Abstract: A real-time image reconstruction method for scanning transmission electron microscopy (STEM) is proposed. With an algorithm requiring only the center of mass of the diffraction pattern at one probe position at a time, it is able to update the resulting image each time a new probe position is visited without storing any intermediate diffraction patterns. The results show clear features at high spatial frequency, such as atomic column positions. It is also demonstrated that some common post-processing methods, such as band-pass filtering, can be directly integrated in the real-time processing flow. Compared with other reconstruction methods, the proposed method produces high-quality reconstructions with good noise robustness at extremely low memory and computational requirements. An efficient, interactive open source implementation of the concept is further presented, which is compatible with frame-based, as well as event-based camera/file types. This method provides the attractive feature of immediate feedback that microscope operators have become used to, for example, conventional high-angle annular dark field STEM imaging, allowing for rapid decision-making and fine-tuning to obtain the best possible images for beam-sensitive samples at the lowest possible dose.

Abstract: In this second part of a series we attempt to construct an empirical model that can mimick all experimental observations made regarding the role of an alternative interleaved scan pattern in STEM imaging on the beam damage in a specific zeolite sample. We make use of a 2D diffusion model that describes the dissipation of the deposited beam energy in the sequence of probe positions that are visited during the scan pattern. The diffusion process allows for the concept of trying to ‘outrun’ the beam damage by carefully tuning the dwell time and distance between consecutively visited probe positions. We add a non linear function to include a threshold effect and evaluate the accumulated damage in each part of the image as a function of scan pattern details. Together, these ingredients are able to describe qualitatively all aspects of the experimental data and provide us with a model that could guide a further optimisation towards even lower beam damage without lowering the applied electron dose. We deliberately remain vague on what is diffusing here which avoids introducing too many sample specific details. This provides hope that the model can be applied also in sample classes that were not yet studied in such great detail by adjusting higher level parameters: a sample dependent diffusion constant and damage threshold.

Abstract: Understanding the thermal stability of bimetallic nanoparticles is of vital importance to preserve their functionalities during their use in a variety of applications. In contrast to well-studied bimetallic systems such as Au@Ag, heat-induced morphological and compositional changes in Au@Pt nanoparticles are insufficiently understood, even though Au@Pt is an important material for catalysis. To investigate the thermal instability of Au@Pt nanorods at temperatures below their bulk melting point, we combined in situ heating with two- and three-dimensional electron microscopy techniques, including three-dimensional energy-dispersive X-ray spectroscopy. The experimental results were used as input for molecular dynamics simulations, to unravel the mechanisms behind the morphological transformation of Au@Pt core–shell nanorods. We conclude that thermal stability is influenced not only by the degree of coverage of Pt on Au but also by structural details of the Pt shell.

Abstract: Electron tomography has become a cornerstone technique for the visualization of nanoparticle morphology in three dimensions. However, to obtain in-depth information about a nanoparticle beyond surface faceting and morphology, different electron microscopy signals must be combined. The most notable examples of these combined signals include annular dark-field scanning transmission electron microscopy (ADF-STEM) with different collection angles and the combination of ADF-STEM with energy-dispersive X-ray or electron energy loss spectroscopies. Here, the experimental and computational development of various multimode tomography techniques in connection to the fundamental materials science challenges that multimode tomography has been instrumental to overcoming are summarized. Although the techniques can be applied to a wide variety of compositions, the study is restricted to metal and metal oxide nanoparticles for the sake of simplicity. Current challenges and future directions of multimode tomography are additionally discussed.

Abstract: A new methodology is presented to count the number of atoms in multimetallic nanocrystals by combining energy dispersive X-ray spectroscopy (EDX) and high angle annular dark field scanning transmission electron microscopy (HAADF STEM). For this purpose, the existence of a linear relationship between the incoherent HAADF STEM and EDX images is exploited. Next to the number of atoms for each element in the atomic columns, the method also allows quantification of the error in the obtained number of atoms, which is of importance given the noisy nature of the acquired EDX signals. Using experimental images of an Au@Ag core–shell nanorod, it is demonstrated that 3D structural information can be extracted at the atomic scale. Furthermore, simulated data of an Au@Pt core–shell nanorod show the prospect to characterize heterogeneous nanostructures with adjacent atomic numbers.

Abstract: A robust and reproducible methodology to prepare stable inorganic nanoparticles with chiral morphology might hold the key to the practical utilization of these materials. We describe herein an optimized chiral growth method to prepare 4-fold twisted gold nanorods, where the amino acid cysteine is used as a dissymmetry inducer. Four tilted ridges were found to develop on the surface of single-crystal nanorods upon repeated reduction of HAuCl4, in the presence of cysteine as the chiral inducer and ascorbic acid as a reducing agent. From detailed electron microscopy analysis of the crystallographic structures, we propose that dissymmetry results from the development of chiral facets in the form of protrusions (tilted ridges) on the initial nanorods, eventually leading to a twisted shape. The role of cysteine is attributed to assisting enantioselective facet evolution, which is supported by density functional theory simulations of the surface energies, modified upon adsorption of the chiral molecule. The development of R-type and S-type chiral structures (small facets, terraces, or kinks) would thus be non-equal, removing the mirror symmetry of the Au NR and in turn resulting in a markedly chiral morphology with high plasmonic optical activity.

Abstract: A decade ago, a statistics-based method was introduced to count the number of atoms from annular dark-field scanning transmission electron microscopy (ADF STEM) images. In the past years, this method was successfully applied to nanocrystals of arbitrary shape, size, and composition (and its high accuracy and precision has been demonstrated). However, the counting results obtained from this statistical framework are so far presented without a visualization of the actual uncertainty about this estimate. In this paper, we present three approaches that can be used to represent counting results together with their statistical error, and discuss which approach is most suited for further use based on simulations and an experimental ADF STEM image.

Abstract: The pursuit for the next generation of nanodevices made scientists focus the attention to two dimensional materials. Experimental works of two dimensional materials are hardly free of structural defects, which, in turn, modify drastically the physical properties of its defect-free counterpart. In this work the presence of structural defects is study in two different materials. First, the dependence of the Hall, bend and longitudinal resistances to a perpendicular magnetic field and to vacancy defects in a four-terminal phosphorene single layer Hall bar is investigated. A tight-binding model in combination with the Landauer-Büttiker formalism is used to calculate the energy spectrum, the lead-to-lead transmissions, and the Hall and bend resistances of the system. It is shown that the terminals with zigzag edge orientation are responsible for the absence of quantized plateaus in the Hall resistance and peaks in the longitudinal resistance. A negative bend resistance in the ballistic regime is found due to the presence of high- and low- energy transport modes in the armchair and zigzag terminals, respectively. The system density of states, with single vacancy defects, shows that the presence of in-gap states is proportional to the number of vacancies. Quantized plateaus in the Hall resistance are only formed in a sufficiently clean system. The effects of different kinds of vacancies in the regime where the quantized plateaus are destroyed and a diffusive regime appears in the bend resistance are investigated. Next, we explore effects due to point defect clustering on the electronic and transport properties of bilayer graphene nanoribbons, for AA and AB stacking and zigzag and armchair boundaries, by means of the tight-binding approach and scattering matrix formalism. Evidence of vacancy concentration signatures exhibiting a maximum amplitude and an universality regardless of the system size, stacking and boundary types, in the density of states around the zero-energy level are observed. Our results are explained via the coalescence analysis of the strong sizeable vacancy clustering effect in the system and the breaking of inversion symmetry at high vacancy densities, demonstrating a similar density of states for two equivalent degrees of concentration disorder, below and above the maximum value.

Abstract: Supershapes are used in Parametric Design to model, literally, thou-sands of natural and man-made shapes with a single 6 parameter formula. However, users are left to probe such a rich yet dense collection of supershapes using a set of independent 1-D sliders. Some of the formula’s parameters are non-linear in nature, making them particularly difficult to grasp with conventional 1-D sliders alone. VR appears as a promising setting for Parametric Design with supershapes since it empowers users with more natural visual inspection and shape browsing techniques, with multiple solutions being displayed at once and the possibility to design more interesting forms of slider interaction. In this work, we propose VR shape widgets that allow users to probe and select supershapes from a multitude of solutions. Our designs take leverage on thumbnails, mini-maps, haptic feedback and spatial interaction, while supporting 1-D, 2-D and 3-D supershape parameter spaces. We conducted a user study (N = 18) and found that VR shape widgets are effective, more efficient, and natural than conventional VR 1-D sliders while also usable for users without prior knowledge on supershapes. We also found that the proposed VR widgets provide a quick overview of the main supershapes, and users can easily reach the desired solution without having to perform fine-grain handle manipulations.

Abstract: Biological membranes are under constant attack of reactive oxygen and nitrogen species (RONS), which may lead to a complex mixture of nitro-oxidized lipids that are responsible for structural and dynamic changes on the membrane. Because of that, nitro-oxidized lipids are also associated with several tumors and inflammatory and neurodegenerative diseases. Moreover, lipid oxidation may induce membrane phase-separated domains, which also drastically affect the membrane function. Evidence suggests that domain interfaces are “hot spots” for pore formation, but the underlying mechanisms remain elusive. There is an urgent need for an improved understanding of oxidation-induced phase separation on membrane properties. Likewise, the molecular structure at domain interfaces still needs to be elucidated. To evaluate the effect of lipid nitro-oxidation on the permeability of single-phase (homogeneous) and phase-separated (heterogeneous) phospholipid bilayers (PLBs), we performed atomistic molecular dynamics (MD) simulations using: (1) single-phase PLBs composed of several isomers of nitrated and/or oxidized lipids; (2) phase-separated PLBs composed of coexisting liquid ordered (Lo) and liquid disordered (Ld) domains, where the Ld domain is composed of non-oxidized and/or oxidized lipids. Our results show that nitrated lipids increase the membrane permeability of single-phase PLBs by three-fold compared to oxidized lipids. In addition, we show that oxidized lipids in the presence of nitrated lipids decrease the membrane permeability, suggesting an interaction between nitrated and oxidized lipids. Overall, the permeability of single-phase and phase-separated PLBs was comparable, and the presence of oxidized lipids increases the membrane permeability only in single-phase PLBs. Despite the latter, the presence of only 1.5% of lipid aldehydes at the Lo/Ld domain interfaces of phase-separated PLBs was able to increase the membrane permeability. In consequence of this, we also performed coarse-grained MD simulations to evaluate whether lipid aldehydes have a preference to accumulate at the interface between Lo/Ld domains. Our results show that lipid aldehydes derived from mono-unsaturated lipids accumulate at the interface, but those derived from poly-unsaturated lipids remain in the Ld domain. This study is of interest for photodynamic therapy and plasma medicine for cancer treatment, to understand the effects caused by RONS in cell membranes.

Abstract: Photoactive nanoparticles and their light-driven applications have gained tremendous scientific attention towards remediation of the global environmental problems, meeting alternative energy demands, and other new technological discoveries. The research work presented in this dissertation includes a fundamental investigation of such nanoparticles to gain deeper insights that will ultimately benefit their application. In particular, the study of plasmonic metal nanoparticles and metal oxide nanoparticles for light driven applications is the major theme of this work. The investigation begins with isolated plasmonic Au and Ag nanoparticles, followed by a natural extension to nanoparticle clusters, and then further to nanoparticle films. Next, the application of such plasmonic nanoparticle films for gaseous phase sensing of volatile organic compounds is explored. Finally, the film formation of metal-oxide nanoparticles by self-assembly is investigated for the fabrication of photoactive functional interfaces. The fundamental theoretical investigation of the isolated plasmonic nanoparticles encompasses alloy and core-shell nanostructures of Au-Ag bimetallic compositions. First, the optical properties of bimetallic alloy and core-shell nanoparticles are compared for different structures such as nanospheres, nanotriangles and nanorods. Based on the optical properties, the photothermal properties of these nanostructures are also evaluated for relevant light-driven applications. Further, to bridge the gap between the theoretical and experimental optical properties of colloidal plasmonic nanoparticles, the effect of different statistical parameters pertaining to the particle size distribution is studied. Going from isolated nanoparticles to nanoparticle clusters, the changes in the optical properties of plasmonic nanoparticles when they form finite clusters is investigated. A strong effect of clustering on the absorption intensities of the nanoparticles and hence, on the photothermal properties is found. Next, for the study of plasmonic nanoparticle infinite arrays, Au and Ag nanoparticles films are experimentally obtained by the self-assembly at the air-ethylene glycol interface. Upon further validation of the computational models with the experimental optical properties of these films, the near-field and far-field optical response of the plasmonic nanoparticle arrays is investigated. An application of the self-assembled Au nanoparticle film is then demonstrated in the sensing of volatile organic compounds (VOCs). Finally, the focus is shifted from plasmonic nanoparticles to metal oxide nanoparticles for their self-assembly at the air-water interface to obtain self-assembled films. For this, the hydrophobic functionalization of four metal oxides nanoparticles namely, TiO2, ZnO, WO3 and CuO is investigated. The insights from this work is useful for the design and fabrication of functional nanoparticles and interfaces for light driven applications.

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: 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.