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	Author	Oliveira, M.C.; Cordeiro, R.M.; Bogaerts, A.
	Title	Effect of lipid oxidation on the channel properties of Cx26 hemichannels : a molecular dynamics study			Type	A1 Journal article
	Year	2023	Publication	Archives of biochemistry and biophysics	Abbreviated Journal
	Volume	746	Issue		Pages	109741-12
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Intercellular communication plays a crucial role in cancer, as well as other diseases, such as inflammation, tissue degeneration, and neurological disorders. One of the proteins responsible for this, are connexins (Cxs), which come together to form a hemichannel. When two hemichannels of opposite cells interact with each other, they form a gap junction (GJ) channel, connecting the intracellular space of these cells. They allow the passage of ions, reactive oxygen and nitrogen species (RONS), and signaling molecules from the interior of one cell to another cell, thus playing an essential role in cell growth, differentiation, and homeostasis. The importance of GJs for disease induction and therapy development is becoming more appreciated, especially in the context of oncology. Studies have shown that one of the mechanisms to control the formation and disruption of GJs is mediated by lipid oxidation pathways, but the underlying mechanisms are not well understood. In this study, we performed atomistic molecular dynamics simulations to evaluate how lipid oxidation influences the channel properties of Cx26 hemichannels, such as channel gating and permeability. Our results demonstrate that the Cx26 hemichannel is more compact in the presence of oxidized lipids, decreasing its pore diameter at the extracellular side and increasing it at the amino terminus domains, respectively. The permeability of the Cx26 hemichannel for water and RONS molecules is higher in the presence of oxidized lipids. The latter may facilitate the intracellular accumulation of RONS, possibly increasing oxidative stress in cells. A better understanding of this process will help to enhance the efficacy of oxidative stress-based cancer treatments.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001079100300001	Publication Date	2023-09-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-9861; 1096-0384	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	3.9	Times cited		Open Access
	Notes				Approved	Most recent IF: 3.9; 2023 IF: 3.165
	Call Number	UA @ admin @ c:irua:200282			Serial	9028
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	Author	Rouwenhorst, K.H.R.; Jardali, F.; Bogaerts, A.; Lefferts, L.
	Title	Correction: From the Birkeland–Eyde process towards energy-efficient plasma-based NO_Xsynthesis: a techno-economic analysis			Type	A1 Journal Article
	Year	2023	Publication	Energy & Environmental Science	Abbreviated Journal	Energy Environ. Sci.
	Volume	16	Issue	12	Pages	6170-6173
	Keywords	A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	Correction for ‘From the Birkeland–Eyde process towards energy-efficient plasma-based NO<sub><italic>X</italic></sub>synthesis: a techno-economic analysis’ by Kevin H. R. Rouwenhorst<italic>et al.</italic>,<italic>Energy Environ. Sci.</italic>, 2021,<bold>14</bold>, 2520–2534, https://doi.org/10.1039/D0EE03763J.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2023-11-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1754-5692	ISBN		Additional Links
	Impact Factor	32.5	Times cited		Open Access
	Notes	H2020 European Research Council; Horizon 2020, 810182 ; Ministerie van Economische Zaken en Klimaat;			Approved	Most recent IF: 32.5; 2023 IF: 29.518
	Call Number	PLASMANT @ plasmant @			Serial	8980
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	Author	Snoeckx, R.; Bogaerts, A.
	Title	Plasma technology – a novel solution for CO₂conversion?			Type	A1 Journal article
	Year	2017	Publication	Chemical Society reviews	Abbreviated Journal	Chem Soc Rev
	Volume	46	Issue	19	Pages	5805-5863
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	CO2 conversion into value-added chemicals and fuels is considered as one of the great challenges of the 21st century. Due to the limitations of the traditional thermal approaches, several novel technologies are being developed. One promising approach in this field, which has received little attention to date, is plasma technology. Its advantages include mild operating conditions, easy upscaling, and gas activation by energetic electrons instead of heat. This allows thermodynamically difficult reactions, such as CO2 splitting and the dry reformation of methane, to occur with reasonable energy cost. In this review, after exploring the traditional thermal approaches, we have provided a brief overview of the fierce competition between various novel approaches in a quest to find the most effective and efficient CO2 conversion technology. This is needed to critically assess whether plasma technology can be successful in an already crowded arena. The following questions need to be answered in this regard: are there key advantages to using plasma technology over other novel approaches, and if so, what is the flip side to the use of this technology? Can plasma technology be successful on its own, or can synergies be achieved by combining it with other technologies? To answer these specific questions and to evaluate the potentials and limitations of plasma technology in general, this review presents the current state-of-the-art and a critical assessment of plasma-based CO2 conversion, as well as the future challenges for its practical implementation.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000412141600006	Publication Date	2017-08-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0306-0012	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	38.618	Times cited	168	Open Access	OpenAccess
	Notes	We would like to thank W. Wang (University of Antwerp) for providing the data on the thermal equilibrium conversions. Furthermore, we acknowledge financial support from the IAP/7 (Inter-university Attraction Pole) programme ‘PSI-Physical Chemistry of Plasma-Surface Interactions’ by the Belgian Federal Office for Science Policy (BELSPO), the Methusalem financing of the University of Antwerp, the Fund for Scientific Research Flanders (FWO; Grant no. G.0383.16N, G.0254.14N and G.0217.14N), the TOP research project of the Research Fund of the University of Antwerp (grant ID. 32249).			Approved	Most recent IF: 38.618
	Call Number	PLASMANT @ plasmant @c:irua:145921			Serial	4709
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	Author	Eckert, M.; Neyts, E.; Bogaerts, A.
	Title	Differences between ultrananocrystalline and nanocrystalline diamond growth: theoretical investigation of C_xH_y species at diamond step edges			Type	A1 Journal article
	Year	2010	Publication	Crystal growth & design	Abbreviated Journal	Cryst Growth Des
	Volume	10	Issue	9	Pages	4123-4134
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The behavior of hydrocarbon species at step edges of diamond terraces is investigated by means of combined molecular dynamics−Metropolis Monte Carlo simulations. The results show that the formation of ballas-like diamond films (like UNCD) and well-faceted diamond films (like NCD) can be related to the gas phase concentrations of CxHy in a new manner: Species that have high concentrations above the growing UNCD films suppress the extension of step edges through defect formation. The species that are present above the growing NCD film, however, enhance the extension of diamond terraces, which is believed to result in well-faceted diamond films. Furthermore, it is shown that, during UNCD growth, CxHy species with x ≥ 2 play an important role, in contrast to the currently adopted CVD diamond growth mechanism. Finally, the probabilities for the extension of the diamond (100) terrace are much higher than those for the diamond (111) terrace, which is in full agreement with the experimental observation that diamond (100) facets are more favored than diamond (111) facets during CVD diamond growth.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000281353900042	Publication Date	2010-08-16
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1528-7483;1528-7505;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.055	Times cited	11	Open Access
	Notes				Approved	Most recent IF: 4.055; 2010 IF: 4.390
	Call Number	UA @ lucian @ c:irua:83696			Serial	694
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	Author	Eckert, M.; Neyts, E.; Bogaerts, A.
	Title	Insights into the growth of (ultra)nanocrystalline diamond by combined molecular dynamics and Monte Carlo simulations			Type	A1 Journal article
	Year	2010	Publication	Crystal growth & design	Abbreviated Journal	Cryst Growth Des
	Volume	10	Issue	7	Pages	3005-3021
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this paper, we present the results of combined molecular dynamics−Metropolis Monte Carlo (MD-MMC) simulations of hydrocarbon species at flat diamond (100)2 × 1 and (111)1 × 1 surfaces. The investigated species are considered to be the most important growth species for (ultra)nanocrystalline diamond ((U)NCD) growth. When applying the MMC algorithm to stuck species at monoradical sites, bonding changes are only seen for CH2. The sequence of the bond breaking and formation as put forward by the MMC simulations mimics the insertion of CH2 into a surface dimer as proposed in the standard growth model of diamond. For hydrocarbon species attached to two adjacent radical (biradical) sites, the MMC simulations give rise to significant changes in the bonding structure. For UNCD, the combinations of C3 and C3H2, and C3 and C4H2 (at diamond (100)2 × 1) and C and C2H2 (at diamond (111)1 × 1) are the most successful in nucleating new crystal layers. For NCD, the following combinations pursue the diamond structure the best: C2H2 and C3H2 (at diamond (100)2 × 1) and CH2 and C2H2 (at diamond (111)1 × 1). The different behaviors of the hydrocarbon species at the two diamond surfaces are related to the different sterical hindrances at the diamond surfaces.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000279422700032	Publication Date	2010-05-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1528-7483;1528-7505;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.055	Times cited	13	Open Access
	Notes				Approved	Most recent IF: 4.055; 2010 IF: 4.390
	Call Number	UA @ lucian @ c:irua:83065			Serial	1675
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	Author	Georgieva, V.; Voter, A.F.; Bogaerts, A.
	Title	Understanding the surface diffusion processes during magnetron sputter-deposition of complex oxide Mg-Al-O thin films			Type	A1 Journal article
	Year	2011	Publication	Crystal growth & design	Abbreviated Journal	Cryst Growth Des
	Volume	11	Issue	6	Pages	2553-2558
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	It is known that film structure may change dramatically with the extent of surface diffusion during the film growth process. In the present work, surface diffusion, induced thermally or activated by energetic impacts, is investigated theoretically under conditions appropriate for magnetron sputter-deposition of MgAlO thin films with varying stoichiometry. The distribution of surface diffusion energy barriers available to the system was determined for each stoichiometry, which allowed assessing in a qualitative way how much surface diffusion will take place on the time scale available between deposition events. The activation energy barriers increase with the Al concentration in the film, and therefore, the surface diffusion rates in the time frame of typical deposition rates drop, which can explain the decrease in crystallinity in the film structure and the transition to amorphous structure. The deposition process and the immediate surface diffusion enhanced by the energetic adatoms are simulated by means of a molecular dynamics model. The longer-time thermal surface diffusion and the energy landscape are studied by the temperature accelerated dynamics method, applied in an approximate way. The surface diffusion enhanced by the energetic impacts appears to be very important for the film structure in the low-temperature deposition regime.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000291074600068	Publication Date	2011-04-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1528-7483;1528-7505;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.055	Times cited	14	Open Access
	Notes				Approved	Most recent IF: 4.055; 2011 IF: 4.720
	Call Number	UA @ lucian @ c:irua:89566			Serial	3806
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	Author	Shirazi, M.; Bogaerts, A.; Neyts, E.C.
	Title	A DFT study of H-dissolution into the bulk of a crystalline Ni(111) surface: a chemical identifier for the reaction kinetics			Type	A1 Journal article
	Year	2017	Publication	Physical chemistry, chemical physics	Abbreviated Journal	Phys Chem Chem Phys
	Volume	19	Issue	19	Pages	19150-19158
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this study, we investigated the diffusion of H-atoms to the subsurface and their further diffusion into the bulk of a Ni(111) crystal by means of density functional theory calculations in the context of thermal and plasma-assisted catalysis. The H-atoms at the surface can originate from the dissociative adsorption of H2 or CH4 molecules, determining the surface H-coverage. When a threshold H-coverage is passed, corresponding to 1.00 ML for the crystalline Ni(111) surface, the surface-bound H-atoms start to diffuse to the subsurface. A similar threshold coverage is observed for the interstitial H-coverage. Once the interstitial sites are filled up with a coverage above 1.00 ML of H, dissolution of interstitial H-atoms to the layer below the interstitial sites will be initiated. Hence, by applying a high pressure or inducing a reactive plasma and high temperature, increasing the H-flux to the surface, a large amount of hydrogen can diffuse in a crystalline metal like Ni and can be absorbed. The formation of metal hydride may modify the entire reaction kinetics of the system. Equivalently, the H-atoms in the bulk can easily go back to the surface and release a large amount of heat. In a plasma process, H-atoms are formed in the plasma, and therefore the energy barrier for dissociative adsorption is dismissed, thus allowing achievement of the threshold coverage without applying a high pressure as in a thermal process. As a result, depending on the crystal plane and type of metal, a large number of H-atoms can be dissolved (absorbed) in the metal catalyst, explaining the high efficiency of plasma-assisted catalytic reactions. Here, the mechanism of H-dissolution is established as a chemical identifier for the investigation of the reaction kinetics of a chemical process.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000406334300034	Publication Date	2017-06-22
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1463-9076	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.123	Times cited	10	Open Access	OpenAccess
	Notes	Financial support from the Reactive Atmospheric Plasma processIng – eDucation (RAPID) network, through the EU 7th Framework Programme (grant agreement no. 606889), is gratefully acknowledged. The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government department (EWI) and the Universiteit Antwerpen.			Approved	Most recent IF: 4.123
	Call Number	PLASMANT @ plasmant @ c:irua:144794			Serial	4633
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	Author	Gorbanev, Y.; Verlackt, C.C.W.; Tinck, S.; Tuenter, E.; Foubert, K.; Cos, P.; Bogaerts, A.
	Title	Combining experimental and modelling approaches to study the sources of reactive species induced in water by the COST RF plasma jet			Type	A1 Journal article
	Year	2018	Publication	Physical chemistry, chemical physics	Abbreviated Journal	Phys Chem Chem Phys
	Volume	20	Issue	4	Pages	2797-2808
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The vast biomedical potential of cold atmospheric pressure plasmas (CAPs) is governed by the formation of reactive species. These biologically active species are formed upon the interaction of CAPs with the surroundings. In biological milieu, water plays an essential role. The development of biomedical CAPs thus requires understanding of the sources of the reactive species in aqueous media exposed to the plasma. This is especially important in case of the COST RF plasma jet, which is developed as a reference microplasma system. In this work, we investigated the formation of the OH radicals, H atoms and H2O2 in aqueous solutions exposed to the COST plasma jet. This was done by combining experimental and modelling approaches. The liquid phase species were analysed using UV-Vis spectroscopy and spin trapping with hydrogen isotopes and electron paramagnetic resonance (EPR) spectroscopy. The discrimination between the species formed from the liquid phase and the gas phase molecules was performed by EPR and 1H-NMR analyses of the liquid samples. The concentrations of the reactive species in the gas phase plasma were obtained using a zero-dimensional (0D) chemical kinetics computational model. A three-dimensional (3D) fluid dynamics model was developed to provide information on the induced humidity in the plasma effluent. The comparison of the experimentally obtained trends for the formation of the species as a function of the feed gas and effluent humidity with the modelling results suggest that all reactive species detected in our system are mostly formed in the gas phase plasma inside the COST jet, with minor amounts arising from the plasma effluent humidity.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000423505500066	Publication Date	2018-01-05
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1463-9076	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.123	Times cited	23	Open Access	OpenAccess
	Notes	We are grateful to Volker Schulz-von der Gathen (Experimental Physics II: Application Oriented Plasma Physics, Ruhr-Universita¨t Bochum, Germany) for providing the COST RF plasma jet. We thank our colleagues at the University of Antwerp: Gilles Van Loon (Mechanical Workshop), Karen Leyssens (Research group PLASMANT), and Sylvia Dewilde (Department of Biomedical Sciences) for their help with the equipment. This work was funded by the European Marie Sklodowska-Curie Individual Fellowship ‘LTPAM’ within Horizon2020 (grant no. 657304). Stefan Tinck thanks the Fund for Scientific Research – Flanders (FWO) for supporting his work (grant no. 0880.212.840).			Approved	Most recent IF: 4.123
	Call Number	PLASMANT @ plasmant @c:irua:148365			Serial	4808
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	Author	Verlackt, C.C.W.; Van Boxem, W.; Bogaerts, A.
	Title	Transport and accumulation of plasma generated species in aqueous solution			Type	A1 Journal article
	Year	2018	Publication	Physical chemistry, chemical physics	Abbreviated Journal	Phys Chem Chem Phys
	Volume	20	Issue	10	Pages	6845-6859
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The interaction between cold atmospheric pressure plasma and liquids is receiving increasing attention for various applications. In particular, the use of plasma-treated liquids (PTL) for biomedical applications is of growing importance, in particular for sterilization and cancer treatment. However, insight into the underlying mechanisms of plasma–liquid interactions is still scarce. Here, we present a 2D fluid dynamics model for the interaction between a plasma jet and liquid water. Our results indicate that the formed reactive species originate from either the gas phase (with further solvation) or are formed at the liquid interface. A clear increase in the aqueous density of H2O2, HNO2/NO2- and NO3- is observed as a function of time, while the densities of O3, HO2/O2- and ONOOH/ONOO- are found to quickly reach a maximum due to chemical reactions in solution. The trends observed in our model correlate well with experimental observations from the literature.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000429286100009	Publication Date	2018-02-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1463-9076	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.123	Times cited	35	Open Access	OpenAccess
	Notes	The authors thank Petr Luke`s (Institute of Plasma Physics AS CR, Czech Republic) and Yury Gorbanev (UAntwerp, group PLASMANT) for the fruitful discussions regarding the chemistry in the model and the plasma–liquid interactions.			Approved	Most recent IF: 4.123
	Call Number	PLASMANT @ plasmant @c:irua:149557			Serial	4908
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	Author	Gorbanev, Y.; Van der Paal, J.; Van Boxem, W.; Dewilde, S.; Bogaerts, A.
	Title	Reaction of chloride anion with atomic oxygen in aqueous solutions: can cold plasma help in chemistry research?			Type	A1 Journal article
	Year	2019	Publication	Physical chemistry, chemical physics	Abbreviated Journal	Phys Chem Chem Phys
	Volume	21	Issue	8	Pages	4117-4121
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Cold atmospheric plasma in contact with solutions has many applications, but its chemistry contains many unknowns such as the undescribed reactions with solutes. By combining experiments and modelling, we report the first direct demonstration of the reaction of chloride with oxygen atoms in aqueous solutions exposed to cold plasma.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000461722500001	Publication Date	2019-01-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1463-9076	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.123	Times cited	4	Open Access	Not_Open_Access: Available from 31.01.2020
	Notes	H2020 Marie Skłodowska-Curie Actions, 743151 ; Fonds Wetenschappelijk Onderzoek, 11U5416N ;			Approved	Most recent IF: 4.123
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:157688			Serial	5167
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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	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	Heirman, P.; Van Boxem, W.; Bogaerts, A.
	Title	Reactivity and stability of plasma-generated oxygen and nitrogen species in buffered water solution: a computational study			Type	A1 Journal article
	Year	2019	Publication	Physical chemistry, chemical physics	Abbreviated Journal	Phys Chem Chem Phys
	Volume	21	Issue	24	Pages	12881-12894
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma-treated liquids have great potential for biomedical applications. However, insight into the underlying mechanisms and the exact chemistry is still scarce. In this study, we present the combination of a 0D chemical kinetics and a 2D fluid dynamics model to investigate the plasma treatment of a buffered water solution with the kINPen (R) plasma jet. Using this model, we calculated the gas and liquid flow profiles and the transport and chemistry of all species in the gas and the liquid phase. Moreover, we evaluated the stability of the reactive oxygen and nitrogen species after plasma treatment. We found that of all species, only H2O2, HNO2/NO2-, and HNO3/NO3- are stable in the buffered solution after plasma treatment. This is because both their production and loss processes in the liquid phase are dependent on short-lived radicals (e.g. OH, NO, and NO2). Apart from some discrepancy in the absolute values of the concentrations, which can be explained by the model, all general trends and observations in our model are in qualitative agreement with experimental data and literature.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000472214000012	Publication Date	2019-05-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1463-9076; 1463-9084	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.123	Times cited	7	Open Access
	Notes				Approved	Most recent IF: 4.123
	Call Number	UA @ admin @ c:irua:161314			Serial	6320
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	Author	Neyts, E.; Bogaerts, A.
	Title	Influence of internal energy and impact angle on the sticking behaviour of reactive radicals in thin a-C:H film growth: a molecular dynamics study			Type	A1 Journal article
	Year	2006	Publication	Physical chemistry, chemical physics	Abbreviated Journal	Phys Chem Chem Phys
	Volume	8	Issue	17	Pages	2066-2071
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Cambridge	Editor
	Language		Wos	000236970300011	Publication Date	2006-03-20
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1463-9076;1463-9084;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.123	Times cited	7	Open Access
	Notes				Approved	Most recent IF: 4.123; 2006 IF: 2.892
	Call Number	UA @ lucian @ c:irua:57353			Serial	1625
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	Author	Janssens, K.; Bogaerts, A.; van Grieken, R.
	Title	Colloquium Spectroscopicum Internationale 34, Antwerp, Belgium, 4-9 September 2005: preface			Type	Editorial
	Year	2006	Publication	Talanta : the international journal of pure and applied analytical chemistry	Abbreviated Journal	Talanta
	Volume	70	Issue	5	Pages	907-908
	Keywords	Editorial; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	Pergamon	Place of Publication	Oxford	Editor
	Language		Wos	000242871900001	Publication Date	2006-11-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0039-9140;	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	4.162	Times cited		Open Access
	Notes				Approved	Most recent IF: 4.162; 2006 IF: 2.810
	Call Number	UA @ lucian @ c:irua:61094			Serial	392
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	Author	Khosravian, N.; Kamaraj, B.; Neyts, E.C.; Bogaerts, A.
	Title	Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations			Type	A1 Journal article
	Year	2016	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	6	Issue	6	Pages	19466
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.
	Address	Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Wos	000369573900001	Publication Date	2016-02-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	7	Open Access
	Notes	The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number G012413N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen.”			Approved	Most recent IF: 4.259
	Call Number	c:irua:131610			Serial	4031
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	Author	Attri, P.; Yusupov, M.; Park, J.H.; Lingamdinne, L.P.; Koduru, J.R.; Shiratani, M.; Choi, E.H.; Bogaerts, A.
	Title	Mechanism and comparison of needle-type non-thermal direct and indirect atmospheric pressure plasma jets on the degradation of dyes			Type	A1 Journal article
	Year	2016	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	6	Issue	6	Pages	34419
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Purified water supply for human use, agriculture and industry is the major global priority nowadays. The advanced oxidation process based on atmospheric pressure non-thermal plasma (NTP) has been used for purification of wastewater, although the underlying mechanisms of degradation of organic pollutants are still unknown. In this study we employ two needle-type atmospheric pressure non-thermal plasma jets, i.e., indirect (ID-APPJ) and direct (D-APPJ) jets operating at Ar feed gas, for the treatment of methylene blue, methyl orange and congo red dyes, for two different times (i.e., 20 min and 30 min). Specifically, we study the decolorization/degradation of all three dyes using the above mentioned plasma sources, by means of UV-Vis spectroscopy, HPLC and a density meter. We also employ mass spectroscopy to verify whether only decolorization or also degradation takes place after treatment of the dyes by the NTP jets. Additionally, we analyze the interaction of OH radicals with all three dyes using reactive molecular dynamics simulations, based on the density functional-tight binding method. This investigation represents the first report on the degradation of these three different dyes by two types of NTP setups, analyzed by various methods, and based on both experimental and computational studies.
	Address	Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Wos	000385172300001	Publication Date	2016-10-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	23	Open Access
	Notes	We gratefully acknowledge the grant received from the SRC program of the National Research Foundation of Korea (NRF), funded by the Korean Government (MEST) (No. 20100029418). PA is thankful to FY 2015 Japan Society for the Promotion of Science (JSPS) invitation fellowship. This work was partly supported by MEXT KAKENHI Grant Number 24108009 and JSPS KAKENHI Grant Number JP16H03895. M. Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @ c:irua:135847			Serial	4283
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	Author	Van der Paal, J.; Verheyen, C.; Neyts, E.C.; Bogaerts, A.
	Title	Hampering Effect of Cholesterol on the Permeation of Reactive Oxygen Species through Phospholipids Bilayer: Possible Explanation for Plasma Cancer Selectivity			Type	A1 Journal article
	Year	2017	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	7	Issue	7	Pages	39526
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In recent years, the ability of cold atmospheric pressure plasmas (CAPS) to selectively induce cell death in cancer cells has been widely established. This selectivity has been assigned to the reactive oxygen and nitrogen species (RONS) created in CAPs. To provide new insights in the search for an explanation for the observed selectivity, we calculate the transfer free energy of multiple ROS across membranes containing a varying amount of cholesterol. The cholesterol fraction is investigated as a selectivity parameter because membranes of cancer cells are known to contain lower fractions of cholesterol compared to healthy cells. We find that cholesterol has a significant effect on the permeation of reactive species across a membrane. Indeed, depending on the specific reactive species, an increasing cholesterol fraction can lead to (i) an increase of the transfer free energy barrier height and width, (ii) the formation of a local free energy minimum in the center of the membrane and (iii) the creation of extra free energy barriers due to the bulky sterol rings. In the context of plasma oncology, these observations suggest that the increased ingress of RONS in cancer cells can be explained by the decreased cholesterol fraction of their cell membrane.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000391306900001	Publication Date	2017-01-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	27	Open Access	OpenAccess
	Notes	The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number 11U5416N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @ c:irua:139512			Serial	4340
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	Author	Yusupov, M.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A.
	Title	Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments			Type	A1 Journal article
	Year	2017	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	7	Issue	7	Pages	5761
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000405746500072	Publication Date	2017-07-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	27	Open Access	OpenAccess
	Notes	M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216 N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. S.R. and S.K. acknowledge funding by the BMBF (FKZ: 03Z2DN12). S.R. acknowledges funding by the Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern (AU 15001). The authors thank M. Hammer for the support and discussion in the biophysical studies and J. Van der Paal for the interesting discussions.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @ c:irua:144627			Serial	4630
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	Author	Van Boxem, W.; Van der Paal, J.; Gorbanev, Y.; Vanuytsel, S.; Smits, E.; Dewilde, S.; Bogaerts, A.
	Title	Anti-cancer capacity of plasma-treated PBS: effect of chemical composition on cancer cell cytotoxicity			Type	A1 Journal article
	Year	2017	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	7	Issue	1	Pages	16478
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We evaluate the anti-cancer capacity of plasma-treated PBS (pPBS), by measuring the concentrations of NO2 − and H2O2 in pPBS, treated with a plasma jet, for different values of gas flow rate, gap and plasma treatment time, as well as the effect of pPBS on cancer cell cytotoxicity, for three different glioblastoma cancer cell lines, at exactly the same plasma treatment conditions. Our experiments reveal that pPBS is cytotoxic for all conditions investigated. A small variation in gap between plasma jet and liquid surface (10 mm vs 15 mm) significantly affects the chemical composition of pPBS and its anti-cancer capacity, attributed to the occurrence of discharges onto the liquid. By correlating the effect of gap, gas flow rate and plasma treatment time on the chemical composition and anti-cancer capacity of pPBS, we may conclude that H2O2 is a more important species for the anti-cancer capacity of pPBS than NO2 −. We also used a 0D model, developed for plasma-liquid interactions, to elucidate the most important mechanisms for the generation of H2O2 and NO2 −. Finally, we found that pPBS might be more suitable for practical applications in a clinical setting than (commonly used) plasma-activated media (PAM), because of its higher stability.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000416398100028	Publication Date	2017-11-22
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	40	Open Access	OpenAccess
	Notes	We acknowledge financial support from the Fund for Scientific Research (FWO) Flanders (Grant No. 11U5416N), the Research Council of the University of Antwerp and the European Marie Skłodowska-Curie Individual Fellowship “LTPAM” within Horizon2020 (Grant No. 743151). Finally, we would like to thank P. Attri and A. Privat Maldonado for the valuable discussions.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @c:irua:147192			Serial	4766
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	Author	Klinkhammer, C.; Verlackt, C.; Smilowicz, D.; Kogelheide, F.; Bogaerts, A.; Metzler-Nolte, N.; Stapelmann, K.; Havenith, M.; Lackmann, J.-W.
	Title	Elucidation of plasma-induced chemical modifications on glutathione and glutathione disulphide			Type	A1 Journal article
	Year	2017	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	7	Issue		Pages	13828
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Cold atmospheric pressure plasmas are gaining increased interest in the medical sector and clinical trials to treat skin diseases are underway. Plasmas are capable of producing several reactive oxygen and nitrogen species (RONS). However, there are open questions how plasma-generated RONS interact on a molecular level in a biological environment, e.g. cells or cell components. The redox pair glutathione (GSH) and glutathione disulphide (GSSG) forms the most important redox buffer in organisms responsible for detoxification of intracellular reactive species. We apply Raman spectroscopy, mass spectrometry, and molecular dynamics simulations to identify the time-dependent chemical modifications on GSH and GSSG that are caused by dielectric barrier discharge under ambient conditions. We find GSSG, S-oxidised glutathione species, and S-nitrosoglutathione as oxidation products with the latter two being the final products, while glutathione sulphenic acid, glutathione sulphinic acid, and GSSG are rather reaction intermediates. Experiments using stabilized pH conditions revealed the same main oxidation products as were found in unbuffered solution, indicating that the dominant oxidative or nitrosative reactions are not influenced by acidic pH. For more complex systems these results indicate that too long treatment times can cause difficult-to-handle modifications to the cellular redox buffer which can impair proper cellular function.
	Address
	Corporate Author				Thesis
	Publisher	Nature Publishing Group	Place of Publication	London	Editor
	Language		Wos	000413401300003	Publication Date	2017-10-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	17	Open Access	OpenAccess
	Notes				Approved	Most recent IF: 4.259
	Call Number	UA @ lucian @ c:irua:146666			Serial	4783
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	Author	Lackmann, J.-W.; Wende, K.; Verlackt, C.; Golda, J.; Volzke, J.; Kogelheide, F.; Held, J.; Bekeschus, S.; Bogaerts, A.; Schulz-von der Gathen, V.; Stapelmann, K.
	Title	Chemical fingerprints of cold physical plasmas – an experimental and computational study using cysteine as tracer compound			Type	A1 Journal article
	Year	2018	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	8	Issue	1	Pages	7736
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Reactive oxygen and nitrogen species released by cold physical plasma are being proposed as effectors in various clinical conditions connected to inflammatory processes. As these plasmas can be tailored in a wide range, models to compare and control their biochemical footprint are desired to infer on the molecular mechanisms underlying the observed effects and to enable the discrimination between different plasma sources. Here, an improved model to trace short-lived reactive species is presented. Using FTIR, high-resolution mass spectrometry, and molecular dynamics computational simulation, covalent modifications of cysteine treated with different plasmas were deciphered and the respective product pattern used to generate a fingerprint of each plasma source. Such, our experimental model allows a fast and reliable grading of the chemical potential of plasmas used for medical purposes. Major reaction products were identified to be cysteine sulfonic acid, cystine, and cysteine fragments. Less abundant products, such as oxidized cystine derivatives or S-nitrosylated cysteines, were unique to different plasma sources or operating conditions. The data collected point at hydroxyl radicals, atomic O, and singlet oxygen as major contributing species that enable an impact on cellular thiol groups when applying cold plasma in vitro or in vivo.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000432275800035	Publication Date	2018-05-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	19	Open Access	OpenAccess
	Notes	This work was supported by the German Research Foundation (DFG, grant PAK816 to V.SvdG.), the Federal German Ministry of Education and Research (grant number 03Z22DN12 to K.W. and 03Z22DN11 to S.B.), and the FWO-Flanders (grant number G012413N to A.B.). K.W. likes to thank T. von Woedtke and K.-D. Weltmann for constant support. The authors thank K. Kartaschew for fruitful discussion and G. Bruno for support during mock studies.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @c:irua:151241			Serial	4957
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	Author	Vanraes, P.; Nikiforov, A.; Bogaerts, A.; Leys, C.
	Title	Study of an AC dielectric barrier single micro-discharge filament over a water film			Type	A1 Journal article
	Year	2018	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	8	Issue	1	Pages	10919
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In the last decades, AC powered atmospheric dielectric barrier discharges (DBDs) in air with a liquid electrode have been proposed as a promising plasma technology with versatile applicability in medicine agriculture and water treatment. The fundamental features of the micro-discharge filaments that make up this type of plasma have, however, not been studied yet in sufficient detail. In order to address this need, we investigated a single DBD micro-discharge filament over a water film in a sphere-to-sphere electrode configuration, by means of ICCD imaging and optical emission spectroscopy. When the water film temporarily acts as the cathode, the plasma duration is remarkably long and shows a clear similarity with a resistive barrier discharge, which we attribute to the resistive nature of the water film and the formation of a cathode fall. As another striking difference to DBD with solid electrodes, a constant glow-like plasma is observed at the water surface during the entire duration of the applied voltage cycle, indicating continuous plasma treatment of the liquid. We propose several elementary mechanisms that might underlie the observed unique behavior, based on the specific features of a water electrode.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000439101600018	Publication Date	2018-07-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	3	Open Access	OpenAccess
	Notes	P. Vanraes acknowledges funding by a University of Antwerp BOF grant.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @c:irua:152822c:irua:152411			Serial	4999
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	Author	Attri, P.; Han, J.; Choi, S.; Choi, E.H.; Bogaerts, A.; Lee, W.
	Title	CAP modifies the structure of a model protein from thermophilic bacteria: mechanisms of CAP-mediated inactivation			Type	A1 Journal article
	Year	2018	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	8	Issue	1	Pages	10218
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Cold atmospheric plasma (CAP) has great potential for sterilization in the food industry, by deactivation of thermophilic bacteria, but the underlying mechanisms are largely unknown. Therefore, we investigate here whether CAP is able to denature/modify protein from thermophilic bacteria. We focus on MTH1880 (MTH) from Methanobacterium thermoautotrophicum as model protein, which we treated with dielectric barrier discharge (DBD) plasma operating in air for 10, 15 and 20 mins. We analysed the structural changes of MTH using circular dichroism, fluorescence and NMR spectroscopy, as well as the thermal and chemical denaturation, upon CAP treatment. Additionally, we performed molecular dynamics (MD) simulations to determine the stability, flexibility and solvent accessible surface area (SASA) of both the native and oxidised protein.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000437414500004	Publication Date	2018-06-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	6	Open Access	OpenAccess
	Notes	We gratefully acknowledge the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by NRF-2017R1A2B2008483 to W.L. through the National Research Foundation of Korea (NRF) and BK+ program (J.H.). E.H.C. acknowledges the NRF (NRF-2016K1A4A3914113 and No. 20100027963). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @c:irua:152817c:irua:152431			Serial	5002
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	Author	Shaw, P.; Kumar, N.; Kwak, H.S.; Park, J.H.; Uhm, H.S.; Bogaerts, A.; Choi, E.H.; Attri, P.
	Title	Bacterial inactivation by plasma treated water enhanced by reactive nitrogen species			Type	A1 Journal article
	Year	2018	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	8	Issue	1	Pages	11268
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	There is a growing body of literature that recognizes the importance of plasma treated water (PTW)for inactivation of microorganism. However, very little attention has been paid to the role of reactive nitrogen species (RNS) in deactivation of bacteria. The aim of this study is to explore the role of RNS in bacterial killing, and to develop a plasma system with increased sterilization efficiency. To increase the concentration of reactive oxygen and nitrogen species (RONS) in solution, we have used vapor systems (DI water/HNO3 at different wt%) combined with plasma using N2 as working gas. The results show that the addition of the vapor system yields higher RONS contents. Furthermore, PTW produced by N2 + 0.5 wt% HNO3 vapor comprises a large amount of both RNS and ROS, while PTW created by N2 + H2O vapor consists of a large amount of ROS, but much less RNS. Interestingly, we observed more deactivation of E. Coli with PTW created by N2 + 0.5 wt% HNO3 vapor plasma as compared to PTW generated by the other plasma systems. This work provides new insight into the role of RNS along with ROS for deactivation of bacteria.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000439805700029	Publication Date	2018-07-20
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	17	Open Access	OpenAccess
	Notes	We gratefully acknowledge the Leading Foreign Research Institute Recruitment program (Grant # NRF- 2016K1A4A3914113) throughout the Basic Science Research Program of the National Research Foundation (NRF) of Korea and in part by Kwangwoon University 2018. JHP thanks to NRF Grant No. NRF- 2017R1D1A1B03033495. We also acknowledge financial support from the Research Foundation – Flanders (FWO) (Grant Number 12J5617N) and from the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon 2020 (Grant Number 743546).			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @c:irua:152821			Serial	5003
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	Author	Snoeckx, R.; Wang, W.; Zhang, X.; Cha, M.S.; Bogaerts, A.
	Title	Plasma-based multi-reforming for Gas-To-Liquid: tuning the plasma chemistry towards methanol			Type	A1 Journal article
	Year	2018	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	8	Issue	1	Pages	15929
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Because of its unique properties, plasma technology has gained much prominence in the microelectronics industry. Recently, environmental and energy applications of plasmas have gained a lot of attention. In this area, the focus is on converting CO 2 and reforming hydrocarbons, with the goal of developing an efficient single-step ‘gas-to-liquid’ (GTL) process. Here we show that applying tri-reforming principles to plasma—further called ‘plasma-based multi-reforming’—allows us to better control the plasma chemistry and thus the formed products. To demonstrate this, we used chemical kinetics calculations supported by experiments and reveal that better control of the plasma chemistry can be achieved by adding O 2 or H 2 O to a mixture containing CH 4 and CO 2 (diluted in N 2 ). Moreover, by adding O 2 and H 2 O simultaneously, we can tune the plasma chemistry even further, improving the conversions, thermal efficiency and methanol yield. Unlike thermocatalytic reforming, plasma-based reforming is capable of producing methanol in a single step; and compared with traditional plasma-based dry reforming, plasma-based multi-reforming increases the methanol yield by more than seven times and the thermal efficiency by 49%, as revealed by our model calculations. Thus, we believe that by using plasma-based multi-reforming, ‘gas-to-liquid’ conversion may be made efficient and scalable.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000448589200005	Publication Date	2018-10-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited		Open Access	OpenAccess
	Notes	The authors acknowledge financial support from the Competitive Research Funding from King Abdullah University of Science and Technology (KAUST), the European Marie Skłodowska-Curie Individual Fellowship “GlidArc” within Horizon2020 (Grant No. 657304), the Fund for Scientific Research Flanders (FWO) (grant nos G.0217.14 N, G.0254.14 N and G.0383.16 N) and the IAP/7 (Inter-university Attraction Pole) program ‘PSI-Physical Chemistry of Plasma-Surface Interactions’, financially supported by the Belgian Federal Office for Science Policy (BELSPO). 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: 4.259
	Call Number	PLASMANT @ plasmant @c:irua:154868			Serial	5066
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	Author	Razzokov, J.; Yusupov, M.; Bogaerts, A.
	Title	Oxidation destabilizes toxic amyloid beta peptide aggregation			Type	A1 Journal article
	Year	2019	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	9	Issue	1	Pages	5476
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000462990000018	Publication Date	2019-04-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	5	Open Access	OpenAccess
	Notes	M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant 1200216N and 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.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:159367			Serial	5182
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	Author	Shaw, P.; Kumar, N.; Mumtaz, S.; Lim, J.S.; Jang, J.H.; Kim, D.; Sahu, B.D.; Bogaerts, A.; Choi, E.H.
	Title	Evaluation of non-thermal effect of microwave radiation and its mode of action in bacterial cell inactivation			Type	A1 Journal Article
	Year	2021	Publication	Scientific Reports	Abbreviated Journal	Sci Rep-Uk
	Volume	11	Issue	1	Pages	14003
	Keywords	A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	A growing body of literature has recognized the non-thermal effect of pulsed microwave radiation (PMR) on bacterial systems. However, its mode of action in deactivating bacteria has not yet been extensively investigated. Nevertheless, it is highly important to advance the applications of PMR from simple to complex biological systems. In this study, we first optimized the conditions of the PMR device and we assessed the results by simulations, using ANSYS HFSS (High Frequency Structure Simulator) and a 3D particle-in-cell code for the electron behavior, to provide a better overview of the bacterial cell exposure to microwave radiation. To determine the sensitivity of PMR,<italic>Escherichia coli</italic> and<italic>Staphylococcus aureus</italic>cultures were exposed to PMR (pulse duration: 60 ns, peak frequency: 3.5 GHz) with power density of 17 kW/cm<sup>2</sup>at the free space of sample position, which would induce electric field of 8.0 kV/cm inside the PBS solution of falcon tube in this experiment at 25 °C. At various discharges (D) of microwaves, the colony forming unit curves were analyzed. The highest ratios of viable count reductions were observed when the doses were increased from 20D to 80D, which resulted in an approximate 6 log reduction in <italic>E. coli</italic>and 4 log reduction in<italic>S. aureus.</italic>Moreover, scanning electron microscopy also revealed surface damage in both bacterial strains after PMR exposure. The bacterial inactivation was attributed to the deactivation of oxidation-regulating genes and DNA damage.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000674547300011	Publication Date	2021-07-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited		Open Access	OpenAccess
	Notes	Department of Biotechnology, Ministry of Science and Technology, India, D.O.NO.BT/HRD/35/02/2006 ; National Research Foundation of Korea, NRF-2016K1A4A3914113 ; This research was supported by the National Research Foundation (NRF) of Korea, funded by the Korean government (MSIT) under the Grant Number NRF-2016K1A4A3914113, and in part by Kwangwoon University, Seoul, Korea, 2021. We also gratefully acknowledge the financial support obtained from Department of Biotechnology (DBT) Ramalingaswami Re-entry Fellowship, India, Grant Number D.O.NO.BT/HRD/35/02/2006.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @c:irua:179844			Serial	6800
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	Author	Hoon Park, J.; Kumar, N.; Hoon Park, D.; Yusupov, M.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A.; Ho Kang, M.; Sup Uhm, H.; Ha Choi, E.; Attri, P.;
	Title	A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma			Type	A1 Journal article
	Year	2015	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	5	Issue	5	Pages	13849
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG.
	Address
	Corporate Author				Thesis
	Publisher	Nature Publishing Group	Place of Publication	London	Editor
	Language		Wos	000360909000001	Publication Date	2015-09-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	32	Open Access
	Notes				Approved	Most recent IF: 4.259; 2015 IF: 5.578
	Call Number	c:irua:127410			Serial	419
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	Author	Sun, S.R.; Wang, H.X.; Mei, D.H.; Tu, X.; Bogaerts, A.
	Title	CO2 conversion in a gliding arc plasma: Performance improvement based on chemical reaction modeling			Type	A1 Journal article
	Year	2017	Publication	Journal of CO2 utilization	Abbreviated Journal	J Co2 Util
	Volume	17	Issue	17	Pages	220-234
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	CO2 conversion into value-added chemicals is gaining increasing interest in recent years, and a gliding arc plasma has great potential for this purpose, because of its high energy efficiency. In this study, a chemical reaction kinetics model is presented to study the CO2 splitting in a gliding arc discharge. The calculated conversion and energy efficiency are in good agreement with experimental data in a range of different operating conditions. Therefore, this reaction kinetics model can be used to elucidate the dominant chemical reactions contributing to CO2 destruction and formation. Based on this reaction pathway analysis, the restricting factors for CO2 conversion are figured out, i.e., the reverse reactions and the small treated gas fraction. This allows us to propose some solutions in order to improve the CO2 conversion, such as decreasing the gas temperature, by using a high frequency discharge, or increasing the power density, by using a micro-scale gliding arc reactor, or by removing the reverse reactions, which could be realized in practice by adding possible scavengers for O atoms, such as CH4. Finally, we compare our results with other types of plasmas in terms of conversion and energy efficiency, and the results illustrate that gliding arc discharges are indeed quite promising for CO2 conversion, certainly when keeping in mind the possible solutions for further performance improvement.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000393928500023	Publication Date	2016-12-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2212-9820	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.292	Times cited	41	Open Access	Not_Open_Access
	Notes	We acknowledge financial support from the IAP/7 (Inter- university Attraction Pole) program ‘PSI-Physical Chemistry of Plasma-Surface Interactions’ by the Belgian Federal Office for Science Policy (BELSPO) and the Fund for Scientific Research Flanders (FWO; Grant no. G.0383.16N). The calculations were carried out 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 is also supported by National Natural Science Foundation of China (grant nos. 11275021, 11575019). S R Sun thanks the financial support from the China Scholarship Council (CSC).			Approved	Most recent IF: 4.292
	Call Number	PLASMANT @ plasmant @ c:irua:138986			Serial	4332
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	Author	Berthelot, A.; Bogaerts, A.
	Title	Pinpointing energy losses in CO 2 plasmas – Effect on CO 2 conversion			Type	A1 Journal article
	Year	2018	Publication	Journal of CO2 utilization	Abbreviated Journal	J Co2 Util
	Volume	24	Issue		Pages	479-499
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma technology is gaining increasing interest for CO2 conversion, but to maximize the energy efficiency, it is important to track the different energy transfers taking place in the plasma. In this paper, we study these mechanisms by a 0D chemical kinetics model, including the vibrational kinetics, for different conditions of reduced electric field, gas temperature and ionization degree, at a pressure of 100 mbar. Our model predicts a maximum conversion and energy efficiency of 32% and 47%, respectively, at conditions that are particularly beneficial for energy efficient CO2 conversion, i.e. a low reduced electric field (10 Td) and a low gas temperature (300 K). We study the effect of the efficiency by which the vibrational energy is used to dissociate CO2, as well as of the activation energy of the reaction CO2+O→CO+O2, to elucidate the theoretical limitations to the energy efficiency. Our model reveals that these parameters are mainly responsible for the limitations in the energy efficiency. By varying these parameters, we can reach a maximum conversion and energy efficiency of 86%. Finally, we derive an empirical formula to estimate the maximum possible energy efficiency that can be reached under the assumptions of the model.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000428234500054	Publication Date	2018-03-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2212-9820	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.292	Times cited	6	Open Access	Not_Open_Access: Available from 16.03.2020
	Notes	We acknowledge financial support from the European Union's Seventh Framework Program for research, technological development and demonstration under grant agreement no. 606889. The calculations were 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. We would also like to thank Prof. Richard van de Sanden (DIFFER) for the interesting talks.			Approved	Most recent IF: 4.292
	Call Number	PLASMANT @ plasmant @c:irua:149645			Serial	4912
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