2018-04-13 08:46

6 files changed, 124 insertions, 71 deletions

diff --git a/MX2/chapter.tex b/MX2/chapter.tex
index 88b496e..6e5bdb1 100644
--- a/MX2/chapter.tex
+++ b/MX2/chapter.tex
@@ -1,6 +1,20 @@
-\chapter{Transition metal dichalcogenide thin films} \label{cha:mx2}
-
-\textit{This Chapter borrows extensively from \textcite{CzechKyleJonathan2015a}.}
+\chapter{Measurement of Ultrafast Excitonic Dynamics of Few-Layer MoS$\mathbf{_2}$ using
+  State-Selective Coherent Multidimensional Spectroscopy} \label{cha:mx2}
+
+\textit{This Chapter borrows extensively from \textcite{CzechKyleJonathan2015a}. The authors are:
+  \begin{denumerate}
+    \item Kyle J. Czech
+    \item Blaise J. Thompson
+    \item Schuyler Kain
+    \item Qi Ding
+    \item Melinda J. Shearer
+    \item Robert J. Hamers
+    \item Song Jin
+    \item John C. Wright
+  \end{denumerate}
+}
+
+\clearpage
 
 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
diff --git a/PEDOT_PSS/chapter.tex b/PEDOT_PSS/chapter.tex
index 10c5af2..b7fba1f 100644
--- a/PEDOT_PSS/chapter.tex
+++ b/PEDOT_PSS/chapter.tex
@@ -1,6 +1,28 @@
-\chapter{PEDOT:PSS}
-
-\section{Introduction}
+\chapter{PEDOT:PSS}  \label{cha:pps}
+
+
+\textit{This Chapter presents content first published in \textcite{HorakErikH2018a}.
+  The authors are:
+  \begin{denumerate}
+    \item Erik H. Horak
+    \item Morgan T. Rea
+    \item Kevin D. Heylman
+    \item David Gelbwaser-Klimovsky
+    \item Semion K. Saikin
+    \item Blaise J. Thompson
+    \item Daniel D. Kohler
+    \item Kassandra A. Knapper
+    \item Wei Wei
+    \item Feng Pan
+    \item Padma Gopalan
+    \item John C. Wright
+    \item Alán Aspuru-Guzik
+    \item Randall H. Goldsmith
+  \end{denumerate}
+  This Chapter focuses on my contribution.  %
+}
+
+\section{Introduction}  % =========================================================================
 
 Poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) is a transparent, electrically
 conductive (up to 4380 S cm$^{-1}$ \cite{KimNara2013a}) polymer.  %
@@ -15,7 +37,7 @@ even more structural inhomogeneity.  %
 Nonlinear spectroscopy may be able to shed light on the microscopic environment of electronic
 states within PEDOT:PSS.  %
 
-\section{Background}
+\section{Background}  % ===========================================================================
 
 Complex microstructure:
 \begin{enumerate}
@@ -38,7 +60,7 @@ These electronic perturbations arise from injected holes producing a quinoidal d
 over 4-5 monomers of the CP aromatic backbone, collectively called a polaron.  %
 Energetically favorable to be spin-silent bipolaron.  %
 
-\section{Methods}
+\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.  %
@@ -65,7 +87,7 @@ Signal was detected using an InSb photodiode (Teledyne Judson J10D-M204-R01M-3C-
 Four wave mixing was isolated from excitation scatter using dual chopping and digital signal
 processing.  %
 
-\section{Transmittance and reflectance}
+\section{Transmittance and reflectance}  % ========================================================
 
 \autoref{fig:PEDOTPSS_linear} shows the transmission, reflectance, and extinction spectrum of the
 thin film used in this work.  %
@@ -83,7 +105,7 @@ thin film used in this work.  %
 \end{figure}
 \clearpage
 
-\section{Three-pulse echo spectroscopy}  % --------------------------------------------------------
+\section{Three-pulse echo spectroscopy}  % ========================================================
 
 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}} =
@@ -296,8 +318,6 @@ Regardless, these contributions do not affect our analysis.  %
 Extremely fast (single fs) carrier scattering time constants have also been observed for PEDOT-base
 conductive films. [CITES]
 
-\section{Frequency-domain transient grating spectroscopy}  % --------------------------------------
-
-This section describes preliminary, unpublished work accomplished on PEDOT:PSS.  %
-
+\section{Conclusions}  % ==========================================================================
 
+% TODO
\ No newline at end of file
diff --git a/abstract.tex b/abstract.tex
index 1a1060d..fdaf7b9 100644
--- a/abstract.tex
+++ b/abstract.tex
@@ -22,9 +22,8 @@ tunable output frequencies.  %
 These pulses are directed into a material under investigation.  %
 The pulses interact with the material, and due to the specific interference between the multiple
 fields the material is driven to emit a new pulse: the MR-CMDS signal.  %
-This signal may be different in frequency from the input pulses, and it may travel in a new
-direction depending on the exact experiment being performed.  %
-% BJT: flip proceeding sentence around
+This signal may have a different frequency and/or direction than the input pulses, depending on the
+exact experiment being performed.  % 
 The MR-CMDS experiment involves tracking the intensity of this output signal as a function of
 different properties of the excitation pulses.  %
 These properties include
@@ -40,12 +39,12 @@ Because MR-CMDS is a family of related-but-separate experiments, each of them a
 space, there are special challenges that must be addressed when designing a general-purpose MR-CMDS
 instrument.  % BJT: be more specific about the challenge at hand
 These issues require development of software, hardware, and theory.  %
-Five different improvements to MR-CMDS are presented in this dissertation: 1. processing software
-(\autoref{cha:pro}), 2. acquisition software (\autoref{cha:acq}) 3, active artifact correction
-(\autoref{cha:act}), 4. automated OPA calibration (\autoref{cha:opa}), and 5. finite pulse
-accountancy (\autoref{cha:mix}).  %
 \hyperref[prt:background]{Part I: Background} introduces relevant literature which informs on this
 development work.  %
+\hyperref[prt:development]{Part II: Development} presents five strategies used to improve MR-CMDS:
+1. processing software (\autoref{cha:pro}), 2. acquisition software (\autoref{cha:acq}) 3, active
+artifact correction (\autoref{cha:act}), 4. automated OPA calibration (\autoref{cha:opa}), and 5.
+finite pulse accountancy (\autoref{cha:mix}).  %
 Finally, \hyperref[prt:applications]{Part III: Applications} presents three examples where these
-instruments, with these improvements, have been used to address chemical questions in
-semiconductor systems.  %
\ No newline at end of file
+instruments, with these improvements, have been used to address chemical questions in semiconductor
+systems.  %
\ No newline at end of file
diff --git a/bibliography.bib b/bibliography.bib
index f0d3d2d..86191ef 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -1177,6 +1177,21 @@ year = {1998}
   month =        {nov},

 }

 

+@article{HorakErikH2018a,

+  author =       {Horak, Erik H. and Rea, Morgan T. and Heylman, Kevin D. and Gelbwaser-Klimovsky,

+                  David and Saikin, Semion K. and Thompson, Blaise J. and Kohler, Daniel D. and

+                  Knapper, Kassandra A. and Wei, Wei and Pan, Feng and Gopalan, Padma and Wright,

+                  John C. and Aspuru-Guzik, Alán and Goldsmith, Randall H.},

+  title =        {Exploring Electronic Structure and Order in Polymers via Single-Particle

+                  Microresonator Spectroscopy},

+  journal =      {Nano Letters},

+  volume =       18,

+  number =       3,

+  pages =        {1600-1607},

+  year =         2018,

+  doi =          {10.1021/acs.nanolett.7b04211},

+}

+

 @article{HunterJohnD2007a,

   author =       {John D. Hunter},

   title =        {Matplotlib: A 2D Graphics Environment},

@@ -3060,6 +3075,20 @@ year = {1998}
   month =        {jan},

 }

 

+@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{YursLenaA2012a,

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

                   and Jin, Song and Wright, John},

@@ -3075,20 +3104,6 @@ year = {1998}
   month =        {mar},

 }

 

-@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{ZanniMartinT2001a,

   author =       {Zanni, Martin T and Asplund, Matthew C and Hochstrasser, Robin M},

   title =        {{Two-dimensional heterodyned and stimulated infrared photon echoes of

diff --git a/dissertation.tex b/dissertation.tex
index e1a3014..bff81b7 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -64,21 +64,21 @@ This dissertation is approved by the following members of the Final Oral Committ
 \include{introduction/chapter}

 

 \part{Background} \label{prt:background}

-%\include{spectroscopy/chapter}

-%\include{software/chapter}  % sof

+\include{spectroscopy/chapter}

+\include{software/chapter}  % sof

 

 \part{Development} \label{prt:development}

-%\include{processing/chapter}  % pro

-%\include{acquisition/chapter}  % acq

-%\include{active_correction/chapter}  % act

-%\include{opa/chapter}  % opa

-%\include{mixed_domain/chapter}

+\include{processing/chapter}  % pro

+\include{acquisition/chapter}  % acq

+\include{active_correction/chapter}  % act

+\include{opa/chapter}  % opa

+\include{mixed_domain/chapter}

 

 \part{Applications} \label{prt:applications}

 \include{PbSe_susceptibility/chapter}  % pss

 \include{PbSe_global_analysis/chapter}  % psg

-%\include{MX2/chapter}

-%\include{PEDOT_PSS/chapter}

+\include{MX2/chapter}  % mx2

+\include{PEDOT_PSS/chapter}  % pps

 

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

 

@@ -86,16 +86,15 @@ This dissertation is approved by the following members of the Final Oral Committ
 

 \part{Appendix} \label{prt:appendix}

 \begin{appendix}

-%\include{public/chapter}

-%\include{procedures/chapter}

-%\include{hardware/chapter}

-% TODO: consider inserting WrightTools documentation as PDF

-%\include{irf/chapter}

-%\include{quantitative_ta/chapter}

-%\include{tg/chapter}

-%\include{opa_phase/chapter}  % rpa

+% AFTER DEFENSE \include{public/chapter}

+\include{procedures/chapter}

+\include{hardware/chapter}

+\include{irf/chapter}

+\include{quantitative_ta/chapter}

+\include{tg/chapter}

+\include{opa_phase/chapter}  % rpa

 %\include{errata/chapter}

-%\include{colophon/chapter}

+% AFTER DEFENSE \include{colophon/chapter}

 \end{appendix}

 

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

diff --git a/todo.org b/todo.org
index f6d000a..45021e4 100644
--- a/todo.org
+++ b/todo.org
@@ -1,20 +1,21 @@
-* TODO headers                                                 :introduction:
-* TODO cite important CMDS discoveries, reviews                :introduction:
-* TODO incorporate Nancy's comments                            :introduction:
-* TODO incorporate Claire's comments                           :introduction:
-* TODO summarize PbSe chapter                                  :introduction:
-* TODO summarize MX2 chapter                                   :introduction:
-* TODO summarize PEDOT:PSS chapter                             :introduction:
-* TODO verify light-matter interaction content                 :spectroscopy:
-* TODO finish instrumentation section (darien)                 :spectroscopy:
-* IDEA linear vs multidimensional figure                       :spectroscopy:
-* IDEA see Paul's dissertation                                 :spectroscopy:
+* TODO headers                                                          :int:
+* TODO cite important CMDS discoveries, reviews                         :int:
+* TODO incorporate Nancy's comments                                     :int:
+* TODO incorporate Claire's comments                                    :int:
+* TODO summarize PbSe chapter                                           :int:
+* TODO summarize MX2 chapter                                            :int:
+* TODO summarize PEDOT:PSS chapter                                      :int:
+* TODO verify light-matter interaction content                          :spc:
+* TODO finish instrumentation section (darien)                          :spc:
+* IDEA linear vs multidimensional figure                                :spc:
+* IDEA see Paul's dissertation                                          :spc:
 ** re: loss of resonance advantage with very fast pulses
 * TODO more references for object oriented programming                  :sof:
 ** in inbox
 * IDEA incorporate StoddenVictoria2016a                                 :sof:
 * IDEA incorporate idea "most people over-trust software"               :sof:
 * IDEA consider refactoring or expanding OOP section                    :sof:
+* IDEA insert content from SI                                           :mix:
 * TODO summary paragraphs in introduction                               :pro:
 * TODO finish discussing interpolation types                            :pro:
 ** TODO describe figure
@@ -55,10 +56,15 @@
 * TODO generalizability                                                 :opa:
 * TODO future directions                                                :opa:
 * TODO figure captions                                                  :opa:
-* TODO insert content from main                                         :pss:
-* TODO insert content from SI                                           :pss:
-* TODO insert content from main                                         :psg:
-* TODO insert content from SI                                           :psg:
-* TODO insert content from SI                                  :mixed_domain:
+* DONE insert content from main                                         :pss:
+  CLOSED: [2018-04-12 Thu 21:04]
+* IDEA insert content from SI                                           :pss:
+* DONE insert content from main                                         :psg:
+  CLOSED: [2018-04-12 Thu 21:04]
+* IDEA insert content from SI                                           :psg:
+* TODO include errata, remove errata as chapter                         :mx2:
+* TODO better title                                                     :pps:
+* TODO first draft                                                      :pps:
+* IDEA unpublished data summary                                         :pps:
 * TODO verify all references                                         :polish:
 * TODO read through and make links where appropriate                 :polish: