From 986041f724da53f069ab4c444c8365b05bb195cc Mon Sep 17 00:00:00 2001 From: Blaise Thompson Date: Sat, 21 Apr 2018 15:24:59 -0500 Subject: 2018-04-21 15:25 --- literature/BrownEmilyJ1999a.pdf | Bin 0 -> 27493229 bytes literature/BrownEmilyJ1999a_1.png | Bin 0 -> 74019 bytes presentation.pdf | Bin 1331020 -> 5916984 bytes presentation.tex | 331 +++++++++++++++++++++----------------- 4 files changed, 186 insertions(+), 145 deletions(-) create mode 100644 literature/BrownEmilyJ1999a.pdf create mode 100644 literature/BrownEmilyJ1999a_1.png diff --git a/literature/BrownEmilyJ1999a.pdf b/literature/BrownEmilyJ1999a.pdf new file mode 100644 index 0000000..3b3b524 Binary files /dev/null and b/literature/BrownEmilyJ1999a.pdf differ diff --git a/literature/BrownEmilyJ1999a_1.png b/literature/BrownEmilyJ1999a_1.png new file mode 100644 index 0000000..3de5ad3 Binary files /dev/null and b/literature/BrownEmilyJ1999a_1.png differ diff --git a/presentation.pdf b/presentation.pdf index b840c9f..011e2f0 100644 Binary files a/presentation.pdf and b/presentation.pdf differ 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