\subsection{Atomic force microscopy}
\label{sec.afm}

We obtain unfolding forces for proteins by mechanically pulling with an AFM (see Figure~\ref{fig.afm_schematic}).
\begin{figure}[btp]
 \centering
 \includegraphics[width=0.6\textwidth]{AFM_bw_schematic} \\
 \caption{Basic AFM operation\cite{warr}.
          The laser bounces off of the reflective back of the cantilever and hits a four-segment photodiode, which records the location of the laser spot.
	  The force on the tip can be measured indirectly by watching the deflection of the laser spot and modeling the cantilever as a spring obeying Hooke's Law.
          The specimen is mounted on a piezoelectric scanner, which allows it to be positioned in three dimensions relative to the tip.
          In our setup, the entire cantilever-surface system is enclosed by a buffer-filled fluid cell.}
 \label{fig.afm_schematic}
\end{figure}
The AFM gives us access to picoNewton forces over nanometer distances, which allows the unfolding of individual protein to be monitored directly.

Because AFMs have traditionally been used for imaging, commercial control systems and software are geared towards those applications.
Our AFM control hardware (NanoScope IIIa, from Digital Instruments, Santa Barbara, CA) has been significantly modified to give direct access to the piezo control lines and photodiode signals.
We have also almost completely replaced the commercial software with home-built programs, which we discuss in Section~\ref{sec.server}.
Our AFM itself (MultiMode, from Digital Instruments) also has some minor modifications which we discuss in Section~\ref{sec.stepper}.


