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Author Wang, W.; Patil, B.; Heijkers, S.; Hessel, V.; Bogaerts, A.
Title Nitrogen fixation by gliding arc plasma : better insight by chemical kinetics modelling Type A1 Journal article
Year 2017 Publication Chemsuschem Abbreviated Journal Chemsuschem
Volume 10 Issue 10 Pages 2145-2157
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The conversion of atmospheric nitrogen into valuable compounds, that is, so-called nitrogen fixation, is gaining increased interest, owing to the essential role in the nitrogen cycle of the biosphere. Plasma technology, and more specifically gliding arc plasma, has great potential in this area, but little is known about the underlying mechanisms. Therefore, we developed a detailed chemical kinetics model for a pulsed-power gliding-arc reactor operating at atmospheric pressure for nitrogen oxide synthesis. Experiments are performed to validate the model and reasonable agreement is reached between the calculated and measured NO and NO2 yields and the corresponding energy efficiency for NOx formation for different N2/O2 ratios, indicating that the model can provide a realistic picture of the plasma chemistry. Therefore, we can use the model to investigate the reaction pathways for the formation and loss of NOx. The results indicate that vibrational excitation of N2 in the gliding arc contributes significantly to activating the N2 molecules, and leads to an energy efficient way of NOx production, compared to the thermal process. Based on the underlying chemistry, the model allows us to propose solutions on how to further improve the NOx formation by gliding arc technology. Although the energy efficiency of the gliding-arc-based nitrogen fixation process at the present stage is not comparable to the world-scale HaberBosch process, we believe our study helps us to come up with more realistic scenarios of entering a cutting-edge innovation in new business cases for the decentralised production of fertilisers for agriculture, in which low-temperature plasma technology might play an important role.
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Corporate Author Thesis
Publisher Place of Publication Weinheim Editor
Language Wos 000402122100006 Publication Date 2017-03-08
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1864-5631 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.226 Times cited 42 Open Access OpenAccess
Notes Approved (down) Most recent IF: 7.226
Call Number UA @ lucian @ c:irua:143261 Serial 4672
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Author Cleiren, E.; Heijkers, S.; Ramakers, M.; Bogaerts, A.
Title Dry Reforming of Methane in a Gliding Arc Plasmatron: Towards a Better Understanding of the Plasma Chemistry Type A1 Journal article
Year 2017 Publication Chemsuschem Abbreviated Journal Chemsuschem
Volume 10 Issue 20 Pages 4025-4036
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Dry reforming of methane (DRM) in a gliding arc plasmatron is studied for different CH4 fractions in the mixture. The CO2 and CH4 conversions reach their highest values of approximately 18 and 10%, respectively, at 25% CH4 in the gas mixture, corresponding to an overall energy cost of 10 kJ L@1 (or 2.5 eV per molecule) and an energy efficiency of 66%. CO and H2 are the major products, with the formation of smaller fractions of C2Hx (x=2, 4, or 6) compounds and H2O. A chemical kinetics model is used to investigate the underlying chemical processes. The calculated CO2 and CH4 conversion and the energy efficiency are in good agreement with the experimental data. The model calculations reveal that the reaction of CO2 (mainly at vibrationally excited levels) with H radicals is mainly responsible for

the CO2 conversion, especially at higher CH4 fractions in the mixture, which explains why the CO2 conversion increases with increasing CH4 fraction. The main process responsible for CH4 conversion is the reaction with OH radicals. The excellent energy efficiency can be explained by the non-equilibrium character of the plasma, in which the electrons mainly activate the gas molecules, and by the important role of the vibrational kinetics of CO2. The results demonstrate that a gliding arc plasmatron is very promising for DRM.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000413565100012 Publication Date 2017-10-02
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1864-5631 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.226 Times cited 23 Open Access OpenAccess
Notes Fonds Wetenschappelijk Onderzoek, G.0383.16N ; Federaal Wetenschapsbeleid; Approved (down) Most recent IF: 7.226
Call Number PLASMANT @ plasmant @c:irua:146665 Serial 4759
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Author Andersen, J.A.; Christensen, J.M.; Østberg, M.; Bogaerts, A.; Jensen, A.D.
Title Plasma-catalytic ammonia decomposition using a packed-bed dielectric barrier discharge reactor Type A1 Journal article
Year 2022 Publication International Journal Of Hydrogen Energy Abbreviated Journal Int J Hydrogen Energ
Volume 47 Issue 75 Pages 32081-32091
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Plasma-catalytic ammonia decomposition as a method for producing hydrogen was studied in a packed-bed dielectric barrier discharge (DBD) reactor at ambient pressure and a fixed plasma power. The influence of packing the plasma zone with various dielectric materials, typically used as catalyst supports, was examined. At conditions (21 W, 75 Nml/min NH3) where an NH3 conversion of 5% was achieved with plasma alone, an improved decomposition was found when introducing dielectric materials with dielectric constants between 4 and 30. Of the tested materials, MgAl2O4 yielded the highest conversion (15.1%). The particle size (0.3-1.4 mm) of the MgAl2O4 packing was found to have a modest influence on the conversion, which dropped from 15.1% to 12.6% with increasing particle size. Impregnation of MgAl2O4 with different metals was found to decrease the NH3 conversion, with the Ni impregnation still showing an improved conversion (7%) compared to plasma-only. The plasma-assisted ammonia decomposition occurs in the gas phase due to micro-discharges, as evident from a linear correlation between the conversion and the frequency of micro-discharges for both plasma alone and with the various solid packing materials. The primary function of the solid is thus to facilitate the gas phase reaction by assisting the creation of micro-discharges. Lastly, insulation of the reactor to raise the temperature to 230 degrees C in the plasma zone was found to have a negative effect on the conversion, as a change from volume discharges to surface discharges occurred. The study shows that NH3 can be decomposed to provide hydrogen by exposure to a non-thermal plasma, but further developments are needed for it to become an energy efficient technology. (C)2022 The Author(s). Published by Elsevier Ltd on behalf of Hydrogen Energy Publications LLC.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000865421200012 Publication Date 2022-08-17
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0360-3199 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.2 Times cited Open Access OpenAccess
Notes Approved (down) Most recent IF: 7.2
Call Number UA @ admin @ c:irua:191512 Serial 7191
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Author De Backer, J.; Maric, D.; Zuhra, K.; Bogaerts, A.; Szabo, C.; Vanden Berghe, W.; Hoogewijs, D.
Title Cytoglobin Silencing Promotes Melanoma Malignancy but Sensitizes for Ferroptosis and Pyroptosis Therapy Response Type A1 Journal article
Year 2022 Publication Antioxidants Abbreviated Journal Antioxidants
Volume 11 Issue 8 Pages 1548
Keywords A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
Abstract Despite recent advances in melanoma treatment, there are still patients that either do not respond or develop resistance. This unresponsiveness and/or acquired resistance to therapy could be explained by the fact that some melanoma cells reside in a dedifferentiated state. Interestingly, this dedifferentiated state is associated with greater sensitivity to ferroptosis, a lipid peroxidation-reliant, iron-dependent form of cell death. Cytoglobin (CYGB) is an iron hexacoordinated globin that is highly enriched in melanocytes and frequently downregulated during melanomagenesis. In this study, we investigated the potential effect of CYGB on the cellular sensitivity towards (1S, 3R)-RAS-selective lethal small molecule (RSL3)-mediated ferroptosis in the G361 melanoma cells with abundant endogenous expression. Our findings show that an increased basal ROS level and higher degree of lipid peroxidation upon RSL3 treatment contribute to the increased sensitivity of CYGB knockdown G361 cells to ferroptosis. Furthermore, transcriptome analysis demonstrates the enrichment of multiple cancer malignancy pathways upon CYGB knockdown, supporting a tumor-suppressive role for CYGB. Remarkably, CYGB knockdown also triggers activation of the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome and subsequent induction of pyroptosis target genes. Altogether, we show that silencing of CYGB expression modulates cancer therapy sensitivity via regulation of ferroptosis and pyroptosis cell death signaling pathways.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000846411000001 Publication Date 2022-08-10
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2076-3921 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7 Times cited Open Access OpenAccess
Notes Approved (down) Most recent IF: 7
Call Number PLASMANT @ plasmant @c:irua:190686 Serial 7102
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Author Wardenier, N.; Gorbanev, Y.; Van Moer, I.; Nikiforov, A.; Van Hulle, S.W.H.; Surmont, P.; Lynen, F.; Leys, C.; Bogaerts, A.; Vanraes, P.
Title Removal of alachlor in water by non-thermal plasma: Reactive species and pathways in batch and continuous process Type A1 Journal article
Year 2019 Publication Water research Abbreviated Journal Water Res
Volume 161 Issue Pages 549-559
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Pesticides are emerging contaminants frequently detected in the aquatic environment. In this work, a novel approach combining activated carbon adsorption, oxygen plasma treatment and ozonation was studied for the removal of the persistent chlorinated pesticide alachlor. A comparison was made between the removal efficiency and energy consumption for two different reactor operation modes: batchrecirculation and single-pass mode. The kinetics study revealed that the insufficient removal of alachlor by adsorption was significantly improved in terms of degradation efficiency and energy consumption when combined with the plasma treatment. The best efficiency (ca. 80% removal with an energy cost of 19.4 kWh mÀ3) was found for the single-pass operational mode of the reactor. In the batch-recirculating process, a complete elimination of alachlor by plasma treatment was observed after 30 min of treatment. Analysis of the reactive species induced by plasma in aqueous solutions showed that the decomposition of alachlor mainly occurred through a radical oxidation mechanism, with a minor contribution of long-living oxidants (O3, H2O2). Investigation of the alachlor oxidation pathways revealed six different oxidation mechanisms, including the loss of aromaticity which was never before reported for plasma-assisted degradation of aromatic pesticides. It was revealed that the removal rate and energy cost could be further improved with more than 50% by additional O3 gas bubbling in the solution reservoir.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000475999400054 Publication Date 2019-06-10
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0043-1354 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.942 Times cited 2 Open Access
Notes PlasmaTex project IWT, 1408/2 ; the European Marie Sklodowska-Curie Individual Fellowship within Horizon2020, 743151 ; Flemish Knowledge Centre Water; This work was financially supported by the PlasmaTex project IWT 1408/2 and the European Marie Sklodowska-Curie Individual Fellowship within Horizon2020 (‘LTPAM’, grant no. 743151). This research was initiated within the LED H2O project which is financially supported by the Flemish Knowledge Centre Water (Vlakwa). Approved (down) Most recent IF: 6.942
Call Number PLASMANT @ plasmant @c:irua:161173 Serial 5288
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Author Scalise, E.; Houssa, M.; Cinquanta, E.; Grazianetti, C.; van den Broek, B.; Pourtois, G.; Stesmans, A.; Fanciulli, M.; Molle, A.
Title Engineering the electronic properties of silicene by tuning the composition of MoX2 and GaX (X = S,Se,Te) chalchogenide templates Type A1 Journal article
Year 2014 Publication 2D materials Abbreviated Journal 2D Mater
Volume 1 Issue 1 Pages 011010
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract By using first-principles simulations, we investigate the interaction of a 2D silicon layer with two classes of chalcogenide-layered compounds, namely MoX2 and GaX (X = S, Se, Te). A rather weak (van der Waals) interaction between the silicene layers and the chalcogenide layers is predicted. We found that the buckling of the silicene layer is correlated to the lattice mismatch between the silicene layer and the MoX2 or GaX template. The electronic properties of silicene on these different templates largely depend on the buckling of the silicene layer: highly buckled silicene on MoS2 is predicted to be metallic, while low buckled silicene on GaS and GaSe is predicted to be semi-metallic, with preserved Dirac cones at the K points. These results indicate new routes for artificially engineering silicene nanosheets, providing tailored electronic properties of this 2D layer on non-metallic substrates. These non-metallic templates also open the way to the possible integration of silicene in future nanoelectronic devices.
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Corporate Author Thesis
Publisher IOP Publishing Place of Publication Bristol Editor
Language Wos 000353649900011 Publication Date 2014-05-29
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2053-1583; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.937 Times cited 49 Open Access
Notes Approved (down) Most recent IF: 6.937; 2014 IF: NA
Call Number UA @ lucian @ c:irua:126032 Serial 1048
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Author van den Broek, B.; Houssa, M.; Scalise, E.; Pourtois, G.; Afanas'ev, V.V.; Stesmans, A.
Title Two-dimensional hexagonal tin : ab initio geometry, stability, electronic structure and functionalization Type A1 Journal article
Year 2014 Publication 2D materials Abbreviated Journal 2D Mater
Volume 1 Issue Pages 021004
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract We study the structural, mechanical and electronic properties of the two-dimensional (2D) allotrope of tin: tinene/stanene using first-principles calculation within density functional theory, implemented in a set of computer codes. Continuing the trend of the group-IV 2D materials graphene, silicene and germanene; tinene is predicted to have a honeycomb lattice with lattice parameter of a(0) = 4.62 angstrom and a buckling of d(0) = 0.92 angstrom. The electronic dispersion shows a Dirac cone with zero gap at the Fermi energy and a Fermi velocity of v(F) = 0.97 x 10(6) m s(-1); including spin-orbit coupling yields a bandgap of 0.10 eV. The monolayer is thermally stable up to 700 K, as indicated by first-principles molecular dynamics, and has a phonon dispersion without imaginary frequencies. We explore applied electric field and applied strain as functionalization mechanisms. Combining these two mechanisms allows for an induced bandgap up to 0.21 eV, whilst retaining the linear dispersion, albeit with degraded electronic transport parameters.
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Corporate Author Thesis
Publisher IOP Publishing Place of Publication Bristol Editor
Language Wos 000353650400004 Publication Date 2014-08-27
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2053-1583 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.937 Times cited 58 Open Access
Notes Approved (down) Most recent IF: 6.937; 2014 IF: NA
Call Number UA @ lucian @ c:irua:134432 Serial 4530
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Author van den Broek, B.; Houssa, M.; Iordanidou, K.; Pourtois, G.; Afanas'ev, V.V.; Stesmans, A.
Title Functional silicene and stanene nanoribbons compared to graphene: electronic structure and transport Type A1 Journal article
Year 2016 Publication 2D materials Abbreviated Journal 2D Mater
Volume 3 Issue 1 Pages 015001
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Since the advent of graphene, other 2D materials have garnered interest; notably the single element materials silicene, germanene, and stanene. Weinvestigate the ballistic current-voltage (I-V) characteristics of armchair silicene and stanene armchair nanoribbons (AXNRs with X = Si, Sn) using a combination of density functional theory and non-equilibrium Green's functions. The impact of out-of-plane electric field and in-plane uniaxial strain on the ribbon geometries, electronic structure, and (I-V)s are considered and contrasted with graphene. Since silicene and stanene are sp(2)/sp(3) buckled layers, the electronic structure can be tuned by an electric field that breaks the sublattice symmetry, an effect absent in graphene. This decreases the current by similar to 50% for Sn, since it has the largest buckling. Uniaxial straining of the ballistic channel affects the AXNR electronic structure in multiple ways: it changes the bandgap and associated effective carrier mass, and creates a local buckling distortion at the lead-channel interface which induces a interface dipole. Due to the increasing sp(3) hybridization character with increasing element mass, large reconstructions rectify the strained systems, an effect absent in sp(2) bonded graphene. This results in a smaller strain effect on the current: a decrease of 20% for Sn at 15% tensile strain compared to a similar to 75% decrease for C.
Address
Corporate Author Thesis
Publisher IOP Publishing Place of Publication Bristol Editor
Language Wos 000373936300021 Publication Date 2016-01-06
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2053-1583 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.937 Times cited 19 Open Access
Notes Approved (down) Most recent IF: 6.937
Call Number UA @ lucian @ c:irua:144746 Serial 4658
Permanent link to this record
 
 
Author Heyne, M.H.; Marinov, D.; Braithwaite, N.; Goodyear, A.; de Marneffe, J.-F.; Cooke, M.; Radu, I.; Neyts, E.C.; De Gendt, S.
Title A route towards the fabrication of 2D heterostructures using atomic layer etching combined with selective conversion Type A1 Journal article
Year 2019 Publication 2D materials Abbreviated Journal 2D Mater
Volume 6 Issue 3 Pages 035030
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Heterostructures of low-dimensional semiconducting materials, such as transition metal dichalcogenides (MX2), are promising building blocks for future electronic and optoelectronic devices. The patterning of one MX2 material on top of another one is challenging due to their structural similarity. This prevents an intrinsic etch stop when conventional anisotropic dry etching processes are used. An alternative approach consist in a two-step process, where a sacrificial silicon layer is pre-patterned with a low damage plasma process, stopping on the underlying MoS2 film. The pre-patterned layer is used as sacrificial template for the formation of the top WS2 film. This study describes the optimization of a cyclic Ar/Cl-2 atomic layer etch process applied to etch silicon on top of MoS2, with minimal damage, followed by a selective conversion of the patterned Si into WS2. The impact of the Si atomic layer etch towards the MoS2 is evaluated: in the ion energy range used for this study, MoS2 removal occurs in the over-etch step over 1-2 layers, leading to the appearance of MoOx but without significant lattice distortions to the remaining layers. The combination of Si atomic layer etch, on top of MoS2, and subsequent Si-to-WS2 selective conversion, allows to create a WS2/MoS2 heterostructure, with clear Raman signals and horizontal lattice alignment. These results demonstrate a scalable, transfer free method to achieve horizontally individually patterned heterostacks and open the route towards wafer-level processing of 2D materials.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000468335500004 Publication Date 2019-04-23
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2053-1583 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.937 Times cited Open Access Not_Open_Access
Notes Approved (down) Most recent IF: 6.937
Call Number UA @ admin @ c:irua:160229 Serial 5266
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Author Hu, L.; Amini, M.N.; Wu, Y.; Jin, Z.; Yuan, J.; Lin, R.; Wu, J.; Dai, Y.; He, H.; Lu, Y.; Lu, J.; Ye, Z.; Han, S.-T.; Ye, J.; Partoens, B.; Zeng, Y.-J.; Ruan, S.
Title Charge transfer doping modulated raman scattering and enhanced stability of black phosphorus quantum dots on a ZnO nanorod Type A1 Journal article
Year 2018 Publication Advanced Optical Materials Abbreviated Journal Adv Opt Mater
Volume 6 Issue 15 Pages 1800440
Keywords A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Black phosphorus (BP) has recently triggered an unprecedented interest in the 2D community. However, many of its unique properties are not exploited and the well-known environmental vulnerability is not conquered. Herein, a type-I mixed-dimensional (0D-1D) van der Waals heterojunction is developed, where three-atomic-layer BP quantum dots (QDs) are assembled on a single ZnO nanorod (NR). By adjusting the indium (In) content in ZnO NRs, the degree and even the direction of surface charge transfer doping within the heterojunction can be tuned, which result in selective Raman scattering enhancements between ZnO and BP. The maximal enhancement factor is determined as 4340 for BP QDs with sub-ppm level. Furthermore, an unexpected long-term ambient stability (more than six months) of BP QDs is revealed, which is ascribed to the electron doping from ZnO:In NRs. The first demonstration of selective Raman enhancements between two inorganic semiconductors as well as the improved stability of BP shed light on this emerging 2D material.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000440815200023 Publication Date 2018-05-18
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2195-1071 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.875 Times cited 37 Open Access Not_Open_Access
Notes ; L. Hu and M. N. Amini contributed equally to this work. This work was supported by the National Natural Science Foundation of China under Grant Nos. 51502178, 81571763 and 81622026, the Shenzhen Science and Technology Project under Grant Nos. JCYJ20150324141711644, JCYJ20170412105400428, KQJSCX20170727101208249 and JCYJ20170302153853962. Parts of the computational calculations were carried out using the HPC infrastructure at University of Antwerp (CalcUA), a division of the Flemish Supercomputer Center VSC, supported financially by the FWO-Vlaanderen and the Flemish Government (EWI Department). L. H. acknowledges the PhD Start-up Fund of Natural Science Foundation of Guangdong Province under Grand No. 2017A030310072. J. Y. acknowledges the funding of Shanghai Jiao Tong University (Nos. YG2016MS51 and YG2017MS54). ; Approved (down) Most recent IF: 6.875
Call Number UA @ lucian @ c:irua:153112UA @ admin @ c:irua:153112 Serial 5082
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Author Nematollahi, P.
Title Selectivity of Mo-NC sites for electrocatalytic N₂ reduction : a function of the single atom position on the surface and local carbon topologies Type A1 Journal article
Year 2023 Publication Applied surface science Abbreviated Journal
Volume 612 Issue Pages 155908-155909
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Transition metal (TM) doped two-dimensional single-atom catalysts are known as a promising class of catalysts for electrocatalytic gas conversion. However, the detailed mechanisms that occur at the surface of these catalysts are still unknown. In the present work, we simulate three Mo-doped nitrogenated graphene structures. In each catalyst, the position of the Mo active site and the corresponding local carbon topologies are different, i.e. MoN4C10 with in-plane Mo atom, MoN4C8 in which Mo atom bridges two adjacent armchair-like graphitic edges, and MoN2C3 in which Mo is doped at the edge of the graphene sheet. Using Density Functional Theory (DFT) calculations we discuss the electrocatalytic activity of Mosingle bondNsingle bondC structures for nitrogen reduction reaction (NRR) with a focus on unraveling the corresponding mechanisms concerning different Mo site positions and C topologies. Our results indicate that the position of the active site centers has a great effect on its electrocatalytic behavior. The gas phase N2 efficiently reduces to ammonia on MoN4C8 via the distal mechanism with an onset potential of −0.51 V. We confirm that the proposed pyridinic structure, MoN4C8, can catalyze NRR effectively with a low overpotential of 0.35 V.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000901469900003 Publication Date 2022-11-30
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0169-4332 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.7 Times cited Open Access OpenAccess
Notes Approved (down) Most recent IF: 6.7; 2023 IF: 3.387
Call Number UA @ admin @ c:irua:192430 Serial 7275
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Author Faraji, F.; Neek-Amal, M.; Neyts, E.C.; Peeters, F.M.
Title Indentation of graphene nano-bubbles Type A1 Journal article
Year 2022 Publication Nanoscale Abbreviated Journal Nanoscale
Volume 14 Issue 15 Pages 5876-5883
Keywords A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Molecular dynamics simulations are used to investigate the effect of an AFM tip when indenting graphene nano bubbles filled by a noble gas (i.e. He, Ne and Ar) up to the breaking point. The failure points resemble those of viral shells as described by the Foppl-von Karman (FvK) dimensionless number defined in the context of elasticity theory of thin shells. At room temperature, He gas inside the bubbles is found to be in the liquid state while Ne and Ar atoms are in the solid state although the pressure inside the nano bubble is below the melting pressure of the bulk. The trapped gases are under higher hydrostatic pressure at low temperatures than at room temperature.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000776763000001 Publication Date 2022-03-30
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2040-3364; 2040-3372 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.7 Times cited 2 Open Access OpenAccess
Notes Approved (down) Most recent IF: 6.7
Call Number UA @ admin @ c:irua:187924 Serial 7171
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Author Tampieri, F.; Espona-Noguera, A.; Labay, C.; Ginebra, M.-P.; Yusupov, M.; Bogaerts, A.; Canal, C.
Title Does non-thermal plasma modify biopolymers in solution? A chemical and mechanistic study for alginate Type A1 Journal Article
Year 2023 Publication Biomaterials Science Abbreviated Journal
Volume Issue Pages
Keywords A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Abstract In the last decades, non-thermal plasma has been extensively investigated as a relevant tool for various biomedical applications, ranging from tissue decontamination to regeneration and from skin treatment to tumor therapies. This high versatility is due to the different kinds and amount of reactive oxygen and nitrogen species that can be generated during a plasma treatment and put in contact with the biological target. Some recent studies report that solutions of biopolymers with the ability to generate hydrogels, when treated with plasma, can enhance the generation of reactive species and influence their stability, resulting thus in the ideal media for indirect treatments of biological targets. The direct effects of the plasma treatment on the structure of biopolymers in water solution, as well as the chemical mechanisms responsible for the enhanced generation of RONS, are not yet fully understood. In this study, we aim at filling this gap by investigating, on the one hand, the nature and extent of the modifications induced by plasma treatment in alginate solutions, and, on the other hand, at using this information to explain the mechanisms responsible for the enhanced generation of reactive species as a consequence of the treatment. The approach we use is twofold: (i) investigating the effects of plasma treatment on alginate solutions, by size exclusion chromatography, rheology and scanning electron microscopy and (ii) study of a molecular model (glucuronate) sharing its chemical structure, by chromatography coupled with mass spectrometry and by molecular dynamics simulations. Our results point out the active role of the biopolymer chemistry during direct plasma treatment. Short-lived reactive species, such as OH radicals and O atoms, can modify the polymer structure, affecting its functional groups and causing partial fragmentation. Some of these chemical modifications, like the generation of organic peroxide, are likely responsible for the secondary generation of long-lived reactive species such as hydrogen peroxide and nitrite ions. This is relevant in view of using biocompatible hydrogels as vehicles for storage and delivery reactive species for targeted therapies.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000973699000001 Publication Date 2023-04-11
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2047-4830 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.6 Times cited Open Access Not_Open_Access
Notes Agència de Gestió d’Ajuts Universitaris i de Recerca, SGR2022-1368 ; H2020 European Research Council, 714793 ; European Cooperation in Science and Technology, CA19110 CA20114 ; Secretaría de Estado de Investigación, Desarrollo e Innovación, PID2019-103892RB-I00/AEI/10.13039/501100011033 ; We thank Gonzalo Rodríguez Cañada and Xavier Solé-Martí (Universitat Politècnica de Catalunya) for help in collecting some of the experimental data and for the useful discussions. This work has been primarily funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 714793). The authors acknowledge MINECO for PID2019103892RB-I00/AEI/10.13039/501100011033 project (CC). The authors belong to SGR2022-1368 (FT, AEN, CL, MPG, CC) and acknowledge Generalitat de Catalunya for the ICREA Academia Award for Excellence in Research of CC. We thank also COST Actions CA20114 (Therapeutical Applications of Cold Plasmas) and CA19110 (Plasma Applications for Smart and Sustainable Agriculture) for the stimulating environment provided. Approved (down) Most recent IF: 6.6; 2023 IF: 4.21
Call Number PLASMANT @ plasmant @c:irua:196773 Serial 8794
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Author Deben, C.; Cardenas De La Hoz, E.; Le Compte, M.; Van Schil, P.; Hendriks, J.M.H.; Lauwers, P.; Yogeswaran, S.K.; Lardon, F.; Pauwels, P.; van Laere, S.; Bogaerts, A.; Smits, E.; Vanlanduit, S.; Lin, A.
Title OrBITS : label-free and time-lapse monitoring of patient derived organoids for advanced drug screening Type A1 Journal article
Year 2022 Publication Cellular Oncology (2211-3428) Abbreviated Journal Cell Oncol
Volume Issue Pages 1-16
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Center for Oncological Research (CORE)
Abstract Background Patient-derived organoids are invaluable for fundamental and translational cancer research and holds great promise for personalized medicine. However, the shortage of available analysis methods, which are often single-time point, severely impede the potential and routine use of organoids for basic research, clinical practise, and pharmaceutical and industrial applications. Methods Here, we developed a high-throughput compatible and automated live-cell image analysis software that allows for kinetic monitoring of organoids, named Organoid Brightfield Identification-based Therapy Screening (OrBITS), by combining computer vision with a convolutional network machine learning approach. The OrBITS deep learning analysis approach was validated against current standard assays for kinetic imaging and automated analysis of organoids. A drug screen of standard-of-care lung and pancreatic cancer treatments was also performed with the OrBITS platform and compared to the gold standard, CellTiter-Glo 3D assay. Finally, the optimal parameters and drug response metrics were identified to improve patient stratification. Results OrBITS allowed for the detection and tracking of organoids in routine extracellular matrix domes, advanced Gri3D (R)-96 well plates, and high-throughput 384-well microplates, solely based on brightfield imaging. The obtained organoid Count, Mean Area, and Total Area had a strong correlation with the nuclear staining, Hoechst, following pairwise comparison over a broad range of sizes. By incorporating a fluorescent cell death marker, infra-well normalization for organoid death could be achieved, which was tested with a 10-point titration of cisplatin and validated against the current gold standard ATP-assay, CellTiter-Glo 3D. Using this approach with OrBITS, screening of chemotherapeutics and targeted therapies revealed further insight into the mechanistic action of the drugs, a feature not achievable with the CellTiter-Glo 3D assay. Finally, we advise the use of the growth rate-based normalised drug response metric to improve accuracy and consistency of organoid drug response quantification. Conclusion Our findings validate that OrBITS, as a scalable, automated live-cell image analysis software, would facilitate the use of patient-derived organoids for drug development and therapy screening. The developed wet-lab workflow and software also has broad application potential, from providing a launching point for further brightfield-based assay development to be used for fundamental research, to guiding clinical decisions for personalized medicine.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000898426100001 Publication Date 2022-12-12
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2211-3428; 2211-3436 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.6 Times cited Open Access OpenAccess
Notes Approved (down) Most recent IF: 6.6
Call Number UA @ admin @ c:irua:192698 Serial 7272
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Author Chirumamilla, C.S.; Palagani, A.; Kamaraj, B.; Declerck, K.; Verbeek, M.W.C.; Ryabtsova, O.; De Bosscher, K.; Bougarne, N.; Ruttens, B.; Gevaert, K.; Houtman, R.; De Vos, W.H.; Joossens, J.; van der Veken, P.; Augustyns, K.; van Ostade, X.; Bogaerts, A.; De Winter, H.; Vanden Berghe, W.
Title Selective glucocorticoid receptor properties of GSK866 analogs with cysteine reactive warheads Type Administrative Services
Year 2017 Publication Frontiers in immunology Abbreviated Journal Front Immunol
Volume 8 Issue Pages 1324
Keywords Administrative Services; A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Medicinal Chemistry (UAMC)
Abstract Synthetic glucocorticoids (GC) are the mainstay therapy for treatment of acute and chronic inflammatory disorders. Due to the high adverse effects associated with long-term use, GC pharmacology has focused since the nineties on more selective GC ligand-binding strategies, classified as selective glucocorticoid receptor (GR) agonists (SEGRAs) or selective glucocorticoid receptor modulators (SEGRMs). In the current study, GSK866 analogs with electrophilic covalent-binding warheads were developed with potential SEGRA properties to improve their clinical safety profile for long-lasting topical skin disease applications. Since the off-rate of a covalently binding drug is negligible compared to that of a non-covalent drug, its therapeutic effects can be prolonged and typically, smaller doses of the drug are necessary to reach the same level of therapeutic efficacy, thereby potentially reducing systemic side effects. Different analogs of SEGRA GSK866 coupled to cysteine reactive warheads were characterized for GR potency and selectivity in various biochemical and cellular assays. GR- and NFκB-dependent reporter gene studies show favorable anti-inflammatory properties with reduced GR transactivation of two non-steroidal GSK866 analogs UAMC-1217 and UAMC-1218, whereas UAMC-1158 and UAMC-1159 compounds failed to modulate cellular GR activity. These results were further supported by GR immuno-localization and S211 phospho-GR western analysis, illustrating significant GR phosphoactivation and nuclear translocation upon treatment of GSK866, UAMC-1217, or UAMC-1218, but not in case of UAMC-1158 or UAMC-1159. Furthermore, mass spectrometry analysis of tryptic peptides of recombinant GR ligand-binding domain (LBD) bound to UAMC-1217 or UAMC-1218 confirmed covalent cysteine-dependent GR binding. Finally, molecular dynamics simulations, as well as glucocorticoid receptor ligand-binding domain (GR-LBD) coregulator interaction profiling of the GR-LBD bound to GSK866 or its covalently binding analogs UAMC-1217 or UAMC-1218 revealed subtle conformational differences that might underlie their SEGRA properties. Altogether, GSK866 analogs UAMC-1217 and UAMC-1218 hold promise as a novel class of covalent-binding SEGRA ligands for the treatment of topical inflammatory skin disorders.
Address
Corporate Author Thesis
Publisher Place of Publication Place of publication unknown Editor
Language Wos 000414136300001 Publication Date 2017-11-01
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1664-3224 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.429 Times cited 2 Open Access OpenAccess
Notes Approved (down) Most recent IF: 6.429
Call Number UA @ lucian @ c:irua:146485 Serial 4750
Permanent link to this record
 
 
Author Neyts, E.C.; Bogaerts, A.
Title Ion irradiation for improved graphene network formation in carbon nanotube growth Type A1 Journal article
Year 2014 Publication Carbon Abbreviated Journal Carbon
Volume 77 Issue Pages 790-795
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Ion irradiation of carbon nanotubes very often leads to defect formation. However, we have recently shown that Ar ion irradiation in a limited energy window of 1025 eV may enhance the initial cap nucleation process, when the carbon network is in contact with the metal nanocatalyst. Here, we employ reactive molecular dynamics simulations to demonstrate that ion irradiation in a higher energy window of 1035 eV may also heal network defects after the nucleation stage through a non-metal-mediated mechanism, when the carbon network is no longer in contact with the metal nanocatalyst. The results demonstrate the possibility of beneficially utilizing ions in e.g. plasma-enhanced chemical vapour deposition of carbon nanotubes.
Address
Corporate Author Thesis
Publisher Place of Publication Oxford Editor
Language Wos 000340689400083 Publication Date 2014-06-11
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0008-6223; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited 7 Open Access
Notes Approved (down) Most recent IF: 6.337; 2014 IF: 6.196
Call Number UA @ lucian @ c:irua:118062 Serial 1745
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Author Shariat, M.; Hosseini, S.I.; Shokri, B.; Neyts, E.C.
Title Plasma enhanced growth of single walled carbon nanotubes at low temperature : a reactive molecular dynamics simulation Type A1 Journal article
Year 2013 Publication Carbon Abbreviated Journal Carbon
Volume 65 Issue Pages 269-276
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Low-temperature growth of carbon nanotubes (CNTs) has been claimed to provide a route towards chiral-selective growth, enabling a host of applications. In this contribution, we employ reactive molecular dynamics simulations to demonstrate how plasma-based deposition allows such low-temperature growth. We first show how ion bombardment during the growth affects the carbon dissolution and precipitation process. We then continue to demonstrate how a narrow ion energy window allows CNT growth at 500 K. Finally, we also show how CNTs in contrast cannot be grown in thermal CVD at this low temperature, but only at high temperature, in agreement with experimental data. (C) 2013 Elsevier Ltd. All rights reserved.
Address
Corporate Author Thesis
Publisher Place of Publication Oxford Editor
Language Wos 000326773200031 Publication Date 2013-08-23
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0008-6223; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited 21 Open Access
Notes Approved (down) Most recent IF: 6.337; 2013 IF: 6.160
Call Number UA @ lucian @ c:irua:112697 Serial 2635
Permanent link to this record
 
 
Author Neyts, E.; Maeyens, A.; Pourtois, G.; Bogaerts, A.
Title A density-functional theory simulation of the formation of Ni-doped fullerenes by ion implantation Type A1 Journal article
Year 2011 Publication Carbon Abbreviated Journal Carbon
Volume 49 Issue 3 Pages 1013-1017
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Using self-consistent KohnSham density-functional theory molecular dynamics simulations, we demonstrate the theoretical possibility to synthesize NiC60, the incarfullerene Ni@C60 and the heterofullerene C59Ni in an ion implantation setup. The corresponding formation mechanisms of all three complexes are elucidated as a function of the ion implantation energy and impact location, suggesting possible routes for selectively synthesizing these complexes.
Address
Corporate Author Thesis
Publisher Place of Publication Oxford Editor
Language Wos 000286683500032 Publication Date 2010-11-14
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0008-6223; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited 13 Open Access
Notes Approved (down) Most recent IF: 6.337; 2011 IF: 5.378
Call Number UA @ lucian @ c:irua:85139 Serial 639
Permanent link to this record
 
 
Author Neyts, E.C.; Bogaerts, A.
Title Formation of endohedral Ni@C60 and exohedral NiC60 metallofullerene complexes by simulated ion implantation Type A1 Journal article
Year 2009 Publication Carbon Abbreviated Journal Carbon
Volume 47 Issue 4 Pages 1028-1033
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The interaction of thermal and hyperthermal Ni ions with gas-phase C60 fullerene was investigated at two temperatures with classical molecular dynamics simulations using a recently developed interatomic many-body potential. The interaction between Ni and C60 is characterized in terms of the NiC60 binding sites, complex formation, and the collision and temperature induced deformation of the C60 cage structure. The simulations show how ion implantation theoretically allows the synthesis of both endohedral Ni@C60 and exohedral NiC60 metallofullerene complexes.
Address
Corporate Author Thesis
Publisher Place of Publication Oxford Editor
Language Wos 000264252900012 Publication Date 2008-12-25
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0008-6223; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited 15 Open Access
Notes Approved (down) Most recent IF: 6.337; 2009 IF: 4.504
Call Number UA @ lucian @ c:irua:76434 Serial 1260
Permanent link to this record
 
 
Author Khalilov, U.; Bogaerts, A.; Neyts, E.C.
Title Atomic-scale mechanisms of plasma-assisted elimination of nascent base-grown carbon nanotubes Type A1 Journal article
Year 2017 Publication Carbon Abbreviated Journal Carbon
Volume 118 Issue 118 Pages 452-457
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Selective etching allows for obtaining carbon nanotubes with a specific chirality. While plasma-assisted etching has already been used to separate metallic tubes from their semiconducting counterparts, little is known about the nanoscale mechanisms of the etching process. We combine (reactive) molecular dynamics (MD) and force-bias Monte Carlo (tfMC) simulations to study H-etching of CNTs. In particular, during the hydrogenation and subsequent etching of both the carbon cap and the tube, they sequentially transform to different carbon nanostructures, including carbon nanosheet, nanowall, and polyyne chains, before they are completely removed from the surface of a substrate-bound Ni-nanocluster.We also found that onset of the etching process is different in the cases of the cap and the tube, although the overall etching scenario is similar in both cases. The entire hydrogenation/etching process for both cases is analysed in detail, comparing with available theoretical and experimental evidences.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000401120800053 Publication Date 2017-03-26
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0008-6223 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited 2 Open Access OpenAccess
Notes U. K. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), Belgium (Grant No. 12M1315N). The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. The authors also thank Prof. A. C. T. van Duin for sharing the ReaxFF code. Approved (down) Most recent IF: 6.337
Call Number PLASMANT @ plasmant @ c:irua:141915 Serial 4531
Permanent link to this record
 
 
Author Aussems, D.U.B.; Bal, K.M.; Morgan, T.W.; van de Sanden, M.C.M.; Neyts, E.C.
Title Mechanisms of elementary hydrogen ion-surface interactions during multilayer graphene etching at high surface temperature as a function of flux Type A1 Journal article
Year 2018 Publication Carbon Abbreviated Journal Carbon
Volume 137 Issue Pages 527-532
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract In order to optimize the plasma-synthesis and modification process of carbon nanomaterials for applications such as nanoelectronics and energy storage, a deeper understanding of fundamental hydrogengraphite/graphene interactions is required. Atomistic simulations by Molecular Dynamics have proven to be indispensable to illuminate these phenomena. However, severe time-scale limitations restrict them to very fast processes such as reflection, while slow thermal processes such as surface diffusion and molecular desorption are commonly inaccessible. In this work, we could however reach these thermal processes for the first time at time-scales and surface temperatures (1000 K) similar to high-flux plasma exposure experiments during the simulation of multilayer graphene etching by 5 eV H ions. This was achieved by applying the Collective Variable-Driven Hyperdynamics biasing technique, which extended the inter-impact time over a range of six orders of magnitude, down to a more realistic ion-flux of 1023m2s1. The results show that this not only causes a strong shift from predominant ion-to thermally induced interactions, but also significantly affects the hydrogen uptake and surface evolution. This study thus elucidates H ion-graphite/graphene interaction mechanisms and stresses the importance of including long time-scales in atomistic simulations at high surface temperatures to understand the dynamics of the ion-surface system.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000440661700056 Publication Date 2018-05-24
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0008-6223 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited 4 Open Access Not_Open_Access: Available from 25.05.2020
Notes DIFFER is part of the Netherlands Organisation for Scientific Research (NWO). K.M.B. is funded as PhD fellow (aspirant) of the FWO-Flanders (Fund for Scientific Research-Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government e department EWI. Approved (down) Most recent IF: 6.337
Call Number PLASMANT @ plasmant @c:irua:152172 Serial 4993
Permanent link to this record
 
 
Author De Backer, J.; Razzokov, J.; Hammerschmid, D.; Mensch, C.; Hafideddine, Z.; Kumar, N.; van Raemdonck, G.; Yusupov, M.; Van Doorslaer, S.; Johannessen, C.; Sobott, F.; Bogaerts, A.; Dewilde, S.
Title The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor Type A1 Journal article
Year 2018 Publication Redox Biology Abbreviated Journal Redox Biol
Volume 19 Issue Pages 1-10
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec)
Abstract Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000449722100002 Publication Date 2018-07-24
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2213-2317 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited Open Access OpenAccess
Notes M.Y. and N.K. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grant nos. 1200216N and 12J5617N. 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). C.M acknowledges the financial support provided by the Flemish Community and the University of Antwerp (BOF-NOI) for the pre-doctoral scholarship is under grant number/project ID: 28465. S.V.D., S. D. and Z.H. acknowledge the FWO (Grant G.0687.13) and the GOA-BOF UA 2013–2016 (project-ID 28312) for funding. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI. Approved (down) Most recent IF: 6.337
Call Number PLASMANT @ plasmant @c:irua:152818 Serial 5006
Permanent link to this record
 
 
Author Khalilov, U.; Vets, C.; Neyts, E.C.
Title Catalyzed growth of encapsulated carbyne Type A1 Journal article
Year 2019 Publication Carbon Abbreviated Journal Carbon
Volume 153 Issue Pages 1-5
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Carbyne is a novel material of current interest in nanotechnology. As is typically the case for nanomaterials, the growth process determines the resulting properties. While endohedral carbyne has been successfully synthesized, its catalyst and feedstock-dependent growth mechanism is still elusive. We here study the nucleation and growth mechanism of different carbon chains in a Ni-containing double walled carbon nanotube using classical molecular dynamics simulations and first-principles calculations. We find that the understanding the competitive role of the metal catalyst and the hydrocarbon is important to control the growth of 1-dimensional carbon chains, including Ni or H-terminated carbyne. Also, we find that the electronic property of the Ni-terminated carbyne can be tuned by steering the H concentration along the chain. These results suggest catalyst-containing carbon nanotubes as a possible synthesis route for carbyne formation.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000485054200001 Publication Date 2019-07-01
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0008-6223 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited Open Access Not_Open_Access
Notes Fund of Scientific Research Flanders (FWO), Belgium, 12M1318N 1S22516N ; Flemish Supercomputer Centre VSC; Hercules Foundation; Flemish Government; University of Antwerp; The authors gratefully acknowledge the financial support from the Fund of Scientific Research Flanders (FWO), Belgium, Grant numbers 12M1318N and 1S22516N. The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the University of Antwerp. Approved (down) Most recent IF: 6.337
Call Number PLASMANT @ plasmant @c:irua:160695 Serial 5187
Permanent link to this record
 
 
Author Khalilov, U.; Neyts, E.C.
Title Mechanisms of selective nanocarbon synthesis inside carbon nanotubes Type A1 Journal article
Year 2021 Publication Carbon Abbreviated Journal Carbon
Volume 171 Issue Pages 72-78
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The possibility of confinement effects inside a carbon nanotube provides new application opportunities, e.g., growth of novel carbon nanostructures. However, the understanding the precise role of catalystfeedstock in the nanostructure synthesis is still elusive. In our simulation-based study, we investigate the Ni-catalyzed growth mechanism of encapsulated carbon nanostructures, viz. double-wall carbon nanotube and graphene nanoribbon, from carbon and hydrocarbon growth precursors, respectively. Specifically, we find that the tube and ribbon growth is determined by a catalyst-vs-feedstock competition effect. We compare our results, i.e., growth mechanism and structure morphology with all available theoretical and experimental data. Our calculations show that all encapsulated nanostructures contain metal (catalyst) atoms and such structures are less stable than their pure counterparts. Therefore, we study the purification mechanism of these structures. In general, this study opens a possible route to the controllable synthesis of tubular and planar carbon nanostructures for today’s nanotechnology.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000598371500009 Publication Date 2020-09-02
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0008-6223 ISBN Additional Links UA library record; WoS full record
Impact Factor 6.337 Times cited Open Access OpenAccess
Notes Fund of Scientific Research Flanders, 12M1318N ; Universiteit Antwerpen; Flemish Supercomputer Centre; Hercules Foundation; Flemish Government; The authors gratefully acknowledge the financial support from the Fund of Scientific Research Flanders (FWO), Belgium, Grant number 12M1318N. The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Centre (VSC), funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA, Belgium. Approved (down) Most recent IF: 6.337
Call Number PLASMANT @ plasmant @c:irua:172459 Serial 6414
Permanent link to this record
 
 
Author Fukuhara, S.; Bal, K.M.; Neyts, E.C.; Shibuta, Y.
Title Entropic and enthalpic factors determining the thermodynamics and kinetics of carbon segregation from transition metal nanoparticles Type A1 Journal article
Year 2021 Publication Carbon Abbreviated Journal Carbon
Volume 171 Issue Pages 806-813
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The free energy surface (FES) for carbon segregation from nickel nanoparticles is obtained from advanced molecular dynamics simulations. A suitable reaction coordinate is developed that can distinguish dissolved carbon atoms from segregated dimers, chains and junctions on the nanoparticle surface. Because of the typically long segregation time scale (up to ms), metadynamics simulations along the developed reaction coordinate are used to construct FES over a wide range of temperatures and carbon concentrations. The FES revealed the relative stability of different stages in the segregation process, and free energy barriers and rates of the individual steps could then be calculated and decomposed into enthalpic and entropic contributions. As the carbon concentration in the nickel nanoparticle increases, segregated carbon becomes more stable in terms of both enthalpy and entropy. The activation free energy of the reaction also decreases with the increase of carbon concentration, which can be mainly attributed to entropic effects. These insights and the methodology developed to obtain them improve our understanding of carbon segregation process across materials science in general, and the nucleation and growth of carbon nanotube in particular.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000598371500084 Publication Date 2020-09-25
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0008-6223 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited Open Access OpenAccess
Notes Scientific Research, 19H02415 ; JSPS, 18J22727 ; Japan Society for the Promotion of Science; JSPS; JSPS; FWO; Research Foundation; Flanders, 12ZI420N ; This work was supported by Grant-in-Aid for Scientific Research (B) (No.19H02415) and Grant-in-Aid for JSPS Research Fellow (No.18J22727) from Japan Society for the Promotion of Science (JSPS), Japan. S.F. was supported by JSPS through the Program for 812 Approved (down) Most recent IF: 6.337
Call Number PLASMANT @ plasmant @c:irua:172452 Serial 6421
Permanent link to this record
 
 
Author Yusupov, M.; Privat-Maldonado, A.; Cordeiro, R.M.; Verswyvel, H.; Shaw, P.; Razzokov, J.; Smits, E.; Bogaerts, A.
Title Oxidative damage to hyaluronan–CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy Type A1 Journal article
Year 2021 Publication Redox Biology Abbreviated Journal Redox Biol
Volume 43 Issue Pages 101968
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Abstract Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44–HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44–HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44–HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000657371800005 Publication Date 2021-04-14
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2213-2317 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited Open Access OpenAccess
Notes Fwo; The authors acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA, where all computational work was performed. Approved (down) Most recent IF: 6.337
Call Number PLASMANT @ plasmant @c:irua:177780 Serial 6750
Permanent link to this record
 
 
Author Bings, N.H.; Bogaerts, A.; Broekaert, J.A.C.
Title Atomic spectroscopy Type A1 Journal article
Year 2013 Publication Analytical chemistry Abbreviated Journal Anal Chem
Volume 85 Issue 2 Pages 670-704
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos 000313668400013 Publication Date 2012-11-07
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.32 Times cited 29 Open Access
Notes Approved (down) Most recent IF: 6.32; 2013 IF: 5.825
Call Number UA @ lucian @ c:irua:104719 Serial 190
Permanent link to this record
 
 
Author Lindner, H.; Murtazin, A.; Groh, S.; Niemax, K.; Bogaerts, A.
Title Simulation and experimental studies on plasma temperature, flow velocity, and injector diameter effects for an inductively coupled plasma Type A1 Journal article
Year 2011 Publication Analytical chemistry Abbreviated Journal Anal Chem
Volume 83 Issue 24 Pages 9260-9266
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract An inductively coupled plasma (ICP) is analyzed by means of experiments and numerical simulation. Important plasma properties are analyzed, namely, the effective temperature inside the central channel and the mean flow velocity inside the plasma. Furthermore, the effect of torches with different injector diameters is studied by the model. The temperature inside the central channel is determined from the end-on collected line-to-background ratio in dependence of the injector gas flow rates. Within the limits of 3% deviation, the results of the simulation and the experiments are in good agreement in the range of flow rates relevant for the analysis of relatively large droplets, i.e., 50 μm. The deviation increases for higher gas flow rates but stays below 6% for all flow rates studied. The velocity of the gas inside the coil region was determined by side-on analyte emission measurements with single monodisperse droplet introduction and by the analysis of the injector gas path lines in the simulation. In the downstream region significantly higher velocities were found than in the upstream region in both the simulation and the experiment. The quantitative values show good agreement in the downstream region. In the upstream region, deviations were found in the absolute values which can be attributed to the flow conditions in that region and because the methods used for velocity determination are not fully consistent. Eddy structures are found in the simulated flow lines. These affect strongly the way taken by the path lines of the injector gas and they can explain the very long analytical signals found in the experiments at low flow rates. Simulations were performed for different injector diameters in order to find conditions where good analyte transport and optimum signals can be expected. The results clearly show the existence of a transition flow rate which marks the lower limit for effective analyte transport conditions through the plasma. A rule-of-thumb equation was extracted from the results from which the transition flow rate can be estimated for different injector diameters and different injector gas compositions.
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos 000297946900013 Publication Date 2011-07-29
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.32 Times cited 34 Open Access
Notes Approved (down) Most recent IF: 6.32; 2011 IF: 5.856
Call Number UA @ lucian @ c:irua:94001 Serial 3009
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Author Bings, N.H.; Bogaerts, A.; Broekaert, J.A.C.
Title Atomic spectroscopy: a review Type A1 Journal article
Year 2010 Publication Analytical chemistry Abbreviated Journal Anal Chem
Volume 82 Issue 12 Pages 4653-4681
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos 000278616100001 Publication Date 2010-05-13
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.32 Times cited 65 Open Access
Notes Approved (down) Most recent IF: 6.32; 2010 IF: 5.874
Call Number UA @ lucian @ c:irua:82675 Serial 195
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Author Lindner, H.; Autrique, D.; Garcia, C.C.; Niemax, K.; Bogaerts, A.
Title Optimized transport setup for high repetition rate pulse-separated analysis in laser ablation-inductively coupled plasma mass spectrometry Type A1 Journal article
Year 2009 Publication Analytical chemistry Abbreviated Journal Anal Chem
Volume 81 Issue 11 Pages 4241-4248
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract An optimized laser ablation setup, proposed for high repetition rate inductively coupled plasma mass spectrometry (ICPMS) analyses such as 2D imaging or depth profiling, is presented. For such applications, the particle washout time needs to be as short as possible to allow high laser pulse frequencies for reduced analysis time. Therefore, it is desirable to have an ablation setup that operates as a laminar flow reactor (LFR). A top-down strategy was applied that resulted in the present design. In the first step, a previously applied ablation setup was analyzed on the basis of computational fluid dynamics (CFD) results presented by D. Autrique et al. (Spectrochim. Acta, B 2008, 63, 257−270). By means of CFD simulations, the design was modified in such a way that it operated in the LFR regime. Experimental results demonstrate that the current design can indeed be regarded as an LFR. Furthermore, the operation under LFR conditions allowed some insight into the initial radial concentration distribution if the experimental ICPMS signal and analytical expressions are taken into account. Recommendations for a modified setup for more resilient spatial distributions are given. With the present setup, a washout time of 140 ms has been achieved for a 3% signal area criterion. Therefore, 7 Hz repetition rates can be applied with the present setup. Using elementary formulas of the analytical model, an upper bound for the washout times for similar setups can be predicted. The authors believe that the presented setup geometry comes close to the achievable limit for reliable short washout times.
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos 000266601800014 Publication Date 2009-04-29
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.32 Times cited 18 Open Access
Notes Approved (down) Most recent IF: 6.32; 2009 IF: 5.214
Call Number UA @ lucian @ c:irua:76935 Serial 2492
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