NANOlab Center of Excellence literature database -- Query Results

	NANOlab Center of Excellence literature database Home \| Show All \| Simple Search \| Advanced Search	Login Quick Search: Field: contains: ...
	31–59 of 59 records found matching your query (RSS \| history):

Select All Deselect All

<< 1 2 >>

List View

Citations

Details

	Records
	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	Han, I.; Song, I.S.; Choi, S.A.; Lee, T.; Yusupov, M.; Shaw, P.; Bogaerts, A.; Choi, E.H.; Ryu, J.J.
	Title	Bioactive Nonthermal Biocompatible Plasma Enhances Migration on Human Gingival Fibroblasts			Type	A1 Journal article
	Year	2023	Publication	Advanced healthcare materials	Abbreviated Journal
	Volume	12	Issue	4	Pages	2200527
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	This study hypothesizes that the application of low-dose nonthermal biocompatible dielectric barrier discharge plasma (DBD-NBP) to human gingival fibroblasts (HGFs) will inhibit colony formation but not cell death and induce matrix metalloproteinase (MMP) expression, extracellular matrix (ECM) degradation, and subsequent cell migration, which can result in enhanced wound healing. HGFs treated with plasma for 3 min migrate to each other across the gap faster than those in the control and 5-min treatment groups on days 1 and 3. The plasma-treated HGFs show significantly high expression levels of the cell cycle arrest-related p21 gene and enhanced MMP activity. Focal adhesion kinase (FAK) mediated attenuation of wound healing or actin cytoskeleton rearrangement, and plasma-mediated reversal of this attenuation support the migratory effect of DBD-NBP. Further, this work performs computer simulations to investigate the effect of oxidation on the stability and conformation of the catalytic kinase domain (KD) of FAK. It is found that the oxidation of highly reactive amino acids (AAs) Cys427, Met442, Cys559, Met571, Met617, and Met643 changes the conformation and increases the structural flexibility of the FAK protein and thus modulates its function and activity. Low-dose DBD-NBP-induces host cell cycle arrest, ECM breakdown, and subsequent migration, thus contributing to the enhanced wound healing process.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000897762100001	Publication Date	2022-11-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2192-2640	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	10	Times cited		Open Access	OpenAccess
	Notes	National Research Foundation of Korea; Kementerian Pendidikan, 2020R1I1A1A01073071 2021R1A6A1A03038785 ;			Approved	Most recent IF: 10; 2023 IF: 5.11
	Call Number	PLASMANT @ plasmant @c:irua:192804			Serial	7242
Permanent link to this record



	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
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	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
Permanent link to this record



	Author	Ghasemitarei, M.; Ghorbi, T.; Yusupov, M.; Zhang, Y.; Zhao, T.; Shali, P.; Bogaerts, A.
	Title	Effects of Nitro-Oxidative Stress on Biomolecules: Part 1—Non-Reactive Molecular Dynamics Simulations			Type	A1 Journal Article
	Year	2023	Publication	Biomolecules	Abbreviated Journal	Biomolecules
	Volume	13	Issue	9	Pages	1371
	Keywords	A1 Journal Article; plasma medicine; reactive oxygen and; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001071356400001	Publication Date	2023-09-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2218-273X	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	This research received no external funding.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:200380			Serial	8958
Permanent link to this record



	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	Yusupov, M.; Neyts, E.C.; Khalilov, U.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A.
	Title	Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls			Type	A1 Journal article
	Year	2012	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	14	Issue	9	Pages	093043
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. CO, CN and CC bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000309393400001	Publication Date	2012-09-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	47	Open Access
	Notes				Approved	Most recent IF: 3.786; 2012 IF: 4.063
	Call Number	UA @ lucian @ c:irua:101014			Serial	189
Permanent link to this record



	Author	Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A.
	Title	Behavior of electrons in a dual-magnetron sputter deposition system : a Monte Carlo model			Type	A1 Journal article
	Year	2011	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	13	Issue		Pages	033018-033018,17
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	A Monte Carlo model has been developed for investigating the electron behavior in a dual-magnetron sputter deposition system. To describe the three-dimensional (3D) geometry, different reference frames, i.e. a local and a global coordinate system, were used. In this study, the influence of both closed and mirror magnetic field configurations on the plasma properties is investigated. In the case of a closed magnetic field configuration, the calculated electron trajectories show that if an electron is emitted in (or near) the center of the cathode, where the influence of the magnetic field is low, it is able to travel from one magnetron to the other. On the other hand, when an electron is created at the race track area, it is more or less trapped in the strong magnetic field and cannot easily escape to the second magnetron region. In the case of a mirror magnetic field configuration, irrespective of where the electron is emitted from the cathode, it cannot travel from one magnetron to the other because the magnetic field lines guide the electron to the substrate. Moreover, the electron density and electron impact ionization rate have been calculated and studied in detail for both configurations.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000289064600001	Publication Date	2011-03-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	12	Open Access
	Notes				Approved	Most recent IF: 3.786; 2011 IF: 4.177
	Call Number	UA @ lucian @ c:irua:87544			Serial	224
Permanent link to this record



	Author	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
Permanent link to this record



	Author	Neyts, E.C.; Yusupov, M.; Verlackt, C.C.; Bogaerts, A.
	Title	Computer simulations of plasmabiomolecule and plasmatissue interactions for a better insight in plasma medicine			Type	A1 Journal article
	Year	2014	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	47	Issue	29	Pages	293001
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficultif not impossibleto obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasmabiomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance the field.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000338860300001	Publication Date	2014-06-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727;1361-6463;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	28	Open Access
	Notes				Approved	Most recent IF: 2.588; 2014 IF: 2.721
	Call Number	UA @ lucian @ c:irua:117853			Serial	472
Permanent link to this record



	Author	Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A.
	Title	Elucidating the asymmetric behavior of the discharge in a dual magnetron sputter deposition system			Type	A1 Journal article
	Year	2011	Publication	Applied physics letters	Abbreviated Journal	Appl Phys Lett
	Volume	98	Issue	13	Pages	131502-131502,3
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	A magnetron discharge is characterized by drifts of the charged particles guiding center, caused by the magnetic field, in contrast to unmagnetized discharges. Because of these drifts, a pronounced asymmetry of the discharge can be observed in a dual magnetron setup. In this work, it is found that the shape of the discharge in a dual magnetron configuration depends on the magnetic field configuration. In a closed configuration, strong drifts were observed in one preferential direction, whereas in a mirror configuration the deflection of the discharge was not so pronounced. Our calculations confirm experimental observations.
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000289153600017	Publication Date	2011-04-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-6951;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.411	Times cited	4	Open Access
	Notes				Approved	Most recent IF: 3.411; 2011 IF: 3.844
	Call Number	UA @ lucian @ c:irua:87867			Serial	1026
Permanent link to this record



	Author	Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C.
	Title	How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations			Type	A1 Journal article
	Year	2015	Publication	Biointerphases	Abbreviated Journal	Biointerphases
	Volume	10	Issue	10	Pages	029501
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000357195600019	Publication Date	2014-12-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1934-8630;1559-4106;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.603	Times cited	10	Open Access
	Notes				Approved	Most recent IF: 2.603; 2015 IF: 3.374
	Call Number	c:irua:121371			Serial	1492
Permanent link to this record



	Author	Yusupov, M.; Neyts, E.C.; Verlackt, C.C.; Khalilov, U.; van Duin, A.C.T.; Bogaerts, A.
	Title	Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species : a reactive molecular dynamics study			Type	A1 Journal article
	Year	2015	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	12	Issue	12	Pages	162-171
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Reactive molecular dynamics simulations are performed to study the interaction of reactive oxygen species, such as OH, HO2 and H2O2, with the endotoxic biomolecule lipid A of the gram-negative bacterium Escherichia coli. It is found that the aforementioned plasma species can destroy the lipid A, which consequently results in reducing its toxic activity. All bond dissociation events are initiated by hydrogen-abstraction reactions. However, the mechanisms behind these dissociations are dependent on the impinging plasma species, i.e. a clear difference is observed in the mechanisms upon impact of HO2 radicals and H2O2 molecules on one hand and OH radicals on the other hand. Our simulation results are in good agreement with experimental observations.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Weinheim	Editor
	Language		Wos	000350275400005	Publication Date	2014-09-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1612-8850;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.846	Times cited	18	Open Access
	Notes				Approved	Most recent IF: 2.846; 2015 IF: 2.453
	Call Number	c:irua:123540			Serial	1589
Permanent link to this record



	Author	Bogaerts, A.; Aerts, R.; Snoeckx, R.; Somers, W.; Van Gaens, W.; Yusupov, M.; Neyts, E.
	Title	Modeling of plasma and plasma-surface interactions for medical, environmental and nano applications			Type	A1 Journal article
	Year	2012	Publication	Journal of physics : conference series	Abbreviated Journal
	Volume	399	Issue		Pages	012011
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this paper, an overview is given of modeling investigations carried out in our research group for a better understanding of plasmas used for medical, environmental and nano applications. The focus is both on modeling the plasma chemistry and the plasma-surface interactions. The plasma chemistry provides the densities and fluxes of the important plasma species. This information can be used as input when modeling the plasma-surface interactions. The combination of plasma simulations and plasma – surface interaction simulations provides a more comprehensive understanding of the underlying processes for these applications.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000312261700011	Publication Date	2012-11-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1742-6588;1742-6596;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited	7	Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:104727			Serial	2130
Permanent link to this record



	Author	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	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	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	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	Tit, N.; Al Ezzi, M.M.; Abdullah, H.M.; Yusupov, M.; Kouser, S.; Bahlouli, H.; Yamani, Z.H.
	Title	Detection of CO2 using CNT-based sensors: Role of Fe catalyst on sensitivity and selectivity			Type	A1 Journal article
	Year	2017	Publication	Materials chemistry and physics	Abbreviated Journal	Mater Chem Phys
	Volume	186	Issue	186	Pages	353-364
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The adsorption of CO2 on surfaces of graphene and carbon nanotubes (CNTs), decorated with Fe atoms, are investigated using the self-consistent-charge density-functional tight-binding (SCC-DFTB) method, neglecting the heat effects. Fe ad-atoms are more stable when they are dispersed on hollow sites. They introduce a large density of states at the Fermi level (N-F); where keeping such density low would help in gas sensing. Furthermore, the Fe ad-atom can weaken the C=O double bonds of the chemisorbed CO2 molecule, paving the way for oxygen atoms to drain more charges from Fe. Consequently, chemisorption of CO2 molecules reduces both N-F and the conductance while it enhances the sensitivity with the increasing gas dose. Conducting armchair CNTs (ac-CNTs) have higher sensitivity than graphene and semiconducting zigzag CNTs (zz-CNT5). Comparative study of sensitivity of ac-CNT-Fe composite towards various gases (e.g., O-2, N-2, H-2, H2O, CO and CO2) has shown high sensitivity and selectivity towards CO, CO2 and H2O gases. (C) 2016 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Lausanne	Editor
	Language		Wos	000390621200044	Publication Date	2016-11-04
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0254-0584	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.084	Times cited	17	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 2.084
	Call Number	UA @ lucian @ c:irua:140333			Serial	4465
Permanent link to this record



	Author	Van der Paal, J.; Hong, S.-H.; Yusupov, M.; Gaur, N.; Oh, J.-S.; Short, R.D.; Szili, E.J.; Bogaerts, A.
	Title	How membrane lipids influence plasma delivery of reactive oxygen species into cells and subsequent DNA damage : an experimental and computational study			Type	A1 Journal article
	Year	2019	Publication	Physical chemistry, chemical physics	Abbreviated Journal	Phys Chem Chem Phys
	Volume	21	Issue	35	Pages	19327-19341
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000486175400045	Publication Date	2019-08-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1463-9076; 1463-9084	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.123	Times cited	1	Open Access
	Notes				Approved	Most recent IF: 4.123
	Call Number	UA @ admin @ c:irua:162782			Serial	6303
Permanent link to this record



	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.
	Address
	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
Permanent link to this record



	Author	Khalilov, U.; Uljayev, U.; Mehmonov, K.; Nematollahi, P.; Yusupov, M.; Neyts, E.C.; Neyts, E.C.
	Title	Can endohedral transition metals enhance hydrogen storage in carbon nanotubes?			Type	A1 Journal article
	Year	2024	Publication	International journal of hydrogen energy	Abbreviated Journal
	Volume	55	Issue		Pages	640-610
	Keywords	A1 Journal article; Engineering sciences. Technology; Modelling and Simulation in Chemistry (MOSAIC); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The safe and efficient use of hydrogen energy, which is in high demand worldwide today, requires efficient hydrogen storage. Despite significant advances in hydrogen storage using carbon-based nanomaterials, including carbon nanotubes (CNTs), efforts to substantially increase the storage capacity remain less effective. In this work, we demonstrate the effect of endohedral transition metal atoms on the hydrogen storage capacity of CNTs using reactive molecular dynamics simulations. We find that an increase in the volume fraction of endohedral nickel atoms leads to an increase in the concentration of physisorbed hydrogen molecules around single-walled CNTs (SWNTs) by approximately 1.6 times compared to pure SWNTs. The obtained results provide insight into the underlying mechanisms of how endohedral transition metal atoms enhance the hydrogen storage ability of SWNTs under nearly ambient conditions.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001142427400001	Publication Date	2023-11-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0360-3199	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	7.2	Times cited		Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 7.2; 2024 IF: 3.582
	Call Number	UA @ admin @ c:irua:202315			Serial	9006
Permanent link to this record



	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	2.1	Times cited		Open Access
	Notes				Approved	Most recent IF: 2.1; 2023 IF: 1.254
	Call Number	UA @ admin @ c:irua:199261			Serial	9027
Permanent link to this record



	Author	Rezaei, M.; Ghasemitarei, M.; Razzokov, J.; Yusupov, M.; Ghorbanalilu, M.; Ejtehadi, M.R.
	Title	In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel			Type	A1 Journal article
	Year	2024	Publication	Archives of biochemistry and biophysics	Abbreviated Journal
	Volume	751	Issue		Pages	109835-109837
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g., by cold atmospheric plasma (CAP)) on the pyruvate (Pyr) uptake by VDAC1. Inhibiting Pyr uptake through VDAC1 can suppress cancer cell proliferation. Our primary target was to study the translocation of Pyr across the native and oxidized forms of hVDAC1, the human VDAC1. Specifically, we employed MD simulations to analyze the hVDAC1 structure by modifying certain cysteine residues to cysteic acids and methionine residues to methionine sulfoxides, which allowed us to investigate the effect of oxidation. Our results showed that the free energy barrier for Pyr translocation through the native and oxidized channel was approximately 4.3 +/- 0.7 kJ mol-1 and 10.8 +/- 1.8 kJ mol-1, respectively. An increase in barrier results in a decrease in rate of Pyr permeation through the oxidized channel. Thus, our results indicate that low levels of CAP oxidation reduce Pyr translocation, resulting in decreased cancer cell proliferation. Therefore, low levels of oxidation are likely sufficient to treat cancer cells given the inhibition of Pyr uptake.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001127850500001	Publication Date	2023-11-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-9861; 1096-0384	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	3.9	Times cited		Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 3.9; 2024 IF: 3.165
	Call Number	UA @ admin @ c:irua:202185			Serial	9046
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	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