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	Author	Amini, M.N.; Altantzis, T.; Lobato, I.; Grzelczak, M.; Sánchez-Iglesias, A.; Van Aert, S.; Liz-Marzán, L.M.; Partoens, B.; Bals, S.; Neyts, E.C.
	Title	Understanding the Effect of Iodide Ions on the Morphology of Gold Nanorods			Type	A1 Journal article
	Year	2018	Publication	Particle and particle systems characterization	Abbreviated Journal	Part Part Syst Char
	Volume	35	Issue	35	Pages	1800051
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The presence of iodide ions during the growth of gold nanorods strongly affects the shape of the final products, which is proposed to be due to selective iodide adsorption on certain crystallographic facets. Therefore, a detailed structural and morphological characterization of the starting rods is crucial toward understanding this effect. Electron tomography is used to determine the crystallographic indices of the lateral facets of gold nanorods, as well as those present at the tips. Based on this information, density functional theory calculations are used to determine the surface and interface energies of the observed facets and provide insight into the relationship between the amount of iodide ions in the growth solution and the final morphology of anisotropic gold nanoparticles.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000441893400002	Publication Date	2018-06-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0934-0866	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.474	Times cited	6	Open Access	OpenAccess
	Notes	This work was supported by the European Research Council (grant 335078 COLOURATOM to S.B.). T.A., S.V.A. S.B. and E.C.N., acknowledge funding from the Research Foundation Flanders (FWO, Belgium), through project funding (G.0218.14N and G.0369.15N) and a postdoctoral grant to T.A. L.M.L.-M. and M.G. acknowledge funding from the Spanish Ministerio de Economía y Competitividad (grant MAT2013-46101-R). Mozhgan N. Amini and Thomas Altantzis contributed equally to this work. (ROMEO:yellow; preprint:; postprint:restricted ; pdfversion:cannot); ecas_sara			Approved	Most recent IF: 4.474
	Call Number	EMAT @ emat @c:irua:152998UA @ admin @ c:irua:152998			Serial	5010
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	Author	Razzokov, J.; Yusupov, M.; Vanuytsel, S.; Neyts, E.C.; Bogaerts, A.
	Title	Phosphatidylserine flip-flop induced by oxidation of the plasma membrane: a better insight by atomic scale modeling			Type	A1 Journal article
	Year	2017	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	14	Issue	10	Pages	1700013
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000413045800010	Publication Date	2017-04-05
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1612-8850	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.846	Times cited	9	Open Access	Not_Open_Access
	Notes	Fonds Wetenschappelijk Onderzoek, 1200216N ;			Approved	Most recent IF: 2.846
	Call Number	PLASMANT @ plasmant @c:irua:149567			Serial	4910
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	Author	Neyts, E.C.; Bal, K.M.
	Title	Effect of electric fields on plasma catalytic hydrocarbon oxidation from atomistic simulations			Type	A1 Journal article
	Year	2017	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	14	Issue	6	Pages	e1600158
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The catalytic oxidative dehydrogenation of hydrocarbons is an industrially important process, in which selectivity is a key issue. We here investigate the conversion of methanol to formaldehyde on a vanadia surface employing long timescale simulations, reaching a time scale of seconds. In particular, we compare the thermal process to the case where an additional external electric field is applied, as would be the case in a direct plasma-catalysis setup. We find that the electric field influences the retention time of the molecules at the catalyst surface. These simulations provide an atomic scale insight in the thermal catalytic oxidative dehydrogenation process, and in how an external electric field may affect this process.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Weinheim	Editor
	Language		Wos	000403699900013	Publication Date	2016-11-08
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1612-8850	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.846	Times cited	2	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 2.846
	Call Number	UA @ lucian @ c:irua:144210			Serial	4647
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	Author	Neyts, E.C.; Brault, P.
	Title	Molecular Dynamics Simulations for Plasma-Surface Interactions: Molecular Dynamics Simulations…			Type	A1 Journal article
	Year	2017	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	14	Issue	14	Pages	1600145
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma-surface interactions are in general highly complex due to the interplay of many concurrent processes. Molecular dynamics simulations provide insight in some of these processes, subject to the accessible time and length scales, and the availability of suitable force fields. In this introductory tutorial-style review, we aim to describe the current capabilities and limitations of molecular dynamics simulations in this field, restricting ourselves to low-temperature nonthermal plasmas. Attention is paid to the simulation of the various fundamental processes occurring, including sputtering, etching, implantation, and deposition, as well as to what extent the basic plasma components can be accounted for, including ground state and excited species, electric fields, ions, photons, and electrons. A number of examples is provided, giving an bird’s eye overview of the current state of the field.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000393184600009	Publication Date	2016-09-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1612-8850	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.846	Times cited	13	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 2.846
	Call Number	PLASMANT @ plasmant @ c:irua:141758			Serial	4488
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	Author	Van der Paal, J.; Aernouts, S.; van Duin, A.C.T.; Neyts, E.C.; Bogaerts, A.
	Title	Interaction of O and OH radicals with a simple model system for lipids in the skin barrier : a reactive molecular dynamics investigation for plasma medicine			Type	A1 Journal article
	Year	2013	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	46	Issue	39	Pages	395201
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma medicine has been claimed to provide a novel route to heal wounds and regenerate skin, although very little is currently known about the elementary processes taking place. We carried out a series of ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of O and OH radicals with lipids, more specifically with α-linolenic acid as a model for the free fatty acids present in the upper skin layer. Our calculations predict that the O and OH radicals most typically abstract a H atom from the fatty acids, which can lead to the formation of a conjugated double bond, but also to the incorporation of alcohol or aldehyde groups, thereby increasing the hydrophilic character of the fatty acids and changing the general lipid composition of the skin. Within the limitations of the investigated model, no formation of possibly toxic products was observed.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000324810400007	Publication Date	2013-09-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727;1361-6463;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	36	Open Access
	Notes				Approved	Most recent IF: 2.588; 2013 IF: 2.521
	Call Number	UA @ lucian @ c:irua:109904			Serial	1684
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	Author	Bal, K.M.; Neyts, E.C.
	Title	Quantifying the impact of vibrational nonequilibrium in plasma catalysis: insights from a molecular dynamics model of dissociative chemisorption			Type	A1 Journal Article;plasma catalysis
	Year	2021	Publication	Journal Of Physics D-Applied Physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	54	Issue	39	Pages	394004
	Keywords	A1 Journal Article;plasma catalysis; vibrational nonequilibrium; dissociative chemisorption; free energy barriers; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	The rate, selectivity and efficiency of plasma-based conversion processes is strongly affected by nonequilibrium phenomena. High concentrations of vibrationally excited molecules are such a plasma-induced effect. It is frequently assumed that vibrationally excited molecules are important in plasma catalysis because their presence lowers the apparent activation energy of dissociative chemisorption reactions and thus increases the conversion rate. A detailed atomic-level understanding of vibrationally stimulated catalytic reactions in the context of plasma catalysis is however lacking. Here, we couple a recently developed statistical model of a plasma-induced vibrational nonequilibrium to molecular dynamics simulations, enhanced sampling methods, and machine learning techniques. We quantify the impact of a vibrational nonequilibrium on the dissociative chemisorption barrier of H2 and CH4 on nickel catalysts over a wide range of vibrational temperatures. We investigate the effect of surface structure and compare the role of different vibrational modes of methane in the dissociation process. For low vibrational temperatures, very high vibrational efficacies are found, and energy in bend vibrations appears to dominate the dissociation of methane. The relative impact of vibrational nonequilibrium is much higher on terrace sites than on surface steps. We then show how our simulations can help to interpret recent experimental results, and suggest new paths to a better understanding of plasma catalysis.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000674464100001	Publication Date	2021-09-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited		Open Access	OpenAccess
	Notes	Fonds Wetenschappelijk Onderzoek, 12ZI420N ; K M B was funded as a junior postdoctoral fellow of the FWO (Research Foundation—Flanders), Grant 12ZI420N. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. HLDA calculations were performed with a script provided by G Piccini.			Approved	Most recent IF: 2.588
	Call Number	PLASMANT @ plasmant @c:irua:179830			Serial	6808
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	Author	Tinck, S.; Tillocher, T.; Dussart, R.; Neyts, E.C.; Bogaerts, A.
	Title	Elucidating the effects of gas flow rate on an SF₆inductively coupled plasma and on the silicon etch rate, by a combined experimental and theoretical investigation			Type	A1 Journal article
	Year	2016	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	49	Issue	49	Pages	385201
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Experiments show that the etch rate of Si with SF6 inductively coupled plasma (ICP) is significantly influenced by the absolute gas flow rate in the range of 50–600 sccm, with a maximum at around 200 sccm. Therefore, we numerically investigate the effects of the gas flow rate on the bulk plasma properties and on the etch rate, to obtain more insight in the underlying reasons of this effect. A hybrid Monte Carlo—fluid model is applied to simulate an SF6 ICP. It is found that the etch rate is influenced by two simultaneous effects: (i) the residence time of the gas and (ii) the temperature profile of the plasma in the ICP volume, resulting indeed in a maximum etch rate at 200 sccm.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000384095900011	Publication Date	2016-08-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	1	Open Access
	Notes	We are very grateful to Mark Kushner for providing the computational model. The Fund for Scientific Research Flanders (FWO; grant no. 0880.212.840) is acknowledged for financial support of this work. The work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the University of Antwerp.			Approved	Most recent IF: 2.588
	Call Number	c:irua:134867			Serial	4108
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	Author	Neyts, E.C.; Yusupov, M.; Verlackt, C.C.; Bogaerts, A.
	Title	Computer simulations of plasmabiomolecule and plasmatissue interactions for a better insight in plasma medicine			Type	A1 Journal article
	Year	2014	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	47	Issue	29	Pages	293001
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficultif not impossibleto obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasmabiomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance the field.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000338860300001	Publication Date	2014-06-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727;1361-6463;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	28	Open Access
	Notes				Approved	Most recent IF: 2.588; 2014 IF: 2.721
	Call Number	UA @ lucian @ c:irua:117853			Serial	472
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	Author	Neyts, E.C.; Bogaerts, A.
	Title	Understanding plasma catalysis through modelling and simulation : a review			Type	A1 Journal article
	Year	2014	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	47	Issue	22	Pages	224010
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma catalysis holds great promise for environmental applications, provided that the process viability can be maximized in terms of energy efficiency and product selectivity. This requires a fundamental understanding of the various processes taking place and especially the mutual interactions between plasma and catalyst. In this review, we therefore first examine the various effects of the plasma on the catalyst and of the catalyst on the plasma that have been described in the literature. Most of these studies are purely experimental. The urgently needed fundamental understanding of the mechanisms underpinning plasma catalysis, however, may also be obtained through modelling and simulation. Therefore, we also provide here an overview of the modelling efforts that have been developed already, on both the atomistic and the macroscale, and we identify the data that can be obtained with these models to illustrate how modelling and simulation may contribute to this field. Last but not least, we also identify future modelling opportunities to obtain a more complete understanding of the various underlying plasma catalytic effects, which is needed to provide a comprehensive picture of plasma catalysis.
	Address
	Corporate Author				Thesis
	Publisher	Iop publishing ltd	Place of Publication	Bristol	Editor
	Language		Wos	000336207900011	Publication Date	2014-05-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727;1361-6463;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	130	Open Access
	Notes				Approved	Most recent IF: 2.588; 2014 IF: 2.721
	Call Number	UA @ lucian @ c:irua:116920			Serial	3803
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	Author	Dufour, T.; Minnebo, J.; Abou Rich, S.; Neyts, E.C.; Bogaerts, A.; Reniers, F.
	Title	Understanding polyethylene surface functionalization by an atmospheric He/O₂ plasma through combined experiments and simulations			Type	A1 Journal article
	Year	2014	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	47	Issue	22	Pages	224007
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	High density polyethylene surfaces were exposed to the atmospheric post-discharge of a radiofrequency plasma torch supplied in helium and oxygen. Dynamic water contact angle measurements were performed to evaluate changes in surface hydrophilicity and angle resolved x-ray photoelectron spectroscopy was carried out to identify the functional groups responsible for wettability changes and to study their subsurface depth profiles, up to 9 nm in depth. The reactions leading to the formation of CO, C = O and OC = O groups were simulated by molecular dynamics. These simulations demonstrate that impinging oxygen atoms do not react immediately upon impact but rather remain at or close to the surface before eventually reacting. The simulations also explain the release of gaseous species in the ambient environment as well as the ejection of low molecular weight oxidized materials from the surface.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000336207900008	Publication Date	2014-05-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727;1361-6463;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	13	Open Access
	Notes				Approved	Most recent IF: 2.588; 2014 IF: 2.721
	Call Number	UA @ lucian @ c:irua:116919			Serial	3804
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	Author	Bogaerts, A.; Neyts, E.C.; Rousseau, A.
	Title	Special issue on fundamentals of plasmasurface interactions			Type	Editorial
	Year	2014	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	47	Issue	22	Pages	220301
	Keywords	Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	Iop publishing ltd	Place of Publication	Bristol	Editor
	Language		Wos	000336207900001	Publication Date	2014-05-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727;1361-6463;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	2	Open Access
	Notes				Approved	Most recent IF: 2.588; 2014 IF: 2.721
	Call Number	UA @ lucian @ c:irua:116917			Serial	3068
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	Author	Bal, K.M.; Neyts, E.C.
	Title	On the time scale associated with Monte Carlo simulations			Type	A1 Journal article
	Year	2014	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	141	Issue	20	Pages	204104
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000345641400005	Publication Date	2014-11-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9606;1089-7690;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.965	Times cited	26	Open Access
	Notes				Approved	Most recent IF: 2.965; 2014 IF: 2.952
	Call Number	UA @ lucian @ c:irua:120667			Serial	2459
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	Author	Bal, K.M.; Neyts, E.C.
	Title	Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory			Type	A1 Journal article
	Year	2022	Publication	Journal Of Chemical Physics	Abbreviated Journal	J Chem Phys
	Volume	157	Issue	18	Pages	184113-10
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000885260600002	Publication Date	2022-11-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9606	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.4	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 4.4
	Call Number	UA @ admin @ c:irua:192076			Serial	7266
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	Author	Khalilov, U.; Bogaerts, A.; Hussain, S.; Kovacevic, E.; Brault, P.; Boulmer-Leborgne, C.; Neyts, E.C.
	Title	Nanoscale mechanisms of CNT growth and etching in plasma environment			Type	A1 Journal article
	Year	2017	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	50	Issue	50	Pages	184001
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma-enhanced chemical deposition (PECVD) of carbon nanotubes has already been shown to allow chirality control to some extent. In PECVD, however, etching may occur simultaneously with the growth, and the occurrence of intermediate processes further significantly complicates the growth process. We here employ a computational approach with experimental support to study the plasma-based formation of Ni nanoclusters, Ni-catalyzed CNT growth and subsequent etching processes, in order to understand the underpinning nanoscale mechanisms. We find that hydrogen is the dominant factor in both the re-structuring of a Ni film and the subsequent appearance of Ni nanoclusters, as well as in the CNT nucleation and etching processes. The obtained results are compared with available theoretical and experimental studies and provide a deeper understanding of the occurring nanoscale mechanisms in plasma-assisted CNT nucleation and growth.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000398300900001	Publication Date	2017-04-03
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	6	Open Access	OpenAccess
	Notes	UK gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), Belgium (Grant No. 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. The authors also thank Prof A C T van Duin for sharing the ReaxFF code.			Approved	Most recent IF: 2.588
	Call Number	PLASMANT @ plasmant @ c:irua:141918			Serial	4533
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	Author	Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A.
	Title	Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine			Type	A1 Journal article
	Year	2015	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	48	Issue	48	Pages	155202
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000351856600007	Publication Date	2015-03-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727;1361-6463;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	20	Open Access
	Notes				Approved	Most recent IF: 2.588; 2015 IF: 2.721
	Call Number	c:irua:124230			Serial	3242
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	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
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	Author	Mees, M.J.; Pourtois, G.; Neyts, E.C.; Thijsse, B.J.; Stesmans, A.
	Title	Uniform-acceptance force-bias Monte Carlo method with time scale to study solid-state diffusion			Type	A1 Journal article
	Year	2012	Publication	Physical review : B : condensed matter and materials physics	Abbreviated Journal	Phys Rev B
	Volume	85	Issue	13	Pages	134301-134301,9
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Monte Carlo (MC) methods have a long-standing history as partners of molecular dynamics (MD) to simulate the evolution of materials at the atomic scale. Among these techniques, the uniform-acceptance force-bias Monte Carlo (UFMC) method [ G. Dereli Mol. Simul. 8 351 (1992)] has recently attracted attention [ M. Timonova et al. Phys. Rev. B 81 144107 (2010)] thanks to its apparent capacity of being able to simulate physical processes in a reduced number of iterations compared to classical MD methods. The origin of this efficiency remains, however, unclear. In this work we derive a UFMC method starting from basic thermodynamic principles, which leads to an intuitive and unambiguous formalism. The approach includes a statistically relevant time step per Monte Carlo iteration, showing a significant speed-up compared to MD simulations. This time-stamped force-bias Monte Carlo (tfMC) formalism is tested on both simple one-dimensional and three-dimensional systems. Both test-cases give excellent results in agreement with analytical solutions and literature reports. The inclusion of a time scale, the simplicity of the method, and the enhancement of the time step compared to classical MD methods make this method very appealing for studying the dynamics of many-particle systems.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000302290500001	Publication Date	2012-04-03
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1098-0121;1550-235X;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.836	Times cited	31	Open Access
	Notes				Approved	Most recent IF: 3.836; 2012 IF: 3.767
	Call Number	UA @ lucian @ c:irua:97160			Serial	3809
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	Author	Kovács, A.; Yusupov, M.; Cornet, I.; Billen, P.; Neyts, E.C.
	Title	Effect of natural deep eutectic solvents of non-eutectic compositions on enzyme stability			Type	A1 Journal article
	Year	2022	Publication	Journal Of Molecular Liquids	Abbreviated Journal	J Mol Liq
	Volume	366	Issue		Pages	120180-17
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS)
	Abstract	Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000865431800010	Publication Date	2022-08-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0167-7322	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	6	Times cited		Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 6
	Call Number	UA @ admin @ c:irua:191538			Serial	7265
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	Author	Nematollahi, P.; Neyts, E.C.
	Title	Direct oxidation of methane to methanol on Co embedded N-doped graphene: Comparing the role of N₂O and O₂ as oxidants			Type	A1 Journal article
	Year	2020	Publication	Applied Catalysis A-General	Abbreviated Journal	Appl Catal A-Gen
	Volume	602	Issue		Pages	117716-10
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this work, the effects of N-doping into the Co-doped single vacancy (Co-SV-G) and di-vacancy graphene flake (Co-dV-G) are investigated and compared toward direct oxidation of methane to methanol (DOMM) employing two different oxidants (N2O and O-2) using density functional theory (DFT) calculation. We found that DOMM on CoN3-G utilizing the N2O molecule as oxygen-donor proceeds via a two-step reaction with low activation energies. In addition, we found that although CoN3-G might be a good catalyst for methane conversion, it can also catalyze the oxidation of methanol to CO2 and H2O due to the required low activation barriers. Moreover, the adsorption behaviors of CHx (x = 0-4) species and dehydrogenation of CHx (x = 1-4) species on CoN3-G are investigated. We concluded that CoN3-G can be used as an efficient catalyst for DOMM and N-2O reduction at ambient conditions which may serve as a guide for fabricating effective C/N catalysts in energy-related devices.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000554006800046	Publication Date	2020-06-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0926-860x	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.5	Times cited		Open Access
	Notes	; This work was performed with the financial support from the Doctoral Fund of the Antwerp University (NO. BOFLP33099). All the simulations are performed on resources provided by the high-performance computing center of Antwerp University. ;			Approved	Most recent IF: 5.5; 2020 IF: 4.339
	Call Number	UA @ admin @ c:irua:171219			Serial	6485
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	Author	Bal, K.M.; Fukuhara, S.; Shibuta, Y.; Neyts, E.C.
	Title	Free energy barriers from biased molecular dynamics simulations			Type	A1 Journal article
	Year	2020	Publication	Journal Of Chemical Physics	Abbreviated Journal	J Chem Phys
	Volume	153	Issue	11	Pages	114118
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000574665600004	Publication Date	2020-09-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9606	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.4	Times cited		Open Access
	Notes	Japan Society for the Promotion of Science, 19H02415 18J22727 ; Fonds Wetenschappelijk Onderzoek, 12ZI420N ; This work was supported, in part, by a Grant-in-Aid for Scientific Research (B) (Grant No. 19H02415) and Grant-in-Aid for a JSPS Research Fellow (Grant No. 18J22727) from the Japan Society for the Promotion of Science (JSPS), Japan. K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation – Flanders), Grant No. 12ZI420N. S.F. was supported by JSPS through the Program for Leading Graduate Schools (MERIT). The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. The authors are grateful to Pablo Piaggi for making the pair entropy CV code publicly available.			Approved	Most recent IF: 4.4; 2020 IF: 2.965
	Call Number	PLASMANT @ plasmant @c:irua:172456			Serial	6420
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	Author	Fukuhara, S.; Bal, K.M.; Neyts, E.C.; Shibuta, Y.
	Title	Accelerated molecular dynamics simulation of large systems with parallel collective variable-driven hyperdynamics			Type	A1 Journal article
	Year	2020	Publication	Computational Materials Science	Abbreviated Journal	Comp Mater Sci
	Volume	177	Issue		Pages	109581
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The limitation in time and length scale is a major issue of molecular dynamics (MD) simulation. Although several methods have been developed to extend the MD time scale, their performance usually deteriorates with increasing system size. Therefore, an acceleration method which is applicable to large systems is required to bridge the gap between the MD simulations and target phenomena. In this study, an accelerated MD method for large system is developed based on the collective variable-driven hyperdynamics (CVHD) method [K.M. Bal and E.C. Neyts, 2015]. The key idea is to run CVHD in parallel with rate control and accelerate multiple possible events simultaneously. Using this novel method, carbon diﬀusion in bcc-iron bicrystal with grain boundary is examined as an application for practical materials. Carbon atoms reaching at the grain boundary are trapped whereas carbon atoms in the bulk region diﬀuse randomly, and both dynamic regimes can be simultaneously accelerated with the parallel CVHD technique.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000519576300001	Publication Date	2020-02-08
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0927-0256	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.3	Times cited		Open Access
	Notes	JSPS, J22727 ; Japan Society for the Promotion of Science; This work was supported by Grant-in-Aid for Scientiﬁc Research (B) (No.19H02415) and Grant-in-Aid for JSPS Research Fellow (No.18J22727) from Japan Society for the Promotion of Science (JSPS), Japan. S.F. was supported by JSPS through the Program for Leading Graduate Schools (MERIT). Data availability The data required to reproduce these ﬁndings are available from the corresponding authors upon reasonable request.			Approved	Most recent IF: 3.3; 2020 IF: 2.292
	Call Number	PLASMANT @ plasmant @c:irua:166773			Serial	6333
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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.; 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	Neyts, E.C.; Ostrikov, K.; Han, Z.J.; Kumar, S.; van Duin, A.C.T.; Bogaerts, A.
	Title	Defect healing and enhanced nucleation of carbon nanotubes by low-energy ion bombardment			Type	A1 Journal article
	Year	2013	Publication	Physical review letters	Abbreviated Journal	Phys Rev Lett
	Volume	110	Issue	6	Pages	065501-65505
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Structural defects inevitably appear during the nucleation event that determines the structure and properties of single-walled carbon nanotubes. By combining ion bombardment experiments with atomistic simulations we reveal that ion bombardment in a suitable energy range allows these defects to be healed resulting in an enhanced nucleation of the carbon nanotube cap. The enhanced growth of the nanotube cap is explained by a nonthermal ion-induced graphene network restructuring mechanism.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000314687300022	Publication Date	2013-02-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0031-9007;1079-7114;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.462	Times cited	50	Open Access
	Notes				Approved	Most recent IF: 8.462; 2013 IF: 7.728
	Call Number	UA @ lucian @ c:irua:105306			Serial	616
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	Author	Zhang, Y.-R.; Neyts, E.C.; Bogaerts, A.
	Title	Enhancement of plasma generation in catalyst pores with different shapes			Type	A1 Journal article
	Year	2018	Publication	Plasma sources science and technology	Abbreviated Journal	Plasma Sources Sci T
	Volume	27	Issue	5	Pages	055008
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma generation inside catalyst pores is of utmost importance for plasma catalysis, as the existence of plasma species inside the pores affects the active surface area of the catalyst available to the plasma species for catalytic reactions. In this paper, the electric field enhancement, and thus the plasma production inside catalyst pores with different pore shapes is studied with a two-dimensional fluid model. The results indicate that the electric field will be significantly enhanced near tip-like structures. In a conical pore with small opening, the strongest electric field appears at the opening and bottom corners of the pore, giving rise to a prominent ionization rate throughout the pore. For a cylindrical pore, the electric field is only enhanced at the bottom corners of the pore, with lower absolute value, and thus the ionization rate inside the pore is only slightly enhanced. Finally, in a conical pore with large opening, the electric field is characterized by a maximum at the bottom of the pore, yielding a similar behavior for the ionization rate. These results demonstrate that the shape of the pore has a significantly influence on the electric field enhancement, and thus modifies the plasma properties.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000432351700002	Publication Date	2018-05-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1361-6595	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.302	Times cited	11	Open Access	OpenAccess
	Notes	This work was supported by the Fund for Scientific Research Flanders (FWO) (Grant No. G.0217.14N) and the Fundamental Research Funds for the Central Universities (Grant No. DUT17LK52).			Approved	Most recent IF: 3.302
	Call Number	PLASMANT @ plasmant @c:irua:151546			Serial	4998
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	Author	Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C.
	Title	Multi-level molecular modelling for plasma medicine			Type	A1 Journal article
	Year	2016	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	49	Issue	49	Pages	054002
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000368944100003	Publication Date	2015-12-16
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	11	Open Access
	Notes	This work is financially supported by the Fund for Scientific Research Flanders (FWO) and the Francqui Foundation. The calculations were carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen.			Approved	Most recent IF: 2.588
	Call Number	c:irua:131571			Serial	3985
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	Author	Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C.
	Title	Multi-level molecular modelling for plasma medicine			Type	A1 Journal article
	Year	2016	Publication	Journal Of Physics D-Applied Physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	49	Issue	5	Pages	054002-54019
	Keywords	A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos		Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727	ISBN		Additional Links	UA library record
	Impact Factor	2.588	Times cited		Open Access
	Notes				Approved	Most recent IF: 2.588
	Call Number	UA @ lucian @ c:irua:129798			Serial	4467
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	Author	Bruggeman, P.J.; Kushner, M.J.; Locke, B.R.; Gardeniers, J.G.E.; Graham, W.G.; Graves, D.B.; Hofman-Caris, R.C.H.M.; Maric, D.; Reid, J.P.; Ceriani, E.; Fernandez Rivas, D.; Foster, J.E.; Garrick, S.C.; Gorbanev, Y.; Hamaguchi, S.; Iza, F.; Jablonowski, H.; Klimova, E.; Kolb, J.; Krcma, F.; Lukes, P.; Machala, Z.; Marinov, I.; Mariotti, D.; Mededovic Thagard, S.; Minakata, D.; Neyts, E.C.; Pawlat, J.; Petrovic, Z.L.; Pflieger, R.; Reuter, S.; Schram, D.C.; Schröter, S.; Shiraiwa, M.; Tarabová, B.; Tsai, P.A.; Verlet, J.R.R.; von Woedtke, T.; Wilson, K.R.; Yasui, K.; Zvereva, G.
	Title	Plasma–liquid interactions: a review and roadmap			Type	A1 Journal article
	Year	2016	Publication	Plasma sources science and technology	Abbreviated Journal	Plasma Sources Sci T
	Volume	25	Issue	5	Pages	053002
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma–liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on nonequilibrium plasmas.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000384715400001	Publication Date	2016-09-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1361-6595	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.302	Times cited	460	Open Access
	Notes	This manuscript originated from discussions at the Lorentz Center Workshop ‘Gas/Plasma–Liquid Interface: Transport, Chemistry and Fundamental Data’ that took place at the Lorentz Center, Leiden University in the Netherlands from August 4, through August 8, 2014, and follow-up discussions since the workshop. All authors acknowledge the support of the Lorentz Center, the COST action TD1208 (Electrical Discharges with Liquids for Future Applications) and the Royal Dutch Academy of Sciences for their financial support. PJB, MJK, DBG and JEF acknowledge the support of the ‘Center on Control of Plasma Kinetics’ of the United States Department of Energy Office of Fusion Energy Science (DE-SC0001319). In addition, PJB and BRL acknowledge the support of the National Science Foundation (PHY 1500135 and CBET 1236225, respectively). In addition the enormous help of Mrs. Victoria Piorek (University of Minnesota) in the formatting of the final document including the references is gratefully acknowledged.			Approved	Most recent IF: 3.302
	Call Number	PLASMANT @ plasmant @ c:irua:144654			Serial	4628
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	Author	Van der Paal, J.; Verheyen, C.; Neyts, E.C.; Bogaerts, A.
	Title	Hampering Effect of Cholesterol on the Permeation of Reactive Oxygen Species through Phospholipids Bilayer: Possible Explanation for Plasma Cancer Selectivity			Type	A1 Journal article
	Year	2017	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	7	Issue	7	Pages	39526
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In recent years, the ability of cold atmospheric pressure plasmas (CAPS) to selectively induce cell death in cancer cells has been widely established. This selectivity has been assigned to the reactive oxygen and nitrogen species (RONS) created in CAPs. To provide new insights in the search for an explanation for the observed selectivity, we calculate the transfer free energy of multiple ROS across membranes containing a varying amount of cholesterol. The cholesterol fraction is investigated as a selectivity parameter because membranes of cancer cells are known to contain lower fractions of cholesterol compared to healthy cells. We find that cholesterol has a significant effect on the permeation of reactive species across a membrane. Indeed, depending on the specific reactive species, an increasing cholesterol fraction can lead to (i) an increase of the transfer free energy barrier height and width, (ii) the formation of a local free energy minimum in the center of the membrane and (iii) the creation of extra free energy barriers due to the bulky sterol rings. In the context of plasma oncology, these observations suggest that the increased ingress of RONS in cancer cells can be explained by the decreased cholesterol fraction of their cell membrane.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000391306900001	Publication Date	2017-01-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	27	Open Access	OpenAccess
	Notes	The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number 11U5416N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @ c:irua:139512			Serial	4340
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	Author	Grubova, I.Y.; Surmeneva, M.A.; Surmenev, R.A.; Neyts, E.C.
	Title	Effect of van der Waals interactions on the adhesion strength at the interface of the hydroxyapatite-titanium biocomposite : a first-principles study			Type	A1 Journal article
	Year	2020	Publication	RSC advances	Abbreviated Journal
	Volume	10	Issue	62	Pages	37800-37805
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Hydroxyapatite (HAP) is frequently used as biocompatible coating on Ti-based implants. In this context, the HAP-Ti adhesion is of crucial importance. Here, we report ab initio calculations to investigate the influence of Si incorporation into the amorphous calcium-phosphate (a-HAP) structure on the interfacial bonding mechanism between the a-HAP coating and an amorphous titanium dioxide (a-TiO2) substrate, contrasting two different density functionals: PBE-GGA, and DFT-D3, which are capable of describing the influence of the van der Waals (vdW) interactions. In particular, we discuss the effect of dispersion on the work of adhesion (W-ad), equilibrium geometries, and charge density difference (CDD). We find that replacement of P by Si in a-HAP (a-Si-HAP) with the creation of OH vacancies as charge compensation results in a significant increase in the bond strength between the coating and substrate in the case of using the PBE-GGA functional. However, including the vdW interactions shows that these forces considerably contribute to the W-ad. We show that the difference (W-ad – W-ad(vdW)) is on average more than 1.1 J m(-2) and 0.5 J m(-2) for a-HAP/a-TiO2 and a-Si-HAP/a-TiO2, respectively. These results reveal that including vdW interactions is essential for accurately describing the chemical bonding at the a-HAP/a-TiO2 interface.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000583523300025	Publication Date	2020-10-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access
	Notes	; The authors gratefully acknowledge financial support from the Russian president's grant MK-330.2020.8 and BOF Fellowships for International Joint PhD students funded by University of Antwerp (UAntwerp, project number 32545). The work was carried out at Tomsk Polytechnic University within the framework of Tomsk Polytechnic University Competitiveness Enhancement Program grant and in part using the Turing HPC infrastructure of the CalcUA core facility of the UAntwerp, a division of the Flemish Supercomputer Centre (VSC), funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerp, Belgium. ;			Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:173603			Serial	6499
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