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\title{Calculating equilibrium free energies with nonequilibrium path sampling methods}

\author{Harald Oberhofer}

\begin{document}
\pagenumbering{roman}
% \maketitle
\input{src/title.tex}
\cleardoublepage
\input{src/acknowl.tex}
\cleardoublepage
\input{src/abstracts.tex}
\cleardoublepage
\tableofcontents
\listoffigures
\listoftables
\newpage
\cleardoublepage
\pagenumbering{arabic}

	\chapter{Introduction}
		\input{src/intro.tex}
	\chapter{Theory}
		\label{theory}
		\input{src/theorygen.tex}
		\section{Thermodynamics: free rnergy}
			\input{src/freeenergy.tex}
		\section{The Jarzynski theorem}
			\label{jarzgeneral}
			\input{src/jarzgeneral.tex}

	\chapter[Previous efforts]{Previous efforts to achieve better sampling with Jarzynski's equality}
		\label{previous}
		\input{src/effortsgeneral.tex}
		\section{A sketch of Sun's method}
			\input{src/effortssun.tex}
		\section{Other methods}
			\input{src/effortsother.tex}

	\chapter{Methods}
		\label{methods}
		\input{src/methodsgeneral.tex}
		\section{Transition path sampling}
			\label{methodstps}
			\input{src/methodstps.tex}
		\section{Umbrella Sampling}
			\label{methodsumb}
			\input{src/methodsumb.tex}
		\section{Wang-Landau sampling}
			\label{methodswanlan}
			\input{src/methodswal.tex}
		\section[Comparing umbrella and Wang-Landau sampling]{A comparison between umbrella sampling and Wang-Landau sampling in the 
				context of paths sampling}
			\label{methodscomp}
			\input {src/methodscomp.tex}
		\section{General simulation details}
		\input{src/details.tex}

	\chapter{Dragged harmonic oscillator}
		\label{mypot}
		\input{src/dhogeneral.tex}
		\section{General remarks}
			\label{simplegeneral}
			\input{src/simplegeneral.tex}
		\section{Analytical solution}
			\label{simpleanalytical}
			\input{src/simpleanalytical.tex}
		\section{Simulations}
			\subsection{Straightforward simulation}
				\input{src/simmystraight.tex}
			\subsection{Wang-Landau sampling simulation}
				\input{src/simmywal.tex}
			\subsection{Umbrella sampling simulation}
				\label{mypotumb}
				\input{src/mypotumb.tex}
				\input{src/simmyumb.tex}
% 		\section{Conclusion}
% 			\input{src/myconc.tex}

	\chapter[Sun's model]{Double well to single well transition (Sun's model)}
		\label{sunpot}
		\input{src/sunint.tex}
		\section{General remarks}
			\label{sungeneral}
			\input{src/sungeneral.tex}
		\section{Simulations}
			\label{sunsim}
			\subsection{Straightforward simulation}
				\input{src/simsunstraight.tex}
			\subsection{Wang-Landau sampling simulation}
				\input{src/simsunwal}
			\subsection{Umbrella sampling simulation}
				\label{sunpotumb}
				\input{src/sunpotumb.tex}
				\input{src/simsunumb.tex}
% 		\section{Conclusion}
% 			\input{src/sunconc.tex}

	\chapter{Comparison with non-Jarzinsky methods}
		\label{comp}
		\input{src/nonjcomp.tex}
	\chapter{Final remarks}
		\input{src/finalconc.tex}

	\newpage
	\appendix
% 	\pagenumbering{alph}
	\chapter{Adiabatic invariants}
		\label{adiabinv}
		\input{src/adiabinv.tex}
	\chapter{Tables}
		\label{tables}
		\input{src/tables.tex}
	\bibliography{src/bibliography}
\end{document}