Nano Home

NANOlab Center of Excellence literature database

Home |  Show All |  Simple Search |  Advanced Search
Quick Search:
1–30 of 59 records found matching your query (RSS | history):
toggle visibility
Search within Results:
Display Options:
Select All    Deselect All << 1 2 >>
List View
 | 
Citations
 | 
Details
   print
  Records Links
Author Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. pdf  url
doi  openurl
  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 (down)  
  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  
Permanent link to this record
 
 
Author Oliveira, M.C.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A. pdf  url
doi  openurl
  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 (down)  
  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 Tampieri, F.; Espona-Noguera, A.; Labay, C.; Ginebra, M.-P.; Yusupov, M.; Bogaerts, A.; Canal, C. pdf  url
doi  openurl
  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 (down)  
  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 Abduvokhidov, D.; Yusupov, M.; Shahzad, A.; Attri, P.; Shiratani, M.; Oliveira, M.C.; Razzokov, J. url  doi
openurl 
  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 (down)  
  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. url  doi
openurl 
  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 (down)  
  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 Yusupov, M. openurl 
  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 (down)  
  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. url  doi
openurl 
  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 Bristol Editor  
  Language Wos 000309393400001 Publication Date 2012-09-27  
  Series Editor Series Title Abbreviated Series Title (down)  
  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  
Permanent link to this record
 
 
Author Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. url  doi
openurl 
  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 Bristol Editor  
  Language Wos 000289064600001 Publication Date 2011-03-15  
  Series Editor Series Title Abbreviated Series Title (down)  
  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  
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.; url  doi
openurl 
  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 London Editor  
  Language Wos 000360909000001 Publication Date 2015-09-09  
  Series Editor Series Title Abbreviated Series Title (down)  
  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  
Permanent link to this record
 
 
Author Neyts, E.C.; Yusupov, M.; Verlackt, C.C.; Bogaerts, A. pdf  doi
openurl 
  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 London Editor  
  Language Wos 000338860300001 Publication Date 2014-06-26  
  Series Editor Series Title Abbreviated Series Title (down)  
  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  
Permanent link to this record
 
 
Author Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. doi  openurl
  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 (down)  
  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 Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C. url  doi
openurl 
  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 (down)  
  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.; Neyts, E.C.; Verlackt, C.C.; Khalilov, U.; van Duin, A.C.T.; Bogaerts, A. pdf  url
doi  openurl
  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 Weinheim Editor  
  Language Wos 000350275400005 Publication Date 2014-09-17  
  Series Editor Series Title Abbreviated Series Title (down)  
  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.; Aerts, R.; Snoeckx, R.; Somers, W.; Van Gaens, W.; Yusupov, M.; Neyts, E. url  doi
openurl 
  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 (down)  
  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 Yusupov, M.; Bogaerts, A.; Huygh, S.; Snoeckx, R.; van Duin, A.C.T.; Neyts, E.C. pdf  doi
openurl 
  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 Washington, D.C. Editor  
  Language Wos 000316773000056 Publication Date 2013-02-23  
  Series Editor Series Title Abbreviated Series Title (down)  
  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 Bogaerts, A.; Yusupov, M.; Van der Paal, J.; Verlackt, C.C.W.; Neyts, E.C. pdf  doi
openurl 
  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 Weinheim Editor  
  Language Wos 000346034700007 Publication Date 2014-09-29  
  Series Editor Series Title Abbreviated Series Title (down)  
  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
 
 
Author Yusupov, M.; Neyts, E.C.; Simon, P.; Berdiyorov, G.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A. pdf  doi
openurl 
  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 London Editor  
  Language Wos 000329108000013 Publication Date 2013-12-13  
  Series Editor Series Title Abbreviated Series Title (down)  
  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 Yusupov, M.; Saraiva, M.; Depla, D.; Bogaerts, A. url  doi
openurl 
  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 Bristol Editor  
  Language Wos 000307072500003 Publication Date 2012-07-21  
  Series Editor Series Title Abbreviated Series Title (down)  
  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  
Permanent link to this record
 
 
Author Elmonov, A.A.; Yusupov, M.S.; Dzhurakhalov, A.A.; Bogaerts, A. openurl 
  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 (down)  
  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
 
 
Author Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A. pdf  url
doi  openurl
  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 London Editor  
  Language Wos 000351856600007 Publication Date 2015-03-25  
  Series Editor Series Title Abbreviated Series Title (down)  
  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. pdf  url
doi  openurl
  Title Multi-level molecular modelling for plasma medicine Type A1 Journal article
  Year 2016 Publication Journal of physics: D: applied physics Abbreviated Journal J Phys D Appl Phys  
  Volume 49 Issue 49 Pages 054002  
  Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000368944100003 Publication Date 2015-12-16  
  Series Editor Series Title Abbreviated Series Title (down)  
  Series Volume Series Issue Edition  
  ISSN 0022-3727 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.588 Times cited 11 Open Access  
  Notes This work is financially supported by the Fund for Scientific Research Flanders (FWO) and the Francqui Foundation. The calculations were carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. Approved Most recent IF: 2.588  
  Call Number c:irua:131571 Serial 3985  
Permanent link to this record
 
 
Author Khalilov, U.; Yusupov, M.; Bogaerts, A.; Neyts, E.C. url  doi
openurl 
  Title Selective Plasma Oxidation of Ultrasmall Si Nanowires Type A1 Journal article
  Year 2016 Publication The journal of physical chemistry: C : nanomaterials and interfaces Abbreviated Journal J Phys Chem C  
  Volume 120 Issue 120 Pages 472-477  
  Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract Device performance of Si|SiOx core-shell based nanowires critically depends on the exact control over the oxide thickness. Low-temperature plasma oxidation is a highly promising alternative to thermal oxidation allowing for improved control over the oxidation process, in particular for ultrasmall Si nanowires. We here elucidate the room temperature plasma oxidation mechanisms of ultrasmall Si nanowires using hybrid molecular dynamics / force-bias Monte Carlo simulations. We demonstrate how the oxidation and concurrent water formation mechanisms are a function of the oxidizing plasma species and we demonstrate how the resulting core-shell oxide thickness can be controlled through these species. A new mechanism of water formation is discussed in detail. The results provide a detailed atomic level explanation of the oxidation process of highly curved Si surfaces. These results point out a route toward plasma-based formation of ultrathin core-shell Si|SiOx nanowires at room temperature.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000368562200057 Publication Date 2015-12-21  
  Series Editor Series Title Abbreviated Series Title (down)  
  Series Volume Series Issue Edition  
  ISSN 1932-7447 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 4.536 Times cited 3 Open Access  
  Notes U.K. and M.Y. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grants 12M1315N and 1200216N. This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. We thank Prof. A. C. T. van Duin for sharing the ReaxFF code. Approved Most recent IF: 4.536  
  Call Number c:irua:130677 Serial 4002  
Permanent link to this record
 
 
Author Attri, P.; Yusupov, M.; Park, J.H.; Lingamdinne, L.P.; Koduru, J.R.; Shiratani, M.; Choi, E.H.; Bogaerts, A. pdf  url
doi  openurl
  Title Mechanism and comparison of needle-type non-thermal direct and indirect atmospheric pressure plasma jets on the degradation of dyes Type A1 Journal article
  Year 2016 Publication Scientific reports Abbreviated Journal Sci Rep-Uk  
  Volume 6 Issue 6 Pages 34419  
  Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract Purified water supply for human use, agriculture and industry is the major global priority nowadays. The advanced oxidation process based on atmospheric pressure non-thermal plasma (NTP) has been used for purification of wastewater, although the underlying mechanisms of degradation of organic pollutants are still unknown. In this study we employ two needle-type atmospheric pressure non-thermal plasma jets, i.e., indirect (ID-APPJ) and direct (D-APPJ) jets operating at Ar feed gas, for the treatment of methylene blue, methyl orange and congo red dyes, for two different times (i.e., 20 min and 30 min). Specifically, we study the decolorization/degradation of all three dyes using the above mentioned plasma sources, by means of UV-Vis spectroscopy, HPLC and a density meter. We also employ mass spectroscopy to verify whether only decolorization or also degradation takes place after treatment of the dyes by the NTP jets. Additionally, we analyze the interaction of OH radicals with all three dyes using reactive molecular dynamics simulations, based on the density functional-tight binding method. This investigation represents the first report on the degradation of these three different dyes by two types of NTP setups, analyzed by various methods, and based on both experimental and computational studies.  
  Address Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language English Wos 000385172300001 Publication Date 2016-10-06  
  Series Editor Series Title Abbreviated Series Title (down)  
  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 23 Open Access  
  Notes We gratefully acknowledge the grant received from the SRC program of the National Research Foundation of Korea (NRF), funded by the Korean Government (MEST) (No. 20100029418). PA is thankful to FY 2015 Japan Society for the Promotion of Science (JSPS) invitation fellowship. This work was partly supported by MEXT KAKENHI Grant Number 24108009 and JSPS KAKENHI Grant Number JP16H03895. M. Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Approved Most recent IF: 4.259  
  Call Number PLASMANT @ plasmant @ c:irua:135847 Serial 4283  
Permanent link to this record
 
 
Author Yusupov, M.; Van der Paal, J.; Neyts, E.C.; Bogaerts, A. pdf  url
doi  openurl
  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 (down)  
  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 Tit, N.; Al Ezzi, M.M.; Abdullah, H.M.; Yusupov, M.; Kouser, S.; Bahlouli, H.; Yamani, Z.H. pdf  url
doi  openurl
  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 Lausanne Editor  
  Language Wos 000390621200044 Publication Date 2016-11-04  
  Series Editor Series Title Abbreviated Series Title (down)  
  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 Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. pdf  url
openurl 
  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 (down)  
  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.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A. url  doi
openurl 
  Title Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments Type A1 Journal article
  Year 2017 Publication Scientific reports Abbreviated Journal Sci Rep-Uk  
  Volume 7 Issue 7 Pages 5761  
  Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000405746500072 Publication Date 2017-07-12  
  Series Editor Series Title Abbreviated Series Title (down)  
  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 27 Open Access OpenAccess  
  Notes M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216 N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. S.R. and S.K. acknowledge funding by the BMBF (FKZ: 03Z2DN12). S.R. acknowledges funding by the Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern (AU 15001). The authors thank M. Hammer for the support and discussion in the biophysical studies and J. Van der Paal for the interesting discussions. Approved Most recent IF: 4.259  
  Call Number PLASMANT @ plasmant @ c:irua:144627 Serial 4630  
Permanent link to this record
 
 
Author Yusupov, M.; Yan, D.; Cordeiro, R.M.; Bogaerts, A. pdf  url
doi  openurl
  Title Atomic scale simulation of H2O2permeation through aquaporin: toward the understanding of plasma cancer treatment Type A1 Journal article
  Year 2018 Publication Journal of physics: D: applied physics Abbreviated Journal J Phys D Appl Phys  
  Volume 51 Issue 12 Pages 125401  
  Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract Experiments have demonstrated the potential selective anticancer capacity of cold atmospheric plasmas (CAPs), but the underlying mechanisms remain unclear. Using computer simulations, we try to shed light on the mechanism of selectivity, based on aquaporins (AQPs), i.e. transmembrane protein channels transferring external H 2 O 2 and other reactive oxygen species, created e.g. by CAPs, to the cell interior. Specifically, we perform molecular dynamics simulations for the permeation of H 2 O 2 through AQP1 (one of the members of the AQP family) and the palmitoyl-oleoyl-phosphatidylcholine (POPC) phospholipid bilayer (PLB). The free energy barrier of H 2 O 2 across AQP1 is lower than for the POPC PLB, while the permeability coefficient, calculated using the free energy and diffusion rate profiles, is two orders of magnitude higher. This indicates that the delivery of H 2 O 2 into the cell interior should be through AQP. Our study gives a better insight into the role of AQPs in the selectivity of CAPs for treating cancer cells.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000426378100001 Publication Date 2018-02-28  
  Series Editor Series Title Abbreviated Series Title (down)  
  Series Volume Series Issue Edition  
  ISSN 0022-3727 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.588 Times cited 7 Open Access OpenAccess  
  Notes MY gratefully acknowledges financial support from the Research Foundation—Flanders (FWO) via Grant No. 1200216N and a travel grant to George Washington University (GWU). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Super- computer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Work at GWU was supported by the National Science Foundation, grant 1465061. RMC thanks FAPESP and CNPq for finan- cial support (Grant Nos. 2012/50680-5 and 459270/2014-1, respectively). Approved Most recent IF: 2.588  
  Call Number PLASMANT @ plasmant @c:irua:149382 Serial 4811  
Permanent link to this record
 
 
Author Kumar, N.; Shaw, P.; Razzokov, J.; Yusupov, M.; Attri, P.; Uhm, H.S.; Choi, E.H.; Bogaerts, A. url  doi
openurl 
  Title Enhancement of cellular glucose uptake by reactive species: a promising approach for diabetes therapy Type A1 Journal article
  Year 2018 Publication RSC advances Abbreviated Journal Rsc Adv  
  Volume 8 Issue 18 Pages 9887-9894  
  Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract It is generally known that antidiabetic activity is associated with an increased level of glucose uptake in adipocytes and skeletal muscle cells. However, the role of exogenous reactive oxygen and nitrogen species (RONS) in muscle development and more importantly in glucose uptake is largely unknown. We investigate the effect of RONS generated by cold atmospheric plasma (CAP) in glucose uptake. We show that the glucose uptake is significantly enhanced in differentiated L6 skeletal muscle cells after CAP treatment. We also observe a significant increase of the intracellular Ca++ and ROS level, without causing toxicity. One of the possible reasons for an elevated level of glucose uptake as well as intracellular ROS and Ca++ ions is probably the increased oxidative stress leading to glucose transport.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000430451800036 Publication Date 2018-03-08  
  Series Editor Series Title Abbreviated Series Title (down)  
  Series Volume Series Issue Edition  
  ISSN 2046-2069 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.108 Times cited 1 Open Access OpenAccess  
  Notes We gratefully acknowledge nancial support from the Research Foundation – Flanders (FWO), grant numbers 12J5617N, 1200216N and from the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). We are also thankful to the Plasma Bioscience Research Center at Kwangwoon University for providing the core facilities for the experimental work as well as nancial support by the Leading Foreign Research Institute Recruitment program (Grant # NRF-2016K1A4A3914113) through the Basic Science Research Program of the National Research Founda Approved Most recent IF: 3.108  
  Call Number PLASMANT @ plasmant @c:irua:149564 Serial 4909  
Permanent link to this record
 
 
Author Razzokov, J.; Yusupov, M.; Vanuytsel, S.; Neyts, E.C.; Bogaerts, A. pdf  url
doi  openurl
  Title Phosphatidylserine flip-flop induced by oxidation of the plasma membrane: a better insight by atomic scale modeling Type A1 Journal article
  Year 2017 Publication Plasma processes and polymers Abbreviated Journal Plasma Process Polym  
  Volume 14 Issue 10 Pages 1700013  
  Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000413045800010 Publication Date 2017-04-05  
  Series Editor Series Title Abbreviated Series Title (down)  
  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 9 Open Access Not_Open_Access  
  Notes Fonds Wetenschappelijk Onderzoek, 1200216N ; Approved Most recent IF: 2.846  
  Call Number PLASMANT @ plasmant @c:irua:149567 Serial 4910  
Permanent link to this record
Select All    Deselect All << 1 2 >>
List View
 | 
Citations
 | 
Details
   print
toggle visibility
Save Citations:
Export Records:
Home CQL Search  |  Library Search  |  Show Record  |  Extract Citations Help