Abstract: In this study, we investigated the diffusion of H-atoms to the subsurface and their further diffusion into the bulk of a Ni(111) crystal by means of density functional theory calculations in the context of thermal and plasma-assisted catalysis. The H-atoms at the surface can originate from the dissociative adsorption of H2 or CH4 molecules, determining the surface H-coverage. When a threshold H-coverage is passed, corresponding to 1.00 ML for the crystalline Ni(111) surface, the surface-bound H-atoms start to diffuse to the subsurface. A similar threshold coverage is observed for the interstitial H-coverage. Once the interstitial sites are filled up with a coverage above 1.00 ML of H, dissolution of interstitial H-atoms to the layer below the interstitial sites will be initiated. Hence, by applying a high pressure or inducing a reactive plasma and high temperature, increasing the H-flux to the surface, a large amount of hydrogen can diffuse in a crystalline metal like Ni and can be absorbed. The formation of metal hydride may modify the entire reaction kinetics of the system. Equivalently, the H-atoms in the bulk can easily go back to the surface and release a large amount of heat. In a plasma process, H-atoms are formed in the plasma, and therefore the energy barrier for dissociative adsorption is dismissed, thus allowing achievement of the threshold coverage without applying a high pressure as in a thermal process. As a result, depending on the crystal plane and type of metal, a large number of H-atoms can be dissolved (absorbed) in the metal catalyst, explaining the high efficiency of plasma-assisted catalytic reactions. Here, the mechanism of H-dissolution is established as a chemical identifier for the investigation of the reaction kinetics of a chemical process.

Abstract: SIRT6 and COX-2 are oncogenes target that promote the expression of proinflammatory and pro-survival proteins through a signaling pathway, which leads to increased survival and proliferation of tumor cells. However, COX-2 also suppresses skin tumorigenesis and their relationship with SIRT6, making it an interesting target for the discovery of drugs with anti-inflammatory and anti-cancer properties. Herein, we studied the interaction of thieno[3,2-c] pyran analogs and RONS species with SIRT6 and COX-2 through the use of molecular docking and molecular dynamic simulations. Molecular docking studies revealed the importance of hydrophobic and hydrophilic amino acid residues for the stability. The molecular dynamics study examined conformational changes in the enzymes caused by the binding of the substrates and how those changes affected the stability of the protein-drug complex. The average RMSD values of the backbone atoms in compounds 6 and 10 were calculated from 1000 ps to 10000 ps and were found to be 0.13 nm for both compounds. Similarly, the radius of gyration values for compounds 6 and 10 were found to be 1.87 +/- 0.03 nm and 1.86 +/- 0.02 nm, respectively. The work presented here, will be of great help in lead identification and optimization for early drug discovery.

Abstract: When confined between graphene layers, water behaves differently from the bulk and exhibits unusual properties such as fast water flow and ordering into a crystal. The hydrogen-bonded network is affected by the limited space and by the characteristics of the confining walls. The presence of an extraordinary number of hydronium and hydroxide ions in narrow channels has the following effects: (i) they affect water permeation through the channel, (ii) they may interact with functional groups on the graphene oxide surface and on the edges, and (iii) they change the thermochemistry of water, which are fundamentally important to understand, especially when confined water is subjected to an external electric field. Here we study the physical properties of water when confined between two graphene sheets and containing hydronium and hydroxide. We found that: (i) there is a disruption in the solvation structure of the ions, which is also affected by the layered structure of confined water, (ii) hydronium and hydroxide occupy specific regions inside the nanochannel, with a prevalence of hydronium (hydroxide) ions at the edges (interior), and (iii) ions recombine more slowly in confined systems than in bulk water, with the recombination process depending on the channel height and commensurability between the size of the molecules and the nanochannel height – a decay of 20% (40%) in the number of ions in 8 ps is observed for a channel height of h = 7 angstrom (bulk water). Our work reveals distinctive properties of water confined in a nanocapillary in the presence of additional hydronium and hydroxide ions.

Abstract: A hybrid model is used to investigate the fragmentation of C4F8 inductive discharges. Indeed, the resulting reactive species are crucial for the optimization of the Si-based etching process, since they determine the mechanisms of fluorination, polymerization, and sputtering. In this paper, we present the dissociation degree, the density ratio of F vs. CxFy (i.e., fluorocarbon (fc) neutrals), the neutral vs. positive ion density ratio, details on the neutral and ion components, and fractions of various fc neutrals (or ions) in the total fc neutral (or ion) density in a C4F8 inductively coupled plasma source, as well as the effect of pressure and power on these results. To analyze the fragmentation behavior, the electron density and temperature and electron energy probability function (EEPF) are investigated. Moreover, the main electron-impact generation sources for all considered neutrals and ions are determined from the complicated C4F8 reaction set used in the model. The C4F8 plasma fragmentation is explained, taking into account many factors, such as the EEPF characteristics, the dominance of primary and secondary processes, and the thresholds of dissociation and ionization. The simulation results are compared with experiments from literature, and reasonable agreement is obtained. Some discrepancies are observed, which can probably be attributed to the simplified polymer surface kinetics assumed in the model.

Abstract: In this paper, an O2 inductively coupled plasma used for plasma enhanced atomic layer deposition of Al2O3 thin films is investigated by means of modeling. This work intends to provide more information about basic plasma properties such as species densities and species fluxes to the substrate as a function of power and pressure, which might be hard to measure experimentally. For this purpose, a hybrid model developed by Kushner et al is applied to calculate the plasma characteristics in the reactor volume for different chamber pressures ranging from 1 to 10 mTorr and different coil powers ranging from 50 to 500 W. Density profiles of the various oxygen containing plasma species are reported as well as fluxes to the substrate under various operating conditions. Furthermore, different orientations of the substrate, which can be placed vertically or horizontally in the reactor, are taken into account. In addition, special attention is paid to the recombination process of atomic oxygen on the different reactor walls under the stated operating conditions. From this work it can be concluded that the plasma properties change significantly in different locations of the reactor. The plasma density near the cylindrical coil is high, while it is almost negligible in the neighborhood of the substrate. Ion and excited species fluxes to the substrate are found to be very low and negligible. Finally, the orientation of the substrate has a minor effect on the flux of O2, while it has a significant effect on the flux of O. In the horizontal configuration, the flux of atomic oxygen can be up to one order of magnitude lower than in the vertical configuration.

Abstract: The chemical complexity of non-equilibrium plasmas poses a challenge for plasma modeling because of the computational load. This paper presents a dimension reduction method for such chemically complex plasmas based on principal component analysis (PCA). PCA is used to identify a low-dimensional manifold in chemical state space that is described by a small number of parameters: the principal components. Reduction is obtained since continuity equations only need to be solved for these principal components and not for all the species. Application of the presented method to a CO2 plasma model including state-to-state vibrational kinetics of CO2 and CO demonstrates the potential of the PCA method for dimension reduction. A manifold described by only two principal components is able to predict the CO2 to CO conversion at varying ionization degrees very accurately.

Abstract: In this work, a hybrid model is used to investigate the effect of different gas ratios on the Si etching and polymer film deposition characteristics in an Ar/CF4 inductively coupled plasma. The influence of the surface processes on the bulk plasma properties is studied, and also the spatial characteristics of important gas phase and etched species. The densities of F and CF2 decrease when the surface module is included in the simulations, due to the species consumption caused by etching and polymer deposition. The influence of the surface processes on the bulk plasma depends on the Ar/CF4 gas ratio. The deposited polymer becomes thicker at high CF4 content because of more abundant CFx radicals. As a result of the competition between the polymer thickness and the F flux, the etch rate first increases and then decreases upon increasing the CF4 content. The electron properties, more specifically the electron density profile, affect the Si etch characteristics substantially by determining the radical density and flux profiles. In fact, the radial profile of the etch rate is more uniform at low CF4 content since the electron density has a smooth distribution. At high CF4 content, the etch rate is less uniform with a minimum halfway along the wafer radius, because the electron density distribution is more localized. Therefore, our calculations predict that it is better to work at relatively high Ar/CF4 gas ratios, in order to obtain high etch rate and good profile uniformity for etch applications. This, in fact, corresponds to the typical experimental etch conditions in Ar/CF4 gas mixtures as found in the literature, where Ar is typically present at a much higher concentration than CF4.

Abstract: A detailed account is given of neutron and γ-ray attenuation effects in 14-MeV neutron activation analysis of oxygen. Appropriate neutron cross-section values have been determined in two different ways and compared with literature values. It appears that the attenuation process is best described in terms of nonelastic scattering cross-sections. It is also shown that the narrow beam total γ-ray attenuation coefficients at 6 MeV, given in the literature are suitable for correction purposes if 16N γ-rays are counted with a window of 4.56.5 MeV. Attention was paid to the contribution of β-rays when the 16N activity is counted in this energy interval with a NaI(Tl) detector.

Abstract: Cold atmospheric pressure plasmas in and in contact with liquids represent a growing field of research for various applications. Understanding the interactions between the plasma generated species and the liquid is crucial. In this work we perform molecular dynamics (MD) simulations based on a quantum mechanical method, i.e. density-functional based tight-binding (DFTB), to examine the interactions of OH radicals and O atoms in bulk water. Our calculations reveal that the transport of OH radicals through water is not only governed by diffusion, but also by an equilibrium reaction of H-abstraction with water molecules. Furthermore, when two OH radicals encounter each other, they either form a stable cluster, or react, resulting in the formation of a new water molecule and an O atom. In addition,
the O atoms form either oxywater (when in singlet configuration) or they remain stable in solution (when in triplet configuration), stressing the important role that O atoms can play in aqueous solution, and in contact with biomolecules. Our observations are in line with both experimental and ab initio results from the literature.

Abstract: In this study we quantitatively investigate for the first time the plasma characteristics of an argon gliding arc with a 3D model. The model is validated by comparison with available experimental data from literature and a reasonable agreement is obtained for the calculated gas temperature and electron density. A complete arc cycle is modeled from initial ignition to arc decay. We investigate how the plasma characteristics, i.e., the electron temperature, gas temperature,
reduced electric field, and the densities of electrons, Ar+ and Ar2+ ions and Ar(4s) excited states, vary over one complete arc cycle, including their behavior in the discharge and post-discharge. These plasma characteristics exhibit a different evolution over one arc cycle, indicating that either the active discharge stage or the post-discharge stage can be beneficial for certain applications.