Abstract: Biological membranes are under constant attack of free radicals, which may lead to lipid nitro-oxidation, pro­ ducing a complex mixture of nitro-oxidized lipids that are responsible for structural and dynamic changes on the membrane. Despite the latter, nitro-oxidized lipids are also associated with several inflammatory and neuro­ degenerative diseases, the underlying mechanisms of which remain elusive. We perform atomistic molecular dynamics simulations using several isomers of nitro-oxidized lipids to study their effect on the structure and permeability of the membrane, as well as the interaction between the mixture of these products in the phos­pholipid membrane environment. Our results show that the stereo- and positional isomers have a stronger effect on the properties of the membrane composed of oxidized lipids compared to that containing nitrated lipids. Nevertheless, nitrated lipids lead to three-fold increase in water permeability compared to oxidized lipids. In addition, we show that in a membrane consisting of combined nitro-oxidized lipid products, the presence of oxidized lipids protects the membrane from transient pores. Is well stablished that plasma application and photodynamic therapy produces a number of oxidative species used to kill cancer cells, through membrane damage induced by nitro-oxidative stress. This study is important to elucidate the mechanisms and the molecular level properties involving the reactive species produced during that cancer therapies.

Abstract: Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells.

Abstract: Reactive oxygen and nitrogen species (RONS) are involved in many biochemical processes, including nitrooxidative stress that causes cancer cell death, observed in cancer therapies such as photodynamic therapy and cold atmospheric plasma. However, their mechanisms of action and selectivity still remain elusive due to the complexity of biological cells. For example, it is not well known how RONS generated by cancer therapies permeate the cell membrane to cause nitro-oxidative damage. There are many studies dedicated to the perme­ation of RONS across native and oxidized membranes, but not across nitrated membranes, another lipid product also generated during nitro-oxidative stress. Herein, we performed molecular dynamics (MD) simulations to calculate the free energy barrier of RONS permeation across nitrated membranes. Our results show that hy­drophilic RONS, such as hydroperoxyl radical (HO2) and peroxynitrous acid (ONOOH), have relatively low barriers compared to hydrogen peroxide (H2O2) and hydroxyl radical (HO), and are more prone to permeate the membrane than for the native or peroxidized membranes, and similar to aldehyde-oxidized membranes. Hy­drophobic RONS like molecular oxygen (O2), nitrogen dioxide (NO2) and nitric oxide (NO) even have insignif­icant barriers for permeation. Compared to native and peroxidized membranes, nitrated membranes are more permeable, suggesting that we must not only consider oxidized membranes during nitro-oxidative stress, but also nitrated membranes, and their role in cancer therapies.

Abstract: Plasma, the fourth and most pervasive state of matter in the visible universe, is a fascinating medium that is connected to the beginning of our universe itself. Man-made plasmas are at the core of many technological advances that include the fabrication of semiconductor devices, which enabled the modern computer and communication revolutions. The introduction of low temperature, atmospheric pressure plasmas to the biomedical field has ushered a new revolution in the healthcare arena that promises to introduce plasma-based therapies to combat some thorny and long-standing medical challenges. This article presents an overview of where research is at today and discusses innovative concepts and approaches to overcome present challenges and take the field to the next level. It is written by a team of experts who took an in-depth look at the various applications of plasma in hygiene, decontamination, and medicine, made critical analysis, and proposed ideas and concepts that should help the research community focus their efforts on clear and practical steps necessary to keep the field advancing for decades to come.

Abstract: Cold atmospheric plasma (CAP) is a promising technology for several medical applications, including the removal of biofilms from surfaces. However, the molecular mechanisms of CAP treatment are still poorly understood. Here we unravel the possible mechanisms of CAP‐induced oxidation of oligosaccharides, employing reactive molecular dynamics simulations based on the density functional‐tight binding potential. Specifically, we find that the interaction of oxygen atoms (used as CAP‐generated reactive species) with cellotriose (a model system for the oligosaccharides) can break structurally important glycosidic bonds, which subsequently leads to the disruption of the oligosaccharide molecule. The overall results help to shed light on our experimental evidence for cellotriose CAP. This oxidation by study provides atomic‐level insight into the onset of plasma‐induced removal of biofilms, as oligosaccharides are one of the main components of biofilm.

Abstract: In the last decades, non-thermal plasma has been extensively investigated as a relevant tool for various biomedical applications, ranging from tissue decontamination to regeneration and from skin treatment to tumor therapies. This high versatility is due to the different kinds and amount of reactive oxygen and nitrogen species that can be generated during a plasma treatment and put in contact with the biological target. Some recent studies report that solutions of biopolymers with the ability to generate hydrogels, when treated with plasma, can enhance the generation of reactive species and influence their stability, resulting thus in the ideal media for indirect treatments of biological targets. The direct effects of the plasma treatment on the structure of biopolymers in water solution, as well as the chemical mechanisms responsible for the enhanced generation of RONS, are not yet fully understood. In this study, we aim at filling this gap by investigating, on the one hand, the nature and extent of the modifications induced by plasma treatment in alginate solutions, and, on the other hand, at using this information to explain the mechanisms responsible for the enhanced generation of reactive species as a consequence of the treatment. The approach we use is twofold: (i) investigating the effects of plasma treatment on alginate solutions, by size exclusion chromatography, rheology and scanning electron microscopy and (ii) study of a molecular model (glucuronate) sharing its chemical structure, by chromatography coupled with mass spectrometry and by molecular dynamics simulations. Our results point out the active role of the biopolymer chemistry during direct plasma treatment. Short-lived reactive species, such as OH radicals and O atoms, can modify the polymer structure, affecting its functional groups and causing partial fragmentation. Some of these chemical modifications, like the generation of organic peroxide, are likely responsible for the secondary generation of long-lived reactive species such as hydrogen peroxide and nitrite ions. This is relevant in view of using biocompatible hydrogels as vehicles for storage and delivery reactive species for targeted therapies.

Abstract: A Monte Carlo model has been developed for investigating the electron behavior in a dual-magnetron sputter deposition system. To describe the three-dimensional (3D) geometry, different reference frames, i.e. a local and a global coordinate system, were used. In this study, the influence of both closed and mirror magnetic field configurations on the plasma properties is investigated. In the case of a closed magnetic field configuration, the calculated electron trajectories show that if an electron is emitted in (or near) the center of the cathode, where the influence of the magnetic field is low, it is able to travel from one magnetron to the other. On the other hand, when an electron is created at the race track area, it is more or less trapped in the strong magnetic field and cannot easily escape to the second magnetron region. In the case of a mirror magnetic field configuration, irrespective of where the electron is emitted from the cathode, it cannot travel from one magnetron to the other because the magnetic field lines guide the electron to the substrate. Moreover, the electron density and electron impact ionization rate have been calculated and studied in detail for both configurations.

Abstract: A multi-species Monte Carlo (MC) model, combined with an analytical surface model, has been developed in order to investigate the general plasma processes occurring during the sputter deposition of complex oxide films in a dual-magnetron sputter deposition system. The important plasma species, such as electrons, Ar+ ions, fast Ar atoms and sputtered metal atoms (i.e. Mg and Al atoms) are described with the so-called multi-species MC model, whereas the deposition of MgxAlyOz films is treated by an analytical surface model. Targetsubstrate distances for both magnetrons in the dual-magnetron setup are varied for the purpose of growing stoichiometric complex oxide thin films. The metal atoms are sputtered from pure metallic targets, whereas the oxygen flux is only directed toward the substrate and is high enough to obtain fully oxidized thin films but low enough to avoid target poisoning. The calculations correspond to typical experimental conditions applied to grow these complex oxide films. In this paper, some calculation results are shown, such as the densities of various plasma species, their fluxes toward the targets and substrate, the deposition rates, as well as the film stoichiometry. Moreover, some results of the combined model are compared with experimental observations. Note that this is the first complete model, which can be applied for large and complicated magnetron reactor geometries, such as dual-magnetron configurations. With this model, we are able to describe all important plasma species as well as the deposition process. It can also be used to predict film stoichiometries of complex oxide films on the substrate.

Abstract: Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG.

Abstract: The application of atmospheric pressure plasmas in medicine is increasingly gaining attention in recent years, although very little is currently known about the plasma-induced processes occurring on the surface of living organisms. It is known that most bio-organisms, including bacteria, are coated by a liquid film surrounding them, and there might be many interactions between plasma species and the liquid layer before the plasma species reach the surface of the bio-organisms. Therefore, it is essential to study the behaviour of the reactive species in a liquid film, in order to determine whether these species can travel through this layer and reach the biomolecules, or whether new species are formed along the way. In this work, we investigate the interaction of reactive oxygen species (i.e. O, OH, HO2 and H2O2) with water, which is assumed as a simple model system for the liquid layer surrounding biomolecules. Our computational investigations show that OH, HO2 and H2O2 can travel deep into the liquid layer and are hence in principle able to reach the bio-organism. Furthermore, O, OH and HO2 radicals react with water molecules through hydrogen-abstraction reactions, whereas no H-abstraction reaction takes place in the case of H2O2. This study is important to gain insight into the fundamental operating mechanisms in plasma medicine, in general, and the interaction mechanisms of plasma species with a liquid film, in particular.

Abstract: Nonthermal atmospheric pressure plasmas are gaining increasing attention for biomedical applications. However, very little fundamental information on the interaction mechanisms between the plasma species and biological cells is currently available. We investigate the interaction of important plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, with bacterial peptidoglycan by means of reactive molecular dynamics simulations, aiming for a better understanding of plasma disinfection. Our results show that OH, O, O3, and H2O2 can break structurally important bonds of peptidoglycan (i.e., CO, CN, or CC bonds), which consequently leads to the destruction of the bacterial cell wall. The mechanisms behind these breakups are, however, dependent on the impinging plasma species, and this also determines the effectiveness of the cell wall destruction.

Abstract: In this review paper, we present several examples of reactive molecular dynamics simulations, which contribute to a better understanding of the underlying mechanisms in plasma medicine on the atomic scale. This includes the interaction of important reactive oxygen plasma species with the outer cell wall of both gram-positive and gram-negative bacteria, and with lipids present in human skin. Moreover, as most biomolecules are surrounded by a liquid biofilm, the behavior of these plasma species in a liquid (water) layer is presented as well. Finally, a perspective for future atomic scale modeling studies is given, in the field of plasma medicine in general, and for cancer treatment in particular.