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Records |
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Author |
Yusupov, M.; Bogaerts, A.; Huygh, S.; Snoeckx, R.; van Duin, A.C.T.; Neyts, E.C. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
Plasma-induced destruction of bacterial cell wall components : a reactive molecular dynamics simulation |
Type |
A1 Journal article |
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Year |
2013 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
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Volume |
117 |
Issue |
11 |
Pages |
5993-5998 |
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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 |
Nonthermal atmospheric pressure plasmas are gaining increasing attention for biomedical applications. However, very little fundamental information on the interaction mechanisms between the plasma species and biological cells is currently available. We investigate the interaction of important plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, with bacterial peptidoglycan by means of reactive molecular dynamics simulations, aiming for a better understanding of plasma disinfection. Our results show that OH, O, O3, and H2O2 can break structurally important bonds of peptidoglycan (i.e., CO, CN, or CC bonds), which consequently leads to the destruction of the bacterial cell wall. The mechanisms behind these breakups are, however, dependent on the impinging plasma species, and this also determines the effectiveness of the cell wall destruction. |
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Place of Publication |
Washington, D.C. |
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Wos |
000316773000056 |
Publication Date |
2013-02-23 |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1932-7447;1932-7455; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.536 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
59 |
Open Access |
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Notes |
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Approved |
Most recent IF: 4.536; 2013 IF: 4.835 |
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Call Number |
UA @ lucian @ c:irua:107154 |
Serial |
2636 |
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Permanent link to this record |
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Author |
Yusupov, M.; Neyts, E.C.; Simon, P.; Berdiyorov, G.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
Reactive molecular dynamics simulations of oxygen species in a liquid water layer of interest for plasma medicine |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
47 |
Issue |
2 |
Pages |
025205-25209 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The application of atmospheric pressure plasmas in medicine is increasingly gaining attention in recent years, although very little is currently known about the plasma-induced processes occurring on the surface of living organisms. It is known that most bio-organisms, including bacteria, are coated by a liquid film surrounding them, and there might be many interactions between plasma species and the liquid layer before the plasma species reach the surface of the bio-organisms. Therefore, it is essential to study the behaviour of the reactive species in a liquid film, in order to determine whether these species can travel through this layer and reach the biomolecules, or whether new species are formed along the way. In this work, we investigate the interaction of reactive oxygen species (i.e. O, OH, HO2 and H2O2) with water, which is assumed as a simple model system for the liquid layer surrounding biomolecules. Our computational investigations show that OH, HO2 and H2O2 can travel deep into the liquid layer and are hence in principle able to reach the bio-organism. Furthermore, O, OH and HO2 radicals react with water molecules through hydrogen-abstraction reactions, whereas no H-abstraction reaction takes place in the case of H2O2. This study is important to gain insight into the fundamental operating mechanisms in plasma medicine, in general, and the interaction mechanisms of plasma species with a liquid film, in particular. |
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Place of Publication |
London |
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Wos |
000329108000013 |
Publication Date |
2013-12-13 |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0022-3727;1361-6463; |
ISBN |
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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 ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
51 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.588; 2014 IF: 2.721 |
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Call Number |
UA @ lucian @ c:irua:112286 |
Serial |
2823 |
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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. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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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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Corporate Author |
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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 ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
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 |
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Permanent link to this record |
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Author |
Hoon Park, J.; Kumar, N.; Hoon Park, D.; Yusupov, M.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A.; Ho Kang, M.; Sup Uhm, H.; Ha Choi, E.; Attri, P.; |
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Title |
A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
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Volume |
5 |
Issue |
5 |
Pages |
13849 |
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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 |
Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG. |
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Corporate Author |
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Thesis |
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Publisher |
Nature Publishing Group |
Place of Publication |
London |
Editor |
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Language |
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Wos |
000360909000001 |
Publication Date |
2015-09-09 |
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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 |
2045-2322; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.259 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
32 |
Open Access |
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Notes |
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Approved |
Most recent IF: 4.259; 2015 IF: 5.578 |
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Call Number |
c:irua:127410 |
Serial |
419 |
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Permanent link to this record |
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Author |
Neyts, E.C.; Yusupov, M.; Verlackt, C.C.; Bogaerts, A. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
Computer simulations of plasmabiomolecule and plasmatissue interactions for a better insight in plasma medicine |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
47 |
Issue |
29 |
Pages |
293001 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficultif not impossibleto obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasmabiomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance 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 |
London |
Editor |
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Language |
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Wos |
000338860300001 |
Publication Date |
2014-06-26 |
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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 |
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 ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
28 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.588; 2014 IF: 2.721 |
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Call Number |
UA @ lucian @ c:irua:117853 |
Serial |
472 |
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Permanent link to this record |
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Author |
Yusupov, M.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A. |
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Title |
Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
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Volume |
7 |
Issue |
7 |
Pages |
5761 |
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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 |
We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level. |
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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 |
000405746500072 |
Publication Date |
2017-07-12 |
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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 |
2045-2322 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.259 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
27 |
Open Access |
OpenAccess |
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Notes |
M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216 N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. S.R. and S.K. acknowledge funding by the BMBF (FKZ: 03Z2DN12). S.R. acknowledges funding by the Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern (AU 15001). The authors thank M. Hammer for the support and discussion in the biophysical studies and J. Van der Paal for the interesting discussions. |
Approved |
Most recent IF: 4.259 |
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Call Number |
PLASMANT @ plasmant @ c:irua:144627 |
Serial |
4630 |
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Permanent link to this record |
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Author |
Attri, P.; Yusupov, M.; Park, J.H.; Lingamdinne, L.P.; Koduru, J.R.; Shiratani, M.; Choi, E.H.; Bogaerts, A. |
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Title |
Mechanism and comparison of needle-type non-thermal direct and indirect atmospheric pressure plasma jets on the degradation of dyes |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
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Volume |
6 |
Issue |
6 |
Pages |
34419 |
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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 |
Purified water supply for human use, agriculture and industry is the major global priority nowadays. The advanced oxidation process based on atmospheric pressure non-thermal plasma (NTP) has been used for purification of wastewater, although the underlying mechanisms of degradation of organic pollutants are still unknown. In this study we employ two needle-type atmospheric pressure non-thermal plasma jets, i.e., indirect (ID-APPJ) and direct (D-APPJ) jets operating at Ar feed gas, for the treatment of methylene blue, methyl orange and congo red dyes, for two different times (i.e., 20 min and 30 min). Specifically, we study the decolorization/degradation of all three dyes using the above mentioned plasma sources, by means of UV-Vis spectroscopy, HPLC and a density meter. We also employ mass spectroscopy to verify whether only decolorization or also degradation takes place after treatment of the dyes by the NTP jets. Additionally, we analyze the interaction of OH radicals with all three dyes using reactive molecular dynamics simulations, based on the density functional-tight binding method. This investigation represents the first report on the degradation of these three different dyes by two types of NTP setups, analyzed by various methods, and based on both experimental and computational studies. |
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Address |
Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium |
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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 |
English |
Wos |
000385172300001 |
Publication Date |
2016-10-06 |
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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 |
2045-2322 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.259 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
23 |
Open Access |
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Notes |
We gratefully acknowledge the grant received from the SRC program of the National Research Foundation of Korea (NRF), funded by the Korean Government (MEST) (No. 20100029418). PA is thankful to FY 2015 Japan Society for the Promotion of Science (JSPS) invitation fellowship. This work was partly supported by MEXT KAKENHI Grant Number 24108009 and JSPS KAKENHI Grant Number JP16H03895. M. Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. |
Approved |
Most recent IF: 4.259 |
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Call Number |
PLASMANT @ plasmant @ c:irua:135847 |
Serial |
4283 |
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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. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
Reactive molecular dynamics simulations for a better insight in plasma medicine |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
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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) |
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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 |
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Series Issue |
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Edition |
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ISSN |
1612-8850; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.846 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
22 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.846; 2014 IF: 2.453 |
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Call Number |
UA @ lucian @ c:irua:121269 |
Serial |
2822 |
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Permanent link to this record |
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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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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
London |
Editor |
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Language |
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Wos |
000351856600007 |
Publication Date |
2015-03-25 |
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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 |
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 ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
20 |
Open Access |
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Notes |
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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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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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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 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.846 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
18 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.846; 2015 IF: 2.453 |
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Call Number |
c:irua:123540 |
Serial |
1589 |
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Permanent link to this record |
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Author |
Tit, N.; Al Ezzi, M.M.; Abdullah, H.M.; Yusupov, M.; Kouser, S.; Bahlouli, H.; Yamani, Z.H. |
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Title |
Detection of CO2 using CNT-based sensors: Role of Fe catalyst on sensitivity and selectivity |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Materials chemistry and physics |
Abbreviated Journal |
Mater Chem Phys |
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Volume |
186 |
Issue |
186 |
Pages |
353-364 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The adsorption of CO2 on surfaces of graphene and carbon nanotubes (CNTs), decorated with Fe atoms, are investigated using the self-consistent-charge density-functional tight-binding (SCC-DFTB) method, neglecting the heat effects. Fe ad-atoms are more stable when they are dispersed on hollow sites. They introduce a large density of states at the Fermi level (N-F); where keeping such density low would help in gas sensing. Furthermore, the Fe ad-atom can weaken the C=O double bonds of the chemisorbed CO2 molecule, paving the way for oxygen atoms to drain more charges from Fe. Consequently, chemisorption of CO2 molecules reduces both N-F and the conductance while it enhances the sensitivity with the increasing gas dose. Conducting armchair CNTs (ac-CNTs) have higher sensitivity than graphene and semiconducting zigzag CNTs (zz-CNT5). Comparative study of sensitivity of ac-CNT-Fe composite towards various gases (e.g., O-2, N-2, H-2, H2O, CO and CO2) has shown high sensitivity and selectivity towards CO, CO2 and H2O gases. (C) 2016 Elsevier B.V. All rights reserved. |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Lausanne |
Editor |
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Language |
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Wos |
000390621200044 |
Publication Date |
2016-11-04 |
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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 |
0254-0584 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.084 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
17 |
Open Access |
Not_Open_Access |
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Notes |
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Approved |
Most recent IF: 2.084 |
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Call Number |
UA @ lucian @ c:irua:140333 |
Serial |
4465 |
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Permanent link to this record |
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Author |
Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. |
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Title |
Behavior of electrons in a dual-magnetron sputter deposition system : a Monte Carlo model |
Type |
A1 Journal article |
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Year |
2011 |
Publication |
New journal of physics |
Abbreviated Journal |
New J Phys |
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Volume |
13 |
Issue |
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Pages |
033018-033018,17 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
A Monte Carlo model has been developed for investigating the electron behavior in a dual-magnetron sputter deposition system. To describe the three-dimensional (3D) geometry, different reference frames, i.e. a local and a global coordinate system, were used. In this study, the influence of both closed and mirror magnetic field configurations on the plasma properties is investigated. In the case of a closed magnetic field configuration, the calculated electron trajectories show that if an electron is emitted in (or near) the center of the cathode, where the influence of the magnetic field is low, it is able to travel from one magnetron to the other. On the other hand, when an electron is created at the race track area, it is more or less trapped in the strong magnetic field and cannot easily escape to the second magnetron region. In the case of a mirror magnetic field configuration, irrespective of where the electron is emitted from the cathode, it cannot travel from one magnetron to the other because the magnetic field lines guide the electron to the substrate. Moreover, the electron density and electron impact ionization rate have been calculated and studied in detail for both configurations. |
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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 |
000289064600001 |
Publication Date |
2011-03-15 |
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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 |
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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 ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
12 |
Open Access |
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Notes |
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Approved |
Most recent IF: 3.786; 2011 IF: 4.177 |
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Call Number |
UA @ lucian @ c:irua:87544 |
Serial |
224 |
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Permanent link to this record |
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Author |
Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. |
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Title |
Multi-level molecular modelling for plasma medicine |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
49 |
Issue |
49 |
Pages |
054002 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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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. |
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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 |
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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 |
0022-3727 |
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 ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
11 |
Open Access |
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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 |
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Call Number |
c:irua:131571 |
Serial |
3985 |
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Permanent link to this record |
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Author |
Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C. |
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Title |
How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Biointerphases |
Abbreviated Journal |
Biointerphases |
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Volume |
10 |
Issue |
10 |
Pages |
029501 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms. |
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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 |
000357195600019 |
Publication Date |
2014-12-17 |
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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 |
1934-8630;1559-4106; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.603 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
10 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.603; 2015 IF: 3.374 |
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Call Number |
c:irua:121371 |
Serial |
1492 |
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Permanent link to this record |
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Author |
Razzokov, J.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A. |
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Title |
Atomic scale understanding of the permeation of plasma species across native and oxidized membranes |
Type |
A1 Journal article |
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Year |
2018 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
51 |
Issue |
36 |
Pages |
365203 |
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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 plasmas (CAPs) have attracted significant interest for their potential benefits in medical applications, including cancer therapy. The therapeutic effects of CAPs are related to reactive oxygen and nitrogen species (ROS and RNS) present in the plasma. The impact of ROS has been extensively studied, but the role of RNS in CAP-treatment remains poorly understood at the molecular level. Here, we investigate the permeation of RNS and ROS across native and oxidized phospholipid bilayers (PLBs) by means of computer simulations. The results reveal significantly lower free energy barriers for RNS (i.e. NO, NO2, N2O4) and O3 compared to hydrophilic ROS, such as OH, HO2 and H2O2. This suggests that the investigated RNS and O3 can permeate more easily through both native and oxidized PLBs in comparison to hydrophilic ROS, indicating their potentially important role in plasma medicine. |
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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 |
000441182400002 |
Publication Date |
2018-08-08 |
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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 |
0022-3727 |
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 ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
10 |
Open Access |
OpenAccess |
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Notes |
M Y gratefully acknowledges financial support from the Research Foundation—Flanders (FWO), grant 1200216N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. RMC thanks FAPESP and CNPq for financial support (grants 2012/50680-5 and 459270/2014-1, respectively). |
Approved |
Most recent IF: 2.588 |
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Call Number |
PLASMANT @ plasmant @c:irua:152824 |
Serial |
5005 |
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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 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.846 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
9 |
Open Access |
Not_Open_Access |
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Notes |
Fonds Wetenschappelijk Onderzoek, 1200216N ; |
Approved |
Most recent IF: 2.846 |
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Call Number |
PLASMANT @ plasmant @c:irua:149567 |
Serial |
4910 |
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Permanent link to this record |
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Author |
Bogaerts, A.; Aerts, R.; Snoeckx, R.; Somers, W.; Van Gaens, W.; Yusupov, M.; Neyts, E. |
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Title |
Modeling of plasma and plasma-surface interactions for medical, environmental and nano applications |
Type |
A1 Journal article |
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Year |
2012 |
Publication |
Journal of physics : conference series |
Abbreviated Journal |
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Volume |
399 |
Issue |
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Pages |
012011 |
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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 investigations carried out in our research group for a better understanding of plasmas used for medical, environmental and nano applications. The focus is both on modeling the plasma chemistry and the plasma-surface interactions. The plasma chemistry provides the densities and fluxes of the important plasma species. This information can be used as input when modeling the plasma-surface interactions. The combination of plasma simulations and plasma – surface interaction simulations provides a more comprehensive understanding of the underlying processes for these applications. |
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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 |
000312261700011 |
Publication Date |
2012-11-26 |
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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 |
1742-6588;1742-6596; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
7 |
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:104727 |
Serial |
2130 |
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Permanent link to this record |
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Author |
Yusupov, M.; Yan, D.; Cordeiro, R.M.; Bogaerts, A. |
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Title |
Atomic scale simulation of H2O2permeation through aquaporin: toward the understanding of plasma cancer treatment |
Type |
A1 Journal article |
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Year |
2018 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
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Volume |
51 |
Issue |
12 |
Pages |
125401 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Experiments have demonstrated the potential selective anticancer capacity of cold atmospheric plasmas (CAPs), but the underlying mechanisms remain unclear. Using computer simulations, we try to shed light on the mechanism of selectivity, based on aquaporins (AQPs), i.e. transmembrane protein channels transferring external H 2 O 2 and other reactive oxygen species, created e.g. by CAPs, to the cell interior. Specifically, we perform molecular dynamics simulations for the permeation of H 2 O 2 through AQP1 (one of the members of the AQP family) and the palmitoyl-oleoyl-phosphatidylcholine (POPC) phospholipid bilayer (PLB). The free energy barrier of H 2 O 2 across AQP1 is lower than for the POPC PLB, while the permeability coefficient, calculated using the free energy and diffusion rate profiles, is two orders of magnitude higher. This indicates that the delivery of H 2 O 2 into the cell interior should be through AQP. Our study gives a better insight into the role of AQPs in the selectivity of CAPs for treating cancer 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 |
000426378100001 |
Publication Date |
2018-02-28 |
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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 |
0022-3727 |
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 ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
7 |
Open Access |
OpenAccess |
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Notes |
MY gratefully acknowledges financial support from the Research Foundation—Flanders (FWO) via Grant No. 1200216N and a travel grant to George Washington University (GWU). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Super- computer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Work at GWU was supported by the National Science Foundation, grant 1465061. RMC thanks FAPESP and CNPq for finan- cial support (Grant Nos. 2012/50680-5 and 459270/2014-1, respectively). |
Approved |
Most recent IF: 2.588 |
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Call Number |
PLASMANT @ plasmant @c:irua:149382 |
Serial |
4811 |
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Permanent link to this record |
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Author |
Yusupov, M.; Lackmann, J.-W.; Razzokov, J.; Kumar, S.; Stapelmann, K.; Bogaerts, A. |
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Title |
Impact of plasma oxidation on structural features of human epidermal growth factor |
Type |
A1 Journal article |
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Year |
2018 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
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Volume |
15 |
Issue |
8 |
Pages |
1800022 |
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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 computer simulations supported by experiments to investigate the oxidation of an important signaling protein, that is, human epidermal growth factor (hEGF), caused by cold atmospheric plasma (CAP) treatment. Specifically, we study the conformational changes of hEGF with different degrees of oxidation, to mimic short and long CAP treatment times. Our results indicate that the oxidized structures become more flexible, due to their conformational changes and breakage of the disulfide bonds, especially at higher oxidation degrees. MM/GBSA calculations reveal that an increasing oxidation level leads to a lower binding free energy of hEGF with its receptor. These results help to understand the fundamentals of the use of CAP for wound healing versus cancer treatment at short and longer treatment times. |
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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 |
000441895700004 |
Publication Date |
2018-05-07 |
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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 |
1612-8850 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.846 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
7 |
Open Access |
Not_Open_Access |
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Notes |
Fonds Wetenschappelijk Onderzoek, 1200216N ; Bundesministerium für Bildung und Forschung, 03Z22DN12 ; |
Approved |
Most recent IF: 2.846 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:152815 |
Serial |
5008 |
|
Permanent link to this record |
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|
|
|
Author |
Bogaerts, A.; Yusupov, M.; Razzokov, J.; Van der Paal, J. |
![goto web page url](http://nano.uantwerpen.be/nanorefs/img/www.gif)
![find record details (via OpenURL) openurl](img/xref.gif)
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Title |
Plasma for cancer treatment: How can RONS penetrate through the cell membrane? Answers from computer modeling |
Type |
A1 Journal article |
|
Year |
2019 |
Publication |
Frontiers of Chemical Science and Engineering |
Abbreviated Journal |
Front Chem Sci Eng |
|
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Volume |
|
Issue |
|
Pages |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Plasma is gaining increasing interest for cancer
treatment, but the underlying mechanisms are not yet fully
understood. Using computer simulations at the molecular
level, we try to gain better insight in how plasma-generated
reactive oxygen and nitrogen species (RONS) can
penetrate through the cell membrane. Specifically, we
compare the permeability of various (hydrophilic and
hydrophobic) RONS across both oxidized and nonoxidized cell membranes. We also study pore formation,
and how it is hampered by higher concentrations of
cholesterol in the cell membrane, and we illustrate the
much higher permeability of H2O2 through aquaporin
channels. Both mechanisms may explain the selective
cytotoxic effect of plasma towards cancer cells. Finally, we
also discuss the synergistic effect of plasma-induced
oxidation and electric fields towards pore formation.
Keywords plasma medicine, cancer treatment, computer
modelling, cell membrane, reactive oxygen and nitrogen
species |
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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 |
000468848400004 |
Publication Date |
2019-03-22 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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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 ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
5 |
Open Access |
Not_Open_Access: Available from 23.05.2020
|
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|
Notes |
We acknowledge financial support from the Research Foundation–Flanders (FWO; Grant Nos. 1200216N and 11U5416N). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. We are also very thankful to R. Cordeiro for the very interesting discussions. |
Approved |
Most recent IF: 1.712 |
|
|
Call Number |
PLASMANT @ plasmant @UA @ admin @ c:irua:159977 |
Serial |
5172 |
|
Permanent link to this record |
|
|
|
|
Author |
Yusupov, M.; Razzokov, J.; Cordeiro, R.M.; Bogaerts, A. |
![goto web page url](http://nano.uantwerpen.be/nanorefs/img/www.gif)
![find record details (via OpenURL) openurl](img/xref.gif)
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Title |
Transport of Reactive Oxygen and Nitrogen Species across Aquaporin: A Molecular Level Picture |
Type |
A1 Journal article |
|
Year |
2019 |
Publication |
Oxidative medicine and cellular longevity |
Abbreviated Journal |
Oxid Med Cell Longev |
|
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Volume |
2019 |
Issue |
|
Pages |
1-11 |
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|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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|
Abstract |
Aquaporins (AQPs) are transmembrane proteins that conduct not only water molecules across the cell membrane but also other solutes, such as reactive oxygen and nitrogen species (RONS), produced (among others) by cold atmospheric plasma (CAP). These RONS may induce oxidative stress in the cell interior, which plays a role in cancer treatment. The underlying mechanisms of the transport of RONS across AQPs, however, still remain obscure. We apply molecular dynamics simulations to investigate the permeation of both hydrophilic (H<sub>2</sub>O<sub>2</sub>and OH) and hydrophobic (NO<sub>2</sub>and NO) RONS through AQP1. Our simulations show that these RONS can all penetrate across the pores of AQP1. The permeation free energy barrier of OH and NO is lower than that of H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>, indicating that these radicals may have easier access to the pore interior and interact with the amino acid residues of AQP1. We also study the effect of RONS-induced oxidation of both the phospholipids and AQP1 (i.e., sulfenylation of Cys<sub>191</sub>) on the transport of the above-mentioned RONS across AQP1. Both lipid and protein oxidation seem to slightly increase the free energy barrier for H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>permeation, while for OH and NO, we do not observe a strong effect of oxidation. The simulation results help to gain insight in the underlying mechanisms of the noticeable rise of CAP-induced RONS in cancer cells, thereby improving our understanding on the role of AQPs in the selective anticancer capacity of CAP. |
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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 |
000492999000001 |
Publication Date |
2019-06-17 |
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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 |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1942-0900 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
4.593 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
5 |
Open Access |
OpenAccess |
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|
Notes |
The authors 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. M.Y. gratefully acknowledges Dr. U. Khalilov for the fruitful discussions. This work was financially supported by the Research Foundation Flanders (FWO) (grant number 1200219N). |
Approved |
Most recent IF: 4.593 |
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|
Call Number |
PLASMANT @ plasmant @UA @ admin @ c:irua:160118 |
Serial |
5180 |
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Permanent link to this record |
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|
|
|
Author |
Razzokov, J.; Yusupov, M.; Bogaerts, A. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
Oxidation destabilizes toxic amyloid beta peptide aggregation |
Type |
A1 Journal article |
|
Year |
2019 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
|
|
Volume |
9 |
Issue |
1 |
Pages |
5476 |
|
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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 |
The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease. |
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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 |
000462990000018 |
Publication Date |
2019-04-02 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2045-2322 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
4.259 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
5 |
Open Access |
OpenAccess |
|
|
Notes |
M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant 1200216N and 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. |
Approved |
Most recent IF: 4.259 |
|
|
Call Number |
PLASMANT @ plasmant @UA @ admin @ c:irua:159367 |
Serial |
5182 |
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Permanent link to this record |
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Author |
Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. |
![find record details (via OpenURL) openurl](img/xref.gif)
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Title |
Elucidating the asymmetric behavior of the discharge in a dual magnetron sputter deposition system |
Type |
A1 Journal article |
|
Year |
2011 |
Publication |
Applied physics letters |
Abbreviated Journal |
Appl Phys Lett |
|
|
Volume |
98 |
Issue |
13 |
Pages |
131502-131502,3 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
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Abstract |
A magnetron discharge is characterized by drifts of the charged particles guiding center, caused by the magnetic field, in contrast to unmagnetized discharges. Because of these drifts, a pronounced asymmetry of the discharge can be observed in a dual magnetron setup. In this work, it is found that the shape of the discharge in a dual magnetron configuration depends on the magnetic field configuration. In a closed configuration, strong drifts were observed in one preferential direction, whereas in a mirror configuration the deflection of the discharge was not so pronounced. Our calculations confirm experimental observations. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
American Institute of Physics |
Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000289153600017 |
Publication Date |
2011-04-01 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
|
|
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ISSN |
0003-6951; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.411 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
4 |
Open Access |
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|
Notes |
|
Approved |
Most recent IF: 3.411; 2011 IF: 3.844 |
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|
Call Number |
UA @ lucian @ c:irua:87867 |
Serial |
1026 |
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Permanent link to this record |
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Author |
Khalilov, U.; Yusupov, M.; Bogaerts, A.; Neyts, E.C. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
Selective Plasma Oxidation of Ultrasmall Si Nanowires |
Type |
A1 Journal article |
|
Year |
2016 |
Publication |
The journal of physical chemistry: C : nanomaterials and interfaces |
Abbreviated Journal |
J Phys Chem C |
|
|
Volume |
120 |
Issue |
120 |
Pages |
472-477 |
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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 |
Device performance of Si|SiOx core-shell based nanowires critically depends on the exact control over the oxide thickness. Low-temperature plasma oxidation is a highly promising alternative to thermal oxidation allowing for improved control over the oxidation process, in particular for ultrasmall Si nanowires. We here elucidate the room temperature plasma oxidation mechanisms of ultrasmall Si nanowires using hybrid molecular dynamics / force-bias Monte Carlo simulations. We demonstrate how the oxidation and concurrent water formation mechanisms are a function of the oxidizing plasma species and we demonstrate how the resulting core-shell oxide thickness can be controlled through these species. A new mechanism of water formation is discussed in detail. The results provide a detailed atomic level explanation of the oxidation process of highly curved Si surfaces. These results point out a route toward plasma-based formation of ultrathin core-shell Si|SiOx nanowires at room temperature. |
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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 |
000368562200057 |
Publication Date |
2015-12-21 |
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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 |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1932-7447 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
4.536 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
3 |
Open Access |
|
|
|
Notes |
U.K. and M.Y. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grants 12M1315N and 1200216N. This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. We thank Prof. A. C. T. van Duin for sharing the ReaxFF code. |
Approved |
Most recent IF: 4.536 |
|
|
Call Number |
c:irua:130677 |
Serial |
4002 |
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Permanent link to this record |
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Author |
Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A. |
![goto web page url](http://nano.uantwerpen.be/nanorefs/img/www.gif)
![find record details (via OpenURL) openurl](img/xref.gif)
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Title |
Transport of cystine across xC-antiporter |
Type |
A1 Journal article |
|
Year |
2019 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
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Volume |
664 |
Issue |
|
Pages |
117-126 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Extracellular cystine (CYC) uptake by xC antiporter is important for the cell viability. Especially in cancer cells, the upregulation of xC activity is observed, which protects these cells from intracellular oxidative stress. Hence, inhibition of the CYC uptake may eventually lead to cancer cell death. Up to now, the molecular level mechanism of the CYC uptake by xC antiporter has not been studied in detail. In this study, we applied several different simulation techniques to investigate the transport of CYC through xCT, the light subunit of the xC antiporter, which is responsible for the CYC and glutamate translocation. Specifically, we studied the permeation of CYC across three model systems, i.e., outward facing (OF), occluded (OCC) and inward facing (IF) configurations of xCT. We also investigated the effect of mutation of Cys327 to Ala within xCT, which was also studied experimentally in literature. This allowed us to qualitatively compare our computation results with experimental observations, and thus, to validate our simulations. In summary, our simulations provide a molecular level mechanism of the transport of CYC across the xC antiporter, more specifically, which amino acid residues in the xC antiporter play a key role in the uptake, transport and release of CYC. |
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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 |
000461411200014 |
Publication Date |
2019-02-07 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
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ISSN |
0003-9861 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.165 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
3 |
Open Access |
OpenAccess |
|
|
Notes |
Research Foundation − FlandersResearch Foundation − Flanders (FWO), 1200216N 1200219N ; Hercules FoundationHercules Foundation; Flemish GovernmentFlemish Government (department EWI); UAUA; M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant numbers 1200216N and 1200219N. The computational 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 (department EWI) and the UA. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript. |
Approved |
Most recent IF: 3.165 |
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|
Call Number |
PLASMANT @ plasmant @UA @ admin @ c:irua:158571 |
Serial |
5183 |
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Permanent link to this record |
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|
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Author |
Yusupov, M.; Saraiva, M.; Depla, D.; Bogaerts, A. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
Sputter deposition of MgxAlyOz thin films in a dual-magnetron device : a multi-species Monte Carlo model |
Type |
A1 Journal article |
|
Year |
2012 |
Publication |
New journal of physics |
Abbreviated Journal |
New J Phys |
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Volume |
14 |
Issue |
7 |
Pages |
073043 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
A multi-species Monte Carlo (MC) model, combined with an analytical surface model, has been developed in order to investigate the general plasma processes occurring during the sputter deposition of complex oxide films in a dual-magnetron sputter deposition system. The important plasma species, such as electrons, Ar+ ions, fast Ar atoms and sputtered metal atoms (i.e. Mg and Al atoms) are described with the so-called multi-species MC model, whereas the deposition of MgxAlyOz films is treated by an analytical surface model. Targetsubstrate distances for both magnetrons in the dual-magnetron setup are varied for the purpose of growing stoichiometric complex oxide thin films. The metal atoms are sputtered from pure metallic targets, whereas the oxygen flux is only directed toward the substrate and is high enough to obtain fully oxidized thin films but low enough to avoid target poisoning. The calculations correspond to typical experimental conditions applied to grow these complex oxide films. In this paper, some calculation results are shown, such as the densities of various plasma species, their fluxes toward the targets and substrate, the deposition rates, as well as the film stoichiometry. Moreover, some results of the combined model are compared with experimental observations. Note that this is the first complete model, which can be applied for large and complicated magnetron reactor geometries, such as dual-magnetron configurations. With this model, we are able to describe all important plasma species as well as the deposition process. It can also be used to predict film stoichiometries of complex oxide films on the substrate. |
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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 |
000307072500003 |
Publication Date |
2012-07-21 |
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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 |
|
Series Issue |
|
Edition |
|
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ISSN |
1367-2630; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
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Impact Factor |
3.786 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
2 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 3.786; 2012 IF: 4.063 |
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Call Number |
UA @ lucian @ c:irua:100100 |
Serial |
3111 |
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Permanent link to this record |
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Author |
Kumar, N.; Shaw, P.; Razzokov, J.; Yusupov, M.; Attri, P.; Uhm, H.S.; Choi, E.H.; Bogaerts, A. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
Enhancement of cellular glucose uptake by reactive species: a promising approach for diabetes therapy |
Type |
A1 Journal article |
|
Year |
2018 |
Publication |
RSC advances |
Abbreviated Journal |
Rsc Adv |
|
|
Volume |
8 |
Issue |
18 |
Pages |
9887-9894 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
It is generally known that antidiabetic activity is associated with an increased level of glucose uptake in adipocytes and skeletal muscle cells. However, the role of exogenous reactive oxygen and nitrogen species (RONS) in muscle development and more importantly in glucose uptake is largely unknown. We investigate the effect of RONS generated by cold atmospheric plasma (CAP) in glucose uptake. We show that the glucose uptake is significantly enhanced in differentiated L6 skeletal muscle cells after CAP treatment. We also observe a significant increase of the intracellular Ca++ and ROS level, without causing toxicity. One of the possible reasons for an elevated level of glucose uptake as well as intracellular ROS and Ca++ ions is probably the increased oxidative stress leading to glucose transport. |
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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 |
000430451800036 |
Publication Date |
2018-03-08 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2046-2069 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.108 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
1 |
Open Access |
OpenAccess |
|
|
Notes |
We gratefully acknowledge nancial support from the Research Foundation – Flanders (FWO), grant numbers 12J5617N, 1200216N and from the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). We are also thankful to the Plasma Bioscience Research Center at Kwangwoon University for providing the core facilities for the experimental work as well as nancial support by the Leading Foreign Research Institute Recruitment program (Grant # NRF-2016K1A4A3914113) through the Basic Science Research Program of the National Research Founda |
Approved |
Most recent IF: 3.108 |
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|
Call Number |
PLASMANT @ plasmant @c:irua:149564 |
Serial |
4909 |
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Permanent link to this record |
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Author |
Van der Paal, J.; Hong, S.-H.; Yusupov, M.; Gaur, N.; Oh, J.-S.; Short, R.D.; Szili, E.J.; Bogaerts, A. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
How membrane lipids influence plasma delivery of reactive oxygen species into cells and subsequent DNA damage : an experimental and computational study |
Type |
A1 Journal article |
|
Year |
2019 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
|
|
Volume |
21 |
Issue |
35 |
Pages |
19327-19341 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted. |
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Wos |
000486175400045 |
Publication Date |
2019-08-21 |
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1463-9076; 1463-9084 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.123 |
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Most recent IF: 4.123 |
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Call Number |
UA @ admin @ c:irua:162782 |
Serial |
6303 |
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Author |
Elmonov, A.A.; Yusupov, M.S.; Dzhurakhalov, A.A.; Bogaerts, A. |
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Title |
Sputtering of Si(001) and SiC(001) by grazing ion bombardment |
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P1 Proceeding |
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2008 |
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209-213 |
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P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The peculiarities of sputtering processes at 0.5-5 keV Ne grazing ion bombardment of Si(001) and SiC(001) surfaces and their possible application for the surface modification have been studied by computer simulation. Sputtering yields in the primary knock-on recoil atoms regime versus the initial energy of incident ions (E(0) = 0.5-5 keV) and angle of incidence (psi = 0-30 degrees) counted from a target surface have been calculated. Comparative studies of layer-by-layer sputtering for Si(001) and SiC(001) surfaces versus the initial energy of incident ions as well as an effective sputtering and sputtering threshold are discussed. |
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0000-00-00 |
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84 |
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978-86-80019-27-7 |
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UA library record; WoS full record; |
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Most recent IF: NA |
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UA @ lucian @ c:irua:95704 |
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3112 |
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Author |
Yusupov, M.; Van der Paal, J.; Neyts, E.C.; Bogaerts, A. |
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Title |
Synergistic effect of electric field and lipid oxidation on the permeability of cell membranes |
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A1 Journal article |
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2017 |
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Biochimica et biophysica acta : G : general subjects |
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Bba-Gen Subjects |
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1861 |
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1861 |
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839-847 |
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A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Background: Strong electric fields are knownto affect cell membrane permeability,which can be applied for therapeutic purposes, e.g., in cancer therapy. A synergistic enhancement of this effect may be accomplished by the presence of reactive oxygen species (ROS), as generated in cold atmospheric plasmas. Little is known about the synergy between lipid oxidation by ROS and the electric field, nor on howthis affects the cell membrane permeability.
Method: We here conduct molecular dynamics simulations to elucidate the dynamics of the permeation process under the influence of combined lipid oxidation and electroporation. A phospholipid bilayer (PLB), consisting of di-oleoyl-phosphatidylcholine molecules covered with water layers, is used as a model system for the plasma membrane.
Results and conclusions:Weshow howoxidation of the lipids in the PLB leads to an increase of the permeability of the bilayer to ROS, although the permeation free energy barriers still remain relatively high. More importantly, oxidation of the lipids results in a drop of the electric field threshold needed for pore formation (i.e., electroporation) in the PLB. The created pores in the membrane facilitate the penetration of reactive plasma species deep into the cell interior, eventually causing oxidative damage.
General significance: This study is of particular interest for plasma medicine, as plasma generates both ROS and electric fields, but it is also of more general interest for applications where strong electric fields and ROS both come into play. |
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000397366200012 |
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2017-01-27 |
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0304-4165 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.702 |
Times cited ![sorted by Times cited field, descending order (down)](img/sort_desc.gif) |
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Open Access |
OpenAccess |
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Notes |
This work is financially supported by the Fund for Scientific Research Flanders (FWO; grant numbers: 1200216N and 11U5416N). The work was carried out 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 Flem |
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Most recent IF: 4.702 |
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PLASMANT @ plasmant @ c:irua:140095 |
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4413 |
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