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Author Attri, P.; Bogaerts, A. pdf  url
doi  openurl
  Title Perspectives of Plasma-treated Solutions as Anticancer Drugs Type A1 Journal article
  Year 2019 Publication Anti-cancer agents in medicinal chemistry Abbreviated Journal Anti-Cancer Agent Me  
  Volume 19 Issue 4 Pages 436-438  
  Keywords (up) A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000472726300001 Publication Date 2019-06-26  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1871-5206 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.598 Times cited 2 Open Access Not_Open_Access  
  Notes Approved Most recent IF: 2.598  
  Call Number PLASMANT @ plasmant @UA @ admin @ c:irua:160694 Serial 5189  
Permanent link to this record
 

 
Author Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R. url  doi
openurl 
  Title Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations Type A1 Journal article
  Year 2022 Publication Journal Of Chemical Information And Modeling Abbreviated Journal J Chem Inf Model  
  Volume 62 Issue 1 Pages 129-141  
  Keywords (up) A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000740019000001 Publication Date 2022-01-10  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1549-9596 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 5.6 Times cited Open Access Not_Open_Access  
  Notes Fonds Wetenschappelijk Onderzoek, 1200219N ; Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. Approved Most recent IF: 5.6  
  Call Number PLASMANT @ plasmant @c:irua:185485 Serial 7050  
Permanent link to this record
 

 
Author Lin, A.; Biscop, E.; Gorbanev, Y.; Smits, E.; Bogaerts, A. pdf  url
doi  openurl
  Title Toward defining plasma treatment dose : the role of plasma treatment energy of pulsed‐dielectric barrier discharge in dictating in vitro biological responses Type A1 Journal article
  Year 2022 Publication Plasma Processes And Polymers Abbreviated Journal Plasma Process Polym  
  Volume 19 Issue 3 Pages e2100151  
  Keywords (up) A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract The energy dependence of a pulsed-dielectric barrier discharge (DBD) plasma treatment on chemical species production and biological responses was investigated. We hypothesized that the total plasma energy delivered during treatment encompasses the influence of major application parameters. A microsecond-pulsed DBD system was used to treat three different cancer cell lines and cell viability was analyzed. The energy per pulse was measured and the total plasma treatment energy was controlled by adjusting the pulse frequency, treatment time, and application distance. Our data suggest that the delivered plasma energy plays a predominant role in stimulating a biological response in vitro. This study aids in developing steps toward defining a plasma treatment unit and treatment dose for biomedical and clinical research.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000711907800001 Publication Date 2021-10-28  
  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 Approved Most recent IF: 3.5  
  Call Number UA @ admin @ c:irua:182916 Serial 7219  
Permanent link to this record
 

 
Author Van Loenhout, J.; Peeters, M.; Bogaerts, A.; Smits, E.; Deben, C. pdf  url
doi  openurl
  Title Oxidative Stress-Inducing Anticancer Therapies: Taking a Closer Look at Their Immunomodulating Effects Type A1 Journal article
  Year 2020 Publication Antioxidants Abbreviated Journal Antioxidants  
  Volume 9 Issue 12 Pages 1188  
  Keywords (up) A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)  
  Abstract Cancer cells are characterized by higher levels of reactive oxygen species (ROS) compared to normal cells as a result of an imbalance between oxidants and antioxidants. However, cancer cells maintain their redox balance due to their high antioxidant capacity. Recently, a high level of oxidative stress is considered a novel target for anticancer therapy. This can be induced by increasing exogenous ROS and/or inhibiting the endogenous protective antioxidant system. Additionally, the immune system has been shown to be a significant ally in the fight against cancer. Since ROS levels are important to modulate the antitumor immune response, it is essential to consider the effects of oxidative stress-inducing treatments on this response. In this review, we provide an overview of the mechanistic cellular responses of cancer cells towards exogenous and endogenous ROS-inducing treatments, as well as the indirect and direct antitumoral immune effects, which can be both immunostimulatory and/or immunosuppressive. For future perspectives, there is a clear need for comprehensive investigations of different oxidative stress-inducing treatment strategies and their specific immunomodulating effects, since the effects cannot be generalized over different treatment modalities. It is essential to elucidate all these underlying immune effects to make oxidative stress-inducing treatments effective anticancer therapy.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000602288600001 Publication Date 2020-11-27  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2076-3921 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 7 Times cited Open Access  
  Notes This research was funded by the Olivia Hendrickx Research Fund (21OCL06) and the University of Antwerp (FFB160231). Approved Most recent IF: 7; 2020 IF: NA  
  Call Number PLASMANT @ plasmant @c:irua:173865 Serial 6441  
Permanent link to this record
 

 
Author Shaw, P.; Kumar, N.; Sahun, M.; Smits, E.; Bogaerts, A.; Privat-Maldonado, A. url  doi
openurl 
  Title Modulating the Antioxidant Response for Better Oxidative Stress-Inducing Therapies: How to Take Advantage of Two Sides of the Same Medal? Type A1 Journal article
  Year 2022 Publication Biomedicines Abbreviated Journal Biomedicines  
  Volume 10 Issue 4 Pages 823  
  Keywords (up) A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)  
  Abstract Oxidative stress-inducing therapies are characterized as a specific treatment that involves the production of reactive oxygen and nitrogen species (RONS) by external or internal sources. To protect cells against oxidative stress, cells have evolved a strong antioxidant defense system to either prevent RONS formation or scavenge them. The maintenance of the redox balance ensures signal transduction, development, cell proliferation, regulation of the mechanisms of cell death, among others. Oxidative stress can beneficially be used to treat several diseases such as neurodegenerative disorders, heart disease, cancer, and other diseases by regulating the antioxidant system. Understanding the mechanisms of various endogenous antioxidant systems can increase the therapeutic efficacy of oxidative stress-based therapies, leading to clinical success in medical treatment. This review deals with the recent novel findings of various cellular endogenous antioxidant responses behind oxidative stress, highlighting their implication in various human diseases, such as ulcers, skin pathologies, oncology, and viral infections such as SARS-CoV-2.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000785420400001 Publication Date 2022-03-31  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2227-9059 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor Times cited Open Access OpenAccess  
  Notes Science and Engineering Research Board (SERB), Core Research Grant, Department of Science and Technology, India., (CRG/2021/001935) ; Department of Biotechnology, BT/RLF/Re-entry/27/2019 ; We are grateful to Charlotta Bengtson for her valuable input. Approved Most recent IF: NA  
  Call Number PLASMANT @ plasmant @c:irua:187931 Serial 7051  
Permanent link to this record
 

 
Author De Backer, J.; Maric, D.; Zuhra, K.; Bogaerts, A.; Szabo, C.; Vanden Berghe, W.; Hoogewijs, D. url  doi
openurl 
  Title Cytoglobin Silencing Promotes Melanoma Malignancy but Sensitizes for Ferroptosis and Pyroptosis Therapy Response Type A1 Journal article
  Year 2022 Publication Antioxidants Abbreviated Journal Antioxidants  
  Volume 11 Issue 8 Pages 1548  
  Keywords (up) A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)  
  Abstract Despite recent advances in melanoma treatment, there are still patients that either do not respond or develop resistance. This unresponsiveness and/or acquired resistance to therapy could be explained by the fact that some melanoma cells reside in a dedifferentiated state. Interestingly, this dedifferentiated state is associated with greater sensitivity to ferroptosis, a lipid peroxidation-reliant, iron-dependent form of cell death. Cytoglobin (CYGB) is an iron hexacoordinated globin that is highly enriched in melanocytes and frequently downregulated during melanomagenesis. In this study, we investigated the potential effect of CYGB on the cellular sensitivity towards (1S, 3R)-RAS-selective lethal small molecule (RSL3)-mediated ferroptosis in the G361 melanoma cells with abundant endogenous expression. Our findings show that an increased basal ROS level and higher degree of lipid peroxidation upon RSL3 treatment contribute to the increased sensitivity of CYGB knockdown G361 cells to ferroptosis. Furthermore, transcriptome analysis demonstrates the enrichment of multiple cancer malignancy pathways upon CYGB knockdown, supporting a tumor-suppressive role for CYGB. Remarkably, CYGB knockdown also triggers activation of the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome and subsequent induction of pyroptosis target genes. Altogether, we show that silencing of CYGB expression modulates cancer therapy sensitivity via regulation of ferroptosis and pyroptosis cell death signaling pathways.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000846411000001 Publication Date 2022-08-10  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2076-3921 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 7 Times cited Open Access OpenAccess  
  Notes Approved Most recent IF: 7  
  Call Number PLASMANT @ plasmant @c:irua:190686 Serial 7102  
Permanent link to this record
 

 
Author Slaets, J.; Loenders, B.; Bogaerts, A. pdf  url
doi  openurl
  Title Plasma-based dry reforming of CH4: Plasma effects vs. thermal conversion Type A1 Journal Article
  Year 2024 Publication Fuel Abbreviated Journal Fuel  
  Volume 360 Issue Pages 130650  
  Keywords (up) A1 Journal Article; Plasma kinetics Computer modelling Dry reforming of methane; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;  
  Abstract In this work we evaluate the chemical kinetics of dry reforming of methane in warm plasmas (1000–4000 K) using modelling with a newly developed chemistry set, for a broad range of parameters (temperature, power density and CO2/CH4 ratio). We compare the model against thermodynamic equilibrium concentrations, serving as validation of the thermal chemical kinetics. Our model reveals that plasma-specific reactions (i.e., electron impact collisions) accelerate the kinetics compared to thermal conversion, rather than altering the overall kinetics pathways and intermediate products, for gas temperatures below 2000 K. For higher temperatures, the kinetics are dominated by heavy species collisions and are strictly thermal, with negligible influence of the electrons and ions on the overall kinetics. When studying the effects of different gas mixtures on the kinetics, we identify important intermediate species, side reactions and side products. The use of excess CO2 leads to H2O formation, at the expense of H2 formation, and the CO2 conversion itself is limited, only approaching full conversion near 4000 K. In contrast, full conversion of both reactants is only kinetically limited for mixtures with excess CH4, which also gives rise to the formation of C2H2, alongside syngas. Within the given parameter space, our model predicts the 30/70 ratio of CO2/CH4 to be the most optimal for syngas formation with a H2/CO ratio of 2.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 001138077700001 Publication Date 2023-12-15  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0016-2361 ISBN Additional Links UA library record; WoS full record  
  Impact Factor 7.4 Times cited Open Access Not_Open_Access  
  Notes This research was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 810182 – SCOPE ERC Synergy project), the Catalisti-ICON project BluePlasma (Project No. HBC.2022.0445), the FWO-SBO project PlasMaCatDESIGN (FWO Grant ID S001619N), the Independent Research Fund Denmark (Project No. 0217-00231B) and through long-term structural funding (Methusalem). 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. We also thank Bart Wanten, Roel Michiels, Pepijn Heirman, Claudia Verheyen, dr. Senne Van Alphen, dr. Elise Vervloessem, dr. Kevin van ’t Veer, dr. Joshua Boothroyd, dr. Omar Biondo and dr. Eduardo Morais for their expertise and feedback regarding the kinetics scheme. Approved Most recent IF: 7.4; 2024 IF: 4.601  
  Call Number PLASMANT @ plasmant @c:irua:201669 Serial 8973  
Permanent link to this record
 

 
Author Herrebout, D.; Bogaerts, A.; Yan, M.; Goedheer, W.; Dekempeneer, E.; Gijbels, R. doi  openurl
  Title 1D fluid model for an rf methane plasma of interest in deposition of diamond-like carbon layers Type A1 Journal article
  Year 2001 Publication Journal of applied physics Abbreviated Journal J Appl Phys  
  Volume 90 Issue Pages 570-579  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher American Institute of Physics Place of Publication New York, N.Y. Editor  
  Language Wos 000169660000007 Publication Date 2002-07-26  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0021-8979; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.068 Times cited 83 Open Access  
  Notes Approved Most recent IF: 2.068; 2001 IF: 2.128  
  Call Number UA @ lucian @ c:irua:37250 c:irua:37250 c:irua:37250 c:irua:37250 Serial 2  
Permanent link to this record
 

 
Author Kolev, S.; Bogaerts, A. pdf  url
doi  openurl
  Title A 2D model for a gliding arc discharge Type A1 Journal article
  Year 2015 Publication Plasma sources science and technology Abbreviated Journal Plasma Sources Sci T  
  Volume 24 Issue 24 Pages 015025  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract In this study we report on a 2D fluid model of a gliding arc discharge in argon. Despite the 3D nature of the discharge, 2D models are found to be capable of providing very useful information about the operation of the discharge. We employ two modelsan axisymmetric and a Cartesian one. We show that for the considered experiment and the conditions of a low current arc (around 30 mA) in argon, there is no significant heating of the cathode surface and the discharge is sustained by field electron emission from the cathode accompanied by the formation of a cathode spot. The obtained discharge power and voltage are relatively sensitive to the surface properties and particularly to the surface roughness, causing effectively an amplification of the normal electric field. The arc body and anode region are not influenced by this and depend mainly on the current value. The gliding of the arc is modelled by means of a 2D Cartesian model. The arcelectrode contact points are analysed and the gliding mechanism along the electrode surface is discussed. Following experimental observations, the cathode spot is simulated as jumping from one point to another. A complete arc cycle is modelled from initial ignition to arc decay. The results show that there is no interaction between the successive gliding arcs.  
  Address  
  Corporate Author Thesis  
  Publisher Institute of Physics Place of Publication Bristol Editor  
  Language Wos 000348298200026 Publication Date 2014-12-23  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0963-0252;1361-6595; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.302 Times cited 34 Open Access  
  Notes Approved Most recent IF: 3.302; 2015 IF: 3.591  
  Call Number c:irua:122538 c:irua:122538 c:irua:122538 c:irua:122538 Serial 3  
Permanent link to this record
 

 
Author Bogaerts, A. url  doi
openurl 
  Title The afterglow mystery of pulsed glow discharges and the role of dissociative electron-ion recombination Type A1 Journal article
  Year 2007 Publication Journal of analytical atomic spectrometry Abbreviated Journal J Anal Atom Spectrom  
  Volume 22 Issue Pages 502-512  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication London Editor  
  Language Wos 000246889200012 Publication Date 2007-04-18  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0267-9477;1364-5544; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.379 Times cited 56 Open Access  
  Notes Approved Most recent IF: 3.379; 2007 IF: 3.269  
  Call Number UA @ lucian @ c:irua:63859 Serial 81  
Permanent link to this record
 

 
Author Bogaerts, A.; Gijbels, R. doi  openurl
  Title Argon and copper optical emission spectra in a Grimm glow discharge source: mathematical simulations and comparison with experiment Type A1 Journal article
  Year 1998 Publication Journal of analytical atomic spectrometry Abbreviated Journal J Anal Atom Spectrom  
  Volume 13 Issue Pages 721-726  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication London Editor  
  Language Wos 000075385700006 Publication Date 2002-07-26  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0267-9477;1364-5544; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.379 Times cited 25 Open Access  
  Notes Approved Most recent IF: 3.379; 1998 IF: 3.845  
  Call Number UA @ lucian @ c:irua:24127 Serial 149  
Permanent link to this record
 

 
Author de Bleecker, K.; Bogaerts, A.; Goedheer, W. doi  openurl
  Title Aromatic ring generation as a dust precursor in acetylene discharges Type A1 Journal article
  Year 2006 Publication Applied physics letters Abbreviated Journal Appl Phys Lett  
  Volume 88 Issue 15 Pages 151501,1-3  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher American Institute of Physics Place of Publication New York, N.Y. Editor  
  Language Wos 000236796400010 Publication Date 2006-04-10  
  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 20 Open Access  
  Notes Approved Most recent IF: 3.411; 2006 IF: 3.977  
  Call Number UA @ lucian @ c:irua:57218 Serial 150  
Permanent link to this record
 

 
Author Yusupov, M.; Neyts, E.C.; Khalilov, U.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A. url  doi
openurl 
  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 (up) 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 Bings, N.H.; Bogaerts, A.; Broekaert, J.A.C. doi  openurl
  Title Atomic spectroscopy Type A1 Journal article
  Year 2013 Publication Analytical chemistry Abbreviated Journal Anal Chem  
  Volume 85 Issue 2 Pages 670-704  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Washington, D.C. Editor  
  Language Wos 000313668400013 Publication Date 2012-11-07  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 6.32 Times cited 29 Open Access  
  Notes Approved Most recent IF: 6.32; 2013 IF: 5.825  
  Call Number UA @ lucian @ c:irua:104719 Serial 190  
Permanent link to this record
 

 
Author Bings, N.H.; Bogaerts, A.; Broekaert, J.A.C. doi  openurl
  Title Atomic spectroscopy Type A1 Journal article
  Year 2008 Publication Analytical chemistry Abbreviated Journal Anal Chem  
  Volume 80 Issue 12 Pages 4317-4347  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Washington, D.C. Editor  
  Language Wos 000256763400006 Publication Date 2008-05-08  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 6.32 Times cited 53 Open Access  
  Notes Approved Most recent IF: 6.32; 2008 IF: 5.712  
  Call Number UA @ lucian @ c:irua:69437 Serial 191  
Permanent link to this record
 

 
Author Bings, N.H.; Bogaerts, A.; Broekaert, J.A.C. doi  openurl
  Title Atomic spectroscopy Type A1 Journal article
  Year 2006 Publication Analytical chemistry Abbreviated Journal Anal Chem  
  Volume 78 Issue 12 Pages 3917-3945  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Washington, D.C. Editor  
  Language Wos 000238252600007 Publication Date 2006-06-10  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 6.32 Times cited 112 Open Access  
  Notes Approved Most recent IF: 6.32; 2006 IF: 5.646  
  Call Number UA @ lucian @ c:irua:60058 Serial 192  
Permanent link to this record
 

 
Author Bings, N.H.; Bogaerts, A.; Broekaert, J.A.C. doi  openurl
  Title Atomic spectroscopy Type A1 Journal article
  Year 2004 Publication Analytical chemistry Abbreviated Journal Anal Chem  
  Volume 76 Issue 12 Pages 3313-3336  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Washington, D.C. Editor  
  Language Wos 000222011100006 Publication Date 2004-06-14  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 6.32 Times cited 32 Open Access  
  Notes Approved Most recent IF: 6.32; 2004 IF: 5.450  
  Call Number UA @ lucian @ c:irua:46258 Serial 193  
Permanent link to this record
 

 
Author Bings, N.H.; Bogaerts, A.; Broekaert, J.A.C. doi  openurl
  Title Atomic spectroscopy Type A1 Journal article
  Year 2002 Publication Analytical chemistry Abbreviated Journal Anal Chem  
  Volume 74 Issue 12 Pages 2691-2712  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Washington, D.C. Editor  
  Language Wos 000176253700006 Publication Date 2002-07-26  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 6.32 Times cited 18 Open Access  
  Notes Approved Most recent IF: 6.32; 2002 IF: 5.094  
  Call Number UA @ lucian @ c:irua:40192 Serial 194  
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Author Bings, N.H.; Bogaerts, A.; Broekaert, J.A.C. doi  openurl
  Title Atomic spectroscopy: a review Type A1 Journal article
  Year 2010 Publication Analytical chemistry Abbreviated Journal Anal Chem  
  Volume 82 Issue 12 Pages 4653-4681  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Washington, D.C. Editor  
  Language Wos 000278616100001 Publication Date 2010-05-13  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0003-2700;1520-6882; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 6.32 Times cited 65 Open Access  
  Notes Approved Most recent IF: 6.32; 2010 IF: 5.874  
  Call Number UA @ lucian @ c:irua:82675 Serial 195  
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Author Bogaerts, A.; Grozeva, M. doi  openurl
  Title Axial non-uniformity of longitudinal hollow cathode discharges for laser applications: numerical modeling and comparison with experiments Type A1 Journal article
  Year 2002 Publication Applied physics: B: photo-physics and laser chemistry Abbreviated Journal Appl Phys B-Lasers O  
  Volume 75 Issue Pages 731-738  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Berlin Editor  
  Language Wos 000180587100019 Publication Date 2004-03-19  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0946-2171;1432-0649; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 1.696 Times cited 8 Open Access  
  Notes Approved Most recent IF: 1.696; 2002 IF: 2.080  
  Call Number UA @ lucian @ c:irua:44007 Serial 211  
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Author Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. url  doi
openurl 
  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 (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract A Monte Carlo model has been developed for investigating the electron behavior in a dual-magnetron sputter deposition system. To describe the three-dimensional (3D) geometry, different reference frames, i.e. a local and a global coordinate system, were used. In this study, the influence of both closed and mirror magnetic field configurations on the plasma properties is investigated. In the case of a closed magnetic field configuration, the calculated electron trajectories show that if an electron is emitted in (or near) the center of the cathode, where the influence of the magnetic field is low, it is able to travel from one magnetron to the other. On the other hand, when an electron is created at the race track area, it is more or less trapped in the strong magnetic field and cannot easily escape to the second magnetron region. In the case of a mirror magnetic field configuration, irrespective of where the electron is emitted from the cathode, it cannot travel from one magnetron to the other because the magnetic field lines guide the electron to the substrate. Moreover, the electron density and electron impact ionization rate have been calculated and studied in detail for both configurations.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Bristol Editor  
  Language Wos 000289064600001 Publication Date 2011-03-15  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1367-2630; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.786 Times cited 12 Open Access  
  Notes Approved Most recent IF: 3.786; 2011 IF: 4.177  
  Call Number UA @ lucian @ c:irua:87544 Serial 224  
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Author Bogaerts, A.; Gijbels, R. doi  openurl
  Title Behavior of the sputtered copper atoms, ions and excited species in a radio-frequency and direct current glow discharge Type A1 Journal article
  Year 2000 Publication Spectrochimica acta: part B : atomic spectroscopy Abbreviated Journal Spectrochim Acta B  
  Volume 55 Issue Pages 279-297  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Oxford Editor  
  Language Wos 000086340100006 Publication Date 2002-07-26  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0584-8547; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.241 Times cited 17 Open Access  
  Notes Approved Most recent IF: 3.241; 2000 IF: 2.608  
  Call Number UA @ lucian @ c:irua:28325 Serial 226  
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Author Neyts, E.; Shibuta, Y.; Bogaerts, A. doi  openurl
  Title Bond switching regimes in nickel and nickel-carbon nanoclusters Type A1 Journal article
  Year 2010 Publication Chemical physics letters Abbreviated Journal Chem Phys Lett  
  Volume 488 Issue 4/6 Pages 202-205  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract Understanding the fundamental dynamics in carbon nanotube (CNT) catalysts is of primary importance to understand CNT nucleation. This Letter reports on calculated bond switching (BS) rates in pure and carbon containing nickel nanoclusters. The rates are analyzed in terms of their temperature dependent spatial distribution and the mobility of the cluster atoms. The BS mechanism is found to change from vibrational to diffusional at around 900 K, with a corresponding strong increase in activation energy. Furthermore, the BS activation energy is observed to decrease as the carbon content in the cluster increases, resulting in an effective liquification of the cluster.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Amsterdam Editor  
  Language Wos 000275751900020 Publication Date 2010-02-15  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0009-2614; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 1.815 Times cited 20 Open Access  
  Notes Approved Most recent IF: 1.815; 2010 IF: 2.282  
  Call Number UA @ lucian @ c:irua:80998 Serial 248  
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Author Zhao, S.-X.; Zhang, Y.-R.; Gao, F.; Wang, Y.-N.; Bogaerts, A. url  doi
openurl 
  Title Bulk plasma fragmentation in a C4F8 inductively coupled plasma : a hybrid modelling study Type A1 Journal article
  Year 2015 Publication Journal of applied physics Abbreviated Journal J Appl Phys  
  Volume 117 Issue 117 Pages 243303  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract A hybrid model is used to investigate the fragmentation of C4F8 inductive discharges. Indeed, the resulting reactive species are crucial for the optimization of the Si-based etching process, since they determine the mechanisms of fluorination, polymerization, and sputtering. In this paper, we present the dissociation degree, the density ratio of F vs. CxFy (i.e., fluorocarbon (fc) neutrals), the neutral vs. positive ion density ratio, details on the neutral and ion components, and fractions of various fc neutrals (or ions) in the total fc neutral (or ion) density in a C4F8 inductively coupled plasma source, as well as the effect of pressure and power on these results. To analyze the fragmentation behavior, the electron density and temperature and electron energy probability function (EEPF) are investigated. Moreover, the main electron-impact generation sources for all considered neutrals and ions are determined from the complicated C4F8 reaction set used in the model. The C4F8 plasma fragmentation is explained, taking into account many factors, such as the EEPF characteristics, the dominance of primary and secondary processes, and the thresholds of dissociation and ionization. The simulation results are compared with experiments from literature, and reasonable agreement is obtained. Some discrepancies are observed, which can probably be attributed to the simplified polymer surface kinetics assumed in the model.  
  Address  
  Corporate Author Thesis  
  Publisher American Institute of Physics Place of Publication New York, N.Y. Editor  
  Language Wos 000357613900009 Publication Date 2015-06-30  
  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; WoS citing articles  
  Impact Factor 2.068 Times cited 11 Open Access  
  Notes Approved Most recent IF: 2.068; 2015 IF: 2.183  
  Call Number c:irua:126477 Serial 261  
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Author Bogaerts, A.; Gijbels, R. doi  openurl
  Title Calculation of cathode heating in analytical glow discharges Type A1 Journal article
  Year 2004 Publication Journal of analytical atomic spectrometry Abbreviated Journal J Anal Atom Spectrom  
  Volume 19 Issue Pages 1206-1212  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication London Editor  
  Language Wos 000223738000020 Publication Date 2004-09-07  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0267-9477;1364-5544; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.379 Times cited 21 Open Access  
  Notes Approved Most recent IF: 3.379; 2004 IF: 3.926  
  Call Number UA @ lucian @ c:irua:47647 Serial 264  
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Author Bogaerts, A.; Gijbels, R. openurl 
  Title Calculation of crater profiles on a flat cathode in a direct current glow discharge, and comparison with experiment Type A1 Journal article
  Year 1997 Publication Spectrochimica acta: part B : atomic spectroscopy Abbreviated Journal Spectrochim Acta B  
  Volume 52 Issue 6 Pages 765-778  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Oxford Editor  
  Language Wos A1997XH34900009 Publication Date 0000-00-00  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0584-8547; 0038-6987 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.241 Times cited 42 Open Access  
  Notes Approved Most recent IF: 3.241; 1997 IF: 2.448  
  Call Number UA @ lucian @ c:irua:19603 Serial 265  
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Author Kolev, I.; Bogaerts, A. pdf  doi
openurl 
  Title Calculation of gas heating in a dc sputter magnetron Type A1 Journal article
  Year 2008 Publication Journal of applied physics Abbreviated Journal J Appl Phys  
  Volume 104 Issue 9 Pages 093301,1-093301,8  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract The effect of gas heating in laboratory sputter magnetrons is investigated by means of numerical modeling. The model is two-dimensional in the coordinate space and three-dimensional in the velocity space based on the particle-in-cellMonte Carlo collisions technique. It is expanded in a way that allows the inclusion of the neutral plasma particles (fast gas atoms and sputtered atoms), which makes it possible to calculate the gas temperature and its influence on the discharge behavior in a completely self-consistent way. The results of the model are compared to experimental measurements and to other existing simulation results. The results show that gas heating is pressure dependent (rising with the increase in the gas pressure) and should be taken into consideration at pressures above 10 mTorr.  
  Address  
  Corporate Author Thesis  
  Publisher American Institute of Physics Place of Publication New York, N.Y. Editor  
  Language Wos 000260941700017 Publication Date 2008-11-07  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0021-8979; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.068 Times cited 19 Open Access  
  Notes Approved Most recent IF: 2.068; 2008 IF: 2.201  
  Call Number UA @ lucian @ c:irua:71286 Serial 267  
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Author Bogaerts, A.; Gijbels, R.; Serikov, V.V. doi  openurl
  Title Calculation of gas heating in direct current argon glow discharges Type A1 Journal article
  Year 2000 Publication Journal of applied physics Abbreviated Journal J Appl Phys  
  Volume 87 Issue 12 Pages 8334-8344  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher American Institute of Physics Place of Publication New York, N.Y. Editor  
  Language Wos 000087346400013 Publication Date 2002-07-26  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0021-8979; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.068 Times cited 63 Open Access  
  Notes Approved Most recent IF: 2.068; 2000 IF: 2.180  
  Call Number UA @ lucian @ c:irua:28327 Serial 268  
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Author Bogaerts, A.; Temelkov, K.A.; Vuchkov, N.K.; Gijbels, R. doi  openurl
  Title Calculation of rate constants for asymmetric charge transfer, and their effect on relative sensitivity factors in glow discharge mass spectrometry Type A1 Journal article
  Year 2007 Publication Spectrochimica acta: part B : atomic spectroscopy Abbreviated Journal Spectrochim Acta B  
  Volume 62 Issue 4 Pages 325-336  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Oxford Editor  
  Language Wos 000247551800001 Publication Date 2007-03-25  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0584-8547; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.241 Times cited 28 Open Access  
  Notes Approved Most recent IF: 3.241; 2007 IF: 2.957  
  Call Number UA @ lucian @ c:irua:64329 Serial 269  
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Author Bogaerts, A.; Okhrimovskyy, A.; Gijbels, R. doi  openurl
  Title Calculation of the gas flow and its effect on the plasma characteristics for a modified Grimm-type glow discharge cell Type A1 Journal article
  Year 2002 Publication Journal of analytical atomic spectrometry Abbreviated Journal J Anal Atom Spectrom  
  Volume 17 Issue Pages 1076-1082  
  Keywords (up) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication London Editor  
  Language Wos 000177766400012 Publication Date 2002-09-09  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0267-9477;1364-5544; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.379 Times cited 39 Open Access  
  Notes Approved Most recent IF: 3.379; 2002 IF: 4.250  
  Call Number UA @ lucian @ c:irua:40191 Serial 270  
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