“Modelling of a dielectric barrier glow discharge at atmospheric pressure in nitrogen”. Madani M, Bogaerts A, Gijbels R, Vangeneugden D, , 130 (2002)
Keywords: P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|
“Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations”. Ghasemitarei M, Privat-Maldonado A, Yusupov M, Rahnama S, Bogaerts A, Ejtehadi MR, Journal Of Chemical Information And Modeling 62, 129 (2022). http://doi.org/10.1021/acs.jcim.1c00853
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.
Keywords: A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.6
DOI: 10.1021/acs.jcim.1c00853
|
“PIC –, MCC numerical simulation of a DC planar magnetron”. Kolev I, Bogaerts A, Plasma processes and polymers 3, 127 (2006). http://doi.org/10.1002/ppap.200500118
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 27
DOI: 10.1002/ppap.200500118
|
“Low-Temperature Plasma for Biology, Hygiene, and Medicine: Perspective and Roadmap”. Laroussi M, Bekeschus S, Keidar M, Bogaerts A, Fridman A, Lu X, Ostrikov K, Hori M, Stapelmann K, Miller V, Reuter S, Laux C, Mesbah A, Walsh J, Jiang C, Thagard SM, Tanaka H, Liu D, Yan D, Yusupov M, IEEE transactions on radiation and plasma medical sciences 6, 127 (2022). http://doi.org/10.1109/TRPMS.2021.3135118
Abstract: Plasma, the fourth and most pervasive state of matter in the visible universe, is a fascinating medium that is connected to the beginning of our universe itself. Man-made plasmas are at the core of many technological advances that include the fabrication of semiconductor devices, which enabled the modern computer and communication revolutions. The introduction of low temperature, atmospheric pressure plasmas to the biomedical field has ushered a new revolution in the healthcare arena that promises to introduce plasma-based therapies to combat some thorny and long-standing medical challenges. This article presents an overview of where research is at today and discusses innovative concepts and approaches to overcome present challenges and take the field to the next level. It is written by a team of experts who took an in-depth look at the various applications of plasma in hygiene, decontamination, and medicine, made critical analysis, and proposed ideas and concepts that should help the research community focus their efforts on clear and practical steps necessary to keep the field advancing for decades to come.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.1109/TRPMS.2021.3135118
|
“Hybrid Monte Carlo: fluid model for studying the effects of nitrogen addition to argon glow discharges”. Bogaerts A, Spectrochimica acta: part B : atomic spectroscopy 64, 126 (2009). http://doi.org/10.1016/j.sab.2008.11.004
Abstract: A computer model is developed for describing argon/nitrogen glow discharges. The species taken into account in the model include electrons, Ar atoms in the ground state and in the 4s metastable levels, N2 molecules in the ground state and in six different electronically excited levels, N atoms, Ar+ ions, N+, N2+, N3+ and N4+ ions. The fast electrons are simulated with a Monte Carlo model, whereas all other species are treated in a fluid model. 74 different chemical reactions are considered in the model. The calculation results include the densities of all the different plasma species, as well as information on their production and loss processes. The effect of different N2 additions, in the range between 0.1 and 10%, is investigated.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.241
Times cited: 49
DOI: 10.1016/j.sab.2008.11.004
|
“Collisional-radiative model for an argon glow discharge”. Bogaerts A, Gijbels R, Vlcek J, Journal of applied physics 84, 121 (1998). http://doi.org/10.1063/1.368009
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.068
Times cited: 138
DOI: 10.1063/1.368009
|
“Combining CO2 conversion and N2 fixation in a gliding arc plasmatron”. Ramakers M, Heijkers S, Tytgat T, Lenaerts S, Bogaerts A, Journal of CO2 utilization 33, 121 (2019). http://doi.org/10.1016/j.jcou.2019.05.015
Abstract: Industry needs a flexible and efficient technology to convert CO2 into useful products, which fits in the Carbon Capture and Utilization (CCU) philosophy. Plasma technology is intensively being investigated for this purpose. A promising candidate is the gliding arc plasmatron (GAP). Waste streams of CO2 are often not pure and contain N2 as important impurity. Therefore, in this paper we provide a detailed experimental and computational study of the combined CO2 and N2 conversion in a GAP. Is it possible to take advantage of the presence of N2 in the mixture and to combine CO2 conversion with N2 fixation? Our experiments and simulations reveal that N2 actively contributes to the process of CO2 conversion, through its vibrational levels. In addition, NO and NO2 are formed, with concentrations around 7000 ppm, which is slightly too low for valorization, but by improving the reactor design it must be possible to further increase their concentrations. Other NO-based molecules, in particular the strong greenhouse gas N2O, are not formed in the GAP, which is an important result. We also compare our results with those obtained in other plasma reactors to clarify the differences in underlying plasma processes, and to demonstrate the superiority of the GAP.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 4.292
Times cited: 3
DOI: 10.1016/j.jcou.2019.05.015
|
“Transport of cystine across xC-antiporter”. Ghasemitarei M, Yusupov M, Razzokov J, Shokri B, Bogaerts A, Archives of biochemistry and biophysics 664, 117 (2019). http://doi.org/10.1016/j.abb.2019.01.039
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.165
Times cited: 3
DOI: 10.1016/j.abb.2019.01.039
|
“Analysis of the composition of glass objects from Qumran, Israel and the comparison with other Roman glass from western Europe”. Aerts A, Janssens K, Velde B, Adams F, Wouters H page 113 (2000).
Keywords: H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
|
“Computer simulations for processing plasmas”. Bogaerts A, de Bleecker K, Georgieva V, Kolev I, Madani M, Neyts E, Plasma processes and polymers 3, 110 (2006). http://doi.org/10.1002/ppap.200500065
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 8
DOI: 10.1002/ppap.200500065
|
“Comparison of modeling calculations with experimental results for rf glow discharge optical emission spectrometry”. Bogaerts A, Wilken L, Hoffmann V, Gijbels R, Wetzig K, Spectrochimica acta: part B : atomic spectroscopy 57, 109 (2002). http://doi.org/10.1016/S0584-8547(01)00357-3
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.241
Times cited: 14
DOI: 10.1016/S0584-8547(01)00357-3
|
“Numerical study on energy efficiency of a cylindrical dielectric barrier discharge plasma-chemical reactor”. Petrovic D, Martens T, De Bie C, van Dijk J, Brok WJM, Bogaerts A, , 109 (2009)
Keywords: P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|
“Improving dielectric barrier discharge efficiency by optimizing voltage profiles”. Martens T, Brok WJM, van Dijk J, Bogaerts A, , 95 (2009)
Keywords: P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|
“Investigation of laser output power saturation in the He-Cu+ IR hollow cathode discharge laser by experiments and numerical modeling”. Bogaerts A, Gijbels R, Grozeva M, Sabotinov N, Physica scripta T105, 90 (2003). http://doi.org/10.1238/Physica.Topical.105a00090
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.28
DOI: 10.1238/Physica.Topical.105a00090
|
“Microscopic synchroton radiation induced X-ray fluorescence analysis”. Janssens K, Vincze L, Aerts A, Vekemans B, Adams F, Jones K, Knöchel A, Mikrochimica acta: supplementum , 87 (1996)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
|
“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)
|
“Mathematical modelling of an analytical glow discharge”. Bogaerts A, van Straaten M, Gijbels R KD Marketing Services, Milton Keynes, page 82 (1995).
Keywords: H3 Book chapter; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|
“A chemical investigation of altered jade art objects”. Aerts A, Janssens K, Adams F, Orientations , 79 (1995)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
|
“CO2-CH4 conversion and syngas formation at atmospheric pressure using a multi-electrode dielectric barrier discharge”. Ozkan A, Dufour T, Arnoult G, De Keyzer P, Bogaerts A, Reniers F, Journal of CO2 utilization 9, 74 (2015). http://doi.org/10.1016/j.jcou.2015.01.002
Abstract: The conversion of CO2 and CH4 into value-added chemicals is studied in a new geometry of a dielectric barrier discharge (DBD) with multi-electrodes, dedicated to the treatment of high gas flow rates. Gas chromatography is used to define the CO2 and CH4 conversion as well as the yields of the products of decomposition (CO, O2 and H2) and of recombination (C2H4, C2H6 and CH2O). The influence of three parameters is investigated on the conversion: the CO2 and CH4 flow rates, the plasma power and the nature of the carrier gas (argon or helium). The energy efficiency of the CO2 conversion is estimated and compared with those of similar atmospheric plasma sources. Our DBD reactor shows a good compromise between a good energy efficiency and the treatment of a large CO2 flow rate.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.292
Times cited: 57
DOI: 10.1016/j.jcou.2015.01.002
|
“Modeling the growth of SWNTs and graphene on the atomic scale”. Neyts EC, Bogaerts A, ECS transactions 45, 73 (2012). http://doi.org/10.1149/1.3700454
Abstract: The possibility of application of nanomaterials is determined by our ability to control the properties of the materials, which are ultimately determined by their structure and hence their growth processes. We employ hybrid molecular dynamics / Monte Carlo (MD/MC) simulations to explore the growth of SWNTs and graphene on nickel as a catalyst, with the specific goal of unraveling the growth mechanisms. While the general observations are in agreement with the literature, we find a number of interesting phenomena to be operative which are crucial for the growth, and which are not accessible by MD simulations alone due to the associated time scale. Specifically, we observe metal mediated healing and restructuring processes to take place, reorganizing the carbon network during the initial nucleation step. In the case of carbon nanotube growth, this leads to the growth of tubes with a determinable chirality. In the case of graphene formation, we find that graphene is only formed at temperatures above 700 K. These results are of importance for understanding the growth mechanisms of these carbon nanomaterials on the fundamental level.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Times cited: 2
DOI: 10.1149/1.3700454
|
“Use of microscopic XRF for non-destructive analysis in art an archaeometry”. Janssens K, Vittiglio G, Deraedt I, Aerts A, Vekemans B, Vincze L, Wei F, de Ryck I, Schalm O, Adams F, Rindby A, Knöchel A, Simionovici AS, Snigirev A, X-ray spectrometry 29, 73 (2000). http://doi.org/10.1002/(SICI)1097-4539(200001/02)29:1<73::AID-XRS416>3.3.CO;2-D
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 1.298
DOI: 10.1002/(SICI)1097-4539(200001/02)29:1<73::AID-XRS416>3.3.CO;2-D
|
“Recent trends in solids mass spectrometry, with special emphasis on glow discharge mass spectrometry”. Gijbels R, Bogaerts A, , 71 (1996)
Keywords: P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|
“Can plasma spectrochemistry assist in improving the accuracy of chemical analysis?”.Adams F, Adriaens A, Bogaerts A, Analytica chimica acta 456, 63 (2002). http://doi.org/10.1016/S0003-2670(02)00010-7
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.95
Times cited: 6
DOI: 10.1016/S0003-2670(02)00010-7
|
“Modeling of gas discharge plasmas: What can we learn from it?”.Bogaerts A, de Bleecker K, Kolev I, Madani M, Surface and coatings technology 200, 62 (2005). http://doi.org/10.1016/j.surfcoat.2005.02.057
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.589
Times cited: 11
DOI: 10.1016/j.surfcoat.2005.02.057
|
“Langmuir probe diagnostic of high pressure plasmas: study by PIC-MC modelling”. Cenian A, Chernukho A, Bogaerts A, Gijbels R, Leys C, , 61 (2004)
Keywords: P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|
“Modeling of the magnetron discharge”. Bogaerts A, Kolev I, Buyle G Springer, Berlin, page 61 (2008).
Keywords: H1 Book chapter; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|
Berthelot A, Kolev S, Bogaerts A (2015) Different pressure regimes of a surface-wave discharge in argon : a modelling investigation. UCO Press, Cordoba, 57–62
Keywords: P2 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|
“Optimization of operating parameters for inductively coupled plasma mass spectrometry : a computational study”. Aghaei M, Lindner H, Bogaerts A, Spectrochimica acta: part B : atomic spectroscopy 76, 56 (2012). http://doi.org/10.1016/j.sab.2012.06.006
Abstract: An inductively coupled plasma, connected to a mass spectrometer interface, is computationally investigated. The effect of pressure behind the sampler, injector gas flow rate, auxiliary gas flow rate, and applied power is studied. There seems to be an optimum range of injector gas flow rate for each setup which guaranties the presence and also a proper length of the central channel in the torch. Moreover, our modeling results show that for any specific purpose, it is possible to control that either only the central gas flow passes through the sampler orifice or that it is accompanied by the auxiliary gas flow. It was also found that depending on geometry, the variation of outgoing gas flow rate is much less than the variation of the injector gas flow rate and this causes a slightly higher pressure inside the torch. The general effect of increasing the applied power is a rise in the plasma temperature, which results in a higher ionization in the coil region. However, the negative effect is reducing the length of the cool central channel which is important to transfer the sample substances to the sampler. Using a proper applied power can enhance the efficiency of the system. Indeed, by changing the gas path lines, the power can control which flow (i.e., only from injector gas or also from the auxiliary gas) goes to the sampler orifice. Finally, as also reported from experiments in literature, the pressure behind the sampler has no dramatic effect on the plasma characteristics.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.241
Times cited: 18
DOI: 10.1016/j.sab.2012.06.006
|
“Can plasma be formed in catalyst pores? A modeling investigation”. Zhang Y-R, Van Laer K, Neyts EC, Bogaerts A, Applied catalysis : B : environmental 185, 56 (2016). http://doi.org/10.1016/j.apcatb.2015.12.009
Abstract: tWe investigate microdischarge formation inside catalyst pores by a two-dimensional fluid model forvarious pore sizes in the m-range and for various applied voltages. Indeed, this is a poorly understoodphenomenon in plasma catalysis. The calculations are performed for a dielectric barrier discharge inhelium, at atmospheric pressure. The electron and ion densities, electron temperature, electric field andpotential, as well as the electron impact ionization and excitation rate and the densities of excited plasmaspecies, are examined for a better understanding of the characteristics of the plasma inside a pore. Theresults indicate that the pore size and the applied voltage are critical parameters for the formation of amicrodischarge inside a pore. At an applied voltage of 20 kV, our calculations reveal that the ionizationmainly takes place inside the pore, and the electron density shows a significant increase near and inthe pore for pore sizes larger than 200m, whereas the effect of the pore on the total ion density isevident even for 10m pores. When the pore size is fixed at 30m, the presence of the pore has nosignificant influence on the plasma properties at an applied voltage of 2 kV. Upon increasing the voltage,the ionization process is enhanced due to the strong electric field and high electron temperature, andthe ion density shows a remarkable increase near and in the pore for voltages above 10 kV. These resultsindicate that the plasma species can be formed inside pores of structured catalysts (in the m range),and they may interact with the catalyst surface, and affect the plasma catalytic process.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.446
Times cited: 75
DOI: 10.1016/j.apcatb.2015.12.009
|
“De belofte van hoofdhalskankerorganoïden in kankeronderzoek : een blik op de toekomst”. Zaryouh H, Verswyvel H, Bauwens M, Van Haesendonck G, Deben C, Lin A, De Waele J, Vermorken JB, Koljenovic S, Bogaerts A, Lardon F, Smits E, Wouters A, Onco-hemato : multidisciplinair tijdschrift voor oncologie 17, 54 (2023)
Abstract: Hoofd-halskanker vormt een aanzienlijke uitdaging met bijna 900.000 nieuwe diagnoses per jaar, waarbij de jaarlijkse incidentie blijft stijgen. Vaak wordt de diagnose pas in een laat stadium gesteld, wat complexe behandelingen noodzakelijk maakt. Terugval van patiënten is helaas een veelvoorkomend probleem. De gemiddelde overlevingsduur is beperkt tot enkele maanden. Daarom is er een dringende behoefte om nieuwe, veelbelovende behandelingen te ontwikkelen voor patiënten met hoofd-halskanker. Voor het bereiken van deze vooruitgang spelen innovatieve studiemodellen een cruciale rol. Het ontwikkelen van deze nieuwe behandelingen start met laboratoriumonderzoek, waarbij traditionele tweedimensionale celculturen hun beperkingen hebben. Daarom verschuiven onderzoekers hun aandacht meer en meer naar geavanceerdere driedimensionale modellen, met hoofd-halskankerorganoïden als beloftevol nieuw model. Dit model behoudt immers zowel het genetische profiel als de morfologische kenmerken van de originele tumor van de hoofd-halskankerpatiënt. Hoofdhalskankerorganoïden bieden daarom de mogelijkheid om innovatieve behandelingen te testen en kunnen mogelijk zelfs de respons van een patiënt op bepaalde therapieën voorspellen. Hoewel tumororganoïden als ‘patiënt-in-het-lab’ veelbelovend zijn, zijn er uitdagingen te overwinnen, zoals de ontwikkelingstijd en de toepasbaarheid bij alle tumortypes, evenals het ontbreken van immuuncellen en andere micro-omgevingscomponenten. Er is daarom een grote behoefte aan gestandaardiseerde protocollen voor de ontwikkeling van organoïden en verkorting van de ontwikkelingstijd. Concluderend bieden driedimensionale hoofd-halskankerorganoïden een veelbelovend perspectief voor de toekomst van kankerbehandelingen. Ze hebben het potentieel om bij te dragen aan de ontwikkeling van gepersonaliseerde behandelingen en zo de overlevingskansen van kankerpatiënten te verbeteren. Het is echter belangrijk om hun voorspellend vermogen en toepassingsmogelijkheden verder te onderzoeken, voordat ze op grote schaal worden geïmplementeerd.
Keywords: A2 Journal article; Center for Oncological Research (CORE); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|