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“A comparison of floating-electrode DBD and kINPen jet : plasma parameters to achieve similar growth reduction in colon cancer cells under standardized conditions”. Bekeschus S, Lin A, Fridman A, Wende K, Weltmann K-D, Miller V, Plasma chemistry and plasma processing 38, 1 (2018). http://doi.org/10.1007/S11090-017-9845-3
Abstract: A comparative study of two plasma sources (floating-electrode dielectric barrier discharge, DBD, Drexel University; atmospheric pressure argon plasma jet, kINPen, INP Greifswald) on cancer cell toxicity was performed. Cell culture protocols, cytotoxicity assays, and procedures for assessment of hydrogen peroxide (H2O2) were standardized between both labs. The inhibitory concentration 50 (IC50) and its corresponding H2O2 deposition was determined for both devices. For the DBD, IC50 and H2O2 generation were largely dependent on the total energy input but not pulsing frequency, treatment time, or total number of cells. DBD cytotoxicity could not be replicated by addition of H2O2 alone and was inhibited by larger amounts of liquid present during the treatment. Jet plasma toxicity depended on peroxide generation as well as total cell number and amount of liquid. Thus, the amount of liquid present during plasma treatment in vitro is key in attenuating short-lived species or other physical effects from plasmas. These in vitro results suggest a role of liquids in or on tissues during plasma treatment in a clinical setting. Additionally, we provide a platform for correlation between different plasma sources for a predefined cellular response.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.355
Times cited: 12
DOI: 10.1007/S11090-017-9845-3
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“Unveiling the interaction mechanisms of cold atmospheric plasma and amino acids by machine learning”. Chai Z-N, Wang X-C, Yusupov M, Zhang Y-T, Plasma processes and polymers , 1 (2024). http://doi.org/10.1002/PPAP.202300230
Abstract: Plasma medicine has attracted tremendous interest in a variety of medical conditions, ranging from wound healing to antimicrobial applications, even in cancer treatment, through the interactions of cold atmospheric plasma (CAP) and various biological tissues directly or indirectly. The underlying mechanisms of CAP treatment are still poorly understood although the oxidative effects of CAP with amino acids, peptides, and proteins have been explored experimentally. In this study, machine learning (ML) technology is introduced to efficiently unveil the interaction mechanisms of amino acids and reactive oxygen species (ROS) in seconds based on the data obtained from the reactive molecular dynamics (MD) simulations, which are performed to probe the interaction of five types of amino acids with various ROS on the timescale of hundreds of picoseconds but with the huge computational load of several days. The oxidative reactions typically start with H-abstraction, and the details of the breaking and formation of chemical bonds are revealed; the modification types, such as nitrosylation, hydroxylation, and carbonylation, can be observed. The dose effects of ROS are also investigated by varying the number of ROS in the simulation box, indicating agreement with the experimental observation. To overcome the limits of timescales and the size of molecular systems in reactive MD simulations, a deep neural network (DNN) with five hidden layers is constructed according to the reaction data and employed to predict the type of oxidative modification and the probability of occurrence only in seconds as the dose of ROS varies. The well-trained DNN can effectively and accurately predict the oxidative processes and productions, which greatly improves the computational efficiency by almost ten orders of magnitude compared with the reactive MD simulation. This study shows the great potential of ML technology to efficiently unveil the underpinning mechanisms in plasma medicine based on the data from reactive MD simulations or experimental measurements. In this study, since reactive molecular dynamics simulation can currently only describe interactions between a few hundred atoms in a few hundred picoseconds, deep neural networks (DNN) are introduced to enhance the simulation results by predicting more data efficiently. image
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.5
DOI: 10.1002/PPAP.202300230
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“Kinetic modeling of relaxation phenomena after photodetachment in a rf electronegative SiH4 discharge”. Yan M, Bogaerts A, Gijbels R, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 63 (2001). http://doi.org/10.1103/PhysRevE.63.026405
Abstract: The global relaxation process after pulsed laser induced photodetachment in a rf electronegative SIH4 discharge is studied by a self-consistent kinetic one-dimensional particle-in-cell-Monte Carlo model. Our results reveal a comprehensive physical picture of the relaxation process, including the main plasma variables, after a perturbation up to the full recovery of the steady state. A strong influence of the photodetachment on the discharge is found, which results from an increase of the electron density, leading to a weaker bulk field, and hence to a drop in the high energy tail of the electron energy distribution function (EEDF), a reduction of the reaction rates of electron impact attachment and ionization, and a subsequent decrease of the positive and negative ion densities. All the plasma quantities related to electrons recover synchronously. The recovery time of the ion densities is about 1-2 orders of magnitude longer than that of the electrons due to different recovery mechanisms. The modeled behavior of all the charged particles agrees very well with experimental results from the literature. In addition, our work clarifies some unclear processes assumed in the literature, such as the relaxation of the EEDF, the evolution of the electric field, and the recovery of negative ions.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 4
DOI: 10.1103/PhysRevE.63.026405
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“Normal modes of a quasi-one-dimensional multichain complex plasma”. Piacente G, Peeters FM, Betouras JJ, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 70 (2004). http://doi.org/10.1103/PhysRevE.70.036406
Abstract: We studied equally charged particles, suspended in a complex plasma, which move in a plane and interact with a screened Coulomb potential (Yukawa type) and with an additional external confining parabolic potential in one direction, which makes the system quasi-one-dimensional (Q1D). The normal modes of the system are studied in the presence of dissipation. We also investigated how a perpendicular magnetic field couples the phonon modes with each other. Two different ways of exciting the normal modes are discussed: (1) a uniform excitation of the Q1D lattice, and (2) a local forced excitation of the system in which one particle is driven by, e.g., a laser. Our results are in very good agreement with recent experimental findings on a finite single chain system [Liu , Phys. Rev. Lett. 91, 255003 (2003)]. Predictions are made for the normal modes of multichain structures in the presence of damping.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 18
DOI: 10.1103/PhysRevE.70.036406
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“Possible Mechanism of Glucose Uptake Enhanced by Cold Atmospheric Plasma: Atomic Scale Simulations”. Razzokov J, Yusupov M, Bogaerts A, Plasma 1 (2018). http://doi.org/10.3390/plasma1010011
Abstract: Cold atmospheric plasma (CAP) has shown its potential in biomedical applications, such as wound healing, cancer treatment and bacterial disinfection. Recent experiments have provided evidence that CAP can also enhance the intracellular uptake of glucose molecules which is important in diabetes therapy. In this respect, it is essential to understand the underlying mechanisms of intracellular glucose uptake induced by CAP, which is still unclear. Hence, in this study we try to elucidate the possible mechanism of glucose uptake by cells by performing computer simulations. Specifically, we study the transport of glucose molecules through native and oxidized membranes. Our simulation results show that the free energy barrier for the permeation of glucose molecules across the membrane decreases upon increasing the degree of oxidized lipids in the membrane. This indicates that the glucose permeation rate into cells increases when the CAP oxidation level in the cell membrane is increased.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.3390/plasma1010011
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“Modeling for a Better Understanding of Plasma-Based CO2 Conversion”. Bogaerts A, Snoeckx R, Trenchev G, Wang W In: Britun N, Silva T (eds) Plasma Chemistry and Gas Conversion. IntechOpen, Rijeka (2018).
Abstract: This chapter discusses modeling efforts for plasma-based CO2 conversion, which are needed to obtain better insight in the underlying mechanisms, in order to improve this application. We will discuss two types of (complementary) modeling efforts that are most relevant, that is, (i) modeling of the detailed plasma chemistry by zero-dimensional (0D) chemical kinetic models and (ii) modeling of reactor design, by 2D or 3D fluid dynamics models. By showing some characteristic calculation results of both models, for CO2 splitting and in combination with a H-source, and for packed bed DBD and gliding arc plasma, we can illustrate the type of information they can provide.
Keywords: H1 Book Chapter; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
DOI: 10.5772/intechopen.80436
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“The penetration of reactive oxygen and nitrogen species across the stratum corneum”. Duan J, Ma M, Yusupov M, Cordeiro RM, Lu X, Bogaerts A, Plasma Processes And Polymers (2020). http://doi.org/10.1002/ppap.202000005
Abstract: The penetration of reactive oxygen and nitrogen species (RONS) across the stratum corneum (SC) is a necessary and crucial process in many skin‐related plasma medical applications. To gain more insights into this penetration behavior, we combined experimental measurements of the permeability of dry and moist SC layers with computer simulations of model lipid membranes. We measured the permeation of relatively stable molecules, which are typically generated by plasma, namely H2O2, NO3−, and NO2−. Furthermore, we calculated the permeation free energy profiles of the major plasma‐generated RONS and their derivatives (i.e., H2O2, OH, HO2, O2, O3, NO, NO2, N2O4, HNO2, HNO3, NO2−, and NO3−) across native and oxidized SC lipid bilayers, to understand the mechanisms of RONS permeation across the SC. Our results indicate that hydrophobic RONS (i.e., NO, NO2, O2, O3, and N2O4) can translocate more easily across the SC lipid bilayer than hydrophilic RONS (i.e., H2O2, OH, HO2, HNO2, and HNO3) and ions (i.e., NO2− and NO3−) that experience much higher permeation barriers. The permeability of RONS through the SC skin lipids is enhanced when the skin is moist and the lipids are oxidized. These findings may help to understand the underlying mechanisms of plasma interaction with a biomaterial and to optimize the environmental parameters in practice in plasma medical applications.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.5
DOI: 10.1002/ppap.202000005
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“Foundations of plasma catalysis for environmental applications”. Bogaerts A, Neyts EC, Guaitella O, Murphy AB, Plasma Sources Science &, Technology (2022). http://doi.org/10.1088/1361-6595/ac5f8e
Abstract: Plasma catalysis is gaining increasing interest for various applications, but the underlying mechanisms are still far from understood. Hence, more fundamental research is needed to understand these mechanisms. This can be obtained by both modelling and experiments. This foundations paper describes the fundamental insights in plasma catalysis, as well as efforts to gain more insights by modelling and experiments. Furthermore, it discusses the state-of-the-art of the major plasma catalysis applications, as well as successes and challenges of technology transfer of these applications.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.8
DOI: 10.1088/1361-6595/ac5f8e
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“Molecular understanding of the possible mechanisms of oligosaccharide oxidation by cold plasma”. Yusupov M, Dewaele D, Attri P, Khalilov U, Sobott F, Bogaerts A, Plasma processes and polymers (2022). http://doi.org/10.1002/ppap.202200137
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.5
DOI: 10.1002/ppap.202200137
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“Modelling the dynamics of hydrogen synthesis from methane in nanosecond‐pulsed plasmas”. Morais E, Bogaerts A, Plasma processes and polymers 21 (2024). http://doi.org/10.1002/ppap.202300149
Abstract: A chemical kinetics model was developed to characterise the gas‐phase dynamics of H<sub>2</sub>production in nanosecond‐pulsed CH<sub>4</sub>plasmas. Pulsed behaviour was observed in the calculated electric field, electron temperature and species densities at all pressures. The model agrees reasonably with experimental results, showing CH<sub>4</sub>conversion at 30% and C<sub>2</sub>H<sub>2</sub>and H<sub>2</sub>as major products. The underlying mechanisms in CH<sub>4</sub>dissociation and H<sub>2</sub>formation were analysed, highlighting the large contribution of vibrationally excited CH<sub>4</sub>and H<sub>2</sub>to coupling energy from the plasma into gas‐phase heating, and revealing that H<sub>2</sub>synthesis is not affected by applied pressure, with selectivity remaining unchanged at ~42% in the 1–5 bar range.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.5
DOI: 10.1002/ppap.202300149
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“Plasmonic effects in the neutralization of slow ions at a metallic surface”. Bercx M, Mayda S, Depla D, Partoens B, Lamoen D, Contributions to Plasma Physics (2023). http://doi.org/10.1002/ctpp.202300054
Abstract: Secondary electron emission is an important process that plays a significant role in several plasma‐related applications. As measuring the secondary electron yield experimentally is very challenging, quantitative modelling of this process to obtain reliable yield data is critical as input for higher‐scale simulations. Here, we build upon our previous work combining density functional theory calculations with a model originally developed by Hagstrum to extend its application to metallic surfaces. As plasmonic effects play a much more important role in the secondary electron emission mechanism for metals, we introduce an approach based on Poisson point processes to include both surface and bulk plasmon excitations to the process. The resulting model is able to reproduce the yield spectra of several available experimental results quite well but requires the introduction of global fitting parameters, which describe the strength of the plasmon interactions. Finally, we use an in‐house developed workflow to calculate the electron yield for a list of elemental surfaces spanning the periodic table to produce an extensive data set for the community and compare our results with more simplified approaches from the literature.
Keywords: A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
Impact Factor: 1.6
DOI: 10.1002/ctpp.202300054
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