diff options
| -rw-r--r-- | abstract.tex | 7 | ||||
| -rw-r--r-- | acquisition/chapter.tex | 4 | ||||
| -rw-r--r-- | dissertation.cls | 10 | ||||
| -rw-r--r-- | introduction/chapter.tex | 7 | ||||
| -rw-r--r-- | opa/chapter.tex | 2 | ||||
| -rw-r--r-- | processing/chapter.tex | 2 | ||||
| -rw-r--r-- | spectroscopy/chapter.tex | 3 |
7 files changed, 19 insertions, 16 deletions
diff --git a/abstract.tex b/abstract.tex index dd08aa0..2c9b4ed 100644 --- a/abstract.tex +++ b/abstract.tex @@ -5,9 +5,10 @@ Coherent multidimensional spectroscopy (CMDS) encompasses a family of experimental strategies involving the nonlinear interaction between electric fields and a material under investigation. % -This approach has several unique capabilities: 1. resolving congested states [CITE KLUG], 2. -extracting spectra that would otherwise be selection-rule disslowed [CITE BOYLE], 3. resolving -fully coherent dyanmics [CITE], 4. measuring coupling [CITE], and 5. resolving ultrafast dynamics +This approach has several unique capabilities: 1. resolving congested states [CITE KLUG and % JCW Zhao and Wright-JACS], +2. extracting spectra that would otherwise be selection-rule disslowed [CITE BOYLE], 3. resolving +fully coherent dyanmics [CITE % JCW Pakoulev and Wright], +4. measuring coupling [CITE], and 5. resolving ultrafast dynamics [CITE]. % CMDS can be collected in the frequency or the time domain, and each approach has advantages and diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex index 0d3d1c5..0436028 100644 --- a/acquisition/chapter.tex +++ b/acquisition/chapter.tex @@ -36,7 +36,7 @@ for w2 in w2_points: set_d2(d2)
measure_signal()
\end{codefragment}
-In this simple example, there are 5 \python{w1} destinations, 7 \phon{w2} destinations, and 12
+In this simple example, there are 5 \python{w1} destinations, 7 \python{w2} destinations, and 12
\python{d2} destinations, so there are a total of $5\times7\times12=420$ pixels in the
three-dimensional scan. %
The acquisition software must set the hardware to each of these points and acquire data at each of
@@ -732,7 +732,7 @@ We can write the conjugate equation to \ref{eq:simple_exponential_decay}, asking need to get a cerain signal level?'':
\begin{eqnarray}
\log{(S)} &=& -\frac{t}{\tau} \\
-t &=& -\taulog{(S)}.
+t &=& -\tau\log{(S)}.
\end{eqnarray}
So to step linearly in $t$, my step size has to go as $-\tau\log{(S)}$.
diff --git a/dissertation.cls b/dissertation.cls index afb2dc9..aecaaad 100644 --- a/dissertation.cls +++ b/dissertation.cls @@ -118,17 +118,17 @@ colback=bg, boxrule=1pt, colframe=bg, - arc=0, + arc=0pt, shadow=false, - use counter=equation, + new/use counter=equation, boxsep=1ex, top=0pt, left=0pt, right=0pt, bottom=0pt, comment={\hfill(\arabic{chapter}.\arabic{equation})}, listing outside comment, - righthand width=2.5em, + righthand width=3em, sidebyside gap=0pt, minted language=#1, - before skip =-0.5\baselinestretch, - after skip=2\baselinestretch, + %before skip =-0.5\baselinestretch, + %after skip=2\baselinestretch, } \BeforeBeginEnvironment{codefragment}{\begin{singlespace}\stepcounter{equation}} diff --git a/introduction/chapter.tex b/introduction/chapter.tex index be4572d..b8877e6 100644 --- a/introduction/chapter.tex +++ b/introduction/chapter.tex @@ -52,7 +52,7 @@ flexable in the kinds of experiments that they can perform. % This dissertation contains several projects undertaken to improve the reliability and accessibility
of MR-CMDS. %
While MR-CMDS will never be a single-shot experiment, there are many improvements that can improve
-data collection speed. %
+data collection speed. % JCW- NOT SO SURE IT CAN'T BE SINGLE SHOT
Necessary calibration, especially OPA calibration, can be made robust and fully automatic. %
Common artifacts can be addressed through relatively simple modifications in hardware and
software. %
@@ -64,11 +64,12 @@ frequency-domain coherent multidimensional spectroscopy. % Due to its diversity and dimensionality, MR-CMDS data is challenging to process and represent. %
The data processing tools that a scientist develops to process one experiment may not work when she
attempts to process an experiment where different experimental variables are explored. %
-Historically, this has meant that MR-CMDS practitioners have used custom, one-off data processing
+Historically, this % JCW- "THIS" SHOULDN'T BE A NOUN STANDING ALONE AS THE SUBJECT OF THE SENTENCE
+has meant that MR-CMDS practitioners have used custom, one-off data processing
workflows that need to be changed for each particular experiment. %
These changes take time to implement, and can become stumbling blocks or opportunities for
error. %
-Even worse, the challenge of designing a new processing workflow may make dissuade scientist from
+Even worse, the challenge of designing a new processing workflow may dissuade A scientist from
creatively modifying their experimental strategy, or comparing their data with data taken from
another group. %
This limit to creativity and flexibility defeats one of the main advantages of the MR-CMDS
diff --git a/opa/chapter.tex b/opa/chapter.tex index 75459b5..a57847a 100644 --- a/opa/chapter.tex +++ b/opa/chapter.tex @@ -129,7 +129,7 @@ are shown. % \end{figure}
\begin{figure}
- \includegraphics[width=\textwidth]{opa/c2}}
+ \includegraphics[width=\textwidth]{opa/c2}
\caption{
CAPTION TODO
}
diff --git a/processing/chapter.tex b/processing/chapter.tex index 81886c2..baca84c 100644 --- a/processing/chapter.tex +++ b/processing/chapter.tex @@ -128,7 +128,7 @@ It contains a central data ``container'' that is capable of storing all of the i each multidimensional (or one-dimensional) spectra: the \python{Data} class. %
It also defines a \python{Collection} class that contains data objects, collection
objects, and other pieces of metadata in a hierarchical structure. %
-Let's first discuss \mitinline{python}{Data}.
+Let's first discuss \mintinline{python}{Data}.
All spectra are stored within WrightTools as multidimensional arrays. %
Arrays are containers that store many instances of the same data type, typically numerical
diff --git a/spectroscopy/chapter.tex b/spectroscopy/chapter.tex index 3bde7b4..030edd5 100644 --- a/spectroscopy/chapter.tex +++ b/spectroscopy/chapter.tex @@ -67,6 +67,7 @@ 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}
@@ -90,7 +91,7 @@ In Dirac notation \cite{DiracPaulAdrienMaurice1939a}., an observable (such as $\ \end{equation}
The complex wavefunction is called a \emph{ket}, represented $|b>$. %
The complex conjugate is called a \emph{bra}, represented $<a|$. %
-When expanded,
+When expanded, % JCW- MU IS NOT THE OPERATOR. THE OPERATOR IS THE TIME DEPENDENT HAMILTONIAN. MU MULIPLIES ca and cb
\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>
|