Total.tex

% O.K. tot voor Plimpton_{19}95

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% Define convenience functions to use the author name and the thesis title in the PDF document properties.
\newcommand{\authorname}{Jan Stevens} % The author name without titles.
\newcommand{\thesistitle}{Coarse grained simulations of the DNA nanopistion} % The title

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% defining bibliographystyle
% \bibliographystyle{apalike}
\addbibresource{Bibliography/thesis.bib}

% Start of the actual document
\begin{document}

\selectlanguage{english}

\newcommand\mycommfont[1]{\small\ttfamily\textcolor{blue}{#1}}
\SetCommentSty{mycommfont}

% FRONT MATTER
\frontmatter
\rmfamily

\input{Preamble/Titlepage.tex} \cleardoublepage
\input{Preamble/Copyright.tex} \cleardoublepage
\setcounter{page}{0}
\pagenumbering{roman}

\input{Preamble/Abstract.tex}\cleardoublepage
\input{Preamble/Summary.tex} \cleardoublepage
\listoffigures \cleardoublepage
\linespread{0.816}
{\small \tableofcontents}
\cleardoublepage
\linespread{1}

% MAIN MATTER
\mainmatter
\setcounter{page}{0}
\pagenumbering{arabic}

%% Introduction
\chapter{Introduction}
% \epigraph{The career of a young theoretical physicist consists of treating the harmonic
% oscillator in ever-increasing levels of abstraction.}
% {--- \textup{Sidney Coleman}}
\vspace{-0.5cm}
\epigraph{“...if we were to name the most powerful assumption of all, which leads one on
and on in an attempt to understand life, it is that all things are made of atoms, and
that everything that living things do can be understood in terms of the jigglings and
wigglings of atoms.”}
{--- \textup{Richard P. Feynman}, The Feynman Lectures on Physics}
\input{Chapters/Chapter1/ThesisOutline.tex}
\input{Chapters/Chapter1/BiologicalNanopores.tex}
\input{Chapters/Chapter1/DNA.tex}
\input{Chapters/Chapter1/PolymerPhysics.tex}
\input{Chapters/Chapter1/ComputerSimulations.tex} \cleardoublepage

% \vspace{-1cm}
% \epigraph{Given for one instant an intelligence which could comprehend all
% the forces by which nature is animated and the respective positions
% of the beings which compose it, if moreover this intelligence were vast
% enough to submit these data to analysis, it would embrace in the same
% formula both the movements of the largest bodies in the universe and
% those of the lightest atom; to it nothing would be uncertain, and the
% future as the past would be present to its eyes.}
% {--- \textup{Pierre-Simon Laplace}}
\chapter{The DNA Nanopiston}
\input{Chapters/Chapter2/rotaxaneFormation.tex}
\input{Chapters/Chapter2/operatingPrinciples.tex}
\input{Chapters/Chapter2/cgSimulations.tex}

\cleardoublepage
\chapter{Improving the Model}
% \vspace{-1cm}
\epigraph{All models are wrong, but some are useful.}
{--- \textup{George Box}}%\cite{Box1976}}
\input{Chapters/Chapter3/OxDNA.tex}
\input{Chapters/Chapter3/Thermodynamics.tex}
\input{Chapters/Chapter3/FFS.tex}
\input{Chapters/Chapter3/Simulation.tex} \cleardoublepage

\chapter{Simulations of the Rotaxane}
\vspace{0.5cm}
\epigraphfontsize{\small\itshape}
\epigraph{The career of a young theoretical physicist consists of treating the harmonic
oscillator in ever-increasing levels of abstraction.}
{--- \textup{Sidney Coleman}}
\input{Chapters/Chapter4/MixedRotaxane.tex}
\input{Chapters/Chapter4/ConfFluct.tex}
\input{Chapters/Chapter4/Toehold.tex}

\cleardoublepage
\chapter{Conclusions and Perspectives}
\vspace{0.5cm}
\epigraphfontsize{\small\itshape}
\epigraph{“ Blurring the line between life and the artificial.”}
{--- Man-made molecular machines, \textup{Watson \& Cockroft}}%\cite{Watson2016}}
\input{Chapters/Chapter5/ResultsAndConclusions.tex}
\input{Chapters/Chapter5/FuturePerspectives.tex}


% APPENDIX
\begin{appendices}
\addtocontents{toc}{\protect\setcounter{tocdepth}{1}}
\input{Backmatter/Appendix.tex}
\cleardoublepage
\end{appendices}

\newpage
\thispagestyle{empty}
\mbox{}
\newpage

% BIBLIOGRAPHY

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{\small \printbibliography}
\cleardoublepage
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% \onecolumn
% \thispagestyle{empty}
\input{Backmatter/Acknowledgements.tex}
\cleardoublepage
\thispagestyle{empty}

% Back side of book
\cleartoleftpage{} % Make sure the back page is at an even page number
\input{Backmatter/Back.tex}

\end{document}