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	Author	Martin, J.M.L.; François, J.P.; Gijbels, R.; Almlöf, J.
	Title	Structure and infrared spectroscopy of the C₁₁ molecule			Type	A1 Journal article
	Year	1991	Publication	Chemical physics letters	Abbreviated Journal	Chem Phys Lett
	Volume	187	Issue		Pages	367-386
	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	A1991GX46000005	Publication Date	2002-07-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0009-2614;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.897	Times cited	42	Open Access
	Notes				Approved
	Call Number	UA @ lucian @ c:irua:718			Serial	3281
Permanent link to this record



	Author	Tit, N.; Al Ezzi, M.M.; Abdullah, H.M.; Yusupov, M.; Kouser, S.; Bahlouli, H.; Yamani, Z.H.
	Title	Detection of CO2 using CNT-based sensors: Role of Fe catalyst on sensitivity and selectivity			Type	A1 Journal article
	Year	2017	Publication	Materials chemistry and physics	Abbreviated Journal	Mater Chem Phys
	Volume	186	Issue	186	Pages	353-364
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The adsorption of CO2 on surfaces of graphene and carbon nanotubes (CNTs), decorated with Fe atoms, are investigated using the self-consistent-charge density-functional tight-binding (SCC-DFTB) method, neglecting the heat effects. Fe ad-atoms are more stable when they are dispersed on hollow sites. They introduce a large density of states at the Fermi level (N-F); where keeping such density low would help in gas sensing. Furthermore, the Fe ad-atom can weaken the C=O double bonds of the chemisorbed CO2 molecule, paving the way for oxygen atoms to drain more charges from Fe. Consequently, chemisorption of CO2 molecules reduces both N-F and the conductance while it enhances the sensitivity with the increasing gas dose. Conducting armchair CNTs (ac-CNTs) have higher sensitivity than graphene and semiconducting zigzag CNTs (zz-CNT5). Comparative study of sensitivity of ac-CNT-Fe composite towards various gases (e.g., O-2, N-2, H-2, H2O, CO and CO2) has shown high sensitivity and selectivity towards CO, CO2 and H2O gases. (C) 2016 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Lausanne	Editor
	Language		Wos	000390621200044	Publication Date	2016-11-04
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0254-0584	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.084	Times cited	17	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 2.084
	Call Number	UA @ lucian @ c:irua:140333			Serial	4465
Permanent link to this record



	Author	Zhang, Y.-R.; Van Laer, K.; Neyts, E.C.; Bogaerts, A.
	Title	Can plasma be formed in catalyst pores? A modeling investigation			Type	A1 Journal article
	Year	2016	Publication	Applied catalysis : B : environmental	Abbreviated Journal	Appl Catal B-Environ
	Volume	185	Issue	185	Pages	56-67
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	tWe investigate microdischarge formation inside catalyst pores by a two-dimensional fluid model forvarious pore sizes in the m-range and for various applied voltages. Indeed, this is a poorly understoodphenomenon in plasma catalysis. The calculations are performed for a dielectric barrier discharge inhelium, at atmospheric pressure. The electron and ion densities, electron temperature, electric field andpotential, as well as the electron impact ionization and excitation rate and the densities of excited plasmaspecies, are examined for a better understanding of the characteristics of the plasma inside a pore. Theresults indicate that the pore size and the applied voltage are critical parameters for the formation of amicrodischarge inside a pore. At an applied voltage of 20 kV, our calculations reveal that the ionizationmainly takes place inside the pore, and the electron density shows a significant increase near and inthe pore for pore sizes larger than 200m, whereas the effect of the pore on the total ion density isevident even for 10m pores. When the pore size is fixed at 30m, the presence of the pore has nosignificant influence on the plasma properties at an applied voltage of 2 kV. Upon increasing the voltage,the ionization process is enhanced due to the strong electric field and high electron temperature, andthe ion density shows a remarkable increase near and in the pore for voltages above 10 kV. These resultsindicate that the plasma species can be formed inside pores of structured catalysts (in the m range),and they may interact with the catalyst surface, and affect the plasma catalytic process.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000369452000006	Publication Date	2015-12-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0926-3373	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	9.446	Times cited	75	Open Access
	Notes	This work was supported by the Fund for Scientific ResearchFlanders (FWO) (Grant no. G.0217.14N), the National Natural Sci-ence Foundation of China (Grant no. 11405019), and the ChinaPostdoctoral Science Foundation (Grant no. 2015T80244). Theauthors are very grateful to V. Meynen for the useful discussions oncatalysts. This work was carried out in part using the Turing HPCinfrastructure at the CalcUA core facility of the Universiteit Antwer-pen, a division of the Flemish Supercomputer Center VSC, fundedby the Hercules Foundation, the Flemish Government (departmentEWI) and the University of Antwerp.			Approved	Most recent IF: 9.446
	Call Number	c:irua:129808			Serial	3984
Permanent link to this record



	Author	Oleshko, V.; Gijbels, R.; Jacob, W.
	Title	Energy-filtering TEM and electron energy-loss spectroscopy of double structure tabular microcrystals of silver halide emulsions			Type	A1 Journal article
	Year	1996	Publication	Journal of microscopy	Abbreviated Journal	J Microsc-Oxford
	Volume	183	Issue	1	Pages	27-38
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Oxford	Editor
	Language		Wos	A1996UZ02800005	Publication Date	2003-11-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-2720;1365-2818;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.331	Times cited	8	Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:16248			Serial	1039
Permanent link to this record



	Author	Bogaerts, A.; Kozak, T.; van Laer, K.; Snoeckx, R.
	Title	Plasma-based conversion of CO2: current status and future challenges			Type	A1 Journal article
	Year	2015	Publication	Faraday discussions	Abbreviated Journal	Faraday Discuss
	Volume	183	Issue	183	Pages	217-232
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	This paper discusses our recent results on plasma-based CO2 conversion, obtained by a combination of experiments and modeling, for a dielectric barrier discharge (DBD), a microwave plasma and a packed bed DBD reactor. The results illustrate that plasma technology is quite promising for CO2 conversion, but more research is needed to better understand the underlying mechanisms and to further improve the capabilities.
	Address	Research Group PLASMANT, University of Antwerp, Department of Chemistry, Universiteitsplein 1, Antwerp, Belgium. annemie.bogaerts@uantwerpen.be
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Wos	000365914900013	Publication Date	2015-06-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1359-6640	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.588	Times cited	89	Open Access
	Notes	We thank R. Aerts and W. van Gaens for setting up the experimental systems and for the interesting results obtained during their PhD study in our group. We also acknowledge nancial support from the IAP/7 (Inter-university Attraction Pole) program ‘PSI-Physical Chemistry of Plasma-Surface Interactions’ by the Belgian Federal Office for Science Policy (BELSPO), the Fund for Scientic Research Flanders (FWO) and the EU-FP7-ITN network “RAPID”.			Approved	Most recent IF: 3.588; 2015 IF: 4.606
	Call Number	c:irua:130318			Serial	3983
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	Author	Attri, P.; Kaushik, N.K.; Kaushik, N.; Hammerschmid, D.; Privat-Maldonado, A.; De Backer, J.; Shiratani, M.; Choi, E.H.; Bogaerts, A.
	Title	Plasma treatment causes structural modifications in lysozyme, and increases cytotoxicity towards cancer cells			Type	A1 Journal Article
	Year	2021	Publication	International Journal Of Biological Macromolecules	Abbreviated Journal	Int J Biol Macromol
	Volume	182	Issue		Pages	1724-1736
	Keywords	A1 Journal Article; Lysozyme; Cold atmospheric plasma; Cancer cell death; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	Bacterial and mammalian proteins, such as lysozyme, are gaining increasing interest as anticancer drugs. This study aims to modify the lysozyme structure using cold atmospheric plasma to boost its cancer cell killing effect. We investigated the structure at acidic and neutral pH using various experimental techniques (circular dichroism, ﬂuorescence, and mass spectrometry) and molecular dynamics simulations. The controlled structural modiﬁcation of lysozyme at neutral pH enhances its activity, while the activity was lost at acidic pH at the same treatment conditions. Indeed, a larger number of amino acids were oxidized at acidic pH after plasma treatment, which results in a greater distortion of the lysozyme structure, whereas only limited structural changes were observed in lysozyme after plasma treatment at neutral pH. We found that the plasma-treated lysozyme signiﬁcantly induced apoptosis to the cancer cells. Our results reveal that plasma-treated lysozyme could have potential as a new cancer cell killing drug.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000675794700005	Publication Date	2021-05-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0141-8130	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.671	Times cited		Open Access	OpenAccess
	Notes	Japan Society for the Promotion of Science; We gratefully acknowledge the European H2020 Marie SkłodowskaCurie Actions Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. NK thanks to National Research Foundation of Korea under Ministry of Science and ICT (NRF2021R1C1C1013875) of Korean Government. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA.			Approved	Most recent IF: 3.671
	Call Number	PLASMANT @ plasmant @c:irua:178813			Serial	6792
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	Author	Vanraes, P.; Bogaerts, A.
	Title	Laser-induced excitation mechanisms and phase transitions in spectrochemical analysis – Review of the fundamentals			Type	A1 Journal article
	Year	2021	Publication	Spectrochimica Acta Part B-Atomic Spectroscopy	Abbreviated Journal	Spectrochim Acta B
	Volume	179	Issue		Pages	106091
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Nowadays, lasers are commonly applied in spectrochemical analysis methods, for sampling, plasma formation or a combination of both. Despite the numerous investigations that have been performed on these applications, the underlying processes are still insufficiently understood. In order to fasten progress in the field and in honor of the lifework of professor Rick Russo, we here provide a brief overview of the fundamental mechanisms in lasermatter interaction as proposed in literature, and throw the spotlight on some aspects that have not received much attention yet. For an organized discussion, we choose laser ablation, laser desorption and the associated gaseous plasma formation as the central processes in this perspective article, based on a classification of the laserbased spectrochemical analysis techniques and the corresponding laser-matter interaction regimes. First, we put the looking glass over the excitation and thermalization mechanisms in the laser-irradiated condensed phase, for which we propose the so-called multi-plasma model. This novel model can be understood as an extension of the well-known two-temperature model, featuring multiple thermodynamic dimensions, each of which corresponds to a quasi-particle type. Next, the focus is placed on the mass transfer and ionization mechanisms, after which we shortly highlight the possible role of anisotropic and magnetic effects in the laser-excited material. We hope this perspective article motivates more fundamental research on laser-matter interaction, as a continuation of the lifework of Rick Russo.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000631868700005	Publication Date	2021-03-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0584-8547	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.241	Times cited		Open Access	OpenAccess
	Notes	University of Antwerp; We acknowledge funding by a University of Antwerp BOF grant and by a University of Antwerp Methusalem grant.			Approved	Most recent IF: 3.241
	Call Number	PLASMANT @ plasmant @c:irua:176876			Serial	6710
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	Author	Slanina, Z.; Martin, J.M.L.; François, J.P.; Gijbels, R.
	Title	On the relative stabilities of the linear and triangular forms of B₃N			Type	A1 Journal article
	Year	1993	Publication	Chemical physics	Abbreviated Journal	Chem Phys
	Volume	178	Issue		Pages	77-82
	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	A1993MP94200006	Publication Date	2002-07-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0301-0104;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.652	Times cited	9	Open Access
	Notes				Approved	CHEMISTRY, MULTIDISCIPLINARY 65/163 Q2 # CRYSTALLOGRAPHY 10/26 Q2 #
	Call Number	UA @ lucian @ c:irua:6150			Serial	2453
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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	Volkov, V.V.; van Landuyt, J.; Marushkin, K.M.; Gijbels, R.; Férauge, C.; Vasilyev, M.G.; Shelyakin, A.A.; Sokolovsky, A.A.
	Title	Characterization of LPE grown InGaAsP/InP heterostructures: IR-LED at 1.66 μm used for the remote monitoring of methane gas			Type	A1 Journal article
	Year	1997	Publication	Journal of crystal growth	Abbreviated Journal	J Cryst Growth
	Volume	173	Issue		Pages	285-296
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	A1997XC98100008	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-0248	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.751	Times cited	4	Open Access
	Notes				Approved	Most recent IF: 1.751; 1997 IF: 1.259
	Call Number	UA @ lucian @ c:irua:20459			Serial	324
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	Author	Khalilov, U.; Neyts, E.C.
	Title	Mechanisms of selective nanocarbon synthesis inside carbon nanotubes			Type	A1 Journal article
	Year	2021	Publication	Carbon	Abbreviated Journal	Carbon
	Volume	171	Issue		Pages	72-78
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The possibility of conﬁnement effects inside a carbon nanotube provides new application opportunities, e.g., growth of novel carbon nanostructures. However, the understanding the precise role of catalystfeedstock in the nanostructure synthesis is still elusive. In our simulation-based study, we investigate the Ni-catalyzed growth mechanism of encapsulated carbon nanostructures, viz. double-wall carbon nanotube and graphene nanoribbon, from carbon and hydrocarbon growth precursors, respectively. Speciﬁcally, we ﬁnd that the tube and ribbon growth is determined by a catalyst-vs-feedstock competition effect. We compare our results, i.e., growth mechanism and structure morphology with all available theoretical and experimental data. Our calculations show that all encapsulated nanostructures contain metal (catalyst) atoms and such structures are less stable than their pure counterparts. Therefore, we study the puriﬁcation mechanism of these structures. In general, this study opens a possible route to the controllable synthesis of tubular and planar carbon nanostructures for today’s nanotechnology.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000598371500009	Publication Date	2020-09-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0008-6223	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	6.337	Times cited		Open Access	OpenAccess
	Notes	Fund of Scientific Research Flanders, 12M1318N ; Universiteit Antwerpen; Flemish Supercomputer Centre; Hercules Foundation; Flemish Government; The authors gratefully acknowledge the ﬁnancial support from the Fund of Scientiﬁc Research Flanders (FWO), Belgium, Grant number 12M1318N. The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Centre (VSC), funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA, Belgium.			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:172459			Serial	6414
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	Author	Fukuhara, S.; Bal, K.M.; Neyts, E.C.; Shibuta, Y.
	Title	Entropic and enthalpic factors determining the thermodynamics and kinetics of carbon segregation from transition metal nanoparticles			Type	A1 Journal article
	Year	2021	Publication	Carbon	Abbreviated Journal	Carbon
	Volume	171	Issue		Pages	806-813
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The free energy surface (FES) for carbon segregation from nickel nanoparticles is obtained from advanced molecular dynamics simulations. A suitable reaction coordinate is developed that can distinguish dissolved carbon atoms from segregated dimers, chains and junctions on the nanoparticle surface. Because of the typically long segregation time scale (up to ms), metadynamics simulations along the developed reaction coordinate are used to construct FES over a wide range of temperatures and carbon concentrations. The FES revealed the relative stability of different stages in the segregation process, and free energy barriers and rates of the individual steps could then be calculated and decomposed into enthalpic and entropic contributions. As the carbon concentration in the nickel nanoparticle increases, segregated carbon becomes more stable in terms of both enthalpy and entropy. The activation free energy of the reaction also decreases with the increase of carbon concentration, which can be mainly attributed to entropic effects. These insights and the methodology developed to obtain them improve our understanding of carbon segregation process across materials science in general, and the nucleation and growth of carbon nanotube in particular.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000598371500084	Publication Date	2020-09-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0008-6223	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.337	Times cited		Open Access	OpenAccess
	Notes	Scientific Research, 19H02415 ; JSPS, 18J22727 ; Japan Society for the Promotion of Science; JSPS; JSPS; FWO; Research Foundation; Flanders, 12ZI420N ; 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 812			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:172452			Serial	6421
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	Author	Martin, J.M.L.; François, J.P.; Gijbels, R.
	Title	Accurate ab initio quartic force fields for the sulfur compounds H₂S, CS₂, OCS and CS			Type	A1 Journal article
	Year	1995	Publication	Journal of molecular spectroscopy	Abbreviated Journal	J Mol Spectrosc
	Volume	169	Issue		Pages	445-457
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	A1995QD98400014	Publication Date	2002-09-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-2852;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.482	Times cited	37	Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:12277			Serial	45
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	Author	Martin, J.M.L.; François, J.P.; Gijbels, R.
	Title	The anharmonic force field of thioformaldehyde, H₂CS			Type	A1 Journal article
	Year	1994	Publication	Journal of molecular spectroscopy	Abbreviated Journal	J Mol Spectrosc
	Volume	168	Issue		Pages	363-373
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	A1994PU60800015	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-2852	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.482	Times cited	18	Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:10259			Serial	119
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	Author	Martin, J.M.L.; Francois; Gijbels, R.
	Title	The anharmonic-force field of thioformaldehyde, h2cs, by ab-initio methods			Type	A1 Journal article
	Year	1994	Publication	Journal of molecular spectroscopy	Abbreviated Journal	J Mol Spectrosc
	Volume	168	Issue	2	Pages	363-373
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The quartic force field of thioformaldehyde has been calculated ab initio using large basis sets and augmented coupled cluster methods. Calculated fundamentals are in excellent agreement with experiment, as is the most important Coriolis coupling constant. Computed values for the anharmonicity, rovibrational coupling, and centrifugal distortion constants of the four isotopomers (H2CS)-S-32, (H2CS)-S-34, (HDCS)-S-32, and (D2CS)-S-32 have been reported. Predictions have been made for all vibrational transitions from the ground state to excited states with at most two quanta for these isotopomers, both using second-order perturbation theory corrected for Darling-Dennison resonance and using vibrational SCF-CI calculations. For (D2CS)-S-32, perturbation theory performs quite well; for the other isotopomers, performance is poorer for states involving excitation of the out-of-plane bend and, for the (H2CS)-S-32 and (H2CS)-S-34 isotopomers, also for the antisymmetric bend that is in severe Coriolis resonance with it. A possible explanation has been suggested. (C) 1994 Academic Press, Inc.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	A1994PU60800015	Publication Date	2002-10-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-2852;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.482	Times cited	18	Open Access
	Notes				Approved	PHYSICS, APPLIED 47/145 Q2 #
	Call Number	UA @ lucian @ c:irua:95414			Serial	3570
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	Author	Kumar, N.; Perez-Novo, C.; Shaw, P.; Logie, E.; Privat-Maldonado, A.; Dewilde, S.; Smits, E.; Berghe, W.V.; Bogaerts, A.
	Title	Physical plasma-derived oxidants sensitize pancreatic cancer cells to ferroptotic cell death			Type	A1 Journal article
	Year	2021	Publication	Free Radical Biology And Medicine	Abbreviated Journal	Free Radical Bio Med
	Volume	166	Issue		Pages	187-200
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract	Despite modern therapeutic advances, the survival prospects of pancreatic cancer patients remain poor, due to chemoresistance and dysregulated oncogenic kinase signaling networks. We applied a novel kinome activitymapping approach using biological peptide targets as phospho-sensors to identify vulnerable kinase dependencies for therapy sensitization by physical plasma. Ser/Thr-kinome specific activity changes were mapped upon induction of ferroptotic cell death in pancreatic tumor cells exposed to reactive oxygen and nitrogen species of plasma-treated water (PTW). This revealed a broad kinome activity response involving the CAMK, the AGC and CMGC family of kinases. This systems-level kinome network response supports stress adaptive switches between chemoresistant anti-oxidant responses of Kelch-like ECH-associated protein 1 (KEAP1)/Heme Oxygenase 1 (HMOX1) and ferroptotic cell death sensitization upon suppression of Nuclear factor (erythroid derived 2)-like 2 (NRF2) and Glutathione peroxidase 4 (GPX4). This is further supported by ex vivo experiments in the chicken chorioallantoic membrane assay, showing decreased GPX4 and Glutathione (GSH) expression as well as increased lipid peroxidation, along with suppressed BxPC-3 tumor growth in response to PTW. Taken all together, we demonstrate that plasma treated water-derived oxidants sensitize pancreatic cancer cells to ferroptotic cell death by targeting a NRF2-HMOX1-GPX4 specific kinase signaling network.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000632703400001	Publication Date	2021-02-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0891-5849	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.606	Times cited		Open Access	OpenAccess
	Notes	We gratefully acknowledge the financial support obtained from the Research Foundation Flanders (FWO), Belgium, grant number 12J5617 N and Department of Biotechnology (DBT) Ramalingaswami Re-entry Fellowship, India, grant number D.O.NO.BT/HRD/35/02/2006. We are thankful to the Laboratory of Experimental Hematology, for providing the facilities for the experimental and fluorescence microscopy work. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), Belgium. The Kinome profiling was performed at the Epigenetic Signaling service facility (PPES-UA) funded by the Hercules Foundation and Foundation against cancer Belgium (KOTK 7872).			Approved	Most recent IF: 5.606
	Call Number	PLASMANT @ plasmant @c:irua:176878			Serial	6711
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	Author	Attri, P.; Park, J.-H.; De Backer, J.; Kim, M.; Yun, J.-H.; Heo, Y.; Dewilde, S.; Shiratani, M.; Choi, E.H.; Lee, W.; Bogaerts, A.
	Title	Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study			Type	A1 Journal article
	Year	2020	Publication	International Journal Of Biological Macromolecules	Abbreviated Journal	Int J Biol Macromol
	Volume	163	Issue		Pages	2405-2414
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	NADPH oxidases 1 (NOX1) derived reactive oxygen species (ROS) play an important role in the progression of cancer through signaling pathways. Therefore, in this paper, we demonstrate the effect of cold atmospheric plasma (CAP) on the structural changes of Noxa1 SH3 protein, one of the regulatory subunits of NOX1. For this purpose, ﬁrstly we puriﬁed the Noxa1 SH3 protein and analyzed the structure using X-ray crystallography, and subsequently, we treated the protein with two types of CAP reactors such as pulsed dielectric barrier discharge (DBD) and Soft Jet for different time intervals. The structural deformation of Noxa1 SH3 protein was analyzed by various experimental methods (circular dichroism, ﬂuorescence, and NMR spectroscopy) and by MD simulations. Additionally, we demonstrate the effect of CAP (DBD and Soft Jet) on the viability and expression of NOX1 in A375 cancer cells. Our results are useful to understand the structural modiﬁcation/oxidation occur in protein due to reactive oxygen and nitrogen (RONS) species generated by CAP.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000579839600233	Publication Date	2020-09-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0141-8130	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.2	Times cited		Open Access
	Notes	European Marie Skłodowska-Curie Individual Fellowship, 743546 ; JSPS, 20K14454 ; National Research Foundation of Korea, 2019M3A9F6021810 NRF-2017M3A9F6029753 NRF-2019M3E5D6063903 NRF-2016R1A6A3A04010213 ; Brain Korea 21; MSIT, NRF-2016K1A4A3914113 ; Hercules Foundation; Flemish Government; UA; We gratefully acknowledge the European Marie SkłodowskaCurie Individual Fellowship “Anticancer-PAM” within Horizon 2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. Additionally, work was supported by several grants (2019M3A9F6021810, NRF2017M3A9F6029753, NRF-2019M3E5D6063903 to W. Lee), Basic Science Research Program (NRF-2016R1A6A3A04010213 to J.H. Yun) through the National Research Foundation of Korea and in part by the Brain Korea 21 (BK21) PLUS program (J.H.P.). EHC is thankful to National Research Foundation (NRF) of Korea, funded by the Korea government (MSIT) under the grant number (NRF2016K1A4A3914113). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA.			Approved	Most recent IF: 8.2; 2020 IF: 3.671
	Call Number	PLASMANT @ plasmant @c:irua:172451			Serial	6419
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	Author	Xie, L.; Brault, P.; Coutanceau, C.; Bauchire, J.-M.; Caillard, A.; Baranton, S.; Berndt, J.; Neyts, E.C.
	Title	Efficient amorphous platinum catalyst cluster growth on porous carbon : a combined molecular dynamics and experimental study			Type	A1 Journal article
	Year	2015	Publication	Applied catalysis : B : environmental	Abbreviated Journal	Appl Catal B-Environ
	Volume	162	Issue	162	Pages	21-26
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Amorphous platinum clusters supported on porous carbon have been envisaged for high-performance fuel cell electrodes. For this application, it is crucial to control the morphology of the Pt layer and the Ptsubstrate interaction to maximize activity and stability. We thus investigate the morphology evolution during Pt cluster growth on a porous carbon substrate employing atomic scale molecular dynamics simulations. The simulations are based on the Pt-C interaction potential using parameters derived from density functional theory and are found to yield a Pt cluster morphology similar to that observed in low loaded fuel cell electrodes prepared by plasma sputtering. Moreover, the simulations show amorphous Pt cluster growth in agreement with X-ray diffraction and transmission electron microscopy experiments on high performance low Pt content (10 μgPt cm−2) loaded fuel cell electrodes and provide a fundamental insight in the cluster growth mechanism.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000343686900003	Publication Date	2014-06-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0926-3373;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	9.446	Times cited	20	Open Access
	Notes				Approved	Most recent IF: 9.446; 2015 IF: 7.435
	Call Number	c:irua:117949			Serial	874
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	Author	Van 't dack, L.; Gijbels, R.; Walker, C.T.
	Title	Modern developments and applications in microbeam analysis: proceedings of the 10th Workshop of the European Microbeam Analysis Society (EMAS), Antwerp, Belgium, May 6-10, 2007			Type	Editorial
	Year	2008	Publication	Microchimica acta	Abbreviated Journal	Microchim Acta
	Volume	161	Issue	3/4	Pages	285-286
	Keywords	Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000256175600001	Publication Date	2008-05-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0026-3672;1436-5073;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.58	Times cited	1	Open Access
	Notes				Approved	Most recent IF: 4.58; 2008 IF: 1.910
	Call Number	UA @ lucian @ c:irua:69291			Serial	2157
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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	Wardenier, N.; Gorbanev, Y.; Van Moer, I.; Nikiforov, A.; Van Hulle, S.W.H.; Surmont, P.; Lynen, F.; Leys, C.; Bogaerts, A.; Vanraes, P.
	Title	Removal of alachlor in water by non-thermal plasma: Reactive species and pathways in batch and continuous process			Type	A1 Journal article
	Year	2019	Publication	Water research	Abbreviated Journal	Water Res
	Volume	161	Issue		Pages	549-559
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Pesticides are emerging contaminants frequently detected in the aquatic environment. In this work, a novel approach combining activated carbon adsorption, oxygen plasma treatment and ozonation was studied for the removal of the persistent chlorinated pesticide alachlor. A comparison was made between the removal efﬁciency and energy consumption for two different reactor operation modes: batchrecirculation and single-pass mode. The kinetics study revealed that the insufﬁcient removal of alachlor by adsorption was signiﬁcantly improved in terms of degradation efﬁciency and energy consumption when combined with the plasma treatment. The best efﬁciency (ca. 80% removal with an energy cost of 19.4 kWh mÀ3) was found for the single-pass operational mode of the reactor. In the batch-recirculating process, a complete elimination of alachlor by plasma treatment was observed after 30 min of treatment. Analysis of the reactive species induced by plasma in aqueous solutions showed that the decomposition of alachlor mainly occurred through a radical oxidation mechanism, with a minor contribution of long-living oxidants (O3, H2O2). Investigation of the alachlor oxidation pathways revealed six different oxidation mechanisms, including the loss of aromaticity which was never before reported for plasma-assisted degradation of aromatic pesticides. It was revealed that the removal rate and energy cost could be further improved with more than 50% by additional O3 gas bubbling in the solution reservoir.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000475999400054	Publication Date	2019-06-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0043-1354	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.942	Times cited	2	Open Access
	Notes	PlasmaTex project IWT, 1408/2 ; the European Marie Sklodowska-Curie Individual Fellowship within Horizon2020, 743151 ; Flemish Knowledge Centre Water; This work was ﬁnancially supported by the PlasmaTex project IWT 1408/2 and the European Marie Sklodowska-Curie Individual Fellowship within Horizon2020 (‘LTPAM’, grant no. 743151). This research was initiated within the LED H2O project which is ﬁnancially supported by the Flemish Knowledge Centre Water (Vlakwa).			Approved	Most recent IF: 6.942
	Call Number	PLASMANT @ plasmant @c:irua:161173			Serial	5288
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	Author	Grubova, I.Y.; Surmeneva, M.A.; Huygh, S.; Surmenev, R.A.; Neyts, E.C.
	Title	Effects of silicon doping on strengthening adhesion at the interface of the hydroxyapatite-titanium biocomposite : a first-principles study			Type	A1 Journal article
	Year	2019	Publication	Computational materials science	Abbreviated Journal	Comp Mater Sci
	Volume	159	Issue	159	Pages	228-234
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this paper we employ first-principles calculations to investigate the effect of substitutional Si doping in the amorphous calcium-phosphate (a-HAP) structure on the work of adhesion, integral charge transfer, charge density difference and theoretical tensile strengths between an a-HAP coating and amorphous titanium dioxide (a-TiO2) substrate systemically. Our calculations demonstrate that substitution of a P atom by a Si atom in a-HAP (a-Si-HAP) with the creation of OH-vacancies as charge compensation results in a significant increase of the bonding strength of the coating to the substrate. The work of adhesion of the optimized Si-doped interfaces reaches a value of up to -2.52 J m(-2), which is significantly higher than for the stoichiometric a-HAP/a-TiO2. Charge density difference analysis indicates that the dominant interactions at the interface have significant covalent character, and in particular two Ti-O and three Ca-O bonds are formed for a-Si-HAP/a-TiO2 and one Ti-O and three Ca-O bonds for a-HAP/a-TiO2. From the stress-strain curve, the Young's modulus of a-Si-HAP/a-TiO2 is calculated to be about 25% higher than that of the a-HAP/a-TiO2, and the yielding stress is about 2 times greater than that of the undoped model. Our calculations therefore demonstrate that the presence of Si in the a-HAP structure strongly alters not only the bioactivity and resorption rates, but also the mechanical properties of the a-HAP/a-TiO2 interface. The results presented here provide an important theoretical insight into the nature of the chemical bonding at the a-HAP/a-TiO2 interface, and are particularly significant for the practical medical applications of HAP-based biomaterials.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000457856900023	Publication Date	2018-12-18
	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	2.292	Times cited	1	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 2.292
	Call Number	UA @ admin @ c:irua:157480			Serial	5272
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	Author	Marimuthu, P.; Razzokov, J.; Eshonqulov, G.
	Title	Disruption of conserved polar interactions causes a sequential release of Bim mutants from the canonical binding groove of Mcl1			Type	A1 Journal article
	Year	2020	Publication	International Journal Of Biological Macromolecules	Abbreviated Journal	Int J Biol Macromol
	Volume	158	Issue		Pages	364-374
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Mcl1 is an important anti-apoptotic member of the Bcl2 family proteins that are upregulated in several cancer malignancies. The canonical binding groove (CBG) located at the surface of Mcl1 exhibits a critical role in binding partners selectively via the BH3-domain of pro-apoptotic Bcl2 family members that trigger the downregulation of Mcl1 function. There are several crystal structures of point-mutated pro-apoptotic Bim peptides in complex with Mcl1. However, the mechanistic effects of such point-mutations towards peptide binding and complex stability still remain unexplored. Here, the effects of the reported point mutations in Bim peptides and their binding mechanisms to Mcl1 were computationally evaluated using atomistic-level steered molecular dynamics (SMD) simulations. A range of external-forces and constant-velocities were applied to the Bim peptides to uncover the mechanistic basis of peptide dissociation from the CBG of Mcl1. Although the peptides showed similarities in their dissociation pathways, the peak rupture forces varied significantly. According to simulations results, the disruption of the conserved polar contacts at the complex interface causes a sequential release of the peptides from the CBG of Mcl1. Overall, the results obtained from the current study may provide valuable insights for the development of novel anti-cancer peptide-inhibitors that can downregulate Mcl1’s function.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000564486400010	Publication Date	2020-05-03
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0141-8130	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.2	Times cited		Open Access
	Notes	P.M. gratefully acknowledges the Sigrid Jusélius Foundation, Joe, Pentti and Tor Borg Memorial Fund for computational and laboratory infrastructure, the Bioinformatics infrastructure facility supported by Biocenter Finland, CSC-IT Center for Science (Project: 2000461) for the high performance computational facility; Prof. Outi Salo-Ahen, SBL, Pharmacy, Åbo Akademi University and Prof. Olli Pentikäinen, MedChem, University of Turku for valuable discussion; Dr. Jukka Lehtonen for the IT support; and specially thanks Prof. Mark Johnson, SBL, Åbo Akademi University, for providing the lab facility.			Approved	Most recent IF: 8.2; 2020 IF: 3.671
	Call Number	PLASMANT @ plasmant @c:irua:169231			Serial	6365
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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	Bal, K.M.
	Title	Nucleation rates from small scale atomistic simulations and transition state theory			Type	A1 Journal article
	Year	2021	Publication	Journal Of Chemical Physics	Abbreviated Journal	J Chem Phys
	Volume	155	Issue	14	Pages	144111
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion relying only on the free energy barrier, transition state theory, and a simple dynamical correction for diffusive recrossing. In this setup, the time scale problem is overcome by using enhanced sampling methods, in casu metadynamics, whereas the impact of finite size effects can be naturally circumvented by reconstructing the free energy surface from an appropriate ensemble. Approximations from classical nucleation theory are avoided. We demonstrate the accuracy of the approach by calculating macroscopic rates of droplet nucleation from argon vapor, spanning 16 orders of magnitude and in excellent agreement with literature results, all from simulations of very small (512 atom) systems.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000755502100008	Publication Date	2021-09-30
	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	2.965	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 2.965
	Call Number	UA @ admin @ c:irua:184937			Serial	8320
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	Author	Somers, W.; Bogaerts, A.; van Duin, A.C.T.; Neyts, E.C.
	Title	Interactions of plasma species on nickel catalysts : a reactive molecular dynamics study on the influence of temperature and surface structure			Type	A1 Journal article
	Year	2014	Publication	Applied catalysis : B : environmental	Abbreviated Journal	Appl Catal B-Environ
	Volume	154	Issue		Pages	1-8
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Methane reforming by plasma catalysis is a complex process that is far from understood. It requires a multidisciplinary approach which ideally takes into account all effects from the plasma on the catalyst, and vice versa. In this contribution, we focus on the interactions of CHx (x = {1,2,3}) radicals that are created in the plasma with several nickel catalyst surfaces. To this end, we perform reactive molecular dynamics simulations, based on the ReaxFF potential, in a wide temperature range of 4001600 K. First, we focus on the H2 formation as a function of temperature and surface structure. We observe that substantial H2 formation is obtained at 1400 K and above, while the role of the surface structure seems limited. Indeed, in the initial stage, the type of nickel surface influences the CH bond breaking efficiency of adsorbed radicals; however, the continuous carbon diffusion into the surface gradually diminishes the surface crystallinity and therefore reduces the effect of surface structure on the H2 formation probability. Furthermore, we have also investigated to what extent the species adsorbed on the catalyst surface can participate in surface reactions more in general, for the various surface structures and as a function of temperature. These results are part of the ongoing research on the methane reforming by plasma catalysis, a highly interesting yet complex alternative to conventional reforming processes.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000335098800001	Publication Date	2014-02-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0926-3373;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	9.446	Times cited	23	Open Access
	Notes				Approved	Most recent IF: 9.446; 2014 IF: 7.435
	Call Number	UA @ lucian @ c:irua:114607			Serial	1686
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	Author	Khalilov, U.; Vets, C.; Neyts, E.C.
	Title	Catalyzed growth of encapsulated carbyne			Type	A1 Journal article
	Year	2019	Publication	Carbon	Abbreviated Journal	Carbon
	Volume	153	Issue		Pages	1-5
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Carbyne is a novel material of current interest in nanotechnology. As is typically the case for nanomaterials, the growth process determines the resulting properties. While endohedral carbyne has been successfully synthesized, its catalyst and feedstock-dependent growth mechanism is still elusive. We here study the nucleation and growth mechanism of different carbon chains in a Ni-containing double walled carbon nanotube using classical molecular dynamics simulations and ﬁrst-principles calculations. We ﬁnd that the understanding the competitive role of the metal catalyst and the hydrocarbon is important to control the growth of 1-dimensional carbon chains, including Ni or H-terminated carbyne. Also, we ﬁnd that the electronic property of the Ni-terminated carbyne can be tuned by steering the H concentration along the chain. These results suggest catalyst-containing carbon nanotubes as a possible synthesis route for carbyne formation.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000485054200001	Publication Date	2019-07-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0008-6223	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.337	Times cited		Open Access	Not_Open_Access
	Notes	Fund of Scientific Research Flanders (FWO), Belgium, 12M1318N 1S22516N ; Flemish Supercomputer Centre VSC; Hercules Foundation; Flemish Government; University of Antwerp; The authors gratefully acknowledge the ﬁnancial support from the Fund of Scientiﬁc Research Flanders (FWO), Belgium, Grant numbers 12M1318N and 1S22516N. 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 University of Antwerp.			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:160695			Serial	5187
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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	Attri, P.; Razzokov, J.; Yusupov, M.; Koga, K.; Shiratani, M.; Bogaerts, A.
	Title	Influence of osmolytes and ionic liquids on the Bacteriorhodopsin structure in the absence and presence of oxidative stress: A combined experimental and computational study			Type	A1 Journal article
	Year	2020	Publication	International Journal Of Biological Macromolecules	Abbreviated Journal	Int J Biol Macromol
	Volume	148	Issue		Pages	657-665
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Understanding the folding and stability of membrane proteins is of great importance in protein science. Recently, osmolytes and ionic liquids (ILs) are increasingly being used as drug delivery systems in the biopharmaceutical industry. However, the stability of membrane proteins in the presence of osmolytes and ILs is not yet fully understood. Besides, the effect of oxidative stress on membrane proteins with osmolytes or ILs has not been investigated. Therefore, we studied the inﬂuence of osmolytes and ILs as co-solvents on the stability of a model membrane protein (i.e., Bacteriorhodopsin in purple membrane of Halobacterium salinarum), using UV–Vis spectroscopy and molecular dynamics (MD) simulations. The MD simulations allowed us to determine the ﬂexibility and solvent accessible surface area (SASA) of Bacteriorhodopsin protein in the presence and/or absence of cosolvents, as well as to carry out principal component analysis (PCA) to identify the most important movements in this protein. In addition, by means of UV–Vis spectroscopy we studied the effect of oxidative stress generated by cold atmospheric plasma on the stability of Bacteriorhodopsin in the presence and/or absence of co-solvents. This study is important for a better understanding of the stability of proteins in the presence of oxidative stress.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000522094600066	Publication Date	2020-01-20
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0141-8130	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.2	Times cited		Open Access
	Notes	Horizon2020, 743546 ; JSPS, 19H05462 16H03895 ; Nagoya University; We gratefully acknowledge the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI 19H05462 and 16H03895, the joint usage/research program of Center for Low-temperature Plasma Science, Nagoya University and also supported by JSPS and RCL under the Japan-Lithuania Research Cooperative Program. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA.			Approved	Most recent IF: 8.2; 2020 IF: 3.671
	Call Number	PLASMANT @ plasmant @c:irua:165585			Serial	5444
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	Author	de Witte, H.; de Gendt, S.; Douglas, M.; Conard, T.; Kenis, K.; Mertens, P.W.; Vandervorst, W.; Gijbels, R.
	Title	Evaluation of time-of-flight secondary ion mass spectrometry for metal contamination monitoring on wafer surfaces			Type	A1 Journal article
	Year	2000	Publication	Journal of the electrochemical society	Abbreviated Journal	J Electrochem Soc
	Volume	147	Issue	5	Pages	13-17
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000087075200052	Publication Date	2002-07-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0013-4651;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.259	Times cited	14	Open Access
	Notes				Approved	Most recent IF: 3.259; 2000 IF: 2.293
	Call Number	UA @ lucian @ c:irua:34073			Serial	1089
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