Abstract: This Feature addresses the analysis of the reactive species generated by nonthermal atmospheric
pressure plasmas, which are widely employed in industrial and biomedical research, as well as first
clinical applications. We summarize the progress in detection of plasma-generated short-lived
reactive oxygen and nitrogen species in aqueous solutions, discuss the potential and limitations of
various analytical methods in plasma−liquid systems, and provide an outlook on the possible future
research goals in development of short-lived reactive species analysis methods for a general
nonspecialist audience.

Abstract: In this paper we employ first-principles calculations to investigate the effect of substitutional Si doping in the amorphous calcium-phosphate (a-HAP) structure on the work of adhesion, integral charge transfer, charge density difference and theoretical tensile strengths between an a-HAP coating and amorphous titanium dioxide (a-TiO2) substrate systemically. Our calculations demonstrate that substitution of a P atom by a Si atom in a-HAP (a-Si-HAP) with the creation of OH-vacancies as charge compensation results in a significant increase of the bonding strength of the coating to the substrate. The work of adhesion of the optimized Si-doped interfaces reaches a value of up to -2.52 J m(-2), which is significantly higher than for the stoichiometric a-HAP/a-TiO2. Charge density difference analysis indicates that the dominant interactions at the interface have significant covalent character, and in particular two Ti-O and three Ca-O bonds are formed for a-Si-HAP/a-TiO2 and one Ti-O and three Ca-O bonds for a-HAP/a-TiO2. From the stress-strain curve, the Young's modulus of a-Si-HAP/a-TiO2 is calculated to be about 25% higher than that of the a-HAP/a-TiO2, and the yielding stress is about 2 times greater than that of the undoped model. Our calculations therefore demonstrate that the presence of Si in the a-HAP structure strongly alters not only the bioactivity and resorption rates, but also the mechanical properties of the a-HAP/a-TiO2 interface. The results presented here provide an important theoretical insight into the nature of the chemical bonding at the a-HAP/a-TiO2 interface, and are particularly significant for the practical medical applications of HAP-based biomaterials.

Abstract: The thermodynamic aspects of various 2D materials are explored using Density Functional Theory (DFT). Various metal chalcogenides (MX2, M = metal, chalcogen X = S, Se, Te) are investigated with respect to their interaction and stability under different ambient conditions met in the integration process of a transistor device. Their interaction with high- dielectrics is also addressed, in order to assess their possible integration in Complementary Metal Oxide Semiconductor (CMOS) field effect transistors. 2D materials show promise for high performance nanoelectronic devices, but the presence of defects (vacancies, grain boundaries,...) can significantly impact their electronic properties. To assess the impact of defects, their enthalpies of formation and their signature levels in the density of states have been studied. We find, consistently with literature reports, that chalcogen vacancies are the most likely source of defects. It is shown that while pristine 2D materials are in general stable whenever set in contact with different ambient atmospheres, the presence of defective sites affects the electronic properties of the 2D materials to varying degrees. We observe that all the 2D materials studied in the present work show strong reactivity towards radical oxygen plasma treatments while reactivity towards other common gas phase chemical such as O-2 and H2O and groups present at the high- surface varies significantly between species. While energy band-gaps, effective masses and contact resistivities are key criteria in selection of 2D materials for scaled CMOS and tunneling based devices, the phase and ambient stabilities might also play a very important role in the development of reliable nanoelectronic applications.

Abstract: Atomic scale simulations have been shown to be a powerful tool for elucidating the growth mechanisms of carbon nanotubes. The growth picture is however not entirely clear yet due to the gap between current simulations and real experiments. We here simulate for the first time the nucleation and subsequent growth of single-wall carbon nanotubes (SWNTs) from oxygen-containing hydrocarbon feedstocks using the hybrid Molecular Dynamics/Monte Carlo technique. The underlying nucleation mechanisms of Ni-catalysed SWNT growth are discussed in detail. Specifically, we find that as a function of the feedstock, different carbon fractions may emerge as the main growth species, due to a competition between the feedstock decomposition, its rehydroxylation and its contribution to etching of the growing SWNT. This study provides a further understanding of the feedstock effects in SWNT growth in comparison with available experimental evidence as well as with<italic>ab initio</italic>and other simulation data, thereby reducing the simulation–experiment gap.

Abstract: We studied the influence of dense, spherical packing materials, with different chemical compositions, on the dry reforming of methane (DRM) in a dielectric barrier discharge (DBD) reactor. Although not catalytically activated, a vast effect on the conversion and product selectivity could already be observed, an influence which is often neglected when catalytically activated plasma packing materials are being studied. The alpha-Al2O3 packing material of 2.0-2.24 mm size yields the highest total conversion (28%), as well as CO2 (23%) and CH4 (33%) conversion and a high product fraction towards CO (similar to 70%) and ethane (similar to 14%), together with an enhanced CO/H-2 ratio of 9 in a 4.5 mm gap DBD at 60 W and 23 kHz. gamma-Al2O3 is only slightly less active in total conversion (22%) but is even more selective in products formed than alpha-Al2O3 BaTiO3 produces substantially more oxygenated products than the other packing materials but is the least selective in product fractions and has a clear negative impact on CO2 conversion upon addition of CH4. Interestingly, when comparing to pure CO2 splitting and when evaluating differences in products formed, significantly different trends are obtained for the packing materials, indicating a complex impact of the presence of CH4 and the specific nature of the packing materials on the DRM process.

Abstract: Extracellular cystine (CYC) uptake by xC antiporter is important for the cell viability. Especially in cancer cells, the upregulation of xC activity is observed, which protects these cells from intracellular oxidative stress. Hence, inhibition of the CYC uptake may eventually lead to cancer cell death. Up to now, the molecular level mechanism of the CYC uptake by xC antiporter has not been studied in detail. In this study, we applied several different simulation techniques to investigate the transport of CYC through xCT, the light subunit of the xC antiporter, which is responsible for the CYC and glutamate translocation. Specifically, we studied the permeation of CYC across three model systems, i.e., outward facing (OF), occluded (OCC) and inward facing (IF) configurations of xCT. We also investigated the effect of mutation of Cys327 to Ala within xCT, which was also studied experimentally in literature. This allowed us to qualitatively compare our computation results with experimental observations, and thus, to validate our simulations. In summary, our simulations provide a molecular level mechanism of the transport of CYC across the xC antiporter, more specifically, which amino acid residues in the xC antiporter play a key role in the uptake, transport and release of CYC.

Abstract: Plasma catalysis is gaining increasing interest for various gas conversion applications, such as CO2 conversion into value-added chemicals and fuels, N2 fixation for the synthesis of NH3 or NOx, and CH4 conversion into higher hydrocarbons or oxygenates [...]

Abstract: The study presents a 2D fluid plasma model of a gliding arc discharge for dissociation of CO2 which allows its subsequent conversion into value-added chemicals. The model is based on the balance equations of charged and neutral particles, the electron energy balance equation, the gas thermal balance equation and the current continuity equation. By choosing the modeling domain to be the plane perpendicular to the arc current, the numerical calculations are significantly simplified. Thus, the model allows us to explore the influence of the gas instabilities (turbulences) on the energy efficiency of CO2 conversion. This paper presents results for plasma parameters at different values of the effective turbulent thermal conductivity leading to enhanced energy transport.

Abstract: Optimization of catalytic materials for a given application is greatly constrained by linear scaling relations. Recently, however, it has been demonstrated that it is possible to reversibly modulate the chemisorption of molecules on nanomaterials by charging (i.e., injection or removal of electrons) and hence reversibly and selectively modify catalytic activity beyond structure−activity correlations. The fundamental physical relation between the properties of the material, the charging process, and the chemisorption energy, however, remains unclear, and a systematic exploration and optimization of charge-switchable sorbent materials is not yet possible. Using hybrid DFT calculations of CO2 chemisorption on hexagonal boron nitride nanosheets with several types of defects and dopants, we here reveal the existence of fundamental correlations between the electron affinity of a material and charge-induced chemisorption, show how defect engineering can be used to modulate the strength and efficiency of the adsorption process, and demonstrate that excess electrons stabilize many topological defects. We then show how these insights could be exploited in the development of new electrocatalytic materials and the synthesis of doped nanomaterials. Moreover, we demonstrate that calculated chemical properties of charged materials are highly sensitive to the employed computational methodology because of the self-interaction error, which underlines the theoretical challenge posed by such systems.

Abstract: Plasma is gaining increasing interest for cancer
treatment, but the underlying mechanisms are not yet fully
understood. Using computer simulations at the molecular
level, we try to gain better insight in how plasma-generated
reactive oxygen and nitrogen species (RONS) can
penetrate through the cell membrane. Specifically, we
compare the permeability of various (hydrophilic and
hydrophobic) RONS across both oxidized and nonoxidized cell membranes. We also study pore formation,
and how it is hampered by higher concentrations of
cholesterol in the cell membrane, and we illustrate the
much higher permeability of H2O2 through aquaporin
channels. Both mechanisms may explain the selective
cytotoxic effect of plasma towards cancer cells. Finally, we
also discuss the synergistic effect of plasma-induced
oxidation and electric fields towards pore formation.
Keywords plasma medicine, cancer treatment, computer
modelling, cell membrane, reactive oxygen and nitrogen
species

Abstract: Molecular dynamics simulations are carried out for describing growth of Pd and PdO nanoclusters using the ReaxFF force field. The resulting nanocluster structures are successfully compared to those of nanoclusters experimentally grown in a gas aggregation source. The PdO structure is quasi-crystalline as revealed by high resolution transmission microscope analysis for experimental PdO nanoclusters. The role of the nanocluster temperature in the molecular dynamics simulated growth is highlighted.

Abstract: Self-organized striated structure has been observed experimentally and numerically in CF4 plasmas in radio-frequency capacitively coupled plasmas recently (Liu et al 2016 Phys. Rev. Lett. 116 255002). In this work, the striated structure is investigated in a capacitively coupled oxygen discharge with the introduction of the effect from the secondary electron emission, based on a particle-in-cell/Monte Carlo collision model. As we know, the transport of positive and negative ions plays a key role in the formation of striations in electronegative gases, for which, the electronegativity needs to be large enough. As the secondary electron emission increases, electrons in the sheaths gradually contribute more ionization to the discharge. Meanwhile, the increase of the electron density, especially in the plasma bulk, leads to an increased electrical conductivity and a reduced bulk electric field, which would shield the ions' mobility. These changes result in enlarged striation gaps. And then, with more emitted electrons, obvious disruption of the striations is observed accompanied with a transition of electron heating mode. Due to the weakened field, the impact ionization in the plasma bulk is attenuated, compared with the enhanced ionization caused by secondary electrons. This would lead to the electron heating mode transition from striated (STR) mode to gamma-mode. Besides, our investigation further reveals that gamma-mode is more likely to dominate the discharge under high gas pressures or driving voltages.

Abstract: Si:C and Si:C:P alloys are potential candidates for source-drain stressor applications in n-type Fin Field Effect Transistors (FinFETs). Increasing the C content to achieve high strain results in the arrangement of C atoms as third nearest neighbors (3nn) in the Si: C lattice. During thermal annealing, the presence of C atoms as 3nn may promote clustering at the interstitial sites, causing loss of stress. The concentration of C atoms as 3nn is reduced by the incorporation of a small amount of Ge atoms during the growth, whereas in-situ P doping does not influence this 3nn distribution [J Solid State Sci. Technol vol 6, p 755, 2017]. Small amounts of Ge are provided during low temperature selective epitaxial growth scheme, which are based on cyclic deposition and etching (CDE). In this work, we aim to provide physical insights into the aforementioned phenomena, to understand the behavior of 3nn C atoms and the types of defects that are formed in the annealed Si: C films. Using ab-initio simulations, the Ge-C interaction in the Si matrix is investigated and this insight is used to explain how the Ge incorporation leads to a reduced 3nn distribution of the C atoms. The interaction between C and P in the Si: C: P films is also investigated to explain why the P incorporation has not led to a reduction in the 3nn distribution. We then report on the Raman characterization of Si: C layers subjected to post epi annealing. As the penetration depth of the laser is dependent on the wavelength, Raman measurements at two different wavelengths enable us to probe the depth distribution of 3nn C atoms after applying different annealing conditions. We observed a homogeneous loss in 3nn C throughout the layer. Whereas in the kinematic modeling of high resolution X-ray diffraction spectra, a gradient in the substitutional C loss was observed close to the epitaxial layer/substrate interface. This gradient can be due to the out diffusion of C atoms into the Si substrate or to the formation of interstitial C clusters, which cannot be distinguished in HR-XRD. Deep Level Transient Spectroscopy indicated that the prominent out-diffusing species was interstitial CO complex while the interstitial C defects were also prevalent in the epi layer. (c) 2019 The Electrochemical Society.

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.