Abstract: Purple non-sulfur bacteria (PNSB) show great potential for environmental and industrial biotechnology, producing microbial protein, biohydrogen, polyhydroxyalkanoates (PHAs), pigments, etc. When grown photoheterotrophically, the carbon source is typically more reduced than the PNSB biomass, which leads to a redox imbalance. To mitigate the excess of electrons, PNSB can exhibit several ‘electron sinking’ strategies, such as CO2 fixation, N2 fixation, and H2 and PHA production. The lack of a comprehensive (over)view of these redox strategies is hindering the implementation of PNSB for biotechnology applications. This review aims to present the state of the art of redox homeostasis in phototrophically grown PNSB, presenting known and theoretically expected strategies, and discussing them from stoichiometric, thermodynamic, metabolic, and economic points of view.

Abstract: Pretreatment is a critical step in the conversion of lignocellulose into biofuels and biochemicals. During pretreatment, the recalcitrance of lignocellulose is reduced, e.g. by removing lignin, thereby making the carbohydrates more accessible for enzymatic saccharification. Fungal delignification by white-rot fungi is a biotechnological alternative to chemical/physicochemical methods, which is carried out in solid-state fermentation with mild reaction conditions and without the formation of microbial inhibitors. However, fungal pretreatment presents some challenges, such as long pretreatment time, non-selective and low delignification, low enzymatic digestibility and feedstock sterilisation requirement, making its commercial implementation challenging compared to conventional methods. This study investigates the possibility of improving and characterising the solid-state fungal pretreatment of poplar wood by Phanerochaete chrysosporium. The individual and combined effects of MnSO4 and CuSO4 supplements on the delignification of sterilised wood are investigated using response surface methodology to improve the degree and selectivity of fungal delignification. Spore-inoculated solid-state fermentations are carried out for 4 weeks in sterile vented bottles. The mechanism of the concerted action of the metal ions on lignin degradation is then elucidated by relating fungal growth and ligninolytic enzyme activities to lignocellulose degradation as a function of pretreatment time. The optimised metal-supplemented system is then applied to the pretreatment of non-sterilised wood using different inoculation techniques (spores and pre-colonised substrate), nutrients (metal ions with or without glucose and sodium nitrate) and cultivation environments (sterile aerated bottles and open trays). The fermentations are then characterised using infrared spectroscopy, in particular NIR and ATR-FTIR spectroscopy, with the aim of developing rapid lignin quantification methods as an alternative to conventional wet chemical methods. Finally, the feasibility of producing fermentable sugars from sterilised and non-sterilised poplar wood using fungal pretreatment is evaluated through a techno-economic analysis. Supplementing the pretreatment system with 2.01 µmol CuSO4 and 0.77 µmol MnSO4 g-1 wood resulted in 1.9-fold higher lignin degradation, 2.3-fold higher delignification selectivity value and 2.9-fold higher glucose yield. The improved delignification could be explained by the concerted action of Mn2+ and Cu2+ ions, with Mn2+ ions inducing and Cu2+ prolonging manganese peroxidase production responsible for delignification. Fungal pretreatment at non-sterile conditions was obtained using trays in a simple solid-state fermentation set-up without sterile aeration. A 1:3 ratio of pre-colonised and untreated wood was applied for inoculation and only Cu2+, Mn2+ and sodium nitrate as supplements. Remarkably, this technology resulted in a comparably high glucose yield (28.51 ± 0.28%) to the traditional method using sterilised wood, sterile aeration and spores as inoculum, while reducing the amount of wood to be sterilised by 71.2%. Infrared spectroscopy-based methods with high coefficients of determination (R_CV

Abstract: Polarons are quasiparticles emerging in materials from the interaction of extra charge carriers with the surrounding atomic lattice. They appear in a wide va- riety of compounds and can have a profound impact on their properties, making the concept of a polaron a central and ubiquitous topic in material science. Al- though the concept is known for about 75 years, the origin of polarons is not yet fully elucidated. This thesis focuses on WO 3 as a well-known prototypical system for studying polarons, which inherent polaronic nature is linked to its remark- able electrical and chromic properties. The primary objective of this research is to provide a comprehensive atomistic description and understanding of polaron formation in WO 3 using first-principles density functional theory (DFT) calcula- tions. Additionally, the investigation explores the interactions between polarons and the possibility of bipolaron formation. Following a systematic strategy, we first extensively analyze the dielectric and lattice dynamical properties of WO 3 in both the room-temperature P 2 1 /n and ground-state P 2 1 /c phases. Our specific focus is on characterizing the zone-center phonons, which serve as the founda- tion for identifying the phonon modes involved in the polaron formation and charge localization process. Subsequently, we examine the impact of structural distortions on the electronic structure of WO 3 to elucidate the interplay between structural distortions and electronic properties, thereby laying the groundwork for understanding electron-phonon couplings. By incorporating these critical fac- tors, we address our primary research goals. The most common explanation for the polaron formation is associated with the electrostatic screening of the extra charge by the polarizable lattice. Here, we show that, even in ionic crystals, this is not necessarily the case. We demonstrate that polarons in this compound arise primarily from non-polar atomic distortions. We then unveil that this unexpected behavior originates from the undoing of distortive atomic motions, which lowers the bandgap. As such, we coin the name of anti-distortive polaron and validate its appearance through a simple quantum-dot model, in which charge localization is the result of balancing structural, electronic, and confinement energy costs. Then, we also study the polaron-polaron interaction and present the formation of the antiferromagnetic W 4+ bipolaronic state with relatively large formation energy. Our analysis of the W 4+ bipolaronic distortions on the global structure reveals the same behavior as in experiments where the highly distorted monoclinic phase transforms into a tetragonal phase as a function of doping. Additionally, leveraging our previous findings on asymmetric polaronic distortion and examin- ing different merging orientations, we stabilize the antiferromagnetic W 5+ -W 5+ bipolaronic state with an energy lower than the W 4+ state. This thesis clari- fies the formation of unusual medium-size 2D polarons and bipolarons in WO3,which might be relevant to the whole family of ABO 3 perovskites, to which WO 3 is closely related. The simplicity of the concept provides also obvious guidelines for tracking similar behavior in other families of compounds.

Abstract: Plasma-catalytic ammonia synthesis in a dielectric barrier discharge reactor has emerged as a possible route for electrification of nitrogen fixation. In this study, we use a combination of experiments and a plasma kinetic model to investigate the ammonia synthesis from N2 and H2, both with and without a solid packing material in the plasma zone. The effect of plasma power, feed flow rate, N2:H2 feed ratio, gas residence time, temperature, and packing material (MgAl2O4 alone or impregnated with Co or Ru) on the ammonia synthesis rate were examined in the experiments. The kinetic model was employed to improve our understanding of the ammonia formation pathways and identify possible changes in these pathways when altering the N2:H2 feed ratio. A higher NH3 synthesis rate was achieved when increasing the feed flow rate, as well as when increasing the gas tem-perature from 100 to 200 ◦C when a packing material was present in the plasma. At the elevated temperature of 200 ◦C, an optimum in the NH3 synthesis rate was observed at an equimolar feed ratio (N2:H2 =1:1) for the plasma alone and MgAl2O4, while a N2-rich feed was favored for Ru/MgAl2O4 and Co/MgAl2O4. The optimum in the synthesis rate with the N2-rich feed, where high energy electrons are more likely to collide with N2, suggests that the rate-limiting step is the dissociation of N2 in the gas phase. This is supported by the kinetic model when packing material was used. However, for the plasma alone, the model found that the N2 dissociation is only rate limiting in H2-rich feeds, whereas the limited access to H in N2-rich feeds makes the hydrogenation of N species limiting.

Abstract: Plasma-based dry reforming of methane (DRM) into
high-value-added oxygenates is an appealing approach to enable
otherwise thermodynamically unfavorable chemical reactions at
ambient pressure and near room temperature. However, it suffers
from coke deposition due to the deep decomposition of CH4. In this
work, we assess the DRM performance upon O2 addition, as well as
varying temperature, CO2/CH4 ratio, discharge power, and gas
residence time, for optimizing oxygenate production. By adding O2,
the main products can be shifted from syngas (CO + H2) toward
oxygenates. Chemical kinetics modeling shows that the improved
oxygenate production is due to the increased concentration of
oxygen-containing radicals, e.g., O, OH, and HO2, formed by electron
impact dissociation [e + O2 → e + O + O/O(1D)] and subsequent
reactions with H atoms. Our study reveals the crucial role of oxygen-coupling in DRM aimed at oxygenates, providing practical
solutions to suppress carbon deposition and at the same time enhance the oxygenates production in plasma-assisted DRM.

Abstract: Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes.

Abstract: Plasma degradation is one of the most effective methods for the abatement of greenhouse gas sulfur hexafluoride
(SF6). To evaluate the potential of MgO as a catalyst in plasma degradation, we investigate the catalytic properties
of MgO on SF6 adsorption and activation by density functional theory (DFT) where the O-defective and
hydroxylated surfaces are considered as two typical plasma-generated surfaces. Our results show that perfect
MgO (001) and (111) surfaces cannot interact with SF6 and only physical adsorption happens. In case of Odefective
MgO surfaces, the O vacancy is the most stable adsorption site. SF6 undergoes a decomposition to SF5
and F over the O-defective MgO (001) surface and undergoes an elongation of the bottom S-F bond over the Odefective
(111) surface. Besides, SF6 shows a physically adsorption at the stepsite of the MgO (001) surface,
accompanied by small changes in its bond angle and length. Furthermore, SF6 is found to be physically and
chemically adsorbed over 0.5 and 1.0 ML (monolayer) H-covered O-terminated MgO (111) surfaces, respectively.
The SF6 molecule undergoes a self-decomposition on the 1.0 ML hydroxylated surface via a surface bonding
process. This study shows that defective and hydroxylated MgO surfaces have the surface capacities for SF6
activation, which shows that MgO has potential as packing material in SF6 waste treatment in packed-bed
plasmas.

Abstract: Plasma catalysis is emerging for plasma-assisted gas conversion
processes. However, the underlying mechanisms of plasma catalysis are poorly
understood. In this work, we present a 1D heterogeneous catalysis model with axial
dispersion (i.e., accounting for back-mixing and molecular diffusion of fluid elements in
the process stream in the axial direction), for plasma-catalytic NO production from
N2/O2 mixtures. We investigate the concentration and reaction rates of each species
formed as a function of time and position across the catalyst, in order to determine the
underlying mechanisms. To obtain insights into how the performance of the process
can be further improved, we also study how changes in the postplasma gas flow
composition entering the catalyst bed and in the operation conditions of the catalytic
stage affect the performance of NO production.

Abstract: Photocatalytic acetaldehyde degradation exhibits satisfactory performance only at relatively low acetaldehyde flow rates, predominately below 10 × 10-3 mL/min, leaving ample room for improvement. Therefore, it is necessary to prepare more efficient photocatalysts for acetaldehyde degradation. Moreover, the impact of the interaction strength between the titania surface and surface water on the photocatalytic acetaldehyde efficiency is poorly understood. To address these issues, in this work a series of (0 0 1)-faceted anatase titania samples with various surface properties and structures were synthesized via a solvothermal method and tested at high acetaldehyde flow rates under UV light irradiation. With increasing solvothermal time, the pore volume, surface area, and the abundance of surface OH groups all increased, while the crystallite size decreased. These were all identified to be beneficial to promote the degradation performance. When the solvothermal temperature was 180 ℃ and the reaction time was 5 h, the prepared sample displayed the most efficient performance at 19.25× 10-3 mL/min of acetaldehyde (conversion of (74 ± 1)% versus (29 ± 1)% for P25), and achieved a 100 % conversion at 16 × 10-3 mL/min. A weaker interaction strength between surface water and the titania surface was found to improve the acetaldehyde adsorption capacity, thereby promoting the acetaldehyde degradation efficiency. The stability of the best performing sample was tested over 48 h, demonstrating a highly stable performance with no signs of deactivation. Even at a relative humidity of 30 %, the acetaldehyde conversion retains 82% of its efficiency in a dry atmosphere, highlighting its potential in practical applications.

Abstract: Paintings are complex objects containing many different chemical compounds that can react over time. The degradation of arsenic sulfide pigments causes optical changes in paintings. The main degradation product was thought to be white arsenolite (As2O3), but previous research also showed the abundant presence of As(V) species. In this study, we investigate the influence of the presence of a medium on the degradation mechanism of orpiment (As2S3) using synchrotron radiation (SR)-based tomographic transmission X-ray microscopy, SR-based micro-X-ray fluorescence, and Xray absorption near edge structure spectroscopy. Upon direct illumination of dry orpiment powder using UV-visible light, only the formation of As2O3 was observed. When As2S3 was surrounded by a medium and illuminated, As2O3 was only observed in the area directly exposed to light, while As(V) degradation species were found elsewhere in the medium. Without accelerated artificial light aging, As(V)(aq) species are formed and migrate throughout the medium within weeks after preparation. In both scenarios, the As(V) species form via intermediate As(III)(aq) species and the presence of a medium is necessary. As(V)(aq) species can react with available cations to form insoluble metal arsenates, which induces stress within the paint layers (leading to, e.g., cracks and delamination) or can lead to a visual change of the image of the painting.

Abstract: Oxidized cobalt ferrite nanocrystals with a modified distribution of the magnetic cations in their spinel structure give place to an unusual exchange-coupled system with a double reversal of the magnetization, exchange bias, and increased coercivity, but without the presence of a clear physical interface that delimits two well-differentiated magnetic phases. More specifically, the partial oxidation of cobalt cations and the formation of Fe vacancies at the surface region entail the formation of a cobalt-rich mixed ferrite spinel, which is strongly pinned by the ferrimagnetic background from the cobalt ferrite lattice. This particular configuration of exchange-biased magnetic behavior, involving two different magnetic phases but without the occurrence of a crystallographically coherent interface, revolu-tionizes the established concept of exchange bias phenomenology.

Abstract: Out-of-equilibrium self-assembly of metal nanoparticles (NPs) has been devised using different types of strategies and fuels, but the achievement of finite 3D structures with a controlled morphology through this assembly mode is still rare. Here we used a spherical peptide-gold superstructure (PAuSS) as a template to control the out-of-equilibrium self-assembly of Au NPs, obtaining a transient 3D branched Au-nanoshell (BAuNS) stabilized by sodium dodecyl sulphate (SDS). The BAuNS dismantled upon concentration gradient equilibration over time in the solution, leading to NPs disassembly. Notably, BAuNS assembly and disassembly favoured temporary interparticle plasmonic coupling, leading to a remarkable oscillation of their optical properties.

Abstract: Our scientific and technological worldviews are largely dominated by the concepts of entropy and complexity. Originating in 19th-century thermodynamics, the concept of entropy merged with information in the last century, leading to definitions of entropy and complexity by Kolmogorov, Shannon and others. In its simplest form, this worldview is an application of the normal rules of arithmetic. In this worldview, when tossing a coin, a million heads or tails in a row is theoretically possible, but impossible in practice and in real life. On this basis, the impossible (in the binary case, the outermost entries of Pascal's triangle xn and yn for large values of n) can be safely neglected, and one can concentrate fully on what is common and what conforms to the law of large numbers, in fields ranging from physics to sociology and everything in between. However, in recent decades it has been shown that what is most improbable tends to be the rule in nature. Indeed, if one combines the outermost entries xn and yn with the normal rules of arithmetic, either addition or multiplication, one obtains Lamé curves and power laws respectively. In this article, some of these correspondences are highlighted, leading to a double conclusion. First, Gabriel Lamé's geometric footprint in mathematics and the sciences is enormous. Second, conic sections are at the core once more. Whereas mathematics so far has been exclusively the language of patterns in the sciences, the door is opened for mathematics to also become the language of the individual. The probabilistic worldview and Lamé's footprint can be seen as dual methods. In this context, it is to be expected that the notions of information, complexity, simplicity and redundancy benefit from this different viewpoint.

Abstract: Occupancy of different structural positions in a crystal lattice often seems to play a key role in material prop-erties. Several experimental techniques have been developed to uncover this issue, all of them being mostly bulk sensitive. However, many materials including topological insulators (TIs), which are among the most intriguing modern materials, are intended to be used in devices as thin films, for which the sublattice occupancy may differ from the bulk. One of the possible approaches to occupancy analysis is X-ray Photoelectron Diffraction (XPD), a structural method in surface science with chemical sensitivity. We applied this method in a case study of Sb2(Te1-xSex)3 mixed crystals, which belong to prototypical TIs. We used high-angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) as a reference method to verify our analysis. We revealed that the XPD data for vacuum cleaved bulk crystals are in excellent agreement with the reference ones. Also, we demonstrate that the anion occupancy near a naturally formed surface can be rather different from that of the bulk. The present results are relevant for a wide range of compositions where the system remains a topological phase, as we ultimately show by probing the transiently occupied topological surface state above the Fermi level by ultrafast photoemission.

Abstract: Nitrogen (N) is an indispensable building block for all living organisms as well as for pharmaceutical and chemical industry. In a nutshell, N is needed for plants to grow and beings to live and nitrogen fixation (NF) is the process that makes N available for plants as food by converting N2 into a reactive form, such as ammonia (NH3) or nitrogen oxides (NOx), upon reacting with O2 and H2. The aim of this thesis is to elucidate (wet) plasma-based nitrogen fixation with a focus on (1) the role of pulsing in achieving low energy consumption, (2) the role of H2O as a hydrogen source in nitrogen fixation and (3) elucidation of nitrogen fixation pathways in humid air and humid N2 plasma in a combined experimental and computational study. Furthermore, this thesis aims to take into account the knowledge-gaps and challenges identified in the discussion of the state of the art. Specifically, (1) we put our focus on branching out to another way of introducing water into the plasma system, i.e. H2O vapor, (2) we de-couple the problem for pathway elucidation by starting with characterization of the chosen plasma, next a simpler gas mixture and building up from there, (3) we include modelling, though not under wet conditions and (4) we focus on also analyzing species and performance outside liquid H2O. Firstly, based on the reaction analysis of a validated quasi-1D model, we can conclude that pulsing is indeed the key factor for energy-efficient NOx- formation, due to the strong temperature drop it causes. Secondly, the thesis shows that added H2O vapor, and not liquid H2O, is the main source of H for NH3 generation. Related to this, we discuss how the selectivity of plasma-based NF in humid air and humid N2 can be controlled by changing the humidity in the feed gas. Interestingly, NH3 production can be achieved in both N2 and air plasmas using H2O as a H source. Lastly, we identified a significant loss mechanism for NH3 and HNO2 that occurs in systems where these species are synthesized simultaneously, i.e. downstream from the plasma, HNO2 reacts with NH3 to form NH4NO2, which decomposes into N2 and H2O. This reduces the effective NF when not properly addressed, and should therefore be considered in future works aimed at optimizing plasma-based NF. In conclusion, this thesis adds further to the current state of the art of plasma-based NF both in the presence of H2O and in dry systems.