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diff --git a/MX2/chapter.tex b/MX2/chapter.tex
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@@ -1 +1,658 @@
-\chapter{MX2}
\ No newline at end of file
+\chapter{MX2}
+
+
+We report the first coherent multidimensional spectroscopy study of a MoS\textsubscript{2} film.  %
+A four-layer sample of MoS\textsubscript{2} was synthesized on a silica substrate by a simplified
+sulfidation reaction and characterized by absorption and Raman spectroscopy, atomic force
+microscopy, and transmission electron microscopy.  %
+State-selective coherent multidimensional spectroscopy (CMDS) on the as-prepared
+MoS\textsubscript{2} film resolved the dynamics of a series of diagonal and cross-peak features
+involving the spin---orbit split A and B excitonic states and continuum states.  %
+The spectra are characterized by striped features that are similar to those observed in CMDS
+studies of quantum wells where the continuum states contribute strongly to the initial excitation of
+both the diagonal and cross-peak features, while the A and B excitonic states contributed strongly
+to the final output signal.  %
+The strong contribution from the continuum states to the initial excitation of both the diagonal
+and cross-peak features, while the A and B excitonic states contributed strongly to the final
+output signal.  %
+The strong contribution from the continuum states to the initial excitation shows that the continuum
+states are coupled to the A and B excitonic states and that fast intraband relaxation is occurring
+on a sub-70 fs time scale.  %
+A comparison of the CMDS excitation signal and the absorption spectrum shows that the relative
+importance of the continuum states is determined primarily by their absorption strength.  %
+Diagonal and cross-peak features decay with a 680 fs time constant characteristic of exciton
+recombination and/or trapping.  %
+The short time dynamics are complicated by coherent and partially coherent pathways that become
+important when the excitation pulses are temporally overlapped.  %
+In this region, the coherent dynamics create diagonal features involving both the excitonic states
+and continuum states, while the partially coherent pathways contribute to cross-peak features.  %
+
+\section{Introduction}  % -------------------------------------------------------------------------
+
+Transition metal dichalcogenides (TMDCs), such as MoS\textsubscript{2}, are layered semiconductors
+with strong spin-orbit coupling, high charge mobility, and an indirect band gap that becomes direct
+for monolayers. \cite{WangQingHua2012a, MakKinFai2010a}  %
+The optical properties are dominated by the A and B excitonic transitions between two HOMO
+spin-orbit split valence bands and the lowest state of the conduction band at the $K$ and $K^\prime$
+valleys of the two-dimensional hexagonal Brillouin zone. \cite{MolinaSanchezAlejandro2013a}  %
+The spin and valley degrees of freedom are coupled in individual TMDC layers as a result of the
+strong spin-orbit coupling and the loss of inversion symmetry.  %
+The coupling suppresses spin and valley relaxation since both spin and valley must change in a
+transition.  %
+These unusual properties have motivated the development of TMDC monolayers for next-generation
+nano/optoelectronic devices as well as model systems for spintronics and valleytronics
+applications. \cite{MakKinFai2010a, XuXiaodong2014a, XiaoDi2012a}  %
+
+Ultrafast dynamics of the MoS\textsubscript{2} A and B electronic states have been measured by
+pump-probe, transient absorption, and transient reflection spectroscopy. \cite{FangHui2014a,
+  KumarNardeep2013a, NieZhaogang2014a, SunDezheng2014a, SimSangwan2013a}  %
+The spectra contain A and B excitonic features that result from ground-state bleaching (GSB),
+stimulated emission (SE), and excited-state absorption (ESA) pathways.  %
+The excitons exhibit biexponential relaxation times of $\approx$10--20 and $\approx$350--650 fs,
+depending on the fluence and temperature.  %
+The dependence on excitation frequency has not been explored in previous ultrafast experiments on
+MoS\textsubscript{2}, but it has played a central role in understanding exciton cooling dynamics
+and exciton-phonon coupling in studies of quantum dots. \cite{KambhampatiPatanjali2011a}  %
+
+Coherent multidimensional spectroscopy (CMDS) is a complementary four wave mixing (FWM) methodology
+that differs from pump-probe, transient absorption, and transient reflection methods.
+\cite{XiaoDi2012a, FangHui2014a, KumarNardeep2013a, NieZhaogang2014a, SimSangwan2013a,
+  MakKinFai2012a, SunDezheng2014a}  %
+Rather than measuring the intensity change of a probe beam caused by the state population changes
+induced by a pump beam, CMDS measures the intensity of  a coherent output beam created by
+interactions with three excitation pulses.  %
+The interest in CMDS methods arise from their ability to remove inhomogeneous broadening, define
+interstate coupling, and resolve coherent and incoherent dynamics. \cite{CundiffStevenT2008a,
+  TurnerDanielB2009a, KohlerDanielDavid2014a, YursLenaA2011a, GriffinGrahamB2013a, HarelElad2012a,
+  CundiffStevenT1996a, BirkedaDl1996a, WehnerMU1996a}  %
+CMDS typically requires interferometric phase stability between excitation pulses, so CMDS has been
+limited to materials with electronic states within the excitation-pulse bandwidth.  %
+Multiresonant CMDS is a particularly attractive method for the broader range of complex materials
+because it does not require interferometric stability and is able to use independently tunable
+excitation pulses over wide frequency ranges.  %
+
+The multiresonant CMDS used in this work employs two independently tunable excitation beams with
+frequencies $\omega_1$ and $\omega_2$.  %
+The $\omega_2$ beam is split into two beams, denoted by $\omega_2$ and $\omega_2^\prime$.  %
+These three beams are focused onto the MoS\textsubscript{2} thin film at angles, creating an output
+beam in the phase-matched direction
+$\mathbf{k}_{\mathrm{out}}=\mathbf{k}_1-\mathbf{k}_2+\mathbf{k}_{2^\prime}$ where $\mathbf{k}$ is the wave
+vector for each beam and the subscripts label the excitation frequencies.  %
+Multidimensional spectra result from measuring the output intensity dependence on frequency and
+delay times.  %
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=0.5\textwidth]{MX2/01}
+  \caption[CMDS tutorial]{(a) Example delays of the $\omega_1$, $\omega_2$, and
+    $\omega_{2^\prime}$ excitation pulses. (b) Dependence of the output intensity on the
+    $\tau_{22^\prime}$ and $\tau_{21}$ time delays for $\omega_1=\omega_2$. The solid lines define
+    the regions for the six different time orderings of the $\omega_1$, $\omega_2$, and
+    $\omega_{2^\prime}$ excitation pulses. We have developed a convention for numbering these time
+    orderings, as shown. (c) Diagram of the band structure of MoS\textsubscript{2} at the $K$
+    point. The A and B exciton transitions are shown. (d) Two dimensional frequency-frequency plot
+    labeling two diagonal and cross-peak features for the A and B excitons.}
+  \label{fig:Czech01}
+\end{figure}
+
+\autoref{fig:Czech01} introduces our conventions for representing multidimensional spectra.  %
+\autoref{fig:Czech01}b,d are simulated data.  %
+\autoref{fig:Czech01}a shows one of the six time orderings of the three excitation pulses where
+$\tau_{22^\prime}\equiv t_2-t_{2^\prime}>0$ and $\tau_{21}\equiv t_2-t_1<0$; that is, the
+$\omega_{2^\prime}$ pulse interacts first and the $\omega_1$ pulse interacts last.  %
+\autoref{fig:Czech01}b illustrates the 2D delay-delay spectrum for all six time orderings when
+$\omega_1$ and $\omega_2$ are both resonant with the same state.  %
+The color denotes the output amplitude.  %
+Along the negative ordinate where $\tau_{22^\prime}=0$, interactions with the $\omega_2$ and
+$\omega_{2^\prime}$ pulses create a population that is probed by $\omega_1$.  %
+Similarly, along the negative absicissa where $\tau_{21}=0$, interactions with the $\omega_2$ and
+$\omega_1$ pulses create a population that is probed by $\omega_{2\prime}$.  %
+The decay along these axes measures the population relaxation dynamics.  %
+Note that these delay representations differ from previous publications by our group.
+\cite{PakoulevAndreiV2006a}  %
+This paper specifically explores the dynamics along the ordinate where $\tau_{22^\prime}$ is zero
+and the $\tau_{21}$ delay is changed.  %
+
+\autoref{fig:Czech01}c depicts the A and B excitonic transitions between the spin-orbit split
+valence bands and the degenerate conduction band states of MoS\textsubscript{2}.  %
+\autoref{fig:Czech01}d illustrates the 2D frequency-frequency spectrum when $\omega_1$ and
+$\omega_2$ are scanned over two narrow resonances.  %
+The spectrum contains diagonal and cross-peaks that we label according to the excitonic resonances
+AA, AB BA, and BB for illustrative purposes.  %
+The dynamics of the individual quantum states are best visualized by 2D frequency-delay plots,
+which combine the features seen in \autoref{fig:Czech01}b,d.  %
+
+This works reports the first multiresonant CMDS spectra of MoS\textsubscript{2}.  %
+It includes the excitation frequency dependence of the A and B excitonic-state dynamics.  %
+These experiments provide a fundamental understanding of the multidimensional MoS\textsubscript{2}
+spectra and a foundation for interpreting CMDS experiments on more complex TMDC
+heterostructures.  %
+The experimental spectra differ from the simple 2D spectrum shown in \autoref{fig:Czech01}d and
+those of earlier CMDS experiments with model systems.  %
+The line shape of the CMDS excitation spectrum closely matches the absorption spectrum, but the
+line shape of the output coherence is dominated by the A and B excitonic features.  %
+The difference arises from fast, $<70$ fs intraband relaxation from the hot A and B excitons of the
+continuum to the band edge.  %
+A longer, 680 fs relaxation occurs because of trapping and/or exciton dynamics.
+\cite{SimSangwan2013a}  %
+The intensity of the cross-peaks depends on the importance of state filling and intraband
+relaxation of hot A excitons as well as the presence of interband population trnasfer of the A and
+B exciton states.  %
+
+\section{Methods}  % ------------------------------------------------------------------------------
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{MX2/S1}
+  \caption{Schemiatic of the synthetic setup used for Mo thin film sulfidation reactions.}
+  \label{fig:CzechS1}
+\end{figure}
+
+MoS\textsubscript{2} thin films were prepared \textit{via} a Mo film sulfidation reaction, similar
+to methods reported by \textcite{LaskarMasihhurR2013a}.  %
+A 1 nm amount of Mo (Kurt J. Lesker, 99.95\%) metal was electron-beam evaporated onto a fused
+silica substrate at a rate of 0.05 \AA/s.  %
+The prepared Mo thin films were quickly transferred to the center of a 1-inch fused silica tub
+furnace equipped with gas flow controllers (see \autoref{fig:CzechS1}) and purged with Ar.  %
+The temperature of the Mo substrate was increased to 900 $^\circ$C over the course of 15 min, after
+which 200 mg of sulfur was evaporated into the reaction chamber.  %
+Sulfidation was carried out for 30 min, and the furnace was subsequently cooled to room
+temperature; then the reactor tube was returned to atmospheric pressure, and the
+MoS\textsubscript{2} thin film samples were collected.  %
+The MoS\textsubscript{2} samples were characterized and used for CMDS experiments with no further
+preparation.  %
+
+MoS\textsubscript{2} thin film absorption spectra were collected by a Shimadzu 2401PC
+ultraviolet-visible spectraphotometer.  %
+Raman and photoluminescence experiments were carried out in parallel using a Thermo DXR Raman
+microscope with a 100x 0.9 NA focusing objective and a 2.0 mW 532 nm excitation source.  %
+Raman/PL measurements were intentionally performed at an excitation power of $<$8.0 mW to prevent
+sample damage. \cite{CastellanosGomezA2012a}  %
+Contact-mode atomic foce microscopy was performed with an Agilent 5500 AFM.  %
+MoS\textsubscript{2} film thickness was determined by scratching the sample to provide a clean
+step-edge between the MoS\textsubscript{2} film and the fused silica substrate.  %
+TEM samples were prepared following the method outlined by \textcite{ShanmugamMariyappan2012a}
+using concentrated KOH in a 35 $^\circ$C oil bath for 20 minutes.  %
+The delaminated MoS\textsubscript{2} sample was removed from the basic solution, rinsed five times
+with DI water, and transferred to a Cu-mesh TEM grid.  %
+TEM experiments were performed on a FEI Titan aberration corrected (S)TEM under 200 kV accelerating
+voltage.  %
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{MX2/10}
+  \caption[Mask and epi vs transmissive.]{(a) Mask. (b) 2D delay spectra at the BB diagonal
+    ($\omega_1=\omega_2\approx1.95$ eV) for transmissive and reflective geometries. Transmissive
+    signal is a mixture of MoS\textsubscript{2} signal and a large amount of driven signal from the
+    substrate that only appears in the pulse overlap region. Reflective signal is representative of
+    the pure MoS\textsubscript{2} response.}
+  \label{fig:Czech10}
+\end{figure}
+
+The coherent multidimensional spectroscopy system used a 35 fs seed pulse, centered at 800 nm and
+generated by a 1 kHz Tsunami Ti-sapphire oscillator.  %
+The seed was amplified by a Spitfire-Pro regenerative amplifier.  %
+The amplified output was split to pump two TOPAS-C collinear optical parametric amplifiers.  %
+OPA signal output was immediately frequency doubled with BBO crystals, providing two $\approx$50 fs
+independently tunable pulses denoted $\omega_1$ and $\omega_2$ with frequencies ranging from 1.62
+to 2.12 eV.  %
+Signal and idler were not filtered out, but played no role due to their low photon energy.  %
+Pulse $\omega_2$ was split into pulses labeled $\omega_2$ and $\omega_{2^\prime}$ to create a total
+of three excitation pulses.  %
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{MX2/S4}
+  \caption{OPA outputs at each color explored.}
+  \label{fig:CzechS4}
+\end{figure}
+
+In this experiment we use motorized OPAs which allow us to set the output color in software.  %
+OPA1 and OPA2 were used to create the $\omega_1$ and $\omega_2$ frequencies, respectively.  %
+In \autoref{fig:CzechS4} we compare the spectral envelope generated by the OPA at each set
+color.  %
+Negative detuning values correspond to regions of the envelope lower in energy than the
+corresponding set color.  %
+The colorbar allows for comparison between set color intensities.  %
+The fluence values reported correspond to the brightest set color for each OPA.  %
+A single trace of OPA2 output at set color = 1.95 eV can be found in \autoref{fig:Czech02}.
+
+After passing through automated delay stages (Newport SMC100 actuators), all three beams were
+focused onto the sample surface by a 1 meter focal length spherical mirror in a distorted BOXCARS
+geometry to form a 630, 580, and 580 $\mu$m FWHM spot sizes for $\omega_1$, $\omega_2$, and
+$\omega_{2^\prime}$, respectively.  %
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{MX2/S5}
+  \caption{Spectral delay correction.}
+  \label{fig:CzechS5}
+\end{figure}
+
+\autoref{fig:CzechS5} represents delay corrections applied for each OPA.  %
+The corrections were experimentally determined using driven FWM output from fused silica.  %
+Corrections were approximately linear against photon energy, in agreement with the normal dispersion
+of transmissive optics inside our OPAs and between the OPAs and the sample.  %
+OPA2 required a relatively small correction along $\tau_{22^\prime}$ (middle subplot) to account
+for any dispersion experienced differently between the two split beams.  %
+OPA1 was not split and therefore needed no such correction.  %
+
+\autoref{fig:Czech10}a represents the to-scale mask that defines our distorted BOXCARS
+configuration.  %
+Relative to the center of the BOXCARS mask (small black dot), $\omega_1$, $\omega_2$, and
+$\omega_{2^\prime}$ enter the sample at angles of 5.0, 1.5, and 1.0 degrees.  %
+Each is angled only along the vertical or horizontal dimension, as indicated in
+\autoref{fig:Czech10}a.  %
+This distortion allowed us to remove a large amount of unwanted $\omega_2$ and $\omega_{2^\prime}$
+photons from our signal path (\autoref{fig:Czech10}a red star).  %
+$\omega_1$ photons were less efficiently rejected, as we show below.  %
+The center of the BOXCARS mask was brought into the sample at $\approx$45 degrees.  %
+All three beams had S polarization.  %
+After reflection, the output beam was isolated using a series of apertures, spectrally resolved
+with a monochromator (spectral resolution 9 meV). and detected using a photomultiplier (RCA
+C31034A).  %
+
+Our experimental setup allowed for the collection of both transmissive and reflective
+(epi-directional) FWM signal.  %
+The 2D delay spectra in \autoref{fig:Czech10}b show the presence of a large nonresonant
+contribution at the origin for the transmissive FWM signal and weaker signals from the
+MoS\textsubscript{2} thin film at negative values of $\tau_{21}$ and $\tau_{22^\prime}$.  %
+The nonresonant contribution is much weaker than the signals from the film for the reflective
+signal id is the geometry chosen for this experiment.  %
+This discrimination between a film and the substrate was also seen in reflective and transmissive
+CARS microscopy experiments. \cite{VolkmerAndreas2001a}  %
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{MX2/11}
+  \caption[MoS\textsubscript{2} post processing.]{Visualization of data collection and processing.
+    With the exception of (c), each subsequent pane represents an additional processing step on top
+  of previous processing. The color bar of each image is separate. (a) Voltages read by the
+  detector at teach color combination. The large vertical feature is $\omega_1$ scatter; the shape
+  is indicative of the power curve of the OPA. MoS\textsubscript{2} response can be barely seen
+  above this scatter. (b) Data after chopping and active background subtraction at the boxcar (100
+  shots). (c) The portion of chopped signal that is not material response. This portion is
+  extracted by averaging several collections at very positive $\tau_{21}$ values, where no material
+  response is present due to the short coherence times of MoS\textsubscript{2} electronic states.
+  The largest feature is $\omega_2$ scatter. Cross-talk between digital-to-analog channels can also
+  be seen as the negative portion that goes as $\omega_1$ intensity. (d) Signal after (c) is
+  subtracted. (e) Smoothed data. (f) Amplitude level (square root) data. This spectrum corresponds
+  to that at 0 delay in \autoref{fig:Czech03}. Note that the color bar's range is different than in
+  \autoref{fig:Czech03}.}
+  \label{fig:Czech11}
+\end{figure}
+
+Once measured, the FWM signal was sent through a four-stage workup process to create the data set
+shown here.  %
+This workup procedure is visualized in \autoref{fig:Czech11}.  %
+We use a chopper and boxcar in active background subtraction mode (averaging 100 laser shots) to
+extract the FWM signal from $\omega_1$ and $\omega_2$ scatter.  %
+We collect this differential signal (\autoref{fig:Czech11}b) in software with an additional 50
+shots of averaging.  %
+In post-process we subtract $\omega_2$ scatter and smooth the data using a 2D Kaiser window.  %
+Finally, we represent the homodyne collected data as (sig)$^{1/2}$ to make the dynamics and line
+widths comparable to heterodyne-collected techniques like absorbance and pump-probe spectra.  %
+Throughout this work, zero signal on the color bar is set to agree with the average rather than the
+minimum of noise.  %
+Values below zero due to measurement uncertainty underflow the color bar and are plotted in
+white.  %
+This is especially evident in lots such as +120 fs in \autoref{fig:Czech08}, where there is no real
+signal.  %
+IPython \cite{PerezFernando2007a} and matplotlib \cite{HunterJohnD2007a} were important for data
+processing and plotting in this work.
+
+\section{Results and discussion}  % ---------------------------------------------------------------
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=0.75\textwidth]{MX2/02}
+  \caption[Few-layer MoS\textsubscript{2} thin film characterization.]{Characterization of the
+    few-layer MoS\textsubscript{2} film studied in this work. Optical images of the
+    MoS\textsubscript{2} thin film on fused silica substrate in (a) transmission and (b)
+    reflection. (c) Raman spectrum of the $E_{2g}^1$ and $A_{1g}$ vibrational
+    modes. (d) High-resolution TEM image and its corresponding FFT shown in the inset. (e)
+    Absorption (blue), photoluminescence (green), Gaussian fits to the A and B excitons, along with
+    the residules betwen the fits and absorbance (dotted), A and B exciton centers (dotted) and
+    representative excitation pulse shape (red).}
+  \label{fig:Czech02}
+\end{figure}
+
+The few-layer MoS\textsubscript{2} thin film sample studied in this work was prepared on a
+transparent fused silica substrate by a simple sufidation reaction of a Mo thin film using a
+procedure modified from a recent report. \cite{LaskarMasihhurR2013a}  %
+\autoref{fig:Czech02}a and b show the homogeneous deposition and surface smoothness of the sample
+over the centimeter-sized fused silica substrate, respectively.  %
+The Raman spectrum shows the $E_{2g}^1$ and $A_{1g}$ vibrational modes (\autoref{fig:Czech02}c)
+that are characteristic of MoS\textsubscript{2}. \cite{LiSongLin2012a}  %
+The transmission electron micrograph (TEM) in \autoref{fig:Czech02}d shows the lattice fringes of
+the film with an inset fast Fourier transform (FFT) of the TEM image indicative of the hexagonal
+crystal structure of the film corresponding to the 0001 plane of MoS\textsubscript{2}.
+\cite{LukowskiMarkA2013a}  %
+The MoS\textsubscript{2} film thickness was determined to be 2.66 nm by atomic force microscopy and
+corresponds to approximately four monolayers.  %
+\autoref{fig:Czech02}3 shows the absorption and fluorescence spectrum of the film along with the A
+and B excitonic line shapes that were extracted from the absorption spectrum. A representative
+excitation pulse profile is also shown in red for comparison.  %
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{MX2/S3}
+  \caption[MoS\textsubscript{2} absorbance.]{Extraction of excitonic features from absorbance
+    spectrum. (a) Second derivative spectra of absorbance (black) and fit second derivative
+    spectrum (green). Gaussian fit parameters are shown in the inset table. (b) Absorption curve
+    (black), Gaussian fits (blue and red), and remainder (black dotted).}
+  \label{fig:CzechS3}
+\end{figure}
+
+Extracting the exciton absorbance spectrum is complicated by the large ``rising background'' signal
+from other MoS\textsubscript{2} bands.  %
+With this in mind, we fit the second derivative absorption spectrum to a sum of two second
+derivative Gaussians, as seen in \autoref{fig:CzechS3}.  %
+Conceptually, this method can be thought of as maximizing the smoothness (as opposed to minimizing
+the amplitude) of the remainder between the fit and the absorption spectrum.  %
+The fit parameters can be found in the inset table in \autoref{fig:CzechS3}.  %
+The Gaussians themselves and the remainder can be found in \autoref{fig:CzechS3}.  %
+
+The multiresonant CMDS experiment uses $\approx$70 fs excitation pulses created by two
+independently tunable optical parametric amplifiers (OPAs).  %
+Automated delay stages and neutral density filters set the excitation time delays over all values
+of $\tau_{21}$ with $\tau_{22^\prime}=0$ and the pulse fluence to 90 $\mu$J/cm$^2$ (114
+$\mu$J/cm$^2$) for the $\omega_1$ ($\omega_2$ and $\omega_{2^\prime}$) beam(s).  %
+Each pulse was focused onto the sample using a distorted BOXCARS configuration.
+\cite{EckbrethAlanC1978a}  %
+The FWM signal was spatially isolated and detected with a monochromator that tracks the output
+frequency so $\omega_m = \omega_1$.  %
+In order to compare the FWM spectra with the absorption spectrum, the signal has been defined as
+the square root of the measured FWM signal since FWM depends quadratically on the sample
+concentration and path length.  %
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{MX2/03}
+  \caption[MoS\textsubscript{2} frequency-frequency slices.]{2D frequency-frequency spectra of the
+    MoS\textsubscript{2} sample in the epi configuration. In all spectra $\tau_{22^\prime}=0$ fs,
+    while $\tau_{21}$ is designated in the bottom-right corner of each spectral panel. The color
+    bar defines the square root of the intensity normalized to the most intense feature in the
+    series of spectra. The integration of the signal onto the $\hbar\omega_1=\hbar\omega_m$ and
+    $\hbar\omega_2$ axes are represented ans the blue curves in the top and right side plots,
+    respectively. The side plots also contain the absorbance spectrum (black line) to aid
+    intepretation of the dynamics of the integrated 2D signals. The dashed lines mark the centers
+    of the A and B excitons, as designated from the absorption spectrum.}
+  \label{fig:Czech03}
+\end{figure}
+
+The main set of data presented in this work is an $\omega_1\omega_2\tau_{21}$ ``movie'' with
+$\tau_{22\prime}=0$. 
+\autoref{fig:Czec03} shows representative 2D frequency-frequency slices from this movie at
+increasingly negative $\tau_{21}$ times.  %
+Each 2D frequency spectrum contains side plots along both axes that compare the absorbance spectrum
+(black) to the projection of the integrated signal onto the axis (blue).  %
+Along $\omega_1$ (which for negative $\tau_{21}$ times acts as the ``probe'') we observe two peaks
+corresponding to the A and B excitons.  %
+In contrast, we see no well-defined excitonic peaks along the $\omega_2$ ``pump'' axis.  %
+Instead, the signal amplitude increases toward bluer $\omega_2$ values.  %
+The decrease in FWM above 2.05 eV is caused by a drop in the $\omega_2$ OPA power.
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=0.75\textwidth]{MX2/04}
+  \caption[MoS\textsubscript{2} $\omega_1$ Wigner progression.]{Mixed $\omega_1$---$\tau_{21}$
+    time---frequency representations of the 3D data set at five ascending $\omega_2$ excitation
+    frequencies (solid black lines) showing the impact of the $\omega_2$ excitation frequency on
+    the $\omega_1$ spectral line shape as a function of time. The A and B exciton energies are
+    marked as dashed lines within each spectrum.}
+  \label{fig:Czech04}
+\end{figure}
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=0.75\textwidth]{MX2/05}
+  \caption[MoS\textsubscript{2} $\omega_2$ Wigner progression.]{Mixed $\omega_2$---$\tau_{21}$
+    time---frequency representations of the 3D data set at five ascending $\omega_1$ probe
+    frequencies (solid black lines) showing the impact of the $\omega_1$ excitation frequency on
+    the $\omega_2$ spectral line shape as a function of time. The A and B exciton energies are
+    marked as dashed lines within each spectrum.}
+  \label{fig:Czech05}
+\end{figure}
+
+Figures \ref{fig:Czech04} and \ref{fig:Czech05} show representative 2D frequency-delay slices from
+this movie, where the absicissa is the $\omega_1$ or $\omega_2$ frequency, respectively, the
+ordinate is the $\tau_{21}$ delay time, and the solid bold lines represent five different
+$\omega_2$ or $\omega_1$ frequencies.  %
+The color bar is normalized to the brightest feature in each subplot.  %
+This normalization allows comparison of the time dependence of the line shapes, positions, and
+relative signal amplitudes along the $\omega_1$ or $\omega_2$ axis directly.  %
+
+Each subplot in \autoref{fig:Czech04} is similar to published pump-probe, transient absorption, multidimensionaland
+transient reflection experiments that have measured the electronc dynamics of the A and B excitons.
+\cite{XiaoDi2012a, FangHui2014a, KumarNardeep2013a, NieZhaogang2014a, SunDezheng2014a,
+  SimSangwan2013a, MakKinFai2012a, ThomallaMarkus2006a}  %
+These previous experiments measure relaxation dynamics on the same $\approx$400-600 fs time scale
+that is characteristic of \autoref{fig:Czech04}.  %
+
+Our experiments also show how the spectral features change as a function of the $\omega_2$
+excitation frequency.  %
+The top to subplots of \autoref{fig:Czech04} reflect the changes in the AA and BA features, while
+the bottom two subplots reflect the changes in the AB and BB features.  %
+The figure highlights the changes in the relative amplitude of the A and B features as a function
+of excitation frequency.  %
+Both the line shapes and the dynamics of the spectral features are very similar.  %
+\autoref{fig:Czech05} is an excitation spectrum that shows that the dynamics of the spectral
+features do not depend strongly on the $\omega_1$ frequency.
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=0.5\textwidth]{MX2/06}
+  \caption[Pathway V, VI liouville pathways.]{Liouville pathways for \autoref{fig:Czech04}. gg and
+    ee designate ground- and excited-state populations, the eg, 2e,e, and e$^\prime$+e,e represent
+    the excitonic and biexcitonic output coherences, and the arrows are labeled with the
+    frequencies or population transfer responsible for the transitions. e and e$^\prime$ represent
+    either A or B excitonic states.}
+  \label{fig:Czech06}
+\end{figure}
+
+The spectral features in Figures \ref{fig:Czech03}, \ref{fig:Czech04} and \ref{fig:Czech05} depend
+on the quantum mechanical interference effects caused by the different pathways.  %
+\autoref{fig:Czech06} shows all of the Liouville pathways required to understand the spectral
+features. \cite{PakoulevAndreiV2010a, PakoulevAndreiV2009a}  %
+These pathways correspond to the time orderings labeled V and VI in \autoref{fig:Czech02}b. The
+letters denote the density matrix elements, $\rho_{ij}$, where g representest the ground state and
+e, e$^\prime$ represent any excitonic state.  %
+Interaction with the temporally overlapped $\omega_2$ and $\omega_{2^\prime}$ pulses excites the ee
+excited-state population and bleaches the ground-state population.  %
+Subsequent interaction with $\omega_1$ creates the output coherences for the diagonal spectral
+features when $\omega_1=\omega_2$ or the cross-peak features when $\omega_1\neq\omega_2$.  %
+The stimulated emission (SE) and ground-state bleaching (GSB) pathways create the eg or e$^\prime$g
+output coherences from the ee and gg populations, respectively, while the excited-state absorption
+pathway creates the 2e,e or e$^\prime$+e,e biexcitonic output coherences.  %
+\autoref{fig:Czech06} also includes a population transfer pathway from the ee excited-state
+population to an e$^\prime$e$^\prime$ population from which similar SE and ESA pathways occur.  %
+Since the ESA pathways destructively interfere with the SE and GSB pathways, the output singal
+depends on the differences between the pathways.  %
+Factors that change the biexcitonic output coherences such as the transition moments, state filling
+(Pauli blocking), frequency shifts, or dephasing rate changes will control the output signal.  %
+State filling and ground-state depletion are important factors for MoS\textsubscript{2} since the
+transitions excite specific electron and hole spin and valley states in individual layers.  %
+
+The state-filling and ground-state bleaching effects on the diagonal and cross-peak features in
+\autoref{fig:Czech03} depend on the spin and valley states in the output coherence.
+\cite{XuXiaodong2014a}  %
+The effects of these spins will disappear as the spin and valley states return to equilibrium.
+\cite{ZengHualing2012a, ZhuBairen2014a, MaiCong2013a}
+If we assume spin relaxation is negligible, the FWM transitions that create the diagonal features
+involve either the A or B ESA transitions, so the resulting 2e,e state includes two spin-aligned
+conduction band electrons and valence band holes.  %
+Similarly, the cross-peak regions denoted by AB or BA in \autoref{fig:Czech01}d will have two
+transitions involving an A exciton, so the initial e$^\prime$+e,e state will include antialigned
+spins.  %
+A quantitative treatment of the cancellation effects between the GSB, SE, and ESA pathways requries
+knowledge of the transition moments and state degeneracies and is beyond the scope of this paper.
+\cite{WongCathyY2011a}  %
+
+The most important characteristic of the experimental spectra is the contrast between the absence
+of well-resolved excitonic features that depend on $\omega_2$ in Figures \ref{fig:Czech03} and
+\ref{fig:Czech05} and the well-defined excitonic features that depend on $\omega_1$.  %
+It is also important to note that the projections of the signal amplitude onto the $\omega_2$ axis
+in \autoref{fig:Czech03} match closely with the continuum features in the absorption spectrum and
+that the line shapes of the features along the $\omega_2$ axis in \autoref{fig:Czech05} do not
+change appreciably for different delay times or $\omega_1$ values. %
+It shoudl be noted that the excitation pulse bandwidth (see \autoref{fig:Czech02}e) contributes to
+the absence of well-resolved A and B excitonic features along $\omega_2$.  %
+The similarity to the continuum states in the absorption spectrum and the absence of a strong
+dependence on $\omega_1$ show that the continuum states observed at higher $\omega_2$ frequencies
+participate directly in creating the final output coherences and that their increasing importance
+reflects the increasing absorption strength of higher energy continuum states.  %
+In contrast, the features dependent on $\omega_1$ in Figures \ref{fig:Czech03} and
+\ref{fig:Czech04} match the line shapes of the A and B excitonic resonances.  %
+Although the relative amplitudes of the spectral features depend on the $\omega_2$ frequency, they
+do not depend strongly on the delay times.  %
+These characteristics show that hot A and B excitonic states undergo rapid intraband population
+relaxation over a $<$70 fs time scale set by excitation pulses to the A and B excitonic states
+excited by $\omega_1$.
+
+A central feature of Figures \ref{fig:Czech03} and \ref{fig:Czech04} is that the AB region is much
+brighter than the BA region.  %
+This difference is suprising because simple models predict cross-peaks of equal amplitude, as
+depicted in \autoref{fig:Czech01}d.  %
+The symmetry in simple models arises because the AB and BA cross-peaks involve the same four
+transitions.  %
+The symmetry between AB and BA may be broken by material processes such as population relaxation
+and transfer, the output coherence dephasing rates, and the bleaching and state-filling effects of
+the valence and conduction band states involved in the transitions.  %
+
+We believe that ultrafast intraband population transfer breaks the symmetry of AB and BA
+cross-peaks.  %
+For the BA peak, the interactions with $\omega_2$ and $\omega_{2^\prime}$ generate only A excitons
+that do not relax on $<$70 fs time scales.  %
+For the AB peak, $\omega_2$ and $\omega_{2^\prime}$ generate two kinds of excitons: (1) B excitons
+and (2) hot excitons in the A band.  %
+Relaxation to A may occur by interband transitions of B excitons or intraband transitions of hot A
+excitons.  %
+Either will lead to the GSB, SE, and ESA shown in the ee $\rightarrow$ e$^\prime$e$^\prime$
+population transfer pathways of \autoref{fig:Czech06}.  %
+This relaxation must occur on the time scale of our pulse-width since the cross-peak asymmetry is
+observed even during temporal overlap.  %
+We believe that intraband relaxation of hot A excitons is the main factor in breaking the symmetry
+between AB and BA cross-peaks.  %
+\autoref{fig:Czech04} shows that B $\rightarrow$ A interband relaxation occurs on a longer time
+scale.  %
+The B/A ratio is higher when $\omega_2$ is resonant with the B excitonic transition than when
+$\omega_2$ is lower than the A exciton frequency (the top subplot).  %
+If population transfer of holes from the B to A valence bands occurred during temporal overlap, the
+B/A ratio would be independent of pump frequency at $\tau_21<0$.
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{MX2/07}
+  \caption[MoS\textsubscript{2} transients.]{Transients taken at the different $\omega_1$ and
+    $\omega_2$ frequencies indicated by the colored markers on the 2D spectrum. The dynamics are
+    assigned to a 680 fs fast time constant (black solid line) and a slow time constant represented
+    as an unchanging offset over this timescale (black dashed line).}
+  \label{fig:Czech07}
+\end{figure}
+
+\autoref{fig:Czech07} shows the delay transients at the different frequencies shown in the 2D
+spectrum.  %
+The colors of the dots on the 2D frequency-frequency spectrum match the colors of the
+transients.  %
+The transients were taken with a smaller step size and a longer time scale than the delay space
+explored in the 3D data set.  %
+The transients are quite similar.  %
+Our data are consistent with both monomolecular biexponential and bimolecular kinetic models and
+cannot discriminate between them.  %
+We have fit the decay kinetics to a single exponential model with a time constant of 680 fs and an
+offset that represents the long time decay.  %
+The 680 fs decay is similar to previously published pump-probe and transient absorption
+experiments. \cite{NieZhaogang2014a, SunDezheng2014a, DochertyCallumJ2014a}  %
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{MX2/08}
+  \caption[MoS\textsubscript{2} frequency-frequency slices near pulse overlap.]{2D
+    frequency-frquency spectra near zero $\tau_{21}$ delay times. The signal amplitude is
+    normalized to the brightest features in each spectrum.}
+  \label{fig:Czech08}
+\end{figure}
+
+The spectral features change quantitatively for delay times near temporal overlap.  %
+\autoref{fig:Czech08} shows a series of 2D spectra for both positive and negative $\tau_{21}$ delay
+times with $\tau_{22^\prime}=0$.  %
+Each spectrum is normalized to its brightest feature.  %
+The spectra at positive $\tau_{21}$ delay times become rapidly weaker as the delay times become
+more positive until the features vanish into the noise at +120 fs.  %
+The spectra also develop more diagonal character as the delay time moves from negative to positive
+values.  %
+The AB cross-peak is also a strong feature in the spectrum at early times.  %
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=0.5\textwidth]{MX2/09}
+  \caption[Pathways I, III Liouville pathways.]{Liouville pathways for the $\omega_1$, $\omega_2$,
+    and $\omega_{2^\prime}$ time ordering of pulse interactions. e and e$^\prime$ represent either
+    A or B excitonic states.}
+  \label{fig:Czech09}
+\end{figure}
+
+The pulse overlap region is complicated by the multiple Liouville pathways that must be
+considered.  %
+Additionally, interference between scattered light from the $\omega_1$ excitation beam and the
+output signal becomes a larger factor as the FWM signal decreases.  %
+\autoref{fig:Czech09} shows the $\omega_1$, $\omega_2$, and $\omega_{2^\prime}$ time ordered
+pathway that becomes and important consideration for positive $\tau_{21}$ delay times.  %
+Since $\tau_{22^\prime}=0$, the initial $\omega_1$ pulse creates an excited-state coherence, while
+the subsequent $\omega_2$ and $\omega_{2^\prime}$ pulses create the output coherence.  %
+The output signal is only important at short $\tau_{21}>0$ values because the initially excited
+coherence dephases very rapidly.  %
+When $\omega_1\neq\omega_2$, the first two interactions create an e$^\prime$e zero quantum
+coherence that also dephases rapidly.  %
+However, when $\omega_1=\omega_2$, the first two interactions create an ee, gg population
+difference that relaxes on linger time scales.  %
+The resulting signal will therefore appear as the diagonal feature in \autoref{fig:Czech08}
+(\textit{e.g.}, see the +40 fs 2D spectrum).  %
+In addition to the diagonal feature in \autoref{fig:Czech08}, there is also a vertical feature when
+$\omega_1$ is resonant with the A excitonic transition as well as the AB cross-peak.  %
+These features are attributed to the pathways in \autoref{fig:Czech06}.  %
+Although these pathways are depressed when $\tau_{21}>0$, there is sufficient temporal overlap
+between the $\omega_2$, $\omega_{2^\prime}$, and $\omega_1$ pulses to make their contribution
+comparable to those in \autoref{fig:Czech09}.  %
+More positie values of $\tau_{21}$ emphasize the \autoref{fig:Czech09} pathways over the
+\autoref{fig:Czech06} pathways, accounting for the increasing percentage of diagonal character at
+increasingly positive delays.  %
+
+\section{Conclusions}  % --------------------------------------------------------------------------
+
+This paper presents the first coherent multidimensional spectroscopy of MoS\textsubscript{2} thin
+films.  %
+CMDS methods are related to the earlier ultrafast pump-probe and transient absorption methods since
+they all share bleaching, stimulated emission, Pauli blocking, and excited-state absorption
+pathways, but they differ in how these pathways define the spectra.  %
+In addition, CMDS methods have many additional pathways that become important when the coherence
+dephasing times are longer than the excitation pulse widths.  %
+In this work, the dephasing times are short so the pathways are identical to transient
+absorption.  %
+This work reports the first frequency-frequency-delay spectra of MX\textsubscript{2} samples.  %
+These spectra are complementary to previous work because they allow a direct comparison between the
+initially excited excitonic states and the states creating the final output coherence.  %
+The spectra show that the same hot A and B exciton continuum states that are observed in the
+absorption spectrum also dominate the CMDS excitation spectra.  %
+They also show that rapid, <70 fs intraband relaxation occurs to create the band-edge A and B
+excitonic features observed in the CMSD spectrum.  %
+The relative intensity of the diagonal peak features depends on the relative absorption strength of
+the A and B excitons.  %
+The relative intensity of cross-peak features in the 2D spectra depends on the excitation
+frequency.  %
+Excitation at or above the B exciton feature creates strong cross-peaks associated with hot A and B
+excitons that undergo ultrafast intraband population transfer.  %
+Excitation below the B excitonic feature creates a weak cross-peak indicating A-induced B-state
+bleaching but at a lower signal level corresponding to the lower optical density at this energy.  %
+Population relaxation occurs over $\approx$680 fs, either by transfer to traps or by bimolecular
+charge recombination.  %
+
+These experiments provide the understanding of MoS\textsubscript{2} coherent multidimensional
+spectra that will form the foundation required to measure the dynamical processes occurring in more
+complex MoS\textsubscript{2} and other TMDC heterostructures with quantum-state resolution.  %
+The frequency domain based multiresonant CMDS methods described in this paper will play a central
+role in these measurements.  %
+They use longer, independently tunable pulses that provide state-selective excitation over a wide
+spectral range without the requirement for interferometric stability.  %
+
diff --git a/PEDOT:PSS/chapter.tex b/PEDOT:PSS/chapter.tex
new file mode 100644
index 0000000..c7dc807
--- /dev/null
+++ b/PEDOT:PSS/chapter.tex
@@ -0,0 +1 @@
+\chapter{PEDOT:PSS}
\ No newline at end of file
diff --git a/bibliography.bib b/bibliography.bib
index 88fede4..6b2a454 100644
--- a/bibliography.bib
+++ b/bibliography.bib
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+}

+

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+  month =        {dec},

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+}

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+}

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+@article{HuygensChristiaan1913a,

 	author = {Huygens, Christiaan},

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@@ -95,7 +250,7 @@
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+@book{KahnemanDaniel2013a,

 	author = {Kahneman, Daniel},

 	title = {Thinking, Fast and Slow},

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@@ -103,31 +258,128 @@
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-}

-

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+@article{KambhampatiPatanjali2011a,

+  author =       {Patanjali Kambhampati},

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+                  Semiconductor Quantum Dots},

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+  year =         2011,

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+}

+

+@article{KohlerDanielDavid2014a,

+  author =       {Daniel D. Kohler and Stephen B. Block and Schuyler Kain and

+                  Andrei V. Pakoulev and John C. Wright},

+  title =        {Ultrafast Dynamics within the 1S Exciton Band of Colloidal

+                  {PbSe} Quantum Dots Using Multiresonant Coherent

+                  Multidimensional Spectroscopy},

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+  month =        {mar},

+  publisher =    {American Chemical Society ({ACS})},

+}

+

+@article{KumarNardeep2013a,

+  author =       {Kumar, Nardeep and He, Jiaqi and He, Dawei and Wang, Yongsheng

+                  and Zhao, Hui},

+  title =        {Charge carrier dynamics in bulk MoS2 crystal studied by

+                  transient absorption microscopy},

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+  pages =        133702,

+  year =         2013,

+  doi =          {10.1063/1.4799110},

+}

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+@article{LaskarMasihhurR2013a,

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+                  Rajan},

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+  month =        {jun},

+  publisher =    {{AIP} Publishing},

+}

+

+@incollection{LeeDuckhwan1985a,

+  address =      {London; New York},

+  author =       {Lee, Duckhwan and Albrecht, Andreas C.},

+  booktitle =    {Advances in infrared and Raman Spectroscopy},

+  chapter =      {4},

+  edition =      {1},

+  editor =       {Clark, R. J. H. and Hester, R. E.},

+  isbn =         {9780471906742},

+  pages =        {179--213},

+  title =        {A Unified View of Raman, Resonance Raman, and Fluorescence Spectroscopy (and

+                  their Analogues in Two-Photon Absorption},

+  year =         {1985},

+}

+

+@article{LiSongLin2012a,

+  author =       {Song-Lin Li and Hisao Miyazaki and Haisheng Song and Hiromi Kuramochi and Shu

+                  Nakaharai and Kazuhito Tsukagoshi},

+  title =        {Quantitative Raman Spectrum and Reliable Thickness Identification for Atomic

+                  Layers on Insulating Substrates},

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+  month =        {aug},

+  publisher =    {American Chemical Society ({ACS})},

+}

+

+@article{LukowskiMarkA2013a,

+  author =       {Mark A. Lukowski and Andrew S. Daniel and Fei Meng and Audrey Forticaux and

+                  Linsen Li and Song Jin},

+  title =        {Enhanced Hydrogen Evolution Catalysis from Chemically Exfoliated Metallic {MoS}2

+                  Nanosheets},

+  journal =      {Journal of the American Chemical Society},

+  volume =       135,

+  number =       28,

+  pages =        {10274--10277},

+  year =         2013,

+  doi =          {10.1021/ja404523s},

+  url =          {https://doi.org/10.1021/ja404523s},

+  month =        {jul},

+  publisher =    {American Chemical Society ({ACS})},

+}

+

+@article{MaiCong2013a,

+  author =       {Cong Mai and Andrew Barrette and Yifei Yu and Yuriy G. Semenov and Ki Wook Kim

+                  and Linyou Cao and Kenan Gundogdu},

+  title =        {Many-Body Effects in Valleytronics: Direct Measurement of Valley Lifetimes in

+                  Single-Layer {MoS}2},

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+  year =         2013,

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+  url =          {https://doi.org/10.1021/nl403742j},

+  month =        {dec},

+  publisher =    {American Chemical Society ({ACS})},

+}

+

+@article{MaimanTheodore1960a,

 	author = {Maiman, Theodore},

 	title = {Stimulated Optical Radiation in Ruby},

 	year = {1960},

@@ -139,31 +391,136 @@
 	doi = {10.1038/187493a0},

 }

 

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+@article{MakKinFai2010a,

+  author =       {Kin Fai Mak and Changgu Lee and James Hone and Jie Shan and

+                  Tony F. Heinz},

+  title =        {Atomically {ThinMoS}2: A New Direct-Gap Semiconductor},

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+  doi =          {10.1103/physrevlett.105.136805},

+  month =        {sep},

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-@article{MeyerKentA2004.000,

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+  author =       {Kin Fai Mak and Keliang He and Jie Shan and Tony F. Heinz},

+  title =        {Control of valley polarization in monolayer {MoS}2 by optical

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-@book{PankoveJacques1975.000,

+@article{McClainBrianL2004a,

+  author =       {McClain, Brian L. and Finkelstein, Ilya J. and Fayer, M. D.},

+  title =        {Vibrational echo experiments on red blood cells: Comparison of the dynamics of

+                  cytoplasmic and aqueous hemoglobin},

+  journal =      {Chemical Physics Letters},

+  volume =       392,

+  number =       {4-6},

+  pages =        {324--329},

+  year =         2004,

+  doi =          {10.1016/j.cplett.2004.05.080},

+  month =        {jul},

+}

+

+@article{MeyerKentA2004a,

+  author =       {Meyer, Kent A and Wright, John C. and Thompson, David E},

+  title =        {Frequency and Time-Resolved Triply Vibrationally Enhanced Four-Wave Mixing

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+}

+

+@article{PakoulevAndreiV2009a,

+  author =       {Andrei V. Pakoulev and Mark A. Rickard and Kathryn M. Kornau and Nathan A. Mathew

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+  title =        {Mixed Frequency-/Time-Domain Coherent Multidimensional Spectroscopy: Research

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+

+@article{PakoulevAndreiV2010a,

+  author =       {Andrei V. Pakoulev and Stephen B. Block and Lena A. Yurs and Nathan A. Mathew and

+                  Kathryn M. Kornau and John C. Wright},

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 }

 

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+@article{PerezFernando2007a,

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+}

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 	author = {Judith Segal},

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+}

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+  author =       {Sangwan Sim and Jusang Park and Jeong-Gyu Song and Chihun In

+                  and Yun-Shik Lee and Hyungjun Kim and Hyunyong Choi},

+  title =        {Exciton dynamics in atomically thin {MoS}2: Interexcitonic

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 }

 

-@article{SpencerAustinP2015.000,

+@article{SpencerAustinP2015a,

 	author = {Spencer, Austin P. and Li, Hebin and Cundiff, Steven T. and Jonas, David M.},

 	title = {Pulse Propagation Effects in Optical 2D Fourier-Transform Spectroscopy: Theory},

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+                  {GaAs} quantum wells},

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+  number =       11,

+  pages =        {699--712},

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+  doi =          {10.1038/nnano.2012.193},

+  url =          {https://doi.org/10.1038/nnano.2012.193},

+  month =        {nov},

+  publisher =    {Springer Nature},

+}

+

+@article{WehnerMU1996a,

+  author =       {M. U. Wehner and D. Steinbach and M. Wegener},

+  title =        {Ultrafast coherent transients due to exciton-continuum scattering in bulk {GaAs}},

+  journal =      {Physical Review B},

+  volume =       54,

+  number =       8,

+  pages =        {R5211--R5214},

+  year =         1996,

+  doi =          {10.1103/physrevb.54.r5211},

+  url =          {https://doi.org/10.1103/physrevb.54.r5211},

+  month =        {aug},

+  publisher =    {American Physical Society ({APS})},

+}

+

+@article{WongCathyY2011a,

+  author =       {Cathy Y. Wong and Gregory D. Scholes},

+  title =        {Using two-dimensional photon echo spectroscopy to probe the fine structure of the

+                  ground state biexciton of {CdSe} nanocrystals},

+  journal =      {Journal of Luminescence},

+  volume =       131,

+  number =       3,

+  pages =        {366--374},

+  year =         2011,

+  doi =          {10.1016/j.jlumin.2010.09.015},

+  url =          {https://doi.org/10.1016/j.jlumin.2010.09.015},

+  month =        {mar},

+  publisher =    {Elsevier {BV}},

+}

+

+@article{XiaoDi2012a,

+  author =       {Di Xiao and Gui-Bin Liu and Wanxiang Feng and Xiaodong Xu and

+                  Wang Yao},

+  title =        {Coupled Spin and Valley Physics in Monolayers {ofMoS}2and

+                  Other Group-{VI} Dichalcogenides},

+  journal =      {Physical Review Letters},

+  volume =       108,

+  number =       19,

+  year =         2012,

+  doi =          {10.1103/physrevlett.108.196802 },

+  month =        {may},

+}

+

+@article{XuXiaodong2014a,

+	author = {Xiaodong Xu and Wang Yao and Di Xiao and Tony F. Heinz},

+	title = {Spin and pseudospins in layered transition metal dichalcogenides},

+	journal = {Nature Physics},

+	year = {2014},

+	month = {apr},

+	volume = {10},

+	number = {5},

+	pages = {343--350},

+	doi = {10.1038/nphys2942},

+}

+

+@article{YeeTK1978a,

+  author =       {Yee, T. K. and Gustafson, T. K.},

+  title =        {Diagrammatic analysis of the density operator for nonlinear optical calculations:

+                  Pulsed and cw responses},

+  journal =      {Physical Review A},

+  volume =       18,

+  number =       4,

+  pages =        {1597--1617},

+  year =         1978,

+  doi =          {10.1103/PhysRevA.18.1597},

+  month =        {oct},

+}

+

+@article{YursLenaA2011a,

+  author =       {Yurs, Lena A and Block, Stephen B. and Pakoulev, Andrei V and Selinsky, Rachel S.

+                  and Jin, Song and Wright, John},

+  title =        {Multiresonant Coherent Multidimensional Electronic Spectroscopy of Colloidal PbSe

+                  Quantum Dots},

+  journal =      {The Journal of Physical Chemistry C},

+  volume =       115,

+  number =       46,

+  pages =        {22833--22844},

+  year =         2011,

+  doi =          {10.1021/jp207273x},

+  month =        {nov},

+}

+

+@article{YursLenaA2011a,

+  author =       {Yurs, Lena A and Block, Stephen B. and Pakoulev, Andrei V and

+                  Selinsky, Rachel S. and Jin, Song and Wright, John},

+  title =        {Multiresonant Coherent Multidimensional Electronic

+                  Spectroscopy of Colloidal PbSe Quantum Dots},

+  journal =      {The Journal of Physical Chemistry C},

+  volume =       115,

+  number =       46,

+  pages =        {22833--22844},

+  year =         2011,

+  doi =          {10.1021/jp207273x},

+  month =        {nov},

+}

+

+@article{ZengHualing2012a,

+  author =       {Hualing Zeng and Junfeng Dai and Wang Yao and Di Xiao and Xiaodong Cui},

+  title =        {Valley polarization in {MoS}2 monolayers by optical pumping},

+  journal =      {Nature Nanotechnology},

+  volume =       7,

+  number =       8,

+  pages =        {490--493},

+  year =         2012,

+  doi =          {10.1038/nnano.2012.95},

+  url =          {https://doi.org/10.1038/nnano.2012.95},

+  month =        {jun},

+  publisher =    {Springer Nature},

+}

+

+@article{ZhuBairen2014a,

+  author =       {Bairen Zhu and Hualing Zeng and Junfeng Dai and Xiaodong Cui},

+  title =        {The Study of Spin-Valley Coupling in Atomically Thin Group {VI} Transition Metal

+                  Dichalcogenides},

+  journal =      {Advanced Materials},

+  volume =       26,

+  number =       31,

+  pages =        {5504--5507},

+  year =         2014,

+  doi =          {10.1002/adma.201305367},

+  url =          {https://doi.org/10.1002/adma.201305367},

+  month =        {apr},

+  publisher =    {Wiley-Blackwell},

 }

diff --git a/dissertation.pdf b/dissertation.pdf
index d912182..de1ba62 100644
--- a/dissertation.pdf
+++ b/dissertation.pdf
diff --git a/dissertation.syg b/dissertation.syg
index 816d2c1..48484e6 100644
--- a/dissertation.syg
+++ b/dissertation.syg
@@ -1,3 +1,3 @@
-\glossaryentry{\ensuremath {N}?\glossentry{N}|setentrycounter[]{page}\glsnumberformat}{6}
-\glossaryentry{\ensuremath {N}?\glossentry{N}|setentrycounter[]{page}\glsnumberformat}{6}
-\glossaryentry{\ensuremath {\omega }?\glossentry{omega}|setentrycounter[]{page}\glsnumberformat}{28}
+\glossaryentry{\ensuremath {N}?\glossentry{N}|setentrycounter[]{page}\glsnumberformat}{8}
+\glossaryentry{\ensuremath {N}?\glossentry{N}|setentrycounter[]{page}\glsnumberformat}{8}
+\glossaryentry{\ensuremath {\omega }?\glossentry{omega}|setentrycounter[]{page}\glsnumberformat}{32}
diff --git a/dissertation.tex b/dissertation.tex
index 81f408d..71a5a2d 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -177,7 +177,7 @@ This dissertation is approved by the following members of the Final Oral Committ
   when there are fewer pieces to fit into the puzzle. Our comforting conviction that the world

   makes sense rests on a secure foundation: our almost unlimited ability to ignore our ignorance.}

 

-\hfill -- Daniel Kahneman \cite{KahnemanDaniel2013.000}

+\hfill -- Daniel Kahneman \cite{KahnemanDaniel2013a}

 

 \cleardoublepage

 

@@ -188,17 +188,25 @@ This dissertation is approved by the following members of the Final Oral Committ
 

 % chapters ----------------------------------------------------------------------------------------

 

+\part{Background}

 \include{introduction/chapter}

 \include{spectroscopy/chapter}

 \include{materials/chapter}

+

+\part{Instrumental Development}

 \include{software/chapter}

 \include{instrument/chapter}

+

+\part{Applications}

 \include{PbSe/chapter}

 \include{MX2/chapter}

+\include{PEDOT:PSS/chapter}

+\include{pyrite/chapter}

 \include{BiVO4/chapter}

 

 % appendix -----------------------------------------------------------------------------------------

 

+\part{Appendix}

 \begin{appendix}

 \include{public/chapter}

 \include{procedures/chapter}

diff --git a/instrument/chapter.tex b/instrument/chapter.tex
index 179a629..be8ed71 100644
--- a/instrument/chapter.tex
+++ b/instrument/chapter.tex
@@ -37,7 +37,7 @@ I_{\mathrm{detected}} = \overline{(E_1+E_2)}E_{2^\prime} + (E_1+E_2)\overline{E_
 \end{split}

 \end{equation}

 A similar expression in the case of heterodyne-detected 4WM is derived by

-\textcite{BrixnerTobias2004.000}.  %

+\textcite{BrixnerTobias2004a}.  %

 The goal of any `scatter rejection' processing procedure is to isolate $|E_{\mathrm{4WM}}|^2$ from

 the other terms.  %

 

@@ -81,7 +81,7 @@ The cross term between scatter and signal is the product of $\Phi_\mathrm{sig}$
 \Delta_{2} = \Phi_{\mathrm{sig}}\mathrm{e}^{-\tau_2\omega} &=&  \mathrm{e}^{-\left((\tau_{2^\prime}-2\tau_2)\omega\right)}\\

 \Delta_{2^\prime} = \Phi_{\mathrm{sig}}\mathrm{e}^{-\tau_{2^\prime}\omega} &=& \mathrm{e}^{-\tau_{2}\omega}

 \end{eqnarray}

-Figure \ref{fig:scatterinterferenceinTrEEold} presents numerical simulations of scatter interference as a visual aid. See Yurs 2011 \cite{YursLenaA2011.000}.

+Figure \ref{fig:scatterinterferenceinTrEEold} presents numerical simulations of scatter interference as a visual aid. See Yurs 2011 \cite{YursLenaA2011a}.

 % TODO: Yurs 2011 Data

 

 \begin{figure}[p!] \label{fig:scatterinterferenceinTrEEcurrent}

@@ -130,12 +130,12 @@ separated after light collection.  %
 	\caption[Shot-types in phase shifted parallel modulation.]{Four shot-types in a general phase shifted parallel modulation scheme. The `other' category represents anything that doesn't depend on either chopper, including scatter from other excitation sources, background light, detector voltage offsets, etc.}

 \end{table}

 

-We use the dual chopping scheme developed by \textcite{FurutaKoichi2012.000} called `phase shifted

+We use the dual chopping scheme developed by \textcite{FurutaKoichi2012a} called `phase shifted

 parallel modulation'.  %

 In this scheme, two excitation sources are chopped at 1/4 of the laser repetition rate (two pulses

 on, two pulses off).  %

-Very similar schemes are discussed by \textcite{AugulisRamunas2011.000} and

-\textcite{HeislerIsmael2014.000} for two-dimensional electronic spectroscopy.  %

+Very similar schemes are discussed by \textcite{AugulisRamunas2011a} and

+\textcite{HeislerIsmael2014a} for two-dimensional electronic spectroscopy.  %

 The two chop patterns are phase-shifted to make the four-pulse pattern represented in Table

 \ref{tab:phase_shifted_parallel_modulation}.  %

 In principle this chopping scheme can be achieved with a single judiciously placed mechanical

@@ -170,7 +170,7 @@ To remove such interference terms, you must \textit{fibrillate} your excitation
 An alternative to dual chopping is single-chopping and `leveling'...  %

 this technique was used prior to May 2016 in the Wright Group...  %

 `leveling' and single-chopping is also used in some early 2DES work...

-\cite{BrixnerTobias2004.000}.  %

+\cite{BrixnerTobias2004a}.  %

 

 \begin{figure}[p!] \label{fig:ta-chopping-comparison}

 	\centering

@@ -191,8 +191,8 @@ as the original single chopping.  %
 Fibrillation is the intentional randomization of excitation phase during an experiment.  %

 Because the interference term depends on the phase of the excitation field relative to the signal,

 averaging over many shots with random phase will cause the interference term to approach zero.  %

-This is a well known strategy for removing unwanted interference terms \cite{SpectorIvanC2015.000,

-  McClainBrianL2004.000}.  %

+This is a well known strategy for removing unwanted interference terms \cite{SpectorIvanC2015a,

+  McClainBrianL2004a}.  %

 

 \subsection{Normalization of dual-chopped self-heterodyned signal}

 

diff --git a/introduction/chapter.tex b/introduction/chapter.tex
index 210b1e6..3424a35 100644
--- a/introduction/chapter.tex
+++ b/introduction/chapter.tex
@@ -2,12 +2,11 @@
 

 \section{Coherent Multidimensional Spectroscopy}

 

-\Gls{CMDS}, \gls{coherent multidimensional spectroscopy}

+% Unraveling quantum pathways using optical 3D Fourier-transform spectroscopy doi:10.1038/ncomms2405

 

-\section{Photophysics in Semiconductor Systems}

+\Gls{CMDS}, \gls{coherent multidimensional spectroscopy}

 

-\subsection{Solar Energy Generation}

+\section{The CMDS Instrument}

 

-I like to do \acrlong{TA}

+\section{Scientific Software}

 

-% TODO: discuss Schottky-Quasar, strategies for overcoming

diff --git a/principles/chapter.tex b/principles/chapter.tex
new file mode 100644
index 0000000..9098035
--- /dev/null
+++ b/principles/chapter.tex
@@ -0,0 +1,10 @@
+\chapter{Principles of Instrumental Development}
+
+
+\section{Quality in Science}
+
+% TODO: move to beginning of part II
+% Accessible Reproducible Research doi:10.1126/science.1179653 
+% Quality Uncertainty Erodes Trust in Science doi:10.1525/collabra.74
+% https://software-carpentry.org/blog/2016/11/reproducibility-reading-list.html
+
diff --git a/pyrite/chapter.tex b/pyrite/chapter.tex
new file mode 100644
index 0000000..deb8e2e
--- /dev/null
+++ b/pyrite/chapter.tex
@@ -0,0 +1 @@
+\chapter{Pyrite}
\ No newline at end of file
diff --git a/software/chapter.tex b/software/chapter.tex
index e2c9652..d991410 100644
--- a/software/chapter.tex
+++ b/software/chapter.tex
@@ -1,11 +1,11 @@
-% TODO: add StoddenVictoria2016.000 (Enhancing reproducibility for computational methods)

-% TODO: add MillmanKJarrod2011.000 (Python for Scientists and Engineers)

-% TODO: add vanderWaltStefan2011.000 (The NumPy Array: A Structure for Efficient Numerical Computation)

+% TODO: add StoddenVictoria2016a (Enhancing reproducibility for computational methods)

+% TODO: add MillmanKJarrod2011a (Python for Scientists and Engineers)

+% TODO: add vanderWaltStefan2011a (The NumPy Array: A Structure for Efficient Numerical Computation)

 % TODO: reference https://www.nsf.gov/pubs/2016/nsf16532/nsf16532.htm (Software Infrastructure for Sustained Innovation (SI2: SSE & SSI))

 

 \chapter{Software}

 

-Cutting-edge science increasingly relies on custom software. In their 2008 survey, \textcite{HannayJoErskine2009.000} demonstrated just how important software is to the modern scientist.

+Cutting-edge science increasingly relies on custom software. In their 2008 survey, \textcite{HannayJoErskine2009a} demonstrated just how important software is to the modern scientist.

 \begin{enumerate}[topsep=-1.5ex, itemsep=0ex, partopsep=0ex, parsep=0ex, label=$\rightarrow$]

 	\item 84.3\% of surveyed scientists state that developing scientific software is important or very important for their own research.

 	\item 91.2\% of surveyed scientists state that using scientific software is important or very important for their own research.

@@ -14,10 +14,10 @@ Cutting-edge science increasingly relies on custom software. In their 2008 surve
 \end{enumerate}

 Despite the importance of software to science and scientists, most scientists are not familiar with basic software engineering concepts.

 % TODO: demonstrate that `most scientists are not familiar with basic software engineering concepts'

-This is in part due to the their general lack of formal training in programming and software development. \textcite{HannayJoErskine2009.000} found that over 90\% of scientists learn software development through `informal self study'. Indeed, I myself have never been formally trained in software development.

+This is in part due to the their general lack of formal training in programming and software development. \textcite{HannayJoErskine2009a} found that over 90\% of scientists learn software development through `informal self study'. Indeed, I myself have never been formally trained in software development.

 

-Software development in a scientific context poses unique challenges. Many traditional software development paradigms demand an upfront articulation of goals and requirements. This allows the developers to carefully design their software, even before a single line of code is written. In her seminal 2005 case study \textcite{SegalJudith2005.000} describes a collaboration between a team of researchers and a contracted team of software engineers. Ultimately 

-% TODO: finish the discussion of SegalJudith2005.000

+Software development in a scientific context poses unique challenges. Many traditional software development paradigms demand an upfront articulation of goals and requirements. This allows the developers to carefully design their software, even before a single line of code is written. In her seminal 2005 case study \textcite{SegalJudith2005a} describes a collaboration between a team of researchers and a contracted team of software engineers. Ultimately 

+% TODO: finish the discussion of SegalJudith2005a

 % TODO: segue to reccomendation of agile development practices: http://agilemanifesto.org/

 

 \section{Overview}

diff --git a/spectroscopy/chapter.tex b/spectroscopy/chapter.tex
index 27d763b..9665558 100644
--- a/spectroscopy/chapter.tex
+++ b/spectroscopy/chapter.tex
@@ -1,6 +1,8 @@
 % TODO: discuss and cite CerulloGiulio2003.000

 % TODO: discuss and cite BrownEmilyJ1999.000

 % TODO: cite and discuss Sheik-Bahae 1990 (first z-scan)

+% Modeling of Transient Absorption Spectra in Exciton–Charge-Transfer Systems 10.1021/acs.jpcb.6b09858

+% TODO: Multidimensional Spectral Fingerprints of a New Family of Coherent Analytical Spectroscopies

 

 \chapter{Spectroscopy}

 

@@ -43,7 +45,7 @@ So-called wave mixing energy level (\gls{WMEL}) diagrams are the most familiar w
 spectroscopy for Wright group members.  %

 \gls{WMEL} diagrams were first proposed by Lee and Albrecht in an appendix to their seminal work

 \emph{A Unified View of Raman, Resonance Raman, and Fluorescence Spectroscopy}

-\cite{LeeDuckhwan1985.000}.  %

+\cite{LeeDuckhwan1985a}.  %

 \gls{WMEL} diagrams are drawn using the following rules.  %

 \begin{enumerate}

 	\item The energy ladder is represented with horizontal lines - solid for real states and dashed

@@ -66,14 +68,14 @@ spectroscopy for Wright group members.  %
 \subsection{Reflectivity}

 

 This derivation adapted from \textit{Optical Processes in Semiconductors} by Jacques I. Pankove

-\cite{PankoveJacques1975.000}.  %

+\cite{PankoveJacques1975a}.  %

 For normal incidence, the reflection coefficient is

 \begin{equation}

 R = \frac{(n-1)^2+k^2}{(n+1)^2+k^2}

 \end{equation}

 % TODO: finish derivation

 

-Further derivation adapted from \cite{KumarNardeep2013.000}.  %

+Further derivation adapted from \cite{KumarNardeep2013a}.  %

 To extend reflectivity to a differential measurement

 % TODO: finish derivation

 

@@ -125,10 +127,10 @@ With very short, broad pulses:  %
 \end{itemize}

 

 This epi-CARS paper might have some useful discussion of non-resonant vs resonant for shorter and

-shorter pulses \cite{ChengJixin2001.000}.  %

+shorter pulses \cite{ChengJixin2001a}.  %

 

 An excellent discussion of pulse distortion phenomena in broadband time-domain experiments was

-published by \textcite{SpencerAustinP2015.000}.  %

+published by \textcite{SpencerAustinP2015a}.  %

 

 Another idea in defense of frequency domain is for the case of power studies.  %

 Since time-domain pulses in-fact possess all colors in them they cannot be trusted as much at