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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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“Numerical study of the size-dependent melting mechanisms of nickel nanoclusters”. Neyts EC, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 113, 2771 (2009)
Abstract: Molecular dynamics simulations were used to investigate the size-dependent melting mechanism of nickel nanoclusters of various sizes. The melting process was monitored by the caloric curve, the overall cluster Lindemann index, and the atomic Lindemann index. Size-dependent melting temperatures were determined, and the correct linear dependence on inverse diameter was recovered. We found that the melting mechanism gradually changes from dynamic coexistence melting to surface melting with increasing cluster size. These findings are of importance in better understanding carbon nanotube growth by catalytic chemical vapor deposition as the phase state of the catalyst nanoparticle codetermines the growth mechanism.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
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“Selective Plasma Oxidation of Ultrasmall Si Nanowires”. Khalilov U, Yusupov M, Bogaerts A, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 120, 472 (2016). http://doi.org/10.1021/acs.jpcc.5b11027
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.
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.5b11027
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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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“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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“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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“Density functional theory study of interface interactions in hydroxyapatite/rutile composites for biomedical applications”. Grubova IY, Surmeneva MA, Huygh S, Surmenev RA, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 121, 15687 (2017). http://doi.org/10.1021/ACS.JPCC.7B02926
Abstract: To gain insight into the nature of the adhesion mechanism between hydroxyapatite (HA) and rutile (rTiO(2)), the mutual affinity between their surfaces was systematically studied using density functional theory (DFT). We calculated both bulk and surface properties of HA and rTiO(2), and explored the interfacial bonding mechanism of amorphous HA (aHA) surface onto amorphous as well as stoichiometric and nonstoichiometric crystalline rTiO(2). Formation energies of bridging and subbridging oxygen vacancies considered in the rTiO(2)(110) surface were evaluated and compared with other theoretical and experimental results. The interfacial interaction was evaluated through the work of adhesion. For the aHA/rTiO(2)(110) interfaces, the work of adhesion is found to depend strongly on the chemical environment of the rTiO(2)(110) surface. Electronic analysis indicates that the charge transfer is very small in the case of interface formation between aHA and crystalline rTiO(2)(110). In contrast, significant charge transfer occurs between aHA and amorphous rTiO(2) (aTiO(2)) slabs during the formation of the interface. Charge density difference (CDD) analysis indicates that the dominant interactions in the interface have significant covalent character, and in particular the Ti-O and Ca-O bonds. Thus, the obtained results reveal that the aHA/aTiO(2) interface shows a more preferable interaction and is thermodynamically more stable than other interfaces. These results are particularly important for improving the long-term stability of HA-based implants.
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.7B02926
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“Stabilities of bimetallic nanoparticles for chirality-selective carbon nanotube growth and the effect of carbon interstitials”. Vets C, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 121, 15430 (2017). http://doi.org/10.1021/ACS.JPCC.7B02880
Abstract: Bimetallic nanoparticles play a crucial role in various applications. A better understanding of their properties would facilitate these applications and possibly even enable chirality-specific growth of carbon nanotubes (CNTs). We here examine the stabilities of NiFe, NiGa, and FeGa nanoparticles and the effect of carbon dissolved in NiFe nanoparticles through density functional theory (DFT) calculations and Born Oppenheimer molecular dynamics (BOMD) simulations. We establish that nanoparticles with more Fe in the core and more Ga on the surface are more stable and compare these results with well-known properties such as surface energy and atom size. Furthermore, we find that the nanoparticles become more stable with increasing carbon content, both at 0 K and at 700 K. These results provide a basis for further research into the chirality-specific growth of CNT's.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 2
DOI: 10.1021/ACS.JPCC.7B02880
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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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“Overcoming Old Scaling Relations and Establishing New Correlations in Catalytic Surface Chemistry: Combined Effect of Charging and Doping”. Bal KM, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 123, 6141 (2019). http://doi.org/10.1021/acs.jpcc.9b01216
Abstract: Optimization of catalytic materials for a given application is greatly constrained by linear scaling relations. Recently, however, it has been demonstrated that it is possible to reversibly modulate the chemisorption of molecules on nanomaterials by charging (i.e., injection or removal of electrons) and hence reversibly and selectively modify catalytic activity beyond structure−activity correlations. The fundamental physical relation between the properties of the material, the charging process, and the chemisorption energy, however, remains unclear, and a systematic exploration and optimization of charge-switchable sorbent materials is not yet possible. Using hybrid DFT calculations of CO2 chemisorption on hexagonal boron nitride nanosheets with several types of defects and dopants, we here reveal the existence of fundamental correlations between the electron affinity of a material and charge-induced chemisorption, show how defect engineering can be used to modulate the strength and efficiency of the adsorption process, and demonstrate that excess electrons stabilize many topological defects. We then show how these insights could be exploited in the development of new electrocatalytic materials and the synthesis of doped nanomaterials. Moreover, we demonstrate that calculated chemical properties of charged materials are highly sensitive to the employed computational methodology because of the self-interaction error, which underlines the theoretical challenge posed by such systems.
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.9b01216
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“CO2 activation on TiO2-supported Cu5 and Ni5 nanoclusters : effect of plasma-induced surface charging”. Jafarzadeh A, Bal KM, Bogaerts A, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 123, 6516 (2019). http://doi.org/10.1021/ACS.JPCC.8B11816
Abstract: Surface charging is an often overlooked factor in many plasma-surface interactions and in particular in plasma catalysis. In this study, we investigate the effect of excess electrons induced by a plasma on the adsorption properties of CO2 on titania-supported Cu-5 and Ni-5 clusters using spin-polarized and dispersion-corrected density functional theory calculations. The effect of excess electrons on the adsorption of Ni and Cu pentamers as well as on CO2 adsorption on a pristine anatase TiO2(101) slab is studied. Our results indicate that adding plasma-induced excess electrons to the system leads to further stabilization of the bent CO2 structure. Also, dissociation of CO2 on charged clusters is energetically more favorable than on neutral clusters. We hypothesize that surface charge is a plausible cause for the synergistic effects sometimes observed in plasma catalysis.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 4
DOI: 10.1021/ACS.JPCC.8B11816
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“Contrasting H-etching to OH-etching in plasma-assisted nucleation of carbon nanotubes”. Van de Sompel P, Khalilov U, Neyts EC, Journal Of Physical Chemistry C 125, 7849 (2021). http://doi.org/10.1021/ACS.JPCC.0C11166
Abstract: To gain full control over the growth of carbon nanotubes (CNTs) using plasma-enhanced chemical vapor deposition (PECVD), a thorough understanding of the underlying plasma-catalyst mechanisms is required. Oxygen-containing species are often used as or added to the growth precursor gas, but these species also yield various radicals and ions, which may simultaneously etch the CNT during the growth. At present, the effect of these reactive species on the growth onset has not yet been thoroughly investigated. We here report on the etching mechanism of incipient CNT structures from OH and O radicals as derived from combined (reactive) molecular dynamics (MD) and force-bias Monte Carlo (tfMC) simulations. Our results indicate that the oxygen-containing radicals initiate a dissociation process. In particular, we show how the oxygen species weaken the interaction between the CNT and the nanocluster. As a result of this weakened interaction, the CNT closes off and dissociates from the cluster in the form of a fullerene. Beyond the specific systems studied in this work, these results are generically important in the context of PECVD-based growth of CNTs using oxygen-containing precursors.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
DOI: 10.1021/ACS.JPCC.0C11166
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“DFT and microkinetic comparison of ru-doped porphyrin-like graphene and nanotubes toward catalytic formic acid decomposition and formation”. Nematollahi P, Ma H, Schneider WF, Neyts EC, Journal Of Physical Chemistry C 125, 18673 (2021). http://doi.org/10.1021/ACS.JPCC.1C03914
Abstract: Immobilization of single metal atoms on a solid host opens numerous possibilities for catalyst designs. If that host is a two-dimensional sheet, sheet curvature becomes a design parameter potentially complementary to host and metal composition. Here, we use a combination of density functional theory calculations and microkinetic modeling to compare the mechanisms and kinetics of formic acid decomposition and formation, chosen for their relevance as a potential hydrogen storage medium, over single Ru atoms anchored to pyridinic nitrogen in a planar graphene flake (RuN4-G) and curved carbon nanotube (RuN4-CNT). Activation barriers are lowered and the predicted turnover frequencies are increased over RuN4-CNT relative to RuN4-CNT. The results highlight the potential of curvature control as a means to achieve high performance and robust catalysts.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
DOI: 10.1021/ACS.JPCC.1C03914
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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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“Understanding the Effect of Iodide Ions on the Morphology of Gold Nanorods”. Amini MN, Altantzis T, Lobato I, Grzelczak M, Sánchez-Iglesias A, Van Aert S, Liz-Marzán LM, Partoens B, Bals S, Neyts EC, Particle and particle systems characterization 35, 1800051 (2018). http://doi.org/10.1002/ppsc.201800051
Abstract: The presence of iodide ions during the growth of gold nanorods strongly affects the shape of the final products, which is proposed to be due to selective iodide adsorption on certain crystallographic facets. Therefore, a detailed structural and morphological characterization of the starting rods is crucial toward understanding this effect. Electron tomography is used to determine the crystallographic indices of the lateral facets of gold nanorods, as well as those present at the tips. Based on this information, density functional theory calculations are used to determine the surface and interface energies of the observed facets and provide insight into the relationship between the amount of iodide ions in the growth solution and the final morphology of anisotropic gold nanoparticles.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.474
Times cited: 6
DOI: 10.1002/ppsc.201800051
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“Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory”. Bal KM, Neyts EC, Journal Of Chemical Physics 157, 184113 (2022). http://doi.org/10.1063/5.0120136
Abstract: We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.4
DOI: 10.1063/5.0120136
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“A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma”. Hoon Park J, Kumar N, Hoon Park D, Yusupov M, Neyts EC, Verlackt CCW, Bogaerts A, Ho Kang M, Sup Uhm H, Ha Choi E, Attri P;, Scientific reports 5, 13849 (2015). http://doi.org/10.1038/srep13849
Abstract: Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.259
Times cited: 32
DOI: 10.1038/srep13849
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“Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations”. Khosravian N, Kamaraj B, Neyts EC, Bogaerts A, Scientific reports 6, 19466 (2016). http://doi.org/10.1038/srep19466
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.259
Times cited: 7
DOI: 10.1038/srep19466
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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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“Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments”. Yusupov M, Wende K, Kupsch S, Neyts EC, Reuter S, Bogaerts A, Scientific reports 7, 5761 (2017). http://doi.org/10.1038/s41598-017-06412-8
Abstract: We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level.
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/s41598-017-06412-8
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“Combined first-principles and experimental study on the microstructure and mechanical characteristics of the multicomponent additive-manufactured Ti-35Nb-7Zr-5Ta alloy”. Grubova IY, Surmenev RA, Neyts EC, Koptyug AV, Volkova AP, Surmeneva MA, ACS Omega 8, 27519 (2023). http://doi.org/10.1021/ACSOMEGA.3C03157
Abstract: New & beta;-stabilizedTi-based alloys are highly promising forbone implants, thanks in part to their low elasticity. The natureof this elasticity, however, is as yet unknown. We here present combinedfirst-principles DFT calculations and experiments on the microstructure,structural stability, mechanical characteristics, and electronic structureto elucidate this origin. Our results suggest that the studied & beta;Ti-35Nb-7Zr-5Ta wt % (TNZT) alloy manufacturedby the electron-beam powder bed fusion (E-PBF) method has homogeneousmechanical properties (H = 2.01 & PLUSMN; 0.22 GPa and E = 69.48 & PLUSMN; 0.03 GPa) along the building direction,which is dictated by the crystallographic texture and microstructuremorphologies. The analysis of the structural and electronic properties,as the main factors dominating the chemical bonding mechanism, indicatesthat TNZT has a mixture of strong metallic and weak covalent bonding.Our calculations demonstrate that the softening in the Cauchy pressure(C & PRIME; = 98.00 GPa) and elastic constant C ̅ ( 44 ) = 23.84 GPa is the originof the low elasticity of TNZT. Moreover, the nature of this softeningphenomenon can be related to the weakness of the second and thirdneighbor bonds in comparison with the first neighbor bonds in theTNZT. Thus, the obtained results indicate that a carefully designedTNZT alloy can be an excellent candidate for the manufacturing oforthopedic internal fixation devices. In addition, the current findingscan be used as guidance not only for predicting the mechanical propertiesbut also the nature of elastic characteristics of the newly developedalloys with yet unknown properties.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.1
DOI: 10.1021/ACSOMEGA.3C03157
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“Stability of Si epoxide defects in Si nanowires : a mixed reactive force field/DFT study”. Schoeters B, Neyts EC, Khalilov U, Pourtois G, Partoens B, Physical chemistry, chemical physics 15, 15091 (2013). http://doi.org/10.1039/c3cp51621k
Abstract: Modeling the oxidation process of silicon nanowires through reactive force field based molecular dynamics simulations suggests that the formation of Si epoxide defects occurs both at the Si/SiOx interface and at the nanowire surface, whereas for flat surfaces, this defect is experimentally observed to occur only at the interface as a result of stress. In this paper, we argue that the increasing curvature stabilizes the defect at the nanowire surface, as suggested by our density functional theory calculations. The latter can have important consequences for the opto-electronic properties of thin silicon nanowires, since the epoxide induces an electronic state within the band gap. Removing the epoxide defect by hydrogenation is expected to be possible but becomes increasingly difficult with a reduction of the diameter of the nanowires.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 3
DOI: 10.1039/c3cp51621k
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“Size-dependent strain and surface energies of gold nanoclusters”. Ali S, Myasnichenko VS, Neyts EC, Physical chemistry, chemical physics 18, 792 (2016). http://doi.org/10.1039/c5cp06153a
Abstract: Gold nanocluster properties exhibit unique size-dependence. In this contribution, we employ reactive molecular dynamics simulations to calculate the size- and temperature-dependent surface energies, strain energies and atomic displacements for icosahedral, cuboctahedral, truncated octahedral and decahedral Au-nanoclusters. The calculations demonstrate that the surface energy decreases with increasing cluster size at 0 K but increases with size at higher temperatures. The calculated melting curves as a function of cluster size demonstrate the Gibbs-Thomson effect. Atomic displacements and strain are found to strongly depend on the cluster size and both are found to increase with increasing cluster size. These results are of importance for understanding the size-and temperature-dependent surface processes on gold nanoclusters.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 37
DOI: 10.1039/c5cp06153a
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“van der Waals density functionals applied to corundum-type sesquioxides : bulk properties and adsorption of CH3 and C6H6 on (0001) surfaces”. Dabaghmanesh S, Neyts EC, Partoens B, Physical chemistry, chemical physics 18, 23139 (2016). http://doi.org/10.1039/c6cp00346j
Abstract: van der Waals (vdW) forces play an important role in the adsorption of molecules on the surface of solids. However, the choice of the most suitable vdW functional for different systems is an essential problem which must be addressed for different systems. The lack of a systematic study on the performance of the vdW functionals in the bulk and adsorption properties of metal-oxides motivated us to examine different vdW approaches and compute the bulk and molecular adsorption properties of alpha-Cr2O3, alpha-Fe2O3, and alpha-Al2O3. For the bulk properties, we compared our results for the heat of formation, cohesive energy, lattice parameters and bond distances between the different vdW functionals and available experimental data. Next we studied the adsorption of benzene and CH3 molecules on top of different oxide surfaces. We employed different approximations to exchange and correlation within DFT, namely, the Perdew-Burke-Ernzerhof (PBE) GGA, (PBE)+U, and vdW density functionals [ DFT(vdW-DF/DF2/optPBE/optB86b/optB88)+U] as well as DFT-D2/D3(+U) methods of Grimme for the bulk calculations and optB86b-vdW(+U) and DFT-D2(+U) for the adsorption energy calculations. Our results highlight the importance of vdW interactions not only in the adsorption of molecules, but importantly also for the bulk properties. Although the vdW contribution in the adsorption of CH3 (as a chemisorption interaction) is less important compared to the adsorption of benzene (as a physisorption interaction), this contribution is not negligible. Also adsorption of benzene on ferryl/chromyl terminated surfaces shows an important chemisorption contribution in which the vdW interactions become less significant.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 6
DOI: 10.1039/c6cp00346j
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“A DFT study of H-dissolution into the bulk of a crystalline Ni(111) surface: a chemical identifier for the reaction kinetics”. Shirazi M, Bogaerts A, Neyts EC, Physical chemistry, chemical physics 19, 19150 (2017). http://doi.org/10.1039/C7CP03662K
Abstract: In this study, we investigated the diffusion of H-atoms to the subsurface and their further diffusion into the bulk of a Ni(111) crystal by means of density functional theory calculations in the context of thermal and plasma-assisted catalysis. The H-atoms at the surface can originate from the dissociative adsorption of H2 or CH4 molecules, determining the surface H-coverage. When a threshold H-coverage is passed, corresponding to 1.00 ML for the crystalline Ni(111) surface, the surface-bound H-atoms start to diffuse to the subsurface. A similar threshold coverage is observed for the interstitial H-coverage. Once the interstitial sites are filled up with a coverage above 1.00 ML of H, dissolution of interstitial H-atoms to the layer below the interstitial sites will be initiated. Hence, by applying a high pressure or inducing a reactive plasma and high temperature, increasing the H-flux to the surface, a large amount of hydrogen can diffuse in a crystalline metal like Ni and can be absorbed. The formation of metal hydride may modify the entire reaction kinetics of the system. Equivalently, the H-atoms in the bulk can easily go back to the surface and release a large amount of heat. In a plasma process, H-atoms are formed in the plasma, and therefore the energy barrier for dissociative adsorption is dismissed, thus allowing achievement of the threshold coverage without applying a high pressure as in a thermal process. As a result, depending on the crystal plane and type of metal, a large number of H-atoms can be dissolved (absorbed) in the metal catalyst, explaining the high efficiency of plasma-assisted catalytic reactions. Here, the mechanism of H-dissolution is established as a chemical identifier for the investigation of the reaction kinetics of a chemical process.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 10
DOI: 10.1039/C7CP03662K
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“A first principles study of p-type defects in LaCrO3”. Dabaghmanesh S, Sarmadian N, Neyts EC, Partoens B, Physical chemistry, chemical physics 19, 22870 (2017). http://doi.org/10.1039/C7CP03575F
Abstract: Recently, Sr-doped LaCrO3 has been experimentally introduced as a new p-type transparent conducting oxide. It is demonstrated that substituting Sr for La results in inducing p-type conductivity in LaCrO3. Performing first principles calculations we study the electronic structure and formation energy of various point defects in LaCrO3. Our results for the formation energies show that in addition to Sr, two more divalent defects, Ca and Ba, substituting for La in LaCrO3, behave as shallow acceptors in line with previous experimental reports. We further demonstrate that under oxygen-poor growth conditions, these shallow acceptors will be compensated by intrinsic donor-like defects (an oxygen vacancy and Cr on an oxygen site), but in the oxygen-rich growth regime the shallow acceptors have the lowest formation energies between all considered defects and will lead to p-type conductivity.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 16
DOI: 10.1039/C7CP03575F
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“Modelling molecular adsorption on charged or polarized surfaces: a critical flaw in common approaches”. Bal KM, Neyts EC, Physical chemistry, chemical physics 20, 8456 (2018). http://doi.org/10.1039/C7CP08209F
Abstract: A number of recent computational material design studies based on density functional theory (DFT) calculations have put forward a new class of materials with electrically switchable chemical characteristics that can be exploited in the development of tunable gas storage and electrocatalytic applications. We find systematic flaws in almost every computational study of gas adsorption on polarized or charged surfaces, stemming from an improper and unreproducible treatment of periodicity, leading to very large errors of up to 3 eV in some cases. Two simple corrective procedures that lead to consistent results are proposed, constituting a crucial course correction to the research in the field.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 8
DOI: 10.1039/C7CP08209F
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“Reaction mechanisms of C(3PJ) and C+(2PJ) with benzene in the interstellar medium from quantum mechanical molecular dynamics simulations”. Izadi ME, Bal KM, Maghari A, Neyts EC, Physical Chemistry Chemical Physics 23, 4205 (2021). http://doi.org/10.1039/D0CP04542J
Abstract: While spectroscopic data on small hydrocarbons in interstellar media in combination with crossed molecular beam (CMB) experiments have provided a wealth of information on astrochemically relevant species, much of the underlying mechanistic pathways of their formation remain elusive. Therefore, in this work, the chemical reaction mechanisms of C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>and C<sup>+</sup>(<sup>2</sup>P) + C<sub>6</sub>H<sub>6</sub>systems using the quantum mechanical molecular dynamics (QMMD) technique at the PBE0-D3(BJ) level of theory is investigated, mimicking a CMB experiment. Both the dynamics of the reactions as well as the electronic structure for the purpose of the reaction network are evaluated. The method is validated for the first reaction by comparison to the available experimental data. The reaction scheme for the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system covers the literature data,<italic>e.g.</italic>the major products are the 1,2-didehydrocycloheptatrienyl radical (C<sub>7</sub>H<sub>5</sub>) and benzocyclopropenyl radical (C<sub>6</sub>H<sub>5</sub>–CH), and it reveals the existence of less common pathways for the first time. The chemistry of the C<sup>+</sup>(<sup>2</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system is found to be much richer, and we have found that this is because of more exothermic reactions in this system in comparison to those in the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system. Moreover, using the QMMD simulation, a number of reaction paths have been revealed that produce three distinct classes of reaction products with different ring sizes. All in all, at all the collision energies and orientations, the major product is the heptagon molecular ion for the ionic system. It is also revealed that the collision orientation has a dominant effect on the reaction products in both systems, while the collision energy mostly affects the charged system. These simulations both prove the applicability of this approach to simulate crossed molecular beams, and provide fundamental information on reactions relevant for the interstellar medium.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
DOI: 10.1039/D0CP04542J
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“Uniform-acceptance force-bias Monte Carlo method with time scale to study solid-state diffusion”. Mees MJ, Pourtois G, Neyts EC, Thijsse BJ, Stesmans A, Physical review : B : condensed matter and materials physics 85, 134301 (2012). http://doi.org/10.1103/PhysRevB.85.134301
Abstract: Monte Carlo (MC) methods have a long-standing history as partners of molecular dynamics (MD) to simulate the evolution of materials at the atomic scale. Among these techniques, the uniform-acceptance force-bias Monte Carlo (UFMC) method [ G. Dereli Mol. Simul. 8 351 (1992)] has recently attracted attention [ M. Timonova et al. Phys. Rev. B 81 144107 (2010)] thanks to its apparent capacity of being able to simulate physical processes in a reduced number of iterations compared to classical MD methods. The origin of this efficiency remains, however, unclear. In this work we derive a UFMC method starting from basic thermodynamic principles, which leads to an intuitive and unambiguous formalism. The approach includes a statistically relevant time step per Monte Carlo iteration, showing a significant speed-up compared to MD simulations. This time-stamped force-bias Monte Carlo (tfMC) formalism is tested on both simple one-dimensional and three-dimensional systems. Both test-cases give excellent results in agreement with analytical solutions and literature reports. The inclusion of a time scale, the simplicity of the method, and the enhancement of the time step compared to classical MD methods make this method very appealing for studying the dynamics of many-particle systems.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.836
Times cited: 31
DOI: 10.1103/PhysRevB.85.134301
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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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