| Home | << 1 2 >> |
|
| Records | |||||
|---|---|---|---|---|---|
| Author | Attri, P.; Yusupov, M.; Park, J.H.; Lingamdinne, L.P.; Koduru, J.R.; Shiratani, M.; Choi, E.H.; Bogaerts, A. | ||||
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 | |||
| 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 | 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 | Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. | ||||
| Title |
Molecular dynamics simulations of mechanical stress on oxidized membranes | Type | A1 Journal article | ||
| Year | 2019 | Publication | Biophysical chemistry | Abbreviated Journal | Biophys Chem |
| Volume | 254 | Issue | Pages | 106266 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Biomembranes are under constant attack of free radicals that may lead to lipid oxidation in conditions of oxidative stress. The products generated during lipid oxidation are responsible for structural and dynamical changes which may jeopardize the membrane function. For instance, the local rearrangements of oxidized lipid molecules may induce membrane rupture. In this study, we investigated the effects of mechanical stress on oxidized phospholipid bilayers (PLBs). Model bilayers were stretched until pore formation (or poration) using nonequilibrium molecular dynamics simulations. We studied single-component homogeneous membranes composed of lipid oxidation products, as well as two-component heterogeneous membranes with coexisting native and oxidized domains. In homogeneous membranes, the oxidation products with —OH and —OOH groups reduced the areal strain required for pore formation, whereas the oxidation product with ]O group behaved similarly to the native membrane. In heterogeneous membranes composed of oxidized and non-oxidized domains, we tested the hypothesis according to which poration may be facilitated at the domain interface region. However, results were inconclusive due to their large statistical variance and sensitivity to simulation setup parameters. We pointed out important technical issues that need to be considered in future simulations of mechanically-induced poration of heterogeneous membranes. This research is of interest for photodynamic therapy and plasma medicine, because ruptured and intact plasma membranes are experimentally considered hallmarks of necrotic and apoptotic cell death. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000502890900015 | Publication Date | 2019-09-13 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0301-4622 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.402 | Times cited | Open Access | ||
| Notes | São Paulo Research Foundation, 2012/50680-5 ; National Counsel of Technological and Scientific Development, 459270/2014-1 ; We are thankful for the financial support received from the São Paulo Research Foundation (FAPESP) (grant no. 2012/50680-5) and from the National Counsel of Technological and Scientific Development (CNPq) (grant no. 459270/2014-1). MCO acknowledges UFABC for the Master's scholarship granted. | Approved | Most recent IF: 2.402 | ||
| Call Number | PLASMANT @ plasmant @c:irua:163477 | Serial | 5374 | ||
| Permanent link to this record | |||||
| Author | Yusupov, M.; Dewaele, D.; Attri, P.; Khalilov, U.; Sobott, F.; Bogaerts, A. | ||||
| Title |
Molecular understanding of the possible mechanisms of oligosaccharide oxidation by cold plasma | Type | A1 Journal article | ||
| Year | 2022 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | Issue | Pages | |||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Cold atmospheric plasma (CAP) is a promising technology for several medical applications, including the removal of biofilms from surfaces. However, the molecular mechanisms of CAP treatment are still poorly understood. Here we unravel the possible mechanisms of CAP‐induced oxidation of oligosaccharides, employing reactive molecular dynamics simulations based on the density functional‐tight binding potential. Specifically, we find that the interaction of oxygen atoms (used as CAP‐generated reactive species) with cellotriose (a model system for the oligosaccharides) can break structurally important glycosidic bonds, which subsequently leads to the disruption of the oligosaccharide molecule. The overall results help to shed light on our experimental evidence for cellotriose CAP. This oxidation by study provides atomic‐level insight into the onset of plasma‐induced removal of biofilms, as oligosaccharides are one of the main components of biofilm. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000865844800001 | Publication Date | 2022-10-11 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1612-8850 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.5 | Times cited | Open Access | OpenAccess | |
| Notes | Fonds Wetenschappelijk Onderzoek, 1200219N ; They also acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UA, where all computational work was performed. This study was financially supported by the Research Foundation–Flanders (FWO) (grant number 1200219N). | Approved | Most recent IF: 3.5 | ||
| Call Number | PLASMANT @ plasmant @c:irua:191404 | Serial | 7113 | ||
| 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. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| 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 | Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. | ||||
| Title |
Multi-level molecular modelling for plasma medicine | Type | A1 Journal article | ||
| Year | 2016 | Publication | Journal Of Physics D-Applied Physics | Abbreviated Journal | J Phys D Appl Phys |
| Volume | 49 | Issue | 5 | Pages | 054002-54019 |
| Keywords | A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | London | Editor | ||
| Language | Wos | Publication Date | 0000-00-00 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0022-3727 | ISBN | Additional Links | UA library record | |
| Impact Factor | 2.588 | Times cited | Open Access | ||
| Notes | Approved | Most recent IF: 2.588 | |||
| Call Number | UA @ lucian @ c:irua:129798 | Serial | 4467 | ||
| Permanent link to this record | |||||
| Author | Razzokov, J.; Yusupov, M.; Bogaerts, A. | ||||
| Title |
Oxidation destabilizes toxic amyloid beta peptide aggregation | Type | A1 Journal article | ||
| Year | 2019 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
| Volume | 9 | Issue | 1 | Pages | 5476 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000462990000018 | Publication Date | 2019-04-02 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.259 | Times cited | 5 | Open Access | OpenAccess |
| Notes | M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant 1200216N and 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. | Approved | Most recent IF: 4.259 | ||
| Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:159367 | Serial | 5182 | ||
| Permanent link to this record | |||||
| Author | Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A. | ||||
| Title |
Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma | Type | A1 Journal article | ||
| Year | 2021 | Publication | Cancers | Abbreviated Journal | Cancers |
| Volume | 13 | Issue | 3 | Pages | 579 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE) | ||||
| Abstract | Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000614960600001 | Publication Date | 2021-02-02 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2072-6694 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | Times cited | Open Access | OpenAccess | ||
| Notes | We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis. | Approved | Most recent IF: NA | ||
| Call Number | PLASMANT @ plasmant @c:irua:176455 | Serial | 6709 | ||
| Permanent link to this record | |||||
| Author | 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. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000657371800005 | Publication Date | 2021-04-14 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2213-2317 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 6.337 | Times cited | Open Access | OpenAccess | |
| Notes | Fwo; The authors acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA, where all computational work was performed. | Approved | Most recent IF: 6.337 | ||
| Call Number | PLASMANT @ plasmant @c:irua:177780 | Serial | 6750 | ||
| Permanent link to this record | |||||
| Author | Cordeiro, R.M.; Yusupov, M.; Razzokov, J.; Bogaerts, A. | ||||
| Title |
Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences | Type | A1 Journal article | ||
| Year | 2020 | Publication | Journal Of Physical Chemistry B | Abbreviated Journal | J Phys Chem B |
| Volume | 124 | Issue | 6 | Pages | 1082-1089 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Nitrogen oxyanions and oxyacids are important agents in atmospheric chemistry and medical biology. Although their chemical behavior in solution is relatively well understood, they may behave very differently at the water/air interface of atmospheric aerosols or at the membrane/water interface of cells. Here, we developed a fully classical model for molecular dynamics simulations of NO3−, NO2−, HNO3, and HNO2 in the framework of the GROMOS 53A6 and 54A7 force field versions. The model successfully accounted for the poorly structured solvation shell and ion pairing tendency of NO3−. Accurate pure-liquid properties and hydration free energies were obtained for the oxyacids. Simulations at the water/air interface showed a local enrichment of HNO3 and depletion of NO3−. The effect was discussed in light of earlier spectroscopic data and ab initio calculations, suggesting that HNO3 behaves as a weaker acid at the surface of water. Our model will hopefully allow for efficient and accurate simulations of nitrogen oxyanions and oxyacids in solution and at microheterogeneous interface environments. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000512222500015 | Publication Date | 2020-02-13 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1520-6106 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.3 | Times cited | Open Access | ||
| Notes | We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work. This study was financed in part by the Coordenaçaõ de Aperfeiçoamento de Pessoal de Nı ́vel Superior – Brasil (CAPES) – Finance Code 001. | Approved | Most recent IF: 3.3; 2020 IF: 3.177 | ||
| Call Number | PLASMANT @ plasmant @c:irua:166488 | Serial | 6340 | ||
| Permanent link to this record | |||||
| Author | 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. | ||||
| Address | |||||
| 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 | ||
| Permanent link to this record | |||||
| Author | Bogaerts, A.; Yusupov, M.; Razzokov, J.; Van der Paal, J. | ||||
| Title |
Plasma for cancer treatment: How can RONS penetrate through the cell membrane? Answers from computer modeling | Type | A1 Journal article | ||
| Year | 2019 | Publication | Frontiers of Chemical Science and Engineering | Abbreviated Journal | Front Chem Sci Eng |
| Volume | Issue | Pages | |||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma is gaining increasing interest for cancer treatment, but the underlying mechanisms are not yet fully understood. Using computer simulations at the molecular level, we try to gain better insight in how plasma-generated reactive oxygen and nitrogen species (RONS) can penetrate through the cell membrane. Specifically, we compare the permeability of various (hydrophilic and hydrophobic) RONS across both oxidized and nonoxidized cell membranes. We also study pore formation, and how it is hampered by higher concentrations of cholesterol in the cell membrane, and we illustrate the much higher permeability of H2O2 through aquaporin channels. Both mechanisms may explain the selective cytotoxic effect of plasma towards cancer cells. Finally, we also discuss the synergistic effect of plasma-induced oxidation and electric fields towards pore formation. Keywords plasma medicine, cancer treatment, computer modelling, cell membrane, reactive oxygen and nitrogen species |
||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000468848400004 | Publication Date | 2019-03-22 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2095-0179 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.712 | Times cited | 5 | Open Access | Not_Open_Access: Available from 23.05.2020 |
| Notes | We acknowledge financial support from the Research Foundation–Flanders (FWO; Grant Nos. 1200216N and 11U5416N). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. We are also very thankful to R. Cordeiro for the very interesting discussions. | Approved | Most recent IF: 1.712 | ||
| Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:159977 | Serial | 5172 | ||
| Permanent link to this record | |||||
| Author | Yusupov, M.; Bogaerts, A.; Huygh, S.; Snoeckx, R.; van Duin, A.C.T.; Neyts, E.C. | ||||
| Title |
Plasma-induced destruction of bacterial cell wall components : a reactive molecular dynamics simulation | Type | A1 Journal article | ||
| Year | 2013 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
| Volume | 117 | Issue | 11 | Pages | 5993-5998 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Nonthermal atmospheric pressure plasmas are gaining increasing attention for biomedical applications. However, very little fundamental information on the interaction mechanisms between the plasma species and biological cells is currently available. We investigate the interaction of important plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, with bacterial peptidoglycan by means of reactive molecular dynamics simulations, aiming for a better understanding of plasma disinfection. Our results show that OH, O, O3, and H2O2 can break structurally important bonds of peptidoglycan (i.e., CO, CN, or CC bonds), which consequently leads to the destruction of the bacterial cell wall. The mechanisms behind these breakups are, however, dependent on the impinging plasma species, and this also determines the effectiveness of the cell wall destruction. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000316773000056 | Publication Date | 2013-02-23 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1932-7447;1932-7455; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 59 | Open Access | |
| Notes | Approved | Most recent IF: 4.536; 2013 IF: 4.835 | |||
| Call Number | UA @ lucian @ c:irua:107154 | Serial | 2636 | ||
| Permanent link to this record | |||||
| Author | 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 | ||
| Permanent link to this record | |||||
| Author | Bogaerts, A.; Yusupov, M.; Van der Paal, J.; Verlackt, C.C.W.; Neyts, E.C. | ||||
| Title |
Reactive molecular dynamics simulations for a better insight in plasma medicine | Type | A1 Journal article | ||
| Year | 2014 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 11 | Issue | 12 | Pages | 1156-1168 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In this review paper, we present several examples of reactive molecular dynamics simulations, which contribute to a better understanding of the underlying mechanisms in plasma medicine on the atomic scale. This includes the interaction of important reactive oxygen plasma species with the outer cell wall of both gram-positive and gram-negative bacteria, and with lipids present in human skin. Moreover, as most biomolecules are surrounded by a liquid biofilm, the behavior of these plasma species in a liquid (water) layer is presented as well. Finally, a perspective for future atomic scale modeling studies is given, in the field of plasma medicine in general, and for cancer treatment in particular. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | 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. | ||||
| 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 | |||
| 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 | Khalilov, U.; Yusupov, M.; Bogaerts, A.; Neyts, E.C. | ||||
| 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 | |||
| 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 | Yusupov, M.; Saraiva, M.; Depla, D.; Bogaerts, A. | ||||
| Title |
Sputter deposition of MgxAlyOz thin films in a dual-magnetron device : a multi-species Monte Carlo model | Type | A1 Journal article | ||
| Year | 2012 | Publication | New journal of physics | Abbreviated Journal | New J Phys |
| Volume | 14 | Issue | 7 | Pages | 073043 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | A multi-species Monte Carlo (MC) model, combined with an analytical surface model, has been developed in order to investigate the general plasma processes occurring during the sputter deposition of complex oxide films in a dual-magnetron sputter deposition system. The important plasma species, such as electrons, Ar+ ions, fast Ar atoms and sputtered metal atoms (i.e. Mg and Al atoms) are described with the so-called multi-species MC model, whereas the deposition of MgxAlyOz films is treated by an analytical surface model. Targetsubstrate distances for both magnetrons in the dual-magnetron setup are varied for the purpose of growing stoichiometric complex oxide thin films. The metal atoms are sputtered from pure metallic targets, whereas the oxygen flux is only directed toward the substrate and is high enough to obtain fully oxidized thin films but low enough to avoid target poisoning. The calculations correspond to typical experimental conditions applied to grow these complex oxide films. In this paper, some calculation results are shown, such as the densities of various plasma species, their fluxes toward the targets and substrate, the deposition rates, as well as the film stoichiometry. Moreover, some results of the combined model are compared with experimental observations. Note that this is the first complete model, which can be applied for large and complicated magnetron reactor geometries, such as dual-magnetron configurations. With this model, we are able to describe all important plasma species as well as the deposition process. It can also be used to predict film stoichiometries of complex oxide films on the substrate. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | 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 | Elmonov, A.A.; Yusupov, M.S.; Dzhurakhalov, A.A.; Bogaerts, A. | ||||
| Title |
Sputtering of Si(001) and SiC(001) by grazing ion bombardment | Type | P1 Proceeding | ||
| Year | 2008 | Publication | Abbreviated Journal | ||
| Volume | Issue | Pages | 209-213 | ||
| Keywords | P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The peculiarities of sputtering processes at 0.5-5 keV Ne grazing ion bombardment of Si(001) and SiC(001) surfaces and their possible application for the surface modification have been studied by computer simulation. Sputtering yields in the primary knock-on recoil atoms regime versus the initial energy of incident ions (E(0) = 0.5-5 keV) and angle of incidence (psi = 0-30 degrees) counted from a target surface have been calculated. Comparative studies of layer-by-layer sputtering for Si(001) and SiC(001) surfaces versus the initial energy of incident ions as well as an effective sputtering and sputtering threshold are discussed. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | Publication Date | 0000-00-00 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | 84 | Edition | ||
| ISSN | 978-86-80019-27-7 | ISBN | Additional Links | UA library record; WoS full record; | |
| Impact Factor | Times cited | Open Access | |||
| Notes | Approved | Most recent IF: NA | |||
| Call Number | UA @ lucian @ c:irua:95704 | Serial | 3112 | ||
| Permanent link to this record | |||||
| Author | Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A. | ||||
| Title |
Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine | Type | A1 Journal article | ||
| Year | 2015 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
| Volume | 48 | Issue | 48 | Pages | 155202 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | 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 | Yusupov, M.; Van der Paal, J.; Neyts, E.C.; Bogaerts, A. | ||||
| Title |
Synergistic effect of electric field and lipid oxidation on the permeability of cell membranes | Type | A1 Journal article | ||
| Year | 2017 | Publication | Biochimica et biophysica acta : G : general subjects | Abbreviated Journal | Bba-Gen Subjects |
| Volume | 1861 | Issue | 1861 | Pages | 839-847 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Background: Strong electric fields are knownto affect cell membrane permeability,which can be applied for therapeutic purposes, e.g., in cancer therapy. A synergistic enhancement of this effect may be accomplished by the presence of reactive oxygen species (ROS), as generated in cold atmospheric plasmas. Little is known about the synergy between lipid oxidation by ROS and the electric field, nor on howthis affects the cell membrane permeability. Method: We here conduct molecular dynamics simulations to elucidate the dynamics of the permeation process under the influence of combined lipid oxidation and electroporation. A phospholipid bilayer (PLB), consisting of di-oleoyl-phosphatidylcholine molecules covered with water layers, is used as a model system for the plasma membrane. Results and conclusions:Weshow howoxidation of the lipids in the PLB leads to an increase of the permeability of the bilayer to ROS, although the permeation free energy barriers still remain relatively high. More importantly, oxidation of the lipids results in a drop of the electric field threshold needed for pore formation (i.e., electroporation) in the PLB. The created pores in the membrane facilitate the penetration of reactive plasma species deep into the cell interior, eventually causing oxidative damage. General significance: This study is of particular interest for plasma medicine, as plasma generates both ROS and electric fields, but it is also of more general interest for applications where strong electric fields and ROS both come into play. |
||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000397366200012 | Publication Date | 2017-01-27 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0304-4165 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.702 | Times cited | Open Access | OpenAccess | |
| Notes | This work is financially supported by the Fund for Scientific Research Flanders (FWO; grant numbers: 1200216N and 11U5416N). The work was carried out using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flem | Approved | Most recent IF: 4.702 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:140095 | Serial | 4413 | ||
| Permanent link to this record | |||||
| Author | 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. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000449722100002 | Publication Date | 2018-07-24 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2213-2317 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 6.337 | Times cited | Open Access | OpenAccess | |
| Notes | 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 | ||
| Permanent link to this record | |||||
| Author | Duan, J.; Ma, M.; Yusupov, M.; Cordeiro, R.M.; Lu, X.; Bogaerts, A. | ||||
| Title |
The penetration of reactive oxygen and nitrogen species across the stratum corneum | Type | A1 Journal article | ||
| Year | 2020 | Publication | Plasma Processes And Polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | Issue | Pages | |||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The penetration of reactive oxygen and nitrogen species (RONS) across the stratum corneum (SC) is a necessary and crucial process in many skin‐related plasma medical applications. To gain more insights into this penetration behavior, we combined experimental measurements of the permeability of dry and moist SC layers with computer simulations of model lipid membranes. We measured the permeation of relatively stable molecules, which are typically generated by plasma, namely H2O2, NO3−, and NO2−. Furthermore, we calculated the permeation free energy profiles of the major plasma‐generated RONS and their derivatives (i.e., H2O2, OH, HO2, O2, O3, NO, NO2, N2O4, HNO2, HNO3, NO2−, and NO3−) across native and oxidized SC lipid bilayers, to understand the mechanisms of RONS permeation across the SC. Our results indicate that hydrophobic RONS (i.e., NO, NO2, O2, O3, and N2O4) can translocate more easily across the SC lipid bilayer than hydrophilic RONS (i.e., H2O2, OH, HO2, HNO2, and HNO3) and ions (i.e., NO2− and NO3−) that experience much higher permeation barriers. The permeability of RONS through the SC skin lipids is enhanced when the skin is moist and the lipids are oxidized. These findings may help to understand the underlying mechanisms of plasma interaction with a biomaterial and to optimize the environmental parameters in practice in plasma medical applications. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000536892900001 | Publication Date | 2020-06-02 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1612-8850 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.5 | Times cited | Open Access | ||
| Notes | National Natural Science Foundation of China, 51625701 51977096 ; Fonds Wetenschappelijk Onderzoek, 1200219N ; China Scholarship Council, 201806160128 ; M. Y. acknowledges the Research Foundation Flanders (FWO) for financial support (Grant No. 1200219N). This study was partially supported by the National Natural Science Foundation of China (Grant No: 51625701 and 51977096) and the China Scholarship Council (Grant No: 201806160128). All computational work was performed using 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. | Approved | Most recent IF: 3.5; 2020 IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @c:irua:169709 | Serial | 6372 | ||
| Permanent link to this record | |||||
| Author | Mehmonov, K.; Ergasheva, A.; Yusupov, M.; Khalilov, U. | ||||
| Title |
The role of carbon monoxide in the catalytic synthesis of endohedral carbyne | Type | A1 Journal article | ||
| Year | 2023 | Publication | Journal of applied physics | Abbreviated Journal | |
| Volume | 134 | Issue | 14 | Pages | 144303-144307 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The unique physical properties of carbyne, a novel carbon nanostructure, have attracted considerable interest in modern nanotechnology. While carbyne synthesis has been accomplished successfully using diverse techniques, the underlying mechanisms governing the carbon monoxide-dependent catalytic synthesis of endohedral carbyne remain poorly understood. In this simulation-based study, we investigate the synthesis of endohedral carbyne from carbon and carbon monoxide radicals in the presence of a nickel catalyst inside double-walled carbon nanotubes with a (5,5)@(10,10) structure. The outcome of our investigation demonstrates that the incorporation of the carbon atom within the Ni-n@(5,5)@(10,10) model system initiates the formation of an elongated carbon chain. In contrast, upon the introduction of carbon monoxide radicals, the growth of the carbyne chain is inhibited as a result of the oxidation of endohedral nickel clusters by oxygen atoms after the initial steps of nucleation. Our findings align with prior theoretical, simulation, and experimental investigations, reinforcing their consistency and providing valuable insights into the synthesis of carbyne-based nanodevices that hold promising potential for future advancements in nanotechnology. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001083993400003 | Publication Date | 2023-10-10 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-8979; 1089-7550 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 3.2 | Times cited | Open Access | ||
| Notes | Approved | Most recent IF: 3.2; 2023 IF: 2.068 | |||
| Call Number | UA @ admin @ c:irua:201233 | Serial | 9106 | ||
| Permanent link to this record | |||||
| Author | Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A. | ||||
| Title |
Transport of cystine across xC-antiporter | Type | A1 Journal article | ||
| Year | 2019 | Publication | Archives of biochemistry and biophysics | Abbreviated Journal | Arch Biochem Biophys |
| Volume | 664 | Issue | Pages | 117-126 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Extracellular cystine (CYC) uptake by xC antiporter is important for the cell viability. Especially in cancer cells, the upregulation of xC activity is observed, which protects these cells from intracellular oxidative stress. Hence, inhibition of the CYC uptake may eventually lead to cancer cell death. Up to now, the molecular level mechanism of the CYC uptake by xC antiporter has not been studied in detail. In this study, we applied several different simulation techniques to investigate the transport of CYC through xCT, the light subunit of the xC antiporter, which is responsible for the CYC and glutamate translocation. Specifically, we studied the permeation of CYC across three model systems, i.e., outward facing (OF), occluded (OCC) and inward facing (IF) configurations of xCT. We also investigated the effect of mutation of Cys327 to Ala within xCT, which was also studied experimentally in literature. This allowed us to qualitatively compare our computation results with experimental observations, and thus, to validate our simulations. In summary, our simulations provide a molecular level mechanism of the transport of CYC across the xC antiporter, more specifically, which amino acid residues in the xC antiporter play a key role in the uptake, transport and release of CYC. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000461411200014 | Publication Date | 2019-02-07 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0003-9861 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.165 | Times cited | 3 | Open Access | OpenAccess |
| Notes | Research Foundation − FlandersResearch Foundation − Flanders (FWO), 1200216N 1200219N ; Hercules FoundationHercules Foundation; Flemish GovernmentFlemish Government (department EWI); UAUA; M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant numbers 1200216N and 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript. | Approved | Most recent IF: 3.165 | ||
| Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:158571 | Serial | 5183 | ||
| Permanent link to this record | |||||
| Author | Yusupov, M.; Razzokov, J.; Cordeiro, R.M.; Bogaerts, A. | ||||
| Title |
Transport of Reactive Oxygen and Nitrogen Species across Aquaporin: A Molecular Level Picture | Type | A1 Journal article | ||
| Year | 2019 | Publication | Oxidative medicine and cellular longevity | Abbreviated Journal | Oxid Med Cell Longev |
| Volume | 2019 | Issue | Pages | 1-11 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Aquaporins (AQPs) are transmembrane proteins that conduct not only water molecules across the cell membrane but also other solutes, such as reactive oxygen and nitrogen species (RONS), produced (among others) by cold atmospheric plasma (CAP). These RONS may induce oxidative stress in the cell interior, which plays a role in cancer treatment. The underlying mechanisms of the transport of RONS across AQPs, however, still remain obscure. We apply molecular dynamics simulations to investigate the permeation of both hydrophilic (H<sub>2</sub>O<sub>2</sub>and OH) and hydrophobic (NO<sub>2</sub>and NO) RONS through AQP1. Our simulations show that these RONS can all penetrate across the pores of AQP1. The permeation free energy barrier of OH and NO is lower than that of H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>, indicating that these radicals may have easier access to the pore interior and interact with the amino acid residues of AQP1. We also study the effect of RONS-induced oxidation of both the phospholipids and AQP1 (i.e., sulfenylation of Cys<sub>191</sub>) on the transport of the above-mentioned RONS across AQP1. Both lipid and protein oxidation seem to slightly increase the free energy barrier for H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>permeation, while for OH and NO, we do not observe a strong effect of oxidation. The simulation results help to gain insight in the underlying mechanisms of the noticeable rise of CAP-induced RONS in cancer cells, thereby improving our understanding on the role of AQPs in the selective anticancer capacity of CAP. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000492999000001 | Publication Date | 2019-06-17 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1942-0900 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.593 | Times cited | 5 | Open Access | OpenAccess |
| Notes | 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. M.Y. gratefully acknowledges Dr. U. Khalilov for the fruitful discussions. This work was financially supported by the Research Foundation Flanders (FWO) (grant number 1200219N). | Approved | Most recent IF: 4.593 | ||
| Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:160118 | Serial | 5180 | ||
| Permanent link to this record | |||||
| Author | Oliveira, M.C.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A. | ||||
| Title |
Unraveling the permeation of reactive species across nitrated membranes by computer simulations | Type | A1 Journal Article;Reactive oxygen and nitrogen species | ||
| Year | 2021 | Publication | Computers In Biology And Medicine | Abbreviated Journal | Comput Biol Med |
| Volume | 136 | Issue | Pages | 104768 | |
| Keywords | A1 Journal Article;Reactive oxygen and nitrogen species; Nitro-oxidative stress; Molecular dynamics simulations; Nitrated membranes; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| Abstract | Reactive oxygen and nitrogen species (RONS) are involved in many biochemical processes, including nitrooxidative stress that causes cancer cell death, observed in cancer therapies such as photodynamic therapy and cold atmospheric plasma. However, their mechanisms of action and selectivity still remain elusive due to the complexity of biological cells. For example, it is not well known how RONS generated by cancer therapies permeate the cell membrane to cause nitro-oxidative damage. There are many studies dedicated to the permeation of RONS across native and oxidized membranes, but not across nitrated membranes, another lipid product also generated during nitro-oxidative stress. Herein, we performed molecular dynamics (MD) simulations to calculate the free energy barrier of RONS permeation across nitrated membranes. Our results show that hydrophilic RONS, such as hydroperoxyl radical (HO2) and peroxynitrous acid (ONOOH), have relatively low barriers compared to hydrogen peroxide (H2O2) and hydroxyl radical (HO), and are more prone to permeate the membrane than for the native or peroxidized membranes, and similar to aldehyde-oxidized membranes. Hydrophobic RONS like molecular oxygen (O2), nitrogen dioxide (NO2) and nitric oxide (NO) even have insignificant barriers for permeation. Compared to native and peroxidized membranes, nitrated membranes are more permeable, suggesting that we must not only consider oxidized membranes during nitro-oxidative stress, but also nitrated membranes, and their role in cancer therapies. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000696938800003 | Publication Date | 2021-08-17 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0010-4825 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.836 | Times cited | Open Access | OpenAccess | |
| Notes | We thank University of Antwerp and Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted and for providing the computational resources needed for completion of this work. M. Yusupov acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. | Approved | Most recent IF: 1.836 | ||
| Call Number | PLASMANT @ plasmant @c:irua:181082 | Serial | 6807 | ||
| Permanent link to this record | |||||
| Author | Abduvokhidov, D.; Yusupov, M.; Shahzad, A.; Attri, P.; Shiratani, M.; Oliveira, M.C.; Razzokov, J. | ||||
| Title |
Unraveling the Transport Properties of RONS across Nitro-Oxidized Membranes | Type | A1 Journal Article | ||
| Year | 2023 | Publication | Biomolecules | Abbreviated Journal | Biomolecules |
| Volume | 13 | Issue | 7 | Pages | 1043 |
| Keywords | A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| Abstract | The potential of cold atmospheric plasma (CAP) in biomedical applications has received significant interest, due to its ability to generate reactive oxygen and nitrogen species (RONS). Upon exposure to living cells, CAP triggers alterations in various cellular components, such as the cell membrane. However, the permeation of RONS across nitrated and oxidized membranes remains understudied. To address this gap, we conducted molecular dynamics simulations, to investigate the permeation capabilities of RONS across modified cell membranes. This computational study investigated the translocation processes of less hydrophilic and hydrophilic RONS across the phospholipid bilayer (PLB), with various degrees of oxidation and nitration, and elucidated the impact of RONS on PLB permeability. The simulation results showed that less hydrophilic species, i.e., NO, NO2, N2O4, and O3, have a higher penetration ability through nitro-oxidized PLB compared to hydrophilic RONS, i.e., HNO3, s-cis-HONO, s-trans-HONO, H2O2, HO2, and OH. In particular, nitro-oxidation of PLB, induced by, e.g., cold atmospheric plasma, has minimal impact on the penetration of free energy barriers of less hydrophilic species, while it lowers these barriers for hydrophilic RONS, thereby enhancing their translocation across nitro-oxidized PLB. This research contributes to a better understanding of the translocation abilities of RONS in the field of plasma biomedical applications and highlights the need for further analysis of their role in intracellular signaling pathways. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001035160000001 | Publication Date | 2023-06-27 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2218-273X | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | Times cited | Open Access | Not_Open_Access | ||
| Notes | This research was funded by the Innovative Development Agency of the Republic of Uzbekistan, grant number FZ-2020092817. | Approved | Most recent IF: NA | ||
| Call Number | PLASMANT @ plasmant @c:irua:198154 | Serial | 8803 | ||
| Permanent link to this record | |||||
| Author | Chai, Z.-N.; Wang, X.-C.; Yusupov, M.; Zhang, Y.-T. | ||||
| Title |
Unveiling the interaction mechanisms of cold atmospheric plasma and amino acids by machine learning | Type | A1 Journal article | ||
| Year | 2024 | Publication | Plasma processes and polymers | Abbreviated Journal | |
| Volume | Issue | Pages | 1-26 | ||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma medicine has attracted tremendous interest in a variety of medical conditions, ranging from wound healing to antimicrobial applications, even in cancer treatment, through the interactions of cold atmospheric plasma (CAP) and various biological tissues directly or indirectly. The underlying mechanisms of CAP treatment are still poorly understood although the oxidative effects of CAP with amino acids, peptides, and proteins have been explored experimentally. In this study, machine learning (ML) technology is introduced to efficiently unveil the interaction mechanisms of amino acids and reactive oxygen species (ROS) in seconds based on the data obtained from the reactive molecular dynamics (MD) simulations, which are performed to probe the interaction of five types of amino acids with various ROS on the timescale of hundreds of picoseconds but with the huge computational load of several days. The oxidative reactions typically start with H-abstraction, and the details of the breaking and formation of chemical bonds are revealed; the modification types, such as nitrosylation, hydroxylation, and carbonylation, can be observed. The dose effects of ROS are also investigated by varying the number of ROS in the simulation box, indicating agreement with the experimental observation. To overcome the limits of timescales and the size of molecular systems in reactive MD simulations, a deep neural network (DNN) with five hidden layers is constructed according to the reaction data and employed to predict the type of oxidative modification and the probability of occurrence only in seconds as the dose of ROS varies. The well-trained DNN can effectively and accurately predict the oxidative processes and productions, which greatly improves the computational efficiency by almost ten orders of magnitude compared with the reactive MD simulation. This study shows the great potential of ML technology to efficiently unveil the underpinning mechanisms in plasma medicine based on the data from reactive MD simulations or experimental measurements. In this study, since reactive molecular dynamics simulation can currently only describe interactions between a few hundred atoms in a few hundred picoseconds, deep neural networks (DNN) are introduced to enhance the simulation results by predicting more data efficiently. image | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001202061200001 | Publication Date | 2024-04-15 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1612-8850 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 3.5 | Times cited | Open Access | ||
| Notes | Approved | Most recent IF: 3.5; 2024 IF: 2.846 | |||
| Call Number | UA @ admin @ c:irua:205512 | Serial | 9181 | ||
| Permanent link to this record | |||||