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main.tex
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% University of Michigan Dissertation LaTeX Template for 2023
% Created by John Meluso and Shreyas Kousik
% 9 Jul 2020
% Use the University of Michigan thesis class.
\documentclass[thesis]{thesis-umich}
\input{packages}
%--- Set the font styles -----
% As of this writing, Rackham does not have strict font requirements, but they
% suggest "standard fonts" such as Times, Arial, or Times New Roman.
% In practice, they allow the default LaTeX font (Computer Modern).
% The fonts available to you depend on the typesetting engine you use, e.g.
% pdflatex (the overleaf default), xelatex, or lualatex.
% Set the font to whatever you like, as long as it's compatible with the tex
% engine you're using.
% More information from Overleaf on font selection with:
% - pdflatex: https://www.overleaf.com/learn/latex/Font_typefaces
% - xelatex: https://www.overleaf.com/learn/latex/XeLaTeX
% See examples below depending on your engine and uncomment the usepackage
% commands and any subsequent commands as needed.
%-------------------------------------------------------------------------------
%--- pdflatex -----
%\usepackage{times}
%\usepackage{newtxtext}
%\usepackage{newtxmath}
%-------------------------------------------------------------------------------
%--- xelatex / lualatex -----
%\usepackage{fontspec}
%\setromanfont{Times New Roman}
%\setsansfont{Arial}
%\setmonofont{Courier New}
%-------------------------------------------------------------------------------
% If you are using the alpha bibliography style, keep these next three lines in your preamble, so that the references are left-aligned; or, you can comment it out and see what happens
\makeatletter
\renewcommand{\@biblabel}[1]{[#1]\hfill}
\makeatother
% Title of the thesis
\title{Methods development toward non-equilibrium studies
of transcription initiation by \textit{E. coli} RNA Polymerase}
% Author name
\author{Maya A. Segal}
% Department
%\department{Chemistry}
% Year of completion
\year=2023
% Author email
\email{mayasegala@gmail.com}
% Author ORCID iD
\orcid{0000-0002-1828-7682}
% Frontispiece
% if you want to add a frontispiece, add an image named `frontispiece.png1
%\frontispiece{\includegraphics[width=4in]{front_materials/frontispiece.png}}
% Default style for front pages
\frontpagestyle{7} % 7 is preferred by Rackham, but should be set individually for each front page
% Dedication (the input [7] determines the style -- 7 is Rackham's preferred style)
% \hidededication{%
\dedication[7]{\input{front_materials/dedication}}
% Acknowledgments (the input [7] determines the style -- 7 is Rackham's preferred style)
\acknowledgments[7]{\input{front_materials/acknowledgments}}
% Vita
\vita[7]{\input{front_materials/vita}}
% Committee
\committee{ %
Professor Shimon S. Weiss, Chair \\
Professor Justin R. Caram \\
Professor William M. Gelbart \\
Professor Charles M. Knobler \\
}
% Chair must be entered separately for formatting reasons.
\chair{Professor Shimon S. Weiss}
%\cochair{Co-chair One \& Co-chair Two}
% Commands to hide or show lists of figures, tables, etc.
% To hide a list, change the word "show" in the command to "hide".
%\showlistoftables
\showlistofprograms
\showlistofappendices
\showlistofacronyms
% Definition of any acronyms used.
% To add an acronym, add an \acro{}{} command on a new line within the \acronyms{} command. For \acro, field 1 is the acronym and field 2 is the corresponding expression. For example: \acro{TLA}{Three Letter Acronym}.
\acronyms{
\acro{FRET}{Fluorescence Resonance Energy Transfer}
\acro{PAX}{Periodic Acceptor Excitation}
\acro{E. coli}{Escherichia coli}
\acro{RNAP}{RNA Polymerase}
\acro{mRNA}{messenger RNA}
\acro{$RP_c$}{RNAP closed complex}
\acro{$RP_o$}{RNAP open bubble complex}
\acro{$RP_{ITC}$}{RNAP initial transcription complex}
\acro{BOIs}{bubble opening intermediates}
\acro{PBIIs}{paused-backtracked initiation intermediates}
\acro{TS}{template strand}
\acro{NTS}{non-template strand}
\acro{dsDNA}{duble-stranded DNA}
\acro{lacCONS}{\textit{lac} consensus sequence}
\acro{bp}{base pair}
\acro{PDB}{Protein Data Bank}
\acro{NTP}{ribonucleoside triphosphate}
\acro{DPBB}{double$-\psi-\beta-$barrel}
\acro{FRET}{Fluorescence Resonance Energy Transfer}
\acro{smFRET}{single-molecule FRET}
\acro{ALEX}{Alternating Laser Excitation}
\acro{FAMS}{Fluorescence Aided Molecular Sorting}
\acro{TIRF}{Total Internal Reflection Fluorescence}
\acro{STED}{Stimulated Emission Depletion}
\acro{SMLM}{Single Molecule Localization Microscopy}
\acro{FLIM}{Fluorescence Lifetime Imaging Microscopy}
\acro{TCSPC}{Time-Correlated Single-Photon Counting}
\acro{FCS}{Fluorescence Correlation Spectroscopy}
\acro{FCCS}{Fluorescence Cross-Correlation Spectroscopy}
\acro{CW}{continuous-wave}
\acro{SPAD}{Single Photon Avalanche Diode}
\acro{AOM}{Acousto-optic Modulator}
\acro{nsALEX}{nanosecond ALEX}
\acro{PIE}{Periodic Interleaved Excitation}
\acro{POLIMI}{Politecnico di Milano}
\acro{iAQC}{integrated active quenching circuit}
\acro{CMOS}{Complementary Metal Oxide Semiconductor}
\acro{MVUE}{Minimum Variance Unbiased Estimator}
\acro{DCR}{dark count rate}
\acro{LCOS-SLM}{liquid crystal on silicon spatial light modulator}
\acro{NA}{numerical aperture}
\acro{FPGA}{field-programmable gate array}
\acro{TTL}{transistor-transistor logic}
\acro{NIM}{nuclear instrumentation module}
\acro{BNC}{Bayonet Neill–Concelman}
\acro{LVDS}{low-voltage differential signaling}
\acro{TACs}{time-to-amplitude converters}
\acro{MLE}{Maximum Likelihood Estimator}
\acro{PSF}{Point Spread Function}
\acro{SBR}{signal-to-background rate}
\acro{APBS}{all-photon burst search}
\acro{DCBS}{dual-channel burst search}
\acro{HT-smFRET}{high-throughput smFRET}
\acro{HT-FCS}{high-throughput Fluorescence Correlation Spectroscopy}
\acro{PDE}{photon detection efficiency}
\acro{ACF}{autocorrelation function}
\acro{CCF}{cross-correlation function}
\acro{PCR}{polymerase chain reaction}
\acro{wt-rpoD}{wildtype $\sigma^{70}$ gene}
\acro{ITS}{initial transcription sequence}
\acro{ssDNA}{single stranded DNA}
\acro{PDMS}{polydimethylsiloxane}
}
% Some abstract text
\abstract{
\input{front_materials/abstract}
}
%\hideabstractpagenumber
%% DOCUMENT AREA
\begin{document}
% Place your chapters here using the \input{} command
\input{chapters/chpt_1-RNAP}
\input{chapters/chpt_2-smFRET}
\input{chapters/chpt_3-HT-smFRET}
\input{chapters/chpt_4-Applications_of_HT-smFRET}
\input{chapters/chpt_5-promoter_escape_experiments}
\input{chapters/chpt_6-conclusion}
% Appendices
\appendix
\input{appendices/appendix_1}
\input{appendices/appendix_2}
\input{appendices/appendix_3}
% citations in ACS style using achemso package
%\bibliographystyle{plain}
% Give this command the relative path to the .bib file.
\bibliography{bib.bib}
\end{document}