Records |
Author |
de Bleecker, K.; Bogaerts, A.; Goedheer, W.J. |
Title |
Nanoparticle growth and transport mechanisms in capacitively coupled silane discharges: a numerical investigation |
Type |
P1 Proceeding |
Year |
2005 |
Publication |
|
Abbreviated Journal |
|
Volume |
|
Issue |
|
Pages |
201-204 |
Keywords |
P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
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Corporate Author |
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Thesis |
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Publisher |
American Institute of Physics |
Place of Publication |
Melville, N.Y. |
Editor |
|
Language |
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Wos |
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Publication Date |
0000-00-00 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
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ISBN |
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Additional Links |
UA library record; WoS full record; |
Impact Factor |
|
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: NA |
Call Number |
UA @ lucian @ c:irua:56576 |
Serial |
2260 |
Permanent link to this record |
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|
|
Author |
Kamaraj, B.; Purohit, R. |
Title |
Mutational Analysis on Membrane Associated Transporter Protein (MATP) and Their Structural Consequences in Oculocutaeous Albinism Type 4 (OCA4)A Molecular Dynamics Approach |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Journal of cellular biochemistry |
Abbreviated Journal |
J Cell Biochem |
Volume |
117 |
Issue |
11 |
Pages |
2608-2619 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
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Corporate Author |
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Thesis |
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Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
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Language |
|
Wos |
000383626800017 |
Publication Date |
2016-03-28 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0730-2312 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.085 |
Times cited |
28 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 3.085 |
Call Number |
UA @ lucian @ c:irua:144634 |
Serial |
4671 |
Permanent link to this record |
|
|
|
Author |
Vanraes, P.; Parayil Venugopalan, S.; Bogaerts, A. |
Title |
Multiscale modeling of plasma–surface interaction—General picture and a case study of Si and SiO2etching by fluorocarbon-based plasmas |
Type |
A1 Journal Article |
Year |
2021 |
Publication |
Applied Physics Reviews |
Abbreviated Journal |
Appl Phys Rev |
Volume |
8 |
Issue |
4 |
Pages |
041305 |
Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
Abstract |
The physics and chemistry of plasma–surface interaction is a broad domain relevant to various applications and several natural processes, including plasma etching for microelectronics fabrication, plasma deposition, surface functionalization, nanomaterial synthesis, fusion reactors, and some astrophysical and meteorological phenomena. Due to their complex nature, each of these processes is generally investigated in separate subdomains, which are considered to have their own theoretical, modeling, and experimental challenges. In this review, however, we want to emphasize the overarching nature of plasma–surface interaction physics and chemistry, by focusing on the general strategy for its computational simulation. In the first half of the review, we provide a menu card with standard and less standardized computational methods to be used for the multiscale modeling of the underlying processes. In the second half, we illustrate the benefits and potential of the multiscale modeling strategy with a case study of Si and SiO2 etching by fluorocarbon plasmas and identify the gaps in knowledge still present on this intensely investigated plasma–material combination, both on a qualitative and quantitative level. Remarkably, the dominant etching mechanisms remain the least understood. The resulting new insights are of general relevance, for all plasmas and materials, including their various applications. We therefore hope to motivate computational and experimental scientists and engineers to collaborate more intensely on filling the existing gaps in knowledge. In this way, we expect that research will overcome a bottleneck stage in the development and optimization of multiscale models, and thus the fundamental understanding of plasma–surface interaction. |
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 |
000754799700001 |
Publication Date |
2021-10-07 |
Series Editor |
|
Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1931-9401 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
13.667 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
Asml; P. Vanraes acknowledges funding by ASML for the project “Computational simulation of plasma etching of trench structures.” P. Vanraes wishes to thank Violeta Georgieva and Stefan Tinck for the fruitful discussions on the HPEM code, Yu-Ru Zhang for an example of the CCP reactor code, and Karel Venken for his technical help with the server maintenance and use. P. Vanraes and A. Bogaerts want to express their gratitude to Mark J. Kushner (University of Michigan) for the sharing of the HPEM and MCFPM codes and for the interesting exchange of views. S. P. Venugopalan wishes to thank Sander Wuister, Coen Verschuren, Michael Kubis, Mohammad Kamali, |
Approved |
Most recent IF: 13.667 |
Call Number |
PLASMANT @ plasmant @c:irua:183287 |
Serial |
6814 |
Permanent link to this record |
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|
|
Author |
Bleiner, D.; Bogaerts, A. |
Title |
Multiplicity and contiguity of ablation mechanisms in laser-assisted analytical micro-sampling |
Type |
A1 Journal article |
Year |
2006 |
Publication |
Spectrochimica acta: part B : atomic spectroscopy |
Abbreviated Journal |
Spectrochim Acta B |
Volume |
61 |
Issue |
4 |
Pages |
421-432 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
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Corporate Author |
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Thesis |
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Publisher |
|
Place of Publication |
Oxford |
Editor |
|
Language |
|
Wos |
000238887600008 |
Publication Date |
2006-03-30 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0584-8547; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.241 |
Times cited |
48 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 3.241; 2006 IF: 3.092 |
Call Number |
UA @ lucian @ c:irua:58156 |
Serial |
2234 |
Permanent link to this record |
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|
|
Author |
Liu, Y.H.; Chen, Z.Y.; Yu, M.Y.; Bogaerts, A. |
Title |
Multiple void formation in plasmas containing multispecies charged grains |
Type |
A1 Journal article |
Year |
2006 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
Volume |
74 |
Issue |
|
Pages |
056401,1-6 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
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Corporate Author |
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Thesis |
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Publisher |
|
Place of Publication |
Lancaster, Pa |
Editor |
|
Language |
|
Wos |
000242408800037 |
Publication Date |
2006-11-14 |
Series Editor |
|
Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.366 |
Times cited |
21 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.366; 2006 IF: 2.438 |
Call Number |
UA @ lucian @ c:irua:60424 |
Serial |
2233 |
Permanent link to this record |
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Author |
Autrique, D. |
Title |
Multiphase modelling of a ns-laser-irradiated copper sample |
Type |
Doctoral thesis |
Year |
2014 |
Publication |
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Abbreviated Journal |
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Volume |
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Issue |
|
Pages |
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Keywords |
Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Antwerpen |
Editor |
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Language |
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Wos |
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Publication Date |
0000-00-00 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
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ISBN |
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Additional Links |
UA library record |
Impact Factor |
|
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: NA |
Call Number |
UA @ lucian @ c:irua:116428 |
Serial |
2224 |
Permanent link to this record |
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|
|
Author |
Le Compte, M.; Cardenas De La Hoz, E.; Peeters, S.; Smits, E.; Lardon, F.; Roeyen, G.; Vanlanduit, S.; Prenen, H.; Peeters, M.; Lin, A.; Deben, C. |
Title |
Multiparametric tumor organoid drug screening using widefield live-cell imaging for bulk and single-organoid analysis |
Type |
A1 Journal article |
Year |
2022 |
Publication |
Jove-Journal Of Visualized Experiments |
Abbreviated Journal |
Jove-J Vis Exp |
Volume |
|
Issue |
190 |
Pages |
1-18 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Center for Oncological Research (CORE) |
Abstract |
Patient-derived tumor organoids (PDTOs) hold great promise for preclinical and translational research and predicting the patient therapy response from ex vivo drug screenings. However, current adenosine triphosphate (ATP)-based drug screening assays do not capture the complexity of a drug response (cytostatic or cytotoxic) and intratumor heterogeneity that has been shown to be retained in PDTOs due to a bulk readout. Live-cell imaging is a powerful tool to overcome this issue and visualize drug responses more in-depth. However, image analysis software is often not adapted to the three-dimensionality of PDTOs, requires fluorescent viability dyes, or is not compatible with a 384-well microplate format. This paper describes a semi-automated methodology to seed, treat, and image PDTOs in a high-throughput, 384-well format using conventional, widefield, live-cell imaging systems. In addition, we developed viability marker-free image analysis software to quantify growth rate-based drug response metrics that improve reproducibility and correct growth rate variations between different PDTO lines. Using the normalized drug response metric, which scores drug response based on the growth rate normalized to a positive and negative control condition, and a fluorescent cell death dye, cytotoxic and cytostatic drug responses can be easily distinguished, profoundly improving the classification of responders and non-responders. In addition, drug-response heterogeneity can by quantified from single-organoid drug response analysis to identify potential, resistant clones. Ultimately, this method aims to improve the prediction of clinical therapy response by capturing a multiparametric drug response signature, which includes kinetic growth arrest and cell death quantification. , |
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 |
000928020400010 |
Publication Date |
2022-12-24 |
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 |
1940-087x |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
1.2 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 1.2 |
Call Number |
UA @ admin @ c:irua:193168 |
Serial |
7271 |
Permanent link to this record |
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|
|
Author |
Heyne, M.H.; Chiappe, D.; Meersschaut, J.; Nuytten, T.; Conard, T.; Bender, H.; Huyghebaert, C.; Radu, I.P.; Caymax, M.; de Marneffe, J.F.; Neyts, E.C.; De Gendt, S.; |
Title |
Multilayer MoS2 growth by metal and metal oxide sulfurization |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Journal of materials chemistry C : materials for optical and electronic devices |
Abbreviated Journal |
J Mater Chem C |
Volume |
4 |
Issue |
4 |
Pages |
1295-1304 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
We investigated the deposition of MoS2 multilayers on large area substrates. The pre-deposition of metal or metal oxide with subsequent sulfurization is a promising technique to achieve layered films. We distinguish a different reaction behavior in metal oxide and metallic films and investigate the effect of the temperature, the H2S/H-2 gas mixture composition, and the role of the underlying substrate on the material quality. The results of the experiments suggest a MoS2 growth mechanism consisting of two subsequent process steps. At first, the reaction of the sulfur precursor with the metal or metal oxide occurs, requiring higher temperatures in the case of metallic film compared to metal oxide. At this stage, the basal planes assemble towards the diffusion direction of the reaction educts and products. After the sulfurization reaction, the material recrystallizes and the basal planes rearrange parallel to the substrate to minimize the surface energy. Therefore, substrates with low roughness show basal plane assembly parallel to the substrate. These results indicate that the substrate character has a significant impact on the assembly of low dimensional MoS2 films. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000370723300020 |
Publication Date |
2016-01-05 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2050-7526; 2050-7534 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
5.256 |
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: 5.256 |
Call Number |
UA @ lucian @ c:irua:132327 |
Serial |
4211 |
Permanent link to this record |
|
|
|
Author |
Jochum, K.P.; Gijbels, R.; Adriaens, A. |
Title |
Multielementmassenspektrometrie (MMS) |
Type |
H3 Book chapter |
Year |
2000 |
Publication |
|
Abbreviated Journal |
|
Volume |
|
Issue |
|
Pages |
188-203 |
Keywords |
H3 Book chapter; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
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Corporate Author |
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Thesis |
|
Publisher |
Schweizerbart |
Place of Publication |
Stuttgart |
Editor |
|
Language |
|
Wos |
|
Publication Date |
0000-00-00 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
|
ISBN |
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Additional Links |
UA library record |
Impact Factor |
|
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: NA |
Call Number |
UA @ lucian @ c:irua:31705 |
Serial |
2217 |
Permanent link to this record |
|
|
|
Author |
Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. |
Title |
Multi-level molecular modelling for plasma medicine |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
Volume |
49 |
Issue |
49 |
Pages |
054002 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000368944100003 |
Publication Date |
2015-12-16 |
Series Editor |
|
Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0022-3727 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.588 |
Times cited |
11 |
Open Access |
|
Notes |
This work is financially supported by the Fund for Scientific Research Flanders (FWO) and the Francqui Foundation. The calculations were carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. |
Approved |
Most recent IF: 2.588 |
Call Number |
c:irua:131571 |
Serial |
3985 |
Permanent link to this record |
|
|
|
Author |
Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. |
Title |
Multi-level molecular modelling for plasma medicine |
Type |
A1 Journal article |
Year |
2016 |
Publication |
Journal Of Physics D-Applied Physics |
Abbreviated Journal |
J Phys D Appl Phys |
Volume |
49 |
Issue |
5 |
Pages |
054002-54019 |
Keywords |
A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT) |
Abstract |
|
Address |
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Corporate Author |
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Thesis |
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Publisher |
|
Place of Publication |
London |
Editor |
|
Language |
|
Wos |
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Publication Date |
0000-00-00 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0022-3727 |
ISBN |
|
Additional Links |
UA library record |
Impact Factor |
2.588 |
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.588 |
Call Number |
UA @ lucian @ c:irua:129798 |
Serial |
4467 |
Permanent link to this record |
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|
|
Author |
Vandelannoote, R.; Blommaert, W.; Van 't dack, L.; van Grieken, R.; Gijbels, R. |
Title |
Multi-element trace analysis of geothermal waters : problems, characteristics and applicability |
Type |
P3 Proceeding |
Year |
1985 |
Publication |
|
Abbreviated Journal |
|
Volume |
|
Issue |
|
Pages |
523-527 |
Keywords |
P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
Abstract |
|
Address |
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Corporate Author |
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Thesis |
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Publisher |
Chemie |
Place of Publication |
Heidelberg |
Editor |
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Language |
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Wos |
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Publication Date |
0000-00-00 |
Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
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ISBN |
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Additional Links |
UA library record |
Impact Factor |
|
Times cited |
|
Open Access |
|
Notes |
|
Approved |
no |
Call Number |
UA @ lucian @ c:irua:111511 |
Serial |
2210 |
Permanent link to this record |
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|
|
Author |
Lindner, H.; Bogaerts, A. |
Title |
Multi-element model for the simulation of inductively coupled plasmas : effects of helium addition to the central gas stream |
Type |
A1 Journal article |
Year |
2011 |
Publication |
Spectrochimica acta: part B : atomic spectroscopy |
Abbreviated Journal |
Spectrochim Acta B |
Volume |
66 |
Issue |
6 |
Pages |
421-431 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
A model for an atmospheric pressure inductively coupled plasma (ICP) is developed which allows rather easy extension to a variable number of species and ionisation degrees. This encompasses an easy calculation of transport parameters for mixtures, ionisation and heat capacity. The ICP is modeled in an axisymmetric geometry, taking into account the gas streaming into a flowing ambient gas. A mixture of argon and helium is applied in the injector gas stream as it is often done in laser ablation ICP spectrometry. The results show a strong influence of the added helium on the center of the ICP, which is important for chemical analysis. The length of the central channel is significantly increased and the temperature inside is significantly higher than in the case of pure argon. This means that higher gas volume flow rates can be applied by addition of helium compared to the use of pure argon. This has the advantage that the gas velocity in the transport system towards the ICP can be increased, which allows shorter washout-times. Consequently, shorter measurement times can be achieved, e.g. for spatial mapping analyses in laser ablation ICP spectrometry. Furthermore, the higher temperature and the longer effective plasma length will increase the maximum size of droplets or particles injected into the ICP that are completely evaporated at the detection site. Thus, we expect an increase of the analytical performance of the ICP by helium addition to the injector gas. |
Address |
|
Corporate Author |
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Thesis |
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Publisher |
|
Place of Publication |
Oxford |
Editor |
|
Language |
|
Wos |
000293488700003 |
Publication Date |
2011-04-20 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0584-8547; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.241 |
Times cited |
28 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 3.241; 2011 IF: 2.876 |
Call Number |
UA @ lucian @ c:irua:90190 |
Serial |
2209 |
Permanent link to this record |
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|
|
Author |
Zhang, H.; Zhang, H.; Trenchev, G.; Li, X.; Wu, Y.; Bogaerts, A. |
Title |
Multi-dimensional modelling of a magnetically stabilized gliding arc plasma in argon and CO2 |
Type |
A1 Journal article |
Year |
2020 |
Publication |
Plasma Sources Science & Technology |
Abbreviated Journal |
Plasma Sources Sci T |
Volume |
29 |
Issue |
4 |
Pages |
045019 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
This study focuses on a magnetically stabilized gliding arc (MGA) plasma. Two fully coupled flow-plasma models (in 3D and 2D) are presented. The 3D model is applied to compare the arc dynamics of the MGA with a traditional gas-driven gliding arc. The 2D model is used for a detailed parametric study on the effect of the external magnetic field. The results show that the relative velocity between the plasma and feed gas is generated due to the Lorentz force, which can increase the plasma-treated gas fraction. The magnetic field also helps to decrease the gas temperature by enhancing heat transfer and to increase the electron number density. This work shows the potential of an external magnetic field to control the gliding arc behavior, for enhanced gas conversion at low gas flow rates. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000570241800001 |
Publication Date |
2020-04-09 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1361-6595 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.8 |
Times cited |
|
Open Access |
|
Notes |
Fonds Wetenschappelijk Onderzoek, G.0383.16N ; National Natural Science Foundation of China, 51706204 51707144 ; State Key Laboratory of Electrical Insulation and Power Equipment, EIPE19302 ; The authors acknowledge financial support from the Fund for Scientific Research—Flanders (FWO; Grant G.0383.16 N), National Natural Science Foundation of China under Grant Nos. 51706204, 51707144, and State Key Laboratory of Electrical Insulation and Power Equipment (EIPE19302). The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (Department EWI), and Universiteit Antwerpen. Finally, Hantian Zhang acknowledges financial support from the China Scholarship Council. |
Approved |
Most recent IF: 3.8; 2020 IF: 3.302 |
Call Number |
PLASMANT @ plasmant @c:irua:169218 |
Serial |
6360 |
Permanent link to this record |
|
|
|
Author |
Bogaerts, A.; van Straaten, M.; Gijbels, R. |
Title |
Monte Carlo simulation of an analytical glow discharge: motion of electrons, ions and fast neutrals in the cathode dark space |
Type |
A1 Journal article |
Year |
1995 |
Publication |
Spectrochimica acta: part B : atomic spectroscopy |
Abbreviated Journal |
Spectrochim Acta B |
Volume |
50 |
Issue |
|
Pages |
179-196 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
Oxford |
Editor |
|
Language |
|
Wos |
A1995QW79100005 |
Publication Date |
2002-07-26 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0584-8547; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.176 |
Times cited |
95 |
Open Access |
|
Notes |
|
Approved |
no |
Call Number |
UA @ lucian @ c:irua:12268 |
Serial |
2198 |
Permanent link to this record |
|
|
|
Author |
Bogaerts, A.; Gijbels, R. |
Title |
Monte Carlo model for the argon ions and fast argon atoms in a radio-frequency discharge |
Type |
A1 Journal article |
Year |
1999 |
Publication |
IEEE transactions on plasma science |
Abbreviated Journal |
Ieee T Plasma Sci |
Volume |
27 |
Issue |
5 |
Pages |
1406-1415 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
Language |
|
Wos |
000083453000023 |
Publication Date |
2002-08-24 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0093-3813; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
1.052 |
Times cited |
15 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 1.052; 1999 IF: 1.085 |
Call Number |
UA @ lucian @ c:irua:28321 |
Serial |
2197 |
Permanent link to this record |
|
|
|
Author |
Liu, Y.H.; Neyts, E.; Bogaerts, A. |
Title |
Monte Carlo method for simulations of adsorbed atom diffusion on a surface |
Type |
A1 Journal article |
Year |
2006 |
Publication |
Diamond and related materials |
Abbreviated Journal |
Diam Relat Mater |
Volume |
15 |
Issue |
10 |
Pages |
1629-1635 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
Language |
|
Wos |
000241224000021 |
Publication Date |
2006-03-01 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0925-9635; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.561 |
Times cited |
5 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.561; 2006 IF: 1.935 |
Call Number |
UA @ lucian @ c:irua:59633 |
Serial |
2196 |
Permanent link to this record |
|
|
|
Author |
Martín, A.; Bordel, N.; Pereiro, R.; Bogaerts, A. |
Title |
Monte Carlo analysis of the electron thermalization process in the afterglow of a microsecond dc pulsed glow discharge |
Type |
A1 Journal article |
Year |
2008 |
Publication |
Spectrochimica acta: part B : atomic spectroscopy |
Abbreviated Journal |
Spectrochim Acta B |
Volume |
63 |
Issue |
11 |
Pages |
1274-1282 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
A Monte Carlo model is utilized for studying the behavior of electrons in the afterglow of an analytical microsecond dc pulsed glow discharge. This model uses several quantities as input data, such as electric field and potential, ion flux at the cathode, the fast argon ion and atom impact ionization rates, slow electron density, the electrical characterization of the pulse (voltage and current profiles) and temperature profile. These quantities were obtained by earlier Monte Carlo fluid calculations for a pulsed discharge. Our goal is to study the behavior of the so-called Monte Carlo electrons (i.e., those electrons created at the cathode or by ionization collisions in the plasma which are followed by using the Monte Carlo model) from their origin to the moment when they are absorbed at the cell walls or when they have lost their energy by collisions (being transferred to the group of slow electrons) in the afterglow of the pulsed discharge. The thermalization of the electrons is a phenomenon where the electron-electron Coulomb collisions acquire a special importance. Indeed, in the afterglow the cross sections of the other electron reactions taken into account in the model are very low, because of the very low electron energy. We study the electron energy distributions at several times during and after the pulse and at several positions in the plasma cell, focusing on the thermalization and on the behavior of the electrons in the afterglow. Also, the time evolution of the rates of the various collision processes, the average electron energy, the densities of Monte Carlo and slow electrons and the ionization degree are investigated. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
Oxford |
Editor |
|
Language |
|
Wos |
000261905500008 |
Publication Date |
2008-10-05 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0584-8547; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.241 |
Times cited |
9 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 3.241; 2008 IF: 2.853 |
Call Number |
UA @ lucian @ c:irua:71271 |
Serial |
2195 |
Permanent link to this record |
|
|
|
Author |
Yusupov, M.; Dewaele, D.; Attri, P.; Khalilov, U.; Sobott, F.; Bogaerts, A. |
Title |
Molecular understanding of the possible mechanisms of oligosaccharide oxidation by cold plasma |
Type |
A1 Journal article |
Year |
2022 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
Volume |
|
Issue |
|
Pages |
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Cold atmospheric plasma (CAP) is a promising technology for several medical applications, including the removal of biofilms from surfaces. However, the molecular mechanisms of CAP treatment are still poorly understood. Here we unravel the possible mechanisms of CAP‐induced oxidation of oligosaccharides, employing reactive molecular dynamics simulations based on the density functional‐tight binding potential. Specifically, we find that the interaction of oxygen atoms (used as CAP‐generated reactive species) with cellotriose (a model system for the oligosaccharides) can break structurally important glycosidic bonds, which subsequently leads to the disruption of the oligosaccharide molecule. The overall results help to shed light on our experimental evidence for cellotriose CAP. This oxidation by study provides atomic‐level insight into the onset of plasma‐induced removal of biofilms, as oligosaccharides are one of the main components of biofilm. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000865844800001 |
Publication Date |
2022-10-11 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1612-8850 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.5 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
Fonds Wetenschappelijk Onderzoek, 1200219N ; They also acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UA, where all computational work was performed. This study was financially supported by the Research Foundation–Flanders (FWO) (grant number 1200219N). |
Approved |
Most recent IF: 3.5 |
Call Number |
PLASMANT @ plasmant @c:irua:191404 |
Serial |
7113 |
Permanent link to this record |
|
|
|
Author |
Ignatova, V.A.; van Vaeck, L.; Gijbels, R.; Adams, F. |
Title |
Molecular speciation of inorganic mixtures by Fourier transform laser microprobe mass sepctrometry |
Type |
A1 Journal article |
Year |
2003 |
Publication |
International journal of mass spectrometry |
Abbreviated Journal |
Int J Mass Spectrom |
Volume |
225 |
Issue |
|
Pages |
213-224 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
Language |
|
Wos |
000181179500002 |
Publication Date |
2003-02-17 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1387-3806; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
1.702 |
Times cited |
9 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 1.702; 2003 IF: 2.361 |
Call Number |
UA @ lucian @ c:irua:41595 |
Serial |
2183 |
Permanent link to this record |
|
|
|
Author |
Razzokov, J. |
Title |
Molecular level simulations for plasma medicine applications |
Type |
Doctoral thesis |
Year |
2019 |
Publication |
|
Abbreviated Journal |
|
Volume |
|
Issue |
|
Pages |
173 p. |
Keywords |
Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
|
Publication Date |
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
|
ISBN |
|
Additional Links |
UA library record |
Impact Factor |
|
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: NA |
Call Number |
UA @ admin @ c:irua:159654 |
Serial |
5277 |
Permanent link to this record |
|
|
|
Author |
Yadav, D.K.; Kumar, S.; Saloni; Misra, S.; Yadav, L.; Teli, M.; Sharma, P.; Chaudhary, S.; Kumar, N.; Choi, E.H.; Kim, H.S.; Kim, M.-hyun |
Title |
Molecular Insights into the Interaction of RONS and Thieno[3,2-c]pyran Analogs with SIRT6/COX-2: A Molecular Dynamics Study |
Type |
A1 Journal article |
Year |
2018 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
Volume |
8 |
Issue |
8 |
Pages |
4777 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
SIRT6 and COX-2 are oncogenes target that promote the expression of proinflammatory and pro-survival proteins through a signaling pathway, which leads to increased survival and proliferation of tumor cells. However, COX-2 also suppresses skin tumorigenesis and their relationship with SIRT6, making it an interesting target for the discovery of drugs with anti-inflammatory and anti-cancer properties. Herein, we studied the interaction of thieno[3,2-c] pyran analogs and RONS species with SIRT6 and COX-2 through the use of molecular docking and molecular dynamic simulations. Molecular docking studies revealed the importance of hydrophobic and hydrophilic amino acid residues for the stability. The molecular dynamics study examined conformational changes in the enzymes caused by the binding of the substrates and how those changes affected the stability of the protein-drug complex. The average RMSD values of the backbone atoms in compounds 6 and 10 were calculated from 1000 ps to 10000 ps and were found to be 0.13 nm for both compounds. Similarly, the radius of gyration values for compounds 6 and 10 were found to be 1.87 +/- 0.03 nm and 1.86 +/- 0.02 nm, respectively. The work presented here, will be of great help in lead identification and optimization for early drug discovery. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
Nature Publishing Group |
Place of Publication |
London |
Editor |
|
Language |
|
Wos |
000427685200002 |
Publication Date |
2018-03-13 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2045-2322 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.259 |
Times cited |
10 |
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 4.259 |
Call Number |
UA @ lucian @ c:irua:150841 |
Serial |
4974 |
Permanent link to this record |
|
|
|
Author |
van Ham, R.; Adriaens, A.; van Vaeck, L.; Gijbels, R.; Adams, F. |
Title |
Molecular information in static SIMS for the speciation of inorganic compounds |
Type |
A1 Journal article |
Year |
2000 |
Publication |
Nuclear instruments and methods in physics research: B: beam interactions with materials and atoms |
Abbreviated Journal |
Nucl Instrum Meth B |
Volume |
161/163 |
Issue |
|
Pages |
245-249 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
Language |
|
Wos |
000086204100043 |
Publication Date |
2003-04-05 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0168-583X; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
1.109 |
Times cited |
19 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 1.109; 2000 IF: 0.955 |
Call Number |
UA @ lucian @ c:irua:27853 |
Serial |
2178 |
Permanent link to this record |
|
|
|
Author |
Khalilov, U.; Vets, C.; Neyts, E.C. |
Title |
Molecular evidence for feedstock-dependent nucleation mechanisms of CNTs |
Type |
A1 Journal article |
Year |
2019 |
Publication |
Nanoscale Horizons |
Abbreviated Journal |
Nanoscale Horiz. |
Volume |
4 |
Issue |
3 |
Pages |
674-682 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Atomic scale simulations have been shown to be a powerful tool for elucidating the growth mechanisms of carbon nanotubes. The growth picture is however not entirely clear yet due to the gap between current simulations and real experiments. We here simulate for the first time the nucleation and subsequent growth of single-wall carbon nanotubes (SWNTs) from oxygen-containing hydrocarbon feedstocks using the hybrid Molecular Dynamics/Monte Carlo technique. The underlying nucleation mechanisms of Ni-catalysed SWNT growth are discussed in detail. Specifically, we find that as a function of the feedstock, different carbon fractions may emerge as the main growth species, due to a competition between the feedstock decomposition, its rehydroxylation and its contribution to etching of the growing SWNT. This study provides a further understanding of the feedstock effects in SWNT growth in comparison with available experimental evidence as well as with<italic>ab initio</italic>and other simulation data, thereby reducing the simulation–experiment gap. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000471816500011 |
Publication Date |
2019-01-02 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2055-6756 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
|
Times cited |
1 |
Open Access |
Not_Open_Access: Available from 03.01.2020
|
Notes |
Fonds Wetenschappelijk Onderzoek, 12M1318N 1S22516N ; The authors gratefully acknowledge financial support from the Research Foundation Flanders (FWO), Belgium (Grant numbers 12M1318N and 1S22516N). The work was carried out in part using the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by FWO and the Flemish Government (Department EWI). We thank Prof. A. C. T. van Duin for sharing the reax-code and forcefield parameters. |
Approved |
Most recent IF: NA |
Call Number |
PLASMANT @ plasmant @UA @ admin @ c:irua:159658 |
Serial |
5169 |
Permanent link to this record |
|
|
|
Author |
Eckert, M.; Neyts, E.; Bogaerts, A. |
Title |
Molecular dynamics simulations of the sticking and etch behavior of various growth species of (ultra)nanocrystalline diamond films |
Type |
A1 Journal article |
Year |
2008 |
Publication |
Chemical vapor deposition |
Abbreviated Journal |
Chem Vapor Depos |
Volume |
14 |
Issue |
7/8 |
Pages |
213-223 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
The reaction behavior of species that may affect the growth of ultrananocrystal line and nanocrystalline diamond ((U)NCD) films is investigated by means of molecular dynamics simulations. Impacts of CHx (x = 0 – 4), C2Hx (x=0-6), C3Hx (x=0-2), C4Hx (x = 0 – 2), H, and H-2 on clean and hydrogenated diamond (100)2 x 1 and (111) 1 x 1 surfaces at two different substrate temperatures are simulated. We find that the different bonding structures of the two surfaces cause different temperature effects on the sticking efficiency. These results predict a temperature-dependent ratio of diamond (100) and (111) growth. Furthermore, predictions of which are the most important hydrocarbon species for (U)NCD growth are made. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
Weinheim |
Editor |
|
Language |
|
Wos |
000259302700008 |
Publication Date |
2008-08-18 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0948-1907;1521-3862; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
1.333 |
Times cited |
25 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 1.333; 2008 IF: 1.483 |
Call Number |
UA @ lucian @ c:irua:70001 |
Serial |
2177 |
Permanent link to this record |
|
|
|
Author |
Neyts, E.; Eckert, M.; Bogaerts, A. |
Title |
Molecular dynamics simulations of the growth of thin a-C:H films under additional ion bombardment: influence of the growth species and the Ar+ ion kinetic energy |
Type |
A1 Journal article |
Year |
2007 |
Publication |
Chemical vapor deposition |
Abbreviated Journal |
Chem Vapor Depos |
Volume |
13 |
Issue |
6/7 |
Pages |
312-318 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
|
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
Weinheim |
Editor |
|
Language |
|
Wos |
000248381800007 |
Publication Date |
2007-07-10 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0948-1907;1521-3862; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
1.333 |
Times cited |
14 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 1.333; 2007 IF: 1.936 |
Call Number |
UA @ lucian @ c:irua:64532 |
Serial |
2176 |
Permanent link to this record |
|
|
|
Author |
Brault, P.; Neyts, E.C. |
Title |
Molecular dynamics simulations of supported metal nanocatalyst formation by plasma sputtering |
Type |
A1 Journal article |
Year |
2015 |
Publication |
Catalysis today |
Abbreviated Journal |
Catal Today |
Volume |
256 |
Issue |
256 |
Pages |
3-12 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Magnetron sputtering is a widely used physical vapor deposition technique for deposition and formation of nanocatalyst thin films and clusters. Nevertheless, so far only few studies investigated this formation process at the fundamental level. We here review atomic scale molecular dynamics simulations aimed at elucidating the nanocatalyst growth process through magnetron sputtering. We first introduce the basic magnetron sputtering background and machinery of molecular dynamics simulations, and then describe the studies conducted in this field so far. We also present a perspective view on how the field may be developed further. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
Language |
|
Wos |
000360085300002 |
Publication Date |
2015-02-28 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0920-5861; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.636 |
Times cited |
18 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 4.636; 2015 IF: 3.893 |
Call Number |
c:irua:127408 |
Serial |
2174 |
Permanent link to this record |
|
|
|
Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
Title |
Molecular dynamics simulations of mechanical stress on oxidized membranes |
Type |
A1 Journal article |
Year |
2019 |
Publication |
Biophysical chemistry |
Abbreviated Journal |
Biophys Chem |
Volume |
254 |
Issue |
|
Pages |
106266 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Biomembranes are under constant attack of free radicals that may lead to lipid oxidation in conditions of oxidative stress. The products generated during lipid oxidation are responsible for structural and dynamical changes which may jeopardize the membrane function. For instance, the local rearrangements of oxidized lipid molecules may induce membrane rupture. In this study, we investigated the effects of mechanical stress on oxidized phospholipid bilayers (PLBs). Model bilayers were stretched until pore formation (or poration) using nonequilibrium molecular dynamics simulations. We studied single-component homogeneous membranes composed of lipid oxidation products, as well as two-component heterogeneous membranes with coexisting native and oxidized domains. In homogeneous membranes, the oxidation products with —OH and —OOH groups reduced the areal strain required for pore formation, whereas the oxidation product with ]O group behaved similarly to the native membrane. In heterogeneous membranes composed of oxidized and non-oxidized domains, we tested the hypothesis according to which poration may be facilitated at the domain interface region. However, results were inconclusive due to their large statistical variance and sensitivity to simulation setup parameters. We pointed out important technical issues that need to be considered in future simulations of mechanically-induced poration of heterogeneous membranes. This research is of interest for photodynamic therapy and plasma medicine, because ruptured and intact plasma membranes are experimentally considered hallmarks of necrotic and apoptotic cell death. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000502890900015 |
Publication Date |
2019-09-13 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0301-4622 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.402 |
Times cited |
|
Open Access |
|
Notes |
São Paulo Research Foundation, 2012/50680-5 ; National Counsel of Technological and Scientific Development, 459270/2014-1 ; We are thankful for the financial support received from the São Paulo Research Foundation (FAPESP) (grant no. 2012/50680-5) and from the National Counsel of Technological and Scientific Development (CNPq) (grant no. 459270/2014-1). MCO acknowledges UFABC for the Master's scholarship granted. |
Approved |
Most recent IF: 2.402 |
Call Number |
PLASMANT @ plasmant @c:irua:163477 |
Serial |
5374 |
Permanent link to this record |
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|
|
Author |
Brault, P.; Chamorro-Coral, W.; Chuon, S.; Caillard, A.; Bauchire, J.-M.; Baranton, S.; Coutanceau, C.; Neyts, E. |
Title |
Molecular dynamics simulations of initial Pd and PdO nanocluster growth in a magnetron gas aggregation source |
Type |
A1 Journal article |
Year |
2019 |
Publication |
Frontiers of Chemical Science and Engineering |
Abbreviated Journal |
Front Chem Sci Eng |
Volume |
13 |
Issue |
2 |
Pages |
324-329 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Molecular dynamics simulations are carried out for describing growth of Pd and PdO nanoclusters using the ReaxFF force field. The resulting nanocluster structures are successfully compared to those of nanoclusters experimentally grown in a gas aggregation source. The PdO structure is quasi-crystalline as revealed by high resolution transmission microscope analysis for experimental PdO nanoclusters. The role of the nanocluster temperature in the molecular dynamics simulated growth is highlighted. |
Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
|
Editor |
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Language |
|
Wos |
000468848400009 |
Publication Date |
2019-03-26 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2095-0179 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
1.712 |
Times cited |
3 |
Open Access |
Not_Open_Access |
Notes |
|
Approved |
Most recent IF: 1.712 |
Call Number |
UA @ admin @ c:irua:160278 |
Serial |
5276 |
Permanent link to this record |
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|
|
Author |
Gou, F.; Neyts, E.; Eckert, M.; Tinck, S.; Bogaerts, A. |
Title |
Molecular dynamics simulations of Cl+ etching on a Si(100) surface |
Type |
A1 Journal article |
Year |
2010 |
Publication |
Journal of applied physics |
Abbreviated Journal |
J Appl Phys |
Volume |
107 |
Issue |
11 |
Pages |
113305,1-113305,6 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Molecular dynamics simulations using improved TersoffBrenner potential parameters were performed to investigate Cl+ etching of a {2×1} reconstructed Si(100) surface. Steady-state Si etching accompanying the Cl coverage of the surface is observed. Furthermore, a steady-state chlorinated reaction layer is formed. The thickness of this reaction layer is found to increase with increasing energy. The stoichiometry of SiClx species in the reaction layer is found to be SiCl:SiCl2:SiCl3 = 1.0:0.14:0.008 at 50 eV. These results are in excellent agreement with available experimental data. While elemental Si products are created by physical sputtering, most SiClx (0<x<4) etch products are produced by chemical-enhanced physical sputtering. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
American Institute of Physics |
Place of Publication |
New York, N.Y. |
Editor |
|
Language |
|
Wos |
000278907100018 |
Publication Date |
2010-06-04 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0021-8979; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.068 |
Times cited |
15 |
Open Access |
|
Notes |
|
Approved |
Most recent IF: 2.068; 2010 IF: 2.079 |
Call Number |
UA @ lucian @ c:irua:82663 |
Serial |
2175 |
Permanent link to this record |