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| Author | Bogaerts, A.; Neyts, E.C.; Guaitella, O.; Murphy, A.B. | ||||
| Title | Foundations of plasma catalysis for environmental applications | Type | A1 Journal article | ||
| Year | 2022 | Publication | Plasma Sources Science & Technology | Abbreviated Journal | Plasma Sources Sci T |
| Volume | Issue | Pages | |||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma catalysis is gaining increasing interest for various applications, but the underlying mechanisms are still far from understood. Hence, more fundamental research is needed to understand these mechanisms. This can be obtained by both modelling and experiments. This foundations paper describes the fundamental insights in plasma catalysis, as well as efforts to gain more insights by modelling and experiments. Furthermore, it discusses the state-of-the-art of the major plasma catalysis applications, as well as successes and challenges of technology transfer of these applications. | ||||
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| Language | Wos | 000804396200001 | Publication Date | 2022-03-21 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor  |
3.8 | Times cited | Open Access | OpenAccess | |
| Notes | H2020 Marie Skłodowska-Curie Actions, 823745 ; H2020 European Research Council, 810182 ; We acknowldege financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation programme (Grant Agreement No. 810182 – SCOPE ERC Synergy project) and the European Union’s Horizon 2020 Research and Innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 813393 (PIONEER). | Approved | Most recent IF: 3.8 | ||
| Call Number | PLASMANT @ plasmant @c:irua:188539 | Serial | 7070 | ||
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| Author | Bissonnette-Dulude, J.; Heirman, P.; Coulombe, S.; Bogaerts, A.; Gervais, T.; Reuter, S. | ||||
| Title | Coupling the COST reference plasma jet to a microfluidic device: a computational study | Type | A1 Journal Article | ||
| Year | 2024 | Publication | Plasma sources science and technology | Abbreviated Journal | Plasma Sources Sci. Technol. |
| Volume | 33 | Issue | 1 | Pages | 015001 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The use of microfluidic devices in the field of plasma-liquid interaction can unlock unique possibilities to investigate the effects of plasma-generated reactive species for environmental and biomedical applications. So far, very little simulation work has been performed on microfluidic devices in contact with a plasma source. We report on the modelling and computational simulation of physical and chemical processes taking place in a novel plasma-microfluidic platform. The main production and transport pathways of reactive species both in plasma and liquid are modelled by a novel modelling approach that combines 0D chemical kinetics and 2D transport mechanisms. This combined approach, applicable to systems where the transport of chemical species occurs in unidirectional flows at high Péclet numbers, decreases calculation times considerably compared to regular 2D simulations. It takes advantage of the low computational time of the 0D reaction models while providing spatial information through multiple plug-flow simulations to yield a quasi-2D model. The gas and liquid flow profiles are simulated entirely in 2D, together with the chemical reactions and transport of key chemical species. The model correctly predicts increased transport of hydrogen peroxide into the liquid when the microfluidic opening is placed inside the plasma effluent region, as opposed to inside the plasma region itself. Furthermore, the modelled hydrogen peroxide production and transport in the microfluidic liquid differs by less than 50% compared with experimental results. To explain this discrepancy, the limits of the 0D–2D combined approach are discussed. | ||||
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| Language | Wos | 001136607100001 | Publication Date | 2024-01-01 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
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| ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor |
3.8 | Times cited | Open Access | Not_Open_Access | |
| Notes | Natural Sciences and Engineering Research Council of Canada, RGPIN-06820 ; FWO, 1100421N ; McGill University, the TransMedTech Institute; | Approved | Most recent IF: 3.8; 2024 IF: 3.302 | ||
| Call Number | PLASMANT @ plasmant @c:irua:202783 | Serial | 8990 | ||
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| Author | Biondo, O.; Fromentin, C.; Silva, T.; Guerra, V.; van Rooij, G.; Bogaerts, A. | ||||
| Title | Insights into the limitations to vibrational excitation of CO2: validation of a kinetic model with pulsed glow discharge experiments | Type | A1 Journal article | ||
| Year | 2022 | Publication | Plasma Sources Science & Technology | Abbreviated Journal | Plasma Sources Sci T |
| Volume | 31 | Issue | 7 | Pages | 074003 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Vibrational excitation represents an efficient channel to drive the dissociation of CO<sub>2</sub>in a non-thermal plasma. Its viability is investigated in low-pressure pulsed discharges, with the intention of selectively exciting the asymmetric stretching mode, leading to stepwise excitation up to the dissociation limit of the molecule. Gas heating is crucial for the attainability of this process, since the efficiency of vibration–translation (V–T) relaxation strongly depends on temperature, creating a feedback mechanism that can ultimately thermalize the discharge. Indeed, recent experiments demonstrated that the timeframe of V–T non-equilibrium is limited to a few milliseconds at ca. 6 mbar, and shrinks to the<italic>μ</italic>s-scale at 100 mbar. With the aim of backtracking the origin of gas heating in pure CO<sub>2</sub>plasma, we perform a kinetic study to describe the energy transfers under typical non-thermal plasma conditions. The validation of our kinetic scheme with pulsed glow discharge experiments enables to depict the gas heating dynamics. In particular, we pinpoint the role of vibration–vibration–translation relaxation in redistributing the energy from asymmetric to symmetric levels of CO<sub>2</sub>, and the importance of collisional quenching of CO<sub>2</sub>electronic states in triggering the heating feedback mechanism in the sub-millisecond scale. This latter finding represents a novelty for the modelling of low-pressure pulsed discharges and we suggest that more attention should be paid to it in future studies. Additionally, O atoms convert vibrational energy into heat, speeding up the feedback loop. The efficiency of these heating pathways, even at relatively low gas temperature and pressure, underpins the lifetime of V–T non-equilibrium and suggests a redefinition of the optimal conditions to exploit the ‘ladder-climbing’ mechanism in CO<sub>2</sub>discharges. | ||||
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| Language | Wos | 000839466500001 | Publication Date | 2022-07-01 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
3.8 | Times cited | Open Access | OpenAccess | |
| Notes | Fundação para a Ciência e a Tecnologia, PLA/0076/2021 ; H2020 Marie Skłodowska-Curie Actions, 813393 ; This research was supported by the European Union’s Horizon 2020 Research and Innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 813393 (PIONEER). V Guerra and T Silva were partially funded by the Portuguese ‘FCT-Fundação para a Ciência e a Tecnologia’, under Projects UIDB/50010/2020, UIDP/50010/2020, PTDC/FISPLA/1616/2021 and EXPL/FIS-PLA/0076/2021. 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: 3.8 | ||
| Call Number | PLASMANT @ plasmant @c:irua:190008 | Serial | 7106 | ||
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| Author | Tennyson, J.; Mohr, S.; Hanicinec, M.; Dzarasova, A.; Smith, C.; Waddington, S.; Liu, B.; Alves, L.L.; Bartschat, K.; Bogaerts, A.; Engelmann, S.U.; Gans, T.; Gibson, A.R.; Hamaguchi, S.; Hamilton, K.R.; Hill, C.; O’Connell, D.; Rauf, S.; van ’t Veer, K.; Zatsarinny, O. | ||||
| Title | The 2021 release of the Quantemol database (QDB) of plasma chemistries and reactions | Type | A1 Journal article | ||
| Year | 2022 | Publication | Plasma Sources Science & Technology | Abbreviated Journal | Plasma Sources Sci T |
| Volume | 31 | Issue | 9 | Pages | 095020 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The Quantemol database (QDB) provides cross sections and rates of processes important for plasma models; heavy particle collisions (chemical reactions) and electron collision processes are considered. The current version of QDB has data on 28 917 processes between 2485 distinct species plus data for surface processes. These data are available via a web interface or can be delivered directly to plasma models using an application program interface; data are available in formats suitable for direct input into a variety of popular plasma modeling codes including HPEM, COMSOL, ChemKIN, CFD-ACE+, and VisGlow. QDB provides ready assembled plasma chemistries plus the ability to build bespoke chemistries. The database also provides a Boltzmann solver for electron dynamics and a zero-dimensional model. Thesedevelopments, use cases involving O<sub>2</sub>, Ar/NF<sub>3</sub>, Ar/NF<sub>3</sub>/O<sub>2</sub>, and He/H<sub>2</sub>O/O<sub>2</sub>chemistries, and plans for the future are presented. | ||||
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| Language | Wos | 000895762200001 | Publication Date | 2022-09-01 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
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| ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor |
3.8 | Times cited | Open Access | OpenAccess | |
| Notes | Engineering and Physical Sciences Research Council, EP/N509577/1 ; Fundação para a Ciência e a Tecnologia, UIDB/50010/2020 ; Science and Technology Facilities Council, ST/K004069/1 ; National Science Foundation, OAC-1834740 ; | Approved | Most recent IF: 3.8 | ||
| Call Number | PLASMANT @ plasmant @c:irua:192845 | Serial | 7245 | ||
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| Author | Biondo, O.; Hughes, A.; van der Steeg, A.; Maerivoet, S.; Loenders, B.; van Rooij, G.; Bogaerts, A. | ||||
| Title | Power concentration determined by thermodynamic properties in complex gas mixtures : the case of plasma-based dry reforming of methane | Type | A1 Journal article | ||
| Year | 2023 | Publication | Plasma sources science and technology | Abbreviated Journal | |
| Volume | 32 | Issue | 4 | Pages | 045001-45020 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We investigate discharge contraction in a microwave plasma at sub-atmospheric pressure, operating in CO2 and CO2/CH4 mixtures. The rise of the electron number density with plasma contraction intensifies the gas heating in the core of the plasma. This, in turn, initiates fast core-periphery transport and defines the rate of thermal chemistry over plasma chemistry. In this context, power concentration describes the overall mechanism including plasma contraction and chemical kinetics. In a complex chemistry such as dry reforming of methane, transport of reactive species is essential to define the performance of the reactor and achieve the desired outputs. Thus, we couple experimental observations and thermodynamic calculations for model validation and understanding of reactor performance. Adding CH4 alters the thermodynamic properties of the mixture, especially the reactive component of the heat conductivity. The increase in reactive heat conductivity increases the pressure at which plasma contraction occurs, because higher rates of gas heating are required to reach the same temperature. In addition, we suggest that the predominance of heat conduction over convection is a key condition to observe the effect of heat conductivity on gas temperature. | ||||
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| Language | Wos | 000963579500001 | Publication Date | 2023-03-23 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
3.8 | Times cited | Open Access | Not_Open_Access | |
| Notes | Approved | Most recent IF: 3.8; 2023 IF: 3.302 | |||
| Call Number | UA @ admin @ c:irua:196044 | Serial | 8397 | ||
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| Author | Tsonev, I.; Boothroyd, J.; Kolev, S.; Bogaerts, A. | ||||
| Title | Simulation of glow and arc discharges in nitrogen: effects of the cathode emission mechanisms | Type | A1 Journal Article | ||
| Year | 2023 | Publication | PLASMA SOURCES SCIENCE & TECHNOLOGY | Abbreviated Journal | |
| Volume | 32 | Issue | 5 | Pages | 054002 |
| Keywords | A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| Abstract | Experimental evidence in the literature has shown that low-current direct current nitrogen discharges can exist in both glow and arc regimes at atmospheric pressure. However, modelling investigations of the positive column that include the influence of the cathode phenomena are scarce. In this work we developed a 2D axisymmetric model of a plasma discharge in flowing nitrogen gas, studying the influence of the two cathode emission mechanisms—thermionic field emission and secondary electron emission—on the cathode region and the positive column. We show for an inlet gas flow velocity of 1 m s<sup>−1</sup>in the current range of 80–160 mA, that the electron emission mechanism from the cathode greatly affects the size and temperature of the cathode region, but does not significantly influence the discharge column at atmospheric pressure. We also demonstrate that in the discharge column the electron density balance is local and the electron production and destruction is dominated by volume processes. With increasing flow velocity, the discharge contraction is enhanced due to the increased convective heat loss. The cross sectional area of the conductive region is strongly dependent on the gas velocity and heat conductivity of the gas. | ||||
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| Language | Wos | 000987841800001 | Publication Date | 2023-05-01 | |
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| ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor |
3.8 | Times cited | Open Access | Not_Open_Access | |
| Notes | This research is financially supported by the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 965546. | Approved | Most recent IF: 3.8; 2023 IF: 3.302 | ||
| Call Number | PLASMANT @ plasmant @c:irua:196972 | Serial | 8788 | ||
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| Author | Vanraes, P.; Parayil Venugopalan, S.; Besemer, M.; Bogaerts, A. | ||||
| Title | Assessing neutral transport mechanisms in aspect ratio dependent etching by means of experiments and multiscale plasma modeling | Type | A1 Journal Article | ||
| Year | 2023 | Publication | Plasma Sources Science and Technology | Abbreviated Journal | Plasma Sources Sci. Technol. |
| Volume | 32 | Issue | 6 | Pages | 064004 |
| Keywords | A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| Abstract | Since the onset of pattern transfer technologies for chip manufacturing, various strategies have been developed to circumvent or overcome aspect ratio dependent etching (ARDE). These methods have, however, their own limitations in terms of etch non-idealities, throughput or costs. Moreover, they have mainly been optimized for individual in-device features and die-scale patterns, while occasionally ending up with poor patterning of metrology marks, affecting the alignment and overlay in lithography. Obtaining a better understanding of the underlying mechanisms of ARDE and how to mitigate them therefore remains a relevant challenge to date, for both marks and advanced nodes. In this work, we accordingly assessed the neutral transport mechanisms in ARDE by means of experiments and multiscale modeling for SiO<sub>2</sub>etching with CHF<sub>3</sub>/Ar and CF<sub>4</sub>/Ar plasmas. The experiments revealed a local maximum in the etch rate for an aspect ratio around unity, i.e. the simultaneous occurrence of regular and inverse reactive ion etching lag for a given etch condition. We were able to reproduce this ARDE trend in the simulations without taking into account charging effects and the polymer layer thickness, suggesting shadowing and diffuse reflection of neutrals as the primary underlying mechanisms. Subsequently, we explored four methods with the simulations to regulate ARDE, by varying the incident plasma species fluxes, the amount of polymer deposition, the ion energy and angular distribution and the initial hardmask sidewall angle, for which the latter was found to be promising in particular. Although our study focusses on feature dimensions characteristic to metrology marks and back-end-of-the-line integration, the obtained insights have a broader relevance, e.g. to the patterning of advanced nodes. Additionally, this work supports the insight that physisorption may be more important in plasma etching at room temperature than originally thought, in line with other recent studies, a topic on which we recommend further research. | ||||
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| Language | Wos | 001021250100001 | Publication Date | 2023-06-01 | |
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| ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
3.8 | Times cited | Open Access | Not_Open_Access | |
| Notes | P Vanraes acknowledges funding by ASML for the project ‘Computational simulation of plasma etching of trench structures’. P Vanraes and A Bogaerts want to express their gratitude to Mark J Kushner (University of Michigan) for the sharing of the HPEM and MCFPM codes, and for the interesting exchange of views. P Vanraes wishes to thank Violeta Georgieva and Stefan Tinck for the fruitful discussions on the HPEM code, Yu-Ru Zhang for an example of the CCP reactor code and Karel Venken for his technical help with the server maintenance and use. S P Venugopalan and M Besemer wish to thank Luigi Scaccabarozzi, Sander Wuister, Coen Verschuren, Michael Kubis, Kuan-Ming Chen, Ruben Maas, Huaichen Zhang and Julien Mailfert (ASML) for the insightful discussions. | Approved | Most recent IF: 3.8; 2023 IF: 3.302 | ||
| Call Number | PLASMANT @ plasmant @c:irua:197760 | Serial | 8811 | ||
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| Author | Albrechts, M.; Tsonev, I.; Bogaerts, A. | ||||
| Title | Investigation of O atom kinetics in O2plasma and its afterglow | Type | A1 Journal Article | ||
| Year | 2024 | Publication | Plasma Sources Science and Technology | Abbreviated Journal | Plasma Sources Sci. Technol. |
| Volume | 33 | Issue | 4 | Pages | 045017 |
| Keywords | A1 Journal Article; oxygen plasma, pseudo-1D plug-flow kinetic model, O atoms, low-pressure validation, atmospheric pressure microwave torch; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| Abstract | We have developed a comprehensive kinetic model to study the O atom kinetics in an O<sub>2</sub>plasma and its afterglow. By adopting a pseudo-1D plug-flow formalism within the kinetic model, our aim is to assess how far the O atoms travel in the plasma afterglow, evaluating its potential as a source of O atoms for post-plasma gas conversion applications. Since we could not find experimental data for pure O<sub>2</sub>plasma at atmospheric pressure, we first validated our model at low pressure (1–10 Torr) where very good experimental data are available. Good agreement between our model and experiments was achieved for the reduced electric field, gas temperature and the densities of the dominant neutral species, i.e. O<sub>2</sub>(a), O<sub>2</sub>(b) and O. Subsequently, we confirmed that the chemistry set is consistent with thermodynamic equilibrium calculations at atmospheric pressure. Finally, we investigated the O atom densities in the O<sub>2</sub>plasma and its afterglow, for which we considered a microwave O<sub>2</sub>plasma torch, operating at a pressure between 0.1 and 1 atm, for a flow rate of 20 slm and an specific energy input of 1656 kJ mol<sup>−1</sup>. Our results show that for both pressure conditions, a high dissociation degree of ca. 92% is reached within the discharge. However, the O atoms travel much further in the plasma afterglow for<italic>p</italic>= 0.1 atm (9.7 cm) than for<italic>p</italic>= 1 atm (1.4 cm), attributed to the longer lifetime (3.8 ms at 0.1 atm vs 1.8 ms at 1 atm) resulting from slower three-body recombination kinetics, as well as a higher volumetric flow rate. | ||||
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| Language | Wos | 001209453500001 | Publication Date | 2024-04-01 | |
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| ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor |
3.8 | Times cited | Open Access | ||
| Notes | This research was supported by the Horizon Europe Framework Program ‘Research and Innovation Actions’ (RIA), Project CANMILK (Grant No. 101069491). | Approved | Most recent IF: 3.8; 2024 IF: 3.302 | ||
| Call Number | PLASMANT @ plasmant @c:irua:205920 | Serial | 9125 | ||
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| Author | Hayne, M.; Jones, C.L.; Bogaerts, R.; Riva, C.; Usher, A.; Peeters, F.M.; Herlach, F.; Moshchalkov, V.V.; Henini, M. | ||||
| Title | Photoluminescence of negatively charged excitons in high magnetic fields | Type | A1 Journal article | ||
| Year | 1999 | Publication | Physical review : B : condensed matter and materials physics | Abbreviated Journal | Phys Rev B |
| Volume | 59 | Issue | Pages | 2927-2931 | |
| Keywords | A1 Journal article; Condensed Matter Theory (CMT) | ||||
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| Publisher | Place of Publication | Lancaster, Pa | Editor | ||
| Language | Wos | 000078463100064 | Publication Date | 2002-07-27 | |
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| ISSN | 0163-1829;1095-3795; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
3.836 | Times cited | 86 | Open Access | |
| Notes | Approved | Most recent IF: 3.836; 1999 IF: NA | |||
| Call Number | UA @ lucian @ c:irua:24158 | Serial | 2614 | ||
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| Author | Uytdenhouwen, Y.; Meynen, V.; Cool, P.; Bogaerts, A. | ||||
| Title | The Potential Use of Core-Shell Structured Spheres in a Packed-Bed DBD Plasma Reactor for CO2 Conversion | Type | A1 Journal article | ||
| Year | 2020 | Publication | Catalysts | Abbreviated Journal | Catalysts |
| Volume | 10 | Issue | 5 | Pages | 530 |
| Keywords | A1 Journal article; Laboratory of adsorption and catalysis (LADCA); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | This work proposes to use core-shell structured spheres to evaluate whether it allows to individually optimize bulk and surface effects of a packing material, in order to optimize conversion and energy efficiency. Different core-shell materials have been prepared by spray coating, using dense spheres (as core) and powders (as shell) of SiO2, Al2O3, and BaTiO3. The materials are investigated for their performance in CO2 dissociation and compared against a benchmark consisting of a packed-bed reactor with the pure dense spheres, as well as an empty reactor. The results in terms of CO2 conversion and energy efficiency show various interactions between the core and shell material, depending on their combination. Al2O3 was found as the best core material under the applied conditions here, followed by BaTiO3 and SiO2, in agreement with their behaviour for the pure spheres. Applying a thin shell layer on the cores showed equal performance between the different shell materials. Increasing the layer thickness shifts this behaviour, and strong combination effects were observed depending on the specific material. Therefore, this method of core-shell spheres has the potential to allow tuning of the packing properties more closely to the application by designing an optimal combination of core and shell. | ||||
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| Language | Wos | 000546007000092 | Publication Date | 2020-05-11 | |
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| ISSN | 2073-4344 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
3.9 | Times cited | Open Access | ||
| Notes | Interreg, Project EnOp ; Fonds Wetenschappelijk Onderzoek, G.0254.14N ; Universiteit Antwerpen, Project SynCO2Chem ; We want to thank Jasper Lefevre (VITO) for assistance in the development of the coating suspension for the core-shell spheres. | Approved | Most recent IF: 3.9; 2020 IF: 3.082 | ||
| Call Number | PLASMANT @ plasmant @c:irua:169222 | Serial | 6364 | ||
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| Author | Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. | ||||
| Title | How do nitrated lipids affect the properties of phospholipid membranes? | Type | A1 Journal article | ||
| Year | 2020 | Publication | Archives Of Biochemistry And Biophysics | Abbreviated Journal | Arch Biochem Biophys |
| Volume | 695 | Issue | Pages | 108548 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Biological membranes are under constant attack of free radicals, which may lead to lipid nitro-oxidation, pro ducing a complex mixture of nitro-oxidized lipids that are responsible for structural and dynamic changes on the membrane. Despite the latter, nitro-oxidized lipids are also associated with several inflammatory and neuro degenerative diseases, the underlying mechanisms of which remain elusive. We perform atomistic molecular dynamics simulations using several isomers of nitro-oxidized lipids to study their effect on the structure and permeability of the membrane, as well as the interaction between the mixture of these products in the phospholipid membrane environment. Our results show that the stereo- and positional isomers have a stronger effect on the properties of the membrane composed of oxidized lipids compared to that containing nitrated lipids. Nevertheless, nitrated lipids lead to three-fold increase in water permeability compared to oxidized lipids. In addition, we show that in a membrane consisting of combined nitro-oxidized lipid products, the presence of oxidized lipids protects the membrane from transient pores. Is well stablished that plasma application and photodynamic therapy produces a number of oxidative species used to kill cancer cells, through membrane damage induced by nitro-oxidative stress. This study is important to elucidate the mechanisms and the molecular level properties involving the reactive species produced during that cancer therapies. | ||||
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| Language | Wos | 000594173400010 | Publication Date | 0000-00-00 | |
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| ISSN | 0003-9861 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
3.9 | Times cited | Open Access | ||
| Notes | CAPES; Flanders Research Foundation, 1200219N ; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. | Approved | Most recent IF: 3.9; 2020 IF: 3.165 | ||
| Call Number | PLASMANT @ plasmant @c:irua:173861 | Serial | 6440 | ||
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| Author | Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. | ||||
| Title | Distribution of lipid aldehydes in phase-separated membranes: A molecular dynamics study | Type | A1 Journal article | ||
| Year | 2022 | Publication | Archives Of Biochemistry And Biophysics | Abbreviated Journal | Arch Biochem Biophys |
| Volume | 717 | Issue | Pages | 109136 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | It is well established that lipid aldehydes (LAs) are able to increase the permeability of cell membranes and induce their rupture. However, it is not yet clear how LAs are distributed in phase-separated membranes (PSMs), which are responsible for the transport of selected molecules and intracellular signaling. Thus, we investigate here the distribution of LAs in a PSM by coarse-grained molecular dynamics simulations. Our results reveal that LAs derived from mono-unsaturated lipids tend to accumulate at the interface between the liquid-ordered/liquiddisordered domains, whereas those derived from poly-unsaturated lipids remain in the liquid-disordered domain. These results are important for understanding the effects caused by oxidized lipids in membrane structure, properties and organization. | ||||
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| Language | Wos | 000767632000001 | Publication Date | 2022-01-24 | |
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| ISSN | 0003-9861 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor |
3.9 | Times cited | Open Access | OpenAccess | |
| Notes | We thank the University of Antwerp and the Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted. 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: 3.9 | ||
| Call Number | PLASMANT @ plasmant @c:irua:185874 | Serial | 6905 | ||
| Permanent link to this record | |||||
| Author | Lamonier, J.-F.; Bogaerts, A. | ||||
| Title | Feature Papers to Celebrate “Environmental Catalysis”—Trends & Outlook | Type | Editorial | ||
| Year | 2022 | Publication | Catalysts | Abbreviated Journal | Catalysts |
| Volume | 12 | Issue | 7 | Pages | 720 |
| Keywords | Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | This Special Issue collects three reviews, eight articles, and two communications related to the design of catalysts for environmental applications, such as the transformation of several pollutants into harmless or valuable products [...] | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000831734700001 | Publication Date | 2022-06-30 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2073-4344 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor |
3.9 | Times cited | Open Access | OpenAccess | |
| Notes | Approved | Most recent IF: 3.9 | |||
| Call Number | PLASMANT @ plasmant @c:irua:189202 | Serial | 7074 | ||
| Permanent link to this record | |||||
| Author | Oliveira, M.C.; Cordeiro, R.M.; Bogaerts, A. | ||||
| Title | Effect of lipid oxidation on the channel properties of Cx26 hemichannels : a molecular dynamics study | Type | A1 Journal article | ||
| Year | 2023 | Publication | Archives of biochemistry and biophysics | Abbreviated Journal | |
| Volume | 746 | Issue | Pages | 109741-12 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Intercellular communication plays a crucial role in cancer, as well as other diseases, such as inflammation, tissue degeneration, and neurological disorders. One of the proteins responsible for this, are connexins (Cxs), which come together to form a hemichannel. When two hemichannels of opposite cells interact with each other, they form a gap junction (GJ) channel, connecting the intracellular space of these cells. They allow the passage of ions, reactive oxygen and nitrogen species (RONS), and signaling molecules from the interior of one cell to another cell, thus playing an essential role in cell growth, differentiation, and homeostasis. The importance of GJs for disease induction and therapy development is becoming more appreciated, especially in the context of oncology. Studies have shown that one of the mechanisms to control the formation and disruption of GJs is mediated by lipid oxidation pathways, but the underlying mechanisms are not well understood. In this study, we performed atomistic molecular dynamics simulations to evaluate how lipid oxidation influences the channel properties of Cx26 hemichannels, such as channel gating and permeability. Our results demonstrate that the Cx26 hemichannel is more compact in the presence of oxidized lipids, decreasing its pore diameter at the extracellular side and increasing it at the amino terminus domains, respectively. The permeability of the Cx26 hemichannel for water and RONS molecules is higher in the presence of oxidized lipids. The latter may facilitate the intracellular accumulation of RONS, possibly increasing oxidative stress in cells. A better understanding of this process will help to enhance the efficacy of oxidative stress-based cancer treatments. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001079100300001 | Publication Date | 2023-09-07 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0003-9861; 1096-0384 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor |
3.9 | Times cited | Open Access | ||
| Notes | Approved | Most recent IF: 3.9; 2023 IF: 3.165 | |||
| Call Number | UA @ admin @ c:irua:200282 | Serial | 9028 | ||
| Permanent link to this record | |||||
| Author | Eckert, M.; Neyts, E.; Bogaerts, A. | ||||
| Title | Differences between ultrananocrystalline and nanocrystalline diamond growth: theoretical investigation of CxHy species at diamond step edges | Type | A1 Journal article | ||
| Year | 2010 | Publication | Crystal growth & design | Abbreviated Journal | Cryst Growth Des |
| Volume | 10 | Issue | 9 | Pages | 4123-4134 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The behavior of hydrocarbon species at step edges of diamond terraces is investigated by means of combined molecular dynamics−Metropolis Monte Carlo simulations. The results show that the formation of ballas-like diamond films (like UNCD) and well-faceted diamond films (like NCD) can be related to the gas phase concentrations of CxHy in a new manner: Species that have high concentrations above the growing UNCD films suppress the extension of step edges through defect formation. The species that are present above the growing NCD film, however, enhance the extension of diamond terraces, which is believed to result in well-faceted diamond films. Furthermore, it is shown that, during UNCD growth, CxHy species with x ≥ 2 play an important role, in contrast to the currently adopted CVD diamond growth mechanism. Finally, the probabilities for the extension of the diamond (100) terrace are much higher than those for the diamond (111) terrace, which is in full agreement with the experimental observation that diamond (100) facets are more favored than diamond (111) facets during CVD diamond growth. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000281353900042 | Publication Date | 2010-08-16 | |
| 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 | 11 | Open Access | |
| Notes | Approved | Most recent IF: 4.055; 2010 IF: 4.390 | |||
| Call Number | UA @ lucian @ c:irua:83696 | Serial | 694 | ||
| Permanent link to this record | |||||
| Author | Eckert, M.; Neyts, E.; Bogaerts, A. | ||||
| Title | Insights into the growth of (ultra)nanocrystalline diamond by combined molecular dynamics and Monte Carlo simulations | Type | A1 Journal article | ||
| Year | 2010 | Publication | Crystal growth & design | Abbreviated Journal | Cryst Growth Des |
| Volume | 10 | Issue | 7 | Pages | 3005-3021 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In this paper, we present the results of combined molecular dynamics−Metropolis Monte Carlo (MD-MMC) simulations of hydrocarbon species at flat diamond (100)2 × 1 and (111)1 × 1 surfaces. The investigated species are considered to be the most important growth species for (ultra)nanocrystalline diamond ((U)NCD) growth. When applying the MMC algorithm to stuck species at monoradical sites, bonding changes are only seen for CH2. The sequence of the bond breaking and formation as put forward by the MMC simulations mimics the insertion of CH2 into a surface dimer as proposed in the standard growth model of diamond. For hydrocarbon species attached to two adjacent radical (biradical) sites, the MMC simulations give rise to significant changes in the bonding structure. For UNCD, the combinations of C3 and C3H2, and C3 and C4H2 (at diamond (100)2 × 1) and C and C2H2 (at diamond (111)1 × 1) are the most successful in nucleating new crystal layers. For NCD, the following combinations pursue the diamond structure the best: C2H2 and C3H2 (at diamond (100)2 × 1) and CH2 and C2H2 (at diamond (111)1 × 1). The different behaviors of the hydrocarbon species at the two diamond surfaces are related to the different sterical hindrances at the diamond surfaces. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000279422700032 | Publication Date | 2010-05-25 | |
| 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 | 13 | Open Access | |
| Notes | Approved | Most recent IF: 4.055; 2010 IF: 4.390 | |||
| Call Number | UA @ lucian @ c:irua:83065 | Serial | 1675 | ||
| 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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| 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 | Neyts, E.; Bogaerts, A. | ||||
| Title | Influence of internal energy and impact angle on the sticking behaviour of reactive radicals in thin a-C:H film growth: a molecular dynamics study | Type | A1 Journal article | ||
| Year | 2006 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 8 | Issue | 17 | Pages | 2066-2071 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Cambridge | Editor | ||
| Language | Wos | 000236970300011 | Publication Date | 2006-03-20 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076;1463-9084; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.123 | Times cited | 7 | Open Access | |
| Notes | Approved | Most recent IF: 4.123; 2006 IF: 2.892 | |||
| Call Number | UA @ lucian @ c:irua:57353 | Serial | 1625 | ||
| Permanent link to this record | |||||
| Author | Shirazi, M.; Bogaerts, A.; Neyts, E.C. | ||||
| Title | A DFT study of H-dissolution into the bulk of a crystalline Ni(111) surface: a chemical identifier for the reaction kinetics | Type | A1 Journal article | ||
| Year | 2017 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 19 | Issue | 19 | Pages | 19150-19158 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In this study, we investigated the diffusion of H-atoms to the subsurface and their further diffusion into the bulk of a Ni(111) crystal by means of density functional theory calculations in the context of thermal and plasma-assisted catalysis. The H-atoms at the surface can originate from the dissociative adsorption of H2 or CH4 molecules, determining the surface H-coverage. When a threshold H-coverage is passed, corresponding to 1.00 ML for the crystalline Ni(111) surface, the surface-bound H-atoms start to diffuse to the subsurface. A similar threshold coverage is observed for the interstitial H-coverage. Once the interstitial sites are filled up with a coverage above 1.00 ML of H, dissolution of interstitial H-atoms to the layer below the interstitial sites will be initiated. Hence, by applying a high pressure or inducing a reactive plasma and high temperature, increasing the H-flux to the surface, a large amount of hydrogen can diffuse in a crystalline metal like Ni and can be absorbed. The formation of metal hydride may modify the entire reaction kinetics of the system. Equivalently, the H-atoms in the bulk can easily go back to the surface and release a large amount of heat. In a plasma process, H-atoms are formed in the plasma, and therefore the energy barrier for dissociative adsorption is dismissed, thus allowing achievement of the threshold coverage without applying a high pressure as in a thermal process. As a result, depending on the crystal plane and type of metal, a large number of H-atoms can be dissolved (absorbed) in the metal catalyst, explaining the high efficiency of plasma-assisted catalytic reactions. Here, the mechanism of H-dissolution is established as a chemical identifier for the investigation of the reaction kinetics of a chemical process. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000406334300034 | Publication Date | 2017-06-22 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.123 | Times cited | 10 | Open Access | OpenAccess |
| Notes | Financial support from the Reactive Atmospheric Plasma processIng – eDucation (RAPID) network, through the EU 7th Framework Programme (grant agreement no. 606889), is gratefully acknowledged. The calculations were performed 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 Universiteit Antwerpen. | Approved | Most recent IF: 4.123 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:144794 | Serial | 4633 | ||
| Permanent link to this record | |||||
| Author | Gorbanev, Y.; Verlackt, C.C.W.; Tinck, S.; Tuenter, E.; Foubert, K.; Cos, P.; Bogaerts, A. | ||||
| Title | Combining experimental and modelling approaches to study the sources of reactive species induced in water by the COST RF plasma jet | Type | A1 Journal article | ||
| Year | 2018 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 20 | Issue | 4 | Pages | 2797-2808 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The vast biomedical potential of cold atmospheric pressure plasmas (CAPs) is governed by the formation of reactive species. These biologically active species are formed upon the interaction of CAPs with the surroundings. In biological milieu, water plays an essential role. The development of biomedical CAPs thus requires understanding of the sources of the reactive species in aqueous media exposed to the plasma. This is especially important in case of the COST RF plasma jet, which is developed as a reference microplasma system. In this work, we investigated the formation of the OH radicals, H atoms and H2O2 in aqueous solutions exposed to the COST plasma jet. This was done by combining experimental and modelling approaches. The liquid phase species were analysed using UV-Vis spectroscopy and spin trapping with hydrogen isotopes and electron paramagnetic resonance (EPR) spectroscopy. The discrimination between the species formed from the liquid phase and the gas phase molecules was performed by EPR and 1H-NMR analyses of the liquid samples. The concentrations of the reactive species in the gas phase plasma were obtained using a zero-dimensional (0D) chemical kinetics computational model. A three-dimensional (3D) fluid dynamics model was developed to provide information on the induced humidity in the plasma effluent. The comparison of the experimentally obtained trends for the formation of the species as a function of the feed gas and effluent humidity with the modelling results suggest that all reactive species detected in our system are mostly formed in the gas phase plasma inside the COST jet, with minor amounts arising from the plasma effluent humidity. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000423505500066 | Publication Date | 2018-01-05 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.123 | Times cited | 23 | Open Access | OpenAccess |
| Notes | We are grateful to Volker Schulz-von der Gathen (Experimental Physics II: Application Oriented Plasma Physics, Ruhr-Universita¨t Bochum, Germany) for providing the COST RF plasma jet. We thank our colleagues at the University of Antwerp: Gilles Van Loon (Mechanical Workshop), Karen Leyssens (Research group PLASMANT), and Sylvia Dewilde (Department of Biomedical Sciences) for their help with the equipment. This work was funded by the European Marie Sklodowska-Curie Individual Fellowship ‘LTPAM’ within Horizon2020 (grant no. 657304). Stefan Tinck thanks the Fund for Scientific Research – Flanders (FWO) for supporting his work (grant no. 0880.212.840). | Approved | Most recent IF: 4.123 | ||
| Call Number | PLASMANT @ plasmant @c:irua:148365 | Serial | 4808 | ||
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| Author | Verlackt, C.C.W.; Van Boxem, W.; Bogaerts, A. | ||||
| Title | Transport and accumulation of plasma generated species in aqueous solution | Type | A1 Journal article | ||
| Year | 2018 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 20 | Issue | 10 | Pages | 6845-6859 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The interaction between cold atmospheric pressure plasma and liquids is receiving increasing attention for various applications. In particular, the use of plasma-treated liquids (PTL) for biomedical applications is of growing importance, in particular for sterilization and cancer treatment. However, insight into the underlying mechanisms of plasma–liquid interactions is still scarce. Here, we present a 2D fluid dynamics model for the interaction between a plasma jet and liquid water. Our results indicate that the formed reactive species originate from either the gas phase (with further solvation) or are formed at the liquid interface. A clear increase in the aqueous density of H2O2, HNO2/NO2- and NO3- is observed as a function of time, while the densities of O3, HO2/O2- and ONOOH/ONOO- are found to quickly reach a maximum due to chemical reactions in solution. The trends observed in our model correlate well with experimental observations from the literature. |
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000429286100009 | Publication Date | 2018-02-06 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.123 | Times cited | 35 | Open Access | OpenAccess |
| Notes | The authors thank Petr Luke`s (Institute of Plasma Physics AS CR, Czech Republic) and Yury Gorbanev (UAntwerp, group PLASMANT) for the fruitful discussions regarding the chemistry in the model and the plasma–liquid interactions. | Approved | Most recent IF: 4.123 | ||
| Call Number | PLASMANT @ plasmant @c:irua:149557 | Serial | 4908 | ||
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| Author | Gorbanev, Y.; Van der Paal, J.; Van Boxem, W.; Dewilde, S.; Bogaerts, A. | ||||
| Title | Reaction of chloride anion with atomic oxygen in aqueous solutions: can cold plasma help in chemistry research? | Type | A1 Journal article | ||
| Year | 2019 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 21 | Issue | 8 | Pages | 4117-4121 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Cold atmospheric plasma in contact with solutions has many applications, but its chemistry contains many unknowns such as the undescribed reactions with solutes. By combining experiments and modelling, we report the first direct demonstration of the reaction of chloride with oxygen atoms in aqueous solutions exposed to cold plasma. | ||||
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| Language | Wos | 000461722500001 | Publication Date | 2019-01-30 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.123 | Times cited | 4 | Open Access | Not_Open_Access: Available from 31.01.2020 |
| Notes | H2020 Marie Skłodowska-Curie Actions, 743151 ; Fonds Wetenschappelijk Onderzoek, 11U5416N ; | Approved | Most recent IF: 4.123 | ||
| Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:157688 | Serial | 5167 | ||
| Permanent link to this record | |||||
| Author | Van der Paal, J.; Hong, S.-H.; Yusupov, M.; Gaur, N.; Oh, J.-S.; Short, R.D.; Szili, E.J.; Bogaerts, A. | ||||
| Title | How membrane lipids influence plasma delivery of reactive oxygen species into cells and subsequent DNA damage : an experimental and computational study | Type | A1 Journal article | ||
| Year | 2019 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 21 | Issue | 35 | Pages | 19327-19341 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted. | ||||
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| Language | Wos | 000486175400045 | Publication Date | 2019-08-21 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076; 1463-9084 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.123 | Times cited | 1 | Open Access | |
| Notes | Approved | Most recent IF: 4.123 | |||
| Call Number | UA @ admin @ c:irua:162782 | Serial | 6303 | ||
| Permanent link to this record | |||||
| Author | Heirman, P.; Van Boxem, W.; Bogaerts, A. | ||||
| Title | Reactivity and stability of plasma-generated oxygen and nitrogen species in buffered water solution: a computational study | Type | A1 Journal article | ||
| Year | 2019 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 21 | Issue | 24 | Pages | 12881-12894 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma-treated liquids have great potential for biomedical applications. However, insight into the underlying mechanisms and the exact chemistry is still scarce. In this study, we present the combination of a 0D chemical kinetics and a 2D fluid dynamics model to investigate the plasma treatment of a buffered water solution with the kINPen (R) plasma jet. Using this model, we calculated the gas and liquid flow profiles and the transport and chemistry of all species in the gas and the liquid phase. Moreover, we evaluated the stability of the reactive oxygen and nitrogen species after plasma treatment. We found that of all species, only H2O2, HNO2/NO2-, and HNO3/NO3- are stable in the buffered solution after plasma treatment. This is because both their production and loss processes in the liquid phase are dependent on short-lived radicals (e.g. OH, NO, and NO2). Apart from some discrepancy in the absolute values of the concentrations, which can be explained by the model, all general trends and observations in our model are in qualitative agreement with experimental data and literature. | ||||
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| Language | Wos | 000472214000012 | Publication Date | 2019-05-29 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076; 1463-9084 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.123 | Times cited | 7 | Open Access | |
| Notes | Approved | Most recent IF: 4.123 | |||
| Call Number | UA @ admin @ c:irua:161314 | Serial | 6320 | ||
| Permanent link to this record | |||||
| Author | Janssens, K.; Bogaerts, A.; van Grieken, R. | ||||
| Title | Colloquium Spectroscopicum Internationale 34, Antwerp, Belgium, 4-9 September 2005: preface | Type | Editorial | ||
| Year | 2006 | Publication | Talanta : the international journal of pure and applied analytical chemistry | Abbreviated Journal | Talanta |
| Volume | 70 | Issue | 5 | Pages | 907-908 |
| Keywords | Editorial; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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| Publisher | Pergamon | Place of Publication | Oxford | Editor | |
| Language | Wos | 000242871900001 | Publication Date | 2006-11-01 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0039-9140; | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor |
4.162 | Times cited | Open Access | ||
| Notes | Approved | Most recent IF: 4.162; 2006 IF: 2.810 | |||
| Call Number | UA @ lucian @ c:irua:61094 | Serial | 392 | ||
| Permanent link to this record | |||||
| Author | Hoon Park, J.; Kumar, N.; Hoon Park, D.; Yusupov, M.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A.; Ho Kang, M.; Sup Uhm, H.; Ha Choi, E.; Attri, P.; | ||||
| Title | A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma | Type | A1 Journal article | ||
| Year | 2015 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
| Volume | 5 | Issue | 5 | Pages | 13849 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Nature Publishing Group | Place of Publication | London | Editor | |
| Language | Wos | 000360909000001 | Publication Date | 2015-09-09 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2045-2322; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.259 | Times cited | 32 | Open Access | |
| Notes | Approved | Most recent IF: 4.259; 2015 IF: 5.578 | |||
| Call Number | c:irua:127410 | Serial | 419 | ||
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| Author | Khosravian, N.; Kamaraj, B.; Neyts, E.C.; Bogaerts, A. | ||||
| Title | Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations | Type | A1 Journal article | ||
| Year | 2016 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
| Volume | 6 | Issue | 6 | Pages | 19466 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment. | ||||
| Address | Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium | ||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | English | Wos | 000369573900001 | Publication Date | 2016-02-09 |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.259 | Times cited | 7 | Open Access | |
| Notes | The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number G012413N. The calculations were performed in part using the Turing HPC infrastructure of 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 Universiteit Antwerpen.” | Approved | Most recent IF: 4.259 | ||
| Call Number | c:irua:131610 | Serial | 4031 | ||
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| Author | Attri, P.; Yusupov, M.; Park, J.H.; Lingamdinne, L.P.; Koduru, J.R.; Shiratani, M.; Choi, E.H.; Bogaerts, A. | ||||
| Title | Mechanism and comparison of needle-type non-thermal direct and indirect atmospheric pressure plasma jets on the degradation of dyes | Type | A1 Journal article | ||
| Year | 2016 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
| Volume | 6 | Issue | 6 | Pages | 34419 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Purified water supply for human use, agriculture and industry is the major global priority nowadays. The advanced oxidation process based on atmospheric pressure non-thermal plasma (NTP) has been used for purification of wastewater, although the underlying mechanisms of degradation of organic pollutants are still unknown. In this study we employ two needle-type atmospheric pressure non-thermal plasma jets, i.e., indirect (ID-APPJ) and direct (D-APPJ) jets operating at Ar feed gas, for the treatment of methylene blue, methyl orange and congo red dyes, for two different times (i.e., 20 min and 30 min). Specifically, we study the decolorization/degradation of all three dyes using the above mentioned plasma sources, by means of UV-Vis spectroscopy, HPLC and a density meter. We also employ mass spectroscopy to verify whether only decolorization or also degradation takes place after treatment of the dyes by the NTP jets. Additionally, we analyze the interaction of OH radicals with all three dyes using reactive molecular dynamics simulations, based on the density functional-tight binding method. This investigation represents the first report on the degradation of these three different dyes by two types of NTP setups, analyzed by various methods, and based on both experimental and computational studies. | ||||
| Address | Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium | ||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | English | Wos | 000385172300001 | Publication Date | 2016-10-06 |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.259 | Times cited | 23 | Open Access | |
| Notes | We gratefully acknowledge the grant received from the SRC program of the National Research Foundation of Korea (NRF), funded by the Korean Government (MEST) (No. 20100029418). PA is thankful to FY 2015 Japan Society for the Promotion of Science (JSPS) invitation fellowship. This work was partly supported by MEXT KAKENHI Grant Number 24108009 and JSPS KAKENHI Grant Number JP16H03895. M. Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216N. 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. | Approved | Most recent IF: 4.259 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:135847 | Serial | 4283 | ||
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| Author | Van der Paal, J.; Verheyen, C.; Neyts, E.C.; Bogaerts, A. | ||||
| Title | Hampering Effect of Cholesterol on the Permeation of Reactive Oxygen Species through Phospholipids Bilayer: Possible Explanation for Plasma Cancer Selectivity | Type | A1 Journal article | ||
| Year | 2017 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
| Volume | 7 | Issue | 7 | Pages | 39526 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In recent years, the ability of cold atmospheric pressure plasmas (CAPS) to selectively induce cell death in cancer cells has been widely established. This selectivity has been assigned to the reactive oxygen and nitrogen species (RONS) created in CAPs. To provide new insights in the search for an explanation for the observed selectivity, we calculate the transfer free energy of multiple ROS across membranes containing a varying amount of cholesterol. The cholesterol fraction is investigated as a selectivity parameter because membranes of cancer cells are known to contain lower fractions of cholesterol compared to healthy cells. We find that cholesterol has a significant effect on the permeation of reactive species across a membrane. Indeed, depending on the specific reactive species, an increasing cholesterol fraction can lead to (i) an increase of the transfer free energy barrier height and width, (ii) the formation of a local free energy minimum in the center of the membrane and (iii) the creation of extra free energy barriers due to the bulky sterol rings. In the context of plasma oncology, these observations suggest that the increased ingress of RONS in cancer cells can be explained by the decreased cholesterol fraction of their cell membrane. |
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| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000391306900001 | Publication Date | 2017-01-06 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.259 | Times cited | 27 | Open Access | OpenAccess |
| Notes | The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number 11U5416N. The calculations were performed in part using the Turing HPC infrastructure of 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 Universiteit Antwerpen. | Approved | Most recent IF: 4.259 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:139512 | Serial | 4340 | ||
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| Author | Yusupov, M.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A. | ||||
| Title | Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments | Type | A1 Journal article | ||
| Year | 2017 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
| Volume | 7 | Issue | 7 | Pages | 5761 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000405746500072 | Publication Date | 2017-07-12 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor |
4.259 | Times cited | 27 | Open Access | OpenAccess |
| Notes | M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216 N. 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. S.R. and S.K. acknowledge funding by the BMBF (FKZ: 03Z2DN12). S.R. acknowledges funding by the Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern (AU 15001). The authors thank M. Hammer for the support and discussion in the biophysical studies and J. Van der Paal for the interesting discussions. | Approved | Most recent IF: 4.259 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:144627 | Serial | 4630 | ||
| Permanent link to this record | |||||