Abstract: An extensive CO2 plasmamodel is presented that is relevant for the production of ‘‘solar fuels.’’ It is based on reaction rate coefficients fromrigorously reviewed literature, and is augmented with reactionrate coefficients that are obtained fromscaling laws.The input data set,which is suitable for usage with the plasma simulation software Plasimo (https://plasimo.phys.tue.nl/), is available via the Plasimo and publisher’s websites.1 The correctness of this model implementation has been established by independent ZDPlasKin implementation (http://www.zdplaskin.
laplace.univ-tlse.fr/), to verify that the results agree. Results of these ‘‘global models’’ are presented for a DBD plasma reactor.

Abstract: The modelling of a gliding arc discharge (GAD) is studied by means of the quasineutral (QN) plasma modelling approach. The model is first evaluated for reliability and proper description of a gliding arc discharge at atmospheric pressure, by comparing with a more elaborate non-quasineutral (NQN) plasma model in two different geometries – a 2D axisymmetric and a Cartesian geometry. The NQN model is considered as a reference, since it provides a continuous self-consistent plasma description, including the near electrode regions. In general, the results of the QN model agree very well with those obtained from the NQN model. The small differences between both models are attributed to the approximations in the derivation of the QN model. The use of the QN model provides a substantial reduction of the computation time compared to the NQN model, which is crucial for the development of more complex models in three dimensions or with complicated chemistries. The latter is illustrated for (i) a reverse vortex flow(RVF) GAD in argon, and (ii) a GAD in CO2. The RVF discharge is modelled in three dimensions and the effect of the turbulent heat transport on the plasma and gas characteristics is
discussed. The GAD model in CO2 is in a 1D geometry with axial symmetry and provides results for the time evolution of the electron, gas and vibrational temperature of CO2, as well as for the molar fractions of the different species.

Abstract: This paper gives an overview of our plasma chemistry modeling for CO2 and CH4 conversion in a dielectric barrier discharge (DBD) and microwave (MW) plasma. We focus on pure CO2 splitting and pure CH4 reforming, as well as mixtures of CO2/CH4, CH4/O2, and CO2/H2O. We show calculation results for the conversion, energy efficiency, and product formation, in comparison with experiments where possible. We also present the underlying chemical reaction pathways, to explain the observed
trends. For pure CO2, a comparison is made between a DBD and MW plasma, illustrating that the higher energy efficiency of the latter is attributed to the more important role of the vibrational levels.

Abstract: The catalytic oxidative dehydrogenation of hydrocarbons is an industrially important process, in which selectivity is a key issue. We here investigate the conversion of methanol to formaldehyde on a vanadia surface employing long timescale simulations, reaching a time scale of seconds. In particular, we compare the thermal process to the case where an additional external electric field is applied, as would be the case in a direct plasma-catalysis setup. We find that the electric field influences the retention time of the molecules at the catalyst surface. These simulations provide an atomic scale insight in the thermal catalytic oxidative dehydrogenation process, and in how an external electric field may affect this process.

Abstract: Cryogenic plasma etching is a promising technique for high-control wafer development with limited plasma induced damage. Cryogenic wafer temperatures effectively reduce surface damage during etching, but the fundamental mechanism is not well understood. In this study, the influences of wafer temperature, gas mixture and substrate bias on the (cryogenic) etch rates of Si with SF6/O2 inductively coupled plasmas are experimentally and computationally investigated. The etch rates are measured in situ with double-point reflectometry and a hybrid computational Monte Carlo – fluid model is applied to calculate plasma properties. This work allows the reader to obtain a better insight in the effects of wafer temperature on the etch rate and to find operating conditions for successful anisotropic (cryo)etching.

Abstract: We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells.

Abstract: We perform computer simulations supported by experiments to investigate the oxidation of an important signaling protein, that is, human epidermal growth factor (hEGF), caused by cold atmospheric plasma (CAP) treatment. Specifically, we study the conformational changes of hEGF with different degrees of oxidation, to mimic short and long CAP treatment times. Our results indicate that the oxidized structures become more flexible, due to their conformational changes and breakage of the disulfide bonds, especially at higher oxidation degrees. MM/GBSA calculations reveal that an increasing oxidation level leads to a lower binding free energy of hEGF with its receptor. These results help to understand the fundamentals of the use of CAP for wound healing versus cancer treatment at short and longer treatment times.

Abstract: In recent years, cold atmospheric plasma (CAP) has been proposed as a novel method to enhance transdermal drug delivery, while avoiding tissue damage. However, the underlying mechanism for the increasing skin permeability upon CAP treatment is still undefined. We propose a mechanism in which CAP-generated reactive species induce cross-linking of skin lipids, leading to the generation of nanopores, thereby facilitating the permeation of drug molecules. Molecular dynamics simulations support this proposed mechanism. Furthermore, our results indicate that to achieve maximum enhancement of the permeability, the optimal treatment will depend on the exact lipid composition of the skin, as well as on the CAP source used.

Abstract: Quantitative annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique to characterise nano-particles on an atomic scale. Because of their limited size and beam sensitivity, the atomic structure of such particles may become extremely challenging to determine. Therefore keeping the incoming electron dose to a minimum is important. However, this may reduce the reliability of quantitative ADF STEM which will here be demonstrated for nano-particle atom-counting. Based on experimental ADF STEM images of a real industrial catalyst, we discuss the limits for counting the number of atoms in a projected atomic column with single atom sensitivity. We diagnose these limits by combining a thorough statistical method and detailed image simulations.

Abstract: The electronic properties of quaternary AlInGaN devices significantly depend on the homogeneity of the alloy. The identification of compositional fluctuations or verification of random-alloy distribution is hence of grave importance. Here, a comprehensive multiprobe study of composition and compositional homogeneity is presented, investigating AlInGaN layers with indium concentrations ranging from 0 to 17 at% and aluminium concentrations between 0 and 39 at% employing high-angle annular dark field scanning electron microscopy (HAADF STEM), energy dispersive X-ray spectroscopy (EDX) and atom probe tomography (APT). EDX mappings reveal distributions of local concentrations which are in good agreement with random alloy atomic distributions. This was hence investigated with HAADF STEM by comparison with theoretical random alloy expectations using statistical tests. To validate the performance of these tests, HAADF STEM image simulations were carried out for the case of a random-alloy distribution of atoms and for the case of In-rich clusters with nanometer dimensions. The investigated samples, which were grown by metal-organic vapor phase epitaxy (MOVPE), were thereby found to be homogeneous on this nanometer scale. Analysis of reconstructions obtained from APT measurements yielded matching results. Though HAADF STEM only allows for the reduction of possible combinations of indium and aluminium concentrations to the proximity of isolines in the two-dimensional composition space. The observed ranges of composition are in good agreement with the EDX and APT results within the respective precisions.

Abstract: Electron tomography is currently a versatile tool to investigate the connection between the structure and properties of nanomaterials. However, a quantitative interpretation of electron tomography results is still far from straightforward. Especially accurate quantification of pore-space is hampered by artifacts introduced in all steps of the processing chain, i.e., acquisition, reconstruction, segmentation and quantification. Furthermore, most common approaches require subjective manual user input. In this paper, the PORES algorithm POre REconstruction and Segmentation is introduced; it is a tailor-made, integral approach, for the reconstruction, segmentation, and quantification of porous nanomaterials. The PORES processing chain starts by calculating a reconstruction with a nanoporous-specific reconstruction algorithm: the Simultaneous Update of Pore Pixels by iterative REconstruction and Simple Segmentation algorithm (SUPPRESS). It classifies the interior region to the pores during reconstruction, while reconstructing the remaining region by reducing the error with respect to the acquired electron microscopy data. The SUPPRESS reconstruction can be directly plugged into the remaining processing chain of the PORES algorithm, resulting in accurate individual pore quantification and full sample pore statistics. The proposed approach was extensively validated on both simulated and experimental data, indicating its ability to generate accurate statistics of nanoporous materials.

Abstract: Annular dark-field (ADF) scanning transmission electron microscopy (STEM) has become widely used in quantitative studies based on the opportunity to directly compare experimental and simulated images. This comparison merely requires the experimental data to be normalised and expressed in units of fractional beam-current. However, inhomogeneities in the response of electron detectors can complicate this normalisation. The quantification procedure becomes both experiment and instrument specific, requiring new simulations for the particular response of each instrument's detector, and for every camera-length used. This not only impedes the comparison between different instruments and research groups, but can also be computationally very time consuming. Furthermore, not all image simulation methods allow for the inclusion of an inhomogeneous detector response. In this work, we propose an alternative method for normalising experimental data in order to compare these with simulations that consider a homogeneous detector response. To achieve this, we determine the electron flux distribution reaching the detector by means of a camera-length series or a so-called atomic column cross-section averaged convergent beam electron diffraction (XSACBED) pattern. The result is then used to determine the relative weighting of the detector response. Here we show that the results obtained by this new electron flux weighted (EFW) method are comparable to the currently used method, while considerably simplifying the needed simulation libraries. The proposed method also allows one to obtain a metric that describes the quality of the detector response in comparison with the ideal detector response.

Abstract: The main features and the GPU implementation of the MULTEM program are presented and described. This new program performs accurate and fast multislice simulations by including higher order expansion of the multislice solution of the high energy Schrodinger equation, the correct subslicing of the three-dimensional potential and top-bottom surfaces. The program implements different kinds of simulation for CTEM, STEM, ED, PED, CBED, ADF-TEM and ABF-HC with proper treatment of the spatial and temporal incoherences. The multislice approach described here treats the specimen as amorphous material which allows a straightforward implementation of the frozen phonon approximation. The generalized transmission function for each slice is calculated when is needed and then discarded. This allows us to perform large simulations that can include millions of atoms and keep the computer memory requirements to a reasonable level. (C) 2015 Elsevier B.V. All rights reserved.

Abstract: We demonstrate the production of an ordered array of electron vortices making use of an electron optical setup consisting of two electrostatic biprisms. The biprism filaments are oriented nearly orthogonal with respect to each other in a transmission electron microscope. Matching the position of the filaments, we can choose to form different topological features in the electron wave. We outline the working principle of the setup and demonstrate fist experimental results. This setup partially bridges the gap between angular momentum carried by electron spin, which is intrinsic and therefore present in any position of the wave, and angular momentum carried by the vortex character of the wave, which can be extrinsic depending on the axis around which it is measured. (C) 2013 Elsevier B.V. All rights reserved.