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| -rw-r--r-- | presentation.pdf | bin | 1331020 -> 5916984 bytes | |||
| -rw-r--r-- | presentation.tex | 331 |
4 files changed, 186 insertions, 145 deletions
diff --git a/literature/BrownEmilyJ1999a.pdf b/literature/BrownEmilyJ1999a.pdf Binary files differnew file mode 100644 index 0000000..3b3b524 --- /dev/null +++ b/literature/BrownEmilyJ1999a.pdf diff --git a/literature/BrownEmilyJ1999a_1.png b/literature/BrownEmilyJ1999a_1.png Binary files differnew file mode 100644 index 0000000..3de5ad3 --- /dev/null +++ b/literature/BrownEmilyJ1999a_1.png diff --git a/presentation.pdf b/presentation.pdf Binary files differindex b840c9f..011e2f0 100644 --- a/presentation.pdf +++ b/presentation.pdf 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}
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