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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 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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“Sulfur-alloyed Cr2O3: a new p-type transparent conducting oxide host”. Dabaghmanesh S, Saniz R, Neyts E, Partoens B, RSC advances 7, 4453 (2017). http://doi.org/10.1039/C6RA27852C
Abstract: Doped Cr2O3 has been shown to be a p-type transparent conducting oxide (TCO). Its conductivity, however, is low. As for most p-type TCOs, the main problem is the high effective hole mass due to flat valence bands. We use first-principles methods to investigate whether one can increase the valence band dispersion (i.e. reduce the hole mass) by anion alloying with sulfur, while keeping the band gap large enough for transparency. The alloying concentrations considered are given by Cr(4)SxO(6-x), with x = 1-5. To be able to describe the electronic properties of these materials accurately, we first study Cr2O3, examining critically the accuracy of different density functionals and methods, including PBE, PBE+U, HSE06, as well as perturbative approaches within the GW approximation. Our results demonstrate that Cr4S2O4 has an optical band gap of 3.08 eV and an effective hole mass of 1.8 m(e). This suggests Cr4S2O4 as a new p-type TCO host candidate.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.108
Times cited: 9
DOI: 10.1039/C6RA27852C
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“The formation of Cr2O3 nanoclusters over graphene sheet and carbon nanotubes”. Dabaghmanesh S, Neek-Amal M, Partoens B, Neyts EC, Chemical physics letters 687, 188 (2017). http://doi.org/10.1016/J.CPLETT.2017.09.005
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.815
Times cited: 2
DOI: 10.1016/J.CPLETT.2017.09.005
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“Direct oxidation of methane to methanol on Co embedded N-doped graphene: Comparing the role of N₂O and O₂, as oxidants”. Nematollahi P, Neyts EC, Applied Catalysis A-General 602, 117716 (2020). http://doi.org/10.1016/J.APCATA.2020.117716
Abstract: In this work, the effects of N-doping into the Co-doped single vacancy (Co-SV-G) and di-vacancy graphene flake (Co-dV-G) are investigated and compared toward direct oxidation of methane to methanol (DOMM) employing two different oxidants (N2O and O-2) using density functional theory (DFT) calculation. We found that DOMM on CoN3-G utilizing the N2O molecule as oxygen-donor proceeds via a two-step reaction with low activation energies. In addition, we found that although CoN3-G might be a good catalyst for methane conversion, it can also catalyze the oxidation of methanol to CO2 and H2O due to the required low activation barriers. Moreover, the adsorption behaviors of CHx (x = 0-4) species and dehydrogenation of CHx (x = 1-4) species on CoN3-G are investigated. We concluded that CoN3-G can be used as an efficient catalyst for DOMM and N-2O reduction at ambient conditions which may serve as a guide for fabricating effective C/N catalysts in energy-related devices.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.5
DOI: 10.1016/J.APCATA.2020.117716
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“Effect of van der Waals interactions on the adhesion strength at the interface of the hydroxyapatite-titanium biocomposite : a first-principles study”. Grubova IY, Surmeneva MA, Surmenev RA, Neyts EC, RSC advances 10, 37800 (2020). http://doi.org/10.1039/D0RA06006B
Abstract: Hydroxyapatite (HAP) is frequently used as biocompatible coating on Ti-based implants. In this context, the HAP-Ti adhesion is of crucial importance. Here, we report ab initio calculations to investigate the influence of Si incorporation into the amorphous calcium-phosphate (a-HAP) structure on the interfacial bonding mechanism between the a-HAP coating and an amorphous titanium dioxide (a-TiO2) substrate, contrasting two different density functionals: PBE-GGA, and DFT-D3, which are capable of describing the influence of the van der Waals (vdW) interactions. In particular, we discuss the effect of dispersion on the work of adhesion (W-ad), equilibrium geometries, and charge density difference (CDD). We find that replacement of P by Si in a-HAP (a-Si-HAP) with the creation of OH vacancies as charge compensation results in a significant increase in the bond strength between the coating and substrate in the case of using the PBE-GGA functional. However, including the vdW interactions shows that these forces considerably contribute to the W-ad. We show that the difference (W-ad – W-ad(vdW)) is on average more than 1.1 J m(-2) and 0.5 J m(-2) for a-HAP/a-TiO2 and a-Si-HAP/a-TiO2, respectively. These results reveal that including vdW interactions is essential for accurately describing the chemical bonding at the a-HAP/a-TiO2 interface.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.1039/D0RA06006B
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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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“Thermal conductivity of titanium nitride/titanium aluminum nitride multilayer coatings deposited by lateral rotating cathode arc”. Samani MK, Ding XZ, Khosravian N, Amin-Ahmadi B, Yi Y, Chen G, Neyts EC, Bogaerts A, Tay BK, Thin solid films : an international journal on the science and technology of thin and thick films 578, 133 (2015). http://doi.org/10.1016/j.tsf.2015.02.032
Abstract: A seriesof [TiN/TiAlN]nmultilayer coatingswith different bilayer numbers n=5, 10, 25, 50, and 100 were deposited on stainless steel substrate AISI 304 by a lateral rotating cathode arc technique in a flowing nitrogen atmosphere. The composition and microstructure of the coatings have been analyzed by using energy dispersive X-ray spectroscopy, X-ray diffraction (XRD), and conventional and high-resolution transmission electron microscopy (HRTEM). XRD analysis shows that the preferential orientation growth along the (111) direction is reduced in the multilayer coatings. TEM analysis reveals that the grain size of the coatings decreases with increasing bilayer number. HRTEMimaging of the multilayer coatings shows a high density misfit dislocation between the TiN and TiAlN layers. The cross-plane thermal conductivity of the coatings was measured by a pulsed photothermal reflectance technique. With increasing bilayer number, the multilayer coatings' thermal conductivity decreases gradually. This reduction of thermal conductivity can be ascribed to increased phonon scattering due to the disruption of columnar structure, reduced preferential orientation, decreased grain size of the coatings and present misfit dislocations at the interfaces.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.879
Times cited: 41
DOI: 10.1016/j.tsf.2015.02.032
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“Thermodynamics at the nanoscale : phase diagrams of nickel-carbon nanoclusters and equilibrium constants for face transitions”. Engelmann Y, Bogaerts A, Neyts EC, Nanoscale 6, 11981 (2014). http://doi.org/10.1039/C4NR02354D
Abstract: Using reactive molecular dynamics simulations, the melting behavior of nickelcarbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickelcarbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method.
Keywords: A1 Journal article; PLASMANT
Impact Factor: 7.367
Times cited: 20
DOI: 10.1039/C4NR02354D
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“Multi-level molecular modelling for plasma medicine”. Bogaerts A, Khosravian N, Van der Paal J, Verlackt CCW, Yusupov M, Kamaraj B, Neyts EC, Journal Of Physics D-Applied Physics 49, 054002 (2016)
Keywords: A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT)
Impact Factor: 2.588
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“Molecular Dynamics Simulations for Plasma-Surface Interactions: Molecular Dynamics Simulations…”. Neyts EC, Brault P, Plasma processes and polymers 14, 1600145 (2017). http://doi.org/10.1002/ppap.201600145
Abstract: Plasma-surface interactions are in general highly complex due to the interplay of many concurrent processes. Molecular dynamics simulations provide insight in some of these processes, subject to the accessible time and length scales, and the availability of suitable force fields. In this introductory tutorial-style review, we aim to describe the current capabilities and limitations of molecular dynamics simulations in this field, restricting ourselves to low-temperature nonthermal plasmas. Attention is paid to the simulation of the various fundamental processes occurring, including sputtering, etching, implantation, and deposition, as well as to what extent the basic plasma components can be accounted for, including ground state and excited species, electric fields, ions, photons, and electrons. A number of examples is provided, giving an bird’s eye overview of the current state of the field.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 13
DOI: 10.1002/ppap.201600145
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“Adsorption of C and CHx radicals on anatase (001) and the influence of oxygen vacancies”. Huygh S, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 119, 4908 (2015). http://doi.org/10.1021/jp5127249
Abstract: The adsorption of C and CHx radicals on anatase (001) was studied using DFT within the generalized gradient approximation using the Perde-Burke-Ernzerhof (PBE) functional. We have studied the influence of oxygen vacancies in and at the surface on the adsorption properties of the radicals. For the oxygen vacancies in anatase (001), the most stable vacancy is located at the surface. For this vacancy, the maximal adsorption strength of C and CH decreases compared to the adsorption on the stoichiometric surface, but it increases for CH2 and CH3. If an oxygen vacancy is present in the first subsurface layer, the maximal adsorption strength increases for C, CH, CH2, and CH3. When the vacancy is present in the next subsurface layer, we find that only the CH3 adsorption is enhanced, while the maximal adsorption energies for the other radical species decrease. Not only does the precise location of the oxygen vacancy determine the maximal adsorption interaction, it also influences the adsorption strengths of the radicals at different surface configurations. This determines the probability of finding a certain adsorption configuration at the surface, which in turn influences the possible surface reactions. We find that C preferentially adsorbs far away from the oxygen vacancy, while CH2 and CH3 adsorb preferentially at the oxygen vacancy site. A fraction of CH partially adsorbs at the oxygen vacancy, and another fraction adsorbs further away from the vacancy.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 13
DOI: 10.1021/jp5127249
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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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“Catalyzed growth of carbon nanotube with definable chirality by hybrid molecular dynamics-force biased Monte Carlo simulations”. Neyts EC, Shibuta Y, van Duin ACT, Bogaerts A, ACS nano 4, 6665 (2010). http://doi.org/10.1021/nn102095y
Abstract: Metal-catalyzed growth mechanisms of carbon nanotubes (CNTs) were studied by hybrid molecular dynamics−Monte Carlo simulations using a recently developed ReaxFF reactive force field. Using this novel approach, including relaxation effects, a CNT with definable chirality is obtained, and a step-by-step atomistic description of the nucleation process is presented. Both root and tip growth mechanisms are observed. The importance of the relaxation of the network is highlighted by the observed healing of defects.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 13.942
Times cited: 129
DOI: 10.1021/nn102095y
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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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“Characterization of nano-crystalline diamond films grown under continuous DC bias during plasma enhanced chemical vapor deposition”. Mortet V, Zhang L, Echert M, Soltani A, d' Haen J, Douheret O, Moreau M, Osswald S, Neyts E, Troadec D, Wagner P, Bogaerts A, Van Tendeloo G, Haenen K, Materials Research Society symposium proceedings (2009). http://doi.org/10.1557/PROC-1203-J05-03
Abstract: Nanocrystalline diamond films have generated much interested due to their diamond-like properties and low surface roughness. Several techniques have been used to obtain a high re-nucleation rate, such as hydrogen poor or high methane concentration plasmas. In this work, the properties of nano-diamond films grown on silicon substrates using a continuous DC bias voltage during the complete duration of growth are studied. Subsequently, the layers were characterised by several morphological, structural and optical techniques. Besides a thorough investigation of the surface structure, using SEM and AFM, special attention was paid to the bulk structure of the films. The application of FTIR, XRD, multi wavelength Raman spectroscopy, TEM and EELS yielded a detailed insight in important properties such as the amount of crystallinity, the hydrogen content and grain size. Although these films are smooth, they are under a considerable compressive stress. FTIR spectroscopy points to a high hydrogen content in the films, while Raman and EELS indicate a high concentration of sp2 carbon. TEM and EELS show that these films consist of diamond nano-grains mixed with an amorphous sp2 bonded carbon, these results are consistent with the XRD and UV Raman spectroscopy data.
Keywords: A3 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.1557/PROC-1203-J05-03
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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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“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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“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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