2018-04-13 22:39

6 files changed, 85 insertions, 73 deletions

diff --git a/bibliography.bib b/bibliography.bib
index 86191ef..b6f050e 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -1,3 +1,16 @@
+@article{HendersonGiles1994a,

+  author =       {Giles Henderson and Robert C. Rittenhouse and John C. Wright and Jon L. Holmes},

+  title =        {How a Photon is Created or Absorbed},

+  journal =      {Journal of Chemical Education},

+  volume =       71,

+  number =       4,

+  pages =        300,

+  year =         1994,

+  doi =          {10.1021/ed071p300.2},

+  month =        {apr},

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

+}

+

 @article{AartsmaThijsJ1976a,

   author =       {Aartsma, Thijs J and Wiersma, Douwe A},

   title =        {{Photon-echo relaxation in molecular mixed crystals}},

diff --git a/dissertation.tex b/dissertation.tex
index e0edd73..72b351e 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -2,6 +2,8 @@
 

 \begin{document}

 

+\raggedbottom

+

 % --- preamble ------------------------------------------------------------------------------------

 

 \begin{centering}

@@ -61,7 +63,7 @@ This dissertation is approved by the following members of the Final Oral Committ
 

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

 

-\include{introduction/chapter}

+\include{introduction/chapter}  % int

 

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

 \include{spectroscopy/chapter}

diff --git a/software/chapter.tex b/software/chapter.tex
index e6707dd..06fcff9 100644
--- a/software/chapter.tex
+++ b/software/chapter.tex
@@ -1,14 +1,3 @@
-%A whole set of licenses have been written to use for this purpose.  %

-%Briefly, strong copyleft licenses do not allow for software to be modified or enhancements without

-%sharing those enhancements under the same licenses.  %

-%These ``viral'' licenses are meant to force companies and individuals who would otherwise not open

-%source to share their code.  %

-%The strongest copyleft licenses do not even allow others to link against the licensed software

-%without themselves being copyleft.  %

-%This strategy has been moderately successful, but is becoming less popular.  % TODO: cite

-%Open source licenses are less opinionated, merely granting users the right to copy, modify,

-%distribute, and publish code without restriction except perhaps credit to the source.  %

-

 \chapter{Software} \label{cha:sof}

 

 \begin{dquote}

@@ -117,24 +106,22 @@ Other funding agencies have similar projects.  %
 

 Software development ``by-and-for'' scientists poses unique challenges.  %

 In this section, I attempt to summarize the literature about these challenges, with a focus on

-those challenges that I have found most relevant.  %

+those that I have found most relevant.  %

 

 \textbf{``End-user developers.''} \cite{SegalJudith2005a, HannayJoErskine2009a, JoppaLucasN2013a}

 % TODO: see Joppa ref 17, 21 22

 Typically the developers of scientific software are not trained software developers.  %

 This is perfectly appropriate, because scientific software development typically requires a large

-amount of domain knowledge that only ``end-users'' possess.  %

+amount of domain-specific knowledge that only ``end-users'' possess.  %

 Software development practices may not be valued in a scientific environment.  %

 End-users may lack the skill and knowledge required to develop high quality, maintainable

 software.  %

 They may not be aware of best practices in software development.  %

 They focus on feature additions and neglect documentation and maintenance.  %

-% BJT: what are the consequences of end-users

-

 

 \textbf{Shifting goals.} \cite{SegalJudith2005a, CarverJeffreyC2007a, HannayJoErskine2009a,

   PrabhuPrakash2011a}

-Many traditional software development paradigms demand an upfront articulation of goals and

+Traditional software development paradigms typically 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.  %

@@ -181,8 +168,8 @@ loop of critical self assessment that science depends upon.  %
 On the positive side, testing can be an easy-to-add development practice with huge rewards.  %

 Well written tests can be a programmers best friend: helping her to ensure that her code has met

 all of the given requirements.  %

-Well written tests allow programmers to optimize without worrying about breaking crucial components

-of their software.  %

+This allows programmers to optimize without worrying about breaking crucial components of their

+software.  %

 

 \textbf{Struggles with optimization.} \cite{PrabhuPrakash2011a}

 Sometimes, a scientific application requires performant code.  %

@@ -219,7 +206,7 @@ Make your dependencies explicit, in machine readable ways where possible.  %
 \textbf{Do not duplicate.} \cite{WilsonGreg2017a}  %

 If you do need to write some software, make sure that you do not duplicate code within your own

 work.  %

-Instead of writing the same 10 lines of code again and again with small tweaks, write a function

+Instead of writing the same few lines of code again and again with small tweaks, write a function

 that accepts a set of arguments.  %

 If you are doing the same operation in many different contexts, consider defining a library to that

 operation that can be imported and shared between your different projects.  %

@@ -292,7 +279,7 @@ As Nick Barnes says, \emph{``Publish your computer code: it is good enough''}.
 \cite{BarnesNick2010a}  %

 

 \textbf{Write human readable code, and document it well.} \cite{WilsonGreg2017a}  %

-Let the computer do the work, but write the program to be read by a human.  %

+Let the computer do the work, but write the source code to be read by a human.  %

 Give classes, functions, attributes and variables meaningful names.  %

 Don't be afraid to be verbose, most programming environments have tab completion so long names are

 not all that hard to type.  %

@@ -301,6 +288,8 @@ Try to follow the recommended style for your language, but don't obsess about it
 \textbf{Avoid premature optimization.} \cite{WilsonGreg2014a, WilsonGreg2017a}

 Don't get pulled into the trap of trying to make things perfect the first time.  %

 Software design is typically a very iterative process, and for good reason.  %

+This is particularly true in a scientific context, where goals may evolve during the development

+process.  %

 Write for correctness first, and if it works, consider optimization.  %

 If you do need to make your software faster, use profiling tools like cProfile

 \cite{PythonProfilers} and SnakeViz \cite{SnakeViz} to empirically determine what operations are

diff --git a/spectroscopy/auto/chapter.el b/spectroscopy/auto/chapter.el
index 4966739..731ac34 100644
--- a/spectroscopy/auto/chapter.el
+++ b/spectroscopy/auto/chapter.el
@@ -3,6 +3,7 @@
  (lambda ()
    (LaTeX-add-labels
     "cha:spc"
-    "spc:fig:power_curves"))
+    "spc:eqn:E"
+    "spc:fig:ranges"))
  :latex)
 
diff --git a/spectroscopy/chapter.tex b/spectroscopy/chapter.tex
index cdd3955..819fe94 100644
--- a/spectroscopy/chapter.tex
+++ b/spectroscopy/chapter.tex
@@ -14,9 +14,9 @@
   

 \clearpage

 

-In this chapter I lay out the foundations of spectroscopy as relevant to this dissertation.  %

-Spectroscopy is the study of the interaction of light (electromagnetic radiation) and matter

-(molecules, crystals, solids, liquids etc).  %

+%In this chapter I lay out the foundations of spectroscopy as relevant to this dissertation.  %

+%Spectroscopy is the study of the interaction of light (electromagnetic radiation) and matter

+%(molecules, crystals, solids, liquids etc).  %

 

 \section{Light-matter interaction}  % =============================================================

 

@@ -36,7 +36,12 @@ many photons.  %
 

 % TODO: language from 'how a photon is created or destroyed'

 

-For simplicity, consider a two state system: ``a'' and ``b''.  %

+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}.  %

+Here I present a very minimal overview.  %

+

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

 These two states might be the inital and final states in a transition.  %

 The wavefunction for this system can be written as a sum of the stationary states (eigenstates)

 with appropriate scaling coefficients:

@@ -47,42 +52,41 @@ The time dependence lies in the $c_a$ and $c_b$ coefficients, and the spatial de
 the $\psi_a$ and $\psi_b$ eigienstates.  %

 

 Now we will expose this two-state system to an electric field:

-\begin{equation}

-  E = E^{\circ}\left[ \me^{i(kz-\omega t)} + \me^{-i(kz-\omega t)} \right]

+\begin{equation} \label{spc:eqn:E}

+  E = E^{0}\left[ \me^{i(kz-\omega t)} + \me^{-i(kz-\omega t)} \right]

 \end{equation}

 

 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

-...:

-% jcw- ISN'T IT JUST MU DOT E WHERE E IS A VECTOR THAT IS TIME DEPENDENT, NOT A TIME DERIVATIVE 

-\begin{equation}

-  H = H_{\circ} - \mu \dot E

-\end{equation}

+\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]

+\end{eqnarray}

 

 Solving for the time-dependent coefficients, then:

 \begin{eqnarray}

   c_a(t) &=& \cos{\frac{\Omega t}{2}} \me^{-i\omega_at} \\

   c_b(5) &=& \sin{\frac{\Omega t}{2}} \me^{-i\omega_bt}

 \end{eqnarray}

-Fast and slow parts...

-Bohr and Rabi freuencies...

-

-Where $\Omega$ is the \emph{Rabi frequency}:  %

+Where $\omega_a$ and $\omega_b$ are the fast (and familiar) Bohr frequencies and $\Omega$ is the

+\emph{Rabi frequency}:  %

 \begin{equation}

   \Omega \equiv \frac{\mu E^\circ}{\hbar}

 \end{equation}

 

-In Dirac notation \cite{DiracPaulAdrienMaurice1939a}., an observable (such as $\mu(t)$) can be written simply:  %

+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{\mu} \right| c_aa + c_bb \right>

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

 \end{equation}

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

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

-When expanded,  % JCW- MU IS NOT THE OPERATOR. THE OPERATOR IS THE TIME DEPENDENT HAMILTONIAN. MU MULIPLIES ca and cb

+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{mu} \right| c_bb \right> +

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

+  \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

@@ -91,18 +95,9 @@ with the time-dependent electric field.  %
 We commonly represent quantum mechanical systems using density matrices, where diagonal elements

 are populations and off-diagonal elements are coherences.  %

 Each density matrix element has the form $\rho_{kb}$, where $k$ is the ket and $b$ is the bra.  %

-% TODO: 4 member density matrix representing system above

 A more complete discussion of the formalism we use to describe light-matter interaction is

 presented in \autoref{cha:mix}.  %

 

-% TODO: homogeneous line-width

-

-Spectroscopic experiments are typically performed on an ensemble of states.  %

-In such circumstances, inhomogeneous broadening becomes relevant.  %

-Inhomogeneous broadening arises from permanent differences between different oscillators in the

-ensemble.  %

-% TODO: why is inhomogeneous broadening important?

-

 Many strategies have been introduced for diagrammatically representing the interaction of multiple

 electric fields in an experiment.  %

 Spectroscopists have used diagrams to represent nonlinear optical phenomena since 1965.

@@ -139,9 +134,8 @@ WMELs can be found throughout this dissertation.  %
 Scientists have come up with many ways of exploiting light-matter interaction for measurement

 purposes.  %

 This section discusses several of these strategies.  %

-I start broadly, by comparing and contrasting differences across categories of spectroscopies.  %

-I then go into detail regarding a few experiments that are particularly relevant to this

-dissertation.  %

+I take a compare-and-contrast approach, rather than getting too caught up in the infinite diversity

+of possible spectroscopic strategies.  %

 

 \subsection{Linear vs multidimensional}  % --------------------------------------------------------

 

@@ -172,6 +166,8 @@ The most obvious advantage of multidimensional spectroscopy comes directly from
 itself.  %

 Multidimensional spectroscopy can \emph{decongest} spectra with overlapping peaks by isolating

 peaks in a multidimensional resonance landscape.  %

+This decongestion arises directly from the multiple resonances the multidimensional spectroscopy

+demands of a material.  %

 

 \subsection{Frequency vs time domain}  % ----------------------------------------------------------

 

@@ -188,30 +184,32 @@ This relies on pulsed light sources with tunable frequencies.  %
 Time domain experiments use an interferometric technique to resolve frequency axes.  %

 Broadband excitation pulses which contain all of the necessary frequencies are used to excite the

 sample.  %

-The delay (time) between pulses is scanned, and the resonances along that axis are resolved through

-Fourier transform of the resulting interferogram.  %

+The delay (phase) between pulses is scanned, and the resonances along that axis are resolved

+through Fourier transform of the resulting interferogram.  %

 In modern experiments, pulse shapers are used to control the delay between pulses in a very

 precise, fast, and reproducible way.  %

 The time domain strategy is by-far the most popular technique in multidimensional spectroscopy

 because these technologies allow for rapid, robust data collection.  %

 

-This dissertation focuses on frequency domain strategies, so some discussion of the advantages of

-frequency domain when compared to time domain are warranted.  %

+This dissertation focuses on less-popular frequency domain strategies, so some discussion of the

+advantages of frequency domain when compared to time domain are warranted.  %

 

 One of the biggest instrumental limitations of multidimensional spectroscopy is bandwidth.  %

 It is easy to get absorbance spectra over the entire visible spectrum, and even into the

 ultraviolet and near infrared.  %

+Not so for multidimensional spectroscopy.  %

 Multidimensional spectroscopy is limited by the bandwidth of our (tunable) light sources.  %

 For frequency domain techniques, this limitation is incidental: sources with greater tunability

 will be easy to incorporate into these instruments, and creating such sources is only a matter of

-more optomechanical engineering.  %

+more optomechanical engineering---more moving parts.  %

 Time domain techniques, on the other hand, have a more fundamental issue with bandwidth.  %

 Time domain requires that all of the desired frequencies be present within the single excitation

 pulse, and pulses with very large frequency bandwidth (very short in time) become very hard to use

 and control.   %

 With short, broad pulses:

 \begin{ditemize}

-	\item Non-resonant signal becomes brighter relative to resonant signal. \cite{ChengJixin2001a}

+	\item Non-resonant signal becomes brighter relative to resonant signal (the resonance advantage

+    is lost). \cite{ChengJixin2001a}

 	\item Pulse distortions become essentially unavoidable. \cite{SpencerAustinP2015a}

 \end{ditemize}

 

@@ -268,13 +266,14 @@ heterodyne-detected data.  %
 \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 [CITE].  %

+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}  %

@@ -298,23 +297,31 @@ idler the lower energy photon.  %
 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:power_curves}.  %

+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.  %

 

-\begin{figure}

-  \caption[TOPAS-C optical processes]{

-    CAPTION TODO.

-  }

-  \label{spc:fig:power_curves}

-\end{figure}

-

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

 

-Delay stages are simple, one-motor devices which...

+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...
\ No newline at end of file
+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/spectroscopy/ranges.png b/spectroscopy/ranges.png
new file mode 100644
index 0000000..ae4f421
--- /dev/null
+++ b/spectroscopy/ranges.png