“Analysis of silver halide microcrystals using different modes of a scanning transmission electron microscope and digital image processing”. Geuens I, Gijbels R, Jacob WA, Verbeeck A, de Keyzer R, The journal of imaging science and technology 36, 534 (1992)
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 0.349
Times cited: 10
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“Application of neural networks in image analysis: the classification of geometrical shapes”. Geuens I, Nys B, Gijbels R, Jacob W, CC-AI: the journal for the integrated study of artificial intelligence, cognitive science and applied epistemology 10, 61 (1993)
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“The primary energy dependence of backscattered electron images up to 100 keV”. Geuens I, Nys B, Naudts J, Gijbels R, Jacob W, van Espen P, Scanning microscopy 5, 339 (1991)
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Chemometrics (Mitac 3)
Times cited: 3
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Ghasemitarei M (2019) Study of the interaction of plasma radicals with malignant tumor cells by means of Molecular Dynamics simulation. 117 p
Abstract: abstract not available
Keywords: Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Effects of Nitro-Oxidative Stress on Biomolecules: Part 1—Non-Reactive Molecular Dynamics Simulations”. Ghasemitarei M, Ghorbi T, Yusupov M, Zhang Y, Zhao T, Shali P, Bogaerts A, Biomolecules 13, 1371 (2023). http://doi.org/10.3390/biom13091371
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.
Keywords: A1 Journal Article; plasma medicine; reactive oxygen and; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
DOI: 10.3390/biom13091371
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“Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations”. Ghasemitarei M, Privat-Maldonado A, Yusupov M, Rahnama S, Bogaerts A, Ejtehadi MR, Journal Of Chemical Information And Modeling 62, 129 (2022). http://doi.org/10.1021/acs.jcim.1c00853
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.
Keywords: A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.6
DOI: 10.1021/acs.jcim.1c00853
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“Transport of cystine across xC-antiporter”. Ghasemitarei M, Yusupov M, Razzokov J, Shokri B, Bogaerts A, Archives of biochemistry and biophysics 664, 117 (2019). http://doi.org/10.1016/j.abb.2019.01.039
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.165
Times cited: 3
DOI: 10.1016/j.abb.2019.01.039
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“Effect of oxidative stress on cystine transportation by xC&oline, antiporter”. Ghasemitarei M, Yusupov M, Razzokov J, Shokri B, Bogaerts A, Archives of biochemistry and biophysics 674, 108114 (2019). http://doi.org/10.1016/j.abb.2019.108114
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.165
DOI: 10.1016/j.abb.2019.108114
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“The role of UV photolysis and molecular transport in the generation of reactive species in a tissue model with a cold atmospheric pressure plasma jet”. Ghimire B, Szili EJ, Lamichhane P, Short RD, Lim JS, Attri P, Masur K, Weltmann K-D, Hong S-H, Choi EH, Applied physics letters 114, 093701 (2019). http://doi.org/10.1063/1.5086522
Abstract: Cold atmospheric pressure plasma jets (plasma) operated in ambient air provide a rich source of reactive oxygen and nitrogen species (RONS), which are known to influence biological processes important in disease. In the plasma treatment of diseased tissue such as subcutaneous cancer tumors, plasma RONS need to first traverse an interface between the plasma-skin surface and second be transported to millimeter depths in order to reach deep-seated diseased cells. However, the mechanisms in the plasma generation of RONS within soft tissues are not understood. In this study, we track the plasma jet delivery of RONS into a tissue model target and we delineate two processes: through target delivery of RONS generated (primarily) in the plasma jet and in situ RONS generation by UV photolysis within the target. We demonstrate that UV photolysis promotes the rapid generation of RONS in the tissue model target’s surface after which the RONS are transported to millimeter depths via a slower molecular process. Our results imply that the flux of UV photons from plasma jets is important for delivering RONS through seemingly impenetrable barriers such as skin. The findings have implications not only in treatments of living tissues but also in the functionalization of soft hydrated biomaterials such as hydrogels and extracellular matrix derived tissue scaffolds.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.411
Times cited: 12
DOI: 10.1063/1.5086522
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Ghorbanfekr Kalashami H (2019) Graphene-based membranes and nanoconfined water : molecular dynamics simulation study. 243 p
Keywords: Doctoral thesis; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Insights into water permeation through hBN nanocapillaries by ab initio machine learning molecular dynamics simulations”. Ghorbanfekr H, Behler J, Peeters FM, Journal Of Physical Chemistry Letters 11, 7363 (2020). http://doi.org/10.1021/ACS.JPCLETT.0C01739
Abstract: Water permeation between stacked layers of hBN sheets forming 2D nanochannels is investigated using large-scale ab initio-quality molecular dynamics simulations. A high-dimensional neural network potential trained on density-functional theory calculations is employed. We simulate water in van der Waals nanocapillaries and study the impact of nanometric confinement on the structure and dynamics of water using both equilibrium and nonequilibrium methods. At an interlayer distance of 10.2 A confinement induces a first-order phase transition resulting in a well-defined AA-stacked bilayer of hexagonal ice. In contrast, for h < 9 A, the 2D water monolayer consists of a mixture of different locally ordered patterns of squares, pentagons, and hexagons. We found a significant change in the transport properties of confined water, particularly for monolayer water where the water-solid friction coefficient decreases to half and the diffusion coefficient increases by a factor of 4 as compared to bulk water. Accordingly, the slip-velocity is found to increase under confinement and we found that the overall permeation is dominated by monolayer water adjacent to the hBN membranes at extreme confinements. We conclude that monolayer water in addition to bilayer ice has a major contribution to water transport through 2D nanochannels.
Keywords: A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.7
Times cited: 24
DOI: 10.1021/ACS.JPCLETT.0C01739
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“Chemical analysis in metal processing: overview and future needs in refined and ultrapure metals”. Gijbels R, Acta technica Belgica: metallurgie 30, 91 (1991)
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Development of a Fourier transform laser microprobe mass spectrometer with external ion source”. Gijbels R, ICR/Ion trap newsletter 30 (1993)
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“The many faces of TOF-SIMS for the characterization of solid (sub)surfaces”. Gijbels R, , 101 (2003)
Keywords: P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Oppervlakte en in-diepte analyse via SIMS, SNMS en GDMS”. Gijbels R, Physicalia magazine 14, 49 (1992)
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Einleitung zu den massenspektrometrischen Methoden”. Gijbels R, Adriaens A Schweizerbart, Stuttgart, page 159 (2000).
Keywords: H3 Book chapter; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Modeling of glow discharge ion sources for mass spectrometry: potentials and limitations”. Gijbels R, Bogaerts A, Spectroscopy 9, 8 (1997)
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Recent trends in solids mass spectrometry: GDMS and other methods”. Gijbels R, Bogaerts A, Fresenius' journal of analytical chemistry 359, 326 (1997). http://doi.org/10.1007/s002160050581
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Times cited: 5
DOI: 10.1007/s002160050581
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“Recent trends in solids mass spectrometry, with special emphasis on glow discharge mass spectrometry”. Gijbels R, Bogaerts A, , 71 (1996)
Keywords: P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Determination of silicon in natural and pollution aerosols by 14-MeV neutron activation analysis”. Gijbels R, Dams R, Analytica chimica acta 63, 369 (1973). http://doi.org/10.1016/S0003-2670(01)82362-X
Abstract: The determination of silicon via the 28Si(n,p)28 Al reaction by means of 14-MeV neutrons is applied to the analysis of pollution and natural aerosols. A Whatman 41 filter (40 cm2) on which airborne particulate material has been collected is compressed into a 3 × 12.7 mm pellet. Standards are prepared in the same way from clean filters spiked with a silicate solution. After a 50-s irradiation and a 75-s decay time, the sample is counted for 2 min with 5 × 5 NaI(Tl) well detector. The 1.779-MeV photopeak of 28Al is measured with a single channel sealer chain or with a multichannel analyser. The reproducibility, sensitivity and liability to interference from other elements were investigated for both counting systems. The homogeneity of the pellets and the filters was checked. The overall precision of one single-channel determination was estimated to be 3.5% after a 24-h high-volume sampling time. Samples collected in urban, industrial and remote areas with concentrations ranging from 0.05 to 15 μg Si m-3 air were analysed and the results are discussed.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.513
Times cited: 16
DOI: 10.1016/S0003-2670(01)82362-X
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“Atomic mass spectrometry”. Gijbels R, Oksenoid KG Academic Press, London, page 2839 (1995).
Keywords: H3 Book chapter; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Scanning microanalysis”. Gijbels R, Oleshko V s.l., page 427 (1998).
Keywords: H3 Book chapter; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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Gijbels R, van Grieken R (1977) Application of analytical methods for trace elements in geothermal waters : part 1 : Amélie-les-Bains (Eastern Pyrenees). S.l
Keywords: MA3 Book as author; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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Gijbels R, van Grieken R (1985) Trace element geochemistry in thermal waters from the Eastern Pyrenees. S.l
Keywords: MA3 Book as author; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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Gijbels R, van Grieken R, Blommaert W, Van 't dack L, van Espen P, Nullens H, Saelens R (1983) Application of analytical methods for trace elements in geothermal waters : part 2 : Plombières, Bains-les-Bains, Bourbonne (Vosges). S.l
Keywords: MA3 Book as author; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Chemometrics (Mitac 3)
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“Application of trace element analysis to geothermal waters”. Gijbels R, van Grieken R, Blommaert W, Vandelannoote R, Van 't dack L, , 429 (1977)
Keywords: P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Trace element geochemistry in thermal waters from Plombières and Bains (Vosges)”. Gijbels R, van Grieken R, Blommaert W, Vandelannoote R, Van 't dack L, , 396 (1980)
Keywords: P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Trace element geochemistry in thermal waters from Amélie-les-Bains (Eastern Pyrenees, France)”. Gijbels R, van Grieken R, Vandelannoote R, Blommaert W, Van 't dack L, , 123 (1980)
Keywords: P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Mass spectrometric analysis of inorganic solids: GDMS and other methods”. Gijbels R, van Straaten M, Bogaerts A, Advances in mass spectrometry 13, 241 (1995)
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Times cited: 12
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“SIMS/TOF-SIMS study of microparticles: surface analysis, imaging and quantification”. Gijbels R, Verlinden G, Geuens I London Institute of Physics, Bristol, page 331 (2000).
Keywords: H1 Book chapter; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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