%-----------------------end preamble-------------------------

\begin{document}

\maketitle

\begin{frame}
 \titlepage
\end{frame}

\section{Protein unfolding}

\subsection{Introduction}

\begin{frame}
 \frametitle{Proteins from DNA}
 \begin{center}
  \includegraphics[width=0.6\textwidth]{translation} \\
  Transcription and translation\cite{nih}.
 \end{center}
\end{frame}

\begin{frame}
 \frametitle{The many-many-many body problem}
 \begin{columns}[c]
  \column{\evencolwidth}
   \begin{center}
   \includegraphics[width=\textwidth]{folding_paradox} \\
    Levinthal paradox%\cite{nolting00}
   \end{center}
  \column{\evencolwidth}
   \begin{center}
    \includegraphics[width=\textwidth]{golfFunnel} \\
    A hypothetical energy landscape %\cite{nolting05}
   \end{center}
 \end{columns}
\end{frame}


\subsection{Motivation}

\begin{frame}
 \frametitle{The principle of minimum frustration}
 \begin{columns}[c]
  \column{\evencolwidth}
   \begin{center}
    \includegraphics[width=\textwidth]{timescale} \\
    Protein folding timescales at 25{\dg}C and pH 7\cite{nolting05}
   \end{center}
  \column{\evencolwidth}
   \begin{center}
    \includegraphics[width=0.6\textwidth]{lock_in} \\
    The principle of minimum frustration\cite{saito97}.
   \end{center}
 \end{columns}
\end{frame}

\begin{frame}
 \frametitle{More nice funnel potentials}
 \begin{columns}
  \column{\evencolwidth}
   \begin{center}
    \includegraphics[width=\textwidth]{smoothFunnel} \\
   \end{center}
  \column{\evencolwidth}
   \begin{center}
    \includegraphics[width=\textwidth]{bumpyBowl} \\
   \end{center}
 \end{columns}
\end{frame}

\subsubsection{Measuring energy roughness}

\begin{frame}
 \frametitle{Energy roughness $\varepsilon$}
 \begin{center}
  \includegraphics[width=0.7\textwidth]{hyeon_landscape} \\
  Proposed energy roughness model\cite{hyeon03}.
           $F(x) = F_0(x) + F_1(x)$
 \end{center}
\end{frame}

\begin{frame}
 \frametitle{Kramers' problem}
 \begin{align}
  k_R^{-1}(f) &= \frac{2 \pi \gamma}{\omega_0 \omega_{ts}}
                 \langle e^{-\beta F_1}\rangle
		 \langle e^{\beta F_1} \rangle
		 e^{\beta (\Delta F_0^\ddagger - f \Delta x)}
		                                    & \text{Hyeon Eqn. 3}
		                                    \nonumber
 \end{align}
 Where
 \begin{itemize}
 \item $\gamma$ is the coefficient of ``friction'',
 \item $\omega_{0,ts}$ are the angular velocities at the relevant extrema from expanding the effective potential
  $F^*(x) = F_0(x) - fx - k_B T \psi^-$ with
  $e^{\psi^-(z)} = \langle e^{-\beta F_1(z)} \rangle$,
 \item $\beta \equiv 1/k_B T$,
 \item $F_0(x)$ is the large-scale smooth potential,
 \item $F_1(x)$ is the small-scale rough potential, and
 \item $F_0^\ddagger$ is the activation energy.
 \end{itemize}
\end{frame}

\begin{frame}
 \frametitle{Simplifying}
 \begin{align}
  k_R^{-1}(f) &= \frac{2 \pi \gamma}{\omega_0 \omega_{ts}}
                 \langle e^{-\beta F_1}\rangle
		 \langle e^{\beta F_1} \rangle
		 e^{\beta (\Delta F_0^\ddagger - f \Delta x)}
		                                    & \text{Hyeon Eqn. 3}
		                                    \nonumber \\
  \log(k_R^{-1}(f)/k_0^{-1}) &= 
     \beta [ \Delta F_0^\ddagger - f (\Delta x) ]
     + \log \langle e^{\beta F_1} \rangle^2 
                                              & \text{Hyeon Eqn. 4} 
                                              \nonumber \\
  \log(k_R^{-1}(f)/k_0^{-1}) &= 
     \beta [ \Delta F_0^\ddagger - f (\Delta x) ]
     + \beta^2 \langle F_1^2 \rangle 
                                              & \text{Hyeon Eqn. 5}
                                              \nonumber
 \end{align}
% And because $k^{-1} = \tau$(Hanngi 7.1), where $\tau$ is the mean first passage time through $x_{ts}$.
 Or
 \begin{align}
  \log(\tau) &= -log(k_0) + \frac{k_B[ \Delta F_0^\ddagger - f (\Delta x) ]}{T} + \frac{k_B^2 \langle F_1^2 \rangle}{T^2} \nonumber
 \end{align}
\end{frame}

\begin{frame}
 \frametitle{Simulated experiment}
 \begin{center}
  \includegraphics[width=0.6\textwidth]{hyeon_const_f_sim} \\
  Simulated relationship between $\tau$ and $T$\cite{hyeon03}.\\
  Note $3.8\U{pN nm} = 2.2{\dg}C$ and $4.4\U{pN nm} = 46{\dg}C$.
% pN nm = 10^(-12-9) J
% kB = 1.37e-23 J/K
% C = K-273.15
% 
% For simulation a, the quad term is 9.89 pN.nm
%  the average amplitude of F1 was 3.0 pN.nm
%  odd, I'd expect <F1^2> = 1/2 Amplitude^2 = 4.5
 \end{center}
\end{frame}

\subsection{How we do it}

\begin{frame}
 \frametitle{Atomic force microscopy}
 \begin{center}
  \includegraphics[width=0.70\textwidth]{AFM_schematic} \\
  Basic AFM operation\cite{warr}.
 \end{center}
\end{frame}

\begin{frame}
 \frametitle{Atomic force microscopy}
 \begin{columns}[c]
  \column{0.7\textwidth}
   \begin{center}
    \includegraphics[width=0.8\textwidth]{multimode_head} \\
    Multimode head.
   \end{center}
  \column{0.3\textwidth}
   \begin{center}
    \includegraphics[width=\textwidth]{multimode_cell_bottom} \\
    Fluid cell.
   \end{center}
 \end{columns}
\end{frame}

\begin{frame}
 \frametitle{Protein unfolding}
 \begin{center}
  \includegraphics[width=0.70\textwidth]{AFM_schematic} \\
 \end{center}
\end{frame}

\begin{frame}
 \frametitle{Equipment layout}
 \begin{center}
  \includegraphics[width=0.90\textwidth]{equipment_layout} \\
 \end{center}
\end{frame}

\begin{frame}
 \frametitle{The sawtooth}
 \begin{center}
  \includegraphics[height=0.85\textheight]{mp/unfolding.2}
 \end{center}
\end{frame}

\section{What I've done}%------------------------------------------------------

\begin{frame}
 \frametitle{Overview}
 \begin{center}
  \includegraphics[width=0.95\textwidth]{protein_unfolding_expt} \\
  My contributions.
 \end{center}
\end{frame}

\subsection{Experiment server}% -   -   -   -   -   -   -   -   -   -   -   -

\subsubsection{Motivation}

\begin{frame}
 \frametitle{Architecture comparison}
 \begin{columns}
  \column{0.5\textwidth}
   \begin{center}
    %\includegraphics{arch_tree} \\
    \includegraphics[width=1.1\textwidth]{arch_tree} \\
    Tree.
   \end{center}
  \column{0.5\textwidth}
   \begin{center}
    \includegraphics[width=\textwidth]{arch_net} \\
    %\includegraphics{arch_net} \\
    Network.
   \end{center}
 \end{columns}
\end{frame}

\begin{frame}
 \frametitle{Current situation}
 LabVIEW for the experiment, Igor for the analysis.

 (Screen-shots?).
\end{frame}

\subsubsection{The goal}

\begin{frame}[fragile]
 \frametitle{The goal: Flexible control scripts in action}
\begin{verbatim}
 > approach_surface
 Lost signal!
 > approach_surface
 > piezo_measure_distance
 372 nm
 > pull_protein --save 'D:\data\' &
 saving data to 'D:\data\070510\'
 > monitor_unfolding
 > sort_data --dir 'D:\data\070510\'
 ...
 > ls
 pulls_good
 pulls_bad_structure
 ...
\end{verbatim}
\end{frame}

\begin{frame}[label=approach_surface_script,fragile]
 \frametitle{Example script: \texttt{approach\_surface}}
\begin{verbatim}
#!/bin/sh
TARG_DEF=1 # Volts
MIN_TOT=3 # Volts
get_feedback() {
  DEF=`cmmdline -c ':AFM|Get:Deflection'`
  TOT=`cmmdline -c ':AFM|Get:TotalPhotodiode'`
}
step_closer() {
  ANS=`cmmdline -c 'Stepper|Set:RelPos 1'`
}
get_feedback
while [ $DEF -lt $TARG_DEF ] && [ $TOT -gt $MIN_TOT ]; do
  step_closer
  get_feedback
done
\end{verbatim}
\end{frame}

\subsubsection{Server design}

\begin{frame}
 \frametitle{Process architecture}
 \begin{center}
  %   \vskip 0.25in
  \includegraphics[width=.6\textwidth]{arch_net}
  %  \caption{}
 \end{center}
\end{frame}

\begin{frame}
 \frametitle{Tracing commands}
 \begin{columns}
  \column{.38\textwidth}
   \begin{center}
    \includegraphics[width=\textwidth]{ipc_example}
   \end{center}
  \column{.62\textwidth}
   \begin{center}
    \ttfamily
    %\small
    \begin{tabular}{l|l|l}
     From & To & Message \\
     \hline
     Cmmdline & Stepper & Set:AbsPos 3 \\
     Stepper & Dig. Out & Set:Output 1 \\
     Dig. Out & Stepper & DONE \\
     Stepper & Dig. Out & Set:Output 2 \\
     Dig. Out & Stepper & DONE \\
     Stepper & Dig. Out & Set:Output 3 \\
     Dig. Out & Stepper & DONE \\
     Stepper & Cmmdline & DONE
    \end{tabular}
   \end{center}
 \end{columns}
\end{frame}

\begin{frame}
 \frametitle{Under the hood}
 \begin{center}
  \includegraphics[width=0.95\textwidth]{program_threading}
 \end{center}
\end{frame}

\begin{frame}
 \frametitle{Message handling logic}
 \begin{center}
  \includegraphics[width=0.89\textwidth]{handler}
 \end{center}
\end{frame}


\subsubsection{Client design}

You want to write a socket-able process when you have some state information you'd like to preserve, you want to continuously monitor something, or you are used often enough that the connection-per-message overhead slows you down considerably.
Otherwise, you can use simpler scripts as seen in the stepper\_approach example.

\begin{frame}
 \frametitle{Client design}
 Stand-alone client processes allow
 \begin{itemize}
  \item Preserving
 \end{itemize} 
\end{frame}

\subsubsection{The future}

\begin{frame}
 \frametitle{The future}
 Ideally, robust modularization of code will
 \begin{itemize}
  \item Allow easy testing of individual modules.
  \item Allow new users to learn the software in manageable chunks.
 \end{itemize}
 The hot-pluggable client-server architecture will
 \begin{itemize}
  \item Allow diagnostic tools to be loaded on the fly.
  \item Allow quick and dirty logging of the entire experiment \\
    (including initialization and shutdown).
  \item Allow several processes to easily share limited resources \\
    (eg. NIDAQ boards).
 \end{itemize}
 And the text based interface will
 \begin{itemize}
  \item Leverage the power of ASCII and the Unix toolbox.
  \item Allow several formats for accomplishing the same task (easy migration).
 \end{itemize}
\end{frame}

\subsection{Stepper control}% -   -   -   -   -   -   -   -   -   -   -   -   -

\subsubsection{Motivation}

\begin{frame}
 \frametitle{Drift}
\end{frame}

\subsubsection{Implementation}

\begin{frame}
 \frametitle{Multimode interior}
  \begin{center}
   \includegraphics[width=0.6\textwidth]{multimode_interior} \\
  \end{center}
\end{frame}

\begin{frame}
 \frametitle{Multimode main board}
  \begin{center}
   \includegraphics[width=0.6\textwidth]{multimode_main_board} \\
  \end{center}
\end{frame}

\begin{frame}
 \frametitle{Break in box version 1}
  \begin{center}
   \includegraphics[width=0.6\textwidth]{break_in_box_1} \\
  \end{center}
\end{frame}


\begin{frame}
 \frametitle{Total photodiode voltage}
  \begin{center}
   \includegraphics[width=0.9\textwidth]{multimode_main_connector} \\
  \end{center}
\end{frame}

\begin{frame}
 \frametitle{Total photodiode voltage}
  \begin{center}
   \includegraphics[width=0.4\textwidth]{total_voltage_grabber} \\
  \end{center}
\end{frame}

\begin{frame}
 \frametitle{Total photodiode voltage, installed}
  \begin{center}
   \includegraphics[width=0.7\textwidth]{total_voltage_grabber_action} \\
  \end{center}
\end{frame}


\begin{frame}
 \frametitle{DB9 to wires}
  \begin{center}
   \includegraphics[width=0.9\textwidth]{DB9_to_wires} \\
  \end{center}
\end{frame}

\begin{frame}
 \frametitle{DB9 to wires, installed}
  \begin{center}
   \includegraphics[width=0.9\textwidth]{DB9_to_wires_action} \\
  \end{center}
\end{frame}

\begin{frame}
 \frametitle{Break in box version 2}
  \begin{center}
   \includegraphics[width=0.6\textwidth]{break_in_box_1} \\
  \end{center}
\end{frame}

\begin{frame}
 \frametitle{Complete stepper control setup}
  \begin{center}
   \includegraphics[width=0.6\textwidth]{break_in_box_1} \\
  \end{center}
\end{frame}

\againframe{approach_surface_script}

\subsection{Temperature control}% -   -   -   -   -   -   -   -   -   -   -   -

\subsection{Automatically sorting pulling curves}% -  -  -  -  -  -  -  -  -  -

\subsubsection{Introduction and motivation}

\begin{frame}
 \frametitle{Automatically sorted pulling curves}
 Motivation:
 \begin{itemize}
  \item Clarify sorting criteria.
  \item Allow rational tuning of experiment parameters.
  \item Easing sorting of large data sets.
 \end{itemize}
\end{frame}

\subsubsection{Sorting criteria}

\begin{frame}
 \frametitle{Sorting procedure}
 \begin{columns}[T]
  \column{0.5\textwidth}
   \includegraphics[height=0.8\textheight]{data_sorter}
  \column{0.5\textwidth}
   \hspace{\stretch{1}}
   \makebox[0.25\textwidth][r] {
    \includegraphics[width=0.9\textwidth]{force_curve}
   }
 \end{columns}
\end{frame}

\subsubsection{Some examples}


\section{Next year}

\appendix

\begin{frame}
 \frametitle{Constant loading temperature dependence}
\end{frame}

\addcontentsline{toc}{section}{References}
\begin{frame}
 \frametitle{References}
 \input{mainref}	% include bibliography
\end{frame}

\end{document}
