+The unfolding system is stored as a chain of \emph{domains} (Figure
+\ref{fig.domain_chain}). Domains can be folded, globular protein
+domains, unfolded protein linkers, AFM cantilevers, or other
+stretchable system components. The system is modeled as graph of
+possible domain states with transitions between them (Figure
+\ref{fig.domain_states}).
+
+\begin{figure}
+\begin{center}
+\subfloat[][]{\label{fig.domain_chain}
+\begin{tikzpicture}[->,node distance=2cm,font=\footnotesize]
+ \tikzstyle{every state}=[fill,draw=red!50,very thick,fill=red!20]
+ \node[state] (A) {domain 1};
+ \node[state] (B) [below of=A] {domain 2};
+ \node[state] (C) [below of=B] {.~.~.};
+ \node[state] (D) [below of=C] {domain $N$};
+ \node (S) [below of=D] {Surface};
+ \node (E) [above of=A] {};
+
+ \path[-] (A) edge (B)
+ (B) edge node [right] {Tension} (C)
+ (C) edge (D)
+ (D) edge (S);
+ \path[->,green] (A) edge node [right,black] {Extension} (E);
+\end{tikzpicture}
+}
+\qquad
+\subfloat[][]{\label{fig.domain_states}
+\begin{tikzpicture}[->,node distance=2.5cm,shorten <=1pt,shorten >=1pt,font=\footnotesize]
+ \tikzstyle{every state}=[fill,draw=blue!50,very thick,fill=blue!20]
+ \node[state] (A) {cantilever};
+ \node[state] (C) [below of=A] {transition};
+ \node[state] (B) [left of=C] {folded};
+ \node[state] (D) [right of=C] {unfolded};
+
+ \path (B) edge [bend left] node [above] {$k_1$} (C)
+ (C) edge [bend left] node [below] {$k_1'$} (B)
+ edge [bend left] node [above] {$k_2$} (D)
+ (D) edge [bend left] node [below] {$k_2'$} (C);
+\end{tikzpicture}
+}
+\caption{\subref{fig.domain_chain} Extending a chain of domains. One end
+ of the chain is fixed, while the other is extended at a constant
+ speed. The domains are coupled with rigid linkers, so the domains
+ themselves must stretch to accomodate the extension.
+ \subref{fig.domain_states} Each domain exists in a discrete state. At
+ each timestep, it may transition into another state following a
+ user-defined state matrix such as this one, showing a metastable
+ transition state and an explicit ``cantilever'' domain.}
+\end{center}
+\end{figure}