From 617926e81e3c073f18bcaf9784a474638f2c4447 Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Sun, 1 Apr 2018 16:56:35 -0500
Subject: 2018-04-01 16:56

---
 introduction/chapter.tex | 157 ++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 147 insertions(+), 10 deletions(-)

(limited to 'introduction/chapter.tex')

diff --git a/introduction/chapter.tex b/introduction/chapter.tex
index 81a6b97..be4572d 100644
--- a/introduction/chapter.tex
+++ b/introduction/chapter.tex
@@ -1,14 +1,89 @@
-\chapter{Introduction}
+\cleardoublepage
+\chapter{Introduction} \label{cha:int}
 
-\section{Coherent Multidimensional Spectroscopy}
+% TODO: cool quote, if I can think of one...
 
-% Unraveling quantum pathways using optical 3D Fourier-transform spectroscopy doi:10.1038/ncomms2405
+\clearpage
 
-\Gls{CMDS}, \gls{coherent multidimensional spectroscopy}
+Coherent multidimensional spectroscopy (CMDS) is a family of experimental strategies capable of
+providing unique insights into microscopic material physics.  %
+It is similar to the more familiar [NMR EXPERIMENTS], although the implementation is different due
+to differences between the behavior of nuclear spin states (probed by NMR) and electronic and
+vibrational states (probed by CMDS).  %
+CMDS can resolve couplings between states, and can decongest spectra by taking advantage of
+dimensionality and selection rules.  %
+With the advent of ultrafast lasers, CMDS can resolve dynamics in excited states and the coupling
+between them.  %
 
-\section{The CMDS Instrument}
+CMDS is most often performed in the time domain, where multiple broadband pulses are scanned in
+time to collect a multidimensional interferogram.  [CITE]  %
+This technique is fast and robust---it has even been performed on a single shot. [CITE]  %
+However time-domain CMDS has some fundamental limitations:
+\begin{ditemize}
+  \item The frequency bandwidth must be contained within the excitation pulse---and ultrabroadband
+    pulses are hard to make and control.  [CITE JONAS]
+  \item A phase-locked local oscillator is required, and preparing a local oscillator for experiments
+    with unique output colors is challenging.
+\end{ditemize}
+Scientists in the time-domain CMDS community are taking both of these challenges head-on, pushing
+the envelope in excitation pulse bandwidth [CITE 2DWL] and performing two-stage experiments in
+which excitation pulses are used to generate a local oscillator in non-resonant media [CITE
+ZANNI].  %
 
-From an instrumental perspective, MR-CMDS is a problem of calibration and coordination.  %
+An alternative strategy is frequency domain ``multi-resonant'' CMDS (MR-CMDS).  %
+Rather than using a single broadband excitation pulse, MR-CMDS employs a relatively narrow-band
+source with a tunable frequency.  %
+Motorized optical parametric amplifiers (OPAs) are typically used to provide this tunability.  %
+In MR-CMDS, frequency axes are resolved directly by scanning these motorized OPAs.  %
+This process is time intensive, and it can be challenging to ensure that the OPAs are well
+calibrated and that the experiment is not affected by the motion of crystals and other optics
+inside these automated OPAs.  %
+Despite these challenges, MR-CMDS is an incredibly flexible strategy that can be a very powerful
+analytical tool.  %
+Because MR-CMDS does not require that all frequencies be contained within one broadband source,
+there is no theoretical limit to the frequency range that can be resolved in this way.  %
+MR-CMDS can be homodyne-detected, so experiments with unique output colors are much more
+accessible.  %
+Finally, because the components are more self-contained, MR-CMDS instruments tend to be more
+flexable in the kinds of experiments that they can perform.  %
+
+% TODO: boilerplate about the kinds of things that make up an MR-CMDS instrument... OPAs, delays...
+
+This dissertation contains several projects undertaken to improve the reliability and accessibility
+of MR-CMDS.  %
+While MR-CMDS will never be a single-shot experiment, there are many improvements that can improve
+data collection speed.  %
+Necessary calibration, especially OPA calibration, can be made robust and fully automatic.  %
+Common artifacts can be addressed through relatively simple modifications in hardware and
+software.  %
+Finally, the complexity that arises from finite pulses with ``marginal'' resolution in frequency
+and time can be understood and accounted for through numerical simulation.  %
+Taken together, these improvements represent a significant improvement in the accessibility of
+frequency-domain coherent multidimensional spectroscopy.  %
+
+Due to its diversity and dimensionality, MR-CMDS data is challenging to process and represent.  %
+The data processing tools that a scientist develops to process one experiment may not work when she
+attempts to process an experiment where different experimental variables are explored.  %
+Historically, this has meant that MR-CMDS practitioners have used custom, one-off data processing
+workflows that need to be changed for each particular experiment.  %
+These changes take time to implement, and can become stumbling blocks or opportunities for
+error.  %
+Even worse, the challenge of designing a new processing workflow may make dissuade scientist from
+creatively modifying their experimental strategy, or comparing their data with data taken from
+another group.  %
+This limit to creativity and flexibility defeats one of the main advantages of the MR-CMDS
+strategy.  %
+\autoref{cha:pro} describes a new software package, WrightTools, that greatly simplifies CMDS data
+processing.  %
+WrightTools defines a \emph{universal format} that is capable of representing any CMDS dataset,
+regardless of dimensionality or the axes scanned.  %
+A set of simple functions are used to convert raw data into this universal format.  %
+Once converted, the data can be manipulated with a set of powerful methods that encompass the
+majority of operations needed to process such data.  %
+Finally, simple tools are defined to quickly and beautifully represent the datasets.  %
+WrightTools is made to be extended, so it will continue to evolve along with its users.  %
+
+From an instrumental perspective, MR-CMDS is a problem of calibration and coordination.  % 
 Within the Wright Group, each of our two main instruments are composed of roughly ten actively
 moving component hardwares. %
 Many of these components are purchased directly from vendors such as SpectraPhysics, National
@@ -17,8 +92,6 @@ Others are created or heavily modified by graduate students.  %
 The Wright Group has always maintained custom acquisition software packages which control the
 complex, many-stepped dance that these components must perform to acquire MR-CMDS spectra.  %
 
-\section{Scientific Software}
-
 When I joined the Wright Group, I saw that acquisition software was a real barrier to experimental
 progress and flexibility.  %
 Graduate students had ideas for instrumental enhancements that were infeasible because of the
@@ -45,5 +118,69 @@ It offers more fine-grained control of data acquisition and timing, enabling mor
 algorithms to quickly acquire artifact-free results.  %
 In conjunction with other algorithmic and hardware improvements that I have made, PyCMDS has
 decreased acquisition times by up to two orders of magnitude.  %
-A companion software, WrightTools (which I also created), solves some of the processing and
-representation challenges of multidimensional data.  %
\ No newline at end of file
+
+Like any analytical technique, MR-CMDS is subject to artifacts: features of the data that are
+caused by instrumental imperfections or limitations, and do not reflect the intrinsic material
+response that is of interest.  %
+% HOW THE EXPERIMENT WAS DONE, NOT WHAT IT IS HOPING TO MEASURE
+For example, M-factors are ... [CITE] and [CITE JONAS PULSE PROPAGATION].  %
+Since MR-CMDS is a very active experiment, with many moving motors, an active approach to artifact
+correction is particularly appropriate.  %
+\autoref{cha:act} describes strategies for implementing such corrections.  %
+Spectral delay correction can be applied to account for the fact that not all output colors arrive
+at the same time.  %
+Dual chopping can correct for scatter and other unwanted processes, ensuring that the observed
+signal depends on all of the excitation beams.  %
+Fibrillation can wash out interference between desired and undesired processes, and is
+complementary with chopping.  %
+Automated poynting correction and power correction can account for non-idealities in OPA
+performance.  %
+
+The theory that is used to describe CMDS is typically derived in one of two limits.  %
+In the impulsive limit, pulses are broad in frequency and short in time compared to material
+resonances.  %
+Resonant responses are impulsive, like a hammer hitting a bell.  %
+The impulsive limit is particularly well suited for describing time domain experiments.  %
+In the driven limit, pulses are narrow in frequency and long in time compared to material
+response.  %
+Resonant responses are driven, like a jello dessert sitting on a washing machine.  %
+The expected spectrum in both of these limits can be computed analytically. [CITE]  %
+Things get more complicated in the mixed domain, where pulses have similar bandwidth as the
+material response. %
+Experiments in this domain are a practical necessity as CMDS addresses systems with very fast
+dephasing times [CITE].  %
+% TODO: cite smallwood and similar somewhere around here
+At the same time, the marginal resolution in frequency \emph{and} time that the mixed domain
+possess promises huge potential in pathway resolution and decongestion. [CITE JOHN OR ANDREI]  %
+\autoref{cha:mix} describes the pitfalls and opportunities contained in the mixed domain
+approach.  %
+An intuitive description of mixed-domain experiments is given.  %
+False signatures of material correlation are discussed, and strategies for resolving true material
+correlation are defined.  %
+
+In \hyperref[prt:applications]{Part III: Applications}, three projects in which MR-CMDS was used to
+answer chemical questions in materials systems are described.  %
+These chapters do not directly address improvements to the MR-CMDS methodology, but instead serve
+as case studies in the potential of MR-CMDS and the utility of the improvements described in
+\autoref{prt:development}.  %
+
+Chapter [...] describes a series of experiments performed on PbSe quantum dots.
+PbSe quantum dots are useful because [...]  %
+We learned [...]  %
+
+Chapter [...] describes an experiment performed on MoS2.
+MoS2 is useful because [...]  %
+We learned [...]  %
+
+Chapter [...] describes an experiment performed on PEDOT:PSS.
+useful because...
+we learned...
+
+Despite challenges in software, hardware, and theory MR-CMDS is a crucial tool in the hands of
+scientists.  %
+This dissertation describes several ways to make MR-CMDS more accessible through software and
+hardware development.  %
+PyCMDS has made data collection faster and more artifact-free.  %
+WrightTools has trivialized data processing, tightening the loop between idea and execution.  %
+Theory can be used to guide experimental insight in the promising, if challenging, mixed domain.  %
+Applications of these ideas in three materials are presented.  %
-- 
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