Records |
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 ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
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 |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Cambridge |
Editor |
|
Language |
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Wos |
000343000800049 |
Publication Date |
2014-07-24 |
Series Editor |
|
Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
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 |
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Author |
Neyts, E.C.; Khalilov, U.; Pourtois, G.; van Duin, A.C.T. |
Title |
Hyperthermal oxygen interacting with silicon surfaces : adsorption, implantation, and damage creation |
Type |
A1 Journal article |
Year |
2011 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
Volume |
115 |
Issue |
15 |
Pages |
4818-4823 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
Using reactive molecular dynamics simulations, we have investigated the effect of single-impact, low-energy (thermal-100 eV) bombardment of a Si(100){2 × 1} surface by atomic and molecular oxygen. Penetration probability distributions, as well as defect formation distributions, are presented as a function of the impact energy for both species. It is found that at low impact energy, defects are created chemically due to the chemisorption process in the top layers of the surface, while at high impact energy, additional defects are created by a knock-on displacement of Si. These results are of particular importance for understanding device performances of silica-based microelectronic and photovoltaic devices. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Washington, D.C. |
Editor |
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Language |
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Wos |
000288401200060 |
Publication Date |
2011-03-02 |
Series Editor |
|
Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1932-7447;1932-7455; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.536 |
Times cited |
28 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 4.536; 2011 IF: 4.805 |
Call Number |
UA @ lucian @ c:irua:89858 |
Serial |
1543 |
Permanent link to this record |
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|
Author |
Neyts, E.; Maeyens, A.; Pourtois, G.; Bogaerts, A. |
Title |
A density-functional theory simulation of the formation of Ni-doped fullerenes by ion implantation |
Type |
A1 Journal article |
Year |
2011 |
Publication |
Carbon |
Abbreviated Journal |
Carbon |
Volume |
49 |
Issue |
3 |
Pages |
1013-1017 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
Using self-consistent KohnSham density-functional theory molecular dynamics simulations, we demonstrate the theoretical possibility to synthesize NiC60, the incarfullerene Ni@C60 and the heterofullerene C59Ni in an ion implantation setup. The corresponding formation mechanisms of all three complexes are elucidated as a function of the ion implantation energy and impact location, suggesting possible routes for selectively synthesizing these complexes. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Oxford |
Editor |
|
Language |
|
Wos |
000286683500032 |
Publication Date |
2010-11-14 |
Series Editor |
|
Series Title |
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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 |
13 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 6.337; 2011 IF: 5.378 |
Call Number |
UA @ lucian @ c:irua:85139 |
Serial |
639 |
Permanent link to this record |
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|
|
Author |
Dabaghmanesh, S.; Neyts, E.C.; Partoens, B. |
Title |
van der Waals density functionals applied to corundum-type sesquioxides : bulk properties and adsorption of CH3 and C6H6 on (0001) surfaces |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
Volume |
18 |
Issue |
18 |
Pages |
23139-23146 |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
van der Waals (vdW) forces play an important role in the adsorption of molecules on the surface of solids. However, the choice of the most suitable vdW functional for different systems is an essential problem which must be addressed for different systems. The lack of a systematic study on the performance of the vdW functionals in the bulk and adsorption properties of metal-oxides motivated us to examine different vdW approaches and compute the bulk and molecular adsorption properties of alpha-Cr2O3, alpha-Fe2O3, and alpha-Al2O3. For the bulk properties, we compared our results for the heat of formation, cohesive energy, lattice parameters and bond distances between the different vdW functionals and available experimental data. Next we studied the adsorption of benzene and CH3 molecules on top of different oxide surfaces. We employed different approximations to exchange and correlation within DFT, namely, the Perdew-Burke-Ernzerhof (PBE) GGA, (PBE)+U, and vdW density functionals [ DFT(vdW-DF/DF2/optPBE/optB86b/optB88)+U] as well as DFT-D2/D3(+U) methods of Grimme for the bulk calculations and optB86b-vdW(+U) and DFT-D2(+U) for the adsorption energy calculations. Our results highlight the importance of vdW interactions not only in the adsorption of molecules, but importantly also for the bulk properties. Although the vdW contribution in the adsorption of CH3 (as a chemisorption interaction) is less important compared to the adsorption of benzene (as a physisorption interaction), this contribution is not negligible. Also adsorption of benzene on ferryl/chromyl terminated surfaces shows an important chemisorption contribution in which the vdW interactions become less significant. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
|
Place of Publication |
Cambridge |
Editor |
|
Language |
|
Wos |
000382109300040 |
Publication Date |
2016-07-27 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1463-9076; 1463-9084 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.123 |
Times cited |
6 |
Open Access |
|
Notes |
; This work was supported by the Strategic Initiative Materials in Flanders (SIM). The computational resources and services used in this work were provided by the Vlaams Supercomputer Centrum (VSC) and the HPC infrastructure of the University of Antwerp. ; |
Approved |
Most recent IF: 4.123 |
Call Number |
UA @ lucian @ c:irua:135701 |
Serial |
4311 |
Permanent link to this record |
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|
|
Author |
Bal, K.M.; Neyts, E.C. |
Title |
Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory |
Type |
A1 Journal article |
Year |
2022 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
Volume |
157 |
Issue |
18 |
Pages |
184113-10 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000885260600002 |
Publication Date |
2022-11-14 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0021-9606 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.4 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 4.4 |
Call Number |
UA @ admin @ c:irua:192076 |
Serial |
7266 |
Permanent link to this record |
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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 ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
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 |
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Corporate Author |
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Thesis |
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Publisher |
|
Place of Publication |
Cambridge |
Editor |
|
Language |
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Wos |
000321675600003 |
Publication Date |
2013-06-06 |
Series Editor |
|
Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
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 |
Permanent link to this record |
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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 ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
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 |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Cambridge |
Editor |
|
Language |
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Wos |
000322315600019 |
Publication Date |
2013-04-26 |
Series Editor |
|
Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
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 |
Permanent link to this record |
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|
Author |
Heyne, M.H.; Chiappe, D.; Meersschaut, J.; Nuytten, T.; Conard, T.; Bender, H.; Huyghebaert, C.; Radu, I.P.; Caymax, M.; de Marneffe, J.F.; Neyts, E.C.; De Gendt, S.; |
Title |
Multilayer MoS2 growth by metal and metal oxide sulfurization |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Journal of materials chemistry C : materials for optical and electronic devices |
Abbreviated Journal |
J Mater Chem C |
Volume |
4 |
Issue |
4 |
Pages |
1295-1304 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
We investigated the deposition of MoS2 multilayers on large area substrates. The pre-deposition of metal or metal oxide with subsequent sulfurization is a promising technique to achieve layered films. We distinguish a different reaction behavior in metal oxide and metallic films and investigate the effect of the temperature, the H2S/H-2 gas mixture composition, and the role of the underlying substrate on the material quality. The results of the experiments suggest a MoS2 growth mechanism consisting of two subsequent process steps. At first, the reaction of the sulfur precursor with the metal or metal oxide occurs, requiring higher temperatures in the case of metallic film compared to metal oxide. At this stage, the basal planes assemble towards the diffusion direction of the reaction educts and products. After the sulfurization reaction, the material recrystallizes and the basal planes rearrange parallel to the substrate to minimize the surface energy. Therefore, substrates with low roughness show basal plane assembly parallel to the substrate. These results indicate that the substrate character has a significant impact on the assembly of low dimensional MoS2 films. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000370723300020 |
Publication Date |
2016-01-05 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2050-7526; 2050-7534 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
5.256 |
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: 5.256 |
Call Number |
UA @ lucian @ c:irua:132327 |
Serial |
4211 |
Permanent link to this record |
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|
|
Author |
Razzokov, J.; Yusupov, M.; Vanuytsel, S.; Neyts, E.C.; Bogaerts, A. |
Title |
Phosphatidylserine flip-flop induced by oxidation of the plasma membrane: a better insight by atomic scale modeling |
Type |
A1 Journal article |
Year |
2017 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
Volume |
14 |
Issue |
10 |
Pages |
1700013 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000413045800010 |
Publication Date |
2017-04-05 |
Series Editor |
|
Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1612-8850 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.846 |
Times cited |
9 |
Open Access |
Not_Open_Access |
Notes |
Fonds Wetenschappelijk Onderzoek, 1200216N ; |
Approved |
Most recent IF: 2.846 |
Call Number |
PLASMANT @ plasmant @c:irua:149567 |
Serial |
4910 |
Permanent link to this record |
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Author |
Van der Paal, J.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A. |
Title |
Effect of lipid peroxidation on membrane permeability of cancer and normal cells subjected to oxidative stress |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Chemical science |
Abbreviated Journal |
Chem Sci |
Volume |
7 |
Issue |
7 |
Pages |
489-498 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
We performed molecular dynamics simulations to investigate the effect of lipid peroxidation products on the structural and dynamic properties of the cell membrane. Our simulations predict that the lipid order in a phospholipid bilayer, as a model system for the cell membrane, decreases upon addition of lipid peroxidation products. Eventually, when all phospholipids are oxidized, pore formation can occur. This will allow reactive species, such as reactive oxygen and nitrogen species (RONS), to enter the cell and cause oxidative damage to intracellular macromolecules, such as DNA or proteins. On the other hand, upon increasing the cholesterol fraction of lipid bilayers, the cell membrane order increases, eventually reaching a certain threshold, from which cholesterol is able to protect the membrane against pore formation. This finding is crucial for cancer treatment by plasma technology, producing a large number of RONS, as well as for other cancer treatment methods that cause an increase in the concentration of extracellular RONS. Indeed, cancer cells contain less cholesterol than their healthy counterparts. Thus, they will be more vulnerable to the consequences of lipid peroxidation, eventually enabling the penetration of RONS into the interior of the cell, giving rise to oxidative stress, inducing pro-apoptotic factors. This provides, for the first time, molecular level insight why plasma can selectively treat cancer cells, while leaving their healthy counterparts undamaged, as is indeed experimentally demonstrated. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000366826900058 |
Publication Date |
2015-10-16 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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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 |
106 |
Open Access |
|
Notes |
The authors acknowledge nancial support from the Fund for Scientic Research (FWO) Flanders, grant number G012413N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. |
Approved |
Most recent IF: 8.668 |
Call Number |
c:irua:131058 |
Serial |
3986 |
Permanent link to this record |
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Author |
Heyne, M.H.; de Marneffe, J.-F.; Delabie, A.; Caymax, M.; Neyts, E.C.; Radu, I.; Huyghebaert, C.; De Gendt, S. |
Title |
Two-dimensional WS2 nanoribbon deposition by conversion of pre-patterned amorphous silicon |
Type |
A1 Journal article |
Year |
2017 |
Publication |
Nanotechnology |
Abbreviated Journal |
Nanotechnology |
Volume |
28 |
Issue |
28 |
Pages |
04LT01 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
We present a method for area selective deposition of 2D WS2 nanoribbons with tunable thickness on a dielectric substrate. The process is based on a complete conversion of a prepatterned, H-terminated Si layer to metallic W by WF6, followed by in situ sulfidation by H2S. The reaction process, performed at 450 degrees C, yields nanoribbons with lateral dimension down to 20 nm and with random basal plane orientation. The thickness of the nanoribbons is accurately controlled by the thickness of the pre-deposited Si layer. Upon rapid thermal annealing at 900 degrees C under inert gas, the WS2 basal planes align parallel to the substrate. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Bristol |
Editor |
|
Language |
|
Wos |
000391445100001 |
Publication Date |
2016-12-15 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0957-4484 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.44 |
Times cited |
13 |
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 3.44 |
Call Number |
UA @ lucian @ c:irua:140382 |
Serial |
4471 |
Permanent link to this record |
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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 ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
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 |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
|
Wos |
000508473400008 |
Publication Date |
2020-01-16 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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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 |
Permanent link to this record |
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|
|
Author |
Neyts, E.; Bogaerts, A.; van de Sanden, M.C.M. |
Title |
Modeling PECVD growth of nanostructured carbon materials |
Type |
A1 Journal article |
Year |
2009 |
Publication |
High temperature material processes |
Abbreviated Journal |
High Temp Mater P-Us |
Volume |
13 |
Issue |
3/4 |
Pages |
399-412 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
We present here some of our modeling efforts for PECVD growth of nanostructured carbon materials with focus on amorphous hydrogenated carbon. Experimental data from an expanding thermal plasma setup were used as input for the simulations. Attention was focused both on the film growth mechanism, as well as on the hydrocarbon reaction mechanisms during growth of the films. It is found that the reaction mechanisms and sticking coefficients are dependent on the specific surface sites, and the structural properties of the growth radicals. The film growth results are in correspondence with the experiment. Furthermore, it is found that thin a-C:H films can be densified using an additional H-flux towards the substrate. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
|
Wos |
000274202300012 |
Publication Date |
2010-02-01 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1093-3611; |
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:80991 |
Serial |
2138 |
Permanent link to this record |
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Author |
Yusupov, M.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A. |
Title |
Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments |
Type |
A1 Journal article |
Year |
2017 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
Volume |
7 |
Issue |
7 |
Pages |
5761 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
|
Wos |
000405746500072 |
Publication Date |
2017-07-12 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2045-2322 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.259 |
Times cited |
27 |
Open Access |
OpenAccess |
Notes |
M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216 N. 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. S.R. and S.K. acknowledge funding by the BMBF (FKZ: 03Z2DN12). S.R. acknowledges funding by the Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern (AU 15001). The authors thank M. Hammer for the support and discussion in the biophysical studies and J. Van der Paal for the interesting discussions. |
Approved |
Most recent IF: 4.259 |
Call Number |
PLASMANT @ plasmant @ c:irua:144627 |
Serial |
4630 |
Permanent link to this record |
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Author |
Villarreal, R.; Lin, P.-C.; Faraji, F.; Hassani, N.; Bana, H.; Zarkua, Z.; Nair, M.N.; Tsai, H.-C.; Auge, M.; Junge, F.; Hofsaess, H.C.; De Gendt, S.; De Feyter, S.; Brems, S.; Ahlgren, E.H.; Neyts, E.C.; Covaci, L.; Peeters, F.M.; Neek-Amal, M.; Pereira, L.M.C. |
Title |
Breakdown of universal scaling for nanometer-sized bubbles in graphene |
Type |
A1 Journal article |
Year |
2021 |
Publication |
Nano Letters |
Abbreviated Journal |
Nano Lett |
Volume |
21 |
Issue |
19 |
Pages |
8103-8110 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
We report the formation of nanobubbles on graphene with a radius of the order of 1 nm, using ultralow energy implantation of noble gas ions (He, Ne, Ar) into graphene grown on a Pt(111) surface. We show that the universal scaling of the aspect ratio, which has previously been established for larger bubbles, breaks down when the bubble radius approaches 1 nm, resulting in much larger aspect ratios. Moreover, we observe that the bubble stability and aspect ratio depend on the substrate onto which the graphene is grown (bubbles are stable for Pt but not for Cu) and trapped element. We interpret these dependencies in terms of the atomic compressibility of the noble gas as well as of the adhesion energies between graphene, the substrate, and trapped atoms. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
|
Wos |
000709549100026 |
Publication Date |
2021-09-14 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1530-6984 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
12.712 |
Times cited |
24 |
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 12.712 |
Call Number |
UA @ admin @ c:irua:184137 |
Serial |
6857 |
Permanent link to this record |
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|
Author |
Neyts, E.C. |
Title |
The role of ions in plasma catalytic carbon nanotube growth : a review |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Frontiers of Chemical Science and Engineering |
Abbreviated Journal |
Front Chem Sci Eng |
Volume |
9 |
Issue |
9 |
Pages |
154-162 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
While it is well-known that the plasma-enhanced catalytic chemical vapor deposition (PECVD) of carbon nanotubes (CNTs) offers a number of advantages over thermal CVD, the influence of the various individual contributing factors is not well understood. Especially the role of ions is unclear, since ions in plasmas are generally associated with sputtering rather than with growing a material. Even so, various studies have demonstrated the beneficial effects of ion bombardment during the growth of CNTs. This review looks at the role of the ions in plasma-enhanced CNT growth as deduced from both experimental and simulation studies. Specific attention is paid to the beneficial effects of ion bombardment. Based on the available literature, it can be concluded that ions can be either beneficial or detrimental for carbon nanotube growth, depending on the exact conditions and the control over the growth process. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000360319600003 |
Publication Date |
2015-06-11 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2095-0179 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
1.712 |
Times cited |
8 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 1.712; 2015 IF: NA |
Call Number |
UA @ lucian @ c:irua:127815 |
Serial |
4239 |
Permanent link to this record |
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Author |
Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A. |
Title |
Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
Volume |
48 |
Issue |
48 |
Pages |
155202 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
London |
Editor |
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Language |
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Wos |
000351856600007 |
Publication Date |
2015-03-25 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
ISSN |
0022-3727;1361-6463; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.588 |
Times cited |
20 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.588; 2015 IF: 2.721 |
Call Number |
c:irua:124230 |
Serial |
3242 |
Permanent link to this record |
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Author |
Izadi, M.E.; Bal, K.M.; Maghari, A.; Neyts, E.C. |
Title |
Reaction mechanisms of C(3PJ) and C+(2PJ) with benzene in the interstellar medium from quantum mechanical molecular dynamics simulations |
Type |
A1 Journal article |
Year |
2021 |
Publication |
Physical Chemistry Chemical Physics |
Abbreviated Journal |
Phys Chem Chem Phys |
Volume |
23 |
Issue |
7 |
Pages |
4205-4216 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract ![sorted by Abstract field, ascending order (up)](img/sort_asc.gif) |
While spectroscopic data on small hydrocarbons in interstellar media in combination with crossed molecular beam (CMB) experiments have provided a wealth of information on astrochemically relevant species, much of the underlying mechanistic pathways of their formation remain elusive. Therefore, in this work, the chemical reaction mechanisms of C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>and C<sup>+</sup>(<sup>2</sup>P) + C<sub>6</sub>H<sub>6</sub>systems using the quantum mechanical molecular dynamics (QMMD) technique at the PBE0-D3(BJ) level of theory is investigated, mimicking a CMB experiment. Both the dynamics of the reactions as well as the electronic structure for the purpose of the reaction network are evaluated. The method is validated for the first reaction by comparison to the available experimental data. The reaction scheme for the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system covers the literature data,<italic>e.g.</italic>the major products are the 1,2-didehydrocycloheptatrienyl radical (C<sub>7</sub>H<sub>5</sub>) and benzocyclopropenyl radical (C<sub>6</sub>H<sub>5</sub>–CH), and it reveals the existence of less common pathways for the first time. The chemistry of the C<sup>+</sup>(<sup>2</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system is found to be much richer, and we have found that this is because of more exothermic reactions in this system in comparison to those in the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system. Moreover, using the QMMD simulation, a number of reaction paths have been revealed that produce three distinct classes of reaction products with different ring sizes. All in all, at all the collision energies and orientations, the major product is the heptagon molecular ion for the ionic system. It is also revealed that the collision orientation has a dominant effect on the reaction products in both systems, while the collision energy mostly affects the charged system. These simulations both prove the applicability of this approach to simulate crossed molecular beams, and provide fundamental information on reactions relevant for the interstellar medium. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
|
Wos |
000621595300016 |
Publication Date |
2021-01-18 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1463-9076 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.123 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
Fonds Wetenschappelijk Onderzoek, 12ZI420N ; Ministry of Science Research and Technology; Universiteit Antwerpen; The financial support from the Iran Ministry of Science, Research and Technology and PLASMANT Research Group University of Antwerp is highly acknowledged by the authors. K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation – Flanders), Grant 12ZI420N. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. |
Approved |
Most recent IF: 4.123 |
Call Number |
PLASMANT @ plasmant @c:irua:176672 |
Serial |
6742 |
Permanent link to this record |