“Flowing Atmospheric Pressure Afterglow for Ambient Ionization: Reaction Pathways Revealed by Modeling”. Aghaei M, Bogaerts A, Analytical Chemistry 93, 6620 (2021). http://doi.org/10.1021/acs.analchem.0c04076
Abstract: We describe the plasma chemistry in a helium flowing atmospheric pressure afterglow (FAPA) used for analytical spectrometry, by means of a quasione-dimensional (1D) plasma chemical kinetics model. We study the effect of typical impurities present in the feed gas, as well as the afterglow in ambient humid air. The model provides the species density profiles in the discharge and afterglow regions and the chemical pathways. We demonstrate that H, N, and O atoms are formed in the discharge region, while the dominant reactive neutral species in the afterglow are O3 and NO. He* and He2* are responsible for Penning ionization of O2, N2, H2O, H2, and N, and especially O and H atoms. Besides, He2+ also contributes to ionization of N2, O2, H2O, and O through charge transfer reactions. From the pool of ions created in the discharge, NO+ and (H2O)3H+ are the dominant ions in the afterglow. Moreover, negatively charged clusters, such as NO3H2O− and NO2H2O−, are formed and their pathway is discussed as well. Our model predictions are in line with earlier observations in the literature about the important reagent ions and provide a comprehensive overview of the underlying pathways. The model explains in detail why helium provides a high analytical sensitivity because of high reagent ion formation by both Penning ionization and charge transfer. Such insights are very valuable for improving the analytical performance of this (and other) ambient desorption/ionization source(s).
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.32
DOI: 10.1021/acs.analchem.0c04076
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“A density-functional theory simulation of the formation of Ni-doped fullerenes by ion implantation”. Neyts E, Maeyens A, Pourtois G, Bogaerts A, Carbon 49, 1013 (2011). http://doi.org/10.1016/j.carbon.2010.11.009
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 13
DOI: 10.1016/j.carbon.2010.11.009
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“Formation of endohedral Ni@C60 and exohedral NiC60 metallofullerene complexes by simulated ion implantation”. Neyts EC, Bogaerts A, Carbon 47, 1028 (2009). http://doi.org/10.1016/j.carbon.2008.12.023
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 15
DOI: 10.1016/j.carbon.2008.12.023
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“Ion irradiation for improved graphene network formation in carbon nanotube growth”. Neyts EC, Bogaerts A, Carbon 77, 790 (2014). http://doi.org/10.1016/j.carbon.2014.05.083
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 7
DOI: 10.1016/j.carbon.2014.05.083
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“Plasma enhanced growth of single walled carbon nanotubes at low temperature : a reactive molecular dynamics simulation”. Shariat M, Hosseini SI, Shokri B, Neyts EC, Carbon 65, 269 (2013). http://doi.org/10.1016/j.carbon.2013.08.025
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 21
DOI: 10.1016/j.carbon.2013.08.025
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“Atomic-scale mechanisms of plasma-assisted elimination of nascent base-grown carbon nanotubes”. Khalilov U, Bogaerts A, Neyts EC, Carbon 118, 452 (2017). http://doi.org/10.1016/j.carbon.2017.03.068
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 2
DOI: 10.1016/j.carbon.2017.03.068
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“Mechanisms of elementary hydrogen ion-surface interactions during multilayer graphene etching at high surface temperature as a function of flux”. Aussems DUB, Bal KM, Morgan TW, van de Sanden MCM, Neyts EC, Carbon 137, 527 (2018). http://doi.org/10.1016/j.carbon.2018.05.051
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 4
DOI: 10.1016/j.carbon.2018.05.051
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“The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor”. De Backer J, Razzokov J, Hammerschmid D, Mensch C, Hafideddine Z, Kumar N, van Raemdonck G, Yusupov M, Van Doorslaer S, Johannessen C, Sobott F, Bogaerts A, Dewilde S, Redox Biology 19, 1 (2018). http://doi.org/10.1016/j.redox.2018.07.019
Abstract: Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec)
Impact Factor: 6.337
DOI: 10.1016/j.redox.2018.07.019
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“Catalyzed growth of encapsulated carbyne”. Khalilov U, Vets C, Neyts EC, Carbon 153, 1 (2019). http://doi.org/10.1016/j.carbon.2019.06.110
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
DOI: 10.1016/j.carbon.2019.06.110
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“Mechanisms of selective nanocarbon synthesis inside carbon nanotubes”. Khalilov U, Neyts EC, Carbon 171, 72 (2021). http://doi.org/10.1016/j.carbon.2020.08.060
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
DOI: 10.1016/j.carbon.2020.08.060
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“Entropic and enthalpic factors determining the thermodynamics and kinetics of carbon segregation from transition metal nanoparticles”. Fukuhara S, Bal KM, Neyts EC, Shibuta Y, Carbon 171, 806 (2021). http://doi.org/10.1016/j.carbon.2020.09.059
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
DOI: 10.1016/j.carbon.2020.09.059
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“Oxidative damage to hyaluronan–CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy”. Yusupov M, Privat-Maldonado A, Cordeiro RM, Verswyvel H, Shaw P, Razzokov J, Smits E, Bogaerts A, Redox Biology 43, 101968 (2021). http://doi.org/10.1016/j.redox.2021.101968
Abstract: Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44–HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44–HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44–HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Impact Factor: 6.337
DOI: 10.1016/j.redox.2021.101968
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Chirumamilla CS, Palagani A, Kamaraj B, Declerck K, Verbeek MWC, Ryabtsova O, De Bosscher K, Bougarne N, Ruttens B, Gevaert K, Houtman R, De Vos WH, Joossens J, van der Veken P, Augustyns K, van Ostade X, Bogaerts A, De Winter H, Vanden Berghe W (2017) Selective glucocorticoid receptor properties of GSK866 analogs with cysteine reactive warheads. Place of publication unknown, 1324
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.
Keywords: Administrative Services; A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Medicinal Chemistry (UAMC)
Impact Factor: 6.429
Times cited: 2
DOI: 10.3389/FIMMU.2017.01324
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“OrBITS : label-free and time-lapse monitoring of patient derived organoids for advanced drug screening”. Deben C, Cardenas De La Hoz E, Le Compte M, Van Schil P, Hendriks JMH, Lauwers P, Yogeswaran SK, Lardon F, Pauwels P, van Laere S, Bogaerts A, Smits E, Vanlanduit S, Lin A, Cellular Oncology (2211-3428) , 1 (2022). http://doi.org/10.1007/S13402-022-00750-0
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.
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)
Impact Factor: 6.6
DOI: 10.1007/S13402-022-00750-0
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“Does non-thermal plasma modify biopolymers in solution? A chemical and mechanistic study for alginate”. Tampieri F, Espona-Noguera A, Labay C, Ginebra M-P, Yusupov M, Bogaerts A, Canal C, Biomaterials Science (2023). http://doi.org/10.1039/D3BM00212H
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.
Keywords: A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 6.6
DOI: 10.1039/D3BM00212H
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“Indentation of graphene nano-bubbles”. Faraji F, Neek-Amal M, Neyts EC, Peeters FM, Nanoscale 14, 5876 (2022). http://doi.org/10.1039/D2NR01207C
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.7
Times cited: 2
DOI: 10.1039/D2NR01207C
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“Selectivity of Mo-NC sites for electrocatalytic N₂, reduction : a function of the single atom position on the surface and local carbon topologies”. Nematollahi P, Applied surface science 612, 155908 (2023). http://doi.org/10.1016/J.APSUSC.2022.155908
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.7
DOI: 10.1016/J.APSUSC.2022.155908
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“Charge transfer doping modulated raman scattering and enhanced stability of black phosphorus quantum dots on a ZnO nanorod”. Hu L, Amini MN, 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, Advanced Optical Materials 6, 1800440 (2018). http://doi.org/10.1002/ADOM.201800440
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.875
Times cited: 37
DOI: 10.1002/ADOM.201800440
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“Engineering the electronic properties of silicene by tuning the composition of MoX2 and GaX (X = S,Se,Te) chalchogenide templates”. Scalise E, Houssa M, Cinquanta E, Grazianetti C, van den Broek B, Pourtois G, Stesmans A, Fanciulli M, Molle A, 2D materials 1, 011010 (2014). http://doi.org/10.1088/2053-1583/1/1/011010
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.937
Times cited: 49
DOI: 10.1088/2053-1583/1/1/011010
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“Two-dimensional hexagonal tin : ab initio geometry, stability, electronic structure and functionalization”. van den Broek B, Houssa M, Scalise E, Pourtois G, Afanas'ev VV, Stesmans A, 2D materials 1, 021004 (2014). http://doi.org/10.1088/2053-1583/1/2/021004
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.937
Times cited: 58
DOI: 10.1088/2053-1583/1/2/021004
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“Functional silicene and stanene nanoribbons compared to graphene: electronic structure and transport”. van den Broek B, Houssa M, Iordanidou K, Pourtois G, Afanas'ev VV, Stesmans A, 2D materials 3, 015001 (2016). http://doi.org/10.1088/2053-1583/3/1/015001
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.937
Times cited: 19
DOI: 10.1088/2053-1583/3/1/015001
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“A route towards the fabrication of 2D heterostructures using atomic layer etching combined with selective conversion”. Heyne MH, Marinov D, Braithwaite N, Goodyear A, de Marneffe J-F, Cooke M, Radu I, Neyts EC, De Gendt S, 2D materials 6, 035030 (2019). http://doi.org/10.1088/2053-1583/AB1BA7
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.937
DOI: 10.1088/2053-1583/AB1BA7
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“Removal of alachlor in water by non-thermal plasma: Reactive species and pathways in batch and continuous process”. Wardenier N, Gorbanev Y, Van Moer I, Nikiforov A, Van Hulle SWH, Surmont P, Lynen F, Leys C, Bogaerts A, Vanraes P, Water research 161, 549 (2019). http://doi.org/10.1016/j.watres.2019.06.022
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.942
Times cited: 2
DOI: 10.1016/j.watres.2019.06.022
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“Oxidative Stress-Inducing Anticancer Therapies: Taking a Closer Look at Their Immunomodulating Effects”. Van Loenhout J, Peeters M, Bogaerts A, Smits E, Deben C, Antioxidants 9, 1188 (2020). http://doi.org/10.3390/antiox9121188
Abstract: Cancer cells are characterized by higher levels of reactive oxygen species (ROS) compared to normal cells as a result of an imbalance between oxidants and antioxidants. However, cancer cells maintain their redox balance due to their high antioxidant capacity. Recently, a high level of oxidative stress is considered a novel target for anticancer therapy. This can be induced by increasing exogenous ROS and/or inhibiting the endogenous protective antioxidant system. Additionally, the immune system has been shown to be a significant ally in the fight against cancer. Since ROS levels are important to modulate the antitumor immune response, it is essential to consider the effects of oxidative stress-inducing treatments on this response. In this review, we provide an overview of the mechanistic cellular responses of cancer cells towards exogenous and endogenous ROS-inducing treatments, as well as the indirect and direct antitumoral immune effects, which can be both immunostimulatory and/or immunosuppressive. For future perspectives, there is a clear need for comprehensive investigations of different oxidative stress-inducing treatment strategies and their specific immunomodulating effects, since the effects cannot be generalized over different treatment modalities. It is essential to elucidate all these underlying immune effects to make oxidative stress-inducing treatments effective anticancer therapy.
Keywords: A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Impact Factor: 7
DOI: 10.3390/antiox9121188
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“Cytoglobin Silencing Promotes Melanoma Malignancy but Sensitizes for Ferroptosis and Pyroptosis Therapy Response”. De Backer J, Maric D, Zuhra K, Bogaerts A, Szabo C, Vanden Berghe W, Hoogewijs D, Antioxidants 11, 1548 (2022). http://doi.org/10.3390/antiox11081548
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.
Keywords: A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
Impact Factor: 7
DOI: 10.3390/antiox11081548
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“Plasma-catalytic ammonia decomposition using a packed-bed dielectric barrier discharge reactor”. Andersen JA, Christensen JM, Østberg M, Bogaerts A, Jensen AD, International Journal Of Hydrogen Energy 47, 32081 (2022). http://doi.org/10.1016/J.IJHYDENE.2022.07.102
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.2
DOI: 10.1016/J.IJHYDENE.2022.07.102
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“Can endohedral transition metals enhance hydrogen storage in carbon nanotubes?”.Khalilov U, Uljayev U, Mehmonov K, Nematollahi P, Yusupov M, Neyts EC, Neyts EC, International journal of hydrogen energy 55, 640 (2024). http://doi.org/10.1016/J.IJHYDENE.2023.11.195
Abstract: The safe and efficient use of hydrogen energy, which is in high demand worldwide today, requires efficient hydrogen storage. Despite significant advances in hydrogen storage using carbon-based nanomaterials, including carbon nanotubes (CNTs), efforts to substantially increase the storage capacity remain less effective. In this work, we demonstrate the effect of endohedral transition metal atoms on the hydrogen storage capacity of CNTs using reactive molecular dynamics simulations. We find that an increase in the volume fraction of endohedral nickel atoms leads to an increase in the concentration of physisorbed hydrogen molecules around single-walled CNTs (SWNTs) by approximately 1.6 times compared to pure SWNTs. The obtained results provide insight into the underlying mechanisms of how endohedral transition metal atoms enhance the hydrogen storage ability of SWNTs under nearly ambient conditions.
Keywords: A1 Journal article; Engineering sciences. Technology; Modelling and Simulation in Chemistry (MOSAIC); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.2
DOI: 10.1016/J.IJHYDENE.2023.11.195
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“Carbon dioxide splitting in a dielectric barrier discharge plasma : a combined experimental and computational study”. Aerts R, Somers W, Bogaerts A, Chemsuschem 8, 702 (2015). http://doi.org/10.1002/cssc.201402818
Abstract: Plasma technology is gaining increasing interest for the splitting of CO2 into CO and O2. We have performed experiments to study this process in a dielectric barrier discharge (DBD) plasma with a wide range of parameters. The frequency and dielectric material did not affect the CO2 conversion and energy efficiency, but the discharge gap can have a considerable effect. The specific energy input has the most important effect on the CO2 conversion and energy efficiency. We have also presented a plasma chemistry model for CO2 splitting, which shows reasonable agreement with the experimental conversion and energy efficiency. This model is used to elucidate the critical reactions that are mostly responsible for the CO2 conversion. Finally, we have compared our results with other CO2 splitting techniques and we identified the limitations as well as the benefits and future possibilities in terms of modifications of DBD plasmas for greenhouse gas conversion in general.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.226
Times cited: 131
DOI: 10.1002/cssc.201402818
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“The Quest for Value-Added Products from Carbon Dioxide and Water in a Dielectric Barrier Discharge: A Chemical Kinetics Study”. Snoeckx R, Ozkan A, Reniers F, Bogaerts A, Chemsuschem 10, 409 (2017). http://doi.org/10.1002/cssc.201601234
Abstract: Recycling of carbon dioxide by its conversion into value-added products has gained significant interest owing to the role it can play for use in an anthropogenic carbon cycle. The combined conversion with H2O could even mimic the natural photosynthesis process. An interesting gas conversion technique currently being considered in the field of CO2 conversion is plasma technology. To investigate whether it is also promising for this combined conversion, we performed a series of experiments and developed a chemical kinetics plasma chemistry model for a deeper understanding of the process. The main products formed were the syngas components CO and H2, as well as O2 and H2O2, whereas methanol formation was only observed in the parts-per-billion to parts-per-million range. The syngas ratio, on the other hand, could easily be controlled by varying both the water content and/or energy input. On the basis of the model, which was validated with experimental results, a chemical kinetics analysis was performed, which allowed the construction and investigation of the different pathways leading to the observed experimental results and which helped to clarify these results. This approach allowed us to evaluate this technology on the basis of its underlying chemistry and to propose solutions on how to further improve the formation of value-added products by using plasma technology.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.226
Times cited: 25
DOI: 10.1002/cssc.201601234
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“The Chemical Route to a Carbon Dioxide Neutral World”. Martens JA, Bogaerts A, De Kimpe N, Jacobs PA, Marin GB, Rabaey K, Saeys M, Verhelst S, Chemsuschem 10, 1039 (2017). http://doi.org/10.1002/cssc.201601051
Abstract: Excessive CO2 emissions in the atmosphere from anthropogenic activity can be divided into point sources and diffuse sources. The capture of CO2 from flue gases of large industrial installations and its conversion into fuels and chemicals with fast catalytic processes seems technically possible. Some emerging technologies are already being demonstrated on an industrial scale. Others are still being tested on a laboratory or pilot scale. These emerging chemical technologies can be implemented in a time window ranging from 5 to 20 years. The massive amounts of energy needed for capturing processes and the conversion of CO2 should come from low-carbon energy sources, such as tidal, geothermal, and nuclear energy, but also, mainly, from the sun. Synthetic methane gas that can be formed from CO2 and hydrogen gas is an attractive renewable energy carrier with an existing distribution system. Methanol offers advantages as a liquid fuel and is also a building block for the chemical industry. CO2 emissions from diffuse sources is a difficult problem to solve, particularly for CO2 emissions from road, water, and air transport, but steady progress in the development of technology for capturing CO2 from air is being made. It is impossible to ban carbon from the entire energy
supply of mankind with the current technological knowledge, but a transition to a mixed carbon–hydrogen economy can reduce net CO2 emissions and ultimately lead to a CO2-neutral world.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.226
Times cited: 75
DOI: 10.1002/cssc.201601051
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