Abstract: Physical plasmas generate unique mixes of reactive oxygen and nitrogen species (RONS or ROS). Only a bit more than a decade ago, these plasmas, operating at body temperature, started to be considered for medical therapy with considerably little mechanistic redox chemistry or biomedical research existing on that topic at that time. Today, a vast body of evidence is available on physical plasma-derived ROS, from their spatiotemporal resolution in the plasma gas phase to sophisticated chemical and biochemical analysis of these species once dissolved in liquids. Data from<italic>in silico</italic>analysis dissected potential reaction pathways of plasma-derived reactive species with biological membranes, and<italic>in vitro</italic>and<italic>in vivo</italic>experiments in cell and animal disease models identified molecular mechanisms and potential therapeutic benefits of physical plasmas. In 2013, the first medical plasma systems entered the European market as class IIa devices and have proven to be a valuable resource in dermatology, especially for supporting the healing of chronic wounds. The first results in cancer patients treated with plasma are promising, too. Due to the many potentials of this blooming new field ahead, there is a need to highlight the main concepts distilled from plasma research in chemistry and biology that serve as a mechanistic link between plasma physics (how and which plasma-derived ROS are produced) and therapy (what is the medical benefit). This inevitably puts cellular membranes in focus, as these are the natural interphase between ROS produced by plasmas and translation of their chemical reactivity into distinct biological responses.

Abstract: Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.

Abstract: In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. CO, CN and CC bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale.

Abstract: In this paper we study two cold atmospheric pressure plasma jets, operating in Ar + 2% air, with a different electrode geometry but with the same power dissipated in the plasma. The density profiles of the biomedically active NO and O species throughout the plasma jet, previously obtained by laser diagnostics, are calculated by means of a zero-dimensional semi-empirical reaction kinetics model. A good agreement between the calculated and measured data is demonstrated. Furthermore, the most probable spatial power distribution in an RF driven plasma jet is obtained for the first time by comparing measured and calculated species density profiles. This was possible due to the strong effect of the power distribution on the NO and O density profiles. In addition the dominant reaction pathways for both the NO and the O species are identified. The model allows us to obtain key information on the reactive species production inside the jet, which is difficult to access by laser diagnostics in a coaxial geometry. Finally, we demonstrate that water impurities in the order of 100 ppm in the gas feed can have a significant effect on the spatial distribution of the NO and O density.

Abstract: The physical processes in an Ar/O2 magnetron discharge used for the reactive sputter deposition of TiOx thin films were simulated with a 2d3v particle-in-cell/Monte Carlo collisions (PIC/MCC) model. The plasma species taken into account are electrons, Ar+ ions, fast Arf atoms, metastable Arm* atoms, Ti+ ions, Ti atoms, O+ ions, O2+ ions, O− ions and O atoms. This model accounts for plasmatarget interactions, such as secondary electron emission and target sputtering, and the effects of target poisoning. Furthermore, the deposition process is described by an analytical surface model. The influence of the O2/Ar gas ratio on the plasma potential and on the species densities and fluxes is investigated. Among others, it is shown that a higher O2 pressure causes the region of positive plasma potential and the O− density to be more spread, and the latter to decrease. On the other hand, the deposition rates of Ti and O are not much affected by the O2/Ar proportion. Indeed, the predicted stoichiometry of the deposited TiOx film approaches x=2 for nearly all the investigated O2/Ar proportions.

Abstract: Cold atmospheric pressure plasmas have proven to provide an alternative treatment of cancer by targeting tumorous cells while leaving their healthy counterparts unharmed. However, the underlying mechanisms of the plasma–cell interactions are not yet fully understood. Reactive oxygen species, and in particular hydroxyl radicals (OH), are known to play a crucial role in plasma driven apoptosis of
malignant cells. In this paper we investigate the interaction of OH radicals, as well as H2O2 molecules and HO2 radicals, with DNA by means of reactive molecular dynamics simulations using the ReaxFF force field. Our results provide atomic-scale insight into the dynamics of oxidative stress on DNA caused by the OH radicals, while H2O2 molecules appear not reactive within the considered timescale. Among the observed processes are the formation of 8-OH-adduct radicals, forming the first stages towards the formation of 8-oxoGua and 8-oxoAde, H-abstraction reactions of the amines, and the partial opening of loose DNA ends in aqueous solution.

Abstract: The plasma behavior in a parallel-plate dielectric barrier discharge (DBD) is simulated by a two-dimensional particle-in-cell/Monte Carlo collision model, comparing for the first time an unpacked (empty) DBD with a packed bed DBD, i.e., a DBD filled with dielectric spheres in the gas gap. The calculations are performed in air, at atmospheric pressure. The discharge is powered by a pulse with a voltage amplitude of −20 kV. When comparing the packed and unpacked DBD reactors with the same dielectric barriers, it is clear that the presence of the dielectric packing leads to a transition in discharge behavior from a combination of negative streamers and unlimited surface streamers on the bottom dielectric surface to a combination of predominant positive streamers and limited surface discharges on the dielectric surfaces of the beads and plates. Furthermore, in the packed bed DBD, the electric field is locally enhanced inside the dielectric material, near the contact points between the beads and the plates, and therefore also in the plasma between the packing beads and between a bead and the dielectric wall, leading to values of $4\times {10}

Abstract: We investigate the theoretical possibility of single layer graphene formation on a nickel surface at different substrate temperatures under far-from-equilibrium high precursor flux conditions, employing state-of-the-art hybrid reactive molecular dynamics/uniform acceptance force bias Monte Carlo simulations. It is predicted that under these conditions, the formation of a single layer graphene-like film may proceed through a combined depositionsegregation mechanism on a nickel substrate, rather than by pure surface segregation as is typically observed for metals with high carbon solubility. At 900 K and above, nearly continuous graphene layers are obtained. These simulations suggest that single layer graphene deposition is theoretically possible on Ni under high flux conditions.

Abstract: The application of coreshell SiSiO2 nanowires as nanoelectronic devices strongly depends on their structure, which is difficult to tune precisely. In this work, we investigate the formation of the coreshell nanowires at the atomic scale, by reactive molecular dynamics simulations. The occurrence of two temperature-dependent oxidation mechanisms of ultra-small diameter Si-NWs is demonstrated. We found that control over the Si-core radius and the SiOx (x ≤ 2) oxide shell is possible by tuning the growth temperature and the initial Si-NW diameter. Two different structures were obtained, i.e., ultrathin SiO2 silica nanowires at high temperature and Si core|ultrathin SiO2 silica nanowires at low temperature. The transition temperature is found to linearly decrease with the nanowire curvature. Finally, the interfacial stress is found to be responsible for self-limiting oxidation, depending on both the initial Si-NW radius and the oxide growth temperature. These novel insights allow us to gain control over the exact morphology and structure of the wires, as is needed for their application in nanoelectronics.

Abstract: Using reactive molecular dynamics simulations, the melting behavior of nickel-carbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickel-carbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method.

Abstract: Cold atmospheric plasma and nanomedicine originally emerged as individual domains, but are increasingly applied in combination with each other. Most research is performed in the context of cancer treatment, with only little focus yet on the possible synergies. Many questions remain on the potential of this promising hybrid technology, particularly regarding regenerative medicine and tissue engineering. In this perspective article, we therefore start from the fundamental mechanisms in the individual technologies, in order to envision possible synergies for wound healing and tissue recovery, as well as research strategies to discover and optimize them. Among these strategies, we demonstrate how cold plasmas and nanomaterials can enhance each other’s strengths and overcome each other’s limitations. The parallels with cancer research, biotechnology and plasma surface modification further serve as inspiration for the envisioned synergies in tissue regeneration. The discovery and optimization of synergies may also be realized based on a profound understanding of the underlying redox- and field-related biological processes. Finally, we emphasize the toxicity concerns in plasma and nanomedicine, which may be partly remediated by their combination, but also partly amplified. A widespread use of standardized protocols and materials is therefore strongly recommended, to ensure both a fast and safe clinical implementation.

Abstract: Plasma-catalytic dry reforming of CH4 (DRM) is promising to convert the greenhouse gasses CH4 and CO2 into value-added chemicals, thus simultaneously providing an alternative to fossil resources as feedstock for the chemical industry. However, while many experiments have been dedicated to plasma-catalytic DRM, there is no consensus yet in literature on the optimal choice of catalyst for targeted products, because the underlying mechanisms are far from understood. Indeed, plasma catalysis is very complex, as it encompasses various chemical and physical interactions between plasma and catalyst, which depend on many parameters. This complexity hampers the comparison of experimental results from different studies, which, in our opinion, is an important bottleneck in the further development of this promising research field. Hence, in this perspective paper, we describe the important physical and chemical effects that should be accounted for when designing plasma-catalytic experiments in general, highlighting the need for standardized experimental setups, as well as careful documentation of packing properties and reaction conditions, to further advance this research field. On the other hand, many parameters also create many windows of opportunity for further optimizing plasma-catalytic systems. Finally, various experiments also reveal the lack of improvement in plasma catalysis compared to plasma-only, specifically for DRM, but the underlying mechanisms are unclear. Therefore, we present our newly developed coupled plasma-surface kinetics model for DRM, to provide more insight in the underlying reasons. Our model illustrates that transition metal catalysts can adversely affect plasmacatalytic DRM, if radicals dominate the plasma-catalyst interactions. Thus, we demonstrate that a good understanding of the plasma-catalyst interactions is crucial to avoiding conditions at which these interactions negatively affect the results, and we provide some recommendations for improvement. For instance, we believe that plasma-catalytic DRM may benefit more from higher reaction temperatures, at which vibrational excitation can enhance the surface reactions.

Abstract: This study investigates the dry reformation of methane (DRM) over Ni/Al2O3 catalysts in a dielectric barrier discharge (DBD) non-thermal plasma reactor. A novel hybrid machine learning (ML) model is developed to optimize the plasma-catalytic DRM reaction with limited experimental data. To address the non-linear and complex nature of the plasma-catalytic DRM process, the hybrid ML model integrates three well-established algorithms: regression trees, support vector regression, and artificial neural networks. A genetic algorithm (GA) is then used to optimize the hyperparameters of each algorithm within the hybrid ML model. The ML model achieved excellent agreement with the experimental data, demonstrating its efficacy in accurately predicting and optimizing the DRM process. The model was subsequently used to investigate the impact of various operating parameters on the plasma-catalytic DRM performance. We found that the optimal discharge power (20 W), CO2/CH4 molar ratio (1.5), and Ni loading (7.8 wt%) resulted in the maximum energy yield at a total flow rate of
51 mL/min. Furthermore, we investigated the relative significance of each operating parameter on the performance of the plasmacatalytic DRM process. The results show that the total flow rate had the greatest influence on the conversion, with a significance exceeding 35% for each output, while the Ni loading had the least impact on the overall reaction performance. This hybrid model demonstrates a remarkable ability to extract valuable insights from limited datasets, enabling the development and optimization of more efficient and selective plasma-catalytic chemical processes.