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“Evolution of charged particle densities after laser-induced photodetachment in a strongly electronegative RF discharge”. Yan M, Bogaerts A, Gijbels R, IEEE transactions on plasma science 30, 132 (2002). http://doi.org/10.1109/TPS.2002.1003959
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.052
DOI: 10.1109/TPS.2002.1003959
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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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“Local and fast relaxation phenomena after laser-induced photodetachment in a strongly electronegative rf discharge”. Yan M, Bogaerts A, Gijbels R, Goedheer WJ, Physical review : E : statistical, nonlinear, and soft matter physics 65, 016408 (2002). http://doi.org/10.1103/PhysRevE.65.016408
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 2
DOI: 10.1103/PhysRevE.65.016408
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“Spatial behavior of energy relaxation of electrons in capacitively coupled discharges: comparison between Ar and SiH4”. Yan M, Bogaerts A, Gijbels R, Goedheer WJ, Journal of applied physics 87, 3628 (2000). http://doi.org/10.1063/1.372392
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.068
Times cited: 14
DOI: 10.1063/1.372392
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“Electron energy distribution function in capacitively coupled RF discharges: differences between electropositive Ar and electronegative SiH4 discharges”. Yan M, Bogaerts A, Goedheer WJ, Gijbels R, Plasma sources science and technology 9, 583 (2000). http://doi.org/10.1088/0963-0252/9/4/314
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 21
DOI: 10.1088/0963-0252/9/4/314
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“Conductivity and electron density of undoped model compounds of poly(phenylene vinylene)”. Yang Z, Geise HJ, Mehbod M, Debrue G, Visser JW, Sonneveld EJ, Van 't dack L, Gijbels R, Synthetic metals 39, 137 (1990). http://doi.org/10.1016/0379-6779(90)90179-O
Abstract: Fourteen derivatives of trans,trans-1,4-bis[2-phenylethenyl]benzene were synthesized by Wittig reactions as model compounds of poly(paraphenylene vinylene). Structure, configurational homogeneity and absence of ionic impurities were controlled by mass spectrometry, infrared and neutron activation analysis, respectively. Crystallographic unit cell parameters were obtained from X-ray powder patterns and measurements of electrical conductivities were performed on undoped samples. The data of four more compounds containing one or more thiophene rings instead of phenyl rings were added from the 3iterature. If NO2 and Cl groups are excluded from the electron count a good linear correlation is found between the logarithm of the conductivity and the non-σ electron density (View the MathML source). The position of the substituents, on the central or on the terminal ring, also plays a role in as much as it affects the molecular volume of the compound but not the non-σ electron density. The correlation between the logarithm of the conductivity and the absorption coefficient of the longest wavelength of UV absorption identifies the π electrons in the chromophore as the principal charge carriers.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.252
Times cited: 25
DOI: 10.1016/0379-6779(90)90179-O
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Yi Y, Li S, Cui Z, Hao Y, Zhang Y, Wang L, Liu P, Tu X, Xu X, Guo H, Bogaerts A (2021) Selective oxidation of CH4 to CH3OH through plasma catalysis: Insights from catalyst characterization and chemical kinetics modelling. 120384
Abstract: The selective oxidation of methane to methanol (SOMTM) by molecular oxygen is a holy grail in catalytic chemistry and remains a challenge in chemical industry. We perform SOMTM in a CH4/O2 plasma, at low temperature and atmospheric pressure, promoted by Ni-based catalysts, reaching 81 % liquid oxygenates selectivity and 50 % CH3OH selectivity, with an excellent catalytic stability. Chemical kinetics modelling shows that CH3OH in the plasma is mainly produced through radical reactions, i.e., CH4 + O(1D) → CH3O + H, followed by CH3O + H + M→ CH3OH + M and CH3O + HCO → CH3OH + CO. The catalyst characterization shows that the improved production of CH3OH is attributed to abundant chemisorbed oxygen species, originating from highly dispersed NiO phase with strong oxide support interaction with γ-Al2O3, which are capable of promoting CH3OH formation through E-R reactions and activating H2O molecules to facilitate CH3OH desorption.
Keywords: A1 Journal Article;Methane conversion; Plasma catalysis; Selective oxidation; Methanol synthesis; Plasma chemistry; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 9.446
DOI: 10.1016/j.apcatb.2021.120384
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“Plasma-Catalytic Ammonia Reforming of Methane over Cu-Based Catalysts for the Production of HCN and H2at Reduced Temperature”. Yi Y, Wang X, Jafarzadeh A, Wang L, Liu P, He B, Yan J, Zhang R, Zhang H, Liu X, Guo H, Neyts EC, Bogaerts A, Acs Catalysis 11, 1765 (2021). http://doi.org/10.1021/acscatal.0c04940
Abstract: Industrial production of HCN from NH3 and CH4 not only uses precious Pt or Pt−Rh catalysts but also requires extremely high temperatures (∼1600 K). From an energetic, operational, and safety perspective, a drastic decrease in temperature is highly desirable. Here, we report ammonia reforming of methane for the production of HCN and H2 at 673 K by the combination of CH4/NH3 plasma and a supported Cu/silicalite-1 catalyst. 30% CH4 conversion has been achieved with 79% HCN selectivity. Catalyst characterization and plasma diagnostics reveal that the excellent reaction performance is attributed to metallic Cu active sites. In addition, we propose a possible reaction pathway, viz. E-R reactions with N, NH, NH2, and CH radicals produced in the plasma, for the production of HCN, based on density functional theory calculations. Importantly, the Cu/silicalite-1 catalyst costs less than 5% of the commercial Pt mesh catalyst.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 10.614
DOI: 10.1021/acscatal.0c04940
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“Titanium (germano-)silicides featuring 10-9 Ω.cm2 contact resistivity and improved compatibility to advanced CMOS technology”. Yu H, Schaekers M, Chew SA, Eyeraert J-L, Dabral A, Pourtois G, Horiguchi N, Mocuta D, Collaert N, De Meyer K, 2018 18th International Workshop On Junction Technology (iwjt) , 80 (2018)
Abstract: uIn this work, we discuss three novel Ti (germano-)silicidation techniques featuring respectively the pre-contact amorphization implantation (PCAI), the TiSi co-deposition, and Ti atomic layer deposition (ALD). All three techniques form TiSix(Ge-y) contacts with ultralow contact resistivity (rho(c)) of (1-3)x10(-9) Omega.cm(2) on both highly doped n-Si and p-SiGe substrates: these techniques meet rho(c) requirement of 5-14 nm CMOS technology and feature unified CMOS contact solutions. We further discuss the compatibility of these techniques to the realistic CMOS transistor fabrication.
Keywords: P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Electron acceleration by an intense short-pulse laser in underdense plasma”. Yu MY, Yu W, Chen ZY, Zhang J, Yin Y, Cao LH, Lu PX, Xu ZZ, Physics of plasmas 10, 2468 (2003). http://doi.org/10.1063/1.1572158
Abstract: Electron acceleration from the interaction of an intense short-pulse laser with low density plasma is considered. The relation between direct electron acceleration within the laser pulse and that in the wake is investigated analytically. The magnitude and location of the ponderomotive-force-caused charge separation field with respect to that of the pulse determine the relative effectiveness of the two acceleration mechanisms. It is shown that there is an optimum condition for acceleration in the wake. Electron acceleration within the pulse dominates as the pulse becomes sufficiently short, and the latter directly drives and even traps the electrons. The latter can reach ultrahigh energies and can be extracted by impinging the pulse on a solid target. (C) 2003 American Institute of Physics.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.115
Times cited: 41
DOI: 10.1063/1.1572158
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“Long-distance channeling and focusing of lasers in plasmas”. Yuan X, Yu W, Yu MY, Chen ZY, Liu JR, Lu PX, Li RX, Qian LJ, Lu BD, Physica scripta 66, 381 (2002). http://doi.org/10.1238/Physica.Regular.066a00381
Abstract: The propagation of a short laser beam in plasma is investigated analytically Relativistic ponderomotive force and space charge effects are included, and an equation describing the evolution of the laser spot size is derived. It is shown that self-consistent electron cavitation can lead to self channelling and thus long-distance self-focusing of the laser. The condition for the latter to occur is given.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.28
Times cited: 2
DOI: 10.1238/Physica.Regular.066a00381
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“Numerical simulation on particle density and reaction pathways in methane needle-plane discharge plasma at atmospheric pressure”. Yue-Feng Z, Chao W, Wang W-Z, Li L, Hao S, Tao S, Jie P, Wuli xuebao 67, 085202 (2018). http://doi.org/10.7498/APS.67.20172192
Abstract: Methane needle-plane discharge has practical application prospect and scientific research significance since methane conversion heavy oil hydrogenation is formed by coupling methane needle-plane discharge with heavy oil hydrogenation, which can achieve high-efficient heavy oil hydrogenation and increase the yields of high value-added light olefins. In this paper, a two-dimensional fluid model is built up for numerically simulating the methane needle-plane discharge plasma at atmospheric pressure. Spatial and axial distributions of electric intensity, electron temperature and particle densities are obtained. Reaction yields are summarized and crucial pathways to produce various kinds of charged and neutral particles are found out. Simulation results indicate that axial evolutions of CH3+ and CH4+ densities, electric intensity and electron temperature are similar and closely related. The CH5+ and C2H5+ densities first increase and then decrease along the axial direction. The CH3 and H densities have nearly identical spatial and axial distributions. Particle density distributions of CH2, C2H4 and C2H5 are obviously different in the area near the cathode but comparatively resemblant in the positive column region. The CH3+ and CH4+ are produced by electron impact ionizations between electrons and CH4. The CH5+ and C2H5+ are respectively generated by molecular impact dissociations between CH3+ and CH4 and between CH4+ and CH4. Electron impact decomposition between electrons and CH4 is a dominated reaction to produce CH3, CH2, CH and H. The reactions between CH2 and CH4 and between electrons and C2H4 are critical pathways to produce C2H4 and C2H2, respectively. In addition, the yields of electron impact decomposition reactions between electrons and CH4 and reactions between CH2 and CH4 account for 52.15% and 47.85% of total yields of H-2 respectively.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 0.624
DOI: 10.7498/APS.67.20172192
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Yusupov M (2014) Atomic scale simulations for a better insight in plasma medicine. Antwerpen
Keywords: Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Plasma-induced destruction of bacterial cell wall components : a reactive molecular dynamics simulation”. Yusupov M, Bogaerts A, Huygh S, Snoeckx R, van Duin ACT, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 117, 5993 (2013). http://doi.org/10.1021/jp3128516
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 59
DOI: 10.1021/jp3128516
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“Behavior of electrons in a dual-magnetron sputter deposition system : a Monte Carlo model”. Yusupov M, Bultinck E, Depla D, Bogaerts A, New journal of physics 13, 033018 (2011). http://doi.org/10.1088/1367-2630/13/3/033018
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.786
Times cited: 12
DOI: 10.1088/1367-2630/13/3/033018
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“Elucidating the asymmetric behavior of the discharge in a dual magnetron sputter deposition system”. Yusupov M, Bultinck E, Depla D, Bogaerts A, Applied physics letters 98, 131502 (2011). http://doi.org/10.1063/1.3574365
Abstract: A magnetron discharge is characterized by drifts of the charged particles guiding center, caused by the magnetic field, in contrast to unmagnetized discharges. Because of these drifts, a pronounced asymmetry of the discharge can be observed in a dual magnetron setup. In this work, it is found that the shape of the discharge in a dual magnetron configuration depends on the magnetic field configuration. In a closed configuration, strong drifts were observed in one preferential direction, whereas in a mirror configuration the deflection of the discharge was not so pronounced. Our calculations confirm experimental observations.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.411
Times cited: 4
DOI: 10.1063/1.3574365
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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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“Impact of plasma oxidation on structural features of human epidermal growth factor”. Yusupov M, Lackmann J-W, Razzokov J, Kumar S, Stapelmann K, Bogaerts A, Plasma processes and polymers 15, 1800022 (2018). http://doi.org/10.1002/ppap.201800022
Abstract: We perform computer simulations supported by experiments to investigate the oxidation of an important signaling protein, that is, human epidermal growth factor (hEGF), caused by cold atmospheric plasma (CAP) treatment. Specifically, we study the conformational changes of hEGF with different degrees of oxidation, to mimic short and long CAP treatment times. Our results indicate that the oxidized structures become more flexible, due to their conformational changes and breakage of the disulfide bonds, especially at higher oxidation degrees. MM/GBSA calculations reveal that an increasing oxidation level leads to a lower binding free energy of hEGF with its receptor. These results help to understand the fundamentals of the use of CAP for wound healing versus cancer treatment at short and longer treatment times.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 7
DOI: 10.1002/ppap.201800022
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“Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls”. Yusupov M, Neyts EC, Khalilov U, Snoeckx R, van Duin ACT, Bogaerts A, New journal of physics 14, 093043 (2012). http://doi.org/10.1088/1367-2630/14/9/093043
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.786
Times cited: 47
DOI: 10.1088/1367-2630/14/9/093043
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“Reactive molecular dynamics simulations of oxygen species in a liquid water layer of interest for plasma medicine”. Yusupov M, Neyts EC, Simon P, Berdiyorov G, Snoeckx R, van Duin ACT, Bogaerts A, Journal of physics: D: applied physics 47, 025205 (2014). http://doi.org/10.1088/0022-3727/47/2/025205
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 51
DOI: 10.1088/0022-3727/47/2/025205
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“Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species : a reactive molecular dynamics study”. Yusupov M, Neyts EC, Verlackt CC, Khalilov U, van Duin ACT, Bogaerts A, Plasma processes and polymers 12, 162 (2015). http://doi.org/10.1002/ppap.201400064
Abstract: Reactive molecular dynamics simulations are performed to study the interaction of reactive oxygen species, such as OH, HO2 and H2O2, with the endotoxic biomolecule lipid A of the gram-negative bacterium Escherichia coli. It is found that the aforementioned plasma species can destroy the lipid A, which consequently results in reducing its toxic activity. All bond dissociation events are initiated by hydrogen-abstraction reactions. However, the mechanisms behind these dissociations are dependent on the impinging plasma species, i.e. a clear difference is observed in the mechanisms upon impact of HO2 radicals and H2O2 molecules on one hand and OH radicals on the other hand. Our simulation results are in good agreement with experimental observations.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 18
DOI: 10.1002/ppap.201400064
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“Oxidative damage to hyaluronan–CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy”. Yusupov M, Privat-Maldonado A, Cordeiro RM, Verswyvel H, Shaw P, Razzokov J, Smits E, Bogaerts A, Redox Biology 43, 101968 (2021). http://doi.org/10.1016/j.redox.2021.101968
Abstract: Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44–HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44–HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44–HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Impact Factor: 6.337
DOI: 10.1016/j.redox.2021.101968
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“Transport of Reactive Oxygen and Nitrogen Species across Aquaporin: A Molecular Level Picture”. Yusupov M, Razzokov J, Cordeiro RM, Bogaerts A, Oxidative medicine and cellular longevity 2019, 1 (2019). http://doi.org/10.1155/2019/2930504
Abstract: Aquaporins (AQPs) are transmembrane proteins that conduct not only water molecules across the cell membrane but also other solutes, such as reactive oxygen and nitrogen species (RONS), produced (among others) by cold atmospheric plasma (CAP). These RONS may induce oxidative stress in the cell interior, which plays a role in cancer treatment. The underlying mechanisms of the transport of RONS across AQPs, however, still remain obscure. We apply molecular dynamics simulations to investigate the permeation of both hydrophilic (H<sub>2</sub>O<sub>2</sub>and OH) and hydrophobic (NO<sub>2</sub>and NO) RONS through AQP1. Our simulations show that these RONS can all penetrate across the pores of AQP1. The permeation free energy barrier of OH and NO is lower than that of H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>, indicating that these radicals may have easier access to the pore interior and interact with the amino acid residues of AQP1. We also study the effect of RONS-induced oxidation of both the phospholipids and AQP1 (i.e., sulfenylation of Cys<sub>191</sub>) on the transport of the above-mentioned RONS across AQP1. Both lipid and protein oxidation seem to slightly increase the free energy barrier for H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>permeation, while for OH and NO, we do not observe a strong effect of oxidation. The simulation results help to gain insight in the underlying mechanisms of the noticeable rise of CAP-induced RONS in cancer cells, thereby improving our understanding on the role of AQPs in the selective anticancer capacity of CAP.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.593
Times cited: 5
DOI: 10.1155/2019/2930504
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“Sputter deposition of MgxAlyOz thin films in a dual-magnetron device : a multi-species Monte Carlo model”. Yusupov M, Saraiva M, Depla D, Bogaerts A, New journal of physics 14, 073043 (2012). http://doi.org/10.1088/1367-2630/14/7/073043
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.786
Times cited: 2
DOI: 10.1088/1367-2630/14/7/073043
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“Synergistic effect of electric field and lipid oxidation on the permeability of cell membranes”. Yusupov M, Van der Paal J, Neyts EC, Bogaerts A, Biochimica et biophysica acta : G : general subjects 1861, 839 (2017). http://doi.org/10.1016/j.bbagen.2017.01.030
Abstract: Background: Strong electric fields are knownto affect cell membrane permeability,which can be applied for therapeutic purposes, e.g., in cancer therapy. A synergistic enhancement of this effect may be accomplished by the presence of reactive oxygen species (ROS), as generated in cold atmospheric plasmas. Little is known about the synergy between lipid oxidation by ROS and the electric field, nor on howthis affects the cell membrane permeability.
Method: We here conduct molecular dynamics simulations to elucidate the dynamics of the permeation process under the influence of combined lipid oxidation and electroporation. A phospholipid bilayer (PLB), consisting of di-oleoyl-phosphatidylcholine molecules covered with water layers, is used as a model system for the plasma membrane.
Results and conclusions:Weshow howoxidation of the lipids in the PLB leads to an increase of the permeability of the bilayer to ROS, although the permeation free energy barriers still remain relatively high. More importantly, oxidation of the lipids results in a drop of the electric field threshold needed for pore formation (i.e., electroporation) in the PLB. The created pores in the membrane facilitate the penetration of reactive plasma species deep into the cell interior, eventually causing oxidative damage.
General significance: This study is of particular interest for plasma medicine, as plasma generates both ROS and electric fields, but it is also of more general interest for applications where strong electric fields and ROS both come into play.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.702
DOI: 10.1016/j.bbagen.2017.01.030
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“Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments”. Yusupov M, Wende K, Kupsch S, Neyts EC, Reuter S, Bogaerts A, Scientific reports 7, 5761 (2017). http://doi.org/10.1038/s41598-017-06412-8
Abstract: We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.259
Times cited: 27
DOI: 10.1038/s41598-017-06412-8
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“Atomic scale simulation of H2O2permeation through aquaporin: toward the understanding of plasma cancer treatment”. Yusupov M, Yan D, Cordeiro RM, Bogaerts A, Journal of physics: D: applied physics 51, 125401 (2018). http://doi.org/10.1088/1361-6463/aaae7a
Abstract: Experiments have demonstrated the potential selective anticancer capacity of cold atmospheric plasmas (CAPs), but the underlying mechanisms remain unclear. Using computer simulations, we try to shed light on the mechanism of selectivity, based on aquaporins (AQPs), i.e. transmembrane protein channels transferring external H 2 O 2 and other reactive oxygen species, created e.g. by CAPs, to the cell interior. Specifically, we perform molecular dynamics simulations for the permeation of H 2 O 2 through AQP1 (one of the members of the AQP family) and the palmitoyl-oleoyl-phosphatidylcholine (POPC) phospholipid bilayer (PLB). The free energy barrier of H 2 O 2 across AQP1 is lower than for the POPC PLB, while the permeability coefficient, calculated using the free energy and diffusion rate profiles, is two orders of magnitude higher. This indicates that the delivery of H 2 O 2 into the cell interior should be through AQP. Our study gives a better insight into the role of AQPs in the selectivity of CAPs for treating cancer cells.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 7
DOI: 10.1088/1361-6463/aaae7a
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“Synergism of the initial stage of removal of dielectric materials during electrical erosion processing in electrolytes”. Zaripov AA, Khalilov UB, Ashurov KB, Surface engineering and applied electrochemistry 59, 712 (2023). http://doi.org/10.3103/S1068375523060194
Abstract: Ceramics and composites, many of whose physicochemical properties significantly exceed similar properties of metals and their alloys, are processed qualitatively mainly by the electroerosion method. Despite the existing works, the mechanism of the initial stage of the removal of materials has not yet been identified. For a comprehensive understanding of the mechanism of the removal of dielectrics, a new model is proposed based on the experimental results obtained on an improved electroerosion installation. It was revealed that the initial stage of the removal of a dielectric material consists of three successive stages that are associated with the synergistic effect on the process of the anionic group of electrolytes, plasma flare, and the cavitation shock. This makes it possible to better understand the mechanism of the removal of composite and ceramic materials, which should contribute to ensuring the machinability of those materials and their wide use in promising technologies.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.3103/S1068375523060194
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“De belofte van hoofdhalskankerorganoïden in kankeronderzoek : een blik op de toekomst”. Zaryouh H, Verswyvel H, Bauwens M, Van Haesendonck G, Deben C, Lin A, De Waele J, Vermorken JB, Koljenovic S, Bogaerts A, Lardon F, Smits E, Wouters A, Onco-hemato : multidisciplinair tijdschrift voor oncologie 17, 54 (2023)
Abstract: Hoofd-halskanker vormt een aanzienlijke uitdaging met bijna 900.000 nieuwe diagnoses per jaar, waarbij de jaarlijkse incidentie blijft stijgen. Vaak wordt de diagnose pas in een laat stadium gesteld, wat complexe behandelingen noodzakelijk maakt. Terugval van patiënten is helaas een veelvoorkomend probleem. De gemiddelde overlevingsduur is beperkt tot enkele maanden. Daarom is er een dringende behoefte om nieuwe, veelbelovende behandelingen te ontwikkelen voor patiënten met hoofd-halskanker. Voor het bereiken van deze vooruitgang spelen innovatieve studiemodellen een cruciale rol. Het ontwikkelen van deze nieuwe behandelingen start met laboratoriumonderzoek, waarbij traditionele tweedimensionale celculturen hun beperkingen hebben. Daarom verschuiven onderzoekers hun aandacht meer en meer naar geavanceerdere driedimensionale modellen, met hoofd-halskankerorganoïden als beloftevol nieuw model. Dit model behoudt immers zowel het genetische profiel als de morfologische kenmerken van de originele tumor van de hoofd-halskankerpatiënt. Hoofdhalskankerorganoïden bieden daarom de mogelijkheid om innovatieve behandelingen te testen en kunnen mogelijk zelfs de respons van een patiënt op bepaalde therapieën voorspellen. Hoewel tumororganoïden als ‘patiënt-in-het-lab’ veelbelovend zijn, zijn er uitdagingen te overwinnen, zoals de ontwikkelingstijd en de toepasbaarheid bij alle tumortypes, evenals het ontbreken van immuuncellen en andere micro-omgevingscomponenten. Er is daarom een grote behoefte aan gestandaardiseerde protocollen voor de ontwikkeling van organoïden en verkorting van de ontwikkelingstijd. Concluderend bieden driedimensionale hoofd-halskankerorganoïden een veelbelovend perspectief voor de toekomst van kankerbehandelingen. Ze hebben het potentieel om bij te dragen aan de ontwikkeling van gepersonaliseerde behandelingen en zo de overlevingskansen van kankerpatiënten te verbeteren. Het is echter belangrijk om hun voorspellend vermogen en toepassingsmogelijkheden verder te onderzoeken, voordat ze op grote schaal worden geïmplementeerd.
Keywords: A2 Journal article; Center for Oncological Research (CORE); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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Zhang H (2020) Optical diagnostics of spatiotemporal evolution characteristics of nanosecond laser-induced plasma in gases. 117 p
Keywords: Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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