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“Formation of single layer graphene on nickel under far-from-equilibrium high flux conditions”. Neyts EC, van Duin ACT, Bogaerts A, Nanoscale 5, 7250 (2013). http://doi.org/10.1039/c3nr00153a
Abstract: We investigate the theoretical possibility of single layer graphene formation on a nickel surface at different substrate temperatures under far-from-equilibrium high precursor flux conditions, employing state-of-the-art hybrid reactive molecular dynamics/uniform acceptance force bias Monte Carlo simulations. It is predicted that under these conditions, the formation of a single layer graphene-like film may proceed through a combined depositionsegregation mechanism on a nickel substrate, rather than by pure surface segregation as is typically observed for metals with high carbon solubility. At 900 K and above, nearly continuous graphene layers are obtained. These simulations suggest that single layer graphene deposition is theoretically possible on Ni under high flux conditions.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 25
DOI: 10.1039/c3nr00153a
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“Foundations of plasma catalysis for environmental applications”. Bogaerts A, Neyts EC, Guaitella O, Murphy AB, Plasma Sources Science &, Technology (2022). http://doi.org/10.1088/1361-6595/ac5f8e
Abstract: Plasma catalysis is gaining increasing interest for various applications, but the underlying mechanisms are still far from understood. Hence, more fundamental research is needed to understand these mechanisms. This can be obtained by both modelling and experiments. This foundations paper describes the fundamental insights in plasma catalysis, as well as efforts to gain more insights by modelling and experiments. Furthermore, it discusses the state-of-the-art of the major plasma catalysis applications, as well as successes and challenges of technology transfer of these applications.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.8
DOI: 10.1088/1361-6595/ac5f8e
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“Free energy barriers from biased molecular dynamics simulations”. Bal KM, Fukuhara S, Shibuta Y, Neyts EC, Journal Of Chemical Physics 153, 114118 (2020). http://doi.org/10.1063/5.0020240
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.4
DOI: 10.1063/5.0020240
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“Hampering Effect of Cholesterol on the Permeation of Reactive Oxygen Species through Phospholipids Bilayer: Possible Explanation for Plasma Cancer Selectivity”. Van der Paal J, Verheyen C, Neyts EC, Bogaerts A, Scientific reports 7, 39526 (2017). http://doi.org/10.1038/srep39526
Abstract: In recent years, the ability of cold atmospheric pressure plasmas (CAPS) to selectively induce cell death in cancer cells has been widely established. This selectivity has been assigned to the reactive oxygen and nitrogen species (RONS) created in CAPs. To provide new insights in the search for an explanation
for the observed selectivity, we calculate the transfer free energy of multiple ROS across membranes containing a varying amount of cholesterol. The cholesterol fraction is investigated as a selectivity parameter because membranes of cancer cells are known to contain lower fractions of cholesterol compared to healthy cells. We find that cholesterol has a significant effect on the permeation of
reactive species across a membrane. Indeed, depending on the specific reactive species, an increasing cholesterol fraction can lead to (i) an increase of the transfer free energy barrier height and width, (ii) the formation of a local free energy minimum in the center of the membrane and (iii) the creation of extra free energy barriers due to the bulky sterol rings. In the context of plasma oncology, these observations suggest that the increased ingress of RONS in cancer cells can be explained by the decreased cholesterol fraction of their cell membrane.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.259
Times cited: 27
DOI: 10.1038/srep39526
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“High Coke Resistance of a TiO2Anatase (001) Catalyst Surface during Dry Reforming of Methane”. Huygh S, Bogaerts A, Bal KM, Neyts EC, Journal Of Physical Chemistry C 122, 9389 (2018). http://doi.org/10.1021/acs.jpcc.7b10963
Abstract: The resistance of a TiO2 anatase (001) surface to coke formation was studied in the context of dry reforming of methane using density functional theory (DFT) calculations. As carbon atoms act as precursors for coke formation, the resistance to coke formation can be measured by the carbon coverage of the surface. This is related to the stability of different CHx (x = 0−3) species and their rate of hydrogenation and dehydrogenation on the TiO2 surface. Therefore, we studied the reaction mechanisms and their corresponding rates as a function of the temperature for the dehydrogenation of the species on the surface. We found that the stabilities of C and CH are significantly lower than those of CH3 and CH2. The hydrogenation rates of the different species are significantly higher than the dehydrogenation rates in a temperature range of 300−1000 K. Furthermore, we found that dehydrogenation of CH3, CH2, and CH will only occur at appreciable rates starting from 600, 900, and 900 K, respectively. On the basis of these results, it is clear that the anatase (001) surface has a high coke resistance, and it is thus not likely that the surface will become poisoned by coke during dry reforming of methane. As the rate limiting step in dry reforming is the dissociative adsorption of CH4, we studied an alternative approach to thermal catalysis. We found that the temperature threshold for dry reforming is at least 700 K. This threshold temperature may be lowered by the use of plasma-catalysis, where the appreciable rates of adsorption of plasma-generated CHx radicals result in bypassing the rate limiting step of the reaction.
Keywords: A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 4.536
Times cited: 1
DOI: 10.1021/acs.jpcc.7b10963
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“How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations”. Khosravian N, Bogaerts A, Huygh S, Yusupov M, Neyts EC, Biointerphases 10, 029501 (2015). http://doi.org/10.1116/1.4904339
Abstract: The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.603
Times cited: 10
DOI: 10.1116/1.4904339
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“How Oxygen Vacancies Activate CO2 Dissociation on TiO2 Anatase (001)”. Huygh S, Bogaerts A, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 120, 21659 (2016). http://doi.org/10.1021/acs.jpcc.6b07459
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 49
DOI: 10.1021/acs.jpcc.6b07459
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“How the alignment of adsorbed ortho H pairs determines the onset of selective carbon nanotube etching”. Khalilov U, Bogaerts A, Xu B, Kato T, Kaneko T, Neyts EC, Nanoscale 9, 1653 (2017). http://doi.org/10.1039/C6NR08005G
Abstract: Unlocking the enormous technological potential of carbon nanotubes strongly depends on our ability to specifically produce metallic or semiconducting tubes. While selective etching of both has already been demonstrated, the underlying reasons, however, remain elusive as yet. We here present computational and experimental evidence on the operative mechanisms at the atomic scale. We demonstrate that during the adsorption of H atoms and their coalescence, the adsorbed ortho hydrogen pairs on single-walled carbon nanotubes induce higher shear stresses than axial stresses, leading to the elongation of HC–CH bonds as a function of their alignment with the tube chirality vector, which we denote as the γ-angle. As a result, the C–C cleavage occurs more rapidly in nanotubes containing ortho H-pairs with a small γ-angle. This phenomenon can explain the selective etching of small-diameter semiconductor nanotubes with a similar curvature. Both theoretical and experimental results strongly indicate the important role of the γ-angle in the selective etching mechanisms of carbon nanotubes, in addition to the nanotube curvature and metallicity effects and lead us to clearly understand the onset of selective synthesis/removal of CNT-based materials.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 6
DOI: 10.1039/C6NR08005G
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“Hyperthermal oxidation of Si(100)2x1 surfaces : effect of growth temperature”. Khalilov U, Pourtois G, van Duin ACT, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 116, 8649 (2012). http://doi.org/10.1021/jp300506g
Abstract: Using reactive molecular dynamics simulations based on the ReaxFF potential, we studied the growth mechanism of ultrathin silica (SiO2) layers during hyperthermal oxidation as a function of temperature in the range 100-1300 K. Oxidation of Si(100){2 x 1} surfaces by both atomic and molecular oxygen was investigated for hyperthermal impact energies in the range of 1 to 5 eV. Two different growth mechanisms are found, corresponding to a low temperature oxidation and a high temperature one. The transition temperature between these mechanisms is estimated to be about 700 K. Also, the initial step of the Si oxidation process is analyzed in detail. Where possible, we validated our results with experimental and ab initio data, and good agreement was obtained. This study is important for the fabrication of silica-based devices in the micro- and nanoelectronics industry and, more specifically, for the fabrication of metal oxide semiconductor devices.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 32
DOI: 10.1021/jp300506g
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“Hyperthermal oxygen interacting with silicon surfaces : adsorption, implantation, and damage creation”. Neyts EC, Khalilov U, Pourtois G, van Duin ACT, The journal of physical chemistry: C : nanomaterials and interfaces 115, 4818 (2011). http://doi.org/10.1021/jp112068z
Abstract: Using reactive molecular dynamics simulations, we have investigated the effect of single-impact, low-energy (thermal-100 eV) bombardment of a Si(100){2 × 1} surface by atomic and molecular oxygen. Penetration probability distributions, as well as defect formation distributions, are presented as a function of the impact energy for both species. It is found that at low impact energy, defects are created chemically due to the chemisorption process in the top layers of the surface, while at high impact energy, additional defects are created by a knock-on displacement of Si. These results are of particular importance for understanding device performances of silica-based microelectronic and photovoltaic devices.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 28
DOI: 10.1021/jp112068z
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“Identification of a Robust and Durable FeN4CxCatalyst for ORR in PEM Fuel Cells and the Role of the Fifth Ligand”. Nematollahi P, Barbiellini B, Bansil A, Lamoen D, Qingying J, Mukerjee S, Neyts EC, ACS catalysis , 7541 (2022). http://doi.org/10.1021/acscatal.2c01294
Abstract: Although recent studies have advanced the understanding of pyrolyzed
Fe−N−C materials as oxygen reduction reaction (ORR) catalysts, the atomic and
electronic structures of the active sites and their detailed reaction mechanisms still remain unknown. Here, based on first-principles density functional theory (DFT) computations, we discuss the electronic structures of three FeN4 catalytic centers with different local topologies of the surrounding C atoms with a focus on unraveling the mechanism of their ORR activity in acidic electrolytes. Our study brings back a forgotten, synthesized pyridinic Fe−N coordinate to the community’s attention, demonstrating that this catalyst can exhibit excellent activity for promoting direct four-electron ORR through the addition of a fifth ligand such as −NH2, −OH, and −SO4. We also identify sites with good stability properties through the combined use of our DFT calculations and Mössbauer spectroscopy data.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 12.9
DOI: 10.1021/acscatal.2c01294
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“Identification of a unique pyridinic FeN4Cx electrocatalyst for N₂, reduction : tailoring the coordination and carbon topologies”. Nematollahi P, Neyts EC, Journal Of Physical Chemistry C 126, 14460 (2022). http://doi.org/10.1021/ACS.JPCC.2C03577
Abstract: Although the heterogeneity of pyrolyzed Fe???N???C materials is known and has been reported previously, the atomic structure of the active sites and their detailed reaction mechanisms are still unknown. Here, we identified two pyridinic Fe???N4-like centers with different local C coordinates, i.e., FeN4C8 and FeN4C10, and studied their electrocatalytic activity for the nitrogen reduction reaction (NRR) based on density functional theory (DFT) calculations. We also discovered the influence of the adsorption of NH2 as a functional ligand on catalyst performance on the NRR. We confirmed that the NRR selectivity of the studied catalysts is essentially governed either by the local C coordination or by the dynamic structure associated with the FeII/FeIII. Our investigations indicate that the proposed traditional pyridinic FeN4C10 has higher catalytic activity and selectivity for the NRR than the robust FeN4C8 catalyst, while it may have outstanding activity for promoting other (electro)catalytic reactions. <comment>Superscript/Subscript Available</comment
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.7
DOI: 10.1021/ACS.JPCC.2C03577
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“Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species : a reactive molecular dynamics study”. Yusupov M, Neyts EC, Verlackt CC, Khalilov U, van Duin ACT, Bogaerts A, Plasma processes and polymers 12, 162 (2015). http://doi.org/10.1002/ppap.201400064
Abstract: Reactive molecular dynamics simulations are performed to study the interaction of reactive oxygen species, such as OH, HO2 and H2O2, with the endotoxic biomolecule lipid A of the gram-negative bacterium Escherichia coli. It is found that the aforementioned plasma species can destroy the lipid A, which consequently results in reducing its toxic activity. All bond dissociation events are initiated by hydrogen-abstraction reactions. However, the mechanisms behind these dissociations are dependent on the impinging plasma species, i.e. a clear difference is observed in the mechanisms upon impact of HO2 radicals and H2O2 molecules on one hand and OH radicals on the other hand. Our simulation results are in good agreement with experimental observations.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 18
DOI: 10.1002/ppap.201400064
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“Incorporation of fluorescent dyes in atmospheric pressure plasma coatings for in-line monitoring of coating homogeneity”. Somers W, Dubreuil MF, Neyts EC, Vangeneugden D, Bogaerts A, Plasma processes and polymers 11, 678 (2014). http://doi.org/10.1002/ppap.201300178
Abstract: This paper reports on the incorporation of three commercial fluorescent dyes, i.e., rhodamine 6G, fluorescein, and fluorescent brightener 184, in plasma coatings, by utilizing a dielectric barrier discharge (DBD) reactor, and the subsequent monitoring of the coatings homogeneity based on the emitted fluorescent light. The plasma coatings are qualitatively characterized with fluorescence microscopy, UVvis spectroscopy and profilometry for the determination of the coating thickness. The emitted fluorescent light of the coating correlates to the amount of dye per area, and deviations of these factors can hence be observed by monitoring the intensity of this light. This allows monitoring the homogeneity of the plasma coatings in a fast and simple way, without making major adjustments to the process.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 3
DOI: 10.1002/ppap.201300178
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“Indentation of graphene nano-bubbles”. Faraji F, Neek-Amal M, Neyts EC, Peeters FM, Nanoscale 14, 5876 (2022). http://doi.org/10.1039/D2NR01207C
Abstract: Molecular dynamics simulations are used to investigate the effect of an AFM tip when indenting graphene nano bubbles filled by a noble gas (i.e. He, Ne and Ar) up to the breaking point. The failure points resemble those of viral shells as described by the Foppl-von Karman (FvK) dimensionless number defined in the context of elasticity theory of thin shells. At room temperature, He gas inside the bubbles is found to be in the liquid state while Ne and Ar atoms are in the solid state although the pressure inside the nano bubble is below the melting pressure of the bulk. The trapped gases are under higher hydrostatic pressure at low temperatures than at room temperature.
Keywords: A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.7
Times cited: 2
DOI: 10.1039/D2NR01207C
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“Influence of the Material Dielectric Constant on Plasma Generation inside Catalyst Pores”. Zhang Y-R, Neyts EC, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 120, 25923 (2016). http://doi.org/10.1021/acs.jpcc.6b09038
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 34
DOI: 10.1021/acs.jpcc.6b09038
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“Insights in the plasma-assisted growth of carbon nanotubes through atomic scale simulations : effect of electric field”. Neyts EC, van Duin ACT, Bogaerts A, Journal of the American Chemical Society 134, 1256 (2012). http://doi.org/10.1021/ja2096317
Abstract: Carbon nanotubes (CNTs) are nowadays routinely grown in a thermal CVD setup. State-of-the-art plasma-enhanced CVD (PECVD) growth, however, offers advantages over thermal CVD. A lower growth temperature and the growth of aligned freestanding single-walled CNTs (SWNTs) makes the technique very attractive. The atomic scale growth mechanisms of PECVD CNT growth, however, remain currently entirely unexplored. In this contribution, we employed molecular dynamics simulations to focus on the effect of applying an electric field on the SWNT growth process, as one of the effects coming into play in PECVD. Using sufficiently strong fields results in (a) alignment of the growing SWNTs, (b) a better ordering of the carbon network, and (c) a higher growth rate relative to thermal growth rate. We suggest that these effects are due to the small charge transfer occurring in the Ni/C system. These simulations constitute the first study of PECVD growth of SWNTs on the atomic level.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 13.858
Times cited: 56
DOI: 10.1021/ja2096317
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“Integrated atomistic chemical imaging and reactive force field molecular dynamic simulations on silicon oxidation”. Dumpala S, Broderick SR, Khalilov U, Neyts EC, van Duin ACT, Provine J, Howe RT, Rajan K, Applied physics letters 106, 011602 (2015). http://doi.org/10.1063/1.4905442
Abstract: In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO2 and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.411
Times cited: 19
DOI: 10.1063/1.4905442
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“Interaction of O and OH radicals with a simple model system for lipids in the skin barrier : a reactive molecular dynamics investigation for plasma medicine”. Van der Paal J, Aernouts S, van Duin ACT, Neyts EC, Bogaerts A, Journal of physics: D: applied physics 46, 395201 (2013). http://doi.org/10.1088/0022-3727/46/39/395201
Abstract: Plasma medicine has been claimed to provide a novel route to heal wounds and regenerate skin, although very little is currently known about the elementary processes taking place. We carried out a series of ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of O and OH radicals with lipids, more specifically with α-linolenic acid as a model for the free fatty acids present in the upper skin layer. Our calculations predict that the O and OH radicals most typically abstract a H atom from the fatty acids, which can lead to the formation of a conjugated double bond, but also to the incorporation of alcohol or aldehyde groups, thereby increasing the hydrophilic character of the fatty acids and changing the general lipid composition of the skin. Within the limitations of the investigated model, no formation of possibly toxic products was observed.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 36
DOI: 10.1088/0022-3727/46/39/395201
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“Interactions of plasma species on nickel catalysts : a reactive molecular dynamics study on the influence of temperature and surface structure”. Somers W, Bogaerts A, van Duin ACT, Neyts EC, Applied catalysis : B : environmental 154, 1 (2014). http://doi.org/10.1016/j.apcatb.2014.01.061
Abstract: Methane reforming by plasma catalysis is a complex process that is far from understood. It requires a multidisciplinary approach which ideally takes into account all effects from the plasma on the catalyst, and vice versa. In this contribution, we focus on the interactions of CHx (x = {1,2,3}) radicals that are created in the plasma with several nickel catalyst surfaces. To this end, we perform reactive molecular dynamics simulations, based on the ReaxFF potential, in a wide temperature range of 4001600 K. First, we focus on the H2 formation as a function of temperature and surface structure. We observe that substantial H2 formation is obtained at 1400 K and above, while the role of the surface structure seems limited. Indeed, in the initial stage, the type of nickel surface influences the CH bond breaking efficiency of adsorbed radicals; however, the continuous carbon diffusion into the surface gradually diminishes the surface crystallinity and therefore reduces the effect of surface structure on the H2 formation probability. Furthermore, we have also investigated to what extent the species adsorbed on the catalyst surface can participate in surface reactions more in general, for the various surface structures and as a function of temperature. These results are part of the ongoing research on the methane reforming by plasma catalysis, a highly interesting yet complex alternative to conventional reforming processes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.446
Times cited: 23
DOI: 10.1016/j.apcatb.2014.01.061
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“Ion irradiation for improved graphene network formation in carbon nanotube growth”. Neyts EC, Bogaerts A, Carbon 77, 790 (2014). http://doi.org/10.1016/j.carbon.2014.05.083
Abstract: Ion irradiation of carbon nanotubes very often leads to defect formation. However, we have recently shown that Ar ion irradiation in a limited energy window of 1025 eV may enhance the initial cap nucleation process, when the carbon network is in contact with the metal nanocatalyst. Here, we employ reactive molecular dynamics simulations to demonstrate that ion irradiation in a higher energy window of 1035 eV may also heal network defects after the nucleation stage through a non-metal-mediated mechanism, when the carbon network is no longer in contact with the metal nanocatalyst. The results demonstrate the possibility of beneficially utilizing ions in e.g. plasma-enhanced chemical vapour deposition of carbon nanotubes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 7
DOI: 10.1016/j.carbon.2014.05.083
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“Kinetics of energy selective Cs encapsulation in single-walled carbon nanotubes for damage-free and position-selective doping”. Kato T, Neyts EC, Abiko Y, Akama T, Hatakeyama R, Kaneko T, The journal of physical chemistry: C : nanomaterials and interfaces 119, 11903 (2015). http://doi.org/10.1021/acs.jpcc.5b00300
Abstract: A method has been developed for damage-free cesium (Cs) encapsulation within single-walled carbon nanotubes (SWNTs) with fine position selectivity. Precise energy tuning of Cs-ion irradiation revealed that there is a clear energy window (2060 eV) for the efficient encapsulation of Cs through the hexagonal network of SWNT sidewalls without causing significant damage. This minimum energy threshold of Cs-ion encapsulation (∼20 eV) matches well with the value obtained by ab initio simulation (∼22 eV). Furthermore, position-selective Cs encapsulation was carried out, resulting in the successful formation of pn-junction SWNT thin films with excellent environmental stability.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 3
DOI: 10.1021/acs.jpcc.5b00300
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“Linking bi-metal distribution patterns in porous carbon nitride fullerene to its catalytic activity toward gas adsorption”. Nematollahi P, Neyts EC, Nanomaterials 11, 1794 (2021). http://doi.org/10.3390/NANO11071794
Abstract: Immobilization of two single transition metal (TM) atoms on a substrate host opens numerous possibilities for catalyst design. If the substrate contains more than one vacancy site, the combination of TMs along with their distribution patterns becomes a design parameter potentially complementary to the substrate itself and the bi-metal composition. By means of DFT calculations, we modeled three dissimilar bi-metal atoms (Ti, Mn, and Cu) doped into the six porphyrin-like cavities of porous C24N24 fullerene, considering different bi-metal distribution patterns for each binary complex, viz. TixCuz@C24N24, TixMny@C24N24, and MnyCuz@C24N24 (with x, y, z = 0-6). We elucidate whether controlling the distribution of bi-metal atoms into the C24N24 cavities can alter their catalytic activity toward CO2, NO2, H-2, and N-2 gas capture. Interestingly, Ti2Mn4@C24N24 and Ti2Cu4@C24N24 complexes showed the highest activity and selectively toward gas capture. Our findings provide useful information for further design of novel few-atom carbon-nitride-based catalysts.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.553
DOI: 10.3390/NANO11071794
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“Mechanisms of elementary hydrogen ion-surface interactions during multilayer graphene etching at high surface temperature as a function of flux”. Aussems DUB, Bal KM, Morgan TW, van de Sanden MCM, Neyts EC, Carbon 137, 527 (2018). http://doi.org/10.1016/j.carbon.2018.05.051
Abstract: In order to optimize the plasma-synthesis and modification process of carbon nanomaterials for applications such as nanoelectronics and energy storage, a deeper understanding of fundamental hydrogengraphite/graphene interactions is required. Atomistic simulations by Molecular Dynamics have proven to be indispensable to illuminate these phenomena. However, severe time-scale limitations restrict them to very fast processes such as reflection, while slow thermal processes such as surface diffusion and molecular desorption are commonly inaccessible. In this work, we could however reach these thermal processes for the first time at time-scales and surface temperatures (1000 K) similar to high-flux plasma exposure experiments during the simulation of multilayer graphene etching by 5 eV H ions. This was achieved by applying the Collective Variable-Driven Hyperdynamics biasing technique, which extended the inter-impact time over a range of six orders of magnitude, down to a more realistic ion-flux of 1023m2s1. The results show that this not only causes a strong shift from predominant ion-to thermally induced interactions, but also significantly affects the hydrogen uptake and surface evolution. This study thus elucidates H ion-graphite/graphene interaction mechanisms and stresses the importance of including long time-scales in atomistic simulations at high surface temperatures to understand the dynamics of the ion-surface system.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 4
DOI: 10.1016/j.carbon.2018.05.051
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“Mechanisms of Peptide Oxidation by Hydroxyl Radicals: Insight at the Molecular Scale”. Verlackt CCW, Van Boxem W, Dewaele D, Lemière F, Sobott F, Benedikt J, Neyts EC, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 121, 5787 (2017). http://doi.org/10.1021/acs.jpcc.6b12278
Abstract: Molecular dynamics (MD) simulations were performed to provide atomic scale insight in the initial interaction between hydroxyl radicals (OH) and peptide systems in solution. These OH radicals are representative reactive oxygen species produced by cold atmospheric plasmas. The use of plasma for biomedical applications is gaining increasing interest, but the fundamental mechanisms behind the plasma modifications still remain largely elusive. This study helps to gain more insight in the underlying mechanisms of plasma medicine but is also more generally applicable to peptide oxidation, of interest for other applications. Combining both reactive and nonreactive MD simulations, we are able to elucidate the reactivity of the amino acids inside the peptide systems and their effect on their structure up to 1 μs. Additionally, experiments were performed, treating the simulated peptides with a plasma jet. The computational results presented here correlate well with the obtained experimental data and highlight the importance of the chemical environment for the reactivity of the individual amino acids, so that specific amino acids are attacked in higher numbers than expected. Furthermore, the long time scale simulations suggest that a single oxidation has an effect on the 3D conformation due to an increase in hydrophilicity and intra- and intermolecular interactions.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 5
DOI: 10.1021/acs.jpcc.6b12278
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“Mechanisms of selective nanocarbon synthesis inside carbon nanotubes”. Khalilov U, Neyts EC, Carbon 171, 72 (2021). http://doi.org/10.1016/j.carbon.2020.08.060
Abstract: The possibility of confinement effects inside a carbon nanotube provides new application opportunities, e.g., growth of novel carbon nanostructures. However, the understanding the precise role of catalystfeedstock in the nanostructure synthesis is still elusive. In our simulation-based study, we investigate the Ni-catalyzed growth mechanism of encapsulated carbon nanostructures, viz. double-wall carbon nanotube and graphene nanoribbon, from carbon and hydrocarbon growth precursors, respectively. Specifically, we find that the tube and ribbon growth is determined by a catalyst-vs-feedstock competition effect. We compare our results, i.e., growth mechanism and structure morphology with all available theoretical and experimental data. Our calculations show that all encapsulated nanostructures contain metal (catalyst) atoms and such structures are less stable than their pure counterparts. Therefore, we study the purification mechanism of these structures. In general, this study opens a possible route to the controllable synthesis of tubular and planar carbon nanostructures for today’s nanotechnology.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
DOI: 10.1016/j.carbon.2020.08.060
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“Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds”. Bal KM, Neyts EC, Journal of chemical theory and computation 11, 4545 (2015). http://doi.org/10.1021/acs.jctc.5b00597
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.245
Times cited: 41
DOI: 10.1021/acs.jctc.5b00597
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“Microscopic mechanisms of vertical graphene and carbon nanotube cap nucleation from hydrocarbon growth precursors”. Khalilov U, Bogaerts A, Neyts EC, Nanoscale 6, 9206 (2014). http://doi.org/10.1039/c4nr00669k
Abstract: Controlling and steering the growth of single walled carbon nanotubes is often believed to require controlling of the nucleation stage. Yet, little is known about the microscopic mechanisms governing the nucleation from hydrocarbon molecules. Specifically, we address here the dehydrogenation of hydrocarbon molecules and the formation of all-carbon graphitic islands on metallic nanoclusters from hydrocarbon molecules under conditions typical for carbon nanotube growth. Employing reactive molecular dynamics simulations, we demonstrate for the first time that the formation of a graphitic network occurs through the intermediate formation of vertically oriented, not fully dehydrogenated graphitic islands. Upon dehydrogenation of these vertical graphenes, the islands curve over the surface, thereby forming a carbon network covering the nanoparticle. The results indicate that controlling the extent of dehydrogenation offers an additional parameter to control the nucleation of carbon nanotubes.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 21
DOI: 10.1039/c4nr00669k
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“Modeling the growth of SWNTs and graphene on the atomic scale”. Neyts EC, Bogaerts A, ECS transactions 45, 73 (2012). http://doi.org/10.1149/1.3700454
Abstract: The possibility of application of nanomaterials is determined by our ability to control the properties of the materials, which are ultimately determined by their structure and hence their growth processes. We employ hybrid molecular dynamics / Monte Carlo (MD/MC) simulations to explore the growth of SWNTs and graphene on nickel as a catalyst, with the specific goal of unraveling the growth mechanisms. While the general observations are in agreement with the literature, we find a number of interesting phenomena to be operative which are crucial for the growth, and which are not accessible by MD simulations alone due to the associated time scale. Specifically, we observe metal mediated healing and restructuring processes to take place, reorganizing the carbon network during the initial nucleation step. In the case of carbon nanotube growth, this leads to the growth of tubes with a determinable chirality. In the case of graphene formation, we find that graphene is only formed at temperatures above 700 K. These results are of importance for understanding the growth mechanisms of these carbon nanomaterials on the fundamental level.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Times cited: 2
DOI: 10.1149/1.3700454
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“Modeling the physicochemical properties of natural deep eutectic solvents : a review”. Kovács A, Billen P, Cornet I, Wijnants M, Neyts EC, Chemsuschem 13, 3789 (2020). http://doi.org/10.1002/CSSC.202000286
Abstract: Natural deep eutectic solvents (NADES) are mixtures of naturally derived compounds with a significantly decreased melting point due to the specific interactions among the constituents. NADES have benign properties (low volatility, flammability, toxicity, cost) and tailorable physicochemical properties (by altering the type and molar ratio of constituents), hence they are often considered as a green alternative to common organic solvents. Modeling the relation between their composition and properties is crucial though, both for understanding and predicting their behavior. Several efforts were done to this end, yet this review aims at structuring the present knowledge as an outline for future research. First, we reviewed the key properties of NADES and relate them to their structure based on the available experimental data. Second, we reviewed available modeling methods applicable to NADES. At the molecular level, density functional theory and molecular dynamics allow interpreting density differences and vibrational spectra, and computation of interaction energies. Additionally, properties at the level of the bulk media can be explained and predicted by semi-empirical methods based on ab initio methods (COSMO-RS) and equation of state models (PC-SAFT). Finally, methods based on large datasets are discussed; models based on group contribution methods and machine learning. A combination of bulk media and dataset modeling allows qualitative prediction and interpretation of phase equilibria properties on the one hand, and quantitative prediction of melting point, density, viscosity, surface tension and refractive indices on the other hand. In our view, multiscale modeling, combining the molecular and macroscale methods, will strongly enhance the predictability of NADES properties and their interaction with solutes, yielding truly tailorable solvents to accommodate (bio)chemical reactions.
Keywords: A1 Journal article; Engineering sciences. Technology; Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE)
Impact Factor: 8.4
DOI: 10.1002/CSSC.202000286
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