Abstract: Plasma catalysis is gaining increasing interest for various environmental applications, but the crucial question is whether plasma can be created inside catalyst pores and under which conditions. In practice, various catalytic support materials are used, with various dielectric constants. We investigate here the influence of the dielectric constant on the plasma properties inside catalyst pores and in the sheath in front of the pores, for various pore sizes. The calculations are performed by a two-dimensional fluid model for an atmospheric pressure dielectric barrier discharge in helium. The electron impact ionization rate, electron temperature, electron and ion density, as well as the potential distribution and surface charge density, are analyzed for a better understanding of the discharge behavior inside catalyst pores. The results indicate that, in a 100 μm pore, the electron impact ionization in the pore, which is characteristic for the plasma generation inside the pore, is greatly enhanced for dielectric constants below 300. Smaller pore sizes only yield enhanced ionization for smaller dielectric constants, i.e., up to εr = 200, 150, and 50 for pore sizes of 50, 30, and 10 μm. Thus, the most common catalyst supports, i.e., Al2O3 and SiO2, which have dielectric constants around εr = 8−11 and 4.2, respectively, should allow more easily that microdischarges can be formed inside catalyst pores, even for smaller pore sizes. On the other hand, ferroelectric materials with dielectric constants above 300 never seem to yield plasma enhancement inside catalyst pores, not even for 100 μm pore sizes. Furthermore, it is clear that the dielectric constant of the material has a large effect on the extent of plasma enhancement inside the catalyst pores, especially in the range between εr = 4 and εr = 200. The obtained results are explained in detail based on the surface charge density at the pore walls,
and the potential distribution and electron temperature inside and above the pores. The results obtained with this model are
important for plasma catalysis, as the production plasma species in catalyst pores might affect the catalyst properties, and thus
improve the applications of plasma catalysis.

Abstract: Molecular dynamics (MD) simulations were performed to provide atomic scale insight in the initial interaction between hydroxyl radicals (OH) and peptide systems in solution. These OH radicals are representative reactive oxygen species produced by cold atmospheric plasmas. The use of plasma for biomedical applications is gaining increasing interest, but the fundamental mechanisms behind the plasma modifications still remain largely elusive. This study helps to gain more insight in the underlying mechanisms of plasma medicine but is also more generally applicable to peptide oxidation, of interest for other applications. Combining both reactive and nonreactive MD simulations, we are able to elucidate the reactivity of the amino acids inside the peptide systems and their effect on their structure up to 1 μs. Additionally, experiments were performed, treating the simulated peptides with a plasma jet. The computational results presented here correlate well with the obtained experimental data and highlight the importance of the chemical environment for the reactivity of the individual amino acids, so that specific amino acids are attacked in higher numbers than expected. Furthermore, the long time scale simulations suggest that a single oxidation has an effect on the 3D conformation due to an increase in hydrophilicity and intra- and intermolecular interactions.

Abstract: A number of recent computational material design studies based on density functional theory (DFT) calculations have put forward a new class of materials with electrically switchable chemical characteristics that can be exploited in the development of tunable gas storage and electrocatalytic applications. We find systematic flaws in almost every computational study of gas adsorption on polarized or charged surfaces, stemming from an improper and unreproducible treatment of periodicity, leading to very large errors of up to 3 eV in some cases. Two simple corrective procedures that lead to consistent results are proposed, constituting a crucial course correction to the research in the field.

Abstract: Plasma-surface interactions are in general highly complex due to the interplay of many concurrent processes. Molecular dynamics simulations provide insight in some of these processes, subject to the accessible time and length scales, and the availability of suitable force fields. In this introductory tutorial-style review, we aim to describe the current capabilities and limitations of molecular dynamics simulations in this field, restricting ourselves to low-temperature nonthermal plasmas. Attention is paid to the simulation of the various fundamental processes occurring, including sputtering, etching, implantation, and deposition, as well as to what extent the basic plasma components can be accounted for, including ground state and excited species, electric fields, ions, photons, and electrons. A number of examples is provided, giving an bird’s eye overview of the current state of the field.

Abstract: We discuss the synthesis of carbon nanotubes (CNTs) and graphene by catalytic chemical vapour deposition (CCVD) and plasma-enhanced CVD (PECVD), summarising the state-of-the-art understanding of mechanisms controlling their growth rate, chiral angle, number of layers (walls), diameter, length and quality (defects), before presenting a new model for 2D nucleation of a graphene sheet from amorphous carbon on a nickel surface. Although many groups have modelled this process using a variety of techniques, we ask whether there are any complementary ideas emerging from the different proposed growth mechanisms, and whether different modelling techniques can give the same answers for a given mechanism. Subsequently, by comparing the results of tight-binding, semi-empirical molecular orbital theory and reactive bond order force field calculations, we demonstrate that graphene on crystalline Ni(111) is thermodynamically stable with respect to the corresponding amorphous metal and carbon structures. Finally, we show in principle how a complementary heterogeneous nucleation step may play a key role in the transformation from amorphous carbon to graphene on the metal surface. We conclude that achieving the conditions under which this complementary crystallisation process can occur may be a promising method to gain better control over the growth processes of both graphene from flat metal surfaces and CNTs from catalyst nanoparticles.

Abstract: Using reactive molecular dynamics simulations, we have investigated the effect of single-impact, low-energy (thermal-100 eV) bombardment of a Si(100){2 × 1} surface by atomic and molecular oxygen. Penetration probability distributions, as well as defect formation distributions, are presented as a function of the impact energy for both species. It is found that at low impact energy, defects are created chemically due to the chemisorption process in the top layers of the surface, while at high impact energy, additional defects are created by a knock-on displacement of Si. These results are of particular importance for understanding device performances of silica-based microelectronic and photovoltaic devices.

Abstract: The deposition of ultra-thin tungsten films and their related 2D chalcogen compounds on large area dielectric substrates by gas phase reactions is challenging. The lack of nucleation sites complicates the adsorption of W-related precursors and subsequent sulfurization usually requires high temperatures. We propose here a technique in which a thin solid amorphous silicon film is used as reductant for the gas phase precursor WF6 leading to the conversion to metallic W. The selectivity of the W conversion towards the underlying dielectric surfaces is demonstrated. The role of the Si surface preparation, the conversion temperature, and Si thickness on the formation process is investigated. Further, the in situ conversion of the metallic tungsten into thin stoichiometric WS2 is achieved by a cyclic approach based on WF6 and H2S pulses at the moderate temperature of 450 1C, which is much lower than usual oxide sulfurization processes.

Abstract: Natural deep eutectic solvents (NADES) are mixtures of naturally derived compounds with a significantly decreased melting point due to the specific interactions among the constituents. NADES have benign properties (low volatility, flammability, toxicity, cost) and tailorable physicochemical properties (by altering the type and molar ratio of constituents), hence they are often considered as a green alternative to common organic solvents. Modeling the relation between their composition and properties is crucial though, both for understanding and predicting their behavior. Several efforts were done to this end, yet this review aims at structuring the present knowledge as an outline for future research. First, we reviewed the key properties of NADES and relate them to their structure based on the available experimental data. Second, we reviewed available modeling methods applicable to NADES. At the molecular level, density functional theory and molecular dynamics allow interpreting density differences and vibrational spectra, and computation of interaction energies. Additionally, properties at the level of the bulk media can be explained and predicted by semi-empirical methods based on ab initio methods (COSMO-RS) and equation of state models (PC-SAFT). Finally, methods based on large datasets are discussed; models based on group contribution methods and machine learning. A combination of bulk media and dataset modeling allows qualitative prediction and interpretation of phase equilibria properties on the one hand, and quantitative prediction of melting point, density, viscosity, surface tension and refractive indices on the other hand. In our view, multiscale modeling, combining the molecular and macroscale methods, will strongly enhance the predictability of NADES properties and their interaction with solutes, yielding truly tailorable solvents to accommodate (bio)chemical reactions.

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: Amorphous platinum clusters supported on porous carbon have been envisaged for high-performance fuel cell electrodes. For this application, it is crucial to control the morphology of the Pt layer and the Ptsubstrate interaction to maximize activity and stability. We thus investigate the morphology evolution during Pt cluster growth on a porous carbon substrate employing atomic scale molecular dynamics simulations. The simulations are based on the Pt-C interaction potential using parameters derived from density functional theory and are found to yield a Pt cluster morphology similar to that observed in low loaded fuel cell electrodes prepared by plasma sputtering. Moreover, the simulations show amorphous Pt cluster growth in agreement with X-ray diffraction and transmission electron microscopy experiments on high performance low Pt content (10 μgPt cm−2) loaded fuel cell electrodes and provide a fundamental insight in the cluster growth mechanism.

Abstract: The resistance of a TiO2 anatase (001) surface to coke formation was studied in the context of dry reforming of methane using density functional theory (DFT) calculations. As carbon atoms act as precursors for coke formation, the resistance to coke formation can be measured by the carbon coverage of the surface. This is related to the stability of different CHx (x = 0−3) species and their rate of hydrogenation and dehydrogenation on the TiO2 surface. Therefore, we studied the reaction mechanisms and their corresponding rates as a function of the temperature for the dehydrogenation of the species on the surface. We found that the stabilities of C and CH are significantly lower than those of CH3 and CH2. The hydrogenation rates of the different species are significantly higher than the dehydrogenation rates in a temperature range of 300−1000 K. Furthermore, we found that dehydrogenation of CH3, CH2, and CH will only occur at appreciable rates starting from 600, 900, and 900 K, respectively. On the basis of these results, it is clear that the anatase (001) surface has a high coke resistance, and it is thus not likely that the surface will become poisoned by coke during dry reforming of methane. As the rate limiting step in dry reforming is the dissociative adsorption of CH4, we studied an alternative approach to thermal catalysis. We found that the temperature threshold for dry reforming is at least 700 K. This threshold temperature may be lowered by the use of plasma-catalysis, where the appreciable rates of adsorption of plasma-generated CHx radicals result in bypassing the rate limiting step of the reaction.

Abstract: van der Waals (vdW) forces play an important role in the adsorption of molecules on the surface of solids. However, the choice of the most suitable vdW functional for different systems is an essential problem which must be addressed for different systems. The lack of a systematic study on the performance of the vdW functionals in the bulk and adsorption properties of metal-oxides motivated us to examine different vdW approaches and compute the bulk and molecular adsorption properties of alpha-Cr2O3, alpha-Fe2O3, and alpha-Al2O3. For the bulk properties, we compared our results for the heat of formation, cohesive energy, lattice parameters and bond distances between the different vdW functionals and available experimental data. Next we studied the adsorption of benzene and CH3 molecules on top of different oxide surfaces. We employed different approximations to exchange and correlation within DFT, namely, the Perdew-Burke-Ernzerhof (PBE) GGA, (PBE)+U, and vdW density functionals [ DFT(vdW-DF/DF2/optPBE/optB86b/optB88)+U] as well as DFT-D2/D3(+U) methods of Grimme for the bulk calculations and optB86b-vdW(+U) and DFT-D2(+U) for the adsorption energy calculations. Our results highlight the importance of vdW interactions not only in the adsorption of molecules, but importantly also for the bulk properties. Although the vdW contribution in the adsorption of CH3 (as a chemisorption interaction) is less important compared to the adsorption of benzene (as a physisorption interaction), this contribution is not negligible. Also adsorption of benzene on ferryl/chromyl terminated surfaces shows an important chemisorption contribution in which the vdW interactions become less significant.

Abstract: Recent experiments have revealed that the macroscopic Kelvin equation remains surprisingly accurate even for nanoscale capillaries. This phenomenon was so far explained by the oscillatory behavior of the solid−liquid interfacial free energy. We here demonstrate thermodynamic and capillarity inconsistencies with this explanation. After revising the Kelvin equation, we ascribe its validity at nanoscale confinement to the effect of disjoining pressure.
To substantiate our hypothesis, we employed molecular dynamics simulations to evaluate interfacial heat transfer and wetting properties. Our assessments unveil a breakdown in a previously established proportionality between the work of adhesion and the Kapitza conductance at capillary heights below 1.3 nm, where the dominance of the work of adhesion shifts primarily from energy to entropy. Alternatively, the peak density of the initial water layer can effectively probe the work of adhesion. Unlike under bulk conditions, high confinement renders the work of adhesion entropically unfavorable.

Abstract: Background: Strong electric fields are knownto affect cell membrane permeability,which can be applied for therapeutic purposes, e.g., in cancer therapy. A synergistic enhancement of this effect may be accomplished by the presence of reactive oxygen species (ROS), as generated in cold atmospheric plasmas. Little is known about the synergy between lipid oxidation by ROS and the electric field, nor on howthis affects the cell membrane permeability.
Method: We here conduct molecular dynamics simulations to elucidate the dynamics of the permeation process under the influence of combined lipid oxidation and electroporation. A phospholipid bilayer (PLB), consisting of di-oleoyl-phosphatidylcholine molecules covered with water layers, is used as a model system for the plasma membrane.
Results and conclusions:Weshow howoxidation of the lipids in the PLB leads to an increase of the permeability of the bilayer to ROS, although the permeation free energy barriers still remain relatively high. More importantly, oxidation of the lipids results in a drop of the electric field threshold needed for pore formation (i.e., electroporation) in the PLB. The created pores in the membrane facilitate the penetration of reactive plasma species deep into the cell interior, eventually causing oxidative damage.
General significance: This study is of particular interest for plasma medicine, as plasma generates both ROS and electric fields, but it is also of more general interest for applications where strong electric fields and ROS both come into play.