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+\bibcite{florian_forster}{{4}{}{{}}{{}}}
+\bibcite{bhaskar}{{5}{}{{}}{{}}}
+\bibcite{SEM_book}{{6}{}{{}}{{}}}
+\bibcite{Mask_Aligner}{{7}{}{{}}{{}}}
+\bibcite{SiN_dielectric}{{8}{}{{}}{{}}}
+\bibcite{Beeker}{{9}{}{{}}{{}}}
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diff --git a/bibliography.bib b/bibliography.bib
index 979ca735e62e3512a0c2e551269da5bec8baa02e..2b272c0abe3ccd171392a1720eb57629f2a4bce5 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -21,11 +21,11 @@
 }
 %Check this citation
 @manual{switch_datasheet,
-    organization  = "Analog Devices Inc.",
-    title         = "IC SWITCH SPDTX2 1.8OHM 16TSSOP",
-    number        = "ADG1436",
-    year          =  2016, 
-    note          = "Rev. B"
+    organization  = {Analog Devices Inc.},
+    title         = {IC SWITCH SPDTX2 1.8OHM 16TSSOP},
+    number        = {ADG1436},
+    year          = {2016}, 
+    note          = {Rev. B}
 }
 
 @book{SEM_book,
@@ -36,4 +36,106 @@ pages = {1-522},
 title = {Scanning Microscopy for Nanotechnology. Techniques and Applications},
 isbn = {978-0-387-33325-0},
 doi = {10.1007/978-0-387-39620-0}
-}
\ No newline at end of file
+}
+
+@book{AFM_book,
+  title={Atomic Force Microscopy},
+  author={Eaton, P. and West, P.},
+  isbn={9780199570454},
+  lccn={2010280406},
+  url={https://books.google.be/books?id=VB0UDAAAQBAJ},
+  year={2010},
+  publisher={OUP Oxford}
+}
+
+@thesis{Bhaskar,
+author       = {Bhaskar, Priyamvada},
+      othercontributors = {Morgenstern, Markus and Ternes, Markus Peter},
+      title        = {{F}abrication and investigation of ultrahigh vacuum
+                      compatible interfaces of topological insulators and
+                      superconductors},
+      school       = {RWTH Aachen University},
+      type         = {Dissertation},
+      address      = {Aachen},
+      publisher    = {RWTH Aachen University},
+      reportid     = {RWTH-2023-08222},
+      pages        = {1 Online-Ressource : Illustrationen, Diagramme},
+      year         = {2023},
+      note         = {Published on the publication server of RWTH Aachen
+                      University; Dissertation, RWTH Aachen University, 2023},
+      cin          = {132310 / 130000},
+      ddc          = {530},
+      cid          = {$I:(DE-82)132310_20140620$ / $I:(DE-82)130000_20140620$},
+      typ          = {PUB:(DE-HGF)11},
+      doi          = {10.18154/RWTH-2023-08222},
+      url          = {https://publications.rwth-aachen.de/record/964278},
+}
+
+@thesis{Beeker,
+	author = {Beeker, Jonas},
+	title = {Growth of {P}b islands with the help of an {U}ltrahigh {V}acuum {M}ask {A}ligner},
+	school       = {RWTH Aachen University},
+	type         = {Masters},
+    address      = {Aachen},
+    publisher    = {RWTH Aachen University},
+	year         = {2022},
+	note         = {unpublished, but viewable on the Server of the 2nd institute of physics B},
+}
+
+@thesis{Olschewski,
+	author = {Olschewski, Tim},
+	title = {Konstruktion und Aufbau eines Mask Aligners für Ultrahochvakuum},
+	school       = {RWTH Aachen University},
+	type         = {Masters},
+    address      = {Aachen},
+    publisher    = {RWTH Aachen University},
+	year         = {2015},
+	note         = {unpublished, but viewable on the Server of the 2nd institute of physics B},
+}
+
+@thesis{Florian_forster,
+	author = {Forster, Florian},
+	title = {Aufbau und {T}est eines {M}olekularstrahlverdampfers},
+	school       = {RWTH Aachen University},
+	type         = {Masters},
+    address      = {Aachen},
+    publisher    = {RWTH Aachen University},
+	year         = {2009},
+	note         = {unpublished, but viewable on the Server of the 2nd institute of physics B},
+}
+
+@article{SiN_dielectric,
+author = {Jan Kischkat and Sven Peters and Bernd Gruska et al.},
+journal = {Appl. Opt.},
+number = {28},
+pages = {6789--6798},
+publisher = {Optica Publishing Group},
+title = {Mid-infrared optical properties of thin films of aluminum oxide, titanium dioxide, silicon dioxide, aluminum nitride, and silicon nitride},
+volume = {51},
+month = {Oct},
+year = {2012},
+url = {https://opg.optica.org/ao/abstract.cfm?URI=ao-51-28-6789},
+doi = {10.1364/AO.51.006789},
+}
+
+@book{Tungsten_melt,
+author = {Cardarelli, François},
+year = {2008},
+month = {01},
+pages = {529-530, },
+title = {Materials Handbook: A Concise Desktop Reference. Third Edition},
+isbn = {978-1-84628-668-1},
+doi = {10.1007/978-1-84628-669-8}
+}
+
+@book{Tungsten_evap,
+title = {Handbook of Chemical Compound Data for Process Safety},
+editor = {Carl L. Yaws},
+publisher = {Gulf Professional Publishing},
+address = {Houston},
+pages = {vi},
+year = {1997},
+isbn = {978-0-88415-381-8},
+doi = {https://doi.org/10.1016/B978-088415381-8/50015-2},
+url = {https://www.sciencedirect.com/science/article/pii/B9780884153818500152}
+}
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diff --git a/chap01.tex b/chap01.tex
index 4f31481b4382e94f858b9c94291937d0337c08a1..eea82506a292fdf1630806d3fd159be12a69abec 100644
--- a/chap01.tex
+++ b/chap01.tex
@@ -2,7 +2,7 @@
 Page left unintentionally blank
 \todo{This section needs citations}
 \chapter{Mask Aligner Background}
-
+The Mask Aligner and its Molecular Beam Evaporation chamber are used to create thin films on samples with high accuracy. This chapter will introduce the required background behind the evaporation of thin films on sample surface as well as explain the basic evaporation and alignment setup the Mask Aligner uses.
 
 \section{Electron beam evaporation}
 Electron beam evaporation is a physical vapor deposition (PVD) technique used in vacuum and particularly Ultra high vacuum conditions, to deposit material onto a substrates surface. The general setup of an electron beam evaporator is seen in Figure \ref{fig:e-beam_evap}. The source material, which is the material to be deposited on the samples surface is placed as ultra pure pellets inside a crucible.
@@ -14,9 +14,9 @@ Electron beam evaporation is a physical vapor deposition (PVD) technique used in
     \label{fig:e-beam_evap}
 \end{figure}
  
-The crucible is also heated during the evaporation process, in order to prevent the crucible itself from being damaged or even partially evaporated a material with high melting point has to be chosen. Tungsten with a melting point of 3695 K \cite{todo}\todo{citation} is usually chosen. Additionally, the crucible usually has to be water cooled to prevent damaging the system.
+The crucible is also heated during the evaporation process, in order to prevent the crucible itself from being damaged or even partially evaporated a material with high melting point has to be 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 prevent damaging the system.
 
-In order to heat the source material locally beyond its boiling point it is hit with a high current electron beam ($\mathcal{O}$(1 kV)), this beam usually has to be focused using magnetic fields to hit the source material. The highly energetic electrons interact with the atomic nuclei and the atomic electrons of the source material and transfer energy. This energy transfer heats the hit atoms locally and eventually causes the system to reach its melting and then its boiling point, if enough current is applied to give the required heating power. The penetration depth of electron with ($<5$ kV) is less than 0.4 $\mu$m (estimated using CASINO Monte Carlo software)\cite{CASINO_Software} so the heating occurs only very near to the source materials 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.\\
+In order to heat the source material locally beyond its boiling point it is hit with a high current electron beam ($\mathcal{O}$(1 kV)), emitted by either an electron gun or a filament, this beam usually has to be focused using magnetic fields to hit the source material. The highly energetic electrons interact with the atomic nuclei and the atomic electrons of the source material and transfer energy. This energy transfer heats the hit atoms locally and eventually causes the system to reach its melting and then its boiling point, if enough current is applied to give the required heating power. The penetration depth of electron with ($<5$ kV) is less than 0.4 $\mu$m (estimated using CASINO Monte Carlo software)\cite{CASINO_Software} so the heating occurs only very near to the source materials 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 reaches its boiling point it forms a vapor, which is directed through a funnel to the samples surface. The sample is kept at a temperature much colder than the source materials boiling temperature, due to this the material beam will deposit and condense on the substrates surface forming a thin film. \\
 
@@ -31,7 +31,7 @@ where $N$ is the number of gas molecules deposited, $A$ is the surface area, $t$
 
 \todo{Quartz balance???}
 
-Some of the advantages that e-beam evaporation has over other techniques such as thermal evaporation or sputtering \cite{} are that due to the high energy localized heating materials which require high temperature to reach their boiling point, like tungsten ($5828$ K) or niobium ($5017$ K) can be evaporated using e-beam evaporation. The deposition rate can also be controlled with high precision using the current applied to create the electron beam.\cite{Vapor_depo_princ} \\
+Some of the advantages that e-beam evaporation has over other techniques such as thermal evaporation or sputtering \cite{} are that due to the high energy localized heating materials which require high temperature to reach their boiling point, like tungsten ($5828$ K)\cite{Tungsten_evap} or niobium ($5017$ K)\cite{Tungsten_evap} can be evaporated using e-beam evaporation. The deposition rate can also be controlled with high precision using the current applied to create the electron beam.\cite{Vapor_depo_princ} \\
 The high energy electron beam is directed directly at the source material and is unlikely to interact with the samples surface, unlike for example sputtering, where the high energy particles depositing the material can interact and either implant unwanted material or dislodge substrate material damaging the substrate surface. \cite{todo}\todo{citation}
 
 E-beam evaporation offers more control over deposition rate than thermal evaporation, and it is easier to evaporate material which require high evaporation temperatures with e-beam evaporation. \todo{citation}
@@ -39,16 +39,16 @@ E-beam evaporation offers more control over deposition rate than thermal evapora
 In order to control the length of the evaporation precisely a shutter is usually included in the evaporation chamber which 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. By closing the shutter this can be avoided.
 
 \subsection{Mask Aligner Lead Evaporator}
-The electron beam evaporator used for the lead evaporation in the mask aligner chamber was built by Florian Forster in 2009. The crucible of this evaporator, as is usual, is made from tungsten and the evaporator uses a filament . The crucible is surrounded by a tungsten filament, that heats the crucible and additionally a voltage of up to 1kV can be applied between crucible and filament causing e-beam evaporation to take place. Surrounding the heating elements is a cooper cylinder that needs to be water cooled to prevent damage to the evaporator. In order to see if the cooling failed or too much current/voltage is applied to the controls, a thermocouple measures the temperature of the copper cylinder. \\
-In order to control the molecular flow, one can change the current applied to the filament or the voltage accelerating the electron beam towards the source. Additionally, the crucible can be shifted on the z-axis closer or further away from the filament, controlling the amount of heat is received, this method is however not used in this thesis. In order to determine if the applied controls have the desired effect, the current of $\text{Pb}^+$ ions leaving the crucible is measured by a flux monitor positioned at the top of the evaporator, below the shutter, which can be used to open the molecular flow to the mask aligner chamber.
+The electron beam evaporator used for the lead evaporation in the mask aligner chamber was built by Florian Forster in 2009\cite{florian_forster}. The crucible of this evaporator, as is usual, is made from tungsten and the evaporator uses a filament placed near the crucible to bombard the material placed inside the crucible with highly energetic electrons. To accomplish this a high current (up to $1$ kV) is applied between filament and crucible to direct electrons emitted from the filament to the crucible. Additionally the system can be heated with radiative heat from the filament. Surrounding the heating elements is a cooper cylinder, that functions as a heat sink for the system and that needs to be water cooled to prevent damage to the evaporator. In order to see if the cooling failed or too much current/voltage is applied to the controls, a thermal sensor measures the temperature of the copper cylinder. \\
+In order to control the molecular flow, one can change the current applied to the filament or the voltage accelerating the electron beam towards the source. Additionally, the crucible can be shifted on the z-axis closer or further away from the filament, controlling the amount of heating that is received by the source material. This method of temperature control was unused in this thesis as the distance was previously optimized already. In order to determine if the applied controls have the desired effect, the current of $\text{Pb}^+$ ions leaving the crucible is measured by a flux monitor positioned at the top of the evaporator, below the shutter, which can be used to open the molecular flow to the mask aligner chamber. \\
 
 \section{Stencil Lithography}
-Stencil lithography is a method of depositing pattened structures on a nanometer scale on substrates (sample) using a stencil. The stencil is 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 on the substrates surface, while the mask is placed on top of the sample. The mask protects the substrate from the molecular beam, expect in the places where the pattern has been cut into the mask. In this way the 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 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 on the substrates surface, while the mask is placed on top of the sample. The mask protects the substrate from the molecular beam, expect in the places where the pattern has been cut into the mask. In this way the pattern is transferred from the mask to the sample. \\
 Stencil Lithography can also be used for etching where patterns are cut into the substrates surface, using reactive ion etching, in the places where the mask has been patterned, while the rest of the sample remains protected. \\
 Stencil lithography requires no resist, heat or other chemical treatment and thus protects the substrate from possible contamination or damage that chemicals or heat can cause. Masks can also be reused many times and the process is relatively simple to use and fast in execution. In stencil lithography the fabrication speed is only limited by the possible deposition rate of the depositon material and the complexity of applying the mask to the sample and can be on the order of minutes.
 While versatile since any pattern can be deposited or etched using stencil lithography, stencil lithography comes with challenges. 
 Material is also deposited on the masks including in the aperture of the pattern, which reduces the effective aperture over time. This means that while masks can be reused, they cannot be reused indefinitely.
-One of the biggest challenges is that in order to get sharp patterns on the substrates surface the mask has ideally to be placed directly on the surface of the sample as otherwise effects resulting from the limited coherence length of the molecular beam used in physical vapor deposition result in a "blurring" of the structures. However direct placement of the mask on the substrates surface has the potential to contaminate or damage both mask and substrate and should be avoided. \\
+One of the biggest challenges is that in order to get sharp patterns on the substrates surface the mask has ideally to be placed directly on the surface of the sample as otherwise effects resulting from the limited coherence length of the molecular beam used in physical vapor deposition result in a "blurring" of the structures. However, direct placement of the mask on the substrates surface has the potential to contaminate or damage both mask and sample and should be avoided for materials very sensitive to mechanical damage or when measurement of the sample in highly sensitive devices such as \textbf{S}canning \textbf{T}unneling \textbf{M}icroscopes is intended.  \\
 
 The Mask Aligner is a tool designed to overcome the challenge of sample mask alignment, allowing precise control of mask sample distance. 
 
@@ -85,11 +85,11 @@ The mask and the sample also have to be kept parallel as a tilt would result in
 	\label{fig:penumbra_explanation_tilt_2d}
 	\end{subfigure}
 	\begin{subfigure}{0.45\textwidth}
-    \includegraphics[width=\linewidth]{img/CalibrationUHV_Z2_Z3.png}
+    \includegraphics[width=\linewidth]{img/Plots/Background/Penumbra_ImageTilt.pdf}
     \caption{}
-	\label{fig:penumbra_explanation_tilt_3d}
+	\label{fig:penumbra_explanation_tilt_sim}
 	\end{subfigure}
-	\caption{}
+	\caption{A diagram of the evaporation happening with a tilted mask for only one hole (\subref{fig:penumbra_explanation_tilt_2d}) showing the 2 different penumbral radii that appear in a cross-section of the evaporation at the tilt angle. (\subref{fig:penumbra_explanation_tilt_sim}) shows a simulated evaporation with large penumbra for a tilt angle of $45^\circ$ the "half-moon" shaped penumbra, that is wider on on side than on the other, can be seen easily.}
     \label{fig:penumbra_explanation_tilt}
 \end{figure}\todo{colors}
 
@@ -148,4 +148,6 @@ There are more ways to get useful sample information from an AFM, the tip can fo
 \todo{Image of SEM Setup}
 A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope is a microscope in which an image of the topography of a sample is created via a focused electron beam. In order to do this a sample is hit with a focused beam of electrons, while suspended in vacuum. When an electron hits the surface of the sample the electron can undergo various interactions with the sample. The main matter interaction that is measured in an SEM is the is inelastic scattering of the beam electron with a sample electron. The sample electron is ejected at a different angle from the incoming beam electron. This ejected electron is called secondary electron.\cite{SEM_book} The secondary electron are ejected from the sample at relatively low energy of $<50$ eV and can thus be attracted with a positive bias voltage ($>10$ kV) applied to a scintillator, which then converts the attracted electrons into light photons, which are then detected via photo multiplier tube (PMT). Such a detector is called Everhart–Thornley detector (ET) detector. Using these detectors it is now possible to detect the amount of secondary electrons emitted at the current beam location. This amount is based on the surfaces topography and thus by measuring the voltage given at the PMT a topographical image of the sample can be obtained. Other types of electron are also emitted in beam sample interaction and can be detected in an SEM setup, but for this thesis only the secondary electrons are relevant.\\
 SEMs give high contrast large area images with good spatial resolution and were thus used in this thesis to initially locate evaporated fields on silicon samples, but SEM imaging comes with some downsides which is why they are not sufficient to fully characterize the samples in this thesis.
-On insulating or semi conducting samples the electron beam of the SEM causes areas of the sample to charge up, which changes the SEM image over time and can potentially cause damage to the sample. For this reason the electron beam has to be operated at the lower end of beam energy. In theory this limits the spatial resolution as higher energy electron have a better De-Broglie wavelength, but optical effects arising from focussing the electron beam bottleneck the resolution rather than wavelength. SEMs give good topographical images, but exact quantitative heights of features cannot be directly obtained from an SEM image without a known reference and thus they are not sufficient for sample characterization.
\ No newline at end of file
+On insulating or semi conducting samples the electron beam of the SEM causes areas of the sample to charge up, which changes the SEM image over time and can potentially cause damage to the sample. For this reason the electron beam has to be operated at the lower end of beam energy. In theory this limits the spatial resolution as higher energy electron have a better De-Broglie wavelength, but optical effects arising from focussing the electron beam bottleneck the resolution rather than wavelength. SEMs give good topographical images, but exact quantitative heights of features cannot be directly obtained from an SEM image without a known reference and thus they are not sufficient for sample characterization.
+
+\subsection{Energy-dispersive X-ray spectroscopy}
diff --git a/chap02.aux b/chap02.aux
index 982c4f28b59155c6de8b59727b0207fce7099f57..9794447d8144360aa6c665a593a7f718c35dbe4b 100644
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+\newlabel{fig:calibration_example}{{2.7}{23}{Example of a linear fit for the measured calibration data. From the slope of the fit, the step size of a single step can be obtained. This calibration was performed during a time in which repairs at the Z3 motor were performed. The Z3 motor has a stronger difference in step size between approach/retract than the other motors here}{figure.caption.38}{}}
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+\newlabel{fig:camera_alignment_example}{{2.9}{24}{Examples of camera views for different alignment situations. Camera placed or angled too low (a), too high (b) and placed in good alignment (c). In (a) the surface of the sample can be seen, which means the camera is not in line with the sample, but rather tilted too far up or too low in height. In (b) one can see the surface of the sample holder on the upper side as well as an upwards shift on the side of the sample indicating that the sample is tilted with respect to the camera, this is cause by a camera too high up or tilted too far down}{figure.caption.42}{}}
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+\@writefile{tdo}{\contentsline {todo}{Placeholder}{25}{section*.44}\protected@file@percent }
 \citation{SiN_dielectric}
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.2.3}Approach Curves}{26}{subsection.2.2.3}\protected@file@percent }
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 \newlabel{eq:plate_capacitor}{{2.1}{26}{Approach Curves}{equation.2.2.1}{}}
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-\newlabel{fig:approach_curve_example}{{2.11}{27}{A capacitance (approach) curve, for one of the capacitive sensors, as an example (a) and the difference of each capacitance value to the last (b). Only one sensor is pictured. Marked are the important point where the slope of the $\frac {1}{r}$ curve changes. These points, where the geometry of the alignment process changes are marked labeled First, Second and Full contact. Before each of these points the difference goes to a local maximum. These are marked with blue dashed lines. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points mark where the mask is touching the sample}{figure.caption.51}{}}
+\newlabel{fig:approach_curve_example_cap}{{2.12a}{27}{\relax }{figure.caption.46}{}}
+\newlabel{sub@fig:approach_curve_example_cap}{{a}{27}{\relax }{figure.caption.46}{}}
+\newlabel{fig:approach_curve_example_cap_diff}{{2.12b}{27}{\relax }{figure.caption.46}{}}
+\newlabel{sub@fig:approach_curve_example_cap_diff}{{b}{27}{\relax }{figure.caption.46}{}}
+\newlabel{fig:approach_curve_example_first}{{2.12c}{27}{\relax }{figure.caption.46}{}}
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+\newlabel{fig:approach_curve_example}{{2.12}{27}{A capacitance (approach) curve, for one of the capacitive sensors, as an example (a) and the difference of each capacitance value to the last (b). Only one sensor is pictured. Marked are the important point where the slope of the $\frac {1}{r}$ curve changes. These points, where the geometry of the alignment process changes are marked labeled First, Second and Full contact. Before each of these points the difference goes to a local maximum. These are marked with blue dashed lines. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points mark where the mask is touching the sample}{figure.caption.46}{}}
 \citation{Beeker}
 \newlabel{eq:cap_slope_change}{{2.3}{28}{Approach Curves}{equation.2.2.3}{}}
 \citation{Beeker}
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+\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces Plot of data of approach curves recorded on two different days. The second curve was recorded after retraction and subsequent approach. The 2 curves do not start at the same distance away from sample, which is why they are not aligned on the x-axis. A clear drop in capacitance can be observed from one measurement to the other regardless.}}{29}{figure.caption.47}\protected@file@percent }
+\newlabel{fig:approach_subsequent}{{2.13}{29}{Plot of data of approach curves recorded on two different days. The second curve was recorded after retraction and subsequent approach. The 2 curves do not start at the same distance away from sample, which is why they are not aligned on the x-axis. A clear drop in capacitance can be observed from one measurement to the other regardless}{figure.caption.47}{}}
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-\newlabel{fig:cross_cap_approach_sim}{{2.15}{31}{The 3 capacitance curves of one example measurement multiplied with a factor, found by fitting, to ensure same scale (upper), the differences from $C_1$ to $C_2$ and $C_3$ (lower left) and the differences $C_2$ to $C_3$ (lower right). The plot shows heavy correlation between $C_1$, $C_2$ and $C_3$, since the shape of the graph is nearly identical. Most approach curves obtained with the newer mask holders are of similar shape}{figure.caption.57}{}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the SiNi layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample.}}{32}{figure.caption.59}\protected@file@percent }
-\newlabel{fig:leakage_current}{{2.16}{32}{Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the SiNi layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample}{figure.caption.59}{}}
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+\@writefile{tdo}{\contentsline {todo}{If you do not have data for this maybe scratch line, me!}{29}{section*.50}\protected@file@percent }
+\newlabel{fig:approach_replicability_cap}{{2.14a}{30}{\relax }{figure.caption.51}{}}
+\newlabel{sub@fig:approach_replicability_cap}{{a}{30}{\relax }{figure.caption.51}{}}
+\newlabel{fig:approach_replicability_cap_diff}{{2.14b}{30}{\relax }{figure.caption.51}{}}
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+\@writefile{tdo}{\contentsline {todo}{Find chapter ref}{30}{section*.53}\protected@file@percent }
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+\@writefile{tdo}{\contentsline {todo}{Plot too smol}{31}{section*.55}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{31}{subsection.2.2.5}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces \relax }}{31}{figure.caption.56}\protected@file@percent }
+\newlabel{fig:explanation_curve_difference}{{2.15}{31}{\relax }{figure.caption.56}{}}
+\@writefile{tdo}{\contentsline {todo}{Better plort}{31}{section*.57}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces The 3 capacitance curves of one example measurement multiplied with a factor, found by fitting, to ensure same scale (upper), the differences from $C_1$ to $C_2$ and $C_3$ (lower left) and the differences $C_2$ to $C_3$ (lower right). The plot shows heavy correlation between $C_1$, $C_2$ and $C_3$, since the shape of the graph is nearly identical. Most approach curves obtained with the newer mask holders are of similar shape.}}{32}{figure.caption.58}\protected@file@percent }
+\newlabel{fig:cross_cap_approach_sim}{{2.16}{32}{The 3 capacitance curves of one example measurement multiplied with a factor, found by fitting, to ensure same scale (upper), the differences from $C_1$ to $C_2$ and $C_3$ (lower left) and the differences $C_2$ to $C_3$ (lower right). The plot shows heavy correlation between $C_1$, $C_2$ and $C_3$, since the shape of the graph is nearly identical. Most approach curves obtained with the newer mask holders are of similar shape}{figure.caption.58}{}}
+\@writefile{tdo}{\contentsline {todo}{Plot of heavily correlated approach curves}{32}{section*.59}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.17}{\ignorespaces Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the SiNi layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample.}}{33}{figure.caption.60}\protected@file@percent }
+\newlabel{fig:leakage_current}{{2.17}{33}{Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the SiNi layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample}{figure.caption.60}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.1}{\ignorespaces Table of cross capacitance measurement to determine possible causes for large values in approach curves. All measurements were done with Mask shuttle in Mask aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII.}}{34}{table.caption.61}\protected@file@percent }
+\newlabel{tab:cross_cap}{{2.1}{34}{Table of cross capacitance measurement to determine possible causes for large values in approach curves. All measurements were done with Mask shuttle in Mask aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII}{table.caption.61}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\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 error.}}{35}{figure.caption.62}\protected@file@percent }
+\newlabel{fig:mask_old_caps}{{2.18}{35}{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 error}{figure.caption.62}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via linear fit, first to C2 and C3 fit to C1 and then C3 fit to C2. If the function follows a $\frac  {1}{r}$ shape, one should not be able to fit the plots to each other, via a linear function, unless they are heavily correlated. The residuals show the variation to be well within the error bars and overall within less then $1$ \%.}}{35}{figure.caption.63}\protected@file@percent }
+\newlabel{fig:mask_old_correl}{{2.19}{35}{The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via linear fit, first to C2 and C3 fit to C1 and then C3 fit to C2. If the function follows a $\frac {1}{r}$ shape, one should not be able to fit the plots to each other, via a linear function, unless they are heavily correlated. The residuals show the variation to be well within the error bars and overall within less then $1$ \%}{figure.caption.63}{}}
+\@writefile{tdo}{\contentsline {todo}{Axis labels}{35}{section*.64}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.20}{\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.}}{36}{figure.caption.65}\protected@file@percent }
+\newlabel{fig:cross_cap_diagramm}{{2.20}{36}{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.65}{}}
+\@writefile{tdo}{\contentsline {todo}{Make into 1 curve}{36}{section*.66}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Leakage current}{36}{section*.67}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Improved gold pin fitting}{36}{section*.68}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{37}{subsection.2.2.6}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{High correlation between capacitance curves}{37}{section*.69}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Write this but understandable}{37}{section*.70}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Plot stop condition}{37}{section*.71}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Low correlation between capacitance curves}{37}{section*.72}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Check}{37}{section*.73}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {2.3}Mask Aligner Operation}{37}{section.2.3}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Sample Preparation}{37}{subsection.2.3.1}\protected@file@percent }
 \@setckpt{chap02}{
-\setcounter{page}{38}
+\setcounter{page}{39}
 \setcounter{equation}{4}
 \setcounter{enumi}{10}
 \setcounter{enumii}{0}
@@ -129,12 +132,12 @@
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-\setcounter{figure}{19}
+\setcounter{figure}{20}
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+\setcounter{bookmark@seq@number}{20}
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@@ -143,7 +146,7 @@
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+\setcounter{@todonotes@numberoftodonotes}{31}
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diff --git a/chap02.tex b/chap02.tex
index 6b76c7753a3e3284dc8c4c5775e4945ca807815e..62fcbe1c769047f40911a93aff7252adb37e193c 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -102,13 +102,13 @@ affect the given motors step size. A point where the 3 motors are in agreement
 has to be found iteratively. The jumps in signal after certain rotations come
 from the CuBe plate slipping across the winding of the screw at certain spots.}
     \label{fig:screw_firmness}
-\end{figure}\todo{Make Plot better}
+\end{figure}
 
 In order for the motors to perform similarly a common point has to be found on
 these screw curves at which the screws are then left. This is done by measuring
 the time it takes for a motor to travel a known distance. For example the
 distance of one solder \todo{Image for this} anchor can be used as it is known
-to be \todo{Write distance}. This gives a measurement with large error, but
+to be $2$ mm. This gives a measurement with large error, but
 enough precision to determine a good screw position, while not taking up a large
 amount of time and allowing for quick iteration. \\
 
@@ -122,9 +122,9 @@ view when looking at the motors separately. \\
 steps, a specific remarkable point has to be found, that does not change upon
 motor movement and that can be observed after and before a given amount of steps
 were driven. Outside UHV the best points are small scratches on the prisms
-\todo{Thing on prism}, since these are already in a focal plane with the motors,
+\ce{Al2O3} plate, since these are already in a focal plane with the motors,
 and it is easy to determine their center since their are usually only a few
-pixels in diameter, while remaining stable after driving. However when scratches
+pixels in diameter, while remaining stable after driving. However, when scratches
 in the metal are chosen as a point of reference the lighting conditions must not
 be changed during the calibration as this can hinder their visibility.\\
 Inside UHV it is a little more complicated since only one angle is available for
@@ -133,12 +133,19 @@ be chosen, since it is directly in view, but for the motors Z2 and Z3 this
 procedure is not possible since they cannot be directly seen. Instead, the 2
 screws very close to the motors are chosen (seen in Figure
 \ref{fig:calibration_uhv_points_of_interest}
-\subref{fig:calibration_uhv_points_of_interest_z2z3})\todo{Find out error this
-produces} and their movement is instead observed. For camera calibration their
-diameter is chosen as this is also known to be \todo{Screw diameter}. The
+\subref{fig:calibration_uhv_points_of_interest_z2z3}) and their movement is instead observed. For camera calibration their
+diameter is chosen as this is also known to be $3$ mm. The
 distance driven in this instance is still good to measure, but the screws are a
-little closer to the camera than the motors themselves, leading to a small error
-in calibration. The error can be estimated to be about \todo{Make model}\\
+little closer to the camera than the motors themselves, if one neglects the small deviation of the screw from the imaginary line connecting the motor pivot point from the line to the center one can estimate the distance the screw moves per unit of movement for the motor itself using an equilateral triangle. The model for this can be seen in Figure \ref{fig:calibration_screw_diff_explain}. 
+
+\begin{figure}[H]
+    \centering
+    \includegraphics[width=0.6\linewidth]{img/Plots/Calibrations/screw_diff_explain.pdf}
+    \caption{Diagram explaining how to derive the deviation of measured step size on the screws near the Z2 and Z3 motors from the actual step size of the motors.}
+    \label{fig:calibration_screw_diff_explain}
+\end{figure} \todo{Maybe leave out}
+
+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. \\
 
 \begin{figure}[H]
     \centering
@@ -220,14 +227,14 @@ The behavior is linear in the voltage, but the slope is slightly different for
 each motor causing an optimum voltage for driving all 3 motors with the same
 voltage to be around $80$ V. Also noticeable is a strong difference in slope for
 Z3. Z3 is much more influenced by voltage than the other motors where the
-stepsize/V is larger by about a factor of $\approx 0.3$. From this plot the
+step size/V is larger by about a factor of $\approx 0.3$. From this plot the
 slope for each motor can be obtained and with this possible variations in motor
 behavior can be compensated by adjusting the voltage to each channel. This has
 to be done by driving each motor separately, since the current setup does not
 allow for different voltage pulses to be applied to each of the motor
-simultaneaously. This should allow for corrections should the driving behavior
+simultaneously. This should allow for corrections should the driving behavior
 of any of the motors change or if compensation for potential deviations in
-stepsize is needed.\\
+step size is needed.\\
 
 \subsection{Optical Alignment}
 To align mask and sample it is first necessary to get the sample aligned and
@@ -239,12 +246,12 @@ To do this a Bresser MicroCam II camera with a resolution of 20 megapixel is
 mounted on a stand in front of the window of the mask aligner chamber. The
 mounting of it can be controlled via 3 micrometer screws in x, y and z
 direction. Additionally, the camera can be rotated on 2 axis allowing full
-control of the camera angle.\todo{Maybe image} No optical alignment can be done
-in the axis in which the camera is pointed as depth information is difficult to
+control of the camera angle.\todo{Maybe image} No optical adjustment can be done
+in the axis, in which the camera is pointed as depth information is difficult to
 obtain. For this reason the sample has to be aligned so that its surface normal
 is perpendicular to the cameras view direction i.e. no sample surface can be
 seen in camera view and 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.
+edge of the sample, and the upper side of the sample holder cannot be observed.
 \\
 
 \begin{figure}[H]
@@ -279,7 +286,7 @@ the sample leaving a decently sized gap between mask and sample still. Now the
 mask is aligned until only a very small gap can be seen. The size of the gap can
 be optically estimated using the Bresser software. A known length can be used to
 calibrate lengths within the software. As an object of known length the sample
-can be for example chosen since its edge is known to be $3000 \pm 100 $ $\mu$m.
+can be for example chosen since its edge is known to be $5940 \pm 20 $ $\mu$m.
 In camera view direction the mask and sample should now be aligned within
 possible optical accuracy. 
  
@@ -464,7 +471,7 @@ do not start at the same distance away from sample, which is why they are not
 aligned on the x-axis. A clear drop in capacitance can be observed from one
 measurement to the other regardless.}
     \label{fig:approach_subsequent}
-\end{figure}
+\end{figure}\todo{Plot too smol}
 
 \subsection{Reproducibility}
 One of the questions about the efficacy of Mask Aligner as an alignment tool is
@@ -475,6 +482,8 @@ and before after evaporation was discussed.\cite{Beeker}
 
 \subsubsection{Reproducibility when removing sample/mask}
 
+One reproducibility question is whether the approach curve is strongly affected by the exchange of mask or sample or even just the reinsertion of mask or sample. This is important since an exchange of sample to perform a new evaporation is a common operation in the creation of patterned samples. The process could be accelerated and be made less propable to damage the sample, when any approach curve made with the same mask can be used and no additional calibration approach to full contact has to be done for each sample. \todo{If you do not have data for this maybe scratch line, me!}
+
 \begin{figure}[H]
     \centering
 	\begin{subfigure}{0.45\textwidth}
@@ -487,9 +496,19 @@ and before after evaporation was discussed.\cite{Beeker}
     \caption{}
 	\label{fig:approach_replicability_cap_diff}
 	\end{subfigure}
-	\caption{}
+	\caption{3 subsequent approach curves \subref{fig:approach_replicability_cap} and differences in capacitance for each step \subref{fig:approach_replicability_cap_diff} recorded. \textcolor{tab_green}{Green} is initial curve. \textcolor{tab_blue}{Blue} curve is after sample has been carefully removed and reinserted. For \textcolor{tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor{tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier.}
     \label{fig:approach_replicability}
-\end{figure}
+\end{figure} \todo{Plot needs labels and bigger}
+
+First the reproducibility between exchanging just the mask and sample and reinserting it is looked at. When reinserting the mask the approach curve changed drastically, which can likely be attributed to newly induced tilt on the mask. This can be seen in the shift between the \textcolor{tab_green}{green} and \textcolor{tab_red}{red} curves in Figure \ref{fig:approach_replicability}. This might be feature of the particular batch of masks this thesis worked with as the gold pins connecting the mask holder and mask stage do not have fully stable contact between the male and female side and allow for a certain level of movement. The process of moving the mask out and back in to the mask frame might induce enough perturbation to the mask holder to move it slightly in the mask. This fault could potentially be fixed with better gold pin design, when designing newer mask mentioned further in \ref{todo} \todo{Find chapter ref}\\
+
+Another reason might be small movement of the mask frame on the \ce{Nd} magnets tilting the mask, when reinserting the mask. This problem cannot be fixed without a complete redesign of the Mask Aligner. \\
+
+Reinserting the sample also induced a difference in approach curves, but the difference is much smaller as can be seen in \textcolor{tab_blue}{blue} and \textcolor{tab_green}{green}, but the same curve is followed and the point of first contact has only shifted upwards slightly. In the difference curve it is clear that the stop condition however changed by some amount. A stop condition developed on the peak of the \textcolor{tab_green}{green} curve (for example $0.04$ pF) would overshoot the point of first contact on the \textcolor{tab_blue}{blue} curve and the stop condition would never trigger. If left unsupervised the mask would in this instance eventually crash into the sample, unless a point near the point of second or full contact satisfies the stop condition as well. This should be taken into account when deciding on a stop condition. \\
+
+\subsubsection{Reproducibility for different sample, but same mask}
+
+\todo{Plot too smol}
 
 
 \subsection{Cross capacitances}
diff --git a/chap03.aux b/chap03.aux
index 65df692f4b8cc7d4b087f8cdefa6ce6eb25f632e..267a3335ecbf31fbe6a520454ab4f4c426933ed2 100644
--- a/chap03.aux
+++ b/chap03.aux
@@ -1,69 +1,69 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
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+\@writefile{toc}{\contentsline {chapter}{\numberline {3}Electronics}{39}{chapter.3}\protected@file@percent }
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+\newlabel{fig:kim0001_pulse_shape}{{3.4}{42}{Plots showing both an approach step (a) and a retract step for the KIM0001 device. It is noticeable that the pulse shapes for approach and retract are not similar in shape, and due to this a difference in behavior would be expected. The slow flank of the signals also has noticeable aliasing artifacts, which can cause the piezo to move in very small steps that are within the slip rather than the stick regime}{figure.caption.81}{}}
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+\newlabel{fig:kim0001_voltage_behaviour}{{3.6}{43}{4 Plots showing the Voltage of the retract steps of the KIM0001 after setting the Voltage to 125 on the device, after 1 step (a), ~50 steps (b), ~120 steps (c) and ~200 steps (d). The voltage spikes beyond the desired voltage at the start and after 200 steps settles on a voltage of ~118 V. Also noticeable is an inconsistency in peak shape in (c) as compared to the others. No settings were changed during the recording of this data}{figure.caption.82}{}}
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+\newlabel{fig:bessel_filter}{{3.8}{45}{Plots showing both an aliased signal (a) and the same signal, but smoothed out with an 8th order Bessel filter (b). The amount of aliasing is not representative of our electronics and is simply for illustration purposes. After filtering, the signal appears very smooth and without sharp steps}{figure.caption.90}{}}
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+\newlabel{fig:walker_pulse_shape_slow}{{3.10}{48}{Plots showing both an approach step (a) and a retract step (b) for the new Walker device \textcolor {tab_red}{(red)} and for comparison the RHK in \textcolor {tab_blue}{(blue)} in an unloaded state for a nominal voltage of 80 V. The dashed \textcolor {tab_green}{green} lines show a timeframe of 1000 $\mu $s around the fast flank, which should be the length of 1 pulse exactly. The Walker keeps the Voltage of 80 V both in the maxima and minima, while the RHK undershoots in the maximum for approach and overshoots in the minimum and vice versa in the retract. Noticeable is a voltage peak in the RHK behavior after the fast flank, that is absent in the Walkers pulse}{figure.caption.101}{}}
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+\newlabel{fig:walker_pulse_shape_fast}{{3.11}{49}{Plots showing the fast Flank of the Walker Signal and the fast flank of the RHK Signal, for both approach (a) and retract (b), for a nominal voltage of 80 V (without load). The fast flank of the walker is more stable showing no signs of peaking, and it saturates at the desired voltage of 80 V, while the RHK signal over/undershoots the desired voltage, by about 20 V, before going back down/up}{figure.caption.103}{}}
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diff --git a/chap03.tex b/chap03.tex
index 1b2e72c44399499840cc55192a89a29f0cd166c6..4e33e746372dcdd9956419107827fa3b21e6d841 100644
--- a/chap03.tex
+++ b/chap03.tex
@@ -153,7 +153,7 @@ The polarity of the generated signal. Negative polarity is chosen as an approach
 The frequency is not adjustable as of the writing of this thesis, though in principle multiples changable frequencies are possible to be implemented through code. Since all previous approach curves and alignment operations were always performed at $1$ kHz it was deemed not necessary to implement. Frequencies higher than $1$ kHz are also difficult, as the timing accuracy of the Arduino is already close to its limits and the signal would also lose sampling rate since the output rate of the DAC is fixed. 
 
 \subsection{Measured Pulse shape}
-In order to verify the ability to drive the Mask Aligner with the new electronics, test measurements of both the new Walker and the RHK were performed to see if the new Walker can support both the slip-stick behavior and give consistent pulse shape. For the Mask Aligner a voltage of 80 V was determined to be the default voltage to run experiments (see \ref{TODO}) in, for this reason most of these comparisons will be made at 80 V. \\
+In order to verify the ability to drive the Mask Aligner with the new electronics, test measurements of both the new Walker and the RHK were performed to see if the new Walker can support both the slip-stick behavior and give consistent pulse shape. For the Mask Aligner a voltage of 80 V was determined to be the default voltage to run experiments (see \ref{fig:calibration_voltage}) in, for this reason the comparisons will be made at 80 V, unless otherwise specified. \\
 A measurement of the slow flank, without any attached load, is shown in Figure (\ref{fig:walker_pulse_shape_slow}). The Walker compares favorably to the RHK. It has a more consistent peak shape and its peak voltage corresponds to the one given as a parameter more closely than the RHK, which both under- and overshoots the specified 80 V, by up to $\approx$20 V. The walker pulses are also more symmetric around the fast flank than the one from the RHK. Both the Walker and the RHK show no aliasing artifacts, that are not explainable with the limited time resolution of the oscilloscope. Given this data the Walker seems to outperform the RHK at least in the unloaded state and should give the same, or a better driving behavior as the RHK.\todo{This sentence}
 
 \begin{figure}[H]
@@ -188,8 +188,6 @@ The slow flank was also measured for both the RHK and the Walker, again in an un
 
 \todo{The x-axis for all these plots is wrong!}
 
-For a system with a load of $9$ nF attached the signal looks very different for the Walker.
-
 \subsection{Driving the Mask Aligner}
-Due to hardware issues with the Walker, no final test with the Mask Aligner attached as a load could be performed and the driving performance could not be tested. Some hardware failure caused the positive polarity to no longer reach full $120$ V and with a load attached it could no longer reach beyond $0$ V.
+Due to hardware issues with the Walker, no final test with the Mask Aligner attached as a load could not be performed and the driving performance could not be tested. Some hardware failure caused the positive polarity to no longer reach full $120$ V peak and with a load attached it could no longer reach beyond $0$ V giving a unipolar piezo driving signal in approach direction and no slip stick driving signal in retract.
 
diff --git a/chap04.aux b/chap04.aux
index 44c83fab24c8bff476f5265386a69521a0d519b3..1fa7e663ea17da8fc5962909c4ef24a59978e9fb 100644
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 \citation{olschewski}
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+\newlabel{fig:solder_anchors_diagram_SmallerDot}{{4.3b}{54}{\relax }{figure.caption.115}{}}
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+\newlabel{fig:solder_anchors_examples}{{4.3}{54}{The problem with the solder anchors, that emerged with the Mask Aligner over time (a) as well as the 3 different measures that were taken to fix the problem. Making the solder point smaller (b), replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate (c) and putting the anchor with glue on the top/bottom of the solder ceramic (d). All 3 measures (b-d) fix the same issue depicted in (a) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably}{figure.caption.115}{}}
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+\newlabel{fig:Z3_weaker_stack}{{4.9}{60}{The measured capacitance values for the piezos stacks of the motor Z3. The ones both showing $1.62$ nF were only measured together since they were always wired in parallel, when measurements were taken. The plate stacks were also only measured together. Measurements were taken by measuring capacitance of the entire motor Z3 with the piezos detached from the circuit}{figure.caption.128}{}}
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diff --git a/chap04.tex b/chap04.tex
index 35567f45a802133d9645288290095bcd6b0eb8a6..76d376278ea9fbcfa8d98dfee225db643b209b24 100644
--- a/chap04.tex
+++ b/chap04.tex
@@ -70,6 +70,32 @@ The last course of action that could be taken was to glue the soldering anchor o
 EPO-TEK H70E is recommended to cure at 150°C for at least 1 hour, since it would be difficult and dangerous to heat the entire Mask Aligner to 150°C, since the piezo stacks depolarize at temperatures near 150°C\todo{Check}, and it would be also be difficult to heat the glue locally to 150°C, it was determined that a different glue should be used. \\
 Thorseal was instead used for all gluing purposes. Torr Seal is a two component epoxy, that can cure at room temperature and follows the requirements, with regard to out gassing, that allows usage in UHV conditions. It however has the disadvantage of reaching its flash point at 175°C, for this reason soldering on anything affixed with Torr Seal should be done with care as prolonged exposure to the heat of a soldering iron will lead the glue to deteriorate quickly. Also of note is that Torr Seal cannot operate at temperatures below -45°C, so usage in a cryonically cooled environment is no longer possible, since the Mask Aligner is however not intended for usage in a cooled environment anyway this was determined not to be an issue.
 
+\begin{figure}[H]
+    \centering
+    \begin{subfigure}{0.4\textwidth}
+        \includegraphics[width=0.8\linewidth]{img/Repairs/SolderAnchorsBase.pdf}
+        \caption{}
+        \label{fig:solder_anchors_diagram_base}
+    \end{subfigure}
+    \begin{subfigure}{0.4\textwidth}
+        \includegraphics[width=0.8\linewidth]{img/Repairs/SolderAnchorsSmallerDot.pdf}
+        \caption{}
+        \label{fig:solder_anchors_diagram_SmallerDot}
+    \end{subfigure}
+    \begin{subfigure}{0.4\textwidth}
+        \includegraphics[width=0.8\linewidth]{img/Repairs/SolderAnchorsAlO.pdf}
+        \caption{}
+        \label{fig:solder_anchors_diagram_AlO}
+    \end{subfigure}
+    \begin{subfigure}{0.4\textwidth}
+        \includegraphics[width=0.8\linewidth]{img/Repairs/SolderAnchorsGlueTop.pdf}
+        \caption{}
+        \label{fig:solder_anchors_diagram_GlueTop}
+    \end{subfigure}
+    \caption{The problem with the solder anchors, that emerged with the Mask Aligner over time (a) as well as the 3 different measures that were taken to fix the problem. Making the solder point smaller (b), replacing the solder anchor ceramic with a much smaller \ce{Al2O3} plate (c) and putting the anchor with glue on the top/bottom of the solder ceramic (d). All 3 measures (b-d) fix the same issue depicted in (a) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably.}
+    \label{fig:solder_anchors_examples}
+\end{figure}
+
 All motors were checked for soldering anchor points that could potentially interfere with the prism, and one of these actions was taken for all ceramics where problems could be found.\todo{show examples} \\
 After this step, the prism would no longer get stuck when driving and could cleanly drive the whole range of possible motion. \\
 
diff --git a/chap05.aux b/chap05.aux
index 6e1f4af4402b92c39165ef25ad65eff4cf7390c4..5a7060a4478e097389e8cb798edc7f42c8ef44cc 100644
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--- a/chap05.tex
+++ b/chap05.tex
@@ -74,12 +74,12 @@ Also obtained by this method are the height and the umbral width of each dot.
     \label{fig:evaporation_analysis}
 \end{figure}
 
-This process was performed for every recorded dot and with multiple line cuts near the line in which the tilt is pointing as well as for both trace and retrace images. This gives multiple datapoints for each image for both $\sigma$. 
+This process was performed for every recorded dot and with multiple line cuts near the line in which the tilt is pointing as well as for both trace and retrace images. This gives multiple datapoints for each image for both $\sigma_s$ and $\sigma_l$. 
 
 \subsection{Tilt}
-All evaporated dots, even when the capacitance signal was within the full contact regime showed signs of a tilt between mask hole and sample in the form of a half moon shaped second penumbra. If this was due to a misalignement between the entire mask and the sample one would expect the direction of the tilt to be the same for the entire evaporated field and the size of the second penumbra to diminish along the direction of the tilt. But as seen in Figure \ref{fig:evaporation_tilts} the direction of the tilt is not uniform and instead seems to point outwards for the dots on the edge. This suggests the mask itself is slightly bent towards the edges resulting in an alignment error.\todo{write about mask deformatiuon}\\
+All evaporated dots, even when the capacitance signal was within the full contact regime showed signs of a tilt between mask hole and sample in the form of a half moon shaped second penumbra. If this was due to a misalignement between the entire mask and the sample one would expect the direction of the tilt to be the same for the entire evaporated field and the size of the second penumbra to diminish along the direction of the tilt. But as seen in Figure \ref{fig:evaporation_tilts} the direction of the tilt is not uniform and instead seems to point outwards for the dots on the edge. This suggests the mask itself is slightly bent towards the edges resulting in an alignment error. \\
 
-For the fields 2 and 3 a stronger tilt would be expected than for the fields 3 and 5, since the latter where evaporated in full contact, while the former near the spot of first contact.
+The smallest minor that was found in the AFM data was $2.15 \pm 0.08$ $\mu$m against the $3.01\pm 0.05$ $\mu$m of the evaporated circle. This would imply a tilt from one side of the dot on the mask to the other of $44 \pm 9 ^\circ$, which implies a difference in mask sample distance from one side of the hole in the mask to the other side of it of $1.96 \pm 0.31$ $\mu$m. Even with a mask sample distance on average of $1$ $\mu$m this is still possible since one side can be retraced from the mask by $1.96 \pm 0.31$ $\mu$m rather than the other being closer, but this still implies a massive deformation of the mask membrane.
 
 
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diff --git a/thesis.bbl b/thesis.bbl
index b1bfaa39a6494b6042179447815f1854186d57e8..48d941c4c7dc7e26f72ccbd0debab8c2c2dc9db8 100644
--- a/thesis.bbl
+++ b/thesis.bbl
@@ -1,10 +1,33 @@
-\begin{thebibliography}{1}
+\begin{thebibliography}{10}
+
+\bibitem{Tungsten_melt}
+François Cardarelli.
+\newblock {\em Materials Handbook: A Concise Desktop Reference. Third Edition}.
+\newblock 01 2008.
+
+\bibitem{Tungsten_evap}
+Carl~L. Yaws, editor.
+\newblock {\em Handbook of Chemical Compound Data for Process Safety}.
+\newblock Gulf Professional Publishing, Houston, 1997.
 
 \bibitem{Vapor_depo_princ}
 P.K.S.K.S.S. Harsha.
 \newblock {\em Principles of Vapor Deposition of Thin Films}.
 \newblock Elsevier Science, 2005.
 
+\bibitem{florian_forster}
+Florian Forster.
+\newblock Aufbau und {T}est eines {M}olekularstrahlverdampfers, 2009.
+\newblock unpublished, but viewable on the Server of the 2nd institute of
+  physics B.
+
+\bibitem{bhaskar}
+Priyamvada Bhaskar.
+\newblock {F}abrication and investigation of ultrahigh vacuum compatible
+  interfaces of topological insulators and superconductors, 2023.
+\newblock Published on the publication server of RWTH Aachen University;
+  Dissertation, RWTH Aachen University, 2023.
+
 \bibitem{SEM_book}
 W.~Zhou and Z.L. Wang.
 \newblock {\em Scanning Microscopy for Nanotechnology. Techniques and
@@ -17,9 +40,29 @@ Priyamvada Bhaskar, Simon Mathioudakis, Tim Olschewski, Florian Muckel,
 \newblock Mask aligner for ultrahigh vacuum with capacitive distance control.
 \newblock {\em Applied Physics Letters}, 112(16), apr 2018.
 
+\bibitem{SiN_dielectric}
+Jan Kischkat, Sven Peters, and Bernd~Gruska et~al.
+\newblock Mid-infrared optical properties of thin films of aluminum oxide,
+  titanium dioxide, silicon dioxide, aluminum nitride, and silicon nitride.
+\newblock {\em Appl. Opt.}, 51(28):6789--6798, Oct 2012.
+
+\bibitem{Beeker}
+Jonas Beeker.
+\newblock Growth of {P}b islands with the help of an {U}ltrahigh {V}acuum
+  {M}ask {A}ligner, 2022.
+\newblock unpublished, but viewable on the Server of the 2nd institute of
+  physics B.
+
 \bibitem{switch_datasheet}
 Analog Devices Inc.
 \newblock {\em IC SWITCH SPDTX2 1.8OHM 16TSSOP}, 2016.
 \newblock Rev. B.
 
+\bibitem{olschewski}
+Tim Olschewski.
+\newblock Konstruktion und aufbau eines mask aligners für ultrahochvakuum,
+  2015.
+\newblock unpublished, but viewable on the Server of the 2nd institute of
+  physics B.
+
 \end{thebibliography}
diff --git a/thesis.blg b/thesis.blg
index df06741c63d857c90a280a71f280a9b351a90baf..5aa033efdd0839dfdb28f43cc34598de47374ead 100644
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 Reallocating 'name_of_file' (item size: 1) to 20 items.
 A level-1 auxiliary file: acknowledgments.aux
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diff --git a/thesis.out b/thesis.out
index d9e68055075050bdb6404dab315c37290ab32e11..634e00a2a25371902caae18dcbe57debbbbd6ad9 100644
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diff --git a/thesis.pdf b/thesis.pdf
index 0ef5ac98c82009a40c26275b64a2c8c4bfb4df51..187d7fc9f52787124e65cce3559788f361858189 100644
Binary files a/thesis.pdf and b/thesis.pdf differ
diff --git a/thesis.synctex.gz b/thesis.synctex.gz
index 16f01f9b2c1e0d5f192cda99e8b8b34a21d5604c..bd929c413ba6c172b18e5e057a03d3d5ad017fa0 100644
Binary files a/thesis.synctex.gz and b/thesis.synctex.gz differ
diff --git a/thesis.toc b/thesis.toc
index e9ea46894ad5fe24351f3a3c99547ed93273b9ee..5a5ea4451993d43090d6aa2cef7b291e2ebc9158 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -3,16 +3,17 @@
 \contentsline {section}{\numberline {1.1}Electron beam evaporation}{5}{section.1.1}%
 \contentsline {subsection}{\numberline {1.1.1}Mask Aligner Lead Evaporator}{7}{subsection.1.1.1}%
 \contentsline {section}{\numberline {1.2}Stencil Lithography}{7}{section.1.2}%
-\contentsline {subsubsection}{Penumbra}{8}{section*.10}%
-\contentsline {subsubsection}{Tilt induced Penumbra}{9}{section*.14}%
+\contentsline {subsubsection}{Penumbra}{8}{section*.9}%
+\contentsline {subsubsection}{Tilt induced Penumbra}{9}{section*.13}%
 \contentsline {section}{\numberline {1.3}Measurement Techniques}{11}{section.1.3}%
 \contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{11}{subsection.1.3.1}%
-\contentsline {subsubsection}{}{11}{section*.19}%
-\contentsline {subsubsection}{Modes}{12}{section*.21}%
-\contentsline {paragraph}{Contact}{12}{section*.22}%
-\contentsline {paragraph}{Non-Contact}{13}{section*.23}%
-\contentsline {paragraph}{Tapping}{13}{section*.24}%
+\contentsline {subsubsection}{}{11}{section*.18}%
+\contentsline {subsubsection}{Modes}{12}{section*.20}%
+\contentsline {paragraph}{Contact}{12}{section*.21}%
+\contentsline {paragraph}{Non-Contact}{13}{section*.22}%
+\contentsline {paragraph}{Tapping}{13}{section*.23}%
 \contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{14}{subsection.1.3.2}%
+\contentsline {subsection}{\numberline {1.3.3}Energy-dispersive X-ray spectroscopy}{15}{subsection.1.3.3}%
 \contentsline {chapter}{\numberline {2}Mask Aligner Setup}{16}{chapter.2}%
 \contentsline {section}{\numberline {2.1}Molecular Beam Evaporation Chamber}{18}{section.2.1}%
 \contentsline {section}{\numberline {2.2}Shadow Mask Alignment}{19}{section.2.2}%
@@ -20,62 +21,63 @@
 \contentsline {subsection}{\numberline {2.2.2}Optical Alignment}{24}{subsection.2.2.2}%
 \contentsline {subsection}{\numberline {2.2.3}Approach Curves}{26}{subsection.2.2.3}%
 \contentsline {subsection}{\numberline {2.2.4}Reproducibility}{29}{subsection.2.2.4}%
-\contentsline {subsubsection}{Reproducibility when removing sample/mask}{29}{section*.53}%
-\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{30}{subsection.2.2.5}%
-\contentsline {paragraph}{Leakage current}{35}{section*.66}%
-\contentsline {paragraph}{Improved gold pin fitting}{35}{section*.67}%
-\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{36}{subsection.2.2.6}%
-\contentsline {paragraph}{High correlation between capacitance curves}{36}{section*.68}%
-\contentsline {paragraph}{Low correlation between capacitance curves}{36}{section*.71}%
-\contentsline {section}{\numberline {2.3}Mask Aligner Operation}{36}{section.2.3}%
-\contentsline {subsection}{\numberline {2.3.1}Sample Preparation}{36}{subsection.2.3.1}%
-\contentsline {chapter}{\numberline {3}Electronics}{38}{chapter.3}%
-\contentsline {section}{\numberline {3.1}Slip Stick Principle}{38}{section.3.1}%
-\contentsline {section}{\numberline {3.2}RHK}{39}{section.3.2}%
-\contentsline {subsection}{\numberline {3.2.1}Overview}{39}{subsection.3.2.1}%
-\contentsline {paragraph}{amplitude}{39}{section*.74}%
-\contentsline {paragraph}{sweep period}{39}{section*.75}%
-\contentsline {paragraph}{time between sweeps}{39}{section*.76}%
-\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{39}{subsection.3.2.2}%
-\contentsline {section}{\numberline {3.3}KIM001}{40}{section.3.3}%
-\contentsline {subsection}{\numberline {3.3.1}Overview}{40}{subsection.3.3.1}%
-\contentsline {subsection}{\numberline {3.3.2}Pulse shape}{40}{subsection.3.3.2}%
-\contentsline {subsection}{\numberline {3.3.3}Voltage behavior}{41}{subsection.3.3.3}%
-\contentsline {section}{\numberline {3.4}Mask Aligner Controller "Walker"}{42}{section.3.4}%
-\contentsline {subsection}{\numberline {3.4.1}Overview}{42}{subsection.3.4.1}%
-\contentsline {subsection}{\numberline {3.4.2}Signal generation}{43}{subsection.3.4.2}%
-\contentsline {subsection}{\numberline {3.4.3}Fast flank}{44}{subsection.3.4.3}%
-\contentsline {subsection}{\numberline {3.4.4}Amplification}{45}{subsection.3.4.4}%
-\contentsline {subsection}{\numberline {3.4.5}Parameters}{45}{subsection.3.4.5}%
-\contentsline {paragraph}{Amplitude (amp)}{45}{section*.94}%
-\contentsline {paragraph}{Voltage (volt)}{46}{section*.95}%
-\contentsline {paragraph}{Channel}{46}{section*.96}%
-\contentsline {paragraph}{Max Step}{46}{section*.97}%
-\contentsline {paragraph}{Polarity}{46}{section*.98}%
-\contentsline {subsection}{\numberline {3.4.6}Measured Pulse shape}{46}{subsection.3.4.6}%
-\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{48}{subsection.3.4.7}%
-\contentsline {chapter}{\numberline {4}Mask Aligner Repairs and Optimizations}{49}{chapter.4}%
-\contentsline {section}{\numberline {4.1}Overview}{49}{section.4.1}%
-\contentsline {section}{\numberline {4.2}General UHV device preparation}{49}{section.4.2}%
-\contentsline {subsection}{\numberline {4.2.1}Adding components}{49}{subsection.4.2.1}%
-\contentsline {subsection}{\numberline {4.2.2}Soldering}{50}{subsection.4.2.2}%
-\contentsline {section}{\numberline {4.3}Soldering Anchors}{50}{section.4.3}%
-\contentsline {section}{\numberline {4.4}Piezo Reglueing}{53}{section.4.4}%
-\contentsline {section}{\numberline {4.5}Z3 Motor}{55}{section.4.5}%
-\contentsline {subsection}{\numberline {4.5.1}Front Plate repair}{56}{subsection.4.5.1}%
-\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{59}{subsection.4.5.2}%
-\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{60}{section.4.6}%
-\contentsline {section}{\numberline {4.7}Final Test}{60}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and Measurement}{63}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Silicon}{63}{section.5.1}%
-\contentsline {subsection}{\numberline {5.1.1}Sample Preparation}{63}{subsection.5.1.1}%
-\contentsline {subsection}{\numberline {5.1.2}Contamination}{64}{subsection.5.1.2}%
-\contentsline {subsection}{\numberline {5.1.3}Penumbra}{65}{subsection.5.1.3}%
-\contentsline {subsection}{\numberline {5.1.4}Tilt}{67}{subsection.5.1.4}%
-\contentsline {subsection}{\numberline {5.1.5}Simulation}{68}{subsection.5.1.5}%
-\contentsline {paragraph}{Improvements}{71}{section*.151}%
-\contentsline {chapter}{Conclusions and Outlook}{72}{chapter*.152}%
-\contentsline {chapter}{Bibliography}{73}{chapter*.153}%
-\contentsline {chapter}{List of Abbreviations}{74}{chapter*.154}%
-\contentsline {section}{\numberline {5.2}New Driver Electronics}{75}{section.5.2}%
-\contentsline {chapter}{Acknowledgments}{77}{chapter*.157}%
+\contentsline {subsubsection}{Reproducibility when removing sample/mask}{29}{section*.49}%
+\contentsline {subsubsection}{Reproducibility for different sample, but same mask}{31}{section*.54}%
+\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{31}{subsection.2.2.5}%
+\contentsline {paragraph}{Leakage current}{36}{section*.67}%
+\contentsline {paragraph}{Improved gold pin fitting}{36}{section*.68}%
+\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{37}{subsection.2.2.6}%
+\contentsline {paragraph}{High correlation between capacitance curves}{37}{section*.69}%
+\contentsline {paragraph}{Low correlation between capacitance curves}{37}{section*.72}%
+\contentsline {section}{\numberline {2.3}Mask Aligner Operation}{37}{section.2.3}%
+\contentsline {subsection}{\numberline {2.3.1}Sample Preparation}{37}{subsection.2.3.1}%
+\contentsline {chapter}{\numberline {3}Electronics}{39}{chapter.3}%
+\contentsline {section}{\numberline {3.1}Slip Stick Principle}{39}{section.3.1}%
+\contentsline {section}{\numberline {3.2}RHK}{40}{section.3.2}%
+\contentsline {subsection}{\numberline {3.2.1}Overview}{40}{subsection.3.2.1}%
+\contentsline {paragraph}{amplitude}{40}{section*.75}%
+\contentsline {paragraph}{sweep period}{40}{section*.76}%
+\contentsline {paragraph}{time between sweeps}{40}{section*.77}%
+\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{40}{subsection.3.2.2}%
+\contentsline {section}{\numberline {3.3}KIM001}{41}{section.3.3}%
+\contentsline {subsection}{\numberline {3.3.1}Overview}{41}{subsection.3.3.1}%
+\contentsline {subsection}{\numberline {3.3.2}Pulse shape}{41}{subsection.3.3.2}%
+\contentsline {subsection}{\numberline {3.3.3}Voltage behavior}{42}{subsection.3.3.3}%
+\contentsline {section}{\numberline {3.4}Mask Aligner Controller "Walker"}{43}{section.3.4}%
+\contentsline {subsection}{\numberline {3.4.1}Overview}{43}{subsection.3.4.1}%
+\contentsline {subsection}{\numberline {3.4.2}Signal generation}{44}{subsection.3.4.2}%
+\contentsline {subsection}{\numberline {3.4.3}Fast flank}{45}{subsection.3.4.3}%
+\contentsline {subsection}{\numberline {3.4.4}Amplification}{46}{subsection.3.4.4}%
+\contentsline {subsection}{\numberline {3.4.5}Parameters}{46}{subsection.3.4.5}%
+\contentsline {paragraph}{Amplitude (amp)}{46}{section*.95}%
+\contentsline {paragraph}{Voltage (volt)}{47}{section*.96}%
+\contentsline {paragraph}{Channel}{47}{section*.97}%
+\contentsline {paragraph}{Max Step}{47}{section*.98}%
+\contentsline {paragraph}{Polarity}{47}{section*.99}%
+\contentsline {subsection}{\numberline {3.4.6}Measured Pulse shape}{47}{subsection.3.4.6}%
+\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{49}{subsection.3.4.7}%
+\contentsline {chapter}{\numberline {4}Mask Aligner Repairs and Optimizations}{50}{chapter.4}%
+\contentsline {section}{\numberline {4.1}Overview}{50}{section.4.1}%
+\contentsline {section}{\numberline {4.2}General UHV device preparation}{50}{section.4.2}%
+\contentsline {subsection}{\numberline {4.2.1}Adding components}{50}{subsection.4.2.1}%
+\contentsline {subsection}{\numberline {4.2.2}Soldering}{51}{subsection.4.2.2}%
+\contentsline {section}{\numberline {4.3}Soldering Anchors}{51}{section.4.3}%
+\contentsline {section}{\numberline {4.4}Piezo Reglueing}{54}{section.4.4}%
+\contentsline {section}{\numberline {4.5}Z3 Motor}{56}{section.4.5}%
+\contentsline {subsection}{\numberline {4.5.1}Front Plate repair}{57}{subsection.4.5.1}%
+\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{60}{subsection.4.5.2}%
+\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{61}{section.4.6}%
+\contentsline {section}{\numberline {4.7}Final Test}{61}{section.4.7}%
+\contentsline {chapter}{\numberline {5}Evaporations and Measurement}{64}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Silicon}{64}{section.5.1}%
+\contentsline {subsection}{\numberline {5.1.1}Sample Preparation}{64}{subsection.5.1.1}%
+\contentsline {subsection}{\numberline {5.1.2}Contamination}{65}{subsection.5.1.2}%
+\contentsline {subsection}{\numberline {5.1.3}Penumbra}{66}{subsection.5.1.3}%
+\contentsline {subsection}{\numberline {5.1.4}Tilt}{68}{subsection.5.1.4}%
+\contentsline {subsection}{\numberline {5.1.5}Simulation}{69}{subsection.5.1.5}%
+\contentsline {paragraph}{Improvements}{72}{section*.152}%
+\contentsline {chapter}{Conclusions and Outlook}{73}{chapter*.153}%
+\contentsline {chapter}{Bibliography}{74}{chapter*.154}%
+\contentsline {chapter}{List of Abbreviations}{75}{chapter*.155}%
+\contentsline {section}{\numberline {5.2}New Driver Electronics}{76}{section.5.2}%
+\contentsline {chapter}{Acknowledgments}{78}{chapter*.158}%