Abstract: Ammonia (NH3) synthesis is crucial for the production of artificial fertilizer and is carried out through the Haber-Bosch process. With an energy consumption of 30 GJ/t-NH3 and the emission of 2 kg-CO2/kg-NH3, ammonia is the chemical with the largest environmental footprint. Haber-Bosch operates under high pressure and high temperature conditions. Plasma technology potentially allows greener ammonia production. Dielectric barrier discharges are a popular plasma source in which a catalyst is easily incorporated. The combination of plasma and catalyst can circumvent the harsh reaction conditions of the Haber-Bosch process. Plasma kinetics modelling is used to gain insight into the mechanisms of such plasma-catalytic systems. Special attention is given to the instantaneous power absorbed by the electrons, the relevant fraction of the microdischarges and the discharge volumes. The importance of vibrational excitation is investigated. Depending on the exact discharge conditions, it was found that both the strong microdischarges and vibrational excitation can be simultaneously important for the ammonia yield. The temporal behavior of filamentary dielectric barrier discharges was explicitly taken into account. Ammonia was found to decompose during the microdischarges due to electron impact dissociation. At the same time atomic nitrogen and other excited species are created. Those reactive species recombine to ammonia in the afterglow through various elementary Eley-Rideal and Langmuir-Hinshelwood surface reaction steps with a net ammonia gain. Finally, the concept of the fraction of microdischarges was generalized. It directly represents the efficiency with which the applied electric power is transferred to each individual particle in the plasma reactor. It is argued that any type of spatial or temporal non-uniformity of the plasma will cause unequal treatment of the gas molecules in the reactor, corresponding to a lower efficiency at which the power is transferred to the gas molecules. All of those insights aid in an increased understanding of plasma-catalytic ammonia synthesis as a potential green chemistry solution to the synthesis of ammonia on small scale.  

Abstract: The human population is projected to grow to 9.7 billion by 2050, resulting in an estimated increase in protein demand of 50%. From an environmental perspective, the current and future demand of protein cannot be sustainably met as the conventional food production chain is severely altering biogeochemical cycles of nitrogen and phosphorus, biodiversity and land-use, with flows towards the biosphere and oceans that are exceeding the planetary boundaries. Microbial protein (protein derived from microorganisms) has been suggested as an excellent sustainable protein source, a fortiori when produced in a land- and fossil free manner. The photoautohydrogenotrophic cultivation (i.e. with light, CO2 and H2) of purple bacteria links up perfectly with the upcoming green electrification of industry (green H2) and the need for carbon capture and utilization. However, this metabolism represented a gap in literature, and thus this thesis aimed to establish a basic knowledge platform on its kinetic, stoichiometric and nutritional performance. At first, three originally photoheterotrophically enriched purple bacteria were studied of which Rhodobacter capsulatus reached the highest protein productivity of 0.16 g protein/L/d, which aligned well with the commonly-known photoautotrophic microalgae. Moreover, a full dietary essential amino acid match was found for human food, while the fatty acid content was dominated by the health-stimulating vaccenic acid (82-86%). Lastly, the achieved protein yield in photoautohydrogenotrophic purple bacteria was 2.3 times higher compared to hydrogen oxidizing bacteria, indicating a resource-efficient use of H2. Next, a photoautohydrogenotrophic enrichment of wastewater treatment microbiomes was performed in search for specialist species. While the isolates of this enrichment showed improvements in their performance during acclimation, the kinetic and nutritional performance of Rhodobacter capsulatus still excelled. Subsequently, the influence of nutrient limitations (C or N) and nitrogen gas fixation was studied on the nutritional tuning potential. Both the limitations as well as the N2 fixation resulted in the shift of the essential amino acid profiles. Additionally, the limitations significantly decreased the pigment content, while an increase in the storage of poly-P was seen in case of carbon limitations. The next major challenge was the production intensification in a photobioreactor of which the design was linked to minimizing both H2 and light limitations. The chosen bubble-column photobioreactor already resulted in a doubled biomass productivity. Finally, the remaining technological and non-technological challenges ahead for the production of a high-value, cost-efficient, environment-friendly microbial protein that complies with legislative requirements and appeals to future consumers were discussed.

Abstract: Lignin determination in lignocellulose with the conventional two-step acid hydrolysis method is highly laborious and time-consuming. However, its quantification is crucial to monitor fungal pretreatment of wood, as the increase of acid-insoluble lignin (AIL) degradation linearly correlates with the achievable enzymatic saccharification yield. Therefore, in this study, a new attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy method was developed to track fungal delignification in an easy and rapid manner. Partial least square regression (PLSR) with cross-validation (CV) was applied to correlate the ATR-FTIR spectra with the AIL content (19.9%–27.1%). After variable selection and normalization, a PLSR model with a high coefficient of determination (

Abstract: Memristors are considered to be the fourth circuit element and have great potential in areas like logic operations, information storage, and neuromorphic computing. The functional material in a memristor, which has a nonlinear resistance, is the key component to be developed. Herein, resistive switching is demonstrated and the structural evolutions in Ag2Te are examined under an external electric field. It is shown that the electroresistance effect is originating from an electronically triggered phase transition together with directional Ag+-ion diffusion. Using in situ transmission electron microscopy, the phase transition from the monoclinic alpha-Ag2Te into the face-centered cubic beta-Ag2Te, accompanied by a change in resistance, is directly observed. Diffusion of Ag+-ions modulates the localized density of Ag+-ion vacancies, leading to a change in electrical conductivity and influences the threshold voltage to trigger the phase transition. During the electric field-driven phase transition, the spontaneous and localized multiple polarizations from the low-symmetry alpha-Ag2Te (referring to an antiferroelectric structure) are vanishing in the cubic beta-Ag2Te (referring to a paraelectric structure). The abrupt resistance change of thin Ag2Te caused by the phase transition and modulated by the applied electric field demonstrates its great potential as functional material in volatile memory and memristors with a low-energy consumption.

Abstract: Scanning electron microscopy coupled with microanalysis (SEM-EDX) is an important analytical tool for the morphological and chemical characterization of different types of materials. In many applications, SEM-EDX elemental maps are usually used and processed as images, thus flattening and reducing the spectroscopic information contained in EDX hyperspectral data cubes. The exploitation of the full hyperspectral dataset could be indeed very useful for the study of complex matrices like soil. In order to maximize the information attainable by SEM-EDX data cubes analysis, the software package “Datamuncher Gamma” was implemented and applied to study soil aggregates. By using this approach, different phases (silicates, aluminosilicates, Ca-carbonates, Ca-phosphates, organic matter, iron oxides) inside soil aggregates were successfully identified and segmented. The advantages of this method over the common ROI imaging approach are presented. Finally, this method was used to compare different aggregates in a Cr-polluted soil and understand their possible pedological history. The present method can be used for the analysis of every type of SEM-EDX data cubes, allowing its application to different types of samples and fields of study.

Abstract: Groundwater fluxes in tidal marshes largely control key ecosystem functions and services, such as vegetation growth, soil carbon sequestration, and nutrient cycling. In tidal marshes restored on formerly embanked agricultural land, groundwater fluxes are often limited as compared to nearby natural marshes, as a result of historical agricultural soil compaction. To improve the functioning of restored tidal marshes, knowledge is needed on how much certain design options can optimize soil-groundwater interactions in future restoration projects. Based on measured data on soil properties and tidally induced groundwater dynamics, we calibrated and evaluated a 2D vertical model of a creek-marsh cross-section, accounting for both saturated and unsaturated groundwater flow and solute transport in a variably saturated groundwater flow model. We found that model simulations of common restoration practices such as soil amendments (increasing the depth of porous soil on top of the compact layer) and creek excavation (increasing the creek density) increase the soil aeration depth and time, the drainage depth and the solute flux, and decrease the residence time of solutes in the porewater. Our simulations indicate that increasing the depth to the compact layer from 20 cm to 40 cm, or increasing the creek density from 1 creek to 2 creeks along a 50 m marsh transect (while maintaining the total creek cross-sectional area), in both cases more than doubles the volume of water processed by the marsh soil. We discuss that this may stimulate nutrient cycling. As such, our study demonstrates that groundwater modelling can support the design of marsh restoration measures aiming to optimize groundwater fluxes and related ecosystem services.

Abstract: The effect of pore size on plasma catalysis is crucial but still unclear. Studies have shown plasma cannot enter micropores and mesopores, so catalysts for traditional thermocatalysis may not fit plasma catalysis. Here, 3D porous Cu and CuO with different pore sizes were prepared using uniform silica particles (10–2000 nm) as templates, and compared in plasma-catalytic dry reforming. In most cases, the smaller the pore size, the higher the conversion of CH4 and CO2. Large pores reachable by more electrons did not improve the reaction efficiency. We attribute this to the small surface area and large crystallite size, as indicated by N2-sorption, mercury intrusion and XRD. While the smaller pores might not be reachable by electrons, due to the sheath formed in front of them, as predicted by modeling, they can still be reached by radicals formed in the plasma, and ions can even be attracted into these pores. An exception are the samples synthesized from 1 μm silica, which show better performance. We believe this is due to the electric field enhancement for pore sizes close to the Debye length. The performances of CuO and Cu with different pore sizes can provide references for future research on oxide supports and metal components of plasma catalysts.

Abstract: Ever since the industrial revolution, the emission of greenhouse gasses dramatically increased, resulting in high CO2 concentration in the atmosphere. The electrochemical conversion of CO2 to value added products, such as carbon monoxide, formic acid, methane, ethylene and ethanol is a very promising strategy to inhibit CO2 emissions. Nevertheless, at the moment, the electrochemical CO2 reduction (eCO2R) is not yet industrially viable, mainly due to the lack of good electrocatalysts. On the other hand, core-shell nanoparticles (NPs) have emerged over the last couple of years as promising candidates. It is believed that bimetallic enhancement effects are behind the improved performance of these core-shell NPs when compared to the individual metals. Although widely investigated, there are still some remaining issues and/or open questions. Indeed, the development of a robust and straightforward synthesis method along with fundamental insight into their resistance towards electrochemical stress remains absent. A good control over morphology, size and composition is key in determining which properties are beneficial for the eCO2R. Since these catalysts are designed to be implemented in electrolyzers, they have to maintain long-term performance. This makes the design of a reproducible method, unveiling structure-performance relationships the effect of electrochemical stress, a crucial aspect. Exploring and modifying existing synthesis methods, have led to the acquisition of a robust and reproducible synthesis method where thermal decomposition of the Cu core is combined with the galvanic replacement of Ag in organic solvents. The implementation of this method has led to the design of a wide variety of Cu-Ag bimetallic NPs and enabled to investigate their composition-selectivity profile. Introducing Ag on Cu suppressed hydrogen and increased the CO formation. CO production was boosted by using Cu@Ag core-shells and was promoted even more by changing the type of electrolyte. As these nanoparticles suffered from degradation, the 3D mapping of the structural changes of Cu@Ag core-shells under operating conditions led to the hypothesis of a two-step degradation mechanism where initially Cu leaching was observed with the subsequent sintering of the Ag shells. One approach to avoid this electrochemical degradation, investigated in this research, was the application of an ultrathin carbon layer to protect the active layer. This ultrathin carbon layer operated as a protective layer, suppressing hydrogen production and increasing the stability of the electrocatalyst. In conclusion, the product selectivity can be tuned by using different Cu-Ag bimetallic nanoparticles synthesized through a robust method. Their unique degradation pathway of Cu@Ag core-shell nanoparticles has led to the proposition of a more accurate stabilization strategy. These findings can contribute significantly in the quest for improved electrocatalysts for the eCO2R.

Abstract: This piece of work is twofold. First, the time evolution of wave-packets in 2D systems is analyzed by the Split-Operator technique in three different scenarios: in multilayer phosphorene, the transient oscillations in the time-dependent average of position and momentum were observed due to the zitterbewegung effect, and the wave packet propagates non-uniformly along the space deforming itself into an elliptical shape. These results were corroborated by the Green’s function formalism except for large values of the wave-vector and long times; in 2D semiconductor quantum wires (QWs) with anisotropic effective masses and different angle orientations with respect to the anisotropic axis. We have shown that the greater this angle, the smaller is the energy levels spacing implying in an increase of the accessible electronic states. Additionally, for non-null magnetic field, the quantum Hall edge states are significantly affected by the edge orientation. In the anisotropic case damped oscillations in the average values of velocity in both x and y directions where obtained. Theses oscillations are originated by the QW geometry but also from subwavepackets with different momentum orientations, whereas for isotropic QWs the wavepacket disperses without splitting; in the third scenario the split-operator technique was used to study the Landau levels, the wave packet trajectories and velocities of electrons in graphene at low-energy regime described by a modified Dirac equation where the momentum-operator is written in a generalized form as result of applying the position-dependent translation operator formalism (PDTO). In the second part of this thesis, the electronic and tunneling properties of α − T3 lattices were studied. Electrons in these lattices behave analogous to integer-spin Dirac Fermions. The presence of a third atomic site in the unit cell leads to a flat band in the energy spectrum, providing unique electronic and tunneling properties. The presence of a super-periodic potential and the inclusion of symmetry-breaking terms results in deviations of the atomic equivalence between the atomic sites affecting the Dirac points and the band-gap. Small deviations in the equivalence between the atomic sites and the number of barriers change the transmission properties in these lattices. Additionally, new tunneling regions are possible by adjusting the symmetry between the atomic sites and affect the omnidirectional total transmission called super-Klein tunneling observed in these lattices. We compare those results to the tunneling probabilities through regions where the energy spectrum changes from linear with a middle flat band to a hyperbolic dispersion.

Abstract: Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved.

Abstract: As recently highlighted by the SARS-CoV-2 pandemic, viruses have become an increasing burden for health, global economy, and environment. The control of transmission by contact with contaminated materials represents a major challenge, particularly in hospital environments. However, the current disinfection methods in hospital settings suffer from numerous drawbacks. As a result, several medical supplies that cannot be properly disinfected are not reused, leading to severe shortages and increasing amounts of waste, thus prompting the search for alternative solutions. In this work, we report that non-thermal plasma (NTP) can effectively inactivate SARS-CoV-2 from non-porous and porous materials commonly found in healthcare facilities. We demonstrated that 5 min treatment with a dielectric barrier discharge NTP can inactivate 100% of SARS-CoV-2 (Wuhan and Omicron strains) from plastic material. Using porcine respiratory coronavirus (surrogate for SARS-CoV-2) and coxsackievirus B3 (highly resistant non-enveloped virus), we tested the NTP virucidal activity on hospital materials and obtained complete inactivation after 5 and 10 min, respectively. We hypothesize that the produced reactive species and local acidification contribute to the overall virucidal effect of NTP. Our results demonstrate the potential of dielectric barrier discharge NTPs for the rapid, efficient, and low-cost disinfection of healthcare materials.

Abstract: Background Patient-derived organoids are invaluable for fundamental and translational cancer research and holds great promise for personalized medicine. However, the shortage of available analysis methods, which are often single-time point, severely impede the potential and routine use of organoids for basic research, clinical practise, and pharmaceutical and industrial applications. Methods Here, we developed a high-throughput compatible and automated live-cell image analysis software that allows for kinetic monitoring of organoids, named Organoid Brightfield Identification-based Therapy Screening (OrBITS), by combining computer vision with a convolutional network machine learning approach. The OrBITS deep learning analysis approach was validated against current standard assays for kinetic imaging and automated analysis of organoids. A drug screen of standard-of-care lung and pancreatic cancer treatments was also performed with the OrBITS platform and compared to the gold standard, CellTiter-Glo 3D assay. Finally, the optimal parameters and drug response metrics were identified to improve patient stratification. Results OrBITS allowed for the detection and tracking of organoids in routine extracellular matrix domes, advanced Gri3D (R)-96 well plates, and high-throughput 384-well microplates, solely based on brightfield imaging. The obtained organoid Count, Mean Area, and Total Area had a strong correlation with the nuclear staining, Hoechst, following pairwise comparison over a broad range of sizes. By incorporating a fluorescent cell death marker, infra-well normalization for organoid death could be achieved, which was tested with a 10-point titration of cisplatin and validated against the current gold standard ATP-assay, CellTiter-Glo 3D. Using this approach with OrBITS, screening of chemotherapeutics and targeted therapies revealed further insight into the mechanistic action of the drugs, a feature not achievable with the CellTiter-Glo 3D assay. Finally, we advise the use of the growth rate-based normalised drug response metric to improve accuracy and consistency of organoid drug response quantification. Conclusion Our findings validate that OrBITS, as a scalable, automated live-cell image analysis software, would facilitate the use of patient-derived organoids for drug development and therapy screening. The developed wet-lab workflow and software also has broad application potential, from providing a launching point for further brightfield-based assay development to be used for fundamental research, to guiding clinical decisions for personalized medicine.

Abstract: Transition metal (TM) doped two-dimensional single-atom catalysts are known as a promising class of catalysts for electrocatalytic gas conversion. However, the detailed mechanisms that occur at the surface of these catalysts are still unknown. In the present work, we simulate three Mo-doped nitrogenated graphene structures. In each catalyst, the position of the Mo active site and the corresponding local carbon topologies are different, i.e. MoN4C10 with in-plane Mo atom, MoN4C8 in which Mo atom bridges two adjacent armchair-like graphitic edges, and MoN2C3 in which Mo is doped at the edge of the graphene sheet. Using Density Functional Theory (DFT) calculations we discuss the electrocatalytic activity of Mosingle bondNsingle bondC structures for nitrogen reduction reaction (NRR) with a focus on unraveling the corresponding mechanisms concerning different Mo site positions and C topologies. Our results indicate that the position of the active site centers has a great effect on its electrocatalytic behavior. The gas phase N2 efficiently reduces to ammonia on MoN4C8 via the distal mechanism with an onset potential of −0.51 V. We confirm that the proposed pyridinic structure, MoN4C8, can catalyze NRR effectively with a low overpotential of 0.35 V.

Abstract: Since its discovery 20 years ago, many studies have been performed to gain insight into the functional role of cytoglobin (Cygb). However, Cygb has been proven to be a promiscuous protein. Yet, there is a consensus that Cygb is a cytoprotective protein involved in redox homeostasis. CYGB is a ubiquitously expressed hexacoordinated globin that is highly expressed in melanocytes and is often found to be downregulated during melanocyte-to-melanoma transition. In Chapter III, we investigated the molecular mechanism through which CYGB could be involved in redox regulation. Here, we showed that CYGB contains two redox-sensitive cysteine residues and that the formation of an intramolecular disulfide bridge resulted in the heme group becoming more accessible to external ligands. This supports the hypothesis that Cys38 and Cys83 serve as sensitive redox sensors. In Chapter IV we showed that CYGB mRNA and protein levels were elevated upon exposure to hypoxia. Interestingly, this upregulation was most likely HIF-2α-dependent. We propose that in melanoma, HIF-2α, rather than HIF-1α, positively regulates CYGB under hypoxic conditions in a cell type specific way. In Chapter V, the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels was investigated. We confirmed that NTP endows cytotoxicity that induces cell death through apoptosis and that this was mediated through the production of ROS. Moreover, we showed that CYGB protects melanoma cells from ROS-induced apoptosis by the scavenging of ROS. Interestingly, CYGB expression influenced the expression of NRF2 and HO-1. We identified the lncRNA MEG3 as a possible mechanism through which NRF2 expression and its downstream target HO-1 can be regulated by CYGB. In chapter VI, increased basal ROS levels and higher degree of lipid peroxidation upon RSL3 treatment contributed to the increased sensitivity of CYGB knockdown G361 cells to ferroptosis. Furthermore, transcriptome analysis demonstrates the enrichment of multiple cancer malignancy pathways upon CYGB knockdown, supporting a tumor-suppressive role for CYGB. Remarkably, CYGB expression regulation was identified as a critical determinant of the ferroptosis–pyroptosis therapy response. This suggests that CYGB is involved in the regulation of multiple modes of programmed cell death. FInally, we sought to delineate the RONS that are responsible for plasma-induced ICD. Our results highlight the importance of the short-lived species. Furthermore, we are first to demonstrate that NTP-created vaccine is safely prepared and offers complete protection. Moreover, we provide conclusive evidence that direct application of NTP induces ICD in melanoma.

Abstract: Gas-solid vortex chambers are a promising alternative for reactive and non-reactive processes requiring enhanced heat and mass transfer rates and order-of-milliseconds contact time. The conservation of angular momentum is instrumental in understanding how the interactions between gas, particulate solids, and chamber walls influence the formation of a rotating solids bed. Therefore, this work applies the conservation of angular momentum to derive a model that gives the average angular velocity of solids in terms of gas injection velocity, wall-solids bed drag coefficient, gas and particle properties, and chamber geometry. Three datasets from published studies, comprising 1 g-Geldart B- and d-type particles in different vortex chambers, validate the model results. Using a sensitivity analysis, we assessed the effect of input variables on the average angular velocity of solids, average void fraction, and average bed height. Results indicate that the top and bottom end-wall boundaries exert the most significant braking effect on the rotating solids bed compared with the cylindrical outer wall and gas injection boundaries. The wall-solids bed drag coefficient appears independent of the gas injection velocity for a wide range of operating conditions. The proposed model is a valuable tool for analyzing and comparing gas–solid vortex typologies, unraveling improvement opportunities, and scale-up.