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Over the past few decades, Single-Particle Analysis (SPA), in combination with cryo-transmission electron microscopy, has evolved into one of the leading technologies for structural analysis of biological macromolecules. It allows the investigation of biological structures in a close to native state at the molecular level. Within the last five years the achievable resolution of SPA surpassed 2°A and is now approaching atomic resolution, which so far has only been possible with Xray crystallography in a far from native environment. One remaining problem of Cryo-Electron Microscopy (cryo-EM) is the weak image contrast. Since the introduction of cryo-EM in the 1980s phase plates have been investigated as a potential tool to overcome these contrast limitations. Until now, technical problems and instrumental deficiencies have made the use of phase plates difficult; an automated workflow, crucial for the acquisition of 1000s of micrographs needed for SPA, was not possible. In this thesis, a new Zernike-type Phase Plate (PP) was developed and investigated. Freestanding metal films were used as a PP material to overcome the ageing and contamination problems of standard carbon-based PPs. Several experiments, evaluating and testing various metals, ended with iridium as the best-suited material. A thorough investigation of the properties of iridium PP followed in the second part of this thesis. One key outcome is a new operation mode, the rocking PP. By using this rocking-mode, fringing artifacts, another obstacle of Zernike PPs, could be solved. In the last part of this work, acquisition and reconstruction of SPA data of apoferritin was performed using the iridium PP in rocking-mode. A special semi-automated workflow for the acquisition of PP data was developed and tested. The recorded PP data was compared to an additional reference dataset without a PP, acquired following a conventional workflow.
Nanotemplates for the combined structural and functional analysis of membrane-associated proteins
(2019)
Plasma membranes are essential for life because they give cells an identity. Plasma membranes are almost impermeable to fluids and substances. Still, transport between inside and outside needs to be possible. An important transport way is endocytosis. This mechanism relies on membrane-associated proteins that sense and induce curvature to the plasma membrane. However, the physics and structural dynamics behind proteins acting on membranes is not well understood. There is a standard method in vitro to investigate membrane-associated proteins sensing spherical geometries: They are incubated on unilamellar vesicles. This procedure allows to analyze these proteins in their bound state. This approach is inappropriate for GRAF1 (GTPase Regulator Associated with Focal Adhesion Kinase-1), a key player in endocytosis because it senses tubular geometries instead. However, GRAF1 extrudes lipid tubes from vesicles that can be analyzed. Still, this is a limited method because these tubes suffer from inhomogeneity and they do not enable the observation of intermediate and lower concentration binding states. To overcome this issue they can be incubated on pre-tubular structures called nanotemplates. There have been studies using carbon nanotubes and Galactosylceramide lipid tubes as nanotemplates. These approaches require complex chemical modifications or expensive components and they are not necessarily flexible. In this work we present a simple and easy new approach to prepare nanotemplates using Folch lipid mixture. We show on the basis of BPG, a truncate of GRAF1, that our nanotemplates are suitable for Cryo-EM and that it is possible to use IHRSR (Iterative Helical Real Space Reconstruction) to analyze the structure of BPG in its bound state. Moreover, the qualification for Cryo-EM allows to use plunge freezing to interrupt the incubation on our nanotemplates abruptly. This enables the analysis of intermediate binding states to understand the binding process.
The three biodegradable polymers polylactic acid (PLA), polyhydroxybutyrate (PHB) and polybutylene adipate terephthalate (PBAT) were coated with hydrogenated amorphous carbon layers (a-C:H) in the context of this thesis. A direct alignment of the sample surface to the source was chosen, resulting in the deposition of a robust, r-type a-C:H. At the same time, a partly covered silicon wafer was placed together with the polymers in the coating chamber and was coated. Silicon is a hard material and serves as a reference for the applied layers. Due to the hardness of the material, no mixed phase occurs between the substrate and the applied layer (no interlayer formation). In addition, the thickness of the applied layer can be estimated with the help of the silicon sample.
The deposition of the layer was realized by radio frequency plasma enhanced chemical vapor deposition (RF-PECVD). For the coating the samples were pre-treated with an oxygen plasma. Acetylene was used as precursor gas for the plasma coating. Coatings with increasing thickness in 50 nm steps from 0-500 nm were realised.
The surface analysis was performed using several techniques: The morphology and layer stability were analyzed with scanning electron microscopy (SEM) measurements. The wettability was determined by contact angle technique. In addition, the contact angles provide macroscopic information about the bond types of the carbon atoms present on the surface. For microscopic analysis of the chemical composition of the sample and layer surfaces, diffuse reflectance Fourier transform infrared spectroscopy (DRIFT) as well as synchrotron based X-ray photon spectroscopy (XPS) and near edge X-ray absorption fine structure spectroscopy (NEXAFS) were used.
All coated polymers showed several cases of layer failure due to internal stress in the layers. However, these were at different layer thicknesses, so there was a substrate effect. In addition, it is visible in the SEM images that the coatings of PLA and PHB can cause the applied layer to wave, the so-called cord buckling. This does not occur with polymer PBAT, which indicates a possible better bonding of the layer to the polymer. The chemical analyses of the layer surfaces show for each material a layer thickness dependent ratio of sp² to sp³ bonds of carbon, which alternately dominate the layer. In all polymers, the sp³ bond initially dominates, but the sp² to sp³ ratio changes at different intervals. Although the polymers were coated in the same plasma, i.e. the respective layer thicknesses (50 nm, 100 nm, ...) were applied in the same plasma process, the respective systems differed considerably from each other. A substrate effect is therefore demonstrably present. In addition, it was found that a change in the dominant bond from sp³ to sp² is an indication ofan upcoming layer failure of the a-C:H layer deposited on the polymer. In the case of PLA, this occurs immediately with change to sp² as the dominant bond; in the case of PHB and PBAT, this occurs with different delay to increased layer thicknesses (at PHB 100 nm, at PBAT approx. 200 nm.
Overall, this thesis shows that there is a substrate effect in the coating of the biodegradable polymers PLA, PHB and PBAT, since despite the same coating there is a different chemical composition of the surface at the respective layer thicknesses. In addition, a layer failure can be predicted by analyzing the existing bond.
Spektroskopie zweiatomiger Moleküle bei Einstrahlung ultrakurzer Laserpulse und ihre Anwendung
(2020)
Even with moderate pulse energies and average powers, ultrashort pulse lasers achieve very high peak powers, whose effect on matter is fundamentally different from that of other light sources. The high electric field strength does not only cause an increase of optically nonlinear effects such as second harmonic generation, but it is also responsible for the “cold“ ablation, which leads to colder plasmas. An investigation of these two circumstances in terms of a simplification of the pulse duration measurement and an improvement of the molecular formation in cooling plasmas is the topic of this work. In this context, it is shown that when selecting suitable process parameters, especially when purposefully defocusing the medium, the use of ultrashort pulse lasers improves the spectroscopy of several emitting molecules such as aluminum oxide. Therefore, their detection is possible even without the time-resolving spectrometers required in literature. In addition, ultrashort pulses enable spatially resolved crystallization of zinc oxide on zinc surfaces prepared by basic means. The resulting wurtzites usually align their c-axis approximately perpendicular to the underlying surface and can be used to generate scattered second harmonics. Fiber-based femtosecond lasers with pulse energies in the microjoule range, pulse durations of a few 100fs and very low maintenance requirements have proven to be a powerful instrument for these purposes. For measuring the pulse duration, the high pulse energy also enables the usage of frequency doublers with much lower conversion eciencies. Despite nonuniform crystal axes, the scattering second harmonic generating aluminum nitride has proven to be particularly suitable for optical autocorrelation. Compared to the commonly used monocrystalline beta-barium borate, the sintered aluminum nitride ceramic plates facilitate the adjustment, simplify the material handling and reduce the expenses by two to three orders of magnitude. The method developed in this work is therefore also suitable for confirmatory measurements of the pulse duration during the production process of such systems – especially when the occurring pulse energies are high or rather too high for beta-barium borate.
The analysis of three-dimensional and complex motion sequences
of human gait and therefore the most important question
of kenesiology ”why are we falling?” is the essence of this
paper. The gerontology and its science of movement is currently
limited to simple and one-dimensional methods and models. An
extensive literature research shows the latest state of research of
the three common methods to determine the stability of human
gait. To assess the margin of stability, local stability and orbital
stability it is shown, how those methods are applicable to evaluate
the subject’s ability to recover from any disturbences of
the subject’s gait. Based on this assessment and the method’s
advantages and disadvantages a new method will be derived
that allows spatial analysis of dynamic instability of linear and
non-linear human gait. A motion capture system and the timed
up and go test serve as a basis for this new method and will be
explained. A numerical approximation to optimise the number
of markers within a marker-set of a motion capture analysis
and its maximum correlation with the full-body-marker-set will
be given. This simplification is very helpful for further clinical
or scientific research. To validate the new method a trial
with subjects will be shown and discussed. New appreciable
variables and snapshots of specific situations during the gait
offer new and different interpretations of the human gait. The
new method is the most applicable and appropriate assessment
of human gait and the individual development of the human
gait while aging, as well as to detect and prevent falling and
associated injuries. Especially directional change of a non-linear
gait become assessable with the new method.
The biodegradable polymers polylactic acid (PLA) and polyhydroxybutyrate (PHB) produced from renewable raw materials were coated with hydrogenated amorphous carbon layers (a-C:H) at different deposition angles with various thicknesses as part of this thesis. Similar to conventional polymers, biopolymers often have unsuitable surface properties for industrial purposes, e.g. low hardness. For some applications, it is therefore necessary and advantageous to modify the surface properties of biopolymers while retaining the main properties of the substrate material. A suitable surface modification is the deposition of thin a-C:H layers. Their properties depend essentially on the sp² and sp³ hybridization ratio of the carbon atoms and the content of hydrogen atoms. The sp²/sp³ ratio was to be controlled in the present work by varying the coating geometry. Since coatings at 0°, directly in front of the plasma source, contain a higher percentage of sp³ and indirectly coated (180°) a higher amount of sp², it is shown in this work that it is possible to control the sp²/sp³ ratio. For this purpose, the samples are placed in front of the plasma source at angles of 0, 30, 60, 90, 120, 150 and 180° and coated for 2.5, 5.0, 7.5 and 10.0 minutes. For the angles 0°, the layer thicknesses were 25, 50, 75 and 100 nm. The a-C:H layers were all deposited using radio-frequency plasma-enhanced chemical vapor deposition and acetylene as C and H sources after being pretreated with an oxygen plasma for 10 minutes. Following the O₂ treatment and the a-C:H deposition, the surfaces are examined using macroscopic and microscopic measurement methods and the data is then analyzed. The surface morphology is recorded using scanning electron microscopy and atomic force microscopy. In addition, data on the stability of the layer and the surface roughness can be collected. Contact angle (CA) measurements are used to determine not only the wettability, but also the contact angle hysteresis by pumping the drop volume up and down. By measuring the CA with different liquids and comparing them, the surface free energy (SFE) and its polar and disperse components are determined. The changes in barrier properties are verified by water vapor transmission rate tests (WVTR). The chemical analysis of the surface is carried out on the one hand by Fourier transform infrared spectroscopy with specular reflection and on the other hand by synchrotron-supported techniques such as near-edge X-ray absorption fine structure and X-ray photoelectron spectroscopy. When analyzing the surfaces after the O₂ treatment, which was initially assumed to serve only to clean and activate the surface for the a-C:H coating, it was found that the changes were more drastic than originally assumed. For example, if PLA is treated at 0° for 10 minutes, the roughness increases fivefold. As the angle increases, it decreases again until it returns to the initial value at 180°. This can be recognized to a lesser extent with PHB at 30°. For both polymers, it can be shown that the polar fraction of the SFE increases. In the WVTR, a decrease in permeability can be observed for PLA and an increase in the initial value for PHB. The chemical surface analysis shows that the O₂ treatment has little effect on the surface bonds. Overall, it can be shown in this work that the O₂ treatment has an effect on the properties of the surface and cannot be regarded exclusively as a cleaning and activation process. With direct a-C:H coating (at 0°), a layer failure due to internal stress can be observed for both PLA and PHB. This also occurs with PHB at 30°, but to a lesser extent. Permeability of the polymers is reduced by 47% with a five-minute coating and the layer at 10.0 minutes continues to have this effect despite cracks appearing. The application of a-C:H layers shows a dominance of sp³ bonds for both polymer types with direct coating. This decreases with increasing angle and sp² bonds become dominant for indirect coatings. This result is similar for all coating thicknesses, only the angle at which the change of the dominant bond takes place is different. It is shown that it is possible to control the surface properties by an angle-dependent coating and thus to control the ratio sp²/sp³.