|
Records |
Links |
|
Author |
Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. |
|
|
Title |
Multi-level molecular modelling for plasma medicine |
Type |
A1 Journal article |
|
Year |
2016 |
Publication |
Journal Of Physics D-Applied Physics |
Abbreviated Journal |
J Phys D Appl Phys |
|
|
Volume |
49 |
Issue |
5 |
Pages |
054002-54019 |
|
|
Keywords |
A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT) |
|
|
Abstract |
|
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
London |
Editor |
|
|
|
Language |
|
Wos |
|
Publication Date |
0000-00-00 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0022-3727 |
ISBN |
|
Additional Links |
UA library record |
|
|
Impact Factor |
2.588 |
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: 2.588 |
|
|
Call Number |
UA @ lucian @ c:irua:129798 |
Serial |
4467 |
|
Permanent link to this record |
|
|
|
|
Author |
Bogaerts, A.; Aerts, R.; Snoeckx, R.; Somers, W.; Van Gaens, W.; Yusupov, M.; Neyts, E. |
|
|
Title |
Modeling of plasma and plasma-surface interactions for medical, environmental and nano applications |
Type |
A1 Journal article |
|
Year |
2012 |
Publication |
Journal of physics : conference series |
Abbreviated Journal |
|
|
|
Volume |
399 |
Issue |
|
Pages |
012011 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
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. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
Bristol |
Editor |
|
|
|
Language |
|
Wos |
000312261700011 |
Publication Date |
2012-11-26 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1742-6588;1742-6596; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
|
Times cited |
7 |
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: NA |
|
|
Call Number |
UA @ lucian @ c:irua:104727 |
Serial |
2130 |
|
Permanent link to this record |
|
|
|
|
Author |
Cordeiro, R.M.; Yusupov, M.; Razzokov, J.; Bogaerts, A. |
|
|
Title |
Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences |
Type |
A1 Journal article |
|
Year |
2020 |
Publication |
Journal Of Physical Chemistry B |
Abbreviated Journal |
J Phys Chem B |
|
|
Volume |
124 |
Issue |
6 |
Pages |
1082-1089 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
Nitrogen oxyanions and oxyacids are important agents in atmospheric chemistry and medical biology. Although their chemical behavior in solution is relatively well understood, they may behave very differently at the water/air interface of atmospheric aerosols or at the membrane/water interface of cells. Here, we developed a fully classical model for molecular dynamics simulations of NO3−, NO2−, HNO3, and HNO2 in the framework of the GROMOS 53A6 and 54A7 force field versions. The model successfully accounted for the poorly structured solvation shell and ion pairing tendency of NO3−. Accurate pure-liquid properties and hydration free energies were obtained for the oxyacids. Simulations at the water/air interface showed a local enrichment of HNO3 and depletion of NO3−. The effect was discussed in light of earlier spectroscopic data and ab initio calculations, suggesting that HNO3 behaves as a weaker acid at the surface of water. Our model will hopefully allow for efficient and accurate simulations of nitrogen oxyanions and oxyacids in solution and at microheterogeneous interface environments. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000512222500015 |
Publication Date |
2020-02-13 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1520-6106 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.3 |
Times cited |
|
Open Access |
|
|
|
Notes |
We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work. This study was financed in part by the Coordenaçaõ de Aperfeiçoamento de Pessoal de Nı ́vel Superior – Brasil (CAPES) – Finance Code 001. |
Approved |
Most recent IF: 3.3; 2020 IF: 3.177 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:166488 |
Serial |
6340 |
|
Permanent link to this record |
|
|
|
|
Author |
Kovács, A.; Yusupov, M.; Cornet, I.; Billen, P.; Neyts, E.C. |
|
|
Title |
Effect of natural deep eutectic solvents of non-eutectic compositions on enzyme stability |
Type |
A1 Journal article |
|
Year |
2022 |
Publication |
Journal Of Molecular Liquids |
Abbreviated Journal |
J Mol Liq |
|
|
Volume |
366 |
Issue |
|
Pages |
120180-17 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS) |
|
|
Abstract |
Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000865431800010 |
Publication Date |
2022-08-25 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0167-7322 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
|
|
Impact Factor |
6 |
Times cited |
|
Open Access |
Not_Open_Access |
|
|
Notes |
|
Approved |
Most recent IF: 6 |
|
|
Call Number |
UA @ admin @ c:irua:191538 |
Serial |
7265 |
|
Permanent link to this record |
|
|
|
|
Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
|
|
Title |
Lipid Oxidation: Role of Membrane Phase-Separated Domains |
Type |
A1 Journal Article |
|
Year |
2021 |
Publication |
Journal Of Chemical Information And Modeling |
Abbreviated Journal |
J Chem Inf Model |
|
|
Volume |
61 |
Issue |
6 |
Pages |
2857-2868 |
|
|
Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
|
|
Abstract |
Lipid oxidation is associated with several inflammatory and neurodegenerative diseases, but many questions to unravel its effects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a significant effect on membrane function. It is reported that domain interfaces are “hot spots” for pore formation, but the underlying mechanisms and the effect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Specifically, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any effect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000669541400034 |
Publication Date |
2021-06-28 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1549-9596 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.76 |
Times cited |
|
Open Access |
OpenAccess |
|
|
Notes |
Fonds Wetenschappelijk Onderzoek, 1200219N ; Coordenação de Aperfeiçoamento de Pessoal de NÃvel Superior; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for the scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. |
Approved |
Most recent IF: 3.76 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:179766 |
Serial |
6806 |
|
Permanent link to this record |
|
|
|
|
Author |
Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R. |
|
|
Title |
Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations |
Type |
A1 Journal article |
|
Year |
2022 |
Publication |
Journal Of Chemical Information And Modeling |
Abbreviated Journal |
J Chem Inf Model |
|
|
Volume |
62 |
Issue |
1 |
Pages |
129-141 |
|
|
Keywords |
A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000740019000001 |
Publication Date |
2022-01-10 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1549-9596 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
5.6 |
Times cited |
|
Open Access |
Not_Open_Access |
|
|
Notes |
Fonds Wetenschappelijk Onderzoek, 1200219N ; Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. |
Approved |
Most recent IF: 5.6 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:185485 |
Serial |
7050 |
|
Permanent link to this record |
|
|
|
|
Author |
Mehmonov, K.; Ergasheva, A.; Yusupov, M.; Khalilov, U. |
|
|
Title |
The role of carbon monoxide in the catalytic synthesis of endohedral carbyne |
Type |
A1 Journal article |
|
Year |
2023 |
Publication |
Journal of applied physics |
Abbreviated Journal |
|
|
|
Volume |
134 |
Issue |
14 |
Pages |
144303-144307 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
The unique physical properties of carbyne, a novel carbon nanostructure, have attracted considerable interest in modern nanotechnology. While carbyne synthesis has been accomplished successfully using diverse techniques, the underlying mechanisms governing the carbon monoxide-dependent catalytic synthesis of endohedral carbyne remain poorly understood. In this simulation-based study, we investigate the synthesis of endohedral carbyne from carbon and carbon monoxide radicals in the presence of a nickel catalyst inside double-walled carbon nanotubes with a (5,5)@(10,10) structure. The outcome of our investigation demonstrates that the incorporation of the carbon atom within the Ni-n@(5,5)@(10,10) model system initiates the formation of an elongated carbon chain. In contrast, upon the introduction of carbon monoxide radicals, the growth of the carbyne chain is inhibited as a result of the oxidation of endohedral nickel clusters by oxygen atoms after the initial steps of nucleation. Our findings align with prior theoretical, simulation, and experimental investigations, reinforcing their consistency and providing valuable insights into the synthesis of carbyne-based nanodevices that hold promising potential for future advancements in nanotechnology. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
001083993400003 |
Publication Date |
2023-10-10 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0021-8979; 1089-7550 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
|
|
Impact Factor |
3.2 |
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: 3.2; 2023 IF: 2.068 |
|
|
Call Number |
UA @ admin @ c:irua:201233 |
Serial |
9106 |
|
Permanent link to this record |
|
|
|
|
Author |
Khalilov, U.; Uljayev, U.; Mehmonov, K.; Nematollahi, P.; Yusupov, M.; Neyts, E.C.; Neyts, E.C. |
|
|
Title |
Can endohedral transition metals enhance hydrogen storage in carbon nanotubes? |
Type |
A1 Journal article |
|
Year |
2024 |
Publication |
International journal of hydrogen energy |
Abbreviated Journal |
|
|
|
Volume |
55 |
Issue |
|
Pages |
640-610 |
|
|
Keywords |
A1 Journal article; Engineering sciences. Technology; Modelling and Simulation in Chemistry (MOSAIC); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
The safe and efficient use of hydrogen energy, which is in high demand worldwide today, requires efficient hydrogen storage. Despite significant advances in hydrogen storage using carbon-based nanomaterials, including carbon nanotubes (CNTs), efforts to substantially increase the storage capacity remain less effective. In this work, we demonstrate the effect of endohedral transition metal atoms on the hydrogen storage capacity of CNTs using reactive molecular dynamics simulations. We find that an increase in the volume fraction of endohedral nickel atoms leads to an increase in the concentration of physisorbed hydrogen molecules around single-walled CNTs (SWNTs) by approximately 1.6 times compared to pure SWNTs. The obtained results provide insight into the underlying mechanisms of how endohedral transition metal atoms enhance the hydrogen storage ability of SWNTs under nearly ambient conditions. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
001142427400001 |
Publication Date |
2023-11-24 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0360-3199 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
7.2 |
Times cited |
|
Open Access |
Not_Open_Access |
|
|
Notes |
|
Approved |
Most recent IF: 7.2; 2024 IF: 3.582 |
|
|
Call Number |
UA @ admin @ c:irua:202315 |
Serial |
9006 |
|
Permanent link to this record |
|
|
|
|
Author |
Attri, P.; Razzokov, J.; Yusupov, M.; Koga, K.; Shiratani, M.; Bogaerts, A. |
|
|
Title |
Influence of osmolytes and ionic liquids on the Bacteriorhodopsin structure in the absence and presence of oxidative stress: A combined experimental and computational study |
Type |
A1 Journal article |
|
Year |
2020 |
Publication |
International Journal Of Biological Macromolecules |
Abbreviated Journal |
Int J Biol Macromol |
|
|
Volume |
148 |
Issue |
|
Pages |
657-665 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
Understanding the folding and stability of membrane proteins is of great importance in protein science. Recently, osmolytes and ionic liquids (ILs) are increasingly being used as drug delivery systems in the biopharmaceutical industry. However, the stability of membrane proteins in the presence of osmolytes and ILs is not yet fully understood. Besides, the effect of oxidative stress on membrane proteins with osmolytes or ILs has not been investigated. Therefore, we studied the influence of osmolytes and ILs as co-solvents on the stability of a model membrane protein (i.e., Bacteriorhodopsin in purple membrane of Halobacterium salinarum), using UV–Vis spectroscopy and molecular dynamics (MD) simulations. The MD simulations allowed us to determine the flexibility and solvent accessible surface area (SASA) of Bacteriorhodopsin protein in the presence and/or absence of cosolvents, as well as to carry out principal component analysis (PCA) to identify the most important movements in this protein. In addition, by means of UV–Vis spectroscopy we studied the effect of oxidative stress generated by cold atmospheric plasma on the stability of Bacteriorhodopsin in the presence and/or absence of co-solvents. This study is important for a better understanding of the stability of proteins in the presence of oxidative stress. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000522094600066 |
Publication Date |
2020-01-20 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0141-8130 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
8.2 |
Times cited |
|
Open Access |
|
|
|
Notes |
Horizon2020, 743546 ; JSPS, 19H05462 16H03895 ; Nagoya University; We gratefully acknowledge the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI 19H05462 and 16H03895, the joint usage/research program of Center for Low-temperature Plasma Science, Nagoya University and also supported by JSPS and RCL under the Japan-Lithuania Research Cooperative Program. 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: 8.2; 2020 IF: 3.671 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:165585 |
Serial |
5444 |
|
Permanent link to this record |
|
|
|
|
Author |
Laroussi, M.; Bekeschus, S.; Keidar, M.; Bogaerts, A.; Fridman, A.; Lu, X.; Ostrikov, K.; Hori, M.; Stapelmann, K.; Miller, V.; Reuter, S.; Laux, C.; Mesbah, A.; Walsh, J.; Jiang, C.; Thagard, S.M.; Tanaka, H.; Liu, D.; Yan, D.; Yusupov, M. |
|
|
Title |
Low-Temperature Plasma for Biology, Hygiene, and Medicine: Perspective and Roadmap |
Type |
A1 Journal article |
|
Year |
2022 |
Publication |
IEEE transactions on radiation and plasma medical sciences |
Abbreviated Journal |
IEEE Trans. Radiat. Plasma Med. Sci. |
|
|
Volume |
6 |
Issue |
2 |
Pages |
127-157 |
|
|
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
Plasma, the fourth and most pervasive state of matter in the visible universe, is a fascinating medium that is connected to the beginning of our universe itself. Man-made plasmas are at the core of many technological advances that include the fabrication of semiconductor devices, which enabled the modern computer and communication revolutions. The introduction of low temperature, atmospheric pressure plasmas to the biomedical field has ushered a new revolution in the healthcare arena that promises to introduce plasma-based therapies to combat some thorny and long-standing medical challenges. This article presents an overview of where research is at today and discusses innovative concepts and approaches to overcome present challenges and take the field to the next level. It is written by a team of experts who took an in-depth look at the various applications of plasma in hygiene, decontamination, and medicine, made critical analysis, and proposed ideas and concepts that should help the research community focus their efforts on clear and practical steps necessary to keep the field advancing for decades to come. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000750257400005 |
Publication Date |
2021-12-14 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2469-7311 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
|
Times cited |
|
Open Access |
OpenAccess |
|
|
Notes |
Research Foundation—Flanders, 1200219N ; |
Approved |
Most recent IF: NA |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:185875 |
Serial |
6907 |
|
Permanent link to this record |
|
|
|
|
Author |
Bogaerts, A.; Yusupov, M.; Razzokov, J.; Van der Paal, J. |
|
|
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 |
|
|
Volume |
|
Issue |
|
Pages |
|
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
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 |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000468848400004 |
Publication Date |
2019-03-22 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2095-0179 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
1.712 |
Times cited |
5 |
Open Access |
Not_Open_Access: Available from 23.05.2020
|
|
|
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 |
Khalilov, U.; Yusupov, M.; Eshonqulov, Gb.; Neyts, Ec.; Berdiyorov, Gr. |
|
|
Title |
Atomic level mechanisms of graphene healing by methane-based plasma radicals |
Type |
A1 Journal article |
|
Year |
2023 |
Publication |
FlatChem |
Abbreviated Journal |
FlatChem |
|
|
Volume |
39 |
Issue |
|
Pages |
100506 |
|
|
Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
|
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000990342500001 |
Publication Date |
2023-04-19 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2452-2627 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
|
|
Impact Factor |
6.2 |
Times cited |
|
Open Access |
OpenAccess |
|
|
Notes |
U.K., M.Y. and G.B.E. acknowledge the support of the Agency for Innovative Development of the Republic of Uzbekistan (Grant numbers F-FA-2021-512 and FZ-2020092435). The computational resources and services used in this work were partially provided by the HPC core facility CalcUA of the Universiteit Antwerpen and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. |
Approved |
Most recent IF: 6.2; 2023 IF: NA |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:197442 |
Serial |
8813 |
|
Permanent link to this record |
|
|
|
|
Author |
Oliveira, M.C.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A. |
|
|
Title |
Unraveling the permeation of reactive species across nitrated membranes by computer simulations |
Type |
A1 Journal Article;Reactive oxygen and nitrogen species |
|
Year |
2021 |
Publication |
Computers In Biology And Medicine |
Abbreviated Journal |
Comput Biol Med |
|
|
Volume |
136 |
Issue |
|
Pages |
104768 |
|
|
Keywords |
A1 Journal Article;Reactive oxygen and nitrogen species; Nitro-oxidative stress; Molecular dynamics simulations; Nitrated membranes; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
|
|
Abstract |
Reactive oxygen and nitrogen species (RONS) are involved in many biochemical processes, including nitrooxidative stress that causes cancer cell death, observed in cancer therapies such as photodynamic therapy and cold atmospheric plasma. However, their mechanisms of action and selectivity still remain elusive due to the complexity of biological cells. For example, it is not well known how RONS generated by cancer therapies permeate the cell membrane to cause nitro-oxidative damage. There are many studies dedicated to the permeation of RONS across native and oxidized membranes, but not across nitrated membranes, another lipid product also generated during nitro-oxidative stress. Herein, we performed molecular dynamics (MD) simulations to calculate the free energy barrier of RONS permeation across nitrated membranes. Our results show that hydrophilic RONS, such as hydroperoxyl radical (HO2) and peroxynitrous acid (ONOOH), have relatively low barriers compared to hydrogen peroxide (H2O2) and hydroxyl radical (HO), and are more prone to permeate the membrane than for the native or peroxidized membranes, and similar to aldehyde-oxidized membranes. Hydrophobic RONS like molecular oxygen (O2), nitrogen dioxide (NO2) and nitric oxide (NO) even have insignificant barriers for permeation. Compared to native and peroxidized membranes, nitrated membranes are more permeable, suggesting that we must not only consider oxidized membranes during nitro-oxidative stress, but also nitrated membranes, and their role in cancer therapies. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000696938800003 |
Publication Date |
2021-08-17 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0010-4825 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
1.836 |
Times cited |
|
Open Access |
OpenAccess |
|
|
Notes |
We thank University of Antwerp and Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted and for providing the computational resources needed for completion of this work. M. Yusupov acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. |
Approved |
Most recent IF: 1.836 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:181082 |
Serial |
6807 |
|
Permanent link to this record |
|
|
|
|
Author |
Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A. |
|
|
Title |
Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma |
Type |
A1 Journal article |
|
Year |
2021 |
Publication |
Cancers |
Abbreviated Journal |
Cancers |
|
|
Volume |
13 |
Issue |
3 |
Pages |
579 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE) |
|
|
Abstract |
Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000614960600001 |
Publication Date |
2021-02-02 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2072-6694 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
|
Times cited |
|
Open Access |
OpenAccess |
|
|
Notes |
We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis. |
Approved |
Most recent IF: NA |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:176455 |
Serial |
6709 |
|
Permanent link to this record |
|
|
|
|
Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
|
|
Title |
Molecular dynamics simulations of mechanical stress on oxidized membranes |
Type |
A1 Journal article |
|
Year |
2019 |
Publication |
Biophysical chemistry |
Abbreviated Journal |
Biophys Chem |
|
|
Volume |
254 |
Issue |
|
Pages |
106266 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
Biomembranes are under constant attack of free radicals that may lead to lipid oxidation in conditions of oxidative stress. The products generated during lipid oxidation are responsible for structural and dynamical changes which may jeopardize the membrane function. For instance, the local rearrangements of oxidized lipid molecules may induce membrane rupture. In this study, we investigated the effects of mechanical stress on oxidized phospholipid bilayers (PLBs). Model bilayers were stretched until pore formation (or poration) using nonequilibrium molecular dynamics simulations. We studied single-component homogeneous membranes composed of lipid oxidation products, as well as two-component heterogeneous membranes with coexisting native and oxidized domains. In homogeneous membranes, the oxidation products with —OH and —OOH groups reduced the areal strain required for pore formation, whereas the oxidation product with ]O group behaved similarly to the native membrane. In heterogeneous membranes composed of oxidized and non-oxidized domains, we tested the hypothesis according to which poration may be facilitated at the domain interface region. However, results were inconclusive due to their large statistical variance and sensitivity to simulation setup parameters. We pointed out important technical issues that need to be considered in future simulations of mechanically-induced poration of heterogeneous membranes. This research is of interest for photodynamic therapy and plasma medicine, because ruptured and intact plasma membranes are experimentally considered hallmarks of necrotic and apoptotic cell death. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000502890900015 |
Publication Date |
2019-09-13 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0301-4622 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
2.402 |
Times cited |
|
Open Access |
|
|
|
Notes |
São Paulo Research Foundation, 2012/50680-5 ; National Counsel of Technological and Scientific Development, 459270/2014-1 ; We are thankful for the financial support received from the São Paulo Research Foundation (FAPESP) (grant no. 2012/50680-5) and from the National Counsel of Technological and Scientific Development (CNPq) (grant no. 459270/2014-1). MCO acknowledges UFABC for the Master's scholarship granted. |
Approved |
Most recent IF: 2.402 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:163477 |
Serial |
5374 |
|
Permanent link to this record |
|
|
|
|
Author |
Abduvokhidov, D.; Yusupov, M.; Shahzad, A.; Attri, P.; Shiratani, M.; Oliveira, M.C.; Razzokov, J. |
|
|
Title |
Unraveling the Transport Properties of RONS across Nitro-Oxidized Membranes |
Type |
A1 Journal Article |
|
Year |
2023 |
Publication |
Biomolecules |
Abbreviated Journal |
Biomolecules |
|
|
Volume |
13 |
Issue |
7 |
Pages |
1043 |
|
|
Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
|
|
Abstract |
The potential of cold atmospheric plasma (CAP) in biomedical applications has received significant interest, due to its ability to generate reactive oxygen and nitrogen species (RONS). Upon exposure to living cells, CAP triggers alterations in various cellular components, such as the cell membrane. However, the permeation of RONS across nitrated and oxidized membranes remains understudied. To address this gap, we conducted molecular dynamics simulations, to investigate the permeation capabilities of RONS across modified cell membranes. This computational study investigated the translocation processes of less hydrophilic and hydrophilic RONS across the phospholipid bilayer (PLB), with various degrees of oxidation and nitration, and elucidated the impact of RONS on PLB permeability. The simulation results showed that less hydrophilic species, i.e., NO, NO2, N2O4, and O3, have a higher penetration ability through nitro-oxidized PLB compared to hydrophilic RONS, i.e., HNO3, s-cis-HONO, s-trans-HONO, H2O2, HO2, and OH. In particular, nitro-oxidation of PLB, induced by, e.g., cold atmospheric plasma, has minimal impact on the penetration of free energy barriers of less hydrophilic species, while it lowers these barriers for hydrophilic RONS, thereby enhancing their translocation across nitro-oxidized PLB. This research contributes to a better understanding of the translocation abilities of RONS in the field of plasma biomedical applications and highlights the need for further analysis of their role in intracellular signaling pathways. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
001035160000001 |
Publication Date |
2023-06-27 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2218-273X |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
|
Times cited |
|
Open Access |
Not_Open_Access |
|
|
Notes |
This research was funded by the Innovative Development Agency of the Republic of Uzbekistan, grant number FZ-2020092817. |
Approved |
Most recent IF: NA |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:198154 |
Serial |
8803 |
|
Permanent link to this record |
|
|
|
|
Author |
Ghasemitarei, M.; Ghorbi, T.; Yusupov, M.; Zhang, Y.; Zhao, T.; Shali, P.; Bogaerts, A. |
|
|
Title |
Effects of Nitro-Oxidative Stress on Biomolecules: Part 1—Non-Reactive Molecular Dynamics Simulations |
Type |
A1 Journal Article |
|
Year |
2023 |
Publication |
Biomolecules |
Abbreviated Journal |
Biomolecules |
|
|
Volume |
13 |
Issue |
9 |
Pages |
1371 |
|
|
Keywords |
A1 Journal Article; plasma medicine; reactive oxygen and; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
|
|
Abstract |
Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
001071356400001 |
Publication Date |
2023-09-11 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2218-273X |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
|
Times cited |
|
Open Access |
Not_Open_Access |
|
|
Notes |
This research received no external funding. |
Approved |
Most recent IF: NA |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:200380 |
Serial |
8958 |
|
Permanent link to this record |
|
|
|
|
Author |
Tampieri, F.; Espona-Noguera, A.; Labay, C.; Ginebra, M.-P.; Yusupov, M.; Bogaerts, A.; Canal, C. |
|
|
Title |
Does non-thermal plasma modify biopolymers in solution? A chemical and mechanistic study for alginate |
Type |
A1 Journal Article |
|
Year |
2023 |
Publication |
Biomaterials Science |
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
|
|
|
Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
|
|
Abstract |
In the last decades, non-thermal plasma has been extensively investigated as a relevant tool for various biomedical applications, ranging from tissue decontamination to regeneration and from skin treatment to tumor therapies. This high versatility is due to the different kinds and amount of reactive oxygen and nitrogen species that can be generated during a plasma treatment and put in contact with the biological target. Some recent studies report that solutions of biopolymers with the ability to generate hydrogels, when treated with plasma, can enhance the generation of reactive species and influence their stability, resulting thus in the ideal media for indirect treatments of biological targets. The direct effects of the plasma treatment on the structure of biopolymers in water solution, as well as the chemical mechanisms responsible for the enhanced generation of RONS, are not yet fully understood. In this study, we aim at filling this gap by investigating, on the one hand, the nature and extent of the modifications induced by plasma treatment in alginate solutions, and, on the other hand, at using this information to explain the mechanisms responsible for the enhanced generation of reactive species as a consequence of the treatment. The approach we use is twofold: (i) investigating the effects of plasma treatment on alginate solutions, by size exclusion chromatography, rheology and scanning electron microscopy and (ii) study of a molecular model (glucuronate) sharing its chemical structure, by chromatography coupled with mass spectrometry and by molecular dynamics simulations. Our results point out the active role of the biopolymer chemistry during direct plasma treatment. Short-lived reactive species, such as OH radicals and O atoms, can modify the polymer structure, affecting its functional groups and causing partial fragmentation. Some of these chemical modifications, like the generation of organic peroxide, are likely responsible for the secondary generation of long-lived reactive species such as hydrogen peroxide and nitrite ions. This is relevant in view of using biocompatible hydrogels as vehicles for storage and delivery reactive species for targeted therapies. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000973699000001 |
Publication Date |
2023-04-11 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2047-4830 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
6.6 |
Times cited |
|
Open Access |
Not_Open_Access |
|
|
Notes |
Agència de Gestió d’Ajuts Universitaris i de Recerca, SGR2022-1368 ; H2020 European Research Council, 714793 ; European Cooperation in Science and Technology, CA19110 CA20114 ; Secretaría de Estado de Investigación, Desarrollo e Innovación, PID2019-103892RB-I00/AEI/10.13039/501100011033 ; We thank Gonzalo Rodríguez Cañada and Xavier Solé-Martí (Universitat Politècnica de Catalunya) for help in collecting some of the experimental data and for the useful discussions. This work has been primarily funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 714793). The authors acknowledge MINECO for PID2019103892RB-I00/AEI/10.13039/501100011033 project (CC). The authors belong to SGR2022-1368 (FT, AEN, CL, MPG, CC) and acknowledge Generalitat de Catalunya for the ICREA Academia Award for Excellence in Research of CC. We thank also COST Actions CA20114 (Therapeutical Applications of Cold Plasmas) and CA19110 (Plasma Applications for Smart and Sustainable Agriculture) for the stimulating environment provided. |
Approved |
Most recent IF: 6.6; 2023 IF: 4.21 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:196773 |
Serial |
8794 |
|
Permanent link to this record |
|
|
|
|
Author |
Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C. |
|
|
Title |
How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
Biointerphases |
Abbreviated Journal |
Biointerphases |
|
|
Volume |
10 |
Issue |
10 |
Pages |
029501 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
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. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000357195600019 |
Publication Date |
2014-12-17 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1934-8630;1559-4106; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
2.603 |
Times cited |
10 |
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: 2.603; 2015 IF: 3.374 |
|
|
Call Number |
c:irua:121371 |
Serial |
1492 |
|
Permanent link to this record |
|
|
|
|
Author |
Yusupov, M.; Van der Paal, J.; Neyts, E.C.; Bogaerts, A. |
|
|
Title |
Synergistic effect of electric field and lipid oxidation on the permeability of cell membranes |
Type |
A1 Journal article |
|
Year |
2017 |
Publication |
Biochimica et biophysica acta : G : general subjects |
Abbreviated Journal |
Bba-Gen Subjects |
|
|
Volume |
1861 |
Issue |
1861 |
Pages |
839-847 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
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. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000397366200012 |
Publication Date |
2017-01-27 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0304-4165 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
4.702 |
Times cited |
|
Open Access |
OpenAccess |
|
|
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 |
Approved |
Most recent IF: 4.702 |
|
|
Call Number |
PLASMANT @ plasmant @ c:irua:140095 |
Serial |
4413 |
|
Permanent link to this record |
|
|
|
|
Author |
Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A. |
|
|
Title |
Transport of cystine across xC-antiporter |
Type |
A1 Journal article |
|
Year |
2019 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
|
|
Volume |
664 |
Issue |
|
Pages |
117-126 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
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. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000461411200014 |
Publication Date |
2019-02-07 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0003-9861 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.165 |
Times cited |
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 |
|
|
Call Number |
PLASMANT @ plasmant @UA @ admin @ c:irua:158571 |
Serial |
5183 |
|
Permanent link to this record |
|
|
|
|
Author |
Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A. |
|
|
Title |
Effect of oxidative stress on cystine transportation by xC‾ antiporter |
Type |
A1 Journal article |
|
Year |
2019 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
|
|
Volume |
674 |
Issue |
|
Pages |
108114 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
We performed computer simulations to investigate the effect of oxidation on the extracellular cystine (CYC) uptake by the xC− antiporter. The latter is important for killing of cancer cells. Specifically, applying molecular dynamics (MD) simulations we studied the transport of CYC across xCT, i.e., the light subunit of the xC− antiporter, in charge of bidirectional transport of CYC and glutamate. We considered the outward facing (OF) configuration of xCT, and to study the effect of oxidation, we modified the Cys327 residue, located in the vicinity of the extracellular milieu, to cysteic acid (CYO327). Our computational results showed that oxidation of Cys327 results in a free energy barrier for CYC translocation, thereby blocking the access of CYC to the substrate binding site of the OF system. The formation of the energy barrier was found to be due to the conformational changes in the channel. Analysis of the MD trajectories revealed that the reorganization of the side chains of the Tyr244 and CYO327 residues play a critical role in the OF channel blocking. Indeed, the calculated distance between Tyr244 and either Cys327 or CYO327 showed a narrowing of the channel after oxidation. The obtained free energy barrier for CYC translocation was found to be 33.9kJmol−1, indicating that oxidation of Cys327, by e.g., cold atmospheric plasma, is more effective in inhibiting the xC− antiporter than in the mutation of this amino acid to Ala (yielding a barrier of 32.4kJmol−1). The inhibition of the xC− antiporter may lead to Cys starvation in some cancer cells, eventually resulting in cancer cell death. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000525439700011 |
Publication Date |
2019-09-23 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0003-9861 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.165 |
Times cited |
|
Open Access |
|
|
|
Notes |
Ministry of Science, Research and Technology of Iran; University of Antwerp; Research Foundation − Flanders, 1200219N ; Universiteit Antwerpen; Hercules Foundation; Flemish Government; UA; M. G. acknowledges funding from the Ministry of Science, Research and Technology of Iran and from the University of Antwerp in Belgium. M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant number 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. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript. |
Approved |
Most recent IF: 3.165 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:163474 |
Serial |
5372 |
|
Permanent link to this record |
|
|
|
|
Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
|
|
Title |
How do nitrated lipids affect the properties of phospholipid membranes? |
Type |
A1 Journal article |
|
Year |
2020 |
Publication |
Archives Of Biochemistry And Biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
|
|
Volume |
695 |
Issue |
|
Pages |
108548 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
Biological membranes are under constant attack of free radicals, which may lead to lipid nitro-oxidation, pro ducing a complex mixture of nitro-oxidized lipids that are responsible for structural and dynamic changes on the membrane. Despite the latter, nitro-oxidized lipids are also associated with several inflammatory and neuro degenerative diseases, the underlying mechanisms of which remain elusive. We perform atomistic molecular dynamics simulations using several isomers of nitro-oxidized lipids to study their effect on the structure and permeability of the membrane, as well as the interaction between the mixture of these products in the phospholipid membrane environment. Our results show that the stereo- and positional isomers have a stronger effect on the properties of the membrane composed of oxidized lipids compared to that containing nitrated lipids. Nevertheless, nitrated lipids lead to three-fold increase in water permeability compared to oxidized lipids. In addition, we show that in a membrane consisting of combined nitro-oxidized lipid products, the presence of oxidized lipids protects the membrane from transient pores. Is well stablished that plasma application and photodynamic therapy produces a number of oxidative species used to kill cancer cells, through membrane damage induced by nitro-oxidative stress. This study is important to elucidate the mechanisms and the molecular level properties involving the reactive species produced during that cancer therapies. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000594173400010 |
Publication Date |
0000-00-00 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0003-9861 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.9 |
Times cited |
|
Open Access |
|
|
|
Notes |
CAPES; Flanders Research Foundation, 1200219N ; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. |
Approved |
Most recent IF: 3.9; 2020 IF: 3.165 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:173861 |
Serial |
6440 |
|
Permanent link to this record |
|
|
|
|
Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
|
|
Title |
Distribution of lipid aldehydes in phase-separated membranes: A molecular dynamics study |
Type |
A1 Journal article |
|
Year |
2022 |
Publication |
Archives Of Biochemistry And Biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
|
|
Volume |
717 |
Issue |
|
Pages |
109136 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
It is well established that lipid aldehydes (LAs) are able to increase the permeability of cell membranes and induce their rupture. However, it is not yet clear how LAs are distributed in phase-separated membranes (PSMs), which are responsible for the transport of selected molecules and intracellular signaling. Thus, we investigate here the distribution of LAs in a PSM by coarse-grained molecular dynamics simulations. Our results reveal that LAs derived from mono-unsaturated lipids tend to accumulate at the interface between the liquid-ordered/liquiddisordered domains, whereas those derived from poly-unsaturated lipids remain in the liquid-disordered domain. These results are important for understanding the effects caused by oxidized lipids in membrane structure, properties and organization. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000767632000001 |
Publication Date |
2022-01-24 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0003-9861 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
|
|
Impact Factor |
3.9 |
Times cited |
|
Open Access |
OpenAccess |
|
|
Notes |
We thank the University of Antwerp and the Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted. The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerpen. |
Approved |
Most recent IF: 3.9 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:185874 |
Serial |
6905 |
|
Permanent link to this record |
|
|
|
|
Author |
Rezaei, M.; Ghasemitarei, M.; Razzokov, J.; Yusupov, M.; Ghorbanalilu, M.; Ejtehadi, M.R. |
|
|
Title |
In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel |
Type |
A1 Journal article |
|
Year |
2024 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
|
|
|
Volume |
751 |
Issue |
|
Pages |
109835-109837 |
|
|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g., by cold atmospheric plasma (CAP)) on the pyruvate (Pyr) uptake by VDAC1. Inhibiting Pyr uptake through VDAC1 can suppress cancer cell proliferation. Our primary target was to study the translocation of Pyr across the native and oxidized forms of hVDAC1, the human VDAC1. Specifically, we employed MD simulations to analyze the hVDAC1 structure by modifying certain cysteine residues to cysteic acids and methionine residues to methionine sulfoxides, which allowed us to investigate the effect of oxidation. Our results showed that the free energy barrier for Pyr translocation through the native and oxidized channel was approximately 4.3 +/- 0.7 kJ mol-1 and 10.8 +/- 1.8 kJ mol-1, respectively. An increase in barrier results in a decrease in rate of Pyr permeation through the oxidized channel. Thus, our results indicate that low levels of CAP oxidation reduce Pyr translocation, resulting in decreased cancer cell proliferation. Therefore, low levels of oxidation are likely sufficient to treat cancer cells given the inhibition of Pyr uptake. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
001127850500001 |
Publication Date |
2023-11-23 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0003-9861; 1096-0384 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
|
|
Impact Factor |
3.9 |
Times cited |
|
Open Access |
Not_Open_Access |
|
|
Notes |
|
Approved |
Most recent IF: 3.9; 2024 IF: 3.165 |
|
|
Call Number |
UA @ admin @ c:irua:202185 |
Serial |
9046 |
|
Permanent link to this record |
|
|
|
|
Author |
Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. |
|
|
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) |
|
|
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. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
American Institute of Physics |
Place of Publication |
New York, N.Y. |
Editor |
|
|
|
Language |
|
Wos |
000289153600017 |
Publication Date |
2011-04-01 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0003-6951; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.411 |
Times cited |
4 |
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: 3.411; 2011 IF: 3.844 |
|
|
Call Number |
UA @ lucian @ c:irua:87867 |
Serial |
1026 |
|
Permanent link to this record |
|
|
|
|
Author |
Han, I.; Song, I.S.; Choi, S.A.; Lee, T.; Yusupov, M.; Shaw, P.; Bogaerts, A.; Choi, E.H.; Ryu, J.J. |
|
|
Title |
Bioactive Nonthermal Biocompatible Plasma Enhances Migration on Human Gingival Fibroblasts |
Type |
A1 Journal article |
|
Year |
2023 |
Publication |
Advanced healthcare materials |
Abbreviated Journal |
|
|
|
Volume |
12 |
Issue |
4 |
Pages |
2200527 |
|
|
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
This study hypothesizes that the application of low-dose nonthermal biocompatible dielectric barrier discharge plasma (DBD-NBP) to human gingival fibroblasts (HGFs) will inhibit colony formation but not cell death and induce matrix metalloproteinase (MMP) expression, extracellular matrix (ECM) degradation, and subsequent cell migration, which can result in enhanced wound healing. HGFs treated with plasma for 3 min migrate to each other across the gap faster than those in the control and 5-min treatment groups on days 1 and 3. The plasma-treated HGFs show significantly high expression levels of the cell cycle arrest-related p21 gene and enhanced MMP activity. Focal adhesion kinase (FAK) mediated attenuation of wound healing or actin cytoskeleton rearrangement, and plasma-mediated reversal of this attenuation support the migratory effect of DBD-NBP. Further, this work performs computer simulations to investigate the effect of oxidation on the stability and conformation of the catalytic kinase domain (KD) of FAK. It is found that the oxidation of highly reactive amino acids (AAs) Cys427, Met442, Cys559, Met571, Met617, and Met643 changes the conformation and increases the structural flexibility of the FAK protein and thus modulates its function and activity. Low-dose DBD-NBP-induces host cell cycle arrest, ECM breakdown, and subsequent migration, thus contributing to the enhanced wound healing process. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
000897762100001 |
Publication Date |
2022-11-14 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2192-2640 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
10 |
Times cited |
|
Open Access |
OpenAccess |
|
|
Notes |
National Research Foundation of Korea; Kementerian Pendidikan, 2020R1I1A1A01073071 2021R1A6A1A03038785 ; |
Approved |
Most recent IF: 10; 2023 IF: 5.11 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:192804 |
Serial |
7242 |
|
Permanent link to this record |
|
|
|
|
Author |
Yusupov, M. |
|
|
Title |
Atomic scale simulations for a better insight in plasma medicine |
Type |
Doctoral thesis |
|
Year |
2014 |
Publication |
|
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
|
|
|
Keywords |
Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
|
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
Antwerpen |
Editor |
|
|
|
Language |
|
Wos |
|
Publication Date |
0000-00-00 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
|
ISBN |
|
Additional Links |
UA library record |
|
|
Impact Factor |
|
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: NA |
|
|
Call Number |
UA @ lucian @ c:irua:117837 |
Serial |
188 |
|
Permanent link to this record |
|
|
|
|
Author |
Elmonov, A.A.; Yusupov, M.S.; Dzhurakhalov, A.A.; Bogaerts, A. |
|
|
Title |
Sputtering of Si(001) and SiC(001) by grazing ion bombardment |
Type |
P1 Proceeding |
|
Year |
2008 |
Publication |
|
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
209-213 |
|
|
Keywords |
P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
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. |
|
|
Address |
|
|
|
Corporate Author |
|
Thesis |
|
|
|
Publisher |
|
Place of Publication |
|
Editor |
|
|
|
Language |
|
Wos |
|
Publication Date |
0000-00-00 |
|
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
|
Series Volume |
|
Series Issue |
84 |
Edition |
|
|
|
ISSN |
978-86-80019-27-7 |
ISBN |
|
Additional Links |
UA library record; WoS full record; |
|
|
Impact Factor |
|
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: NA |
|
|
Call Number |
UA @ lucian @ c:irua:95704 |
Serial |
3112 |
|
Permanent link to this record |