Abstract: Artemisinin (ART) is a vital medicinal compound that is used alone or as part of a combination therapy against malaria. ART is thought to function by attaching to heme covalently and alkylating a range of proteins. Using a combination of biophysical methods, we demonstrate that ART is bound by three-way junction and duplex containing DNA molecules. Binding of ART by DNA is first shown for the cocaine-binding DNA aptamer and extensively studied using this DNA molecule. Isothermal titration calorimetry methods show that the binding of ART is both entropically and enthalpically driven at physiological NaCl concentration. Native mass spectrometry methods confirm DNA binding and show that a non-covalent complex is formed. Nuclear magnetic resonance spectroscopy shows that ART binds at the three-way junction of the cocaine-binding aptamer, and that binding results in the folding of the structure-switching variant of this aptamer. This structure-switching ability was exploited using the photochrome aptamer switch assay to demonstrate that ART can be detected using this biosensing assay. This study is the first to demonstrate the DNA binding ability of ART and should lay the foundation for further work to study implications of DNA binding for the antimalarial activity of ART.

Abstract: Encompassing a broad spectrum of methodological approaches and aims, the scholars contributing to this volume offer renewed perspectives on the multifaceted oeuvre of Diego Velázquez. The seventeenth-century artist’s exceptional religious works as well as his numerous portraits are examined within the social and historical context of Velázquez’s milieu which included both the Spanish court as well as circles comprising important intellectual figures of his time. Following a close investigation of his works, which also includes the results of recent technological examinations on his paintings, the contributors to this volume offer new, exciting findings and discussions on the inspirations, sources and possible intentions of Velázquez.

Abstract: Currently, a large variety of materials are studied by transmission electron microscopy (TEM) as it offers the possibility to perform structural and elemental analysis at a local scale. Relatively recent advances in aberration correctors and electron sources allow the instrument to achieve atomic resolution. Along with these advances, a state-of-the-art technology has been reached in TEM. However, the instrument is far from being perfect and imperfections or external sources can make the interpretation of information troublesome. Environmental factors such as acoustic and mechanical vibrations, temperature fluctuations, etc., can induce sample drift and create image distortions. These distortions are enhanced in scanning operation because of the serial acquisition of the information, which are more apparent at atomic resolution as small field of views are imaged. In addition, scanning distortions are induced due to the finite time response of the scan coils. These types of distortions would reduce precision in atomic-scale strain analysis, for instance, in semiconductors. Most of the efforts to correct these distortions are focused on data processing techniques post-acquisition. Another limitation in TEM is beam damage effects. Beam damage arises because of the energy transferred to the sample in electron-sample interactions. In scanning TEM, at atomic resolution, the increased electron charge density (electron dose) carried on a sub-Å size electron probe may aggravate beam damage effects. Soft materials such as zeolites, organic, biological materials, etc., can be destroyed under irradiation limiting the amount of information that can be acquired. Current efforts to circumvent beam damage are mostly based on low electron dose acquisitions and data processing methods to maximize the signal at low dose conditions. In this thesis, a different approach is given to address drift and scanning distortions, as well as beam damage effects. Novel scan strategies are proposed for that purpose, which are shown to substantially overcome these issues compared to the standard scan method in TEM.

Abstract: A new equation for predicting the generated bremsstrahlung background intensity in electron-probe x-ray microanalysis has been verified experimentally. This equation is applicable to all bulk composite specimens and reduces to Kramers' equation for pure elements only. The experimental verification has been carried out for Al2O3, Fe2O3 and ZrO2 with radiation energies from 4.2 to 14.8 keV. The predicted bremsstrahlung intensities are in good agreement with the experimental data.

Abstract: In the last few decades, nanostructuring has driven significant attention towards the development of novel metallic materials with advanced mechanical properties. Nanocrystalline (nc) metals are a class of nanostructured materials with grain sizes smaller than about 100 nm. These exhibit outstanding mechanical strength and fatigue properties compared to their coarse-grained (cg) counterparts. These are promising candidates for application as structural or functional materials. Nc metals in the form of thin films are employed as hard coatings on bulk components, structural components, and conductive layers in various micro-/nanoscale devices. These structural components and devices are often subjected to cyclic stresses or fatigue loading. Under these cyclic stresses, nc metals tend to exhibit the Bauschinger effect (BE). The strength loss during the BE is of great importance concerning the strength-ductility trade-off in nc metals. Furthermore, contact surfaces of the engineering components in service often undergo relative motion and are subject to both friction and wear. These extreme loading conditions demand nc metals with tailored interfacial characteristics for improved tribological performance. Aiming at ensuring high reliability and mechanical robustness for optimum performance of these components, there has been a strong motivation for understanding the mechanical properties and governing deformation mechanisms in nc metallic materials. This thesis aimed at in-depth investigation of microstructures at micro-/nanoscales using state-of-the-art in situ and ex situ transmission electron microscopy (TEM) to develop a closer link between the deformation structure and underlying deformation mechanisms in some nc metallic materials. The thesis has primarily focused on the in situ TEM nanomechanics of the BE and rotational deformation of grains in nc palladium thin films. A sputtered thin film of nc Pd was deformed inside TEM by cyclic loading-unloading experiments and the evolving microstructure was studied in real-time under different TEM imaging modes. The stress-strain response of the film exhibited a characteristic non-linear unloading behavior confirming the BE in the film. The corresponding bright-field TEM imaging revealed evidence of partially reversible dislocation activity. Towards a quantitative understanding of the deformation structure in real-time, in situ nanomechanical testing was coupled with precession-assisted automated crystal orientation mapping in scanning TEM (ACOM-STEM). Global ACOM-STEM analysis offered crystal orientation of a large number of grains at different states of deformation and confirmed partially reversible rotations of nanosized grains fitting to the observed BE during loading and unloading. Analysis of intragranular rotations showed substantial changes in the sub-structure within most of these grains indicating a dominant role of dislocation-based processes in driving these rotations. Globally, an unusually random evolution of texture was seen that demonstrated the influence of deformation heterogeneity and grain interactions on the resulting texture characteristics in nc metals. In the quest of understanding the grain interactions, local investigations based on annular dark-field STEM imaging during loading-unloading showed reversible changes in the contrast of grains with sets of adjoining grains exhibiting a unique cooperative rotation. Local analysis of the density of geometrically necessary dislocations (GNDs) showed the formation of dislocation pile-up at grain boundaries due to the generation of back-stresses during unloading. Critical observations of the evolution of GND density offered greater insights into the mechanism of cooperative grain rotations and these rotations were related to grain structure and grain boundary characteristics. In addition to understanding the influence of grain structure and grain boundaries, the thesis has further investigated the role of heterointerfaces in sputtered Au-Cu and Cu-Cr nanocrystalline multilayered composites (NMCs) deformed under cyclic sliding contact. The microstructural evolution in the NMCs was investigated at different deformation states by classical TEM imaging, ACOM-STEM as well as energy-filtered TEM (EFTEM). Au-Cu NMC with an initial high density of twin boundaries deformed by stress-driven detwinning with a concurrent change in grain structure in both Au and Cu. The formation of a vortex structure was observed due to plastic flow instabilities at Au-Cu interfaces that led to codeformation and mechanical intermixing. Cu-Cr NMC showed a preferential grain growth in Cu layers whereas no noticeable change in the grain sizes was seen in Cr layers. The phase maps revealed sharp interfaces between Cu and Cr layers indicating no intermixing between the immiscible phases. EFTEM results exposed the cracking processes in Cr layers with a concurrent migration of Cu in the cracks. Overall, the thesis has attempted to analyze the competing deformation processes and relate these with the microstructural heterogeneity in terms of grain structure and GB and interfacial characteristics in nc metallic materials.

Abstract: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal diseases, characterized by a treatment-resistant and invasive nature. In line with these inherent aggressive characteristics, only a subset of patients shows a clinical response to the standard of care therapies, thereby highlighting the need for a more personalized treatment approach. In this study, we comprehensively unraveled the intra-patient response heterogeneity and intrinsic aggressive nature of PDAC on bulk and single-organoid resolution. We leveraged a fully characterized PDAC organoid panel ( N  = 8) and matched our artificial intelligence-driven, live-cell organoid image analysis with retrospective clinical patient response. In line with the clinical outcomes, we identified patient-specific sensitivities to the standard of care therapies (gemcitabine-paclitaxel and FOLFIRINOX) using a growth rate-based and normalized drug response metric. Moreover, the single-organoid analysis was able to detect resistant as well as invasive PDAC organoid clones, which was orchestrates on a patient, therapy, drug, concentration and time-specific level. Furthermore, our in vitro organoid analysis indicated a correlation with the matched patient progression-free survival (PFS) compared to the current, conventional drug response readouts. This work not only provides valuable insights on the response complexity in PDAC, but it also highlights the potential applications (extendable to other tumor types) and clinical translatability of our approach in drug discovery and the emerging era of personalized medicine.

Abstract: Nanoscience and nanotechnologies are of immense importance across many fields of science and for numerous practical applications. In this context, scanning transmission electron microscopy (STEM) and 4D-STEM are among the most powerful characterization methods at the atomic scale. Annular dark-field (ADF)-STEM can be used to quantify atomic structures in 3D by counting atoms based on a single projection image. In 4D-STEM a full diffraction pattern is recorded at each scan step, which enables more dose efficient imaging and the utilization of various advanced imaging modalities, which can however be complex and slow. Both, STEM and 4D-STEM suffer from noise and distortions. In the first section of this work the most important of these distortions are discussed and it is shown how image restoration with a dedicated convolutional neural network (CNN) can be beneficial for atomic structure quantifications in ADF-STEM. In the second part, a new 4D-STEM imaging method real-time-integrated-centre-of-mass (riCOM) is introduced, which is a very dose-efficient and fast algorithm that enables unprecedented live-imaging capabilities for 4D-STEM. It is based on the integrated centre-of-mass approach, but is reformulated with variable integration ranges and optional filters, which allows for a tunable contrast transfer function. This enables the imaging of light and heavy elements simultaneously at very low doses. In the third part another new 4D-STEM method, coined AIRPI (AI-assisted rapid phase imaging) is introduced, which uses a CNN to retrieve a patch of the specimen's phase image for each scan position, based on the diffraction patterns in the probe's immediate surroundings. This allows also live imaging in principle and surpasses comparable state-of-the-art algorithms in terms of resolution also at low doses. Different atomic columns can be reliably distinguished over a wide range of atomic numbers, enabling a very good image interpretability. Further, AIRPI can recover low frequency image components, which preserves thickness information. This is a unique and important feature which could make quantitative 4D-STEM feasible.