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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.
Address
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 (down) 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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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 (down) 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 Khalilov, U.; Bogaerts, A.; Neyts, E.C.
Title Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors Type A1 Journal article
Year 2015 Publication Nature communications Abbreviated Journal Nat Commun
Volume 6 Issue 6 Pages 10306
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level.
Address PLASMANT research group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium
Corporate Author Thesis
Publisher Place of Publication Editor
Language English Wos 000367584500001 Publication Date 2015-12-22
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2041-1723 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 12.124 Times cited 37 Open Access
Notes The authors gratefully acknowledge financial support from the Fund of Scientific Research Flanders (FWO), Belgium, grant number 12M1315N. The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. We thank Professor Adri C. T. van Duin for sharing the ReaxFF code. Approved Most recent IF: 12.124; 2015 IF: 11.470
Call Number c:irua:129975 Serial 3990
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Author Elliott, J.A.; Shibuta, Y.; Amara, H.; Bichara, C.; Neyts, E.C.
Title Atomistic modelling of CVD synthesis of carbon nanotubes and graphene Type A1 Journal article
Year 2013 Publication Nanoscale Abbreviated Journal Nanoscale
Volume 5 Issue 15 Pages 6662-6676
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract We discuss the synthesis of carbon nanotubes (CNTs) and graphene by catalytic chemical vapour deposition (CCVD) and plasma-enhanced CVD (PECVD), summarising the state-of-the-art understanding of mechanisms controlling their growth rate, chiral angle, number of layers (walls), diameter, length and quality (defects), before presenting a new model for 2D nucleation of a graphene sheet from amorphous carbon on a nickel surface. Although many groups have modelled this process using a variety of techniques, we ask whether there are any complementary ideas emerging from the different proposed growth mechanisms, and whether different modelling techniques can give the same answers for a given mechanism. Subsequently, by comparing the results of tight-binding, semi-empirical molecular orbital theory and reactive bond order force field calculations, we demonstrate that graphene on crystalline Ni(111) is thermodynamically stable with respect to the corresponding amorphous metal and carbon structures. Finally, we show in principle how a complementary heterogeneous nucleation step may play a key role in the transformation from amorphous carbon to graphene on the metal surface. We conclude that achieving the conditions under which this complementary crystallisation process can occur may be a promising method to gain better control over the growth processes of both graphene from flat metal surfaces and CNTs from catalyst nanoparticles.
Address
Corporate Author Thesis
Publisher Place of Publication Cambridge Editor
Language Wos 000321675600003 Publication Date 2013-06-06
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2040-3364;2040-3372; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.367 Times cited 52 Open Access
Notes Approved Most recent IF: 7.367; 2013 IF: 6.739
Call Number UA @ lucian @ c:irua:109231 Serial 200
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Author Neyts, E.C.; van Duin, A.C.T.; Bogaerts, A.
Title Formation of single layer graphene on nickel under far-from-equilibrium high flux conditions Type A1 Journal article
Year 2013 Publication Nanoscale Abbreviated Journal Nanoscale
Volume 5 Issue 16 Pages 7250-7255
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract We investigate the theoretical possibility of single layer graphene formation on a nickel surface at different substrate temperatures under far-from-equilibrium high precursor flux conditions, employing state-of-the-art hybrid reactive molecular dynamics/uniform acceptance force bias Monte Carlo simulations. It is predicted that under these conditions, the formation of a single layer graphene-like film may proceed through a combined depositionsegregation mechanism on a nickel substrate, rather than by pure surface segregation as is typically observed for metals with high carbon solubility. At 900 K and above, nearly continuous graphene layers are obtained. These simulations suggest that single layer graphene deposition is theoretically possible on Ni under high flux conditions.
Address
Corporate Author Thesis
Publisher Place of Publication Cambridge Editor
Language Wos 000322315600019 Publication Date 2013-04-26
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2040-3364;2040-3372; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.367 Times cited 25 Open Access
Notes Approved Most recent IF: 7.367; 2013 IF: 6.739
Call Number UA @ lucian @ c:irua:109249 Serial 1264
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Author Khalilov, U.; Bogaerts, A.; Neyts, E.C.
Title Microscopic mechanisms of vertical graphene and carbon nanotube cap nucleation from hydrocarbon growth precursors Type A1 Journal article
Year 2014 Publication Nanoscale Abbreviated Journal Nanoscale
Volume 6 Issue 15 Pages 9206-9214
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Controlling and steering the growth of single walled carbon nanotubes is often believed to require controlling of the nucleation stage. Yet, little is known about the microscopic mechanisms governing the nucleation from hydrocarbon molecules. Specifically, we address here the dehydrogenation of hydrocarbon molecules and the formation of all-carbon graphitic islands on metallic nanoclusters from hydrocarbon molecules under conditions typical for carbon nanotube growth. Employing reactive molecular dynamics simulations, we demonstrate for the first time that the formation of a graphitic network occurs through the intermediate formation of vertically oriented, not fully dehydrogenated graphitic islands. Upon dehydrogenation of these vertical graphenes, the islands curve over the surface, thereby forming a carbon network covering the nanoparticle. The results indicate that controlling the extent of dehydrogenation offers an additional parameter to control the nucleation of carbon nanotubes.
Address
Corporate Author Thesis
Publisher Place of Publication Cambridge Editor
Language Wos 000339861500103 Publication Date 2014-05-27
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2040-3364;2040-3372; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.367 Times cited 21 Open Access
Notes Approved Most recent IF: 7.367; 2014 IF: 7.394
Call Number UA @ lucian @ c:irua:117950 Serial 2027
Permanent link to this record
 
 
Author Khalilov, U.; Pourtois, G.; Bogaerts, A.; van Duin, A.C.T.; Neyts, E.C.
Title Reactive molecular dynamics simulations on SiO2-coated ultra-small Si-nanowires Type A1 Journal article
Year 2013 Publication Nanoscale Abbreviated Journal Nanoscale
Volume 5 Issue 2 Pages 719-725
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The application of coreshell SiSiO2 nanowires as nanoelectronic devices strongly depends on their structure, which is difficult to tune precisely. In this work, we investigate the formation of the coreshell nanowires at the atomic scale, by reactive molecular dynamics simulations. The occurrence of two temperature-dependent oxidation mechanisms of ultra-small diameter Si-NWs is demonstrated. We found that control over the Si-core radius and the SiOx (x ≤ 2) oxide shell is possible by tuning the growth temperature and the initial Si-NW diameter. Two different structures were obtained, i.e., ultrathin SiO2 silica nanowires at high temperature and Si core|ultrathin SiO2 silica nanowires at low temperature. The transition temperature is found to linearly decrease with the nanowire curvature. Finally, the interfacial stress is found to be responsible for self-limiting oxidation, depending on both the initial Si-NW radius and the oxide growth temperature. These novel insights allow us to gain control over the exact morphology and structure of the wires, as is needed for their application in nanoelectronics.
Address
Corporate Author Thesis
Publisher Place of Publication Cambridge Editor
Language Wos 000313426200036 Publication Date 2012-11-16
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2040-3364;2040-3372; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.367 Times cited 17 Open Access
Notes Approved Most recent IF: 7.367; 2013 IF: 6.739
Call Number UA @ lucian @ c:irua:102584 Serial 2824
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Author Engelmann, Y.; Bogaerts, A.; Neyts, E.C.
Title Thermodynamics at the nanoscale : phase diagrams of nickel-carbon nanoclusters and equilibrium constants for face transitions Type A1 Journal article
Year 2014 Publication Nanoscale Abbreviated Journal Nanoscale
Volume 6 Issue Pages 11981-11987
Keywords A1 Journal article; PLASMANT
Abstract Using reactive molecular dynamics simulations, the melting behavior of nickelcarbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickelcarbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method.
Address
Corporate Author Thesis
Publisher Place of Publication Cambridge Editor
Language Wos 000343000800049 Publication Date 2014-07-24
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2040-3364;2040-3372; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.367 Times cited 20 Open Access
Notes Approved Most recent IF: 7.367; 2014 IF: 7.394
Call Number UA @ lucian @ c:irua:119408 Serial 3636
Permanent link to this record
 
 
Author Engelmann; Bogaerts, A.; Neyts, E.C.
Title Thermodynamics at the nanoscale: phase diagrams of nickel-carbon nanoclusters and equilibrium constants for phase transitions Type A1 Journal article
Year 2014 Publication Nanoscale Abbreviated Journal Nanoscale
Volume 6 Issue 20 Pages 11981-11987
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Using reactive molecular dynamics simulations, the melting behavior of nickel-carbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickel-carbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method.
Address
Corporate Author Thesis
Publisher Place of Publication Cambridge Editor
Language Wos 000343000800049 Publication Date 2014-07-24
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2040-3364;2040-3372; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.367 Times cited 20 Open Access
Notes Approved Most recent IF: 7.367; 2014 IF: 7.394
Call Number UA @ lucian @ c:irua:121106 Serial 3637
Permanent link to this record
 
 
Author Faraji, F.; Neek-Amal, M.; Neyts, E.C.; Peeters, F.M.
Title Indentation of graphene nano-bubbles Type A1 Journal article
Year 2022 Publication Nanoscale Abbreviated Journal Nanoscale
Volume 14 Issue 15 Pages 5876-5883
Keywords A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Molecular dynamics simulations are used to investigate the effect of an AFM tip when indenting graphene nano bubbles filled by a noble gas (i.e. He, Ne and Ar) up to the breaking point. The failure points resemble those of viral shells as described by the Foppl-von Karman (FvK) dimensionless number defined in the context of elasticity theory of thin shells. At room temperature, He gas inside the bubbles is found to be in the liquid state while Ne and Ar atoms are in the solid state although the pressure inside the nano bubble is below the melting pressure of the bulk. The trapped gases are under higher hydrostatic pressure at low temperatures than at room temperature.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000776763000001 Publication Date 2022-03-30
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2040-3364; 2040-3372 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.7 Times cited Open Access OpenAccess
Notes Approved Most recent IF: 6.7
Call Number UA @ admin @ c:irua:187924 Serial 7171
Permanent link to this record
 
 
Author Khalilov, U.; Bogaerts, A.; Xu, B.; Kato, T.; Kaneko, T.; Neyts, E.C.
Title How the alignment of adsorbed ortho H pairs determines the onset of selective carbon nanotube etching Type A1 Journal article
Year 2017 Publication Nanoscale Abbreviated Journal Nanoscale
Volume 9 Issue 9 Pages 1653-1661
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Unlocking the enormous technological potential of carbon nanotubes strongly depends on our ability to specifically produce metallic or semiconducting tubes. While selective etching of both has already been demonstrated, the underlying reasons, however, remain elusive as yet. We here present computational and experimental evidence on the operative mechanisms at the atomic scale. We demonstrate that during the adsorption of H atoms and their coalescence, the adsorbed ortho hydrogen pairs on single-walled carbon nanotubes induce higher shear stresses than axial stresses, leading to the elongation of HC–CH bonds as a function of their alignment with the tube chirality vector, which we denote as the γ-angle. As a result, the C–C cleavage occurs more rapidly in nanotubes containing ortho H-pairs with a small γ-angle. This phenomenon can explain the selective etching of small-diameter semiconductor nanotubes with a similar curvature. Both theoretical and experimental results strongly indicate the important role of the γ-angle in the selective etching mechanisms of carbon nanotubes, in addition to the nanotube curvature and metallicity effects and lead us to clearly understand the onset of selective synthesis/removal of CNT-based materials.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000395422800036 Publication Date 2016-12-19
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2040-3364 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.367 Times cited 6 Open Access OpenAccess
Notes U. K. gratefully acknowledges financial support from the Fund of Scientific Research Flanders (FWO), Belgium (Grant No. 12M1315N). This work was also supported in part by Grant-in- Aid for Young Scientists A (Grant No. 25706028), Grant-in-Aid for Scientific Research on Innovative Areas (Grant No. 26107502) from JSPS KAKENHI. This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. The authors also thank Prof. A. C. T. van Duin for sharing the ReaxFF code and J. Razzokov for his assistance to perform the DFT calculations. Approved Most recent IF: 7.367
Call Number PLASMANT @ plasmant @ c:irua:140091 Serial 4417
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Author Zaryouh, H.; Verswyvel, H.; Bauwens, M.; Van Haesendonck, G.; Deben, C.; Lin, A.; De Waele, J.; Vermorken, J.B.; Koljenovic, S.; Bogaerts, A.; Lardon, F.; Smits, E.; Wouters, A.
Title De belofte van hoofdhalskankerorganoïden in kankeronderzoek : een blik op de toekomst Type A2 Journal article
Year 2023 Publication Onco-hemato : multidisciplinair tijdschrift voor oncologie Abbreviated Journal
Volume 17 Issue 7 Pages 54-58
Keywords A2 Journal article; Center for Oncological Research (CORE); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Hoofd-halskanker vormt een aanzienlijke uitdaging met bijna 900.000 nieuwe diagnoses per jaar, waarbij de jaarlijkse incidentie blijft stijgen. Vaak wordt de diagnose pas in een laat stadium gesteld, wat complexe behandelingen noodzakelijk maakt. Terugval van patiënten is helaas een veelvoorkomend probleem. De gemiddelde overlevingsduur is beperkt tot enkele maanden. Daarom is er een dringende behoefte om nieuwe, veelbelovende behandelingen te ontwikkelen voor patiënten met hoofd-halskanker. Voor het bereiken van deze vooruitgang spelen innovatieve studiemodellen een cruciale rol. Het ontwikkelen van deze nieuwe behandelingen start met laboratoriumonderzoek, waarbij traditionele tweedimensionale celculturen hun beperkingen hebben. Daarom verschuiven onderzoekers hun aandacht meer en meer naar geavanceerdere driedimensionale modellen, met hoofd-halskankerorganoïden als beloftevol nieuw model. Dit model behoudt immers zowel het genetische profiel als de morfologische kenmerken van de originele tumor van de hoofd-halskankerpatiënt. Hoofdhalskankerorganoïden bieden daarom de mogelijkheid om innovatieve behandelingen te testen en kunnen mogelijk zelfs de respons van een patiënt op bepaalde therapieën voorspellen. Hoewel tumororganoïden als ‘patiënt-in-het-lab’ veelbelovend zijn, zijn er uitdagingen te overwinnen, zoals de ontwikkelingstijd en de toepasbaarheid bij alle tumortypes, evenals het ontbreken van immuuncellen en andere micro-omgevingscomponenten. Er is daarom een grote behoefte aan gestandaardiseerde protocollen voor de ontwikkeling van organoïden en verkorting van de ontwikkelingstijd. Concluderend bieden driedimensionale hoofd-halskankerorganoïden een veelbelovend perspectief voor de toekomst van kankerbehandelingen. Ze hebben het potentieel om bij te dragen aan de ontwikkeling van gepersonaliseerde behandelingen en zo de overlevingskansen van kankerpatiënten te verbeteren. Het is echter belangrijk om hun voorspellend vermogen en toepassingsmogelijkheden verder te onderzoeken, voordat ze op grote schaal worden geïmplementeerd.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos Publication Date
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 2030-2738 ISBN Additional Links UA library record
Impact Factor Times cited Open Access
Notes Approved Most recent IF: NA
Call Number UA @ admin @ c:irua:202271 Serial 9004
Permanent link to this record
 
 
Author Scalise, E.; Houssa, M.; Pourtois, G.; Afanas'ev, V.; Stesmans, A.
Title Strain-induced semiconductor to metal transition in the two-dimensional honeycomb structure of MoS2 Type A1 Journal article
Year 2012 Publication Nano Research Abbreviated Journal Nano Res
Volume 5 Issue 1 Pages 43-48
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The electronic properties of two-dimensional honeycomb structures of molybdenum disulfide (MoS(2)) subjected to biaxial strain have been investigated using first-principles calculations based on density functional theory. On applying compressive or tensile bi-axial strain on bi-layer and mono-layer MoS(2), the electronic properties are predicted to change from semiconducting to metallic. These changes present very interesting possibilities for engineering the electronic properties of two-dimensional structures of MoS(2).
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000299085200006 Publication Date 2011-11-10
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1998-0124;1998-0000; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.354 Times cited 407 Open Access
Notes Approved Most recent IF: 7.354; 2012 IF: 7.392
Call Number UA @ lucian @ c:irua:96262 Serial 3169
Permanent link to this record
 
 
Author Scalise, E.; Houssa, M.; Pourtois, G.; van den Broek, B.; Afanas'ev, V.; Stesmans, A.
Title Vibrational properties of silicene and germanene Type A1 Journal article
Year 2013 Publication Nano Research Abbreviated Journal Nano Res
Volume 6 Issue 1 Pages 19-28
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The structural and vibrational properties of two-dimensional hexagonal silicon (silicene) and germanium (germanene) are investigated by means of first-principles calculations. It is predict that the silicene (germanene) structure with a small buckling of 0.44 (0.7 ) and bond lengths of 2.28 (2.44 ) is energetically the most favorable, and it does not exhibit imaginary phonon mode. The calculated non-resonance Raman spectra of silicene is characterized by a main peak at about 575 cm(-1), namely the G-like peak. For germanene, the highest peak is at about 290 cm(-1). Extensive calculations on armchair silicene nanoribbons and armchair germanene nanoribbons are also performed, with and without hydrogenation of the edges. The studies reveal other Raman peaks mainly distributed at lower frequencies than the G-like peak which could be attributed to the defects at the edges of the ribbons, thus not present in the Raman spectra of non-defective silicene and germanene. Particularly the Raman peak corresponding to the D mode is found to be located at around 515 cm(-1) for silicene and 270 cm(-1) for germanene. The calculated G-like and the D peaks are likely the fingerprints of the Raman spectra of the low-buckled structures of silicene and germanene.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000313658800003 Publication Date 2012-12-17
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1998-0124;1998-0000; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.354 Times cited 105 Open Access
Notes Approved Most recent IF: 7.354; 2013 IF: 6.963
Call Number UA @ lucian @ c:irua:110106 Serial 3846
Permanent link to this record
 
 
Author van den Broek, B.; Houssa, M.; Lu, A.; Pourtois, G.; Afanas'ev, V.; Stesmans, A.
Title Silicene nanoribbons on transition metal dichalcogenide substrates : effects on electronic structure and ballistic transport Type A1 Journal article
Year 2016 Publication Nano Research Abbreviated Journal Nano Res
Volume 9 Issue 9 Pages 3394-3406
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The idea of stacking multiple monolayers of different two-dimensional materials has become a global pursuit. In this work, a silicene armchair nanoribbon of width W and van der Waals-bonded to different transition-metal dichalcogenide (TMD) bilayer substrates MoX2 and WX2, where X = S, Se, Te is considered. The orbital resolved electronic structure and ballistic transport properties of these systems are simulated by employing van der Waals-corrected density functional theory and nonequilibrium Green's functions. We find that the lattice mismatch with the underlying substrate determines the electronic structure, correlated with the silicene buckling distortion and ultimately with the contact resistance of the two-terminal system. The smallest lattice mismatch, obtained with the MoTe2 substrate, results in the silicene ribbon properties coming close to those of a freestanding one. With the TMD bilayer acting as a dielectric layer, the electronic structure is tunable from a direct to an indirect semiconducting layer, and subsequently to a metallic electronic dispersion layer, with a moderate applied perpendicular electric field.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000386770300018 Publication Date 2016-08-20
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1998-0124 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.354 Times cited 2 Open Access
Notes Approved Most recent IF: 7.354
Call Number UA @ lucian @ c:irua:138210 Serial 4469
Permanent link to this record
 
 
Author Rezaei, F.; Vanraes, P.; Nikiforov, A.; Morent, R.; De Geyter, N.
Title Applications of plasma-liquid systems : a review Type A1 Journal article
Year 2019 Publication Materials Abbreviated Journal Materials
Volume 12 Issue 17 Pages 2751
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Plasma-liquid systems have attracted increasing attention in recent years, owing to their high potential in material processing and nanoscience, environmental remediation, sterilization, biomedicine, and food applications. Due to the multidisciplinary character of this scientific field and due to its broad range of established and promising applications, an updated overview is required, addressing the various applications of plasma-liquid systems till now. In the present review, after a brief historical introduction on this important research field, the authors aimed to bring together a wide range of applications of plasma-liquid systems, including nanomaterial processing, water analytical chemistry, water purification, plasma sterilization, plasma medicine, food preservation and agricultural processing, power transformers for high voltage switching, and polymer solution treatment. Although the general understanding of plasma-liquid interactions and their applications has grown significantly in recent decades, it is aimed here to give an updated overview on the possible applications of plasma-liquid systems. This review can be used as a guide for researchers from different fields to gain insight in the history and state-of-the-art of plasma-liquid interactions and to obtain an overview on the acquired knowledge in this field up to now.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000488880300104 Publication Date 2019-08-27
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1996-1944 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.654 Times cited 4 Open Access
Notes Approved Most recent IF: 2.654
Call Number UA @ admin @ c:irua:163805 Serial 6285
Permanent link to this record
 
 
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 (down) 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 Ghorbanfekr, H.; Behler, J.; Peeters, F.M.
Title Insights into water permeation through hBN nanocapillaries by ab initio machine learning molecular dynamics simulations Type A1 Journal article
Year 2020 Publication Journal Of Physical Chemistry Letters Abbreviated Journal J Phys Chem Lett
Volume 11 Issue 17 Pages 7363-7370
Keywords A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Water permeation between stacked layers of hBN sheets forming 2D nanochannels is investigated using large-scale ab initio-quality molecular dynamics simulations. A high-dimensional neural network potential trained on density-functional theory calculations is employed. We simulate water in van der Waals nanocapillaries and study the impact of nanometric confinement on the structure and dynamics of water using both equilibrium and nonequilibrium methods. At an interlayer distance of 10.2 A confinement induces a first-order phase transition resulting in a well-defined AA-stacked bilayer of hexagonal ice. In contrast, for h < 9 A, the 2D water monolayer consists of a mixture of different locally ordered patterns of squares, pentagons, and hexagons. We found a significant change in the transport properties of confined water, particularly for monolayer water where the water-solid friction coefficient decreases to half and the diffusion coefficient increases by a factor of 4 as compared to bulk water. Accordingly, the slip-velocity is found to increase under confinement and we found that the overall permeation is dominated by monolayer water adjacent to the hBN membranes at extreme confinements. We conclude that monolayer water in addition to bilayer ice has a major contribution to water transport through 2D nanochannels.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000569375400061 Publication Date 2020-08-10
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1948-7185 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 5.7 Times cited 24 Open Access
Notes ; This work was supported by the Flemish Science Foundation (FWO-Vl) and the Methusalem program (Grant Number: G099219N). The authors thank Arham Amouei for the helpful discussion regarding MD simulations. ; Approved Most recent IF: 5.7; 2020 IF: 9.353
Call Number UA @ admin @ c:irua:171996 Serial 6546
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Author Javdani, Z.; Hassani, N.; Faraji, F.; Zhou, R.; Sun, C.; Radha, B.; Neyts, E.; Peeters, F.M.; Neek-Amal, M.
Title Clogging and unclogging of hydrocarbon-contaminated nanochannels Type A1 Journal article
Year 2022 Publication The journal of physical chemistry letters Abbreviated Journal J Phys Chem Lett
Volume 13 Issue 49 Pages 11454-11463
Keywords A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The recent advantages of the fabrication of artificial nanochannels enabled new research on the molecular transport, permeance, and selectivity of various gases and molecules. However, the physisorption/chemisorption of the unwanted molecules (usually hydrocarbons) inside nanochannels results in the alteration of the functionality of the nanochannels. We investigated contamination due to hydrocarbon molecules, nanochannels made of graphene, hexagonal boron nitride, BC2N, and molybdenum disulfide using molecular dynamics simulations. We found that for a certain size of nanochannel (i.e., h = 0.7 nm), as a result of the anomalous hydrophilic nature of nanochannels made of graphene, the hydrocarbons are fully adsorbed in the nanochannel, giving rise to full uptake. An increasing temperature plays an important role in unclogging, while pressure does not have a significant role. The results of our pioneering work contribute to a better understanding and highlight the important factors in alleviating the contamination and unclogging of nanochannels, which are in good agreement with the results of recent experiments.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000893147700001 Publication Date 2022-12-05
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1948-7185 ISBN Additional Links UA library record; WoS full record
Impact Factor 5.7 Times cited Open Access OpenAccess
Notes Approved Most recent IF: 5.7
Call Number UA @ admin @ c:irua:192815 Serial 7263
Permanent link to this record
 
 
Author Gerrits, N.
Title Accurate simulations of the reaction of H₂ on a curved Pt crystal through machine learning Type A1 Journal article
Year 2021 Publication Journal Of Physical Chemistry Letters Abbreviated Journal J Phys Chem Lett
Volume 12 Issue 51 Pages 12157-12164
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Theoretical studies on molecule-metal surface reactions have so far been limited to small surface unit cells due to computational costs. Here, for the first time molecular dynamics simulations on very large surface unit cells at the level of density functional theory are performed, allowing a direct comparison to experiments performed on a curved crystal. Specifically, the reaction of D-2 on a curved Pt crystal is investigated with a neural network potential (NNP). The developed NNP is also accurate for surface unit cells considerably larger than those that have been included in the training data, allowing dynamical simulations on very large surface unit cells that otherwise would have been intractable. Important and complex aspects of the reaction mechanism are discovered such as diffusion and a shadow effect of the step. Furthermore, conclusions from simulations on smaller surface unit cells cannot always be transfered to larger surface unit cells, limiting the applicability of theoretical studies of smaller surface unit cells to heterogeneous catalysts with small defect densities.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000734045900001 Publication Date 2021-12-17
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1948-7185 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 9.353 Times cited Open Access OpenAccess
Notes Approved Most recent IF: 9.353
Call Number UA @ admin @ c:irua:184717 Serial 7413
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Author Gerrits, N.; Jackson, B.; Bogaerts, A.
Title Accurate Reaction Probabilities for Translational Energies on Both Sides of the Barrier of Dissociative Chemisorption on Metal Surfaces Type A1 Journal Article
Year 2024 Publication The Journal of Physical Chemistry Letters Abbreviated Journal J. Phys. Chem. Lett.
Volume 15 Issue 9 Pages 2566-2572
Keywords A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Abstract Molecular dynamics simulations are essential for a better understanding of dissociative chemisorption on metal surfaces, which is often the rate-controlling step in heterogeneous and plasma catalysis. The workhorse quasi-classical trajectory approach ubiquitous in molecular dynamics is able to accurately predict reactivity only for high translational and low vibrational energies. In contrast, catalytically relevant conditions generally involve low translational and elevated vibrational energies. Existing quantum dynamics approaches are intractable or approximate as a result of the large number of degrees of freedom present in molecule−metal surface reactions. Here, we extend a ring polymer molecular dynamics approach to fully include, for the first time, the degrees of freedom of a moving metal surface. With this approach, experimental sticking probabilities for the dissociative chemisorption of methane on Pt(111) are reproduced for a large range of translational and vibrational energies by including nuclear quantum effects and employing full-dimensional simulations.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001177959900001 Publication Date 2024-03-07
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1948-7185 ISBN Additional Links UA library record; WoS full record
Impact Factor 5.7 Times cited Open Access
Notes Nick Gerrits has been financially supported through a Dutch Research Council (NWO) Rubicon grant (019.202EN.012). The computational resources and services used in this work were provided by the high performance computing (HPC) core facility CalcUA of the Universiteit Antwerpen and the Flemish Supercomputer Center (VSC) funded by the Research Foundation−Flanders (FWO) and the Flemish Government. The authors thank Mark Somers for useful discussions. Approved Most recent IF: 5.7; 2024 IF: 9.353
Call Number PLASMANT @ plasmant @c:irua:204818 Serial 9114
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Author Mortet, V.; Zhang, L.; Echert, M.; Soltani, A.; d' Haen, J.; Douheret, O.; Moreau, M.; Osswald, S.; Neyts, E.; Troadec, D.; Wagner, P.; Bogaerts, A.; Van Tendeloo, G.; Haenen, K.
Title Characterization of nano-crystalline diamond films grown under continuous DC bias during plasma enhanced chemical vapor deposition Type A3 Journal article
Year 2009 Publication Materials Research Society symposium proceedings Abbreviated Journal
Volume Issue 1203 Pages
Keywords A3 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Nanocrystalline diamond films have generated much interested due to their diamond-like properties and low surface roughness. Several techniques have been used to obtain a high re-nucleation rate, such as hydrogen poor or high methane concentration plasmas. In this work, the properties of nano-diamond films grown on silicon substrates using a continuous DC bias voltage during the complete duration of growth are studied. Subsequently, the layers were characterised by several morphological, structural and optical techniques. Besides a thorough investigation of the surface structure, using SEM and AFM, special attention was paid to the bulk structure of the films. The application of FTIR, XRD, multi wavelength Raman spectroscopy, TEM and EELS yielded a detailed insight in important properties such as the amount of crystallinity, the hydrogen content and grain size. Although these films are smooth, they are under a considerable compressive stress. FTIR spectroscopy points to a high hydrogen content in the films, while Raman and EELS indicate a high concentration of sp2 carbon. TEM and EELS show that these films consist of diamond nano-grains mixed with an amorphous sp2 bonded carbon, these results are consistent with the XRD and UV Raman spectroscopy data.
Address
Corporate Author Thesis
Publisher Place of Publication Wuhan Editor
Language Wos Publication Date 2010-03-27
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1946-4274; ISBN Additional Links UA library record
Impact Factor Times cited Open Access
Notes Approved Most recent IF: NA
Call Number UA @ lucian @ c:irua:81646 Serial 327
Permanent link to this record
 
 
Author Lu, A.K.A.; Houssa, M.; Radu, I.P.; Pourtois, G.
Title Toward an understanding of the electric field-induced electrostatic doping in van der Waals heterostructures : a first-principles study Type A1 Journal article
Year 2017 Publication ACS applied materials and interfaces Abbreviated Journal Acs Appl Mater Inter
Volume 9 Issue 8 Pages 7725-7734
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Since the discovery of graphene, a broad range of two-dimensional (2D) materials has captured the attention of the scientific communities. Materials, such as hexagonal boron nitride (hBN) and the transition metal dichalcogenides (TMDs) family, have shown promising semiconducting and insulating properties that are very appealing for the semiconductor industry. Recently, the possibility of taking advantage of the properties of 2D-based heterostructures has been investigated for low-power nanoelectronic applications. In this work, we aim at evaluating the relation between the nature of the materials used in such heterostructures and the amplitude of the layer-to-layer charge transfer induced by an external electric field, as is typically present in nanoelectronic gated devices. A broad range of combinations of TMDs, graphene, and hBN has been investigated using density functional theory. Our results show that the electric field induced charge transfer strongly depends on the nature of the 2D materials used in the van der Waals heterostructures and to a lesser extent on the relative orientation of the materials in the structure. Our findings contribute to the building of the fundamental understanding required to engineer electrostatically the doping of 2D materials and to establish the factors that drive the charge transfer mechanisms in electron tunneling-based devices. These are key ingredients for the development of 2D -based nanoelectronic devices.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000395494200119 Publication Date 2017-02-13
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1944-8244 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.504 Times cited 10 Open Access Not_Open_Access
Notes Approved Most recent IF: 7.504
Call Number UA @ lucian @ c:irua:142483 Serial 4696
Permanent link to this record
 
 
Author Gogoi, A.; Neyts, E.C.; Milošević, M.V.; Peeters, F.M.
Title Arresting aqueous swelling of layered graphene-oxide membranes with H3O+ and OH- ions Type A1 Journal article
Year 2022 Publication ACS applied materials and interfaces Abbreviated Journal Acs Appl Mater Inter
Volume 14 Issue 30 Pages 34946-34954
Keywords A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Over the past decade, graphene oxide (GO) has emerged as a promising membrane material with superior separation performance and intriguing mechanical/chemical stability. However, its practical implementation remains very challenging primarily because of its undesirable swelling in an aqueous environment. Here, we demonstrated that dissociation of water molecules into H3O+ and OH- ions inside the interlayer gallery of a layered GO membrane can strongly affect its stability and performance. We reveal that H3O+ and OH- ions form clusters inside the GO laminates that impede the permeance of water and salt ions through the membrane. Dynamics of those clusters is sensitive to an external ac electric field, which can be used to tailor the membrane performance. The presence of H3O+ and OH- ions also leads to increased stability of the hydrogen bond (H-bond) network among the water molecules and the GO layers, which further reduces water permeance through the membrane, while crucially imparting stability to the layered GO membrane against undesirable swelling. KEYWORDS: layered graphene-oxide membrane, aqueous stability, H3O+ and OH- ions, external electric field, molecular dynamics
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000835946500001 Publication Date 2022-07-25
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1944-8244 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 9.5 Times cited 1 Open Access OpenAccess
Notes Approved Most recent IF: 9.5
Call Number UA @ admin @ c:irua:189467 Serial 7127
Permanent link to this record
 
 
Author Yusupov, M.; Razzokov, J.; Cordeiro, R.M.; Bogaerts, A.
Title Transport of Reactive Oxygen and Nitrogen Species across Aquaporin: A Molecular Level Picture Type A1 Journal article
Year 2019 Publication Oxidative medicine and cellular longevity Abbreviated Journal Oxid Med Cell Longev
Volume 2019 Issue Pages 1-11
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Aquaporins (AQPs) are transmembrane proteins that conduct not only water molecules across the cell membrane but also other solutes, such as reactive oxygen and nitrogen species (RONS), produced (among others) by cold atmospheric plasma (CAP). These RONS may induce oxidative stress in the cell interior, which plays a role in cancer treatment. The underlying mechanisms of the transport of RONS across AQPs, however, still remain obscure. We apply molecular dynamics simulations to investigate the permeation of both hydrophilic (H<sub>2</sub>O<sub>2</sub>and OH) and hydrophobic (NO<sub>2</sub>and NO) RONS through AQP1. Our simulations show that these RONS can all penetrate across the pores of AQP1. The permeation free energy barrier of OH and NO is lower than that of H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>, indicating that these radicals may have easier access to the pore interior and interact with the amino acid residues of AQP1. We also study the effect of RONS-induced oxidation of both the phospholipids and AQP1 (i.e., sulfenylation of Cys<sub>191</sub>) on the transport of the above-mentioned RONS across AQP1. Both lipid and protein oxidation seem to slightly increase the free energy barrier for H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>permeation, while for OH and NO, we do not observe a strong effect of oxidation. The simulation results help to gain insight in the underlying mechanisms of the noticeable rise of CAP-induced RONS in cancer cells, thereby improving our understanding on the role of AQPs in the selective anticancer capacity of CAP.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000492999000001 Publication Date 2019-06-17
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1942-0900 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.593 Times cited 5 Open Access OpenAccess
Notes The authors acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UA, where all computational work was performed. M.Y. gratefully acknowledges Dr. U. Khalilov for the fruitful discussions. This work was financially supported by the Research Foundation Flanders (FWO) (grant number 1200219N). Approved Most recent IF: 4.593
Call Number PLASMANT @ plasmant @UA @ admin @ c:irua:160118 Serial 5180
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Author Privat-Maldonado, A.; Schmidt, A.; Lin, A.; Weltmann, K.-D.; Wende, K.; Bogaerts, A.; Bekeschus, S.
Title ROS from Physical Plasmas: Redox Chemistry for Biomedical Therapy Type A1 Journal article
Year 2019 Publication Oxidative medicine and cellular longevity Abbreviated Journal Oxid Med Cell Longev
Volume 2019 Issue Pages 1-29
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Physical plasmas generate unique mixes of reactive oxygen and nitrogen species (RONS or ROS). Only a bit more than a decade ago, these plasmas, operating at body temperature, started to be considered for medical therapy with considerably little mechanistic redox chemistry or biomedical research existing on that topic at that time. Today, a vast body of evidence is available on physical plasma-derived ROS, from their spatiotemporal resolution in the plasma gas phase to sophisticated chemical and biochemical analysis of these species once dissolved in liquids. Data from<italic>in silico</italic>analysis dissected potential reaction pathways of plasma-derived reactive species with biological membranes, and<italic>in vitro</italic>and<italic>in vivo</italic>experiments in cell and animal disease models identified molecular mechanisms and potential therapeutic benefits of physical plasmas. In 2013, the first medical plasma systems entered the European market as class IIa devices and have proven to be a valuable resource in dermatology, especially for supporting the healing of chronic wounds. The first results in cancer patients treated with plasma are promising, too. Due to the many potentials of this blooming new field ahead, there is a need to highlight the main concepts distilled from plasma research in chemistry and biology that serve as a mechanistic link between plasma physics (how and which plasma-derived ROS are produced) and therapy (what is the medical benefit). This inevitably puts cellular membranes in focus, as these are the natural interphase between ROS produced by plasmas and translation of their chemical reactivity into distinct biological responses.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000493001000003 Publication Date 2019-10-08
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1942-0900 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.593 Times cited Open Access
Notes KW and SB acknowledge funding by the German Federal Ministry of Education and Research (grant numbers 03Z22DN11 and 03Z22DN12). The work of SB is further supported by the European Social Fund (grant number ESF/14-BM-A55-0006). APM and AB acknowledge funding by the Methusalem Project. AL acknowledges funding from the Research Foundation Flanders (grant number 12S9218N). APM thanks Yury Gorbanev for his assistance with the preparation of this review. Approved Most recent IF: 4.593
Call Number PLASMANT @ plasmant @c:irua:163476 Serial 5373
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Author Lin, A.; Biscop, E.; Breen, C.; Butler, S.J.; Smits, E.; Bogaerts, A.; Jakovljevic, V.
Title Critical Evaluation of the Interaction of Reactive Oxygen and Nitrogen Species with Blood to Inform the Clinical Translation of Nonthermal Plasma Therapy Type A1 Journal article
Year 2020 Publication Oxidative Medicine And Cellular Longevity Abbreviated Journal Oxid Med Cell Longev
Volume 2020 Issue Pages 1-10
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Abstract Non-thermal plasma (NTP), an ionized gas generated at ambient pressure and temperature, has been an emerging technology for medical applications. Through controlled delivery of reactive oxygen and nitrogen species (ROS/RNS), NTP can elicit hormetic cellular responses, thus stimulating broad therapeutic effects. To enable clinical translation of the promising preclinical research into NTP therapy, a deeper understanding of NTP interactions with clinical substrates is profoundly needed. Since NTP-generated ROS/RNS will inevitably interact with blood in several clinical contexts, understanding their stability in this system is crucial. In this study, two medically relevant NTP delivery modalities were used to assess the stability of NTP-generated ROS/RNS in three aqueous solutions with increasing organic complexities: phosphate-buffered saline (PBS), blood plasma (BP), and processed whole blood. NTP-generated RNS collectively (NO2−, ONOO−), H2O2, and ONOO− exclusively were analyzed over time. We demonstrated that NTP-generated RNS and H2O2 were stable in PBS but scavenged by different components of the blood. While RNS remained stable in BP after initial scavenging effects, it was completely reduced in processed whole blood. On the other hand, H2O2 was completely scavenged in both liquids over time. Our previously developed luminescent probe europium(III) was used for precision measurement of ONOO− concentration. NTP-generated ONOO− was detected in all three liquids for up to at least 30 seconds, thus highlighting its therapeutic potential. Based on our results, we discussed the necessary considerations to choose the most optimal NTP modality for delivery of ROS/RNS to and via blood in the clinical context.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000600343500001 Publication Date 2020-12-03
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1942-0900 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.593 Times cited Open Access
Notes This work was supported in part by the Research Foundation Flanders grant 12S9218N (A.L.) ,12S9221N (A.L) and G044420N (A.B. and A.L). This work was also supported by the Methusalem grant (A.B.). Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @c:irua:174000 Serial 6658
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Author Le Compte, M.; Cardenas De La Hoz, E.; Peeters, S.; Smits, E.; Lardon, F.; Roeyen, G.; Vanlanduit, S.; Prenen, H.; Peeters, M.; Lin, A.; Deben, C.
Title Multiparametric tumor organoid drug screening using widefield live-cell imaging for bulk and single-organoid analysis Type A1 Journal article
Year 2022 Publication Jove-Journal Of Visualized Experiments Abbreviated Journal Jove-J Vis Exp
Volume Issue 190 Pages 1-18
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Center for Oncological Research (CORE)
Abstract Patient-derived tumor organoids (PDTOs) hold great promise for preclinical and translational research and predicting the patient therapy response from ex vivo drug screenings. However, current adenosine triphosphate (ATP)-based drug screening assays do not capture the complexity of a drug response (cytostatic or cytotoxic) and intratumor heterogeneity that has been shown to be retained in PDTOs due to a bulk readout. Live-cell imaging is a powerful tool to overcome this issue and visualize drug responses more in-depth. However, image analysis software is often not adapted to the three-dimensionality of PDTOs, requires fluorescent viability dyes, or is not compatible with a 384-well microplate format. This paper describes a semi-automated methodology to seed, treat, and image PDTOs in a high-throughput, 384-well format using conventional, widefield, live-cell imaging systems. In addition, we developed viability marker-free image analysis software to quantify growth rate-based drug response metrics that improve reproducibility and correct growth rate variations between different PDTO lines. Using the normalized drug response metric, which scores drug response based on the growth rate normalized to a positive and negative control condition, and a fluorescent cell death dye, cytotoxic and cytostatic drug responses can be easily distinguished, profoundly improving the classification of responders and non-responders. In addition, drug-response heterogeneity can by quantified from single-organoid drug response analysis to identify potential, resistant clones. Ultimately, this method aims to improve the prediction of clinical therapy response by capturing a multiparametric drug response signature, which includes kinetic growth arrest and cell death quantification. ,
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000928020400010 Publication Date 2022-12-24
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1940-087x ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 1.2 Times cited Open Access OpenAccess
Notes Approved Most recent IF: 1.2
Call Number UA @ admin @ c:irua:193168 Serial 7271
Permanent link to this record
 
 
Author Neyts, E.C.; Bogaerts, A.
Title Modeling the growth of SWNTs and graphene on the atomic scale Type A1 Journal article
Year 2012 Publication ECS transactions Abbreviated Journal
Volume 45 Issue 4 Pages 73-78
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The possibility of application of nanomaterials is determined by our ability to control the properties of the materials, which are ultimately determined by their structure and hence their growth processes. We employ hybrid molecular dynamics / Monte Carlo (MD/MC) simulations to explore the growth of SWNTs and graphene on nickel as a catalyst, with the specific goal of unraveling the growth mechanisms. While the general observations are in agreement with the literature, we find a number of interesting phenomena to be operative which are crucial for the growth, and which are not accessible by MD simulations alone due to the associated time scale. Specifically, we observe metal mediated healing and restructuring processes to take place, reorganizing the carbon network during the initial nucleation step. In the case of carbon nanotube growth, this leads to the growth of tubes with a determinable chirality. In the case of graphene formation, we find that graphene is only formed at temperatures above 700 K. These results are of importance for understanding the growth mechanisms of these carbon nanomaterials on the fundamental level.
Address
Corporate Author Thesis
Publisher Electrochemical Society Place of Publication Pennington Editor
Language Wos 000316890000008 Publication Date 2012-04-27
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1938-6737;1938-5862; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor Times cited 2 Open Access
Notes Approved Most recent IF: NA
Call Number UA @ lucian @ c:irua:108535 Serial 2144
Permanent link to this record
 
 
Author Sorée, B.; Magnus, W.; Szepieniec, M.; Vandenbreghe, W.; Verhulst, A.; Pourtois, G.; Groeseneken, G.; de Gendt, S.; Heyns, M.
Title Novel device concepts for nanotechnology : the nanowire pinch-off FET and graphene tunnelFET Type A2 Journal article
Year 2010 Publication ECS transactions Abbreviated Journal
Volume 28 Issue Pages 15-26
Keywords A2 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract We explain the basic operation of a nanowire pinch-off FET and graphene nanoribbon tunnelFET. For the nanowire pinch-off FET we construct an analytical model to obtain the threshold voltage as a function of radius and doping density. We use the gradual channel approximation to calculate the current-voltage characteristics of this device and we show that the nanowire pinch-off FET has a subthreshold slope of 60 mV/dec and good ION and ION/IOFF ratios. For the graphene nanoribbon tunnelFET we show that an improved analytical model yields more realistic results for the transmission probability and hence the tunneling current. The first simulation results for the graphene nanoribbon tunnelFET show promising subthreshold slopes.
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Publisher Place of Publication Editor
Language Wos Publication Date 0000-00-00
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Series Volume Series Issue Edition
ISSN (down) 1938-5862 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor Times cited Open Access
Notes Approved Most recent IF: NA
Call Number UA @ lucian @ c:irua:89510 Serial 2375
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