From 986041f724da53f069ab4c444c8365b05bb195cc Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Sat, 21 Apr 2018 15:24:59 -0500
Subject: 2018-04-21 15:25

---
 presentation.tex | 331 +++++++++++++++++++++++++++++++------------------------
 1 file changed, 186 insertions(+), 145 deletions(-)

(limited to 'presentation.tex')

diff --git a/presentation.tex b/presentation.tex
index 9f4a3f1..1729bb2 100644
--- a/presentation.tex
+++ b/presentation.tex
@@ -1,6 +1,7 @@
 \documentclass{presentation}
 
 \title{Development of \\ Frequency Domain Multidimensional Spectroscopy}
+\subtitle{---Beyond Two Dimensions---}
 \author{Blaise Thompson}
 
 \institute{University of Wisconsin--Madison}
@@ -9,141 +10,137 @@
 \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]
+\begin{frame}{Brown et al. (1999)}
+  \begin{columns}
+    \begin{column}{0.5\textwidth}
+      \fbox{\adjincludegraphics[width=\textwidth]{"literature/BrownEmilyJ1999a"}}
+    \end{column}
+    \begin{column}{0.5\textwidth}
+      \includegraphics[width=\textwidth]{"literature/BrownEmilyJ1999a_1"}
+      \centering
+      \\
+      \vspace{2\baselineskip}
+      $\vec{k_{\text{sig}}} = \vec{k_a} - \vec{k_b} + \vec{k_c}$
+    \end{column}
+  \end{columns}
 \end{frame}
 
-\begin{frame}{Coherence transfer}
-  \fbox{\adjincludegraphics[width=\textwidth]{literature/ChenuAurelia2014a}}
+\begin{frame}{Overview}
+  \adjincludegraphics[width=\textwidth]{"mixed_domain/simulation overview"}
 \end{frame}
 
-\begin{frame}{Analytical}
-  But wait! I'm an \emph{Analytical} Chemist...
+\begin{frame}{Diversity}
+  Great diversity of experimental strategies.
   \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
+  Different phase matching conditions...
   \begin{itemize}
-    \item detection (selectivity)
-    \item unknown identification
-    \item quantification
+    \item transient grating $\vec{k_a} - \vec{k_b} + \vec{k_c}$
+    \item transient absorption
+    \item DOVE
+    % TODO: darien's experiments
   \end{itemize}
+  But also different color combinations and dimensions explored.
+  % SAY: based on the same basic ability to scan pulses in frequency, delay etc
 \end{frame}
 
-% TODO: in fact, 2DIR is already used regularly...
-
-\begin{frame}{Pakoulev et al. (2009)}  
-  \fbox{\adjincludegraphics[width=\textwidth]{literature/PakoulevAndreiV2009a}}
+\begin{frame}{MR-CMDS development}
+  [SUMMARY SLIDE FOR REMAINDER OF PRESENTATION]
 \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}
+\section{Tunability}  % ===========================================================================
 
-\begin{frame}{Donaldson et al. (2010)}
-  \fbox{\adjincludegraphics[width=\textwidth]{literature/DonaldsonPaulMurray2010a}}
+\begin{frame}{Tunability}
+  \centering \huge
+  Control and Calibration of \\
+  Optical Parametric Amplifiers
 \end{frame}
 
-\begin{frame}{Fournier et al. (2009)}
-  \fbox{\adjincludegraphics[width=\textwidth]{literature/FournierFrederic2009a}}
+\begin{frame}{Two strategies for CMDS}
+  Two strategies for collecting multidimensional spectra:
+  \vspace{\baselineskip} \\
+  \begin{columns}
+    \begin{column}{0.4\textwidth}
+      Time Domain
+      \begin{itemize}
+        \item broadband pulses
+        \item resolve spectra interferometrically
+        \item fast (even single shot)
+        \item robust
+      \end{itemize} 
+    \end{column}
+    \begin{column}{0.4\textwidth}
+      Frequency Domain
+      \begin{itemize}
+        \item narrowband pulses
+        \item resolve spectra by tuning OPAs directly
+        \item slow (lots of motor motion)
+        \item fragile
+      \end{itemize}
+    \end{column}
+  \end{columns}
+\end{frame}
+
+\begin{frame}{Postage stamp}
+  [FIGURE FROM LIT]
+\end{frame}
+
+\begin{frame}{Czech}
+  [FIGURE FROM CZECH]
 \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}
+\begin{frame}{Bandwidth}
+  \adjincludegraphics[width=\textwidth]{opa/OPA_ranges}
 \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}
+\begin{frame}{TOPAS-C}
+  \includegraphics[width=\textwidth]{opa/TOPAS-C}
+  Two ``stages'', each with two motorized optics.
 \end{frame}
 
-\begin{frame}{Time domain}
-  Multiple broadband pulses are scanned in \emph{time} to collect a multidimensional interferogram
-  (analogous to FTIR, NMR).
+\begin{frame}{Tuning}
+  % TODO: curve plot?
+  Tuning curves---recorded correspondence between motor positions and output color.
   \vspace{\baselineskip} \\
-  A local oscillator must be used to measure the \emph{phase} of the output.
+  Exquisite sensitivity to alignment and lab conditions---tuning required roughly once a week.
   \vspace{\baselineskip} \\
-  This technique is...
+  Manual tuning is difficult...
   \begin{itemize}
-    \item fast (even single shot)
-    \item robust
+    \item high dimensional motor space
+    \item difficult to asses overall quality
+    \item several hours of work per OPA (sometimes, an entire day for one OPA)
   \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.  
+\begin{frame}{Preamp}
+  \includegraphics[width=\textwidth]{opa/preamp}
 \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}
+\begin{frame}{Automation}
+  \begin{columns}
+    \begin{column}{0.5\textwidth}
+      \adjincludegraphics[width=\textwidth]{opa/autotune_preamp}
+    \end{column}
+    \begin{column}{0.5\textwidth}
+      Fully automated OPA tuning
+      \begin{itemize}
+        \item less than 1 hour per OPA
+        \item can be scheduled for odd times
+        \item high quality from global analysis 
+        \item reproducible
+        \item unambiguous representations
+      \end{itemize}
+      \vspace{\baselineskip} \\
+      Other calibration steps also automated.
+    \end{column}
+  \end{columns}
 \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}  % =======================================================================
+\section{Acquisition}  % ==========================================================================
 
-\begin{frame}{The instrument}
-  [PICTURE OF LASER LAB]
+\begin{frame}{Acquisition}
+  \centering \huge
+  Control of the MR-CMDS \\
+  Instrument
 \end{frame}
 
 \begin{frame}{The instrument}
@@ -166,33 +163,6 @@
   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}
@@ -203,18 +173,6 @@
   \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.
@@ -241,9 +199,25 @@
   \end{itemize}
 \end{frame}
 
-\section{Tuning}  % ===============================================================================
+\subsection{Extensibility}  % ---------------------------------------------------------------------
 
-\begin{frame}{Tuning}
+% DARIEN ADDED AEROTECH STAGE---1 DAY
+
+% SUNDEN ADDED CUSTOM POYNTING TUNE IN A FEW DAYS (including testing)
+
+\section{Processing}  % ===========================================================================
+
+\begin{frame}{Processing}
+  WrightTools.
+\end{frame}
+
+\begin{frame}{TOC}
+\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{Conclusion}  % ===========================================================================
@@ -252,6 +226,73 @@
 \end{frame}
 
 \section{Supplement}  % ===========================================================================
+ 
+\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}{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}{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}{Selection rules}
+  MR-CMDS can easily collect data without an external local oscillator.
+  \vspace{\baselineskip} \\
+  This means... [BOYLE]
+\end{frame}
 
 \begin{frame}{MR-CMDS theory}
 \end{frame}
-- 
cgit v1.2.3

