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+++ 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.  %