Abstract: During the past decades, metallic nanoparticles (NPs) have attracted great attention in materials science due to their specific optical properties based on surface plasmon resonances. Because of these phenomena, plasmonic NPs (or nanoplasmonics) are very promising for application in biosensing, photocatalysts, medicine, data storage, solar energy conversion, etc. Currently, colloidal synthesis techniques enable scientists to routinely produce mono and bimetallic NPs of various shapes, sizes, composition, and elemental distribution, with superior properties for plasmonic applications. Two primary directions for further advancing nanoplasmonic-based technologies include synthesizing novel morphologies, such as highly asymmetric chiral NPs, and gaining deeper insights into the factors affecting the stability of produced nanoplasmonics. With the increasing complexity of nanoplasmonics morphologies and higher stability requirements, there is a pressing need for thorough investigations into their 3D structures and their evolution under different conditions, with high resolution. Electron tomography (ET) emerges as an ideal tool to retrieve shape and element-sensitive information about individual nanoparticles in 3D, achieving resolutions down to the atomic level. Moreover, ET techniques can be combined with in situ holders, enabling detailed studies of processes mimicking real applications of nanoplasmonic-based devices. The first part of this thesis will focus on detailed studies of chiral Au NPs, promising for spectroscopy techniques based on the differential absorption of left- and right-handed circularly polarized light. Specifically, I will discuss the primary strategies for wet-colloidal growth of the various types of intrinsically chiral Au NPs. Advanced ET methods will be demonstrated as powerful tools for characterizing the final helical morphologies of the produced Au NPs and for studying the chiral growth mechanisms by examining intermediate structures obtained during chiral growth. The second part will focus on the heat-induced stability of various Au@Ag core-shell NPs. Operating in real conditions, such as elevated temperatures, may cause particle reshaping and redistribution of metals between the core and shell, gradually altering nanoplasmonics properties. Hence, a thorough understanding of the influence of size, shape, and defects on these processes is crucial for further developments. Recently developed techniques, combining fast ET with in-situ heating holders, have allowed me to evaluate the influence of various parameters (size, shape, defect structure) on heat-induced elemental redistribution in Au@Ag core-shell nanoparticles qualitatively and quantitatively. Additionally, I will discuss the prospects of high-resolution ET for visualizing the diffusion of individual atoms within complex nanostructures.

Abstract: The treatment of a well plate by an atmospheric pressure plasma jet is common for<italic>in vitro</italic>plasma medicine research. Here, reactive species are largely produced through the mixing of the jet effluent with the surrounding atmosphere. This mixing can be influenced not only by the ambient conditions, but also by the geometry of the treated well. To limit this influence and control the atmosphere, a shielding gas is sometimes applied. However, the interplay between the gas shield and the well geometry has not been investigated. In this work, we developed a 2D-axisymmetric computational fluid dynamics model of the kINPen plasma jet, to study the mixing of the jet effluent with the surrounding atmosphere, with and without gas shield. Our computational and experimental results show that the choice of well type can have a significant influence on the effluent conditions, as well as on the effectiveness of the gas shield. Furthermore, the geometry of the shielding gas device can substantially influence the mixing as well. Our results provide a deeper understanding of how the choice of setup geometry can influence the plasma treatment, even when all other operating parameters are unchanged.

Abstract: The use of microfluidic devices in the field of plasma-liquid interaction can unlock unique possibilities to investigate the effects of plasma-generated reactive species for environmental and biomedical applications. So far, very little simulation work has been performed on microfluidic devices in contact with a plasma source. We report on the modelling and computational simulation of physical and chemical processes taking place in a novel plasma-microfluidic platform. The main production and transport pathways of reactive species both in plasma and liquid are modelled by a novel modelling approach that combines 0D chemical kinetics and 2D transport mechanisms. This combined approach, applicable to systems where the transport of chemical species occurs in unidirectional flows at high Péclet numbers, decreases calculation times considerably compared to regular 2D simulations. It takes advantage of the low computational time of the 0D reaction models while providing spatial information through multiple plug-flow simulations to yield a quasi-2D model. The gas and liquid flow profiles are simulated entirely in 2D, together with the chemical reactions and transport of key chemical species. The model correctly predicts increased transport of hydrogen peroxide into the liquid when the microfluidic opening is placed inside the plasma effluent region, as opposed to inside the plasma region itself. Furthermore, the modelled hydrogen peroxide production and transport in the microfluidic liquid differs by less than 50% compared with experimental results. To explain this discrepancy, the limits of the 0D–2D combined approach are discussed.

Abstract: Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.

Abstract: Urine nitrification is pH-sensitive due to limited alkalinity and high residual ammonium concentrations. This study aimed to investigate how the pH affects nitrogen conversion and the microbial community of urine nitrification with a pH-based feeding strategy. First, kinetic parameters for NH3, HNO2, and NO2– limitation and inhibition were determined for nitrifiers from a urine nitrification reactor. The turning point for ammonia-oxidizing bacteria (AOB), i.e., the substrate concentration at which a further increase would lead to a decrease in activity due to inhibitory effects, was at an NH3 concentration of 12 mg-N L–1, which was reached only at pH values above 7. The total nitrite turning point for nitrite-oxidizing bacteria (NOB) was pH-dependent, e.g., 18 mg-N L–1 at pH 6.3. Second, four years of data from two 120 L reactors were analyzed, showing that stable nitrification with low nitrite was most likely between pH 5.8 and 6.7. And third, six 12 L urine nitrification reactors were operated at total nitrogen concentrations of 1300 and 3600 mg-N L–1 and pH values between 2.5 and 8.5. At pH 6, the AOB Nitrosomonas europaea was found, and the NOB belonged to the genus Nitrobacter. At pH 7, nitrite accumulated, and Nitrosomonas halophila was the dominant AOB. NOB were inhibited by HNO2 accumulation. At pH 8.5, the AOB Nitrosomonas stercoris became dominant, and NH3 inhibited NOB. Without influent, the pH dropped to 2.5 due to the growth of the acid-tolerant AOB “Candidatus Nitrosacidococcus urinae”. In conclusion, pH is a decisive process control parameter for urine nitrification by influencing the selection and kinetics of nitrifiers.

Abstract: In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy.

Abstract: Ptychography provides high dose efficiency images that can reveal light elements next to heavy atoms. However, despite ptychography having an otherwise single signed contrast transfer function, contrast reversals can occur when the projected potential becomes strong for both direct and iterative inversion ptychography methods. It has recently been shown that these reversals can often be counteracted in direct ptychography methods by adapting the focus. Here we provide an explanation of why the best contrast is often found with the probe focused to the middle of the sample. The phase contribution due to defocus at each sample slice above and below the central plane in this configuration effectively cancels out, which can prevent contrast reversals when dynamical scattering effects are not overly strong. In addition we show that the convergence angle can be an important consideration for removal of contrast reversals in relatively thin samples.

Abstract: A recently developed healable Al-Mg2Si designed by the programmed damage and repair (PDR) strategy is studied considering the role microstructural defects play on precipitation, damage, and healing. The alloy incorporates sacrificial Mg2Si particles that precipitate after friction stir processing (FSP). They act as damage localization sites and are healable based on the solid-state diffusion of Al-matrix. A combination of different transmission electron microscopy (TEM) imaging techniques enabled the visualization and quantification of various crystallographic defects and the spatial distribution of Mg2Si precipitates. Intragrain nucleation is found to be the dominant mechanism for precipitation during FSP whereas grain boundaries and subgrain boundaries mainly lead to coarsening of the precipitates. The statistical and spatial analyses of the damaged particles have shown particle fracture as the dominant damage mechanism which is strongly dependent on the size and aspect ratio of the particles whereas the damage was not found to depend on the location of the precipitates within the matrix. The damaged particles are associated with dislocations accumulated around them. The interplay of these dislocations is directly visualized during healing based on in situ TEM heating which revealed recovery in the matrix as an operative mechanism during the diffusion healing of the PDR alloy.

Abstract: We explored the potential of plasma-based In-Situ Resource Utilization (ISRU) for Mars through the conversion of Martian atmosphere (~96% CO2, 2% N2, and 2% Ar) into life-sustaining chemicals. As the Martian surface pressure is about 1% of the Earth’s surface pressure, it is an ideal environment for plasma-based gas conversion using microwave reactors. At 1000 W and 10 Ln/min (normal liters per minute), we produced ~76 g/h of O2 and ~3 g/h of NOx using a 2.45 GHz waveguided reactor at 25 mbar, which is ~3.5 times Mars ambient pressure. The energy cost required to produce O2 was ~0.013 kWh/g, which is very promising compared to recently concluded MOXIE experiments on the Mars surface. This marks a crucial step towards realizing the extension of human exploration.

Abstract: Warm plasma offers a promising route for CO2 splitting into valuable CO, yet recombination reactions of CO with oxygen, forming again CO2, have recently emerged as critical limitation. This study combines experiments and fluid dynamics + chemical kinetics modelling to comprehensively analyse the recombination reactions upon CO2 splitting in an atmospheric plasmatron. We introduce an innovative in-situ gas sampling technique, enabling 2D spatial mapping of gas product compositions and temperatures, experimentally confirming for the first time the substantial limiting effect of CO recombination reactions in the afterglow region. Our results show that the CO mole fraction at a 5 L/min flow rate drops significantly from 11.9 % at a vertical distance of z = 20 mm in the afterglow region to 8.6 % at z = 40 mm. We constructed a comprehensive 2D model that allows for spatial reaction rates analysis incorporating crucial reactions, and we validated it to kinetically elucidate this phenomenon. CO2 +M⇌O+CO+M and CO2 +O⇌CO+O2 are the dominant reactions, with the forward reactions prevailing in the plasma region and the backward reactions becoming prominent in the afterglow region. These results allow us to propose an afterglow quenching strategy for performance enhancement, which is further demonstrated through a meticulously developed plasmatron reactor with two-stage cooling. Our approach substantially increases the CO2 conversion (e.g., from 6.6 % to 19.5 % at 3 L/min flow rate) and energy efficiency (from 13.5 % to 28.5 %, again at 3 L/min) and significantly shortens the startup time (from ~ 150 s to 25 s). Our study underscores the critical role of inhibiting recombination reactions in plasma-based CO2 conversion and offers new avenues for performance enhancement.

Abstract: The number and composition of species in a community can be quantified with alpha-diversity indices, including species richness (R), Simpson's index (D), and the Shannon-Wiener index (HGREEK TONOS). In forest communities, there are large variations in tree size among species and individuals of the same species, which result in differences in ecological processes and ecosystem functions. However, tree size inequality (TSI) has been largely neglected in studies using the available diversity indices. The TSI in the diameter at breast height (DBH) data for each of 999 20 m x 20 m forest census quadrats was quantified using the Gini index (GI), a measure of the inequality of size distribution. The generalized performance equation was used to describe the rotated and right-shifted Lorenz curve of the cumulative proportion of DBH and the cumulative proportion of number of trees per quadrat. We also examined the relationships of alpha-diversity indices with the GI using correlation tests. The generalized performance equation effectively described the rotated and right-shifted Lorenz curve of DBH distributions, with most root-mean-square errors (990 out of 999 quadrats) being < 0.0030. There were significant positive correlations between each of three alpha-diversity indices (i.e., R, D, and H') and the GI. Nevertheless, the total abundance of trees in each quadrat did not significantly influence the GI. This means that the TSI increased with increasing species diversity. Thus, two new indices are proposed that can balance alpha-diversity against the extent of TSI in the community: (1 – GI) x D, and (1 – GI) x H'. These new indices were significantly correlated with the original D and HGREEK TONOS, and did not increase the extent of variation within each group of indices. This study presents a useful tool for quantifying both species diversity and the variation in tree sizes in forest communities, especially in the face of cumulative species loss under global climate change.

Abstract: Complex transition-metal oxides exhibit a wide variety of chemical and physical properties which are a strong function the local electronic states of the transition-metal centres, as determined by a combination of metal oxidation state and local coordination environment. Topochemical reduction of the double perovskite oxide, LaSrCoRuO6, using Zr, yields LaSrCoRuO5. This reduced phase contains an ordered array of apex-linked square-based pyramidal Ru3+O5, square-planar Co1+O4 and octahedral Co3+O6 units, consistent with the coordination-geometry driven disproportionation of Co2+. Coordination-geometry driven disproportionation of d(7) transition-metal cations (e.g. Rh2+, Pd3+, Pt3+) is common in complex oxides containing 4d and 5d metals. However, the weak ligand field experienced by a 3d transition-metal such as cobalt leads to the expectation that d(7+) Co2+ should be stable to disproportionation in oxide environments, so the presence of Co1+O4 and Co3+O6 units in LaSrCoRuO5 is surprising. Low-temperature measurements indicate LaSrCoRuO5 adopts a ferromagnetically ordered state below 120 K due to couplings between S=(1)/(2) Ru3+ and S=1 Co1+.

Abstract: Optical hyperspectral cameras capture the spectral reflectance of materials. Since many materials behave as heterogeneous intimate mixtures with which each photon interacts differently, the relationship between spectral reflectance and material composition is very complex. Quantitative validation of spectral unmixing algorithms requires high-quality ground truth fractional abundance data, which are very difficult to obtain. In this work, we generated a comprehensive laboratory ground truth dataset of intimately mixed mineral powders. For this, five clay powders (Kaolin, Roof clay, Red clay, mixed clay, and Calcium hydroxide) were mixed homogeneously to prepare 325 samples of 60 binary, 150 ternary, 100 quaternary, and 15 quinary mixtures. Thirteen different hyperspectral sensors have been used to acquire the reflectance spectra of these mixtures in the visible, near, short, mid, and long-wavelength infrared regions (350-15385) nm. Overlaps in wavelength regions due to the operational ranges of each sensor and variations in acquisition conditions resulted in a large amount of spectral variability. Ground truth composition is given by construction, but to verify that the generated samples are sufficiently homogeneous, XRD and XRF elemental analysis is performed. We believe these data will be beneficial for validating advanced methods for nonlinear unmixing and material composition estimation, including studying spectral variability and training supervised unmixing approaches. The datasets can be downloaded from the following link: https://github.com/VisionlabHyperspectral/Multisensor_datasets.

Abstract: Electronic devices that work in the quantum regime often employ hybrid nanostructures to bring about a nonlinear behaviour. The nonlinearity that these can provide has proven to be useful, in particular, for applications in quantum computation. Here we present a hybrid device that acts as a capacitor with a nonlinear charge-voltage relation. The device consists of a nanowire placed between the plates of a coplanar capacitor, with a co-parallel alignment. At low temperatures, due to the finite density of states on the nanowire, the charge distribution in the capacitor is uneven and energy-dependent, resulting in a charge-dependent effective capacitance. We study this system analytically and numerically, and show that the nonlinearity of the capacitance is significant enough to be utilized in circuit quantum electrodynamics. The resulting nonlinearity can be switched on, modulated, and switched off by an external potential, thus making this capacitive device highly versatile for uses in quantum computation.