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“Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences”. Cordeiro RM, Yusupov M, Razzokov J, Bogaerts A, Journal Of Physical Chemistry B 124, 1082 (2020). http://doi.org/10.1021/acs.jpcb.9b08172
Abstract: Nitrogen oxyanions and oxyacids are important agents in atmospheric chemistry and medical biology. Although their chemical behavior in solution is relatively well understood, they may behave very differently at the water/air interface of atmospheric aerosols or at the membrane/water interface of cells. Here, we developed a fully classical model for molecular dynamics simulations of NO3−, NO2−, HNO3, and HNO2 in the framework of the GROMOS 53A6 and 54A7 force field versions. The model successfully accounted for the poorly structured solvation shell and ion pairing tendency of NO3−. Accurate pure-liquid properties and hydration free energies were obtained for the oxyacids. Simulations at the water/air interface showed a local enrichment of HNO3 and depletion of NO3−. The effect was discussed in light of earlier spectroscopic data and ab initio calculations, suggesting that HNO3 behaves as a weaker acid at the surface of water. Our model will hopefully allow for efficient and accurate simulations of nitrogen oxyanions and oxyacids in solution and at microheterogeneous interface environments.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.3
DOI: 10.1021/acs.jpcb.9b08172
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“Dry reforming of methane in a nanosecond repetitively pulsed discharge: chemical kinetics modeling”. Zhang L, Heijkers S, Wang W, Martini LM, Tosi P, Yang D, Fang Z, Bogaerts A, Plasma Sources Science &, Technology 31, 055014 (2022). http://doi.org/10.1088/1361-6595/ac6bbc
Abstract: Nanosecond pulsed discharge plasma shows a high degree of non-equilibrium, and exhibits relatively high conversions in the dry reforming of methane. To further improve the application, a good insight of the underlying mechanisms is desired. We developed a chemical kinetics model to explore the underlying plasma chemistry in nanosecond pulsed discharge. We compared the calculated conversions and product selectivities with experimental results, and found reasonable agreement in a wide range of specific energy input. Hence, the chemical kinetics model is able to provide insight in the underlying plasma chemistry. The modeling results predict that the most important dissociation reaction of CO<sub>2</sub>and CH<sub>4</sub>is electron impact dissociation. C<sub>2</sub>H<sub>2</sub>is the most abundant hydrocarbon product, and it is mainly formed upon reaction of two CH<sub>2</sub>radicals. Furthermore, the vibrational excitation levels of CO<sub>2</sub>contribute for 85% to the total dissociation of CO<sub>2</sub>.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.8
DOI: 10.1088/1361-6595/ac6bbc
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“Characterization of nano-crystalline diamond films grown under continuous DC bias during plasma enhanced chemical vapor deposition”. Mortet V, Zhang L, Echert M, Soltani A, d' Haen J, Douheret O, Moreau M, Osswald S, Neyts E, Troadec D, Wagner P, Bogaerts A, Van Tendeloo G, Haenen K, Materials Research Society symposium proceedings (2009). http://doi.org/10.1557/PROC-1203-J05-03
Abstract: Nanocrystalline diamond films have generated much interested due to their diamond-like properties and low surface roughness. Several techniques have been used to obtain a high re-nucleation rate, such as hydrogen poor or high methane concentration plasmas. In this work, the properties of nano-diamond films grown on silicon substrates using a continuous DC bias voltage during the complete duration of growth are studied. Subsequently, the layers were characterised by several morphological, structural and optical techniques. Besides a thorough investigation of the surface structure, using SEM and AFM, special attention was paid to the bulk structure of the films. The application of FTIR, XRD, multi wavelength Raman spectroscopy, TEM and EELS yielded a detailed insight in important properties such as the amount of crystallinity, the hydrogen content and grain size. Although these films are smooth, they are under a considerable compressive stress. FTIR spectroscopy points to a high hydrogen content in the films, while Raman and EELS indicate a high concentration of sp2 carbon. TEM and EELS show that these films consist of diamond nano-grains mixed with an amorphous sp2 bonded carbon, these results are consistent with the XRD and UV Raman spectroscopy data.
Keywords: A3 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.1557/PROC-1203-J05-03
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“Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study”. Attri P, Park J-H, De Backer J, Kim M, Yun J-H, Heo Y, Dewilde S, Shiratani M, Choi EH, Lee W, Bogaerts A, International Journal Of Biological Macromolecules 163, 2405 (2020). http://doi.org/10.1016/j.ijbiomac.2020.09.120
Abstract: NADPH oxidases 1 (NOX1) derived reactive oxygen species (ROS) play an important role in the progression of cancer through signaling pathways. Therefore, in this paper, we demonstrate the effect of cold atmospheric plasma (CAP) on the structural changes of Noxa1 SH3 protein, one of the regulatory subunits of NOX1. For this purpose, firstly we purified the Noxa1 SH3 protein and analyzed the structure using X-ray crystallography, and subsequently, we treated the protein with two types of CAP reactors such as pulsed dielectric barrier discharge (DBD) and Soft Jet for different time intervals. The structural deformation of Noxa1 SH3 protein was analyzed by various experimental methods (circular dichroism, fluorescence, and NMR spectroscopy) and by MD simulations. Additionally, we demonstrate the effect of CAP (DBD and Soft Jet) on the viability and expression of NOX1 in A375 cancer cells. Our results are useful to understand the structural modification/oxidation occur in protein due to reactive oxygen and nitrogen (RONS) species generated by CAP.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 8.2
DOI: 10.1016/j.ijbiomac.2020.09.120
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“Al2O3-Supported Transition Metals for Plasma-Catalytic NH3 Synthesis in a DBD Plasma: Metal Activity and Insights into Mechanisms”. Gorbanev Y, Engelmann Y, van’t Veer K, Vlasov E, Ndayirinde C, Yi Y, Bals S, Bogaerts A, Catalysts 11, 1230 (2021). http://doi.org/10.3390/catal11101230
Abstract: N2 fixation into NH3 is one of the main processes in the chemical industry. Plasma catalysis is among the environmentally friendly alternatives to the industrial energy-intensive Haber-Bosch process. However, many questions remain open, such as the applicability of the conventional catalytic knowledge to plasma. In this work, we studied the performance of Al2O3-supported Fe, Ru, Co and Cu catalysts in plasma-catalytic NH3 synthesis in a DBD reactor. We investigated the effects of different active metals, and different ratios of the feed gas components, on the concentration and production rate of NH3, and the energy consumption of the plasma system. The results show that the trend of the metal activity (common for thermal catalysis) does not appear in the case of plasma catalysis: here, all metals exhibited similar performance. These findings are in good agreement with our recently published microkinetic model. This highlights the virtual independence of NH3 production on the metal catalyst material, thus validating the model and indicating the potential contribution of radical adsorption and Eley-Rideal reactions to the plasma-catalytic mechanism of NH3 synthesis.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Movement Antwerp (MOVANT)
Impact Factor: 3.082
Times cited: 19
DOI: 10.3390/catal11101230
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“Special Issue on “Dielectric Barrier Discharges and their Applications&rdquo, in Commemoration of the 20th Anniversary of Dr. Ulrich Kogelschatz’s Work”. Bogaerts A, Plasma Chemistry and Plasma Processing 43, 1281 (2023). http://doi.org/10.1007/s11090-023-10431-x
Abstract: n/a
Keywords: A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 3.6
DOI: 10.1007/s11090-023-10431-x
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“Sustainable NOxproduction from air in pulsed plasma: elucidating the chemistry behind the low energy consumption”. Vervloessem E, Gorbanev Y, Nikiforov A, De Geyter N, Bogaerts A, Green Chemistry 24, 916 (2022). http://doi.org/10.1039/D1GC02762J
Abstract: N-Based fertilisers are paramount to support our still-growing world population. Current industrial N<sub>2</sub>fixation is heavily fossil fuel-dependent, therefore, a lot of work is put into the development of fossil-free pathways. Plasma technology offers a fossil-free and flexible method for N<sub>2</sub>fixation that is compatible with renewable energy sources. We present here a pulsed plasma jet for direct NO<sub><italic>x</italic></sub>production from air. The pulsed power allows for a record-low energy consumption (EC) of 0.42 MJ (mol N)<sup>−1</sup>. This is the lowest reported EC in plasma-based N<sub>2</sub>fixation at atmospheric pressure thus far. We compare our experimental data with plasma chemistry modelling, and obtain very good agreement. Hence, we can use our model to explain the underlying mechanisms responsible for this low EC. The pulsed power and the corresponding pulsed gas temperature are the reason for the very low EC: they provide a strong vibrational–translational non-equilibrium and promote the non-thermal Zeldovich mechanism. This insight is important for the development of the next generation of plasma sources for energy-efficient NO<sub><italic>x</italic></sub>production.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.8
DOI: 10.1039/D1GC02762J
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“Covalent Cysteine Targeting of Bruton’s Tyrosine Kinase (BTK) Family by Withaferin-A Reduces Survival of Glucocorticoid-Resistant Multiple Myeloma MM1 Cells”. Logie E, Chirumamilla CS, Perez-Novo C, Shaw P, Declerck K, Palagani A, Rangarajan S, Cuypers B, De Neuter N, Mobashar Hussain Urf Turabe F, Kumar Verma N, Bogaerts A, Laukens K, Offner F, Van Vlierberghe P, Van Ostade X, Berghe WV, Cancers 13, 1618 (2021). http://doi.org/10.3390/cancers13071618
Abstract: Multiple myeloma (MM) is a hematological malignancy characterized by plasma cells’ uncontrolled growth. The major barrier in treating MM is the occurrence of primary and acquired therapy resistance to anticancer drugs. Often, this therapy resistance is associated with constitutive hyperactivation of tyrosine kinase signaling. Novel covalent kinase inhibitors, such as the clinically approved BTK inhibitor ibrutinib (IBR) and the preclinical phytochemical withaferin A (WA), have, therefore, gained pharmaceutical interest. Remarkably, WA is more effective than IBR in killing BTK-overexpressing glucocorticoid (GC)-resistant MM1R cells. To further characterize the kinase inhibitor profiles of WA and IBR in GC-resistant MM cells, we applied phosphopeptidome- and transcriptome-specific tyrosine kinome profiling. In contrast to IBR, WA was found to reverse BTK overexpression in GC-resistant MM1R cells. Furthermore, WA-induced cell death involves covalent cysteine targeting of Hinge-6 domain type tyrosine kinases of the kinase cysteinome classification, including inhibition of the hyperactivated BTK. Covalent interaction between WA and BTK could further be confirmed by biotin-based affinity purification and confocal microscopy. Similarly, molecular modeling suggests WA preferably targets conserved cysteines in the Hinge-6 region of the kinase cysteinome classification, favoring inhibition of multiple B-cell receptors (BCR) family kinases. Altogether, we show that WA’s promiscuous inhibition of multiple BTK family tyrosine kinases represents a highly effective strategy to overcome GC-therapy resistance in MM.
Keywords: A1 Journal article; ADReM Data Lab (ADReM); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.3390/cancers13071618
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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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“Synchrotron radiation induced X-ray microfluorescence analysis”. Janssens K, Vincze L, Vekemans B, Aerts A, Adams F, Jones KW, Knöchel A, Microchimica acta
T2 –, 4th Workshop of the European-Microanalysis-Society on Modern, Developments and Applications in Microbeam Analysis, MAY, 1995, ST MALO, FRANCE , 87 (1996)
Abstract: mu-XRF is the microscopic equivalent of the well-established multielement analytical technique. In this paper, after comparing the interaction of X-ray photons, electrons and protons with matter and an introduction to synchrotron rings and microfocussing of X-rays, the instrumentation for mu-XRF is discussed, both for laboratory source and synchrotron based setups and the analytical characteristics of mu-XRF are contrasted to that of other microanalytical techniques, Also, this issue of quantification of mu-XRF data is addressed; the applicability of the method in archeological and geological analysis is illustrated.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Numerical study of the size-dependent melting mechanisms of nickel nanoclusters”. Neyts EC, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 113, 2771 (2009)
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
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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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“Reaction mechanisms and thin a-C:H film growth from low energy hydrocarbon radicals”. Neyts E, Bogaerts A, van de Sanden MCM, Journal of physics : conference series 86, 12020 (2007). http://doi.org/10.1088/1742-6596/86/1/012020
Abstract: Molecular dynamics simulations using the Brenner potential have been performed to investigate reaction mechanisms of various hydrocarbon radicals with low kinetic energies on amorphous hydrogenated carbon (a-C:H) surfaces and to simulate thin a-C:H film growth. Experimental data from an expanding thermal plasma setup were used as input for the simulations. The hydrocarbon reaction mechanisms were studied both during growth of the films and on a set of surface sites specific for a-C:H surfaces. Thin film growth was studied using experimentally detected growth species. It is found that the reaction mechanisms and sticking coefficients are dependent on the specific surface sites, and the structural properties of the growth radicals. Furthermore, it is found that thin a-C:H films can be densified using an additional H-flux towards the substrate.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Times cited: 22
DOI: 10.1088/1742-6596/86/1/012020
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“Molecular dynamics simulations of Cl+ etching on a Si(100) surface”. Gou F, Neyts E, Eckert M, Tinck S, Bogaerts A, Journal of applied physics 107, 113305 (2010). http://doi.org/10.1063/1.3361038
Abstract: Molecular dynamics simulations using improved TersoffBrenner potential parameters were performed to investigate Cl+ etching of a {2×1} reconstructed Si(100) surface. Steady-state Si etching accompanying the Cl coverage of the surface is observed. Furthermore, a steady-state chlorinated reaction layer is formed. The thickness of this reaction layer is found to increase with increasing energy. The stoichiometry of SiClx species in the reaction layer is found to be SiCl:SiCl2:SiCl3 = 1.0:0.14:0.008 at 50 eV. These results are in excellent agreement with available experimental data. While elemental Si products are created by physical sputtering, most SiClx (0<x<4) etch products are produced by chemical-enhanced physical sputtering.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.068
Times cited: 15
DOI: 10.1063/1.3361038
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“Accurate Reaction Probabilities for Translational Energies on Both Sides of the Barrier of Dissociative Chemisorption on Metal Surfaces”. Gerrits N, Jackson B, Bogaerts A, The Journal of Physical Chemistry Letters 15, 2566 (2024). http://doi.org/10.1021/acs.jpclett.3c03408
Abstract: Molecular dynamics simulations are essential for a better understanding of dissociative chemisorption on metal surfaces, which is often the rate-controlling step in heterogeneous and plasma catalysis. The workhorse quasi-classical trajectory approach ubiquitous in molecular dynamics is able to accurately predict reactivity only for high translational and low vibrational energies. In contrast, catalytically relevant conditions generally involve low translational and elevated vibrational energies. Existing quantum dynamics approaches are intractable or approximate as a result of the large number of degrees of freedom present in molecule−metal surface reactions. Here, we extend a ring polymer molecular dynamics approach to fully include, for the first time, the degrees of freedom of a moving metal surface. With this approach, experimental sticking probabilities for the dissociative chemisorption of methane on Pt(111) are reproduced for a large range of translational and vibrational energies by including nuclear quantum effects and employing full-dimensional simulations.
Keywords: A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 5.7
DOI: 10.1021/acs.jpclett.3c03408
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“Molecular dynamics simulation of temperature effects on CF(3)(+) etching of Si surface”. Jian-Ping N, Xiao-Dan L, Cheng-Li Z, You-Min Q, Ping-Ni H, Bogaerts A, Fu-Jun G, Wuli xuebao 59, 7225 (2010)
Abstract: Molecular dynamics method was employed to investigate the effects of the reaction layer formed near the surface region on CF(3)(+) etching of Si at different temperatures. The simulation results show that the coverages of F and C are sensitive to the surface temperature. With increasing temperature, the physical etching is enhanced, while the chemical etching is weakened. It is found that with increasing surface temperature, the etching rate of Si increases. As to the etching products, the yields of SiF and SiF(2) increase with temperature, whereas the yield of SiF(3) is not sensitive to the surface temperature. And the increase of the etching yield is mainly due to the increased desorption of SiF and SiF(2). The comparison shows that the reactive layer plays an important part in the subsequeat impacting, which enhances the etching rate of Si and weakens the chemical etching intensity.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 0.624
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“Mechanisms of Peptide Oxidation by Hydroxyl Radicals: Insight at the Molecular Scale”. Verlackt CCW, Van Boxem W, Dewaele D, Lemière F, Sobott F, Benedikt J, Neyts EC, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 121, 5787 (2017). http://doi.org/10.1021/acs.jpcc.6b12278
Abstract: Molecular dynamics (MD) simulations were performed to provide atomic scale insight in the initial interaction between hydroxyl radicals (OH) and peptide systems in solution. These OH radicals are representative reactive oxygen species produced by cold atmospheric plasmas. The use of plasma for biomedical applications is gaining increasing interest, but the fundamental mechanisms behind the plasma modifications still remain largely elusive. This study helps to gain more insight in the underlying mechanisms of plasma medicine but is also more generally applicable to peptide oxidation, of interest for other applications. Combining both reactive and nonreactive MD simulations, we are able to elucidate the reactivity of the amino acids inside the peptide systems and their effect on their structure up to 1 μs. Additionally, experiments were performed, treating the simulated peptides with a plasma jet. The computational results presented here correlate well with the obtained experimental data and highlight the importance of the chemical environment for the reactivity of the individual amino acids, so that specific amino acids are attacked in higher numbers than expected. Furthermore, the long time scale simulations suggest that a single oxidation has an effect on the 3D conformation due to an increase in hydrophilicity and intra- and intermolecular interactions.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 5
DOI: 10.1021/acs.jpcc.6b12278
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“Multi-level molecular modelling for plasma medicine”. Bogaerts A, Khosravian N, Van der Paal J, Verlackt CCW, Yusupov M, Kamaraj B, Neyts EC, Journal of physics: D: applied physics 49, 054002 (2016). http://doi.org/10.1088/0022-3727/49/5/054002
Abstract: Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 11
DOI: 10.1088/0022-3727/49/5/054002
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“Modeling SiH4/O2/Ar inductively coupled plasmas used for filling of microtrenches in shallow trench isolation (STI)”. Tinck S, Bogaerts A, Plasma processes and polymers 9, 522 (2012). http://doi.org/10.1002/ppap.201100093
Abstract: Modeling results are presented to gain a better insight in the properties of a SiH4/O2/Ar inductively coupled plasma (ICP) and how it interacts with a silicon substrate (wafer), as applied in the microelectronics industry for the fabrication of electronic devices. The SiH4/O2/Ar ICP is used for the filling of microtrenches with isolating material (SiO2), as applied in shallow trench isolation (STI). In this article, a detailed reaction set that describes the plasma chemistry of SiH4/O2/Ar discharges as well as surface processes, such as sputtering, oxidation, and deposition, is presented. Results are presented on the plasma properties during the plasma enhanced chemical vapor deposition process (PECVD) for different gas ratios, as well as on the shape of the filled trenches and the surface compositions of the deposited layers. For the operating conditions under study it is found that the most important species accounting for deposition are SiH2, SiH3O, SiH3 and SiH2O, while SiH+2, SiH+3, O+2 and Ar+ are the dominant species for sputtering of the surface. By diluting the precursor gas (SiH4) in the mixture, the deposition rate versus sputtering rate can be controlled for a desired trench filling process. From the calculation results it is clear that a high deposition rate will result in undesired void formation during the trench filling, while a small deposition rate will result in undesired trench bottom and mask damage by sputtering. By varying the SiH4/O2 ratio, the chemical composition of the deposited layer will be influenced. However, even at the highest SiH4/O2 ratio investigated (i.e., 3.2:1; low oxygen content), the bulk deposited layer consists mainly of SiO2, suggesting that low-volatile silane species deposit first and subsequently become oxidized instead of being oxidized first in the plasma before deposition. Finally, it was found that the top surface of the deposited layer contained less oxygen due to preferential sputtering of O atoms, making the top layer more Si-rich. However, this effect is negligible at a SiH4/O2 ratio of 2:1 or lower.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 5
DOI: 10.1002/ppap.201100093
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“Modeling of CO2Splitting in a Microwave Plasma: How to Improve the Conversion and Energy Efficiency”. Berthelot A, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 121, 8236 (2017). http://doi.org/10.1021/acs.jpcc.6b12840
Abstract: Microwave plasmas are one of the most promising techniques for CO2 conversion into value-added chemicals and fuels since they are very energy efficient. Nevertheless, experiments show that this high energy efficiency is only reached at low pressures and significantly drops toward atmospheric pressure, which is a clear limitation for industrial applications. In this paper, we use a zerodimensional reaction kinetics model to simulate a CO2 microwave plasma in a pressure range from 50 mbar to 1 bar, in order to evaluate the reasons for this decrease in energy efficiency at atmospheric pressure. The code includes a detailed description of the vibrational kinetics of CO2, CO, and O2 as well as the energy exchanges between them because the vibrational kinetics is known to be crucial for energy efficient CO2 splitting. First, we use a self-consistent gas temperature calculation in order to assess the key performance indicators for CO2 splitting, i.e., the CO2 conversion and corresponding energy efficiency. Our results indicate that lower pressures and higher power densities lead to more vibrational excitation, which is beneficial for the conversion. We also demonstrate the key role of the gas temperature. The model predicts the highest conversion and energy efficiencies at pressures around 300 mbar, which is in agreement with experiments from the literature. We also show the beneficial aspect of fast gas cooling in the afterglow at high pressure. In a second step, we study in more detail the effects of pressure, gas temperature, and power density on the vibrational distribution function and on the dissociation and recombination mechanisms of CO2, which define the CO2 splitting efficiency. This study allows us to identify the limiting factors of CO2 conversion and to propose potential solutions to improve the process.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 47
DOI: 10.1021/acs.jpcc.6b12840
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“Carbon dioxide dissociation in a microwave plasma reactor operating in a wide pressure range and different gas inlet configurations”. Belov I, Vermeiren V, Paulussen S, Bogaerts A, Journal of CO2 utilization 24, 386 (2018). http://doi.org/10.1016/j.jcou.2017.12.009
Abstract: Microwave (MW) plasmas represent a promising solution for efficient CO2 dissociation. MW discharges are also very versatile and can be sustained at various pressure and gas flow regimes. To identify the most favorable conditions for the further scale-up of the CO2 decomposition reaction, a MW plasma reactor operating in pure CO2 in a wide pressure range (200 mbar–1 bar) is studied. Three different gas flow configurations are explored: a direct, reverse and a vortex regime. The CO2 conversion and energy efficiency drop almost linearly with increasing pressure, regardless of the gas flow regime. The results obtained in the direct flow configuration underline the importance of post-discharge cooling, as the exhaust of the MW plasma reactor in this regime expanded into the vacuum chamber without additional quenching. As a result, this system yields exhaust temperatures of up to 1000 K, which explains the lowest conversion (∼3.5% at 200 mbar and 2% at 1 bar). A post-discharge cooling step is introduced for the reverse gas inlet regime and allows the highest conversion to be achieved (∼38% at 200 mbar and 6.2% at 1 bar, with energy efficiencies of 23% and 3.7%). Finally, a tangential gas inlet is utilized in the vortex configuration to generate a swirl flow pattern. This results in the generation of a stable discharge in a broader range of CO2 flows (15–30 SLM) and the highest energy efficiencies obtained in this study (∼25% at 300 mbar and ∼13% at 1 bar, at conversions of 21% and 12%). The experimental results are complemented with computational fluid dynamics simulations and with the analysis of the latest literature to identify the further research directions.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.292
Times cited: 8
DOI: 10.1016/j.jcou.2017.12.009
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“In Situ Plasma Studies Using a Direct Current Microplasma in a Scanning Electron Microscope”. Grünewald L, Chezganov D, De Meyer R, Orekhov A, Van Aert S, Bogaerts A, Bals S, Verbeeck J, Advanced Materials Technologies (2024). http://doi.org/10.1002/admt.202301632
Abstract: Microplasmas can be used for a wide range of technological applications and to improve the understanding of fundamental physics. Scanning electron microscopy, on the other hand, provides insights into the sample morphology and chemistry of materials from the mm‐ down to the nm‐scale. Combining both would provide direct insight into plasma‐sample interactions in real‐time and at high spatial resolution. Up till now, very few attempts in this direction have been made, and significant challenges remain. This work presents a stable direct current glow discharge microplasma setup built inside a scanning electron microscope. The experimental setup is capable of real‐time in situ imaging of the sample evolution during plasma operation and it demonstrates localized sputtering and sample oxidation. Further, the experimental parameters such as varying gas mixtures, electrode polarity, and field strength are explored and experimental<italic>V</italic>–<italic>I</italic>curves under various conditions are provided. These results demonstrate the capabilities of this setup in potential investigations of plasma physics, plasma‐surface interactions, and materials science and its practical applications. The presented setup shows the potential to have several technological applications, for example, to locally modify the sample surface (e.g., local oxidation and ion implantation for nanotechnology applications) on the µm‐scale.
Keywords: A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
Impact Factor: 6.8
DOI: 10.1002/admt.202301632
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“Interactions of plasma species on nickel catalysts : a reactive molecular dynamics study on the influence of temperature and surface structure”. Somers W, Bogaerts A, van Duin ACT, Neyts EC, Applied catalysis : B : environmental 154, 1 (2014). http://doi.org/10.1016/j.apcatb.2014.01.061
Abstract: Methane reforming by plasma catalysis is a complex process that is far from understood. It requires a multidisciplinary approach which ideally takes into account all effects from the plasma on the catalyst, and vice versa. In this contribution, we focus on the interactions of CHx (x = {1,2,3}) radicals that are created in the plasma with several nickel catalyst surfaces. To this end, we perform reactive molecular dynamics simulations, based on the ReaxFF potential, in a wide temperature range of 4001600 K. First, we focus on the H2 formation as a function of temperature and surface structure. We observe that substantial H2 formation is obtained at 1400 K and above, while the role of the surface structure seems limited. Indeed, in the initial stage, the type of nickel surface influences the CH bond breaking efficiency of adsorbed radicals; however, the continuous carbon diffusion into the surface gradually diminishes the surface crystallinity and therefore reduces the effect of surface structure on the H2 formation probability. Furthermore, we have also investigated to what extent the species adsorbed on the catalyst surface can participate in surface reactions more in general, for the various surface structures and as a function of temperature. These results are part of the ongoing research on the methane reforming by plasma catalysis, a highly interesting yet complex alternative to conventional reforming processes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.446
Times cited: 23
DOI: 10.1016/j.apcatb.2014.01.061
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“Catalyzed growth of carbon nanotube with definable chirality by hybrid molecular dynamics-force biased Monte Carlo simulations”. Neyts EC, Shibuta Y, van Duin ACT, Bogaerts A, ACS nano 4, 6665 (2010). http://doi.org/10.1021/nn102095y
Abstract: Metal-catalyzed growth mechanisms of carbon nanotubes (CNTs) were studied by hybrid molecular dynamics−Monte Carlo simulations using a recently developed ReaxFF reactive force field. Using this novel approach, including relaxation effects, a CNT with definable chirality is obtained, and a step-by-step atomistic description of the nucleation process is presented. Both root and tip growth mechanisms are observed. The importance of the relaxation of the network is highlighted by the observed healing of defects.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 13.942
Times cited: 129
DOI: 10.1021/nn102095y
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“Preparation of sulfonated ordered mesoporous carbon and its use for the esterification of fatty acids”. Peng L, Philippaerts A, Ke X, van Noyen J, de Cleppel F, Van Tendeloo G, Jacobs PA, Sels BF, Catalysis today 150, 140 (2010). http://doi.org/10.1016/j.cattod.2009.07.066
Abstract: Mesoporous carbon, which can be replicated from mesoporous silica and whose surface is hydrophobic, can be an ideal catalyst for the esterification of fatty acids. Here we report an easy and low cost way to prepare sulfonic acid group-functionalized mesoporous carbon. A sample of calcined mesoporous silica SBA-15 was added to an aqueous sucrose solution followed by drying and calcination at different temperatures. In contrast to existing procedures, the obtained hybrid Si/C material was then first sulfonated in H2SO4, before the final removal of the silica template in order to stabilize the porous structure towards the liquid phase sulfonation treatment. Thus the silicacarbon composites, instead of the mesoporous carbon, were successfully sulfonated to introduce SO3H groups, while keeping the ordered mesoporous structure intact. The influence of carbonization temperature was investigated, suggesting an optimum temperature of 873 K. The SO3H group-functionalized mesoporous carbon, denoted as CMK-3-873-SO3H, was characterized by means of XRD, N2 physisorption, SEM, FT-IR, elemental analysis and TEM. It followed that a uniform mesoporous carbon was obtained with an average pore size of 3.89 nm, a specific surface of 807 m2/g and a SO3H group loading of 0.39 meq/g of dry material. Compared with other solid acid catalysts, the resulting material shows enhanced activity in the acid-catalyzed esterification of oleic acid with methanol, and can be used repeatedly. The increased catalytic performance is attributed to the hydrophobic surface and larger pore size of the new catalyst. It can effectively accommodate long chain fatty acids and reject formed water, making the active sites easily accessible.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 4.636
Times cited: 132
DOI: 10.1016/j.cattod.2009.07.066
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“Synergistic Effects of Melittin and Plasma Treatment: A Promising Approach for Cancer Therapy”. Shaw P, Kumar N, Hammerschmid D, Privat-Maldonado A, Dewilde S, Bogaerts A, Cancers 11, 1109 (2019). http://doi.org/10.3390/cancers11081109
Abstract: Melittin (MEL), a small peptide component of bee venom, has been reported to exhibit anti-cancer effects in vitro and in vivo. However, its clinical applicability is disputed because of its non-specific cytotoxicity and haemolytic activity in high treatment doses. Plasma-treated phosphate buffered saline solution (PT-PBS), a solution rich in reactive oxygen and nitrogen species (RONS) can disrupt the cell membrane integrity and induce cancer cell death through oxidative stress-mediated pathways. Thus, PT-PBS could be used in combination with MEL to facilitate its access into cancer cells and to reduce the required therapeutic dose. The aim of our study is to determine the reduction of the effective dose of MEL required to eliminate cancer cells by its combination with PT-PBS. For this purpose, we have optimised the MEL threshold concentration and tested the combined treatment of MEL and PT-PBS on A375 melanoma and MCF7 breast cancer cells, using in vitro, in ovo and in silico approaches. We investigated the cytotoxic effect of MEL and PT-PBS alone and in combination to reveal their synergistic cytological effects. To support the in vitro and in ovo experiments, we showed by computer simulations that plasma-induced oxidation of the phospholipid bilayer leads to a decrease of the free energy barrier for translocation of MEL in comparison with the non-oxidized bilayer, which also suggests a synergistic effect of MEL with plasma induced oxidation. Overall, our findings suggest that MEL in combination with PT-PBS can be a promising combinational therapy to circumvent the non-specific toxicity of MEL, which may help for clinical applicability in the future.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Times cited: 1
DOI: 10.3390/cancers11081109
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Lin A, De Backer J, Quatannens D, Cuypers B, Verswyvel H, De La Hoz EC, Ribbens B, Siozopoulou V, Van Audenaerde J, Marcq E, Lardon F, Laukens K, Vanlanduit S, Smits E, Bogaerts A (2022) The effect of local non‐thermal plasma therapy on the<scp>cancer‐immunity</scp>cycle in a melanoma mouse model
Abstract: Melanoma remains a deadly cancer despite significant advances in immune checkpoint blockade and targeted therapies. The incidence of melanoma is also growing worldwide, which highlights the need for novel treatment options and strategic combination of therapies. Here, we investigate non-thermal plasma (NTP), an ionized gas, as a promising, therapeutic option. In a melanoma mouse model, direct treatment of tumors with NTP results in reduced tumor burden and prolonged survival. Physical characterization of NTP treatment in situ reveals the deposited NTP energy and temperature associated with therapy response, and whole transcriptome analysis of the tumor identified several modulated pathways. NTP treatment also enhances the cancer-immunity cycle, as immune cells in both the tumor and tumor-draining lymph nodes appear more stimulated to perform their anti-cancer functions. Thus, our data suggest that local NTP therapy stimulates systemic, anti-cancer immunity. We discuss, in detail, how these fundamental insights will help direct the translation of NTP technology into the clinic and inform rational combination strategies to address the challenges in melanoma therapy.
Keywords: University Hospital Antwerp; A1 Journal article; Pharmacology. Therapy; Engineering sciences. Technology; ADReM Data Lab (ADReM); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES)
DOI: 10.1002/btm2.10314
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“Cytoglobin inhibits non-thermal plasma-induced apoptosis in melanoma cells through regulation of the NRF2-mediated antioxidant response”. De Backer J, Lin A, Berghe WV, Bogaerts A, Hoogewijs D, Redox Biology 55, 102399 (2022). http://doi.org/10.1016/j.redox.2022.102399
Abstract: Melanoma arises from pigment-producing cells called melanocytes located in the basal layers of the epidermis of the skin. Cytoglobin (CYGB) is a ubiquitously expressed hexacoordinated globin that is highly enriched in melanocytes and frequently downregulated during melanomagenesis. Previously, we showed that non-thermal plasma (NTP)-produced reactive oxygen and nitrogen species (RONS) lead to the formation of an intra molecular disulfide bridge that would allow CYGB to function as a redox-sensitive protein. Here, we investigate the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels, and we explore the role of CYGB in determining treatment outcome. Our findings are consistent with previous studies supporting that NTP cytotoxicity is mediated through the production of RONS and leads to apoptotic cell death in melanoma cells. Furthermore, we show that NTP-treated solutions elicit an antioxidant response through the activation of nuclear factor erythroid 2–related factor 2 (NRF2). The knock down and overexpression of CYGB respectively sensitizes and protects melanoma cells from RONS-induced apoptotic cell death. The presence of CYGB enhances heme-oxygenase 1 (HO-1) and NRF2 protein expression levels, whereas the absence impairs their expression. Moreover, analysis of the CYGB-dependent transcriptome demonstrates the tumor suppressor long non-coding RNA maternally expressed 3 (MEG3) as a hitherto unde scribed link between CYGB and NRF2. Thus, the presence of CYGB, at least in melanoma cells, seems to play a central role in determining the therapeutic outcome of RONS-inducing anticancer therapies, like NTP-treated solutions, possessing both tumor-suppressive and oncogenic features. Hence, CYGB expression could be of in terest either as a biomarker or as a candidate for future targeted therapies in melanoma.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
Impact Factor: 11.4
DOI: 10.1016/j.redox.2022.102399
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“Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide—Mcl1 Complexes”. Marimuthu P, Razzokov J, Singaravelu K, Bogaerts A, Biomolecules 10, 1114 (2020). http://doi.org/10.3390/biom10081114
Abstract: Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.3390/biom10081114
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“The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor”. De Backer J, Razzokov J, Hammerschmid D, Mensch C, Hafideddine Z, Kumar N, van Raemdonck G, Yusupov M, Van Doorslaer S, Johannessen C, Sobott F, Bogaerts A, Dewilde S, Redox Biology 19, 1 (2018). http://doi.org/10.1016/j.redox.2018.07.019
Abstract: Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec)
Impact Factor: 6.337
DOI: 10.1016/j.redox.2018.07.019
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