Abstract: van der Waals (vdW) forces play an important role in the adsorption of molecules on the surface of solids. However, the choice of the most suitable vdW functional for different systems is an essential problem which must be addressed for different systems. The lack of a systematic study on the performance of the vdW functionals in the bulk and adsorption properties of metal-oxides motivated us to examine different vdW approaches and compute the bulk and molecular adsorption properties of alpha-Cr2O3, alpha-Fe2O3, and alpha-Al2O3. For the bulk properties, we compared our results for the heat of formation, cohesive energy, lattice parameters and bond distances between the different vdW functionals and available experimental data. Next we studied the adsorption of benzene and CH3 molecules on top of different oxide surfaces. We employed different approximations to exchange and correlation within DFT, namely, the Perdew-Burke-Ernzerhof (PBE) GGA, (PBE)+U, and vdW density functionals [ DFT(vdW-DF/DF2/optPBE/optB86b/optB88)+U] as well as DFT-D2/D3(+U) methods of Grimme for the bulk calculations and optB86b-vdW(+U) and DFT-D2(+U) for the adsorption energy calculations. Our results highlight the importance of vdW interactions not only in the adsorption of molecules, but importantly also for the bulk properties. Although the vdW contribution in the adsorption of CH3 (as a chemisorption interaction) is less important compared to the adsorption of benzene (as a physisorption interaction), this contribution is not negligible. Also adsorption of benzene on ferryl/chromyl terminated surfaces shows an important chemisorption contribution in which the vdW interactions become less significant.

Abstract: Doped Cr2O3 has been shown to be a p-type transparent conducting oxide (TCO). Its conductivity, however, is low. As for most p-type TCOs, the main problem is the high effective hole mass due to flat valence bands. We use first-principles methods to investigate whether one can increase the valence band dispersion (i.e. reduce the hole mass) by anion alloying with sulfur, while keeping the band gap large enough for transparency. The alloying concentrations considered are given by Cr(4)SxO(6-x), with x = 1-5. To be able to describe the electronic properties of these materials accurately, we first study Cr2O3, examining critically the accuracy of different density functionals and methods, including PBE, PBE+U, HSE06, as well as perturbative approaches within the GW approximation. Our results demonstrate that Cr4S2O4 has an optical band gap of 3.08 eV and an effective hole mass of 1.8 m(e). This suggests Cr4S2O4 as a new p-type TCO host candidate.

Abstract: The thermodynamic aspects of various 2D materials are explored using Density Functional Theory (DFT). Various metal chalcogenides (MX2, M = metal, chalcogen X = S, Se, Te) are investigated with respect to their interaction and stability under different ambient conditions met in the integration process of a transistor device. Their interaction with high- dielectrics is also addressed, in order to assess their possible integration in Complementary Metal Oxide Semiconductor (CMOS) field effect transistors. 2D materials show promise for high performance nanoelectronic devices, but the presence of defects (vacancies, grain boundaries,...) can significantly impact their electronic properties. To assess the impact of defects, their enthalpies of formation and their signature levels in the density of states have been studied. We find, consistently with literature reports, that chalcogen vacancies are the most likely source of defects. It is shown that while pristine 2D materials are in general stable whenever set in contact with different ambient atmospheres, the presence of defective sites affects the electronic properties of the 2D materials to varying degrees. We observe that all the 2D materials studied in the present work show strong reactivity towards radical oxygen plasma treatments while reactivity towards other common gas phase chemical such as O-2 and H2O and groups present at the high- surface varies significantly between species. While energy band-gaps, effective masses and contact resistivities are key criteria in selection of 2D materials for scaled CMOS and tunneling based devices, the phase and ambient stabilities might also play a very important role in the development of reliable nanoelectronic applications.

Abstract: The structure of Bi0.81Pb0.19FeO2.905 was investigated on different length scales using a combination of electron diffraction, high-resolution scanning transmission electron microscopy, synchrotron X-ray powder diffraction, and Mössbauer spectroscopy. In the 80300 K temperature range, the average crystal structure of Bi0.81Pb0.19FeO2.905 is a cubic Pm3̅m perovskite with a = 3.95368(3) Å at T = 300 K. The (Pb2+, Bi3+) cations and O2 anions are randomly displaced along the 110 cubic directions, indicating the steric activity of the lone pair on the Pb2+ and Bi3+ cations and a tilting distortion of the perovskite framework. The charge imbalance induced by the heterovalent Bi3+ → Pb2+ substitution is compensated by the formation of oxygen vacancies preserving the trivalent state of the Fe cations. On a short scale, oxygen vacancies are located in anion-deficient (FeO1.25) layers that are approximately 6 perovskite unit cells apart and transform every sixth layer of the FeO6 octahedra into a layer with a 1:1 mixture of corner-sharing FeO4 tetrahedra and FeO5 tetragonal pyramids. The anion-deficient layers act as twin planes for the octahedral tilting pattern of adjacent perovskite blocks. They effectively randomize the octahedral tilting and prevent the cooperative distortion of the perovskite framework. The disorder in the anion sublattice impedes cooperative interactions of the local dipoles induced by the off-center displacements of the Pb and Bi cations. Magnetic susceptibility measurements evidence the antiferromagnetic ordering in Bi0.81Pb0.19FeO2.905 at low temperatures.

Abstract: This study focuses on four textile industries (DH-GEDA, NOYA, ALMHADI, and ALSAR) established between 2005 and 2008 in the peri-urban areas of Dukem and Gelan. The objectives of the study were to generate baseline information regarding the concentration levels of selected pollutants and to analyze their effects on biophysical environments. This study also attempts to explore the level of exposure that humans and livestock have to polluted effluents and the effects thereof. The findings of this study are based on data empirically collected from two sources: laboratory analysis of sample effluents from the four selected textile plants and quantitative as well as qualitative socioeconomic data collection. As part of the latter, a household survey and focus group discussions (FGDs) with elderly and other focal persons were employed in the towns of Dukem and Gelan. The results of the study show that large concentrations of biological oxygen demand (BOD5), chemical oxygen demand (COD), total suspended solids (TSS), and pH were found in all the observed textile industries, at levels beyond the permissible discharge limit set by the national Environmental Protection Authority (EPA). Furthermore, sulfide (S2), R-phosphate (R-PO43), and Zn were found in large concentrations in DH-GEDA and ALMHADI, while high concentrations were also identified in samples taken from ALSAR and ALMHADI. In spite of the clear-cut legal tools, this study shows that the local environment, people, and their livestock are exposed to highly contaminated effluents. We therefore recommend that the respective federal and regional government bodies should reexamine the compliance to and actual implementation of the existing legal procedures and regulations and respond appropriately.

Abstract: Although most state-of-the-art Sn-based electrocatalysts yield promising results in terms of selectivity and catalyst activity, their stability remains insufficient to date. Here, we demonstrate the successful application of the recently developed pomegranate-structured SnO2 (Pom. SnO2) and SnO2@C (Pom. SnO2@C) nanocomposite electrocatalysts for the efficient electrochemical conversion of CO2 to formate. With an initial selectivity of 83 and 86% towards formate and an operating potential of -0.72 V and -0.64 V vs. RHE, respectively, these pomegranate SnO2 electrocatalysts are able to compete with most of the current state-of-the-art Sn-based electrocatalysts in terms of activity and selectivity. Given the importance of electrocatalyst stability, long-term experiments (24 h) were performed and a temporary loss in selectivity for the Pom. SnO2@C electrocatalyst was largely restored to its initial selectivity upon drying and exposure to air. Of all the used (24 h) electrocatalysts, the pomegranate SnO2@C had the highest selectivity over a time period of one hour, reaching an average recovered FE of 85%, while the commercial SnO2 and bare pomegranate SnO2 electrocatalysts reached an average of 79 and 80% FE towards formate, respectively. Furthermore, the pomegranate structure of Pom. SnO2@C was largely preserved due to the presence of the heterogeneous carbon shell, which acts as a protective layer, physically inhibiting particle segregation/pulverisation and agglomeration.

Abstract: The ability to detect low concentrations of protein biomarkers is crucial for the early-stage detection of many diseases and therefore indispensable for improving diagnostic devices for healthcare. Here, we demonstrate that by integrating DNA nanotechnologies like DNA origami and aptamers, we can design innovative biosensing concepts for reproducible and sensitive detection of specific targets. DNA origami structures decorated with aptamers were studied as a novel tool to structure the biosensor surface with nanoscale precision in a digital detection bioassay, enabling control of the density, orientation, and accessibility of the bioreceptor to optimize the interaction between target and aptamer. DNA origami was used to control the spatial distribution of an in-house-generated aptamer on superparamagnetic microparticles, resulting in an origami-linked digital aptamer bioassay to detect the main peanut antigen Ara h1 with 2-fold improved signal-to-noise ratio and 15-fold improved limit of detection compared to a digital bioassay without DNA origami. Moreover, the sensitivity achieved was 4 orders of magnitude higher than commercially available and literature-reported enzyme-linked immunosorbent assay techniques. In conclusion, this novel and innovative approach to engineer biosensing interfaces will be of major interest to scientists and clinicians looking for new molecular insights and ultrasensitive detection of a broad range of targets, and, for the next generation of diagnostics.

Abstract: Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application.

Abstract: The range of applications for aptamers, small oligonucleotide-based receptors binding to their targets with high specificity and affinity, has been steadily expanding. Our understanding of the mechanisms governing aptamer-ligand recognition and binding is however lagging, stymieing the progress in the rational design of new aptamers and optimization of the known ones. Here we demonstrate the capabilities and limitations of native ion mobility-mass spectrometry for the analysis of their higher-order structure and non-covalent interactions. A set of related cocaine-binding aptamers, displaying a range of folding properties and ligand binding affinities, was used as a case study in both positive and negative electrospray ionization modes. Using carefully controlled experimental conditions, we probed their conformational behavior and interactions with the high-affinity ligand quinine as a surrogate for cocaine. The ratios of bound and unbound aptamers in the mass spectra were used to rank them according to their apparent quinine-binding affinity, qualitatively matching the published ranking order. The arrival time differences between the free aptamer and aptamer-quinine complexes were consistent with a small ligand-induced conformational change, and found to inversely correlate with the affinity of binding. This mass spectrometry-based approach provides a fast and convenient way to study the molecular basis of aptamer-ligand recognition.

Abstract: Aptamers are promising biorecognition elements with a wide applicability from therapeutics to bio-sensing. However, to successfully use these biomolecules, a complete characterisation of their bindingperformance in the presence of the target is crucial. Several multi-analytical approaches have been re-ported including techniques to describe kinetic and thermodynamic aspects of the aptamer-targetinteraction, and techniques which allow an in-depth understanding of the aptamer-target structures.Recent literature shows the need of a critical data interpretation, a combination of characterisationtechniques and suggests the key role of the characterisation protocol design. Indeed, thefinal applicationof the aptamer should be considered before choosing the characterisation method. All the limitations andcapabilities of the analytical tools in use for aptamer characterisation should be taken into account. Here,we present a critical overview of the current methods and multi-analytical approaches to study aptamer-target binding, aiming to provide researchers with guidelines for the design of characterisation protocols.

Abstract: Different cement samples commonly used in building construction in Turkey have been analyzed for natural radioactivity using gamma-ray spectrometry. The mean activity concentrations observed in the cement samples were 52, 40 and 324 Bq kg−1 for 226Ra, 232Th and 40K, respectively. The measured activity concentrations for these radionuclides were compared with the reported data of other countries and world average limits. The radiological hazard parameters such as radium equivalent activities (Raeq), gamma index (Iγ) and alpha index (Iα) indices as well as terrestrial absorbed dose and annual effective dose rate were calculated and compared with the international data. The Raeq values of cement are lower than the limit of 370 Bq kg−1, equivalent to a gamma dose of 1.5 mSv y−1. Moreover, the mass attenuation coefficients were determined experimentally and calculated theoretically using XCOM in some cement samples. Also, chemical compositions analyses of the cement samples were investigated.

Abstract: An important issue in biodiversity valuation is gaining a better understanding of how biodiversity conservation affects economic activities and human welfare. Quantifying the economic benefits of biodiversity for human well-being is not straightforward. Here, we expand the ecosystem service cascade by (i) attributing a methodology to the different steps of the cascade to assess the effects of changes in functional group diversity on economic activities; (ii) including multiple attributes for defining functional diversity and (iii) integrating a dynamic ecological model simulating complex interactions and feedbacks between species with an economic model assessing the effects of changes in functional group diversity for gross revenues. The stepwise methodological framework integrates a production function approach with a market price-based approach in order to investigate the indirect use value of functional group diversity based on the ecological role of species in the ecosystem. The methodology is applied to estimate the relationship between the gross economic value of Chinook salmon (Pacific Northwest, United States) and the diversity of freshwater macroinvertebrates. The results of our analysis emphasize the importance of biological diversity for sustaining ecosystem goods and services. The analysis provides a tractable framework for quantitatively exploring the economic consequences of changes in functional group diversity.

Abstract: We numerically study the vortex-vortex interaction in multicomponent homogeneous Bose-Einstein condensates within the realm of the Gross-Pitaevskii theory. We provide strong evidence that pairwise vortex interaction captures the underlying mechanisms which determine the geometric configuration of the vortices, such as different lattices in many-vortex states, as well as the bound vortex states with two (dimer) or three (trimer) vortices. Specifically, we discuss and apply our theoretical approach to investigate intra- and intercomponent vortex-vortex interactions in two- and three-component Bose-Einstein condensates, thereby shedding light on the formation of the exotic vortex configurations. These results correlate with current experimental efforts in multicomponent Bose-Einstein condensates and the understanding of the role of vortex interactions in multiband superconductors.