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Author |
Verlackt, C.C.W.; Van Boxem, W.; Dewaele, D.; Lemière, F.; Sobott, F.; Benedikt, J.; Neyts, E.C.; Bogaerts, A. |
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Title |
Mechanisms of Peptide Oxidation by Hydroxyl Radicals: Insight at the Molecular Scale |
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A1 Journal article |
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Year  |
2017 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
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Volume |
121 |
Issue |
121 |
Pages |
5787-5799 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Molecular dynamics (MD) simulations were performed to provide atomic scale insight in the initial interaction between hydroxyl radicals (OH) and peptide systems in solution. These OH radicals are representative reactive oxygen species produced by cold atmospheric plasmas. The use of plasma for biomedical applications is gaining increasing interest, but the fundamental mechanisms behind the plasma modifications still remain largely elusive. This study helps to gain more insight in the underlying mechanisms of plasma medicine but is also more generally applicable to peptide oxidation, of interest for other applications. Combining both reactive and nonreactive MD simulations, we are able to elucidate the reactivity of the amino acids inside the peptide systems and their effect on their structure up to 1 μs. Additionally, experiments were performed, treating the simulated peptides with a plasma jet. The computational results presented here correlate well with the obtained experimental data and highlight the importance of the chemical environment for the reactivity of the individual amino acids, so that specific amino acids are attacked in higher numbers than expected. Furthermore, the long time scale simulations suggest that a single oxidation has an effect on the 3D conformation due to an increase in hydrophilicity and intra- and intermolecular interactions. |
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Wos |
000396969900037 |
Publication Date |
2017-03-16 |
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Series Issue |
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Edition |
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ISSN |
1932-7447 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.536 |
Times cited |
5 |
Open Access |
OpenAccess |
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Notes |
Fonds Wetenschappelijk Onderzoek, G012413N ; |
Approved |
Most recent IF: 4.536 |
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Call Number |
PLASMANT @ plasmant @ c:irua:142202 |
Serial |
4537 |
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Author |
Mao, M.; Benedikt, J.; Consoli, A.; Bogaerts, A. |
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Title |
New pathways for nanoparticle formation in acetylene dusty plasmas: a modelling investigation and comparison with experiments |
Type |
A1 Journal article |
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Year |
2008 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
41 |
Issue |
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Pages |
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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, the initial mechanisms of nanoparticle formation and growth in radiofrequency acetylene (C2H2) plasmas are investigated by means of a comprehensive self-consistent one-dimensional (1D) fluid model. This model is an extension of the 1D fluid model, developed earlier by De Bleecker et al. Based on the comparison of our previous results with available experimental data for acetylene plasmas in the literature, some new mechanisms for negative ion formation and growth are proposed. Possible routes are considered for the formation of larger (linear and branched) hydrocarbons C2nH2 (n = 3, 4, 5), which contribute to the generation of C2nH− anions (n = 3, 4, 5) due to dissociative electron attachment. Moreover, the vinylidene anion (H2CC−) and higher anions (n = 24) are found to be important plasma species. |
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Place of Publication |
London |
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Wos |
000260738100024 |
Publication Date |
2008-10-24 |
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ISSN |
0022-3727;1361-6463; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.588 |
Times cited |
47 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.588; 2008 IF: 2.104 |
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Call Number |
UA @ lucian @ c:irua:71018 |
Serial |
2330 |
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Author |
Neyts, E.; Bogaerts, A.; Gijbels, R.; Benedikt, J.; van de Sanden, M.C.M. |
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Title |
Molecular dynamics simulation of the impact behaviour of various hydrocarbon species on DLC |
Type |
A1 Journal article |
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Year |
2005 |
Publication |
Nuclear instruments and methods in physics research: B: beam interactions with materials and atoms |
Abbreviated Journal |
Nucl Instrum Meth B |
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Volume |
228 |
Issue |
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Pages |
315-318 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Place of Publication |
Amsterdam |
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Wos |
000226669800052 |
Publication Date |
2004-12-06 |
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Series Issue |
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Edition |
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ISSN |
0168-583X; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
1.109 |
Times cited |
19 |
Open Access |
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Notes |
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Approved |
Most recent IF: 1.109; 2005 IF: 1.181 |
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Call Number |
UA @ lucian @ c:irua:49873 |
Serial |
2172 |
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Author |
Neyts, E.; Bogaerts, A.; Gijbels, R.; Benedikt, J.; van den Sanden, M.C.M. |
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Title |
Molecular dynamics simulations for the growth of diamond-like carbon films from low kinetic energy species |
Type |
A1 Journal article |
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Year |
2004 |
Publication |
Diamond and related materials |
Abbreviated Journal |
Diam Relat Mater |
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Volume |
13 |
Issue |
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Pages |
1873-1881 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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Place of Publication |
Amsterdam |
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Wos |
000223883400021 |
Publication Date |
2004-07-30 |
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Series Issue |
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Edition |
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ISSN |
0925-9635; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.561 |
Times cited |
53 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.561; 2004 IF: 1.670 |
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Call Number |
UA @ lucian @ c:irua:48276 |
Serial |
2173 |
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Author |
Hamon, A.-L.; Verbeeck, J.; Schryvers, D.; Benedikt, J.; van den Sanden, R.M.C.M. |
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Title |
ELNES study of carbon K-edge spectra of plasma deposited carbon films |
Type |
A1 Journal article |
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Year |
2004 |
Publication |
Journal of materials chemistry |
Abbreviated Journal |
J Mater Chem |
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Volume |
14 |
Issue |
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Pages |
2030-2035 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
Electron energy loss spectroscopy was used to investigate the bonding of plasma deposited carbon films. The experimental conditions include the use of a specific collection angle for which the shape of the spectra is free of the orientation dependency usually encountered in graphite due to its anisotropic structure. The first quantification process of the energy loss near-edge structure was performed by a standard fit of the collected spectrum, corrected for background and multiple scattering, with three Gaussian functions followed by a comparison with the graphite spectrum obtained under equivalent experimental conditions. In a second approach a fitting model directly incorporating the background subtraction and multiple scattering removal was applied. The final numerical results are interpreted in view of the deposition conditions of the films and the actual fitting procedure with the related choice of parameters. |
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Publisher |
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Place of Publication |
Cambridge |
Editor |
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Wos |
000222312500017 |
Publication Date |
2004-06-28 |
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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 |
0959-9428;1364-5501; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
6.626 |
Times cited |
61 |
Open Access |
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Notes |
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Approved |
Most recent IF: NA |
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Call Number |
UA @ lucian @ c:irua:48782UA @ admin @ c:irua:48782 |
Serial |
1025 |
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