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Author | Kovács, A.; Yusupov, M.; Cornet, I.; Billen, P.; Neyts, E.C. | ||||
Title | Effect of natural deep eutectic solvents of non-eutectic compositions on enzyme stability | Type | A1 Journal article | ||
Year | 2022 | Publication | Journal Of Molecular Liquids | Abbreviated Journal | J Mol Liq |
Volume | 366 | Issue | Pages | 120180-17 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS) | ||||
Abstract | Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved. | ||||
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Language | Wos | 000865431800010 | Publication Date | 2022-08-25 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0167-7322 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | 6 | Times cited | Open Access | Not_Open_Access | |
Notes | Approved | Most recent IF: 6 | |||
Call Number | UA @ admin @ c:irua:191538 | Serial | 7265 | ||
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Author | Faraji, F.; Neek-Amal, M.; Neyts, E.C.; Peeters, F.M. | ||||
Title | Cation-controlled permeation of charged polymers through nanocapillaries | Type | A1 Journal article | ||
Year | 2023 | Publication | Physical review E | Abbreviated Journal | Phys Rev E |
Volume | 107 | Issue | 3 | Pages | 034501-34510 |
Keywords | A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Molecular dynamics simulations are used to study the effects of different cations on the permeation of charged polymers through flat capillaries with heights below 2 nm. Interestingly, we found that, despite being monovalent, Li+ , Na+ , and K+ cations have different effects on polymer permeation, which consequently affects their transmission speed throughout those capillaries. We attribute this phenomenon to the interplay of the cations' hydration free energies and the hydrodynamic drag in front of the polymer when it enters the capillary. Different alkali cations exhibit different surface versus bulk preferences in small clusters of water under the influence of an external electric field. This paper presents a tool to control the speed of charged polymers in confined spaces using cations. | ||||
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Language | Wos | 000955986000006 | Publication Date | 2023-03-17 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2470-0053 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.4 | Times cited | 1 | Open Access | Not_Open_Access |
Notes | Approved | Most recent IF: 2.4; 2023 IF: 2.366 | |||
Call Number | UA @ admin @ c:irua:196089 | Serial | 7586 | ||
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Author | Khalilov, U.; Uljayev, U.; Mehmonov, K.; Nematollahi, P.; Yusupov, M.; Neyts, E.C.; Neyts, E.C. | ||||
Title | Can endohedral transition metals enhance hydrogen storage in carbon nanotubes? | Type | A1 Journal article | ||
Year | 2024 | Publication | International journal of hydrogen energy | Abbreviated Journal | |
Volume | 55 | Issue | Pages | 640-610 | |
Keywords | A1 Journal article; Engineering sciences. Technology; Modelling and Simulation in Chemistry (MOSAIC); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The safe and efficient use of hydrogen energy, which is in high demand worldwide today, requires efficient hydrogen storage. Despite significant advances in hydrogen storage using carbon-based nanomaterials, including carbon nanotubes (CNTs), efforts to substantially increase the storage capacity remain less effective. In this work, we demonstrate the effect of endohedral transition metal atoms on the hydrogen storage capacity of CNTs using reactive molecular dynamics simulations. We find that an increase in the volume fraction of endohedral nickel atoms leads to an increase in the concentration of physisorbed hydrogen molecules around single-walled CNTs (SWNTs) by approximately 1.6 times compared to pure SWNTs. The obtained results provide insight into the underlying mechanisms of how endohedral transition metal atoms enhance the hydrogen storage ability of SWNTs under nearly ambient conditions. | ||||
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Language | Wos | 001142427400001 | Publication Date | 2023-11-24 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0360-3199 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7.2 | Times cited | Open Access | Not_Open_Access | |
Notes | Approved | Most recent IF: 7.2; 2024 IF: 3.582 | |||
Call Number | UA @ admin @ c:irua:202315 | Serial | 9006 | ||
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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 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1367-2630; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.786 | Times cited | 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 | Engelmann, Y.; Bogaerts, A.; Neyts, E.C. | ||||
Title | Thermodynamics at the nanoscale : phase diagrams of nickel-carbon nanoclusters and equilibrium constants for face transitions | Type | A1 Journal article | ||
Year | 2014 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
Volume | 6 | Issue | Pages | 11981-11987 | |
Keywords | A1 Journal article; PLASMANT | ||||
Abstract | Using reactive molecular dynamics simulations, the melting behavior of nickelcarbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickelcarbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method. | ||||
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Publisher | Place of Publication | Cambridge | Editor | ||
Language | Wos | 000343000800049 | Publication Date | 2014-07-24 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 2040-3364;2040-3372; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7.367 | Times cited | 20 | Open Access | |
Notes | Approved | Most recent IF: 7.367; 2014 IF: 7.394 | |||
Call Number | UA @ lucian @ c:irua:119408 | Serial | 3636 | ||
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Author | Zhang, Y.-R.; Van Laer, K.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Can plasma be formed in catalyst pores? A modeling investigation | Type | A1 Journal article | ||
Year | 2016 | Publication | Applied catalysis : B : environmental | Abbreviated Journal | Appl Catal B-Environ |
Volume | 185 | Issue | 185 | Pages | 56-67 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | tWe investigate microdischarge formation inside catalyst pores by a two-dimensional fluid model forvarious pore sizes in the m-range and for various applied voltages. Indeed, this is a poorly understoodphenomenon in plasma catalysis. The calculations are performed for a dielectric barrier discharge inhelium, at atmospheric pressure. The electron and ion densities, electron temperature, electric field andpotential, as well as the electron impact ionization and excitation rate and the densities of excited plasmaspecies, are examined for a better understanding of the characteristics of the plasma inside a pore. Theresults indicate that the pore size and the applied voltage are critical parameters for the formation of amicrodischarge inside a pore. At an applied voltage of 20 kV, our calculations reveal that the ionizationmainly takes place inside the pore, and the electron density shows a significant increase near and inthe pore for pore sizes larger than 200m, whereas the effect of the pore on the total ion density isevident even for 10m pores. When the pore size is fixed at 30m, the presence of the pore has nosignificant influence on the plasma properties at an applied voltage of 2 kV. Upon increasing the voltage,the ionization process is enhanced due to the strong electric field and high electron temperature, andthe ion density shows a remarkable increase near and in the pore for voltages above 10 kV. These resultsindicate that the plasma species can be formed inside pores of structured catalysts (in the m range),and they may interact with the catalyst surface, and affect the plasma catalytic process. | ||||
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Language | Wos | 000369452000006 | Publication Date | 2015-12-11 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0926-3373 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 9.446 | Times cited | 75 | Open Access | |
Notes | This work was supported by the Fund for Scientific ResearchFlanders (FWO) (Grant no. G.0217.14N), the National Natural Sci-ence Foundation of China (Grant no. 11405019), and the ChinaPostdoctoral Science Foundation (Grant no. 2015T80244). Theauthors are very grateful to V. Meynen for the useful discussions oncatalysts. This work was carried out in part using the Turing HPCinfrastructure at the CalcUA core facility of the Universiteit Antwer-pen, a division of the Flemish Supercomputer Center VSC, fundedby the Hercules Foundation, the Flemish Government (departmentEWI) and the University of Antwerp. | Approved | Most recent IF: 9.446 | ||
Call Number | c:irua:129808 | Serial | 3984 | ||
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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 | |
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 | |
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 | Van der Paal, J.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A. | ||||
Title | Effect of lipid peroxidation on membrane permeability of cancer and normal cells subjected to oxidative stress | Type | A1 Journal article | ||
Year | 2016 | Publication | Chemical science | Abbreviated Journal | Chem Sci |
Volume | 7 | Issue | 7 | Pages | 489-498 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | We performed molecular dynamics simulations to investigate the effect of lipid peroxidation products on the structural and dynamic properties of the cell membrane. Our simulations predict that the lipid order in a phospholipid bilayer, as a model system for the cell membrane, decreases upon addition of lipid peroxidation products. Eventually, when all phospholipids are oxidized, pore formation can occur. This will allow reactive species, such as reactive oxygen and nitrogen species (RONS), to enter the cell and cause oxidative damage to intracellular macromolecules, such as DNA or proteins. On the other hand, upon increasing the cholesterol fraction of lipid bilayers, the cell membrane order increases, eventually reaching a certain threshold, from which cholesterol is able to protect the membrane against pore formation. This finding is crucial for cancer treatment by plasma technology, producing a large number of RONS, as well as for other cancer treatment methods that cause an increase in the concentration of extracellular RONS. Indeed, cancer cells contain less cholesterol than their healthy counterparts. Thus, they will be more vulnerable to the consequences of lipid peroxidation, eventually enabling the penetration of RONS into the interior of the cell, giving rise to oxidative stress, inducing pro-apoptotic factors. This provides, for the first time, molecular level insight why plasma can selectively treat cancer cells, while leaving their healthy counterparts undamaged, as is indeed experimentally demonstrated. | ||||
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Language | Wos | 000366826900058 | Publication Date | 2015-10-16 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2041-6520 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.668 | Times cited | 106 | Open Access | |
Notes | The authors acknowledge nancial support from the Fund for Scientic Research (FWO) Flanders, grant number G012413N. The calculations were performed 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: 8.668 | ||
Call Number | c:irua:131058 | Serial | 3986 | ||
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Author | Khalilov, U.; Bogaerts, A.; Neyts, E.C. | ||||
Title | Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors | Type | A1 Journal article | ||
Year | 2015 | Publication | Nature communications | Abbreviated Journal | Nat Commun |
Volume | 6 | Issue | 6 | Pages | 10306 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level. | ||||
Address | PLASMANT research group, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium | ||||
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Publisher | Place of Publication | Editor | |||
Language | English | Wos | 000367584500001 | Publication Date | 2015-12-22 |
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ISSN | 2041-1723 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 12.124 | Times cited | 37 | Open Access | |
Notes | The authors gratefully acknowledge financial support from the Fund of Scientific Research Flanders (FWO), Belgium, grant number 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. We thank Professor Adri C. T. van Duin for sharing the ReaxFF code. | Approved | Most recent IF: 12.124; 2015 IF: 11.470 | ||
Call Number | c:irua:129975 | Serial | 3990 | ||
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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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Language | Wos | 000362921700004 | Publication Date | 2015-09-02 | |
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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 | ||
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Author | Neyts, E.C.; Ostrikov, K.K.; Sunkara, M.K.; Bogaerts, A. | ||||
Title | Plasma Catalysis: Synergistic Effects at the Nanoscale | Type | A1 Journal article | ||
Year | 2015 | Publication | Chemical reviews | Abbreviated Journal | Chem Rev |
Volume | 115 | Issue | 115 | Pages | 13408-13446 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Thermal-catalytic gas processing is integral to many current industrial processes. Ever-increasing demands on conversion and energy efficiencies are a strong driving force for the development of alternative approaches. Similarly, synthesis of several functional materials (such as nanowires and nanotubes) demands special processing conditions. Plasma catalysis provides such an alternative, where the catalytic process is complemented by the use of plasmas that activate the source gas. This combination is often observed to result in a synergy between plasma and catalyst. This Review introduces the current state-of-the-art in plasma catalysis, including numerous examples where plasma catalysis has demonstrated its benefits or shows future potential, including CO2 conversion, hydrocarbon reforming, synthesis of nanomaterials, ammonia production, and abatement of toxic waste gases. The underlying mechanisms governing these applications, as resulting from the interaction between the plasma and the catalyst, render the process highly complex, and little is known about the factors leading to the often-observed synergy. This Review critically examines the catalytic mechanisms relevant to each specific application. | ||||
Address | Department of Chemistry, Research Group PLASMANT, Universiteit Antwerpen , Universiteitsplein 1, 2610 Wilrijk-Antwerp, Belgium | ||||
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Language | English | Wos | 000367563000006 | Publication Date | 2015-11-30 |
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ISSN | 0009-2665 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 47.928 | Times cited | 204 | Open Access | |
Notes | ECN and AB gratefully acknowledge financial support from the Fund of Scientific Research Flanders (FWO), Belgium, Grant Number G.0217.14N. KO acknowledges partial support by the Australian Research Council and CSIRO’s OCE Science Leaders Program. MKS acknowledges partial support from US National Science Foundation through grants DMS 1125909 and EPSCoR 1355448 and also PhD students Babajide Ajayi, Apolo Nambo and Maria Carreon for their help. | Approved | Most recent IF: 47.928; 2015 IF: 46.568 | ||
Call Number | c:irua:130001 | Serial | 3993 | ||
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Author | Khalilov, U.; Yusupov, M.; Bogaerts, A.; Neyts, E.C. | ||||
Title | Selective Plasma Oxidation of Ultrasmall Si Nanowires | Type | A1 Journal article | ||
Year | 2016 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
Volume | 120 | Issue | 120 | Pages | 472-477 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Device performance of Si|SiOx core-shell based nanowires critically depends on the exact control over the oxide thickness. Low-temperature plasma oxidation is a highly promising alternative to thermal oxidation allowing for improved control over the oxidation process, in particular for ultrasmall Si nanowires. We here elucidate the room temperature plasma oxidation mechanisms of ultrasmall Si nanowires using hybrid molecular dynamics / force-bias Monte Carlo simulations. We demonstrate how the oxidation and concurrent water formation mechanisms are a function of the oxidizing plasma species and we demonstrate how the resulting core-shell oxide thickness can be controlled through these species. A new mechanism of water formation is discussed in detail. The results provide a detailed atomic level explanation of the oxidation process of highly curved Si surfaces. These results point out a route toward plasma-based formation of ultrathin core-shell Si|SiOx nanowires at room temperature. | ||||
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Language | Wos | 000368562200057 | Publication Date | 2015-12-21 | |
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ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.536 | Times cited | 3 | Open Access | |
Notes | U.K. and M.Y. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grants 12M1315N and 1200216N. This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. We thank Prof. A. C. T. van Duin for sharing the ReaxFF code. | Approved | Most recent IF: 4.536 | ||
Call Number | c:irua:130677 | Serial | 4002 | ||
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Author | Neyts, E.C. | ||||
Title | Plasma-Surface Interactions in Plasma Catalysis | Type | A1 Journal article | ||
Year | 2016 | Publication | Plasma chemistry and plasma processing | Abbreviated Journal | Plasma Chem Plasma P |
Volume | 36 | Issue | 36 | Pages | 185-212 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | In this paper the various elementary plasma—surface interaction processes occurring in plasma catalysis are critically evaluated. Specifically, plasma catalysis at atmospheric pressure is considered. The importance of the various processes is analyzed for the most common plasma catalysis sources, viz. the dielectric barrier discharge and the gliding arc. The role and importance of surface chemical reactions (including adsorption, surface-mediated association and dissociation reactions, and desorption), plasma-induced surface modification, photocatalyst activation, heating, charging, surface discharge formation and electric field enhancement are discussed in the context of plasma catalysis. Numerous examples are provided to demonstrate the importance of the various processes. | ||||
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Language | Wos | 000370720800011 | Publication Date | 2015-10-16 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0272-4324 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.355 | Times cited | 66 | Open Access | |
Notes | The author is indebted to many colleagues for fruitful discussions. In particular discussions with A. Bogaerts (University of Antwerp, Belgium), H.-H. Kim (AIST, Japan), J. C. Whitehead (University of Manchester, UK) and T. Nozaki (Tokyo Institute of Technology, Japan) are greatfully acknowledged and appreciated. | Approved | Most recent IF: 2.355 | ||
Call Number | c:irua:130742 | Serial | 4004 | ||
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Author | Khosravian, N.; Kamaraj, B.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations | Type | A1 Journal article | ||
Year | 2016 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
Volume | 6 | Issue | 6 | Pages | 19466 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment. | ||||
Address | Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium | ||||
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Publisher | Place of Publication | Editor | |||
Language | English | Wos | 000369573900001 | Publication Date | 2016-02-09 |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.259 | Times cited | 7 | Open Access | |
Notes | The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number G012413N. The calculations were performed 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: 4.259 | ||
Call Number | c:irua:131610 | Serial | 4031 | ||
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Author | Bal, K.M.; Neyts, E.C. | ||||
Title | Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations | Type | A1 Journal article | ||
Year | 2016 | Publication | Chemical science | Abbreviated Journal | Chem Sci |
Volume | 7 | Issue | 7 | Pages | 5280-5286 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Atomistic simulations can in principle provide an unbiased description of all mechanisms, intermediates, and products of complex chemical processes. However, due to the severe time scale limitation of conventional simulation techniques, unrealistically high simulation temperatures are usually applied, which are a poor approximation of most practically relevant low-temperature applications. In this work, we demonstrate the direct observation at the atomic scale of the pyrolysis and oxidation of n-dodecane at temperatures as low as 700 K through the use of a novel simulation technique, collective variable-driven hyperdynamics (CVHD). A simulated timescale of up to 39 seconds is reached. Product compositions and dominant mechanisms are found to be strongly temperature-dependent, and are consistent with experiments and kinetic models. These simulations provide a first atomic-level look at the full dynamics of the complicated fuel combustion process at industrially relevant temperatures and time scales, unattainable by conventional molecular dynamics simulations. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000380893900059 | Publication Date | 2016-05-05 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2041-6520 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.668 | Times cited | 22 | Open Access | |
Notes | K. M. B. is funded as PhD fellow (aspirant) of the FWO-Flanders (Fund for Scientic Research-Flanders), Grant 11V8915N. 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. The authors would also like to thank S. Banerjee for assisting with the interpretation of the experimental results. | Approved | Most recent IF: 8.668 | ||
Call Number | c:irua:134577 c:irua:135670 | Serial | 4105 | ||
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Author | Tinck, S.; Tillocher, T.; Dussart, R.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Elucidating the effects of gas flow rate on an SF6inductively coupled plasma and on the silicon etch rate, by a combined experimental and theoretical investigation | 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 | 385201 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Experiments show that the etch rate of Si with SF6 inductively coupled plasma (ICP) is significantly influenced by the absolute gas flow rate in the range of 50–600 sccm, with a maximum at around 200 sccm. Therefore, we numerically investigate the effects of the gas flow rate on the bulk plasma properties and on the etch rate, to obtain more insight in the underlying reasons of this effect. A hybrid Monte Carlo—fluid model is applied to simulate an SF6 ICP. It is found that the etch rate is influenced by two simultaneous effects: (i) the residence time of the gas and (ii) the temperature profile of the plasma in the ICP volume, resulting indeed in a maximum etch rate at 200 sccm. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000384095900011 | Publication Date | 2016-08-24 | |
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 | 1 | Open Access | |
Notes | We are very grateful to Mark Kushner for providing the computational model. The Fund for Scientific Research Flanders (FWO; grant no. 0880.212.840) is acknowledged for financial support of this work. The work 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. | Approved | Most recent IF: 2.588 | ||
Call Number | c:irua:134867 | Serial | 4108 | ||
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Author | Huygh, S.; Bogaerts, A.; Neyts, E.C. | ||||
Title | How Oxygen Vacancies Activate CO2 Dissociation on TiO2 Anatase (001) | Type | A1 Journal article | ||
Year | 2016 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
Volume | 120 | Issue | 120 | Pages | 21659-21669 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The adsorption, dissociation, and diffusion of CO2 on the anatase (001) surface was studied using DFT by means of the generalized gradient approximation using the Perdew−Burcke−Ernzerhof (PBE)-functional and applying corrections for long-range dispersion interactions. Different stable adsorption configurations were identified for the fully oxidized surface. The most stable adsorption configuration is the monodentated carbonate-like structure. Small energy barriers were identified for the conversion of a physisorbed to a chemisorbed configuration. CO2 dissociation is found to be unfeasible on the stoichiometric surface. The introduction of oxygen vacancy defects gives rise to new highly stable adsorption configurations with a stronger activation of the C−O bonds. This leads to the possibility of exothermic dissociation of CO2 with barriers up to 22.2 kcal/mol, corresponding to chemical lifetimes of less than 4 s at 300 K. These reactions cause a CO molecule to be formed, which will easily desorb, and the reduced surface to become oxidized. It is clear that oxygen vacancy defects play a key role in the catalytic activity of an anatase (001) surface. Oxygen vacancies play an important role in the dissociation of CO2 on the anatase (001) surface, and will play a significant role in complex problems, such as the catalytic conversion of CO2 to value-added chemicals. |
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000384626800055 | Publication Date | 2016-09-02 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.536 | Times cited | 49 | Open Access | |
Notes | Stijn Huygh is funded as an aspirant of the Research Foundation Flanders (FWO, project number 11C0115N). This work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UAntwerpen. | Approved | Most recent IF: 4.536 | ||
Call Number | PLASMANT @ plasmant @ c:irua:136164 | Serial | 4291 | ||
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Author | Zhang, Y.-R.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Influence of the Material Dielectric Constant on Plasma Generation inside Catalyst Pores | Type | A1 Journal article | ||
Year | 2016 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
Volume | 120 | Issue | 120 | Pages | 25923-25934 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Plasma catalysis is gaining increasing interest for various environmental applications, but the crucial question is whether plasma can be created inside catalyst pores and under which conditions. In practice, various catalytic support materials are used, with various dielectric constants. We investigate here the influence of the dielectric constant on the plasma properties inside catalyst pores and in the sheath in front of the pores, for various pore sizes. The calculations are performed by a two-dimensional fluid model for an atmospheric pressure dielectric barrier discharge in helium. The electron impact ionization rate, electron temperature, electron and ion density, as well as the potential distribution and surface charge density, are analyzed for a better understanding of the discharge behavior inside catalyst pores. The results indicate that, in a 100 μm pore, the electron impact ionization in the pore, which is characteristic for the plasma generation inside the pore, is greatly enhanced for dielectric constants below 300. Smaller pore sizes only yield enhanced ionization for smaller dielectric constants, i.e., up to εr = 200, 150, and 50 for pore sizes of 50, 30, and 10 μm. Thus, the most common catalyst supports, i.e., Al2O3 and SiO2, which have dielectric constants around εr = 8−11 and 4.2, respectively, should allow more easily that microdischarges can be formed inside catalyst pores, even for smaller pore sizes. On the other hand, ferroelectric materials with dielectric constants above 300 never seem to yield plasma enhancement inside catalyst pores, not even for 100 μm pore sizes. Furthermore, it is clear that the dielectric constant of the material has a large effect on the extent of plasma enhancement inside the catalyst pores, especially in the range between εr = 4 and εr = 200. The obtained results are explained in detail based on the surface charge density at the pore walls, and the potential distribution and electron temperature inside and above the pores. The results obtained with this model are important for plasma catalysis, as the production plasma species in catalyst pores might affect the catalyst properties, and thus improve the applications of plasma catalysis. |
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000388429100029 | Publication Date | 2016-11-17 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.536 | Times cited | 34 | Open Access | |
Notes | This work was supported by the Fund for Scientific Research Flanders (FWO) (Grant G.0217.14N), the National Natural Science Foundation of China (Grant 11405019), and the China Postdoctoral Science Foundation (Grant 2015T80244). This work 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. | Approved | Most recent IF: 4.536 | ||
Call Number | PLASMANT @ plasmant @ c:irua:138602 | Serial | 4319 | ||
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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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Series Volume | Series Issue | Edition | |||
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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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 | |
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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 | Bal, K.M.; Bogaerts, A.; Neyts, E.C. | ||||
Title | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | Type | A1 Journal article | ||
Year | 2020 | Publication | Journal Of Physical Chemistry Letters | Abbreviated Journal | J Phys Chem Lett |
Volume | 11 | Issue | 2 | Pages | 401-406 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | We present an approach to incorporate the effect of vibrational nonequilibrium in molecular dynamics (MD) simulations. A perturbed canonical ensemble, in which selected modes are excited to higher temperature while all others remain equilibrated at low temperature, is simulated by applying a specifically tailored bias potential. Our method can be readily applied to any (classical or quantum mechanical) MD setup at virtually no additional computational cost and allows the study of reactions of vibrationally excited molecules in nonequilibrium environments such as plasmas. In combination with enhanced sampling methods, the vibrational efficacy and mode selectivity of vibrationally stimulated reactions can then be quantified in terms of chemically relevant observables, such as reaction rates and apparent free energy barriers. We first validate our method for the prototypical hydrogen exchange reaction and then show how it can capture the effect of vibrational excitation on a symmetric SN2 reaction and radical addition on CO2. | ||||
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Language | Wos | 000508473400008 | Publication Date | 2020-01-16 | |
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ISSN | 1948-7185 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 5.7 | Times cited | Open Access | ||
Notes | Universiteit Antwerpen; Fonds Wetenschappelijk Onderzoek, 12ZI420N ; Departement Economie, Wetenschap en Innovatie van de Vlaamse Overheid; K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation − Flanders), Grant 12ZI420N, and through a TOP-BOF research project of the University of Antwerp. 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: 5.7; 2020 IF: 9.353 | ||
Call Number | PLASMANT @ plasmant @c:irua:165587 | Serial | 5442 | ||
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Author | Fukuhara, S.; Bal, K.M.; Neyts, E.C.; Shibuta, Y. | ||||
Title | Accelerated molecular dynamics simulation of large systems with parallel collective variable-driven hyperdynamics | Type | A1 Journal article | ||
Year | 2020 | Publication | Computational Materials Science | Abbreviated Journal | Comp Mater Sci |
Volume | 177 | Issue | Pages | 109581 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The limitation in time and length scale is a major issue of molecular dynamics (MD) simulation. Although several methods have been developed to extend the MD time scale, their performance usually deteriorates with increasing system size. Therefore, an acceleration method which is applicable to large systems is required to bridge the gap between the MD simulations and target phenomena. In this study, an accelerated MD method for large system is developed based on the collective variable-driven hyperdynamics (CVHD) method [K.M. Bal and E.C. Neyts, 2015]. The key idea is to run CVHD in parallel with rate control and accelerate multiple possible events simultaneously. Using this novel method, carbon diffusion in bcc-iron bicrystal with grain boundary is examined as an application for practical materials. Carbon atoms reaching at the grain boundary are trapped whereas carbon atoms in the bulk region diffuse randomly, and both dynamic regimes can be simultaneously accelerated with the parallel CVHD technique. | ||||
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Language | Wos | 000519576300001 | Publication Date | 2020-02-08 | |
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ISSN | 0927-0256 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.3 | Times cited | Open Access | ||
Notes | JSPS, J22727 ; Japan Society for the Promotion of Science; This work was supported by Grant-in-Aid for Scientific Research (B) (No.19H02415) and Grant-in-Aid for JSPS Research Fellow (No.18J22727) from Japan Society for the Promotion of Science (JSPS), Japan. S.F. was supported by JSPS through the Program for Leading Graduate Schools (MERIT). Data availability The data required to reproduce these findings are available from the corresponding authors upon reasonable request. | Approved | Most recent IF: 3.3; 2020 IF: 2.292 | ||
Call Number | PLASMANT @ plasmant @c:irua:166773 | Serial | 6333 | ||
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Author | Jafarzadeh, A.; Bal, K.M.; Bogaerts, A.; Neyts, E.C. | ||||
Title | Activation of CO2on Copper Surfaces: The Synergy between Electric Field, Surface Morphology, and Excess Electrons | Type | A1 Journal article | ||
Year | 2020 | Publication | Journal Of Physical Chemistry C | Abbreviated Journal | J Phys Chem C |
Volume | 124 | Issue | 12 | Pages | 6747-6755 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | In this work, we use density functional theory calculations to study the combined effect of external electric fields, surface morphology, and surface charge on CO2 activation over Cu(111), Cu(211), Cu(110), and Cu(001) surfaces. We observe that the binding energy of the CO2 molecule on Cu surfaces increases significantly upon increasing the applied electric field strength. In addition, rougher surfaces respond more effectively to the presence of the external electric field toward facilitating the formation of a carbonate-like CO2 structure and the transformation of the most stable adsorption mode from physisorption to chemisorption. The presence of surface charges further strengthens the electric field effect and consequently causes an improved bending of the CO2 molecule and C−O bond length elongation. On the other hand, a net charge in the absence of an externally applied electric field shows only a marginal effect on CO2 binding. The chemisorbed CO2 is more stable and further activated when the effects of an external electric field, rough surface, and surface charge are combined. These results can help to elucidate the underlying factors that control CO2 activation in heterogeneous and plasma catalysis, as well as in electrochemical processes. | ||||
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Language | Wos | 000526396900030 | Publication Date | 2020-03-26 | |
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ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.7 | Times cited | Open Access | ||
Notes | Bijzonder Onderzoeksfonds, 32249 ; The financial support from the TOP research project of the Research Fund of the University of Antwerp (grant ID: 32249) is highly acknowledged by the authors. The computational resources used in this study were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Governmentdepartment EWI. | Approved | Most recent IF: 3.7; 2020 IF: 4.536 | ||
Call Number | PLASMANT @ plasmant @c:irua:168606 | Serial | 6361 | ||
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Author | Engelmann, Y.; Mehta, P.; Neyts, E.C.; Schneider, W.F.; Bogaerts, A. | ||||
Title | Predicted Influence of Plasma Activation on Nonoxidative Coupling of Methane on Transition Metal Catalysts | Type | A1 Journal article | ||
Year | 2020 | Publication | Acs Sustainable Chemistry & Engineering | Abbreviated Journal | Acs Sustain Chem Eng |
Volume | 8 | Issue | 15 | Pages | 6043-6054 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Movement Antwerp (MOVANT) | ||||
Abstract | The combination of catalysis and nonthermal plasma holds promise for enabling difficult chemical conversions. The possible synergy between both depends strongly on the nature of the reactive plasma species and the catalyst material. In this paper, we show how vibrationally excited species and plasma-generated radicals interact with transition metal catalysts and how changing the catalyst material can improve the conversion rates and product selectivity. We developed a microkinetic model to investigate the impact of vibrational excitations and plasma-generated radicals on the nonoxidative coupling of methane over transition metal surfaces. We predict a significant increase in ethylene formation for vibrationally excited methane. Plasma-generated radicals have a stronger impact on the turnover frequencies with high selectivity toward ethylene on noble catalysts and mixed selectivity on non-noble catalysts. In general, we show how the optimal catalyst material depends on the desired products as well as the plasma conditions. | ||||
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Language | Wos | 000526884000025 | Publication Date | 2020-04-20 | |
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ISSN | 2168-0485 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.4 | Times cited | Open Access | ||
Notes | Herculesstichting; University of Notre Dame; Universiteit Antwerpen; Division of Engineering Education and Centers, EEC-1647722 ; We would like to thank Tom Butterworth for his work on methane vibrational distribution functions (VDF) and for sharing his thoughts and experiences on this matter, specifically regarding the VDF of the degenerate modes of methane. We ACS Sustainable Chemistry & Engineering pubs.acs.org/journal/ascecg Research Article https://dx.doi.org/10.1021/acssuschemeng.0c00906 ACS Sustainable Chem. Eng. 2020, 8, 6043−6054 6052 also acknowledge financial support from the DOC-PRO3 and the TOP-BOF projects of the University of Antwerp. This work 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. Support for W.F.S. was provided by the National Science Foundation under cooperative agreement no. EEC-1647722, an Engineering Research Center for the Innovative and Strategic Transformation of Alkane Resources (CISTAR). P.M. acknowledges support through the Eilers Graduate Fellowship of the University of Notre Dame. | Approved | Most recent IF: 8.4; 2020 IF: 5.951 | ||
Call Number | PLASMANT @ plasmant @c:irua:169228 | Serial | 6366 | ||
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Author | Bal, K.M.; Fukuhara, S.; Shibuta, Y.; Neyts, E.C. | ||||
Title | Free energy barriers from biased molecular dynamics simulations | Type | A1 Journal article | ||
Year | 2020 | Publication | Journal Of Chemical Physics | Abbreviated Journal | J Chem Phys |
Volume | 153 | Issue | 11 | Pages | 114118 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory. | ||||
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Language | Wos | 000574665600004 | Publication Date | 2020-09-21 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0021-9606 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.4 | Times cited | Open Access | ||
Notes | Japan Society for the Promotion of Science, 19H02415 18J22727 ; Fonds Wetenschappelijk Onderzoek, 12ZI420N ; This work was supported, in part, by a Grant-in-Aid for Scientific Research (B) (Grant No. 19H02415) and Grant-in-Aid for a JSPS Research Fellow (Grant No. 18J22727) from the Japan Society for the Promotion of Science (JSPS), Japan. K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation – Flanders), Grant No. 12ZI420N. S.F. was supported by JSPS through the Program for Leading Graduate Schools (MERIT). 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. The authors are grateful to Pablo Piaggi for making the pair entropy CV code publicly available. | Approved | Most recent IF: 4.4; 2020 IF: 2.965 | ||
Call Number | PLASMANT @ plasmant @c:irua:172456 | Serial | 6420 | ||
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Author | Faraji, F.; Neyts, E.C.; Milošević, M.V.; Peeters, F.M. | ||||
Title | Comment on “Misinterpretation of the Shuttleworth equation” | Type | A1 Journal Article | ||
Year | 2024 | Publication | Scripta Materialia | Abbreviated Journal | Scripta Materialia |
Volume | 250 | Issue | Pages | 116186 | |
Keywords | A1 Journal Article; CMT | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2024-05-24 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1359-6462 | ISBN | Additional Links | ||
Impact Factor | 6 | Times cited | Open Access | ||
Notes | Research Foundation Flanders; | Approved | Most recent IF: 6; 2024 IF: 3.747 | ||
Call Number | UA @ lucian @ CMT | Serial | 9116 | ||
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Author | Faraji, F.; Neyts, E.C.; Milošević, M.V.; Peeters, F.M. | ||||
Title | Capillary Condensation of Water in Graphene Nanocapillaries | Type | A1 Journal Article | ||
Year | 2024 | Publication | Nano Letters | Abbreviated Journal | Nano Lett. |
Volume | 24 | Issue | 18 | Pages | 5625-5630 |
Keywords | A1 Journal Article; CMT | ||||
Abstract | Recent experiments have revealed that the macroscopic Kelvin equation remains surprisingly accurate even for nanoscale capillaries. This phenomenon was so far explained by the oscillatory behavior of the solid−liquid interfacial free energy. We here demonstrate thermodynamic and capillarity inconsistencies with this explanation. After revising the Kelvin equation, we ascribe its validity at nanoscale confinement to the effect of disjoining pressure. To substantiate our hypothesis, we employed molecular dynamics simulations to evaluate interfacial heat transfer and wetting properties. Our assessments unveil a breakdown in a previously established proportionality between the work of adhesion and the Kapitza conductance at capillary heights below 1.3 nm, where the dominance of the work of adhesion shifts primarily from energy to entropy. Alternatively, the peak density of the initial water layer can effectively probe the work of adhesion. Unlike under bulk conditions, high confinement renders the work of adhesion entropically unfavorable. |
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2024-05-08 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1530-6984 | ISBN | Additional Links | ||
Impact Factor | 10.8 | Times cited | Open Access | ||
Notes | This work was supported by Research Foundation-Flanders (FWO, project No. G099219N). The computational resources used in this work were provided by the HPC core facility CalcUA of the University of Antwerp, and the Flemish Supercomputer Center (VSC), funded by FWO and the Flemish Government. | Approved | Most recent IF: 10.8; 2024 IF: 12.712 | ||
Call Number | UA @ lucian @ | Serial | 9123 | ||
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Author | Huygh, S.; Neyts, E.C. | ||||
Title | Adsorption of C and CHx radicals on anatase (001) and the influence of oxygen vacancies | Type | A1 Journal article | ||
Year | 2015 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
Volume | 119 | Issue | 119 | Pages | 4908-4921 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The adsorption of C and CHx radicals on anatase (001) was studied using DFT within the generalized gradient approximation using the Perde-Burke-Ernzerhof (PBE) functional. We have studied the influence of oxygen vacancies in and at the surface on the adsorption properties of the radicals. For the oxygen vacancies in anatase (001), the most stable vacancy is located at the surface. For this vacancy, the maximal adsorption strength of C and CH decreases compared to the adsorption on the stoichiometric surface, but it increases for CH2 and CH3. If an oxygen vacancy is present in the first subsurface layer, the maximal adsorption strength increases for C, CH, CH2, and CH3. When the vacancy is present in the next subsurface layer, we find that only the CH3 adsorption is enhanced, while the maximal adsorption energies for the other radical species decrease. Not only does the precise location of the oxygen vacancy determine the maximal adsorption interaction, it also influences the adsorption strengths of the radicals at different surface configurations. This determines the probability of finding a certain adsorption configuration at the surface, which in turn influences the possible surface reactions. We find that C preferentially adsorbs far away from the oxygen vacancy, while CH2 and CH3 adsorb preferentially at the oxygen vacancy site. A fraction of CH partially adsorbs at the oxygen vacancy, and another fraction adsorbs further away from the vacancy. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Washington, D.C. | Editor | ||
Language | Wos | 000350840700052 | Publication Date | 2015-02-18 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1932-7447;1932-7455; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.536 | Times cited | 13 | Open Access | |
Notes | Approved | Most recent IF: 4.536; 2015 IF: 4.772 | |||
Call Number | c:irua:124909 | Serial | 63 | ||
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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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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Bristol | Editor | ||
Language | Wos | 000309393400001 | Publication Date | 2012-09-27 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1367-2630; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.786 | Times cited | 47 | Open Access | |
Notes | Approved | Most recent IF: 3.786; 2012 IF: 4.063 | |||
Call Number | UA @ lucian @ c:irua:101014 | Serial | 189 | ||
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Author | Elliott, J.A.; Shibuta, Y.; Amara, H.; Bichara, C.; Neyts, E.C. | ||||
Title | Atomistic modelling of CVD synthesis of carbon nanotubes and graphene | Type | A1 Journal article | ||
Year | 2013 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
Volume | 5 | Issue | 15 | Pages | 6662-6676 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | We discuss the synthesis of carbon nanotubes (CNTs) and graphene by catalytic chemical vapour deposition (CCVD) and plasma-enhanced CVD (PECVD), summarising the state-of-the-art understanding of mechanisms controlling their growth rate, chiral angle, number of layers (walls), diameter, length and quality (defects), before presenting a new model for 2D nucleation of a graphene sheet from amorphous carbon on a nickel surface. Although many groups have modelled this process using a variety of techniques, we ask whether there are any complementary ideas emerging from the different proposed growth mechanisms, and whether different modelling techniques can give the same answers for a given mechanism. Subsequently, by comparing the results of tight-binding, semi-empirical molecular orbital theory and reactive bond order force field calculations, we demonstrate that graphene on crystalline Ni(111) is thermodynamically stable with respect to the corresponding amorphous metal and carbon structures. Finally, we show in principle how a complementary heterogeneous nucleation step may play a key role in the transformation from amorphous carbon to graphene on the metal surface. We conclude that achieving the conditions under which this complementary crystallisation process can occur may be a promising method to gain better control over the growth processes of both graphene from flat metal surfaces and CNTs from catalyst nanoparticles. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Cambridge | Editor | ||
Language | Wos | 000321675600003 | Publication Date | 2013-06-06 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2040-3364;2040-3372; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7.367 | Times cited | 52 | Open Access | |
Notes | Approved | Most recent IF: 7.367; 2013 IF: 6.739 | |||
Call Number | UA @ lucian @ c:irua:109231 | Serial | 200 | ||
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