Abstract: Inelastic image simulation software is presented, implementing the double channeling approximation which takes into account the combination of multiple elastic and single inelastic scattering in a crystal. The approach is described with a density matrix formalism. Two applications in high resolution energy filtered (EFTEM) transmission electron microscopy (TEM) images are presented: thickness-defocus maps for SrTiO3 and exit plane intensities for an (LaAlO3)3(SrTiO3)3 multilayer system. Both systems show a severe breakdown in direct interpretability which becomes worse for higher acceleration voltages, thicker samples and lower excitation edge energies. Since this effect already occurs in the exit plane intensity, it is a fundamental limit and image simulations in EFTEM are indispensable just as they are indispensable for elastic high resolution TEM images.

Abstract: A model-based method is proposed to relatively quantify the chemical composition of atomic columns using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. The method is based on a quantification of the total intensity of the scattered electrons for the individual atomic columns using statistical parameter estimation theory. In order to apply this theory, a model is required describing the image contrast of the HAADF STEM images. Therefore, a simple, effective incoherent model has been assumed which takes the probe intensity profile into account. The scattered intensities can then be estimated by fitting this model to an experimental HAADF STEM image. These estimates are used as a performance measure to distinguish between different atomic column types and to identify the nature of unknown columns with good accuracy and precision using statistical hypothesis testing. The reliability of the method is supported by means of simulated HAADF STEM images as well as a combination of experimental images and electron energy-loss spectra. It is experimentally shown that statistically meaningful information on the composition of individual columns can be obtained even if the difference in averaged atomic number Z is only 3. Using this method, quantitative mapping at atomic resolution using HAADF STEM images only has become possible without the need of simultaneously recorded electron energy loss spectra.

Abstract: We present a new method to measure structure factors from electron spot diffraction patterns recorded under almost parallel illumination in transmission electron microscopes. Bloch wave refinement routines have been developed to refine the crystal thickness, its orientation and structure factors by comparison of experimentally recorded and calculated intensities. Our method requires a modicum of computational effort, making it suitable for contemporary personal computers. Frozen lattice and Bloch wave simulations of GaAs diffraction patterns are used to derive optimised experimental conditions. Systematic errors are estimated from the application of the method to simulated diffraction patterns and rules for the recognition of physically reasonable initial refinement conditions are derived. The method is applied to the measurement of the 200 structure factor for GaAs. We found that the influence of inelastically scattered electrons is negligible. Additionally, we measured the 200 structure factor from zero loss filtered two-dimensional convergent beam electron diffraction patterns. The precision of both methods is found to be comparable and the results agree well with each other. A deviation of more than 20% from isolated atom scattering data is observed, whereas close agreement is found with structure factors obtained from density functional theory [A. Rosenauer, M. Schowalter, F. Glas, D. Lamoen, Phys. Rev. B 72 (2005), 085326-1], which account for the redistribution of electrons due to chemical bonding via modified atomic scattering amplitudes.

Abstract: Recording the electron energy loss spectroscopy data cube with a series of energy filtered images is a dose inefficient process because the energy slit blocks most of the electrons. When recording the data cube by scanning an electron probe over the sample, perfect dose efficiency is attained; but due to the low current in nanoprobes, this often is slower, with a smaller field of view. In W. Van den Broek et al. [Ultramicroscopy, 106 (2006) 269], we proposed a new method to record the data cube, which is more dose efficient than an energy filtered series. It produces a set of projections of the data cube and then tomographically reconstructs it. In this article, we demonstrate these projections in practice, we present a simple geometrical model that allows for quantification of the projection angles and we present the first successful experimental reconstruction, all on a standard post-column instrument.

Abstract: It is well known that, in bulk, the solution of the Bogoliubovde Gennes equations is the same whether or not the HartreeFock term is included. Here the HartreeFock potential is position independent and so gives the same contribution to both the single-electron energies and the Fermi level (the chemical potential). Thus, the single-electron energies measured from the Fermi level (they control the solution) stay the same. This is not the case for nanostructured superconductors, where quantum confinement breaks the translational symmetry and results in a position-dependent HartreeFock potential. In this case its contribution to the single-electron energies depends on the relevant quantum numbers. We numerically solved the Bogoliubovde Gennes equations with the HartreeFock term for a clean superconducting nanocylinder and found a shift of the curve representing the thickness-dependent oscillations of the critical superconducting temperature to larger diameters.

Abstract: The effect of trigonal warping on the transmission of electrons tunneling through potential barriers in graphene is investigated. We present calculations of the transmission coefficient for single and double barriers as a function of energy, incidence angle and barrier heights. The results show remarkable valley-dependent directional effects for barriers oriented parallel to the armchair or parallel to the zigzag direction. These results indicate that electrostatic gates can be used as valley filters in graphene-based devices.

Abstract: In this paper, some modelling approaches to describe direct current (dc) magnetron discharges developed in our research groups will be presented, including an analytical model, Monte Carlo simulations for the electrons and for the sputtered atoms, a hybrid Monte Carlo-fluid model and particle-in-cell-Monte Carlo collision simulations. The strengths and limitations of the various modelling approaches will be explained, and some characteristic simulation results will be illustrated. Furthermore, some other simulation methods related to the magnetron device will be briefly explained, more specifically for calculating the magnetic field distribution inside the discharge, and for describing the (reactive) sputtering.

Abstract: In this paper, a simulation method is described to predict the etching behaviour of Cl2/O2/Ar inductively coupled plasmas on a Si substrate, as used in shallow trench isolation for the production of electronic devices. The hybrid plasma equipment model (HPEM) developed by Kushner et al is applied to calculate the plasma characteristics in the reactor chamber and two additional Monte Carlo simulations are performed to predict the fluxes, angles and energy of the plasma species bombarding the Si substrate, as well as the resulting surface processes such as etching and deposition. The simulations are performed for a wide variety of operating conditions such as gas composition, chamber pressure, power deposition and substrate bias. It is predicted by the simulations that when the fraction of oxygen in the gas mixture is too high, the oxidation of the Si substrate is superior to the etching of Si by chlorine species, resulting in an etch rate close to zero as is also observed in the experiments.

Abstract: Plasma modelling is an exciting subject in which virtually all physical disciplines are represented. Plasma models combine the electromagnetic, statistical and fluid dynamical theories that have their roots in the 19th century with the modern insights concerning the structure of matter that were developed throughout the 20th century. The present cluster issue consists of 20 invited contributions, which are representative of the state of the art in plasma modelling and numerical simulation. These contributions provide an in-depth discussion of the major theories and modelling and simulation strategies, and their applications to contemporary plasma-based technologies. In this editorial review, we introduce and complement those papers by providing a bird's eye perspective on plasma modelling and discussing the historical context in which it has surfaced.

Abstract: Background Cell transplantation is likely to become an important therapeutic tool for the treatment of various traumatic and ischemic injuries to the central nervous system (CNS). However, in many pre-clinical cell therapy studies, reporter gene-assisted imaging of cellular implants in the CNS and potential reporter gene and/or cell-based immunogenicity, still remain challenging research topics. Results In this study, we performed cell implantation experiments in the CNS of immunocompetent mice using autologous (syngeneic) luciferase-expressing bone marrow-derived stromal cells (BMSC-Luc) cultured from ROSA26-L-S-L-Luciferase transgenic mice, and BMSC-Luc genetically modified using a lentivirus encoding the enhanced green fluorescence protein (eGFP) and the puromycin resistance gene (Pac) (BMSC-Luc/eGFP/Pac). Both reporter gene-modified BMSC populations displayed high engraftment capacity in the CNS of immunocompetent mice, despite potential immunogenicity of introduced reporter proteins, as demonstrated by real-time bioluminescence imaging (BLI) and histological analysis at different time-points post-implantation. In contrast, both BMSC-Luc and BMSC-Luc/eGFP/Pac did not survive upon intramuscular cell implantation, as demonstrated by real-time BLI at different time-points post-implantation. In addition, ELISPOT analysis demonstrated the induction of IFN-ã-producing CD8+ T-cells upon intramuscular cell implantation, but not upon intracerebral cell implantation, indicating that BMSC-Luc and BMSC-Luc/eGFP/Pac are immune-tolerated in the CNS. However, in our experimental transplantation model, results also indicated that reporter gene-specific immune-reactive T-cell responses were not the main contributors to the immunological rejection of BMSC-Luc or BMSC-Luc/eGFP/Pac upon intramuscular cell implantation. Conclusion We here demonstrate that reporter gene-modified BMSC derived from ROSA26-L-S-L-Luciferase transgenic mice are immune-tolerated upon implantation in the CNS of syngeneic immunocompetent mice, providing a research model for studying survival and localisation of autologous BMSC implants in the CNS by real-time BLI and/or histological analysis in the absence of immunosuppressive therapy.

Abstract: Using Brownian dynamics simulations, we investigate the dynamics of colloids confined in two-dimensional narrow channels driven by a nonuniform force Fdr(y). We considered linear-gradient, parabolic, and deltalike driving-force profiles. This driving force induces melting of the colloidal solid (i.e., shear-induced melting), and the colloidal motion experiences a transition from elastic to plastic regime with increasing Fdr. For intermediate Fdr (i.e., in the transition region) the response of the system, i.e., the distribution of the velocities of the colloidal chains õi(y), in general does not coincide with the profile of the driving force Fdr(y), and depends on the magnitude of Fdr, the width of the channel, and the density of colloids. For example, we show that the onset of plasticity is first observed near the boundaries while the motion in the central region is elastic. This is explained by: (i) (in)commensurability between the chains due to the larger density of colloids near the boundaries, and (ii) the gradient in Fdr. Our study provides a deeper understanding of the dynamics of colloids in channels and could be accessed in experiments on colloids (or in dusty plasma) with, e.g., asymmetric channels or in the presence of a gradient potential field.

Abstract: A combination of synchrotron radiation based X-ray microscopic techniques (ì-XRF, ì-XANES, ì-XRD) applied on single depleted uranium (DU) particles and semi-bulk leaching experiments has been employed to link the potential bioavailability of DU particles to site-specific particle characteristics. The oxidation states and crystallographic forms of U in DU particles have been determined for individual particles isolated from selected samples collected at different sites in Kosovo and Kuwait that were contaminated by DU ammunition during the 1999 Balkan conflict and the 1991 Gulf war. Furthermore, small soil or sand samples heavily contaminated with DU particles were subjected to simulated gastrointestinal fluid (0.16 M HCl) extractions. Characteristics of DU particles in Kosovo soils collected in 2000 and in Kuwait soils collected in 2002 varied significantly depending on the release scenario and to some extent on weathering conditions. Oxidized U (+6) was determined in large, fragile and bright yellow DU particles released during fire at a DU ammunition storage facility and crystalline phases such as schoepite (UO3·2.25H2O), dehydrated schoepite (UO3·0.75H2O) and metaschoepite (UO3·2.0H2O) were identified. As expected, these DU particles were rapidly dissolved in 0.16 M HCl (84 ± 3% extracted after 2 h) indicating a high degree of potential mobility and bioavailability. In contrast, the 2 h extraction of samples contaminated with DU particles originating either from corrosion of unspent DU penetrators or from impacted DU ammunition appeared to be much slower (2030%) as uranium was less oxidized (+4 to +6). Crystalline phases such as UO2, UC and metallic U or UTi alloy were determined in impacted DU particles from Kosovo and Kuwait, while the UO2,34 phase, only determined in particles from Kosovo, could reflect a more corrosive environment. Although the results are based on a limited number of DU particles, they indicate that the structure and extractability of DU particles released from similar sources (metallic U penetrators) will depend on the release scenarios (fire, impact) and to some extent environmental conditions. However, most of the DU particles (7396%) in all investigated samples were dissolved in 0.16 M HCl after one week indicating that a majority of the DU material is bioaccessible.

Abstract: Single crystals of Ln5Ru2O12 (Ln=Pr, Nd, SmTb) were grown out of either NaOH or KOH fluxes in sealed silver tubes. The crystals of all the phases were observed to be twinned as confirmed by TEM studies. The series crystallize in the C2/m monoclinic system with lattice parameters, a=12.4049(4)12.7621(6) Å, b=5.8414(2)5.9488(3) Å, c=7.3489(2)7.6424(4) Å, β=107.425(3)107.432(2)° and Z=2. The crystal structure is isotypic with the defect/disorder model of Ln5Re2O12 (Ln = Y, Gd) and consists of one dimensional edge shared RuO6 octahedral chains separated by a two dimensional LnOx polyhedral framework. Magnetic measurements indicate paramagnetic and antiferromagnetic behavior for Ln=Nd, SmGd and Ln=Tb, respectively.

Abstract: The ground states of a few electrons confined in two vertically coupled quantum rings in the presence of an external magnetic field are studied systematically within the current spin-density functional theory. Electron-electron interactions combined with inter-ring tunneling affect the electronic structure and the persistent current. For small values of the external magnetic field, we recover the zero magnetic field molecular quantum ring ground state configurations. Increasing the magnetic field many angular momentum, spin, and isospin transitions are predicted to occur in the ground state. We show that these transitions follow certain rules, which are governed by the parity of the number of electrons, the single-particle picture, Hunds rules, and many-body effects.

Abstract: We study the properties of a capacitive 13.56 MHz discharge with a mixture of Ar/C₂H₂ taking into account the plasmochemistry and growth of heavy hydrocarbons. A hybrid model was developed to combine the kinetic description for electron motion and the fluid approach for negative and positive ion transports and plasmochemical processes. A significant change in plasma parameters related to injection of 5.8% portion of acetylene in argon was observed and analyzed. We found that the electronegativity of the mixture is about 30%. The densities of negatively and positively charged heavy hydrocarbons are sufficiently large to be precursors for the formation of nanoparticles in the discharge volume.