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Records |
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Author |
Zhang, Y.-R.; Neyts, E.C.; Bogaerts, A. |
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Title |
Enhancement of plasma generation in catalyst pores with different shapes |
Type |
A1 Journal article |
|
Year |
2018 |
Publication |
Plasma sources science and technology |
Abbreviated Journal |
Plasma Sources Sci T |
|
Volume |
27 |
Issue |
5 |
Pages |
055008 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Plasma generation inside catalyst pores is of utmost importance for plasma catalysis, as the existence of plasma species inside the pores affects the active surface area of the catalyst available to the plasma species for catalytic reactions. In this paper, the electric field enhancement, and thus the plasma production inside catalyst pores with different pore shapes is studied with a two-dimensional fluid model. The results indicate that the electric field will be significantly enhanced near tip-like structures. In a conical pore with small opening, the strongest electric field appears at the opening and bottom corners of the pore, giving rise to a prominent ionization rate throughout the pore. For a cylindrical pore, the electric field is only enhanced at the bottom corners of the pore, with lower absolute value, and thus the ionization rate inside the pore is only slightly enhanced. Finally, in a conical pore with large opening, the electric field is characterized by a maximum at the bottom of the pore, yielding a similar behavior for the ionization rate. These results demonstrate that the shape of the pore has a significantly influence on the electric field enhancement, and thus modifies the plasma properties. |
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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 |
000432351700002 |
Publication Date |
2018-05-15 |
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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 |
1361-6595 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.302 |
Times cited |
11 |
Open Access |
OpenAccess |
|
Notes |
This work was supported by the Fund for Scientific Research Flanders (FWO) (Grant No. G.0217.14N) and the Fundamental Research Funds for the Central Universities (Grant No. DUT17LK52). |
Approved |
Most recent IF: 3.302 |
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Call Number |
PLASMANT @ plasmant @c:irua:151546 |
Serial |
4998 |
Permanent link to this record |
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Author |
Bogaerts, A.; De Bie, C.; Eckert, M.; Georgieva, V.; Martens, T.; Neyts, E.; Tinck, S. |
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Title |
Modeling of the plasma chemistry and plasmasurface interactions in reactive plasmas |
Type |
A1 Journal article |
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Year |
2010 |
Publication |
Pure and applied chemistry |
Abbreviated Journal |
Pure Appl Chem |
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Volume |
82 |
Issue |
6 |
Pages |
1283-1299 |
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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, an overview is given of modeling activities going on in our research group, for describing the plasma chemistry and plasmasurface interactions in reactive plasmas. The plasma chemistry is calculated by a fluid approach or by hybrid Monte Carlo (MC)fluid modeling. An example of both is illustrated in the first part of the paper. The example of fluid modeling is given for a dielectric barrier discharge (DBD) in CH4/O2, to describe the partial oxidation of CH4 into value-added chemicals. The example of hybrid MCfluid modeling concerns an inductively coupled plasma (ICP) etch reactor in Ar/Cl2/O2, including also the description of the etch process. The second part of the paper deals with the treatment of plasmasurface interactions on the atomic level, with molecular dynamics (MD) simulations or a combination of MD and MC simulations. |
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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 |
000279063900010 |
Publication Date |
2010-04-21 |
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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 |
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Series Issue |
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Edition |
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ISSN |
1365-3075;0033-4545; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.626 |
Times cited |
13 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.626; 2010 IF: 2.134 |
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Call Number |
UA @ lucian @ c:irua:82108 |
Serial |
2134 |
Permanent link to this record |
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Author |
Yusupov, M.; Neyts, E.C.; Khalilov, U.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A. |
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Title |
Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls |
Type |
A1 Journal article |
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Year |
2012 |
Publication |
New journal of physics |
Abbreviated Journal |
New J Phys |
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Volume |
14 |
Issue |
9 |
Pages |
093043 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. CO, CN and CC bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale. |
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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 |
Bristol |
Editor |
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Language |
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Wos |
000309393400001 |
Publication Date |
2012-09-27 |
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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 |
1367-2630; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.786 |
Times cited |
47 |
Open Access |
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Notes |
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Approved |
Most recent IF: 3.786; 2012 IF: 4.063 |
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Call Number |
UA @ lucian @ c:irua:101014 |
Serial |
189 |
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 |
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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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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 |
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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 |
1367-2630; |
ISBN |
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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 |
Permanent link to this record |
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Author |
Neyts, E.C.; Bogaerts, A. |
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Title |
Combining molecular dynamics with Monte Carlo simulations : implementations and applications |
Type |
A1 Journal article |
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Year |
2013 |
Publication |
Theoretical chemistry accounts : theory, computation, and modeling |
Abbreviated Journal |
Theor Chem Acc |
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Volume |
132 |
Issue |
2 |
Pages |
1320-12 |
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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 contribution, we present an overview of the various techniques for combining atomistic molecular dynamics with Monte Carlo simulations, mainly in the context of condensed matter systems, as well as a brief summary of the main accelerated dynamics techniques. Special attention is given to the force bias Monte Carlo technique and its combination with molecular dynamics, in view of promising recent developments, including a definable timescale. Various examples of the application of combined molecular dynamics / Monte Carlo simulations are given, in order to demonstrate the enhanced simulation efficiency with respect to either pure molecular dynamics or Monte Carlo. |
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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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Wos |
000318294700010 |
Publication Date |
2012-12-19 |
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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 |
1432-881X;1432-2234; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
1.89 |
Times cited |
27 |
Open Access |
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Notes |
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Approved |
Most recent IF: 1.89; 2013 IF: 2.143 |
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Call Number |
UA @ lucian @ c:irua:104725 |
Serial |
404 |
Permanent link to this record |
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Author |
Cassimon, J.; Kovács, A.; Neyts, E.; Cornet, I.; Billen, P. |
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Title |
Deacetylation of mannosylerythritol lipids in hydrophobic natural deep eutectic solvents |
Type |
A1 Journal article |
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Year |
2023 |
Publication |
European journal of organic chemistry |
Abbreviated Journal |
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Volume |
27 |
Issue |
5 |
Pages |
e202300934-10 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS) |
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Abstract |
Mannosylerythritol lipids (MELs) are a promising group of biosurfactants due to their high fermentation yield, selfassembly and biological activity. During fermentation by Pseudozyma aphidis, a mixture of MELs with different levels of acylation is formed, of which the fully deacetylated form is the most valuable. In order to reduce the environmental impact of deacetylation, an enzymatic process using natural deep eutectic solvents (NADES) has been developed. We tested the deacetylation of a purified MELs mixture with immobilized Candida antarctica lipase B enzyme and 2-ethylhexanol as co-substrate in 140 h reactions with different NADES. We identified hydrophobic NADES systems with similar yields and kinetics as in pure 2-ethylhexanol solvent. Our results indicate that deacetylation of MELs mixtures in NADES as a solvent is possible with yields comparable to pure co-substrate and that hydrophobic NADES without carboxylic acid compounds facilitate the reaction to the greatest extent. |
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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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Wos |
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Publication Date |
2023-12-12 |
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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 |
1434-193x; 1099-0690 |
ISBN |
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Additional Links |
UA library record |
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Impact Factor |
2.8 |
Times cited |
|
Open Access |
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Notes |
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Approved |
Most recent IF: 2.8; 2023 IF: 2.834 |
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Call Number |
UA @ admin @ c:irua:201382 |
Serial |
9017 |
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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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 |
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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 |
Permanent link to this record |
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Author |
Shirazi, M.; Bogaerts, A.; Neyts, E.C. |
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Title |
A DFT study of H-dissolution into the bulk of a crystalline Ni(111) surface: a chemical identifier for the reaction kinetics |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
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Volume |
19 |
Issue |
19 |
Pages |
19150-19158 |
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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 study, we investigated the diffusion of H-atoms to the subsurface and their further diffusion into the bulk of a Ni(111) crystal by means of density functional theory calculations in the context of thermal and plasma-assisted catalysis. The H-atoms at the surface can originate from the dissociative adsorption of H2 or CH4 molecules, determining the surface H-coverage. When a threshold H-coverage is passed, corresponding to 1.00 ML for the crystalline Ni(111) surface, the surface-bound H-atoms start to diffuse to the subsurface. A similar threshold coverage is observed for the interstitial H-coverage. Once the interstitial sites are filled up with a coverage above 1.00 ML of H, dissolution of interstitial H-atoms to the layer below the interstitial sites will be initiated. Hence, by applying a high pressure or inducing a reactive plasma and high temperature, increasing the H-flux to the surface, a large amount of hydrogen can diffuse in a crystalline metal like Ni and can be absorbed. The formation of metal hydride may modify the entire reaction kinetics of the system. Equivalently, the H-atoms in the bulk can easily go back to the surface and release a large amount of heat. In a plasma process, H-atoms are formed in the plasma, and therefore the energy barrier for dissociative adsorption is dismissed, thus allowing achievement of the threshold coverage without applying a high pressure as in a thermal process. As a result, depending on the crystal plane and type of metal, a large number of H-atoms can be dissolved (absorbed) in the metal catalyst, explaining the high efficiency of plasma-assisted catalytic reactions. Here, the mechanism of H-dissolution is established as a chemical identifier for the investigation of the reaction kinetics of a chemical process. |
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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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Wos |
000406334300034 |
Publication Date |
2017-06-22 |
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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 |
1463-9076 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
4.123 |
Times cited |
10 |
Open Access |
OpenAccess |
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Notes |
Financial support from the Reactive Atmospheric Plasma processIng – eDucation (RAPID) network, through the EU 7th Framework Programme (grant agreement no. 606889), is gratefully acknowledged. The calculations were performed 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 Universiteit Antwerpen. |
Approved |
Most recent IF: 4.123 |
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Call Number |
PLASMANT @ plasmant @ c:irua:144794 |
Serial |
4633 |
Permanent link to this record |
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Author |
Bal, K.M.; Neyts, E.C. |
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Title |
Modelling molecular adsorption on charged or polarized surfaces: a critical flaw in common approaches |
Type |
A1 Journal article |
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Year |
2018 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
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Volume |
20 |
Issue |
13 |
Pages |
8456-8459 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
A number of recent computational material design studies based on density functional theory (DFT) calculations have put forward a new class of materials with electrically switchable chemical characteristics that can be exploited in the development of tunable gas storage and electrocatalytic applications. We find systematic flaws in almost every computational study of gas adsorption on polarized or charged surfaces, stemming from an improper and unreproducible treatment of periodicity, leading to very large errors of up to 3 eV in some cases. Two simple corrective procedures that lead to consistent results are proposed, constituting a crucial course correction to the research in the field. |
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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 |
000428779700007 |
Publication Date |
2018-03-12 |
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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 |
8 |
Open Access |
OpenAccess |
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Notes |
K. M. B. is funded as PhD fellow (aspirant) of the FWO-Flanders (Research Foundation – Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government – department EWI. |
Approved |
Most recent IF: 4.123 |
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Call Number |
PLASMANT @ plasmant @c:irua:150357 |
Serial |
4916 |
Permanent link to this record |
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Author |
Izadi, M.E.; Bal, K.M.; Maghari, A.; Neyts, E.C. |
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Title |
Reaction mechanisms of C(3PJ) and C+(2PJ) with benzene in the interstellar medium from quantum mechanical molecular dynamics simulations |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Physical Chemistry Chemical Physics |
Abbreviated Journal |
Phys Chem Chem Phys |
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Volume |
23 |
Issue |
7 |
Pages |
4205-4216 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
While spectroscopic data on small hydrocarbons in interstellar media in combination with crossed molecular beam (CMB) experiments have provided a wealth of information on astrochemically relevant species, much of the underlying mechanistic pathways of their formation remain elusive. Therefore, in this work, the chemical reaction mechanisms of C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>and C<sup>+</sup>(<sup>2</sup>P) + C<sub>6</sub>H<sub>6</sub>systems using the quantum mechanical molecular dynamics (QMMD) technique at the PBE0-D3(BJ) level of theory is investigated, mimicking a CMB experiment. Both the dynamics of the reactions as well as the electronic structure for the purpose of the reaction network are evaluated. The method is validated for the first reaction by comparison to the available experimental data. The reaction scheme for the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system covers the literature data,<italic>e.g.</italic>the major products are the 1,2-didehydrocycloheptatrienyl radical (C<sub>7</sub>H<sub>5</sub>) and benzocyclopropenyl radical (C<sub>6</sub>H<sub>5</sub>–CH), and it reveals the existence of less common pathways for the first time. The chemistry of the C<sup>+</sup>(<sup>2</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system is found to be much richer, and we have found that this is because of more exothermic reactions in this system in comparison to those in the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system. Moreover, using the QMMD simulation, a number of reaction paths have been revealed that produce three distinct classes of reaction products with different ring sizes. All in all, at all the collision energies and orientations, the major product is the heptagon molecular ion for the ionic system. It is also revealed that the collision orientation has a dominant effect on the reaction products in both systems, while the collision energy mostly affects the charged system. These simulations both prove the applicability of this approach to simulate crossed molecular beams, and provide fundamental information on reactions relevant for the interstellar medium. |
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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 |
000621595300016 |
Publication Date |
2021-01-18 |
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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 |
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Open Access |
OpenAccess |
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Notes |
Fonds Wetenschappelijk Onderzoek, 12ZI420N ; Ministry of Science Research and Technology; Universiteit Antwerpen; The financial support from the Iran Ministry of Science, Research and Technology and PLASMANT Research Group University of Antwerp is highly acknowledged by the authors. K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation – Flanders), Grant 12ZI420N. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. |
Approved |
Most recent IF: 4.123 |
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Call Number |
PLASMANT @ plasmant @c:irua:176672 |
Serial |
6742 |
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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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 |
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 |
|
|
ISSN |
1463-9076; 1463-9084 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
4.123 |
Times cited |
6 |
Open Access |
|
|
Notes |
; This work was supported by the Strategic Initiative Materials in Flanders (SIM). The computational resources and services used in this work were provided by the Vlaams Supercomputer Centrum (VSC) and the HPC infrastructure of the University of Antwerp. ; |
Approved |
Most recent IF: 4.123 |
|
Call Number |
UA @ lucian @ c:irua:135701 |
Serial |
4311 |
Permanent link to this record |
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Author |
Dabaghmanesh, S.; Sarmadian, N.; Neyts, E.C.; Partoens, B. |
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Title |
A first principles study of p-type defects in LaCrO3 |
Type |
A1 Journal article |
|
Year |
2017 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
|
Volume |
19 |
Issue |
34 |
Pages |
22870-22876 |
|
Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
Abstract |
Recently, Sr-doped LaCrO3 has been experimentally introduced as a new p-type transparent conducting oxide. It is demonstrated that substituting Sr for La results in inducing p-type conductivity in LaCrO3. Performing first principles calculations we study the electronic structure and formation energy of various point defects in LaCrO3. Our results for the formation energies show that in addition to Sr, two more divalent defects, Ca and Ba, substituting for La in LaCrO3, behave as shallow acceptors in line with previous experimental reports. We further demonstrate that under oxygen-poor growth conditions, these shallow acceptors will be compensated by intrinsic donor-like defects (an oxygen vacancy and Cr on an oxygen site), but in the oxygen-rich growth regime the shallow acceptors have the lowest formation energies between all considered defects and will lead to p-type conductivity. |
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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 |
Cambridge |
Editor |
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Language |
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Wos |
000408671600026 |
Publication Date |
2017-08-01 |
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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 |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
4.123 |
Times cited |
16 |
Open Access |
OpenAccess |
|
Notes |
; This work was supported by SIM vzw, Technologiepark 935, BE-9052 Zwijnaarde, Belgium, within the InterPoCo project of the H-INT-S horizontal program. The computational resources and services were provided by the Flemish Supercomputer Center and the HPC infrastructure of the University of Antwerp (CalcUA), both funded by the FWO-Vlaanderen and the Flemish Government. ; |
Approved |
Most recent IF: 4.123 |
|
Call Number |
UA @ lucian @ c:irua:145621 |
Serial |
4735 |
Permanent link to this record |
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Author |
Gogoi, A.; Neyts, E.C.; Peeters, F.M. |
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Title |
Reduction-enhanced water flux through layered graphene oxide (GO) membranes stabilized with H3O+ and OH- ions |
Type |
A1 Journal article |
|
Year |
2024 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
|
|
Volume |
26 |
Issue |
13 |
Pages |
10265-10272 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Modelling and Simulation in Chemistry (MOSAIC) |
|
Abstract |
Graphene oxide (GO) is one of the most promising candidates for next generation of atomically thin membranes. Nevertheless, one of the major issues for real world application of GO membranes is their undesirable swelling in an aqueous environment. Recently, we demonstrated that generation of H3O+ and OH- ions (e.g., with an external electric field) in the interlayer gallery could impart aqueous stability to the layered GO membranes (A. Gogoi, ACS Appl. Mater. Interfaces, 2022, 14, 34946). This, however, compromises the water flux through the membrane. In this study, we report on reducing the GO nanosheets as a solution to this issue. With the reduction of the GO nanosheets, the water flux through the layered GO membrane initially increases and then decreases again beyond a certain degree of reduction. Here, two key factors are at play. Firstly, the instability of the H-bond network between water molecules and the GO nanosheets, which increases the water flux. Secondly, the pore size reduction in the interlayer gallery of the membranes, which decreases the water flux. We also observe a significant improvement in the salt rejection of the membranes, due to the dissociation of water molecules in the interlayer gallery. In particular, for the case of 10% water dissociation, the water flux through the membranes can be enhanced without altering its selectivity. This is an encouraging observation as it breaks the traditional tradeoff between water flux and salt rejection of a membrane. |
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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 |
001186465400001 |
Publication Date |
2024-03-15 |
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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 |
|
Edition |
|
|
ISSN |
1463-9076; 1463-9084 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
|
Impact Factor |
3.3 |
Times cited |
|
Open Access |
|
|
Notes |
|
Approved |
Most recent IF: 3.3; 2024 IF: 4.123 |
|
Call Number |
UA @ admin @ c:irua:204792 |
Serial |
9168 |
Permanent link to this record |
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Author |
Neyts, E.; Bogaerts, A. |
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Title |
Influence of internal energy and impact angle on the sticking behaviour of reactive radicals in thin a-C:H film growth: a molecular dynamics study |
Type |
A1 Journal article |
|
Year |
2006 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
|
Volume |
8 |
Issue |
17 |
Pages |
2066-2071 |
|
Keywords |
A1 Journal article; 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 |
Cambridge |
Editor |
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Language |
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Wos |
000236970300011 |
Publication Date |
2006-03-20 |
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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 |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
4.123 |
Times cited |
7 |
Open Access |
|
|
Notes |
|
Approved |
Most recent IF: 4.123; 2006 IF: 2.892 |
|
Call Number |
UA @ lucian @ c:irua:57353 |
Serial |
1625 |
Permanent link to this record |
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Author |
Schoeters, B.; Neyts, E.C.; Khalilov, U.; Pourtois, G.; Partoens, B. |
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Title |
Stability of Si epoxide defects in Si nanowires : a mixed reactive force field/DFT study |
Type |
A1 Journal article |
|
Year |
2013 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
|
Volume |
15 |
Issue |
36 |
Pages |
15091-15097 |
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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 |
Modeling the oxidation process of silicon nanowires through reactive force field based molecular dynamics simulations suggests that the formation of Si epoxide defects occurs both at the Si/SiOx interface and at the nanowire surface, whereas for flat surfaces, this defect is experimentally observed to occur only at the interface as a result of stress. In this paper, we argue that the increasing curvature stabilizes the defect at the nanowire surface, as suggested by our density functional theory calculations. The latter can have important consequences for the opto-electronic properties of thin silicon nanowires, since the epoxide induces an electronic state within the band gap. Removing the epoxide defect by hydrogenation is expected to be possible but becomes increasingly difficult with a reduction of the diameter of the nanowires. |
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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 |
Cambridge |
Editor |
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Language |
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Wos |
000323520600029 |
Publication Date |
2013-07-16 |
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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 |
1463-9076;1463-9084; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
4.123 |
Times cited |
3 |
Open Access |
|
|
Notes |
; BS gratefully acknowledges financial support of the IWT, Institute for the Promotion of Innovation by Science and Technology in Flanders, via the SBO project “SilaSol”. This work was carried out 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 and the Universiteit Antwerpen. ; |
Approved |
Most recent IF: 4.123; 2013 IF: 4.198 |
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Call Number |
UA @ lucian @ c:irua:110793 |
Serial |
3130 |
Permanent link to this record |
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Author |
Eckert, M.; Neyts, E.; Bogaerts, A. |
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Title |
Modeling adatom surface processes during crystal growth: a new implementation of the Metropolis Monte Carlo algorithm |
Type |
A1 Journal article |
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Year |
2009 |
Publication |
CrystEngComm |
Abbreviated Journal |
Crystengcomm |
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Volume |
11 |
Issue |
8 |
Pages |
1597-1608 |
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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, a new implementation of the Metropolis Monte Carlo (MMC) algorithm is presented. When combining the MMC model with a molecular dynamics (MD) code, crystal growth by plasma-enhanced chemical vapor deposition can be simulated. As the MD part simulates impacts of growth species onto the surface on a time scale of picoseconds, the MMC algorithm simulates the slower adatom surface processes. The implementation includes a criterion for the selection of atoms that are allowed to be displaced during the simulation, and a criterion of after how many MMC cycles the simulation is stopped. We performed combined MD-MMC simulations for hydrocarbon species that are important for the growth of ultrananocrystalline diamond (UNCD) films at partially hydrogenated diamond surfaces, since this implementation is part of a study of the growth mechanisms of (ultra)nanocrystalline diamond films. Exemplary for adatom arrangements during the growth of UNCD, the adatom surface behavior of C and C2H2 at diamond (111)1 × 1, C and C4H2 at diamond (111)1 × 1 and C3 at diamond (100)2 × 1 has been investigated. For all cases, the diamond crystal structure is pursued under the influence of MMC simulation. Additional longer time-scale MD simulations put forward very similar structures, verifying the MMC algorithm. Nevertheless, the MMC simulation time is typically one order of magnitude shorter than the MD simulation time. |
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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 |
000268184300021 |
Publication Date |
2009-04-07 |
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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 |
1466-8033; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
3.474 |
Times cited |
15 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 3.474; 2009 IF: 4.183 |
|
Call Number |
UA @ lucian @ c:irua:77374 |
Serial |
2106 |
Permanent link to this record |
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Author |
Eckert, M.; Neyts, E.; Bogaerts, A. |
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Title |
Differences between ultrananocrystalline and nanocrystalline diamond growth: theoretical investigation of CxHy species at diamond step edges |
Type |
A1 Journal article |
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Year |
2010 |
Publication |
Crystal growth & design |
Abbreviated Journal |
Cryst Growth Des |
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Volume |
10 |
Issue |
9 |
Pages |
4123-4134 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The behavior of hydrocarbon species at step edges of diamond terraces is investigated by means of combined molecular dynamics−Metropolis Monte Carlo simulations. The results show that the formation of ballas-like diamond films (like UNCD) and well-faceted diamond films (like NCD) can be related to the gas phase concentrations of CxHy in a new manner: Species that have high concentrations above the growing UNCD films suppress the extension of step edges through defect formation. The species that are present above the growing NCD film, however, enhance the extension of diamond terraces, which is believed to result in well-faceted diamond films. Furthermore, it is shown that, during UNCD growth, CxHy species with x ≥ 2 play an important role, in contrast to the currently adopted CVD diamond growth mechanism. Finally, the probabilities for the extension of the diamond (100) terrace are much higher than those for the diamond (111) terrace, which is in full agreement with the experimental observation that diamond (100) facets are more favored than diamond (111) facets during CVD diamond growth. |
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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 |
000281353900042 |
Publication Date |
2010-08-16 |
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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 |
1528-7483;1528-7505; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
4.055 |
Times cited |
11 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 4.055; 2010 IF: 4.390 |
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Call Number |
UA @ lucian @ c:irua:83696 |
Serial |
694 |
Permanent link to this record |
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Author |
Eckert, M.; Neyts, E.; Bogaerts, A. |
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Title |
Insights into the growth of (ultra)nanocrystalline diamond by combined molecular dynamics and Monte Carlo simulations |
Type |
A1 Journal article |
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Year |
2010 |
Publication |
Crystal growth & design |
Abbreviated Journal |
Cryst Growth Des |
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Volume |
10 |
Issue |
7 |
Pages |
3005-3021 |
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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 present the results of combined molecular dynamics−Metropolis Monte Carlo (MD-MMC) simulations of hydrocarbon species at flat diamond (100)2 × 1 and (111)1 × 1 surfaces. The investigated species are considered to be the most important growth species for (ultra)nanocrystalline diamond ((U)NCD) growth. When applying the MMC algorithm to stuck species at monoradical sites, bonding changes are only seen for CH2. The sequence of the bond breaking and formation as put forward by the MMC simulations mimics the insertion of CH2 into a surface dimer as proposed in the standard growth model of diamond. For hydrocarbon species attached to two adjacent radical (biradical) sites, the MMC simulations give rise to significant changes in the bonding structure. For UNCD, the combinations of C3 and C3H2, and C3 and C4H2 (at diamond (100)2 × 1) and C and C2H2 (at diamond (111)1 × 1) are the most successful in nucleating new crystal layers. For NCD, the following combinations pursue the diamond structure the best: C2H2 and C3H2 (at diamond (100)2 × 1) and CH2 and C2H2 (at diamond (111)1 × 1). The different behaviors of the hydrocarbon species at the two diamond surfaces are related to the different sterical hindrances at the diamond surfaces. |
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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 |
000279422700032 |
Publication Date |
2010-05-25 |
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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 |
1528-7483;1528-7505; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
4.055 |
Times cited |
13 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 4.055; 2010 IF: 4.390 |
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Call Number |
UA @ lucian @ c:irua:83065 |
Serial |
1675 |
Permanent link to this record |
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Author |
Villarreal, R.; Lin, P.-C.; Faraji, F.; Hassani, N.; Bana, H.; Zarkua, Z.; Nair, M.N.; Tsai, H.-C.; Auge, M.; Junge, F.; Hofsaess, H.C.; De Gendt, S.; De Feyter, S.; Brems, S.; Ahlgren, E.H.; Neyts, E.C.; Covaci, L.; Peeters, F.M.; Neek-Amal, M.; Pereira, L.M.C. |
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Title |
Breakdown of universal scaling for nanometer-sized bubbles in graphene |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Nano Letters |
Abbreviated Journal |
Nano Lett |
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Volume |
21 |
Issue |
19 |
Pages |
8103-8110 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
We report the formation of nanobubbles on graphene with a radius of the order of 1 nm, using ultralow energy implantation of noble gas ions (He, Ne, Ar) into graphene grown on a Pt(111) surface. We show that the universal scaling of the aspect ratio, which has previously been established for larger bubbles, breaks down when the bubble radius approaches 1 nm, resulting in much larger aspect ratios. Moreover, we observe that the bubble stability and aspect ratio depend on the substrate onto which the graphene is grown (bubbles are stable for Pt but not for Cu) and trapped element. We interpret these dependencies in terms of the atomic compressibility of the noble gas as well as of the adhesion energies between graphene, the substrate, and trapped atoms. |
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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 |
000709549100026 |
Publication Date |
2021-09-14 |
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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 |
1530-6984 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
12.712 |
Times cited |
24 |
Open Access |
OpenAccess |
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Notes |
|
Approved |
Most recent IF: 12.712 |
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Call Number |
UA @ admin @ c:irua:184137 |
Serial |
6857 |
Permanent link to this record |
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Author |
Faraji, F.; Neyts, E.C.; Milošević, M.V.; Peeters, F.M. |
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Title |
Capillary Condensation of Water in Graphene Nanocapillaries |
Type |
A1 Journal Article |
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Year |
2024 |
Publication |
Nano Letters |
Abbreviated Journal |
Nano Lett. |
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Volume |
24 |
Issue |
18 |
Pages |
5625-5630 |
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Keywords |
A1 Journal Article; CMT |
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Abstract |
Recent experiments have revealed that the macroscopic Kelvin equation remains surprisingly accurate even for nanoscale capillaries. This phenomenon was so far explained by the oscillatory behavior of the solid−liquid interfacial free energy. We here demonstrate thermodynamic and capillarity inconsistencies with this explanation. After revising the Kelvin equation, we ascribe its validity at nanoscale confinement to the effect of disjoining pressure.
To substantiate our hypothesis, we employed molecular dynamics simulations to evaluate interfacial heat transfer and wetting properties. Our assessments unveil a breakdown in a previously established proportionality between the work of adhesion and the Kapitza conductance at capillary heights below 1.3 nm, where the dominance of the work of adhesion shifts primarily from energy to entropy. Alternatively, the peak density of the initial water layer can effectively probe the work of adhesion. Unlike under bulk conditions, high confinement renders the work of adhesion entropically unfavorable. |
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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 |
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Publication Date |
2024-05-08 |
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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 |
1530-6984 |
ISBN |
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Additional Links |
|
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Impact Factor |
10.8 |
Times cited |
|
Open Access |
|
|
Notes |
This work was supported by Research Foundation-Flanders (FWO, project No. G099219N). The computational resources used in this work were provided by the HPC core facility CalcUA of the University of Antwerp, and the Flemish Supercomputer Center (VSC), funded by FWO and the Flemish Government. |
Approved |
Most recent IF: 10.8; 2024 IF: 12.712 |
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Call Number |
UA @ lucian @ |
Serial |
9123 |
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 |
|
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 |
Neyts, E.C.; Thijsse, B.J.; Mees, M.J.; Bal, K.M.; Pourtois, G. |
|
Title |
Establishing uniform acceptance in force biased Monte Carlo simulations |
Type |
A1 Journal article |
|
Year |
2012 |
Publication |
Journal of chemical theory and computation |
Abbreviated Journal |
J Chem Theory Comput |
|
Volume |
8 |
Issue |
6 |
Pages |
1865-1869 |
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
Abstract |
Uniform acceptance force biased Monte Carlo (UFMC) simulations have previously been shown to be a powerful tool to simulate atomic scale processes, enabling one to follow the dynamical path during the simulation. In this contribution, we present a simple proof to demonstrate that this uniform acceptance still complies with the condition of detailed balance, on the condition that the characteristic parameter lambda = 1/2 and that the maximum allowed step size is chosen to be sufficiently small. Furthermore, the relation to Metropolis Monte Carlo (MMC) is also established, and it is shown that UFMC reduces to MMC by choosing the characteristic parameter lambda = 0 [Rao, M. et al. Mol. Phys. 1979, 37, 1773]. Finally, a simple example compares the UFMC and MMC methods. |
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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 |
|
Wos |
000305092400002 |
Publication Date |
2012-05-16 |
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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 |
|
Series Issue |
|
Edition |
|
|
ISSN |
1549-9618;1549-9626; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
5.245 |
Times cited |
20 |
Open Access |
|
|
Notes |
|
Approved |
Most recent IF: 5.245; 2012 IF: 5.389 |
|
Call Number |
UA @ lucian @ c:irua:99090 |
Serial |
1082 |
Permanent link to this record |
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|
|
Author |
Berdiyorov, G.R.; Khalilov, U.; Hamoudi, H.; Neyts, E.C. |
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Title |
Effect of chemical modification on electronic transport properties of carbyne |
Type |
A1 Journal article |
|
Year |
2021 |
Publication |
Journal Of Computational Electronics |
Abbreviated Journal |
J Comput Electron |
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Volume |
|
Issue |
|
Pages |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
Abstract |
Using density functional theory in combination with the Green’s functional formalism, we study the effect of surface functionalization on the electronic transport properties of 1D carbon allotrope—carbyne. We found that both hydrogenation and fluorination result in structural changes and semiconducting to metallic transition. Consequently, the current in the functionalization systems increases significantly due to strong delocalization of electronic states along the carbon chain. We also study the electronic transport in partially hydrogenated carbyne and interface structures consisting of pristine and functionalized carbyne. In the latter case, current rectification is obtained in the system with rectification ratio up to 50%. These findings can be useful for developing carbyne-based structures with tunable electronic transport properties. |
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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 |
000617664900001 |
Publication Date |
2021-02-13 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
ISSN |
1569-8025 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
1.526 |
Times cited |
|
Open Access |
OpenAccess |
|
Notes |
Computational resources were provided by the research computing facilities of Qatar Environment and Energy Research Institute. Calculations are also conducted 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 University of Antwerp. U. Khalilov gratefully acknowledges financial support from the Fund of Scientific Research Flanders (FWO), Belgium, Grant number 12M1315N. |
Approved |
Most recent IF: 1.526 |
|
Call Number |
PLASMANT @ plasmant @c:irua:176169 |
Serial |
6708 |
Permanent link to this record |
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Author |
Neyts, E.C.; Brault, P. |
|
Title |
Molecular Dynamics Simulations for Plasma-Surface Interactions: Molecular Dynamics Simulations… |
Type |
A1 Journal article |
|
Year |
2017 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
|
Volume |
14 |
Issue |
14 |
Pages |
1600145 |
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
Abstract |
Plasma-surface interactions are in general highly complex due to the interplay of many concurrent processes. Molecular dynamics simulations provide insight in some of these processes, subject to the accessible time and length scales, and the availability of suitable force fields. In this introductory tutorial-style review, we aim to describe the current capabilities and limitations of molecular dynamics simulations in this field, restricting ourselves to low-temperature nonthermal plasmas. Attention is paid to the simulation of the various fundamental processes occurring, including sputtering, etching, implantation, and deposition, as well as to what extent the basic plasma components can be accounted for, including ground state and excited species, electric fields, ions, photons, and electrons. A number of examples is provided, giving an bird’s eye overview of the current state of 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 |
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Editor |
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Language |
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Wos |
000393184600009 |
Publication Date |
2016-09-07 |
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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 |
|
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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 |
13 |
Open Access |
Not_Open_Access |
|
Notes |
|
Approved |
Most recent IF: 2.846 |
|
Call Number |
PLASMANT @ plasmant @ c:irua:141758 |
Serial |
4488 |
Permanent link to this record |
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Author |
Neyts, E.C.; Bal, K.M. |
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Title |
Effect of electric fields on plasma catalytic hydrocarbon oxidation from atomistic simulations |
Type |
A1 Journal article |
|
Year |
2017 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
|
Volume |
14 |
Issue |
6 |
Pages |
e1600158 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
Abstract |
The catalytic oxidative dehydrogenation of hydrocarbons is an industrially important process, in which selectivity is a key issue. We here investigate the conversion of methanol to formaldehyde on a vanadia surface employing long timescale simulations, reaching a time scale of seconds. In particular, we compare the thermal process to the case where an additional external electric field is applied, as would be the case in a direct plasma-catalysis setup. We find that the electric field influences the retention time of the molecules at the catalyst surface. These simulations provide an atomic scale insight in the thermal catalytic oxidative dehydrogenation process, and in how an external electric field may affect this 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 |
Weinheim |
Editor |
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Language |
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Wos |
000403699900013 |
Publication Date |
2016-11-08 |
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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 |
2 |
Open Access |
Not_Open_Access |
|
Notes |
|
Approved |
Most recent IF: 2.846 |
|
Call Number |
UA @ lucian @ c:irua:144210 |
Serial |
4647 |
Permanent link to this record |
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Author |
Tinck, S.; Tillocher, T.; Georgieva, V.; Dussart, R.; Neyts, E.; Bogaerts, A. |
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Title |
Concurrent effects of wafer temperature and oxygen fraction on cryogenic silicon etching with SF6/O2plasmas |
Type |
A1 Journal article |
|
Year |
2017 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
|
Volume |
14 |
Issue |
9 |
Pages |
1700018 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Cryogenic plasma etching is a promising technique for high-control wafer development with limited plasma induced damage. Cryogenic wafer temperatures effectively reduce surface damage during etching, but the fundamental mechanism is not well understood. In this study, the influences of wafer temperature, gas mixture and substrate bias on the (cryogenic) etch rates of Si with SF6/O2 inductively coupled plasmas are experimentally and computationally investigated. The etch rates are measured in situ with double-point reflectometry and a hybrid computational Monte Carlo – fluid model is applied to calculate plasma properties. This work allows the reader to obtain a better insight in the effects of wafer temperature on the etch rate and to find operating conditions for successful anisotropic (cryo)etching. |
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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 |
000410773200012 |
Publication Date |
2017-04-03 |
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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 |
|
Open Access |
Not_Open_Access |
|
Notes |
Fonds Wetenschappelijk Onderzoek, 0880.212.840 ; Hercules Foundation; Flemish Government (Department EWI); Universiteit Antwerpen; |
Approved |
Most recent IF: 2.846 |
|
Call Number |
PLASMANT @ plasmant @c:irua:145637 |
Serial |
4708 |
Permanent link to this record |
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Author |
Razzokov, J.; Yusupov, M.; Vanuytsel, S.; Neyts, E.C.; Bogaerts, A. |
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Title |
Phosphatidylserine flip-flop induced by oxidation of the plasma membrane: a better insight by atomic scale modeling |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
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Volume |
14 |
Issue |
10 |
Pages |
1700013 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells. |
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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 |
000413045800010 |
Publication Date |
2017-04-05 |
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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 |
1612-8850 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
Impact Factor |
2.846 |
Times cited |
9 |
Open Access |
Not_Open_Access |
|
Notes |
Fonds Wetenschappelijk Onderzoek, 1200216N ; |
Approved |
Most recent IF: 2.846 |
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Call Number |
PLASMANT @ plasmant @c:irua:149567 |
Serial |
4910 |
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 |
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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 |
|
|
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 |
Somers, W.; Dubreuil, M.F.; Neyts, E.C.; Vangeneugden, D.; Bogaerts, A. |
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Title |
Incorporation of fluorescent dyes in atmospheric pressure plasma coatings for in-line monitoring of coating homogeneity |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
|
Volume |
11 |
Issue |
7 |
Pages |
678-684 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
This paper reports on the incorporation of three commercial fluorescent dyes, i.e., rhodamine 6G, fluorescein, and fluorescent brightener 184, in plasma coatings, by utilizing a dielectric barrier discharge (DBD) reactor, and the subsequent monitoring of the coatings homogeneity based on the emitted fluorescent light. The plasma coatings are qualitatively characterized with fluorescence microscopy, UVvis spectroscopy and profilometry for the determination of the coating thickness. The emitted fluorescent light of the coating correlates to the amount of dye per area, and deviations of these factors can hence be observed by monitoring the intensity of this light. This allows monitoring the homogeneity of the plasma coatings in a fast and simple way, without making major adjustments to the 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 |
Weinheim |
Editor |
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Language |
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Wos |
000340416300007 |
Publication Date |
2014-05-03 |
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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 |
3 |
Open Access |
|
|
Notes |
|
Approved |
Most recent IF: 2.846; 2014 IF: 2.453 |
|
Call Number |
UA @ lucian @ c:irua:118063 |
Serial |
1598 |
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. |
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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 |
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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. |
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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 |
000346034700007 |
Publication Date |
2014-09-29 |
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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 |
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 |