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	Author	Yusupov, M.
	Title	Atomic scale simulations for a better insight in plasma medicine			Type	Doctoral thesis
	Year	2014	Publication		Abbreviated Journal
	Volume		Issue		Pages
	Keywords	Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Antwerpen	Editor
	Language		Wos		Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:117837			Serial	188
Permanent link to this record



	Author	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
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	Author	Khalilov, U.; Yusupov, M.; Eshonqulov, Gb.; Neyts, Ec.; Berdiyorov, Gr.
	Title	Atomic level mechanisms of graphene healing by methane-based plasma radicals			Type	A1 Journal Article
	Year	2023	Publication	FlatChem	Abbreviated Journal	FlatChem
	Volume	39	Issue		Pages	100506
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000990342500001	Publication Date	2023-04-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2452-2627	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	6.2	Times cited		Open Access	OpenAccess
	Notes	U.K., M.Y. and G.B.E. acknowledge the support of the Agency for Innovative Development of the Republic of Uzbekistan (Grant numbers F-FA-2021-512 and FZ-2020092435). The computational resources and services used in this work were partially provided by the HPC core facility CalcUA of the Universiteit Antwerpen and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government.			Approved	Most recent IF: 6.2; 2023 IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:197442			Serial	8813
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	Author	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
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	Author	Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A.
	Title	Behavior of electrons in a dual-magnetron sputter deposition system : a Monte Carlo model			Type	A1 Journal article
	Year	2011	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	13	Issue		Pages	033018-033018,17
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	A Monte Carlo model has been developed for investigating the electron behavior in a dual-magnetron sputter deposition system. To describe the three-dimensional (3D) geometry, different reference frames, i.e. a local and a global coordinate system, were used. In this study, the influence of both closed and mirror magnetic field configurations on the plasma properties is investigated. In the case of a closed magnetic field configuration, the calculated electron trajectories show that if an electron is emitted in (or near) the center of the cathode, where the influence of the magnetic field is low, it is able to travel from one magnetron to the other. On the other hand, when an electron is created at the race track area, it is more or less trapped in the strong magnetic field and cannot easily escape to the second magnetron region. In the case of a mirror magnetic field configuration, irrespective of where the electron is emitted from the cathode, it cannot travel from one magnetron to the other because the magnetic field lines guide the electron to the substrate. Moreover, the electron density and electron impact ionization rate have been calculated and studied in detail for both configurations.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000289064600001	Publication Date	2011-03-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	12	Open Access
	Notes				Approved	Most recent IF: 3.786; 2011 IF: 4.177
	Call Number	UA @ lucian @ c:irua:87544			Serial	224
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	Author	Yusupov, M.; Saraiva, M.; Depla, D.; Bogaerts, A.
	Title	Sputter deposition of Mg_xAl_yO_z 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	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
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	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
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	Author	Hoon Park, J.; Kumar, N.; Hoon Park, D.; Yusupov, M.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A.; Ho Kang, M.; Sup Uhm, H.; Ha Choi, E.; Attri, P.;
	Title	A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma			Type	A1 Journal article
	Year	2015	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	5	Issue	5	Pages	13849
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG.
	Address
	Corporate Author				Thesis
	Publisher	Nature Publishing Group	Place of Publication	London	Editor
	Language		Wos	000360909000001	Publication Date	2015-09-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	32	Open Access
	Notes				Approved	Most recent IF: 4.259; 2015 IF: 5.578
	Call Number	c:irua:127410			Serial	419
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	Author	Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R.
	Title	Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations			Type	A1 Journal article
	Year	2022	Publication	Journal Of Chemical Information And Modeling	Abbreviated Journal	J Chem Inf Model
	Volume	62	Issue	1	Pages	129-141
	Keywords	A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they aﬀect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the eﬀect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this diﬀerence is not signiﬁcant. Overall, these ﬁndings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000740019000001	Publication Date	2022-01-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1549-9596	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.6	Times cited		Open Access	Not_Open_Access
	Notes	Fonds Wetenschappelijk Onderzoek, 1200219N ; Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they aﬀect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the eﬀect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this diﬀerence is not signiﬁcant. Overall, these ﬁndings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.			Approved	Most recent IF: 5.6
	Call Number	PLASMANT @ plasmant @c:irua:185485			Serial	7050
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	Author	Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M.
	Title	How do nitrated lipids affect the properties of phospholipid membranes?			Type	A1 Journal article
	Year	2020	Publication	Archives Of Biochemistry And Biophysics	Abbreviated Journal	Arch Biochem Biophys
	Volume	695	Issue		Pages	108548
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Biological membranes are under constant attack of free radicals, which may lead to lipid nitro-oxidation, pro ducing a complex mixture of nitro-oxidized lipids that are responsible for structural and dynamic changes on the membrane. Despite the latter, nitro-oxidized lipids are also associated with several inflammatory and neuro degenerative diseases, the underlying mechanisms of which remain elusive. We perform atomistic molecular dynamics simulations using several isomers of nitro-oxidized lipids to study their effect on the structure and permeability of the membrane, as well as the interaction between the mixture of these products in the phospholipid membrane environment. Our results show that the stereo- and positional isomers have a stronger effect on the properties of the membrane composed of oxidized lipids compared to that containing nitrated lipids. Nevertheless, nitrated lipids lead to three-fold increase in water permeability compared to oxidized lipids. In addition, we show that in a membrane consisting of combined nitro-oxidized lipid products, the presence of oxidized lipids protects the membrane from transient pores. Is well stablished that plasma application and photodynamic therapy produces a number of oxidative species used to kill cancer cells, through membrane damage induced by nitro-oxidative stress. This study is important to elucidate the mechanisms and the molecular level properties involving the reactive species produced during that cancer therapies.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000594173400010	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-9861	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.9	Times cited		Open Access
	Notes	CAPES; Flanders Research Foundation, 1200219N ; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for financial support.			Approved	Most recent IF: 3.9; 2020 IF: 3.165
	Call Number	PLASMANT @ plasmant @c:irua:173861			Serial	6440
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	Author	Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M.
	Title	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
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	Author	Matnazarova, S.; Khalilov, U.; Yusupov, M.
	Title	Effect of endohedral nickel atoms on the hydrophilicity of carbon nanotubes			Type	A1 Journal article
	Year	2023	Publication	Molecular simulation	Abbreviated Journal
	Volume	49	Issue	17	Pages	1575-1581
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Carbon nanotubes (CNTs) have been successfully used in biomedicine, including cancer therapy, due to their unique physico-chemical properties. Because pristine CNTs exhibit hydrophobic behaviour, they can have a cytotoxic effect on cells, which limits their practical use in biomedicine. The toxicity of CNTs can be reduced by adding water-soluble functional radicals to their surface, i.e. by increasing their hydrophilicity. Another possibility for increasing the hydrophilicity of CNTs is probably filling them with endohedral metal atoms, which has not yet been studied. Thus, in this study, we use computer simulations to investigate the combined effect of endohedral nickel atoms and functional groups on the hydrophilicity of CNTs. Our simulation results show that the introduction of endohedral nickel atoms into CNTs increases their binding energy with functional groups. We also find that the addition of functional groups to the surface of CNT, along with filling it with endohedral nickel atoms, leads to an increase in the dipole moment of the CNT as well as its interaction energy with water, thereby increasing the hydrophilicity of the CNT and, consequently, its solubility in water. This, in turn, can lead to a decrease in CNT toxicity.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001059544800001	Publication Date	2023-09-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0892-7022	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor		Times cited		Open Access
	Notes				Approved	no
	Call Number	UA @ admin @ c:irua:199261			Serial	9027
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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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	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
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	Author	Razzokov, J.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A.
	Title	Atomic scale understanding of the permeation of plasma species across native and oxidized membranes			Type	A1 Journal article
	Year	2018	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	51	Issue	36	Pages	365203
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Cold atmospheric plasmas (CAPs) have attracted significant interest for their potential benefits in medical applications, including cancer therapy. The therapeutic effects of CAPs are related to reactive oxygen and nitrogen species (ROS and RNS) present in the plasma. The impact of ROS has been extensively studied, but the role of RNS in CAP-treatment remains poorly understood at the molecular level. Here, we investigate the permeation of RNS and ROS across native and oxidized phospholipid bilayers (PLBs) by means of computer simulations. The results reveal significantly lower free energy barriers for RNS (i.e. NO, NO2, N2O4) and O3 compared to hydrophilic ROS, such as OH, HO2 and H2O2. This suggests that the investigated RNS and O3 can permeate more easily through both native and oxidized PLBs in comparison to hydrophilic ROS, indicating their potentially important role in plasma medicine.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000441182400002	Publication Date	2018-08-08
	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	10	Open Access	OpenAccess
	Notes	M Y gratefully acknowledges financial support from the Research Foundation—Flanders (FWO), grant 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. RMC thanks FAPESP and CNPq for financial support (grants 2012/50680-5 and 459270/2014-1, respectively).			Approved	Most recent IF: 2.588
	Call Number	PLASMANT @ plasmant @c:irua:152824			Serial	5005
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	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
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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.
	Address
	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	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
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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
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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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000973699000001	Publication Date	2023-04-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2047-4830	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.6	Times cited		Open Access	Not_Open_Access
	Notes	Agència de Gestió d’Ajuts Universitaris i de Recerca, SGR2022-1368 ; H2020 European Research Council, 714793 ; European Cooperation in Science and Technology, CA19110 CA20114 ; Secretaría de Estado de Investigación, Desarrollo e Innovación, PID2019-103892RB-I00/AEI/10.13039/501100011033 ; We thank Gonzalo Rodríguez Cañada and Xavier Solé-Martí (Universitat Politècnica de Catalunya) for help in collecting some of the experimental data and for the useful discussions. This work has been primarily funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 714793). The authors acknowledge MINECO for PID2019103892RB-I00/AEI/10.13039/501100011033 project (CC). The authors belong to SGR2022-1368 (FT, AEN, CL, MPG, CC) and acknowledge Generalitat de Catalunya for the ICREA Academia Award for Excellence in Research of CC. We thank also COST Actions CA20114 (Therapeutical Applications of Cold Plasmas) and CA19110 (Plasma Applications for Smart and Sustainable Agriculture) for the stimulating environment provided.			Approved	Most recent IF: 6.6; 2023 IF: 4.21
	Call Number	PLASMANT @ plasmant @c:irua:196773			Serial	8794
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	Author	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
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	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
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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.
	Address
	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	Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M.
	Title	Distribution of lipid aldehydes in phase-separated membranes: A molecular dynamics study			Type	A1 Journal article
	Year	2022	Publication	Archives Of Biochemistry And Biophysics	Abbreviated Journal	Arch Biochem Biophys
	Volume	717	Issue		Pages	109136
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	It is well established that lipid aldehydes (LAs) are able to increase the permeability of cell membranes and induce their rupture. However, it is not yet clear how LAs are distributed in phase-separated membranes (PSMs), which are responsible for the transport of selected molecules and intracellular signaling. Thus, we investigate here the distribution of LAs in a PSM by coarse-grained molecular dynamics simulations. Our results reveal that LAs derived from mono-unsaturated lipids tend to accumulate at the interface between the liquid-ordered/liquiddisordered domains, whereas those derived from poly-unsaturated lipids remain in the liquid-disordered domain. These results are important for understanding the effects caused by oxidized lipids in membrane structure, properties and organization.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000767632000001	Publication Date	2022-01-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-9861	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	3.9	Times cited		Open Access	OpenAccess
	Notes	We thank the University of Antwerp and the Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted. The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerpen.			Approved	Most recent IF: 3.9
	Call Number	PLASMANT @ plasmant @c:irua:185874			Serial	6905
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	Author	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.
	Address
	Corporate Author				Thesis
	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 ; CoordenaÃ§Ã£o de AperfeiÃ§oamento 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	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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	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
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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	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
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	Author	Yusupov, M.; Privat-Maldonado, A.; Cordeiro, R.M.; Verswyvel, H.; Shaw, P.; Razzokov, J.; Smits, E.; Bogaerts, A.
	Title	Oxidative damage to hyaluronan–CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy			Type	A1 Journal article
	Year	2021	Publication	Redox Biology	Abbreviated Journal	Redox Biol
	Volume	43	Issue		Pages	101968
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract	Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44–HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44–HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44–HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000657371800005	Publication Date	2021-04-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2213-2317	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.337	Times cited		Open Access	OpenAccess
	Notes	Fwo; The authors acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA, where all computational work was performed.			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:177780			Serial	6750
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	Author	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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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000865431800010	Publication Date	2022-08-25
	Series Editor		Series Title		Abbreviated Series Title
	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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