Abstract: Bi₂Se₃is a thermoelectric material and a topological insulator. It is slightly conducting in its bulk due to the presence of defects and by controlling the defects different physical properties can be fine tuned. However, studies of the defects in this material are often contradicting or inconclusive. Here, the defect structure of Bi₂Se₃is studied with a combination of techniques: high-resolution scanning transmission electron microscopy (HR-STEM), high-resolution energy-dispersive X-ray (HR-EDX) spectroscopy, precession electron diffraction tomography (PEDT), X-ray diffraction (XRD) and first-principles calculations using density functional theory (DFT). Based on these results, not only the observed defects are discussed, but also the discrepancies in results or possibilities across the techniques. STEM and EDX revealed interstitial defects with mainly Bi character in an octahedral coordination in the van der Waals gap, independent of the applied sample preparation method (focused ion beam milling or cryo-crushing). The inherent character of these defects is supported by their observation in the structure refinement of the EDT data. Moreover, the occupancy probability of the defects determined by EDT is inversely proportional to their corresponding DFT calculated formation energies. STEM also showed the migration of some atoms across and along the van der Waals gap. The kinetic barriers calculated using DFT suggest that some paths are possible at room temperature, while others are most probably beam induced.

Abstract: Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.

Abstract: Plasma catalysis is promising for various environmental, energy and chemical synthesis applications, but the underlying mechanisms are far from understood. Modeling can help to obtain a better insight in these mechanisms. Some burning questions relate to the plasma behavior inside packed bed reactors and whether plasma can penetrate into catalyst pores. In this paper, we try to provide answers to these questions, by means of both fluid modeling and particle-in-cell/Monte Carlo collision simulations. We present a short overview of recent findings obtained in our group by means of modeling, i.e., the enhanced electric field near the contact points and the streamer propagation through the packing in packed bed reactors, as well as the plasma behavior in catalyst pores, to determine the minimum pore size in which plasma streamers can penetrate.

Abstract: Under the constraint of constant illumination, an information criterion is formulated for the Fisher information that compressed sensing measurements in optical and transmission electron microscopy contain about the underlying parameters. Since this approach requires prior knowledge of the signal's support in the sparse basis, we develop a heuristic quantity, the detective quantum efficiency (DQE), that tracks this information criterion well without this knowledge. In this paper, it is shown that for the investigated choice of sensing matrices, and in the absence of read-out noise, i.e., with only Poisson noise present, compressed sensing does not raise the amount of Fisher information in the recordings above that of Shannon sampling. Furthermore, enabled by the DQE's analytical tractability, the experimental designs are optimized by finding out the optimal fraction of on pixels as a function of dose and read-out noise. Finally, we introduce a regularization and demonstrate, through simulations and experiment, that it yields reconstructions attaining minimum mean squared error at experimental settings predicted by the DQE as optimal.

Abstract: Physical plasmas generate unique mixes of reactive oxygen and nitrogen species (RONS or ROS). Only a bit more than a decade ago, these plasmas, operating at body temperature, started to be considered for medical therapy with considerably little mechanistic redox chemistry or biomedical research existing on that topic at that time. Today, a vast body of evidence is available on physical plasma-derived ROS, from their spatiotemporal resolution in the plasma gas phase to sophisticated chemical and biochemical analysis of these species once dissolved in liquids. Data from<italic>in silico</italic>analysis dissected potential reaction pathways of plasma-derived reactive species with biological membranes, and<italic>in vitro</italic>and<italic>in vivo</italic>experiments in cell and animal disease models identified molecular mechanisms and potential therapeutic benefits of physical plasmas. In 2013, the first medical plasma systems entered the European market as class IIa devices and have proven to be a valuable resource in dermatology, especially for supporting the healing of chronic wounds. The first results in cancer patients treated with plasma are promising, too. Due to the many potentials of this blooming new field ahead, there is a need to highlight the main concepts distilled from plasma research in chemistry and biology that serve as a mechanistic link between plasma physics (how and which plasma-derived ROS are produced) and therapy (what is the medical benefit). This inevitably puts cellular membranes in focus, as these are the natural interphase between ROS produced by plasmas and translation of their chemical reactivity into distinct biological responses.

Abstract: The fundamental plasticity mechanisms in thin freestanding Zr65Ni35 metallic glass films are investigated in order to unravel the origin of an outstanding strength/ductility balance. The deformation process is homogenous until fracture with no evidence of catastrophic shear banding. The creep/relaxation behaviour of the films was characterized by on-chip tensile testing, revealing an activation volume in the range 100–200 Å3. Advanced high-resolution transmission electron microscopy imaging and spectroscopy exhibit a very fine glassy nanostructure with well-defined dense Ni-rich clusters embedded in Zr-rich clusters of lower atomic density and a ~2–3 nm characteristic length scale. Nanobeam electron diffraction analysis reveals that the accumulation of plastic deformation at roomtemperature
correlates with monotonously increasing disruption of the local atomic order. These results provide experimental evidences of the dynamics of shear transformation zones activation in metallic glasses. The impact of the nanoscale structural heterogeneities on the mechanical properties including the rate dependent behaviour is discussed, shedding new light on the governing plasticity mechanisms in metallic glasses with initially heterogeneous atomic arrangement.

Abstract: Monolayers of graphene and hexagonal boron nitride (hBN) are highly permeable to thermal protons1,2. For thicker two-dimensional (2D) materials, proton conductivity diminishes exponentially, so that, for example, monolayer MoS2 that is just three atoms thick is completely impermeable to protons1. This seemed to suggest that only one-atom-thick crystals could be used as proton-conducting membranes. Here, we show that few-layer micas that are rather thick on the atomic scale become excellent proton conductors if native cations are ion-exchanged for protons. Their areal conductivity exceeds that of graphene and hBN by one to two orders of magnitude. Importantly, ion-exchanged 2D micas exhibit this high conductivity inside the infamous gap for proton-conducting materials3, which extends from ∼100 °C to 500 °C. Areal conductivity of proton-exchanged monolayer micas can reach above 100 S cm−2 at 500 °C, well above the current requirements for the industry roadmap4. We attribute the fast proton permeation to ~5-Å-wide tubular channels that perforate micas’ crystal structure, which, after ion exchange, contain only hydroxyl groups inside. Our work indicates that there could be other 2D crystals5 with similar nanometre-scale channels, which could help close the materials gap in proton-conducting applications.

Abstract: Despite numerous attempts to use human mesenchymal stem cells (hMSCs) in the field of tissue engineering, the control of their differentiation remains challenging. Here, we investigated possible applications of a non-thermal atmospheric pressure plasma jet (NTAPPJ) to control the differentiation of hMSCs. An air- or nitrogen-based NTAPPJ was applied to hMSCs in culture media, either directly or by media treatment in which the cells were plated after the medium was exposed to the NTAPPJ. The durations of exposure were 1, 2, and 4 min, and the control was not exposed to the NTAPPJ. The initial attachment of the cells was assessed by a water-soluble tetrazolium assay, and the gene expression in the cells was assessed through reverse-transcription polymerase chain reaction and immunofluorescence staining. The results showed that the gene expression in the hMSCs was generally increased by the NTAPPJ exposure, but the enhancement was dependent on the conditions of the exposure, such as the source of the gas and the treatment method used. These results were attributed to the chemicals in the extracellular environment and the reactive oxygen species generated by the plasma. Hence, it was concluded that by applying the best conditions for the NTAPPJ exposure of hMSCs, the control of hMSC differentiation was possible, and therefore, exposure to an NTAPPJ is a promising method for tissue engineering.

Abstract: Tumours are complex systems formed by cellular (malignant, immune, and endothelial cells, fibroblasts) and acellular components (extracellular matrix (ECM) constituents and secreted factors). A close interplay between these factors, collectively called the tumour microenvironment, is required to respond appropriately to external cues and to determine the treatment outcome. Cold plasma (here referred as ‘plasma’) is an emerging anticancer technology that generates a unique cocktail of reactive oxygen and nitrogen species to eliminate cancerous cells via multiple mechanisms of action. While plasma is currently regarded as a local therapy, it can also modulate the mechanisms of cell-to-cell and cell-to-ECM communication, which could facilitate the propagation of its effect in tissue and distant sites. However, it is still largely unknown how the physical interactions occurring between cells and/or the ECM in the tumour microenvironment affect the plasma therapy outcome. In this review, we discuss the effect of plasma on cell-to-cell and cell-to-ECM communication in the context of the tumour microenvironment and suggest new avenues of research to advance our knowledge in the field. Furthermore, we revise the relevant state-of-the-art in three-dimensional in vitro models that could be used to analyse cell-to-cell and cell-to-ECM communication and further strengthen our understanding of the effect of plasma in solid tumours.

Abstract: A detailed microstructural examination endeavoring to understand the interfacial phenomena yielding to cohesion
in solid-state assembling processes was performed. This study focuses on the transition zone of a dissimilar
titanium alloy joint obtained by Linear Friction Welding (LFW) the β-metastable Ti17 to the near-α
Ti6242. The transition zone delimitating both alloys is characterized by a sharp microstructure change from
acicular HCP (Hexagonal Close-Packed) α′ martensitic laths in the Ti6242 to equiaxed BCC β (Body-Centered
Cubic) subgrains in the Ti17; these α′ plates were shown to precipitate within prior-β subgrains remarkably more
rotated than the ones formed in the Ti17. Both α′ and β microstructures were found to be intermingled within
transitional subgrains demarcating a limited gradient from one chemical composition to the other. These peculiar
interfacial grains revealed that the cohesive mechanisms between the rubbing surfaces occurred in the
single-phase β domain under severe strain and high-temperature conditions. During the hot deformation process,
the mutual migration of the crystalline interfaces from one material to another assisted by a continuous dynamic
recrystallization process was identified as the main adhesive mechanism at the junction zone. The latter led to
successful cohesion between the rubbing surfaces. Once the reciprocating motion stopped, fast cooling caused
both materials to experience either a βlean→α′ or βlean→βmetastable transformation in the interfacial zone depending
on their local chemical composition. The limited process time and the subsequent hindered chemical
homogenization at the transition zone led to retaining the so-called intermingled α’/βm subgrains constituting
the border between both Ti-alloys.

Abstract: Magnetic field mapping in transmission electron microscopy is commonplace, but all conventional methods provide only a projection of the components of the magnetic induction perpendicular to the electron trajectory. Recent experimental advances with electron vortices have shown that it is possible to map the out of plane magnetic induction in a TEM setup via interferometry with a specifically prepared electron vortex state carrying high orbital angular momentum (OAM). The method relies on the Aharonov?Bohm phase shift that the electron undergoes when going through a longitudinal field. Here we show how the same effect naturally occurs for any electron wave function, which can always be described as a superposition of OAM modes. This leads to a clear connection between the occurrence of high-OAM partial waves and the amount of azimuthal rotation in the far field angular distribution of the beam. We show that out of plane magnetic field measurement can thus be obtained with a much simpler setup consisting of a ring-like aperture with azimuthal spokes. We demonstrate the experimental setup and explore the achievable sensitivity of the magnetic field measurement.

Abstract: Belgian pork production has faced stagnating prices for decades. It remains unclear whether excessive market power from slaughterhouses or meat retailers has played a role in this trend. While market power studies can reveal some of the market dynamics in this setting, this type of research has not yet been applied to the Belgian pork market. The present paper investigates oligopolies and oligopsonies in the pork production sector. We build a new model that focuses on market power dynamics in the market for live pigs and distinguishes horizontal and vertical market power parameters, both for pig farmers and for slaughterhouses. The results follow from an empirical application using unique slaughterhouse data for 2001–2015. The results indicate that the farmers benefit from a significant power advantage in the live pig market, when very modest price demands are taken as a reference. The final market price of live pigs approaches the price requested by the farmers. On the other hand, the measured vertical market power also suggests that a pig farmer does not receive the (modest) full-wage-based salary. The market power of the slaughterhouses is also limited. Market power as a result of collusion—that is, horizontal market power—is present, but is not strong. However, there are significant differences between the slaughterhouses in terms of mark-up on the input prices. These differences reflect differences in company strategy, and this diversity further reduces the possibility to create sector-wide collusive behaviour.

Abstract: AlGaN/GaN heterostructures were grown on “on-axis” and 2° off (0001) 4H-SiC substrates by metalorganic vapor phase epitaxy (MOVPE). Structural characterization was performed by transmission electron microscopy. The dislocation density, being greater in the on-axis case, is gradually reduced in the GaN layer and is forming
dislocation loops in the lower region. Steps aligned along [11̅00] in the off-axis case give rise to simultaneous defect formation. In the on-axis case, an almost zero density of steps is observed, with the main origin of defects probably being the orientation mismatch at the grain boundaries between the small not fully coalesced AlN grains. V-shaped formations are observed in the AlN nucleation layer, but are more frequent in the off-axis case, probably enhanced by the presence of steps. These V-shaped formations are completely overgrown by the GaN layer, during the subsequent deposition, presenting AlGaN areas in the walls of the defect, indicating an interdiffusion between the layers. Finally, at the AlGaN/GaN heterostructure surface in the on-axis case, V-shapes are observed, with the AlN spacer and AlGaN (21% Al) thickness on relaxed GaN exceeding the critical thickness for relaxation. On the other hand, no relaxation in the form of V-shape creation is observed in the off-axis case, probably due to the smaller AlGaN thickness (less than 21% Al). The AlN spacer layer, grown in between the heterostructure, presents a uniform thickness and clear interfaces.

Abstract: The precipitation mechanism of the Q phase in Al-Mg-Si-Cu alloys has long been the subject of ambiguity and debate since its metastable phase (Q 0) has the same crystal structure and similar lattice parameters as its equilibrium counterparts. In the present work, the evolution of the Q 0 (Q) phase during aging is studied by combination of quantitative atomic-resolution scanning transmission electron microscopy and atom probe tomography. It was found that the transformation from the Q 0 to the Q phase involves changes of the occupancy of Al atoms in atomic columns of the Q 0 (Q) phase. The Al atoms incorporated in the Cu, Si and Mg columns are gradually released into the Al matrix, while mixing between Cu and Si atoms occurs in the Si columns. This transformation process is mainly attributed to the low lattice misfit of the equilibrium Q phase. Besides, the formation of various compositions of the Q phase is due to the different occupancy in the atomic columns of the Q phase. The occupancy changes in the columns of the Q phase are kinetically controlled and are strongly influenced by the alloy composition and aging temperature.