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Author |
Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A. |
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Title |
Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
48 |
Issue |
48 |
Pages |
155202 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract  |
While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function. |
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Place of Publication |
London |
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Wos |
000351856600007 |
Publication Date |
2015-03-25 |
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ISSN |
0022-3727;1361-6463; |
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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 |
20 |
Open Access |
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Approved |
Most recent IF: 2.588; 2015 IF: 2.721 |
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Call Number |
c:irua:124230 |
Serial |
3242 |
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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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Wos |
000621595300016 |
Publication Date |
2021-01-18 |
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ISSN |
1463-9076 |
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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 |
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Author |
Verheyen, C.; van ’t Veer, K.; Snyders, R.; Bogaerts, A. |
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Title |
Atomic oxygen assisted CO2 conversion: A theoretical analysis |
Type |
A1 Journal article |
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Year |
2023 |
Publication |
Journal of CO2 utilization |
Abbreviated Journal |
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Volume |
67 |
Issue |
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Pages |
102347 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
With climate change still a pressing issue, there is a great need for carbon capture, utilisation and storage (CCUS)
methods. We propose a novel concept where CO2 conversion is accomplished by O2 splitting followed by the
addition of O atoms to CO2. The latter is studied here by means of kinetic modelling. In the first instance, we
study various CO2/O ratios, and we observe an optimal CO2 conversion of around 30–40% for 50% O addition.
Gas temperature also has a large influence, with a minimum temperature of around 1000 K to a maximum of
2000 K for optimal conversion. In the second instance, we study various CO2/O/O2 ratios, due to O2 being a
starting gas. Also here we define optimal regions for CO2 conversion, which reach maximum conversion for a
CO2 fraction of 50% and an O/O2 ratio bigger than 1. Those can be expanded by heating on one hand, for low
atomic oxygen availability, and by quenching after reaction on the other hand, for cases where the temperatures
are too high. Our model predictions can serve as a guideline for experimental research in this domain. |
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Wos |
000908384000005 |
Publication Date |
0000-00-00 |
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ISSN |
2212-9820 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
7.7 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
This research was supported by FWO – PhD fellowship-aspirant, Grant 1184820N. We also want to thank Bj¨orn Loenders and Joachim Slaets. |
Approved |
Most recent IF: 7.7; 2023 IF: 4.292 |
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Call Number |
PLASMANT @ plasmant @c:irua:192321 |
Serial |
7231 |
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Author |
Manaigo, F. |
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Title |
Study of a gliding arc discharge for sustainable nitrogen fixation into NOx |
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Doctoral thesis |
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Year |
2024 |
Publication |
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Pages |
xxiv, 114 p. |
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Keywords |
Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
With the growth of the world population, the agricultural sector is required to meet an increasing demand for nutrients and currently relies on industrially produced fertilizers. Among them, nitrogen-based fertilizers are the most common choice and require N2 to be converted into more reactive molecules in a process called “nitrogen fixation”. This is mainly performed through the Haber-Bosch process, which, is not ideal since it requires large-scale facilities to be economical and is associated with a high energy cost and high CO2 emissions, resulting in an environmental impact that is pushing for the study of greener alternatives. Among these, plasma-based nitrogen fixation into NOx is promising, and gliding arc plasma, specifically, proved to be suitable for nitrogen fixation. This thesis aims to study plasma-based nitrogen fixation focusing on an atmospheric pressure gliding arc plasma on three different levels. On a fundamental level, an approach dealing with laser-based excitation of separate rotational lines was successfully developed. This method can be implemented on atmospheric discharges that produce rather high NOx densities and, thus, can impose essential restrictions for the use of “classical” laser-induced fluorescence methods. The approach is then implemented, providing a discussion on the two-dimensional distributions of both the gas temperature and the NO ground state density. A clear correlation between these quantities is found and the effects of both the gas temperature and the plasma power on NO and NO2 concentrations are discussed, revealing how the NO oxidation is already significant in the plasma afterglow region and how the gas flow rate is a crucial parameter affecting the temperature gradients. >From a technological level, the conventional approach of introducing external resistors to stabilize the arc is challenged by studying both its performance and its stability replacing the external resistor with an inductor. We conclude that similar stabilization results can be obtained while significantly lowering the overall energy cost, which decreased from up to a maximum of 7.9 MJ/mol N to 3 MJ/mol N. Finally, we study whether a small-scale fertilizer production facility based on a gliding arc plasma can be a local competitive alternative. This is done by proposing a comparative model to understand how capital, operative expenditures and transport costs affect the production costs. The model highlights how, with the current best available technology, plasma-based nitrogen fixation, while being an interesting alternative for NOx synthesis, still requires a more efficient use of H2 for direct NH3 production. |
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Additional Links |
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no |
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Call Number |
UA @ admin @ c:irua:205259 |
Serial |
9175 |
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Author |
Vanmeert, M.; Razzokov, J.; Mirza, M.U.; Weeks, S.D.; Schepers, G.; Bogaerts, A.; Rozenski, J.; Froeyen, M.; Herdewijn, P.; Pinheiro, V.B.; Lescrinier, E. |
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Title |
Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins |
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A1 Journal article |
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Year |
2019 |
Publication |
Nucleic acids research |
Abbreviated Journal |
Nucleic Acids Res |
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Volume |
47 |
Issue |
13 |
Pages |
7130-7142 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase. |
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Wos |
000490556600047 |
Publication Date |
2019-07-26 |
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ISSN |
0305-1048 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
10.162 |
Times cited |
1 |
Open Access |
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Notes |
European Research Council, FP7/2007-2013 ERC-2012-ADG 20120216/320683 ; KU Leuven, OT/14/128 ; Biotechnology and Biosciences Research Council, BB/N01023X/1 BB/N010221/1 ; Authors are grateful to Prof. Dr A.M.J.J. (Alexandre) Bonvin from the University of Utrecht and the WeNMR institute for his expert contribution. We have greatly benefited from discussions and help from numerous postdocs over the years (in particular, Dr E. Groaz, Dr E. Eremeeva, Dr J. Masschelein, Dr S. Xiaoping and Dr M. Renders) as well as graduate student D. Kestemont and undergraduate student M. Abdel Fattah Ismail. We express our gratitude to L. Margamuljana for helpful discussions and excellent technical assistance on in vitro experiments. |
Approved |
Most recent IF: 10.162 |
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Call Number |
PLASMANT @ plasmant @c:irua:162105 |
Serial |
5359 |
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Armelao, L.; Bertagnolli, H.; Bleiner, D.; Groenewolt, M.; Gross, S.; Krishnan, V.; Sada, C.; Schubert, U.; Tondello, E.; Zattin, A. |
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Highly dispersed mixed zirconia and hafnia nanoparticles in a silica matrix: First example of a ZrO2-HfO2-SiO2 ternary oxide system |
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A1 Journal article |
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2007 |
Publication |
Advanced functional materials |
Abbreviated Journal |
Adv Funct Mater |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
ZrO2 and HfO2 nanoparticles are homogeneously dispersed in SiO2 matrices (supported film and bulk powders) by copolymerization of two oxozirconium and oxohafnium clusters (M4O(2)(OMc)(12), M= Zr, Hf; OMc = OC(O)-C(CH3)=CH2) with (methacryloxypropyl)trimethoxysilane (MAPTMS, (CH2=C(CH3)C(O)O)-(CH2)(3)Si(OCH3)(3)). After calcination (at a temperature >= 800 degrees C), a silica matrix with homogeneously distributed MO2 nanocrystallites is obtained. This route yields a spatially homogeneous dispersion of the metal precursors inside the silica matrix, which is maintained during calcination. The composition of the films and the powders is studied before and after calcination by using Fourier transform infrared (FTIR) analysis, X-ray photoelectron spectroscopy (XPS), secondary ion mass spectrometry (SIMS), and laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). The local environment of the metal atoms in one of the calcined samples is investigated by using X-ray Absorption Fine Structure (XAFS) spectroscopy. Through X-ray diffraction (XRD) the crystallization of Hf and Zr oxides is seen at temperatures higher than those expected for the pure oxides, and transmission electron microscopy (TEM) shows the presence of well-distributed and isolated crystalline oxide nanoparticles (540 nm). |
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Place of Publication |
Weinheim |
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Wos |
000248062100011 |
Publication Date |
2007-05-29 |
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ISSN |
1616-301x |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
12.124 |
Times cited |
34 |
Open Access |
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Approved |
Most recent IF: 12.124; 2007 IF: 7.496 |
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Call Number |
UA @ lucian @ c:irua:95083 |
Serial |
4521 |
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