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Author | Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. | ||||
Title | Multi-level molecular modelling for plasma medicine | Type | A1 Journal article | ||
Year | 2016 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 49 | Issue | 49 | Pages | 054002 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions. | ||||
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Language | Wos | 000368944100003 | Publication Date | 2015-12-16 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0022-3727 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.588 | Times cited | 11 | Open Access | |
Notes | This work is financially supported by the Fund for Scientific Research Flanders (FWO) and the Francqui Foundation. The calculations were carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. | Approved | Most recent IF: 2.588 | ||
Call Number | c:irua:131571 | Serial | 3985 | ||
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Author | Bruggeman, P.J.; Kushner, M.J.; Locke, B.R.; Gardeniers, J.G.E.; Graham, W.G.; Graves, D.B.; Hofman-Caris, R.C.H.M.; Maric, D.; Reid, J.P.; Ceriani, E.; Fernandez Rivas, D.; Foster, J.E.; Garrick, S.C.; Gorbanev, Y.; Hamaguchi, S.; Iza, F.; Jablonowski, H.; Klimova, E.; Kolb, J.; Krcma, F.; Lukes, P.; Machala, Z.; Marinov, I.; Mariotti, D.; Mededovic Thagard, S.; Minakata, D.; Neyts, E.C.; Pawlat, J.; Petrovic, Z.L.; Pflieger, R.; Reuter, S.; Schram, D.C.; Schröter, S.; Shiraiwa, M.; Tarabová, B.; Tsai, P.A.; Verlet, J.R.R.; von Woedtke, T.; Wilson, K.R.; Yasui, K.; Zvereva, G. | ||||
Title | Plasma–liquid interactions: a review and roadmap | Type | A1 Journal article | ||
Year | 2016 | Publication | Plasma sources science and technology | Abbreviated Journal | Plasma Sources Sci T |
Volume | 25 | Issue | 5 | Pages | 053002 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Plasma–liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on nonequilibrium plasmas. | ||||
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Language | Wos | 000384715400001 | Publication Date | 2016-09-30 | |
Series Editor | Series Title | Abbreviated Series Title | |||
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ISSN | 1361-6595 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.302 | Times cited | 460 | Open Access | |
Notes | This manuscript originated from discussions at the Lorentz Center Workshop ‘Gas/Plasma–Liquid Interface: Transport, Chemistry and Fundamental Data’ that took place at the Lorentz Center, Leiden University in the Netherlands from August 4, through August 8, 2014, and follow-up discussions since the workshop. All authors acknowledge the support of the Lorentz Center, the COST action TD1208 (Electrical Discharges with Liquids for Future Applications) and the Royal Dutch Academy of Sciences for their financial support. PJB, MJK, DBG and JEF acknowledge the support of the ‘Center on Control of Plasma Kinetics’ of the United States Department of Energy Office of Fusion Energy Science (DE-SC0001319). In addition, PJB and BRL acknowledge the support of the National Science Foundation (PHY 1500135 and CBET 1236225, respectively). In addition the enormous help of Mrs. Victoria Piorek (University of Minnesota) in the formatting of the final document including the references is gratefully acknowledged. | Approved | Most recent IF: 3.302 | ||
Call Number | PLASMANT @ plasmant @ c:irua:144654 | Serial | 4628 | ||
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Author | Verlackt, C.C.W.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Atomic scale behavior of oxygen-based radicals in water | Type | A1 Journal article | ||
Year | 2017 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 50 | Issue | 50 | Pages | 11LT01 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Cold atmospheric pressure plasmas in and in contact with liquids represent a growing field of research for various applications. Understanding the interactions between the plasma generated species and the liquid is crucial. In this work we perform molecular dynamics (MD) simulations based on a quantum mechanical method, i.e. density-functional based tight-binding (DFTB), to examine the interactions of OH radicals and O atoms in bulk water. Our calculations reveal that the transport of OH radicals through water is not only governed by diffusion, but also by an equilibrium reaction of H-abstraction with water molecules. Furthermore, when two OH radicals encounter each other, they either form a stable cluster, or react, resulting in the formation of a new water molecule and an O atom. In addition, the O atoms form either oxywater (when in singlet configuration) or they remain stable in solution (when in triplet configuration), stressing the important role that O atoms can play in aqueous solution, and in contact with biomolecules. Our observations are in line with both experimental and ab initio results from the literature. |
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Language | Wos | 000415252400001 | Publication Date | 2017-02-13 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0022-3727 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.588 | Times cited | 11 | Open Access | OpenAccess |
Notes | The authors thank Peter Bruggeman (University of Minnesota, USA) and Jan Benedikt (Ruhr-Universität Bochum, Germany) for the interesting discussions regarding the existence of O in aqueous solutions. Furthermore, they acknowledge financial support from the Fund for Scientific Research (FWO) Flanders (project number G012413N). The calculations were performed 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: 2.588 | ||
Call Number | PLASMANT @ plasmant @ c:irua:140845 | Serial | 4420 | ||
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Author | Khalilov, U.; Bogaerts, A.; Hussain, S.; Kovacevic, E.; Brault, P.; Boulmer-Leborgne, C.; Neyts, E.C. | ||||
Title | Nanoscale mechanisms of CNT growth and etching in plasma environment | Type | A1 Journal article | ||
Year | 2017 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 50 | Issue | 50 | Pages | 184001 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Plasma-enhanced chemical deposition (PECVD) of carbon nanotubes has already been shown to allow chirality control to some extent. In PECVD, however, etching may occur simultaneously with the growth, and the occurrence of intermediate processes further significantly complicates the growth process. We here employ a computational approach with experimental support to study the plasma-based formation of Ni nanoclusters, Ni-catalyzed CNT growth and subsequent etching processes, in order to understand the underpinning nanoscale mechanisms. We find that hydrogen is the dominant factor in both the re-structuring of a Ni film and the subsequent appearance of Ni nanoclusters, as well as in the CNT nucleation and etching processes. The obtained results are compared with available theoretical and experimental studies and provide a deeper understanding of the occurring nanoscale mechanisms in plasma-assisted CNT nucleation and growth. |
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Language | Wos | 000398300900001 | Publication Date | 2017-04-03 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0022-3727 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.588 | Times cited | 6 | Open Access | OpenAccess |
Notes | UK gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), Belgium (Grant No. 12M1315N). The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. The authors also thank Prof A C T van Duin for sharing the ReaxFF code. | Approved | Most recent IF: 2.588 | ||
Call Number | PLASMANT @ plasmant @ c:irua:141918 | Serial | 4533 | ||
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Author | Bal, K.M.; Neyts, E.C. | ||||
Title | Quantifying the impact of vibrational nonequilibrium in plasma catalysis: insights from a molecular dynamics model of dissociative chemisorption | Type | A1 Journal Article;plasma catalysis | ||
Year | 2021 | Publication | Journal Of Physics D-Applied Physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 54 | Issue | 39 | Pages | 394004 |
Keywords | A1 Journal Article;plasma catalysis; vibrational nonequilibrium; dissociative chemisorption; free energy barriers; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
Abstract | The rate, selectivity and efficiency of plasma-based conversion processes is strongly affected by nonequilibrium phenomena. High concentrations of vibrationally excited molecules are such a plasma-induced effect. It is frequently assumed that vibrationally excited molecules are important in plasma catalysis because their presence lowers the apparent activation energy of dissociative chemisorption reactions and thus increases the conversion rate. A detailed atomic-level understanding of vibrationally stimulated catalytic reactions in the context of plasma catalysis is however lacking. Here, we couple a recently developed statistical model of a plasma-induced vibrational nonequilibrium to molecular dynamics simulations, enhanced sampling methods, and machine learning techniques. We quantify the impact of a vibrational nonequilibrium on the dissociative chemisorption barrier of H2 and CH4 on nickel catalysts over a wide range of vibrational temperatures. We investigate the effect of surface structure and compare the role of different vibrational modes of methane in the dissociation process. For low vibrational temperatures, very high vibrational efficacies are found, and energy in bend vibrations appears to dominate the dissociation of methane. The relative impact of vibrational nonequilibrium is much higher on terrace sites than on surface steps. We then show how our simulations can help to interpret recent experimental results, and suggest new paths to a better understanding of plasma catalysis. | ||||
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Language | Wos | 000674464100001 | Publication Date | 2021-09-30 | |
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ISSN | 0022-3727 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.588 | Times cited | Open Access | OpenAccess | |
Notes | Fonds Wetenschappelijk Onderzoek, 12ZI420N ; K M B was funded as a junior postdoctoral fellow of the FWO (Research Foundation—Flanders), Grant 12ZI420N. 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 FWO and the Flemish Government. HLDA calculations were performed with a script provided by G Piccini. | Approved | Most recent IF: 2.588 | ||
Call Number | PLASMANT @ plasmant @c:irua:179830 | Serial | 6808 | ||
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Author | Heyne, M.H.; de Marneffe, J.-F.; Delabie, A.; Caymax, M.; Neyts, E.C.; Radu, I.; Huyghebaert, C.; De Gendt, S. | ||||
Title | Two-dimensional WS2 nanoribbon deposition by conversion of pre-patterned amorphous silicon | Type | A1 Journal article | ||
Year | 2017 | Publication | Nanotechnology | Abbreviated Journal | Nanotechnology |
Volume | 28 | Issue | 28 | Pages | 04LT01 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | We present a method for area selective deposition of 2D WS2 nanoribbons with tunable thickness on a dielectric substrate. The process is based on a complete conversion of a prepatterned, H-terminated Si layer to metallic W by WF6, followed by in situ sulfidation by H2S. The reaction process, performed at 450 degrees C, yields nanoribbons with lateral dimension down to 20 nm and with random basal plane orientation. The thickness of the nanoribbons is accurately controlled by the thickness of the pre-deposited Si layer. Upon rapid thermal annealing at 900 degrees C under inert gas, the WS2 basal planes align parallel to the substrate. | ||||
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Publisher | Place of Publication | Bristol | Editor | ||
Language | Wos | 000391445100001 | Publication Date | 2016-12-15 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0957-4484 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.44 | Times cited | 13 | Open Access | OpenAccess |
Notes | Approved | Most recent IF: 3.44 | |||
Call Number | UA @ lucian @ c:irua:140382 | Serial | 4471 | ||
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Author | Bal, K.M.; Huygh, S.; Bogaerts, A.; Neyts, E.C. | ||||
Title | Effect of plasma-induced surface charging on catalytic processes: application to CO2activation | Type | A1 Journal article | ||
Year | 2018 | Publication | Plasma sources science and technology | Abbreviated Journal | Plasma Sources Sci T |
Volume | 27 | Issue | 2 | Pages | 024001 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Understanding the nature and effect of the multitude of plasma–surface interactions in plasma catalysis is a crucial requirement for further process development and improvement. A particularly intriguing and rather unique property of a plasma-catalytic setup is the ability of the plasma to modify the electronic structure, and hence chemical properties, of the catalyst through charging, i.e. the absorption of excess electrons. In this work, we develop a quantum chemical model based on density functional theory to study excess negative surface charges in a heterogeneous catalyst exposed to a plasma. This method is specifically applied to investigate plasma-catalytic CO2 activation on supported M/Al2O3 (M=Ti, Ni, Cu) single atom catalysts. We find that (1) the presence of a negative surface charge dramatically improves the reductive power of the catalyst, strongly promoting the splitting of CO2 to CO and oxygen, and (2) the relative activity of the investigated transition metals is also changed upon charging, suggesting that controlled surface charging is a powerful additional parameter to tune catalyst activity and selectivity. These results strongly point to plasma-induced surface charging of the catalyst as an important factor contributing to the plasma-catalyst synergistic effects frequently reported for plasma catalysis. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000424520100001 | Publication Date | 2018-02-07 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 1361-6595 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.302 | Times cited | 19 | Open Access | OpenAccess |
Notes | KMB is funded as PhD fellow (aspirant) of the FWO-Flanders (Research Foundation—Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government— department EWI. | Approved | Most recent IF: 3.302 | ||
Call Number | PLASMANT @ plasmant @c:irua:149285 | Serial | 4813 | ||
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Author | Zhang, Y.-R.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Enhancement of plasma generation in catalyst pores with different shapes | Type | A1 Journal article | ||
Year | 2018 | Publication | Plasma sources science and technology | Abbreviated Journal | Plasma Sources Sci T |
Volume | 27 | Issue | 5 | Pages | 055008 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Plasma generation inside catalyst pores is of utmost importance for plasma catalysis, as the existence of plasma species inside the pores affects the active surface area of the catalyst available to the plasma species for catalytic reactions. In this paper, the electric field enhancement, and thus the plasma production inside catalyst pores with different pore shapes is studied with a two-dimensional fluid model. The results indicate that the electric field will be significantly enhanced near tip-like structures. In a conical pore with small opening, the strongest electric field appears at the opening and bottom corners of the pore, giving rise to a prominent ionization rate throughout the pore. For a cylindrical pore, the electric field is only enhanced at the bottom corners of the pore, with lower absolute value, and thus the ionization rate inside the pore is only slightly enhanced. Finally, in a conical pore with large opening, the electric field is characterized by a maximum at the bottom of the pore, yielding a similar behavior for the ionization rate. These results demonstrate that the shape of the pore has a significantly influence on the electric field enhancement, and thus modifies the plasma properties. | ||||
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Language | Wos | 000432351700002 | Publication Date | 2018-05-15 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 1361-6595 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.302 | Times cited | 11 | Open Access | OpenAccess |
Notes | This work was supported by the Fund for Scientific Research Flanders (FWO) (Grant No. G.0217.14N) and the Fundamental Research Funds for the Central Universities (Grant No. DUT17LK52). | Approved | Most recent IF: 3.302 | ||
Call Number | PLASMANT @ plasmant @c:irua:151546 | Serial | 4998 | ||
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Author | Bogaerts, A.; Neyts, E.C.; Guaitella, O.; Murphy, A.B. | ||||
Title | Foundations of plasma catalysis for environmental applications | Type | A1 Journal article | ||
Year | 2022 | Publication | Plasma Sources Science & Technology | Abbreviated Journal | Plasma Sources Sci T |
Volume | Issue | Pages | |||
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Plasma catalysis is gaining increasing interest for various applications, but the underlying mechanisms are still far from understood. Hence, more fundamental research is needed to understand these mechanisms. This can be obtained by both modelling and experiments. This foundations paper describes the fundamental insights in plasma catalysis, as well as efforts to gain more insights by modelling and experiments. Furthermore, it discusses the state-of-the-art of the major plasma catalysis applications, as well as successes and challenges of technology transfer of these applications. | ||||
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Language | Wos | 000804396200001 | Publication Date | 2022-03-21 | |
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ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.8 | Times cited | Open Access | OpenAccess | |
Notes | H2020 Marie Skłodowska-Curie Actions, 823745 ; H2020 European Research Council, 810182 ; We acknowldege financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation programme (Grant Agreement No. 810182 – SCOPE ERC Synergy project) and the European Union’s Horizon 2020 Research and Innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 813393 (PIONEER). | Approved | Most recent IF: 3.8 | ||
Call Number | PLASMANT @ plasmant @c:irua:188539 | Serial | 7070 | ||
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Author | Yusupov, M.; Neyts, E.C.; Khalilov, U.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A. | ||||
Title | Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls | Type | A1 Journal article | ||
Year | 2012 | Publication | New journal of physics | Abbreviated Journal | New J Phys |
Volume | 14 | Issue | 9 | Pages | 093043 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. CO, CN and CC bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale. | ||||
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Publisher | Place of Publication | Bristol | Editor | ||
Language | Wos | 000309393400001 | Publication Date | 2012-09-27 | |
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ISSN | 1367-2630; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.786 | Times cited | 47 | Open Access | |
Notes | Approved | Most recent IF: 3.786; 2012 IF: 4.063 | |||
Call Number | UA @ lucian @ c:irua:101014 | Serial | 189 | ||
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Author | Verlackt, C.C.W.; Neyts, E.C.; Jacob, T.; Fantauzzi, D.; Golkaram, M.; Shin, Y.-K.; van Duin, A.C.T.; Bogaerts, A. | ||||
Title | Atomic-scale insight into the interactions between hydroxyl radicals and DNA in solution using the ReaxFF reactive force field | Type | A1 Journal article | ||
Year | 2015 | Publication | New journal of physics | Abbreviated Journal | New J Phys |
Volume | 17 | Issue | 17 | Pages | 103005 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Cold atmospheric pressure plasmas have proven to provide an alternative treatment of cancer by targeting tumorous cells while leaving their healthy counterparts unharmed. However, the underlying mechanisms of the plasma–cell interactions are not yet fully understood. Reactive oxygen species, and in particular hydroxyl radicals (OH), are known to play a crucial role in plasma driven apoptosis of malignant cells. In this paper we investigate the interaction of OH radicals, as well as H2O2 molecules and HO2 radicals, with DNA by means of reactive molecular dynamics simulations using the ReaxFF force field. Our results provide atomic-scale insight into the dynamics of oxidative stress on DNA caused by the OH radicals, while H2O2 molecules appear not reactive within the considered timescale. Among the observed processes are the formation of 8-OH-adduct radicals, forming the first stages towards the formation of 8-oxoGua and 8-oxoAde, H-abstraction reactions of the amines, and the partial opening of loose DNA ends in aqueous solution. |
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Language | Wos | 000367328100001 | Publication Date | 2015-10-02 | |
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ISSN | 1367-2630; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.786 | Times cited | 18 | Open Access | |
Notes | CCWV,ECN and AB acknowledge the contribution of J Van Beeck who is investigating the interaction between H2O2 andDNAusingrMDsimulations. Furthermore, they acknowledge financial support from the Fund for Scientific Research—Flanders (project number G012413N). The calculations were performed using the Turing HPCinfrastructure 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. TJ and DF gratefully acknowledge support from the European Research Council through the ERC-Starting GrantTHEOFUN(Grant Agreement No. 259608). | Approved | Most recent IF: 3.786; 2015 IF: 3.558 | ||
Call Number | c:irua:129178 | Serial | 3955 | ||
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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. | ||||
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Publisher | Place of Publication | Bristol | Editor | ||
Language | Wos | 000312261700011 | Publication Date | 2012-11-26 | |
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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 | Neyts, E.; Bogaerts, A.; van de Sanden, M.C.M. | ||||
Title | Reaction mechanisms and thin a-C:H film growth from low energy hydrocarbon radicals | Type | A1 Journal article | ||
Year | 2007 | Publication | Journal of physics : conference series | Abbreviated Journal | |
Volume | 86 | Issue | Pages | 12020-12020,15 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Molecular dynamics simulations using the Brenner potential have been performed to investigate reaction mechanisms of various hydrocarbon radicals with low kinetic energies on amorphous hydrogenated carbon (a-C:H) surfaces and to simulate thin a-C:H film growth. Experimental data from an expanding thermal plasma setup were used as input for the simulations. The hydrocarbon reaction mechanisms were studied both during growth of the films and on a set of surface sites specific for a-C:H surfaces. Thin film growth was studied using experimentally detected growth species. It is found that the reaction mechanisms and sticking coefficients are dependent on the specific surface sites, and the structural properties of the growth radicals. Furthermore, it is found that thin a-C:H films can be densified using an additional H-flux towards the substrate. | ||||
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Publisher | Place of Publication | Bristol | Editor | ||
Language | Wos | 000256282900020 | Publication Date | 2007-11-22 | |
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ISSN | 1742-6596; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | 22 | Open Access | ||
Notes | Approved | Most recent IF: NA | |||
Call Number | UA @ lucian @ c:irua:65692 | Serial | 2817 | ||
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Author | Mees, M.J.; Pourtois, G.; Neyts, E.C.; Thijsse, B.J.; Stesmans, A. | ||||
Title | Uniform-acceptance force-bias Monte Carlo method with time scale to study solid-state diffusion | Type | A1 Journal article | ||
Year | 2012 | Publication | Physical review : B : condensed matter and materials physics | Abbreviated Journal | Phys Rev B |
Volume | 85 | Issue | 13 | Pages | 134301-134301,9 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Monte Carlo (MC) methods have a long-standing history as partners of molecular dynamics (MD) to simulate the evolution of materials at the atomic scale. Among these techniques, the uniform-acceptance force-bias Monte Carlo (UFMC) method [ G. Dereli Mol. Simul. 8 351 (1992)] has recently attracted attention [ M. Timonova et al. Phys. Rev. B 81 144107 (2010)] thanks to its apparent capacity of being able to simulate physical processes in a reduced number of iterations compared to classical MD methods. The origin of this efficiency remains, however, unclear. In this work we derive a UFMC method starting from basic thermodynamic principles, which leads to an intuitive and unambiguous formalism. The approach includes a statistically relevant time step per Monte Carlo iteration, showing a significant speed-up compared to MD simulations. This time-stamped force-bias Monte Carlo (tfMC) formalism is tested on both simple one-dimensional and three-dimensional systems. Both test-cases give excellent results in agreement with analytical solutions and literature reports. The inclusion of a time scale, the simplicity of the method, and the enhancement of the time step compared to classical MD methods make this method very appealing for studying the dynamics of many-particle systems. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000302290500001 | Publication Date | 2012-04-03 | |
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ISSN | 1098-0121;1550-235X; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.836 | Times cited | 31 | Open Access | |
Notes | Approved | Most recent IF: 3.836; 2012 IF: 3.767 | |||
Call Number | UA @ lucian @ c:irua:97160 | Serial | 3809 | ||
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Author | Neyts, E.C.; Ostrikov, K.; Han, Z.J.; Kumar, S.; van Duin, A.C.T.; Bogaerts, A. | ||||
Title | Defect healing and enhanced nucleation of carbon nanotubes by low-energy ion bombardment | Type | A1 Journal article | ||
Year | 2013 | Publication | Physical review letters | Abbreviated Journal | Phys Rev Lett |
Volume | 110 | Issue | 6 | Pages | 065501-65505 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Structural defects inevitably appear during the nucleation event that determines the structure and properties of single-walled carbon nanotubes. By combining ion bombardment experiments with atomistic simulations we reveal that ion bombardment in a suitable energy range allows these defects to be healed resulting in an enhanced nucleation of the carbon nanotube cap. The enhanced growth of the nanotube cap is explained by a nonthermal ion-induced graphene network restructuring mechanism. | ||||
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Publisher | Place of Publication | New York, N.Y. | Editor | ||
Language | Wos | 000314687300022 | Publication Date | 2013-02-07 | |
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ISSN | 0031-9007;1079-7114; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.462 | Times cited | 50 | Open Access | |
Notes | Approved | Most recent IF: 8.462; 2013 IF: 7.728 | |||
Call Number | UA @ lucian @ c:irua:105306 | Serial | 616 | ||
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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. | ||||
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Language | Wos | 000357195600019 | Publication Date | 2014-12-17 | |
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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 | Nematollahi, P.; Neyts, E.C. | ||||
Title | Linking bi-metal distribution patterns in porous carbon nitride fullerene to its catalytic activity toward gas adsorption | Type | A1 Journal article | ||
Year | 2021 | Publication | Nanomaterials | Abbreviated Journal | Nanomaterials-Basel |
Volume | 11 | Issue | 7 | Pages | 1794 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Immobilization of two single transition metal (TM) atoms on a substrate host opens numerous possibilities for catalyst design. If the substrate contains more than one vacancy site, the combination of TMs along with their distribution patterns becomes a design parameter potentially complementary to the substrate itself and the bi-metal composition. By means of DFT calculations, we modeled three dissimilar bi-metal atoms (Ti, Mn, and Cu) doped into the six porphyrin-like cavities of porous C24N24 fullerene, considering different bi-metal distribution patterns for each binary complex, viz. TixCuz@C24N24, TixMny@C24N24, and MnyCuz@C24N24 (with x, y, z = 0-6). We elucidate whether controlling the distribution of bi-metal atoms into the C24N24 cavities can alter their catalytic activity toward CO2, NO2, H-2, and N-2 gas capture. Interestingly, Ti2Mn4@C24N24 and Ti2Cu4@C24N24 complexes showed the highest activity and selectively toward gas capture. Our findings provide useful information for further design of novel few-atom carbon-nitride-based catalysts. | ||||
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Language | Wos | 000676140500001 | Publication Date | 2021-07-09 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 2079-4991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.553 | Times cited | Open Access | OpenAccess | |
Notes | Approved | Most recent IF: 3.553 | |||
Call Number | UA @ admin @ c:irua:180372 | Serial | 8174 | ||
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Author | Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. | ||||
Title | Multi-level molecular modelling for plasma medicine | Type | A1 Journal article | ||
Year | 2016 | Publication | Journal Of Physics D-Applied Physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 49 | Issue | 5 | Pages | 054002-54019 |
Keywords | A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT) | ||||
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Publisher | Place of Publication | London | Editor | ||
Language | Wos | Publication Date | 0000-00-00 | ||
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ISSN | 0022-3727 | ISBN | Additional Links | UA library record | |
Impact Factor | 2.588 | Times cited | Open Access | ||
Notes | Approved | Most recent IF: 2.588 | |||
Call Number | UA @ lucian @ c:irua:129798 | Serial | 4467 | ||
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