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| Author | Elmonov, A.A.; Yusupov, M.S.; Dzhurakhalov, A.A.; Bogaerts, A. | ||||
| Title | Sputtering of Si(001) and SiC(001) by grazing ion bombardment | Type | P1 Proceeding | ||
| Year | 2008 | Publication | Abbreviated Journal | ||
| Volume | Issue | Pages | 209-213 | ||
Keywords  |
P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The peculiarities of sputtering processes at 0.5-5 keV Ne grazing ion bombardment of Si(001) and SiC(001) surfaces and their possible application for the surface modification have been studied by computer simulation. Sputtering yields in the primary knock-on recoil atoms regime versus the initial energy of incident ions (E(0) = 0.5-5 keV) and angle of incidence (psi = 0-30 degrees) counted from a target surface have been calculated. Comparative studies of layer-by-layer sputtering for Si(001) and SiC(001) surfaces versus the initial energy of incident ions as well as an effective sputtering and sputtering threshold are discussed. | ||||
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| Language | Wos | Publication Date | 0000-00-00 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | 84 | Edition | ||
| ISSN | 978-86-80019-27-7 | ISBN | Additional Links | UA library record; WoS full record; | |
| Impact Factor | Times cited | Open Access | |||
| Notes | Approved | Most recent IF: NA | |||
| Call Number | UA @ lucian @ c:irua:95704 | Serial | 3112 | ||
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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) | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Antwerpen | Editor | ||
| Language | Wos | Publication Date | 0000-00-00 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | ISBN | Additional Links | UA library record | ||
| Impact Factor | Times cited | Open Access | |||
| Notes | Approved | Most recent IF: NA | |||
| Call Number | UA @ lucian @ c:irua:117837 | Serial | 188 | ||
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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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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000696938800003 | Publication Date | 2021-08-17 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0010-4825 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.836 | Times cited | Open Access | OpenAccess | |
| Notes | We thank University of Antwerp and Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted and for providing the computational resources needed for completion of this work. M. Yusupov acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. | Approved | Most recent IF: 1.836 | ||
| Call Number | PLASMANT @ plasmant @c:irua:181082 | Serial | 6807 | ||
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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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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000669541400034 | Publication Date | 2021-06-28 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1549-9596 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.76 | Times cited | Open Access | OpenAccess | |
| Notes | Fonds Wetenschappelijk Onderzoek, 1200219N ; Coordenação de Aperfeiçoamento de Pessoal de NÃvel Superior; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for the scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. | Approved | Most recent IF: 3.76 | ||
| Call Number | PLASMANT @ plasmant @c:irua:179766 | Serial | 6806 | ||
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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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| 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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| 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 | 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) | ||||
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| Publisher | Place of Publication | London | Editor | ||
| Language | Wos | Publication Date | 0000-00-00 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0022-3727 | ISBN | Additional Links | UA library record | |
| Impact Factor | 2.588 | Times cited | Open Access | ||
| Notes | Approved | Most recent IF: 2.588 | |||
| Call Number | UA @ lucian @ c:irua:129798 | Serial | 4467 | ||
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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. | ||||
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| Language | Wos | 001071356400001 | Publication Date | 2023-09-11 | |
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| 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 | De Backer, J.; Razzokov, J.; Hammerschmid, D.; Mensch, C.; Hafideddine, Z.; Kumar, N.; van Raemdonck, G.; Yusupov, M.; Van Doorslaer, S.; Johannessen, C.; Sobott, F.; Bogaerts, A.; Dewilde, S. | ||||
| Title | The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor | Type | A1 Journal article | ||
| Year | 2018 | Publication | Redox Biology | Abbreviated Journal | Redox Biol |
| Volume | 19 | Issue | Pages | 1-10 | |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec) | ||||
| Abstract | Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB. | ||||
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| Language | Wos | 000449722100002 | Publication Date | 2018-07-24 | |
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| 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 | M.Y. and N.K. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grant nos. 1200216N and 12J5617N. 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). C.M acknowledges the financial support provided by the Flemish Community and the University of Antwerp (BOF-NOI) for the pre-doctoral scholarship is under grant number/project ID: 28465. S.V.D., S. D. and Z.H. acknowledge the FWO (Grant G.0687.13) and the GOA-BOF UA 2013–2016 (project-ID 28312) for funding. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI. | Approved | Most recent IF: 6.337 | ||
| Call Number | PLASMANT @ plasmant @c:irua:152818 | Serial | 5006 | ||
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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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| Language | Wos | 000614960600001 | Publication Date | 2021-02-02 | |
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| 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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| Language | Wos | 000657371800005 | Publication Date | 2021-04-14 | |
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| 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 | Kovács, A.; Yusupov, M.; Cornet, I.; Billen, P.; Neyts, E.C. | ||||
| Title | Effect of natural deep eutectic solvents of non-eutectic compositions on enzyme stability | Type | A1 Journal article | ||
| Year | 2022 | Publication | Journal Of Molecular Liquids | Abbreviated Journal | J Mol Liq |
| Volume | 366 | Issue | Pages | 120180-17 | |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS) | ||||
| Abstract | Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved. | ||||
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| Language | Wos | 000865431800010 | Publication Date | 2022-08-25 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 0167-7322 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 6 | Times cited | Open Access | Not_Open_Access | |
| Notes | Approved | Most recent IF: 6 | |||
| Call Number | UA @ admin @ c:irua:191538 | Serial | 7265 | ||
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| 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 | 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 | ||
| Permanent link to this record | |||||
| 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 | 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 | ||
| Permanent link to this record | |||||
| 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 | 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 | ||
| Permanent link to this record | |||||
| Author | Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. | ||||
| Title | Elucidating the asymmetric behavior of the discharge in a dual magnetron sputter deposition system | Type | A1 Journal article | ||
| Year | 2011 | Publication | Applied physics letters | Abbreviated Journal | Appl Phys Lett |
| Volume | 98 | Issue | 13 | Pages | 131502-131502,3 |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | A magnetron discharge is characterized by drifts of the charged particles guiding center, caused by the magnetic field, in contrast to unmagnetized discharges. Because of these drifts, a pronounced asymmetry of the discharge can be observed in a dual magnetron setup. In this work, it is found that the shape of the discharge in a dual magnetron configuration depends on the magnetic field configuration. In a closed configuration, strong drifts were observed in one preferential direction, whereas in a mirror configuration the deflection of the discharge was not so pronounced. Our calculations confirm experimental observations. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | American Institute of Physics | Place of Publication | New York, N.Y. | Editor | |
| Language | Wos | 000289153600017 | Publication Date | 2011-04-01 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0003-6951; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.411 | Times cited | 4 | Open Access | |
| Notes | Approved | Most recent IF: 3.411; 2011 IF: 3.844 | |||
| Call Number | UA @ lucian @ c:irua:87867 | Serial | 1026 | ||
| Permanent link to this record | |||||
| Author | Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C. | ||||
| Title | How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations | Type | A1 Journal article | ||
| Year | 2015 | Publication | Biointerphases | Abbreviated Journal | Biointerphases |
| Volume | 10 | Issue | 10 | Pages | 029501 |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000357195600019 | Publication Date | 2014-12-17 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1934-8630;1559-4106; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.603 | Times cited | 10 | Open Access | |
| Notes | Approved | Most recent IF: 2.603; 2015 IF: 3.374 | |||
| Call Number | c:irua:121371 | Serial | 1492 | ||
| Permanent link to this record | |||||
| Author | Yusupov, M.; 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 | 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.; Aerts, R.; Snoeckx, R.; Somers, W.; Van Gaens, W.; Yusupov, M.; Neyts, E. | ||||
| Title | Modeling of plasma and plasma-surface interactions for medical, environmental and nano applications | Type | A1 Journal article | ||
| Year | 2012 | Publication | Journal of physics : conference series | Abbreviated Journal | |
| Volume | 399 | Issue | Pages | 012011 | |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In this paper, an overview is given of modeling investigations carried out in our research group for a better understanding of plasmas used for medical, environmental and nano applications. The focus is both on modeling the plasma chemistry and the plasma-surface interactions. The plasma chemistry provides the densities and fluxes of the important plasma species. This information can be used as input when modeling the plasma-surface interactions. The combination of plasma simulations and plasma – surface interaction simulations provides a more comprehensive understanding of the underlying processes for these applications. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Bristol | Editor | ||
| Language | Wos | 000312261700011 | Publication Date | 2012-11-26 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1742-6588;1742-6596; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | Times cited | 7 | Open Access | ||
| Notes | Approved | Most recent IF: NA | |||
| Call Number | UA @ lucian @ c:irua:104727 | Serial | 2130 | ||
| Permanent link to this record | |||||
| Author | 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. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | 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 | |||||
| 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. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | 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 | 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. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | 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 | ||
| 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. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | 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 | 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. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000368944100003 | Publication Date | 2015-12-16 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| 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 | Yusupov, M.; Van der Paal, J.; Neyts, E.C.; Bogaerts, A. | ||||
| Title | Synergistic effect of electric field and lipid oxidation on the permeability of cell membranes | Type | A1 Journal article | ||
| Year | 2017 | Publication | Biochimica et biophysica acta : G : general subjects | Abbreviated Journal | Bba-Gen Subjects |
| Volume | 1861 | Issue | 1861 | Pages | 839-847 |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Background: Strong electric fields are knownto affect cell membrane permeability,which can be applied for therapeutic purposes, e.g., in cancer therapy. A synergistic enhancement of this effect may be accomplished by the presence of reactive oxygen species (ROS), as generated in cold atmospheric plasmas. Little is known about the synergy between lipid oxidation by ROS and the electric field, nor on howthis affects the cell membrane permeability. Method: We here conduct molecular dynamics simulations to elucidate the dynamics of the permeation process under the influence of combined lipid oxidation and electroporation. A phospholipid bilayer (PLB), consisting of di-oleoyl-phosphatidylcholine molecules covered with water layers, is used as a model system for the plasma membrane. Results and conclusions:Weshow howoxidation of the lipids in the PLB leads to an increase of the permeability of the bilayer to ROS, although the permeation free energy barriers still remain relatively high. More importantly, oxidation of the lipids results in a drop of the electric field threshold needed for pore formation (i.e., electroporation) in the PLB. The created pores in the membrane facilitate the penetration of reactive plasma species deep into the cell interior, eventually causing oxidative damage. General significance: This study is of particular interest for plasma medicine, as plasma generates both ROS and electric fields, but it is also of more general interest for applications where strong electric fields and ROS both come into play. |
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000397366200012 | Publication Date | 2017-01-27 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0304-4165 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.702 | Times cited | Open Access | OpenAccess | |
| Notes | This work is financially supported by the Fund for Scientific Research Flanders (FWO; grant numbers: 1200216N and 11U5416N). The work was carried out using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flem | Approved | Most recent IF: 4.702 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:140095 | Serial | 4413 | ||
| Permanent link to this record | |||||
| Author | 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. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | 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 | ||
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| Author | Yusupov, M.; Yan, D.; Cordeiro, R.M.; Bogaerts, A. | ||||
| 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. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000426378100001 | Publication Date | 2018-02-28 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| 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 | ||
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| Author | Kumar, N.; Shaw, P.; Razzokov, J.; Yusupov, M.; Attri, P.; Uhm, H.S.; Choi, E.H.; Bogaerts, A. | ||||
| 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. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000430451800036 | Publication Date | 2018-03-08 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| 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 | ||
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| Author | Razzokov, J.; Yusupov, M.; Vanuytsel, S.; Neyts, E.C.; Bogaerts, A. | ||||
| 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. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000413045800010 | Publication Date | 2017-04-05 | |
| 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 | 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 | ||
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| Author | Razzokov, J.; Yusupov, M.; Bogaerts, A. | ||||
| Title | Possible Mechanism of Glucose Uptake Enhanced by Cold Atmospheric Plasma: Atomic Scale Simulations | Type | A1 Journal article | ||
| Year | 2018 | Publication | Plasma | Abbreviated Journal | |
| Volume | 1 | Issue | 1 | Pages | |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Cold atmospheric plasma (CAP) has shown its potential in biomedical applications, such as wound healing, cancer treatment and bacterial disinfection. Recent experiments have provided evidence that CAP can also enhance the intracellular uptake of glucose molecules which is important in diabetes therapy. In this respect, it is essential to understand the underlying mechanisms of intracellular glucose uptake induced by CAP, which is still unclear. Hence, in this study we try to elucidate the possible mechanism of glucose uptake by cells by performing computer simulations. Specifically, we study the transport of glucose molecules through native and oxidized membranes. Our simulation results show that the free energy barrier for the permeation of glucose molecules across the membrane decreases upon increasing the degree of oxidized lipids in the membrane. This indicates that the glucose permeation rate into cells increases when the CAP oxidation level in the cell membrane is increased. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | Publication Date | 2018-06-08 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2571-6182 | ISBN | Additional Links | UA library record | |
| Impact Factor | Times cited | Open Access | OpenAccess | ||
| Notes | The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the Universiteit Antwerpen. | Approved | Most recent IF: NA | ||
| Call Number | PLASMANT @ plasmant @ plasma1010011c:irua:152176 | Serial | 4990 | ||
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