\documentclass{presentation}

\title{Development of \\ Frequency Domain Multidimensional Spectroscopy}
\author{Blaise Thompson}

\institute{University of Wisconsin--Madison}
\date{2018-04-23}

\begin{document}
\maketitle

\section{CMDS}  % =================================================================================

\begin{frame}{CMDS}
	The Wright Group focuses on the development and usage of \\
  Coherent MultiDimensional Spectroscopy (CMDS).
  \vspace{\baselineskip} \\
  CMDS is a family of related nonlinear spectroscopic experiments.
\end{frame}
   
\begin{frame}{Why CMDS?}
  [A BUNCH OF COOL PUBLICATIONS---FOCUSING ON COHERENCE TRANSFER, MECHANISMS ETC]
  [MORE APPLICATIONS]
\end{frame}

\begin{frame}{Coherence transfer}
  \fbox{\adjincludegraphics[width=\textwidth]{literature/ChenuAurelia2014a}}
\end{frame}

\begin{frame}{Analytical}
  But wait! I'm an \emph{Analytical} Chemist...
  \vspace{\baselineskip} \\
  What am I doing in a field so rich with fundamental studies?
  \vspace{\baselineskip} \\
  I hope to convince you that CMDS can be used for analytical work.  % TODO: better
  \begin{itemize}
    \item detection (selectivity)
    \item unknown identification
    \item quantification
  \end{itemize}
\end{frame}

% TODO: in fact, 2DIR is already used regularly...

\begin{frame}{Pakoulev et al. (2009)}  
  \fbox{\adjincludegraphics[width=\textwidth]{literature/PakoulevAndreiV2009a}}
\end{frame}

\begin{frame}{Pakoulev et al. (2009)}
  \begin{shadequote}
    Spectroscopy forms the heart of the analytical methodology used for routine chemical
    measurement.  %
    Of all the analytical spectroscopic methods, NMR spectroscopy is unique in its ability to
    \hl{correlate} spin resonances and \hl{resolve} spectral features from spectra containing
    \hl{thousands of peaks}.  %
    For example, heteronuclear multiple quantum coherence (HMQC) spectroscopy achieves this
    capability by exciting $^1$H, $^{15}$N, $^{13}$ C=O, and $^{13}$C$\alpha$ spins to form a
    multiple quantum coherence \hl{characteristic of a specific position} in a protein’s backbone.
    Three excitations define a specific residue, and a fourth defines the coupling to an adjacent
    residue.
    Not only does it decongest the spectra, it defines the couplings and connectivity between the
    different nuclear spin states.
    Coherent multidimensional spectroscopy (CMDS) has emerged as the \hl{optical analogue} of
    nuclear magnetic resonance (NMR), and there is great interest in using it as a \hl{general
      analytical methodology}.
  \end{shadequote}
\end{frame}

\begin{frame}{Donaldson et al. (2010)}
  \fbox{\adjincludegraphics[width=\textwidth]{literature/DonaldsonPaulMurray2010a}}
\end{frame}

\begin{frame}{Fournier et al. (2009)}
  \fbox{\adjincludegraphics[width=\textwidth]{literature/FournierFrederic2009a}}
\end{frame}

\begin{frame}{Fournier et al. (2009)}
  \begin{shadequote}
    Our protein identification strategy is based on using EVV 2DIR to quantify the amino acid
    content of a protein.  %
    EVV 2DIR is shown to be able to perform \hl{absolute quantification}, something of major
    importance in the field of proteomics but rather difficult and time-consuming to achieve with
    mass spectrometry.  %
    Our technique can be qualified as a top-down \hl{label-free} method; it does not require
    intensive sample preparation, the proteins are intact when analyzed, and it does not have any
    mass restriction on the proteins to be analyzed.  %
    Moreover, EVV 2DIR is a \hl{nondestructive} technique; the samples can be kept for reanalysis
    in the light of further information.  %
  \end{shadequote}
\end{frame}

\section{Frequency domain}  % =====================================================================

\begin{frame}{Domains of CMDS}
  CMDS can be collected in two domains:
  \begin{itemize}
    \item time domain
    \item frequency domain
  \end{itemize}
\end{frame}

\begin{frame}{Time domain}
  Multiple broadband pulses are scanned in \emph{time} to collect a multidimensional interferogram
  (analogous to FTIR, NMR).
  \vspace{\baselineskip} \\
  A local oscillator must be used to measure the \emph{phase} of the output.
  \vspace{\baselineskip} \\
  This technique is...
  \begin{itemize}
    \item fast (even single shot)
    \item robust
  \end{itemize}
  pulse shapers have made time-domain CMDS (2DIR) almost routine.
\end{frame}

\begin{frame}{Frequency domain}
  In the Wright Group, we focus on \emph{frequency} domain ``Multi-Resonant'' (MR)-CMDS.
  \vspace{\baselineskip} \\
  Automated Optical Parametric Amplifiers (OPAs) are used to produce relatively narrow-band pulses.
  Multidimensional spectra are collected ``directly'' by scanning OPAs against each-other.
  \vspace{\baselineskip} \\
  This strategy is...
  \begin{itemize}
    \item slow (must directly visit each pixel)
    \item fragile (many crucial moving pieces)
  \end{itemize}
  but! It is incredibly flexible.  
\end{frame}

\begin{frame}{Bandwidth}
  MR-CMDS has no bandwidth limit!
  \vspace{\baselineskip} \\
  There is just the small matter of making the source continuously tunable...
  \adjincludegraphics[width=\textwidth]{opa/OPA_ranges}
\end{frame}

\begin{frame}{Selection rules}
  MR-CMDS can easily collect data without an external local oscillator.
  \vspace{\baselineskip} \\
  This means... [BOYLE]
\end{frame}

\section{The instrument}  % =======================================================================

\begin{frame}{The instrument}
  [PICTURE OF LASER LAB]
\end{frame}

\begin{frame}{The instrument}
  Many kinds of component hardware
  \begin{itemize}
    \item monochromators
    \item delay stages
    \item filters
    \item OPAs
  \end{itemize}
  $\sim10$ settable devices, $\sim25$ motors. \\
  Multiple detectors.
\end{frame}

\begin{frame}{Pipeline}
  \adjincludegraphics[width=0.5\textwidth]{presentation/pipe}
  What does the ``pipeline'' of MR-CMDS data acquisition and processing look like in the Wright
  Group?
  \vspace{\baselineskip} \\
  How to increase data throughput and quality, while decreasing frustration of experimentalists?  %
\end{frame}

\section{Processing}  % ===========================================================================

\begin{frame}{Processing}
  WrightTools.
\end{frame}

\begin{frame}{Universal format}
  WrightTools defines a \emph{universal file format} for CMDS.
  \begin{itemize}
    \item store multiple multidimensional arrays
    \item metadata
  \end{itemize}
  Import data from a variety of sources.
  \begin{itemize}
    \item previous Wright Group acquisition software
    \item commercial instruments (JASCO, Shimadzu, Ocean Optics)
  \end{itemize}
\end{frame}

\begin{frame}{Flexible data model}
  Flexibility to transform into any desired ``projection'' on component variables.
  \adjincludegraphics[width=\textwidth]{processing/fringes_transform}
  % mention: including expressions
\end{frame}

\section{Acquisition}  % ==========================================================================

\begin{frame}{Acquisition}
  PyCMDS---unified software for controlling hardware and collecting data.
  \adjincludegraphics[width=\textwidth]{acquisition/screenshots/000}
\end{frame}

\begin{frame}{Abstraction}
  Hardware---something that has a \hl{position} that can be \hl{set}.
  \vspace{\baselineskip} \\
  Sensor---something that has a \hl{signal} that can be \hl{read}.
\end{frame}
  
\begin{frame}{Modular hardware model}
  \adjincludegraphics[scale=0.25]{acquisition/hardware_inheritance}
\end{frame}

\begin{frame}{Modular sensor model}
  Can have as many sensors as needed.
  \vspace{\baselineskip} \\
  Each sensor contributes one or more channels.
  \vspace{\baselineskip} \\
  Sensors with size contribute new variables (dimensions).
\end{frame}

\begin{frame}{Central loop}
  Set, wait, read, wait, repeat.
  \vspace{\baselineskip} \\
  Everything is multi-threaded (simultaneous motion, simultaneous read).
\end{frame}
  
\begin{frame}{Acquisitions}
  Acquisition---a particular set of actions.
  \vspace{\baselineskip} \\
  Acquisition modules---a GUI that accepts a user instruction.
\end{frame}

\begin{frame}{Queue}
  Queue.
  \adjincludegraphics[width=\textwidth]{acquisition/screenshots/004}
\end{frame}

\begin{frame}{Queue}
  This strategy can be incredibly productive!
  \begin{itemize}
    \item Soon after the queue was first implemented, we collected more pixels in two weeks than
      had been collected over the previous three years.
  \end{itemize}
\end{frame}

\section{Tuning}  % ===============================================================================

\begin{frame}{Tuning}
\end{frame}

\section{Conclusion}  % ===========================================================================

\begin{frame}{Conclusion}
\end{frame}

\section{Supplement}  % ===========================================================================

\begin{frame}{MR-CMDS theory}
\end{frame}

\begin{frame}{Mixed domain}
  [FIGURES FROM DAN'S PAPER]
\end{frame}

\end{document}