Abstract: The treatment of a well plate by an atmospheric pressure plasma jet is common for<italic>in vitro</italic>plasma medicine research. Here, reactive species are largely produced through the mixing of the jet effluent with the surrounding atmosphere. This mixing can be influenced not only by the ambient conditions, but also by the geometry of the treated well. To limit this influence and control the atmosphere, a shielding gas is sometimes applied. However, the interplay between the gas shield and the well geometry has not been investigated. In this work, we developed a 2D-axisymmetric computational fluid dynamics model of the kINPen plasma jet, to study the mixing of the jet effluent with the surrounding atmosphere, with and without gas shield. Our computational and experimental results show that the choice of well type can have a significant influence on the effluent conditions, as well as on the effectiveness of the gas shield. Furthermore, the geometry of the shielding gas device can substantially influence the mixing as well. Our results provide a deeper understanding of how the choice of setup geometry can influence the plasma treatment, even when all other operating parameters are unchanged.

Abstract: Molecular dynamics method was employed to investigate the effects of the reaction layer formed near the surface region on CF(3)(+) etching of Si at different temperatures. The simulation results show that the coverages of F and C are sensitive to the surface temperature. With increasing temperature, the physical etching is enhanced, while the chemical etching is weakened. It is found that with increasing surface temperature, the etching rate of Si increases. As to the etching products, the yields of SiF and SiF(2) increase with temperature, whereas the yield of SiF(3) is not sensitive to the surface temperature. And the increase of the etching yield is mainly due to the increased desorption of SiF and SiF(2). The comparison shows that the reactive layer plays an important part in the subsequeat impacting, which enhances the etching rate of Si and weakens the chemical etching intensity.

Abstract: Lipid oxidation is associated with several inflammatory and neurodegenerative diseases, but many questions to unravel its effects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a significant effect on membrane function. It is reported that domain interfaces are “hot spots” for pore formation, but the underlying mechanisms and the effect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Specifically, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any effect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy.

Abstract: Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.

Abstract: A Monte Carlo model is utilized for studying the behavior of electrons in the afterglow of an analytical microsecond dc pulsed glow discharge. This model uses several quantities as input data, such as electric field and potential, ion flux at the cathode, the fast argon ion and atom impact ionization rates, slow electron density, the electrical characterization of the pulse (voltage and current profiles) and temperature profile. These quantities were obtained by earlier Monte Carlo fluid calculations for a pulsed discharge. Our goal is to study the behavior of the so-called Monte Carlo electrons (i.e., those electrons created at the cathode or by ionization collisions in the plasma which are followed by using the Monte Carlo model) from their origin to the moment when they are absorbed at the cell walls or when they have lost their energy by collisions (being transferred to the group of slow electrons) in the afterglow of the pulsed discharge. The thermalization of the electrons is a phenomenon where the electron-electron Coulomb collisions acquire a special importance. Indeed, in the afterglow the cross sections of the other electron reactions taken into account in the model are very low, because of the very low electron energy. We study the electron energy distributions at several times during and after the pulse and at several positions in the plasma cell, focusing on the thermalization and on the behavior of the electrons in the afterglow. Also, the time evolution of the rates of the various collision processes, the average electron energy, the densities of Monte Carlo and slow electrons and the ionization degree are investigated.

Abstract: A hybrid model is developed for describing the effects of oxygen addition to argon glow discharges. The species taken into account in the model include Ar atoms in the ground state and the metastable level, O2 gas molecules in the ground state and two metastable levels, O atoms in the ground state and one metastable level, O3 molecules, Ar+, O+, O2+ and O− ions, as well as the electrons. The hybrid model consists of a Monte Carlo model for electrons and fluid models for the other plasma species. In total, 87 different reactions between the various plasma species are taken into account. Calculation results include the species densities and the importance of their production and loss processes, as well as the dissociation degree of oxygen. The effect of different O2 additions on these calculation results, as well as on the sputtering rates, is discussed.

Abstract: A hybrid Monte Carlofluid modeling network is developed for an argon-hydrogen mixture, to predict the effect of small amounts of hydrogen added to a dc argon glow discharge. The species considered in the model include the Ar gas atoms, electrons, Ar+ ions and fast Ar atoms, ArH+, H+, H+2 and H+3 ions, and H atoms and H2 molecules, as well as Ar metastable atoms, sputtered Cu atoms, and the corresponding Cu+ ions. Sixty-five reactions between these species are incorporated in the model. The effect of hydrogen on various calculation results is investigated, such as the species densities, the relative role of different production and loss processes for the various species, the cathode sputtering rate and contributions by different bombarding species, and the dissociation degree of H2 and the ionization degree of Ar and Cu. The calculation results are presented and discussed for 1% H2 addition, and comparison is also made with a pure argon discharge and with only 0.1% H2 addition.

Abstract: In this work, we take a crucial step towards the industrial readiness of plasma-based CO2 conversion. We present a stepwise method to study plasma reactors in series as a first approach to a recycle flow. By means of this procedure, the CO2 conversion is enhanced by a factor of 3, demonstrating that a single-pass plasma treatment performs far below the optimal capacity of the reactor. Furthermore, we explore the effect of O2 in the mixture with our flexible procedure. Addition of O2 in the mixture has a clear detrimental effect on the conversion, in agreement with other experiments in atmospheric pressure plasmas. O2 removal is however highly beneficial, demonstrating a conversion per pass that is 1.6 times higher than the standard procedure. Indeed, extracting one of the products prevents recombination reactions. Based on these insights, we discuss opportunities for further improvements, especially in the field of specialised separation techniques.

Abstract: With climate change still a pressing issue, there is a great need for carbon capture, utilisation and storage (CCUS)
methods. We propose a novel concept where CO2 conversion is accomplished by O2 splitting followed by the
addition of O atoms to CO2. The latter is studied here by means of kinetic modelling. In the first instance, we
study various CO2/O ratios, and we observe an optimal CO2 conversion of around 30–40% for 50% O addition.
Gas temperature also has a large influence, with a minimum temperature of around 1000 K to a maximum of
2000 K for optimal conversion. In the second instance, we study various CO2/O/O2 ratios, due to O2 being a
starting gas. Also here we define optimal regions for CO2 conversion, which reach maximum conversion for a
CO2 fraction of 50% and an O/O2 ratio bigger than 1. Those can be expanded by heating on one hand, for low
atomic oxygen availability, and by quenching after reaction on the other hand, for cases where the temperatures
are too high. Our model predictions can serve as a guideline for experimental research in this domain.