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Author Vanmeert, M.; Razzokov, J.; Mirza, M.U.; Weeks, S.D.; Schepers, G.; Bogaerts, A.; Rozenski, J.; Froeyen, M.; Herdewijn, P.; Pinheiro, V.B.; Lescrinier, E.
Title Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins Type A1 Journal article
Year 2019 Publication Nucleic acids research Abbreviated Journal Nucleic Acids Res
Volume 47 Issue 13 Pages 7130-7142
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000490556600047 Publication Date 2019-07-26
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0305-1048 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 10.162 Times cited 1 Open Access
Notes European Research Council, FP7/2007-2013 ERC-2012-ADG 20120216/320683 ; KU Leuven, OT/14/128 ; Biotechnology and Biosciences Research Council, BB/N01023X/1 BB/N010221/1 ; Authors are grateful to Prof. Dr A.M.J.J. (Alexandre) Bonvin from the University of Utrecht and the WeNMR institute for his expert contribution. We have greatly benefited from discussions and help from numerous postdocs over the years (in particular, Dr E. Groaz, Dr E. Eremeeva, Dr J. Masschelein, Dr S. Xiaoping and Dr M. Renders) as well as graduate student D. Kestemont and undergraduate student M. Abdel Fattah Ismail. We express our gratitude to L. Margamuljana for helpful discussions and excellent technical assistance on in vitro experiments. Approved Most recent IF: 10.162
Call Number PLASMANT @ plasmant @c:irua:162105 Serial 5359
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Author Bekeschus, S.; Freund, E.; Spadola, C.; Privat-Maldonado, A.; Hackbarth, C.; Bogaerts, A.; Schmidt, A.; Wende, K.; Weltmann, K.-D.; von Woedtke, T.; Heidecke, C.-D.; Partecke, L.-I.; Käding, A.
Title Risk Assessment of kINPen Plasma Treatment of Four Human Pancreatic Cancer Cell Lines with Respect to Metastasis Type A1 Journal article
Year 2019 Publication Cancers Abbreviated Journal Cancers
Volume 11 Issue 9 Pages 1237
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Cold physical plasma has limited tumor growth in many preclinical models and is, therefore, suggested as a putative therapeutic option against cancer. Yet, studies investigating the cells’ metastatic behavior following plasma treatment are scarce, although being of prime importance to evaluate the safety of this technology. Therefore, we investigated four human pancreatic cancer cell lines for their metastatic behavior in vitro and in chicken embryos (in ovo). Pancreatic cancer was chosen as it is particularly metastatic to the peritoneum and systemically, which is most predictive for outcome. In vitro, treatment with the kINPen plasma jet reduced pancreatic cancer cell activity and viability, along with unchanged or decreased motility. Additionally, the expression of adhesion markers relevant for metastasis was down-regulated, except for increased CD49d. Analysis of 3D tumor spheroid outgrowth showed a lack of plasma-spurred metastatic behavior. Finally, analysis of tumor tissue grown on chicken embryos validated the absence of an increase of metabolically active cells physically or chemically detached with plasma treatment. We conclude that plasma treatment is a safe and promising therapeutic option and that it does not promote metastatic behavior in pancreatic cancer cells in vitro and in ovo.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000489719000022 Publication Date 2019-08-23
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2072-6694 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor Times cited 4 Open Access
Notes The authors acknowledge that this work was supported by grants funded by the German Federal Ministry of Education and Research (BMBF), grant number 03Z22DN11. We want to thank the Research Foundation – Flanders (FWO) for providing funding to APM under the “long stay abroad” scheme (grant code V415618N). APM and AB acknowledge financial support from the Methusalem project. Technical support by Felix Niessner and Antje Janetzko is gratefully acknowledged. Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @c:irua:162106 Serial 5357
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Author Bogaerts, A.; Gijbels, R.
Title Role of sputtered Cu atoms and ions in a direct current glow discharge: combined fluid and Monte Carlo model Type A1 Journal article
Year 1996 Publication Journal of applied physics Abbreviated Journal J Appl Phys
Volume 79 Issue 3 Pages 1279-1286
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract
Address
Corporate Author Thesis
Publisher American Institute of Physics Place of Publication New York, N.Y. Editor
Language Wos A1996TT92200011 Publication Date 2002-07-26
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0021-8979; ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 2.183 Times cited 81 Open Access
Notes Approved MATERIALS SCIENCE, MULTIDISCIPLINARY 96/271 Q2 #
Call Number UA @ lucian @ c:irua:16239 Serial 2920
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Author Bogaerts, A.; Gijbels, R.; Goedheer, W.J.
Title Two-dimensional model of a direct current glow discharge: description of the electrons, argon ions and fast argon atoms Type A1 Journal article
Year 1996 Publication Analytical chemistry Abbreviated Journal Anal Chem
Volume 68 Issue 14 Pages 2296-2303
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 A1996UY08700002 Publication Date 2002-07-26
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-2700;1520-6882; ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 5.636 Times cited 70 Open Access
Notes Approved no
Call Number UA @ lucian @ c:irua:16241 Serial 3776
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Author Bogaerts, A.; Gijbels, R.
Title Two-dimensional model of a direct current glow discharge : description of the argon metastable atoms, sputtered atoms and ions Type A1 Journal article
Year 1996 Publication Analytical chemistry Abbreviated Journal Anal Chem
Volume 68 Issue 15 Pages 2676-2685
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract A two-dimensional model is presented that describes the behavior of argon metastable atoms, copper atoms, and copper ions in an argon direct. current glow discharge, in the standard cell of the VG9000 glow discharge mass spectrometer for analyzing flat samples. The model is combined with a previously developed model for the electrons, argon ions, and atoms in the same cell to obtain an overall picture of the glow discharge, The results of the present model comprise the number densities of the described plasma species, the relative contributions of different production and loss processes for the argon metastable atoms, the thermalization profile of the sputtered copper atoms, the relative importance of the different ionization mechanisms for the copper atoms, the ionization degree of copper, the copper ion-to-argon ion density ratio, and the relative roles of copper ions, argon ions, and atoms in the sputtering process. All these quantities are calculated for a range of voltages and pressures, Moreover, since the sticking coefficient of copper atoms on solid surfaces is not well-known in the literature, the influence of this parameter on the results is briefly discussed.
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos A1996VA00300042 Publication Date 2002-07-26
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-2700;1520-6882; ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 5.636 Times cited 57 Open Access
Notes Approved no
Call Number UA @ lucian @ c:irua:16242 Serial 3775
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Author Bogaerts, A.; Gijbels, R.
Title Relative sensitivity factors in glow discharge mass spectrometry: the role of charge transfer ionization Type A1 Journal article
Year 1996 Publication Journal of analytical atomic spectrometry Abbreviated Journal J Anal Atom Spectrom
Volume 11 Issue Pages 841-847
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract
Address
Corporate Author Thesis
Publisher Place of Publication London Editor
Language Wos A1996VG92800032 Publication Date 2004-04-20
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0267-9477;1364-5544; ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.466 Times cited 38 Open Access
Notes Approved
Call Number UA @ lucian @ c:irua:16243 Serial 2860
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Author Van der Paal, J.; Hong, S.-H.; Yusupov, M.; Gaur, N.; Oh, J.-S.; Short, R.D.; Szili, E.J.; Bogaerts, A.
Title How membrane lipids influence plasma delivery of reactive oxygen species into cells and subsequent DNA damage : an experimental and computational study Type A1 Journal article
Year 2019 Publication Physical chemistry, chemical physics Abbreviated Journal Phys Chem Chem Phys
Volume 21 Issue 35 Pages 19327-19341
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000486175400045 Publication Date 2019-08-21
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1463-9076; 1463-9084 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 4.123 Times cited 1 Open Access
Notes Approved Most recent IF: 4.123
Call Number UA @ admin @ c:irua:162782 Serial 6303
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Author Van Loenhout, J.; Flieswasser, T.; Freire Boullosa, L.; De Waele, J.; Van Audenaerde, J.; Marcq, E.; Jacobs, J.; Lin, A.; Lion, E.; Dewitte, H.; Peeters, M.; Dewilde, S.; Lardon, F.; Bogaerts, A.; Deben, C.; Smits, E.
Title Cold Atmospheric Plasma-Treated PBS Eliminates Immunosuppressive Pancreatic Stellate Cells and Induces Immunogenic Cell Death of Pancreatic Cancer Cells Type A1 Journal article
Year 2019 Publication Cancers Abbreviated Journal Cancers
Volume 11 Issue 10 Pages 1597
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE)
Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers with a low response to treatment and a five-year survival rate below 5%. The ineffectiveness of treatment is partly because of an immunosuppressive tumor microenvironment, which comprises tumor-supportive pancreatic stellate cells (PSCs). Therefore, new therapeutic strategies are needed to tackle both the immunosuppressive PSC and pancreatic cancer cells (PCCs). Recently, physical cold atmospheric plasma consisting of reactive oxygen and nitrogen species has emerged as a novel treatment option for cancer. In this study, we investigated the cytotoxicity of plasma-treated phosphate-buffered saline (pPBS) using three PSC lines and four PCC lines and examined the immunogenicity of the induced cell death. We observed a decrease in the viability of PSC and PCC after pPBS treatment, with a higher efficacy in the latter. Two PCC lines expressed and released damage-associated molecular patterns characteristic of the induction of immunogenic cell death (ICD). In addition, pPBS-treated PCC were highly phagocytosed by dendritic cells (DCs), resulting in the maturation of DC. This indicates the high potential of pPBS to trigger ICD. In contrast, pPBS induced no ICD in PSC. In general, pPBS treatment of PCCs and PSCs created a more immunostimulatory secretion profile (higher TNF-α and IFN-γ, lower TGF-β) in coculture with DC. Altogether, these data show that plasma treatment via pPBS has the potential to induce ICD in PCCs and to reduce the immunosuppressive tumor microenvironment created by PSCs. Therefore, these data provide a strong experimental basis for further in vivo validation, which might potentially open the way for more successful combination strategies with immunotherapy for PDAC.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000498826000194 Publication Date 2019-10-19
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2072-6694 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor Times cited 6 Open Access
Notes Universiteit Antwerpen, NA ; Fonds Wetenschappelijk Onderzoek, 11E7719N 1121016N 1S32316N 12S9218N 12E3916N ; Agentschap Innoveren en Ondernemen, 141433 ; Kom op tegen Kanker, NA ; Stichting Tegen Kanker, STK2014-155 ; The authors express their gratitude to Christophe Hermans, Céline Merlin, Hilde Lambrechts, and Hans de Reu for technical assistance; and to VITO for the use of the MSD reader (Mol, Belgium). Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @c:irua:163328 Serial 5436
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Author Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A.
Title Effect of oxidative stress on cystine transportation by xC‾ antiporter Type A1 Journal article
Year 2019 Publication Archives of biochemistry and biophysics Abbreviated Journal Arch Biochem Biophys
Volume 674 Issue Pages 108114
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract We performed computer simulations to investigate the effect of oxidation on the extracellular cystine (CYC) uptake by the xC− antiporter. The latter is important for killing of cancer cells. Specifically, applying molecular dynamics (MD) simulations we studied the transport of CYC across xCT, i.e., the light subunit of the xC− antiporter, in charge of bidirectional transport of CYC and glutamate. We considered the outward facing (OF) configuration of xCT, and to study the effect of oxidation, we modified the Cys327 residue, located in the vicinity of the extracellular milieu, to cysteic acid (CYO327). Our computational results showed that oxidation of Cys327 results in a free energy barrier for CYC translocation, thereby blocking the access of CYC to the substrate binding site of the OF system. The formation of the energy barrier was found to be due to the conformational changes in the channel. Analysis of the MD trajectories revealed that the reorganization of the side chains of the Tyr244 and CYO327 residues play a critical role in the OF channel blocking. Indeed, the calculated distance between Tyr244 and either Cys327 or CYO327 showed a narrowing of the channel after oxidation. The obtained free energy barrier for CYC translocation was found to be 33.9kJmol−1, indicating that oxidation of Cys327, by e.g., cold atmospheric plasma, is more effective in inhibiting the xC− antiporter than in the mutation of this amino acid to Ala (yielding a barrier of 32.4kJmol−1). The inhibition of the xC− antiporter may lead to Cys starvation in some cancer cells, eventually resulting in cancer cell death.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000525439700011 Publication Date 2019-09-23
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-9861 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.165 Times cited Open Access
Notes Ministry of Science, Research and Technology of Iran; University of Antwerp; Research Foundation − Flanders, 1200219N ; Universiteit Antwerpen; Hercules Foundation; Flemish Government; UA; M. G. acknowledges funding from the Ministry of Science, Research and Technology of Iran and from the University of Antwerp in Belgium. M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant number 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript. Approved Most recent IF: 3.165
Call Number PLASMANT @ plasmant @c:irua:163474 Serial 5372
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Author Privat-Maldonado, A.; Schmidt, A.; Lin, A.; Weltmann, K.-D.; Wende, K.; Bogaerts, A.; Bekeschus, S.
Title ROS from Physical Plasmas: Redox Chemistry for Biomedical Therapy Type A1 Journal article
Year 2019 Publication Oxidative medicine and cellular longevity Abbreviated Journal Oxid Med Cell Longev
Volume 2019 Issue Pages 1-29
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Physical plasmas generate unique mixes of reactive oxygen and nitrogen species (RONS or ROS). Only a bit more than a decade ago, these plasmas, operating at body temperature, started to be considered for medical therapy with considerably little mechanistic redox chemistry or biomedical research existing on that topic at that time. Today, a vast body of evidence is available on physical plasma-derived ROS, from their spatiotemporal resolution in the plasma gas phase to sophisticated chemical and biochemical analysis of these species once dissolved in liquids. Data from<italic>in silico</italic>analysis dissected potential reaction pathways of plasma-derived reactive species with biological membranes, and<italic>in vitro</italic>and<italic>in vivo</italic>experiments in cell and animal disease models identified molecular mechanisms and potential therapeutic benefits of physical plasmas. In 2013, the first medical plasma systems entered the European market as class IIa devices and have proven to be a valuable resource in dermatology, especially for supporting the healing of chronic wounds. The first results in cancer patients treated with plasma are promising, too. Due to the many potentials of this blooming new field ahead, there is a need to highlight the main concepts distilled from plasma research in chemistry and biology that serve as a mechanistic link between plasma physics (how and which plasma-derived ROS are produced) and therapy (what is the medical benefit). This inevitably puts cellular membranes in focus, as these are the natural interphase between ROS produced by plasmas and translation of their chemical reactivity into distinct biological responses.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000493001000003 Publication Date 2019-10-08
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1942-0900 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 4.593 Times cited Open Access
Notes KW and SB acknowledge funding by the German Federal Ministry of Education and Research (grant numbers 03Z22DN11 and 03Z22DN12). The work of SB is further supported by the European Social Fund (grant number ESF/14-BM-A55-0006). APM and AB acknowledge funding by the Methusalem Project. AL acknowledges funding from the Research Foundation Flanders (grant number 12S9218N). APM thanks Yury Gorbanev for his assistance with the preparation of this review. Approved Most recent IF: 4.593
Call Number PLASMANT @ plasmant @c:irua:163476 Serial 5373
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Author Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M.
Title Molecular dynamics simulations of mechanical stress on oxidized membranes Type A1 Journal article
Year 2019 Publication Biophysical chemistry Abbreviated Journal Biophys Chem
Volume 254 Issue Pages 106266
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Biomembranes are under constant attack of free radicals that may lead to lipid oxidation in conditions of oxidative stress. The products generated during lipid oxidation are responsible for structural and dynamical changes which may jeopardize the membrane function. For instance, the local rearrangements of oxidized lipid molecules may induce membrane rupture. In this study, we investigated the effects of mechanical stress on oxidized phospholipid bilayers (PLBs). Model bilayers were stretched until pore formation (or poration) using nonequilibrium molecular dynamics simulations. We studied single-component homogeneous membranes composed of lipid oxidation products, as well as two-component heterogeneous membranes with coexisting native and oxidized domains. In homogeneous membranes, the oxidation products with —OH and —OOH groups reduced the areal strain required for pore formation, whereas the oxidation product with ]O group behaved similarly to the native membrane. In heterogeneous membranes composed of oxidized and non-oxidized domains, we tested the hypothesis according to which poration may be facilitated at the domain interface region. However, results were inconclusive due to their large statistical variance and sensitivity to simulation setup parameters. We pointed out important technical issues that need to be considered in future simulations of mechanically-induced poration of heterogeneous membranes. This research is of interest for photodynamic therapy and plasma medicine, because ruptured and intact plasma membranes are experimentally considered hallmarks of necrotic and apoptotic cell death.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000502890900015 Publication Date 2019-09-13
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0301-4622 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 2.402 Times cited Open Access
Notes São Paulo Research Foundation, 2012/50680-5 ; National Counsel of Technological and Scientific Development, 459270/2014-1 ; We are thankful for the financial support received from the São Paulo Research Foundation (FAPESP) (grant no. 2012/50680-5) and from the National Counsel of Technological and Scientific Development (CNPq) (grant no. 459270/2014-1). MCO acknowledges UFABC for the Master's scholarship granted. Approved Most recent IF: 2.402
Call Number PLASMANT @ plasmant @c:irua:163477 Serial 5374
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Author Privat-Maldonado, A.; Bengtson, C.; Razzokov, J.; Smits, E.; Bogaerts, A.
Title Modifying the Tumour Microenvironment: Challenges and Future Perspectives for Anticancer Plasma Treatments Type A1 Journal article
Year 2019 Publication Cancers Abbreviated Journal Cancers
Volume 11 Issue 12 Pages 1920
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Abstract Tumours are complex systems formed by cellular (malignant, immune, and endothelial cells, fibroblasts) and acellular components (extracellular matrix (ECM) constituents and secreted factors). A close interplay between these factors, collectively called the tumour microenvironment, is required to respond appropriately to external cues and to determine the treatment outcome. Cold plasma (here referred as ‘plasma’) is an emerging anticancer technology that generates a unique cocktail of reactive oxygen and nitrogen species to eliminate cancerous cells via multiple mechanisms of action. While plasma is currently regarded as a local therapy, it can also modulate the mechanisms of cell-to-cell and cell-to-ECM communication, which could facilitate the propagation of its effect in tissue and distant sites. However, it is still largely unknown how the physical interactions occurring between cells and/or the ECM in the tumour microenvironment affect the plasma therapy outcome. In this review, we discuss the effect of plasma on cell-to-cell and cell-to-ECM communication in the context of the tumour microenvironment and suggest new avenues of research to advance our knowledge in the field. Furthermore, we revise the relevant state-of-the-art in three-dimensional in vitro models that could be used to analyse cell-to-cell and cell-to-ECM communication and further strengthen our understanding of the effect of plasma in solid tumours.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000507382100097 Publication Date 2019-12-02
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2072-6694 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor Times cited Open Access
Notes Figure 4 was created using resources from the ‘Mind the Graph’ platform, free trial version. Spheroid image obtained in collaboration with Sander Bekeschus (INP Greifswald, Germany); organoid image kindly provided by Christophe Deben (Center for Oncological Research, University of Antwerp, Belgium). Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @c:irua:164892 Serial 5437
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Author Attri, P.; Razzokov, J.; Yusupov, M.; Koga, K.; Shiratani, M.; Bogaerts, A.
Title Influence of osmolytes and ionic liquids on the Bacteriorhodopsin structure in the absence and presence of oxidative stress: A combined experimental and computational study Type A1 Journal article
Year 2020 Publication International Journal Of Biological Macromolecules Abbreviated Journal Int J Biol Macromol
Volume 148 Issue Pages 657-665
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Understanding the folding and stability of membrane proteins is of great importance in protein science. Recently, osmolytes and ionic liquids (ILs) are increasingly being used as drug delivery systems in the biopharmaceutical industry. However, the stability of membrane proteins in the presence of osmolytes and ILs is not yet fully understood. Besides, the effect of oxidative stress on membrane proteins with osmolytes or ILs has not been investigated. Therefore, we studied the influence of osmolytes and ILs as co-solvents on the stability of a model membrane protein (i.e., Bacteriorhodopsin in purple membrane of Halobacterium salinarum), using UV–Vis spectroscopy and molecular dynamics (MD) simulations. The MD simulations allowed us to determine the flexibility and solvent accessible surface area (SASA) of Bacteriorhodopsin protein in the presence and/or absence of cosolvents, as well as to carry out principal component analysis (PCA) to identify the most important movements in this protein. In addition, by means of UV–Vis spectroscopy we studied the effect of oxidative stress generated by cold atmospheric plasma on the stability of Bacteriorhodopsin in the presence and/or absence of co-solvents. This study is important for a better understanding of the stability of proteins in the presence of oxidative stress.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000522094600066 Publication Date 2020-01-20
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0141-8130 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 8.2 Times cited Open Access
Notes Horizon2020, 743546 ; JSPS, 19H05462 16H03895 ; Nagoya University; We gratefully acknowledge the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI 19H05462 and 16H03895, the joint usage/research program of Center for Low-temperature Plasma Science, Nagoya University and also supported by JSPS and RCL under the Japan-Lithuania Research Cooperative Program. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Approved Most recent IF: 8.2; 2020 IF: 3.671
Call Number PLASMANT @ plasmant @c:irua:165585 Serial 5444
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Author Van Alphen, S.; Vermeiren, V.; Butterworth, T.; van den Bekerom, D.C.M.; van Rooij, G.J.; Bogaerts, A.
Title Power Pulsing To Maximize Vibrational Excitation Efficiency in N2Microwave Plasma: A Combined Experimental and Computational Study Type A1 Journal article
Year 2020 Publication Journal Of Physical Chemistry C Abbreviated Journal J Phys Chem C
Volume 124 Issue 3 Pages 1765-1779
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Plasma is gaining increasing interest for N2 fixation, being a flexible, electricity-driven alternative for the current conventional fossil fuel-based N2 fixation processes. As the vibrational-induced dissociation of N2 is found to be an energy-efficient pathway to acquire atomic N for the fixation processes, plasmas that are in vibrational nonequilibrium seem promising for this application. However, an important challenge in using nonequilibrium plasmas lies in preventing vibrational−translational (VT) relaxation processes, in which vibrational energy crucial for N2 dissociation is lost to gas heating. We present here both experimental and modeling results for the vibrational and gas temperature in a microsecond-pulsed microwave (MW) N2 plasma, showing how power pulsing can suppress this unfavorable VT relaxation and achieve a maximal vibrational nonequilibrium. By means of our kinetic model, we demonstrate that pulsed plasmas take advantage of the long time scale on which VT processes occur, yielding a very pronounced nonequilibrium over the whole N2 vibrational ladder. Additionally, the effect of pulse parameters like the pulse frequency and pulse width are investigated, demonstrating that the advantage of pulsing to inhibit VT relaxation diminishes for high pulse frequencies (around 7000 kHz) and long power pulses (above 400 μs). Nevertheless, all regimes studied here demonstrate a clear vibrational nonequilibrium while only requiring a limited power-on time, and thus, we may conclude that a pulsed plasma seems very interesting for energyefficient vibrational excitation.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000509438600001 Publication Date 2020-01-23
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1932-7447 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.7 Times cited Open Access
Notes Fonds Wetenschappelijk Onderzoek, 30505023 GoF9618n ; This research was supported by the Excellence of Science FWO-FNRS project (FWO Grant ID GoF9618n, EOS ID 30505023). The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerpen. Approved Most recent IF: 3.7; 2020 IF: 4.536
Call Number PLASMANT @ plasmant @c:irua:165586 Serial 5443
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Author Bal, K.M.; Bogaerts, A.; Neyts, E.C.
Title Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium Type A1 Journal article
Year 2020 Publication Journal Of Physical Chemistry Letters Abbreviated Journal J Phys Chem Lett
Volume 11 Issue 2 Pages 401-406
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract We present an approach to incorporate the effect of vibrational nonequilibrium in molecular dynamics (MD) simulations. A perturbed canonical ensemble, in which selected modes are excited to higher temperature while all others remain equilibrated at low temperature, is simulated by applying a specifically tailored bias potential. Our method can be readily applied to any (classical or quantum mechanical) MD setup at virtually no additional computational cost and allows the study of reactions of vibrationally excited molecules in nonequilibrium environments such as plasmas. In combination with enhanced sampling methods, the vibrational efficacy and mode selectivity of vibrationally stimulated reactions can then be quantified in terms of chemically relevant observables, such as reaction rates and apparent free energy barriers. We first validate our method for the prototypical hydrogen exchange reaction and then show how it can capture the effect of vibrational excitation on a symmetric SN2 reaction and radical addition on CO2.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000508473400008 Publication Date 2020-01-16
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1948-7185 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 5.7 Times cited Open Access
Notes Universiteit Antwerpen; Fonds Wetenschappelijk Onderzoek, 12ZI420N ; Departement Economie, Wetenschap en Innovatie van de Vlaamse Overheid; K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation − Flanders), Grant 12ZI420N, and through a TOP-BOF research project of the University of Antwerp. 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− department EWI. Approved Most recent IF: 5.7; 2020 IF: 9.353
Call Number PLASMANT @ plasmant @c:irua:165587 Serial 5442
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Author Zhou, R.; Zhou, R.; Xian, Y.; Fang, Z.; Lu, X.; Bazaka, K.; Bogaerts, A.; Ostrikov, K.(K.)
Title Plasma-enabled catalyst-free conversion of ethanol to hydrogen gas and carbon dots near room temperature Type A1 Journal article
Year 2020 Publication Chemical Engineering Journal Abbreviated Journal Chem Eng J
Volume 382 Issue 382 Pages 122745
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Selective conversion of bio-renewable ethanol under mild conditions especially at room temperature remains a major challenge for sustainable production of hydrogen and valuable carbon-based materials. In this study, adaptive non-thermal plasma is applied to deliver pulsed energy to rapidly and selectively reform ethanol in the absence of a catalyst. Importantly, the carbon atoms in ethanol that would otherwise be released into the environment in the form of CO or CO2 are effectively captured in the form of carbon dots (CDs). Three modes of non-thermal spark plasma discharges, i.e. single spark mode (SSM), multiple spark mode (MSM) and gliding spark mode (GSM), provide additional flexibility in ethanol reforming by controlling the processes of energy transfer and distribution, thereby affecting the flow rate, gas content, and energy consumption in H-2 production. A favourable combination of low temperature (< 40 degrees C), attractive conversion rate (gas flow rate of similar to 120 mL/min), high hydrogen yield (H-2 content > 90%), low energy consumption (similar to 0.96 kWh/m(3) H-2) and the effective generation of photoluminescent CDs (which are applicable for bioimaging or biolabelling) in the MSM indicate that the proposed strategy may offer a new carbon-negative avenue for comprehensive utilization of alcohols and mitigating the increasingly severe energy and environmental issues.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000503381200200 Publication Date 2019-09-07
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1385-8947; 1873-3212 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 15.1 Times cited 20 Open Access
Notes ; ; Approved Most recent IF: 15.1; 2020 IF: 6.216
Call Number UA @ admin @ c:irua:165648 Serial 6318
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Author Cordeiro, R.M.; Yusupov, M.; Razzokov, J.; Bogaerts, A.
Title Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences Type A1 Journal article
Year 2020 Publication Journal Of Physical Chemistry B Abbreviated Journal J Phys Chem B
Volume 124 Issue 6 Pages 1082-1089
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Nitrogen oxyanions and oxyacids are important agents in atmospheric chemistry and medical biology. Although their chemical behavior in solution is relatively well understood, they may behave very differently at the water/air interface of atmospheric aerosols or at the membrane/water interface of cells. Here, we developed a fully classical model for molecular dynamics simulations of NO3−, NO2−, HNO3, and HNO2 in the framework of the GROMOS 53A6 and 54A7 force field versions. The model successfully accounted for the poorly structured solvation shell and ion pairing tendency of NO3−. Accurate pure-liquid properties and hydration free energies were obtained for the oxyacids. Simulations at the water/air interface showed a local enrichment of HNO3 and depletion of NO3−. The effect was discussed in light of earlier spectroscopic data and ab initio calculations, suggesting that HNO3 behaves as a weaker acid at the surface of water. Our model will hopefully allow for efficient and accurate simulations of nitrogen oxyanions and oxyacids in solution and at microheterogeneous interface environments.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000512222500015 Publication Date 2020-02-13
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1520-6106 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.3 Times cited Open Access
Notes We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work. This study was financed in part by the Coordenaçaõ de Aperfeiçoamento de Pessoal de Nı ́vel Superior – Brasil (CAPES) – Finance Code 001. Approved Most recent IF: 3.3; 2020 IF: 3.177
Call Number PLASMANT @ plasmant @c:irua:166488 Serial 6340
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Author Gorbanev, Y.; Vervloessem, E.; Nikiforov, A.; Bogaerts, A.
Title Nitrogen fixation with water vapor by nonequilibrium plasma : toward sustainable ammonia production Type A1 Journal article
Year 2020 Publication Acs Sustainable Chemistry & Engineering Abbreviated Journal Acs Sustain Chem Eng
Volume 8 Issue 7 Pages 2996-3004
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Ammonia is a crucial nutrient used for plant growth and as a building block in the pharmaceutical and chemical industry, produced via nitrogen fixation of the ubiquitous atmospheric N2. Current industrial ammonia production relies heavily on fossil resources, but a lot of work is put into developing nonfossil-based pathways. Among these is the use of nonequilibrium plasma. In this work, we investigated water vapor as a H source for nitrogen fixation into NH3 by nonequilibrium plasma. The highest selectivity toward NH3 was observed with low amounts of added H2O vapor, but the highest production rate was reached at high H2O vapor contents. We also studied the role of H2O vapor and of the plasma-exposed liquid H2O in nitrogen fixation by using isotopically labeled water to distinguish between these two sources of H2O. We show that added H2O vapor, and not liquid H2O, is the main source of H for NH3 generation. The studied catalyst- and H2-free method offers excellent selectivity toward NH3 (up to 96%), with energy consumption (ca. 95–118 MJ/mol) in the range of many plasma-catalytic H2-utilizing processes.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000516665500045 Publication Date 2020-02-03
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2168-0485 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 8.4 Times cited 14 Open Access
Notes ; This research was supported by the Excellence of Science FWO-FNRS project (FWO grant ID GoF9618n, EOS ID 30505023), the Catalisti Moonshot project P2C, and the Methusalem project of the University of Antwerp. ; Approved Most recent IF: 8.4; 2020 IF: 5.951
Call Number UA @ admin @ c:irua:167134 Serial 6568
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Author Sun, S.R.; Wang, H.X.; Bogaerts, A.
Title Chemistry reduction of complex CO2chemical kinetics: application to a gliding arc plasma Type A1 Journal article
Year 2020 Publication Plasma Sources Science & Technology Abbreviated Journal Plasma Sources Sci T
Volume 29 Issue 2 Pages 025012
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract A gliding arc (GA) plasma has great potential for CO2 conversion into value-added chemicals, because of its high energy efficiency. To improve the application, a 2D/3D fluid model is needed to investigate the CO2 conversion mechanisms in the actual discharge geometry. Therefore, the complex CO2 chemical kinetics description must be reduced due to the huge computational cost associated with 2D/3D models. This paper presents a chemistry reduction method for CO2 plasmas, based on the so-called directed relation graph method. Depending on the defined threshold values, some marginal species are identified. By means of a sensitivity analysis, we can further reduce the chemistry set by removing one by one the marginal species. Based on the socalled flux-sensitivity coupling, we obtain a reduced CO2 kinetics model, consisting of 36 or 15 species (depending on whether the 21 asymmetric mode vibrational states of CO2 are explicitly included or lumped into one group), which is applied to a GA discharge. The results are compared with those predicted with the full chemistry set, and very good agreement is reached. Moreover, the range of validity of the reduced CO2 chemistry set is checked, telling us that this reduced set is suitable for low power GA discharges. Finally, the time and spatial evolution of the CO2 plasma characteristics are presented, based on a 2D model with the reduced kinetics.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000525600600001 Publication Date 2020-02-11
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1361-6595 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.8 Times cited Open Access
Notes We acknowledge financial support from the Fund for Scientific Research Flanders (FWO; Grant No. G.0383.16 N). The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerpen. This work was also supported by the National Natural Science Foundation of China. (Grant Nos. 11735004, 11575019). SR Sun thanks the financial support from the National Postdoctoral Program for Innovative Talents (BX20180029). Approved Most recent IF: 3.8; 2020 IF: 3.302
Call Number PLASMANT @ plasmant @c:irua:167135 Serial 6338
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Author Slaets, J.; Aghaei, M.; Ceulemans, S.; Van Alphen, S.; Bogaerts, A.
Title CO2and CH4conversion in “real” gas mixtures in a gliding arc plasmatron: how do N2and O2affect the performance? Type A1 Journal article
Year 2020 Publication Green Chemistry Abbreviated Journal Green Chem
Volume 22 Issue 4 Pages 1366-1377
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract In this paper we study dry reforming of methane (DRM) in a gliding arc plasmatron (GAP) in the presence of N<sub>2</sub>and O<sub>2</sub>. N<sub>2</sub>is added to create a stable plasma at equal fractions of CO<sub>2</sub>and CH<sub>4</sub>, and because emissions from industrial plants typically contain N<sub>2</sub>, while O<sub>2</sub>is added to enhance the process. We test different gas mixing ratios to evaluate the conversion and energy cost. We obtain conversions between 31 and 52% for CO<sub>2</sub>and between 55 and 99% for CH<sub>4</sub>, with total energy costs between 3.4 and 5.0 eV per molecule, depending on the gas mixture. This is very competitive when benchmarked with the literature. In addition, we present a chemical kinetics model to obtain deeper insight in the underlying plasma chemistry. This allows determination of the major reaction pathways to convert CO<sub>2</sub>and CH<sub>4</sub>, in the presence of O<sub>2</sub>and N<sub>2</sub>, into CO and H<sub>2</sub>. We show that N<sub>2</sub>assists in the CO<sub>2</sub>conversion, but part of the applied energy is also wasted in N<sub>2</sub>excitation. Adding O<sub>2</sub>enhances the CH<sub>4</sub>conversion, and lowers the energy cost, while the CO<sub>2</sub>conversion remains constant, and only slightly drops at the highest O<sub>2</sub>fractions studied, when CH<sub>4</sub>is fully oxidized into CO<sub>2</sub>.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000518034000032 Publication Date 2020-01-30
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1463-9262 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 9.8 Times cited Open Access OpenAccess
Notes H2020 European Research Council, 810182 ; Fonds Wetenschappelijk Onderzoek, GoF9618n 12M7118N ; We acknowledge financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 810182 – SCOPE ERC Synergy project), the Excellence of Science FWO-FNRS project (FWO grant ID GoF9618n, EOS ID 30505023), and the FWO postdoctoral fellowship of M. A. (Grant number 12M7118N). This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the University of Antwerp. Approved Most recent IF: 9.8; 2020 IF: 9.125
Call Number PLASMANT @ plasmant @c:irua:167136 Serial 6339
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Author Trenchev, G.; Bogaerts, A.
Title Dual-vortex plasmatron: A novel plasma source for CO2 conversion Type A1 Journal article
Year 2020 Publication Journal Of Co2 Utilization Abbreviated Journal J Co2 Util
Volume 39 Issue Pages 101152
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Atmospheric pressure gliding arc (GA) discharges are gaining increasing interest for CO2 conversion and other gas conversion applications, due to their simplicity and high energy efficiency. However, they are characterized by some drawbacks, such as non-uniform gas treatment, limiting the conversion, as well as the development of a hot cathode spot, resulting in severe electrode degradation. In this work, we built a dual-vortex plasmatron, which is a GA plasma reactor with innovative electrode configuration, to solve the above problems. The design aims to improve the CO2 conversion capability of the GA reactor by elongating the arc in two directions, to increase the residence time of the gas inside the arc, and to actively cool the cathode spot by rotation of the arc and gas convection. The measured CO2 conversion and corresponding energy efficiency indeed look very promising. In addition, we developed a fluid dynamics non-thermal plasma model with argon chemistry, to study the arc behavior in the reactor and to explain the experimental results.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000546648400008 Publication Date 2020-03-20
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2212-9820 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 7.7 Times cited Open Access
Notes Fund for Scientific Research – Flanders, G.0383.16N 11U53.16N ; Hercules Foundation, the Flemish Government; UAntwerpen; We acknowledge financial support from the Fund for Scientific Research – Flanders (FWO); grant numbers G.0383.16N and 11U53.16N. The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UAntwerpen. We would also like to thank G. Van Loon from the University of Antwerp for building the DVP reactor. Approved Most recent IF: 7.7; 2020 IF: 4.292
Call Number PLASMANT @ plasmant @c:irua:167593 Serial 6356
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Author Heijkers, S.; Aghaei, M.; Bogaerts, A.
Title Plasma-Based CH4Conversion into Higher Hydrocarbons and H2: Modeling to Reveal the Reaction Mechanisms of Different Plasma Sources Type A1 Journal article
Year 2020 Publication Journal Of Physical Chemistry C Abbreviated Journal J Phys Chem C
Volume 124 Issue 13 Pages 7016-7030
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Plasma is gaining interest for CH4 conversion into higher hydrocarbons and H2. However, the performance in terms of conversion and selectivity toward different hydrocarbons is different for different plasma types, and the underlying mechanisms are not yet fully understood. Therefore, we study here these mechanisms in different plasma sources, by means of a chemical kinetics model. The model is first validated by comparing the calculated conversions and hydrocarbon/H2 selectivities with experimental results in these different plasma types and over a wide range of specific energy input (SEI) values. Our model predicts that vibrational−translational nonequilibrium is negligible in all CH4 plasmas investigated, and instead, thermal conversion is important. Higher gas temperatures also lead to a more selective production of unsaturated hydrocarbons (mainly C2H2) due to neutral dissociation of CH4 and subsequent dehydrogenation processes, while three-body recombination reactions into saturated hydrocarbons (mainly C2H6, but also higher hydrocarbons) are dominant in low temperature plasmas.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000526328500007 Publication Date 2020-04-02
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1932-7447 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.7 Times cited Open Access OpenAccess
Notes Universiteit Antwerpen; Vlaamse regering; Fonds Wetenschappelijk Onderzoek, G.0383.16N ; H2020 European Research Council, 810182 ; We acknowledge financial support from the Fund for Scientific Research, Flanders (FWO; Grant No. G.0383.16N), the Methusalem Grant, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 810182 − SCOPE ERC Synergy project). This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the University of Antwerp. Approved Most recent IF: 3.7; 2020 IF: 4.536
Call Number PLASMANT @ plasmant @c:irua:168096 Serial 6358
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Author van ‘t Veer, K.; Reniers, F.; Bogaerts, A.
Title Zero-dimensional modeling of unpacked and packed bed dielectric barrier discharges: the role of vibrational kinetics in ammonia synthesis Type A1 Journal article
Year 2020 Publication Plasma Sources Science & Technology Abbreviated Journal Plasma Sources Sci T
Volume 29 Issue 4 Pages 045020
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract We present a zero-dimensional plasma kinetics model, including both surface and gas phase kinetics, to determine the role of vibrationally excited states in plasma-catalytic ammonia synthesis. We defined a new method to systematically capture the conditions of dielectric barrier discharges (DBDs), including those found in packed bed DBDs. We included the spatial and temporal nature of such discharges by special consideration of the number of micro-discharges in the model. We introduce a parameter that assigns only a part of the plasma power to the microdischarges, to scale the model conditions from filamentary to uniform plasma. Because of the spatial and temporal behaviour of the micro-discharges, not all micro-discharges occurring in the plasma reactor during a certain gas residence time are affecting the molecules. The fraction of power considered in the model ranges from 0.005 %, for filamentary plasma, to 100 %, for uniform plasma. If vibrational excitation is included in the plasma chemistry, these different conditions, however, yield an ammonia density that is only varying within one order of magnitude. At only 0.05 % of the power put into the uniform plasma component, a model neglecting vibrational excitation clearly does not result in adequate amounts of ammonia. Thus, our new model, which accounts for the concept in which not all the power is deposited by the micro-discharges, but some part may also be distributed in between them, suggests that vibrational kinetic processes are really important in (packed bed) DBDs. Indeed, vibrational excitation takes place in both the uniform plasma between the micro-discharges and in the strong micro-discharges, and is responsible for an increased N2 dissociation rate. This is shown here for plasma-catalytic ammonia synthesis, but might also be valid for other gas conversion applications.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000570241500001 Publication Date 2020-04-09
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1361-6595 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.8 Times cited Open Access
Notes This research was supported by the Excellence of Science FWO-FNRS project (FWO grant ID GoF9618n, EOS ID 30505023). The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerpen. The authors would also like to thank Dr. Fatme Jardali for the discussions on plasma kinetic modelling and Dr. Jungmi Hong and Dr. Anthony B. Murphy for their aid in the calculation of the diffusion coefficients. Approved Most recent IF: 3.8; 2020 IF: 3.302
Call Number PLASMANT @ plasmant @c:irua:168097 Serial 6359
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Author Bogaerts, A.
Title Modeling plasmas in analytical chemistry—an example of cross-fertilization Type A1 Journal article
Year 2020 Publication Analytical And Bioanalytical Chemistry Abbreviated Journal Anal Bioanal Chem
Volume 412 Issue 24 Pages 6059-6083
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract This paper gives an overview of the modeling work developed in our group in the last 25 years for various plasmas used in analytical spectrochemistry, i.e., glow discharges (GDs), inductively coupled plasmas (ICPs), and laser ablation (LA) for sample introduction in the ICP and for laser-induced breakdown spectroscopy (LIBS). The modeling approaches are briefly presented, which are different for each case, and some characteristic results are illustrated. These plasmas are used not only in analytical chemistry but also in other applications, and the insights obtained in these other fields were quite helpful for us to develop models for the analytical plasmas. Likewise, there is now a huge interest in plasma–liquid interaction, atmospheric pressure glow discharges (APGDs), and dielectric barrier discharges (DBDs) for environmental, medical, and materials applications of plasmas. The insights obtained in these fields are also very relevant for ambient desorption/ionization sources and for liquid sampling, which are nowadays very popular in analytical chemistry, and they could be very helpful in developing models for these sources as well.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000522701700005 Publication Date 2020-03-31
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1618-2642 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 4.3 Times cited Open Access
Notes M. Aghaei, Z. Chen, D. Autrique, T. Martens, and P. Heirman are gratefully acknowledged for their valuable efforts in the model developments illustrated in this paper. Approved Most recent IF: 4.3; 2020 IF: 3.431
Call Number PLASMANT @ plasmant @c:irua:168600 Serial 6412
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Author Jafarzadeh, A.; Bal, K.M.; Bogaerts, A.; Neyts, E.C.
Title Activation of CO2on Copper Surfaces: The Synergy between Electric Field, Surface Morphology, and Excess Electrons Type A1 Journal article
Year 2020 Publication Journal Of Physical Chemistry C Abbreviated Journal J Phys Chem C
Volume 124 Issue 12 Pages 6747-6755
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract In this work, we use density functional theory calculations to study the combined effect of external electric fields, surface morphology, and surface charge on CO2 activation over Cu(111), Cu(211), Cu(110), and Cu(001) surfaces. We observe that the binding energy of the CO2 molecule on Cu surfaces increases significantly upon increasing the applied electric field strength. In addition, rougher surfaces respond more effectively to the presence of the external electric field toward facilitating the formation of a carbonate-like CO2 structure and the transformation of the most stable adsorption mode from physisorption to chemisorption. The presence of surface charges further strengthens the electric field effect and consequently causes an improved bending of the CO2 molecule and C−O bond length elongation. On the other hand, a net charge in the absence of an externally applied electric field shows only a marginal effect on CO2 binding. The chemisorbed CO2 is more stable and further activated when the effects of an external electric field, rough surface, and surface charge are combined. These results can help to elucidate the underlying factors that control CO2 activation in heterogeneous and plasma catalysis, as well as in electrochemical processes.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000526396900030 Publication Date 2020-03-26
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1932-7447 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.7 Times cited Open Access
Notes Bijzonder Onderzoeksfonds, 32249 ; The financial support from the TOP research project of the Research Fund of the University of Antwerp (grant ID: 32249) is highly acknowledged by the authors. The computational resources used in this study were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Governmentdepartment EWI. Approved Most recent IF: 3.7; 2020 IF: 4.536
Call Number PLASMANT @ plasmant @c:irua:168606 Serial 6361
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Author Zhang, H.; Zhang, H.; Trenchev, G.; Li, X.; Wu, Y.; Bogaerts, A.
Title Multi-dimensional modelling of a magnetically stabilized gliding arc plasma in argon and CO2 Type A1 Journal article
Year 2020 Publication Plasma Sources Science & Technology Abbreviated Journal Plasma Sources Sci T
Volume 29 Issue 4 Pages 045019
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract This study focuses on a magnetically stabilized gliding arc (MGA) plasma. Two fully coupled flow-plasma models (in 3D and 2D) are presented. The 3D model is applied to compare the arc dynamics of the MGA with a traditional gas-driven gliding arc. The 2D model is used for a detailed parametric study on the effect of the external magnetic field. The results show that the relative velocity between the plasma and feed gas is generated due to the Lorentz force, which can increase the plasma-treated gas fraction. The magnetic field also helps to decrease the gas temperature by enhancing heat transfer and to increase the electron number density. This work shows the potential of an external magnetic field to control the gliding arc behavior, for enhanced gas conversion at low gas flow rates.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000570241800001 Publication Date 2020-04-09
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1361-6595 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.8 Times cited Open Access
Notes Fonds Wetenschappelijk Onderzoek, G.0383.16N ; National Natural Science Foundation of China, 51706204 51707144 ; State Key Laboratory of Electrical Insulation and Power Equipment, EIPE19302 ; The authors acknowledge financial support from the Fund for Scientific Research—Flanders (FWO; Grant G.0383.16 N), National Natural Science Foundation of China under Grant Nos. 51706204, 51707144, and State Key Laboratory of Electrical Insulation and Power Equipment (EIPE19302). The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (Department EWI), and Universiteit Antwerpen. Finally, Hantian Zhang acknowledges financial support from the China Scholarship Council. Approved Most recent IF: 3.8; 2020 IF: 3.302
Call Number PLASMANT @ plasmant @c:irua:169218 Serial 6360
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Author Uytdenhouwen, Y.; Meynen, V.; Cool, P.; Bogaerts, A.
Title The Potential Use of Core-Shell Structured Spheres in a Packed-Bed DBD Plasma Reactor for CO2 Conversion Type A1 Journal article
Year 2020 Publication Catalysts Abbreviated Journal Catalysts
Volume 10 Issue 5 Pages 530
Keywords A1 Journal article; Laboratory of adsorption and catalysis (LADCA); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract This work proposes to use core-shell structured spheres to evaluate whether it allows to individually optimize bulk and surface effects of a packing material, in order to optimize conversion and energy efficiency. Different core-shell materials have been prepared by spray coating, using dense spheres (as core) and powders (as shell) of SiO2, Al2O3, and BaTiO3. The materials are investigated for their performance in CO2 dissociation and compared against a benchmark consisting of a packed-bed reactor with the pure dense spheres, as well as an empty reactor. The results in terms of CO2 conversion and energy efficiency show various interactions between the core and shell material, depending on their combination. Al2O3 was found as the best core material under the applied conditions here, followed by BaTiO3 and SiO2, in agreement with their behaviour for the pure spheres. Applying a thin shell layer on the cores showed equal performance between the different shell materials. Increasing the layer thickness shifts this behaviour, and strong combination effects were observed depending on the specific material. Therefore, this method of core-shell spheres has the potential to allow tuning of the packing properties more closely to the application by designing an optimal combination of core and shell.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000546007000092 Publication Date 2020-05-11
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2073-4344 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.9 Times cited Open Access
Notes Interreg, Project EnOp ; Fonds Wetenschappelijk Onderzoek, G.0254.14N ; Universiteit Antwerpen, Project SynCO2Chem ; We want to thank Jasper Lefevre (VITO) for assistance in the development of the coating suspension for the core-shell spheres. Approved Most recent IF: 3.9; 2020 IF: 3.082
Call Number PLASMANT @ plasmant @c:irua:169222 Serial 6364
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Author Engelmann, Y.; Mehta, P.; Neyts, E.C.; Schneider, W.F.; Bogaerts, A.
Title Predicted Influence of Plasma Activation on Nonoxidative Coupling of Methane on Transition Metal Catalysts Type A1 Journal article
Year 2020 Publication Acs Sustainable Chemistry & Engineering Abbreviated Journal Acs Sustain Chem Eng
Volume 8 Issue 15 Pages 6043-6054
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Movement Antwerp (MOVANT)
Abstract The combination of catalysis and nonthermal plasma holds promise for enabling difficult chemical conversions. The possible synergy between both depends strongly on the nature of the reactive plasma species and the catalyst material. In this paper, we show how vibrationally excited species and plasma-generated radicals interact with transition metal catalysts and how changing the catalyst material can improve the conversion rates and product selectivity. We developed a microkinetic model to investigate the impact of vibrational excitations and plasma-generated radicals on the nonoxidative coupling of methane over transition metal surfaces. We predict a significant increase in ethylene formation for vibrationally excited methane. Plasma-generated radicals have a stronger impact on the turnover frequencies with high selectivity toward ethylene on noble catalysts and mixed selectivity on non-noble catalysts. In general, we show how the optimal catalyst material depends on the desired products as well as the plasma conditions.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000526884000025 Publication Date 2020-04-20
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2168-0485 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 8.4 Times cited Open Access
Notes Herculesstichting; University of Notre Dame; Universiteit Antwerpen; Division of Engineering Education and Centers, EEC-1647722 ; We would like to thank Tom Butterworth for his work on methane vibrational distribution functions (VDF) and for sharing his thoughts and experiences on this matter, specifically regarding the VDF of the degenerate modes of methane. We ACS Sustainable Chemistry & Engineering pubs.acs.org/journal/ascecg Research Article https://dx.doi.org/10.1021/acssuschemeng.0c00906 ACS Sustainable Chem. Eng. 2020, 8, 6043−6054 6052 also acknowledge financial support from the DOC-PRO3 and the TOP-BOF projects of the University of Antwerp. This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (Department EWI), and the University of Antwerp. Support for W.F.S. was provided by the National Science Foundation under cooperative agreement no. EEC-1647722, an Engineering Research Center for the Innovative and Strategic Transformation of Alkane Resources (CISTAR). P.M. acknowledges support through the Eilers Graduate Fellowship of the University of Notre Dame. Approved Most recent IF: 8.4; 2020 IF: 5.951
Call Number PLASMANT @ plasmant @c:irua:169228 Serial 6366
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Author Duan, J.; Ma, M.; Yusupov, M.; Cordeiro, R.M.; Lu, X.; Bogaerts, A.
Title The penetration of reactive oxygen and nitrogen species across the stratum corneum Type A1 Journal article
Year 2020 Publication Plasma Processes And Polymers Abbreviated Journal Plasma Process Polym
Volume Issue Pages
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The penetration of reactive oxygen and nitrogen species (RONS) across the stratum corneum (SC) is a necessary and crucial process in many skin‐related plasma medical applications. To gain more insights into this penetration behavior, we combined experimental measurements of the permeability of dry and moist SC layers with computer simulations of model lipid membranes. We measured the permeation of relatively stable molecules, which are typically generated by plasma, namely H2O2, NO3−, and NO2−. Furthermore, we calculated the permeation free energy profiles of the major plasma‐generated RONS and their derivatives (i.e., H2O2, OH, HO2, O2, O3, NO, NO2, N2O4, HNO2, HNO3, NO2−, and NO3−) across native and oxidized SC lipid bilayers, to understand the mechanisms of RONS permeation across the SC. Our results indicate that hydrophobic RONS (i.e., NO, NO2, O2, O3, and N2O4) can translocate more easily across the SC lipid bilayer than hydrophilic RONS (i.e., H2O2, OH, HO2, HNO2, and HNO3) and ions (i.e., NO2− and NO3−) that experience much higher permeation barriers. The permeability of RONS through the SC skin lipids is enhanced when the skin is moist and the lipids are oxidized. These findings may help to understand the underlying mechanisms of plasma interaction with a biomaterial and to optimize the environmental parameters in practice in plasma medical applications.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000536892900001 Publication Date 2020-06-02
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850 ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.5 Times cited Open Access
Notes National Natural Science Foundation of China, 51625701 51977096 ; Fonds Wetenschappelijk Onderzoek, 1200219N ; China Scholarship Council, 201806160128 ; M. Y. acknowledges the Research Foundation Flanders (FWO) for financial support (Grant No. 1200219N). This study was partially supported by the National Natural Science Foundation of China (Grant No: 51625701 and 51977096) and the China Scholarship Council (Grant No: 201806160128). All computational work was performed using 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. Approved Most recent IF: 3.5; 2020 IF: 2.846
Call Number PLASMANT @ plasmant @c:irua:169709 Serial 6372
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Author Bogaerts, A.; Centi, G.
Title Plasma Technology for CO2 Conversion: A Personal Perspective on Prospects and Gaps Type A1 Journal article
Year 2020 Publication Frontiers in energy research Abbreviated Journal Front. Energy Res.
Volume 8 Issue Pages
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract There is increasing interest in plasma technology for CO2 conversion because it can operate at mild conditions and it can store fluctuating renewable electricity into

value-added compounds and renewable fuels. This perspective paper aims to provide a view on the future for non-specialists who want to understand the role of plasma

technology in the new scenario for sustainable and low-carbon energy and chemistry. Thus, it is prepared to give a personal view on future opportunities and challenges. First, we introduce the current state-of-the-art and the potential of plasma-based CO2 conversion. Subsequently, we discuss the challenges to overcome the current limitations and to apply plasma technology on a large scale. The final section discusses the general context and the potential benefits of plasma-based CO2 conversion for our life and the impact on climate change. It also includes a brief analysis on the future scenario for energy and chemical production, and how plasma technology may realize new paths for CO2 utilization.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000553392300001 Publication Date 2020-07-07
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2296-598X ISBN Additional Links (up) UA library record; WoS full record; WoS citing articles
Impact Factor 3.4 Times cited Open Access OpenAccess
Notes We acknowledge financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 810182 – SCOPE ERC Synergy project). We thank A. Berthelot, M. Ramakers, R. Snoeckx, G. Trenchev, and V. Vermeiren for providing the figures used in this article. Approved Most recent IF: 3.4; 2020 IF: NA
Call Number PLASMANT @ plasmant @c:irua:170136 Serial 6390
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