2018-04-07 16:49

5 files changed, 81 insertions, 15 deletions

diff --git a/abstract.tex b/abstract.tex
index 566d95a..c9c8d9e 100644
--- a/abstract.tex
+++ b/abstract.tex
@@ -5,12 +5,16 @@
 
 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 and % JCW Zhao and Wright-JACS], 
-2. extracting spectra that would otherwise be selection-rule disallowed [CITE BOYLE], 3. resolving
-fully coherent dyanmics [CITE % JCW Pakoulev and Wright], 
-4. measuring coupling [CITE], and 5. resolving ultrafast dynamics
-[CITE].  %
-
+This approach has several unique capabilities:
+\begin{denumerate}
+  \item resolving congested states \cite{ZhaoWei1999b, DonaldsonPaulMurray2008a}
+  \item extracting spectra that would otherwise be selection-rule disallowed
+    \cite{BoyleErinSelene2013b, BoyleErinSelene2014b},
+  \item resolving fully coherent dyanmics \cite{PakoulevAndreiV2009a}, 
+  \item measuring coupling \cite{WrightJohnCurtis2011a}, and
+  \item resolving ultrafast dynamics.  % TODO: cite
+\end{denumerate}
+  
 CMDS can be collected in the frequency or the time domain, and each approach has advantages and
 disadvantages.  %
 Frequency domain ``Multi-resonant'' CMDS (MR-CMDS) requires pulsed ultrafast light sources with
@@ -22,8 +26,11 @@ This signal may be different in frequency from the input pulses, and it may trav
 direction 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 1. frequency 2. relative arrival time and separation (delay) 3. fluence
-[CITE Z-SCAN], and 4. polarization [CITE KLUG], among others.  %
+These properties include
+1. frequency
+2. relative arrival time and separation (delay)
+3. fluence \cite{OmariAbdoulghafar2012a, SheikBahaeMansoor1990a}, and
+4. polarization \cite{FournierFrederic2009a}, among others.  %
 Thus MR-CMDS can be thought of as a multidimensional experimental space, where experiments
 typically involve explorations in one to four of the properties above.  %
 
diff --git a/active_correction/chapter.tex b/active_correction/chapter.tex
index 76ae49d..e40ff9d 100644
--- a/active_correction/chapter.tex
+++ b/active_correction/chapter.tex
@@ -1,4 +1,4 @@
-\chapter{Active Correction in MR-CMDS}

+\chapter{Active Correction in MR-CMDS} \label{cha:act}

 

 \begin{dquote}

   Calibrate, \\

diff --git a/bibliography.bib b/bibliography.bib
index 9e5921c..7133357 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -1,3 +1,45 @@
+@article{FournierFrederic2009a,

+  author =       {Frederic Fournier and Rui Guo and Elizabeth M. Gardner and Paul M. Donaldson and

+                  Christian Loeffeld and Ian R. Gould and Keith R. Willison and David R. Klug},

+  title =        {Biological and Biomedical Applications of Two-Dimensional Vibrational

+                  Spectroscopy: Proteomics, Imaging, and Structural Analysis},

+  journal =      {Accounts of Chemical Research},

+  volume =       42,

+  number =       9,

+  pages =        {1322--1331},

+  year =         2009,

+  doi =          {10.1021/ar900074p},

+  month =        {sep},

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

+}

+

+@article{OmariAbdoulghafar2012a,

+  author =       {Abdoulghafar Omari and Iwan Moreels and Francesco Masia and Wolfgang Langbein and

+                  Paola Borri and Dries Van Thourhout and Pascal Kockaert and Zeger Hens},

+  title =        {Role of interband and photoinduced absorption in the nonlinear refraction and

+                  absorption of resonantly excited {PbS} quantum dots around 1550 nm},

+  journal =      {Physical Review B},

+  volume =       85,

+  number =       11,

+  year =         2012,

+  doi =          {10.1103/physrevb.85.115318},

+  month =        {mar},

+  publisher =    {American Physical Society ({APS})},

+}

+

+@article{SheikBahaeMansoor1990a,

+  author =       "Sheik-Bahae, M and Said, AA and Wei, T-H and Hagan, DJ and Van Stryland, EW",

+  title =        "Sensitive measurement of optical nonlinearities using a single beam",

+  journal =      "IEEE journal of quantum electronics.",

+  volume =       26,

+  number =       4,

+  pages =        "760--769",

+  year =         1990,

+  address =      "[New York] :",

+  issn =         "0018-9197",

+  publisher =    "Institute of Electrical and Electronics Engineers",

+}

+

 @article{AartsmaThijsJ1976a,

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

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

@@ -193,7 +235,7 @@
   month =        {nov},

 }

 

-@article{BoyleErinSelene2014a,

+@article{BoyleErinSelene2014b,

   author =       {Boyle, Erin S and Neff-Mallon, Nathan A. and Handali, Jonathan D and Wright, John

                   C},

   title =        {{Resonance IR: A Coherent Multidimensional Analogue of Resonance Raman}},

@@ -2088,6 +2130,19 @@ year = {1998}
   month =        {oct},

 }

 

+@article{WrightJohnCurtis2011a,

+  author =       {John C. Wright},

+  title =        {Multiresonant Coherent Multidimensional Spectroscopy},

+  journal =      {Annual Review of Physical Chemistry},

+  volume =       62,

+  number =       1,

+  pages =        {209--230},

+  year =         2011,

+  doi =          {10.1146/annurev-physchem-032210-103551},

+  month =        {may},

+  publisher =    {Annual Reviews},

+}

+

 @article{WrightJohnCurtis2016a,

   author =       {Wright, John C.},

   title =        {{Analytical chemistry, multidimensional spectral signatures, and the future of

diff --git a/dissertation.tex b/dissertation.tex
index 875a366..b1d10fe 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -72,7 +72,7 @@ This dissertation is approved by the following members of the Final Oral Committ
 \include{acquisition/chapter}

 \include{active_correction/chapter}

 \include{opa/chapter}

-%\include{mixed_domain/chapter}

+\include{mixed_domain/chapter}

 

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

 %\include{PbSe/chapter}

@@ -89,9 +89,9 @@ This dissertation is approved by the following members of the Final Oral Committ
 %\include{procedures/chapter}

 %\include{hardware/chapter}

 % TODO: consider inserting WrightTools documentation as PDF

-\include{irf/chapter}

-\include{quantitative_ta/chapter}

-\include{tg/chapter}

+%\include{irf/chapter}

+%\include{quantitative_ta/chapter}

+%\include{tg/chapter}

 %\include{errata/chapter}

 %\include{colophon/chapter}

 \end{appendix}

diff --git a/todo.org b/todo.org
index fef9ecc..6634005 100644
--- a/todo.org
+++ b/todo.org
@@ -2,7 +2,10 @@
   CLOSED: [2018-04-05 Thu 09:12]
 * DONE quote from RC                                           :introduction:
   CLOSED: [2018-04-07 Sat 11:20]
-* TODO dichotomies                                             :spectroscopy:
+* DONE dichotomies                                             :spectroscopy:
+  CLOSED: [2018-04-07 Sat 15:57]
+* DONE citations                                                   :abstract:
+  CLOSED: [2018-04-07 Sat 16:47]
 * TODO describe spectroscopic instrument                       :spectroscopy:
 * TODO incorporate "most software is not peer reviewed"            :software:
 ** see Joppa reference 6
@@ -16,6 +19,7 @@
 * TODO tables                                                    :processing:
 * TODO distribution section                                      :processing:
 * TODO development section                                       :processing:
+* TODO development history from github                           :processing:
 * TODO insert content                                                  :PbSe:
 * TODO summarize PbSe chapter                                  :introduction:
 * TODO summarize MX2 chapter                                   :introduction: