thesis_main.tex

% Main LaTeX file for thesis

% Template: ut-thesis
% \documentclass[12pt, draft]{ut-thesis}
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\hypersetup{
  colorlinks = true,
  pdfpagelayout = TwoPageLeft,
  pdftitle = {Chemistry in Action: Making Molecular Movies
    with Ultrafast Electron Diffraction and Data Science},
  pdfauthor = {Lai Chung Liu},
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% Cover info
\degree{Doctor of Philosophy}
\department{Physics}
\gradyear{2019}
%\author{Lai Chung Liu (\begin{CJK*}{UTF8}{bkai}廖禮中\end{CJK*})}
\author{Lai Chung Liu}
\title{Chemistry in Action: Making Molecular Movies with Ultrafast Electron Diffraction and Data Science}

% Set formatting
\setlength{\emergencystretch}{6pt} % Fix overfull \hbox
\setcounter{tocdepth}{2} % Set depth of table of content
% \doublespacing % Double-spacing
\flushbottom % Make each page fill up the entire page.

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% Impose hyphenation pattern to fix underfull \hbox in bibliography
\lccode`\(`\(
\lccode`\)`\)
\hyphenation{Bis-(hexa-fluoro-phos-phate)}
\hyphenation{perfluoro-cyclo-pentene}
\hyphenation{ethylene-dioxy-tetra-thia-fulvalene}
\hyphenation{beam-width}

% Silence underfull warnings
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% Main document
\begin{document}

  % Value of \textwidth
  %\the\textwidth
  % textwidth in cm: \printinunitsof{cm}\prntlen{\textwidth}
  % 451.68752 pt = 159.345 mm

  % Set up preliminary sections
  \begin{preliminary}

    \maketitle % Make title page

    % Force blank page between title page and abstract
    \cleardoublepage{}

    % Abstract section
    % (at most 350 words for PhD)
    \begin{abstract}

      A long-held thought experiment of science is the direct observation of the motions
      of atoms and molecules as they undergo chemical reactions and phase transitions.
      The advent of microscopy and diffraction beyond the visible spectrum of light ---
      using X-rays, electrons, and neutrons --- has since enabled such atomic-level elucidation
      of the structure of matter in the steady state.

      Recently, time-resolved techniques have finally enabled the making of
      the titular `molecular movie' on the time scale of chemical physics.
      %
      In this thesis, I report on my works which further this quest
      by using ultrafast electron diffraction and data science to fully resolve
      the photoinduced structural dynamics of five \emph{large}, \emph{low-symmetry},
      and \emph{weakly scattering} molecular systems:
      two Bechgaard-Fabre salts of 4,5-ethylenedioxy-tetrathiafulvalene,
      a ring-closing diarylethene derivative, and two iron(II)-based spin-crossover complexes.

      Leveraging the ultrabright femtosecond electron source presently available,
      large overdetermining time-series maps of reciprocal space
      were measured and structurally refined to track the individual atomic motions
      that lead to each photoproduct: two transient metallic phases, a ring-closed isomer,
      and two expanded high-spin states.
      %
      In all cases, a dramatic and heretofore unknown reduction in dimensionality was found,
      whereby the photoinduced structural dynamics is governed by key reaction modes
      that are much fewer in number than the degrees of freedom expected
      of the respective molecular systems.
      %
      This insight --- along with the experiments and methods presented herein ---
      should find application in uncovering the physics of reduced dimensionality
      as a solution to the problem of how chemistry scales with complexity.
      This work lays the foundation to recast chemistry in terms of
      reduced reaction modes, unifying structure and dynamics
      as a new conceptual basis for chemistry.

      % should find application in the making and understanding of future molecular movies of even greater complexity.

    \end{abstract}

    % Force blank page between abstract and acknowledgement
    \cleardoublepage{}

    % Acknowledgements section
    \begin{acknowledgements}

      This thesis represents not only my work at the computer workstation and on the lab bench;
      herein lies also the result of eight and a half years of studying and working in the Department of Physics
      at the University of Toronto. I am thankful of the University for its institutional support,
      the department staff (in particular, Krystyna Biel and Theresa Baptista of the Graduate
      and Undergraduate Offices respectively), and my doctoral supervisory committee members
      (Profs. Young-June Kim and Erich Poppitz) for their guidance and expertise.
      I would also like to thank the governments of Canada, Qu\'{e}bec, and Ontario
      for the generous financial support that they have awarded me
      through their respective funding agencies:
      the National Science and Engineering Research Council~(NSERC),
      the Fonds de recherche du Québec --- Nature et technologies~(FQRNT),
      and the Ontario Graduate Scholarship~(OGS) program.

      Importantly, I am indebted to my Ph.D. supervisor Prof.~R. J. Dwayne Miller.
      His contagious enthusiasm and unwavering support propelled me forward
      while his deep thinking and visionary perspective helped me develop
      into the well-rounded scientist that I am today.
      For these things, I offer him my most grateful thoughts.

      Beyond Dwayne, I am thankful for the mentoring offered by Profs. Bradley J. Siwick
      and Germ\'{a}n Sciaini, J.~Prof.~Dr.~Henrike M. M\"{u}ller-Werkmeister,
      Drs. Gustavo Moriena, Cheng Lu (\begin{CJK*}{UTF8}{bkai}陸誠\end{CJK*}),
      Meng Gao (\begin{CJK*}{UTF8}{bkai}高蒙\end{CJK*}), and Hubert Jean-Ruel.
      When I first met them, I was still an inexperience graduate student.
      Through their eminent example and extensive experience,
      I learnt the tricks of the scientific trade which has allowed me
      to make my own contribution to our research field.
      In particular, the experiments herein would be impossible
      without the masterful ultramicrotoming of Dr.~Lu.

      Alongside the many other Miller-ite graduate students in the group,
      there were the platoon of wonderful postdoctoral fellows.
      No matter which side of the Atlantic Ocean I am on,
      I can always rely on their knowledge and expertise.
      I extend my most sincere thanks to: Profs. Arash Zarrine-Afsar and Amy L. Stevens,
      and Drs. Francis Talbot and Samansa Maneshi in Toronto;
      Drs. Gaston Corthey,  Masaki Hada (\begin{CJK*}{UTF8}{bkai}羽田真毅\end{CJK*}),
      Stuart A. Hayes, Julian Hirscht, G\"{u}nther H. Kassier, Alexander Marx, Kostyantyn Pichugin,
      and Dongfang Zhang (\begin{CJK*}{UTF8}{bkai}張東方\end{CJK*}) in Hamburg.
      In particular, I must thank my close friends and labmates Drs. Ryan L. Field,
      Yifeng Jiang (\begin{CJK*}{UTF8}{bkai}江熠峰\end{CJK*}), and
      J.~Prof.~Dr.~Henrike M. M\"{u}ller-Werkmeister
      for making my journey less lonely through their wit and companionship.
      % It was a privilege for me to work and collaborate with you.

      Furthermore, all of this would not have been possible without the support and encouragement
      of my family: my father \begin{CJK*}{UTF8}{bkai}廖汝光\end{CJK*},
      mother \begin{CJK*}{UTF8}{bkai}王慧美\end{CJK*}, sister \begin{CJK*}{UTF8}{bkai}廖鳳詩\end{CJK*},
      my nieces, \begin{CJK*}{UTF8}{bkai}廖心悠\end{CJK*} and \begin{CJK*}{UTF8}{bkai}廖心穎\end{CJK*},
      and --- most importantly --- my partner, Herlander D. Pinto.

      Finally, I wish to acknowledge that the research described in this thesis was performed
      on the land that was known as \emph{Tkaronto} ---
      the traditional home of the Wendat, Seneca, and Mississauga of the Credit nations.
      I am grateful to have had this opportunity and hope that the works herein
      will serve to benefit them along with all other Canadians.

        \vspace{1cm}
        \begin{figure*}[h!]
          \raggedleft%
          \includegraphics[width = 0.2\textwidth]{Figures/name.pdf}
        \end{figure*}
        \vspace{-0.5cm}
        \begin{flushright}
          Liu Lai Chung%
          \linebreak%
          Toronto, Canada%
          \linebreak%
          May 23, 2017
        \end{flushright}

    \end{acknowledgements}

    % Force blank page between acknowledgement and epigraph
    \cleardoublepage{}

    % Epigraph
    \newpage
    \renewcommand{\epigraphflush}{center}
    \renewcommand{\sourceflush}{flushright}
    % \setlength\epigraphrule{0pt}
    \setlength\epigraphwidth{0.6\textwidth}
    \vspace*{\fill}
    \epigraph{
    Because as we know, \\
    there are known knowns; \\
    there are things we know we know. \\
    We also know \\
    there are known unknowns; \\
    that is to say we know \\
    there are some things we do not know. \\
    But there are also unknown unknowns: \\
    the ones we don't know we don't know.}%
    {\vspace{0.25\baselineskip}
    \textsc{Donald H. Rumsfeld} \\
    United States Secretary of Defense (2001--2006) \\
    Department of Defense News Briefing, February~12, 2002}

    % Make table of contents
    \newpage
    \pdfbookmark{\contentsname}{toc}
    \tableofcontents

    % list of tables and figures
    \listoffigures
    \addcontentsline{toc}{chapter}{\listfigurename}
    \listoftables
    \addcontentsline{toc}{chapter}{\listtablename}

    % Make list of abbreviations
    \newpage
    \chapter*{List of Abbreviations}
    \addcontentsline{toc}{chapter}{List of Abbreviations}
    %\vspace*{2.52cm}
    %\hspace*{-0.78cm}
    %\textbf{{\Huge List of Abbreviations}\\}

    \begin{multicols}{2}

    \begin{tabbing}
      \hspace*{2.5cm} \= \kill
      \textbf{AZA} \> [Fe\textsuperscript{II}(PM-AzA)\textsubscript{2}(NCS\textsubscript{2})]\\
      \textbf{BBO} \> Beta barium borate \\
      \textbf{BPY} \> [Fe\textsuperscript{II}(bpy)\textsubscript{3}](PF\textsubscript{6})\textsubscript{2}\\
      \textbf{CCD} \> Charge coupled device \\
      \textbf{CF} \> Charge flipping \\
      \textbf{CPA} \> Chirped pulse amplification \\
      \textbf{CPM} \> Cross phase modulation \\
      \textbf{CT} \> Charge-Transfer \\
      \textbf{CWT} \> Continuous wavelet transform \\
      \textbf{DAE} \> Diarylethene \\
      \textbf{DAS} \> Decay-associated spectrum \\
      \textbf{DFT} \> Density functional theory \\
      \textbf{EDO-TTF} \> Ethylenedioxy- \\
        \> tetrathiafulvalene\\
      \textbf{ESA} \> Excited state absorption\\
      \textbf{EXAFS} \> Extended X-ray absorption \\
        \> fine structure\\
      \textbf{FFT} \> Fast Fourier transform \\
      \textbf{FWHM} \> Full width at half maximum \\
      \textbf{GLA} \> Global lifetime analysis \\
      \textbf{GSB} \> Ground state bleach \\
      \textbf{GUI} \> Graphics user interface \\
      \textbf{GVD} \> Group velocity dispersion \\
      \textbf{HOMO} \> Highest occupied molecular \\
        \> orbital\\
      \textbf{HS} \> High-spin \\
      \textbf{HT} \> High-temperature \\
      \textbf{IC} \> Internal conversion \\
      \textbf{IM} \> Insulator--metal \\
      \textbf{IRF} \> Instrument response function\\
      \textbf{ISC} \> Intersystem crossing\\
      \textbf{IVR} \> Intramolecular vibrational-energy \\
        \> relaxation \\
      \textbf{LIESST} \> Light-induced excited-spin-\\
        \> state trapping \\
      \textbf{LS} \> Low-spin \\
      \textbf{LT} \> Low-temperature \\
      \textbf{LUMO} \> Lowest unoccupied \\
        \> molecular orbital\\
      \textbf{MI} \> Metal--insulator\\
      \textbf{MLCT} \> Metal--ligand \\
        \> charge-transfer \\
      \textbf{PFC} \> 1,2-bis(2,4-dimethyl- \\
        \> 5-phenyl-3-thienyl) \\
        \> perfluorocyclopentene \\
      \textbf{PIPT} \> Photoinduced phase \\
        \> transition \\
      \textbf{PSA} \> Product state absorption \\
      \textbf{REGEN} \> Regenerative amplifier \\
      \textbf{RF} \> Radio-frequency \\
      \textbf{RMS} \> Root mean square \\
      \textbf{ROI} \> Region of interest \\
      \textbf{SCO} \> Spin crossover \\
      \textbf{SHG} \> Second harmonic generation \\
      \textbf{SVD} \> Singular value decomposition \\
      \textbf{TA} \> Transient absorption \\
      \textbf{TDMES} \> Time-differential M\"{o}ssbauer \\
        \> emission spectroscopy \\
      \textbf{TEM} \> Transmission electron \\
        \> microscopy\\
      \textbf{THG} \> Third harmonic generation\\
      \textbf{TIS} \> Transient intermediate state\\
      \textbf{Ti:Sapph} \> Titanium-doped sapphire \\
      \textbf{TMC} \> Transition-metal complex\\
      \textbf{UED} \> Ultrafast electron diffraction\\
      \textbf{UV} \> Ultraviolet\\
      \textbf{Vis} \> Visible\\
      \textbf{WLG} \> White light generation\\
      \textbf{WPO} \> Weak phase object\\
      \textbf{XANES} \> X-ray absorption near-edge \\
        \> structure\\
      \textbf{XAS} \> X-ray absorption spectroscopy \\
      \textbf{XES} \> X-ray emission spectroscopy \\
      \textbf{XFEL} \> X-ray free electron laser \\
      \textbf{XRD} \> X-ray diffraction
    \end{tabbing}
    \end{multicols}

    % End of the preliminary sections: reset page style and numbering.
  \end{preliminary}

  \raggedbottom%

  % Include chapter files
  \include{thesis_chap1}
  \include{thesis_chap2}
  \include{thesis_chap3}
  \include{thesis_chap4}
  \include{thesis_chap5}
  \include{thesis_chap6}
  \include{thesis_chap7}

  % Include appendix files
  \appendix
  \include{appendix_intro_timeline}
  \include{appendix_intro_scales}
  \include{appendix_cif}
  \include{appendix_interplanar}
  \include{appendix_MottBethe}
  \include{appendix_fparameters}
  \include{appendix_exPHH}
  \include{appendix_CFT}
  \include{appendix_termsymbols}
  \include{appendix_SCO}
  \include{appendix_SCO_exc}
  \include{appendix_SCO_BPY}
  \include{appendix_permissions}


  % Bibliography section
  \addcontentsline{toc}{chapter}{Bibliography} % Add bibliography to table of content
  \bibliographystyle{ieeetr} % IEEE style
  \bibliography{thesis_biblio} % Bibliography file

\end{document}