\section{Experimental setup and procedure}%-----------------------------------

We mechanically unfold our proteins by pulling them apart with an atomic force microscope (AFM).
A brief review of the operating principle of an AFM is given in Section~\ref{sec.afm}.
We discuss the procedure used to unfold a protein, give an overview of the supporting equipment, and present some example data in Section~\ref{sec.unfold_procedure}.
A temperature control module was built by a former graduate student in order to monitor and control the temperature at which we unfold our proteins. % Y. Yang
We will discuss the temperature control setup in detail in~\ref{sec.temp_control}.

We have been streamlining our experiment to ease the collection of the large datasets required to extract statistically significant amount of data.
In preparation for temperature-dependent protein unfolding experiments, we started making some alterations to our experiment control software and hardware.
One goal was to obtain automatic control of the stepping motor used for coarse positioning, which will allow us to compensate for thermal drift thus extend experiment run times.
We discuss the automatic stepper-control system in Section~\ref{sec.stepper}.

As the stepping motor software evolved, we had difficulty updating the experiment control software to integrate the new features.
After much thought, we decided that the best long term solution would be to scrap our current architecture and rebuild our software in a more modular and flexible fashion.
We discuss our resulting experiment server project in Section~\ref{sec.server}.

In order to extract useful information from the a protein unfolding experiment, the successful protein unfolding curves must be separated from an abundance of force curves without unfolding events.
We discuss a developing procedure for automatically sorting force curves in Section~\ref{sec.auto_sort}.

Finally, we discuss the theory that allows the extraction of frustration from temperature dependent unfolding measurements in Section~\ref{sec.theory}, and apply it to some previous Ubiquitin unfolding data in Section~\ref{sec.ubiquitin}.

\include{afm}
\include{unfold_procedure}
\include{temp_control}
\include{stepper_control}
\include{experiment_server}
\include{sorting}
\include{temp_depend}
\include{temp_ubiq}
