mirror of
https://github.com/dnlbauer/dissertation-template.git
synced 2026-09-10 14:05:30 +00:00
inital commit
This commit is contained in:
Daniel Bauer
250
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## Custom exclusions
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article-template.pdf
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book-template.pdf
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## Core latex/pdflatex auxiliary files:
|
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*.aux
|
||||
*.lof
|
||||
*.log
|
||||
*.lot
|
||||
*.fls
|
||||
*.out
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||||
*.toc
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||||
*.fmt
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||||
*.fot
|
||||
*.cb
|
||||
*.cb2
|
||||
.*.lb
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||||
|
||||
## Intermediate documents:
|
||||
*.dvi
|
||||
*.xdv
|
||||
*-converted-to.*
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||||
# these rules might exclude image files for figures etc.
|
||||
# *.ps
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# *.eps
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# *.pdf
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||||
|
||||
## Generated if empty string is given at "Please type another file name for output:"
|
||||
.pdf
|
||||
|
||||
## Bibliography auxiliary files (bibtex/biblatex/biber):
|
||||
*.bbl
|
||||
*.bcf
|
||||
*.blg
|
||||
*-blx.aux
|
||||
*-blx.bib
|
||||
*.run.xml
|
||||
|
||||
## Build tool auxiliary files:
|
||||
*.fdb_latexmk
|
||||
*.synctex
|
||||
*.synctex(busy)
|
||||
*.synctex.gz
|
||||
*.synctex.gz(busy)
|
||||
*.pdfsync
|
||||
|
||||
## Auxiliary and intermediate files from other packages:
|
||||
# algorithms
|
||||
*.alg
|
||||
*.loa
|
||||
|
||||
# achemso
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||||
acs-*.bib
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||||
|
||||
# amsthm
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||||
*.thm
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||||
|
||||
# beamer
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||||
*.nav
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||||
*.pre
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||||
*.snm
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||||
*.vrb
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||||
|
||||
# changes
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||||
*.soc
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||||
|
||||
# cprotect
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||||
*.cpt
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||||
|
||||
# elsarticle (documentclass of Elsevier journals)
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||||
*.spl
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||||
|
||||
# endnotes
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||||
*.ent
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||||
|
||||
# fixme
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||||
*.lox
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||||
|
||||
# feynmf/feynmp
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||||
*.mf
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||||
*.mp
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||||
*.t[1-9]
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*.t[1-9][0-9]
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||||
*.tfm
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||||
|
||||
#(r)(e)ledmac/(r)(e)ledpar
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*.end
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||||
*.?end
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||||
*.[1-9]
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||||
*.[1-9][0-9]
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||||
*.[1-9][0-9][0-9]
|
||||
*.[1-9]R
|
||||
*.[1-9][0-9]R
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||||
*.[1-9][0-9][0-9]R
|
||||
*.eledsec[1-9]
|
||||
*.eledsec[1-9]R
|
||||
*.eledsec[1-9][0-9]
|
||||
*.eledsec[1-9][0-9]R
|
||||
*.eledsec[1-9][0-9][0-9]
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||||
*.eledsec[1-9][0-9][0-9]R
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||||
|
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# glossaries
|
||||
*.acn
|
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*.acr
|
||||
*.glg
|
||||
*.glo
|
||||
*.gls
|
||||
*.glsdefs
|
||||
|
||||
# gnuplottex
|
||||
*-gnuplottex-*
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||||
|
||||
# gregoriotex
|
||||
*.gaux
|
||||
*.gtex
|
||||
|
||||
# htlatex
|
||||
*.4ct
|
||||
*.4tc
|
||||
*.idv
|
||||
*.lg
|
||||
*.trc
|
||||
*.xref
|
||||
|
||||
# hyperref
|
||||
*.brf
|
||||
|
||||
# knitr
|
||||
*-concordance.tex
|
||||
# TODO Comment the next line if you want to keep your tikz graphics files
|
||||
*.tikz
|
||||
*-tikzDictionary
|
||||
|
||||
# listings
|
||||
*.lol
|
||||
|
||||
# makeidx
|
||||
*.idx
|
||||
*.ilg
|
||||
*.ind
|
||||
*.ist
|
||||
|
||||
# minitoc
|
||||
*.maf
|
||||
*.mlf
|
||||
*.mlt
|
||||
*.mtc[0-9]*
|
||||
*.slf[0-9]*
|
||||
*.slt[0-9]*
|
||||
*.stc[0-9]*
|
||||
|
||||
# minted
|
||||
_minted*
|
||||
*.pyg
|
||||
|
||||
# morewrites
|
||||
*.mw
|
||||
|
||||
# nomencl
|
||||
*.nlg
|
||||
*.nlo
|
||||
*.nls
|
||||
|
||||
# pax
|
||||
*.pax
|
||||
|
||||
# pdfpcnotes
|
||||
*.pdfpc
|
||||
|
||||
# sagetex
|
||||
*.sagetex.sage
|
||||
*.sagetex.py
|
||||
*.sagetex.scmd
|
||||
|
||||
# scrwfile
|
||||
*.wrt
|
||||
|
||||
# sympy
|
||||
*.sout
|
||||
*.sympy
|
||||
sympy-plots-for-*.tex/
|
||||
|
||||
# pdfcomment
|
||||
*.upa
|
||||
*.upb
|
||||
|
||||
# pythontex
|
||||
*.pytxcode
|
||||
pythontex-files-*/
|
||||
|
||||
# thmtools
|
||||
*.loe
|
||||
|
||||
# TikZ & PGF
|
||||
*.dpth
|
||||
*.md5
|
||||
*.auxlock
|
||||
|
||||
# todonotes
|
||||
*.tdo
|
||||
|
||||
# easy-todo
|
||||
*.lod
|
||||
|
||||
# xmpincl
|
||||
*.xmpi
|
||||
|
||||
# xindy
|
||||
*.xdy
|
||||
|
||||
# xypic precompiled matrices
|
||||
*.xyc
|
||||
|
||||
# endfloat
|
||||
*.ttt
|
||||
*.fff
|
||||
|
||||
# Latexian
|
||||
TSWLatexianTemp*
|
||||
|
||||
## Editors:
|
||||
# WinEdt
|
||||
*.bak
|
||||
*.sav
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||||
|
||||
# Texpad
|
||||
.texpadtmp
|
||||
|
||||
# Kile
|
||||
*.backup
|
||||
|
||||
# KBibTeX
|
||||
*~[0-9]*
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||||
|
||||
# auto folder when using emacs and auctex
|
||||
./auto/*
|
||||
*.el
|
||||
|
||||
# expex forward references with \gathertags
|
||||
*-tags.tex
|
||||
|
||||
# standalone packages
|
||||
*.sta
|
||||
|
||||
# generated if using elsarticle.cls
|
||||
*.spl
|
||||
.snakemake
|
||||
|
||||
thesis_stats*
|
||||
*.sec
|
||||
8
.latexmkrc
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8
.latexmkrc
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||||
add_cus_dep('glo', 'gls', 0, 'makeglossaries');
|
||||
add_cus_dep('acn', 'acr', 0, 'makeglossaries');
|
||||
|
||||
sub makeglossaries {
|
||||
system "makeglossaries $_[0]";
|
||||
}
|
||||
|
||||
$pdflatex=q/xelatex -synctex=1 %O %S/
|
||||
28
README.md
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28
README.md
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# A tufte-derived Dissertation/Thesis LaTeX-template
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||||
A LaTeX-template that can be used for dissertations. I developed
|
||||
this template while writing my own PhD thesis. You can see the template in use
|
||||
here: [Example](https://tuprints.ulb.tu-darmstadt.de/18611/)
|
||||
|
||||
### Requirements:
|
||||
- texlive-full
|
||||
- biber (for biblatex)
|
||||
- latexmk, xelatex
|
||||
- Fonts: Vollkorn (http://vollkorn-typeface.com), Gillius ADF No2 (https://blogfonts.com/gillius-adf-no2.font)
|
||||
|
||||
### Compilation
|
||||
|
||||
Compile with `xlatexmk` (there is a `.latexmkrc`):
|
||||
```bash
|
||||
latexmk thesis.tex -pdf
|
||||
```
|
||||
|
||||
or use ninja:
|
||||
```bash
|
||||
ninja thesis.pdf
|
||||
```
|
||||
|
||||
### License
|
||||
Copyright 2017–2021 by Daniel Bauer.
|
||||
|
||||
This template uses a modified version of the original [tufte-latex](https://github.com/Tufte-LaTeX/tufte-latex)
|
||||
template which was published under the Apache 2.0 License, so this work will also use it.
|
||||
6
abstract.tex
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6
abstract.tex
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|
||||
%!TEX root = thesis.tex
|
||||
\chapter{Abstract}
|
||||
\blindtext[4]
|
||||
\glsresetall
|
||||
\chapter{Zusammenfassung}
|
||||
\blindtext[4]
|
||||
9
acknowledgements.tex
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9
acknowledgements.tex
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@@ -0,0 +1,9 @@
|
||||
% -*- Mode:TeX -*-
|
||||
%!TEX root = thesis.tex
|
||||
\chapter*{Acknowledgements}
|
||||
\addcontentsline{toc}{chapter}{Acknowledgements}
|
||||
\doublespacing
|
||||
A page to put acknowledgements.
|
||||
\begin{flushright}
|
||||
\textit{Thank you!}
|
||||
\end{flushright}
|
||||
68
acronyms.tex
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68
acronyms.tex
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|
||||
%!TEX root = thesis.tex
|
||||
|
||||
\makeglossaries
|
||||
\newacronym{MD}{MD}{molecular dynamics}
|
||||
\newacronym{LJ}{LJ}{Lennard-Jones}
|
||||
\newacronym{PME}{PME}{particle-mesh Ewald}
|
||||
\newacronym{HCN}{HCN}{hyperpolarization-activated cyclic nucleotide-gated}
|
||||
\newacronym{VSD}{VSD}{voltage sensor domain}
|
||||
\newacronym{LBD}{LBD}{ligand-binding domain}
|
||||
\newacronym{PD}{PD}{pore domain}
|
||||
\newacronym{SF}{SF}{selectivity filter}
|
||||
\newacronym{TPCs}{TPCs}{two-pore channels}
|
||||
\newacronym{KTN}{KTN}{nucleotide-binding domain}
|
||||
\newacronym{Na}{Na\textsuperscript{+}}{sodium}
|
||||
\newacronym{K}{K\textsuperscript{+}}{potassium}
|
||||
\newacronym{Cl}{Cl\textsuperscript{-}}{chloride}
|
||||
\newacronym{Ca}{Ca\textsuperscript{2+}}{calcium}
|
||||
\newacronym[firstplural=voltage-gated ion channels (VGICs)]{VGIC}{VGIC}{voltage-gated ion channel}
|
||||
\newacronym{If}{I\textsubscript{f}}{funny current}
|
||||
\newacronym[firstplural=transmembrane helices (TMHs)]{TMH}{TMH}{transmembrane helix}
|
||||
\newacronym{Kv}{K\textsubscript{V}}{voltage-gated potassium channel}
|
||||
\newacronym{Kchannel}{K\textsuperscript{+}~channel}{potassium channel}
|
||||
\newacronym{SAN}{SAN}{sinoatrial node}
|
||||
\newacronym{CNBD}{CNBD}{cyclic-nucleotide binding-domain}
|
||||
\newacronym{cAMP}{cAMP}{cyclic-adenosine monophosphate}
|
||||
\newacronym{cGMP}{cGMP}{cyclic-guanosine monophosphate}
|
||||
\newacronym{TRIP8b}{TRIP8b}{tetratricopeptide repeat-containing Rab8b-interacting protein}
|
||||
\newacronym{HCND}{HCND}{HCN domain}
|
||||
\newacronym{AA}{AA}{amino acid}
|
||||
\newacronym{PBC}{PBC}{periodic boundary conditions}
|
||||
\newacronym{PMF}{PMF}{potential of mean force}
|
||||
\newacronym{CV}{CV}{collective variable}
|
||||
\newacronym{MFEP}{MFEP}{minimal free energy pathway}
|
||||
\newacronym{FES}{FES}{free energy surface}
|
||||
\newacronym{US}{US}{umbrella sampling}
|
||||
\newacronym{WHAM}{WHAM}{Weighted Histogram Analysis Method}
|
||||
\newacronym{TEA}{TEA\textsuperscript{+}}{tetraethylazanium}
|
||||
\newacronym{POPC}{POPC}{palmitoyloleoylphosphatidylcholine}
|
||||
\newacronym{VdW}{VdW}{Van der Waals}
|
||||
\newacronym{RDF}{RDF}{radial distribution function}
|
||||
\newacronym{COM}{COM}{center-of-mass}
|
||||
\newacronym{CF}{CF}{cystic fibrosis}
|
||||
\newacronym{CFTR}{CFTR}{cystic fibrosis transmembrane conductance regulator}
|
||||
\newacronym{NEB}{NEB}{nudged elastic band}
|
||||
\newacronym{TST}{TST}{transition state theory}
|
||||
\newacronym{wt}{wt}{wildtype}
|
||||
|
||||
\newcommand{\K}{\gls{K}\xspace}
|
||||
\newcommand{\Na}{\gls{Na}\xspace}
|
||||
\newcommand{\Cl}{\gls{Cl}\xspace}
|
||||
\newcommand{\Ca}{\gls{Ca}\xspace}
|
||||
\newcommand{\Calpha}{C\subs{$\alpha$}\xspace}
|
||||
\newcommand{\s}[1]{s\textsubscript{#1}\xspace}
|
||||
\newcommand{\p}[1]{p\textsubscript{#1}\xspace}
|
||||
\newcommand{\z}[1]{z\textsubscript{#1}\xspace}
|
||||
\newcommand{\Kchannel}{\K~channel\xspace}
|
||||
\newcommand{\Kchannels}{\K~channels\xspace}
|
||||
\newcommand{\KK}{\gls{K}/\gls{K}\xspace}
|
||||
\newcommand{\NaNa}{\gls{Na}/\gls{Na}\xspace}
|
||||
\newcommand{\KNa}{\gls{K}/\gls{Na}\xspace}
|
||||
\newcommand{\NaK}{\gls{Na}/\gls{K}\xspace}
|
||||
\newcommand{\KKK}{\gls{K}/\gls{K}/\gls{K}\xspace}
|
||||
\newcommand{\NaNaNa}{\gls{Na}/\gls{Na}/\gls{Na}\xspace}
|
||||
\newcommand{\KNaNa}{\gls{K}/\gls{Na}/\gls{Na}\xspace}
|
||||
\newcommand{\NaKK}{\gls{Na}/\gls{K}/\gls{K}\xspace}
|
||||
|
||||
\glsaddall
|
||||
|
||||
26
appendix.tex
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26
appendix.tex
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@@ -0,0 +1,26 @@
|
||||
%!TEX root = thesis.tex
|
||||
\chapter{Abbreviations}
|
||||
\vspace{-0.5cm}
|
||||
\begin{tcolorbox}[
|
||||
enhanced,
|
||||
enforce breakable,
|
||||
check odd page,
|
||||
toggle left and right,
|
||||
grow to right by=\marginparwidth+\marginparsep-0.4cm,
|
||||
toggle enlargement=evenpage,
|
||||
notitle after break,
|
||||
vfill before first,
|
||||
nobeforeafter,
|
||||
sharp corners,
|
||||
top=0pt,
|
||||
before upper={\let\clearpage\relax},
|
||||
opacityback=0,
|
||||
opacityframe=0,
|
||||
]
|
||||
|
||||
\renewcommand{\glossarysection}[2][]{} % no glossary title
|
||||
\printglossaries
|
||||
\end{tcolorbox}
|
||||
|
||||
\chapter{Additional Data}
|
||||
\blindtext
|
||||
BIN
athene.png
Normal file
BIN
athene.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 32 KiB |
58
biblio.bib
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58
biblio.bib
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|
||||
|
||||
@article{Abraham2015,
|
||||
title = {{{GROMACS}}: {{High}} Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers},
|
||||
author = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and Páll, Szilárd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik},
|
||||
date = {2015},
|
||||
journaltitle = {SoftwareX},
|
||||
volume = {1},
|
||||
pages = {19--25},
|
||||
issn = {23527110},
|
||||
doi = {10.1016/j.softx.2015.06.001},
|
||||
abstract = {GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.},
|
||||
keywords = {\#nosource},
|
||||
file = {/home/bauer/Zotero/storage/W2EN24B4/Abraham et al_2015_GROMACS.pdf}
|
||||
}
|
||||
|
||||
@article{Alam2009,
|
||||
title = {High-Resolution Structure of the Open {{NaK}} Channel},
|
||||
author = {Alam, Amer and Jiang, Youxing},
|
||||
date = {2009-01-21},
|
||||
journaltitle = {Nature Structural \& Molecular Biology},
|
||||
volume = {16},
|
||||
number = {1},
|
||||
pages = {30--34},
|
||||
issn = {1545-9993},
|
||||
doi = {10.1038/nsmb.1531},
|
||||
abstract = {We report the crystal structure of the nonselective cation channel NaK from Bacillus cereus at a resolution of 1.6 Å . The structure reveals the intracellular gate in an open state, as opposed to the closed form reported previously, making NaK the only channel for which the three-dimensional structures of both conformations are known. Channel opening follows a conserved mechanism of inner helix bending using a flexible glycine residue, the gating hinge, seen in MthK and most other tetrameric cation channels. Additionally, distinct inter and intrasubunit rearrangements involved in channel gating are seen and characterized for the first time along with inner helix twisting motions. Furthermore, we identify a residue deeper within the cavity of the channel pore, Phe92, which is likely to form a constriction point within the open pore, restricting ion flux through the channel. Mutating this residue to alanine causes a subsequent increase in ion-conduction rates as measured by 86 Rb flux assays. The structures of both the open and closed conformations of the NaK channel correlate well with those of equivalent K + channel conformations, namely MthK and KcsA, respectively. The opening and closing of ion channel pores in response to external stimuli such as voltage or ligand binding is a process of extreme importance to ion channel physiology 1 . Until now, our knowledge of the open and closed conformations of tetrameric cation channel pores comes predominantly from the crystal structures of various K + channels, among which the structures of KcsA and MthK have been generally accepted as reasonable models for the closed and open conformations of tetrameric cation channel pores, respectively 2–9 . The closed conformation is characterized by near-straight inner helices and the subsequent bundle crossing that is formed by interactions between their C-terminal residues. In the open conformation seen in the MthK structure, the inner helices seem to bend at a conserved glycine residue, the gating hinge also seen in most other cation channels, resulting in the disruption of the bundle crossing. However, structural information on both states from the same channel has so far been lacking. In the process of studying the ion-selectivity properties of the NaK channel, which shares overall sequence and structural similarities with KcsA, except in the selectivity filter region, and conducts both Na + and K + (refs. 10,11), we crystallized a truncated construct (NaKND19) lacking its N-terminal M0 helix and determined its structure at a resolution of 1.6 Å . Unexpectedly, the NaKND19 structure reveals the intracellular gate in an open conformation. Combined with the closed conformation structure of NaK, the new structure provides a unique opportunity to analyze in detail the structural features underlying pore opening and closing within the same channel. We observe both inner helix twisting and bending at the glycine gating hinge upon pore opening. Our data clearly demonstrate the conservation of central sequence and structural motifs involved in channel opening, while also offering insight into the intricate rearrangements of interactions within and between channel subunits upon undergoing gating transi-tions. In addition, the high-resolution structures also allow us to carry out an analysis of the molecular details of ion binding in the NaK selectivity filter, which we report in our companion paper 12 .},
|
||||
keywords = {\#nosource},
|
||||
file = {/home/bauer/Zotero/storage/L33BLVLV/Alam_Jiang_2009_High-resolution structure of the open NaK channel.pdf}
|
||||
}
|
||||
|
||||
@article{Biggin2000,
|
||||
ids = {biggin2000},
|
||||
title = {Potassium Channel Structure: Domain by Domain},
|
||||
author = {Biggin, Phil C. and Roosild, Tarmo and Choe, Senyon},
|
||||
date = {2000-08},
|
||||
journaltitle = {Current Opinion in Structural Biology},
|
||||
volume = {10},
|
||||
number = {4},
|
||||
eprint = {10981635},
|
||||
eprinttype = {pmid},
|
||||
pages = {456--461},
|
||||
issn = {0959-440X},
|
||||
doi = {10.1016/S0959-440X(00)00114-7},
|
||||
abstract = {Since the determination of the structure of a bacterial potassium channel, the ion channel community has managed to gain momentum in the quest for a complete picture. The information is coming at a steady flow, on a domain by domain basis. Recent discoveries are starting to reveal clues to the complex manner in which potassium channels show enormous diversity of function and also to their methods of regulation. Currently, the structures of four domains are known, with the most recent addition being the Kv?? structure. As efforts continue in the study of the transmembrane domains, especially the voltage-sensing apparatus, there has been a new realization with respect to the identification and role of the cytoplasmic domains in protein-protein interactions in particular. An additional discovery, considerably aided by recent genomic analysis, is that potassium channels comprising subunits with two pore regions and four transmembrane helices combined in a dimeric fashion are abundant and are probable targets for local anesthetics.},
|
||||
isbn = {0959-440X (Print)},
|
||||
keywords = {Anesthetics,Beta subunit,BTB/POZ,Domains,KcsA,NAD,Potassium channels,Protein-protein interaction,Structure,T1},
|
||||
file = {/home/bauer/Zotero/storage/5KMKYJVX/Biggin et al_2000_Potassium channel structure.pdf;/home/bauer/Zotero/storage/KI98GGZ7/Biggin et al_2000_Potassium channel structure.pdf;/home/bauer/Zotero/storage/PG8BRYFT/S0959440X00001147.html}
|
||||
}
|
||||
|
||||
@book{book:1314973,
|
||||
title = {Handbook of Ion Channels},
|
||||
author = {Trudeau, Matthew C. and Zheng, Jie},
|
||||
date = {2015},
|
||||
edition = {1},
|
||||
publisher = {{CRC Press}},
|
||||
isbn = {978-1-4665-5142-8 1-4665-5142-9},
|
||||
file = {/home/bauer/Zotero/storage/A2UIWBQT/Trudeau_2015_Handbook of ion channels.pdf}
|
||||
}
|
||||
52
biblio.tex
Normal file
52
biblio.tex
Normal file
@@ -0,0 +1,52 @@
|
||||
%!TEX root = thesis.tex
|
||||
|
||||
% This is how the bibliography looks like without treatment
|
||||
% Pretty ugly because there is a lot of wasted space
|
||||
%\bibliography{testbib}{}
|
||||
%\bibliographystyle{plain}
|
||||
|
||||
|
||||
% Try to eliminate margins by putting bibliography into a tcolorbox
|
||||
|
||||
|
||||
% \tcolorboxenvironment{thebibliography}{
|
||||
% enhanced,
|
||||
% breakable,
|
||||
% check odd page,
|
||||
% toggle left and right,
|
||||
% grow to right by=\marginparwidth+\marginparsep,
|
||||
% toggle enlargement=evenpage,
|
||||
% notitle after break,
|
||||
% nobeforeafter,
|
||||
% sharp corners,
|
||||
% top=0pt,
|
||||
% before upper={\let\clearpage\relax},
|
||||
% fontupper=\Huge}
|
||||
\chapter{References}
|
||||
\vspace{-0.5cm}
|
||||
\begin{tcolorbox}[
|
||||
enhanced,
|
||||
enforce breakable,
|
||||
check odd page,
|
||||
toggle left and right,
|
||||
grow to right by=\marginparwidth+\marginparsep-0.4cm,
|
||||
toggle enlargement=evenpage,
|
||||
notitle after break,
|
||||
vfill before first,
|
||||
nobeforeafter,
|
||||
sharp corners,
|
||||
top=0pt,
|
||||
left=0pt,
|
||||
bottom=0pt,
|
||||
right=0pt,
|
||||
before upper={\let\clearpage\relax},
|
||||
fontupper=\Huge,
|
||||
opacityback=0,
|
||||
opacityframe=0,
|
||||
]
|
||||
% \begin{thebibliography}
|
||||
% bibliography
|
||||
% \addcontentsline{toc}{chapter}{References}
|
||||
\printbibliography[heading=none] %bibintoc,title={References}]
|
||||
|
||||
\end{tcolorbox}
|
||||
5
build.ninja
Normal file
5
build.ninja
Normal file
@@ -0,0 +1,5 @@
|
||||
rule latex
|
||||
command = latexmk -pdf -interaction=nonstopmode $tex
|
||||
|
||||
build thesis.pdf: latex abstract.tex acknowledgements.tex acronyms.tex appendix.tex biblio.tex config.tex frontpages.tex thesis.tex biblio.bib tufte-common.def tufte-book.cls
|
||||
tex = thesis.tex
|
||||
477
config.tex
Normal file
477
config.tex
Normal file
@@ -0,0 +1,477 @@
|
||||
%!TEX root = thesis.tex
|
||||
|
||||
\usepackage[english]{babel} % Load characters and hyphenation
|
||||
\usepackage{csquotes} % English quotes mess with biblatex quotes
|
||||
\usepackage{ccicons}
|
||||
\usepackage{todonotes}
|
||||
\usepackage{blindtext}
|
||||
\usepackage{amsmath,amssymb}
|
||||
\usepackage{textgreek}
|
||||
\usepackage{tikz}
|
||||
\usepackage{tocloft}
|
||||
\usepackage{siunitx}
|
||||
\usepackage{float}
|
||||
\usepackage{microtype}
|
||||
\usepackage{booktabs}
|
||||
\usepackage{texshade}
|
||||
\usepackage{morefloats}
|
||||
\usepackage{hyperref}
|
||||
\usepackage{hypcap}
|
||||
\usepackage{enumitem}
|
||||
\usepackage{xspace}
|
||||
\usepackage{hyphenat}
|
||||
\usepackage[most]{tcolorbox}
|
||||
\usepackage[noabbrev,nameinlink]{cleveref}
|
||||
|
||||
% required for certain inkscape exports
|
||||
\usepackage{xcolor}
|
||||
|
||||
\xspaceaddexceptions{]\}}
|
||||
|
||||
\usetikzlibrary{shapes,arrows,shapes.multipart}
|
||||
|
||||
|
||||
\sisetup{separate-uncertainty,range-units=single,group-separator = {,}}
|
||||
|
||||
% show a black bar when overfull
|
||||
% \overfullrule=2cm
|
||||
|
||||
% nonbreaking namerefs
|
||||
% \AtBeginDocument{
|
||||
% \let\oldnameref\nameref
|
||||
% \renewcommand\nameref[1]{\ref{#1}~\oldnameref{#1}}
|
||||
% }
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Disable warnings
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{silence}
|
||||
\WarningFilter{biblatex}{Patching footnotes}
|
||||
\WarningFilter{biblatex}{Name format 'last-first' deprecated}
|
||||
\WarningFilter{latex}{Marginpar on page}
|
||||
\WarningFilter{latexfont}{Font shape}
|
||||
\WarningFilter{latexfont}{Some font}
|
||||
\WarningFilter{latexfont}{Font shape}
|
||||
\WarningFilter{biblatex}{No driver for entry type 'software'}
|
||||
\WarningFilter{latex}{`!h' float specifier changed to `!ht'}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Acronyms
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage[nogroupskip,nopostdot,acronym,style=super,nonumberlist,nohypertypes={acronym},automake]{glossaries}
|
||||
\renewcommand*{\glsnamefont}[1]{#1}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% fonts
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{fontspec}
|
||||
% \setmainfont{TeX Gyre Pagella}
|
||||
% \usepackage[libertine,cmintegrals,cmbraces,vvarbb]{newtxmath}
|
||||
% \setmainfont{ETBembo}[
|
||||
% SmallCapsFont={Bembo Small Caps & Oldstyle Fig}
|
||||
% ]
|
||||
\setmainfont{Vollkorn}
|
||||
\setsansfont{Gillius ADF No2}
|
||||
% \setmonofont
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% hyperlinks
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\definecolor{hyperrefcolor}{rgb}{0.2, 0.5, 0.8} % matches pymol slate
|
||||
\hypersetup{
|
||||
colorlinks,
|
||||
allcolors=hyperrefcolor,
|
||||
}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% TOC Style
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% hide something from toc
|
||||
\newcommand{\changelocaltocdepth}[1]{%
|
||||
\addtocontents{toc}{\protect\setcounter{tocdepth}{#1}}%
|
||||
\setcounter{tocdepth}{#1}%
|
||||
}
|
||||
|
||||
% allows to specifically place chapters outside of parts
|
||||
\makeatletter
|
||||
\newcommand{\ChaptersOutsidePart}{%
|
||||
\addtocontents{toc}{\bigskip}
|
||||
\def\toclevel@chapter{-1}\def\toclevel@section{0}\def\toclevel@subsection{1}}
|
||||
\newcommand{\ChaptersInsidePart}{%
|
||||
\def\toclevel@chapter{0}\def\toclevel@section{1}\def\toclevel@subsection{2}}
|
||||
\makeatother
|
||||
|
||||
% TOC style
|
||||
\setlength{\cftbeforechapskip}{0pt}
|
||||
\setlength{\cftbeforepartskip}{10pt}
|
||||
\renewcommand\cftpartfont{\sc\bfseries}
|
||||
\renewcommand\cftchapfont{\small\sc}
|
||||
\renewcommand\cftsecfont{\small}
|
||||
\renewcommand\cftsubsecfont{\small}
|
||||
\renewcommand\cftsubsubsecfont{\small}
|
||||
|
||||
% \renewcommand\cftpartafterpnum{\vspace{-10pt}}
|
||||
|
||||
% Titles of TOC, LOF, LOT
|
||||
\renewcommand\cfttoctitlefont{\vspace{-2.5cm}\relax\huge\rmfamily}
|
||||
\renewcommand\cftaftertoctitle{\vspace{0.35em}}
|
||||
\renewcommand\cftloftitlefont{\vspace{-2.5cm}\relax\huge\rmfamily}
|
||||
\renewcommand\cftafterloftitle{\vspace{0.35em}}
|
||||
\renewcommand\cftlottitlefont{\relax\huge\rmfamily}
|
||||
\renewcommand\cftafterlottitle{\vspace{0.35em}}
|
||||
|
||||
|
||||
\hypersetup{linktocpage} % TOC link on page number
|
||||
|
||||
\setcounter{tocdepth}{1} % number of sections in the toc
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% biblatex
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{hyphenat} % required bc. biblatex uses \nohyphenations
|
||||
\usepackage[
|
||||
backend=biber,
|
||||
style=authoryear,
|
||||
maxnames=3,
|
||||
minbibnames=6,
|
||||
maxbibnames=6,
|
||||
sorting=nyt,
|
||||
isbn=false,
|
||||
doi=true,
|
||||
url=false,
|
||||
backref,
|
||||
giveninits=true, % initials for first names
|
||||
uniquelist=true,
|
||||
uniquename=init,
|
||||
dashed=false, % do not use dashes for same author names
|
||||
]{biblatex}
|
||||
\addbibresource{biblio.bib}
|
||||
\addbibresource{publications.bib}
|
||||
|
||||
% environment with supressed letters after the year for my reference section
|
||||
% https://tex.stackexchange.com/questions/63500/suppress-year-label-letter-in-biblatex-author-year-styles-on-a-per-bibliography
|
||||
\defbibenvironment{nodis}
|
||||
{\list
|
||||
{}
|
||||
{\setlength{\leftmargin}{\bibhang}%
|
||||
\setlength{\itemindent}{-\leftmargin}%
|
||||
\setlength{\itemsep}{\bibitemsep}%
|
||||
\setlength{\parsep}{\bibparsep}}}
|
||||
{\endlist}
|
||||
{\clearfield{extradate}\item}
|
||||
|
||||
|
||||
% my papers section settings
|
||||
\DeclareRefcontext{mypaper}{sorting=none}
|
||||
|
||||
% Reverse names for all authors
|
||||
\DeclareNameAlias{sortname}{last-first}
|
||||
|
||||
% Make title in bibliography link to the doi
|
||||
\newbibmacro{string+doi}[1]{%
|
||||
\iffieldundef{doi}{#1}{\href{http://dx.doi.org/\thefield{doi}}{#1}}}
|
||||
% \DeclareFieldFormat{title}{\usebibmacro{string+doi}{\mkbibemph{#1}}}
|
||||
\DeclareFieldFormat{title}{\usebibmacro{string+doi}{#1}}
|
||||
\DeclareFieldFormat[article]{title}{\usebibmacro{string+doi}{#1}}
|
||||
|
||||
% newline after author (year)
|
||||
\DeclareDelimFormat[bib]{nametitledelim}{\newline\bibsentence}
|
||||
|
||||
% spacing between entries
|
||||
\setlength\bibitemsep{1.5\itemsep}
|
||||
|
||||
% Only years for dates
|
||||
\AtEveryBibitem{\clearfield{month}}
|
||||
\AtEveryBibitem{\clearfield{day}}
|
||||
|
||||
% No pmid
|
||||
\AtEveryBibitem{\clearfield{eprint}}
|
||||
|
||||
% No editors, translators, ...
|
||||
\renewbibmacro*{byeditor+others}{}
|
||||
|
||||
% Supress the in: in references
|
||||
\renewbibmacro{in:}{}
|
||||
|
||||
% Annotate authors
|
||||
% last name
|
||||
\renewcommand*{\mkbibnamefamily}[1]{
|
||||
\ifitemannotation{highlight}
|
||||
{\textbf{#1}}%
|
||||
{\ifitemannotation{highfirst}
|
||||
{\textbf{#1}}%
|
||||
{#1}%
|
||||
}
|
||||
}%%
|
||||
% first name
|
||||
\renewcommand*{\mkbibnamegiven}[1]{
|
||||
\ifitemannotation{highlight}
|
||||
{\textbf{#1}}%
|
||||
{\ifitemannotation{highfirst}
|
||||
{\textbf{#1}}%
|
||||
{#1}
|
||||
}%
|
||||
\ifitemannotation{first}
|
||||
{*}
|
||||
{\ifitemannotation{highfirst}
|
||||
{\textbf{*}}
|
||||
{}
|
||||
}%
|
||||
}%%
|
||||
|
||||
% backreference string
|
||||
\DefineBibliographyStrings{english}{%
|
||||
backrefpage = {cited on p\adddot},%
|
||||
backrefpages = {cited on pp\adddot}%
|
||||
}
|
||||
|
||||
% no header for bibleography
|
||||
\defbibheading{secbib}[\bibname]{%
|
||||
\section*{#1}%
|
||||
\markboth{#1}{#1}}
|
||||
|
||||
% marginnnote with a reduced citing format:
|
||||
% Authors (year), Title. Year links to bibliography
|
||||
\DeclareCiteCommand{\customcite}
|
||||
{\boolfalse{citetracker}% precode
|
||||
\boolfalse{pagetracker}%
|
||||
\usebibmacro{prenote}}
|
||||
{\ifciteindex % loopcode (the actual formatting)
|
||||
{\indexnames{labelname}%
|
||||
\indexfield{indextitle}}
|
||||
{}%
|
||||
\printtext{%
|
||||
\printnames{labelname}%
|
||||
\setunit{\addspace}
|
||||
\printtext[parens]{\printfield[bibhyperref]{year}}% year links to references
|
||||
% \setunit{\labelnamepunct}%
|
||||
% \printfield[citetitle]{labeltitle}%
|
||||
}%
|
||||
}
|
||||
{\multicitedelim} % sepcode: a comma usually
|
||||
{\usebibmacro{postnote}\printtext{\adddot}} % endcode: finish with a dot
|
||||
|
||||
|
||||
% marginnnote with a reduced citing format:
|
||||
% Authors (year), Title. Year links to bibliography
|
||||
\DeclareCiteCommand{\inlinecite}
|
||||
{\boolfalse{citetracker}% precode
|
||||
\boolfalse{pagetracker}%
|
||||
\usebibmacro{prenote}}
|
||||
{\ifciteindex % loopcode (the actual formatting)
|
||||
{\indexnames{labelname}%
|
||||
\indexfield{indextitle}}
|
||||
{}%
|
||||
\printtext{%
|
||||
\printnames{labelname}%
|
||||
\setunit{\addspace}
|
||||
\printtext[parens]{\printfield[bibhyperref]{year}}% year links to references
|
||||
% \setunit{\labelnamepunct}%
|
||||
% \printfield[citetitle]{labeltitle}%
|
||||
}%
|
||||
}
|
||||
{\multicitedelim} % sepcode: a comma usually
|
||||
{\usebibmacro{postnote}\printtext{}} % endcode: finish with a dot
|
||||
|
||||
|
||||
% normal citation -> margin
|
||||
\renewcommand{\cite}[2][0pt]{\sidenote[][#1]{\customcite{#2}}}
|
||||
% inline citation
|
||||
\newcommand{\icite}[2][]{\customcite[#1]{#2}}
|
||||
|
||||
% explanation of a word/phrase
|
||||
\newcommand{\explanation}[2][0pt]{*\marginnote[#1]{*#2}}
|
||||
|
||||
% easier sub and superscripts
|
||||
\newcommand{\sups}[1]{\textsuperscript{#1}}
|
||||
\newcommand{\subs}[1]{\textsubscript{#1}}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Utility functions
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
%% include tex with embedded pdf
|
||||
\newcommand{\pdftex}[2][0.975\textwidth]{
|
||||
\scriptsize\sffamily\selectfont
|
||||
\def\svgwidth{#1}
|
||||
\input{#2}
|
||||
}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% headings
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% headline
|
||||
\newcommand\HUGE{\fontsize{26}{26}\selectfont}
|
||||
\newcommand\CHAPTERSIZE{\fontsize{16}{10}\selectfont}
|
||||
\titleformat{\chapter}%
|
||||
[display]% shape
|
||||
{\vspace{-2.5cm}\relax\begin{fullwidth}}% format applied to label+text
|
||||
{\CHAPTERSIZE \rmfamily\scshape Chapter \thechapter}% label
|
||||
{-1em}% horizontal separation between label and title body
|
||||
{\HUGE\rmfamily}% before the title body
|
||||
[\end{fullwidth}\vspace{-2em}]% after the title body
|
||||
|
||||
% Indent for section number number
|
||||
\titlespacing*{\section}{0pt}{0pt}{0pt}
|
||||
\titleformat{\section}%
|
||||
[hang]% shape
|
||||
{\normalfont\scshape}% format applied to label+text
|
||||
{\thesection\hfill}
|
||||
{1em}% horizontal separation between label and title body
|
||||
{\normalfont\scshape}% before the title body
|
||||
[]% after the title body
|
||||
|
||||
\titlespacing*{\subsection}{0pt}{0pt}{0pt}
|
||||
\titleformat{\subsection}%
|
||||
[hang]% shape
|
||||
{\normalfont\scshape}% format applied to label+text
|
||||
{\thesubsection\hfill}% label
|
||||
{1em}% horizontal separation between label and title body
|
||||
{\normalfont}% before the title body
|
||||
[]% after the title body
|
||||
|
||||
\titleformat{\paragraph}
|
||||
[hang]
|
||||
{\normalfont}
|
||||
{\thesubsubsection}
|
||||
{0em}
|
||||
{\normalfont}
|
||||
[\vspace{-1em}]
|
||||
|
||||
% number of sections that become a counter
|
||||
\setcounter{secnumdepth}{2}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Ref Names
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\creflabelformat{equation}{#2\textup{#1}#3}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Page Style
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% remove paragraph indentation
|
||||
\makeatletter
|
||||
% Paragraph indentation and separation for normal text
|
||||
\renewcommand{\@tufte@reset@par}{%
|
||||
\setlength{\RaggedRightParindent}{0.0pc}%
|
||||
\setlength{\JustifyingParindent}{0.0pc}%
|
||||
\setlength{\parindent}{0pc}%
|
||||
\setlength{\parskip}{\baselineskip}%
|
||||
}
|
||||
\@tufte@reset@par
|
||||
|
||||
% Paragraph indentation and separation for marginal text
|
||||
\renewcommand{\@tufte@margin@par}{%
|
||||
\setlength{\RaggedRightParindent}{0.0pc}%
|
||||
\setlength{\JustifyingParindent}{0.0pc}%
|
||||
\setlength{\parindent}{0.0pc}%
|
||||
\setlength{\parskip}{10pt}%
|
||||
}
|
||||
\makeatother
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Quick fix for xelatex (authors forgot it in tufte)
|
||||
% see https://tex.stackexchange.com/questions/200722/xetex-seems-to-break-headers-in-tufte-handout
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\ifxetex
|
||||
\renewcommand{\textls}[2][5]{%
|
||||
\begingroup\addfontfeatures{LetterSpace=#1}#2\endgroup
|
||||
}
|
||||
\renewcommand{\allcapsspacing}[1]{\textls[15]{#1}}
|
||||
\renewcommand{\smallcapsspacing}[1]{\textls[10]{#1}}
|
||||
\renewcommand{\allcaps}[1]{\textls[15]{\MakeTextUppercase{#1}}}
|
||||
\renewcommand{\smallcaps}[1]{\smallcapsspacing{\scshape\MakeTextLowercase{#1}}}
|
||||
\renewcommand{\textsc}[1]{\smallcapsspacing{\textsmallcaps{#1}}}
|
||||
\fi
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Custom title page
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\makeatletter
|
||||
\newcommand{\fb}[1]{
|
||||
\def\@fb{#1}
|
||||
}
|
||||
\newcommand{\university}[1]{
|
||||
\def\@university{#1}
|
||||
}
|
||||
\newcommand{\refereeA}[1]{
|
||||
\def\@refereeA{#1}
|
||||
}
|
||||
\newcommand{\refereeB}[1]{
|
||||
\def\@refereeB{#1}
|
||||
}
|
||||
\newcommand{\location}[1]{
|
||||
\def\@location{#1}
|
||||
}
|
||||
|
||||
\usepackage{linegoal}% http://ctan.org/pkg/linegoal
|
||||
\usepackage{xparse}% http://ctan.org/pkg/xparse
|
||||
\NewDocumentCommand{\centerrule}{O{0.5ex} O{0.4pt}}{%
|
||||
\leavevmode\rule[#1]{\linegoal}{#2}
|
||||
}
|
||||
|
||||
\renewcommand{\maketitlepage}{
|
||||
\begin{fullwidth}
|
||||
\sffamily
|
||||
\centering
|
||||
{% top
|
||||
\includegraphics[width=3.5cm]{athene}\\
|
||||
\vspace{2pc}
|
||||
\centerrule
|
||||
\fontsize{24}{26}\selectfont\textcolor{darkgray}{\allcaps{\textrm{\thanklesstitle}}}\\
|
||||
\centerrule
|
||||
}
|
||||
\vspace{1pc}
|
||||
\doublespacing
|
||||
{% center
|
||||
\fontsize{14}{14}\selectfont
|
||||
\par
|
||||
dem Fachbereich \@fb\\
|
||||
der \@university\\
|
||||
\vspace{1.5pc}
|
||||
zur Erlangung des Grades\\
|
||||
Doctor rerum naturalium (Dr. rer. nat.)\\
|
||||
\vspace{2pc}
|
||||
vorgelegte Dissertation von\\
|
||||
\vspace{1pc}
|
||||
\Huge\selectfont\hspace{0.4cm}\textcolor{darkgray}{\allcaps{\textrm{\@author}}}
|
||||
}
|
||||
~\vfill
|
||||
{% bottom
|
||||
\begin{tabular}{ll}
|
||||
\fontsize{14}{14}\selectfont\par\noindent{Erstgutachter:} & \fontsize{14}{14}\selectfont\par\noindent{\@refereeA} \\
|
||||
\fontsize{14}{14}\selectfont\par\noindent{Zweitgutachter:} & \fontsize{14}{14}\selectfont\par\noindent{\@refereeB} \\
|
||||
\end{tabular}
|
||||
% \vspace{1pc}
|
||||
\fontsize{14}{14}\selectfont\par\noindent\allcaps{\@location~\the\year}
|
||||
}
|
||||
\end{fullwidth}
|
||||
\thispagestyle{empty}
|
||||
\clearpage
|
||||
}
|
||||
|
||||
\newcommand{\plainsubtitle}{}
|
||||
\newcommand{\subtitle}[1]{%
|
||||
\gdef\@subtitle{#1}%
|
||||
\renewcommand{\plainsubtitle}{#1}% use provided plain-text title
|
||||
\ifthenelse{\isundefined{\hypersetup}}%
|
||||
{}% hyperref is not loaded; do nothing
|
||||
{\hypersetup{pdftitle={\plaintitle: \plainsubtitle{}}}}% set the PDF metadata title
|
||||
}
|
||||
\makeatother
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% My page style
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{fancyhdr}
|
||||
% pagestyle that does not print anything
|
||||
\fancypagestyle{nothing}{
|
||||
\lhead{}
|
||||
\fancyhead[LE]{}
|
||||
\fancyhead[RO]{}
|
||||
}
|
||||
|
||||
% no numbers on part pages
|
||||
\patchcmd{\part}{\thispagestyle{plain}}{\thispagestyle{empty}}
|
||||
{}{\errmessage{Cannot patch \string\part}}
|
||||
\fancypagestyle{plain}{}
|
||||
BIN
deadlines.png
Normal file
BIN
deadlines.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 22 KiB |
34
frontpages.tex
Normal file
34
frontpages.tex
Normal file
@@ -0,0 +1,34 @@
|
||||
%!TEX root = thesis.tex
|
||||
\maketitle
|
||||
|
||||
% copyright stuff
|
||||
\newpage
|
||||
\pagestyle{empty}
|
||||
~\vfill
|
||||
|
||||
\begin{fullwidth}
|
||||
\begin{flushleft}
|
||||
This document was typeset with \href{http://xetex.sourceforge.net/}{Xe\TeX}
|
||||
and a modified version of \href{https://tufte-latex.github.io/tufte-latex}{Tufte-LaTeX}.
|
||||
The\\bibliography was managed with \href{https://www.zotero.org}{Zotero}
|
||||
and processed by \href{https://github.com/plk/biblatex}{Biblatex}.
|
||||
Used fonts were\\Vollkorn (serif), \textsf{Gillius~ADF~No2} (sans serif) and \texttt{TeX~Gyre~Cursor} (monospace).\\
|
||||
Figures and images were generated with \href{https://matplotlib.org}{Matplotlib},
|
||||
\href{https://pymol.org/2}{PyMOL}, and \href{https://chemaxon.com/products/marvin}{MarvinSketch}.
|
||||
|
||||
\textcolor{red}{Hans Wurst}: \plaintitle \\
|
||||
Darmstadt, Technische Universit\"at Darmstadt,\\
|
||||
Jahr der Ver\"offentlichung der Dissertation auf TUprints: xxxx\\
|
||||
URN: \href{http://nbn-resolving.de/urn:nbn:de:tuda-tuprints-xxxxxx}{urn:nbn:de:tuda-tuprints-xxxxx}\\
|
||||
Tag der m\"undlichen Pr\"ufung: xx.xx.xx\\
|
||||
~\\
|
||||
\textbf{\ccbysa~CC BY-SA 4.0 International} \\
|
||||
Attribution - ShareAlike 4.0 International\\
|
||||
\url{https://creativecommons.org/licenses/by-sa/4.0/}
|
||||
\end{flushleft}
|
||||
\end{fullwidth}
|
||||
|
||||
\input{abstract}
|
||||
|
||||
\newpage
|
||||
\cleardoublepage
|
||||
110
publications.bib
Normal file
110
publications.bib
Normal file
@@ -0,0 +1,110 @@
|
||||
%!TEX root = thesis.tex
|
||||
|
||||
@article{mypapermarini2018,
|
||||
title = {{HCN}1 mutation spectrum: from neonatal epileptic encephalopathy to benign generalized epilepsy and beyond},
|
||||
volume = {141},
|
||||
rights = {All rights reserved},
|
||||
issn = {0006-8950},
|
||||
url = {https://academic.oup.com/brain/article/141/11/3160/5142623},
|
||||
doi = {10.1093/brain/awy263},
|
||||
shorttitle = {{HCN}1 mutation spectrum},
|
||||
pages = {3160--3178},
|
||||
number = {11},
|
||||
journaltitle = {Brain},
|
||||
shortjournal = {Brain},
|
||||
author = {Marini, Carla and Porro, Alessandro and Rastetter, Agnès and Dalle, Carine and Rivolta, Ilaria and Bauer, Daniel and Oegema, Renske and Nava, Caroline and Parrini, Elena and Mei, Davide and Mercer, Catherine and Dhamija, Radhika and Chambers, Chelsea and Coubes, Christine and Thévenon, Julien and Kuentz, Paul and Julia, Sophie and Pasquier, Laurent and Dubourg, Christèle and Carré, Wilfrid and Rosati, Anna and Melani, Federico and Pisano, Tiziana and Giardino, Maria and Innes, A. Micheil and Alembik, Yves and Scheidecker, Sophie and Santos, Manuela and Figueiroa, Sonia and Garrido, Cristina and Fusco, Carlo and Frattini, Daniele and Spagnoli, Carlotta and Binda, Anna and Granata, Tiziana and Ragona, Francesca and Freri, Elena and Franceschetti, Silvana and Canafoglia, Laura and Castellotti, Barbara and Gellera, Cinzia and Milanesi, Raffaella and Mancardi, Maria Margherita and Clark, Damien R. and Kok, Fernando and Helbig, Katherine L. and Ichikawa, Shoji and Sadler, Laurie and Neupauerová, Jana and Laššuthova, Petra and Štěrbová, Katalin and Laridon, Annick and Brilstra, Eva and Koeleman, Bobby and Lemke, Johannes R. and Zara, Federico and Striano, Pasquale and Soblet, Julie and Smits, Guillaume and Deconinck, Nicolas and Barbuti, Andrea and {DiFrancesco}, Dario and {LeGuern}, Eric and Guerrini, Renzo and Santoro, Bina and Hamacher, Kay and Thiel, Gerhard and Moroni, Anna and {DiFrancesco}, Jacopo C. and Depienne, Christel},
|
||||
urldate = {2019-12-05},
|
||||
date = {2018-11-01},
|
||||
langid = {english},
|
||||
keywords = {mypaper},
|
||||
author+an = {6=highlight}
|
||||
}
|
||||
|
||||
@article{mypaperporro2019,
|
||||
title = {The {HCN} domain couples voltage gating and {cAMP} response in Hyperpolarization-activated Cyclic Nucleotide-gated channels},
|
||||
volume = {8},
|
||||
rights = {All rights reserved},
|
||||
issn = {2050-084X},
|
||||
url = {https://doi.org/10.7554/eLife.49672},
|
||||
doi = {10.7554/eLife.49672},
|
||||
pages = {e49672},
|
||||
journaltitle = {{eLife}},
|
||||
author = {Porro, Alessandro and Saponaro, Andrea and Gasparri, Federica and Bauer, Daniel and Gross, Christine and Pisoni, Matteo and Abbandonato, Gerardo and Hamacher, Kay and Santoro, Bina and Thiel, Gerhard and Moroni, Anna},
|
||||
editor = {Csanády, László},
|
||||
urldate = {2019-12-05},
|
||||
date = {2019-11-26},
|
||||
keywords = {mypaper},
|
||||
author+an = {4=highlight}
|
||||
}
|
||||
|
||||
@article{mypaperjenewein2020,
|
||||
title = {The mutation L69P in the {PAS} domain of the {hERG} potassium channel results in {LQTS} by trafficking deficiency},
|
||||
rights = {All rights reserved},
|
||||
volume = {13},
|
||||
number = {1},
|
||||
issn = {1933-6950, 1933-6969},
|
||||
url = {https://www.tandfonline.com/doi/full/10.1080/19336950.2020.1751522},
|
||||
doi = {10.1080/19336950.2020.1751522},
|
||||
pages = {163--174},
|
||||
journaltitle = {Channels},
|
||||
shortjournal = {Channels},
|
||||
author = {Jenewein, Tina and Kanner, Scott A. and Bauer, Daniel and Hertel, Brigitte and Colecraft, Henry M. and Moroni, Anna and Thiel, Gerhard and Kauferstein, Silke},
|
||||
urldate = {2020-04-09},
|
||||
date = {2020-04-07},
|
||||
langid = {english},
|
||||
keywords = {mypaper},
|
||||
author+an = {3=highlight}
|
||||
}
|
||||
|
||||
@article{mypaperhauf2020,
|
||||
title = {{GlyT}1 encephalopathy: Characterization of presumably disease causing {GlyT}1 mutations},
|
||||
volume = {139},
|
||||
rights = {All rights reserved},
|
||||
issn = {0197-0186},
|
||||
url = {http://www.sciencedirect.com/science/article/pii/S0197018620302047},
|
||||
doi = {10.1016/j.neuint.2020.104813},
|
||||
shorttitle = {{GlyT}1 encephalopathy},
|
||||
pages = {104813},
|
||||
journaltitle = {Neurochemistry International},
|
||||
shortjournal = {Neurochemistry International},
|
||||
author = {Hauf, K. and Barsch, L. and Bauer, D. and Buchert, R. and Armbruster, A. and Frauenfeld, L. and Grasshoff, U. and Eulenburg, V.},
|
||||
urldate = {2020-07-28},
|
||||
date = {2020-10-01},
|
||||
langid = {english},
|
||||
keywords = {Glycine, Encephalopathy, {GlyT}1, Neurotransmitter, Transporter, mypaper},
|
||||
author+an = {3=highlight}
|
||||
}
|
||||
@article{mypaperschmidt2021,
|
||||
title = {Inferring functional units in ion channel pores via relative entropy},
|
||||
volume = {50},
|
||||
rights = {All rights reserved},
|
||||
issn = {1432-1017},
|
||||
doi = {10.1007/s00249-020-01480-7},
|
||||
pages = {37--57},
|
||||
number = {1},
|
||||
journaltitle = {European biophysics journal},
|
||||
shortjournal = {Eur Biophys J},
|
||||
author = {Schmidt, Michael and Schroeder, Indra and Bauer, Daniel and Thiel, Gerhard and Hamacher, Kay},
|
||||
date = {2021-01-01},
|
||||
pmcid = {PMC7872957},
|
||||
pmid = {33523249},
|
||||
keywords = {mypaper, Anisotropic network model, Mechanical coupling relative entropy, Potassium channel (pores)},
|
||||
author+an = {3=highlight}
|
||||
}
|
||||
@article{mypapersaponaro2021,
|
||||
title = {Gating Movements and Ion Permeation in {HCN}4 Pacemaker Channels},
|
||||
volume = {81},
|
||||
number = {14},
|
||||
pages = {2929--2943.e6},
|
||||
rights = {{CC} {BY}-{NC}-{ND}},
|
||||
url = {https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00446-9},
|
||||
doi = {10.1016/j.molcel.2021.05.033},
|
||||
journaltitle = {Molecular Cell},
|
||||
shortjournal = {Mol. Cell.},
|
||||
author = {Saponaro, Andrea and Bauer, Daniel and Giese, M. Hunter and Swuec, Paolo and Porro, Alessandro and Gasparri, Federica and Sharifzadeh, Atiyeh Sadat and Chaves-Sanjuan, Antonio and Alberio, Laura and Parisi, Giacomo and Cerutti, Gabriele and Clarke, Oliver and Hamacher, Kay and Colecraft, Henry M. and Mancia, Filippo and Hendrickson, Wayne A. and Siegelbaum, Steven A. and {DiFrancesco}, Dario and Bolognesi, Martino and Thiel, Gerhard and Santoro, Bina and Moroni, Anna},
|
||||
date = {2021-07-01},
|
||||
langid = {english},
|
||||
doi = {10.1016/j.molcel.2021.05.033},
|
||||
keywords = {molecular dynamics, gating, cryo-{EM}, pacemaker, selectivity, pore, mypaper, {cAMP}, {HCN}4, permeation},
|
||||
author+an = {1=first; 2=highfirst; 3=first; 4=first}
|
||||
}
|
||||
BIN
thesis.pdf
Normal file
BIN
thesis.pdf
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Binary file not shown.
183
thesis.tex
Normal file
183
thesis.tex
Normal file
@@ -0,0 +1,183 @@
|
||||
% -*- Mode:TeX -*-
|
||||
%!TEX TS-program = xelatex
|
||||
%!TEX spellcheck = en-US
|
||||
\documentclass[a4paper,justified,titlepage,twoside,nobib,symmetric]{tufte-book}
|
||||
\usepackage{etoolbox}
|
||||
|
||||
\include{config}
|
||||
|
||||
\author[H. Wurst]{Hans Wurst}
|
||||
\title[Short thesis title]{Long thesis title}
|
||||
\subtitle{Thesis subtitle}
|
||||
\fb{Biologie}
|
||||
\university{Technischen Universit\"at Darmstadt}
|
||||
\refereeA{Prof. Dr. Musterprof}
|
||||
\refereeB{Prof. Dr. Musterprof2}
|
||||
\location{Darmstadt}
|
||||
|
||||
\DeclareSIUnit\ions{ions}
|
||||
\DeclareSIUnit\molar{M}
|
||||
\DeclareSIUnit\millimolar{mM}
|
||||
\DeclareSIUnit\electrons{e\textsuperscript{-}}
|
||||
|
||||
\include{acronyms}
|
||||
|
||||
\begin{document}
|
||||
\sloppy
|
||||
|
||||
% front
|
||||
\frontmatter
|
||||
\changelocaltocdepth{-1} % hide from toc
|
||||
\pagenumbering{roman}
|
||||
\include{frontpages}
|
||||
\phantomsection
|
||||
\addcontentsline{toc}{chapter}{Contents}
|
||||
\tableofcontents
|
||||
\newpage
|
||||
\phantomsection
|
||||
\addcontentsline{toc}{chapter}{\listfigurename}
|
||||
\listoffigures
|
||||
\phantomsection
|
||||
\addcontentsline{toc}{chapter}{\listtablename}
|
||||
\listoftables
|
||||
\changelocaltocdepth{1}
|
||||
|
||||
% % main text
|
||||
\mainmatter
|
||||
\pagenumbering{arabic}
|
||||
|
||||
\chapter{Prologue}
|
||||
\marginnote{\begin{quote}
|
||||
\textit{"... Ion channels are involved in \mbox{every} thought,
|
||||
every perception,
|
||||
every movement, every heartbeat."}\\
|
||||
\hspace*{\fill}- Clay M. Armstrong (1999)
|
||||
\end{quote}}
|
||||
|
||||
\blindtext
|
||||
\section{Thesis Outline}
|
||||
\blindtext
|
||||
Finally, some text with citations here.\cite{Abraham2015,Alam2009}
|
||||
|
||||
\section{Publications}
|
||||
The following thesis draws on the ideas and writing of the following published
|
||||
works. They are the result of my own research performed during my doctoral
|
||||
studies together with several coworkers and collaborators:
|
||||
\begin{refsection}
|
||||
\nocite{mypapermarini2018,mypaperporro2019,mypaperjenewein2020,mypaperhauf2020,mypaperschmidt2021,mypapersaponaro2021}
|
||||
\begin{refcontext}{mypaper}
|
||||
\vspace{-0.5cm}
|
||||
\printbibliography[keyword=mypaper,heading=none,env=nodis]
|
||||
\end{refcontext}
|
||||
\end{refsection}
|
||||
\begin{flushright}
|
||||
* indicates equal contribution.
|
||||
\end{flushright}
|
||||
|
||||
\chapter{Introduction}
|
||||
\blindtext
|
||||
\begin{figure}
|
||||
\includegraphics[width=0.98\linewidth]{deadlines.png}
|
||||
\caption{Taken from \href{https://www.phdcomics.com}{phdcomics.com}.
|
||||
Here is an inline reference that has nothing to do with the graphic: \customcite{book:1314973}.}
|
||||
\end{figure}
|
||||
\section{Section 1}
|
||||
\blindtext
|
||||
\begin{marginfigure}
|
||||
\includegraphics[width=0.98\linewidth]{cat.jpg}
|
||||
\caption{A cat.}
|
||||
\end{marginfigure}
|
||||
\subsection{Subsection 1}
|
||||
\blindtext
|
||||
\subsection{Subsection 2}
|
||||
\blindtext
|
||||
|
||||
\chapter{Results}
|
||||
\blindtext
|
||||
\section{Section 1}
|
||||
\blindtext
|
||||
\subsection{Subsection 1}
|
||||
\blindtext
|
||||
\subsection{Subsection 2}
|
||||
\blindtext
|
||||
|
||||
\chapter{Discussion}
|
||||
\blindtext
|
||||
\section{Section 1}
|
||||
\blindtext
|
||||
\subsection{Subsection 1}
|
||||
\blindtext
|
||||
\subsection{Subsection 2}
|
||||
\blindtext
|
||||
|
||||
|
||||
\backmatter
|
||||
% bibliography
|
||||
\ChaptersOutsidePart
|
||||
\include{biblio}
|
||||
\ChaptersInsidePart
|
||||
|
||||
\changelocaltocdepth{0}
|
||||
\begin{appendix}
|
||||
\part{Appendix}
|
||||
\chapter{Abbreviations}
|
||||
\vspace{-0.5cm}
|
||||
\begin{tcolorbox}[
|
||||
enhanced,
|
||||
enforce breakable,
|
||||
check odd page,
|
||||
toggle left and right,
|
||||
grow to right by=\marginparwidth+\marginparsep-0.4cm,
|
||||
toggle enlargement=evenpage,
|
||||
notitle after break,
|
||||
vfill before first,
|
||||
nobeforeafter,
|
||||
sharp corners,
|
||||
top=0pt,
|
||||
before upper={\let\clearpage\relax},
|
||||
opacityback=0,
|
||||
opacityframe=0,
|
||||
]
|
||||
|
||||
\renewcommand{\glossarysection}[2][]{} % no glossary title
|
||||
\printglossaries
|
||||
\end{tcolorbox}
|
||||
\chapter{Experimental details}
|
||||
\section*{How to build a flux compensator}
|
||||
\blindtext
|
||||
\section*{Some other Technical Stuff}
|
||||
\blindtext
|
||||
\blindtext
|
||||
\chapter{Additional data}
|
||||
\blindtext
|
||||
\end{appendix}
|
||||
|
||||
|
||||
% Thanks, CV, Erklärung
|
||||
\pagestyle{nothing}
|
||||
\ChaptersOutsidePart
|
||||
\begin{fullwidth}
|
||||
\include{acknowledgements}
|
||||
\chapter*{Ehrenwörtliche Erklärung} %Erklärung gemäß \S9(1) Promotionsordnung
|
||||
\addcontentsline{toc}{chapter}{Ehrenwörtliche Erklärung}
|
||||
|
||||
Ich erkläre hiermit, dass ich die vorliegende Arbeit
|
||||
entsprechend den Regeln guter wissenschaftlicher Praxis selbstständig und ohne
|
||||
unzulässige Hilfe Dritter angefertigt habe.
|
||||
|
||||
Sämtliche aus fremden Quellen direkt oder indirekt übernommenen Gedanken sowie
|
||||
sämtliche von Anderen direkt oder indirekt übernommenen Daten, Techniken und
|
||||
Materialien sind als solche kenntlich gemacht.
|
||||
Die Arbeit wurde bisher bei keiner anderen Hochschule zu Prüfungszwecken
|
||||
eingereicht.
|
||||
|
||||
Die eingereichte elektronische Version stimmt mit der schriftlichen Version
|
||||
überein.
|
||||
|
||||
\vspace{1cm}
|
||||
|
||||
\par\noindent\rule{6cm}{0.4pt} \\
|
||||
\strut \footnotesize Datum und Unterschrift \\
|
||||
\end{fullwidth}
|
||||
\ChaptersInsidePart
|
||||
\end{document}
|
||||
88
tufte-book.cls
Normal file
88
tufte-book.cls
Normal file
@@ -0,0 +1,88 @@
|
||||
\NeedsTeXFormat{LaTeX2e}[1994/06/01]
|
||||
|
||||
\ProvidesClass{tufte-book}[2015/06/30 v3.5.3 Tufte-book class]
|
||||
|
||||
%%
|
||||
% Declare we're tufte-book
|
||||
\newcommand{\@tufte@class}{book}% the base LaTeX class (defaults to the book style)
|
||||
\newcommand{\@tufte@pkgname}{tufte-book}% the name of the package (defaults to tufte-handout)
|
||||
|
||||
%%
|
||||
% Load the common style elements
|
||||
\input{tufte-common.def}
|
||||
|
||||
|
||||
%%
|
||||
% Set up any book-specific stuff now
|
||||
|
||||
%%
|
||||
% The front matter in Tufte's /Beautiful Evidence/ contains everything up
|
||||
% to the opening page of Chapter 1. The running heads, when they appear,
|
||||
% contain only the (arabic) page number in the outside corner.
|
||||
%\newif\if@mainmatter \@mainmattertrue
|
||||
\renewcommand\frontmatter{%
|
||||
\if@openright%
|
||||
\cleardoublepage%
|
||||
\else%
|
||||
\clearpage%
|
||||
\fi%
|
||||
\@mainmatterfalse%
|
||||
\pagenumbering{arabic}%
|
||||
%\pagestyle{plain}%
|
||||
\fancyhf{}%
|
||||
\ifthenelse{\boolean{@tufte@twoside}}%
|
||||
{\fancyhead[LE,RO]{\thepage}}%
|
||||
{\fancyhead[RE,RO]{\thepage}}%
|
||||
}
|
||||
|
||||
|
||||
%%
|
||||
% The main matter in Tufte's /Beautiful Evidence/ doesn't restart the page
|
||||
% numbering---it continues where it left off in the front matter.
|
||||
\renewcommand\mainmatter{%
|
||||
\if@openright%
|
||||
\cleardoublepage%
|
||||
\else%
|
||||
\clearpage%
|
||||
\fi%
|
||||
\@mainmattertrue%
|
||||
\fancyhf{}%
|
||||
\ifthenelse{\boolean{@tufte@twoside}}%
|
||||
{% two-side
|
||||
\renewcommand{\chaptermark}[1]{\markboth{##1}{}}%
|
||||
\fancyhead[LE]{\thepage\quad\smallcaps{\newlinetospace{\plaintitle}}}% book title
|
||||
\fancyhead[RO]{\smallcaps{\newlinetospace{\leftmark}}\quad\thepage}% chapter title
|
||||
}%
|
||||
{% one-side
|
||||
\fancyhead[RE,RO]{\smallcaps{\newlinetospace{\plaintitle}}\quad\thepage}% book title
|
||||
}%
|
||||
}
|
||||
|
||||
|
||||
%%
|
||||
% The back matter contains appendices, indices, glossaries, endnotes,
|
||||
% bibliographies, list of contributors, illustration credits, etc.
|
||||
\renewcommand\backmatter{%
|
||||
\if@openright%
|
||||
\cleardoublepage%
|
||||
\else%
|
||||
\clearpage%
|
||||
\fi%
|
||||
\@mainmatterfalse%
|
||||
}
|
||||
|
||||
%%
|
||||
% Only show the chapter titles in the table of contents
|
||||
\setcounter{tocdepth}{0}
|
||||
|
||||
%%
|
||||
% If there is a `tufte-book-local.sty' file, load it.
|
||||
|
||||
\IfFileExists{tufte-book-local.tex}{%
|
||||
\@tufte@info@noline{Loading tufte-book-local.tex}%
|
||||
\input{tufte-book-local}%
|
||||
}{}
|
||||
|
||||
%%
|
||||
% End of file
|
||||
\endinput
|
||||
2028
tufte-common.def
Normal file
2028
tufte-common.def
Normal file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user