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+\@writefile{lof}{\contentsline {figure}{\numberline {1.6}{\ignorespaces The beam path for an SEM (\subref  {fig:sem_setup_beam}). The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering and X-ray detector. A diagram showing electron matter interactions (\subref  {fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from~\cite  {SEM_image_01} and ~\cite  {SEM_image_02}.}}{13}{figure.caption.14}\protected@file@percent }
+\newlabel{fig:sem_setup}{{1.6}{13}{The beam path for an SEM (\subref {fig:sem_setup_beam}). The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering and X-ray detector. A diagram showing electron matter interactions (\subref {fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from~\cite {SEM_image_01} and ~\cite {SEM_image_02}}{figure.caption.14}{}}
 \citation{self_epitaxy}
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diff --git a/chap01.tex b/chap01.tex
index d19783d4be944144586903f7b3d40116eb5e0e81..1d34ed3142b1334f3ca3167bbb9c7255662e3fb4 100644
--- a/chap01.tex
+++ b/chap01.tex
@@ -3,41 +3,41 @@
 The Mask Aligner is used to create thin patterned films on samples with high accuracy. This chapter will introduce the required background behind the evaporation and explain the basic evaporation and alignment setup.
 
 \section{Electron beam evaporation}
-Electron beam evaporation, also known as \textbf{E}lectron-\textbf{b}eam \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (EBPVD) is a \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) technique that in vacuum or \textbf{U}ltra \textbf{H}igh \textbf{V}acuum (UHV) deposits material onto a substrates surface.
+Electron beam evaporation, also known as \textbf{E}lectron-\textbf{b}eam \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (EBPVD) is a \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) technique that in \textbf{U}ltra \textbf{H}igh \textbf{V}acuum (UHV) deposits material onto a substrates surface.
 
 \begin{figure}[H]
     \centering
     \includegraphics[width=0.5\linewidth]{img/EBeamDep.pdf}
-    \caption{Schematic diagram of a general electron beam evaporation chamber. The B-field is used to focus the beam onto the source. The shutter can interrupt the beam directed to the sample. The funnel is used to focus the vapor beam. }
+    \caption{Schematic of a general electron beam evaporation chamber. The B-field is used to focus the beam onto the source. The shutter can interrupt the beam directed to the sample. The funnel is used to focus the vapor beam. }
     \label{fig:e-beam_evap}
 \end{figure}
  
-The setup of an electron beam evaporator is shown in Figure \ref{fig:e-beam_evap}. The source material is placed inside a crucible as pellets of ultrapure ($>99$ \%) material.
-The crucible is also heated during the evaporation process, in order to prevent it from being damaged, a material with a high melting point is chosen. Tungsten with a melting point of 3695 K ~\cite{Tungsten_melt} is usually chosen. Additionally, the crucible usually has to be water cooled to avoid outgassing during the evaporation process.
+The setup of an electron beam evaporator is shown in Figure \ref{fig:e-beam_evap}. The source material is placed inside a tungsten crucible as pellets of ultrapure ($>99$ \%) material.
+%The crucible is also heated during the evaporation process, in order to prevent it from being damaged, a material with a high melting point is chosen. Tungsten with a melting point of 3695 K ~\cite{Tungsten_melt} is usually chosen. 
+%Additionally, the crucible usually has to be water cooled to avoid outgassing during the evaporation process.
 
-In order to heat the source material it is hit with a high voltage electron beam ($\mathcal{O}$($1$ kV)), emitted by either an electron gun or a filament. This beam usually is focused using magnetic fields to hit the source material. The highly energetic electrons interact chiefly with the atomic electrons of the source material and transfer energy. This energy transfer heats the hit atoms locally and eventually leads to the evaporation of atoms according to its vapor pressure.\\
+In order to heat the source material it is hit with a high voltage electron beam ($\mathcal{O}$($1$ kV)), emitted by either an electron gun or a filament. This beam usually is focused using magnetic fields to hit the source material. Energy transfer heats the hit atoms and eventually leads to the evaporation according to its vapor pressure.\\
 
 %The penetration depth of electron with ($<5$ kV) is less than 0.4 $\mu$m (estimated using CASINO Monte Carlo software)~\cite{CASINO} so the heating occurs only very near to the source material's surface. This allows for less energy loss and more controlled evaporation as the crucible and the rest of the system is not heated by the electron beam directly, but only by the radiant heat emitted by the source material.\\
 
-When the material's vapor pressure exceeds the surrounding environments pressure, a vapor forms. It is directed through a funnel to the sample's surface. The sample is kept at a temperature much colder than the source material's temperature, due to this the material beam will condense on the substrate's surface forming a thin film. \\
+When the material's vapor pressure exceeds the surrounding environments pressure, a vapor forms. The sample is kept at a temperature much colder than the source material's temperature, due to this the material beam will condense on the substrate's surface forming a thin film. \\
 
 In order to ensure the material beam reaches the sample in a direct path, the mean free path (MFP) of a traveling particle has to be larger than the distance to the sample's surface. For this reason, high vacuum (HV) (MFP of $10$ cm to $1$ km) or ultra-high vacuum conditions (UHV) (MFP of $1$ km to $10^5$ km) are used.
 
-The deposition rate of the evaporator can be measured using a molecular flux monitor or a quartz balance. The deposition rate of a material is described by the Hertz-Knudsen equation:
+The deposition rate of the evaporator can be measured using a molecular flux monitor. The deposition rate of a material is described by the Hertz-Knudsen equation:
 \begin{equation}
 	\frac{dN}{A dt} = \frac{\alpha (p_\text{e} - p)}{\sqrt{2 \pi m k_\text{B} T}}
 	\label{eq:hertz_knudsen}
 \end{equation}
 
-where $N$ is the number of gas molecules deposited, $A$ is the surface area, $t$ is time, $\alpha$ is the sticking coefficient, $p$ is the gas pressure of the impinging gas, $m$ is the mass of a single particle, $k_\text{B}$ is the Boltzmann constant, $p_\text{e}$ is the vapor pressure of the material at the sample temperature and $T$ is the temperature~\cite{knudsen}. The sticking parameter of a material can be looked up in literature. With this, the total deposition rate can then be estimated. In practice since the pressure of the impinging gas is difficult to determine this is difficult to estimate. Instead, usually calibration evaporations are performed for different heating powers and different times to determine the deposition rate for a given setup.
+where $N$ is the number of gas molecules deposited, $A$ is the surface area, $t$ is time, $\alpha$ is the sticking coefficient, $p$ is the gas pressure of the impinging gas, $m$ is the mass of a single particle, $k_\text{B}$ is the Boltzmann constant, $p_\text{e}$ is the vapor pressure of the material at the sample temperature and $T$ is the temperature~\cite{knudsen}. The sticking parameter of a material can be looked up in literature. With this, the total deposition rate can then be estimated. In practice since the pressure of the impinging gas is difficult to determine this is difficult to estimate, since it requires precise knowledge on the temperature of the source, that is typically not measured. Instead, usually calibration evaporations are performed for different heating powers and different times to determine the deposition rate for a given setup.
 
 Comparing e-beam evaporation with so-called sputtering of material onto a surface, it offers more controlled deposition~\cite{Vapor_depo_princ}. In sputtering, high energy particles are produced hitting the sample, which can lead to local roughening~\cite{sputter_damage}.
 In contrast to thermal evaporation, where the source is typically heated by Joule heating from a resistive current, higher temperatures are available with e-beam evaporation. This is required, e.g. for \ce{NB}~\cite{tungsten_evaporation}.
-
-In order to control the duration of the evaporation, a shutter is usually included. It can be closed or opened to control when the sample is exposed to the vapor beam. This is also needed for improved deposition rate accuracy, since the source material needs to initially heat up when the electron beam is started, which leads to unstable flux at the start of the evaporation. 
+A shutter is used to control the controls the deposition of the material.
 
 \section{Stencil lithography}
-Stencil lithography is a method of depositing patterned structures on a nanometer scale on substrates (sample) using a stencil. The stencil is typically made of a membrane of \ce{SiN} that is patterned with a lithography process, such as electron beam lithography. Using e-beam lithography, masks can be produced at sub micrometer scales. \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) processes are used to deposit material, through the mask onto the substrate's surface, while the mask is placed above the sample. The molecular beam only reaches the sample through holes in the mask. In this way, a pattern is transferred from the mask to the sample. \\
+Stencil lithography is a method of depositing patterned structures on a nanometer scale on substrates (sample) using a stencil. The stencil is typically made of a membrane of \ce{SiN} that is patterned with a lithography process, such as electron beam lithography. Using e-beam lithography, masks can be produced at sub micrometer scales. \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) processes are used to deposit material. The mask is placed closed to the substrates surface. The molecular beam only reaches the sample through holes in the mask. In this way, a pattern is transferred from the mask to the sample. \\
 Stencil Lithography can also be used for etching where patterns are carved into the substrate's surface, using reactive ion etching. \\
 Stencil lithography requires no resist or other chemical treatment of the sample and thus protects it from possible contamination. Masks can also be reused many times. The process is relatively simple and fast. In stencil lithography, the fabrication speed is only limited by the possible deposition rate and the complexity of applying the mask to the sample. \\
 While versatile since many patterns can be deposited or etched, stencil lithography comes with challenges. 
@@ -46,8 +46,6 @@ One of the biggest challenges is that in order to get sharp patterns on the subs
 
 The Mask Aligner in this work is a tool designed to overcome the challenge of sample mask alignment. It allows precise control of mask sample distance and angle. 
 
-\todo{Here}
-
 \subsubsection{Penumbra}
 The molecular beam, the evaporator generates, is not a set of perfectly parallel beams, rather it will be a spread of beams at slightly different angles. Its aperture is determined by the size of the crucible. It is $a=5$ mm for the setup found on the Mask Aligner. For the purposes of this explanation, the spread can be modeled by two extreme cones (Figure \ref{fig:penumbra_explanation}).\\
 
diff --git a/chap02.aux b/chap02.aux
index 3acc2e0bc03d3511e42fe40519e40aa755aecba2..404227292fa522f9261dc2443427c12144092333 100644
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 \citation{florian_forster}
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\ignorespaces Diagram showing a cross section of the mask at a gold pad location. A small tear in the \ce {SiO2} layer removes insulation between the gold wire and the Si of the mask. Parallel black lines depict plate capacitors illustratively. Larger plate shows larger capacitance. }}{35}{figure.caption.37}\protected@file@percent }
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-\@writefile{lot}{\contentsline {table}{\numberline {2.1}{\ignorespaces Table of cross capacitance measurement results. All measurements were carried out with the mask shuttle the Mask Aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII.}}{36}{table.caption.38}\protected@file@percent }
-\newlabel{tab:cross_cap}{{2.1}{36}{Table of cross capacitance measurement results. All measurements were carried out with the mask shuttle the Mask Aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII}{table.caption.38}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.20}{\ignorespaces The 3 capacitance curves of the Mask labeled "old", the plots look the same, sharing all features and general shape. The main difference is the scale of the y-axis, and due to this the scale of the uncertainty.}}{37}{figure.caption.39}\protected@file@percent }
-\newlabel{fig:mask_old_caps}{{2.20}{37}{The 3 capacitance curves of the Mask labeled "old", the plots look the same, sharing all features and general shape. The main difference is the scale of the y-axis, and due to this the scale of the uncertainty}{figure.caption.39}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.21}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less than $1$ \%.}}{38}{figure.caption.40}\protected@file@percent }
-\newlabel{fig:mask_old_correl}{{2.21}{38}{The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less than $1$ \%}{figure.caption.40}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.22}{\ignorespaces Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger.}}{39}{figure.caption.41}\protected@file@percent }
-\newlabel{fig:cross_cap_diagramm}{{2.22}{39}{Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger}{figure.caption.41}{}}
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-\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.1}Sample preparation}{40}{subsection.2.4.1}\protected@file@percent }
-\newlabel{sec:sample_prep}{{2.4.1}{40}{Sample preparation}{subsection.2.4.1}{}}
+\newlabel{fig:cross_cap_approach_difference}{{2.18a}{34}{\relax }{figure.caption.34}{}}
+\newlabel{sub@fig:cross_cap_approach_difference}{{a}{34}{\relax }{figure.caption.34}{}}
+\newlabel{fig:cross_cap_approach_difference_2}{{2.18b}{34}{\relax }{figure.caption.34}{}}
+\newlabel{sub@fig:cross_cap_approach_difference_2}{{b}{34}{\relax }{figure.caption.34}{}}
+\newlabel{fig:cross_cap_approach_sim}{{2.18c}{34}{\relax }{figure.caption.34}{}}
+\newlabel{sub@fig:cross_cap_approach_sim}{{c}{34}{\relax }{figure.caption.34}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces (\subref  {fig:cross_cap_approach_difference}, \subref  {fig:cross_cap_approach_difference_2}) approach curves of two example measurements of 2 different masks normalized to ensure the same scale. (\subref  {fig:cross_cap_approach_sim}) shows a simple simulation of the approach with tilted sample.}}{34}{figure.caption.34}\protected@file@percent }
+\newlabel{fig:cross_cap_approach}{{2.18}{34}{(\subref {fig:cross_cap_approach_difference}, \subref {fig:cross_cap_approach_difference_2}) approach curves of two example measurements of 2 different masks normalized to ensure the same scale. (\subref {fig:cross_cap_approach_sim}) shows a simple simulation of the approach with tilted sample}{figure.caption.34}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\ignorespaces Diagram showing a cross section of the mask at a gold pad location. A small tear in the \ce {SiO2} layer removes insulation between the gold wire and the Si of the mask. Parallel black lines depict plate capacitors illustratively. Larger plate shows larger capacitance. }}{35}{figure.caption.35}\protected@file@percent }
+\newlabel{fig:leakage_current}{{2.19}{35}{Diagram showing a cross section of the mask at a gold pad location. A small tear in the \ce {SiO2} layer removes insulation between the gold wire and the Si of the mask. Parallel black lines depict plate capacitors illustratively. Larger plate shows larger capacitance}{figure.caption.35}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.1}{\ignorespaces Table of cross capacitance measurement results. All measurements were carried out with the mask shuttle the Mask Aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII.}}{36}{table.caption.36}\protected@file@percent }
+\newlabel{tab:cross_cap}{{2.1}{36}{Table of cross capacitance measurement results. All measurements were carried out with the mask shuttle the Mask Aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII}{table.caption.36}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.20}{\ignorespaces The 3 capacitance curves of the Mask labeled "old". Of note is the difference in scale of the capacitance signal.}}{37}{figure.caption.37}\protected@file@percent }
+\newlabel{fig:mask_old_caps}{{2.20}{37}{The 3 capacitance curves of the Mask labeled "old". Of note is the difference in scale of the capacitance signal}{figure.caption.37}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.21}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within the same range. The lower plots show deviations from comparison curve. }}{37}{figure.caption.38}\protected@file@percent }
+\newlabel{fig:mask_old_correl}{{2.21}{37}{The 3 capacitance curves of the Mask labeled "old" scaled to be within the same range. The lower plots show deviations from comparison curve}{figure.caption.38}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.22}{\ignorespaces Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger.}}{38}{figure.caption.39}\protected@file@percent }
+\newlabel{fig:cross_cap_diagramm}{{2.22}{38}{Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger}{figure.caption.39}{}}
+\@writefile{toc}{\contentsline {paragraph}{Leakage current}{38}{section*.40}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Improved gold pin fitting}{38}{section*.41}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Image of gold pins}{39}{section*.42}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.7}Stop Conditions}{39}{subsection.2.3.7}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{High correlation between capacitance curves}{39}{section*.43}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Low correlation between capacitance curves}{39}{section*.44}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {2.4}Mask Aligner operation}{39}{section.2.4}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.1}Sample preparation}{39}{subsection.2.4.1}\protected@file@percent }
+\newlabel{sec:sample_prep}{{2.4.1}{39}{Sample preparation}{subsection.2.4.1}{}}
 \@setckpt{chap02}{
-\setcounter{page}{42}
+\setcounter{page}{41}
 \setcounter{equation}{4}
 \setcounter{enumi}{10}
 \setcounter{enumii}{0}
@@ -161,7 +160,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{4}
+\setcounter{@todonotes@numberoftodonotes}{2}
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diff --git a/chap02.tex b/chap02.tex
index 65caa78cc00dcfaf35ac7685dbe79427e3e121c3..a5d7ae17b6f8347508965d7219b642a9d010017f 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -14,14 +14,14 @@ path from the \ce{Pb} evaporator. BA stands for Bayard-Alpert pressure gauge. Th
     \label{fig:mask_aligner_chamber}
 \end{figure}
 
-The Mask Aligner vacuum system (Figure \ref{fig:mask_aligner_chamber}) consists of three areas chambers that can be separated with vacuum gate valves~\cite{Mask_Aligner}. The \textbf{M}ain \textbf{C}hamber (MC), the Mask Aligner (MA) chamber, and the evaporator chamber. The second one is the \textbf{L}oad \textbf{L}ock (LL), a vacuum suitcase that is used to insert new samples and masks into the system. The third part is used for pumping down the system to UHV pressures by use of a turbomolecular pump and a prepump (rotary vane). 
+The Mask Aligner vacuum system (Figure \ref{fig:mask_aligner_chamber}) consists of two areas that can be separated with vacuum gate valves~\cite{Mask_Aligner}. The \textbf{M}ain \textbf{C}hamber (MC), the Mask Aligner (MA) chamber, and the evaporator chamber. The second one is the \textbf{L}oad \textbf{L}ock (LL), a vacuum suitcase that is used to insert new samples and masks into the system. The system is pumped to UHV pressures by a turbomolecular pump and a prepump (rotary vane). 
 Between prepump and turbo molecular pump is a pressure sensor to determine if the prepump is providing suitable backing pressure. A valve to a nitrogen bottle allows the system to be vented with an inert gas to avoid contamination.\\
-The main chamber is equipped with an Ion Getter Pump, such that the system can be separated from the turbomolecular pump, without loss of UHV conditions. The pumping system is separated via $2$ \textbf{A}ll \textbf{M}etal \textbf{C}orner \textbf{V}alves (AMCV) (Fig. \ref{fig:mask_aligner_chamber}). Additionally, the Load Lock and the main chamber are separated by a Gate Valve. In order to detect leaks ort contaminants in the vacuum system, a mass spectrometer is attached to the main chamber. \\
-The Load Lock is equipped with a small ion getter pump, that runs on its own, allowing it to keep UHV conditions, even while separated from the main pump loop. A garage with spaces for up to $14$ samples ($10$: $12\times12$ cm$^2$, $4$: Omicron size) is part of the Load lock. Masks can also be stored in these, but require $2$ sample slots. For insertion and removal of masks and sample, a wobble stick is attached to the Load lock chamber. The path of the wobble stick to the Mask Aligner is marked \textcolor{tab_green}{green} in Figure \ref{fig:mask_aligner_chamber}. \\
-Another device, unrelated to this thesis, a gold evaporator, is connected to the vacuum system. It is not further discussed in this thesis, but is drawn in Figure \ref{fig:mask_aligner_chamber} since it was attached to the same system. \\
+The main chamber is equipped with an Ion Getter Pump, such that the Load Lock can be separated from the turbomolecular pump, without loss of UHV conditions. The pumping system is separated via $2$ \textbf{A}ll \textbf{M}etal \textbf{C}orner \textbf{V}alves (AMCV) (Fig. \ref{fig:mask_aligner_chamber}). Additionally, the Load Lock and the main chamber are separated by a Gate Valve. In order to detect leaks or contaminants in the vacuum system, a mass spectrometer is attached to the main chamber. \\
+The Load Lock is equipped with a small ion getter pump, that runs on its own, allowing it to keep UHV conditions, even while separated from the main pump loop. A garage with spaces for up to $14$ samples ($10$: $12\times12$ cm$^2$, $4$: Omicron size) is part of the Load lock. Masks require $2$ sample slots. For insertion and removal of masks and sample into the Mask Aligner, a wobble stick is attached to the Load lock chamber. The path of the wobble stick to the Mask Aligner is marked \textcolor{tab_green}{green} in Figure \ref{fig:mask_aligner_chamber}. \\
+Another device, unrelated to this thesis, a gold evaporator, is connected to the vacuum system. It is not further discussed in this thesis. \\
 
 \subsection{Lead evaporator}
-The electron beam evaporator used for the lead evaporation in the mask aligner chamber was built by Florian Forster in $2009$~\cite{florian_forster}. It is shown schematically in Figure \ref{fig:ma_evap}. The crucible is made from tungsten. The evaporator uses a filament placed near the crucible to bombard the crucible with highly energetic electrons. To accomplish this, a high voltage (up to $1$ kV) is applied between filament and crucible to accelerate electrons to the crucible. In addition, the system is heated by radiative heat from the filament. This heat is used to degas the evaporator and to prevent contaminants from settling on the filament, when no evaporation is taking place. The heating element and crucible are surrounded by a copper cylinder, that functions as a heat sink. The heat sink is water cooled to prevent outgassing of the surrounding due to heating by the filament or crucible. To control the temperature of the \ce{Cu} cylinder during degassing a thermal sensor is placed on the copper cylinder. \\
+The electron beam evaporator used for the lead evaporation in the mask aligner chamber was built by Florian Forster in $2009$~\cite{florian_forster}. It is shown schematically in Figure \ref{fig:ma_evap}. The evaporator uses a filament placed near the crucible to bombard the crucible with electrons. To accomplish this, a high voltage (up to $1$ kV) is applied between filament and crucible to accelerate electrons to the crucible. In addition, the system is heated by radiative heat from the filament current. The resulting heating power is linearly dependent on the voltage applied and quadratic in the current. This heat is used to degas the evaporator and to prevent contaminants from settling on the filament, when no evaporation is taking place. The filament and crucible are surrounded by a copper cylinder, that functions as a heat sink. The heat sink is water cooled to prevent outgassing of the surrounding due to heating by the filament or crucible. To control the temperature of the \ce{Cu} cylinder a thermal sensor is placed on the copper cylinder. \\
 
 \begin{figure}[H]
     \centering
@@ -30,7 +30,7 @@ The electron beam evaporator used for the lead evaporation in the mask aligner c
     \label{fig:ma_evap}
 \end{figure}
 
-In order to control the molecular flux, one can change the current applied to the filament or the voltage accelerating the electrons. Additionally, the crucible can be shifted on the z-axis closer to or further away from the filament. This method of temperature control is the least reliable and was not used in this thesis. The distance was previously optimized. In order to determine the flux current of $\text{Pb}^+$ ions leaving the crucible, it is measured by a flux monitor positioned at the top of the evaporator. Above the flux monitor is a shutter which can be used to open the molecular flux to the MA chamber. \\
+In order to control the molecular flux, one can change the current applied to the filament or the voltage accelerating the electrons. Additionally, the crucible can be shifted on the z-axis closer to or further away from the filament. This method of temperature control is the least reliable and was not used in this thesis. In order to determine the flux current of $\text{Pb}^+$ ions leaving the crucible, it is measured by a flux monitor positioned at the top of the evaporator. Above the flux monitor is a shutter which can be used to open the molecular flux to the MA chamber. \\
 
 \begin{figure}[H]
     \centering
@@ -56,15 +56,15 @@ beam path to the mask is displayed.}
 
 The Mask Aligner can be separated into 3 sections:
 The upper sample module (Fig. \ref{fig:mask_aligner_nomenclature_components}, A-G), the central mask module (Fig. \ref{fig:mask_aligner_nomenclature_components}, I-K) and the lower motor module (Fig. \ref{fig:mask_aligner_nomenclature_components}, L-Q). \\
-The sample module carries the sample and moves of the sample along the x direction. It contains a sliding rail (Fig. \ref{fig:mask_aligner_nomenclature_components} D) along which the sample stage (Fig. \ref{fig:mask_aligner_nomenclature_components}, E) can be moved, by $6$ piezo stacks (Fig. \ref{fig:mask_aligner_nomenclature_components}, B), labeled X in Fig. \ref{fig:mask_aligner_nomenclature_motors}. This setup is referred to as a motor. The sample holder is held with spring tension inside the sample stage (Fig. \ref{fig:mask_aligner_nomenclature_components}, G). Hence, it is fixed, but can be removed in-situ.  \\
+The sample module carries the sample and moves of the sample along the x direction. It contains a sliding rail (Fig. \ref{fig:mask_aligner_nomenclature_components} D) along which the sample stage (Fig. \ref{fig:mask_aligner_nomenclature_components}, E) can be moved. The sample holder is fixed with spring tension inside the sample stage (Fig. \ref{fig:mask_aligner_nomenclature_components}, G). It can be removed in-situ.  \\
 
-The mask module consists of the mask frame (Fig. \ref{fig:mask_aligner_nomenclature_components}, H), which holds the mask shuttle (Fig. \ref{fig:mask_aligner_nomenclature_components}, K) using spring tension. It also provides \ce{CuBe} contacts for the $3$ capacitance detectors on the mask used for capacitive distance measurement. The contacts are connected to shielded coaxial cables running to the vacuum feedthroughs. The shielding is ground to the Mask Aligner body (Fig. \ref{fig:mask_aligner_nomenclature_components}, Q). \\
+The mask module consists of the mask frame (Fig. \ref{fig:mask_aligner_nomenclature_components}, H), which holds the mask shuttle (Fig. \ref{fig:mask_aligner_nomenclature_components}, K). It also contacts the capacitance sensors on the mask using \ce{CuBe} leaf springs. The contacts are connected to shielded coaxial cables running to the vacuum feedthroughs. The shielding is ground to the Mask Aligner body (Fig. \ref{fig:mask_aligner_nomenclature_components}, Q). \\
 
-The motor module consists of $3$ piezo motors. They move the mask along the z axis via $3$ different pivot points. They are labeled Z1, Z2 and Z3 (Figure \ref{fig:mask_aligner_nomenclature_motors}). Each motor consists of a sapphire prism (Fig. \ref{fig:mask_aligner_nomenclature_components}, P) that is clamped by $6$ piezo stacks made up of $4$ piezo plates ($\approx 0.4$ nF) each. Four of the stacks are glued directly to the Mask Aligner body. The last two are attached to a metal plate (Fig. \ref{fig:mask_aligner_nomenclature_components}, O). It is pressed against the sapphire prism via a \ce{CuBe} leaf spring (Fig. \ref{fig:mask_aligner_nomenclature_components}, N). The tension of the \ce{CuBe} spring can be adjusted with a screw mounted on it. This adjustment is critical for the reliable operation of the piezo motor. On top of the sapphire prism, an \ce{Al2O3} plate (Fig. \ref{fig:mask_aligner_nomenclature_components}, M) is attached. It has a small groove in the center, where a neodymium magnet (Fig. \ref{fig:mask_aligner_nomenclature_components}, L) is located. It connects the motor to the mask frame, where a similar \ce{Al2O3} plate is placed. The three pivot points created by the magnets build an equilateral triangle, with the mask in the center. When only one sapphire prism moves up, the mask frame is tilted on the axis defined by the other two motors pivot points and the side of the mask moves closer to the sample. With the three motors arranged in a triangle arbitrary angles can be realized. Since the motor step size is $\approx 70$ nm the angular precision is approximately $\tan^{-1}(\frac{70 \text{ nm}}{23 \text{ mm}}) \approx 1.74 \times 10^{-4}^\circ$. \\
-Often the direction is specified by mathematical sign, where $-$ specifies the approach direction, while $+$ specifies retract (Fig. \ref{fig:mask_aligner_nomenclature_motors}).\\
+The motor module consists of $3$ piezo motors. They move the mask along the z axis via $3$ different pivot points. They are labeled Z1, Z2 and Z3 (Figure \ref{fig:mask_aligner_nomenclature_motors}). Each motor consists of a sapphire prism (Fig. \ref{fig:mask_aligner_nomenclature_components}, P) that is clamped by $6$ piezo stacks made up of $4$ piezo plates ($\approx 0.4$ nF) each. Four of the stacks are glued directly to the Mask Aligner body. The last two are attached to a metal plate (Fig. \ref{fig:mask_aligner_nomenclature_components}, O). It is pressed against the sapphire prism via a \ce{CuBe} leaf spring (Fig. \ref{fig:mask_aligner_nomenclature_components}, N). The tension of the \ce{CuBe} spring can be adjusted with a screw mounted on it. This adjustment is critical for the reliable operation of the piezo motor. On top of the sapphire prism, an \ce{Al2O3} plate (Fig. \ref{fig:mask_aligner_nomenclature_components}, M) is attached. It has a small groove in the center, where a neodymium magnet (Fig. \ref{fig:mask_aligner_nomenclature_components}, L) is located. It connects the motor to the mask frame, where a similar \ce{Al2O3} plate is placed. The three pivot points created by the magnets build an equilateral triangle, with the mask in the center. When only one motor moves up, the mask frame is tilted on the axis defined by the other two motors pivot points and the side of the mask moves closer to the sample. With the three motors arranged in a triangle arbitrary angles can be realized. Since the motor step size is $\approx 70$ nm the angular precision is approximately $\tan^{-1}(\frac{70 \text{ nm}}{23 \text{ mm}}) \approx 1.74 \times 10^{-4}$ degrees. \\
+The direction is specified by mathematical sign, where $-$ specifies the approach direction, while $+$ specifies retract (Fig. \ref{fig:mask_aligner_nomenclature_motors}).\\
 
 \section{Slip stick principle}
-In order to control the movement of the mask stage using the mask aligner, $3$ motors of $6$ piezo stack made of $4$ piezo crystals each are used. Piezo crystals expand/contract upon being supplied with a DC voltage. To enable the piezo crystals to move the stage, a sapphire prism is clamped between the $6$ piezo stacks. When one now applies a voltage amplitude to the piezo stacks, the prism is moved by the stacks. An illustration of the principle is shown in Figure \ref{fig:slip_stick_diagram}. \\
+In order to control the movement of the mask stage using the mask aligner, $3$ motors of $6$ piezo stacks each made up of $4$ piezo crystals are used. Piezo crystals expand/contract upon being supplied with a DC voltage. To enable the piezo crystals to move the stage, a sapphire prism is clamped between the $6$ piezo stacks. When one applies a voltage amplitude to the piezo stacks, the prism is moved by the stacks. An illustration of the principle is shown in Figure \ref{fig:slip_stick_diagram}. \\
 First a slowly rising pulse is applied to the piezo moving the prism along with the piezo. This pulse is referred to as the "slow flank". Afterward, a very fast pulse ($<1$ $\mu$s) is applied, contracting the piezo back into its original position. The prism however due to inertia remains in position. This pulse is referred to as the "fast flank". When repeated, the prism can be moved. The direction depends on the voltage amplitude signal polarity. The simplest pulse shape allowing for this is the saw tooth wave, but other signal shapes that follow the principle can be used.
 
 \begin{figure}[H]
@@ -104,9 +104,15 @@ An example for how the screw firmness affects the step size can be seen in Figur
 \subsection{Motor calibration}
 For the Mask Aligner, the step sizes, of the different motors have to be measured. In the best case they all have the same step size such that the mask is approached without being tilted. The step size calibration is used to determine the distance of mask and sample, when the distance is too small to be optically determined.\\
 
+In order to achieve this, a Bresser MicroCam II camera with a resolution of $20$ megapixel is
+mounted on a frame in front of the window of the mask aligner chamber. The
+frame can be positioned via 3 micrometer screws in x, y and z
+direction. Additionally, the camera can be rotated around $2$ axes allowing full
+control of the camera angle. \\
+
 The procedure for step size calibration is very simple: $2000$, $4000$,
 $6000$, $8000$ and $10000$ steps are driven and after each set of steps the distance
-the prism has traveled in camera view is measured. This is done with the Bresser MicroCam II software. In the software a line is drawn at the initial position. After driving another line is drawn at the end position. The distance between these are measured using the software. An example for motor Z1 and Z2 can be seen in Figure \ref{fig:calibration_uhv_example_driving} for a $1000$ step measurement. If changes to the motors have been performed a calibration has to be performed outside of UHV before reinsertion into UHV. Afterwards the motors have to be calibrated in UHV. \\
+the prism has traveled in the image of the camera is measured. This is done with the Bresser MicroCam II software. In the software a line is drawn at the initial position, from a remarkable point on the motor. After driving another line is drawn at the end position. The distance between these are measured using the software. An example for motor Z1 and Z2 can be seen in Figure \ref{fig:calibration_uhv_example_driving} for a $1000$ step measurement. If changes to the motors have been performed a calibration has to be performed outside of UHV before reinsertion into UHV. Afterwards the motors have to be calibrated in UHV. \\
 
 \begin{figure}[H]
     \centering
@@ -126,20 +132,16 @@ the prism has traveled in camera view is measured. This is done with the Bresser
     \label{fig:calibration_uhv_example_driving}
 \end{figure}
 
-For this measurement a specific remarkable point has to be found. The point has to be stable upon motor driving. After points are chosen, the lighting conditions must not be changed during the calibration, as this can hinder their visibility.\\
+%Outside UHV the best points are small scratches on the prisms
+%\ce{Al2O3} plate, since these are already in a focal plane with the motors.
+The distance measurement using the camera is calibrated by using an object of known size in the focal plane. One example that can be used are the \ce{Nd} magnets ($5$ mm diameter).
 
-Outside UHV the best points are small scratches on the prisms
-\ce{Al2O3} plate, since these are already in a focal plane with the motors.
-It is easy to determine their center since they are usually only a few
-pixels in diameter. The distance measurement using the camera is calibrated by using an object of known size in the focal plane. One example that can be used are the \ce{Nd} magnets ($5$ mm diameter).
-
-Inside UHV the process is more complicated, since only one camera angle is available. For Z1, the previously mentioned notches on the Z1 Motor itself can
-be chosen, but for the motors Z2 and Z3 this procedure is not possible because they cannot be directly seen. Instead, the 2
-screws very close to the motors are chosen (seen in Figure
+Inside UHV the process is more complicated, the motors Z2 and Z3 cannot be directly observed. Instead, the 2
+screws very close to the motors are (seen in Figure
 \ref{fig:calibration_uhv_points_of_interest}
-\subref{fig:calibration_uhv_points_of_interest_z2z3}) and their movement is observed. For camera calibration their diameter is chosen as this is also known to be $3$ mm. 
+\subref{fig:calibration_uhv_points_of_interest_z2z3}) observed. For camera calibration their diameter is chosen as this is also known to be $3$ mm. 
 The screws are a little closer to the camera than the motors themselves, this is accounted for by using a simple trigonometric model seen in Figure \ref{fig:calibration_screw_diff_explain}. 
-With this one gets that for each unit of distance the motor moves, the screws move by $h' = \frac{17.8}{23.74} \approx 0.75$. With this, the actual movement on the motor can be obtained. \\
+With this one gets that for each unit of distance the motor moves, the screws move by $h' = \frac{17.8}{23.74} \approx 0.75$. \\
 
 \begin{figure}[H]
     \centering
@@ -167,7 +169,7 @@ motors Z2/Z3, \textcolor{tab_red}{red:} screws on the motor plate that are close
     \label{fig:calibration_uhv_points_of_interest}
 \end{figure}
 
-A linear fit is performed for the given data and from the slope of the fit the step size for a single step is determined. The results are shown in Figure \ref{fig:calibration_example}. After each set of steps it has to be ensured, that the mask frame is not tilted. Excessive tilt will affect the step size. It should also be taken care that the movement range of the piezos is not exceeded. The \ce{Nd} magnets should not detach from the frame. Moreover, the sapphire prism can fall out of the motor if it is driven too far down. The measurement has to be done for both driving directions separately, since the step sizes will be different. Indeed, in Fig. \ref{fig:calibration_example} shows that the positive retract direction has consistently larger step sizes. The Z3 motor also shows a larger difference in step size for approach and retract than the other $2$ motors.
+A linear fit is performed for the given data. The slope gives the step size. Results are shown in Figure \ref{fig:calibration_example}. After each set of steps it has to be ensured, that the mask frame is not tilted. Excessive tilt will affect the step size. It should also be taken care that the movement range of the piezos is not exceeded. The \ce{Nd} magnets should not detach from the frame. Moreover, the sapphire prism can fall out of the motor if it is driven too far down. The measurement has to be done for both driving directions separately, since the step sizes will be different. Indeed, in Fig. \ref{fig:calibration_example} shows that the positive retract direction has consistently larger step sizes. The Z3 motor also shows a larger difference in step size for approach and retract than the other $2$ motors.
 
 \begin{figure}[H]
     \centering
@@ -188,18 +190,14 @@ seen in Figure \ref{fig:calibration_voltage}
 \end{figure}
 
 The behavior is linear in the voltage, but the slope is slightly different for
-each motor. An optimum, where all motors drive similarly appears at $80$ V. Also noticeable is a strong difference in slope for
+each motor. An optimum, where all motors drive similarly is at $80$ V. Also noticeable is a strong difference in slope for
 Z3. Z3 is much more influenced by voltage than the other motors, where the
 step size/V is larger by $\approx 0.3$. Variations in motor behavior can be compensated using this data. To do this different voltages would have to be applied to each channel. However, the current setup does not allow for this. Due to this new driving electronics are required.\\
 
 \subsection{Optical alignment}
 To align mask and sample one starts optically down to a precision of $50$ $\mu$m. The capacitance sensors provide only
-small signals, at large distances.\\
-In order to achieve this, a Bresser MicroCam II camera with a resolution of $20$ megapixel is
-mounted on a frame in front of the window of the mask aligner chamber. The
-frame can be positioned via 3 micrometer screws in x, y and z
-direction. Additionally, the camera can be rotated around $2$ axes allowing full
-control of the camera angle. The sample has to be aligned so that its surface normal
+small signals, at large distances. \\
+The sample has to be aligned so that its surface normal
 is perpendicular to the camera's view direction. No sample surface can be
 seen in camera view. No upwards tilt can be observed when viewing the side
 edge of the sample, and the upper side of the sample holder, cannot be observed. \\
@@ -233,7 +231,7 @@ placed or angled too low, (b) too high and (c) placed in good alignment. }
 \todo{Fix}
 
 When the camera is aligned with the sample, the mask can be moved close to
-the sample. A visible gap must remain between sample and mask (Fig. \ref{fig:optical_approach_a}). Then the mask is moved toward the sample until only a very small gap remains (Fig. \ref{fig:optical_approach}\subref{fig:optical_approach_b}, \subref{fig:optical_approach_c}). The length of the gap can
+the sample. A visible gap must remain between sample and mask (Fig. \ref{fig:optical_approach_a}). Then the mask is moved toward the sample until only a five pixel gap remains (Fig. \ref{fig:optical_approach}\subref{fig:optical_approach_b}, \subref{fig:optical_approach_c}). The length of the gap can
 be optically estimated using the Bresser software. Direct contact of the sample has to be avoided at this stage. This might require retraction and subsequent approach since the motors are not located directly beneath the mask. To calibrate the length scale of the camera the sample ($5940 \pm 20 $ $\mu$m) is chosen.
 In camera view direction, the mask and sample should now be aligned within
 achievable optical accuracy.
@@ -260,7 +258,6 @@ achievable optical accuracy.
 \end{figure}
 
 \newpage
-\todo{Start here}
 \subsection{Approach curves}
 
 After optical alignment, the mask is further aligned to the sample via capacitive measurement. The 3
diff --git a/chap03.aux b/chap03.aux
index 7b0399fa35bdb1f68197b130c6c1bda270a4465e..5377cb40c83f31383d9635c033d85834bba36b6e 100644
--- a/chap03.aux
+++ b/chap03.aux
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diff --git a/chap04.aux b/chap04.aux
index 5224486453d211e2562323794591f177deeaaf71..f420477f73b3866a9c9ec1c525f6a8e1dd404567 100644
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+++ b/chap04.aux
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+\newlabel{sub@fig:Front_plate_repair_tool}{{a}{61}{\relax }{figure.caption.72}{}}
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+\@writefile{lot}{\contentsline {table}{\numberline {4.1}{\ignorespaces The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}}{63}{table.caption.76}\protected@file@percent }
+\newlabel{tab:cross_cap_after_repair}{{4.1}{63}{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII}{table.caption.76}{}}
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diff --git a/chap05.aux b/chap05.aux
index 128b7b605cb2eeb1f3366d8490d5004f47e99d2b..8408bfec421aeebfbd5007c8f180d06a129f055e 100644
--- a/chap05.aux
+++ b/chap05.aux
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-\newlabel{tab:evaporation_settings}{{5.1}{67}{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}{table.caption.81}{}}
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index 672aafa6f190e4be1444550847c218b329ae907a..113700a7c4cddaf2e4f3909f75d441a45541a386 100644
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diff --git a/img/CameraAlignment_high.png b/img/CameraAlignment_high.png
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 \chapter*{Introduction}
 \addcontentsline{toc}{chapter}{Introduction}
 In condensed matter physics, precise fabrication of nanostructures with sharp patterns is paramount for research in various fields like electronics, photonics and quantum computing. One problem, that is highly sought after in quantum computing, is the creation of Majorana Zero Modes, as these could potentially provide a stable and controllable way to encode information. \textbf{M}ajorana \textbf{Z}ero \textbf{M}odes (MZM) are quasi particles that behave like Majorana fermions with non-Abelian statistics. MZMs are predicted to emerge at the core of vortices at superconductor/topological insulator interfaces~\cite{majorana_zero_modes}. These interfaces require pristine conditions and at the same time patterns, smaller than the coherence length ($<100$ nm) of the superconductor.\\
-
 Atmospheric conditions typically deteriorate surface properties of the required samples. Due to this \textbf{U}ltra \textbf{H}igh \textbf{V}accuum (UHV) conditions are required for the sample. This often limits the pattern creation process, as exposure to ambient conditions or other chemicals are required. \\
 
-Many methods like \textbf{E}lectron \textbf{B}eam \textbf{L}ithography or \textbf{E}xtreme \textbf{U}ltra\textbf{V}iolet \textbf{L}ithography (EUVL or EUV) give the required precision for patterning at the sub $100$ nm scale,~\cite{euv} but require resists, which typically are deposited with the help of solvents. These leave residues after the patterning process, which damage the pristine condition of the substrate. Typically, these methods can also not be performed under UHV conditions. \\
+Many methods like \textbf{E}lectron \textbf{B}eam \textbf{L}ithography (EBL) or \textbf{E}xtreme \textbf{U}ltra\textbf{V}iolet \textbf{L}ithography (EUVL or EUV) give the required precision for patterning at the sub $100$ nm scale,~\cite{euv} but require resists, which typically are deposited with the help of solvents. These leave residues after the patterning process, which damage the pristine condition of the substrate. Typically, these methods can also not be performed under UHV conditions. \\
 
 Other methods of patterning superconductors on topological insulators have been proposed, but many have shortcomings that make their use impractical. There are for example scanning probe approaches,~\cite{afm_pattern} which can directly manipulate single atoms on surfaces, but require 
 long timescales and expensive equipment. Additionally, many Scanning Probe approaches still require resists, leading to the same issues as previously mentioned.\\
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diff --git a/thesis.toc b/thesis.toc
index f2a2684f71271f7189297855564741f140258c8b..2f4a8501e427c8d52674322d6a7344c772c14910 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -1,15 +1,15 @@
 \contentsline {chapter}{Introduction}{3}{chapter*.2}%
 \contentsline {chapter}{\numberline {1}Mask Aligner background}{5}{chapter.1}%
 \contentsline {section}{\numberline {1.1}Electron beam evaporation}{5}{section.1.1}%
-\contentsline {section}{\numberline {1.2}Stencil lithography}{7}{section.1.2}%
-\contentsline {subsubsection}{Penumbra}{7}{section*.5}%
-\contentsline {subsubsection}{Tilt induced penumbra}{8}{section*.7}%
+\contentsline {section}{\numberline {1.2}Stencil lithography}{6}{section.1.2}%
+\contentsline {subsubsection}{Penumbra}{7}{section*.4}%
+\contentsline {subsubsection}{Tilt induced penumbra}{8}{section*.6}%
 \contentsline {section}{\numberline {1.3}Measurement techniques}{9}{section.1.3}%
 \contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{9}{subsection.1.3.1}%
-\contentsline {subsubsection}{Modes}{10}{section*.10}%
-\contentsline {paragraph}{Contact}{11}{section*.12}%
-\contentsline {paragraph}{Non-Contact}{11}{section*.13}%
-\contentsline {paragraph}{Tapping}{12}{section*.14}%
+\contentsline {subsubsection}{Modes}{10}{section*.9}%
+\contentsline {paragraph}{Contact}{11}{section*.11}%
+\contentsline {paragraph}{Non-Contact}{11}{section*.12}%
+\contentsline {paragraph}{Tapping}{12}{section*.13}%
 \contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{12}{subsection.1.3.2}%
 \contentsline {chapter}{\numberline {2}Mask Aligner}{15}{chapter.2}%
 \contentsline {section}{\numberline {2.1}Molecular beam evaporation chamber}{15}{section.2.1}%
@@ -21,99 +21,99 @@
 \contentsline {subsection}{\numberline {2.3.3}Optical alignment}{26}{subsection.2.3.3}%
 \contentsline {subsection}{\numberline {2.3.4}Approach curves}{28}{subsection.2.3.4}%
 \contentsline {subsection}{\numberline {2.3.5}Reproducibility}{32}{subsection.2.3.5}%
-\contentsline {subsubsection}{Reproducibility when removing sample/mask}{32}{section*.34}%
+\contentsline {subsubsection}{Reproducibility when removing sample/mask}{32}{section*.32}%
 \contentsline {subsection}{\numberline {2.3.6}Cross capacitances}{33}{subsection.2.3.6}%
-\contentsline {paragraph}{Leakage current}{39}{section*.42}%
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-\contentsline {subsection}{\numberline {2.3.7}Stop Conditions}{40}{subsection.2.3.7}%
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-\contentsline {paragraph}{Low correlation between capacitance curves}{40}{section*.46}%
-\contentsline {section}{\numberline {2.4}Mask Aligner operation}{40}{section.2.4}%
-\contentsline {subsection}{\numberline {2.4.1}Sample preparation}{40}{subsection.2.4.1}%
-\contentsline {chapter}{\numberline {3}Electronics}{42}{chapter.3}%
-\contentsline {section}{\numberline {3.1}RHK piezo motor controller}{42}{section.3.1}%
-\contentsline {subsection}{\numberline {3.1.1}Overview}{42}{subsection.3.1.1}%
-\contentsline {paragraph}{amplitude}{42}{section*.47}%
-\contentsline {paragraph}{sweep period}{42}{section*.48}%
-\contentsline {paragraph}{time between sweeps}{42}{section*.49}%
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-\contentsline {section}{\numberline {3.2}KIM001}{43}{section.3.2}%
-\contentsline {subsection}{\numberline {3.2.1}Overview}{43}{subsection.3.2.1}%
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-\contentsline {section}{\numberline {3.3}Mask Aligner controller "Walker"}{45}{section.3.3}%
-\contentsline {subsection}{\numberline {3.3.1}Overview}{45}{subsection.3.3.1}%
-\contentsline {subsection}{\numberline {3.3.2}Signal generation}{45}{subsection.3.3.2}%
-\contentsline {subsection}{\numberline {3.3.3}Fast flank}{47}{subsection.3.3.3}%
-\contentsline {subsection}{\numberline {3.3.4}Amplification}{47}{subsection.3.3.4}%
-\contentsline {subsection}{\numberline {3.3.5}Parameters}{48}{subsection.3.3.5}%
-\contentsline {paragraph}{Amplitude (amp)}{48}{section*.58}%
-\contentsline {paragraph}{Voltage (volt)}{48}{section*.59}%
-\contentsline {paragraph}{Channel}{48}{section*.60}%
-\contentsline {paragraph}{Max Step}{48}{section*.61}%
-\contentsline {paragraph}{Polarity}{48}{section*.62}%
-\contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{48}{subsection.3.3.6}%
-\contentsline {subsection}{\numberline {3.3.7}Driving the Mask Aligner}{50}{subsection.3.3.7}%
-\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{52}{chapter.4}%
-\contentsline {section}{\numberline {4.1}Overview}{52}{section.4.1}%
-\contentsline {section}{\numberline {4.2}General UHV device preparation}{53}{section.4.2}%
-\contentsline {subsection}{\numberline {4.2.1}Adding components}{53}{subsection.4.2.1}%
-\contentsline {subsection}{\numberline {4.2.2}Soldering}{53}{subsection.4.2.2}%
-\contentsline {section}{\numberline {4.3}Soldering anchors}{54}{section.4.3}%
-\contentsline {section}{\numberline {4.4}Piezo re-gluing}{57}{section.4.4}%
-\contentsline {section}{\numberline {4.5}Z3 motor}{59}{section.4.5}%
-\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{60}{subsection.4.5.1}%
-\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{63}{subsection.4.5.2}%
-\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{63}{section.4.6}%
-\contentsline {section}{\numberline {4.7}Final test}{65}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and measurement}{66}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Evaporation configuration}{66}{section.5.1}%
-\contentsline {section}{\numberline {5.2}Contamination}{68}{section.5.2}%
-\contentsline {section}{\numberline {5.3}Penumbra}{69}{section.5.3}%
-\contentsline {section}{\numberline {5.4}Tilt and deformation}{74}{section.5.4}%
-\contentsline {section}{\numberline {5.5}Simulation}{77}{section.5.5}%
-\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{77}{subsection.5.5.1}%
-\contentsline {subsection}{\numberline {5.5.2}Results}{79}{subsection.5.5.2}%
-\contentsline {subsection}{\numberline {5.5.3}Software improvements}{83}{subsection.5.5.3}%
-\contentsline {subsection}{\numberline {5.5.4}Final Remark}{84}{subsection.5.5.4}%
-\contentsline {chapter}{Conclusions and Outlook}{85}{chapter*.96}%
-\contentsline {chapter}{Bibliography}{87}{chapter*.97}%
-\contentsline {chapter}{List of Abbreviations}{90}{chapter*.98}%
-\contentsline {chapter}{Appendix}{i}{chapter*.99}%
+\contentsline {paragraph}{Leakage current}{38}{section*.40}%
+\contentsline {paragraph}{Improved gold pin fitting}{38}{section*.41}%
+\contentsline {subsection}{\numberline {2.3.7}Stop Conditions}{39}{subsection.2.3.7}%
+\contentsline {paragraph}{High correlation between capacitance curves}{39}{section*.43}%
+\contentsline {paragraph}{Low correlation between capacitance curves}{39}{section*.44}%
+\contentsline {section}{\numberline {2.4}Mask Aligner operation}{39}{section.2.4}%
+\contentsline {subsection}{\numberline {2.4.1}Sample preparation}{39}{subsection.2.4.1}%
+\contentsline {chapter}{\numberline {3}Electronics}{41}{chapter.3}%
+\contentsline {section}{\numberline {3.1}RHK piezo motor controller}{41}{section.3.1}%
+\contentsline {subsection}{\numberline {3.1.1}Overview}{41}{subsection.3.1.1}%
+\contentsline {paragraph}{amplitude}{41}{section*.45}%
+\contentsline {paragraph}{sweep period}{41}{section*.46}%
+\contentsline {paragraph}{time between sweeps}{41}{section*.47}%
+\contentsline {subsection}{\numberline {3.1.2}Pulse shape}{41}{subsection.3.1.2}%
+\contentsline {section}{\numberline {3.2}KIM001}{42}{section.3.2}%
+\contentsline {subsection}{\numberline {3.2.1}Overview}{42}{subsection.3.2.1}%
+\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{42}{subsection.3.2.2}%
+\contentsline {subsection}{\numberline {3.2.3}Voltage behavior}{43}{subsection.3.2.3}%
+\contentsline {section}{\numberline {3.3}Mask Aligner controller "Walker"}{44}{section.3.3}%
+\contentsline {subsection}{\numberline {3.3.1}Overview}{44}{subsection.3.3.1}%
+\contentsline {subsection}{\numberline {3.3.2}Signal generation}{44}{subsection.3.3.2}%
+\contentsline {subsection}{\numberline {3.3.3}Fast flank}{46}{subsection.3.3.3}%
+\contentsline {subsection}{\numberline {3.3.4}Amplification}{46}{subsection.3.3.4}%
+\contentsline {subsection}{\numberline {3.3.5}Parameters}{47}{subsection.3.3.5}%
+\contentsline {paragraph}{Amplitude (amp)}{47}{section*.56}%
+\contentsline {paragraph}{Voltage (volt)}{47}{section*.57}%
+\contentsline {paragraph}{Channel}{47}{section*.58}%
+\contentsline {paragraph}{Max Step}{47}{section*.59}%
+\contentsline {paragraph}{Polarity}{47}{section*.60}%
+\contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{47}{subsection.3.3.6}%
+\contentsline {subsection}{\numberline {3.3.7}Driving the Mask Aligner}{49}{subsection.3.3.7}%
+\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{51}{chapter.4}%
+\contentsline {section}{\numberline {4.1}Overview}{51}{section.4.1}%
+\contentsline {section}{\numberline {4.2}General UHV device preparation}{52}{section.4.2}%
+\contentsline {subsection}{\numberline {4.2.1}Adding components}{52}{subsection.4.2.1}%
+\contentsline {subsection}{\numberline {4.2.2}Soldering}{52}{subsection.4.2.2}%
+\contentsline {section}{\numberline {4.3}Soldering anchors}{53}{section.4.3}%
+\contentsline {section}{\numberline {4.4}Piezo re-gluing}{56}{section.4.4}%
+\contentsline {section}{\numberline {4.5}Z3 motor}{58}{section.4.5}%
+\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{59}{subsection.4.5.1}%
+\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{62}{subsection.4.5.2}%
+\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{62}{section.4.6}%
+\contentsline {section}{\numberline {4.7}Final test}{64}{section.4.7}%
+\contentsline {chapter}{\numberline {5}Evaporations and measurement}{65}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Evaporation configuration}{65}{section.5.1}%
+\contentsline {section}{\numberline {5.2}Contamination}{67}{section.5.2}%
+\contentsline {section}{\numberline {5.3}Penumbra}{68}{section.5.3}%
+\contentsline {section}{\numberline {5.4}Tilt and deformation}{73}{section.5.4}%
+\contentsline {section}{\numberline {5.5}Simulation}{76}{section.5.5}%
+\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{76}{subsection.5.5.1}%
+\contentsline {subsection}{\numberline {5.5.2}Results}{78}{subsection.5.5.2}%
+\contentsline {subsection}{\numberline {5.5.3}Software improvements}{82}{subsection.5.5.3}%
+\contentsline {subsection}{\numberline {5.5.4}Final Remark}{83}{subsection.5.5.4}%
+\contentsline {chapter}{Conclusions and Outlook}{84}{chapter*.94}%
+\contentsline {chapter}{Bibliography}{86}{chapter*.95}%
+\contentsline {chapter}{List of Abbreviations}{89}{chapter*.96}%
+\contentsline {chapter}{Appendix}{i}{chapter*.97}%
 \contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.5.1}%
 \contentsline {section}{\numberline {B}Walker principle diagram}{ii}{section.5.2}%
 \contentsline {section}{\numberline {C}Walker circuit diagrams}{ii}{section.5.3}%
 \contentsline {section}{\numberline {D}New driver electronics}{vi}{section.5.4}%
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-\contentsline {paragraph}{mstep x}{vi}{section*.109}%
-\contentsline {paragraph}{cancel}{vii}{section*.110}%
-\contentsline {paragraph}{help}{vii}{section*.111}%
+\contentsline {paragraph}{pulse?}{vi}{section*.100}%
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+\contentsline {paragraph}{amp x}{vi}{section*.102}%
+\contentsline {paragraph}{volt x}{vi}{section*.103}%
+\contentsline {paragraph}{channel x}{vi}{section*.104}%
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+\contentsline {paragraph}{cancel}{vii}{section*.108}%
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 \contentsline {section}{\numberline {E}Raycast Simulation}{vii}{section.5.5}%
-\contentsline {paragraph}{radius\_1}{vii}{section*.112}%
-\contentsline {paragraph}{angle}{vii}{section*.113}%
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-\contentsline {chapter}{Acknowledgments}{ix}{chapter*.133}%
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+\contentsline {paragraph}{deposition\_gain}{vii}{section*.117}%
+\contentsline {paragraph}{penalize\_deposition}{vii}{section*.118}%
+\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.119}%
+\contentsline {paragraph}{oscillation\_period}{vii}{section*.120}%
+\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.121}%
+\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.122}%
+\contentsline {paragraph}{save\_intervall}{viii}{section*.123}%
+\contentsline {paragraph}{oscillation\_dir}{viii}{section*.124}%
+\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.125}%
+\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.126}%
+\contentsline {paragraph}{random\_seed}{viii}{section*.127}%
+\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.128}%
+\contentsline {paragraph}{resolution}{viii}{section*.129}%
+\contentsline {paragraph}{path}{viii}{section*.130}%
+\contentsline {chapter}{Acknowledgments}{ix}{chapter*.131}%