Abstract: In this paper, an overview is given of modeling investigations carried out in our research group for a better understanding of plasmas used for medical, environmental and nano applications. The focus is both on modeling the plasma chemistry and the plasma-surface interactions. The plasma chemistry provides the densities and fluxes of the important plasma species. This information can be used as input when modeling the plasma-surface interactions. The combination of plasma simulations and plasma – surface interaction simulations provides a more comprehensive understanding of the underlying processes for these applications.

Abstract: In this paper, an overview is given of modeling activities going on in our research group, for describing the plasma chemistry and plasmasurface interactions in reactive plasmas. The plasma chemistry is calculated by a fluid approach or by hybrid Monte Carlo (MC)fluid modeling. An example of both is illustrated in the first part of the paper. The example of fluid modeling is given for a dielectric barrier discharge (DBD) in CH4/O2, to describe the partial oxidation of CH4 into value-added chemicals. The example of hybrid MCfluid modeling concerns an inductively coupled plasma (ICP) etch reactor in Ar/Cl2/O2, including also the description of the etch process. The second part of the paper deals with the treatment of plasmasurface interactions on the atomic level, with molecular dynamics (MD) simulations or a combination of MD and MC simulations.

Abstract: Because of the unique properties of plasma technology, its use in gas conversion applications is gaining significant interest around the globe. Plasma-based CO2 and CH4 conversion has become a major research area. Many investigations have already been performed regarding the single-component gases, that is, CO2 splitting and CH4 reforming, as well as for two-component mixtures, that is, dry reforming of methane
(CO2/CH4), partial oxidation of methane (CH4/O2), artificial photosynthesis (CO2/H2O), CO2 hydrogenation (CO2/H2), and even first steps toward the influence of N2 impurities have been taken, that is, CO2/N2 and CH4/N2. In this Feature Article we briefly discuss the advances made in literature for these different steps from a plasma chemistry modeling point of view. Subsequently, we present a comprehensive plasma chemistry set, combining the knowledge gathered in this field so far and supported with extensive experimental data. This set can be used for chemical kinetics plasma modeling for all possible combinations of CO2, CH4, N2, O2, and H2O to investigate the bigger picture of the underlying plasmachemical pathways for these mixtures in a dielectric barrier discharge plasma. This is extremely valuable
for the optimization of existing plasma-based CO2 conversion and CH4 reforming processes as well as for investigating the influence of N2, O2, and H2O on these processes and even to support plasma-based multireforming processes.

Abstract: Recently, a process has been proposed for generating negatively-curved carbon schwarzites via zeolite-templating (Braun et al., 2018). However, the proposed process leads to atomistic models which are not very symmetric and often rather defective. In the present work, an improved generation approach is developed, by imposing symmetry constraints, which systematically leads to defect-free, hence more stable, schwarzites. The stability of the newly predicted symmetric schwarzites is also compared to that of other carbon nanostructures (in particular carbon nanotubes – CNTs), which could also be accommodated within the same templates. Our results suggest that only a few of these (such as FAU, SBT and SBS) can fit schwarzites more stable than CNTs. Our predictions could help experimentalists in the crucial choice of the template for the challenging synthesis of schwarzites. Furthermore, being highly symmetric and stable phases, the models could also be synthesized by means of other experimental procedures.

Abstract: The rate of charge deposition in quartz grains irradiated in natural conditions is computed by radiation transport modeling. Quartz luminescence models are modified with the addition of the resulting charge deposition term, and the influence of this process on the optically stimulated luminescence (OSL) signal is analyzed. The results indicate that the charge deposition occurring in the quartz grain during the time of residence within rock could lead to the depletion of trapped holes in the recombination centres. For the two different quartz models investigated here, complete depletion is expected to occur for rock ages between 500 Ma and 1100 Ma. It is predicted that for sedimentary quartz derived from such rocks, the OSL signal is dominated by the slow component. It was also found that the shape and saturation level of the natural sensitivity-corrected dose response curve (DRC) of quartz is affected by the charge deposition; specifically, a linear reduction of the saturation level with the age of the rock is observed.

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: Wastewater reuse provides valuable solutions to solve the societal challenges of decreasing availability and limiting access to secure water resources. The present study quantifies the environmental performance of nectarine orchards irrigation using treated municipal wastewater (TMW) and surface water using a unique dataset based on field experimental data. Climate change, toxicity (for human and freshwater), eutrophication (marine and freshwater) and acidification impacts were analysed using the impact assessment method suggested by the International Reference Life Cycle Data System (ILCD). The water footprint associated to the life cycles of each system has been estimated using the Available WAter REmaining (AWARE) method. Monte Carlo simulation was used to assess data uncertainty. The irrigation of nectarine orchards using TMW performs better than the irrigation using surface water for eutrophication impact categories. Compared with surface water resources, the potential impacts of TMW reuse in agriculture on climate change and toxicity are affected by the wastewater treatment phase (WWT). Only eutrophication and acidification burdens are generated by in-field substitution of surface water with TMW. Considering human and ecosystem water demand, the irrigation with TMW increases water consumption of 19.12 m3 per kg of nectarine produced. Whereas, it shows a positive contribution to water stress (−0.19 m3) if only human water demand is considered. This study provides important results that allow for a better understanding of the potential environmental consequences of TMW reuse in agriculture. It suggests that embracing the type of WWTs, the replacement of fertilizers, the effects on water scarcity and ecosystem quality might be useful to redefine water reuse regulations and increase public acceptance for the reuse of TMW in agriculture. Moreover, this study reveals the need for developing consensus and standardized guidance for life cycle analysis of water reuse applications.

Abstract: The modified atomic scattering amplitudes (MASAs) of mixed Ga_1-xIn_xAs, GaAs_1-xN_x, and InAs_1-xN_x are calculated using the density functional theory approach and the results are compared with those of the binary counterparts. The MASAs of N, Ga, As, and In for various scattering vectors in various chemical environments and in the zinc-blende structure are compared with the frequently used Doyle and Turner values. Deviation from the Doyle and Turner results is found for small scattering vectors (s<0.3 Å^-1) and for these scattering vectors the MASAs are found to be sensitive to the orientation of the scattering vector and on the chemical environment. The chemical environment sensitive MASAs are used within zero pressure classical Metropolis Monte Carlo, finite temperature calculations to investigate the effect of well size on the electron 002 and 220 structure factors (SFs). The implications of the use of the 002 (200) spot for the quantification of nanostructured Ga_1-xIn_xAs systems are examined while the 220 SF across the well is evaluated and is found to be very sensitive to the in-plane static displacements.

Abstract: Oxidative stress-inducing therapies are characterized as a specific treatment that involves the production of reactive oxygen and nitrogen species (RONS) by external or internal sources. To protect cells against oxidative stress, cells have evolved a strong antioxidant defense system to either prevent RONS formation or scavenge them. The maintenance of the redox balance ensures signal transduction, development, cell proliferation, regulation of the mechanisms of cell death, among others. Oxidative stress can beneficially be used to treat several diseases such as neurodegenerative disorders, heart disease, cancer, and other diseases by regulating the antioxidant system. Understanding the mechanisms of various endogenous antioxidant systems can increase the therapeutic efficacy of oxidative stress-based therapies, leading to clinical success in medical treatment. This review deals with the recent novel findings of various cellular endogenous antioxidant responses behind oxidative stress, highlighting their implication in various human diseases, such as ulcers, skin pathologies, oncology, and viral infections such as SARS-CoV-2.

Abstract: Atomic collapse can be observed in graphene because of its large “effective” fine structure constant, which enables this phenomenon to occur for an impurity charge as low as Z(c) similar to 1-2. Here we investigate the effect of the sublattice symmetry on molecular collapse in two spatially separated charge tunable vacancies, which are located on the same (A-A type) or different (A-B type) sublattices. We find that the broken sublattice symmetry: (1) does not affect the location of the main bonding and antibonding molecular collapse peaks, (2) but shifts the position of the satellite peaks, because they are a consequence of the breaking of the local sublattice symmetry, and (3) there are vacancy characteristic collapse peaks that only occur for A-B type vacancies, which can be employed to distinguish them experimentally from the A-A type. As the charge, energy, and separation distance increase, the additional collapse features merge with the main molecular collapse peaks. We show that the spatial distribution around the vacancy site of the collapse states allows us to differentiate the molecular from the frustrated collapse.

Abstract: Finite and infinite three-dimensional dust systems and their configurational and transport properties are investigated by Molecular Dynamics simulation. The model dust-dust interaction potential includes an attraction part. Spherical dust clusters or balls are found and their structural and transport properties studied. Qualitatively, the cluster structure agrees well with recent experimental results.

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.