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Author  |
Engelmann, Y.; Mehta, P.; Neyts, E.C.; Schneider, W.F.; Bogaerts, A. | ||||
| Title | Predicted Influence of Plasma Activation on Nonoxidative Coupling of Methane on Transition Metal Catalysts | Type | A1 Journal article | ||
| Year | 2020 | Publication | Acs Sustainable Chemistry & Engineering | Abbreviated Journal | Acs Sustain Chem Eng |
| Volume | 8 | Issue | 15 | Pages | 6043-6054 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Movement Antwerp (MOVANT) | ||||
| Abstract | The combination of catalysis and nonthermal plasma holds promise for enabling difficult chemical conversions. The possible synergy between both depends strongly on the nature of the reactive plasma species and the catalyst material. In this paper, we show how vibrationally excited species and plasma-generated radicals interact with transition metal catalysts and how changing the catalyst material can improve the conversion rates and product selectivity. We developed a microkinetic model to investigate the impact of vibrational excitations and plasma-generated radicals on the nonoxidative coupling of methane over transition metal surfaces. We predict a significant increase in ethylene formation for vibrationally excited methane. Plasma-generated radicals have a stronger impact on the turnover frequencies with high selectivity toward ethylene on noble catalysts and mixed selectivity on non-noble catalysts. In general, we show how the optimal catalyst material depends on the desired products as well as the plasma conditions. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000526884000025 | Publication Date | 2020-04-20 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2168-0485 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 8.4 | Times cited | Open Access | ||
| Notes | Herculesstichting; University of Notre Dame; Universiteit Antwerpen; Division of Engineering Education and Centers, EEC-1647722 ; We would like to thank Tom Butterworth for his work on methane vibrational distribution functions (VDF) and for sharing his thoughts and experiences on this matter, specifically regarding the VDF of the degenerate modes of methane. We ACS Sustainable Chemistry & Engineering pubs.acs.org/journal/ascecg Research Article https://dx.doi.org/10.1021/acssuschemeng.0c00906 ACS Sustainable Chem. Eng. 2020, 8, 6043−6054 6052 also acknowledge financial support from the DOC-PRO3 and the TOP-BOF projects of the University of Antwerp. This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (Department EWI), and the University of Antwerp. Support for W.F.S. was provided by the National Science Foundation under cooperative agreement no. EEC-1647722, an Engineering Research Center for the Innovative and Strategic Transformation of Alkane Resources (CISTAR). P.M. acknowledges support through the Eilers Graduate Fellowship of the University of Notre Dame. | Approved | Most recent IF: 8.4; 2020 IF: 5.951 | ||
| Call Number | PLASMANT @ plasmant @c:irua:169228 | Serial | 6366 | ||
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| Author |
Engelmann, Y.; van ’t Veer, K.; Gorbanev, Y.; Neyts, E.C.; Schneider, W.F.; Bogaerts, A. | ||||
| Title | Plasma Catalysis for Ammonia Synthesis: A Microkinetic Modeling Study on the Contributions of Eley–Rideal Reactions | Type | A1 Journal Article;Plasma catalysis | ||
| Year | 2021 | Publication | Acs Sustainable Chemistry & Engineering | Abbreviated Journal | Acs Sustain Chem Eng |
| Volume | 9 | Issue | 39 | Pages | 13151-13163 |
| Keywords | A1 Journal Article;Plasma catalysis; Eley−Rideal reactions; Volcano plots; Vibrational excitation; Radical reactions; Dielectric barrier discharge; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| Abstract | Plasma catalysis is an emerging new technology for the electrification and downscaling of NH3 synthesis. Increasing attention is being paid to the optimization of plasma catalysis with respect to the plasma conditions, the catalyst material, and their mutual interaction. In this work we use microkinetic models to study how the total conversion process is impacted by the combination of different plasma conditions and transition metal catalysts. We study how plasma-generated radicals and vibrationally excited N2 (present in a dielectric barrier discharge plasma) interact with the catalyst and impact the NH3 turnover frequencies (TOFs). Both filamentary and uniform plasmas are studied, based on plasma chemistry models that provided plasma phase speciation and vibrational distribution functions. The Langmuir−Hinshelwood reaction rate coefficients (i.e., adsorption reactions and subsequent reactions among adsorbates) are determined using conventional scaling relations. An additional set of Eley−Rideal reactions (i.e., direct reactions of plasma radicals with adsorbates) was added and a sensitivity analysis on the assumed reaction rate coefficients was performed. We first show the impact of different vibrational distribution functions on the catalytic dissociation of N2 and subsequent production of NH3, and we gradually include more radical reactions, to illustrate the contribution of these species and their corresponding reaction pathways. Analysis over a large range of catalysts indicates that different transition metals (metals such as Rh, Ni, Pt, and Pd) optimize the NH3TOFs depending on the population of the vibrational levels of N2. At higher concentrations of plasma-generated radicals, the NH3 TOFs become less dependent on the catalyst material, due to radical adsorptions on the more noble catalysts and Eley−Rideal reactions on the less noble catalysts. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000705367800004 | Publication Date | 2021-10-04 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2168-0485 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.951 | Times cited | Open Access | OpenAccess | |
| Notes | Basic Energy Sciences, DE-SC0021107 ; Vlaamse regering, HBC.2019.0108 ; H2020 European Research Council, 810182 ; Methusalem project – University of Antwerp; Excellence of science FWO-FNRS, GoF9618n ; TOP-BOF – University of Antwerp; DOCPRO3 – University of Antwerp; We acknowledge the financial support from the DOC-PRO3, the TOP-BOF, and the Methusalem project of the University of Antwerp, as well as from the European Research Council (ERC) (grant agreement No, 810182−SCOPE ERC Synergy project), under the European Union’s Horizon 2020 research and innovation programme, the Flemish Government through the Moonshot cSBO project P2C (HBC.2019.0108), and the Excellence of Science FWO-FNRS project (FWO grant ID GoF9618n, EOS ID 30505023). Calculations were carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (Department EWI), 13162 | Approved | Most recent IF: 5.951 | ||
| Call Number | PLASMANT @ plasmant @c:irua:182482 | Serial | 6811 | ||
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| Author |
Engelmann; Bogaerts, A.; Neyts, E.C. | ||||
| Title | Thermodynamics at the nanoscale: phase diagrams of nickel-carbon nanoclusters and equilibrium constants for phase transitions | Type | A1 Journal article | ||
| Year | 2014 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
| Volume | 6 | Issue | 20 | Pages | 11981-11987 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Using reactive molecular dynamics simulations, the melting behavior of nickel-carbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickel-carbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method. | ||||
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| Publisher | Place of Publication | Cambridge | Editor | ||
| Language | Wos | 000343000800049 | Publication Date | 2014-07-24 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2040-3364;2040-3372; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 7.367 | Times cited | 20 | Open Access | |
| Notes | Approved | Most recent IF: 7.367; 2014 IF: 7.394 | |||
| Call Number | UA @ lucian @ c:irua:121106 | Serial | 3637 | ||
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| Author |
Eshtehardi, H.A.; van 't Veer, K.; Delplancke, M.-P.; Reniers, F.; Bogaerts, A. | ||||
| Title | Postplasma Catalytic Model for NO Production: Revealing the Underlying Mechanisms to Improve the Process Efficiency | Type | A1 Journal article | ||
| Year | 2023 | Publication | ACS Sustainable Chemistry and Engineering | Abbreviated Journal | |
| Volume | 11 | Issue | 5 | Pages | 1720-1733 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma catalysis is emerging for plasma-assisted gas conversion processes. However, the underlying mechanisms of plasma catalysis are poorly understood. In this work, we present a 1D heterogeneous catalysis model with axial dispersion (i.e., accounting for back-mixing and molecular diffusion of fluid elements in the process stream in the axial direction), for plasma-catalytic NO production from N2/O2 mixtures. We investigate the concentration and reaction rates of each species formed as a function of time and position across the catalyst, in order to determine the underlying mechanisms. To obtain insights into how the performance of the process can be further improved, we also study how changes in the postplasma gas flow composition entering the catalyst bed and in the operation conditions of the catalytic stage affect the performance of NO production. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000926412800001 | Publication Date | 2023-02-06 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2168-0485 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 8.4 | Times cited | Open Access | OpenAccess | |
| Notes | Fonds Wetenschappelijk Onderzoek, 30505023 GoF9618n ; Fonds De La Recherche Scientifique FNRS, 30505023 GoF9618n ; H2020 European Research Council, 810182 ; | Approved | Most recent IF: 8.4; 2023 IF: 5.951 | ||
| Call Number | PLASMANT @ plasmant @c:irua:195377 | Serial | 7241 | ||
| Permanent link to this record | |||||
| Author |
Eshtehardi, H.A.; Van ‘t Veer, K.; Delplancke, M.-P.; Reniers, F.; Bogaerts, A. | ||||
| Title | Postplasma Catalytic Model for NO Production: Revealing the Underlying Mechanisms to Improve the Process Efficiency | Type | A1 Journal article | ||
| Year | 2023 | Publication | ACS Sustainable Chemistry and Engineering | Abbreviated Journal | |
| Volume | 11 | Issue | 5 | Pages | 1720-1733 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma catalysis is emerging for plasma-assisted gas conversion processes. However, the underlying mechanisms of plasma catalysis are poorly understood. In this work, we present a 1D heterogeneous catalysis model with axial dispersion (i.e., accounting for back-mixing and molecular diffusion of fluid elements in the process stream in the axial direction), for plasma-catalytic NO production from N2/O2 mixtures. We investigate the concentration and reaction rates of each species formed as a function of time and position across the catalyst, in order to determine the underlying mechanisms. To obtain insights into how the performance of the process can be further improved, we also study how changes in the postplasma gas flow composition entering the catalyst bed and in the operation conditions of the catalytic stage affect the performance of NO production. |
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000926412800001 | Publication Date | 2023-02-06 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2168-0485 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 8.4 | Times cited | Open Access | OpenAccess | |
| Notes | This research was supported by the Excellence of Science FWO-FNRS project (FWO grant ID GoF9618n, EOS ID 30505023) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 810182 − SCOPE ERC Synergy project). The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerpen. | Approved | Most recent IF: 8.4; 2023 IF: 5.951 | ||
| Call Number | PLASMANT @ plasmant @c:irua:195377 | Serial | 7257 | ||
| Permanent link to this record | |||||
| Author |
Eshtehardi, H.A.; Van ‘t Veer, K.; Delplancke, M.-P.; Reniers, F.; Bogaerts, A. | ||||
| Title | Postplasma Catalytic Model for NO Production: Revealing the Underlying Mechanisms to Improve the Process Efficiency | Type | A1 Journal article | ||
| Year | 2023 | Publication | ACS Sustainable Chemistry and Engineering | Abbreviated Journal | |
| Volume | 11 | Issue | 5 | Pages | 1720-1733 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma catalysis is emerging for plasma-assisted gas conversion processes. However, the underlying mechanisms of plasma catalysis are poorly understood. In this work, we present a 1D heterogeneous catalysis model with axial dispersion (i.e., accounting for back-mixing and molecular diffusion of fluid elements in the process stream in the axial direction), for plasma-catalytic NO production from N2/O2 mixtures. We investigate the concentration and reaction rates of each species formed as a function of time and position across the catalyst, in order to determine the underlying mechanisms. To obtain insights into how the performance of the process can be further improved, we also study how changes in the postplasma gas flow composition entering the catalyst bed and in the operation conditions of the catalytic stage affect the performance of NO production. |
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000926412800001 | Publication Date | 2023-02-06 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2168-0485 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 8.4 | Times cited | Open Access | OpenAccess | |
| Notes | Fonds Wetenschappelijk Onderzoek, 30505023 GoF9618n ; Fonds De La Recherche Scientifique – FNRS, 30505023 GoF9618n ; H2020 European Research Council, 810182 ; | Approved | Most recent IF: 8.4; 2023 IF: 5.951 | ||
| Call Number | PLASMANT @ plasmant @c:irua:195377 | Serial | 7258 | ||
| Permanent link to this record | |||||
| Author |
Freund, E.; Spadola, C.; Schmidt, A.; Privat-Maldonado, A.; Bogaerts, A.; von Woedtke, T.; Weltmann, K.-D.; Heidecke, C.-D.; Partecke, L.-I.; Käding, A.; Bekeschus, S. | ||||
| Title | Risk Evaluation of EMT and Inflammation in Metastatic Pancreatic Cancer Cells Following Plasma Treatment | Type | A1 Journal article | ||
| Year | 2020 | Publication | Frontiers in physics | Abbreviated Journal | Front. Phys. |
| Volume | 8 | Issue | Pages | ||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The requirements for new technologies to serve as anticancer agents go far beyond their toxicity potential. Novel applications also need to be safe on a molecular and patient level. In a broader sense, this also relates to cancer metastasis and inflammation. In a previous study, the toxicity of an atmospheric pressure argon plasma jet in four human pancreatic cancer cell lines was confirmed and plasma treatment did not promote metastasis in vitro and in ovo. Here, these results are extended by additional types of analysis and new models to validate and define on a molecular level the changes related to metastatic processes in pancreatic cancer cells following plasma treatment in vitro and in ovo. In solid tumors that were grown on the chorion-allantois membrane of fertilized chicken eggs (TUM-CAM), plasma treatment induced modest to profound apoptosis in the tissues. This, however, was not associated with a change in the expression levels of adhesion molecules, as shown using immunofluorescence of ultrathin tissue sections. Culturing of the cells detached from these solid tumors for 6d revealed a similar or smaller total growth area and expression of ZEB1, a transcription factor associated with cancer metastasis, in the plasma-treated pancreatic cancer tissues. Analysis of in vitro and in ovo supernatants of 13 different cytokines and chemokines revealed cell line-specific effects of the plasma treatment but a noticeable increase of, e.g., growth-promoting interleukin 10 was not observed. Moreover, markers of epithelial-to-mesenchymal transition (EMT), a metastasis-promoting cellular program, were investigated. Plasma-treated pancreatic cancer cells did not present an EMT-profile. Finally, a realistic 3D tumor spheroid co-culture model with pancreatic stellate cells was employed, and the invasive properties in a gel-like cellular matrix were investigated. Tumor outgrowth and spread was similar or decreased in the plasma conditions. Altogether, these results provide valuable insights into the effect of plasma treatment on metastasis-related properties of cancer cells and did not suggest EMT-promoting effects of this novel cancer therapy. | ||||
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| Language | Wos | 000581086900001 | Publication Date | 2020-10-09 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2296-424X | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.1 | Times cited | Open Access | ||
| Notes | We thankfully acknowledge the technical support by Felix Niessner and Antje Janetzko. We also thank Jonas Van Audenaerde and Evelien Smits for generating the transduced cell lines used in this study. | Approved | Most recent IF: 3.1; 2020 IF: NA | ||
| Call Number | PLASMANT @ plasmant @c:irua:172448 | Serial | 6425 | ||
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| Author |
Fuchs, J.; Aghaei, M.; Schachel, T.D.; Sperling, M.; Bogaerts, A.; Karst, U. | ||||
| Title | Impact of the Particle Diameter on Ion Cloud Formation from Gold Nanoparticles in ICPMS | Type | A1 Journal article | ||
| Year | 2018 | Publication | Analytical chemistry | Abbreviated Journal | Anal Chem |
| Volume | 90 | Issue | 17 | Pages | 10271-10278 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The unique capabilities of microsecond dwell time (DT) single-particle inductively coupled plasma mass spectrometry (spICPMS) were utilized to characterize the cloud of ions generated from the introduction of suspensions of gold nanoparticles (AuNPs) into the plasma. A set of narrowly distributed particles with diameters ranging from 15.4 to 100.1 nm was synthesized and characterized according to established protocols. Statistically significant numbers of the short transient spICPMS events were evaluated by using 50 μs DT for their summed intensity, maximum intensity, and duration, of which all three were found to depend on the particle diameter. The summed intensity increases from 10 to 1661 counts and the maximum intensity from 6 to 309 counts for AuNPs with diameters from 15.4 to 83.2 nm. The event duration rises from 322 to 1007 μs upon increasing AuNP diameter. These numbers represent a comprehensive set of key data points of the ion clouds generated in ICPMS from AuNPs. The extension of event duration is of high interest to appoint the maximum possible particle number concentration at which separation of consecutive events in spICPMS can still be achieved. Moreover, the combined evaluation of all above-mentioned ion cloud characteristics can explain the regularly observed prolonged single-particle events. The transport and ionization behavior of AuNPs in the ICP was also computationally modeled to gain insight into the size-dependent signal generation. The simulated data reveals that the plasma temperature, and therefore the point of ionization of the particles, is the same for all diameters. However, the maximum number density of Au+, as well as the extent of the ion cloud, depends on the particle diameter, in agreement with the experimental data, and it provides an adequate explanation for the observed ion cloud characteristics. | ||||
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| Language | Wos | 000444060600028 | Publication Date | 2018-09-04 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0003-2700 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 6.32 | Times cited | 5 | Open Access | OpenAccess |
| Notes | We thank Dr. Harald Rösner from the Institute of Materials Physics of the University of Münster for the TEM imaging. | Approved | Most recent IF: 6.32 | ||
| Call Number | PLASMANT @ plasmant @c:irua:153651 | Serial | 5057 | ||
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| Author |
Gamez, G.; Bogaerts, A.; Andrade, F.; Hieftje, G.M. | ||||
| Title | Fundamental studies on a planar-cathode direct current glow discharge: part 1: characterization via laser scattering techniques | Type | A1 Journal article | ||
| Year | 2004 | Publication | Spectrochimica acta: part B : atomic spectroscopy | Abbreviated Journal | Spectrochim Acta B |
| Volume | 59 | Issue | Pages | 435-447 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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| Publisher | Place of Publication | Oxford | Editor | ||
| Language | Wos | 000221577100008 | Publication Date | 2004-03-13 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0584-8547; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.241 | Times cited | 24 | Open Access | |
| Notes | Approved | Most recent IF: 3.241; 2004 IF: 3.086 | |||
| Call Number | UA @ lucian @ c:irua:44505 | Serial | 1310 | ||
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| Author |
Gamez, G.; Bogaerts, A.; Hieftje, G.M. | ||||
| Title | Temporal and spatially resolved laser-scattering plasma diagnostics for the characterization of a ms-pulsed glow discharge | Type | A1 Journal article | ||
| Year | 2006 | Publication | Journal of analytical atomic spectrometry | Abbreviated Journal | J Anal Atom Spectrom |
| Volume | 21 | Issue | Pages | 350-359 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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| Publisher | Place of Publication | London | Editor | ||
| Language | Wos | 000235990200015 | Publication Date | 2006-01-26 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0267-9477;1364-5544; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.379 | Times cited | 17 | Open Access | |
| Notes | Approved | Most recent IF: 3.379; 2006 IF: 3.630 | |||
| Call Number | UA @ lucian @ c:irua:56539 | Serial | 3503 | ||
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| Author |
Gao, M.; Zhang, Y.; Wang, H.; Guo, B.; Zhang, Q.; Bogaerts, A. | ||||
| Title | Mode Transition of Filaments in Packed-Bed Dielectric Barrier Discharges | Type | A1 Journal article | ||
| Year | 2018 | Publication | Catalysts | Abbreviated Journal | Catalysts |
| Volume | 8 | Issue | 6 | Pages | 248 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We investigated the mode transition from volume to surface discharge in a packed bed dielectric barrier discharge reactor by a two-dimensional particle-in-cell/Monte Carlo collision method. The calculations are performed at atmospheric pressure for various driving voltages and for gas mixtures with different N2 and O2 compositions. Our results reveal that both a change of the driving voltage and gas mixture can induce mode transition. Upon increasing voltage, a mode transition from hybrid (volume+surface) discharge to pure surface discharge occurs, because the charged species can escape much more easily to the beads and charge the bead surface due to the strong electric field at high driving voltage. This significant surface charging will further enhance the tangential component of the electric field along the dielectric bead surface, yielding surface ionization waves (SIWs). The SIWs will give rise to a high concentration of reactive species on the surface, and thus possibly enhance the surface activity of the beads, which might be of interest for plasma catalysis. Indeed, electron impact excitation and ionization mainly take place near the bead surface. In addition, the propagation speed of SIWs becomes faster with increasing N2 content in the gas mixture, and slower with increasing O2 content, due to the loss of electrons by attachment to O2 molecules. Indeed, the negative O-2 ion density produced by electron impact attachment is much higher than the electron and positive O+2 ion density. The different ionization rates between N2 and O2 gases will create different amounts of electrons and ions on the dielectric bead surface, which might also have effects in plasma catalysis. |
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| Language | Wos | 000436128600027 | Publication Date | 2018-06-15 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 2073-4344 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.082 | Times cited | 7 | Open Access | OpenAccess |
| Notes | The authors are very grateful to Wei Jiang for the useful discussions on the particle-incell/ Monte-Carlo collision model. | Approved | Most recent IF: 3.082 | ||
| Call Number | PLASMANT @ plasmant @c:irua:152171 | Serial | 4991 | ||
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| Author |
Georgieva, V.; Berthelot, A.; Silva, T.; Kolev, S.; Graef, W.; Britun, N.; Chen, G.; van der Mullen, J.; Godfroid, T.; Mihailova, D.; van Dijk, J.; Snyders, R.; Bogaerts, A.; Delplancke-Ogletree, M.-P. | ||||
| Title | Understanding Microwave Surface-Wave Sustained Plasmas at Intermediate Pressure by 2D Modeling and Experiments: Understanding Microwave Surface-Wave Sustained Plasmas … | Type | A1 Journal article | ||
| Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 14 | Issue | 14 | Pages | 1600185 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | An Ar plasma sustained by a surfaguide wave launcher is investigated at intermediate pressure (200–2667 Pa). Two 2D self-consistent models (quasi-neutral and plasma bulk-sheath) are developed and benchmarked. The complete set of electromagnetic and fluid equations and the boundary conditions are presented. The transformation of fluid equations from a local reference frame, that is, moving with plasma or when the gas flow is zero, to a laboratory reference frame, that is, accounting for the gas flow, is discussed. The pressure range is extended down to 80 Pa by experimental measurements. The electron temperature decreases with pressure. The electron density depends linearly on power, and changes its behavior with pressure depending on the product of pressure and radial plasma size. |
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| Language | Wos | 000403074000012 | Publication Date | 2016-11-17 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 1612-8850 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.846 | Times cited | 8 | Open Access | Not_Open_Access |
| Notes | Federaal Wetenschapsbeleid; European Marie Curie RAPID project; European Union's Seventh Framework Programme, 606889 ; | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:142807 | Serial | 4568 | ||
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| Author |
Georgieva, V.; Bogaerts, A. | ||||
| Title | Negative ion behavior in single- and dual-frequency plasma etching reactors: particle-in-cell/Monte Carlo collision study | Type | A1 Journal article | ||
| Year | 2006 | Publication | Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics | Abbreviated Journal | Phys Rev E |
| Volume | 73 | Issue | 3 | Pages | 036402,1-9 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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| Publisher | Place of Publication | Lancaster, Pa | Editor | ||
| Language | Wos | 000236467700081 | Publication Date | 2006-06-10 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1539-3755;1550-2376; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.366 | Times cited | 7 | Open Access | |
| Notes | Approved | Most recent IF: 2.366; 2006 IF: 2.438 | |||
| Call Number | UA @ lucian @ c:irua:57764 | Serial | 2290 | ||
| Permanent link to this record | |||||
| Author |
Georgieva, V.; Bogaerts, A. | ||||
| Title | Numerical simulation of dual frequency etching reactors: influence of the external process parameters on the plasma characteristics | Type | A1 Journal article | ||
| Year | 2005 | Publication | Journal of applied physics | Abbreviated Journal | J Appl Phys |
| Volume | 98 | Issue | 2 | Pages | 023308,1-13 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | American Institute of Physics | Place of Publication | New York, N.Y. | Editor | |
| Language | Wos | 000230931500016 | Publication Date | 2005-07-27 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-8979; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.068 | Times cited | 75 | Open Access | |
| Notes | Approved | Most recent IF: 2.068; 2005 IF: 2.498 | |||
| Call Number | UA @ lucian @ c:irua:53575 | Serial | 2404 | ||
| Permanent link to this record | |||||
| Author |
Georgieva, V.; Bogaerts, A. | ||||
| Title | Plasma characteristics of an Ar/CF4/N2 discharge in an asymmetric dual frequency reactor: numerical investigation by a PIC/MC model | Type | A1 Journal article | ||
| Year | 2006 | Publication | Plasma sources science and technology | Abbreviated Journal | Plasma Sources Sci T |
| Volume | 15 | Issue | Pages | 368-377 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Institute of Physics | Place of Publication | Bristol | Editor | |
| Language | Wos | 000240655500010 | Publication Date | 2006-04-28 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0963-0252;1361-6595; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.302 | Times cited | 35 | Open Access | |
| Notes | Approved | Most recent IF: 3.302; 2006 IF: 2.346 | |||
| Call Number | UA @ lucian @ c:irua:57550 | Serial | 2630 | ||
| Permanent link to this record | |||||
| Author |
Georgieva, V.; Bogaerts, A.; Gijbels, R. | ||||
| Title | Numerical investigation of ion energy distribution functions in single and dual frequency capacitively coupled plasma reactors | Type | A1 Journal article | ||
| Year | 2004 | Publication | Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics | Abbreviated Journal | Phys Rev E |
| Volume | 69 | Issue | Pages | 026406 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Lancaster, Pa | Editor | ||
| Language | Wos | 000220255500058 | Publication Date | 2004-02-24 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1539-3755;1550-2376; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.366 | Times cited | 97 | Open Access | |
| Notes | Approved | Most recent IF: 2.366; 2004 IF: NA | |||
| Call Number | UA @ lucian @ c:irua:44025 | Serial | 2395 | ||
| Permanent link to this record | |||||
| Author |
Georgieva, V.; Bogaerts, A.; Gijbels, R. | ||||
| Title | Numerical study of Ar/CF4/N2 discharges in single and dual frequency capacitively coupled plasma reactors | Type | A1 Journal article | ||
| Year | 2003 | Publication | Journal of applied physics | Abbreviated Journal | J Appl Phys |
| Volume | 94 | Issue | Pages | 3748-3756 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | American Institute of Physics | Place of Publication | New York, N.Y. | Editor | |
| Language | Wos | 000185419600009 | Publication Date | 2003-12-03 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-8979; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.068 | Times cited | 90 | Open Access | |
| Notes | Approved | Most recent IF: 2.068; 2003 IF: 2.171 | |||
| Call Number | UA @ lucian @ c:irua:44014 | Serial | 2408 | ||
| Permanent link to this record | |||||
| Author |
Georgieva, V.; Bogaerts, A.; Gijbels, R. | ||||
| Title | Particle-in-cell/Monte Carlo simulation of a capacitively coupled radio frequency Ar/Cf4 discharge: effect of gas composition | Type | A1 Journal article | ||
| Year | 2003 | Publication | Journal of applied physics | Abbreviated Journal | J Appl Phys |
| Volume | 93 | Issue | Pages | 2369-2379 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | American Institute of Physics | Place of Publication | New York, N.Y. | Editor | |
| Language | Wos | 000181307000007 | Publication Date | 2003-03-06 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-8979; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.068 | Times cited | 57 | Open Access | |
| Notes | Approved | Most recent IF: 2.068; 2003 IF: 2.171 | |||
| Call Number | UA @ lucian @ c:irua:44011 | Serial | 2561 | ||
| Permanent link to this record | |||||
| Author |
Georgieva, V.; Saraiva, M.; Jehanathan, N.; Lebelev, O.I.; Depla, D.; Bogaerts, A. | ||||
| Title | Sputter-deposited Mg-Al-O thin films: linking molecular dynamics simulations to experiments | Type | A1 Journal article | ||
| Year | 2009 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
| Volume | 42 | Issue | 6 | Pages | 065107,1-065107,8 |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Using a molecular dynamics model the crystallinity of MgxAlyOz thin films with a variation in the stoichiometry of the thin film is studied at operating conditions similar to the experimental operating conditions of a dual magnetron sputter deposition system. The films are deposited on a crystalline or amorphous substrate. The Mg metal content in the film ranged from 100% (i.e. MgO film) to 0% (i.e. Al2O3 film). The radial distribution function and density of the films are calculated. The results are compared with x-ray diffraction and transmission electron microscopy analyses of experimentally deposited thin films by the dual magnetron reactive sputtering process. Both simulation and experimental results show that the structure of the MgAlO film varies from crystalline to amorphous when the Mg concentration decreases. It seems that the crystalline MgAlO films have a MgO structure with Al atoms in between. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | London | Editor | ||
| Language | Wos | 000263824200024 | Publication Date | 2009-03-03 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0022-3727;1361-6463; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.588 | Times cited | 37 | Open Access | |
| Notes | Iwt | Approved | Most recent IF: 2.588; 2009 IF: 2.083 | ||
| Call Number | UA @ lucian @ c:irua:73246 | Serial | 3110 | ||
| Permanent link to this record | |||||
| Author |
Georgieva, V.; Todorov, I.T.; Bogaerts, A. | ||||
| Title | Molecular dynamics simulation of oxide thin film growth: importance of the inter-atomic interaction potential | Type | A1 Journal article | ||
| Year | 2010 | Publication | Chemical physics letters | Abbreviated Journal | Chem Phys Lett |
| Volume | 485 | Issue | 4/6 | Pages | 315-319 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | A molecular dynamics (MD) study of MgxAlyOz thin films grown by magnetron sputtering is presented using an ionic model and comparing two potential sets with formal and partial charges. The applicability of the model and the reliability of the potential sets for the simulation of thin film growth are discussed. The formal charge potential set was found to reproduce the thin film structure in close agreement with the structure of the experimentally grown thin films. Graphical abstract A molecular dynamics study of growth of MgxAlyOz thin films is presented using an ionic model and comparing two potential sets with formal and partial charges. The simulation results with the formal charge potential set showed a transition in the film from a crystalline to an amorphous structure, when the Mg metal content decreases below 50% in very close agreement with the structure of the experimentally deposited films. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Amsterdam | Editor | ||
| Language | Wos | 000273782600010 | Publication Date | 2010-01-05 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0009-2614; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.815 | Times cited | 16 | Open Access | |
| Notes | Approved | Most recent IF: 1.815; 2010 IF: 2.282 | |||
| Call Number | UA @ lucian @ c:irua:80023 | Serial | 2170 | ||
| Permanent link to this record | |||||
| Author |
Georgieva, V.; Voter, A.F.; Bogaerts, A. | ||||
| Title | Understanding the surface diffusion processes during magnetron sputter-deposition of complex oxide Mg-Al-O thin films | Type | A1 Journal article | ||
| Year | 2011 | Publication | Crystal growth & design | Abbreviated Journal | Cryst Growth Des |
| Volume | 11 | Issue | 6 | Pages | 2553-2558 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | It is known that film structure may change dramatically with the extent of surface diffusion during the film growth process. In the present work, surface diffusion, induced thermally or activated by energetic impacts, is investigated theoretically under conditions appropriate for magnetron sputter-deposition of MgAlO thin films with varying stoichiometry. The distribution of surface diffusion energy barriers available to the system was determined for each stoichiometry, which allowed assessing in a qualitative way how much surface diffusion will take place on the time scale available between deposition events. The activation energy barriers increase with the Al concentration in the film, and therefore, the surface diffusion rates in the time frame of typical deposition rates drop, which can explain the decrease in crystallinity in the film structure and the transition to amorphous structure. The deposition process and the immediate surface diffusion enhanced by the energetic adatoms are simulated by means of a molecular dynamics model. The longer-time thermal surface diffusion and the energy landscape are studied by the temperature accelerated dynamics method, applied in an approximate way. The surface diffusion enhanced by the energetic impacts appears to be very important for the film structure in the low-temperature deposition regime. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000291074600068 | Publication Date | 2011-04-11 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1528-7483;1528-7505; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.055 | Times cited | 14 | Open Access | |
| Notes | Approved | Most recent IF: 4.055; 2011 IF: 4.720 | |||
| Call Number | UA @ lucian @ c:irua:89566 | Serial | 3806 | ||
| Permanent link to this record | |||||
| Author |
Gerrits, N.; Jackson, B.; Bogaerts, A. | ||||
| Title | Accurate Reaction Probabilities for Translational Energies on Both Sides of the Barrier of Dissociative Chemisorption on Metal Surfaces | Type | A1 Journal Article | ||
| Year | 2024 | Publication | The Journal of Physical Chemistry Letters | Abbreviated Journal | J. Phys. Chem. Lett. |
| Volume | 15 | Issue | 9 | Pages | 2566-2572 |
| Keywords | A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| 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. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001177959900001 | Publication Date | 2024-03-07 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1948-7185 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 5.7 | Times cited | Open Access | ||
| Notes | Nick Gerrits has been financially supported through a Dutch Research Council (NWO) Rubicon grant (019.202EN.012). The computational resources and services used in this work were provided by the high performance computing (HPC) core facility CalcUA of the Universiteit Antwerpen and the Flemish Supercomputer Center (VSC) funded by the Research Foundation−Flanders (FWO) and the Flemish Government. The authors thank Mark Somers for useful discussions. | Approved | Most recent IF: 5.7; 2024 IF: 9.353 | ||
| Call Number | PLASMANT @ plasmant @c:irua:204818 | Serial | 9114 | ||
| Permanent link to this record | |||||
| Author |
Ghasemitarei, M.; Ghorbi, T.; Yusupov, M.; Zhang, Y.; Zhao, T.; Shali, P.; Bogaerts, A. | ||||
| Title | Effects of Nitro-Oxidative Stress on Biomolecules: Part 1—Non-Reactive Molecular Dynamics Simulations | Type | A1 Journal Article | ||
| Year | 2023 | Publication | Biomolecules | Abbreviated Journal | Biomolecules |
| Volume | 13 | Issue | 9 | Pages | 1371 |
| Keywords | A1 Journal Article; plasma medicine; reactive oxygen and; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| Abstract | Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001071356400001 | Publication Date | 2023-09-11 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2218-273X | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | Times cited | Open Access | Not_Open_Access | ||
| Notes | This research received no external funding. | Approved | Most recent IF: NA | ||
| Call Number | PLASMANT @ plasmant @c:irua:200380 | Serial | 8958 | ||
| Permanent link to this record | |||||
| Author |
Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R. | ||||
| Title | Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations | Type | A1 Journal article | ||
| Year | 2022 | Publication | Journal Of Chemical Information And Modeling | Abbreviated Journal | J Chem Inf Model |
| Volume | 62 | Issue | 1 | Pages | 129-141 |
| Keywords | A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000740019000001 | Publication Date | 2022-01-10 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1549-9596 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.6 | Times cited | Open Access | Not_Open_Access | |
| Notes | Fonds Wetenschappelijk Onderzoek, 1200219N ; Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. | Approved | Most recent IF: 5.6 | ||
| Call Number | PLASMANT @ plasmant @c:irua:185485 | Serial | 7050 | ||
| Permanent link to this record | |||||
| Author |
Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A. | ||||
| Title | Transport of cystine across xC-antiporter | Type | A1 Journal article | ||
| Year | 2019 | Publication | Archives of biochemistry and biophysics | Abbreviated Journal | Arch Biochem Biophys |
| Volume | 664 | Issue | Pages | 117-126 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Extracellular cystine (CYC) uptake by xC antiporter is important for the cell viability. Especially in cancer cells, the upregulation of xC activity is observed, which protects these cells from intracellular oxidative stress. Hence, inhibition of the CYC uptake may eventually lead to cancer cell death. Up to now, the molecular level mechanism of the CYC uptake by xC antiporter has not been studied in detail. In this study, we applied several different simulation techniques to investigate the transport of CYC through xCT, the light subunit of the xC antiporter, which is responsible for the CYC and glutamate translocation. Specifically, we studied the permeation of CYC across three model systems, i.e., outward facing (OF), occluded (OCC) and inward facing (IF) configurations of xCT. We also investigated the effect of mutation of Cys327 to Ala within xCT, which was also studied experimentally in literature. This allowed us to qualitatively compare our computation results with experimental observations, and thus, to validate our simulations. In summary, our simulations provide a molecular level mechanism of the transport of CYC across the xC antiporter, more specifically, which amino acid residues in the xC antiporter play a key role in the uptake, transport and release of CYC. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000461411200014 | Publication Date | 2019-02-07 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0003-9861 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.165 | Times cited | 3 | Open Access | OpenAccess |
| Notes | Research Foundation − FlandersResearch Foundation − Flanders (FWO), 1200216N 1200219N ; Hercules FoundationHercules Foundation; Flemish GovernmentFlemish Government (department EWI); UAUA; M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant numbers 1200216N and 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript. | Approved | Most recent IF: 3.165 | ||
| Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:158571 | Serial | 5183 | ||
| Permanent link to this record | |||||
| Author |
Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A. | ||||
| Title | Effect of oxidative stress on cystine transportation by xC‾ antiporter | Type | A1 Journal article | ||
| Year | 2019 | Publication | Archives of biochemistry and biophysics | Abbreviated Journal | Arch Biochem Biophys |
| Volume | 674 | Issue | Pages | 108114 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We performed computer simulations to investigate the effect of oxidation on the extracellular cystine (CYC) uptake by the xC− antiporter. The latter is important for killing of cancer cells. Specifically, applying molecular dynamics (MD) simulations we studied the transport of CYC across xCT, i.e., the light subunit of the xC− antiporter, in charge of bidirectional transport of CYC and glutamate. We considered the outward facing (OF) configuration of xCT, and to study the effect of oxidation, we modified the Cys327 residue, located in the vicinity of the extracellular milieu, to cysteic acid (CYO327). Our computational results showed that oxidation of Cys327 results in a free energy barrier for CYC translocation, thereby blocking the access of CYC to the substrate binding site of the OF system. The formation of the energy barrier was found to be due to the conformational changes in the channel. Analysis of the MD trajectories revealed that the reorganization of the side chains of the Tyr244 and CYO327 residues play a critical role in the OF channel blocking. Indeed, the calculated distance between Tyr244 and either Cys327 or CYO327 showed a narrowing of the channel after oxidation. The obtained free energy barrier for CYC translocation was found to be 33.9kJmol−1, indicating that oxidation of Cys327, by e.g., cold atmospheric plasma, is more effective in inhibiting the xC− antiporter than in the mutation of this amino acid to Ala (yielding a barrier of 32.4kJmol−1). The inhibition of the xC− antiporter may lead to Cys starvation in some cancer cells, eventually resulting in cancer cell death. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000525439700011 | Publication Date | 2019-09-23 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0003-9861 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.165 | Times cited | Open Access | ||
| Notes | Ministry of Science, Research and Technology of Iran; University of Antwerp; Research Foundation − Flanders, 1200219N ; Universiteit Antwerpen; Hercules Foundation; Flemish Government; UA; M. G. acknowledges funding from the Ministry of Science, Research and Technology of Iran and from the University of Antwerp in Belgium. M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant number 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript. | Approved | Most recent IF: 3.165 | ||
| Call Number | PLASMANT @ plasmant @c:irua:163474 | Serial | 5372 | ||
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| Author |
Gijbels, R.; Bogaerts, A. | ||||
| Title | Modeling of glow discharge ion sources for mass spectrometry: potentials and limitations | Type | A3 Journal article | ||
| Year | 1997 | Publication | Spectroscopy | Abbreviated Journal | |
| Volume | 9 | Issue | 2 | Pages | 8-14 |
| Keywords | A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | Publication Date | 0000-00-00 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | ISBN | Additional Links | UA library record | ||
| Impact Factor | Times cited | Open Access | |||
| Notes | Approved | Most recent IF: NA | |||
| Call Number | UA @ lucian @ c:irua:19600 | Serial | 2123 | ||
| Permanent link to this record | |||||
| Author |
Gijbels, R.; Bogaerts, A. | ||||
| Title | Recent trends in solids mass spectrometry: GDMS and other methods | Type | A1 Journal article | ||
| Year | 1997 | Publication | Fresenius' journal of analytical chemistry | Abbreviated Journal | Fresen J Anal Chem |
| Volume | 359 | Issue | Pages | 326-330 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Berlin | Editor | ||
| Language | Wos | A1997YC02800004 | Publication Date | 2002-08-25 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0937-0633;1432-1130; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | Times cited | 5 | Open Access | ||
| Notes | Approved | Most recent IF: NA | |||
| Call Number | UA @ lucian @ c:irua:19607 | Serial | 2841 | ||
| Permanent link to this record | |||||
| Author |
Gijbels, R.; Bogaerts, A. | ||||
| Title | Recent trends in solids mass spectrometry, with special emphasis on glow discharge mass spectrometry | Type | P3 Proceeding | ||
| Year | 1996 | Publication | Abbreviated Journal | ||
| Volume | Issue | Pages | 71-86 | ||
| Keywords | P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Perfect Prints | Place of Publication | Thane | Editor | |
| Language | Wos | Publication Date | 0000-00-00 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | ISBN | Additional Links | UA library record | ||
| Impact Factor | Times cited | Open Access | |||
| Notes | Approved | ||||
| Call Number | UA @ lucian @ c:irua:16244 | Serial | 2842 | ||
| Permanent link to this record | |||||
| Author |
Gijbels, R.; van Straaten, M.; Bogaerts, A. | ||||
| Title | Mass spectrometric analysis of inorganic solids: GDMS and other methods | Type | A1 Journal article | ||
| Year | 1995 | Publication | Advances in mass spectrometry | Abbreviated Journal | |
| Volume | 13 | Issue | Pages | 241-256 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | London | Editor | ||
| Language | Wos | A1995BG78P00013 | Publication Date | 0000-00-00 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0568-000x | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | Times cited | 12 | Open Access | ||
| Notes | Approved | no | |||
| Call Number | UA @ lucian @ c:irua:12267 | Serial | 1952 | ||
| Permanent link to this record | |||||