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	Author	van den Broek, B.; Houssa, M.; Scalise, E.; Pourtois, G.; Afanas'ev, V.V.; Stesmans, A.
	Title	First-principles electronic functionalization of silicene and germanene by adatom chemisorption			Type	A1 Journal article
	Year	2014	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	291	Issue		Pages	104-108
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	This study presents first-principles results on the electronic functionalization of silicene and germanene monolayers by means of chemisorption of adatom species H, Li, F, Sc, Ti, V. Three general adatom-monolayer configurations are considered, each having its distinct effect on the electronic structure, yielding metallic or semiconducting dispersions depending on the adatom species and configuration. The induced bandgap is a (in)direct F gap ranging from 0.2 to 2.3 eV for both silicene and germanene. In general the alternating configuration was found to be the most energetically stable. The boatlike and chairlike conformers are degenerate with the former having anisotropic effective carrier masses. The top configuration leads to the planar monolayer and predominately to a gapped dispersion. The hollow configuration with V adatoms retains the Dirac cone, but with strong orbital planar hybridization at the Fermi level. We also observe a planar surface state the Fermi level for the latter systems. (C) 2013 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000329327700023	Publication Date	2013-09-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	32	Open Access
	Notes				Approved	Most recent IF: 3.387; 2014 IF: 2.711
	Call Number	UA @ lucian @ c:irua:113766			Serial	1208
Permanent link to this record



	Author	Lenaerts, J.; Gijbels, R.; van Vaeck, L.; Verlinden, G.; Geuens, I.
	Title	Imaging TOF-SIMS for the surface analysis of silver halide microcrystals			Type	A1 Journal article
	Year	2003	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	203/204	Issue		Pages	614-619
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000180527300138	Publication Date	2002-12-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	7	Open Access
	Notes				Approved	Most recent IF: 3.387; 2003 IF: 1.284
	Call Number	UA @ lucian @ c:irua:51974			Serial	1556
Permanent link to this record



	Author	de Witte, H.; Conard, T.; Vandervorst, W.; Gijbels, R.
	Title	Ion-bombardment artifact in TOF-SIMS analysis of ZrO₂/SiO₂/Si stacks			Type	A1 Journal article
	Year	2003	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	203	Issue		Pages	523-526
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We analyzed ultra-thin ZrO2/SiO2/Si gate dielectrics under post-deposition anneals in dry O-2 at temperatures from 500 to 700 degreesC. TOF-SIMS profiling of ZrO2/SiO2/Si stacks is hampered by many sputter induced artifacts. The depletion of oxygen leads to a decrease in SIMS intensities. However, preferential sputtering is accompanied by transport of the depleted species towards the surface. Due to recoil implantation oxygen gets piled-up near the ZrO2/SiO2 interface. Either normal or radiation-enhanced diffusion transports oxygen back to the surface. Simultaneously also segregation of zirconium towards and through the interface is observed, resulting in a large zirconium tail in the underlying silicon substrate. (C) 2002 Elsevier Science B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher	Elsevier science bv	Place of Publication	Amsterdam	Editor
	Language		Wos	000180527300119	Publication Date	2002-12-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	15	Open Access
	Notes				Approved	Most recent IF: 3.387; 2003 IF: 1.284
	Call Number	UA @ lucian @ c:irua:51975			Serial	1743
Permanent link to this record



	Author	Adriaensen, L.; Vangaever, F.; Gijbels, R.
	Title	Organic SIMS: the influence of time on the ion yield enhancement by silver and gold deposition			Type	A1 Journal article
	Year	2004	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	231/232	Issue		Pages	256-260
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000222427700049	Publication Date	2004-04-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	10	Open Access
	Notes				Approved	Most recent IF: 3.387; 2004 IF: 1.497
	Call Number	UA @ lucian @ c:irua:46804			Serial	2510
Permanent link to this record



	Author	Adriaensen, L.; Vangaever, F.; Lenaerts, J.; Gijbels, R.
	Title	S-SIMS and MetA-SIMS study of organic additives in thin polymer coatings			Type	A1 Journal article
	Year	2006	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	252	Issue	19	Pages	6628-6631
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000240609900057	Publication Date	2006-06-20
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	3	Open Access
	Notes				Approved	Most recent IF: 3.387; 2006 IF: 1.436
	Call Number	UA @ lucian @ c:irua:60083			Serial	2937
Permanent link to this record



	Author	Houssa, M.; van den Broek, B.; Scalise, E.; Ealet, B.; Pourtois, G.; Chiappe, D.; Cinquanta, E.; Grazianetti, C.; Fanciulli, M.; Molle, A.; Afanas’ev, V.V.; Stesmans, A.;
	Title	Theoretical aspects of graphene-like group IV semiconductors			Type	A1 Journal article
	Year	2014	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	291	Issue		Pages	98-103
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Silicene and germanene are the silicon and germanium counterparts of graphene, respectively. Recent experimental works have reported the growth of silicene on (1 1 1)Ag surfaces with different atomic configurations, depending on the growth temperature and surface coverage. We first theoretically study the structural and electronic properties of silicene on (1 1 1) Ag surfaces, focusing on the (4 x 4) silicene/Ag structure. Due to symmetry breaking in the silicene layer (nonequivalent number of top and bottom Si atoms), the corrugated silicene layer, with the Ag substrate removed, is predicted to be semiconducting, with a computed energy bandgap of about 0.3 eV. However, the hybridization between the Si 3p orbitals and the Ag 5s orbital in the silicene/(1 1 1)Ag slab model leads to an overall metallic system, with a distribution of local electronic density of states, which is related to the slightly disordered structure of the silicene layer on the (1 1 1)Ag surface. We next study the interaction of silicene and germanene with different hexagonal non-metallic substrates, namely ZnS and ZnSe. On reconstructed (0 0 0 1)ZnS or ZnSe surfaces, which should be more energetically stable for very thin layers, silicene and germanene are found to be semiconducting. Remarkably, the nature and magnitude of their energy bandgap can be controlled by an out-of-plane electric field, an important finding for the potential use of these materials in nanoelectronic devices. (C) 2013 Elsevier B. V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000329327700022	Publication Date	2013-09-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	20	Open Access
	Notes				Approved	Most recent IF: 3.387; 2014 IF: 2.711
	Call Number	UA @ lucian @ c:irua:113765			Serial	3603
Permanent link to this record



	Author	Scalise, E.; Cinquanta, E.; Houssa, M.; van den Broek, B.; Chiappe, D.; Grazianetti, C.; Pourtois, G.; Ealet, B.; Molle, A.; Fanciulli, M.; Afanas’ev, V.V.; Stesmans, A.;
	Title	Vibrational properties of epitaxial silicene layers on (111) Ag			Type	A1 Journal article
	Year	2014	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	291	Issue		Pages	113-117
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The electronic and vibrational properties of three different reconstructions of silicene on Ag(1 1 1) are calculated and compared to experimental results. The 2D epitaxial silicon layers, namely the (4 x 4), (root 13 x root 13) and (2 root 3 x 2 root 3) phases, exhibit different electronic and vibrational properties. Few peaks in the experimental Raman spectrum are identified and attributed to the vibrational modes of the silicene layers. The position and behavior of the Raman peaks with respect to the excitation energy are shown to be a fundamental tool to investigate and discern different phases of silicene on Ag( 1 1 1). (C) 2013 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000329327700025	Publication Date	2013-09-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	36	Open Access
	Notes				Approved	Most recent IF: 3.387; 2014 IF: 2.711
	Call Number	UA @ lucian @ c:irua:113767			Serial	3843
Permanent link to this record



	Author	Nematollahi, P.; Neyts, E.C.
	Title	A comparative DFT study on CO oxidation reaction over Si-doped BC2N nanosheet and nanotube			Type	A1 Journal article
	Year	2018	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	439	Issue	439	Pages	934-945
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this study, we performed density functional theory (DFT) calculations to investigate different reaction mechanisms of CO oxidation catalyzed by the Si atom embedded defective BC2N nanostructures as well as the analysis of the structural and electronic properties. The structures of all the complexes are optimized and characterized by frequency calculations at the M062X/6-31G* computational level. Also, The electronic structures and thermodynamic parameters of adsorbed CO and O-2 molecules over Si-doped BC2N nanostructures are examined in detail. Moreover, to investigate the curvature effect on the CO oxidation reaction, all the adsorption and CO oxidation reactions on a finite-sized armchair (6,6) Si-BC2NNT are also studied. Our results indicate that there can be two possible pathways for the CO oxidation with O-2 molecule: O-2(g) + CO(g) -> O-2(ads) + CO(ads) -> CO2(g) + O-(ads) and O-(ads) + CO(g) -> CO2(g). The first reaction proceeds via the Langmuir-Hinshelwood (LH) mechanism while the second goes through the Eley-Rideal (ER) mechanism. On the other hand, by increasing the tube diameter, the energy barrier increases due to the strong adsorption energy of the O-2 molecule which is related to its dissociation over the tube surface. Our calculations indicate that the two step energy barrier of the oxidation reaction over Si-BC2NNS is less than that over the Si-BC2NNT. Hence, Si-BC2NNS may serve as an efficient and highly activated substrate to CO oxidation rather than (4,4) Si-BC2NNT. (C) 2018 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000427457100112	Publication Date	2018-01-08
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	8	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 3.387
	Call Number	UA @ lucian @ c:irua:150745			Serial	4960
Permanent link to this record



	Author	Nematollahi, P.; Neyts, E.C.
	Title	Direct methane conversion to methanol on M and MN₄ embedded graphene (M = Ni and Si): a comparative DFT study			Type	A1 Journal article
	Year	2019	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	496	Issue	496	Pages	143618
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The ever increasing global production and dispersion of methane requires novel chemistry to transform it into easily condensable energy carriers that can be integrated into the chemical infrastructure. In this context, single atom catalysts have attracted considerable interest due to their outstanding catalytic activity. We here use density functional theory (DFT) computations to compare the reaction and activation energies of M and MN4 embedded graphene (M = Ni and Si) on the methane-to-methanol conversion near room temperature. Thermodynamically, conversion of methane to methanol is energetically favorable at ambient conditions. Both singlet and triplet spin state of the studied systems are considered in all of the calculations. The DFT results show that the barriers are significantly lower when the complexes are in the triplet state than in the singlet state. In particular, Si-G with the preferred spin multiplicity of triplet seems to be viable catalysts for methane oxidation thanks to the corresponding lower energy barriers and higher stability of the obtained configurations. Our results provide insights into the nature of methane conversion and may serve as guidance for fabricating cost-effective graphene-based single atom catalysts.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000488957400004	Publication Date	2019-08-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	2	Open Access
	Notes				Approved	Most recent IF: 3.387
	Call Number	UA @ admin @ c:irua:163695			Serial	6294
Permanent link to this record



	Author	Foumani, A.A.; Forster, D.J.; Ghorbanfekr, H.; Weber, R.; Graf, T.; Niknam, A.R.
	Title	Atomistic simulation of ultra-short pulsed laser ablation of metals with single and double pulses : an investigation of the re-deposition phenomenon			Type	A1 Journal article
	Year	2021	Publication	Applied Surface Science	Abbreviated Journal	Appl Surf Sci
	Volume	537	Issue		Pages	147775
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The demand for higher throughput in the processing of materials with ultra-short pulsed lasers has motivated studies on the use of double pulses (DP). It has been observed in such studies that at relatively high time delays between the two pulses, the ablated volume is lower than that for a single pulse (SP). This has been attributed to the shielding of the second pulse and the re-deposition of the material removed by the first pulse. The investigation of re-deposition in copper with the aid of atomistic simulations is the main objective of this study. Nevertheless, a computational investigation of SP-ablation and experimental measurement of the SP-ablation depths and threshold fluence are also covered. The applied computational apparatus comprises a combination of molecular dynamics with the two-temperature model and the Helmholtz wave equation. The analysis of the simulation results shows that the derived quantities like the SP-ablation threshold fluence and the ratio of DP ablation depth to SP-ablation depth are in agreement with the experimental values. An important finding of this study is that the characteristics of the re-deposition process are highly dependent on the fluence.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000582798700006	Publication Date	2020-09-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	2	Open Access	Not_Open_Access
	Notes	; The authors thank the Center for High-Performance Computing at Shahid Beheshti University of Iran (SARMAD) for making available the computational resources required for this work. ;			Approved	Most recent IF: 3.387
	Call Number	UA @ admin @ c:irua:174299			Serial	6683
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	Author	Adhami Sayad Mahaleh, M.; Narimisa, M.; Nikiforov, A.; Gromov, M.; Gorbanev, Y.; Bitar, R.; Morent, R.; De Geyter, N.
	Title	Nitrogen Oxidation in a Multi-Pin Plasma System in the Presence and Absence of a Plasma/Liquid Interface			Type	A1 Journal Article
	Year	2023	Publication	Applied Sciences	Abbreviated Journal	Applied Sciences
	Volume	13	Issue	13	Pages	7619
	Keywords	A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	The recent energy crisis revealed that there is a strong need to replace hydrocarbon-fueled industrial nitrogen fixation processes by alternative, more sustainable methods. In light of this, plasma-based nitrogen fixation remains one of the most promising options, considering both theoretical and experimental aspects. Lately, plasma interacting with water has received considerable attention in nitrogen fixation applications as it can trigger a unique gas- and liquid-phase chemistry. Within this context, a critical exploration of plasma-assisted nitrogen fixation with or without water presence is of great interest with an emphasis on energy costs, particularly in plasma reactors which have potential for large-scale industrial application. In this work, the presence of water in a multi-pin plasma system on nitrogen oxidation is experimentally investigated by comparing two pulsed negative DC voltage plasmas in metal–metal and metal–liquid electrode configurations. The plasma setups are designed to create similar plasma properties, including plasma power and discharge regime in both configurations. The system energy cost is calculated, considering nitrogen-containing species generated in gas and liquid phases as measured by a gas analyzer, nitrate sensor, and a colorimetry method. The energy cost profile as a function of specific energy input showed a strong dependency on the plasma operational frequency and the gas flow rate, as a result of different plasma operation regimes and initiated reverse processes. More importantly, the presence of the plasma/liquid interface increased the energy cost up to 14 ± 8%. Overall, the results showed that the presence of water in the reaction zone has a negative impact on the nitrogen fixation process.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001031217300001	Publication Date	2023-06-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2076-3417	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.7	Times cited		Open Access	Not_Open_Access
	Notes	NITROPLASM FWO-FNRS Excellence of Science, 30505023 ; European Union-NextGenerationEU, G0G2322N ;			Approved	Most recent IF: 2.7; 2023 IF: 1.679
	Call Number	PLASMANT @ plasmant @c:irua:198153			Serial	8802
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	Author	Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A.
	Title	Transport of cystine across xC-antiporter			Type	A1 Journal article
	Year	2019	Publication	Archives of biochemistry and biophysics	Abbreviated Journal	Arch Biochem Biophys
	Volume	664	Issue		Pages	117-126
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Extracellular cystine (CYC) uptake by xC antiporter is important for the cell viability. Especially in cancer cells, the upregulation of xC activity is observed, which protects these cells from intracellular oxidative stress. Hence, inhibition of the CYC uptake may eventually lead to cancer cell death. Up to now, the molecular level mechanism of the CYC uptake by xC antiporter has not been studied in detail. In this study, we applied several different simulation techniques to investigate the transport of CYC through xCT, the light subunit of the xC antiporter, which is responsible for the CYC and glutamate translocation. Specifically, we studied the permeation of CYC across three model systems, i.e., outward facing (OF), occluded (OCC) and inward facing (IF) configurations of xCT. We also investigated the effect of mutation of Cys327 to Ala within xCT, which was also studied experimentally in literature. This allowed us to qualitatively compare our computation results with experimental observations, and thus, to validate our simulations. In summary, our simulations provide a molecular level mechanism of the transport of CYC across the xC antiporter, more specifically, which amino acid residues in the xC antiporter play a key role in the uptake, transport and release of CYC.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000461411200014	Publication Date	2019-02-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-9861	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.165	Times cited	3	Open Access	OpenAccess
	Notes	Research Foundation − FlandersResearch Foundation − Flanders (FWO), 1200216N 1200219N ; Hercules FoundationHercules Foundation; Flemish GovernmentFlemish Government (department EWI); UAUA; M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant numbers 1200216N and 1200219N. The computational work was carried out 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 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 @UA @ admin @ c:irua:158571			Serial	5183
Permanent link to this record



	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	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	Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M.
	Title	How do nitrated lipids affect the properties of phospholipid membranes?			Type	A1 Journal article
	Year	2020	Publication	Archives Of Biochemistry And Biophysics	Abbreviated Journal	Arch Biochem Biophys
	Volume	695	Issue		Pages	108548
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Biological membranes are under constant attack of free radicals, which may lead to lipid nitro-oxidation, pro ducing a complex mixture of nitro-oxidized lipids that are responsible for structural and dynamic changes on the membrane. Despite the latter, nitro-oxidized lipids are also associated with several inflammatory and neuro degenerative diseases, the underlying mechanisms of which remain elusive. We perform atomistic molecular dynamics simulations using several isomers of nitro-oxidized lipids to study their effect on the structure and permeability of the membrane, as well as the interaction between the mixture of these products in the phospholipid membrane environment. Our results show that the stereo- and positional isomers have a stronger effect on the properties of the membrane composed of oxidized lipids compared to that containing nitrated lipids. Nevertheless, nitrated lipids lead to three-fold increase in water permeability compared to oxidized lipids. In addition, we show that in a membrane consisting of combined nitro-oxidized lipid products, the presence of oxidized lipids protects the membrane from transient pores. Is well stablished that plasma application and photodynamic therapy produces a number of oxidative species used to kill cancer cells, through membrane damage induced by nitro-oxidative stress. This study is important to elucidate the mechanisms and the molecular level properties involving the reactive species produced during that cancer therapies.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000594173400010	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-9861	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.9	Times cited		Open Access
	Notes	CAPES; Flanders Research Foundation, 1200219N ; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for financial support.			Approved	Most recent IF: 3.9; 2020 IF: 3.165
	Call Number	PLASMANT @ plasmant @c:irua:173861			Serial	6440
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	Author	Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M.
	Title	Distribution of lipid aldehydes in phase-separated membranes: A molecular dynamics study			Type	A1 Journal article
	Year	2022	Publication	Archives Of Biochemistry And Biophysics	Abbreviated Journal	Arch Biochem Biophys
	Volume	717	Issue		Pages	109136
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	It is well established that lipid aldehydes (LAs) are able to increase the permeability of cell membranes and induce their rupture. However, it is not yet clear how LAs are distributed in phase-separated membranes (PSMs), which are responsible for the transport of selected molecules and intracellular signaling. Thus, we investigate here the distribution of LAs in a PSM by coarse-grained molecular dynamics simulations. Our results reveal that LAs derived from mono-unsaturated lipids tend to accumulate at the interface between the liquid-ordered/liquiddisordered domains, whereas those derived from poly-unsaturated lipids remain in the liquid-disordered domain. These results are important for understanding the effects caused by oxidized lipids in membrane structure, properties and organization.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000767632000001	Publication Date	2022-01-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-9861	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	3.9	Times cited		Open Access	OpenAccess
	Notes	We thank the University of Antwerp and the Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted. The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerpen.			Approved	Most recent IF: 3.9
	Call Number	PLASMANT @ plasmant @c:irua:185874			Serial	6905
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	Author	Yusupov, M.; Van der Paal, J.; Neyts, E.C.; Bogaerts, A.
	Title	Synergistic effect of electric field and lipid oxidation on the permeability of cell membranes			Type	A1 Journal article
	Year	2017	Publication	Biochimica et biophysica acta : G : general subjects	Abbreviated Journal	Bba-Gen Subjects
	Volume	1861	Issue	1861	Pages	839-847
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Background: Strong electric fields are knownto affect cell membrane permeability,which can be applied for therapeutic purposes, e.g., in cancer therapy. A synergistic enhancement of this effect may be accomplished by the presence of reactive oxygen species (ROS), as generated in cold atmospheric plasmas. Little is known about the synergy between lipid oxidation by ROS and the electric field, nor on howthis affects the cell membrane permeability. Method: We here conduct molecular dynamics simulations to elucidate the dynamics of the permeation process under the influence of combined lipid oxidation and electroporation. A phospholipid bilayer (PLB), consisting of di-oleoyl-phosphatidylcholine molecules covered with water layers, is used as a model system for the plasma membrane. Results and conclusions:Weshow howoxidation of the lipids in the PLB leads to an increase of the permeability of the bilayer to ROS, although the permeation free energy barriers still remain relatively high. More importantly, oxidation of the lipids results in a drop of the electric field threshold needed for pore formation (i.e., electroporation) in the PLB. The created pores in the membrane facilitate the penetration of reactive plasma species deep into the cell interior, eventually causing oxidative damage. General significance: This study is of particular interest for plasma medicine, as plasma generates both ROS and electric fields, but it is also of more general interest for applications where strong electric fields and ROS both come into play.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000397366200012	Publication Date	2017-01-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-4165	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.702	Times cited		Open Access	OpenAccess
	Notes	This work is financially supported by the Fund for Scientific Research Flanders (FWO; grant numbers: 1200216N and 11U5416N). The work was carried out 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 Flem			Approved	Most recent IF: 4.702
	Call Number	PLASMANT @ plasmant @ c:irua:140095			Serial	4413
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	Author	Lin, A.; De Backer, J.; Quatannens, D.; Cuypers, B.; Verswyvel, H.; De La Hoz, E.C.; Ribbens, B.; Siozopoulou, V.; Van Audenaerde, J.; Marcq, E.; Lardon, F.; Laukens, K.; Vanlanduit, S.; Smits, E.; Bogaerts, A.
	Title	The effect of local non‐thermal plasma therapy on the<scp>cancer‐immunity</scp>cycle in a melanoma mouse model			Type	University Hospital Antwerp
	Year	2022	Publication	Bioengineering & Translational Medicine	Abbreviated Journal	Bioengineering & Transla Med
	Volume		Issue		Pages
	Keywords	University Hospital Antwerp; A1 Journal article; Pharmacology. Therapy; Engineering sciences. Technology; ADReM Data Lab (ADReM); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES)
	Abstract	Melanoma remains a deadly cancer despite significant advances in immune checkpoint blockade and targeted therapies. The incidence of melanoma is also growing worldwide, which highlights the need for novel treatment options and strategic combination of therapies. Here, we investigate non-thermal plasma (NTP), an ionized gas, as a promising, therapeutic option. In a melanoma mouse model, direct treatment of tumors with NTP results in reduced tumor burden and prolonged survival. Physical characterization of NTP treatment in situ reveals the deposited NTP energy and temperature associated with therapy response, and whole transcriptome analysis of the tumor identified several modulated pathways. NTP treatment also enhances the cancer-immunity cycle, as immune cells in both the tumor and tumor-draining lymph nodes appear more stimulated to perform their anti-cancer functions. Thus, our data suggest that local NTP therapy stimulates systemic, anti-cancer immunity. We discuss, in detail, how these fundamental insights will help direct the translation of NTP technology into the clinic and inform rational combination strategies to address the challenges in melanoma therapy.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000784103500001	Publication Date	2022-04-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2380-6761	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	Vlaamse regering, 1S67621N 1S76421N G044420N 12S9221N 12S9218N ; The authors would like to thank and acknowledge Christophe Hermans, Ho Wa Lau, and Hilde Lambrechts for their help with sectioning and preparing the IHC slides. The authors would also like to thank Dani Banner for designing the ergonomic NTP applicator handle and Hasan Baysal for 3D printing the pieces used in this experiment. We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr Willy Floren, and the Vereycken family. Some of the resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) The data that support the findings of this study are available from the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9218N (Abraham Lin), 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaert, and Steve Vanlanduit), 1S76421N (Delphine Quatannens), and 1S67621N (Hanne Verswyvel). Figure 7 was created with BioRender.com.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:187909			Serial	7056
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	Author	Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C.
	Title	How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations			Type	A1 Journal article
	Year	2015	Publication	Biointerphases	Abbreviated Journal	Biointerphases
	Volume	10	Issue	10	Pages	029501
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000357195600019	Publication Date	2014-12-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1934-8630;1559-4106;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.603	Times cited	10	Open Access
	Notes				Approved	Most recent IF: 2.603; 2015 IF: 3.374
	Call Number	c:irua:121371			Serial	1492
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	Author	Wende, K.; Williams, P.; Dalluge, J.; Van Gaens, W.; Aboubakr, H.; Bischof, J.; von Woedtke, T.; Goyal, S.M.; Weltmann, K.D.; Bogaerts, A.; Masur, K.; Bruggeman, P.J.;
	Title	Identification of the biologically active liquid chemistry induced by a nonthermal atmospheric pressure plasma jet			Type	A1 Journal article
	Year	2015	Publication	Biointerphases	Abbreviated Journal	Biointerphases
	Volume	10	Issue	10	Pages	029518
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The mechanism of interaction of cold nonequilibrium plasma jets with mammalian cells in physiologic liquid is reported. The major biological active species produced by an argon RF plasma jet responsible for cell viability reduction are analyzed by experimental results obtained through physical, biological, and chemical diagnostics. This is complemented with chemical kinetics modeling of the plasma source to assess the dominant reactive gas phase species. Different plasma chemistries are obtained by changing the feed gas composition of the cold argon based RF plasma jet from argon, humidified argon (0.27%), to argon/oxygen (1%) and argon/air (1%) at constant power. A minimal consensus physiologic liquid was used, providing isotonic and isohydric conditions and nutrients but is devoid of scavengers or serum constituents. While argon and humidified argon plasma led to the creation of hydrogen peroxide dominated action on the mammalian cells, argonoxygen and argonair plasma created a very different biological action and was characterized by trace amounts of hydrogen peroxide only. In particular, for the argonoxygen (1%), the authors observed a strong negative effect on mammalian cell proliferation and metabolism. This effect was distance dependent and showed a half life time of 30 min in a scavenger free physiologic buffer. Neither catalase and mannitol nor superoxide dismutase could rescue the cell proliferation rate. The strong distance dependency of the effect as well as the low water solubility rules out a major role for ozone and singlet oxygen but suggests a dominant role of atomic oxygen. Experimental results suggest that O reacts with chloride, yielding Cl2 − or ClO−. These chlorine species have a limited lifetime under physiologic conditions and therefore show a strong time dependent biological activity. The outcomes are compared with an argon MHz plasma jet (kinpen) to assess the differences between these (at least seemingly) similar plasma sources.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000357195600036	Publication Date	2015-05-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1934-8630;1559-4106;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.603	Times cited	137	Open Access
	Notes				Approved	Most recent IF: 2.603; 2015 IF: 3.374
	Call Number	c:irua:126774			Serial	1549
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	Author	Shaw, P.; Kumar, N.; Sahun, M.; Smits, E.; Bogaerts, A.; Privat-Maldonado, A.
	Title	Modulating the Antioxidant Response for Better Oxidative Stress-Inducing Therapies: How to Take Advantage of Two Sides of the Same Medal?			Type	A1 Journal article
	Year	2022	Publication	Biomedicines	Abbreviated Journal	Biomedicines
	Volume	10	Issue	4	Pages	823
	Keywords	A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract	Oxidative stress-inducing therapies are characterized as a specific treatment that involves the production of reactive oxygen and nitrogen species (RONS) by external or internal sources. To protect cells against oxidative stress, cells have evolved a strong antioxidant defense system to either prevent RONS formation or scavenge them. The maintenance of the redox balance ensures signal transduction, development, cell proliferation, regulation of the mechanisms of cell death, among others. Oxidative stress can beneficially be used to treat several diseases such as neurodegenerative disorders, heart disease, cancer, and other diseases by regulating the antioxidant system. Understanding the mechanisms of various endogenous antioxidant systems can increase the therapeutic efficacy of oxidative stress-based therapies, leading to clinical success in medical treatment. This review deals with the recent novel findings of various cellular endogenous antioxidant responses behind oxidative stress, highlighting their implication in various human diseases, such as ulcers, skin pathologies, oncology, and viral infections such as SARS-CoV-2.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000785420400001	Publication Date	2022-03-31
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2227-9059	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	Science and Engineering Research Board (SERB), Core Research Grant, Department of Science and Technology, India., (CRG/2021/001935) ; Department of Biotechnology, BT/RLF/Re-entry/27/2019 ; We are grateful to Charlotta Bengtson for her valuable input.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:187931			Serial	7051
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	Author	Marimuthu, P.; Razzokov, J.; Singaravelu, K.; Bogaerts, A.
	Title	Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide—Mcl1 Complexes			Type	A1 Journal article
	Year	2020	Publication	Biomolecules	Abbreviated Journal	Biomolecules
	Volume	10	Issue	8	Pages	1114
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000578895600001	Publication Date	2020-07-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2218-273X	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access
	Notes	P.M. gratefully acknowledges the use of the bioinformatics infrastructure facility supported by Biocenter Finland and the CSC-IT Center for Science (Project: 2000461) for the computational facility; Jukka Lehtonen for the IT support; Mark Johnson (SBL) Åbo Akademi University for providing the lab support and Outi Salo-Ahen (Pharmacy) Åbo Akademi University and Olli T. Pentikäinen (Institute of Biomedicine) University of Turku, for their valuable support and discussion.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:170486			Serial	6396
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	Author	Abduvokhidov, D.; Yusupov, M.; Shahzad, A.; Attri, P.; Shiratani, M.; Oliveira, M.C.; Razzokov, J.
	Title	Unraveling the Transport Properties of RONS across Nitro-Oxidized Membranes			Type	A1 Journal Article
	Year	2023	Publication	Biomolecules	Abbreviated Journal	Biomolecules
	Volume	13	Issue	7	Pages	1043
	Keywords	A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	The potential of cold atmospheric plasma (CAP) in biomedical applications has received significant interest, due to its ability to generate reactive oxygen and nitrogen species (RONS). Upon exposure to living cells, CAP triggers alterations in various cellular components, such as the cell membrane. However, the permeation of RONS across nitrated and oxidized membranes remains understudied. To address this gap, we conducted molecular dynamics simulations, to investigate the permeation capabilities of RONS across modified cell membranes. This computational study investigated the translocation processes of less hydrophilic and hydrophilic RONS across the phospholipid bilayer (PLB), with various degrees of oxidation and nitration, and elucidated the impact of RONS on PLB permeability. The simulation results showed that less hydrophilic species, i.e., NO, NO2, N2O4, and O3, have a higher penetration ability through nitro-oxidized PLB compared to hydrophilic RONS, i.e., HNO3, s-cis-HONO, s-trans-HONO, H2O2, HO2, and OH. In particular, nitro-oxidation of PLB, induced by, e.g., cold atmospheric plasma, has minimal impact on the penetration of free energy barriers of less hydrophilic species, while it lowers these barriers for hydrophilic RONS, thereby enhancing their translocation across nitro-oxidized PLB. This research contributes to a better understanding of the translocation abilities of RONS in the field of plasma biomedical applications and highlights the need for further analysis of their role in intracellular signaling pathways.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001035160000001	Publication Date	2023-06-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2218-273X	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	This research was funded by the Innovative Development Agency of the Republic of Uzbekistan, grant number FZ-2020092817.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:198154			Serial	8803
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	Author	Ghasemitarei, M.; Ghorbi, T.; Yusupov, M.; Zhang, Y.; Zhao, T.; Shali, P.; Bogaerts, A.
	Title	Effects of Nitro-Oxidative Stress on Biomolecules: Part 1—Non-Reactive Molecular Dynamics Simulations			Type	A1 Journal Article
	Year	2023	Publication	Biomolecules	Abbreviated Journal	Biomolecules
	Volume	13	Issue	9	Pages	1371
	Keywords	A1 Journal Article; plasma medicine; reactive oxygen and; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001071356400001	Publication Date	2023-09-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2218-273X	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	This research received no external funding.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:200380			Serial	8958
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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.
	Address
	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	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	Bergwerf, I.; de Vocht, N.; Tambuyzer, B.; Verschueren, J.; Reekmans, K.; Daans, J.; Ibrahimi, A.; Van Tendeloo, V.; Chatterjee, S.; Goossens, H.; Jorens, P.G.; Baekelandt, V.; Ysebaert, D.; Van Marck, E.; Berneman, Z.N.; Van Der Linden, A.; Ponsaerts, P.
	Title	Reporter gene-expressing bone marrow-derived stromal cells are immune-tolerated following implantation in the central nervous system of syngeneic immunocompetent mice			Type	A1 Journal article
	Year	2009	Publication	BMC biotechnology	Abbreviated Journal	Bmc Biotechnol
	Volume		Issue		Pages
	Keywords	A1 Journal article; Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP); Bio-Imaging lab; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Background Cell transplantation is likely to become an important therapeutic tool for the treatment of various traumatic and ischemic injuries to the central nervous system (CNS). However, in many pre-clinical cell therapy studies, reporter gene-assisted imaging of cellular implants in the CNS and potential reporter gene and/or cell-based immunogenicity, still remain challenging research topics. Results In this study, we performed cell implantation experiments in the CNS of immunocompetent mice using autologous (syngeneic) luciferase-expressing bone marrow-derived stromal cells (BMSC-Luc) cultured from ROSA26-L-S-L-Luciferase transgenic mice, and BMSC-Luc genetically modified using a lentivirus encoding the enhanced green fluorescence protein (eGFP) and the puromycin resistance gene (Pac) (BMSC-Luc/eGFP/Pac). Both reporter gene-modified BMSC populations displayed high engraftment capacity in the CNS of immunocompetent mice, despite potential immunogenicity of introduced reporter proteins, as demonstrated by real-time bioluminescence imaging (BLI) and histological analysis at different time-points post-implantation. In contrast, both BMSC-Luc and BMSC-Luc/eGFP/Pac did not survive upon intramuscular cell implantation, as demonstrated by real-time BLI at different time-points post-implantation. In addition, ELISPOT analysis demonstrated the induction of IFN-ã-producing CD8+ T-cells upon intramuscular cell implantation, but not upon intracerebral cell implantation, indicating that BMSC-Luc and BMSC-Luc/eGFP/Pac are immune-tolerated in the CNS. However, in our experimental transplantation model, results also indicated that reporter gene-specific immune-reactive T-cell responses were not the main contributors to the immunological rejection of BMSC-Luc or BMSC-Luc/eGFP/Pac upon intramuscular cell implantation. Conclusion We here demonstrate that reporter gene-modified BMSC derived from ROSA26-L-S-L-Luciferase transgenic mice are immune-tolerated upon implantation in the CNS of syngeneic immunocompetent mice, providing a research model for studying survival and localisation of autologous BMSC implants in the CNS by real-time BLI and/or histological analysis in the absence of immunosuppressive therapy.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000262698500001	Publication Date	2009-01-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1472-6750	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.415	Times cited	33	Open Access
	Notes				Approved	Most recent IF: 2.415; 2009 IF: 2.723
	Call Number	UA @ lucian @ c:irua:72911			Serial	4527
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	Author	Bogaerts, A.; Ameye, L.; Bijlholt, M.; Amuli, K.; Heynickx, D.; Devlieger, R.
	Title	INTER-ACT : prevention of pregnancy complications through an e-health driven interpregnancy lifestyle intervention: study protocol of a multicentre randomised controlled trial			Type	A1 Journal article
	Year	2017	Publication	BMC pregnancy and childbirth	Abbreviated Journal	Bmc Pregnancy Childb
	Volume	17	Issue		Pages	154
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Centre for Research and Innovation in Care (CRIC)
	Abstract	Background Excessive maternal pre-pregnancy and gestational weight gain are related to pregnancy- and birth outcomes. The interpregnancy time window offers a unique opportunity to intervene in order to acquire a healthy lifestyle before the start of a new pregnancy. Methods INTER-ACT is an e-health driven multicentre randomised controlled intervention trial targeting women at high risk of pregnancy- and birth related complications. Eligible women are recruited for the study at day 2 or 3 postpartum. At week 6 postpartum, participants are randomised into the intervention or control arm of the study. The intervention focuses on weight, diet, physical activity and mental well-being, and comprises face-to-face coaching, in which behavioural change techniques are central, and use of a mobile application, which is Bluetooth-connected to a weighing scale and activity tracker. The intervention is rolled out postpartum (4 coaching sessions between week 6 and month 6) and in a new pregnancy (3 coaching sessions, one in each trimester of pregnancy); the mobile app is used throughout the two intervention phases. Data collection includes data from the medical record of the participants (pregnancy outcomes and medical history), anthropometric data (height, weight, waist- and hip circumferences, skinfold thickness and body composition by bio-electrical impedance analysis), data from the mobile app (physical activity and weight; intervention group only) and questionnaires (socio-demographics, breastfeeding, food intake, physical activity, lifestyle, psychosocial factors and process evaluation). Medical record data are collected at inclusion and at delivery of the subsequent pregnancy. All other data are collected at week 6 and month 6 postpartum and every subsequent 6 months until a new pregnancy, and in every trimester in the new pregnancy. Primary outcome is the composite endpoint score of pregnancy-induced hypertension, gestational diabetes mellitus, caesarean section, and large-for-gestational-age infant in the subsequent pregnancy.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000402116300002	Publication Date	2017-05-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1471-2393	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.263	Times cited	4	Open Access	OpenAccess
	Notes				Approved	Most recent IF: 2.263
	Call Number	UA @ lucian @ c:irua:143234			Serial	4663
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	Author	Privat-Maldonado, A.; Gorbanev, Y.; Dewilde, S.; Smits, E.; Bogaerts, A.
	Title	Reduction of Human Glioblastoma Spheroids Using Cold Atmospheric Plasma: The Combined Effect of Short- and Long-Lived Reactive Species			Type	A1 Journal article
	Year	2018	Publication	Cancers	Abbreviated Journal	Cancers
	Volume	10	Issue	11	Pages	394
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Cold atmospheric plasma (CAP) is a promising technology against multiple types of cancer. However, the current findings on the effect of CAP on two-dimensional glioblastoma cultures do not consider the role of the tumour microenvironment. The aim of this study was to determine the ability of CAP to reduce and control glioblastoma spheroid tumours in vitro . Three-dimensional glioblastoma spheroid tumours (U87-Red, U251-Red) were consecutively treated directly and indirectly with a CAP using dry He, He + 5% H 2 O or He + 20% H 2 O. The cytotoxicity and spheroid shrinkage were monitored using live imaging. The reactive oxygen and nitrogen species produced in phosphate buffered saline (PBS) were measured by electron paramagnetic resonance (EPR) and colourimetry. Cell migration was also assessed. Our results demonstrate that consecutive CAP treatments (He + 20% H 2 O) substantially shrank U87-Red spheroids and to a lesser degree, U251-Red spheroids. The cytotoxic effect was due to the short- and long-lived species delivered by CAP: they inhibited spheroid growth, reduced cell migration and decreased proliferation in CAP-treated spheroids. Direct treatments were more effective than indirect treatments, suggesting the importance of CAP-generated, short-lived species for the growth inhibition and cell cytotoxicity of solid glioblastoma tumours. We concluded that CAP treatment can effectively reduce glioblastoma tumour size and restrict cell migration, thus demonstrating the potential of CAP therapies for glioblastoma.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000451307700001	Publication Date	2018-10-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2072-6694	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	The authors thank Paul Cos (Department of Pharmaceutical Sciences, University of Antwerp) for providing EPR equipment and Christophe Hermans for his help with the immunohistochemical experiments.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:154871			Serial	5065
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	Author	Shaw, P.; Kumar, N.; Hammerschmid, D.; Privat-Maldonado, A.; Dewilde, S.; Bogaerts, A.
	Title	Synergistic Effects of Melittin and Plasma Treatment: A Promising Approach for Cancer Therapy			Type	A1 Journal article
	Year	2019	Publication	Cancers	Abbreviated Journal	Cancers
	Volume	11	Issue	8	Pages	1109
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Melittin (MEL), a small peptide component of bee venom, has been reported to exhibit anti-cancer effects in vitro and in vivo. However, its clinical applicability is disputed because of its non-specific cytotoxicity and haemolytic activity in high treatment doses. Plasma-treated phosphate buffered saline solution (PT-PBS), a solution rich in reactive oxygen and nitrogen species (RONS) can disrupt the cell membrane integrity and induce cancer cell death through oxidative stress-mediated pathways. Thus, PT-PBS could be used in combination with MEL to facilitate its access into cancer cells and to reduce the required therapeutic dose. The aim of our study is to determine the reduction of the effective dose of MEL required to eliminate cancer cells by its combination with PT-PBS. For this purpose, we have optimised the MEL threshold concentration and tested the combined treatment of MEL and PT-PBS on A375 melanoma and MCF7 breast cancer cells, using in vitro, in ovo and in silico approaches. We investigated the cytotoxic effect of MEL and PT-PBS alone and in combination to reveal their synergistic cytological effects. To support the in vitro and in ovo experiments, we showed by computer simulations that plasma-induced oxidation of the phospholipid bilayer leads to a decrease of the free energy barrier for translocation of MEL in comparison with the non-oxidized bilayer, which also suggests a synergistic effect of MEL with plasma induced oxidation. Overall, our findings suggest that MEL in combination with PT-PBS can be a promising combinational therapy to circumvent the non-specific toxicity of MEL, which may help for clinical applicability in the future.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000484438000069	Publication Date	2019-08-03
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2072-6694	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited	1	Open Access
	Notes	We gratefully acknowledge financial support from the Research Foundation—Flanders (FWO), grant number 12J5617N. We are thankful to Maksudbek Yusupov for his valuable discussions, and to the Center for Oncological Research (CORE), for providing the facilities for the experimental work. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the University Antwerp, 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: NA
	Call Number	PLASMANT @ plasmant @c:irua:161630			Serial	5286
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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	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	Biscop,; Lin,; Boxem,; Loenhout,; Backer,; Deben,; Dewilde,; Smits,; Bogaerts,
	Title	Influence of Cell Type and Culture Medium on Determining Cancer Selectivity of Cold Atmospheric Plasma Treatment			Type	A1 Journal article
	Year	2019	Publication	Cancers	Abbreviated Journal	Cancers
	Volume	11	Issue	9	Pages	1287
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract	Increasing the selectivity of cancer treatments is attractive, as it has the potential to reduce side-effects of therapy. Cold atmospheric plasma (CAP) is a novel cancer treatment that disrupts the intracellular oxidative balance. Several reports claim CAP treatment to be selective, but retrospective analysis of these studies revealed discrepancies in several biological factors and culturing methods. Before CAP can be conclusively stated as a selective cancer treatment, the importance of these factors must be investigated. In this study, we evaluated the influence of the cell type, cancer type, and cell culture medium on direct and indirect CAP treatment. Comparison of cancerous cells with their non-cancerous counterparts was performed under standardized conditions to determine selectivity of treatment. Analysis of seven human cell lines (cancerous: A549, U87, A375, and Malme-3M; non-cancerous: BEAS-2B, HA, and HEMa) and five different cell culture media (DMEM, RPMI1640, AM, BEGM, and DCBM) revealed that the tested parameters strongly influence indirect CAP treatment, while direct treatment was less affected. Taken together, the results of our study demonstrate that cell type, cancer type, and culturing medium must be taken into account before selectivity of CAP treatment can be claimed and overlooking these parameters can easily result in inaccurate conclusions of selectivity.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000489719000072	Publication Date	2019-09-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2072-6694	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited	9	Open Access
	Notes	the Research Foundation Flanders, 12S9218N – ; Universiteit Antwerpen, – ;			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:162097			Serial	5360
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