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	Author	Attri, P.; Han, J.; Choi, S.; Choi, E.H.; Bogaerts, A.; Lee, W.
	Title	CAP modifies the structure of a model protein from thermophilic bacteria: mechanisms of CAP-mediated inactivation			Type	A1 Journal article
	Year	2018	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	8	Issue	1	Pages	10218
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Cold atmospheric plasma (CAP) has great potential for sterilization in the food industry, by deactivation of thermophilic bacteria, but the underlying mechanisms are largely unknown. Therefore, we investigate here whether CAP is able to denature/modify protein from thermophilic bacteria. We focus on MTH1880 (MTH) from Methanobacterium thermoautotrophicum as model protein, which we treated with dielectric barrier discharge (DBD) plasma operating in air for 10, 15 and 20 mins. We analysed the structural changes of MTH using circular dichroism, fluorescence and NMR spectroscopy, as well as the thermal and chemical denaturation, upon CAP treatment. Additionally, we performed molecular dynamics (MD) simulations to determine the stability, flexibility and solvent accessible surface area (SASA) of both the native and oxidised protein.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000437414500004	Publication Date	2018-06-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	6	Open Access	OpenAccess
	Notes	We gratefully acknowledge the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by NRF-2017R1A2B2008483 to W.L. through the National Research Foundation of Korea (NRF) and BK+ program (J.H.). E.H.C. acknowledges the NRF (NRF-2016K1A4A3914113 and No. 20100027963). 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: 4.259
	Call Number	PLASMANT @ plasmant @c:irua:152817c:irua:152431			Serial	5002
Permanent link to this record



	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	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	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	Attri, P.; Yusupov, M.; Park, J.H.; Lingamdinne, L.P.; Koduru, J.R.; Shiratani, M.; Choi, E.H.; Bogaerts, A.
	Title	Mechanism and comparison of needle-type non-thermal direct and indirect atmospheric pressure plasma jets on the degradation of dyes			Type	A1 Journal article
	Year	2016	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	6	Issue	6	Pages	34419
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Purified water supply for human use, agriculture and industry is the major global priority nowadays. The advanced oxidation process based on atmospheric pressure non-thermal plasma (NTP) has been used for purification of wastewater, although the underlying mechanisms of degradation of organic pollutants are still unknown. In this study we employ two needle-type atmospheric pressure non-thermal plasma jets, i.e., indirect (ID-APPJ) and direct (D-APPJ) jets operating at Ar feed gas, for the treatment of methylene blue, methyl orange and congo red dyes, for two different times (i.e., 20 min and 30 min). Specifically, we study the decolorization/degradation of all three dyes using the above mentioned plasma sources, by means of UV-Vis spectroscopy, HPLC and a density meter. We also employ mass spectroscopy to verify whether only decolorization or also degradation takes place after treatment of the dyes by the NTP jets. Additionally, we analyze the interaction of OH radicals with all three dyes using reactive molecular dynamics simulations, based on the density functional-tight binding method. This investigation represents the first report on the degradation of these three different dyes by two types of NTP setups, analyzed by various methods, and based on both experimental and computational studies.
	Address	Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Wos	000385172300001	Publication Date	2016-10-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	23	Open Access
	Notes	We gratefully acknowledge the grant received from the SRC program of the National Research Foundation of Korea (NRF), funded by the Korean Government (MEST) (No. 20100029418). PA is thankful to FY 2015 Japan Society for the Promotion of Science (JSPS) invitation fellowship. This work was partly supported by MEXT KAKENHI Grant Number 24108009 and JSPS KAKENHI Grant Number JP16H03895. M. Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216N. 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: 4.259
	Call Number	PLASMANT @ plasmant @ c:irua:135847			Serial	4283
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	Author	Aussems, D.U.B.; Bal, K.M.; Morgan, T.W.; van de Sanden, M.C.M.; Neyts, E.C.
	Title	Mechanisms of elementary hydrogen ion-surface interactions during multilayer graphene etching at high surface temperature as a function of flux			Type	A1 Journal article
	Year	2018	Publication	Carbon	Abbreviated Journal	Carbon
	Volume	137	Issue		Pages	527-532
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In order to optimize the plasma-synthesis and modification process of carbon nanomaterials for applications such as nanoelectronics and energy storage, a deeper understanding of fundamental hydrogengraphite/graphene interactions is required. Atomistic simulations by Molecular Dynamics have proven to be indispensable to illuminate these phenomena. However, severe time-scale limitations restrict them to very fast processes such as reflection, while slow thermal processes such as surface diffusion and molecular desorption are commonly inaccessible. In this work, we could however reach these thermal processes for the first time at time-scales and surface temperatures (1000 K) similar to high-flux plasma exposure experiments during the simulation of multilayer graphene etching by 5 eV H ions. This was achieved by applying the Collective Variable-Driven Hyperdynamics biasing technique, which extended the inter-impact time over a range of six orders of magnitude, down to a more realistic ion-flux of 1023m2s1. The results show that this not only causes a strong shift from predominant ion-to thermally induced interactions, but also significantly affects the hydrogen uptake and surface evolution. This study thus elucidates H ion-graphite/graphene interaction mechanisms and stresses the importance of including long time-scales in atomistic simulations at high surface temperatures to understand the dynamics of the ion-surface system.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000440661700056	Publication Date	2018-05-24
	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	4	Open Access	Not_Open_Access: Available from 25.05.2020
	Notes	DIFFER is part of the Netherlands Organisation for Scientific Research (NWO). K.M.B. is funded as PhD fellow (aspirant) of the FWO-Flanders (Fund for Scientific Research-Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government e department EWI.			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:152172			Serial	4993
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	Author	Aussems, D.U.B.; Bal, K. M.; Morgan, T.W.; van de Sanden, M.C.M.; Neyts, E.C.
	Title	Atomistic simulations of graphite etching at realistic time scales			Type	A1 Journal article
	Year	2017	Publication	Chemical science	Abbreviated Journal	Chem Sci
	Volume	8	Issue	10	Pages	7160-7168
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Hydrogen–graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe timescale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of 1020 m2 s1. The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C–C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching – chemical erosion – is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000411730500055	Publication Date	2017-08-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2041-6520	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.668	Times cited	3	Open Access	OpenAccess
	Notes	DIFFER is part of the Netherlands Organisation for Scientic Research (NWO). K. M. B. is funded as a PhD fellow (aspirant) of the FWO-Flanders (Fund for Scientic Research-Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI.			Approved	Most recent IF: 8.668
	Call Number	PLASMANT @ plasmant @c:irua:145519			Serial	4707
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	Author	Autrique, D.
	Title	Multiphase modelling of a ns-laser-irradiated copper sample			Type	Doctoral thesis
	Year	2014	Publication		Abbreviated Journal
	Volume		Issue		Pages
	Keywords	Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Antwerpen	Editor
	Language		Wos		Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:116428			Serial	2224
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	Author	Autrique, D.; Bogaerts, A.; Lindner, H.; Garcia, C.C.; Niemax, K.
	Title	Design analysis of a laser ablation cell for inductively coupled plasma mass spectrometry by numerical simulation			Type	A1 Journal article
	Year	2008	Publication	Spectrochimica acta: part B : atomic spectroscopy	Abbreviated Journal	Spectrochim Acta B
	Volume	63	Issue	2	Pages	257-270
	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	000254038900016	Publication Date	2007-12-05
	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	26	Open Access
	Notes				Approved	Most recent IF: 3.241; 2008 IF: 2.853
	Call Number	UA @ lucian @ c:irua:67086			Serial	656
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	Author	Autrique, D.; Clair, G.; L'Hermite, D.; Alexiades, V.; Bogaerts, A.; Rethfeld, B.
	Title	The role of mass removal mechanisms in the onset of ns-laser induced plasma formation			Type	A1 Journal article
	Year	2013	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	114	Issue	2	Pages	023301-23310
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The present study focuses on the role of mass removal mechanisms in ns-laser ablation. A copper sample is placed in argon, initially set at standard pressure and temperature. Calculations are performed for a 6 ns laser pulse with a wavelength of 532 nm and laser fluences up to 10 J/cm2. The transient behavior in and above the copper target is described by a hydrodynamic model. Transmission profiles and ablation depths are compared with experimental results and similar trends are found. Our calculations reveal an interesting self-inhibiting mechanism: volumetric mass removal in the supercritical region triggers plasma shielding and therefore stops proceeding. This self-limiting process indicates that volumetric mass removal does not necessarily result in large ablation depths.
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000321761600006	Publication Date	2013-07-08
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-8979;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.068	Times cited	31	Open Access
	Notes				Approved	Most recent IF: 2.068; 2013 IF: 2.185
	Call Number	UA @ lucian @ c:irua:109237			Serial	2915
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	Author	Autrique, D.; Gornushkin, I.; Alexiades, V.; Chen, Z.; Bogaerts, A.; Rethfeld, B.
	Title	Revisiting the interplay between ablation, collisional, and radiative processes during ns-laser ablation			Type	A1 Journal article
	Year	2013	Publication	Applied physics letters	Abbreviated Journal	Appl Phys Lett
	Volume	103	Issue	17	Pages	174102-174105
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	A study of ns-laser ablation is presented, which focuses on the transient behavior of the physical processes that act in and above a copper sample. A dimensionless multiphase collisional radiative model describes the interplay between the ablation, collisional, and radiative mechanisms. Calculations are done for a 6 ns-Nd:YAG laser pulse operating at 532 nm and fluences up to 15 J/cm2. Temporal intensity profiles as well as transmissivities are in good agreement with experimental results. It is found that volumetric ablation mechanisms and photo-processes both play an essential role in the onset of ns-laser induced breakdown.
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000326455100107	Publication Date	2013-10-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-6951;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.411	Times cited	13	Open Access
	Notes				Approved	Most recent IF: 3.411; 2013 IF: 3.515
	Call Number	UA @ lucian @ c:irua:110944			Serial	2906
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	Author	Baguer, N.; Bogaerts, A.
	Title	Study of the sputtered Cu atoms and Cu⁺ ions in a hollow cathode glow discharge using a hybrid model			Type	A1 Journal article
	Year	2005	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	98	Issue	3	Pages	033303,1-033303,11
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The role of the Cu atoms sputtered from the cathode material in a cylindrical hollow cathode discharge (HCD) and the corresponding Cu+ ions are studied with a self-consistent model based on the principle of Monte Carlo (MC) and fluid simulations. In order to obtain a more realistic view of the discharge processes, this model is coupled with other submodels, which describe the behavior of electrons, fast Ar atoms, Ar+ ions, and Ar metastable atoms, also based on the principles of MC and fluid simulations. Typical results are, among others, the thermalization profile of the Cu atoms, the fast Cu atom, the thermal Cu atom and Cu+ ion fluxes and densities, and the energy distribution of the Cu+ ions. It was found that the contribution of the Ar+ ions to the sputtering was the most significant, followed by the fast Ar atoms. At the cathode bottom, there was no net sputtered flux but a net amount of redeposition. Throughout the discharge volume, at all the conditions investigated, the largest concentration of Cu atoms was found in the lower half of the HCD, close to the bottom. Penning ionization was found the main ionization mechanism for the Cu atoms. The ionization degree of copper atoms was found to be in the same order as for the argon atoms (10-4). (c) 2005 American Institute of Physics.
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000231246100007	Publication Date	2005-08-08
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-8979;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.068	Times cited	18	Open Access
	Notes				Approved	Most recent IF: 2.068; 2005 IF: 2.498
	Call Number	UA @ lucian @ c:irua:54597			Serial	3340
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	Author	Baguer, N.; Bogaerts, A.; Donko, Z.; Gijbels, R.; Sadeghi, N.
	Title	Study of the Ar metastable atom population in a hollow cathode discharge by means of a hybrid model and spectrometric measurements			Type	A1 Journal article
	Year	2005	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	97	Issue		Pages	123305,1-12
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000230278100014	Publication Date	2005-06-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-8979;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.068	Times cited	40	Open Access
	Notes				Approved	Most recent IF: 2.068; 2005 IF: 2.498
	Call Number	UA @ lucian @ c:irua:53102			Serial	3334
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	Author	Baguer, N.; Bogaerts, A.; Gijbels, R.
	Title	Hybrid model for a cylindrical hollow cathode glow discharge and comparison with experiments			Type	A1 Journal article
	Year	2002	Publication	Spectrochimica acta: part B : atomic spectroscopy	Abbreviated Journal	Spectrochim Acta B
	Volume	57	Issue		Pages	311-326
	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	000174639800008	Publication Date	2002-10-15
	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	31	Open Access
	Notes				Approved	Most recent IF: 3.241; 2002 IF: 2.695
	Call Number	UA @ lucian @ c:irua:40180			Serial	1521
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	Author	Baguer, N.; Bogaerts, A.; Gijbels, R.
	Title	Role of the fast Ar atoms, Ar⁺ ions and metastable Ar atoms in a hollow cathode glow discharge: study by a hybrid model			Type	A1 Journal article
	Year	2003	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	94	Issue		Pages	2212-2222
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000184469800011	Publication Date	2003-08-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-8979;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.068	Times cited	19	Open Access
	Notes				Approved	Most recent IF: 2.068; 2003 IF: 2.171
	Call Number	UA @ lucian @ c:irua:44013			Serial	2926
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	Author	Baguer, N.; Bogaerts, A.; Gijbels, R.
	Title	A self-consistent mathematical model of a hollow cathode glow discharge			Type	P1 Proceeding
	Year	1999	Publication		Abbreviated Journal
	Volume		Issue		Pages	157-158
	Keywords	P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	Polish Academyn of Sciences, Space Research Centre	Place of Publication	Warsaw	Editor
	Language		Wos	000165992500079	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record; WoS full record;
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:103981			Serial	2972
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	Author	Baguer, N.; Bogaerts, A.; Gijbels, R.
	Title	Study of a hollow cathode glow discharge in He: Monte Carlo-fluid model combined with a transport model for the metastable atoms			Type	A1 Journal article
	Year	2003	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	93	Issue		Pages	47-55
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000180002500009	Publication Date	2002-12-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-8979;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.068	Times cited	24	Open Access
	Notes				Approved	Most recent IF: 2.068; 2003 IF: 2.171
	Call Number	UA @ lucian @ c:irua:44010			Serial	3324
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	Author	Baguer, N.; Georgieva, V.; Calderin, L.; Todorov, I.T.; van Gils, S.; Bogaerts, A.
	Title	Study of the nucleation and growth of TiO₂ and ZnO thin films by means of molecular dynamics simulations			Type	A1 Journal article
	Year	2009	Publication	Journal of crystal growth	Abbreviated Journal	J Cryst Growth
	Volume	311	Issue	16	Pages	4034-4043
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The nucleation and growth of titanium dioxide (TiO2) and zinc oxide (ZnO) thin films on Fe2O3 (hematite), Al2O3 (á-alumina) and SiO2 (á-quartz) are studied by molecular dynamics simulations. The results show the formation of a strong interface region between the substrate and the film in the six systems studied here. A combination of polycrystalline and amorphous phases are observed in the TiO2 films grown on the three substrates. ZnO deposition on the Fe2O3 and Al2O3 crystals yields a monocrystalline film growth. The ZnO film deposited on the SiO2 crystal exhibits less crystallinity. The simulation results are compared with experimental results available in the literature.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000269580100012	Publication Date	2009-06-24
	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	23	Open Access
	Notes				Approved	Most recent IF: 1.751; 2009 IF: 1.534
	Call Number	UA @ lucian @ c:irua:77453			Serial	3338
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	Author	Baguer, N.; Neyts, E.; van Gils, S.; Bogaerts, A.
	Title	Study of atmospheric MOCVD of TiO₂ thin films by means of computational fluid dynamics simulations			Type	A1 Journal article
	Year	2008	Publication	Chemical vapor deposition	Abbreviated Journal	Chem Vapor Depos
	Volume	14	Issue	11/12	Pages	339-346
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	This paper presents the computational study of the metal-organic (MO) CVD of titanium dioxide (TiO2) films grown using titanium tetraisopropoxide (TTIP) as a precursor and nitrogen as a carrier gas. The TiO2 films are deposited under atmospheric pressure. The effects of the precursor concentration, the substrate temperature, and the hydrolysis reaction on the deposition process are investigated. It is found that hydrolysis of the TTIP decreases the onset temperature of the gas-phase thermal decomposition, and that the deposition rate increases with the precursor concentration and with the decrease of substrate temperature. Concerning the mechanism responsible for the film growth, the model shows that at the lowest precursor concentration, the direct adsorption of the precursor is dominant, while at higher precursor concentrations, the monomer deposition becomes more important.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Weinheim	Editor
	Language		Wos	000262215800003	Publication Date	2008-12-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0948-1907;1521-3862;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.333	Times cited	14	Open Access
	Notes				Approved	Most recent IF: 1.333; 2008 IF: 1.483
	Call Number	UA @ lucian @ c:irua:71905			Serial	3325
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	Author	Bahnamiri, O.S.; Verheyen, C.; Snyders, R.; Bogaerts, A.; Britun, N.
	Title	Nitrogen fixation in pulsed microwave discharge studied by infrared absorption combined with modelling			Type	A1 Journal Article;nitrogen fixation
	Year	2021	Publication	Plasma Sources Science & Technology	Abbreviated Journal	Plasma Sources Sci T
	Volume	30	Issue	6	Pages	065007
	Keywords	A1 Journal Article;nitrogen fixation; pulsed microwave discharge; FTIR spectroscopy; discharge modelling; vibrational excitation; NO yield; energy cost; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	A pulsed microwave surfaguide discharge operating at 2.45 GHz was used for the conversion of molecular nitrogen into valuable compounds in several gas mixtures: N2 :O2 , N2 :O2 :CO2 and N2 :CO2 . The ro-vibrational absorption bands of the molecular species were monitored by a Fourier transform infrared apparatus in the post-discharge region in order to evaluate the relative number density of species, specifically NO production. The effects of specific energy input, pulse frequency, gas flow fraction, gas admixture and gas flow rate were studied for better understanding and optimization of the NO production yield and the corresponding energy cost (EC). By both the experiment and modelling, a highest NO yield is obtained at N2 :O2 (1:1) gas ratio in N2 :O2 mixture. The NO yield reveals a small growth followed by saturation when pulse repetition frequency increases. The energy efficiency start decreasing after the energy input reaches about 5 eV/molec, whereas the NO yield rises steadily at the same time. The lowest EC of about 8 MJ mol−1 corresponding to the yield and the energy efficiency of about 7% and 1% are found, respectively, in an optimum discharge condition in our case.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000659671000001	Publication Date	2021-06-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0963-0252	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.302	Times cited		Open Access	OpenAccess
	Notes	Fonds De La Recherche Scientifique—FNRS, EOS O005118F ; The research is supported by the FNRS-FWO project ‘NITROPLASM’, EOS O005118F. O Samadi also acknowledges PhD student F Manaigo for cooperation in doing the additional measurements.			Approved	Most recent IF: 3.302
	Call Number	PLASMANT @ plasmant @c:irua:179170			Serial	6798
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	Author	Bal, K.
	Title	New ways to bridge the gap between microscopic simulations and macroscopic chemistry			Type	Doctoral thesis
	Year	2018	Publication		Abbreviated Journal
	Volume		Issue		Pages
	Keywords	Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Antwerpen	Editor
	Language		Wos		Publication Date
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:154836			Serial	5118
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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	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	Bal, K.M.; Bogaerts, A.; Neyts, E.C.
	Title	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium			Type	A1 Journal article
	Year	2020	Publication	Journal Of Physical Chemistry Letters	Abbreviated Journal	J Phys Chem Lett
	Volume	11	Issue	2	Pages	401-406
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We present an approach to incorporate the eﬀect of vibrational nonequilibrium in molecular dynamics (MD) simulations. A perturbed canonical ensemble, in which selected modes are excited to higher temperature while all others remain equilibrated at low temperature, is simulated by applying a speciﬁcally tailored bias potential. Our method can be readily applied to any (classical or quantum mechanical) MD setup at virtually no additional computational cost and allows the study of reactions of vibrationally excited molecules in nonequilibrium environments such as plasmas. In combination with enhanced sampling methods, the vibrational eﬃcacy and mode selectivity of vibrationally stimulated reactions can then be quantiﬁed in terms of chemically relevant observables, such as reaction rates and apparent free energy barriers. We ﬁrst validate our method for the prototypical hydrogen exchange reaction and then show how it can capture the eﬀect of vibrational excitation on a symmetric SN2 reaction and radical addition on CO2.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000508473400008	Publication Date	2020-01-16
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1948-7185	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.7	Times cited		Open Access
	Notes	Universiteit Antwerpen; Fonds Wetenschappelijk Onderzoek, 12ZI420N ; Departement Economie, Wetenschap en Innovatie van de Vlaamse Overheid; K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation − Flanders), Grant 12ZI420N, and through a TOP-BOF research project of the University of Antwerp. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government− department EWI.			Approved	Most recent IF: 5.7; 2020 IF: 9.353
	Call Number	PLASMANT @ plasmant @c:irua:165587			Serial	5442
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	Author	Bal, K.M.; Cautereels, J.; Blockhuys, F.
	Title	Structures and spectroscopic properties of sulfur-nitrogen-pnictogen chains : R₂P-N=S=N-PR₂ and R₂P-N=S=N-AsR₂			Type	A1 Journal article
	Year	2017	Publication	Journal of molecular structure	Abbreviated Journal	J Mol Struct
	Volume	1132	Issue		Pages	102-108
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The conformational and configurational preferences of Me2PNSNPMe2 (3) and Me2PNSNAsMe2 (4) have been identified using quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. An approach in which energetic, structural (geometries and bond orders), electronic (analysis of the electron density) and spectroscopic properties are combined leads to the conclusion that these sulfur-nitrogen-pnictogen chains share many of the properties of their chalcogen-nitrogen analogues but that the through-space intramolecular interactions favouring the Z,Z configuration are even weaker than in these latter compounds. The results of this analysis also lead to an unambiguous assignment of the variable-temperature 31P and 15N NMR spectra of these compounds and their structures both in solution and in the solid state.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000393254400015	Publication Date	2016-08-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-2860	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	1.753	Times cited		Open Access	Not_Open_Access: Available from 03.10.2019
	Notes				Approved	Most recent IF: 1.753
	Call Number	UA @ lucian @ c:irua:145533			Serial	4726
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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	Bal, K.M.; Huygh, S.; Bogaerts, A.; Neyts, E.C.
	Title	Effect of plasma-induced surface charging on catalytic processes: application to CO₂activation			Type	A1 Journal article
	Year	2018	Publication	Plasma sources science and technology	Abbreviated Journal	Plasma Sources Sci T
	Volume	27	Issue	2	Pages	024001
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Understanding the nature and effect of the multitude of plasma–surface interactions in plasma catalysis is a crucial requirement for further process development and improvement. A particularly intriguing and rather unique property of a plasma-catalytic setup is the ability of the plasma to modify the electronic structure, and hence chemical properties, of the catalyst through charging, i.e. the absorption of excess electrons. In this work, we develop a quantum chemical model based on density functional theory to study excess negative surface charges in a heterogeneous catalyst exposed to a plasma. This method is specifically applied to investigate plasma-catalytic CO2 activation on supported M/Al2O3 (M=Ti, Ni, Cu) single atom catalysts. We find that (1) the presence of a negative surface charge dramatically improves the reductive power of the catalyst, strongly promoting the splitting of CO2 to CO and oxygen, and (2) the relative activity of the investigated transition metals is also changed upon charging, suggesting that controlled surface charging is a powerful additional parameter to tune catalyst activity and selectivity. These results strongly point to plasma-induced surface charging of the catalyst as an important factor contributing to the plasma-catalyst synergistic effects frequently reported for plasma catalysis.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000424520100001	Publication Date	2018-02-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1361-6595	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.302	Times cited	19	Open Access	OpenAccess
	Notes	KMB is funded as PhD fellow (aspirant) of the FWO-Flanders (Research Foundation—Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government— department EWI.			Approved	Most recent IF: 3.302
	Call Number	PLASMANT @ plasmant @c:irua:149285			Serial	4813
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	Author	Bal, K.M.; Neyts, E.C.
	Title	On the time scale associated with Monte Carlo simulations			Type	A1 Journal article
	Year	2014	Publication	The journal of chemical physics	Abbreviated Journal	J Chem Phys
	Volume	141	Issue	20	Pages	204104
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000345641400005	Publication Date	2014-11-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9606;1089-7690;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.965	Times cited	26	Open Access
	Notes				Approved	Most recent IF: 2.965; 2014 IF: 2.952
	Call Number	UA @ lucian @ c:irua:120667			Serial	2459
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	Author	Bal, K.M.; Neyts, E.C.
	Title	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.; Neyts, E.C.
	Title	Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations			Type	A1 Journal article
	Year	2016	Publication	Chemical science	Abbreviated Journal	Chem Sci
	Volume	7	Issue	7	Pages	5280-5286
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Atomistic simulations can in principle provide an unbiased description of all mechanisms, intermediates, and products of complex chemical processes. However, due to the severe time scale limitation of conventional simulation techniques, unrealistically high simulation temperatures are usually applied, which are a poor approximation of most practically relevant low-temperature applications. In this work, we demonstrate the direct observation at the atomic scale of the pyrolysis and oxidation of n-dodecane at temperatures as low as 700 K through the use of a novel simulation technique, collective variable-driven hyperdynamics (CVHD). A simulated timescale of up to 39 seconds is reached. Product compositions and dominant mechanisms are found to be strongly temperature-dependent, and are consistent with experiments and kinetic models. These simulations provide a first atomic-level look at the full dynamics of the complicated fuel combustion process at industrially relevant temperatures and time scales, unattainable by conventional molecular dynamics simulations.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000380893900059	Publication Date	2016-05-05
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2041-6520	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.668	Times cited	22	Open Access
	Notes	K. M. B. is funded as PhD fellow (aspirant) of the FWO-Flanders (Fund for Scientic Research-Flanders), Grant 11V8915N. 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. The authors would also like to thank S. Banerjee for assisting with the interpretation of the experimental results.			Approved	Most recent IF: 8.668
	Call Number	c:irua:134577 c:irua:135670			Serial	4105
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