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	Author	Larrain, M.; Van Passel, S.; Thomassen, G.; Kresovic, U.; Alderweireldt, N.; Moerman, E.; Billen, P.
	Title	Economic performance of pyrolysis of mixed plastic waste: Open-loop versus closed-loop recycling			Type	A1 Journal Article
	Year	2020	Publication	Journal Of Cleaner Production	Abbreviated Journal	J Clean Prod
	Volume		Issue		Pages	122442
	Keywords	A1 Journal Article; Engineering Management (ENM) ;
	Abstract	In recent decades new recycling technologies for mixed plastic waste have emerged. In pyrolysis, the polymer chains are thermally broken (pyrolyzed) to obtain hydrocarbon materials of different molecular weights such as naphtha, oil or waxes, whose yields can be controlled by varying the reaction parameters. Naphtha represents a closed-loop recycling process as it is a feedstock for (poly)olefins; while the co-production of waxes, having several applications in e.g. the construction industry, exemplifies an open-loop recycling process. This paper compares the economic performance of the pyrolysis of mixed polyolefin waste in a closed-loop and open-loop scheme, including a probabilistic approach to the most important variables. From an economic perspective, open-loop pyrolysis as presented outperforms closed-loop recycling, due to the high prices of wax. However, the results present a high dispersion caused by the volatility of the prices of crude oil and its derivates. Considering the current oil price projections, our case study analysis showed that for open-loop recycling there is a future probability of almost a 98 % of observing positive results and around 57 % of probability in the case of closed-loop recycling, under the assumptions made. Yet, in a future scenario where decarbonized electricity would decrease oil prices, the probability of a positive outcome reduces to 57 % for the open-loop case and to less than 8 % in the case of closed-loop recycling. To make these pathways attractive to investors, the nameplate capacity should be at least 70 kt/year for open-loop recycling and 115 kt/year for closed-loop recycling. A 120 kt/year plant should operate minimally at 80 % of its capacity for open-loop recycling, while closed-loop recycling would demand running close to maximum capacity. Security of feedstock supply therefore is required.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000579071300078	Publication Date	2020-05-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0959-6526	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	11.1	Times cited		Open Access
	Notes	This work was supported by the VLAIO Catalisti-ICON project MATTER (Mechanical and Thermochemical Recycling of mixed plastic waste; project HBC.2018.0262).			Approved	Most recent IF: 11.1; 2020 IF: 5.715
	Call Number	ENM @ enm @c:irua:170005			Serial	6386
Permanent link to this record



	Author	Sui, Y.; Jiang, Y.; Moretti, M.; Vlaeminck, S.E.
	Title	Harvesting time and biomass composition affect the economics of microalgae production			Type	A1 Journal article
	Year	2020	Publication	Journal Of Cleaner Production	Abbreviated Journal	J Clean Prod
	Volume	259	Issue		Pages	120782-10
	Keywords	A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL); Engineering Management (ENM)
	Abstract	Cost simulations provide a strong tool to render the production of microalgae economically viable. This study evaluated the unexplored effect of harvesting time and the corresponding microalgal biomass composition on the overall production cost, under both continuous light and light/dark regime using techno-economic analysis (TEA). At the same time, the TEA gives evidence that a novel product “proteinaceous salt” from Dunaliella microalgae production is a promising high-value product for commercialization with profitability. The optimum production scenario is to employ natural light/dark regime and harvest microalgal biomass around late exponential phase, obtaining the minimum production cost of 11 €/kg and a profitable minimum selling price (MSP) of 14.4 €/kg for the “proteinaceous salt”. For further optimization of the production, increasing microalgal biomass concentration is the most effective way to reduce the total production cost and increase the profits of microalgae products.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000530695500009	Publication Date	2020-02-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0959-6526	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	11.1	Times cited	5	Open Access
	Notes	; This work was supported by the China Scholarship Council (File No. 201507650015) and the MIP i-Cleantech Flanders (Milieu-innovatieplatform; Environment innovation platform) project Microbial Nutrients on Demand (MicroNOD). ;			Approved	Most recent IF: 11.1; 2020 IF: 5.715
	Call Number	UA @ admin @ c:irua:166802			Serial	6531
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	Author	Buyle, M.; Maes, B.; Van Passel, S.; Boonen, K.; Vercalsteren, A.; Audenaert, A.
	Title	Ex-ante LCA of emerging carbon steel slag treatment technologies : fast forwarding lab observations to industrial-scale production			Type	A1 Journal article
	Year	2021	Publication	Journal Of Cleaner Production	Abbreviated Journal	J Clean Prod
	Volume	313	Issue		Pages	127921
	Keywords	A1 Journal article; Engineering sciences. Technology; Energy and Materials in Infrastructure and Buildings (EMIB)
	Abstract	The valuable properties of carbon steel slag are currently underexploited. To date, research mainly focusses on valorising a single property of the slag. In this study an ex-ante life cycle assessment (LCA) was applied to evaluate the environmental profile of a novel technological pathway aimed at the extraction of chromium from carbon steel slag in combination with high quality valorisation of the residual matrix material. A comparison with current practice was made, not only by calculating the environmental impact of the lab scale observations, but more importantly by estimating the impact on an industrial scale. Practical guidance on ex-ante LCA is limited, so this study contributes by incorporating simulations on thermodynamic behaviour, complemented with empirical calculation rules and including information derived from similar technologies to perform the upscaling. These principles of ex-ante LCA were applied to the lab results of two consecutive research iterations. Substantial improvements of the environmental profile were observed: ex-ante results turned out to be a factor 20 lower compared to the results from the lab observations after the first iteration and had decreased by a factor 2 compared to the small pilot scale of the second iteration. All upscaled results are better than those from the worst case reference scenario (landfill). Based on the experience gained after this iterative research cycle, a practical recommendation is that at a low technology readiness level using more simple calculation rules in combination with a flowsheet based on elementary design principles for processes at an industrial scale is a more efficient way of modelling compared to a fully-fledged process design from the start.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000693416000002	Publication Date	2021-06-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0959-6526	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	5.715	Times cited		Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 5.715
	Call Number	UA @ admin @ c:irua:179313			Serial	6922
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	Author	Azadi, H.; Moghaddam, S.M.; Burkart, S.; Mahmoudi, H.; Van Passel, S.; Kurban, A.; Lopez-Carr, D.
	Title	Rethinking resilient agriculture : from Climate-Smart Agriculture to Vulnerable-Smart Agriculture			Type	A1 Journal article
	Year	2021	Publication	Journal Of Cleaner Production	Abbreviated Journal	J Clean Prod
	Volume	319	Issue		Pages	128602
	Keywords	A1 Journal article; Engineering sciences. Technology; Engineering Management (ENM)
	Abstract	Climate-Smart Agriculture (CSA) is seeking to overcome the food security problem and develop rural livelihoods while minimizing negative impacts on the environment. However, when such synergies exist, the situation of small-scale farmers is often overlooked, and they are unable to implement new practices and technologies. Therefore, the main aim of this study is to improve CSA by adding the neglected but very important element “small-scale farmer”, and introduce Vulnerable-Smart Agriculture (VSA) as a complete version of CSA. VSA indicates, based on the results of this study, that none of the decisions made by policymakers can be realistic and functional as long as the voice of the farmers influenced by their decisions is not heard. Therefore, to identify different levels for possible interventions and develop VSA monitoring indicators, a new conceptual framework needs to be developed. This study proposed such a framework consisting of five elements: prediction of critical incidents by farmers, measuring the consequences of incidents, identifying farmers' coping strategies, assessing farmers' livelihood capital when facing an incident, and adapting to climate incidents. The primary focus of this study is on farmers' learning and operational preparation to deal with tension and disasters at farm level. Understanding the implications of threats from climate change and the recognizing of coping mechanisms will contribute to an increase in understanding sustainable management.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000728681500005	Publication Date	2021-08-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0959-6526	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.715	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 5.715
	Call Number	UA @ admin @ c:irua:184869			Serial	6942
Permanent link to this record



	Author	Neyts, E.C.; Thijsse, B.J.; Mees, M.J.; Bal, K.M.; Pourtois, G.
	Title	Establishing uniform acceptance in force biased Monte Carlo simulations			Type	A1 Journal article
	Year	2012	Publication	Journal of chemical theory and computation	Abbreviated Journal	J Chem Theory Comput
	Volume	8	Issue	6	Pages	1865-1869
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Uniform acceptance force biased Monte Carlo (UFMC) simulations have previously been shown to be a powerful tool to simulate atomic scale processes, enabling one to follow the dynamical path during the simulation. In this contribution, we present a simple proof to demonstrate that this uniform acceptance still complies with the condition of detailed balance, on the condition that the characteristic parameter lambda = 1/2 and that the maximum allowed step size is chosen to be sufficiently small. Furthermore, the relation to Metropolis Monte Carlo (MMC) is also established, and it is shown that UFMC reduces to MMC by choosing the characteristic parameter lambda = 0 [Rao, M. et al. Mol. Phys. 1979, 37, 1773]. Finally, a simple example compares the UFMC and MMC methods.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000305092400002	Publication Date	2012-05-16
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1549-9618;1549-9626;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.245	Times cited	20	Open Access
	Notes				Approved	Most recent IF: 5.245; 2012 IF: 5.389
	Call Number	UA @ lucian @ c:irua:99090			Serial	1082
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	Author	Bal, K.M.; Neyts, E.C.
	Title	Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds			Type	A1 Journal article
	Year	2015	Publication	Journal of chemical theory and computation	Abbreviated Journal	J Chem Theory Comput
	Volume	11	Issue	11	Pages	4545-4554
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of reactive processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000362921700004	Publication Date	2015-09-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1549-9618	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.245	Times cited	41	Open Access
	Notes	K.M.B. is funded as Ph.D. fellow (aspirant) of the FWOFlanders (Fund for Scientific Research-Flanders), Grant No. 11 V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) and the HPC infrastructure of the University of Antwerp (CalcUA), funded by the Hercules Foundation and the Flemish Government−Department EWI.			Approved	Most recent IF: 5.245; 2015 IF: 5.498
	Call Number	c:irua:128183			Serial	3991
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	Author	Bal, K.M.
	Title	Reweighted Jarzynski sampling : acceleration of rare events and free energy calculation with a bias potential learned from nonequilibrium work			Type	A1 Journal article
	Year	2021	Publication	Journal Of Chemical Theory And Computation	Abbreviated Journal	J Chem Theory Comput
	Volume	17	Issue	11	Pages	6766-6774
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the reaction coordinate, and the Jarzynski equality is used to learn an approximate free energy surface from the nonequilibrium work distribution. This free energy estimate is represented in a compact form as an artificial neural network and used as an external bias potential to accelerate rare events in a subsequent molecular dynamics simulation. The final free energy estimate is then obtained by reweighting the equilibrium probability distribution of the reaction coordinate sampled under the influence of the external bias. We apply our reweighted Jarzynski sampling recipe to four processes of varying scales and complexities.spanning chemical reaction in the gas phase, pair association in solution, and droplet nucleation in supersaturated vapor. In all cases, we find reweighted Jarzynski sampling to be a very efficient strategy, resulting in rapid convergence of the free energy to high precision.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000718183600008	Publication Date	2021-10-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1549-9618	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.245	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 5.245
	Call Number	UA @ admin @ c:irua:184676			Serial	8479
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	Author	Martin, J.M.L.; François, J.P.; Gijbels, R.
	Title	Ab initio study of the structure, infrared spectra and heat of formation of C₄			Type	A1 Journal article
	Year	1991	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	94	Issue		Pages	3753-3761
	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	A1991FA77800052	Publication Date	0000-00-00
	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	2.952	Times cited	62	Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:715			Serial	38
Permanent link to this record



	Author	Taylor, P.R.; Martin, J.M.L.; François, J.P.; Gijbels, R.
	Title	An ab initio study of the C₃⁺ cation using multireference methods			Type	A1 Journal article
	Year	1991	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	95	Issue		Pages	6530-6534
	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		Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9606	ISBN		Additional Links	UA library record
	Impact Factor	2.952	Times cited		Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:720			Serial	39
Permanent link to this record



	Author	Singh, S.K.; Neek-Amal, M.; Peeters, F.M.
	Title	Electronic properties of graphene nano-flakes : energy gap, permanent dipole, termination effect, and Raman spectroscopy			Type	A1 Journal article
	Year	2014	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	140	Issue	7	Pages	074304-74309
	Keywords	A1 Journal article; Condensed Matter Theory (CMT)
	Abstract	The electronic properties of graphene nano-flakes (GNFs) with different edge passivation are investigated by using density functional theory. Passivation with F and H atoms is considered: C-Nc X-Nx (X = F or H). We studied GNFs with 10 < N-c < 56 and limit ourselves to the lowest energy configurations. We found that: (i) the energy difference Delta between the highest occupied molecular orbital and the lowest unoccupied molecular orbital decreases with N-c, (ii) topological defects (pentagon and heptagon) break the symmetry of the GNFs and enhance the electric polarization, (iii) the mutual interaction of bilayer GNFs can be understood by dipole-dipole interaction which were found sensitive to the relative orientation of the GNFs, (iv) the permanent dipoles depend on the edge terminated atom, while the energy gap is independent of it, and (v) the presence of heptagon and pentagon defects in the GNFs results in the largest difference between the energy of the spin-up and spin-down electrons which is larger for the H-passivated GNFs as compared to F-passivated GNFs. Our study shows clearly the effect of geometry, size, termination, and bilayer on the electronic properties of small GNFs. This study reveals important features of graphene nano-flakes which can be detected using Raman spectroscopy. (C) 2014 AIP Publishing LLC.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000332039900020	Publication Date	2014-02-20
	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	30	Open Access
	Notes	; This work was supported by the EU-Marie Curie IIF postdoctoral Fellowship/ 299855 (for M. N.-A.), the ESF-EuroGRAPHENE project CONGRAN, the Flemish Science Foundation (FWO-Vl), and the Methusalem Foundation of the Flemish Government. ;			Approved	Most recent IF: 2.965; 2014 IF: 2.952
	Call Number	UA @ lucian @ c:irua:115857			Serial	1002
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	Author	Martin, J.M.L.; François, J.P.; Gijbels, R.
	Title	First principles computation of thermo-chemical properties beyond the harmonic approximation: 1: method and application to the water molecule and its isotopomers			Type	A1 Journal article
	Year	1992	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	96	Issue	10	Pages	7633-7645
	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	A1992HU55700047	Publication Date	0000-00-00
	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	2.952	Times cited	59	Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:4195			Serial	1206
Permanent link to this record



	Author	Martin, J.M.L.; François, J.P.; Gijbels, R.
	Title	First principles computation of thermo-chemical properties beyond the harmonic approximation: 2: application to the amino radical and its isotopomers			Type	A1 Journal article
	Year	1992	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	97	Issue	5	Pages	3530-3536
	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	A1992JL37200072	Publication Date	0000-00-00
	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	2.952	Times cited	22	Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:4197			Serial	1207
Permanent link to this record



	Author	Martin, J.M.L.; François, J.P.; Gijbels, R.
	Title	On the effect of centrifugal stretching on the rotational partition function of an asymmetric top			Type	A1 Journal article
	Year	1991	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	95	Issue		Pages	8374-8389
	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	A1991GR66500062	Publication Date	0000-00-00
	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	2.952	Times cited	12	Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:716			Serial	2434
Permanent link to this record



	Author	Martin, J.M.L.; François, J.P.; Gijbels, R.
	Title	On the heat formation of C₈ and higher carbon clusters (letter to the editor)			Type	A1 Journal article
	Year	1991	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	95	Issue		Pages	9420-9421
	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	A1991GV82500076	Publication Date	0000-00-00
	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	2.952	Times cited	27	Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:719			Serial	2437
Permanent link to this record



	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	Euan-Diaz, E.; Herrera-Velarde, S.; Misko, V.R.; Peeters, F.M.; Castaneda-Priego, R.
	Title	Structural transitions and long-time self-diffusion of interacting colloids confined by a parabolic potential			Type	A1 Journal article
	Year	2015	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	142	Issue	142	Pages	024902
	Keywords	A1 Journal article; Condensed Matter Theory (CMT)
	Abstract	We report on the ordering and dynamics of interacting colloidal particles confined by a parabolic potential. By means of Brownian dynamics simulations, we find that by varying the magnitude of the trap stiffness, it is possible to control the dimension of the system and, thus, explore both the structural transitions and the long-time self-diffusion coefficient as a function of the degree of confinement. We particularly study the structural ordering in the directions perpendicular and parallel to the confinement. Further analysis of the local distribution of the first-neighbors layer allows us to identify the different structural phases induced by the parabolic potential. These results are summarized in a structural state diagram that describes the way in which the colloidal suspension undergoes a structural re-ordering while increasing the confinement. To fully understand the particle dynamics, we take into account hydrodynamic interactions between colloids; the parabolic potential constricts the available space for the colloids, but it does not act on the solvent. Our findings show a non-linear behavior of the long-time self-diffusion coefficient that is associated to the structural transitions induced by the external field. (C) 2015 AIP Publishing LLC.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000348129700053	Publication Date	2015-01-10
	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	7	Open Access
	Notes	; This work was partially supported by the “Odysseus” Program of the Flemish Government, the Flemish Science Foundation (FWO-Vl), PIFI 3.4 – PROMEP, and CONACyT (Grant Nos. 61418/2007, 102339/2008, Ph.D. scholarship 230171/2010). R.C.-P. also acknowledges financial support provided by the Marcos Moshinsky fellowship 2013-2014. The authors also thank to the General Coordination of Information and Communications Technologies (CGSTIC) at Cinvestav for providing HPC resources on the Hybrid Cluster Super-computer Xiuhcoatl, which have contributed partially to the research results reported in this paper. ;			Approved	Most recent IF: 2.965; 2015 IF: 2.952
	Call Number	c:irua:123832			Serial	3267
Permanent link to this record



	Author	Michel, K.H.; Verberck, B.; Hulman, M.; Kuzmany, H.; Krause, M.
	Title	Superposition of quantum and classical rotational motions in Sc₂C₂@C₈₄ fullerite			Type	A1 Journal article
	Year	2007	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	126	Issue	6	Pages	064304,1-15
	Keywords	A1 Journal article; Condensed Matter Theory (CMT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000244250200008	Publication Date	2007-02-09
	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	14	Open Access
	Notes				Approved	Most recent IF: 2.965; 2007 IF: 3.044
	Call Number	UA @ lucian @ c:irua:63628			Serial	3381
Permanent link to this record



	Author	Kandemir, A.; Peeters, F.M.; Sahin, H.
	Title	Monitoring the effect of asymmetrical vertical strain on Janus single layers of MoSSe via spectrum			Type	A1 Journal article
	Year	2018	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	149	Issue	8	Pages	084707
	Keywords	A1 Journal article; Condensed Matter Theory (CMT)
	Abstract	Using first principles calculations, we study the structural and phononic properties of the recently synthesized Janus type single layers of molybdenum dichalcogenides. The Janus MoSSe single layer possesses 2H crystal structure with two different chalcogenide sides that lead to out-of-plane anisotropy. By virtue of the asymmetric structure of the ultra-thin Janus type crystal, we induced the out-of-plane anisotropy to show the distinctive vertical pressure effect on the vibrational properties of the Janus material. It is proposed that for the corresponding Raman active optical mode of the Janus structure, the phase modulation and the magnitude ratio of the strained atom and its first neighbor atom adjust the distinctive change in the eigen-frequencies and Raman activity. Moreover, a strong variation in the Raman activity of the Janus structure is obtained under bivertical and univertical strains. Not only eigen-frequency shifts but also Raman activities of the optical modes of the Janus structure exhibit distinguishable features. This study reveals that the vertical anisotropic feature of the Janus structure under Raman measurement allows us to distinguish which side of the Janus crystal interacts with the externals (substrate, functional adlayers, or dopants). Published by AIP Publishing.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000444035800044	Publication Date	2018-08-30
	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	11	Open Access
	Notes	; Computational resources were provided by TUBITAK ULAKBIM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure). H.S. acknowledges financial support from TUBITAK under Project No. 117F095. F.M.P. was supported by the FLAG-ERA-TRANS<INF>2D</INF>TMD. ;			Approved	Most recent IF: 2.965
	Call Number	UA @ lucian @ c:irua:153711UA @ admin @ c:irua:153711			Serial	5115
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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	Baskurt, M.; Yagmurcukardes, M.; Peeters, F.M.; Sahin, H.
	Title	Stable single-layers of calcium halides (CaX₂, X = F, Cl, Br, I)			Type	A1 Journal article
	Year	2020	Publication	Journal Of Chemical Physics	Abbreviated Journal	J Chem Phys
	Volume	152	Issue	16	Pages	164116-164118
	Keywords	A1 Journal article; Condensed Matter Theory (CMT)
	Abstract	By means of density functional theory based first-principles calculations, the structural, vibrational, and electronic properties of 1H- and 1T-phases of single-layer CaX2 (X = F, Cl, Br, or I) structures are investigated. Our results reveal that both the 1H- and 1T-phases are dynamically stable in terms of their phonon band dispersions with the latter being the energetically favorable phase for all single-layers. In both phases of single-layer CaX2 structures, significant phonon softening occurs as the atomic radius increases. In addition, each structural phase exhibits distinctive Raman active modes that enable one to characterize either the phase or the structure via Raman spectroscopy. The electronic band dispersions of single-layer CaX2 structures reveal that all structures are indirect bandgap insulators with a decrease in bandgaps from fluorite to iodide crystals. Furthermore, the calculated linear elastic constants, in-plane stiffness, and Poisson ratio indicate the ultra-soft nature of CaX2 single-layers, which is quite important for their nanoelastic applications. Overall, our study reveals that with their dynamically stable 1T- and 1H-phases, single-layers of CaX2 crystals can be alternative ultra-thin insulators.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000531819100001	Publication Date	2020-04-29
	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	14	Open Access
	Notes	; Computational resources were provided by TUBITAK ULAKBIM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure). H.S. acknowledges financial support from the TUBITAK under Project No. 117F095. H.S. acknowledges support from the Turkish Academy of Sciences under the GEBIP program. M.Y. was supported by a postdoctoral fellowship from the Flemish Science Foundation (FWO-Vl). ;			Approved	Most recent IF: 4.4; 2020 IF: 2.965
	Call Number	UA @ admin @ c:irua:169543			Serial	6615
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	Author	Payne, L.M.; Masia, F.; Zilli, A.; Albrecht, W.; Borri, P.; Langbein, W.
	Title	Quantitative morphometric analysis of single gold nanoparticles by optical extinction microscopy: Material permittivity and surface damping effects			Type	A1 Journal article
	Year	2021	Publication	Journal Of Chemical Physics	Abbreviated Journal	J Chem Phys
	Volume	154	Issue	4	Pages	044702
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000630495600001	Publication Date	2021-01-28
	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	This work was supported by the Welsh Government Life Sciences Bridging Fund (Grant No. LSBF/R6-005), the UK EPSRC (Grant Nos. EP/I005072/1 and EP/M028313/1), and the European Commission (Grant No. EUSMI E191000350). P.B. acknowledges the Royal Society for her Wolfson research merit award (Grant No. WM140077). F.M. acknowledges the Ser Cymru II programme (Case ID 80762-CU-148) which is part-funded by Cardiff University and the European Regional Development Fund through the Welsh Government. W.A. acknowledges an Individual Fellowship from the Marie Skłodowska-Curie actions (MSCA) under the EU’s Horizon 2020 program (Grant No. 797153, SOPMEN) and Sara Bals for supporting the STEM measurements. The brightfield TEM was performed by Thomas Davies at Cardiff University. We acknowledge Iestyn Pope for technical support of the optical equipment.			Approved	Most recent IF: 2.965
	Call Number	EMAT @ emat @c:irua:177566			Serial	6748
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	Author	Hamid, I.; Jalali, H.; Peeters, F.M.; Neek-Amal, M.
	Title	Abnormal in-plane permittivity and ferroelectricity of confined water : from sub-nanometer channels to bulk			Type	A1 Journal article
	Year	2021	Publication	Journal Of Chemical Physics	Abbreviated Journal	J Chem Phys
	Volume	154	Issue	11	Pages	114503
	Keywords	A1 Journal article; Condensed Matter Theory (CMT)
	Abstract	Dielectric properties of nano-confined water are important in several areas of science, i.e., it is relevant in the dielectric double layer that exists in practically all heterogeneous fluid-based systems. Molecular dynamics simulations are used to predict the in-plane dielectric properties of confined water in planar channels of width ranging from sub-nanometer to bulk. Because of suppressed rotational degrees of freedom near the confining walls, the dipole of the water molecules tends to be aligned parallel to the walls, which results in a strongly enhanced in-plane dielectric constant (epsilon (parallel to)) reaching values of about 120 for channels with height 8 angstrom < h < 10 angstrom. With the increase in the width of the channel, we predict that epsilon (parallel to) decreases nonlinearly and reaches the bulk value for h > 70 angstrom. A stratified continuum model is proposed that reproduces the h > 10 angstrom dependence of epsilon (parallel to). For sub-nanometer height channels, abnormal behavior of epsilon (parallel to) is found with two orders of magnitude reduction of epsilon (parallel to) around h similar to 7.5 angstrom, which is attributed to the formation of a particular ice phase that exhibits long-time (similar to mu s) stable ferroelectricity. This is of particular importance for the understanding of the influence of confined water on the functioning of biological systems.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000629831900001	Publication Date	2021-03-17
	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	13	Open Access	OpenAccess
	Notes				Approved	Most recent IF: 2.965
	Call Number	UA @ admin @ c:irua:177579			Serial	6967
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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
Permanent link to this record



	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
Permanent link to this record



	Author	Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M.
	Title	Lipid Oxidation: Role of Membrane Phase-Separated Domains			Type	A1 Journal Article
	Year	2021	Publication	Journal Of Chemical Information And Modeling	Abbreviated Journal	J Chem Inf Model
	Volume	61	Issue	6	Pages	2857-2868
	Keywords	A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	Lipid oxidation is associated with several inﬂammatory and neurodegenerative diseases, but many questions to unravel its eﬀects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a signiﬁcant eﬀect on membrane function. It is reported that domain interfaces are “hot spots” for pore formation, but the underlying mechanisms and the eﬀect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Speciﬁcally, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any eﬀect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000669541400034	Publication Date	2021-06-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1549-9596	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.76	Times cited		Open Access	OpenAccess
	Notes	Fonds Wetenschappelijk Onderzoek, 1200219N ; CoordenaÃ§Ã£o de AperfeiÃ§oamento de Pessoal de NÃvel Superior; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for the scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for ﬁnancial support.			Approved	Most recent IF: 3.76
	Call Number	PLASMANT @ plasmant @c:irua:179766			Serial	6806
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	Author	Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R.
	Title	Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations			Type	A1 Journal article
	Year	2022	Publication	Journal Of Chemical Information And Modeling	Abbreviated Journal	J Chem Inf Model
	Volume	62	Issue	1	Pages	129-141
	Keywords	A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they aﬀect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the eﬀect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this diﬀerence is not signiﬁcant. Overall, these ﬁndings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000740019000001	Publication Date	2022-01-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1549-9596	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.6	Times cited		Open Access	Not_Open_Access
	Notes	Fonds Wetenschappelijk Onderzoek, 1200219N ; Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they aﬀect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the eﬀect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this diﬀerence is not signiﬁcant. Overall, these ﬁndings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.			Approved	Most recent IF: 5.6
	Call Number	PLASMANT @ plasmant @c:irua:185485			Serial	7050
Permanent link to this record



	Author	Verheyen, E.; Jo, C.; Kurttepeli, M.; Vanbutsele, G.; Gobechiya, E.; Korányi, T.I.; Bals, S.; Van Tendeloo, G.; Ryoo, R.; Kirschhock, C.E.A.; Martens, J.A.;
	Title	Molecular shape-selectivity of MFI zeolite nanosheets in n-decane isomerization and hydrocracking			Type	A1 Journal article
	Year	2013	Publication	Journal of catalysis	Abbreviated Journal	J Catal
	Volume	300	Issue		Pages	70-80
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	MFI zeolite nanosheets with thickness of 2 and 8 nm were synthesized, transformed into bifunctional catalysts by loading with platinum and tested in n-decane isomerization and hydrocracking. Detailed analysis of skeletal isomers and hydrocracked products revealed that the MFI nanosheets display transition-state shape-selectivity similar to bulk MFI zeolite crystals. The suppressed formation of bulky skeletal isomers and C5 cracking products are observed both in the nanosheets and the bulk crystals grown in three dimensions. This is typical for restricted transition-state shape-selectivity, characteristic for the MFI type pores. It is a first clear example of transition-state shape-selectivity inside a zeolitic nanosheet. Owing to the short diffusion path across the sheets, expression of diffusion-based discrimination of reaction products in the MFI nanosheets was limited. The 2-methylnonane formation among monobranched C10 isomers and 2,7-dimethyloctane among dibranched C10 isomers, which in MFI zeolite are favored by product diffusion, was much less favored on the nanosheets compared to the reference bulk ZSM-5 material.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	San Diego, Calif.	Editor
	Language		Wos	000317558000009	Publication Date	2013-02-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9517;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.844	Times cited	121	Open Access
	Notes	Methusalem; IAP; Countatoms			Approved	Most recent IF: 6.844; 2013 IF: 6.073
	Call Number	UA @ lucian @ c:irua:106186			Serial	2181
Permanent link to this record



	Author	Dams, M.; Drijkoningen, L.; Pauwels, B.; Van Tendeloo, G.; de Vos, D.E.; Jacobs, P.A.
	Title	Pd-zeolites as heterogeneous catalysts in heck chemistry			Type	A1 Journal article
	Year	2002	Publication	Journal of catalysis	Abbreviated Journal	J Catal
	Volume	209	Issue	1	Pages	225-236
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000176501100027	Publication Date	2002-10-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9517;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.844	Times cited	157	Open Access
	Notes				Approved	Most recent IF: 6.844; 2002 IF: 3.118
	Call Number	UA @ lucian @ c:irua:54844			Serial	2567
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	Author	Philippaerts, A.; Paulussen, S.; Turner, S.; Lebedev, O.I.; Van Tendeloo, G.; Poelman, H.; Bulut, M.; de Clippel, F.; Smeets, P.; Sels, B.; Jacobs, P.
	Title	Selectivity in sorption and hydrogenation of methyl oleate and elaidate on MFI zeolites			Type	A1 Journal article
	Year	2010	Publication	Journal of catalysis	Abbreviated Journal	J Catal
	Volume	270	Issue	1	Pages	172-184
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	Different zeolites were tested for selective removal of methyl elaidate (trans isomer) from an equimolar mixture with methyl oleate (cis isomer). Sorption experiments of the geometric isomers show that only ZSM-5 samples with reduced Al content in the framework are able to discriminate among the bent cis and the linear trans fatty acid methyl esters. Hydrogenation experiments of equimolar methyl oleate and elaidate mixtures at low temperature (65 °C) and high hydrogen pressure (6.0 MPa), using Pt catalysts, confirm this result. Only with a Pt/NaZSM-5 catalyst outspoken selectivity for the hydrogenation of the trans isomer is obtained. In order to prepare a selective Pt/ZSM-5 catalyst, the influence of Pt addition (impregnation, ion-exchange and competitive ion-exchange) and Pt activation (different calcination and reduction temperatures) on the Pt-distribution and Pt particle size was investigated using SEM, bright-field and HR TEM, EDX, electron tomography, CO-chemisorption, XPS, XRD, and UVvis measurements. The best result in terms of hydrogenation activity and selectivity is obtained with a Pt/ZSM-5 catalyst, which is prepared via competitive ion-exchange, followed by slow calcination up to 350 °C under high O2 flow and a reduction up to 500 °C under H2. This preparation method leads to a Pt/ZSM-5 catalyst with the best Pt distribution and the smallest Pt clusters occluded in the zeolite structure. Finally, the influence of zeolite crystal size, morphology, and elemental composition of ZSM-5 on hydrogenation activity and selectivity was investigated in detail.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	San Diego, Calif.	Editor
	Language		Wos	000275966100021	Publication Date	2010-01-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9517;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.844	Times cited	24	Open Access
	Notes	FWO; IAP-IV; Methusalem			Approved	Most recent IF: 6.844; 2010 IF: 5.415
	Call Number	UA @ lucian @ c:irua:82435			Serial	2970
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	Author	Leus, K.; Liu, Y.-Y.; Meledina, M.; Turner, S.; Van Tendeloo, G.; van der Voort, P.
	Title	A Mo^VI grafted metal organic framework : synthesis, characterization and catalytic investigations			Type	A1 Journal article
	Year	2014	Publication	Journal of catalysis	Abbreviated Journal	J Catal
	Volume	316	Issue		Pages	201-209
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	We present the post-modification of a gallium based Metal Organic Framework, COMOC-4, with a Mo-complex. The resulting Mo@COMOC-4 was characterized by means of N2 sorption, XRPD, DRIFT, TGA, XRF, XPS and TEM analysis. The results demonstrate that even at high Mo-complex loadings on the framework, no aggregation or any Mo or Mo oxide species are formed. Moreover, the Mo@COMOC-4 was evaluated as a catalyst in the epoxidation of cyclohexene, cyclooctene and cyclododecene employing TBHP in decane as oxidant. The post-modified COMOC-4 exhibits a very high selectivity toward the epoxide (up to 100%). Regenerability and stability tests have been carried out demonstrating that the catalyst can be recycled without leaching of Mo or loss of crystallinity.
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	Corporate Author				Thesis
	Publisher		Place of Publication	San Diego, Calif.	Editor
	Language		Wos	000340853800020	Publication Date	2014-06-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9517;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.844	Times cited	36	Open Access
	Notes	European Research Council under the Seventh Framework Program (FP7); ; ERC Grant No. 246791 – COUNTATOMS; Hercules; FWO			Approved	Most recent IF: 6.844; 2014 IF: 6.921
	Call Number	UA @ lucian @ c:irua:117416			Serial	3546
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