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Author |
Khosravian, N.; Kamaraj, B.; Neyts, E.C.; Bogaerts, A. |
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Title |
Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
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Volume |
6 |
Issue |
6 |
Pages |
19466 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment. |
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Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium |
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Editor |
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Language |
English |
Wos |
000369573900001 |
Publication Date |
2016-02-09 |
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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 |
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ISSN |
2045-2322 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.259 |
Times cited |
7 |
Open Access |
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Notes |
The authors acknowledge financial support from the Fund for Scientific 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: 4.259 |
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Call Number |
c:irua:131610 |
Serial |
4031 |
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Permanent link to this record |
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Author |
Bal, K.M.; Neyts, E.C. |
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Title |
Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Chemical science |
Abbreviated Journal |
Chem Sci |
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Volume |
7 |
Issue |
7 |
Pages |
5280-5286 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Atomistic simulations can in principle provide an unbiased description of all mechanisms, intermediates, and products of complex chemical processes. However, due to the severe time scale limitation of conventional simulation techniques, unrealistically high simulation temperatures are usually applied, which are a poor approximation of most practically relevant low-temperature applications. In this work, we demonstrate the direct observation at the atomic scale of the pyrolysis and oxidation of n-dodecane at temperatures as low as 700 K through the use of a novel simulation technique, collective variable-driven hyperdynamics (CVHD). A simulated timescale of up to 39 seconds is reached. Product compositions and dominant mechanisms are found to be strongly temperature-dependent, and are consistent with experiments and kinetic models. These simulations provide a first atomic-level look at the full dynamics of the complicated fuel combustion process at industrially relevant temperatures and time scales, unattainable by conventional molecular dynamics simulations. |
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Wos |
000380893900059 |
Publication Date |
2016-05-05 |
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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 |
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ISSN |
2041-6520 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
8.668 |
Times cited |
22 |
Open Access |
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Notes |
K. M. B. is funded as PhD fellow (aspirant) of the FWO-Flanders (Fund for Scientic 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 |
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Call Number |
c:irua:134577 c:irua:135670 |
Serial |
4105 |
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Permanent link to this record |
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Author |
Tinck, S.; Tillocher, T.; Dussart, R.; Neyts, E.C.; Bogaerts, A. |
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Title |
Elucidating the effects of gas flow rate on an SF6inductively coupled plasma and on the silicon etch rate, by a combined experimental and theoretical investigation |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
49 |
Issue |
49 |
Pages |
385201 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Experiments show that the etch rate of Si with SF6 inductively coupled plasma (ICP) is significantly influenced by the absolute gas flow rate in the range of 50–600 sccm, with a maximum at around 200 sccm. Therefore, we numerically investigate the effects of the gas flow rate on the bulk plasma properties and on the etch rate, to obtain more insight in the underlying reasons of this effect. A hybrid Monte Carlo—fluid model is applied to simulate an SF6 ICP. It is found that the etch rate is influenced by two simultaneous effects: (i) the residence time of the gas and (ii) the temperature profile of the plasma in the ICP volume, resulting indeed in a maximum etch rate at 200 sccm. |
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Corporate Author |
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Wos |
000384095900011 |
Publication Date |
2016-08-24 |
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Series Editor |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0022-3727 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.588 |
Times cited |
1 |
Open Access |
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Notes |
We are very grateful to Mark Kushner for providing the computational model. The Fund for Scientific Research Flanders (FWO; grant no. 0880.212.840) is acknowledged for financial support of this work. The work was carried out in part using the Turing HPC infrastructure at 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 University of Antwerp. |
Approved |
Most recent IF: 2.588 |
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Call Number |
c:irua:134867 |
Serial |
4108 |
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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.; |
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Title |
Multilayer MoS2 growth by metal and metal oxide sulfurization |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Journal of materials chemistry C : materials for optical and electronic devices |
Abbreviated Journal |
J Mater Chem C |
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Volume |
4 |
Issue |
4 |
Pages |
1295-1304 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Wos |
000370723300020 |
Publication Date |
2016-01-05 |
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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 |
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ISSN |
2050-7526; 2050-7534 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.256 |
Times cited |
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Open Access |
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Notes |
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Approved |
Most recent IF: 5.256 |
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Call Number |
UA @ lucian @ c:irua:132327 |
Serial |
4211 |
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Permanent link to this record |
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Author |
Ali, S.; Myasnichenko, V.S.; Neyts, E.C. |
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Title |
Size-dependent strain and surface energies of gold nanoclusters |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
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Volume |
18 |
Issue |
18 |
Pages |
792-800 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Gold nanocluster properties exhibit unique size-dependence. In this contribution, we employ reactive molecular dynamics simulations to calculate the size- and temperature-dependent surface energies, strain energies and atomic displacements for icosahedral, cuboctahedral, truncated octahedral and decahedral Au-nanoclusters. The calculations demonstrate that the surface energy decreases with increasing cluster size at 0 K but increases with size at higher temperatures. The calculated melting curves as a function of cluster size demonstrate the Gibbs-Thomson effect. Atomic displacements and strain are found to strongly depend on the cluster size and both are found to increase with increasing cluster size. These results are of importance for understanding the size-and temperature-dependent surface processes on gold nanoclusters. |
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Corporate Author |
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Place of Publication |
Cambridge |
Editor |
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Language |
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Wos |
000369480600017 |
Publication Date |
2015-11-18 |
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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 |
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ISSN |
1463-9076 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.123 |
Times cited |
37 |
Open Access |
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Notes |
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Approved |
Most recent IF: 4.123 |
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Call Number |
UA @ lucian @ c:irua:131626 |
Serial |
4243 |
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Permanent link to this record |
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Author |
Huygh, S.; Bogaerts, A.; Neyts, E.C. |
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Title |
How Oxygen Vacancies Activate CO2 Dissociation on TiO2 Anatase (001) |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
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Volume |
120 |
Issue |
120 |
Pages |
21659-21669 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The adsorption, dissociation, and diffusion of CO2 on the anatase (001) surface was studied using DFT by means of the generalized gradient approximation using the Perdew−Burcke−Ernzerhof (PBE)-functional and applying corrections for long-range dispersion interactions. Different stable adsorption configurations were identified for the fully oxidized surface. The most stable adsorption configuration is the monodentated carbonate-like structure. Small energy barriers were identified for the conversion of a physisorbed to a chemisorbed configuration.
CO2 dissociation is found to be unfeasible on the stoichiometric surface. The introduction of oxygen vacancy defects gives rise to new highly stable adsorption configurations with a stronger activation of the C−O bonds. This leads to the possibility of exothermic dissociation of CO2 with barriers up to 22.2 kcal/mol,
corresponding to chemical lifetimes of less than 4 s at 300 K. These reactions cause a CO molecule to be formed, which will easily desorb, and the reduced surface to become oxidized. It is clear that oxygen vacancy defects play a key role in the catalytic activity of an anatase (001) surface. Oxygen vacancies play an important role in the dissociation of CO2 on the anatase (001) surface, and will play a significant role in complex problems, such as the catalytic conversion of CO2 to value-added chemicals. |
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Wos |
000384626800055 |
Publication Date |
2016-09-02 |
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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 |
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ISSN |
1932-7447 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.536 |
Times cited |
49 |
Open Access |
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Notes |
Stijn Huygh is funded as an aspirant of the Research Foundation Flanders (FWO, project number 11C0115N). This work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UAntwerpen. |
Approved |
Most recent IF: 4.536 |
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Call Number |
PLASMANT @ plasmant @ c:irua:136164 |
Serial |
4291 |
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Permanent link to this record |
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Author |
Dabaghmanesh, S.; Neyts, E.C.; Partoens, B. |
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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 |
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Year |
2016 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
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Volume |
18 |
Issue |
18 |
Pages |
23139-23146 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Corporate Author |
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Publisher |
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Place of Publication |
Cambridge |
Editor |
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Language |
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Wos |
000382109300040 |
Publication Date |
2016-07-27 |
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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 |
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ISSN |
1463-9076; 1463-9084 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.123 |
Times cited |
6 |
Open Access |
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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 |
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Call Number |
UA @ lucian @ c:irua:135701 |
Serial |
4311 |
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Permanent link to this record |
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Author |
Zhang, Y.-R.; Neyts, E.C.; Bogaerts, A. |
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Title |
Influence of the Material Dielectric Constant on Plasma Generation inside Catalyst Pores |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
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Volume |
120 |
Issue |
120 |
Pages |
25923-25934 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Plasma catalysis is gaining increasing interest for various environmental applications, but the crucial question is whether plasma can be created inside catalyst pores and under which conditions. In practice, various catalytic support materials are used, with various dielectric constants. We investigate here the influence of the dielectric constant on the plasma properties inside catalyst pores and in the sheath in front of the pores, for various pore sizes. The calculations are performed by a two-dimensional fluid model for an atmospheric pressure dielectric barrier discharge in helium. The electron impact ionization rate, electron temperature, electron and ion density, as well as the potential distribution and surface charge density, are analyzed for a better understanding of the discharge behavior inside catalyst pores. The results indicate that, in a 100 μm pore, the electron impact ionization in the pore, which is characteristic for the plasma generation inside the pore, is greatly enhanced for dielectric constants below 300. Smaller pore sizes only yield enhanced ionization for smaller dielectric constants, i.e., up to εr = 200, 150, and 50 for pore sizes of 50, 30, and 10 μm. Thus, the most common catalyst supports, i.e., Al2O3 and SiO2, which have dielectric constants around εr = 8−11 and 4.2, respectively, should allow more easily that microdischarges can be formed inside catalyst pores, even for smaller pore sizes. On the other hand, ferroelectric materials with dielectric constants above 300 never seem to yield plasma enhancement inside catalyst pores, not even for 100 μm pore sizes. Furthermore, it is clear that the dielectric constant of the material has a large effect on the extent of plasma enhancement inside the catalyst pores, especially in the range between εr = 4 and εr = 200. The obtained results are explained in detail based on the surface charge density at the pore walls,
and the potential distribution and electron temperature inside and above the pores. The results obtained with this model are
important for plasma catalysis, as the production plasma species in catalyst pores might affect the catalyst properties, and thus
improve the applications of plasma catalysis. |
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Corporate Author |
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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 |
000388429100029 |
Publication Date |
2016-11-17 |
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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 |
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ISSN |
1932-7447 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.536 |
Times cited |
34 |
Open Access |
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Notes |
This work was supported by the Fund for Scientific Research Flanders (FWO) (Grant G.0217.14N), the National Natural Science Foundation of China (Grant 11405019), and the China Postdoctoral Science Foundation (Grant 2015T80244). This work was carried out in part using the Turing HPC infrastructure at 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 University of Antwerp. |
Approved |
Most recent IF: 4.536 |
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Call Number |
PLASMANT @ plasmant @ c:irua:138602 |
Serial |
4319 |
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Permanent link to this record |
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Author |
Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. |
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Title |
Multi-level molecular modelling for plasma medicine |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Journal Of Physics D-Applied Physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
49 |
Issue |
5 |
Pages |
054002-54019 |
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Keywords |
A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT) |
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Abstract |
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Publisher |
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Place of Publication |
London |
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Wos |
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Publication Date |
0000-00-00 |
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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 |
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ISSN |
0022-3727 |
ISBN |
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Additional Links |
UA library record |
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Impact Factor |
2.588 |
Times cited |
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Open Access |
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Notes |
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Approved |
Most recent IF: 2.588 |
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Call Number |
UA @ lucian @ c:irua:129798 |
Serial |
4467 |
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Permanent link to this record |
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Author |
Bruggeman, P.J.; Kushner, M.J.; Locke, B.R.; Gardeniers, J.G.E.; Graham, W.G.; Graves, D.B.; Hofman-Caris, R.C.H.M.; Maric, D.; Reid, J.P.; Ceriani, E.; Fernandez Rivas, D.; Foster, J.E.; Garrick, S.C.; Gorbanev, Y.; Hamaguchi, S.; Iza, F.; Jablonowski, H.; Klimova, E.; Kolb, J.; Krcma, F.; Lukes, P.; Machala, Z.; Marinov, I.; Mariotti, D.; Mededovic Thagard, S.; Minakata, D.; Neyts, E.C.; Pawlat, J.; Petrovic, Z.L.; Pflieger, R.; Reuter, S.; Schram, D.C.; Schröter, S.; Shiraiwa, M.; Tarabová, B.; Tsai, P.A.; Verlet, J.R.R.; von Woedtke, T.; Wilson, K.R.; Yasui, K.; Zvereva, G. |
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Title |
Plasma–liquid interactions: a review and roadmap |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Plasma sources science and technology |
Abbreviated Journal |
Plasma Sources Sci T |
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Volume |
25 |
Issue |
5 |
Pages |
053002 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Plasma–liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on nonequilibrium plasmas. |
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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 |
000384715400001 |
Publication Date |
2016-09-30 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1361-6595 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.302 |
Times cited |
460 |
Open Access |
|
|
|
Notes |
This manuscript originated from discussions at the Lorentz Center Workshop ‘Gas/Plasma–Liquid Interface: Transport, Chemistry and Fundamental Data’ that took place at the Lorentz Center, Leiden University in the Netherlands from August 4, through August 8, 2014, and follow-up discussions since the workshop. All authors acknowledge the support of the Lorentz Center, the COST action TD1208 (Electrical Discharges with Liquids for Future Applications) and the Royal Dutch Academy of Sciences for their financial support. PJB, MJK, DBG and JEF acknowledge the support of the ‘Center on Control of Plasma Kinetics’ of the United States Department of Energy Office of Fusion Energy Science (DE-SC0001319). In addition, PJB and BRL acknowledge the support of the National Science Foundation (PHY 1500135 and CBET 1236225, respectively). In addition the enormous help of Mrs. Victoria Piorek (University of Minnesota) in the formatting of the final document including the references is gratefully acknowledged. |
Approved |
Most recent IF: 3.302 |
|
|
Call Number |
PLASMANT @ plasmant @ c:irua:144654 |
Serial |
4628 |
|
Permanent link to this record |
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Author |
Huygh, S.; Neyts, E.C. |
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|
Title |
Adsorption of C and CHx radicals on anatase (001) and the influence of oxygen vacancies |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
|
|
Volume |
119 |
Issue |
119 |
Pages |
4908-4921 |
|
|
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
The adsorption of C and CHx radicals on anatase (001) was studied using DFT within the generalized gradient approximation using the Perde-Burke-Ernzerhof (PBE) functional. We have studied the influence of oxygen vacancies in and at the surface on the adsorption properties of the radicals. For the oxygen vacancies in anatase (001), the most stable vacancy is located at the surface. For this vacancy, the maximal adsorption strength of C and CH decreases compared to the adsorption on the stoichiometric surface, but it increases for CH2 and CH3. If an oxygen vacancy is present in the first subsurface layer, the maximal adsorption strength increases for C, CH, CH2, and CH3. When the vacancy is present in the next subsurface layer, we find that only the CH3 adsorption is enhanced, while the maximal adsorption energies for the other radical species decrease. Not only does the precise location of the oxygen vacancy determine the maximal adsorption interaction, it also influences the adsorption strengths of the radicals at different surface configurations. This determines the probability of finding a certain adsorption configuration at the surface, which in turn influences the possible surface reactions. We find that C preferentially adsorbs far away from the oxygen vacancy, while CH2 and CH3 adsorb preferentially at the oxygen vacancy site. A fraction of CH partially adsorbs at the oxygen vacancy, and another fraction adsorbs further away from the vacancy. |
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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 |
000350840700052 |
Publication Date |
2015-02-18 |
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Series Editor |
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Series Title |
|
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 |
13 |
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: 4.536; 2015 IF: 4.772 |
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|
Call Number |
c:irua:124909 |
Serial |
63 |
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Permanent link to this record |
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Author |
Hoon Park, J.; Kumar, N.; Hoon Park, D.; Yusupov, M.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A.; Ho Kang, M.; Sup Uhm, H.; Ha Choi, E.; Attri, P.; |
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Title |
A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
|
|
Volume |
5 |
Issue |
5 |
Pages |
13849 |
|
|
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
Nature Publishing Group |
Place of Publication |
London |
Editor |
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Language |
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Wos |
000360909000001 |
Publication Date |
2015-09-09 |
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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 |
2045-2322; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
4.259 |
Times cited |
32 |
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: 4.259; 2015 IF: 5.578 |
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Call Number |
c:irua:127410 |
Serial |
419 |
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Permanent link to this record |
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Author |
Xie, L.; Brault, P.; Coutanceau, C.; Bauchire, J.-M.; Caillard, A.; Baranton, S.; Berndt, J.; Neyts, E.C. |
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Title |
Efficient amorphous platinum catalyst cluster growth on porous carbon : a combined molecular dynamics and experimental study |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
Applied catalysis : B : environmental |
Abbreviated Journal |
Appl Catal B-Environ |
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Volume |
162 |
Issue |
162 |
Pages |
21-26 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Amorphous platinum clusters supported on porous carbon have been envisaged for high-performance fuel cell electrodes. For this application, it is crucial to control the morphology of the Pt layer and the Ptsubstrate interaction to maximize activity and stability. We thus investigate the morphology evolution during Pt cluster growth on a porous carbon substrate employing atomic scale molecular dynamics simulations. The simulations are based on the Pt-C interaction potential using parameters derived from density functional theory and are found to yield a Pt cluster morphology similar to that observed in low loaded fuel cell electrodes prepared by plasma sputtering. Moreover, the simulations show amorphous Pt cluster growth in agreement with X-ray diffraction and transmission electron microscopy experiments on high performance low Pt content (10 μgPt cm−2) loaded fuel cell electrodes and provide a fundamental insight in the cluster growth mechanism. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000343686900003 |
Publication Date |
2014-06-26 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
|
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ISSN |
0926-3373; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
9.446 |
Times cited |
20 |
Open Access |
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Notes |
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Approved |
Most recent IF: 9.446; 2015 IF: 7.435 |
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Call Number |
c:irua:117949 |
Serial |
874 |
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Permanent link to this record |
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Author |
Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C. |
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Title |
How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
Biointerphases |
Abbreviated Journal |
Biointerphases |
|
|
Volume |
10 |
Issue |
10 |
Pages |
029501 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms. |
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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 |
000357195600019 |
Publication Date |
2014-12-17 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
|
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ISSN |
1934-8630;1559-4106; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.603 |
Times cited |
10 |
Open Access |
|
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Notes |
|
Approved |
Most recent IF: 2.603; 2015 IF: 3.374 |
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Call Number |
c:irua:121371 |
Serial |
1492 |
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Permanent link to this record |
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Author |
Yusupov, M.; Neyts, E.C.; Verlackt, C.C.; Khalilov, U.; van Duin, A.C.T.; Bogaerts, A. |
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Title |
Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species : a reactive molecular dynamics study |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
|
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Volume |
12 |
Issue |
12 |
Pages |
162-171 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Reactive molecular dynamics simulations are performed to study the interaction of reactive oxygen species, such as OH, HO2 and H2O2, with the endotoxic biomolecule lipid A of the gram-negative bacterium Escherichia coli. It is found that the aforementioned plasma species can destroy the lipid A, which consequently results in reducing its toxic activity. All bond dissociation events are initiated by hydrogen-abstraction reactions. However, the mechanisms behind these dissociations are dependent on the impinging plasma species, i.e. a clear difference is observed in the mechanisms upon impact of HO2 radicals and H2O2 molecules on one hand and OH radicals on the other hand. Our simulation results are in good agreement with experimental observations. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Weinheim |
Editor |
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Language |
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Wos |
000350275400005 |
Publication Date |
2014-09-17 |
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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 |
|
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|
ISSN |
1612-8850; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
2.846 |
Times cited |
18 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 2.846; 2015 IF: 2.453 |
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Call Number |
c:irua:123540 |
Serial |
1589 |
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Permanent link to this record |
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Author |
Dumpala, S.; Broderick, S.R.; Khalilov, U.; Neyts, E.C.; van Duin, A.C.T.; Provine, J.; Howe, R.T.; Rajan, K. |
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Title |
Integrated atomistic chemical imaging and reactive force field molecular dynamic simulations on silicon oxidation |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
Applied physics letters |
Abbreviated Journal |
Appl Phys Lett |
|
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Volume |
106 |
Issue |
106 |
Pages |
011602 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO2 and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
American Institute of Physics |
Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000347976900008 |
Publication Date |
2015-01-06 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
|
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ISSN |
0003-6951;1077-3118; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.411 |
Times cited |
19 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 3.411; 2015 IF: 3.302 |
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Call Number |
c:irua:122300 |
Serial |
1679 |
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Permanent link to this record |
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Author |
Kato, T.; Neyts, E.C.; Abiko, Y.; Akama, T.; Hatakeyama, R.; Kaneko, T. |
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Title |
Kinetics of energy selective Cs encapsulation in single-walled carbon nanotubes for damage-free and position-selective doping |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
|
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Volume |
119 |
Issue |
119 |
Pages |
11903-11908 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
A method has been developed for damage-free cesium (Cs) encapsulation within single-walled carbon nanotubes (SWNTs) with fine position selectivity. Precise energy tuning of Cs-ion irradiation revealed that there is a clear energy window (2060 eV) for the efficient encapsulation of Cs through the hexagonal network of SWNT sidewalls without causing significant damage. This minimum energy threshold of Cs-ion encapsulation (∼20 eV) matches well with the value obtained by ab initio simulation (∼22 eV). Furthermore, position-selective Cs encapsulation was carried out, resulting in the successful formation of pn-junction SWNT thin films with excellent environmental stability. |
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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 |
000355495600072 |
Publication Date |
2015-05-06 |
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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 |
|
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|
ISSN |
1932-7447;1932-7455; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
4.536 |
Times cited |
3 |
Open Access |
|
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|
Notes |
|
Approved |
Most recent IF: 4.536; 2015 IF: 4.772 |
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Call Number |
c:irua:125928 |
Serial |
1760 |
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Permanent link to this record |
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Author |
Brault, P.; Neyts, E.C. |
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Title |
Molecular dynamics simulations of supported metal nanocatalyst formation by plasma sputtering |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
Catalysis today |
Abbreviated Journal |
Catal Today |
|
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Volume |
256 |
Issue |
256 |
Pages |
3-12 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Magnetron sputtering is a widely used physical vapor deposition technique for deposition and formation of nanocatalyst thin films and clusters. Nevertheless, so far only few studies investigated this formation process at the fundamental level. We here review atomic scale molecular dynamics simulations aimed at elucidating the nanocatalyst growth process through magnetron sputtering. We first introduce the basic magnetron sputtering background and machinery of molecular dynamics simulations, and then describe the studies conducted in this field so far. We also present a perspective view on how the field may be developed further. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000360085300002 |
Publication Date |
2015-02-28 |
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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 |
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ISSN |
0920-5861; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
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Impact Factor |
4.636 |
Times cited |
18 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 4.636; 2015 IF: 3.893 |
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Call Number |
c:irua:127408 |
Serial |
2174 |
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Permanent link to this record |
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Author |
Neyts, E.C.; Ostrikov, K.(K.) |
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Title |
Nanoscale thermodynamic aspects of plasma catalysis |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
Catalysis today |
Abbreviated Journal |
Catal Today |
|
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Volume |
256 |
Issue |
256 |
Pages |
23-28 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Plasma catalysis continues to gain increasing scientific interest, both in established fields like toxic waste abatement and emerging fields like greenhouse gas conversion into value-added chemicals. Attention is typically focused on the obtained conversion process selectivity, rates and energy efficiency. Much less attention is usually paid to the underlying mechanistic aspects of the processes that occur. In this contribution, we critically examine a number of fundamentally important nanoscale thermodynamic aspects of plasma catalysis, which are very relevant to these processes but so far have been overlooked or insufficiently covered in the plasma catalysis literature. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000360085300004 |
Publication Date |
2015-03-25 |
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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 |
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ISSN |
0920-5861; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
4.636 |
Times cited |
14 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 4.636; 2015 IF: 3.893 |
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Call Number |
c:irua:127409 |
Serial |
2274 |
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Permanent link to this record |
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Author |
Nozaki, T.; Neyts, E.C.; Sankaran, M.; Ostrikov, K.(K.); Liu, C.-J. |
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Title |
Plasmas for enhanced catalytic processes (ISPCEM 2014) |
Type |
Editorial |
|
Year |
2015 |
Publication |
Catalysis today |
Abbreviated Journal |
Catal Today |
|
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Volume |
256 |
Issue |
256 |
Pages |
1-2 |
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Keywords |
Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000360085300001 |
Publication Date |
2015-08-21 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
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ISSN |
0920-5861; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
4.636 |
Times cited |
2 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 4.636; 2015 IF: 3.893 |
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Call Number |
c:irua:127407 |
Serial |
2641 |
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Permanent link to this record |
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Author |
Verlackt, C.C.W.; Neyts, E.C.; Jacob, T.; Fantauzzi, D.; Golkaram, M.; Shin, Y.-K.; van Duin, A.C.T.; Bogaerts, A. |
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Title |
Atomic-scale insight into the interactions between hydroxyl radicals and DNA in solution using the ReaxFF reactive force field |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
New journal of physics |
Abbreviated Journal |
New J Phys |
|
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Volume |
17 |
Issue |
17 |
Pages |
103005 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
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Abstract |
Cold atmospheric pressure plasmas have proven to provide an alternative treatment of cancer by targeting tumorous cells while leaving their healthy counterparts unharmed. However, the underlying mechanisms of the plasma–cell interactions are not yet fully understood. Reactive oxygen species, and in particular hydroxyl radicals (OH), are known to play a crucial role in plasma driven apoptosis of
malignant cells. In this paper we investigate the interaction of OH radicals, as well as H2O2 molecules and HO2 radicals, with DNA by means of reactive molecular dynamics simulations using the ReaxFF force field. Our results provide atomic-scale insight into the dynamics of oxidative stress on DNA caused by the OH radicals, while H2O2 molecules appear not reactive within the considered timescale. Among the observed processes are the formation of 8-OH-adduct radicals, forming the first stages towards the formation of 8-oxoGua and 8-oxoAde, H-abstraction reactions of the amines, and the partial opening of loose DNA ends in aqueous solution. |
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Corporate Author |
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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 |
000367328100001 |
Publication Date |
2015-10-02 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1367-2630; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.786 |
Times cited |
18 |
Open Access |
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Notes |
CCWV,ECN and AB acknowledge the contribution of J Van Beeck who is investigating the interaction between H2O2 andDNAusingrMDsimulations. Furthermore, they acknowledge financial support from the Fund for Scientific Research—Flanders (project number G012413N). The calculations were performed using the Turing HPCinfrastructure at 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. TJ and DF gratefully acknowledge support from the European Research Council through the ERC-Starting GrantTHEOFUN(Grant Agreement No. 259608). |
Approved |
Most recent IF: 3.786; 2015 IF: 3.558 |
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Call Number |
c:irua:129178 |
Serial |
3955 |
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Permanent link to this record |
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Author |
Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A. |
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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 |
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|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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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 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
|
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|
ISSN |
0022-3727;1361-6463; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
2.588 |
Times cited |
20 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.588; 2015 IF: 2.721 |
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Call Number |
c:irua:124230 |
Serial |
3242 |
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Permanent link to this record |
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Author |
Samani, M.K.; Ding, X.Z.; Khosravian, N.; Amin-Ahmadi, B.; Yi, Y.; Chen, G.; Neyts, E.C.; Bogaerts, A.; Tay, B.K. |
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Title |
Thermal conductivity of titanium nitride/titanium aluminum nitride multilayer coatings deposited by lateral rotating cathode arc |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Thin solid films : an international journal on the science and technology of thin and thick films |
Abbreviated Journal |
Thin Solid Films |
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Volume |
578 |
Issue |
578 |
Pages |
133-138 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
A seriesof [TiN/TiAlN]nmultilayer coatingswith different bilayer numbers n=5, 10, 25, 50, and 100 were deposited on stainless steel substrate AISI 304 by a lateral rotating cathode arc technique in a flowing nitrogen atmosphere. The composition and microstructure of the coatings have been analyzed by using energy dispersive X-ray spectroscopy, X-ray diffraction (XRD), and conventional and high-resolution transmission electron microscopy (HRTEM). XRD analysis shows that the preferential orientation growth along the (111) direction is reduced in the multilayer coatings. TEM analysis reveals that the grain size of the coatings decreases with increasing bilayer number. HRTEMimaging of the multilayer coatings shows a high density misfit dislocation between the TiN and TiAlN layers. The cross-plane thermal conductivity of the coatings was measured by a pulsed photothermal reflectance technique. With increasing bilayer number, the multilayer coatings' thermal conductivity decreases gradually. This reduction of thermal conductivity can be ascribed to increased phonon scattering due to the disruption of columnar structure, reduced preferential orientation, decreased grain size of the coatings and present misfit dislocations at the interfaces. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Lausanne |
Editor |
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Language |
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Wos |
000351686500019 |
Publication Date |
2015-02-21 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
|
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ISSN |
0040-6090; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
1.879 |
Times cited |
41 |
Open Access |
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Notes |
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Approved |
Most recent IF: 1.879; 2015 IF: 1.759 |
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Call Number |
c:irua:125517 |
Serial |
3626 |
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Permanent link to this record |
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Author |
Khalilov, U.; Bogaerts, A.; Neyts, E.C. |
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Title |
Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Nature communications |
Abbreviated Journal |
Nat Commun |
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Volume |
6 |
Issue |
6 |
Pages |
10306 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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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. |
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Address |
PLASMANT research group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium |
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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 |
English |
Wos |
000367584500001 |
Publication Date |
2015-12-22 |
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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 |
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ISSN |
2041-1723 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
12.124 |
Times cited |
37 |
Open Access |
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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 |
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Call Number |
c:irua:129975 |
Serial |
3990 |
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Permanent link to this record |
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Author |
Bal, K.M.; Neyts, E.C. |
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Title |
Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Journal of chemical theory and computation |
Abbreviated Journal |
J Chem Theory Comput |
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Volume |
11 |
Issue |
11 |
Pages |
4545-4554 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of reactive processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics. |
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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 |
000362921700004 |
Publication Date |
2015-09-02 |
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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 |
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ISSN |
1549-9618 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.245 |
Times cited |
41 |
Open Access |
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Notes |
K.M.B. is funded as Ph.D. fellow (aspirant) of the FWOFlanders (Fund for Scientific Research-Flanders), Grant No. 11 V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) and the HPC infrastructure of the University of Antwerp (CalcUA), funded by the Hercules Foundation and the Flemish Government−Department EWI. |
Approved |
Most recent IF: 5.245; 2015 IF: 5.498 |
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Call Number |
c:irua:128183 |
Serial |
3991 |
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Permanent link to this record |
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Author |
Neyts, E.C.; Ostrikov, K.K.; Sunkara, M.K.; Bogaerts, A. |
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Title |
Plasma Catalysis: Synergistic Effects at the Nanoscale |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Chemical reviews |
Abbreviated Journal |
Chem Rev |
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Volume |
115 |
Issue |
115 |
Pages |
13408-13446 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Thermal-catalytic gas processing is integral to many current industrial processes. Ever-increasing demands on conversion and energy efficiencies are a strong driving force for the development of alternative approaches. Similarly, synthesis of several functional materials (such as nanowires and nanotubes) demands special processing conditions. Plasma catalysis provides such an alternative, where the catalytic process is complemented by the use of plasmas that activate the source gas. This combination is often observed to result in a synergy between plasma and catalyst. This Review introduces the current state-of-the-art in plasma catalysis, including numerous examples where plasma catalysis has demonstrated its benefits or shows future potential, including CO2 conversion, hydrocarbon reforming, synthesis of nanomaterials, ammonia production, and abatement of toxic waste gases. The underlying mechanisms governing these applications, as resulting from the interaction between the plasma and the catalyst, render the process highly complex, and little is known about the factors leading to the often-observed synergy. This Review critically examines the catalytic mechanisms relevant to each specific application. |
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Address |
Department of Chemistry, Research Group PLASMANT, Universiteit Antwerpen , Universiteitsplein 1, 2610 Wilrijk-Antwerp, Belgium |
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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 |
English |
Wos |
000367563000006 |
Publication Date |
2015-11-30 |
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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 |
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ISSN |
0009-2665 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
47.928 |
Times cited |
204 |
Open Access |
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Notes |
ECN and AB gratefully acknowledge financial support from the Fund of Scientific Research Flanders (FWO), Belgium, Grant Number G.0217.14N. KO acknowledges partial support by the Australian Research Council and CSIRO’s OCE Science Leaders Program. MKS acknowledges partial support from US National Science Foundation through grants DMS 1125909 and EPSCoR 1355448 and also PhD students Babajide Ajayi, Apolo Nambo and Maria Carreon for their help. |
Approved |
Most recent IF: 47.928; 2015 IF: 46.568 |
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Call Number |
c:irua:130001 |
Serial |
3993 |
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Permanent link to this record |
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Author |
Neyts, E.C. |
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Title |
The role of ions in plasma catalytic carbon nanotube growth : a review |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Frontiers of Chemical Science and Engineering |
Abbreviated Journal |
Front Chem Sci Eng |
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Volume |
9 |
Issue |
9 |
Pages |
154-162 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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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 |
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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 |
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ISSN |
2095-0179 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
1.712 |
Times cited |
8 |
Open Access |
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Notes |
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Approved |
Most recent IF: 1.712; 2015 IF: NA |
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Call Number |
UA @ lucian @ c:irua:127815 |
Serial |
4239 |
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Permanent link to this record |
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Author |
Neyts, E.C.; Yusupov, M.; Verlackt, C.C.; Bogaerts, A. |
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Title |
Computer simulations of plasmabiomolecule and plasmatissue interactions for a better insight in plasma medicine |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
47 |
Issue |
29 |
Pages |
293001 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficultif not impossibleto obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasmabiomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance the field. |
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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 |
000338860300001 |
Publication Date |
2014-06-26 |
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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 |
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ISSN |
0022-3727;1361-6463; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.588 |
Times cited |
28 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.588; 2014 IF: 2.721 |
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Call Number |
UA @ lucian @ c:irua:117853 |
Serial |
472 |
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Permanent link to this record |
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Author |
Huygh, S.; Bogaerts, A.; van Duin, A.C.T.; Neyts, E.C. |
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Title |
Development of a ReaxFF reactive force field for intrinsic point defects in titanium dioxide |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Computational materials science |
Abbreviated Journal |
Comp Mater Sci |
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Volume |
95 |
Issue |
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Pages |
579-591 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
A reactive ReaxFF force field is developed for studying the influence of intrinsic point defects on the chemistry with TiO2 condensed phases. The force field parameters are optimized to ab initio data for the equations of state, relative phase stabilities for titanium and titanium dioxide, potential energy differences for (TiO2)n-clusters (n = 116). Also data for intrinsic point defects in anatase were added. These data contain formation energies for interstitial titanium and oxygen vacancies, diffusion barriers of the oxygen vacancies and molecular oxygen adsorption on a reduced anatase (101) surface. Employing the resulting force field, we study the influence of concentration of oxygen vacancies and expansion or compression of an anatase surface on the diffusion of the oxygen vacancies. Also the barrier for oxygen diffusion in the subsurface region is evaluated using this force field. This diffusion barrier of 27.7 kcal/mol indicates that the lateral redistribution of oxygen vacancies on the surface and in the subsurface will be dominated by their diffusion in the subsurface, since both this barrier as well as the barriers for diffusion from the surface to the subsurface and vice versa (17.07 kcal/mol and 21.91 kcal/mol, respectively, as calculated with DFT), are significantly lower than for diffusion on the surface (61.12 kcal/mol as calculated with DFT). |
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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 |
000343781700077 |
Publication Date |
2014-09-16 |
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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 |
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ISSN |
0927-0256; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.292 |
Times cited |
15 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.292; 2014 IF: 2.131 |
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Call Number |
UA @ lucian @ c:irua:119409 |
Serial |
682 |
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Permanent link to this record |
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Author |
Tinck, S.; Neyts, E.C.; Bogaerts, A. |
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Title |
Fluorinesilicon surface reactions during cryogenic and near room temperature etching |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
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Volume |
118 |
Issue |
51 |
Pages |
30315-30324 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Cyrogenic etching of silicon is envisaged to enable better control over plasma processing in the microelectronics industry, albeit little is known about the fundamental differences compared to the room temperature process. We here present molecular dynamics simulations carried out to obtain sticking probabilities, thermal desorption rates, surface diffusion speeds, and sputter yields of F, F2, Si, SiF, SiF2, SiF3, SiF4, and the corresponding ions on Si(100) and on SiF13 surfaces, both at cryogenic and near room temperature. The different surface behavior during conventional etching and cryoetching is discussed. F2 is found to be relatively reactive compared to other species like SiF03. Thermal desorption occurs at a significantly lower rate under cryogenic conditions, which results in an accumulation of physisorbed species. Moreover, ion incorporation is often observed for ions with energies of 30400 eV, which results in a relatively low net sputter yield. The obtained results suggest that the actual etching of Si, under both cryogenic and near room temperature conditions, is based on the complete conversion of the Si surface to physisorbed SiF4, followed by subsequent sputtering of these molecules, instead of direct sputtering of the SiF03 surface. |
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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 |
000347360200101 |
Publication Date |
2014-11-25 |
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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 |
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ISSN |
1932-7447;1932-7455; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
4.536 |
Times cited |
11 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 4.536; 2014 IF: 4.772 |
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Call Number |
UA @ lucian @ c:irua:122957 |
Serial |
1239 |
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Permanent link to this record |