Re: Using Org for a dissertation

[suvayu ali <fatkasuvayu+linux@gmail.com>]

[-- Attachment #1: Type: text/plain, Size: 1265 bytes --]

Hi Richard,

On Sat, May 12, 2012 at 8:23 PM, Richard Lawrence
<richard.lawrence@berkeley.edu> wrote:
> I am a graduate student in philosophy, and I am about to begin writing
> my dissertation.  I am wondering about whether I should write it in Org,
> or stick to plain LaTeX.

Since others have added their bits, I'll just say I wrote my Master's
thesis in Physics last year with the then org-mode HEAD. I rather liked
the process and the end result[1]. Although I have to admit, I had to
hack around a bit because of buggy mandatory templates from my
university. Apart from that, everything was very smooth. If you are
interested, my org-mode setup is in a public repo[2]. However I haven't
had the time to make the org source for the thesis publicly available.
In case you are interested, I'm attaching some relevant bits. It has
examples on how to put in tables (with short and long captions),
figures, latex snippets and finally how I included a bibliography and
appendices.

Hope this will help.

Footnotes:

[1] <https://theses.lib.sfu.ca/sites/all/files/public_copies/etd6682_sali_pdf_11110.pdf>
[2] <https://github.com/suvayu/.emacs.d/blob/master/org-mode-config.el>

-- 
Suvayu

Open source is the future. It sets us free.

[-- Attachment #2: shortthesis.txt --]
[-- Type: text/plain, Size: 12741 bytes --]

# -*- mode: org; -*-
#+TITLE:     Estimation and modelling of Standard Model backgrounds in the search for \(W'\) gauge bosons with ATLAS (\mu channel)
#+AUTHOR:    Suvayu Ali
#+EMAIL:     Suvayu.Ali@cern.ch
#+DATE:      \today
#+DESCRIPTION:
#+KEYWORDS:
#+LANGUAGE:  en
#+OPTIONS:   H:4 num:4 toc:nil ::t |:t ^:t -:t f:t *:t <:nil
#+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:nil pri:nil tags:nil

#+EXPORT_SELECT_TAGS: export
#+EXPORT_EXCLUDE_TAGS: noexport

#+STARTUP: content
#+BIND: org-confirm-babel-evaluate nil
#+BIND: org-export-latex-title-command ""

#+LaTeX_CLASS: book
#+LaTeX_CLASS_OPTIONS: [12pt,letterpaper,oneside]
#+LaTeX_HEADER: \usepackage{amsfonts}
#+LaTeX_HEADER: \usepackage{amsmath}
#+LaTeX_HEADER: \usepackage{appendix}
#+LaTeX_HEADER: \usepackage{varioref}
#+LaTeX_HEADER: \usepackage[nokeyprefix]{refstyle}
# more Physics specific packages

# LaTeX Macros
#+LaTeX_HEADER: \newcommand{\p}[1]{\phantom{#1}}
#+LaTeX_HEADER: \newcommand{\modulus}[1]{\ensuremath{\lvert #1 \rvert}}
# some more Physics specific macros

# University stuff
##+LaTeX_HEADER: \usepackage[headings]{thesisstyle}
# ...
# #+LaTeX_HEADER: \include{abstract}
# \include{preamble}

* Introduction

** The Standard Model							 :SM:

   \label{chap:SMintro}

   The Standard Model is a quantum field theoretical approach to
   describe interactions in nature. The theory is primarily built upon
   symmetry arguments supported by experimental data. It describes the
   interactions between all fermions mediated by vector gauge bosons.
   These include the electromagnetic, weak and strong interactions.
   The formulation of the SM does not include gravity. There are
   various approaches to include gravity in BSM theories which are
   discussed elsewhere \cite{ArkaniHamed:1998rs,Randall:1999ee}.

   #+CAPTION: [Interactions and particles described by the SM.]{The interactions and the participating particles described by the Standard Model are tabulated below. Although the $Z^0$ is listed both as force carrier and a particle interacting by the weak force, it should be noted it does not couple with another $Z^0$.}
   #+LABEL: tbl:interactions
   |----------+-----------------+----------------+---------------------------------|
   | Charge   | Force           | Force carrier  | Interacting particles           |
   |----------+-----------------+----------------+---------------------------------|
   | Electric | Electromagnetic | \gamma         | all charged fermions, \(W^\pm\) |
   | Weak     | Weak            | \(W^\pm, Z^0\) | all fermions, \(W^\pm, Z^0\)    |
   | Colour   | Strong          | \(g\)          | all quarks, anti-quarks, \(g\)  |
   |----------+-----------------+----------------+---------------------------------|

   In the SM all particles carry various charges which describe all
   the interactions they undergo: the electric charge is responsible
   for all electromagnetic interactions, the weak charge for all weak
   interactions and the colour charge for all strong interactions.
   Since any quantum fields have bosonic exchange particles, all the
   interactions discussed earlier are associated with different spin-1
   bosons as force carriers. This has been summarised in
   \Tabref{tbl:interactions}.

*** Production and Decay of the \(W'\) Boson				:pdf:

    \label{subsec:Wprod}

    #+CAPTION: A representative diagram for \(W'\) production at the LHC.
    #+LABEL: fig:LO-Wprime
    #+ATTR_LaTeX: width=0.6\textwidth
    [[file:figs/Wprime-s-channel.eps]]

    \noindent *Production:* The $W'$ boson is assumed to have a
    coupling constant that is the same as its lighter SM counterpart.
    This is known as the sequential SM $W'$ boson. The diagrams[fn:1]
    responsible for the production of $W'$ bosons at a hadron
    collider are known as charged current (CC) processes. These are
    flavour changing interactions occurring between up-like and
    down-like quarks (or anti-quarks) where the weak current involved
    is charged as the gauge bosons involved are charged.
    \Figref{fig:LO-Wprime} shows a diagram responsible for $W'$
    production at the LHC.

    The production of a heavy $W'$ boson from a pp collision depends
    strongly on the momenta of the initial state particles. Since
    protons are composite particles made of (anti-)quarks and gluons,
    knowledge about the momentum fraction carried by the initial
    state particles is important. This is achieved by a /Parton
    Distribution Function/ (PDF) determined from deep inelastic
    scattering experiments with hadrons and leptons. In 1968--69,
    Bjorken proposed a dimensionless quantity /x/ which is
    independent of the momentum transfer during a hard scattering
    event. They exhibit a scaling behaviour in the asymptotic limit
    of very high energy collisions, known as /Bjorken scaling/. The
    discovery of scaling behaviour as predicted by Bjorken led to the
    modern formulation of the strong force as an asymptotically free
    quantum field theory \cite{Tung:2009}. The scaling was later
    shown to be only approximately true at low energies due to higher
    order QCD corrections (scaling violations).

    In 1969 Feynman proposed the /parton model/. It describes hadrons
    as composite particles made of its constituent quarks,
    anti-quarks and gluons \cite{PhysRevLett.23.1415}. The
    constituent quarks can be either valence or sea quarks. If the
    quark is one of the three quarks forming the hadron bound state
    and responsible for the quantum number, then it is called the
    /valence quark/. On the other hand if it is a virtual quark
    formed by splitting of gluons, it is called a /sea quark/.
    Modern QCD explains the interaction of hadrons in hard scattering
    experiments using this parton model.

    #+begin_src latex
      \begin{equation}
      \label{eq:partondistribfn}
      \frac{d\sigma}{dm_T} = \sum\limits_{a,b} \int dx_A f_{a/A}(x_A,\mu) \int dx_B f_{b/B}(x_B,\mu) \frac{d\hat{\sigma}}{dm_T}
      \end{equation}
    #+end_src

    The differential production cross section ($d\sigma/dm_T$) for
    observing certain events in a channel in a hadron collider is
    given by \Eqref{eq:partondistribfn}. $f_{a/A}$ and $f_{b/B}$ are
    the parton distribution functions mentioned earlier. They are the
    probability distributions of finding a parton of type /a/ (/b/)
    originating from a hadron of type /A/ (/B/) with the momentum
    fraction $x_A$ ($x_B$). $d\hat{\sigma}/dm_T$ is the parton level
    cross section given by perturbative QCD. The Bjorken scaling
    violations observed earlier could be incorporated into this
    picture by including corrections to the PDFs from perturbative
    QCD. These corrections introduce the dependence on the parameter
    \mu in the PDFs. The parameter \mu is related to the
    renormalisation of the strong coupling in the cross section
    calculation and the QCD corrections to the PDFs. They are often
    referred to separately as /renormalisation scale/ and
    /factorisation scale/ \cite{Soper:1996sn}.

    #+begin_src latex
      \begin{figure}[p]
      \centering
      \begin{tabular}{c}
      \includegraphics[width=0.7\textwidth,trim=0 150 0 150]{plots/PDF-upv.pdf} \\
      \includegraphics[width=0.7\textwidth,trim=0 150 0 150]{plots/PDF-downv.pdf}
      \end{tabular}

      \caption[PDF for the proton at $Q^2 = 1$ TeV/c$^2$]{Proton PDFs
      showing the probability distributions for up (top) and down
      (bottom) quarks at $Q^2 = 1$ TeV/c$^2$. The valence quark PDF
      (black) is compared with the sea quark (red) and gluon (green)
      PDFs. A common choice for the factorisation scale when
      calculating a PDF set is to set it to $Q^2$ of the process
      \cite{website:HepData}.}

      \label{fig:PDF}
      \end{figure}
    #+end_src


* Appendices 						      :ignoreheading:
  :PROPERTIES:
  :VISIBILITY: folded
  :END:

#+LaTeX: \newpage
#+LaTeX: \appendix
# Needs \usepackage{appendix}
#+LaTeX: \addappheadtotoc
#+LaTeX: \appendixpage

** Particle track parametrisation in ATLAS				:trk:

   \label{app:trackparam}

   A particle track in ATLAS is represented by the perigee[fn:2] of the
   track. The perigee is specified by the five parameters:

   + d_0 - transverse impact parameter, the distance of the closest
     approach of helix to beam pipe,
   + z_0 - longitudinal impact parameter, the z value at the point of
     closest approach,
   + \phi_0 - azimuth angle of the momentum at point of closest
     approach, measured in the range $[-\pi,\pi)$,
   + \theta - polar angle in the range $[0,\pi]$,
   + q/p - charge over momentum magnitude.


   In ATLAS the /z/-axis is parallel to the magnetic field (which is
   parallel to the beam axis). \Figref{fig:trkperigee} shows the five
   parameters split into transverse and longitudinal planes.

   #+CAPTION: [Schematic showing all 5 track parameters]{The diagram shows the five parameters, the three longitudinal parameters in the x-y plane and two longitudinal parameters in the r-z plane.}
   #+LABEL: fig:trkperigee
   #+ATTR_LaTeX: width=0.6\textwidth placement=[p]
   [[file:figs/Perigee.png]]


** Limit formalism						     :limits:

   \label{app:limits}

   The limits are set with the observed events in a bin with $m_T$ >
   $m_{Tmin}$, where the lower bin threshold is determined by taking
   the half of the $W'$ mass. The expected number of events are given
   by \Eqref{eq:expevts}, where $\nbg$ is the expected number of
   events from our background model and $N_{sig}$ is the predicted
   number of signal events from \Eqref{eq:sigevts}. $L_{int}$ is the
   integrated luminosity of the recorded data and $\epsilon_{sig}$ is
   the event selection efficiency.

   #+begin_src latex
     \begin{align}
     \label{eq:expevts}
     N_{exp} &= N_{sig} + \nbg \\
     \label{eq:sigevts}
     N_{sig} &= L_{int} \epsilon_{sig} \SB
     \end{align}
   #+end_src

   The likelihood function in \Eqref{eq:likelihood} is obtained from
   Poisson statistics for $N_{obs}$ observed events. Uncertainties are
   included as nuisance parameters in the analysis. They are assumed
   to follow a Gaussian probability distribution. In this analysis we
   consider uncertainties on $L_{int}$, $\epsilon_{sig}$ and $\nbg$ in
   our calculations. Taking the above into consideration we get the
   likelihood function shown in \Eqref{eq:llnuissance}.

   #+begin_src latex
     \begin{align}
     \label{eq:likelihood}
     \mathcal{L}(\SB) &= \frac{(L_{int}\SB + \nbg)^{N_{obs}}e^{-(L_{int}\epsilon_{sig}\SB+\nbg)}}{N_{obs}!} \\
     \label{eq:llnuissance}
     \mathcal{L}(\SB,\theta_1,\dotsc\theta_N) &= \frac{(L_{int}\SB + \nbg)^{N_{obs}}e^{-(L_{int}\epsilon_{sig}\SB+\nbg)}}{N_{obs}!} \prod g_i(\theta_i) \\
     g_i(\theta_i) &= \frac{1}{\sqrt{2\pi}\sigma_i}e^{-\frac{(\theta -\bar{\theta}_i)^2}{2\sigma_i^2}} \nonumber
     \end{align}
   #+end_src

   This likelihood function is used to calculate the log-likelihood
   ratio (LLR) test statistic shown in \Eqref{eq:LLR}
   \cite{Junk:1999kv}. The LLR is used to calculate /p/-values which
   correspond to confidence levels for the signal + background
   (CL_{s+b}) and background (CL_b) only hypotheses. These are
   evaluated by conducting pseudo-experiments and integrating over the
   corresponding LLR distributions.

   #+begin_src latex
     \begin{equation}
     \label{eq:LLR}
     LLR = -2 \ln \frac{\mathcal{L}(data\lvert s+b)}{\mathcal{L}(data\lvert b)}
     \end{equation}
   #+end_src

   The CL_s method finally uses the ratio of the /p/-values to
   determine the exclusion limits (\eqref[name=eq.~]{eq:CLs}). To set
   the limits at 95% confidence level, the signal cross section is
   increased until CL_s = 1 - \alpha where \alpha is 0.95. For a more
   complete discussion of the limit setting procedure see the
   referenced ATLAS internal note \cite{Adams:1317922}.

   #+begin_src latex
     \begin{equation}
     \label{eq:CLs}
     CL_s = \frac{CL_{s+b}}{CL_b}
     \end{equation}
   #+end_src


* Bibliography						      :ignoreheading:

#+LaTeX: \backmatter
#+LaTeX: \newpage
#+LaTeX: \addcontentsline{toc}{chapter}{\bibname}
#+LaTeX: \bibliographystyle{ieeetr}
#+LaTeX: \bibliography{master}


* Footnotes

[fn:1] Here and in the rest of this thesis /diagram/ refers to Feynman
diagrams unless otherwise specified.

[fn:2] The point where the track comes closest to the geometrical
centre of the detector is called the perigee of the track.


* COMMENT local setup

# Local Variables:
# org-export-allow-BIND: t
# org-latex-to-pdf-process: ("pdflatex -interaction nonstopmode %b" "/usr/bin/bibtex %b" "pdflatex -interaction nonstopmode %b" "pdflatex -interaction nonstopmode %b")
# End: