%     Copyright Page 
%
%     The copyright page is optional
%  
%
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\newcommand{\thesiscopyrightpage}{
    \thispagestyle{empty}      %no page number on the copyright page
		\strut \vfill
		\begin{spacing}{1}
   	\begin{center}
        \textcopyright\ \thesisyear, \thesisname. All rights reserved.
    \end{center}
		\end{spacing}
		\newpage
}

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% 
%     Abstract
%
%     The abstract must be 350 words or less
%  
%
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%
\newcommand{\thesisabstract}{
\begin{center}
\MakeUppercase{\thesistitle} \\
ABSTRACT \\
\end{center}
In all known living organisms, every enzyme that synthesizes nucleic acid polymers does so by adding nucleotide 5'-triphosphates to the 3'-hydroxyl group of the growing chain. This results in the well known $5'\to3'$ directionality of all DNA and RNA Polymerases. The lack of any alternative mechanism, e.g. addition in a $3'\to5'$ direction, may indicate a very early founder effect in the evolution of life, or it may be the result of a selective pressure against such an alternative. In an attempt to determine whether the lack of an alternative polymerase directionality is the result of a founder effect or evolutionary selection, we have constructed a basic model of early polymerase evolution. This model is informed by the essential chemical properties of the nucleotide polymerization reaction. With this model, we are able to simulate the growth of organisms with polymerases that synthesize either $5'\to3'$ or $3'\to5'$ in isolation or in competition with each other. We have found that a competition between organisms with $5'\to3'$ polymerases and $3'\to5'$ polymerases only results in a evolutionarily stable strategy under certain conditions. Furthermore, we have found that mutations lead to a much clearer delineation between conditions that lead to a stable coexistence of these populations and conditions which ultimately lead to success for the $5'\to3'$ form. In addition to presenting a plausible explanation for the uniqueness of enzymatic polymerization reactions, we hope these results also provide an example of how whole organism evolution can be understood based on molecular details.
\newpage
% make the author name flush left
\begin{flushleft}
Author: \thesisname \\
Advisor: \thesischairadvisor \\
Date: \thesisdate \\
Department: \thesisdepartment \\
Degree: \thesisdegree \\
\end{flushleft}
    \newpage}


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% 
%     Dedication Page
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%     This section is optional
%  
%
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\newcommand{\thesisdedicationpage}{
	 \begin{center}
		\textbf{Dedication} \\[3.5in]
       This thesis is dedicated to my loving and supportive wife Ceren
    \end{center}
    \vfill \strut
    \newpage}



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% 
%     Acknowledgements
%
%     This section is optional
%  
%
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\newcommand{\thesisacknowledgements}{

\begin{center}
	\textbf{Acknowledgements} \\[6mm]
\end{center}
I would like to acknowledge Marc Mansfield for the years of guidance, inspiration, and instruction that he so graciously provided during both my undergraduate and graduate education. I would also like to acknowledge Francis Jones for making this research possible, for the encouragement that he provided me as an undergraduate and the opportunity he made available to me as a graduate. I would also like to thank the members of my committee, Philip Leopold, A. K. Ganguly, Knut Stamnes, and Nicholas Murgolo, for their input and invaluable insight. Thanks also go out to the faculty and staff of the Department of Chemistry, Chemical Biology, and Biomedical Engineering for all the help they have provided through the years, and most especially to Mary Newell without whom I would not have made it past the first day of graduate school. Finally, I must humbly admit that the thesis presented here would not exist if it were not for the constant support and encouragement of my beautiful wife Ceren \"Ornek-Ballanco.
    \vfill \strut
    \newpage}

\newcommand{\thesisvita}{
\newpage

\noindent \textbf{Vita} \\
%  insert Vita information below
%  the format of the vita is up to the individual.  Some people include photos or personal information
%  such as marital status, birth place or include publications.
%  There is no set format for the vita, so reformat this part as you wish.     
%  
\begin{center}
\textbf{\thesisname}
\end{center}
\begin{spacing}{1}
\begin{tabbing}
\textbf{Place of birth} \hspace{20mm}  \= Hazel Crest, IL \= \\[3mm]
\textbf{Date of birth}  \> October 5, 1980 \\[3mm]

\textbf{Education}  \> Stevens Institute of Technology, Hoboken, NJ \\
\> Doctoral Candidate in Chemical Biology \\
\>  expected date of graduation, May 2011 \\[3mm]

\> Stevens Institute of Technology, Hoboken, NJ \\
\> Masters of Science in Chemistry \\
\> May 2008 \\[3mm]

\> Stevens Institute of Technology, Hoboken, NJ \\
\> Bachelors of Science in Chemistry with Honors \\
\> May 2002 \\[3mm] 

\end{tabbing}
\end{spacing}


    \vfill \strut
    \newpage}