“Deacetylation of mannosylerythritol lipids in hydrophobic natural deep eutectic solvents”. Cassimon J, Kovács A, Neyts E, Cornet I, Billen P, European journal of organic chemistry 27, e202300934 (2023). http://doi.org/10.1002/EJOC.202300934
Abstract: Mannosylerythritol lipids (MELs) are a promising group of biosurfactants due to their high fermentation yield, selfassembly and biological activity. During fermentation by Pseudozyma aphidis, a mixture of MELs with different levels of acylation is formed, of which the fully deacetylated form is the most valuable. In order to reduce the environmental impact of deacetylation, an enzymatic process using natural deep eutectic solvents (NADES) has been developed. We tested the deacetylation of a purified MELs mixture with immobilized Candida antarctica lipase B enzyme and 2-ethylhexanol as co-substrate in 140 h reactions with different NADES. We identified hydrophobic NADES systems with similar yields and kinetics as in pure 2-ethylhexanol solvent. Our results indicate that deacetylation of MELs mixtures in NADES as a solvent is possible with yields comparable to pure co-substrate and that hydrophobic NADES without carboxylic acid compounds facilitate the reaction to the greatest extent.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS)
Impact Factor: 2.8
DOI: 10.1002/EJOC.202300934
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“Predicted Influence of Plasma Activation on Nonoxidative Coupling of Methane on Transition Metal Catalysts”. Engelmann Y, Mehta P, Neyts EC, Schneider WF, Bogaerts A, Acs Sustainable Chemistry &, Engineering 8, 6043 (2020). http://doi.org/10.1021/acssuschemeng.0c00906
Abstract: The combination of catalysis and nonthermal plasma holds promise for enabling difficult chemical conversions. The possible synergy between both depends strongly on the nature of the reactive plasma species and the catalyst material. In this paper, we show how vibrationally excited species and plasma-generated radicals interact with transition metal catalysts and how changing the catalyst material can improve the conversion rates and product selectivity. We developed a microkinetic model to investigate the impact of vibrational excitations and plasma-generated radicals on the nonoxidative coupling of methane over transition metal surfaces. We predict a significant increase in ethylene formation for vibrationally excited methane. Plasma-generated radicals have a stronger impact on the turnover frequencies with high selectivity toward ethylene on noble catalysts and mixed selectivity on non-noble catalysts. In general, we show how the optimal catalyst material depends on the desired products as well as the plasma conditions.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Movement Antwerp (MOVANT)
Impact Factor: 8.4
DOI: 10.1021/acssuschemeng.0c00906
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“Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls”. Yusupov M, Neyts EC, Khalilov U, Snoeckx R, van Duin ACT, Bogaerts A, New journal of physics 14, 093043 (2012). http://doi.org/10.1088/1367-2630/14/9/093043
Abstract: In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. CO, CN and CC bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.786
Times cited: 47
DOI: 10.1088/1367-2630/14/9/093043
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“Atomistic modelling of CVD synthesis of carbon nanotubes and graphene”. Elliott JA, Shibuta Y, Amara H, Bichara C, Neyts EC, Nanoscale 5, 6662 (2013). http://doi.org/10.1039/c3nr01925j
Abstract: We discuss the synthesis of carbon nanotubes (CNTs) and graphene by catalytic chemical vapour deposition (CCVD) and plasma-enhanced CVD (PECVD), summarising the state-of-the-art understanding of mechanisms controlling their growth rate, chiral angle, number of layers (walls), diameter, length and quality (defects), before presenting a new model for 2D nucleation of a graphene sheet from amorphous carbon on a nickel surface. Although many groups have modelled this process using a variety of techniques, we ask whether there are any complementary ideas emerging from the different proposed growth mechanisms, and whether different modelling techniques can give the same answers for a given mechanism. Subsequently, by comparing the results of tight-binding, semi-empirical molecular orbital theory and reactive bond order force field calculations, we demonstrate that graphene on crystalline Ni(111) is thermodynamically stable with respect to the corresponding amorphous metal and carbon structures. Finally, we show in principle how a complementary heterogeneous nucleation step may play a key role in the transformation from amorphous carbon to graphene on the metal surface. We conclude that achieving the conditions under which this complementary crystallisation process can occur may be a promising method to gain better control over the growth processes of both graphene from flat metal surfaces and CNTs from catalyst nanoparticles.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 52
DOI: 10.1039/c3nr01925j
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“Bond switching regimes in nickel and nickel-carbon nanoclusters”. Neyts E, Shibuta Y, Bogaerts A, Chemical physics letters 488, 202 (2010). http://doi.org/10.1016/j.cplett.2010.02.024
Abstract: Understanding the fundamental dynamics in carbon nanotube (CNT) catalysts is of primary importance to understand CNT nucleation. This Letter reports on calculated bond switching (BS) rates in pure and carbon containing nickel nanoclusters. The rates are analyzed in terms of their temperature dependent spatial distribution and the mobility of the cluster atoms. The BS mechanism is found to change from vibrational to diffusional at around 900 K, with a corresponding strong increase in activation energy. Furthermore, the BS activation energy is observed to decrease as the carbon content in the cluster increases, resulting in an effective liquification of the cluster.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.815
Times cited: 20
DOI: 10.1016/j.cplett.2010.02.024
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“Can we control the thickness of ultrathin silica layers by hyperthermal silicon oxidation at room temperature?”.Khalilov U, Neyts EC, Pourtois G, van Duin ACT, The journal of physical chemistry: C : nanomaterials and interfaces 115, 24839 (2011). http://doi.org/10.1021/jp2082566
Abstract: Using reactive molecular dynamics simulations by means of the ReaxFF potential, we studied the growth mechanism of ultrathin silica (SiO2) layers during hyperthermal oxidation at room temperature. Oxidation of Si(100){2 × 1} surfaces by both atomic and molecular oxygen was investigated in the energy range 15 eV. The oxidation mechanism, which differs from thermal oxidation, is discussed. In the case of oxidation by molecular O2, silica is quickly formed and the thickness of the formed layers remains limited compared to oxidation by atomic oxygen. The Si/SiO2 interfaces are analyzed in terms of partial charges and angle distributions. The obtained structures of the ultrathin SiO2 films are amorphous, including some intrinsic defects. 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; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 36
DOI: 10.1021/jp2082566
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“Changing chirality during single-walled carbon nanotube growth : a reactive molecular dynamics/Monte Carlo study”. Neyts EC, van Duin ACT, Bogaerts A, Journal of the American Chemical Society 133, 17225 (2011). http://doi.org/10.1021/ja204023c
Abstract: The growth mechanism and chirality formation of a single-walled carbon nanotube (SWNT) on a surface-bound nickel nanocluster are investigated by hybrid reactive molecular dynamics/force-biased Monte Carlo simulations. The validity of the interatomic potential used, the so-called ReaxFF potential, for simulating catalytic SWNT growth is demonstrated. The SWNT growth process was found to be in agreement with previous studies and observed to proceed through a number of distinct steps, viz., the dissolution of carbon in the metallic particle, the surface segregation of carbon with the formation of aggregated carbon clusters on the surface, the formation of graphitic islands that grow into SWNT caps, and finally continued growth of the SWNT. Moreover, it is clearly illustrated in the present study that during the growth process, the carbon network is continuously restructured by a metal-mediated process, thereby healing many topological defects. It is also found that a cap can nucleate and disappear again, which was not observed in previous simulations. Encapsulation of the nanoparticle is observed to be prevented by the carbon network migrating as a whole over the cluster surface. Finally, for the first time, the chirality of the growing SWNT cap is observed to change from (11,0) over (9,3) to (7,7). It is demonstrated that this change in chirality is due to the metal-mediated restructuring process.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 13.858
Times cited: 116
DOI: 10.1021/ja204023c
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“Combining molecular dynamics with Monte Carlo simulations : implementations and applications”. Neyts EC, Bogaerts A, Theoretical chemistry accounts : theory, computation, and modeling 132, 1320 (2013). http://doi.org/10.1007/s00214-012-1320-x
Abstract: In this contribution, we present an overview of the various techniques for combining atomistic molecular dynamics with Monte Carlo simulations, mainly in the context of condensed matter systems, as well as a brief summary of the main accelerated dynamics techniques. Special attention is given to the force bias Monte Carlo technique and its combination with molecular dynamics, in view of promising recent developments, including a definable timescale. Various examples of the application of combined molecular dynamics / Monte Carlo simulations are given, in order to demonstrate the enhanced simulation efficiency with respect to either pure molecular dynamics or Monte Carlo.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.89
Times cited: 27
DOI: 10.1007/s00214-012-1320-x
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“Computer modeling of plasmas and plasma-surface interactions”. Bogaerts A, Bultinck E, Eckert M, Georgieva V, Mao M, Neyts E, Schwaederlé, L, Plasma processes and polymers 6, 295 (2009). http://doi.org/10.1002/ppap.200800207
Abstract: In this paper, an overview is given of different modeling approaches used for describing gas discharge plasmas, as well as plasma-surface interactions. A fluid model is illustrated for describing the detailed plasma chemistry in capacitively coupled rf discharges. The strengths and limitations of Monte Carlo simulations and of a particle-in-cell-Monte Carlo collisions model are explained for a magnetron discharge, whereas the capabilities of a hybrid Monte Carlo-fluid approach are illustrated for a direct current glow discharge used for spectrochemical analysis of materials. Finally, some examples of molecular dynamics simulations, for the purpose of plasma-deposition, are given.
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.200800207
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“Computer modelling of the plasma chemistry and plasma-based growth mechanisms for nanostructured materials”. Bogaerts A, Eckert M, Mao M, Neyts E, Journal of physics: D: applied physics 44, 174030 (2011). http://doi.org/10.1088/0022-3727/44/17/174030
Abstract: In this review paper, an overview is given of different modelling efforts for plasmas used for the formation and growth of nanostructured materials. This includes both the plasma chemistry, providing information on the precursors for nanostructure formation, as well as the growth processes itself. We limit ourselves to carbon (and silicon) nanostructures. Examples of the plasma modelling comprise nanoparticle formation in silane and hydrocarbon plasmas, as well as the plasma chemistry giving rise to carbon nanostructure formation, such as (ultra)nanocrystalline diamond ((U)NCD) and carbon nanotubes (CNTs). The second part of the paper deals with the simulation of the (plasma-based) growth mechanisms of the same carbon nanostructures, i.e. (U)NCD and CNTs, both by mechanistic modelling and detailed atomistic simulations.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 25
DOI: 10.1088/0022-3727/44/17/174030
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“Computer simulations for processing plasmas”. Bogaerts A, de Bleecker K, Georgieva V, Kolev I, Madani M, Neyts E, Plasma processes and polymers 3, 110 (2006). http://doi.org/10.1002/ppap.200500065
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 8
DOI: 10.1002/ppap.200500065
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“Computer simulations of plasmabiomolecule and plasmatissue interactions for a better insight in plasma medicine”. Neyts EC, Yusupov M, Verlackt CC, Bogaerts A, Journal of physics: D: applied physics 47, 293001 (2014). http://doi.org/10.1088/0022-3727/47/29/293001
Abstract: Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficultif not impossibleto obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasmabiomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance the field.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 28
DOI: 10.1088/0022-3727/47/29/293001
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“Defect healing and enhanced nucleation of carbon nanotubes by low-energy ion bombardment”. Neyts EC, Ostrikov K, Han ZJ, Kumar S, van Duin ACT, Bogaerts A, Physical review letters 110, 065501 (2013). http://doi.org/10.1103/PhysRevLett.110.065501
Abstract: Structural defects inevitably appear during the nucleation event that determines the structure and properties of single-walled carbon nanotubes. By combining ion bombardment experiments with atomistic simulations we reveal that ion bombardment in a suitable energy range allows these defects to be healed resulting in an enhanced nucleation of the carbon nanotube cap. The enhanced growth of the nanotube cap is explained by a nonthermal ion-induced graphene network restructuring mechanism.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 8.462
Times cited: 50
DOI: 10.1103/PhysRevLett.110.065501
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“Densification of thin a-C: H films grown from low-kinetic energy hydrocarbon radicals under the influence of H and C particle fluxes: a molecular dynamics study”. Neyts E, Bogaerts A, van de Sanden MCM, Journal of physics: D: applied physics 39, 1948 (2006). http://doi.org/10.1088/0022-3727/39/9/034
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 3
DOI: 10.1088/0022-3727/39/9/034
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“A density-functional theory simulation of the formation of Ni-doped fullerenes by ion implantation”. Neyts E, Maeyens A, Pourtois G, Bogaerts A, Carbon 49, 1013 (2011). http://doi.org/10.1016/j.carbon.2010.11.009
Abstract: Using self-consistent KohnSham density-functional theory molecular dynamics simulations, we demonstrate the theoretical possibility to synthesize NiC60, the incarfullerene Ni@C60 and the heterofullerene C59Ni in an ion implantation setup. The corresponding formation mechanisms of all three complexes are elucidated as a function of the ion implantation energy and impact location, suggesting possible routes for selectively synthesizing these complexes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 13
DOI: 10.1016/j.carbon.2010.11.009
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“Development of a ReaxFF reactive force field for intrinsic point defects in titanium dioxide”. Huygh S, Bogaerts A, van Duin ACT, Neyts EC, Computational materials science 95, 579 (2014). http://doi.org/10.1016/j.commatsci.2014.07.056
Abstract: A reactive ReaxFF force field is developed for studying the influence of intrinsic point defects on the chemistry with TiO2 condensed phases. The force field parameters are optimized to ab initio data for the equations of state, relative phase stabilities for titanium and titanium dioxide, potential energy differences for (TiO2)n-clusters (n = 116). Also data for intrinsic point defects in anatase were added. These data contain formation energies for interstitial titanium and oxygen vacancies, diffusion barriers of the oxygen vacancies and molecular oxygen adsorption on a reduced anatase (101) surface. Employing the resulting force field, we study the influence of concentration of oxygen vacancies and expansion or compression of an anatase surface on the diffusion of the oxygen vacancies. Also the barrier for oxygen diffusion in the subsurface region is evaluated using this force field. This diffusion barrier of 27.7 kcal/mol indicates that the lateral redistribution of oxygen vacancies on the surface and in the subsurface will be dominated by their diffusion in the subsurface, since both this barrier as well as the barriers for diffusion from the surface to the subsurface and vice versa (17.07 kcal/mol and 21.91 kcal/mol, respectively, as calculated with DFT), are significantly lower than for diffusion on the surface (61.12 kcal/mol as calculated with DFT).
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.292
Times cited: 15
DOI: 10.1016/j.commatsci.2014.07.056
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“Differences between ultrananocrystalline and nanocrystalline diamond growth: theoretical investigation of CxHy species at diamond step edges”. Eckert M, Neyts E, Bogaerts A, Crystal growth &, design 10, 4123 (2010). http://doi.org/10.1021/cg100804v
Abstract: The behavior of hydrocarbon species at step edges of diamond terraces is investigated by means of combined molecular dynamics−Metropolis Monte Carlo simulations. The results show that the formation of ballas-like diamond films (like UNCD) and well-faceted diamond films (like NCD) can be related to the gas phase concentrations of CxHy in a new manner: Species that have high concentrations above the growing UNCD films suppress the extension of step edges through defect formation. The species that are present above the growing NCD film, however, enhance the extension of diamond terraces, which is believed to result in well-faceted diamond films. Furthermore, it is shown that, during UNCD growth, CxHy species with x ≥ 2 play an important role, in contrast to the currently adopted CVD diamond growth mechanism. Finally, the probabilities for the extension of the diamond (100) terrace are much higher than those for the diamond (111) terrace, which is in full agreement with the experimental observation that diamond (100) facets are more favored than diamond (111) facets during CVD diamond growth.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.055
Times cited: 11
DOI: 10.1021/cg100804v
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“Effect of hydrogen on the growth of thin hydrogenated amorphous carbon films from thermal energy radicals”. Neyts E, Bogaerts A, van de Sanden MCM, Applied physics letters 88, 141922 (2006). http://doi.org/10.1063/1.2193803
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.411
Times cited: 35
DOI: 10.1063/1.2193803
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“Efficient amorphous platinum catalyst cluster growth on porous carbon : a combined molecular dynamics and experimental study”. Xie L, Brault P, Coutanceau C, Bauchire J-M, Caillard A, Baranton S, Berndt J, Neyts EC, Applied catalysis : B : environmental 162, 21 (2015). http://doi.org/10.1016/j.apcatb.2014.06.032
Abstract: Amorphous platinum clusters supported on porous carbon have been envisaged for high-performance fuel cell electrodes. For this application, it is crucial to control the morphology of the Pt layer and the Ptsubstrate interaction to maximize activity and stability. We thus investigate the morphology evolution during Pt cluster growth on a porous carbon substrate employing atomic scale molecular dynamics simulations. The simulations are based on the Pt-C interaction potential using parameters derived from density functional theory and are found to yield a Pt cluster morphology similar to that observed in low loaded fuel cell electrodes prepared by plasma sputtering. Moreover, the simulations show amorphous Pt cluster growth in agreement with X-ray diffraction and transmission electron microscopy experiments on high performance low Pt content (10 μgPt cm−2) loaded fuel cell electrodes and provide a fundamental insight in the cluster growth mechanism.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.446
Times cited: 20
DOI: 10.1016/j.apcatb.2014.06.032
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“Establishing uniform acceptance in force biased Monte Carlo simulations”. Neyts EC, Thijsse BJ, Mees MJ, Bal KM, Pourtois G, Journal of chemical theory and computation 8, 1865 (2012). http://doi.org/10.1021/ct2008268
Abstract: Uniform acceptance force biased Monte Carlo (UFMC) simulations have previously been shown to be a powerful tool to simulate atomic scale processes, enabling one to follow the dynamical path during the simulation. In this contribution, we present a simple proof to demonstrate that this uniform acceptance still complies with the condition of detailed balance, on the condition that the characteristic parameter lambda = 1/2 and that the maximum allowed step size is chosen to be sufficiently small. Furthermore, the relation to Metropolis Monte Carlo (MMC) is also established, and it is shown that UFMC reduces to MMC by choosing the characteristic parameter lambda = 0 [Rao, M. et al. Mol. Phys. 1979, 37, 1773]. Finally, a simple example compares the UFMC and MMC methods.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.245
Times cited: 20
DOI: 10.1021/ct2008268
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“Formation of endohedral Ni@C60 and exohedral NiC60 metallofullerene complexes by simulated ion implantation”. Neyts EC, Bogaerts A, Carbon 47, 1028 (2009). http://doi.org/10.1016/j.carbon.2008.12.023
Abstract: The interaction of thermal and hyperthermal Ni ions with gas-phase C60 fullerene was investigated at two temperatures with classical molecular dynamics simulations using a recently developed interatomic many-body potential. The interaction between Ni and C60 is characterized in terms of the NiC60 binding sites, complex formation, and the collision and temperature induced deformation of the C60 cage structure. The simulations show how ion implantation theoretically allows the synthesis of both endohedral Ni@C60 and exohedral NiC60 metallofullerene complexes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.337
Times cited: 15
DOI: 10.1016/j.carbon.2008.12.023
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“Gas discharge plasmas and their applications”. Bogaerts A, Neyts E, Gijbels R, van der Mullen J, Spectrochimica acta: part B : atomic spectroscopy 57, 609 (2002). http://doi.org/10.1016/S0584-8547(01)00406-2
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.241
Times cited: 462
DOI: 10.1016/S0584-8547(01)00406-2
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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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“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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“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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“Influence of internal energy and impact angle on the sticking behaviour of reactive radicals in thin a-C:H film growth: a molecular dynamics study”. Neyts E, Bogaerts A, Physical chemistry, chemical physics 8, 2066 (2006). http://doi.org/10.1039/b517563a
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 7
DOI: 10.1039/b517563a
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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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“Insights into the growth of (ultra)nanocrystalline diamond by combined molecular dynamics and Monte Carlo simulations”. Eckert M, Neyts E, Bogaerts A, Crystal growth &, design 10, 3005 (2010). http://doi.org/10.1021/cg100063c
Abstract: In this paper, we present the results of combined molecular dynamics−Metropolis Monte Carlo (MD-MMC) simulations of hydrocarbon species at flat diamond (100)2 × 1 and (111)1 × 1 surfaces. The investigated species are considered to be the most important growth species for (ultra)nanocrystalline diamond ((U)NCD) growth. When applying the MMC algorithm to stuck species at monoradical sites, bonding changes are only seen for CH2. The sequence of the bond breaking and formation as put forward by the MMC simulations mimics the insertion of CH2 into a surface dimer as proposed in the standard growth model of diamond. For hydrocarbon species attached to two adjacent radical (biradical) sites, the MMC simulations give rise to significant changes in the bonding structure. For UNCD, the combinations of C3 and C3H2, and C3 and C4H2 (at diamond (100)2 × 1) and C and C2H2 (at diamond (111)1 × 1) are the most successful in nucleating new crystal layers. For NCD, the following combinations pursue the diamond structure the best: C2H2 and C3H2 (at diamond (100)2 × 1) and CH2 and C2H2 (at diamond (111)1 × 1). The different behaviors of the hydrocarbon species at the two diamond surfaces are related to the different sterical hindrances at the diamond surfaces.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.055
Times cited: 13
DOI: 10.1021/cg100063c
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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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