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“Feature Papers to Celebrate “Environmental Catalysis”—Trends &, Outlook”. Lamonier J-F, Bogaerts A, Catalysts 12, 720 (2022). http://doi.org/10.3390/catal12070720
Abstract: This Special Issue collects three reviews, eight articles, and two communications related to the design of catalysts for environmental applications, such as the transformation of several pollutants into harmless or valuable products [...]
Keywords: Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.9
DOI: 10.3390/catal12070720
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“Chemical fingerprints of cold physical plasmas &ndash, an experimental and computational study using cysteine as tracer compound”. Lackmann J-W, Wende K, Verlackt C, Golda J, Volzke J, Kogelheide F, Held J, Bekeschus S, Bogaerts A, Schulz-von der Gathen V, Stapelmann K, Scientific reports 8, 7736 (2018). http://doi.org/10.1038/s41598-018-25937-0
Abstract: Reactive oxygen and nitrogen species released by cold physical plasma are being proposed as effectors in various clinical conditions connected to inflammatory processes. As these plasmas can be tailored in a wide range, models to compare and control their biochemical footprint are desired to infer on the molecular mechanisms underlying the observed effects and to enable the discrimination between different plasma sources. Here, an improved model to trace short-lived reactive species is presented. Using FTIR, high-resolution mass spectrometry, and molecular dynamics computational simulation, covalent modifications of cysteine treated with different plasmas were deciphered and the respective product pattern used to generate a fingerprint of each plasma source. Such, our experimental model allows a fast and reliable grading of the chemical potential of plasmas used for medical purposes. Major reaction products were identified to be cysteine sulfonic acid, cystine, and cysteine fragments. Less abundant products, such as oxidized cystine derivatives or S-nitrosylated cysteines, were unique to different plasma sources or operating conditions. The data collected point at hydroxyl radicals, atomic O, and singlet oxygen as major contributing species that enable an impact on cellular thiol groups when applying cold plasma in vitro or in vivo.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.259
Times cited: 19
DOI: 10.1038/s41598-018-25937-0
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“Enhancement of cellular glucose uptake by reactive species: a promising approach for diabetes therapy”. Kumar N, Shaw P, Razzokov J, Yusupov M, Attri P, Uhm HS, Choi EH, Bogaerts A, RSC advances 8, 9887 (2018). http://doi.org/10.1039/C7RA13389H
Abstract: It is generally known that antidiabetic activity is associated with an increased level of glucose uptake in adipocytes and skeletal muscle cells. However, the role of exogenous reactive oxygen and nitrogen species (RONS) in muscle development and more importantly in glucose uptake is largely unknown. We investigate the effect of RONS generated by cold atmospheric plasma (CAP) in glucose uptake. We show that the glucose uptake is significantly enhanced in differentiated L6 skeletal muscle cells after CAP treatment. We also observe a significant increase of the intracellular Ca++ and ROS level, without causing toxicity. One of the possible reasons for an elevated level of glucose uptake as well as intracellular ROS and Ca++ ions is probably the increased oxidative stress leading to glucose transport.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.108
Times cited: 1
DOI: 10.1039/C7RA13389H
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“Physical plasma-derived oxidants sensitize pancreatic cancer cells to ferroptotic cell death”. Kumar N, Perez-Novo C, Shaw P, Logie E, Privat-Maldonado A, Dewilde S, Smits E, Berghe WV, Bogaerts A, Free Radical Biology And Medicine 166, 187 (2021). http://doi.org/10.1016/j.freeradbiomed.2021.02.026
Abstract: Despite modern therapeutic advances, the survival prospects of pancreatic cancer patients remain poor, due to chemoresistance and dysregulated oncogenic kinase signaling networks. We applied a novel kinome activitymapping approach using biological peptide targets as phospho-sensors to identify vulnerable kinase dependencies for therapy sensitization by physical plasma. Ser/Thr-kinome specific activity changes were mapped upon induction of ferroptotic cell death in pancreatic tumor cells exposed to reactive oxygen and nitrogen species of plasma-treated water (PTW). This revealed a broad kinome activity response involving the CAMK, the AGC and CMGC family of kinases. This systems-level kinome network response supports stress adaptive switches between chemoresistant anti-oxidant responses of Kelch-like ECH-associated protein 1 (KEAP1)/Heme Oxygenase 1 (HMOX1) and ferroptotic cell death sensitization upon suppression of Nuclear factor (erythroid derived 2)-like 2 (NRF2) and Glutathione peroxidase 4 (GPX4). This is further supported by ex vivo experiments in the chicken chorioallantoic membrane assay, showing decreased GPX4 and Glutathione (GSH) expression as well as increased lipid peroxidation, along with suppressed BxPC-3 tumor growth in response to PTW. Taken all together, we demonstrate that plasma treated water-derived oxidants sensitize pancreatic cancer cells to ferroptotic cell death by targeting a NRF2-HMOX1-GPX4 specific kinase signaling network.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Impact Factor: 5.606
DOI: 10.1016/j.freeradbiomed.2021.02.026
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“Inactivation of human pancreatic ductal adenocarcinoma with atmospheric plasma treated media and water: a comparative study”. Kumar N, Attri P, Dewilde S, Bogaerts A, Journal of physics: D: applied physics 51, 255401 (2018). http://doi.org/10.1088/1361-6463/aac571
Abstract: In recent years, the interest in treating cancer cells with plasma treated media (PTM) and plasma treated water (PTW) has increased tremendously. However, the actions of PTM and PTW are still not entirely understood. For instance, it is not clear whether the action of PTM is due to a modification in proteins/amino acids after plasma treatment of the media, or due to reactive oxygen and nitrogen species (RONS) generated from the plasma, or a combination of both effects. To differentiate between the actions of RONS and modified proteins/amino acids on the treatment of cancer cells, we compared the effects of PTM and PTW on two different pancreatic ductal adenocarcinomas (MiaPaca-2, BxPc3) and pancreatic stellate cells
(PSCs) (hPSC128-SV). PSCs closely interact with cancer cells to create a tumor-promoting environment that stimulates local tumor progression and metastasis. We treated culture media and deionized water with a cold atmospheric plasma (CAP) jet, and subsequently applied this PTM/PTW at various ratios to the pancreatic cancer and PSC cell lines. We evaluated cell death, intracellular ROS concentrations and the mRNA expression profiles of four oxidative stress-related genes, i.e. Mitogen-activated protein kinase 7 (MAPK7), B-cell lymphoma 2 (BCL2), Checkpoint kinase 1 (CHEK1) and DNA damage-inducible transcript 3, also known as C/EBP homologous protein (CHOP). Our findings demonstrate that PTM and PTW have a similar efficacy to kill pancreatic cancer cells, while PTW is slightly more effective in killing PSCs, as compared to PTM. Furthermore, we observed an enhancement of the intracellular ROS concentrations in both pancreatic cancer cells and PSCs. Thus, it is likely that under our experimental conditions, the anti-cancer activity of PTM can be attributed more to the RONS present in the treated liquid, than to the modification of proteins/amino acids in the media. Furthermore, the fact that the chemo-resistant PSCs were killed by PTM/PTW may offer possibilities for new anti-cancer therapies for pancreatic cancer cells, including PSCs.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 6
DOI: 10.1088/1361-6463/aac571
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“Evaluation of the energy efficiency of CO2 conversion in microwave discharges using a reaction kinetics model”. Kozák T, Bogaerts A, Plasma sources science and technology 24, 015024 (2015). http://doi.org/10.1088/0963-0252/24/1/015024
Abstract: We use a zero-dimensional reaction kinetics model to simulate CO2 conversion in microwave discharges where the excitation of the vibrational levels plays a significant role in the dissociation kinetics. The model includes a description of the CO2 vibrational kinetics, taking into account state-specific VT and VV relaxation reactions and the effect of vibrational excitation on other chemical reactions. The model is used to simulate a general tubular microwave reactor, where a stream of CO2 flows through a plasma column generated by microwave radiation. We study the effects of the internal plasma parameters, namely the reduced electric field, electron density and the total specific energy input, on the CO2 conversion and its energy efficiency. We report the highest energy efficiency (up to 30%) for a specific energy input in the range 0.41.0 eV/molecule and a reduced electric field in the range 50100 Td and for high values of the electron density (an ionization degree greater than 10−5). The energy efficiency is mainly limited by the VT relaxation which contributes dominantly to the vibrational energy losses and also contributes significantly to the heating of the reacting gas. The model analysis provides useful insight into the potential and limitations of CO2 conversion in microwave discharges.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 100
DOI: 10.1088/0963-0252/24/1/015024
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“Splitting of CO2 by vibrational excitation in non-equilibrium plasmas : a reaction kinetics model”. Kozák T, Bogaerts A, Plasma sources science and technology 23, 045004 (2014). http://doi.org/10.1088/0963-0252/23/4/045004
Abstract: We present a zero-dimensional kinetic model of CO2 splitting in non-equilibrium plasmas. The model includes a description of the CO2 vibrational kinetics (25 vibrational levels up to the dissociation limit of the molecule), taking into account state-specific VT and VV relaxation reactions and the effect of vibrational excitation on other chemical reactions. The model is applied to study the reaction kinetics of CO2 splitting in an atmospheric-pressure dielectric barrier discharge (DBD) and in a moderate-pressure microwave discharge. The model results are in qualitative agreement with published experimental works. We show that the CO2 conversion and its energy efficiency are very different in these two types of discharges, which reflects the important dissociation mechanisms involved. In the microwave discharge, excitation of the vibrational levels promotes efficient dissociation when the specific energy input is higher than a critical value (2.0 eV/molecule under the conditions examined). The calculated energy efficiency of the process has a maximum of 23%. In the DBD, vibrationally excited levels do not contribute significantly to the dissociation of CO2 and the calculated energy efficiency of the process is much lower (5%).
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 170
DOI: 10.1088/0963-0252/23/4/045004
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“Quasi-Neutral Modeling of Gliding Arc Plasmas: Quasi-Neutral Modeling of Gliding Arc Plasmas”. Kolev S, Sun S, Trenchev G, Wang W, Wang H, Bogaerts A, Plasma processes and polymers 14, 1600110 (2017). http://doi.org/10.1002/ppap.201600110
Abstract: The modelling of a gliding arc discharge (GAD) is studied by means of the quasineutral (QN) plasma modelling approach. The model is first evaluated for reliability and proper description of a gliding arc discharge at atmospheric pressure, by comparing with a more elaborate non-quasineutral (NQN) plasma model in two different geometries – a 2D axisymmetric and a Cartesian geometry. The NQN model is considered as a reference, since it provides a continuous self-consistent plasma description, including the near electrode regions. In general, the results of the QN model agree very well with those obtained from the NQN model. The small differences between both models are attributed to the approximations in the derivation of the QN model. The use of the QN model provides a substantial reduction of the computation time compared to the NQN model, which is crucial for the development of more complex models in three dimensions or with complicated chemistries. The latter is illustrated for (i) a reverse vortex flow(RVF) GAD in argon, and (ii) a GAD in CO2. The RVF discharge is modelled in three dimensions and the effect of the turbulent heat transport on the plasma and gas characteristics is
discussed. The GAD model in CO2 is in a 1D geometry with axial symmetry and provides results for the time evolution of the electron, gas and vibrational temperature of CO2, as well as for the molar fractions of the different species.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 9
DOI: 10.1002/ppap.201600110
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“Modeling the CO2 dissociation in pulsed atmospheric-pressure discharge”. Kolev S, Paunska T, Trenchev G, Bogaerts A, Technologies , 012007 (2020). http://doi.org/10.1088/1742-6596/1492/1/012007
Abstract: CO2 dissociation and its subsequent conversion into added-value chemicals is a promising strategy for recycling CO2 gas into reusable products. One of the possible methods is direct plasma-induced dissociation. In this work we study the efficiency of CO2 dissociation in pulsed atmospheric-pressure gas discharge between two conducting electrodes by a 0-D numerical plasma model. The purpose of the study is to provide results on the optimal conditions of CO2 conversion with respect to the energy efficiency and dissociation by varying the maximum power density value and the pulse length. The power density is directly related to the discharge current and the reduced electric field in the discharge. We consider pulse lengths in the range from hundreds of nanosecond up to milliseconds. The results obtained show that the dissociation degree and energy efficiency are sensitive to the pulse length (duration) and the power density, so that a considerable improvement of the discharge performance can be achieved by fine-tuning these parameters. The study is intended to provide guidance in designing an experimental set-up and a power supply with the characteristics necessary to achieve optimal conversion.
Keywords: P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.1088/1742-6596/1492/1/012007
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“A 2D model for a gliding arc discharge”. Kolev S, Bogaerts A, Plasma sources science and technology 24, 015025 (2015). http://doi.org/10.1088/0963-0252/24/1/015025
Abstract: In this study we report on a 2D fluid model of a gliding arc discharge in argon. Despite the 3D nature of the discharge, 2D models are found to be capable of providing very useful information about the operation of the discharge. We employ two modelsan axisymmetric and a Cartesian one. We show that for the considered experiment and the conditions of a low current arc (around 30 mA) in argon, there is no significant heating of the cathode surface and the discharge is sustained by field electron emission from the cathode accompanied by the formation of a cathode spot. The obtained discharge power and voltage are relatively sensitive to the surface properties and particularly to the surface roughness, causing effectively an amplification of the normal electric field. The arc body and anode region are not influenced by this and depend mainly on the current value. The gliding of the arc is modelled by means of a 2D Cartesian model. The arcelectrode contact points are analysed and the gliding mechanism along the electrode surface is discussed. Following experimental observations, the cathode spot is simulated as jumping from one point to another. A complete arc cycle is modelled from initial ignition to arc decay. The results show that there is no interaction between the successive gliding arcs.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 34
DOI: 10.1088/0963-0252/24/1/015025
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“Similarities and differences between gliding glow and gliding arc discharges”. Kolev S, Bogaerts A, Plasma sources science and technology 24, 065023 (2015). http://doi.org/10.1088/0963-0252/24/6/065023
Abstract: In this work we have analyzed the properties of a gliding dc discharge in argon at atmospheric pressure. Despite the usual designation of these discharges as ‘gliding arc discharges’, it was found previously that they operate in two different regimes—glow and arc. Here we analyze the differences in both regimes by means of two dimensional fluid modeling. In order to address different aspects of the discharge operation, we use two models—Cartesian and axisymmetric in a cylindrical coordinate system. The obtained results show that the two types of discharges produce a similar plasma column for a similar discharge current. However, the different mechanisms of plasma channel attachment to the cathode could produce certain differences in the plasma parameters (i.e. arc elongation), and this can affect gas treatments applications.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 12
DOI: 10.1088/0963-0252/24/6/065023
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“Three-dimensional modeling of energy transport in a gliding arc discharge in argon”. Kolev S, Bogaerts A, Plasma Sources Science &, Technology 27, 125011 (2018). http://doi.org/10.1088/1361-6595/aaf29c
Abstract: In this work we study energy transport in a gliding arc discharge with two diverging flat
electrodes in argon gas at atmospheric pressure. The discharge is ignited at the shortest electrode
gap and it is pushed downstream by a forced gas flow. The current values considered are
relatively low and therefore a non-equilibrium plasma is produced. We consider two cases, i.e.
with high and low discharge current (28 mA and 2.8mA), and a constant gas flow of 10 lmin −1 ,
with a significant turbulent component to the velocity. The study presents an analysis of the
various energy transport mechanisms responsible for the redistribution of Joule heating to the
plasma species and the moving background gas. The objective of this work is to provide a
general understanding of the role of the different energy transport mechanisms in arc formation
and sustainment, which can be used to improve existing or new discharge designs. The work is
based on a three-dimensional numerical model, combining a fluid plasma model, the shear stress
transport Reynolds averaged Navier–Stokes turbulent gas flow model, and a model for gas
thermal balance. The obtained results show that at higher current the discharge is constricted
within a thin plasma column several hundred kelvin above room temperature, while in the low-
current discharge the combination of intense convective cooling and low Joule heating prevents
discharge contraction and the plasma column evolves to a static non-moving diffusive plasma,
continuously cooled by the flowing gas. As a result, the energy transport in the two cases is
determined by different mechanisms. At higher current and a constricted plasma column, the
plasma column is cooled mainly by turbulent transport, while at low current and an unconstricted
plasma, the major cooling mechanism is energy transport due to non-turbulent gas convection. In
general, the study also demonstrates the importance of turbulent energy transport in
redistributing the Joule heating in the arc and its significant role in arc cooling and the formation
of the gas temperature profile. In general, the turbulent energy transport lowers the average gas
temperature in the arc, thus allowing additional control of thermal non-equilibrium in the
discharge.
Keywords: A1 Journal Article; gliding arc discharge, sliding arc discharge, energy transport, fluid plasma model, atmospheric pressure plasmas; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 3.302
DOI: 10.1088/1361-6595/aaf29c
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“Influence of electron recapture by the cathode upon the discharge characteristics in dc planar magnetrons”. Kolev I, Bogaerts A, Gijbels R, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 72, 056402 (2005). http://doi.org/10.1103/PhysRevE.72.056402
Abstract: In dc magnetrons the electrons emitted from the cathode may return there due to the applied magnetic field. When that happens, they can be recaptured or reflected back into the discharge, depending on the value of the reflection coefficient (RC). A 2d3v (two-dimensional in coordinate and three-dimensional in velocity space) particle-in-cellMonte Carlo model, including an external circuit, is developed to determine the role of the electron recapture in the discharge processes. The detailed discharge structure as a function of RC for two pressures (4 and 25mtorr) is studied. The importance of electron recapture is clearly manifested, especially at low pressures. The results indicate that the discharge characteristics are dramatically changed with varying RC between 0 and 1. Thus, the electron recapture at the cathode appears to be a significant mechanism in magnetron discharges and RC a very important parameter in their correct quantitative description that should be dealt with cautiously.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 29
DOI: 10.1103/PhysRevE.72.056402
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“Calculation of gas heating in a dc sputter magnetron”. Kolev I, Bogaerts A, Journal of applied physics 104, 093301 (2008). http://doi.org/10.1063/1.2970166
Abstract: The effect of gas heating in laboratory sputter magnetrons is investigated by means of numerical modeling. The model is two-dimensional in the coordinate space and three-dimensional in the velocity space based on the particle-in-cellMonte Carlo collisions technique. It is expanded in a way that allows the inclusion of the neutral plasma particles (fast gas atoms and sputtered atoms), which makes it possible to calculate the gas temperature and its influence on the discharge behavior in a completely self-consistent way. The results of the model are compared to experimental measurements and to other existing simulation results. The results show that gas heating is pressure dependent (rising with the increase in the gas pressure) and should be taken into consideration at pressures above 10 mTorr.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.068
Times cited: 19
DOI: 10.1063/1.2970166
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“Detailed numerical investigation of a DC sputter magnetron”. Kolev I, Bogaerts A, IEEE transactions on plasma science 34, 886 (2006). http://doi.org/10.1109/TPS.2006.875843
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.052
Times cited: 28
DOI: 10.1109/TPS.2006.875843
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“Numerical models of the planar magnetron glow discharges”. Kolev I, Bogaerts A, Contributions to plasma physics 44, 582 (2004). http://doi.org/10.1002/ctpp.200410085
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.44
Times cited: 22
DOI: 10.1002/ctpp.200410085
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“Numerical study of the sputtering in a dc magnetron”. Kolev I, Bogaerts A, Journal of vacuum science and technology: A: vacuum surfaces and films 27, 20 (2009). http://doi.org/10.1021/jp8058992
Abstract: Molecular dynamics simulations were used to investigate the size-dependent melting mechanism of nickel nanoclusters of various sizes. The melting process was monitored by the caloric curve, the overall cluster Lindemann index, and the atomic Lindemann index. Size-dependent melting temperatures were determined, and the correct linear dependence on inverse diameter was recovered. We found that the melting mechanism gradually changes from dynamic coexistence melting to surface melting with increasing cluster size. These findings are of importance in better understanding carbon nanotube growth by catalytic chemical vapor deposition as the phase state of the catalyst nanoparticle codetermines the growth mechanism.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 66
DOI: 10.1021/jp8058992
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“PIC –, MCC numerical simulation of a DC planar magnetron”. Kolev I, Bogaerts A, Plasma processes and polymers 3, 127 (2006). http://doi.org/10.1002/ppap.200500118
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 27
DOI: 10.1002/ppap.200500118
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“A Comprehensive Chemical Model for the Splitting of CO2in Non-Equilibrium Plasmas: A Comprehensive Chemical Model for CO2Splitting”. Koelman P, Heijkers S, Tadayon Mousavi S, Graef W, Mihailova D, Kozak T, Bogaerts A, van Dijk J, Plasma processes and polymers 14, 1600155 (2017). http://doi.org/10.1002/ppap.201600155
Abstract: An extensive CO2 plasmamodel is presented that is relevant for the production of ‘‘solar fuels.’’ It is based on reaction rate coefficients fromrigorously reviewed literature, and is augmented with reactionrate coefficients that are obtained fromscaling laws.The input data set,which is suitable for usage with the plasma simulation software Plasimo (https://plasimo.phys.tue.nl/), is available via the Plasimo and publisher’s websites.1 The correctness of this model implementation has been established by independent ZDPlasKin implementation (http://www.zdplaskin.
laplace.univ-tlse.fr/), to verify that the results agree. Results of these ‘‘global models’’ are presented for a DBD plasma reactor.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 21
DOI: 10.1002/ppap.201600155
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“Elucidation of plasma-induced chemical modifications on glutathione and glutathione disulphide”. Klinkhammer C, Verlackt C, Smilowicz D, Kogelheide F, Bogaerts A, Metzler-Nolte N, Stapelmann K, Havenith M, Lackmann J-W, Scientific reports 7, 13828 (2017). http://doi.org/10.1038/S41598-017-13041-8
Abstract: Cold atmospheric pressure plasmas are gaining increased interest in the medical sector and clinical trials to treat skin diseases are underway. Plasmas are capable of producing several reactive oxygen and nitrogen species (RONS). However, there are open questions how plasma-generated RONS interact on a molecular level in a biological environment, e.g. cells or cell components. The redox pair glutathione (GSH) and glutathione disulphide (GSSG) forms the most important redox buffer in organisms responsible for detoxification of intracellular reactive species. We apply Raman spectroscopy, mass spectrometry, and molecular dynamics simulations to identify the time-dependent chemical modifications on GSH and GSSG that are caused by dielectric barrier discharge under ambient conditions. We find GSSG, S-oxidised glutathione species, and S-nitrosoglutathione as oxidation products with the latter two being the final products, while glutathione sulphenic acid, glutathione sulphinic acid, and GSSG are rather reaction intermediates. Experiments using stabilized pH conditions revealed the same main oxidation products as were found in unbuffered solution, indicating that the dominant oxidative or nitrosative reactions are not influenced by acidic pH. For more complex systems these results indicate that too long treatment times can cause difficult-to-handle modifications to the cellular redox buffer which can impair proper cellular function.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.259
Times cited: 17
DOI: 10.1038/S41598-017-13041-8
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“Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations”. Khosravian N, Kamaraj B, Neyts EC, Bogaerts A, Scientific reports 6, 19466 (2016). http://doi.org/10.1038/srep19466
Abstract: This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.259
Times cited: 7
DOI: 10.1038/srep19466
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“How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations”. Khosravian N, Bogaerts A, Huygh S, Yusupov M, Neyts EC, Biointerphases 10, 029501 (2015). http://doi.org/10.1116/1.4904339
Abstract: The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.603
Times cited: 10
DOI: 10.1116/1.4904339
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“Selective Plasma Oxidation of Ultrasmall Si Nanowires”. Khalilov U, Yusupov M, Bogaerts A, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 120, 472 (2016). http://doi.org/10.1021/acs.jpcc.5b11027
Abstract: Device performance of Si|SiOx core-shell based nanowires critically depends on the exact control over the oxide thickness. Low-temperature plasma oxidation is a highly promising alternative to thermal oxidation allowing for improved control over the oxidation process, in particular for ultrasmall Si nanowires. We here elucidate the room temperature plasma oxidation mechanisms of ultrasmall Si nanowires using hybrid molecular dynamics / force-bias Monte Carlo simulations. We demonstrate how the oxidation and concurrent water formation mechanisms are a function of the oxidizing plasma species and we demonstrate how the resulting core-shell oxide thickness can be controlled through these species. A new mechanism of water formation is discussed in detail. The results provide a detailed atomic level explanation of the oxidation process of highly curved Si surfaces. These results point out a route toward plasma-based formation of ultrathin core-shell Si|SiOx nanowires at room temperature.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 3
DOI: 10.1021/acs.jpcc.5b11027
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“New mechanism for oxidation of native silicon oxide”. Khalilov U, Pourtois G, Huygh S, van Duin ACT, Neyts EC, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 117, 9819 (2013). http://doi.org/10.1021/jp400433u
Abstract: Continued miniaturization of metal-oxide-semiconductor field-effect transistors (MOSFETs) requires an ever-decreasing thickness of the gate oxide. The structure of ultrathin silicon oxide films, however, critically depends on the oxidation mechanism. Using reactive atomistic simulations, we here demonstrate how the oxidation mechanism in hyperthermal oxidation of such structures may be controlled by the oxidation temperature and the oxidant energy. Specifically, we study the interaction of hyperthermal oxygen with energies of 15 eV with thin SiOx (x ≤ 2) films with a native oxide thickness of about 10 Å. We analyze the oxygen penetration depth probability and compare with results of the hyperthermal oxidation of a bare Si(100){2 × 1} (c-Si) surface. The temperature-dependent oxidation mechanisms are discussed in detail. Our results demonstrate that, at low (i.e., room) temperature, the penetrated oxygen mostly resides in the oxide region rather than at the SiOx|c-Si interface. However, at higher temperatures, starting at around 700 K, oxygen atoms are found to penetrate and to diffuse through the oxide layer followed by reaction at the c-Si boundary. We demonstrate that hyperthermal oxidation resembles thermal oxidation, which can be described by the DealGrove model at high temperatures. Furthermore, defect creation mechanisms that occur during the oxidation process are also analyzed. This study is useful for the fabrication of ultrathin silicon oxide gate oxides for metal-oxide-semiconductor devices as it links parameters that can be straightforwardly controlled in experiment (oxygen temperature, velocity) with the silicon oxide structure.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 24
DOI: 10.1021/jp400433u
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“Reactive molecular dynamics simulations on SiO2-coated ultra-small Si-nanowires”. Khalilov U, Pourtois G, Bogaerts A, van Duin ACT, Neyts EC, Nanoscale 5, 719 (2013). http://doi.org/10.1039/c2nr32387g
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 17
DOI: 10.1039/c2nr32387g
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“How the alignment of adsorbed ortho H pairs determines the onset of selective carbon nanotube etching”. Khalilov U, Bogaerts A, Xu B, Kato T, Kaneko T, Neyts EC, Nanoscale 9, 1653 (2017). http://doi.org/10.1039/C6NR08005G
Abstract: Unlocking the enormous technological potential of carbon nanotubes strongly depends on our ability to specifically produce metallic or semiconducting tubes. While selective etching of both has already been demonstrated, the underlying reasons, however, remain elusive as yet. We here present computational and experimental evidence on the operative mechanisms at the atomic scale. We demonstrate that during the adsorption of H atoms and their coalescence, the adsorbed ortho hydrogen pairs on single-walled carbon nanotubes induce higher shear stresses than axial stresses, leading to the elongation of HC–CH bonds as a function of their alignment with the tube chirality vector, which we denote as the γ-angle. As a result, the C–C cleavage occurs more rapidly in nanotubes containing ortho H-pairs with a small γ-angle. This phenomenon can explain the selective etching of small-diameter semiconductor nanotubes with a similar curvature. Both theoretical and experimental results strongly indicate the important role of the γ-angle in the selective etching mechanisms of carbon nanotubes, in addition to the nanotube curvature and metallicity effects and lead us to clearly understand the onset of selective synthesis/removal of CNT-based materials.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 6
DOI: 10.1039/C6NR08005G
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“Microscopic mechanisms of vertical graphene and carbon nanotube cap nucleation from hydrocarbon growth precursors”. Khalilov U, Bogaerts A, Neyts EC, Nanoscale 6, 9206 (2014). http://doi.org/10.1039/c4nr00669k
Abstract: Controlling and steering the growth of single walled carbon nanotubes is often believed to require controlling of the nucleation stage. Yet, little is known about the microscopic mechanisms governing the nucleation from hydrocarbon molecules. Specifically, we address here the dehydrogenation of hydrocarbon molecules and the formation of all-carbon graphitic islands on metallic nanoclusters from hydrocarbon molecules under conditions typical for carbon nanotube growth. Employing reactive molecular dynamics simulations, we demonstrate for the first time that the formation of a graphitic network occurs through the intermediate formation of vertically oriented, not fully dehydrogenated graphitic islands. Upon dehydrogenation of these vertical graphenes, the islands curve over the surface, thereby forming a carbon network covering the nanoparticle. The results indicate that controlling the extent of dehydrogenation offers an additional parameter to control the nucleation of carbon nanotubes.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 21
DOI: 10.1039/c4nr00669k
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“Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors”. Khalilov U, Bogaerts A, Neyts EC, Nature communications 6, 10306 (2015). http://doi.org/10.1038/ncomms10306
Abstract: Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 12.124
Times cited: 37
DOI: 10.1038/ncomms10306
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“Atomic-scale mechanisms of plasma-assisted elimination of nascent base-grown carbon nanotubes”. Khalilov U, Bogaerts A, Neyts EC, Carbon 118, 452 (2017). http://doi.org/10.1016/j.carbon.2017.03.068
Abstract: Selective etching allows for obtaining carbon nanotubes with a specific chirality. While plasma-assisted etching has already been used to separate metallic tubes from their semiconducting counterparts, little is known about the nanoscale mechanisms of the etching process. We combine (reactive) molecular dynamics (MD) and force-bias Monte Carlo (tfMC) simulations to study H-etching of CNTs. In particular, during the hydrogenation and subsequent etching of both the carbon cap and the tube, they sequentially transform to different carbon nanostructures, including carbon nanosheet, nanowall, and polyyne chains, before they are completely removed from the surface of a substrate-bound Ni-nanocluster.We also found that onset of the etching process is different in the cases of the cap and the tube, although the overall etching scenario is similar in both cases. The entire hydrogenation/etching process for both cases is analysed in detail, comparing with available theoretical and experimental evidences.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 2
DOI: 10.1016/j.carbon.2017.03.068
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“Toward the Understanding of Selective Si Nano-Oxidation by Atomic Scale Simulations”. Khalilov U, Bogaerts A, Neyts EC, Accounts of chemical research 50, 796 (2017). http://doi.org/10.1021/acs.accounts.6b00564
Abstract: The continuous miniaturization of nanodevices, such as transistors, solar cells, and optical fibers, requires the controlled synthesis of (ultra)thin gate oxides (<10 nm), including Si gate-oxide (SiO2) with high quality at the atomic scale. Traditional thermal growth of SiO2 on planar Si surfaces, however, does not allow one to obtain such ultrathin oxide due to either the high oxygen diffusivity at high temperature or the very low sticking ability of incident oxygen at low temperature. Two recent techniques, both operative at low (room) temperature, have been put forward to overcome these obstacles: (i) hyperthermal oxidation of planar Si surfaces and (ii) thermal or plasma-assisted oxidation of nonplanar Si surfaces, including Si nanowires (SiNWs). These nanooxidation processes are, however, often difficult to study experimentally, due to the key intermediate processes taking place on the nanosecond time scale.
In this Account, these Si nano-oxidation techniques are discussed from a computational point of view and compared to both hyperthermal and thermal oxidation experiments, as well as to well-known models of thermal oxidation, including the Deal−Grove, Cabrera−Mott, and Kao models and several alternative mechanisms. In our studies, we use reactive molecular dynamics (MD) and hybrid MD/Monte Carlo simulation techniques, applying the Reax force field. The incident energy of oxygen species is chosen in the range of 1−5 eV in hyperthermal oxidation of planar Si surfaces in order to prevent energy-induced damage. It turns out that hyperthermal growth allows for two growth modes, where the ultrathin oxide thickness depends on either (1) only the kinetic energy of the incident oxygen species at a growth temperature below Ttrans = 600 K, or (2) both the incident energy and the growth temperature at a growth temperature above Ttrans. These modes are specific to such ultrathin oxides, and are not observed in traditional thermal oxidation, nor theoretically considered by already existing models. In the case of thermal or plasma-assisted oxidation of small Si nanowires, on the other hand, the thickness of the ultrathin oxide is a function of the growth temperature and the nanowire diameter. Below Ttrans, which varies with the nanowire diameter, partially oxidized SiNW are formed, whereas complete oxidation to a SiO2 nanowire occurs only above Ttrans. In both nano-oxidation processes at lower temperature (T < Ttrans), final sandwich c-Si|SiOx|a-SiO2 structures are obtained due to a competition between overcoming the energy barrier to penetrate into Si subsurface layers and the compressive stress (∼2−3 GPa) at the Si crystal/oxide interface. The overall atomic-simulation results strongly indicate that the thickness of the intermediate SiOx (x < 2) region is very limited (∼0.5 nm) and constant irrespective of oxidation parameters. Thus, control over the ultrathin SiO2 thickness with good quality is indeed possible by accurately tuning the oxidant energy, oxidation temperature and surface curvature.
In general, we discuss and put in perspective these two oxidation mechanisms for obtaining controllable ultrathin gate-oxide films, offering a new route toward the fabrication of nanodevices via selective nano-oxidation.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 20.268
Times cited: 5
DOI: 10.1021/acs.accounts.6b00564
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