2018-04-15 17:04

4 files changed, 97 insertions, 94 deletions

diff --git a/bibliography.bib b/bibliography.bib
index 4e1e234..2651b25 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -1537,6 +1537,20 @@
   publisher =    {{AIP} Publishing},

 }

 

+@article{KoivistoinenJuha2017a,

+  author =       {Juha Koivistoinen and Pasi Myllyperki\"{o} and Mika Pettersson},

+  title =        {Time-Resolved Coherent Anti-Stokes Raman Scattering of Graphene: Dephasing

+                  Dynamics of Optical Phonon},

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

+  volume =       8,

+  number =       17,

+  pages =        {4108--4112},

+  year =         2017,

+  doi =          {10.1021/acs.jpclett.7b01711},

+  month =        {aug},

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

+}

+

 @article{KraatzIngvarT2014a,

   author =       {Kraatz, Ingvar T and Booth, Matthew and Whitaker, Benjamin J and Nix, Michael G D

                   and Critchley, Kevin},

@@ -3481,9 +3495,14 @@
   url =          {http://docs.h5py.org/en/latest/high/group.html#groups},

 }

 

+@misc{nanoram,

+  note =         {Accessed: 2018-04-15},

+  title =        {NanoRam Handheld Raman Spectrometer for Material ID},

+  url =          {http://bwtek.com/products/nanoram/},

+}

+

 @misc{pyqtgraph,

   note =         {Accessed: 2018-03-27},

   title =        {PyQtGraph: Scientific Graphics and GUI Library for Python},

   url =          {http://pyqtgraph.org/},

-}

-

+}
\ No newline at end of file
diff --git a/spectroscopy/auto/chapter.el b/spectroscopy/auto/chapter.el
index 731ac34..41829c0 100644
--- a/spectroscopy/auto/chapter.el
+++ b/spectroscopy/auto/chapter.el
@@ -3,7 +3,6 @@
  (lambda ()
    (LaTeX-add-labels
     "cha:spc"
-    "spc:eqn:E"
-    "spc:fig:ranges"))
+    "spc:eqn:E"))
  :latex)
 
diff --git a/spectroscopy/chapter.tex b/spectroscopy/chapter.tex
index 819fe94..805bce8 100644
--- a/spectroscopy/chapter.tex
+++ b/spectroscopy/chapter.tex
@@ -38,7 +38,7 @@ many photons.  %
 

 The basics of light matter interaction have been covered in many texts.  %

 For a beginners introduction I recommend ``How a Photon is Created or Absorbed'' by

-\textref{HendersonGiles1994a}.  %

+\textcite{HendersonGiles1994a}.  %

 Here I present a very minimal overview.  %

 

 Consider a two state system: ``a'' and ``b''.  %

@@ -61,8 +61,8 @@ For simplicity, we consider a single transition dipole, $\mu$.  %
 The Hamiltonian which controls the coupling of or simple system to the electric field described in

 \autoref{spc:eqn:E} can be written.  %

 \begin{eqnarray}

-  H &=& H_{0} - \mu \cdot E \\

-  &=& H_{0} - \mu \cdot \frac{E^0}{2}\left[ \me^{i(kz-\omega t)} + \me^{-i(kz-\omega t)} \right]

+  H &=& H_{0} + \mu \cdot E \\

+  &=& H_{0} + \mu \cdot \frac{E^0}{2}\left[ \me^{i(kz-\omega t)} + \me^{-i(kz-\omega t)} \right]

 \end{eqnarray}

 

 Solving for the time-dependent coefficients, then:

@@ -79,15 +79,11 @@ Where $\omega_a$ and $\omega_b$ are the fast (and familiar) Bohr frequencies and
 In Dirac notation \cite{DiracPaulAdrienMaurice1939a}, an observable (such as $\mu(t)$) can be

 written simply:  %

 \begin{equation}

-  \mu(t) = \left< c_aa + c_bb \left| \hat{H} \right| c_aa + c_bb \right>

+  \mu(t) = |c_a(t)|^2 \langle \phi_a | \mu | \phi_a \rangle + |c_b(t)|^2 \langle \phi_b | \mu | \phi_b \rangle +  c_a(t) c_b^*(t) \langle \phi_b | \mu | \phi_a \rangle  +

+  c_b(t) c_a^*(t) \langle \phi_a | \mu | \phi_b \rangle 

 \end{equation}

 The complex wavefunction is called a \emph{ket}, represented $\left|b\right>$.  %

 The complex conjugate is called a \emph{bra}, represented $\left<a\right|$.  %

-When expanded,

-\begin{equation}

-  \mu(t) = c_a^2\mu_a + c_b^2\mu_b + \left< c_aa \left| \hat{H} \right| c_bb \right> +

-  \left<c_bb \left| \hat{H} \right| c_aa \right>

-\end{equation}

 The first two terms are populations and the final two terms are coherences.  %

 The coherent terms will evolve with the rapid Bohr oscillations, coupling the dipole observable

 with the time-dependent electric field.  %

@@ -146,18 +142,19 @@ These are workhorse experiments, like absorbance, reflectance, FTIR, UV-Vis, and
 ordinary Raman spectroscopy (COORS).  %

 These experiments are incredibly robust, and are typically performed using easy to use commercial

 desktop instruments.  %

-There are now even handheld Raman spectrometers for use in industrial settings. [CITE]  %

+There are now even handheld Raman spectrometers for use in industrial settings. \cite{nanoram}  %

 

 Multidimensional spectroscopy contains a lot more information about the material under

 investigation.  %

 In this work, by ``multidimensional'' I mean higher-order spectroscopy.  %

-I ignore ``correlation spectroscopy'' [CITE], which tracks linear spectral features against

-non-spectral dimensions like lab time, pressure, and temperature.  %

+I ignore ``correlation spectroscopy'' (otherwise known as covariance spectroscopy), which tracks

+linear spectral features against non-spectral dimensions like lab time, pressure, and

+temperature.  %

 So, in the context of this dissertation, multidimensional spectroscopy is synonymous with nonlinear

 spectroscopy.  %

 

 Nonlinear spectroscopy relies upon higher-order terms in the light-matter interaction. In a generic

-system, each term is roughly ten times smaller than the last.  % TODO: cite?

+system, a rule of thumb states that each term is roughly ten times smaller than the last.  %

 This means that nonlinear spectroscopy is typically very weak.  %

 Still, nonlinear signals are fairly easy to isolate and measure using modern instrumentation, as

 this dissertation describes.  %

@@ -261,67 +258,68 @@ space.  %
 Since signal goes as $N^2$, signal decays much faster in homodyne-collected experiments.  %

 If signal decays as a single exponential, the extracted decay is twice as fast for homodyne vs

 heterodyne-detected data.  %

-[CITE DARIEN CORRECTION]

-

-\section{Instrumentation}  % ======================================================================

-

-In this section I introduce the key components of the MR-CMDS instrument.  %

-This also serves to introduce the reader to the particular components used in my research.  %

-

-\subsection{LASER}  % -----------------------------------------------------------------------------

-

-Light Amplified by Stimulated Emission of Radiation (LASER) light sources are absolutely crucial

-components of the modern MR-CMDS instrument.  %

-The first laser was built in 1960 by \textcite{MaimanTheodore1960a}, and pulsed lasers were

-invented soon after.  %

-Today, ultrafast light sources are relatively cheap and reliable.  %

-Our SpectraPhysics ``Tsunami'' oscillator uses passive Kerr-lens mode-locking to generate $\sim$35

-fs seed pulses at $\sim$80 MHz (one pulse every 12.5 nanoseconds). \cite{Tsunami}  %

-This seed is split and fed into two 1 KHz amplifiers, a picosecond ``Spitfire Ace''

-\cite{SpitfireAce} and a femtosecond ``Spitfire Pro'' \cite{SpitfirePro}.  %

-These amplifiers each output several watts of ultrafast pulses at 1 KHz (one pulse per

-millisecond).  %

-

-\subsection{Optical parametric amplifiers}  % -----------------------------------------------------

-

-Optical Parametric Amplifiers (OPAs) are arguably the most crucial component of modern MR-CMDS, as

-they provide the frequency tunable light sources that we require. \cite{CerulloGiulio2003a}  %

-OPAs provide tunability through three-wave sum and difference frequency generation processes.  %

-``Fundamental'' tunability is achieved by splitting the 800 nm photons into two lower energy

-photons, with a splitting ratio determined by motorized optics.  %

-These split photons are called ``signal'' and ``idler'', with signal being the higher energy and

-idler the lower energy photon.  %

-

-% TODO: paragraph about phase matching conditions and polarization

-

-Signal and idler are then either used directly, or amplified through sum or difference frequency

-processes to provide broadband tuneability.  %

-All available optical processes for the TOPAS-C OPAs \cite{TOPAS-C} used on the femtosecond table

-are shown in \autoref{spc:fig:ranges}.  %

-Amazingly, these OPAs offer tunability from the mid-infrared to the ultraviolet.  %

-Currently we do not have proper automated filters to make it possible to continuously scan between

-regions, but such things are possible.  %

-

-On the picosecond table we have three separate kinds of OPAs, including one TOPAS-800

-\cite{TOPAS-800} and two OPA-800 models that have been modified with precision micro control

-\cite{PMC} servo motors to provide automated tunability.  %

-

-\subsection{Delay stages}  % ----------------------------------------------------------------------

-

-Delay stages are simple, one-motor devices which are used to control the relative arrival time of

-pulses at the sample.  %

-The Wright Group currently owns four models of delay stage: 1. Newport MFA-CC [CITE], 2. Aerotech

-... [CITE], 3. Thorlabs LTS300 [CITE].  %

-The fourth ``model'' are actually homemade stages that are driven using PMC motors.  %

-

-\subsection{Spectrometers}  % ---------------------------------------------------------------------

-

-Spectrometers...

-

-\begin{figure}

-  \includegraphics[width=\linewidth]{spectroscopy/ranges}

-  \caption{

-    CAPTION TODO

-  }

-  \label{spc:fig:ranges}

-\end{figure}
\ No newline at end of file
+This fact is often forgotten, and papers have been corrected for forgetting this factor of

+two. \cite{KoivistoinenJuha2017a}  %

+

+% \section{Instrumentation}  % ======================================================================

+

+% In this section I introduce the key components of the MR-CMDS instrument.  %

+% This also serves to introduce the reader to the particular components used in my research.  %

+

+% \subsection{LASER}  % -----------------------------------------------------------------------------

+

+% Light Amplified by Stimulated Emission of Radiation (LASER) light sources are absolutely crucial

+% components of the modern MR-CMDS instrument.  %

+% The first laser was built in 1960 by \textcite{MaimanTheodore1960a}, and pulsed lasers were

+% invented soon after.  %

+% Today, ultrafast light sources are relatively cheap and reliable.  %

+% Our SpectraPhysics ``Tsunami'' oscillator uses passive Kerr-lens mode-locking to generate $\sim$35

+% fs seed pulses at $\sim$80 MHz (one pulse every 12.5 nanoseconds). \cite{Tsunami}  %

+% This seed is split and fed into two 1 KHz amplifiers, a picosecond ``Spitfire Ace''

+% \cite{SpitfireAce} and a femtosecond ``Spitfire Pro'' \cite{SpitfirePro}.  %

+% These amplifiers each output several watts of ultrafast pulses at 1 KHz (one pulse per

+% millisecond).  %

+

+% \subsection{Optical parametric amplifiers}  % -----------------------------------------------------

+

+% Optical Parametric Amplifiers (OPAs) are arguably the most crucial component of modern MR-CMDS, as

+% they provide the frequency tunable light sources that we require. \cite{CerulloGiulio2003a}  %

+% OPAs provide tunability through three-wave sum and difference frequency generation processes.  %

+% ``Fundamental'' tunability is achieved by splitting the 800 nm photons into two lower energy

+% photons, with a splitting ratio determined by motorized optics.  %

+% These split photons are called ``signal'' and ``idler'', with signal being the higher energy and

+% idler the lower energy photon.  %

+

+% % TODO: paragraph about phase matching conditions and polarization

+

+% Signal and idler are then either used directly, or amplified through sum or difference frequency

+% processes to provide broadband tuneability.  %

+% All available optical processes for the TOPAS-C OPAs \cite{TOPAS-C} used on the femtosecond table

+% are shown in \autoref{spc:fig:ranges}.  %

+% Amazingly, these OPAs offer tunability from the mid-infrared to the ultraviolet.  %

+% Currently we do not have proper automated filters to make it possible to continuously scan between

+% regions, but such things are possible.  %

+

+% On the picosecond table we have three separate kinds of OPAs, including one TOPAS-800

+% \cite{TOPAS-800} and two OPA-800 models that have been modified with precision micro control

+% \cite{PMC} servo motors to provide automated tunability.  %

+

+% \subsection{Delay stages}  % ----------------------------------------------------------------------

+

+% Delay stages are simple, one-motor devices which are used to control the relative arrival time of

+% pulses at the sample.  %

+% The Wright Group currently owns four models of delay stage: 1. Newport MFA-CC [CITE], 2. Aerotech

+% ... [CITE], 3. Thorlabs LTS300 [CITE].  %

+% The fourth ``model'' are actually homemade stages that are driven using PMC motors.  %

+

+% \subsection{Spectrometers}  % ---------------------------------------------------------------------

+

+% Spectrometers...

+

+% \begin{figure}

+%   \includegraphics[width=\linewidth]{spectroscopy/ranges}

+%   \caption{

+%     CAPTION TODO

+%   }

+%   \label{spc:fig:ranges}

+% \end{figure}
\ No newline at end of file
diff --git a/todo.org b/todo.org
index 33942ff..54a48d9 100644
--- a/todo.org
+++ b/todo.org
@@ -1,16 +1,3 @@
-* CANCELED headers                                                      :int:
-  CLOSED: [2018-04-15 Sun 15:50]
-* 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: