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	Author	Neyts, E.C.; van Duin, A.C.T.; Bogaerts, A.
	Title	Formation of single layer graphene on nickel under far-from-equilibrium high flux conditions			Type	A1 Journal article
	Year	2013	Publication	Nanoscale	Abbreviated Journal	Nanoscale
	Volume	5	Issue	16	Pages	7250-7255
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We investigate the theoretical possibility of single layer graphene formation on a nickel surface at different substrate temperatures under far-from-equilibrium high precursor flux conditions, employing state-of-the-art hybrid reactive molecular dynamics/uniform acceptance force bias Monte Carlo simulations. It is predicted that under these conditions, the formation of a single layer graphene-like film may proceed through a combined depositionsegregation mechanism on a nickel substrate, rather than by pure surface segregation as is typically observed for metals with high carbon solubility. At 900 K and above, nearly continuous graphene layers are obtained. These simulations suggest that single layer graphene deposition is theoretically possible on Ni under high flux conditions.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Cambridge	Editor
	Language		Wos	000322315600019	Publication Date	2013-04-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364;2040-3372;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	7.367	Times cited	25	Open Access
	Notes				Approved	Most recent IF: 7.367; 2013 IF: 6.739
	Call Number	UA @ lucian @ c:irua:109249			Serial	1264
Permanent link to this record



	Author	Khalilov, U.; Bogaerts, A.; Neyts, E.C.
	Title	Microscopic mechanisms of vertical graphene and carbon nanotube cap nucleation from hydrocarbon growth precursors			Type	A1 Journal article
	Year	2014	Publication	Nanoscale	Abbreviated Journal	Nanoscale
	Volume	6	Issue	15	Pages	9206-9214
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Controlling and steering the growth of single walled carbon nanotubes is often believed to require controlling of the nucleation stage. Yet, little is known about the microscopic mechanisms governing the nucleation from hydrocarbon molecules. Specifically, we address here the dehydrogenation of hydrocarbon molecules and the formation of all-carbon graphitic islands on metallic nanoclusters from hydrocarbon molecules under conditions typical for carbon nanotube growth. Employing reactive molecular dynamics simulations, we demonstrate for the first time that the formation of a graphitic network occurs through the intermediate formation of vertically oriented, not fully dehydrogenated graphitic islands. Upon dehydrogenation of these vertical graphenes, the islands curve over the surface, thereby forming a carbon network covering the nanoparticle. The results indicate that controlling the extent of dehydrogenation offers an additional parameter to control the nucleation of carbon nanotubes.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Cambridge	Editor
	Language		Wos	000339861500103	Publication Date	2014-05-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364;2040-3372;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	7.367	Times cited	21	Open Access
	Notes				Approved	Most recent IF: 7.367; 2014 IF: 7.394
	Call Number	UA @ lucian @ c:irua:117950			Serial	2027
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	Author	Khalilov, U.; Pourtois, G.; Bogaerts, A.; van Duin, A.C.T.; Neyts, E.C.
	Title	Reactive molecular dynamics simulations on SiO₂-coated ultra-small Si-nanowires			Type	A1 Journal article
	Year	2013	Publication	Nanoscale	Abbreviated Journal	Nanoscale
	Volume	5	Issue	2	Pages	719-725
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The application of coreshell SiSiO2 nanowires as nanoelectronic devices strongly depends on their structure, which is difficult to tune precisely. In this work, we investigate the formation of the coreshell nanowires at the atomic scale, by reactive molecular dynamics simulations. The occurrence of two temperature-dependent oxidation mechanisms of ultra-small diameter Si-NWs is demonstrated. We found that control over the Si-core radius and the SiOx (x ≤ 2) oxide shell is possible by tuning the growth temperature and the initial Si-NW diameter. Two different structures were obtained, i.e., ultrathin SiO2 silica nanowires at high temperature and Si core\|ultrathin SiO2 silica nanowires at low temperature. The transition temperature is found to linearly decrease with the nanowire curvature. Finally, the interfacial stress is found to be responsible for self-limiting oxidation, depending on both the initial Si-NW radius and the oxide growth temperature. These novel insights allow us to gain control over the exact morphology and structure of the wires, as is needed for their application in nanoelectronics.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Cambridge	Editor
	Language		Wos	000313426200036	Publication Date	2012-11-16
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364;2040-3372;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	7.367	Times cited	17	Open Access
	Notes				Approved	Most recent IF: 7.367; 2013 IF: 6.739
	Call Number	UA @ lucian @ c:irua:102584			Serial	2824
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	Author	Engelmann, Y.; Bogaerts, A.; Neyts, E.C.
	Title	Thermodynamics at the nanoscale : phase diagrams of nickel-carbon nanoclusters and equilibrium constants for face transitions			Type	A1 Journal article
	Year	2014	Publication	Nanoscale	Abbreviated Journal	Nanoscale
	Volume	6	Issue		Pages	11981-11987
	Keywords	A1 Journal article; PLASMANT
	Abstract	Using reactive molecular dynamics simulations, the melting behavior of nickelcarbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickelcarbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Cambridge	Editor
	Language		Wos	000343000800049	Publication Date	2014-07-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364;2040-3372;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	7.367	Times cited	20	Open Access
	Notes				Approved	Most recent IF: 7.367; 2014 IF: 7.394
	Call Number	UA @ lucian @ c:irua:119408			Serial	3636
Permanent link to this record



	Author	Engelmann; Bogaerts, A.; Neyts, E.C.
	Title	Thermodynamics at the nanoscale: phase diagrams of nickel-carbon nanoclusters and equilibrium constants for phase transitions			Type	A1 Journal article
	Year	2014	Publication	Nanoscale	Abbreviated Journal	Nanoscale
	Volume	6	Issue	20	Pages	11981-11987
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Using reactive molecular dynamics simulations, the melting behavior of nickel-carbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickel-carbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Cambridge	Editor
	Language		Wos	000343000800049	Publication Date	2014-07-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364;2040-3372;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	7.367	Times cited	20	Open Access
	Notes				Approved	Most recent IF: 7.367; 2014 IF: 7.394
	Call Number	UA @ lucian @ c:irua:121106			Serial	3637
Permanent link to this record



	Author	Khalilov, U.; Bogaerts, A.; Xu, B.; Kato, T.; Kaneko, T.; Neyts, E.C.
	Title	How the alignment of adsorbed ortho H pairs determines the onset of selective carbon nanotube etching			Type	A1 Journal article
	Year	2017	Publication	Nanoscale	Abbreviated Journal	Nanoscale
	Volume	9	Issue	9	Pages	1653-1661
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Unlocking the enormous technological potential of carbon nanotubes strongly depends on our ability to specifically produce metallic or semiconducting tubes. While selective etching of both has already been demonstrated, the underlying reasons, however, remain elusive as yet. We here present computational and experimental evidence on the operative mechanisms at the atomic scale. We demonstrate that during the adsorption of H atoms and their coalescence, the adsorbed ortho hydrogen pairs on single-walled carbon nanotubes induce higher shear stresses than axial stresses, leading to the elongation of HC–CH bonds as a function of their alignment with the tube chirality vector, which we denote as the γ-angle. As a result, the C–C cleavage occurs more rapidly in nanotubes containing ortho H-pairs with a small γ-angle. This phenomenon can explain the selective etching of small-diameter semiconductor nanotubes with a similar curvature. Both theoretical and experimental results strongly indicate the important role of the γ-angle in the selective etching mechanisms of carbon nanotubes, in addition to the nanotube curvature and metallicity effects and lead us to clearly understand the onset of selective synthesis/removal of CNT-based materials.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000395422800036	Publication Date	2016-12-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	7.367	Times cited	6	Open Access	OpenAccess
	Notes	U. K. gratefully acknowledges financial support from the Fund of Scientific Research Flanders (FWO), Belgium (Grant No. 12M1315N). This work was also supported in part by Grant-in- Aid for Young Scientists A (Grant No. 25706028), Grant-in-Aid for Scientific Research on Innovative Areas (Grant No. 26107502) from JSPS KAKENHI. This work was carried out in part 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. The authors also thank Prof. A. C. T. van Duin for sharing the ReaxFF code and J. Razzokov for his assistance to perform the DFT calculations.			Approved	Most recent IF: 7.367
	Call Number	PLASMANT @ plasmant @ c:irua:140091			Serial	4417
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	Author	Faraji, F.; Neek-Amal, M.; Neyts, E.C.; Peeters, F.M.
	Title	Indentation of graphene nano-bubbles			Type	A1 Journal article
	Year	2022	Publication	Nanoscale	Abbreviated Journal	Nanoscale
	Volume	14	Issue	15	Pages	5876-5883
	Keywords	A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Molecular dynamics simulations are used to investigate the effect of an AFM tip when indenting graphene nano bubbles filled by a noble gas (i.e. He, Ne and Ar) up to the breaking point. The failure points resemble those of viral shells as described by the Foppl-von Karman (FvK) dimensionless number defined in the context of elasticity theory of thin shells. At room temperature, He gas inside the bubbles is found to be in the liquid state while Ne and Ar atoms are in the solid state although the pressure inside the nano bubble is below the melting pressure of the bulk. The trapped gases are under higher hydrostatic pressure at low temperatures than at room temperature.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000776763000001	Publication Date	2022-03-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364; 2040-3372	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.7	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 6.7
	Call Number	UA @ admin @ c:irua:187924			Serial	7171
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	Author	Khalilov, U.; Vets, C.; Neyts, E.C.
	Title	Molecular evidence for feedstock-dependent nucleation mechanisms of CNTs			Type	A1 Journal article
	Year	2019	Publication	Nanoscale Horizons	Abbreviated Journal	Nanoscale Horiz.
	Volume	4	Issue	3	Pages	674-682
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Atomic scale simulations have been shown to be a powerful tool for elucidating the growth mechanisms of carbon nanotubes. The growth picture is however not entirely clear yet due to the gap between current simulations and real experiments. We here simulate for the first time the nucleation and subsequent growth of single-wall carbon nanotubes (SWNTs) from oxygen-containing hydrocarbon feedstocks using the hybrid Molecular Dynamics/Monte Carlo technique. The underlying nucleation mechanisms of Ni-catalysed SWNT growth are discussed in detail. Specifically, we find that as a function of the feedstock, different carbon fractions may emerge as the main growth species, due to a competition between the feedstock decomposition, its rehydroxylation and its contribution to etching of the growing SWNT. This study provides a further understanding of the feedstock effects in SWNT growth in comparison with available experimental evidence as well as with<italic>ab initio</italic>and other simulation data, thereby reducing the simulation–experiment gap.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000471816500011	Publication Date	2019-01-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2055-6756	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited	1	Open Access	Not_Open_Access: Available from 03.01.2020
	Notes	Fonds Wetenschappelijk Onderzoek, 12M1318N 1S22516N ; The authors gratefully acknowledge financial support from the Research Foundation Flanders (FWO), Belgium (Grant numbers 12M1318N and 1S22516N). The work was carried out in part using the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by FWO and the Flemish Government (Department EWI). We thank Prof. A. C. T. van Duin for sharing the reax-code and forcefield parameters.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:159658			Serial	5169
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	Author	Oleshko, V.P.; van Daele, A.; Gijbels, R.H.; Jacob, W.A.
	Title	Structural and analytical characterization of Ag(Br,I) nanocrystals by cryo-AEM techniques			Type	A1 Journal article
	Year	1998	Publication	Journal of nanostructured materials	Abbreviated Journal	Nanostruct Mater
	Volume	10	Issue	8	Pages	1225-1246
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000079226900001	Publication Date	2002-07-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0965-9773;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited	5	Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:24909			Serial	3190
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	Author	Heyne, M.H.; de Marneffe, J.-F.; Delabie, A.; Caymax, M.; Neyts, E.C.; Radu, I.; Huyghebaert, C.; De Gendt, S.
	Title	Two-dimensional WS2 nanoribbon deposition by conversion of pre-patterned amorphous silicon			Type	A1 Journal article
	Year	2017	Publication	Nanotechnology	Abbreviated Journal	Nanotechnology
	Volume	28	Issue	28	Pages	04LT01
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We present a method for area selective deposition of 2D WS2 nanoribbons with tunable thickness on a dielectric substrate. The process is based on a complete conversion of a prepatterned, H-terminated Si layer to metallic W by WF6, followed by in situ sulfidation by H2S. The reaction process, performed at 450 degrees C, yields nanoribbons with lateral dimension down to 20 nm and with random basal plane orientation. The thickness of the nanoribbons is accurately controlled by the thickness of the pre-deposited Si layer. Upon rapid thermal annealing at 900 degrees C under inert gas, the WS2 basal planes align parallel to the substrate.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000391445100001	Publication Date	2016-12-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0957-4484	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.44	Times cited	13	Open Access	OpenAccess
	Notes				Approved	Most recent IF: 3.44
	Call Number	UA @ lucian @ c:irua:140382			Serial	4471
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	Author	Khalilov, U.; Bogaerts, A.; Neyts, E.C.
	Title	Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors			Type	A1 Journal article
	Year	2015	Publication	Nature communications	Abbreviated Journal	Nat Commun
	Volume	6	Issue	6	Pages	10306
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level.
	Address	PLASMANT research group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Wos	000367584500001	Publication Date	2015-12-22
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2041-1723	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	12.124	Times cited	37	Open Access
	Notes	The authors gratefully acknowledge financial support from the Fund of Scientific Research Flanders (FWO), Belgium, grant number 12M1315N. The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. We thank Professor Adri C. T. van Duin for sharing the ReaxFF code.			Approved	Most recent IF: 12.124; 2015 IF: 11.470
	Call Number	c:irua:129975			Serial	3990
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	Author	Cambré, S.; Campo, J.; Beirnaert, C.; Verlackt, C.; Cool, P.; Wenseleers, W.
	Title	Asymmetric dyes align inside carbon nanotubes to yield a large nonlinear optical response			Type	A1 Journal article
	Year	2015	Publication	Nature nanotechnology	Abbreviated Journal	Nat Nanotechnol
	Volume	10	Issue	10	Pages	248-252
	Keywords	A1 Journal article; Engineering sciences. Technology; Nanostructured and organic optical and electronic materials (NANOrOPT); Laboratory of adsorption and catalysis (LADCA); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Asymmetric dye molecules have unusual optical and electronic properties1, 2, 3. For instance, they show a strong second-order nonlinear optical (NLO) response that has attracted great interest for potential applications in electro-optic modulators for optical telecommunications and in wavelength conversion of lasers2, 3. However, the strong Coulombic interaction between the large dipole moments of these molecules favours a pairwise antiparallel alignment that cancels out the NLO response when incorporated into bulk materials. Here, we show that by including an elongated dipolar dye (p,p′-dimethylaminonitrostilbene, DANS, a prototypical asymmetric dye with a strong NLO response4) inside single-walled carbon nanotubes (SWCNTs)5, 6, an ideal head-to-tail alignment in which all electric dipoles point in the same sense is naturally created. We have applied this concept to synthesize solution-processible DANS-filled SWCNTs that show an extremely large total dipole moment and static hyperpolarizability (β0 = 9,800 × 10−30 e.s.u.), resulting from the coherent alignment of arrays of ∼70 DANS molecules.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000350799700016	Publication Date	2015-02-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1748-3387;1748-3395;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	38.986	Times cited	46	Open Access
	Notes				Approved	Most recent IF: 38.986; 2015 IF: 34.048
	Call Number	c:irua:125405			Serial	158
Permanent link to this record



	Author	Yusupov, M.; Neyts, E.C.; Khalilov, U.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A.
	Title	Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls			Type	A1 Journal article
	Year	2012	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	14	Issue	9	Pages	093043
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. CO, CN and CC bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000309393400001	Publication Date	2012-09-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	47	Open Access
	Notes				Approved	Most recent IF: 3.786; 2012 IF: 4.063
	Call Number	UA @ lucian @ c:irua:101014			Serial	189
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	Author	Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A.
	Title	Behavior of electrons in a dual-magnetron sputter deposition system : a Monte Carlo model			Type	A1 Journal article
	Year	2011	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	13	Issue		Pages	033018-033018,17
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	A Monte Carlo model has been developed for investigating the electron behavior in a dual-magnetron sputter deposition system. To describe the three-dimensional (3D) geometry, different reference frames, i.e. a local and a global coordinate system, were used. In this study, the influence of both closed and mirror magnetic field configurations on the plasma properties is investigated. In the case of a closed magnetic field configuration, the calculated electron trajectories show that if an electron is emitted in (or near) the center of the cathode, where the influence of the magnetic field is low, it is able to travel from one magnetron to the other. On the other hand, when an electron is created at the race track area, it is more or less trapped in the strong magnetic field and cannot easily escape to the second magnetron region. In the case of a mirror magnetic field configuration, irrespective of where the electron is emitted from the cathode, it cannot travel from one magnetron to the other because the magnetic field lines guide the electron to the substrate. Moreover, the electron density and electron impact ionization rate have been calculated and studied in detail for both configurations.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000289064600001	Publication Date	2011-03-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	12	Open Access
	Notes				Approved	Most recent IF: 3.786; 2011 IF: 4.177
	Call Number	UA @ lucian @ c:irua:87544			Serial	224
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	Author	de Bleecker, K.; Bogaerts, A.; Goedheer, W.
	Title	Modelling of nanoparticle coagulation and transport dynamics in dusty silane discharges			Type	A1 Journal article
	Year	2006	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	8	Issue		Pages	178,1-22
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000240503300002	Publication Date	2006-09-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	20	Open Access
	Notes				Approved	Most recent IF: 3.786; 2006 IF: 3.754
	Call Number	UA @ lucian @ c:irua:60269			Serial	2153
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	Author	Van Gaens, W.; Iseni, S.; Schmidt-Bleker, A.; Weltmann, K.-D.; Reuter, S.; Bogaerts, A.
	Title	Numerical analysis of the effect of nitrogen and oxygen admixtures on the chemistry of an argon plasma jet operating at atmospheric pressure			Type	A1 Journal article
	Year	2015	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	17	Issue	17	Pages	033003
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this paper we study the cold atmospheric pressure plasma jet, called kinpen, operating in Ar with different admixture fractions up to 1% pure , and + . Moreover, the device is operating with a gas curtain of dry air. The absolute net production rates of the biologically active ozone () and nitrogen dioxide () species are measured in the far effluent by quantum cascade laser absorption spectroscopy in the mid-infrared. Additionally, a zero-dimensional semi-empirical reaction kinetics model is used to calculate the net production rates of these reactive molecules, which are compared to the experimental data. The latter model is applied throughout the entire plasma jet, starting already within the device itself. Very good qualitative and even quantitative agreement between the calculated and measured data is demonstrated. The numerical model thus yields very useful information about the chemical pathways of both the and the generation. It is shown that the production of these species can be manipulated by up to one order of magnitude by varying the amount of admixture or the admixture type, since this affects the electron kinetics significantly at these low concentration levels.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000352898500003	Publication Date	2015-03-03
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	29	Open Access
	Notes				Approved	Most recent IF: 3.786; 2015 IF: 3.558
	Call Number	c:irua:124228			Serial	2391
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	Author	Van Gaens, W.; Bruggeman, P.J.; Bogaerts, A.
	Title	Numerical analysis of the NO and O generation mechanism in a needle-type plasma jet			Type	A1 Journal article
	Year	2014	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	16	Issue		Pages	063054
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this paper we study two cold atmospheric pressure plasma jets, operating in Ar + 2% air, with a different electrode geometry but with the same power dissipated in the plasma. The density profiles of the biomedically active NO and O species throughout the plasma jet, previously obtained by laser diagnostics, are calculated by means of a zero-dimensional semi-empirical reaction kinetics model. A good agreement between the calculated and measured data is demonstrated. Furthermore, the most probable spatial power distribution in an RF driven plasma jet is obtained for the first time by comparing measured and calculated species density profiles. This was possible due to the strong effect of the power distribution on the NO and O density profiles. In addition the dominant reaction pathways for both the NO and the O species are identified. The model allows us to obtain key information on the reactive species production inside the jet, which is difficult to access by laser diagnostics in a coaxial geometry. Finally, we demonstrate that water impurities in the order of 100 ppm in the gas feed can have a significant effect on the spatial distribution of the NO and O density.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000339081400006	Publication Date	2014-06-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	34	Open Access
	Notes				Approved	Most recent IF: 3.786; 2014 IF: 3.558
	Call Number	UA @ lucian @ c:irua:117946			Serial	2392
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	Author	Jiang, W.; Zhang, Y.; Bogaerts, A.
	Title	Numerical characterization of local electrical breakdown in sub-micrometer metallized film capacitors			Type	A1 Journal article
	Year	2014	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	16	Issue		Pages	113036
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In metallized film capacitors, there exists an air gap of about 0.2 μm between the films, with a pressure ranging generally from 130 atm. Because of the created potential difference between the two films, a microdischarge is formed in this gap. In this paper, we use an implicit particle-in-cell Monte Carlo collision simulation method to study the discharge properties in this direct-current microdischarge with 0.2 μm gap in a range of different voltages and pressures. The discharge process is significantly different from a conventional high pressure discharge. Indeed, the high electric field due to the small gap sustains the discharge by field emission. At low applied voltage (~15 V), only the electrons are generated by field emission, while both electrons and ions are generated as a stable glow discharge at medium applied voltage (~50 V). At still higher applied voltage (~100 V), the number of electrons and ions rapidly multiplies, the electric field reverses, and the discharge changes from a glow to an arc regime.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000346763400006	Publication Date	2014-11-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited		Open Access
	Notes				Approved	Most recent IF: 3.786; 2014 IF: 3.558
	Call Number	UA @ lucian @ c:irua:120455			Serial	2393
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	Author	Bultinck, E.; Bogaerts, A.
	Title	Particle-in-cell/Monte Carlo collisions treatment of an Ar/O₂ magnetron discharge used for the reactive sputter deposition of TiO_x films			Type	A1 Journal article
	Year	2009	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	11	Issue		Pages	103010-103010,24
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The physical processes in an Ar/O2 magnetron discharge used for the reactive sputter deposition of TiOx thin films were simulated with a 2d3v particle-in-cell/Monte Carlo collisions (PIC/MCC) model. The plasma species taken into account are electrons, Ar+ ions, fast Arf atoms, metastable Arm* atoms, Ti+ ions, Ti atoms, O+ ions, O2+ ions, O− ions and O atoms. This model accounts for plasmatarget interactions, such as secondary electron emission and target sputtering, and the effects of target poisoning. Furthermore, the deposition process is described by an analytical surface model. The influence of the O2/Ar gas ratio on the plasma potential and on the species densities and fluxes is investigated. Among others, it is shown that a higher O2 pressure causes the region of positive plasma potential and the O− density to be more spread, and the latter to decrease. On the other hand, the deposition rates of Ti and O are not much affected by the O2/Ar proportion. Indeed, the predicted stoichiometry of the deposited TiOx film approaches x=2 for nearly all the investigated O2/Ar proportions.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000270820900001	Publication Date	2009-10-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	24	Open Access
	Notes				Approved	Most recent IF: 3.786; 2009 IF: 3.312
	Call Number	UA @ lucian @ c:irua:78326			Serial	2559
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	Author	Bultinck, E.; Mahieu, S.; Depla, D.; Bogaerts, A.
	Title	Reactive sputter deposition of TiN_x films, simulated with a particle-in-cell/Monte Carlo collisions model			Type	A1 Journal article
	Year	2009	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	11	Issue		Pages	023039,1-023039,24
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The physical processes in an Ar/N2 magnetron discharge used for the reactive sputter deposition of TiNx thin films were simulated with a 2d3v particle-in-cell/Monte Carlo collisions (PIC/MCC) model. Cathode currents and voltages were calculated self-consistently and compared with experiments. Also, ion fractions were calculated and validated with mass spectrometric measurements. With this PIC/MCC model, the influence of N2/Ar gas ratio on the particle densities and fluxes was investigated, taking into account the effect of the poisoned state of the target.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000263744100001	Publication Date	2009-02-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	23	Open Access
	Notes				Approved	Most recent IF: 3.786; 2009 IF: 3.312
	Call Number	UA @ lucian @ c:irua:73150			Serial	2825
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	Author	Verlackt, C.C.W.; Neyts, E.C.; Jacob, T.; Fantauzzi, D.; Golkaram, M.; Shin, Y.-K.; van Duin, A.C.T.; Bogaerts, A.
	Title	Atomic-scale insight into the interactions between hydroxyl radicals and DNA in solution using the ReaxFF reactive force field			Type	A1 Journal article
	Year	2015	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	17	Issue	17	Pages	103005
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Cold atmospheric pressure plasmas have proven to provide an alternative treatment of cancer by targeting tumorous cells while leaving their healthy counterparts unharmed. However, the underlying mechanisms of the plasma–cell interactions are not yet fully understood. Reactive oxygen species, and in particular hydroxyl radicals (OH), are known to play a crucial role in plasma driven apoptosis of malignant cells. In this paper we investigate the interaction of OH radicals, as well as H2O2 molecules and HO2 radicals, with DNA by means of reactive molecular dynamics simulations using the ReaxFF force field. Our results provide atomic-scale insight into the dynamics of oxidative stress on DNA caused by the OH radicals, while H2O2 molecules appear not reactive within the considered timescale. Among the observed processes are the formation of 8-OH-adduct radicals, forming the first stages towards the formation of 8-oxoGua and 8-oxoAde, H-abstraction reactions of the amines, and the partial opening of loose DNA ends in aqueous solution.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000367328100001	Publication Date	2015-10-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	18	Open Access
	Notes	CCWV,ECN and AB acknowledge the contribution of J Van Beeck who is investigating the interaction between H2O2 andDNAusingrMDsimulations. Furthermore, they acknowledge financial support from the Fund for Scientific Research—Flanders (project number G012413N). The calculations were performed using the Turing HPCinfrastructure 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. TJ and DF gratefully acknowledge support from the European Research Council through the ERC-Starting GrantTHEOFUN(Grant Agreement No. 259608).			Approved	Most recent IF: 3.786; 2015 IF: 3.558
	Call Number	c:irua:129178			Serial	3955
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	Author	Yusupov, M.; Saraiva, M.; Depla, D.; Bogaerts, A.
	Title	Sputter deposition of Mg_xAl_yO_z thin films in a dual-magnetron device : a multi-species Monte Carlo model			Type	A1 Journal article
	Year	2012	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	14	Issue	7	Pages	073043
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	A multi-species Monte Carlo (MC) model, combined with an analytical surface model, has been developed in order to investigate the general plasma processes occurring during the sputter deposition of complex oxide films in a dual-magnetron sputter deposition system. The important plasma species, such as electrons, Ar+ ions, fast Ar atoms and sputtered metal atoms (i.e. Mg and Al atoms) are described with the so-called multi-species MC model, whereas the deposition of MgxAlyOz films is treated by an analytical surface model. Targetsubstrate distances for both magnetrons in the dual-magnetron setup are varied for the purpose of growing stoichiometric complex oxide thin films. The metal atoms are sputtered from pure metallic targets, whereas the oxygen flux is only directed toward the substrate and is high enough to obtain fully oxidized thin films but low enough to avoid target poisoning. The calculations correspond to typical experimental conditions applied to grow these complex oxide films. In this paper, some calculation results are shown, such as the densities of various plasma species, their fluxes toward the targets and substrate, the deposition rates, as well as the film stoichiometry. Moreover, some results of the combined model are compared with experimental observations. Note that this is the first complete model, which can be applied for large and complicated magnetron reactor geometries, such as dual-magnetron configurations. With this model, we are able to describe all important plasma species as well as the deposition process. It can also be used to predict film stoichiometries of complex oxide films on the substrate.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000307072500003	Publication Date	2012-07-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	2	Open Access
	Notes				Approved	Most recent IF: 3.786; 2012 IF: 4.063
	Call Number	UA @ lucian @ c:irua:100100			Serial	3111
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	Author	Zhang, Y.; Wang, H.-yu; Jiang, W.; Bogaerts, A.
	Title	Two-dimensional particle-in cell/Monte Carlo simulations of a packed-bed dielectric barrier discharge in air at atmospheric pressure			Type	A1 Journal article
	Year	2015	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	17	Issue	17	Pages	083056
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The plasma behavior in a parallel-plate dielectric barrier discharge (DBD) is simulated by a two-dimensional particle-in-cell/Monte Carlo collision model, comparing for the first time an unpacked (empty) DBD with a packed bed DBD, i.e., a DBD filled with dielectric spheres in the gas gap. The calculations are performed in air, at atmospheric pressure. The discharge is powered by a pulse with a voltage amplitude of −20 kV. When comparing the packed and unpacked DBD reactors with the same dielectric barriers, it is clear that the presence of the dielectric packing leads to a transition in discharge behavior from a combination of negative streamers and unlimited surface streamers on the bottom dielectric surface to a combination of predominant positive streamers and limited surface discharges on the dielectric surfaces of the beads and plates. Furthermore, in the packed bed DBD, the electric field is locally enhanced inside the dielectric material, near the contact points between the beads and the plates, and therefore also in the plasma between the packing beads and between a bead and the dielectric wall, leading to values of $4\times {10}
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000360957800003	Publication Date	2015-08-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	22	Open Access
	Notes				Approved	Most recent IF: 3.786; 2015 IF: 3.558
	Call Number	c:irua:127650			Serial	3777
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	Author	Marinov, D.; de Marneffe, J.-F.; Smets, Q.; Arutchelvan, G.; Bal, K.M.; Voronina, E.; Rakhimova, T.; Mankelevich, Y.; El Kazzi, S.; Nalin Mehta, A.; Wyndaele, P.-J.; Heyne, M.H.; Zhang, J.; With, P.C.; Banerjee, S.; Neyts, E.C.; Asselberghs, I.; Lin, D.; De Gendt, S.
	Title	Reactive plasma cleaning and restoration of transition metal dichalcogenide monolayers			Type	A1 Journal article
	Year	2021	Publication	npj 2D Materials and Applications	Abbreviated Journal	npj 2D Mater Appl
	Volume	5	Issue	1	Pages	17
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The cleaning of two-dimensional (2D) materials is an essential step in the fabrication of future devices, leveraging their unique physical, optical, and chemical properties. Part of these emerging 2D materials are transition metal dichalcogenides (TMDs). So far there is limited understanding of the cleaning of “monolayer” TMD materials. In this study, we report on the use of downstream H<sub>2</sub>plasma to clean the surface of monolayer WS<sub>2</sub>grown by MOCVD. We demonstrate that high-temperature processing is essential, allowing to maximize the removal rate of polymers and to mitigate damage caused to the WS<sub>2</sub>in the form of sulfur vacancies. We show that low temperature in situ carbonyl sulfide (OCS) soak is an efficient way to resulfurize the material, besides high-temperature H<sub>2</sub>S annealing. The cleaning processes and mechanisms elucidated in this work are tested on back-gated field-effect transistors, confirming that transport properties of WS<sub>2</sub>devices can be maintained by the combination of H<sub>2</sub>plasma cleaning and OCS restoration. The low-damage plasma cleaning based on H<sub>2</sub>and OCS is very reproducible, fast (completed in a few minutes) and uses a 300 mm industrial plasma etch system qualified for standard semiconductor pilot production. This process is, therefore, expected to enable the industrial scale-up of 2D-based devices, co-integrated with silicon technology.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000613258900001	Publication Date	2021-01-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2397-7132	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	Daniil Marinov has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 752164. Ekaterina Voronina, Yuri Mankelevitch, and Tatyana Rakhimova are thankful to the Russian Science Foundation (RSF) for financial support (Grant No. 16-12-10361). This study was carried out using the equipment of the shared research facilities of high-performance computing resources at Lomonosov Moscow State University and the computational resources and services of the HPC core facility CalcUA of the University of Antwerp, and VSC (Flemish Supercomputer Center), funded by the Research Foundation-Flanders (FWO) and the Flemish Government. Patrick With gratefully acknowledges imec’s CTO office for financial support during his stay at imec. The authors thank Mr. Surajit Sutar (imec) for his help during sample electrical characterization, and Patrick Verdonck for lab processing. Jean-François de Marneffe thank Prof. Simone Napolitano from the Free University of Brussels for useful discussions on irreversibly adsorbed polymer layers, and Cédric Huyghebaert (imec) for his continuous support in the framework of the Graphene FET Flagship core project. All authors acknowledge the support of imec’s pilot line and materials characterization and analysis (MCA) group, namely Jonathan Ludwig, Stefanie Sergeant, Thomas Nuytten, Olivier Richard, and Thierry Conard. Finally, Daniil Marinov thank Mikhail Krishtab (imec/KU Leuven) for his help in selecting the optimal plasma etch system for this work. Part of this project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 649953.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:175871			Serial	6671
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	Author	van der Linden, V.; Bultinck, E.; de Ruytter, J.; Schalm, O.; Janssens, K.; Devos, W.; Tiri, W.
	Title	Compositional analysis of 17-18th century archaeological glass fragments, excavated in Mechelen, Belgium: comparison with data from neighboring cities in the Low Countries			Type	A1 Journal article
	Year	2005	Publication	Nuclear instruments and methods in physics research: B: beam interactions with materials and atoms	Abbreviated Journal	Nucl Instrum Meth B
	Volume	239	Issue	1/2	Pages	100-106
	Keywords	A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000233514700013	Publication Date	2005-08-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0168-583X;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.109	Times cited	15	Open Access
	Notes				Approved	Most recent IF: 1.109; 2005 IF: 1.181
	Call Number	UA @ lucian @ c:irua:56068			Serial	444
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	Author	Chen, Z.Y.; Bogaerts, A.; Depla, D.; Ignatova, V.
	Title	Dynamic Monte Carlo simulation for reactive sputtering of aluminium			Type	A1 Journal article
	Year	2003	Publication	Nuclear instruments and methods in physics research: B	Abbreviated Journal	Nucl Instrum Meth B
	Volume	207	Issue		Pages	415-423
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000184051300006	Publication Date	2003-03-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0168-583X;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.109	Times cited	20	Open Access
	Notes				Approved	Most recent IF: 1.109; 2003 IF: 1.041
	Call Number	UA @ lucian @ c:irua:44016			Serial	762
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	Author	Neyts, E.; Bogaerts, A.; Gijbels, R.; Benedikt, J.; van de Sanden, M.C.M.
	Title	Molecular dynamics simulation of the impact behaviour of various hydrocarbon species on DLC			Type	A1 Journal article
	Year	2005	Publication	Nuclear instruments and methods in physics research: B: beam interactions with materials and atoms	Abbreviated Journal	Nucl Instrum Meth B
	Volume	228	Issue		Pages	315-318
	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	000226669800052	Publication Date	2004-12-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0168-583X;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.109	Times cited	19	Open Access
	Notes				Approved	Most recent IF: 1.109; 2005 IF: 1.181
	Call Number	UA @ lucian @ c:irua:49873			Serial	2172
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	Author	van Ham, R.; Adriaens, A.; van Vaeck, L.; Gijbels, R.; Adams, F.
	Title	Molecular information in static SIMS for the speciation of inorganic compounds			Type	A1 Journal article
	Year	2000	Publication	Nuclear instruments and methods in physics research: B: beam interactions with materials and atoms	Abbreviated Journal	Nucl Instrum Meth B
	Volume	161/163	Issue		Pages	245-249
	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	000086204100043	Publication Date	2003-04-05
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0168-583X;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.109	Times cited	19	Open Access
	Notes				Approved	Most recent IF: 1.109; 2000 IF: 0.955
	Call Number	UA @ lucian @ c:irua:27853			Serial	2178
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	Author	Neyts, E.; Yan, M.; Bogaerts, A.; Gijbels, R.
	Title	PIC-MC simulation of an RF capacitively coupled Ar/H₂ discharge			Type	A1 Journal article
	Year	2003	Publication	Nuclear instruments and methods in physics research: B	Abbreviated Journal	Nucl Instrum Meth B
	Volume	202	Issue		Pages	300-304
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000182122500048	Publication Date	2003-03-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0168-583X;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.109	Times cited	8	Open Access
	Notes				Approved	Most recent IF: 1.109; 2003 IF: 1.041
	Call Number	UA @ lucian @ c:irua:44015			Serial	2620
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	Author	Vanmeert, M.; Razzokov, J.; Mirza, M.U.; Weeks, S.D.; Schepers, G.; Bogaerts, A.; Rozenski, J.; Froeyen, M.; Herdewijn, P.; Pinheiro, V.B.; Lescrinier, E.
	Title	Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins			Type	A1 Journal article
	Year	2019	Publication	Nucleic acids research	Abbreviated Journal	Nucleic Acids Res
	Volume	47	Issue	13	Pages	7130-7142
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000490556600047	Publication Date	2019-07-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0305-1048	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	10.162	Times cited	1	Open Access
	Notes	European Research Council, FP7/2007-2013 ERC-2012-ADG 20120216/320683 ; KU Leuven, OT/14/128 ; Biotechnology and Biosciences Research Council, BB/N01023X/1 BB/N010221/1 ; Authors are grateful to Prof. Dr A.M.J.J. (Alexandre) Bonvin from the University of Utrecht and the WeNMR institute for his expert contribution. We have greatly benefited from discussions and help from numerous postdocs over the years (in particular, Dr E. Groaz, Dr E. Eremeeva, Dr J. Masschelein, Dr S. Xiaoping and Dr M. Renders) as well as graduate student D. Kestemont and undergraduate student M. Abdel Fattah Ismail. We express our gratitude to L. Margamuljana for helpful discussions and excellent technical assistance on in vitro experiments.			Approved	Most recent IF: 10.162
	Call Number	PLASMANT @ plasmant @c:irua:162105			Serial	5359
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