21 files changed, 235 insertions, 18 deletions

diff --git a/PEDOT:PSS/beam waist.png b/PEDOT:PSS/beam waist.png
new file mode 100644
index 0000000..1e99afc
--- /dev/null
+++ b/PEDOT:PSS/beam waist.png
diff --git a/PEDOT:PSS/chapter.tex b/PEDOT:PSS/chapter.tex
index c7dc807..9138972 100644
--- a/PEDOT:PSS/chapter.tex
+++ b/PEDOT:PSS/chapter.tex
@@ -1 +1,169 @@
-\chapter{PEDOT:PSS}
\ No newline at end of file
+\chapter{PEDOT:PSS}
+
+\section{Introduction}
+
+Poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) is a transparent, electrically
+conductive (up to 4380 S cm$^{-1}$ \cite{KimNara2013a}) polymer.  %
+It has found widespread use as a flexible, cheap alternative to inorganic transparent electrodes
+such as indium tin oxide.  %
+
+As a polymer, PEDOT:PSS implicitly contains a large amount of structural inhomogeneity.  %
+On top of this, PEDOT:PSS is a two component material, composed of PEDOT (low molecular weight,
+p-doped, highly conductive) and PSS (high molecular-weight, insulating, stabilizing).  %
+These two components segment into domains of conductive and non-conductive material, leading to
+even more structural inhomogeneity.  %
+Nonlinear spectroscopy may be able to shed light on the microscopic environment of electronic
+states within PEDOT:PSS.  %
+
+\section{Background}
+
+Complex microstructure:
+\begin{enumerate}
+  \item PEDOT oligomers (6---18-mers)
+  \item these oligomers $\pi$-stack to form small nanocrystalites, 3 to 14 oligomers for pristine
+    films to as many as 13---14 oligomers for more conductive solvent treated films
+  \item nanocrystallites then arrange into globular conductive particles in a pancakge-like shape
+  \item these particles themselves are then linked via PSS-rich domains and assembled into
+    nanofibril geometry akin to a string of pearls
+  \item nanofibrils interweave to form thin films, with PSS capping layer at surface
+\end{enumerate}
+
+Prior spectroscopy (absorption anisotropy, X-ray scattering, condutivity).  %
+
+% TODO: absorption spectrum of thin film
+
+Broad in the infrared due to midgap states created during doping from charge-induced lattice
+relaxations.  %
+These electronic perturbations arise from injected holes producing a quinoidal distortion spread
+over 4-5 monomers of the CP aromatic backbone, collectively called a polaron.  %
+Energetically favorable to be spin-silent bipolaron.  %
+
+\section{Methods}
+
+PEDOT:PSS (Orgacon Dry, Sigma Aldrich) was dropcast onto a glass microscope slide at 1 mg/mL at a
+tilt to ensure homogeneous film formation.  %
+The sample was heated at 100 $^\circ$C for $\sim$15 min to evaporate water.  %
+
+An ultrafast oscillator (Spectra-Physics Tsunami) was used to prepare $\sim$35 fs seed pulses.  %
+These were amplified (Spectra-Physics Spitfire Pro XP, 1 kHz), split, and converted into 1300 nm 40
+fs pulses using two separate optical parametric amplifiers (Light Conversion TOPAS-C): ``OPA1'' and
+``OPA2''.  %
+Pulses from OPA2 were split again, for a total of three excitation pulses: $\omega_1$, $\omega_2$
+and $\omega_{2^\prime}$.  %
+These were passed through motorized (Newport MFA-CC) retroreflectors to control their relative
+arrival time (``delay'') at the sample: $\tau_{21} = \tau_2 - \tau_1$ and $\tau_{22^\prime} =
+\tau_2 - \tau_{2^\prime}$. The three excitation pulses were focused into the sample in a $1^\circ$
+right-angle isoceles triange, as in the BOXCARS configuration. \cite{EckbrethAlanC1978a}  %
+Each excitation beam was 67 nJ focused into a 375 $\mathsf{\mu m}$ symmetric Gaussian mode for an
+intensity of 67 $\mathsf{\mu J / cm^2}$.  %
+A new beam, emitted coherently from the sample, was isolated with apertures and passed into a
+monochromator (HORIBA Jobin Yvon MicroHR, 140 mm focal length) with a visible grating (500 nm blaze
+300 groves per mm).  %
+The monochromator was set to pass all colors (0 nm, 250 $\mathsf{\mu m}$ slits) to keep the
+measurement impulsive.  %
+Signal was detected using an InSb photodiode (Teledyne Judson J10D-M204-R01M-3C-SP28).  %
+Four wave mixing was isolated from excitation scatter using dual chopping and digital signal
+processing.  %
+
+\section{Transmittance and reflectance}
+
+\afterpage{
+\begin{figure}
+  \centering
+	\includegraphics[width=0.5\linewidth]{"PEDOT:PSS/linear"}
+	\caption[PEDOT:PSS transmission and reflectance spectra.]{
+    Thin film spectra.
+    Transmission, reflectance, and extinction spectrum of the thin film used in this work.  %
+    Extinction is $\log_{10}{\mathsf{(transmission)}}$.  %
+  }
+	\label{fig:PEDOTPSS_linear}
+\end{figure}
+\clearpage}
+
+\autoref{fig:PEDOTPSS_linear} shows the transmission, reflectance, and extinction spectrum of the
+thin film used in this work.  %
+
+\section{Three-pulse echo spectroscopy}
+
+\afterpage{
+\begin{figure}
+  \centering
+	\includegraphics[width=0.5\linewidth]{"PEDOT:PSS/mask"}
+	\caption[PEDOT:PSS 3PE phase matching mask.]{
+    Phase matching mask used in this experiment.
+    Each successive ring subtends 1 degree, such that the excitation pulses are each angled one
+    degree relative to the mask center.
+    The two stars mark the two output poyntings detected in this work.
+  }
+	\label{fig:PEDOTPSS_mask}
+\end{figure}
+\clearpage}
+
+Two dimensional $\tau_{21}, \tau_{22^\prime}$ scans were taken for two phase matching
+configurations: (1) $k_{\mathsf{out}} = k_1 - k_2 + k_{2^\prime}$ (3PE) and (2) $k_{\mathsf{out}} =
+k_1 + k_2 - k_{2^\prime}$ (3PE*).  %
+The rephasing and nonrephasing pathways exchange their time dependance between these two
+configurations.  %
+Comparing both pathways, rephasing-induced peak shifts can be extracted as in 3PE. [CITE]  %
+All data was modeled using numerical integration of the Liouville-von Numann equation.  %
+
+Continuously variable ND filters (THORLABS NDC-100C-4M, THORLABS NDL-10C-4) were used to ensure
+that all three excitation pulse powers were equal within measurement error.  %
+
+\afterpage{
+\begin{figure}
+  \centering
+	\includegraphics[width=0.5\linewidth]{"PEDOT:PSS/raw"}
+	\caption[PEDOT:PSS 3PE raw data.]{
+    CAPTION TODO
+  }
+	\label{fig:PEDOTPSS_raw}
+\end{figure}
+\clearpage}
+
+
+\afterpage{
+\begin{figure}
+  \centering
+	\includegraphics[width=0.5\linewidth]{"PEDOT:PSS/processed"}
+	\caption[PEDOT:PSS 3PE processed data.]{
+    CAPTION TODO
+  }
+	\label{fig:PEDOTPSS_processed}
+\end{figure}
+\clearpage}
+
+\afterpage{
+\begin{figure}
+  \centering
+	\includegraphics[width=0.5\linewidth]{"PEDOT:PSS/delay_space"}
+	\caption[PEDOT:PSS 3PE delay space.]{
+    CAPTION TODO
+  }
+	\label{fig:PEDOTPSS_delay_space}
+\end{figure}
+\clearpage}
+
+\afterpage{
+\begin{figure}
+  \centering
+	\includegraphics[width=0.5\linewidth]{"PEDOT:PSS/traces"}
+	\caption[PEDOT:PSS 3PE traces.]{
+    CAPTION TODO
+  }
+	\label{fig:PEDOTPSS_traces}
+\end{figure}
+\clearpage}
+
+\afterpage{
+\begin{figure}
+  \centering
+	\includegraphics[width=0.5\linewidth]{"PEDOT:PSS/overtraces"}
+	\caption[PEDOT:PSS 3PE traces.]{
+    CAPTION TODO
+  }
+	\label{fig:PEDOTPSS_overtraces}
+\end{figure}
+\clearpage}
+
+\section{Frequency-domain transient grating spectroscopy}
\ No newline at end of file
diff --git a/PEDOT:PSS/compare 2D.png b/PEDOT:PSS/compare 2D.png
new file mode 100644
index 0000000..e42cb42
--- /dev/null
+++ b/PEDOT:PSS/compare 2D.png
diff --git a/PEDOT:PSS/compare slices.png b/PEDOT:PSS/compare slices.png
new file mode 100644
index 0000000..8433b81
--- /dev/null
+++ b/PEDOT:PSS/compare slices.png
diff --git a/PEDOT:PSS/compare.png b/PEDOT:PSS/compare.png
new file mode 100644
index 0000000..2cfd095
--- /dev/null
+++ b/PEDOT:PSS/compare.png
diff --git a/PEDOT:PSS/delay space.png b/PEDOT:PSS/delay space.png
new file mode 100644
index 0000000..1fed3f6
--- /dev/null
+++ b/PEDOT:PSS/delay space.png
diff --git a/PEDOT:PSS/excitation pulse spectra.png b/PEDOT:PSS/excitation pulse spectra.png
new file mode 100644
index 0000000..01d2426
--- /dev/null
+++ b/PEDOT:PSS/excitation pulse spectra.png
diff --git a/PEDOT:PSS/linear.png b/PEDOT:PSS/linear.png
new file mode 100644
index 0000000..7c48bed
--- /dev/null
+++ b/PEDOT:PSS/linear.png
diff --git a/PEDOT:PSS/main.png b/PEDOT:PSS/main.png
new file mode 100644
index 0000000..e1f10d8
--- /dev/null
+++ b/PEDOT:PSS/main.png
diff --git a/PEDOT:PSS/mask.png b/PEDOT:PSS/mask.png
new file mode 100644
index 0000000..418e928
--- /dev/null
+++ b/PEDOT:PSS/mask.png
diff --git a/PEDOT:PSS/overtraces.png b/PEDOT:PSS/overtraces.png
new file mode 100644
index 0000000..767517c
--- /dev/null
+++ b/PEDOT:PSS/overtraces.png
diff --git a/PEDOT:PSS/peak shift.png b/PEDOT:PSS/peak shift.png
new file mode 100644
index 0000000..42e7b43
--- /dev/null
+++ b/PEDOT:PSS/peak shift.png
diff --git a/PEDOT:PSS/processed.png b/PEDOT:PSS/processed.png
new file mode 100644
index 0000000..32b210c
--- /dev/null
+++ b/PEDOT:PSS/processed.png
diff --git a/PEDOT:PSS/raw.png b/PEDOT:PSS/raw.png
new file mode 100644
index 0000000..58cef4a
--- /dev/null
+++ b/PEDOT:PSS/raw.png
diff --git a/PEDOT:PSS/substrate.png b/PEDOT:PSS/substrate.png
new file mode 100644
index 0000000..2a5fe49
--- /dev/null
+++ b/PEDOT:PSS/substrate.png
diff --git a/PEDOT:PSS/traces.png b/PEDOT:PSS/traces.png
new file mode 100644
index 0000000..7ffc5d0
--- /dev/null
+++ b/PEDOT:PSS/traces.png
diff --git a/bibliography.bib b/bibliography.bib
index 6b2a454..66d59c9 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -271,6 +271,21 @@
   month =        {jan},

 }

 

+@article{KimNara2013a,

+  author =       {Nara Kim and Seyoung Kee and Seoung Ho Lee and Byoung Hoon Lee and Yung Ho Kahng

+                  and Yong-Ryun Jo and Bong-Joong Kim and Kwanghee Lee},

+  title =        {Highly Conductive {PEDOT}:{PSS} Nanofibrils Induced by Solution-Processed

+                  Crystallization},

+  journal =      {Advanced Materials},

+  volume =       26,

+  number =       14,

+  pages =        {2268--2272},

+  year =         2013,

+  doi =          {10.1002/adma.201304611},

+  month =        {dec},

+  publisher =    {Wiley-Blackwell},

+}

+

 @article{KohlerDanielDavid2014a,

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

                   Andrei V. Pakoulev and John C. Wright},

diff --git a/dissertation.pdf b/dissertation.pdf
index 5a07659..7cfeb9a 100644
--- a/dissertation.pdf
+++ b/dissertation.pdf
diff --git a/dissertation.syg b/dissertation.syg
index 7b1944a..e69de29 100644
--- a/dissertation.syg
+++ b/dissertation.syg
@@ -1,3 +0,0 @@
-\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}{74}
diff --git a/dissertation.tex b/dissertation.tex
index 3bf6bb6..4bc47a2 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -192,30 +192,30 @@ This dissertation is approved by the following members of the Final Oral Committ
 \include{introduction/chapter}

 

 \part{Background}

-\include{spectroscopy/chapter}

-\include{materials/chapter}

-\include{mixed_domain/chapter}

+%\include{spectroscopy/chapter}

+%\include{materials/chapter}

+%\include{mixed_domain/chapter}

 

 \part{Instrumental Development}

-\include{software/chapter}

-\include{instrument/chapter}

+%\include{software/chapter}

+%\include{instrument/chapter}

 

 \part{Applications}

-\include{PbSe/chapter}

-\include{MX2/chapter}

+%\include{PbSe/chapter}

+%\include{MX2/chapter}

 \include{PEDOT:PSS/chapter}

-\include{pyrite/chapter}

-\include{BiVO4/chapter}

+%\include{pyrite/chapter}

+%\include{BiVO4/chapter}

 

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

 

 \part{Appendix}

 \begin{appendix}

-\include{public/chapter}

-\include{procedures/chapter}

-\include{hardware/chapter}

-\include{errata/chapter}

-\include{colophon/chapter}

+%\include{public/chapter}

+%\include{procedures/chapter}

+%\include{hardware/chapter}

+%\include{errata/chapter}

+%\include{colophon/chapter}

 \end{appendix}

 

 % post --------------------------------------------------------------------------------------------

diff --git a/introduction/chapter.tex b/introduction/chapter.tex
index 3424a35..81a6b97 100644
--- a/introduction/chapter.tex
+++ b/introduction/chapter.tex
@@ -8,5 +8,42 @@
 

 \section{The CMDS Instrument}

 

+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

+Instruments, Horiba, Thorlabs, and Newport.  %

+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

+challenge of incorporating the new components into the existing software ecosystem.  %

+At the same time, students were spending much of their time in lab repeatedly calibrating optical

+parametric amplifiers by hand, a process that sometimes took days.  %

+I chose to spend a significant portion of my graduate career focusing on solving these problems

+through software development.  %

+At first, I focused on improving the existing LabVIEW code.  %

+Eventually, I developed a vision for a deeply modular acquisition software that could not be

+practically created with LabVIEW.  %

+Using Python and Qt, I created a brand new acquisition software PyCMDS: built from the ground up to

+fundamentally solve historical challenges in the Group.  %

+PyCMDS offers a modular hardware model that can ``re-configure'' itself to flexibly control a

+variety of component hardware configurations.  %

+This has enabled graduate students to add and remove hardware whenever necessary, without worrying

+about a heavy additional programming burden.  %

+PyCMDS is now used to drive both MR-CMDS instruments in the Group, allowing for easy sharing of

+component hardware and lessening the total amount of software that the Group needs to maintain.  %

+Besides being more flexible, PyCMDS solves a number of other problems.  %

+It offers fully automated strategies for calibrating component hardwares, making calibration less

+arduous and more reproducible.  %

+It offers more fine-grained control of data acquisition and timing, enabling more complex

+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