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	Author	Elmonov, A.A.; Yusupov, M.S.; Dzhurakhalov, A.A.; Bogaerts, A.
	Title	Sputtering of Si(001) and SiC(001) by grazing ion bombardment			Type	P1 Proceeding
	Year	2008	Publication		Abbreviated Journal
	Volume		Issue		Pages	209-213
	Keywords	P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The peculiarities of sputtering processes at 0.5-5 keV Ne grazing ion bombardment of Si(001) and SiC(001) surfaces and their possible application for the surface modification have been studied by computer simulation. Sputtering yields in the primary knock-on recoil atoms regime versus the initial energy of incident ions (E(0) = 0.5-5 keV) and angle of incidence (psi = 0-30 degrees) counted from a target surface have been calculated. Comparative studies of layer-by-layer sputtering for Si(001) and SiC(001) surfaces versus the initial energy of incident ions as well as an effective sputtering and sputtering threshold are discussed.
	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	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	Laroussi, M.; Bekeschus, S.; Keidar, M.; Bogaerts, A.; Fridman, A.; Lu, X.; Ostrikov, K.; Hori, M.; Stapelmann, K.; Miller, V.; Reuter, S.; Laux, C.; Mesbah, A.; Walsh, J.; Jiang, C.; Thagard, S.M.; Tanaka, H.; Liu, D.; Yan, D.; Yusupov, M.
	Title	Low-Temperature Plasma for Biology, Hygiene, and Medicine: Perspective and Roadmap			Type	A1 Journal article
	Year	2022	Publication	IEEE transactions on radiation and plasma medical sciences	Abbreviated Journal	IEEE Trans. Radiat. Plasma Med. Sci.
	Volume	6	Issue	2	Pages	127-157
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma, the fourth and most pervasive state of matter in the visible universe, is a fascinating medium that is connected to the beginning of our universe itself. Man-made plasmas are at the core of many technological advances that include the fabrication of semiconductor devices, which enabled the modern computer and communication revolutions. The introduction of low temperature, atmospheric pressure plasmas to the biomedical field has ushered a new revolution in the healthcare arena that promises to introduce plasma-based therapies to combat some thorny and long-standing medical challenges. This article presents an overview of where research is at today and discusses innovative concepts and approaches to overcome present challenges and take the field to the next level. It is written by a team of experts who took an in-depth look at the various applications of plasma in hygiene, decontamination, and medicine, made critical analysis, and proposed ideas and concepts that should help the research community focus their efforts on clear and practical steps necessary to keep the field advancing for decades to come.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000750257400005	Publication Date	2021-12-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2469-7311	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	Research Foundation—Flanders, 1200219N ;			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:185875			Serial	6907
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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	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
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	Author	Ghasemitarei, M.; Ghorbi, T.; Yusupov, M.; Zhang, Y.; Zhao, T.; Shali, P.; Bogaerts, A.
	Title	Effects of Nitro-Oxidative Stress on Biomolecules: Part 1—Non-Reactive Molecular Dynamics Simulations			Type	A1 Journal Article
	Year	2023	Publication	Biomolecules	Abbreviated Journal	Biomolecules
	Volume	13	Issue	9	Pages	1371
	Keywords	A1 Journal Article; plasma medicine; reactive oxygen and; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes.
	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
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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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000449722100002	Publication Date	2018-07-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2213-2317	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.337	Times cited		Open Access	OpenAccess
	Notes	M.Y. and N.K. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grant nos. 1200216N and 12J5617N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI). C.M acknowledges the financial support provided by the Flemish Community and the University of Antwerp (BOF-NOI) for the pre-doctoral scholarship is under grant number/project ID: 28465. S.V.D., S. D. and Z.H. acknowledge the FWO (Grant G.0687.13) and the GOA-BOF UA 2013–2016 (project-ID 28312) for funding. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI.			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:152818			Serial	5006
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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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000657371800005	Publication Date	2021-04-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2213-2317	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.337	Times cited		Open Access	OpenAccess
	Notes	Fwo; The authors acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA, where all computational work was performed.			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:177780			Serial	6750
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	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
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	Author	Bogaerts, A.; Yusupov, M.; Razzokov, J.; Van der Paal, J.
	Title	Plasma for cancer treatment: How can RONS penetrate through the cell membrane? Answers from computer modeling			Type	A1 Journal article
	Year	2019	Publication	Frontiers of Chemical Science and Engineering	Abbreviated Journal	Front Chem Sci Eng
	Volume		Issue		Pages
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma is gaining increasing interest for cancer treatment, but the underlying mechanisms are not yet fully understood. Using computer simulations at the molecular level, we try to gain better insight in how plasma-generated reactive oxygen and nitrogen species (RONS) can penetrate through the cell membrane. Speciﬁcally, we compare the permeability of various (hydrophilic and hydrophobic) RONS across both oxidized and nonoxidized cell membranes. We also study pore formation, and how it is hampered by higher concentrations of cholesterol in the cell membrane, and we illustrate the much higher permeability of H2O2 through aquaporin channels. Both mechanisms may explain the selective cytotoxic effect of plasma towards cancer cells. Finally, we also discuss the synergistic effect of plasma-induced oxidation and electric ﬁelds towards pore formation. Keywords plasma medicine, cancer treatment, computer modelling, cell membrane, reactive oxygen and nitrogen species
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000468848400004	Publication Date	2019-03-22
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2095-0179	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.712	Times cited	5	Open Access	Not_Open_Access: Available from 23.05.2020
	Notes	We acknowledge ﬁnancial support from the Research Foundation–Flanders (FWO; Grant Nos. 1200216N and 11U5416N). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. We are also very thankful to R. Cordeiro for the very interesting discussions.			Approved	Most recent IF: 1.712
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:159977			Serial	5172
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	Author	Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A.
	Title	Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma			Type	A1 Journal article
	Year	2021	Publication	Cancers	Abbreviated Journal	Cancers
	Volume	13	Issue	3	Pages	579
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE)
	Abstract	Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000614960600001	Publication Date	2021-02-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2072-6694	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:176455			Serial	6709
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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	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	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	Attri, P.; Yusupov, M.; Park, J.H.; Lingamdinne, L.P.; Koduru, J.R.; Shiratani, M.; Choi, E.H.; Bogaerts, A.
	Title	Mechanism and comparison of needle-type non-thermal direct and indirect atmospheric pressure plasma jets on the degradation of dyes			Type	A1 Journal article
	Year	2016	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	6	Issue	6	Pages	34419
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Purified water supply for human use, agriculture and industry is the major global priority nowadays. The advanced oxidation process based on atmospheric pressure non-thermal plasma (NTP) has been used for purification of wastewater, although the underlying mechanisms of degradation of organic pollutants are still unknown. In this study we employ two needle-type atmospheric pressure non-thermal plasma jets, i.e., indirect (ID-APPJ) and direct (D-APPJ) jets operating at Ar feed gas, for the treatment of methylene blue, methyl orange and congo red dyes, for two different times (i.e., 20 min and 30 min). Specifically, we study the decolorization/degradation of all three dyes using the above mentioned plasma sources, by means of UV-Vis spectroscopy, HPLC and a density meter. We also employ mass spectroscopy to verify whether only decolorization or also degradation takes place after treatment of the dyes by the NTP jets. Additionally, we analyze the interaction of OH radicals with all three dyes using reactive molecular dynamics simulations, based on the density functional-tight binding method. This investigation represents the first report on the degradation of these three different dyes by two types of NTP setups, analyzed by various methods, and based on both experimental and computational studies.
	Address	Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Wos	000385172300001	Publication Date	2016-10-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	23	Open Access
	Notes	We gratefully acknowledge the grant received from the SRC program of the National Research Foundation of Korea (NRF), funded by the Korean Government (MEST) (No. 20100029418). PA is thankful to FY 2015 Japan Society for the Promotion of Science (JSPS) invitation fellowship. This work was partly supported by MEXT KAKENHI Grant Number 24108009 and JSPS KAKENHI Grant Number JP16H03895. M. Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @ c:irua:135847			Serial	4283
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	Author	Yusupov, M.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A.
	Title	Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments			Type	A1 Journal article
	Year	2017	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	7	Issue	7	Pages	5761
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000405746500072	Publication Date	2017-07-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	27	Open Access	OpenAccess
	Notes	M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216 N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. S.R. and S.K. acknowledge funding by the BMBF (FKZ: 03Z2DN12). S.R. acknowledges funding by the Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern (AU 15001). The authors thank M. Hammer for the support and discussion in the biophysical studies and J. Van der Paal for the interesting discussions.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @ c:irua:144627			Serial	4630
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	Author	Razzokov, J.; Yusupov, M.; Bogaerts, A.
	Title	Oxidation destabilizes toxic amyloid beta peptide aggregation			Type	A1 Journal article
	Year	2019	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	9	Issue	1	Pages	5476
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000462990000018	Publication Date	2019-04-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	5	Open Access	OpenAccess
	Notes	M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant 1200216N and 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA.			Approved	Most recent IF: 4.259
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:159367			Serial	5182
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	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	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
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	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
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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	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	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
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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	Razzokov, J.; Yusupov, M.; Vanuytsel, S.; Neyts, E.C.; Bogaerts, A.
	Title	Phosphatidylserine flip-flop induced by oxidation of the plasma membrane: a better insight by atomic scale modeling			Type	A1 Journal article
	Year	2017	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	14	Issue	10	Pages	1700013
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000413045800010	Publication Date	2017-04-05
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1612-8850	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.846	Times cited	9	Open Access	Not_Open_Access
	Notes	Fonds Wetenschappelijk Onderzoek, 1200216N ;			Approved	Most recent IF: 2.846
	Call Number	PLASMANT @ plasmant @c:irua:149567			Serial	4910
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	Author	Yusupov, M.; Lackmann, J.-W.; Razzokov, J.; Kumar, S.; Stapelmann, K.; Bogaerts, A.
	Title	Impact of plasma oxidation on structural features of human epidermal growth factor			Type	A1 Journal article
	Year	2018	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	15	Issue	8	Pages	1800022
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We perform computer simulations supported by experiments to investigate the oxidation of an important signaling protein, that is, human epidermal growth factor (hEGF), caused by cold atmospheric plasma (CAP) treatment. Specifically, we study the conformational changes of hEGF with different degrees of oxidation, to mimic short and long CAP treatment times. Our results indicate that the oxidized structures become more flexible, due to their conformational changes and breakage of the disulfide bonds, especially at higher oxidation degrees. MM/GBSA calculations reveal that an increasing oxidation level leads to a lower binding free energy of hEGF with its receptor. These results help to understand the fundamentals of the use of CAP for wound healing versus cancer treatment at short and longer treatment times.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000441895700004	Publication Date	2018-05-07
	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	7	Open Access	Not_Open_Access
	Notes	Fonds Wetenschappelijk Onderzoek, 1200216N ; Bundesministerium für Bildung und Forschung, 03Z22DN12 ;			Approved	Most recent IF: 2.846
	Call Number	PLASMANT @ plasmant @c:irua:152815			Serial	5008
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	Author	Duan, J.; Ma, M.; Yusupov, M.; Cordeiro, R.M.; Lu, X.; Bogaerts, A.
	Title	The penetration of reactive oxygen and nitrogen species across the stratum corneum			Type	A1 Journal article
	Year	2020	Publication	Plasma Processes And Polymers	Abbreviated Journal	Plasma Process Polym
	Volume		Issue		Pages
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The penetration of reactive oxygen and nitrogen species (RONS) across the stratum corneum (SC) is a necessary and crucial process in many skin‐related plasma medical applications. To gain more insights into this penetration behavior, we combined experimental measurements of the permeability of dry and moist SC layers with computer simulations of model lipid membranes. We measured the permeation of relatively stable molecules, which are typically generated by plasma, namely H2O2, NO3−, and NO2−. Furthermore, we calculated the permeation free energy profiles of the major plasma‐generated RONS and their derivatives (i.e., H2O2, OH, HO2, O2, O3, NO, NO2, N2O4, HNO2, HNO3, NO2−, and NO3−) across native and oxidized SC lipid bilayers, to understand the mechanisms of RONS permeation across the SC. Our results indicate that hydrophobic RONS (i.e., NO, NO2, O2, O3, and N2O4) can translocate more easily across the SC lipid bilayer than hydrophilic RONS (i.e., H2O2, OH, HO2, HNO2, and HNO3) and ions (i.e., NO2− and NO3−) that experience much higher permeation barriers. The permeability of RONS through the SC skin lipids is enhanced when the skin is moist and the lipids are oxidized. These findings may help to understand the underlying mechanisms of plasma interaction with a biomaterial and to optimize the environmental parameters in practice in plasma medical applications.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000536892900001	Publication Date	2020-06-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1612-8850	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.5	Times cited		Open Access
	Notes	National Natural Science Foundation of China, 51625701 51977096 ; Fonds Wetenschappelijk Onderzoek, 1200219N ; China Scholarship Council, 201806160128 ; M. Y. acknowledges the Research Foundation Flanders (FWO) for financial support (Grant No. 1200219N). This study was partially supported by the National Natural Science Foundation of China (Grant No: 51625701 and 51977096) and the China Scholarship Council (Grant No: 201806160128). All computational work was performed using the Turing HPC infrastructure at the CalcUA Core Facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UA.			Approved	Most recent IF: 3.5; 2020 IF: 2.846
	Call Number	PLASMANT @ plasmant @c:irua:169709			Serial	6372
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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	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		Times cited		Open Access
	Notes				Approved	no
	Call Number	UA @ admin @ c:irua:205512			Serial	9181
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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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