Records |
Author |
Bal, K.M.; Neyts, E.C. |
Title |
Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Chemical science |
Abbreviated Journal |
Chem Sci |
Volume |
7 |
Issue |
7 |
Pages |
5280-5286 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Atomistic simulations can in principle provide an unbiased description of all mechanisms, intermediates, and products of complex chemical processes. However, due to the severe time scale limitation of conventional simulation techniques, unrealistically high simulation temperatures are usually applied, which are a poor approximation of most practically relevant low-temperature applications. In this work, we demonstrate the direct observation at the atomic scale of the pyrolysis and oxidation of n-dodecane at temperatures as low as 700 K through the use of a novel simulation technique, collective variable-driven hyperdynamics (CVHD). A simulated timescale of up to 39 seconds is reached. Product compositions and dominant mechanisms are found to be strongly temperature-dependent, and are consistent with experiments and kinetic models. These simulations provide a first atomic-level look at the full dynamics of the complicated fuel combustion process at industrially relevant temperatures and time scales, unattainable by conventional molecular dynamics simulations. |
Address |
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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 |
000380893900059 |
Publication Date |
2016-05-05 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2041-6520 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
8.668 |
Times cited |
22 |
Open Access |
|
Notes |
K. M. B. is funded as PhD fellow (aspirant) of the FWO-Flanders (Fund for 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 |
Call Number |
c:irua:134577 c:irua:135670 |
Serial |
4105 |
Permanent link to this record |
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Author |
Khosravian, N.; Kamaraj, B.; Neyts, E.C.; Bogaerts, A. |
Title |
Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
Volume |
6 |
Issue |
6 |
Pages |
19466 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
Address |
Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium |
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 |
000369573900001 |
Publication Date |
2016-02-09 |
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 |
|
Edition |
|
ISSN |
2045-2322 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.259 |
Times cited |
7 |
Open Access |
|
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 |
Call Number |
c:irua:131610 |
Serial |
4031 |
Permanent link to this record |
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Author |
Heyne, M.H.; Chiappe, D.; Meersschaut, J.; Nuytten, T.; Conard, T.; Bender, H.; Huyghebaert, C.; Radu, I.P.; Caymax, M.; de Marneffe, J.F.; Neyts, E.C.; De Gendt, S.; |
Title |
Multilayer MoS2 growth by metal and metal oxide sulfurization |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Journal of materials chemistry C : materials for optical and electronic devices |
Abbreviated Journal |
J Mater Chem C |
Volume |
4 |
Issue |
4 |
Pages |
1295-1304 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
We investigated the deposition of MoS2 multilayers on large area substrates. The pre-deposition of metal or metal oxide with subsequent sulfurization is a promising technique to achieve layered films. We distinguish a different reaction behavior in metal oxide and metallic films and investigate the effect of the temperature, the H2S/H-2 gas mixture composition, and the role of the underlying substrate on the material quality. The results of the experiments suggest a MoS2 growth mechanism consisting of two subsequent process steps. At first, the reaction of the sulfur precursor with the metal or metal oxide occurs, requiring higher temperatures in the case of metallic film compared to metal oxide. At this stage, the basal planes assemble towards the diffusion direction of the reaction educts and products. After the sulfurization reaction, the material recrystallizes and the basal planes rearrange parallel to the substrate to minimize the surface energy. Therefore, substrates with low roughness show basal plane assembly parallel to the substrate. These results indicate that the substrate character has a significant impact on the assembly of low dimensional MoS2 films. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000370723300020 |
Publication Date |
2016-01-05 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
|
Edition |
|
ISSN |
2050-7526; 2050-7534 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
5.256 |
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: 5.256 |
Call Number |
UA @ lucian @ c:irua:132327 |
Serial |
4211 |
Permanent link to this record |
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Author |
Khalilov, U.; Yusupov, M.; Bogaerts, A.; Neyts, E.C. |
Title |
Selective Plasma Oxidation of Ultrasmall Si Nanowires |
Type |
A1 Journal article |
Year |
2016 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
Volume |
120 |
Issue |
120 |
Pages |
472-477 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Device performance of Si|SiOx core-shell based nanowires critically depends on the exact control over the oxide thickness. Low-temperature plasma oxidation is a highly promising alternative to thermal oxidation allowing for improved control over the oxidation process, in particular for ultrasmall Si nanowires. We here elucidate the room temperature plasma oxidation mechanisms of ultrasmall Si nanowires using hybrid molecular dynamics / force-bias Monte Carlo simulations. We demonstrate how the oxidation and concurrent water formation mechanisms are a function of the oxidizing plasma species and we demonstrate how the resulting core-shell oxide thickness can be controlled through these species. A new mechanism of water formation is discussed in detail. The results provide a detailed atomic level explanation of the oxidation process of highly curved Si surfaces. These results point out a route toward plasma-based formation of ultrathin core-shell Si|SiOx nanowires at room temperature. |
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 |
000368562200057 |
Publication Date |
2015-12-21 |
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 |
1932-7447 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.536 |
Times cited |
3 |
Open Access |
|
Notes |
U.K. and M.Y. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grants 12M1315N and 1200216N. This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. We thank Prof. A. C. T. van Duin for sharing the ReaxFF code. |
Approved |
Most recent IF: 4.536 |
Call Number |
c:irua:130677 |
Serial |
4002 |
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. |
Title |
Multi-level molecular modelling for plasma medicine |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
Volume |
49 |
Issue |
49 |
Pages |
054002 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions. |
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 |
000368944100003 |
Publication Date |
2015-12-16 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0022-3727 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.588 |
Times cited |
11 |
Open Access |
|
Notes |
This work is financially supported by the Fund for Scientific Research Flanders (FWO) and the Francqui Foundation. The calculations were carried out 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: 2.588 |
Call Number |
c:irua:131571 |
Serial |
3985 |
Permanent link to this record |
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Author |
Zhang, Y.-R.; Van Laer, K.; Neyts, E.C.; Bogaerts, A. |
Title |
Can plasma be formed in catalyst pores? A modeling investigation |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Applied catalysis : B : environmental |
Abbreviated Journal |
Appl Catal B-Environ |
Volume |
185 |
Issue |
185 |
Pages |
56-67 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
tWe investigate microdischarge formation inside catalyst pores by a two-dimensional fluid model forvarious pore sizes in the m-range and for various applied voltages. Indeed, this is a poorly understoodphenomenon in plasma catalysis. The calculations are performed for a dielectric barrier discharge inhelium, at atmospheric pressure. The electron and ion densities, electron temperature, electric field andpotential, as well as the electron impact ionization and excitation rate and the densities of excited plasmaspecies, are examined for a better understanding of the characteristics of the plasma inside a pore. Theresults indicate that the pore size and the applied voltage are critical parameters for the formation of amicrodischarge inside a pore. At an applied voltage of 20 kV, our calculations reveal that the ionizationmainly takes place inside the pore, and the electron density shows a significant increase near and inthe pore for pore sizes larger than 200m, whereas the effect of the pore on the total ion density isevident even for 10m pores. When the pore size is fixed at 30m, the presence of the pore has nosignificant influence on the plasma properties at an applied voltage of 2 kV. Upon increasing the voltage,the ionization process is enhanced due to the strong electric field and high electron temperature, andthe ion density shows a remarkable increase near and in the pore for voltages above 10 kV. These resultsindicate that the plasma species can be formed inside pores of structured catalysts (in the m range),and they may interact with the catalyst surface, and affect the plasma catalytic process. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000369452000006 |
Publication Date |
2015-12-11 |
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 |
|
Edition |
|
ISSN |
0926-3373 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
9.446 |
Times cited |
75 |
Open Access |
|
Notes |
This work was supported by the Fund for Scientific ResearchFlanders (FWO) (Grant no. G.0217.14N), the National Natural Sci-ence Foundation of China (Grant no. 11405019), and the ChinaPostdoctoral Science Foundation (Grant no. 2015T80244). Theauthors are very grateful to V. Meynen for the useful discussions oncatalysts. This work was carried out in part using the Turing HPCinfrastructure at the CalcUA core facility of the Universiteit Antwer-pen, a division of the Flemish Supercomputer Center VSC, fundedby the Hercules Foundation, the Flemish Government (departmentEWI) and the University of Antwerp. |
Approved |
Most recent IF: 9.446 |
Call Number |
c:irua:129808 |
Serial |
3984 |
Permanent link to this record |
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Author |
Ali, S.; Myasnichenko, V.S.; Neyts, E.C. |
Title |
Size-dependent strain and surface energies of gold nanoclusters |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
Volume |
18 |
Issue |
18 |
Pages |
792-800 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Cambridge |
Editor |
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Language |
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Wos |
000369480600017 |
Publication Date |
2015-11-18 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
|
Series Volume |
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Series Issue |
|
Edition |
|
ISSN |
1463-9076 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.123 |
Times cited |
37 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 4.123 |
Call Number |
UA @ lucian @ c:irua:131626 |
Serial |
4243 |
Permanent link to this record |
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Author |
Van der Paal, J.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A. |
Title |
Effect of lipid peroxidation on membrane permeability of cancer and normal cells subjected to oxidative stress |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Chemical science |
Abbreviated Journal |
Chem Sci |
Volume |
7 |
Issue |
7 |
Pages |
489-498 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
We performed molecular dynamics simulations to investigate the effect of lipid peroxidation products on the structural and dynamic properties of the cell membrane. Our simulations predict that the lipid order in a phospholipid bilayer, as a model system for the cell membrane, decreases upon addition of lipid peroxidation products. Eventually, when all phospholipids are oxidized, pore formation can occur. This will allow reactive species, such as reactive oxygen and nitrogen species (RONS), to enter the cell and cause oxidative damage to intracellular macromolecules, such as DNA or proteins. On the other hand, upon increasing the cholesterol fraction of lipid bilayers, the cell membrane order increases, eventually reaching a certain threshold, from which cholesterol is able to protect the membrane against pore formation. This finding is crucial for cancer treatment by plasma technology, producing a large number of RONS, as well as for other cancer treatment methods that cause an increase in the concentration of extracellular RONS. Indeed, cancer cells contain less cholesterol than their healthy counterparts. Thus, they will be more vulnerable to the consequences of lipid peroxidation, eventually enabling the penetration of RONS into the interior of the cell, giving rise to oxidative stress, inducing pro-apoptotic factors. This provides, for the first time, molecular level insight why plasma can selectively treat cancer cells, while leaving their healthy counterparts undamaged, as is indeed experimentally demonstrated. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000366826900058 |
Publication Date |
2015-10-16 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
ISSN |
2041-6520 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
8.668 |
Times cited |
106 |
Open Access |
|
Notes |
The authors acknowledge nancial support from the Fund for Scientic Research (FWO) Flanders, grant number G012413N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. |
Approved |
Most recent IF: 8.668 |
Call Number |
c:irua:131058 |
Serial |
3986 |
Permanent link to this record |
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Author |
Neyts, E.C. |
Title |
Plasma-Surface Interactions in Plasma Catalysis |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Plasma chemistry and plasma processing |
Abbreviated Journal |
Plasma Chem Plasma P |
Volume |
36 |
Issue |
36 |
Pages |
185-212 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
In this paper the various elementary plasma—surface interaction processes occurring in plasma catalysis are critically evaluated. Specifically, plasma catalysis at atmospheric pressure is considered. The importance of the various processes is analyzed for the most common plasma catalysis sources, viz. the dielectric barrier discharge and the gliding arc. The role and importance of surface chemical reactions (including adsorption, surface-mediated association and dissociation reactions, and desorption), plasma-induced surface modification, photocatalyst activation, heating, charging, surface discharge formation and electric field enhancement are discussed in the context of plasma catalysis. Numerous examples are provided to demonstrate the importance of the various processes. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000370720800011 |
Publication Date |
2015-10-16 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
ISSN |
0272-4324 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.355 |
Times cited |
66 |
Open Access |
|
Notes |
The author is indebted to many colleagues for fruitful discussions. In particular discussions with A. Bogaerts (University of Antwerp, Belgium), H.-H. Kim (AIST, Japan), J. C. Whitehead (University of Manchester, UK) and T. Nozaki (Tokyo Institute of Technology, Japan) are greatfully acknowledged and appreciated. |
Approved |
Most recent IF: 2.355 |
Call Number |
c:irua:130742 |
Serial |
4004 |
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. |
Title |
Multi-level molecular modelling for plasma medicine |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Journal Of Physics D-Applied Physics |
Abbreviated Journal |
J Phys D Appl Phys |
Volume |
49 |
Issue |
5 |
Pages |
054002-54019 |
Keywords |
A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT) |
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 |
London |
Editor |
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Language |
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Wos |
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Publication Date |
0000-00-00 |
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 |
Impact Factor |
2.588 |
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.588 |
Call Number |
UA @ lucian @ c:irua:129798 |
Serial |
4467 |
Permanent link to this record |
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Author |
Khalilov, U.; Bogaerts, A.; Neyts, E.C. |
Title |
Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Nature communications |
Abbreviated Journal |
Nat Commun |
Volume |
6 |
Issue |
6 |
Pages |
10306 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level. |
Address |
PLASMANT research group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium |
Corporate Author |
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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 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2041-1723 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
12.124 |
Times cited |
37 |
Open Access |
|
Notes |
The authors gratefully acknowledge financial support from the Fund of Scientific Research Flanders (FWO), Belgium, grant number 12M1315N. The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. We thank Professor Adri C. T. van Duin for sharing the ReaxFF code. |
Approved |
Most recent IF: 12.124; 2015 IF: 11.470 |
Call Number |
c:irua:129975 |
Serial |
3990 |
Permanent link to this record |
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Author |
Neyts, E.C.; Ostrikov, K.K.; Sunkara, M.K.; Bogaerts, A. |
Title |
Plasma Catalysis: Synergistic Effects at the Nanoscale |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Chemical reviews |
Abbreviated Journal |
Chem Rev |
Volume |
115 |
Issue |
115 |
Pages |
13408-13446 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
Address |
Department of Chemistry, Research Group PLASMANT, Universiteit Antwerpen , Universiteitsplein 1, 2610 Wilrijk-Antwerp, Belgium |
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 |
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 |
0009-2665 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
47.928 |
Times cited |
204 |
Open Access |
|
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 |
Call Number |
c:irua:130001 |
Serial |
3993 |
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. |
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 |
Volume |
17 |
Issue |
17 |
Pages |
103005 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
000367328100001 |
Publication Date |
2015-10-02 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
ISSN |
1367-2630; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.786 |
Times cited |
18 |
Open Access |
|
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 |
Call Number |
c:irua:129178 |
Serial |
3955 |
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.; |
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. |
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 |
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 |
Call Number |
c:irua:127410 |
Serial |
419 |
Permanent link to this record |
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Author |
Bal, K.M.; Neyts, E.C. |
Title |
Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Journal of chemical theory and computation |
Abbreviated Journal |
J Chem Theory Comput |
Volume |
11 |
Issue |
11 |
Pages |
4545-4554 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of reactive processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics. |
Address |
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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 |
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 |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
5.245 |
Times cited |
41 |
Open Access |
|
Notes |
K.M.B. is funded as Ph.D. fellow (aspirant) of the FWOFlanders (Fund for Scientific Research-Flanders), Grant No. 11 V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) and the HPC infrastructure of the University of Antwerp (CalcUA), funded by the Hercules Foundation and the Flemish Government−Department EWI. |
Approved |
Most recent IF: 5.245; 2015 IF: 5.498 |
Call Number |
c:irua:128183 |
Serial |
3991 |
Permanent link to this record |
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Author |
Nozaki, T.; Neyts, E.C.; Sankaran, M.; Ostrikov, K.(K.); Liu, C.-J. |
Title |
Plasmas for enhanced catalytic processes (ISPCEM 2014) |
Type |
Editorial |
Year |
2015 |
Publication |
Catalysis today |
Abbreviated Journal |
Catal Today |
Volume |
256 |
Issue |
256 |
Pages |
1-2 |
Keywords |
Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
ISSN |
0920-5861; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.636 |
Times cited |
2 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 4.636; 2015 IF: 3.893 |
Call Number |
c:irua:127407 |
Serial |
2641 |
Permanent link to this record |
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Author |
Neyts, E.C. |
Title |
The role of ions in plasma catalytic carbon nanotube growth : a review |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Frontiers of Chemical Science and Engineering |
Abbreviated Journal |
Front Chem Sci Eng |
Volume |
9 |
Issue |
9 |
Pages |
154-162 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
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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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 |
000360319600003 |
Publication Date |
2015-06-11 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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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 |
Impact Factor |
1.712 |
Times cited |
8 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 1.712; 2015 IF: NA |
Call Number |
UA @ lucian @ c:irua:127815 |
Serial |
4239 |
Permanent link to this record |
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Author |
Kato, T.; Neyts, E.C.; Abiko, Y.; Akama, T.; Hatakeyama, R.; Kaneko, T. |
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 |
Volume |
119 |
Issue |
119 |
Pages |
11903-11908 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
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 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.536 |
Times cited |
3 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 4.536; 2015 IF: 4.772 |
Call Number |
c:irua:125928 |
Serial |
1760 |
Permanent link to this record |
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Author |
Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A. |
Title |
Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
Volume |
48 |
Issue |
48 |
Pages |
155202 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
London |
Editor |
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Language |
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Wos |
000351856600007 |
Publication Date |
2015-03-25 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0022-3727;1361-6463; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.588 |
Times cited |
20 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.588; 2015 IF: 2.721 |
Call Number |
c:irua:124230 |
Serial |
3242 |
Permanent link to this record |
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Author |
Neyts, E.C.; Ostrikov, K.(K.) |
Title |
Nanoscale thermodynamic aspects of plasma catalysis |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Catalysis today |
Abbreviated Journal |
Catal Today |
Volume |
256 |
Issue |
256 |
Pages |
23-28 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
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 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.636 |
Times cited |
14 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 4.636; 2015 IF: 3.893 |
Call Number |
c:irua:127409 |
Serial |
2274 |
Permanent link to this record |
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Author |
Brault, P.; Neyts, E.C. |
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 |
Volume |
256 |
Issue |
256 |
Pages |
3-12 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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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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 |
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 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.636 |
Times cited |
18 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 4.636; 2015 IF: 3.893 |
Call Number |
c:irua:127408 |
Serial |
2174 |
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. |
Title |
Thermal conductivity of titanium nitride/titanium aluminum nitride multilayer coatings deposited by lateral rotating cathode arc |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Thin solid films : an international journal on the science and technology of thin and thick films |
Abbreviated Journal |
Thin Solid Films |
Volume |
578 |
Issue |
578 |
Pages |
133-138 |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
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 |
0040-6090; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
1.879 |
Times cited |
41 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 1.879; 2015 IF: 1.759 |
Call Number |
c:irua:125517 |
Serial |
3626 |
Permanent link to this record |
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Author |
Huygh, S.; Neyts, E.C. |
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. |
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 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
ISSN |
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 |
Call Number |
c:irua:124909 |
Serial |
63 |
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. |
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 |
Volume |
106 |
Issue |
106 |
Pages |
011602 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
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 |
|
Edition |
|
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 |
|
Notes |
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Approved |
Most recent IF: 3.411; 2015 IF: 3.302 |
Call Number |
c:irua:122300 |
Serial |
1679 |
Permanent link to this record |
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Author |
Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C. |
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 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
ISSN |
1934-8630;1559-4106; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.603 |
Times cited |
10 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.603; 2015 IF: 3.374 |
Call Number |
c:irua:121371 |
Serial |
1492 |
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. |
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 |
Volume |
12 |
Issue |
12 |
Pages |
162-171 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
ISSN |
1612-8850; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.846 |
Times cited |
18 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.846; 2015 IF: 2.453 |
Call Number |
c:irua:123540 |
Serial |
1589 |
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. |
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 |
Volume |
162 |
Issue |
162 |
Pages |
21-26 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
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 |
0926-3373; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
9.446 |
Times cited |
20 |
Open Access |
|
Notes |
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Approved |
Most recent IF: 9.446; 2015 IF: 7.435 |
Call Number |
c:irua:117949 |
Serial |
874 |
Permanent link to this record |
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Author |
Bal, K.M.; Neyts, E.C. |
Title |
On the time scale associated with Monte Carlo simulations |
Type |
A1 Journal article |
Year |
2014 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
Volume |
141 |
Issue |
20 |
Pages |
204104 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000345641400005 |
Publication Date |
2014-11-26 |
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 |
0021-9606;1089-7690; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.965 |
Times cited |
26 |
Open Access |
|
Notes |
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Approved |
Most recent IF: 2.965; 2014 IF: 2.952 |
Call Number |
UA @ lucian @ c:irua:120667 |
Serial |
2459 |
Permanent link to this record |
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Author |
Tinck, S.; Neyts, E.C.; Bogaerts, A. |
Title |
Fluorinesilicon surface reactions during cryogenic and near room temperature etching |
Type |
A1 Journal article |
Year |
2014 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
Volume |
118 |
Issue |
51 |
Pages |
30315-30324 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
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 |
11 |
Open Access |
|
Notes |
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Approved |
Most recent IF: 4.536; 2014 IF: 4.772 |
Call Number |
UA @ lucian @ c:irua:122957 |
Serial |
1239 |
Permanent link to this record |
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Author |
Bogaerts, A.; Yusupov, M.; Van der Paal, J.; Verlackt, C.C.W.; Neyts, E.C. |
Title |
Reactive molecular dynamics simulations for a better insight in plasma medicine |
Type |
A1 Journal article |
Year |
2014 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
Volume |
11 |
Issue |
12 |
Pages |
1156-1168 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
In this review paper, we present several examples of reactive molecular dynamics simulations, which contribute to a better understanding of the underlying mechanisms in plasma medicine on the atomic scale. This includes the interaction of important reactive oxygen plasma species with the outer cell wall of both gram-positive and gram-negative bacteria, and with lipids present in human skin. Moreover, as most biomolecules are surrounded by a liquid biofilm, the behavior of these plasma species in a liquid (water) layer is presented as well. Finally, a perspective for future atomic scale modeling studies is given, in the field of plasma medicine in general, and for cancer treatment in particular. |
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 |
000346034700007 |
Publication Date |
2014-09-29 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
ISSN |
1612-8850; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.846 |
Times cited |
22 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.846; 2014 IF: 2.453 |
Call Number |
UA @ lucian @ c:irua:121269 |
Serial |
2822 |
Permanent link to this record |