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| Author | Kolev, S.; Sun, S.; Trenchev, G.; Wang, W.; Wang, H.; Bogaerts, A. | ||||
| Title | Quasi-Neutral Modeling of Gliding Arc Plasmas: Quasi-Neutral Modeling of Gliding Arc Plasmas | Type | A1 Journal article | ||
| Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 14 | Issue | 14 | Pages | 1600110 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The modelling of a gliding arc discharge (GAD) is studied by means of the quasineutral (QN) plasma modelling approach. The model is first evaluated for reliability and proper description of a gliding arc discharge at atmospheric pressure, by comparing with a more elaborate non-quasineutral (NQN) plasma model in two different geometries – a 2D axisymmetric and a Cartesian geometry. The NQN model is considered as a reference, since it provides a continuous self-consistent plasma description, including the near electrode regions. In general, the results of the QN model agree very well with those obtained from the NQN model. The small differences between both models are attributed to the approximations in the derivation of the QN model. The use of the QN model provides a substantial reduction of the computation time compared to the NQN model, which is crucial for the development of more complex models in three dimensions or with complicated chemistries. The latter is illustrated for (i) a reverse vortex flow(RVF) GAD in argon, and (ii) a GAD in CO2. The RVF discharge is modelled in three dimensions and the effect of the turbulent heat transport on the plasma and gas characteristics is discussed. The GAD model in CO2 is in a 1D geometry with axial symmetry and provides results for the time evolution of the electron, gas and vibrational temperature of CO2, as well as for the molar fractions of the different species. |
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000403074000011 | Publication Date | 2016-10-04 | |
| 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 | Methusalem financing of the University of Antwerp; | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:142982 | Serial | 4570 | ||
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| Author | Nozaki, T.; Bogaerts, A.; Tu, X.; Sanden, R. | ||||
| Title | Special issue: Plasma Conversion | Type | Editorial | ||
| Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 14 | Issue | 14 | Pages | 1790061 |
| Keywords | Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000403699900015 | Publication Date | 2017-06-16 | |
| 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 | Open Access | Not_Open_Access | |
| Notes | Approved | Most recent IF: 2.846 | |||
| Call Number | PLASMANT @ plasmant @ c:irua:144211 | Serial | 4578 | ||
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| Author | Bogaerts, A.; De Bie, C.; Snoeckx, R.; Koz?k, T. | ||||
| Title | Plasma based CO2and CH4conversion: A modeling perspective | Type | A1 Journal article | ||
| Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 14 | Issue | 14 | Pages | 1600070 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | This paper gives an overview of our plasma chemistry modeling for CO2 and CH4 conversion in a dielectric barrier discharge (DBD) and microwave (MW) plasma. We focus on pure CO2 splitting and pure CH4 reforming, as well as mixtures of CO2/CH4, CH4/O2, and CO2/H2O. We show calculation results for the conversion, energy efficiency, and product formation, in comparison with experiments where possible. We also present the underlying chemical reaction pathways, to explain the observed trends. For pure CO2, a comparison is made between a DBD and MW plasma, illustrating that the higher energy efficiency of the latter is attributed to the more important role of the vibrational levels. |
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000403699900001 | Publication Date | 2016-09-08 | |
| 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 | 17 | Open Access | Not_Open_Access |
| Notes | Inter-university Attraction Pole (IAP/7); Federaal Wetenschapsbeleid; Francqui Research Foundation; Fonds De La Recherche Scientifique – FNRS, G.0383.16N ; Hercules Foundation; Flemish Government; UAntwerpen; | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:144209 | Serial | 4579 | ||
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| Author | Snoeckx, R.; Rabinovich, A.; Dobrynin, D.; Bogaerts, A.; Fridman, A. | ||||
| Title | Plasma-based liquefaction of methane: The road from hydrogen production to direct methane liquefaction | Type | A1 Journal article | ||
| Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 14 | Issue | 14 | Pages | 1600115 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | For the energy industry, a process that is able to transform methane—being the prime component of natural gas—efficiently into a liquid product would be equivalent to a goose with golden eggs. As such it is no surprise that research efforts in this field already date back to the nineteen hundreds. Plasma technology can be considered to be a novel player in this field, but nevertheless one with great potential. Over the past decades this technology has evolved from sole hydrogen production, over indirect methane liquefaction to eventually direct plasma-assisted methane liquefaction processes. An overview of this evolution and these processes is presented, from which it becomes clear that the near future probably lies with the direct two phase plasma-assisted methane liquefaction and the far future with the direct oxidative methane liquefaction. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000403699900008 | Publication Date | 2016-10-28 | |
| 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 | 2.846 | Times cited | 16 | Open Access | Not_Open_Access |
| Notes | Advanced Plasma Solutions; Drexel University; Federaal Wetenschapsbeleid; Fonds De La Recherche Scientifique – FNRS, G038316N V403616N ; | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:144212 | Serial | 4622 | ||
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| Author | Neyts, E.C.; Bal, K.M. | ||||
| Title | Effect of electric fields on plasma catalytic hydrocarbon oxidation from atomistic simulations | Type | A1 Journal article | ||
| Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 14 | Issue | 6 | Pages | e1600158 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The catalytic oxidative dehydrogenation of hydrocarbons is an industrially important process, in which selectivity is a key issue. We here investigate the conversion of methanol to formaldehyde on a vanadia surface employing long timescale simulations, reaching a time scale of seconds. In particular, we compare the thermal process to the case where an additional external electric field is applied, as would be the case in a direct plasma-catalysis setup. We find that the electric field influences the retention time of the molecules at the catalyst surface. These simulations provide an atomic scale insight in the thermal catalytic oxidative dehydrogenation process, and in how an external electric field may affect this process. | ||||
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| Publisher | Place of Publication | Weinheim | Editor | ||
| Language | Wos | 000403699900013 | Publication Date | 2016-11-08 | |
| 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 | 2 | Open Access | Not_Open_Access |
| Notes | Approved | Most recent IF: 2.846 | |||
| Call Number | UA @ lucian @ c:irua:144210 | Serial | 4647 | ||
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| Author | Alves, L.L.; Bogaerts, A. | ||||
| Title | Special Issue on Numerical Modelling of Low-Temperature Plasmas for Various Applications – Part I: Review and Tutorial Papers on Numerical Modelling Approaches | Type | Editorial | ||
| Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 14 | Issue | 14 | Pages | 1690011 |
| Keywords | Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | Publication Date | 2017-01-19 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1612-8850 | ISBN | Additional Links | UA library record | |
| Impact Factor | 2.846 | Times cited | 3 | Open Access | Not_Open_Access |
| Notes | Approved | Most recent IF: 2.846 | |||
| Call Number | PLASMANT @ plasmant @ c:irua:141721 | Serial | 4475 | ||
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| Author | Tinck, S.; Tillocher, T.; Georgieva, V.; Dussart, R.; Neyts, E.; Bogaerts, A. | ||||
| Title | Concurrent effects of wafer temperature and oxygen fraction on cryogenic silicon etching with SF6/O2plasmas | Type | A1 Journal article | ||
| Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 14 | Issue | 9 | Pages | 1700018 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Cryogenic plasma etching is a promising technique for high-control wafer development with limited plasma induced damage. Cryogenic wafer temperatures effectively reduce surface damage during etching, but the fundamental mechanism is not well understood. In this study, the influences of wafer temperature, gas mixture and substrate bias on the (cryogenic) etch rates of Si with SF6/O2 inductively coupled plasmas are experimentally and computationally investigated. The etch rates are measured in situ with double-point reflectometry and a hybrid computational Monte Carlo – fluid model is applied to calculate plasma properties. This work allows the reader to obtain a better insight in the effects of wafer temperature on the etch rate and to find operating conditions for successful anisotropic (cryo)etching. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000410773200012 | Publication Date | 2017-04-03 | |
| 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 | Open Access | Not_Open_Access | |
| Notes | Fonds Wetenschappelijk Onderzoek, 0880.212.840 ; Hercules Foundation; Flemish Government (Department EWI); Universiteit Antwerpen; | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @c:irua:145637 | Serial | 4708 | ||
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| Author | Belov, I.; Paulussen, S.; Bogaerts, A. | ||||
| Title | Pressure as an additional control handle for non-thermal atmospheric plasma processes | Type | A1 Journal article | ||
| Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 14 | Issue | 11 | Pages | 1700046 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | above atmospheric) pressure regimes (1–3.5 bar). It was demonstrated that these operational conditions significantly influence both the discharge dynamics and the process efficiencies of O2 and CO2 discharges. For the case of the O2 DBD, the pressure rise results in the amplification of the discharge current, the appearance of emission lines of the metal electrode material (Fe, Cr, Ni) in the optical emission spectrum and the formation of a granular film of the erosion products (10–300 nm iron oxide nanoparticles) on the reactor walls. Somewhat similar behavior was observed also for the CO2 DBD. The discharge current, the relative intensity of the CO Angstrom band measured by Optical Emission Spectroscopy (OES) and the CO2 conversion rates could be stimulated to some extent by the rise in pressure. The optimal conditions for the O2 DBD (P = 2 bar) and the CO2 DBD (P = 1.5 bar) are demonstrated. It can be argued that the dynamics of the microdischarges (MD) define the underlying process of this behavior. It could be demonstrated that the pressure increase stimulates the formation of more intensive but fewer MDs. In this way, the operating pressure can represent an additional tool to manipulate the properties of the MDs in a DBD, and as a result also the discharge performance. |
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000415339700011 | Publication Date | 2017-06-07 | |
| 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 | 1 | Open Access | Not_Open_Access |
| Notes | Seventh Framework Programme, Grant Agreement № 606889 (RAPID – Reactive Atmospheric Plasma processIng – Education Network) ; | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @c:irua:147024 | Serial | 4763 | ||
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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. | ||||
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| 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 | Rezaei, F.; Gorbanev, Y.; Chys, M.; Nikiforov, A.; Van Hulle, S.W.H.; Cos, P.; Bogaerts, A.; De Geyter, N. | ||||
| Title | Investigation of plasma-induced chemistry in organic solutions for enhanced electrospun PLA nanofibers | Type | A1 Journal article | ||
| Year | 2018 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 15 | Issue | 6 | Pages | 1700226 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Electrospinning is a versatile technique for the fabrication of polymer-based nano/microfibers. Both physical and chemical characteristics of pre-electrospinning polymer solutions affect the morphology and chemistry of electrospun nanofibers. An atmospheric-pressure plasma jet has previously been shown to induce physical modifications in polylactic acid (PLA) solutions. This work aims at investigating the plasma-induced chemistry in organic solutions of PLA, and their effects on the resultant PLA nanofibers. Therefore, very broad range of gas, liquid, and solid (nanofiber) analyzing techniques has been applied. Plasma alters the acidity of the solutions. SEM studies illustrated that complete fiber morphology enhancement only occurred when both PLA and solvent molecules were exposed to preelectrospinning plasma treatment. Additionally, the surface chemistry of the PLA nanofibers was mostly preserved. |
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000436407300005 | Publication Date | 2018-03-24 | |
| 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 | 12 | Open Access | Not_Open_Access |
| Notes | Fonds Wetenschappelijk Onderzoek, G.0379.15N ; FP7 Ideas: European Research Council, 335929 (PLASMATS) ; European Marie Sklodowska-Curie Individual Fellowship “LTPAM”, 657304 ; | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @c:irua:152173 | Serial | 4992 | ||
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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. | ||||
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| Language | Wos | 000441895700004 | Publication Date | 2018-05-07 | |
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| 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 | Brandenburg, R.; Bogaerts, A.; Bongers, W.; Fridman, A.; Fridman, G.; Locke, B.R.; Miller, V.; Reuter, S.; Schiorlin, M.; Verreycken, T.; Ostrikov, K.K. | ||||
| Title | White paper on the future of plasma science in environment, for gas conversion and agriculture | Type | A1 Journal article | ||
| Year | 2019 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 16 | Issue | 1 | Pages | 1700238 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Climate change, environmental pollution control, and resource utilization efficiency, as well as food security, sustainable agriculture, and water supply are among the main challenges facing society today. Expertise across different academic fields, technologies,anddisciplinesisneededtogeneratenewideastomeetthesechallenges. This “white paper” aims to provide a written summary by describing the main aspects and possibilities of the technology. It shows that plasma science and technology can make significant contributions to address the mentioned issues. The paper also addresses to people in the scientific community (inside and outside plasma science) to give inspiration for further work in these fields. | ||||
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| Language | Wos | 000455413600004 | Publication Date | 2018-07-05 | |
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| ISSN |
1612-8850 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.846 | Times cited | 19 | Open Access | Not_Open_Access |
| Notes | This paper is a result of the PlasmaShape project, supported by funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 316216. During this project, young scientists and renowned and outstanding scientists collaborated in the development of a political-scientific consensus paper as well as six scientific, strategic white papers. In an unique format core themes such as energy, optics and glass, medicine and hygiene, aerospace and automotive, plastics and textiles, environment and agriculture and their future development were discussed regarding scientific relevance and economic impact. We would like to thank our colleagues from 18 nations from all over the world (Australia, Belgium, Czech Republic, PR China, France, Germany, Great Britain, Italy, Japan, The Netherlands, Poland, Romania, Russia, Slovakia, Slovenia, Sweden, Switzerland, USA) who have participated both workshops of Future in Plasma Science I and II in Greifswald in 2015/2016. The valuable contribution of all participants during the workshops, the intensive cooperation between the project partners, and the comprehensive input of all working groups of Future in Plasma Science was the base for the present paper. Kindly acknowledged is the support of graphical work by C. Desjardins and K. Drescher. | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:156389 | Serial | 5146 | ||
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| Author | Van der Paal, J.; Fridman, G.; Bogaerts, A. | ||||
| Title | Ceramide cross-linking leads to pore formation: Potential mechanism behind CAP enhancement of transdermal drug delivery | Type | A1 Journal article | ||
| Year | 2019 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 16 | Issue | 16 | Pages | 1900122 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In recent years, cold atmospheric plasma (CAP) has been proposed as a novel method to enhance transdermal drug delivery, while avoiding tissue damage. However, the underlying mechanism for the increasing skin permeability upon CAP treatment is still undefined. We propose a mechanism in which CAP-generated reactive species induce cross-linking of skin lipids, leading to the generation of nanopores, thereby facilitating the permeation of drug molecules. Molecular dynamics simulations support this proposed mechanism. Furthermore, our results indicate that to achieve maximum enhancement of the permeability, the optimal treatment will depend on the exact lipid composition of the skin, as well as on the CAP source used. | ||||
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| Language | Wos | 000479747500001 | Publication Date | 2019-07-30 | |
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| 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 | Open Access | ||
| Notes | Approved | Most recent IF: 2.846 | |||
| Call Number | UA @ admin @ c:irua:161874 | Serial | 6287 | ||
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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. | ||||
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| Language | Wos | 000536892900001 | Publication Date | 2020-06-02 | |
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| 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 | Zhang, Q.‐Z.; Zhang, L.; Yang, D.‐Z.; Schulze, J.; Wang, Y.‐N.; Bogaerts, A. | ||||
| Title | Positive and negative streamer propagation in volume dielectric barrier discharges with planar and porous electrodes | Type | A1 Journal article | ||
| Year | 2021 | Publication | Plasma Processes And Polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 18 | Issue | 4 | Pages | 2000234 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The spatiotemporal dynamics of volume and surface positive and negative streamers in a pintoplate volume dielectric barrier discharge is investigated in this study. The discharge characteristics are found to be completely different for positive and negative streamers. First, the spatial propagation of a positive streamer is found to rely on electron avalanches caused by photo-electrons in front of the streamer head, whereas this is not the case for negative streamers. Second, our simulations reveal an interesting phenomenon of floating positive surface discharges, which develop when a positive streamer reaches a dielectric wall and which explain the experimentally observed branching characteristics. Third, we report for the first time, the interactions between a positive streamer and dielectric pores, in which both the pore diameter and depth affect the evolution of a positive streamer. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000617876700001 | Publication Date | 2021-02-17 | |
| 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 | Open Access | OpenAccess | |
| Notes | Dalian University of Technology, DUT19RC(3)045 ; National Natural Science Foundation of China, 12020101005 ; Deutsche Forschungsgemeinschaft, SFB 1316 project A5 ; Universiteit Antwerpen, TOP‐BOF ; The authors acknowledge financial support from the TOP-BOF project of the University of Antwerp. This study was carried out in part 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 University of Antwerp. Funding by the German Research Foundation (DFG) in the frame of the Collaborative Research Center SFB 1316, project A5, National Natural Science Foundation of China (No. 12020101005), and the Scientific Research Foundation from Dalian University of Technology (DUT19RC(3)045) is also acknowledged. | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @c:irua:176565 | Serial | 6744 | ||
| Permanent link to this record | |||||
| 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. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000865844800001 | Publication Date | 2022-10-11 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1612-8850 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.5 | Times cited | Open Access | OpenAccess | |
| Notes | Fonds Wetenschappelijk Onderzoek, 1200219N ; They also acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UA, where all computational work was performed. This study was financially supported by the Research Foundation–Flanders (FWO) (grant number 1200219N). | Approved | Most recent IF: 3.5 | ||
| Call Number | PLASMANT @ plasmant @c:irua:191404 | Serial | 7113 | ||
| Permanent link to this record | |||||
| Author | Lin, A.; Biscop, E.; Gorbanev, Y.; Smits, E.; Bogaerts, A. | ||||
| 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 | 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 | Tampieri, F.; Gorbanev, Y.; Sardella, E. | ||||
| Title | Plasma‐treated liquids in medicine: Let's get chemical | Type | A1 Journal Article | ||
| Year | 2023 | Publication | Plasma Processes and Polymers | Abbreviated Journal | Plasma Processes & Polymers |
| Volume | 20 | Issue | 9 | Pages | e2300077 |
| Keywords | A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| Abstract | Fundamental and applied research on plasma‐treated liquids for biomedical applications was boosted in the last few years, dictated by their advantages with respect to direct treatments. However, often, the lack of consistent analysis at a molecular level of these liquids, and of the processes used to produce them, have raised doubts of their usefulness in the clinic. The aim of this article is to critically discuss some basic aspects related to the use of plasma‐treated liquids in medicine, with a focus on their chemical composition. We analyze the main liquids used in the field, how they are affected by non‐thermal plasmas, and the possibility to replicate them without plasma treatment. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001005060700001 | Publication Date | 2023-06-08 | |
| 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 | Not_Open_Access | |
| Notes | We thank COST Actions CA20114 (Therapeutical Applications of Cold Plasmas) and CA19110 (Plasma Applications for Smart and Sustainable Agriculture) for the stimulating environment provided. Francesco Tampieri wishes to thank Dr. Cristina Canal for the helpful discussion during the planning stage of this paper. | Approved | Most recent IF: 3.5; 2023 IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @c:irua:197386 | Serial | 8814 | ||
| Permanent link to this record | |||||
| Author | Morais, E.; Bogaerts, A. | ||||
| Title | Modelling the dynamics of hydrogen synthesis from methane in nanosecond‐pulsed plasmas | Type | A1 Journal article | ||
| Year | 2024 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Processes & Polymers |
| Volume | 21 | Issue | 1 | Pages | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | A chemical kinetics model was developed to characterise the gas‐phase dynamics of H<sub>2</sub>production in nanosecond‐pulsed CH<sub>4</sub>plasmas. Pulsed behaviour was observed in the calculated electric field, electron temperature and species densities at all pressures. The model agrees reasonably with experimental results, showing CH<sub>4</sub>conversion at 30% and C<sub>2</sub>H<sub>2</sub>and H<sub>2</sub>as major products. The underlying mechanisms in CH<sub>4</sub>dissociation and H<sub>2</sub>formation were analysed, highlighting the large contribution of vibrationally excited CH<sub>4</sub>and H<sub>2</sub>to coupling energy from the plasma into gas‐phase heating, and revealing that H<sub>2</sub>synthesis is not affected by applied pressure, with selectivity remaining unchanged at ~42% in the 1–5 bar range. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001091258700001 | Publication Date | 2023-10-27 | |
| 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 | Not_Open_Access | |
| Notes | We gratefully acknowledge financial support by the Flemish Government through the Moonshot cSBO project “Power‐to‐Olefins” (P2O; HBC.2020.2620) and funding from the Independent Research Fund Denmark (project nr. 0217‐00231B). | Approved | Most recent IF: 3.5; 2024 IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @c:irua:201192 | Serial | 8983 | ||
| Permanent link to this record | |||||
| Author | Chai, Z.-N.; Wang, X.-C.; Yusupov, M.; Zhang, Y.-T. | ||||
| Title | Unveiling the interaction mechanisms of cold atmospheric plasma and amino acids by machine learning | Type | A1 Journal article | ||
| Year | 2024 | Publication | Plasma processes and polymers | Abbreviated Journal | |
| Volume | Issue | Pages | 1-26 | ||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma medicine has attracted tremendous interest in a variety of medical conditions, ranging from wound healing to antimicrobial applications, even in cancer treatment, through the interactions of cold atmospheric plasma (CAP) and various biological tissues directly or indirectly. The underlying mechanisms of CAP treatment are still poorly understood although the oxidative effects of CAP with amino acids, peptides, and proteins have been explored experimentally. In this study, machine learning (ML) technology is introduced to efficiently unveil the interaction mechanisms of amino acids and reactive oxygen species (ROS) in seconds based on the data obtained from the reactive molecular dynamics (MD) simulations, which are performed to probe the interaction of five types of amino acids with various ROS on the timescale of hundreds of picoseconds but with the huge computational load of several days. The oxidative reactions typically start with H-abstraction, and the details of the breaking and formation of chemical bonds are revealed; the modification types, such as nitrosylation, hydroxylation, and carbonylation, can be observed. The dose effects of ROS are also investigated by varying the number of ROS in the simulation box, indicating agreement with the experimental observation. To overcome the limits of timescales and the size of molecular systems in reactive MD simulations, a deep neural network (DNN) with five hidden layers is constructed according to the reaction data and employed to predict the type of oxidative modification and the probability of occurrence only in seconds as the dose of ROS varies. The well-trained DNN can effectively and accurately predict the oxidative processes and productions, which greatly improves the computational efficiency by almost ten orders of magnitude compared with the reactive MD simulation. This study shows the great potential of ML technology to efficiently unveil the underpinning mechanisms in plasma medicine based on the data from reactive MD simulations or experimental measurements. In this study, since reactive molecular dynamics simulation can currently only describe interactions between a few hundred atoms in a few hundred picoseconds, deep neural networks (DNN) are introduced to enhance the simulation results by predicting more data efficiently. image | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001202061200001 | Publication Date | 2024-04-15 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1612-8850 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 3.5 | Times cited | Open Access | ||
| Notes | Approved | Most recent IF: 3.5; 2024 IF: 2.846 | |||
| Call Number | UA @ admin @ c:irua:205512 | Serial | 9181 | ||
| Permanent link to this record | |||||
| Author | Sorée, B.; Magnus, W.; Pourtois, G. | ||||
| Title | Analytical and self-consistent quantum mechanical model for a surrounding gate MOS nanowire operated in JFET mode | Type | A1 Journal article | ||
| Year | 2008 | Publication | Journal of computational electronics | Abbreviated Journal | J Comput Electron |
| Volume | 7 | Issue | 3 | Pages | 380-383 |
| Keywords | A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We derive an analytical model for the electrostatics and the drive current in a silicon nanowire operating in JFET mode. We show that there exists a range of nanowire radii and doping densities for which the nanowire JFET satisfies reasonable device characteristics. For thin nanowires we have developed a self-consistent quantum mechanical model to obtain the electronic structure. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | S.l. | Editor | ||
| Language | Wos | 000208473800067 | Publication Date | 2008-02-20 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1569-8025;1572-8137; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.526 | Times cited | 70 | Open Access | |
| Notes | Approved | Most recent IF: 1.526; 2008 IF: NA | |||
| Call Number | UA @ lucian @ c:irua:89504 | Serial | 107 | ||
| Permanent link to this record | |||||
| Author | Clima, S.; Belmonte, A.; Degraeve, R.; Fantini, A.; Goux, L.; Govoreanu, B.; Jurczak, M.; Ota, K.; Redolfi, A.; Kar, G.S.; Pourtois, G. | ||||
| Title | Kinetic and thermodynamic heterogeneity : an intrinsic source of variability in Cu-based RRAM memories | Type | A1 Journal article | ||
| Year | 2017 | Publication | Journal of computational electronics | Abbreviated Journal | J Comput Electron |
| Volume | 16 | Issue | 4 | Pages | 1011-1016 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | <script type='text/javascript'>document.write(unpmarked('The resistive random-access memory (RRAM) device concept is close to enabling the development of a new generation of non-volatile memories, provided that their reliability issues are properly understood. The design of a RRAM operating with extrinsic defects based on metallic inclusions, also called conductive bridge RAM, allows the use of a large spectrum of solid electrolytes. However, when scaled to device dimensions that meet the requirements of the latest technological nodes, the discrete nature of the atomic structure of the materials impacts the device operation. Using density functional theory simulations, we evaluated the migration kinetics of Cu conducting species in amorphous and solid electrolyte materials, and established that atomic disorder leads to a large variability in terms of defect stability and kinetic barriers. This variability has a significant impact on the filament resistance and its dynamics, as evidenced during the formation step of the resistive filament. Also, the atomic configuration of the formed filament can age/relax to another metastable atomic configuration, and lead to a modulation of the resistivity of the filament. All these observations are qualitatively explained on the basis of the computed statistical distributions of the defect stability and on the kinetic barriers encountered in RRAM materials.')); | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Place of publication unknown | Editor | ||
| Language | Wos | 000417598100004 | Publication Date | 2017-08-04 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1569-8025 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.526 | Times cited | 2 | Open Access | Not_Open_Access |
| Notes | Approved | Most recent IF: 1.526 | |||
| Call Number | UA @ lucian @ c:irua:148569 | Serial | 4883 | ||
| Permanent link to this record | |||||
| Author | Berdiyorov, G.R.; Khalilov, U.; Hamoudi, H.; Neyts, E.C. | ||||
| Title | Effect of chemical modification on electronic transport properties of carbyne | Type | A1 Journal article | ||
| Year | 2021 | Publication | Journal Of Computational Electronics | Abbreviated Journal | J Comput Electron |
| Volume | Issue | Pages | |||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Using density functional theory in combination with the Green’s functional formalism, we study the effect of surface functionalization on the electronic transport properties of 1D carbon allotrope—carbyne. We found that both hydrogenation and fluorination result in structural changes and semiconducting to metallic transition. Consequently, the current in the functionalization systems increases significantly due to strong delocalization of electronic states along the carbon chain. We also study the electronic transport in partially hydrogenated carbyne and interface structures consisting of pristine and functionalized carbyne. In the latter case, current rectification is obtained in the system with rectification ratio up to 50%. These findings can be useful for developing carbyne-based structures with tunable electronic transport properties. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000617664900001 | Publication Date | 2021-02-13 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1569-8025 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.526 | Times cited | Open Access | OpenAccess | |
| Notes | Computational resources were provided by the research computing facilities of Qatar Environment and Energy Research Institute. Calculations are also conducted 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 University of Antwerp. U. Khalilov gratefully acknowledges financial support from the Fund of Scientific Research Flanders (FWO), Belgium, Grant number 12M1315N. | Approved | Most recent IF: 1.526 | ||
| Call Number | PLASMANT @ plasmant @c:irua:176169 | Serial | 6708 | ||
| Permanent link to this record | |||||
| Author | Khan, A.W.; Jan, F.; Saeed, A.; Zaka-ul-Islam, M.; Abrar, M.; Khattak, N.A.D.; Zakaullah, M. | ||||
| Title | Comparative study of electron temperature and excitation temperature in a magnetic pole enhanced-inductively coupled argon plasma | Type | A1 Journal article | ||
| Year | 2013 | Publication | Current applied physics | Abbreviated Journal | Curr Appl Phys |
| Volume | 13 | Issue | 7 | Pages | 1241-1246 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Magnetic Pole Enhanced-Inductively Coupled Plasmas (MaPE-ICPs) in analogy to the conventional ICPs exhibit two modes of operation, depending on the power coupling mechanism, i.e., a low power mode with dominant capacitive coupling (E-mode) and a high power mode with dominant inductive coupling (H-mode). A comparative study of the electron temperature measured by a Langmuir probe (T-e(LP)) and the electron excitation temperature (T-exc(OES)) determined by Optical Emission Spectroscopy (OES) is reported in the two distinct modes of a MaPE-ICP operated in argon. The dependence of T-e(LP), T-exc(OES) and their ratio (T-e(LP)/T-exc(OES)) on applied power (5-50 W) and gas pressure (15-60 mTorr) is explored, and the validity of T-exc(OES) as an alternative diagnostic to T-e(LP) is tested in the two modes of MaPE-ICP. The OES based non-invasive measurement of the plasma parameters such as electron temperature is very useful for plasma processing applications in which probe measurements are limited. (C) 2013 Elsevier B. V. All rights reserved. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Amsterdam | Editor | ||
| Language | Wos | 000322631400014 | Publication Date | 2013-04-17 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1567-1739; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.971 | Times cited | 13 | Open Access | |
| Notes | Approved | Most recent IF: 1.971; 2013 IF: 2.026 | |||
| Call Number | UA @ lucian @ c:irua:110718 | Serial | 421 | ||
| Permanent link to this record | |||||
| Author | Neyts, E.C.; Thijsse, B.J.; Mees, M.J.; Bal, K.M.; Pourtois, G. | ||||
| Title | Establishing uniform acceptance in force biased Monte Carlo simulations | Type | A1 Journal article | ||
| Year | 2012 | Publication | Journal of chemical theory and computation | Abbreviated Journal | J Chem Theory Comput |
| Volume | 8 | Issue | 6 | Pages | 1865-1869 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Uniform acceptance force biased Monte Carlo (UFMC) simulations have previously been shown to be a powerful tool to simulate atomic scale processes, enabling one to follow the dynamical path during the simulation. In this contribution, we present a simple proof to demonstrate that this uniform acceptance still complies with the condition of detailed balance, on the condition that the characteristic parameter lambda = 1/2 and that the maximum allowed step size is chosen to be sufficiently small. Furthermore, the relation to Metropolis Monte Carlo (MMC) is also established, and it is shown that UFMC reduces to MMC by choosing the characteristic parameter lambda = 0 [Rao, M. et al. Mol. Phys. 1979, 37, 1773]. Finally, a simple example compares the UFMC and MMC methods. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000305092400002 | Publication Date | 2012-05-16 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1549-9618;1549-9626; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.245 | Times cited | 20 | Open Access | |
| Notes | Approved | Most recent IF: 5.245; 2012 IF: 5.389 | |||
| Call Number | UA @ lucian @ c:irua:99090 | Serial | 1082 | ||
| Permanent link to this record | |||||
| Author | Bal, K.M.; Neyts, E.C. | ||||
| Title | Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds | Type | A1 Journal article | ||
| Year | 2015 | Publication | Journal of chemical theory and computation | Abbreviated Journal | J Chem Theory Comput |
| Volume | 11 | Issue | 11 | Pages | 4545-4554 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of reactive processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000362921700004 | Publication Date | 2015-09-02 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1549-9618 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.245 | Times cited | 41 | Open Access | |
| Notes | K.M.B. is funded as Ph.D. fellow (aspirant) of the FWOFlanders (Fund for Scientific Research-Flanders), Grant No. 11 V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) and the HPC infrastructure of the University of Antwerp (CalcUA), funded by the Hercules Foundation and the Flemish Government−Department EWI. | Approved | Most recent IF: 5.245; 2015 IF: 5.498 | ||
| Call Number | c:irua:128183 | Serial | 3991 | ||
| Permanent link to this record | |||||
| Author | Tchakoua, T.; Gerrits, N.; Smeets, E.W.F.; Kroes, G.-J. | ||||
| Title | SBH17 : benchmark database of barrier heights for dissociative chemisorption on transition metal surfaces | Type | A1 Journal article | ||
| Year | 2023 | Publication | Journal of chemical theory and computation | Abbreviated Journal | |
| Volume | 19 | Issue | 1 | Pages | 245-270 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Accurate barriers for rate controlling elementary reactions on metal surfaces are key to understanding, controlling, and predicting the rate of heterogeneously catalyzed processes. While barrier heights for gas phase reactions have been extensively benchmarked, dissociative chemisorption barriers for the reactions of molecules on metal surfaces have received much less attention. The first database called SBH10 and containing 10 entries was recently constructed based on the specific reaction parameter approach to density functional theory (SRP-DFT) and experimental results. We have now constructed a new and improved database (SBH17) containing 17 entries based on SRP-DFT and experiments. For this new SBH17 benchmark study, we have tested three algorithms (high, medium, and light) for calculating barrier heights for dissociative chemisorption on metals, which we have named for the amount of computational effort involved in their use. We test the performance of 14 density functionals at the GGA, GGA+vdW-DF, and meta-GGA rungs. Our results show that, in contrast with the previous SBH10 study where the BEEF-vdW-DF2 functional seemed to be most accurate, the workhorse functional PBE and the MS2 density functional are the most accurate of the GGA and meta-GGA functionals tested. Of the GGA+vdW functionals tested, the SRP32-vdW-DF1 functional is the most accurate. Additionally, we found that the medium algorithm is accurate enough for assessing the performance of the density functionals tested, while it avoids geometry optimizations of minimum barrier geometries for each density functional tested. The medium algorithm does require metal lattice constants and interlayer distances that are optimized separately for each functional. While these are avoided in the light algorithm, this algorithm is found not to give a reliable description of functional performance. The combination of relative ease of use and demonstrated reliability of the medium algorithm will likely pave the way for incorporation of the SBH17 database in larger databases used for testing new density functionals and electronic structure methods. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000903286100001 | Publication Date | 2022-12-19 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1549-9618 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.5 | Times cited | Open Access | OpenAccess | |
| Notes | Approved | Most recent IF: 5.5; 2023 IF: 5.245 | |||
| Call Number | UA @ admin @ c:irua:193426 | Serial | 7274 | ||
| Permanent link to this record | |||||
| Author | Bal, K.M. | ||||
| Title | Reweighted Jarzynski sampling : acceleration of rare events and free energy calculation with a bias potential learned from nonequilibrium work | Type | A1 Journal article | ||
| Year | 2021 | Publication | Journal Of Chemical Theory And Computation | Abbreviated Journal | J Chem Theory Comput |
| Volume | 17 | Issue | 11 | Pages | 6766-6774 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the reaction coordinate, and the Jarzynski equality is used to learn an approximate free energy surface from the nonequilibrium work distribution. This free energy estimate is represented in a compact form as an artificial neural network and used as an external bias potential to accelerate rare events in a subsequent molecular dynamics simulation. The final free energy estimate is then obtained by reweighting the equilibrium probability distribution of the reaction coordinate sampled under the influence of the external bias. We apply our reweighted Jarzynski sampling recipe to four processes of varying scales and complexities.spanning chemical reaction in the gas phase, pair association in solution, and droplet nucleation in supersaturated vapor. In all cases, we find reweighted Jarzynski sampling to be a very efficient strategy, resulting in rapid convergence of the free energy to high precision. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000718183600008 | Publication Date | 2021-10-29 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN |
1549-9618 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.245 | Times cited | Open Access | OpenAccess | |
| Notes | Approved | Most recent IF: 5.245 | |||
| Call Number | UA @ admin @ c:irua:184676 | Serial | 8479 | ||
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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. | ||||
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| 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 ; Coordenação de Aperfeiçoamento 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 | ||
| Permanent link to this record | |||||
| Author | Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R. | ||||
| Title | Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations | Type | A1 Journal article | ||
| Year | 2022 | Publication | Journal Of Chemical Information And Modeling | Abbreviated Journal | J Chem Inf Model |
| Volume | 62 | Issue | 1 | Pages | 129-141 |
| Keywords | A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. | ||||
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| 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 | |||||