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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 (up) 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
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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.
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Corporate Author Thesis
Publisher Place of Publication (up) 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 Nível 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
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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.
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Corporate Author Thesis
Publisher Place of Publication (up) 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
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Author Yusupov, M.; Privat-Maldonado, A.; Cordeiro, R.M.; Verswyvel, H.; Shaw, P.; Razzokov, J.; Smits, E.; Bogaerts, A.
Title Oxidative damage to hyaluronan–CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy Type A1 Journal article
Year 2021 Publication Redox Biology Abbreviated Journal Redox Biol
Volume 43 Issue Pages 101968
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Abstract Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44–HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44–HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44–HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.
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Corporate Author Thesis
Publisher Place of Publication (up) Editor
Language Wos 000657371800005 Publication Date 2021-04-14
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2213-2317 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.337 Times cited Open Access OpenAccess
Notes Fwo; The authors acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA, where all computational work was performed. Approved Most recent IF: 6.337
Call Number PLASMANT @ plasmant @c:irua:177780 Serial 6750
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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.
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Corporate Author Thesis
Publisher Place of Publication (up) 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
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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.
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Corporate Author Thesis
Publisher Place of Publication (up) 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
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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.
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Corporate Author Thesis
Publisher Place of Publication (up) 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
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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.
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Corporate Author Thesis
Publisher Place of Publication (up) 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
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Author Yusupov, M.; Dewaele, D.; Attri, P.; Khalilov, U.; Sobott, F.; Bogaerts, A.
Title Molecular understanding of the possible mechanisms of oligosaccharide oxidation by cold plasma Type A1 Journal article
Year 2022 Publication Plasma processes and polymers Abbreviated Journal Plasma Process Polym
Volume Issue Pages
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Cold atmospheric plasma (CAP) is a promising technology for several medical applications, including the removal of biofilms from surfaces. However, the molecular mechanisms of CAP treatment are still poorly understood. Here we unravel the possible mechanisms of CAP‐induced oxidation of oligosaccharides, employing reactive molecular dynamics simulations based on the density functional‐tight binding potential. Specifically, we find that the interaction of oxygen atoms (used as CAP‐generated reactive species) with cellotriose (a model system for the oligosaccharides) can break structurally important glycosidic bonds, which subsequently leads to the disruption of the oligosaccharide molecule. The overall results help to shed light on our experimental evidence for cellotriose CAP. This oxidation by study provides atomic‐level insight into the onset of plasma‐induced removal of biofilms, as oligosaccharides are one of the main components of biofilm.
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Corporate Author Thesis
Publisher Place of Publication (up) Editor
Language Wos 000865844800001 Publication Date 2022-10-11
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.5 Times cited Open Access OpenAccess
Notes Fonds Wetenschappelijk Onderzoek, 1200219N ; They also acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UA, where all computational work was performed. This study was financially supported by the Research Foundation–Flanders (FWO) (grant number 1200219N). Approved Most recent IF: 3.5
Call Number PLASMANT @ plasmant @c:irua:191404 Serial 7113
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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.
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Corporate Author Thesis
Publisher Place of Publication (up) 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
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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.
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Corporate Author Thesis
Publisher Place of Publication (up) 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
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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.
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Corporate Author Thesis
Publisher Place of Publication (up) 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
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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 (up) 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
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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 (up) 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
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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 (up) 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 Yusupov, M.; Neyts, E.C.; Khalilov, U.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A.
Title Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls Type A1 Journal article
Year 2012 Publication New journal of physics Abbreviated Journal New J Phys
Volume 14 Issue 9 Pages 093043
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. CO, CN and CC bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale.
Address
Corporate Author Thesis
Publisher Place of Publication (up) Bristol Editor
Language Wos 000309393400001 Publication Date 2012-09-27
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1367-2630; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.786 Times cited 47 Open Access
Notes Approved Most recent IF: 3.786; 2012 IF: 4.063
Call Number UA @ lucian @ c:irua:101014 Serial 189
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Author Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A.
Title Behavior of electrons in a dual-magnetron sputter deposition system : a Monte Carlo model Type A1 Journal article
Year 2011 Publication New journal of physics Abbreviated Journal New J Phys
Volume 13 Issue Pages 033018-033018,17
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract A Monte Carlo model has been developed for investigating the electron behavior in a dual-magnetron sputter deposition system. To describe the three-dimensional (3D) geometry, different reference frames, i.e. a local and a global coordinate system, were used. In this study, the influence of both closed and mirror magnetic field configurations on the plasma properties is investigated. In the case of a closed magnetic field configuration, the calculated electron trajectories show that if an electron is emitted in (or near) the center of the cathode, where the influence of the magnetic field is low, it is able to travel from one magnetron to the other. On the other hand, when an electron is created at the race track area, it is more or less trapped in the strong magnetic field and cannot easily escape to the second magnetron region. In the case of a mirror magnetic field configuration, irrespective of where the electron is emitted from the cathode, it cannot travel from one magnetron to the other because the magnetic field lines guide the electron to the substrate. Moreover, the electron density and electron impact ionization rate have been calculated and studied in detail for both configurations.
Address
Corporate Author Thesis
Publisher Place of Publication (up) Bristol Editor
Language Wos 000289064600001 Publication Date 2011-03-15
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1367-2630; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.786 Times cited 12 Open Access
Notes Approved Most recent IF: 3.786; 2011 IF: 4.177
Call Number UA @ lucian @ c:irua:87544 Serial 224
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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 (up) 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
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Author Yusupov, M.; Saraiva, M.; Depla, D.; Bogaerts, A.
Title Sputter deposition of MgxAlyOz thin films in a dual-magnetron device : a multi-species Monte Carlo model Type A1 Journal article
Year 2012 Publication New journal of physics Abbreviated Journal New J Phys
Volume 14 Issue 7 Pages 073043
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract A multi-species Monte Carlo (MC) model, combined with an analytical surface model, has been developed in order to investigate the general plasma processes occurring during the sputter deposition of complex oxide films in a dual-magnetron sputter deposition system. The important plasma species, such as electrons, Ar+ ions, fast Ar atoms and sputtered metal atoms (i.e. Mg and Al atoms) are described with the so-called multi-species MC model, whereas the deposition of MgxAlyOz films is treated by an analytical surface model. Targetsubstrate distances for both magnetrons in the dual-magnetron setup are varied for the purpose of growing stoichiometric complex oxide thin films. The metal atoms are sputtered from pure metallic targets, whereas the oxygen flux is only directed toward the substrate and is high enough to obtain fully oxidized thin films but low enough to avoid target poisoning. The calculations correspond to typical experimental conditions applied to grow these complex oxide films. In this paper, some calculation results are shown, such as the densities of various plasma species, their fluxes toward the targets and substrate, the deposition rates, as well as the film stoichiometry. Moreover, some results of the combined model are compared with experimental observations. Note that this is the first complete model, which can be applied for large and complicated magnetron reactor geometries, such as dual-magnetron configurations. With this model, we are able to describe all important plasma species as well as the deposition process. It can also be used to predict film stoichiometries of complex oxide films on the substrate.
Address
Corporate Author Thesis
Publisher Place of Publication (up) Bristol Editor
Language Wos 000307072500003 Publication Date 2012-07-21
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1367-2630; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.786 Times cited 2 Open Access
Notes Approved Most recent IF: 3.786; 2012 IF: 4.063
Call Number UA @ lucian @ c:irua:100100 Serial 3111
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Author Tit, N.; Al Ezzi, M.M.; Abdullah, H.M.; Yusupov, M.; Kouser, S.; Bahlouli, H.; Yamani, Z.H.
Title Detection of CO2 using CNT-based sensors: Role of Fe catalyst on sensitivity and selectivity Type A1 Journal article
Year 2017 Publication Materials chemistry and physics Abbreviated Journal Mater Chem Phys
Volume 186 Issue 186 Pages 353-364
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The adsorption of CO2 on surfaces of graphene and carbon nanotubes (CNTs), decorated with Fe atoms, are investigated using the self-consistent-charge density-functional tight-binding (SCC-DFTB) method, neglecting the heat effects. Fe ad-atoms are more stable when they are dispersed on hollow sites. They introduce a large density of states at the Fermi level (N-F); where keeping such density low would help in gas sensing. Furthermore, the Fe ad-atom can weaken the C=O double bonds of the chemisorbed CO2 molecule, paving the way for oxygen atoms to drain more charges from Fe. Consequently, chemisorption of CO2 molecules reduces both N-F and the conductance while it enhances the sensitivity with the increasing gas dose. Conducting armchair CNTs (ac-CNTs) have higher sensitivity than graphene and semiconducting zigzag CNTs (zz-CNT5). Comparative study of sensitivity of ac-CNT-Fe composite towards various gases (e.g., O-2, N-2, H-2, H2O, CO and CO2) has shown high sensitivity and selectivity towards CO, CO2 and H2O gases. (C) 2016 Elsevier B.V. All rights reserved.
Address
Corporate Author Thesis
Publisher Place of Publication (up) Lausanne Editor
Language Wos 000390621200044 Publication Date 2016-11-04
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0254-0584 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.084 Times cited 17 Open Access Not_Open_Access
Notes Approved Most recent IF: 2.084
Call Number UA @ lucian @ c:irua:140333 Serial 4465
Permanent link to this record
 
 
Author Hoon Park, J.; Kumar, N.; Hoon Park, D.; Yusupov, M.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A.; Ho Kang, M.; Sup Uhm, H.; Ha Choi, E.; Attri, P.;
Title A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma Type A1 Journal article
Year 2015 Publication Scientific reports Abbreviated Journal Sci Rep-Uk
Volume 5 Issue 5 Pages 13849
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG.
Address
Corporate Author Thesis
Publisher Nature Publishing Group Place of Publication (up) London Editor
Language Wos 000360909000001 Publication Date 2015-09-09
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2045-2322; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.259 Times cited 32 Open Access
Notes Approved Most recent IF: 4.259; 2015 IF: 5.578
Call Number c:irua:127410 Serial 419
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Author Neyts, E.C.; Yusupov, M.; Verlackt, C.C.; Bogaerts, A.
Title Computer simulations of plasmabiomolecule and plasmatissue interactions for a better insight in plasma medicine Type A1 Journal article
Year 2014 Publication Journal of physics: D: applied physics Abbreviated Journal J Phys D Appl Phys
Volume 47 Issue 29 Pages 293001
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficultif not impossibleto obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasmabiomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance the field.
Address
Corporate Author Thesis
Publisher Place of Publication (up) London Editor
Language Wos 000338860300001 Publication Date 2014-06-26
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0022-3727;1361-6463; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.588 Times cited 28 Open Access
Notes Approved Most recent IF: 2.588; 2014 IF: 2.721
Call Number UA @ lucian @ c:irua:117853 Serial 472
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Author Yusupov, M.; Neyts, E.C.; Simon, P.; Berdiyorov, G.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A.
Title Reactive molecular dynamics simulations of oxygen species in a liquid water layer of interest for plasma medicine Type A1 Journal article
Year 2014 Publication Journal of physics: D: applied physics Abbreviated Journal J Phys D Appl Phys
Volume 47 Issue 2 Pages 025205-25209
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The application of atmospheric pressure plasmas in medicine is increasingly gaining attention in recent years, although very little is currently known about the plasma-induced processes occurring on the surface of living organisms. It is known that most bio-organisms, including bacteria, are coated by a liquid film surrounding them, and there might be many interactions between plasma species and the liquid layer before the plasma species reach the surface of the bio-organisms. Therefore, it is essential to study the behaviour of the reactive species in a liquid film, in order to determine whether these species can travel through this layer and reach the biomolecules, or whether new species are formed along the way. In this work, we investigate the interaction of reactive oxygen species (i.e. O, OH, HO2 and H2O2) with water, which is assumed as a simple model system for the liquid layer surrounding biomolecules. Our computational investigations show that OH, HO2 and H2O2 can travel deep into the liquid layer and are hence in principle able to reach the bio-organism. Furthermore, O, OH and HO2 radicals react with water molecules through hydrogen-abstraction reactions, whereas no H-abstraction reaction takes place in the case of H2O2. This study is important to gain insight into the fundamental operating mechanisms in plasma medicine, in general, and the interaction mechanisms of plasma species with a liquid film, in particular.
Address
Corporate Author Thesis
Publisher Place of Publication (up) London Editor
Language Wos 000329108000013 Publication Date 2013-12-13
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0022-3727;1361-6463; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.588 Times cited 51 Open Access
Notes Approved Most recent IF: 2.588; 2014 IF: 2.721
Call Number UA @ lucian @ c:irua:112286 Serial 2823
Permanent link to this record
 
 
Author Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A.
Title Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine Type A1 Journal article
Year 2015 Publication Journal of physics: D: applied physics Abbreviated Journal J Phys D Appl Phys
Volume 48 Issue 48 Pages 155202
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function.
Address
Corporate Author Thesis
Publisher Place of Publication (up) London Editor
Language Wos 000351856600007 Publication Date 2015-03-25
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0022-3727;1361-6463; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.588 Times cited 20 Open Access
Notes Approved Most recent IF: 2.588; 2015 IF: 2.721
Call Number c:irua:124230 Serial 3242
Permanent link to this record
 
 
Author Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C.
Title Multi-level molecular modelling for plasma medicine Type A1 Journal article
Year 2016 Publication Journal Of Physics D-Applied Physics Abbreviated Journal J Phys D Appl Phys
Volume 49 Issue 5 Pages 054002-54019
Keywords A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT)
Abstract
Address
Corporate Author Thesis
Publisher Place of Publication (up) 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 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 (up) 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 Yusupov, M.; Bogaerts, A.; Huygh, S.; Snoeckx, R.; van Duin, A.C.T.; Neyts, E.C.
Title Plasma-induced destruction of bacterial cell wall components : a reactive molecular dynamics simulation Type A1 Journal article
Year 2013 Publication The journal of physical chemistry: C : nanomaterials and interfaces Abbreviated Journal J Phys Chem C
Volume 117 Issue 11 Pages 5993-5998
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Nonthermal atmospheric pressure plasmas are gaining increasing attention for biomedical applications. However, very little fundamental information on the interaction mechanisms between the plasma species and biological cells is currently available. We investigate the interaction of important plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, with bacterial peptidoglycan by means of reactive molecular dynamics simulations, aiming for a better understanding of plasma disinfection. Our results show that OH, O, O3, and H2O2 can break structurally important bonds of peptidoglycan (i.e., CO, CN, or CC bonds), which consequently leads to the destruction of the bacterial cell wall. The mechanisms behind these breakups are, however, dependent on the impinging plasma species, and this also determines the effectiveness of the cell wall destruction.
Address
Corporate Author Thesis
Publisher Place of Publication (up) Washington, D.C. Editor
Language Wos 000316773000056 Publication Date 2013-02-23
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1932-7447;1932-7455; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.536 Times cited 59 Open Access
Notes Approved Most recent IF: 4.536; 2013 IF: 4.835
Call Number UA @ lucian @ c:irua:107154 Serial 2636
Permanent link to this record
 
 
Author Yusupov, M.; Neyts, E.C.; Verlackt, C.C.; Khalilov, U.; van Duin, A.C.T.; Bogaerts, A.
Title Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species : a reactive molecular dynamics study Type A1 Journal article
Year 2015 Publication Plasma processes and polymers Abbreviated Journal Plasma Process Polym
Volume 12 Issue 12 Pages 162-171
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Reactive molecular dynamics simulations are performed to study the interaction of reactive oxygen species, such as OH, HO2 and H2O2, with the endotoxic biomolecule lipid A of the gram-negative bacterium Escherichia coli. It is found that the aforementioned plasma species can destroy the lipid A, which consequently results in reducing its toxic activity. All bond dissociation events are initiated by hydrogen-abstraction reactions. However, the mechanisms behind these dissociations are dependent on the impinging plasma species, i.e. a clear difference is observed in the mechanisms upon impact of HO2 radicals and H2O2 molecules on one hand and OH radicals on the other hand. Our simulation results are in good agreement with experimental observations.
Address
Corporate Author Thesis
Publisher Place of Publication (up) Weinheim Editor
Language Wos 000350275400005 Publication Date 2014-09-17
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.846 Times cited 18 Open Access
Notes Approved Most recent IF: 2.846; 2015 IF: 2.453
Call Number c:irua:123540 Serial 1589
Permanent link to this record
 
 
Author Bogaerts, A.; Yusupov, M.; Van der Paal, J.; Verlackt, C.C.W.; Neyts, E.C.
Title Reactive molecular dynamics simulations for a better insight in plasma medicine Type A1 Journal article
Year 2014 Publication Plasma processes and polymers Abbreviated Journal Plasma Process Polym
Volume 11 Issue 12 Pages 1156-1168
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract In this review paper, we present several examples of reactive molecular dynamics simulations, which contribute to a better understanding of the underlying mechanisms in plasma medicine on the atomic scale. This includes the interaction of important reactive oxygen plasma species with the outer cell wall of both gram-positive and gram-negative bacteria, and with lipids present in human skin. Moreover, as most biomolecules are surrounded by a liquid biofilm, the behavior of these plasma species in a liquid (water) layer is presented as well. Finally, a perspective for future atomic scale modeling studies is given, in the field of plasma medicine in general, and for cancer treatment in particular.
Address
Corporate Author Thesis
Publisher Place of Publication (up) Weinheim Editor
Language Wos 000346034700007 Publication Date 2014-09-29
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.846 Times cited 22 Open Access
Notes Approved Most recent IF: 2.846; 2014 IF: 2.453
Call Number UA @ lucian @ c:irua:121269 Serial 2822
Permanent link to this record