“Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine”. Van der Paal J, Verlackt CC, Yusupov M, Neyts EC, Bogaerts A, Journal of physics: D: applied physics 48, 155202 (2015). http://doi.org/10.1088/0022-3727/48/15/155202
Abstract: While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 20
DOI: 10.1088/0022-3727/48/15/155202
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“Study of atmospheric MOCVD of TiO2 thin films by means of computational fluid dynamics simulations”. Baguer N, Neyts E, van Gils S, Bogaerts A, Chemical vapor deposition 14, 339 (2008). http://doi.org/10.1002/cvde.200806708
Abstract: This paper presents the computational study of the metal-organic (MO) CVD of titanium dioxide (TiO2) films grown using titanium tetraisopropoxide (TTIP) as a precursor and nitrogen as a carrier gas. The TiO2 films are deposited under atmospheric pressure. The effects of the precursor concentration, the substrate temperature, and the hydrolysis reaction on the deposition process are investigated. It is found that hydrolysis of the TTIP decreases the onset temperature of the gas-phase thermal decomposition, and that the deposition rate increases with the precursor concentration and with the decrease of substrate temperature. Concerning the mechanism responsible for the film growth, the model shows that at the lowest precursor concentration, the direct adsorption of the precursor is dominant, while at higher precursor concentrations, the monomer deposition becomes more important.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.333
Times cited: 14
DOI: 10.1002/cvde.200806708
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“Temperature influence on the reactivity of plasma species on a nickel catalyst surface : an atomic scale study”. Somers W, Bogaerts A, van Duin ACT, Huygh S, Bal KM, Neyts EC, Catalysis today 211, 131 (2013). http://doi.org/10.1016/j.cattod.2013.02.010
Abstract: In recent years, the potential use of hydrogen as a clean energy source has gained considerable attention. Especially H2 formation by Ni-catalyzed reforming of methane at elevated temperatures is an attractive process. However, a more fundamental knowledge at the atomic level is needed for a full comprehension of the reactions at the catalyst surface. In this contribution, we therefore investigate the H2 formation after CHx impacts on a Ni(1 1 1) surface in the temperature range 4001600 K, by means of reactive molecular dynamics (MD) simulations using the ReaxFF potential. While some H2 formation is already observed at the lower temperatures, substantial H2 formation is only obtained at elevated temperatures of 1400 K and above. At 1600 K, the H2 molecules are even the most frequently formed species. In direct correlation with the increasing dehydrogenation at elevated temperatures, an increased surface-to-subsurface C-diffusivity is observed as well. This study highlights the major importance of the temperature on the H2 formation.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.636
Times cited: 27
DOI: 10.1016/j.cattod.2013.02.010
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“Theoretical investigation of grain size tuning during prolonged bias-enhanced nucleation”. Eckert M, Mortet V, Zhang L, Neyts E, Verbeeck J, Haenen ken, Bogaerts A, Chemistry of materials 23, 1414 (2011). http://doi.org/10.1021/cm102481y
Abstract: In this paper, the effects of prolonged bias-enhanced nucleation (prolonged BEN) on the growth mechanisms of diamond are investigated by molecular dynamics (MD) and combined MD-Metropolis Monte Carlo (MD-MMC) simulations. First, cumulative impacts of CxHy+ and Hx+ on an a-C:H/nanodiamond composite were simulated; second, nonconsecutive impacts of the dominant ions were simulated in order to understand the observed phenomena in more detail. As stated in the existing literature, the growth of diamond structures during prolonged BEN is a process that takes place below the surface of the growing film. The investigation of the penetration behavior of CxHy+ and Hx+ species shows that the carbon-containing ions remain trapped within this amorphous phase where they dominate mechanisms like precipitation of sp3 carbon clusters. The H+ ions, however, penetrate into the crystalline phase at high bias voltages (>100 V), destroying the perfect diamond structure. The experimentally measured reduction of grain sizes at high bias voltage, reported in the literature, might thus be related to penetrating H+ ions. Furthermore, the CxHy+ ions are found to be the most efficient sputtering agents, preventing the build up of defective material.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.466
Times cited: 9
DOI: 10.1021/cm102481y
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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 phase transitions”. Engelmann, Bogaerts A, Neyts EC, Nanoscale 6, 11981 (2014). http://doi.org/10.1039/c4nr02354d
Abstract: Using reactive molecular dynamics simulations, the melting behavior of nickel-carbon 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 nickel-carbon 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; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 20
DOI: 10.1039/c4nr02354d
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“Understanding plasma catalysis through modelling and simulation : a review”. Neyts EC, Bogaerts A, Journal of physics: D: applied physics 47, 224010 (2014). http://doi.org/10.1088/0022-3727/47/22/224010
Abstract: Plasma catalysis holds great promise for environmental applications, provided that the process viability can be maximized in terms of energy efficiency and product selectivity. This requires a fundamental understanding of the various processes taking place and especially the mutual interactions between plasma and catalyst. In this review, we therefore first examine the various effects of the plasma on the catalyst and of the catalyst on the plasma that have been described in the literature. Most of these studies are purely experimental. The urgently needed fundamental understanding of the mechanisms underpinning plasma catalysis, however, may also be obtained through modelling and simulation. Therefore, we also provide here an overview of the modelling efforts that have been developed already, on both the atomistic and the macroscale, and we identify the data that can be obtained with these models to illustrate how modelling and simulation may contribute to this field. Last but not least, we also identify future modelling opportunities to obtain a more complete understanding of the various underlying plasma catalytic effects, which is needed to provide a comprehensive picture of plasma catalysis.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 130
DOI: 10.1088/0022-3727/47/22/224010
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“Understanding polyethylene surface functionalization by an atmospheric He/O2 plasma through combined experiments and simulations”. Dufour T, Minnebo J, Abou Rich S, Neyts EC, Bogaerts A, Reniers F, Journal of physics: D: applied physics 47, 224007 (2014). http://doi.org/10.1088/0022-3727/47/22/224007
Abstract: High density polyethylene surfaces were exposed to the atmospheric post-discharge of a radiofrequency plasma torch supplied in helium and oxygen. Dynamic water contact angle measurements were performed to evaluate changes in surface hydrophilicity and angle resolved x-ray photoelectron spectroscopy was carried out to identify the functional groups responsible for wettability changes and to study their subsurface depth profiles, up to 9 nm in depth. The reactions leading to the formation of CO, C = O and OC = O groups were simulated by molecular dynamics. These simulations demonstrate that impinging oxygen atoms do not react immediately upon impact but rather remain at or close to the surface before eventually reacting. The simulations also explain the release of gaseous species in the ambient environment as well as the ejection of low molecular weight oxidized materials from the surface.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 13
DOI: 10.1088/0022-3727/47/22/224007
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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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“Unraveling the deposition mechanism in a-C:H thin-film growth: a molecular-dynamics study for the reaction behavior of C3 and C3H radicals with a-C:H surfaces”. Neyts E, Bogaerts A, van de Sanden MCM, Journal of applied physics 99, 014902 (2006). http://doi.org/10.1063/1.2150149
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.068
Times cited: 25
DOI: 10.1063/1.2150149
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“Can plasma be formed in catalyst pores? A modeling investigation”. Zhang Y-R, Van Laer K, Neyts EC, Bogaerts A, Applied catalysis : B : environmental 185, 56 (2016). http://doi.org/10.1016/j.apcatb.2015.12.009
Abstract: tWe investigate microdischarge formation inside catalyst pores by a two-dimensional fluid model forvarious pore sizes in the m-range and for various applied voltages. Indeed, this is a poorly understoodphenomenon in plasma catalysis. The calculations are performed for a dielectric barrier discharge inhelium, at atmospheric pressure. The electron and ion densities, electron temperature, electric field andpotential, as well as the electron impact ionization and excitation rate and the densities of excited plasmaspecies, are examined for a better understanding of the characteristics of the plasma inside a pore. Theresults indicate that the pore size and the applied voltage are critical parameters for the formation of amicrodischarge inside a pore. At an applied voltage of 20 kV, our calculations reveal that the ionizationmainly takes place inside the pore, and the electron density shows a significant increase near and inthe pore for pore sizes larger than 200m, whereas the effect of the pore on the total ion density isevident even for 10m pores. When the pore size is fixed at 30m, the presence of the pore has nosignificant influence on the plasma properties at an applied voltage of 2 kV. Upon increasing the voltage,the ionization process is enhanced due to the strong electric field and high electron temperature, andthe ion density shows a remarkable increase near and in the pore for voltages above 10 kV. These resultsindicate that the plasma species can be formed inside pores of structured catalysts (in the m range),and they may interact with the catalyst surface, and affect the plasma catalytic process.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.446
Times cited: 75
DOI: 10.1016/j.apcatb.2015.12.009
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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). http://doi.org/10.1088/0022-3727/49/5/054002
Abstract: Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 11
DOI: 10.1088/0022-3727/49/5/054002
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“Effect of lipid peroxidation on membrane permeability of cancer and normal cells subjected to oxidative stress”. Van der Paal J, Neyts EC, Verlackt CCW, Bogaerts A, Chemical science 7, 489 (2016). http://doi.org/10.1039/C5SC02311D
Abstract: We performed molecular dynamics simulations to investigate the effect of lipid peroxidation products on the structural and dynamic properties of the cell membrane. Our simulations predict that the lipid order in a phospholipid bilayer, as a model system for the cell membrane, decreases upon addition of lipid peroxidation products. Eventually, when all phospholipids are oxidized, pore formation can occur. This will allow reactive species, such as reactive oxygen and nitrogen species (RONS), to enter the cell and cause oxidative damage to intracellular macromolecules, such as DNA or proteins. On the other hand, upon increasing the cholesterol fraction of lipid bilayers, the cell membrane order increases, eventually reaching a certain threshold, from which cholesterol is able to protect the membrane against pore formation. This finding is crucial for cancer treatment by plasma technology, producing a large number of RONS, as well as for other cancer treatment methods that cause an increase in the concentration of extracellular RONS. Indeed, cancer cells contain less cholesterol than their healthy counterparts. Thus, they will be more vulnerable to the consequences of lipid peroxidation, eventually enabling the penetration of RONS into the interior of the cell, giving rise to oxidative stress, inducing pro-apoptotic factors. This provides, for the first time, molecular level insight why plasma can selectively treat cancer cells, while leaving their healthy counterparts undamaged, as is indeed experimentally demonstrated.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 8.668
Times cited: 106
DOI: 10.1039/C5SC02311D
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“Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors”. Khalilov U, Bogaerts A, Neyts EC, Nature communications 6, 10306 (2015). http://doi.org/10.1038/ncomms10306
Abstract: Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 12.124
Times cited: 37
DOI: 10.1038/ncomms10306
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“Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds”. Bal KM, Neyts EC, Journal of chemical theory and computation 11, 4545 (2015). http://doi.org/10.1021/acs.jctc.5b00597
Abstract: The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of reactive processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.245
Times cited: 41
DOI: 10.1021/acs.jctc.5b00597
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“Plasma Catalysis: Synergistic Effects at the Nanoscale”. Neyts EC, Ostrikov KK, Sunkara MK, Bogaerts A, Chemical reviews 115, 13408 (2015). http://doi.org/10.1021/acs.chemrev.5b00362
Abstract: Thermal-catalytic gas processing is integral to many current industrial processes. Ever-increasing demands on conversion and energy efficiencies are a strong driving force for the development of alternative approaches. Similarly, synthesis of several functional materials (such as nanowires and nanotubes) demands special processing conditions. Plasma catalysis provides such an alternative, where the catalytic process is complemented by the use of plasmas that activate the source gas. This combination is often observed to result in a synergy between plasma and catalyst. This Review introduces the current state-of-the-art in plasma catalysis, including numerous examples where plasma catalysis has demonstrated its benefits or shows future potential, including CO2 conversion, hydrocarbon reforming, synthesis of nanomaterials, ammonia production, and abatement of toxic waste gases. The underlying mechanisms governing these applications, as resulting from the interaction between the plasma and the catalyst, render the process highly complex, and little is known about the factors leading to the often-observed synergy. This Review critically examines the catalytic mechanisms relevant to each specific application.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 47.928
Times cited: 204
DOI: 10.1021/acs.chemrev.5b00362
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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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“Plasma-Surface Interactions in Plasma Catalysis”. Neyts EC, Plasma chemistry and plasma processing 36, 185 (2016). http://doi.org/10.1007/s11090-015-9662-5
Abstract: In this paper the various elementary plasma—surface interaction processes occurring in plasma catalysis are critically evaluated. Specifically, plasma catalysis at atmospheric pressure is considered. The importance of the various processes is analyzed for the most common plasma catalysis sources, viz. the dielectric barrier discharge and the gliding arc. The role and importance of surface chemical reactions (including adsorption, surface-mediated association and dissociation reactions, and desorption), plasma-induced surface modification, photocatalyst activation, heating, charging, surface discharge formation and electric field enhancement are discussed in the context of plasma catalysis. Numerous examples are provided to demonstrate the importance of the various processes.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.355
Times cited: 66
DOI: 10.1007/s11090-015-9662-5
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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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“Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations”. Bal KM, Neyts EC, Chemical science 7, 5280 (2016). http://doi.org/10.1039/C6SC00498A
Abstract: Atomistic simulations can in principle provide an unbiased description of all mechanisms, intermediates, and products of complex chemical processes. However, due to the severe time scale limitation of conventional simulation techniques, unrealistically high simulation temperatures are usually applied, which are a poor approximation of most practically relevant low-temperature applications. In this work, we demonstrate the direct observation at the atomic scale of the pyrolysis and oxidation of n-dodecane at temperatures as low as 700 K through the use of a novel simulation technique, collective variable-driven hyperdynamics (CVHD). A simulated timescale of up to 39 seconds is reached. Product compositions and dominant mechanisms are found to be strongly temperature-dependent, and are consistent with experiments and kinetic models. These simulations provide a first atomic-level look at the full dynamics of the complicated fuel combustion process at industrially relevant temperatures and time scales, unattainable by conventional molecular dynamics simulations.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 8.668
Times cited: 22
DOI: 10.1039/C6SC00498A
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“Elucidating the effects of gas flow rate on an SF6inductively coupled plasma and on the silicon etch rate, by a combined experimental and theoretical investigation”. Tinck S, Tillocher T, Dussart R, Neyts EC, Bogaerts A, Journal of physics: D: applied physics 49, 385201 (2016). http://doi.org/10.1088/0022-3727/49/38/385201
Abstract: Experiments show that the etch rate of Si with SF6 inductively coupled plasma (ICP) is significantly influenced by the absolute gas flow rate in the range of 50–600 sccm, with a maximum at around 200 sccm. Therefore, we numerically investigate the effects of the gas flow rate on the bulk plasma properties and on the etch rate, to obtain more insight in the underlying reasons of this effect. A hybrid Monte Carlo—fluid model is applied to simulate an SF6 ICP. It is found that the etch rate is influenced by two simultaneous effects: (i) the residence time of the gas and (ii) the temperature profile of the plasma in the ICP volume, resulting indeed in a maximum etch rate at 200 sccm.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 1
DOI: 10.1088/0022-3727/49/38/385201
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“Multilayer MoS2 growth by metal and metal oxide sulfurization”. Heyne MH, Chiappe D, Meersschaut J, Nuytten T, Conard T, Bender H, Huyghebaert C, Radu IP, Caymax M, de Marneffe JF, Neyts EC, De Gendt S;, Journal of materials chemistry C : materials for optical and electronic devices 4, 1295 (2016). http://doi.org/10.1039/c5tc04063a
Abstract: We investigated the deposition of MoS2 multilayers on large area substrates. The pre-deposition of metal or metal oxide with subsequent sulfurization is a promising technique to achieve layered films. We distinguish a different reaction behavior in metal oxide and metallic films and investigate the effect of the temperature, the H2S/H-2 gas mixture composition, and the role of the underlying substrate on the material quality. The results of the experiments suggest a MoS2 growth mechanism consisting of two subsequent process steps. At first, the reaction of the sulfur precursor with the metal or metal oxide occurs, requiring higher temperatures in the case of metallic film compared to metal oxide. At this stage, the basal planes assemble towards the diffusion direction of the reaction educts and products. After the sulfurization reaction, the material recrystallizes and the basal planes rearrange parallel to the substrate to minimize the surface energy. Therefore, substrates with low roughness show basal plane assembly parallel to the substrate. These results indicate that the substrate character has a significant impact on the assembly of low dimensional MoS2 films.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.256
DOI: 10.1039/c5tc04063a
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“The role of ions in plasma catalytic carbon nanotube growth : a review”. Neyts EC, Frontiers of Chemical Science and Engineering 9, 154 (2015). http://doi.org/10.1007/s11705-015-1515-5
Abstract: While it is well-known that the plasma-enhanced catalytic chemical vapor deposition (PECVD) of carbon nanotubes (CNTs) offers a number of advantages over thermal CVD, the influence of the various individual contributing factors is not well understood. Especially the role of ions is unclear, since ions in plasmas are generally associated with sputtering rather than with growing a material. Even so, various studies have demonstrated the beneficial effects of ion bombardment during the growth of CNTs. This review looks at the role of the ions in plasma-enhanced CNT growth as deduced from both experimental and simulation studies. Specific attention is paid to the beneficial effects of ion bombardment. Based on the available literature, it can be concluded that ions can be either beneficial or detrimental for carbon nanotube growth, depending on the exact conditions and the control over the growth process.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.712
Times cited: 8
DOI: 10.1007/s11705-015-1515-5
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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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“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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“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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“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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“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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“DFT study of Ni-catalyzed plasma dry reforming of methane”. Shirazi M, Neyts EC, Bogaerts A, Applied catalysis : B : environmental 205, 605 (2017). http://doi.org/10.1016/j.apcatb.2017.01.004
Abstract: tWe investigated the plasma-assisted catalytic reactions for the production of value-added chemicalsfrom Ni-catalyzed plasma dry reforming of methane by means of density functional theory (DFT). Weinspected many activation barriers, from the early stage of adsorption of the major chemical fragmentsderived fromCH4andCO2molecules up to the formation of value-added chemicals at the surface, focusingon the formation of methanol, as well as the hydrogenation of C1and C2hydrocarbon fragments. Theactivation barrier calculations show that the presence of surface-bound H atoms and in some cases alsoremaining chemical fragments at the surface facilitates the formation of products. This implies that thehydrogenation of a chemical fragment on the hydrogenated crystalline surface is energetically favouredcompared to the simple hydrogenation of the chemical fragment at the bare Ni(111) surface. Indeed, thepresence of hydrogen modifies the electronic structure of the surface and the course of the reactions.We therefore conclude that surface-bound H atoms, and to some extent also the remaining chemicalfragments at the crystalline surface, induce the following effects: they facilitate associative desorption ofmethanol and ethane by increasing the rate of H-transfer to the adsorbed fragments while they impedehydrogenation of ethylene to ethane, thus promoting again the desorption of ethylene. Overall, they thusfacilitate the catalytic conversion of the formed fragments from CH4and CO2, into value-added chemicals.Finally, we believe that the retention of methane fragments, especially CH3, in the presence of surface-boundHatoms (as observed here for Ni) can be regarded as an identifier for the proper choice of a catalystfor the production of value-added chemicals.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.446
Times cited: 26
DOI: 10.1016/j.apcatb.2017.01.004
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“Synergistic effect of electric field and lipid oxidation on the permeability of cell membranes”. Yusupov M, Van der Paal J, Neyts EC, Bogaerts A, Biochimica et biophysica acta : G : general subjects 1861, 839 (2017). http://doi.org/10.1016/j.bbagen.2017.01.030
Abstract: Background: Strong electric fields are knownto affect cell membrane permeability,which can be applied for therapeutic purposes, e.g., in cancer therapy. A synergistic enhancement of this effect may be accomplished by the presence of reactive oxygen species (ROS), as generated in cold atmospheric plasmas. Little is known about the synergy between lipid oxidation by ROS and the electric field, nor on howthis affects the cell membrane permeability.
Method: We here conduct molecular dynamics simulations to elucidate the dynamics of the permeation process under the influence of combined lipid oxidation and electroporation. A phospholipid bilayer (PLB), consisting of di-oleoyl-phosphatidylcholine molecules covered with water layers, is used as a model system for the plasma membrane.
Results and conclusions:Weshow howoxidation of the lipids in the PLB leads to an increase of the permeability of the bilayer to ROS, although the permeation free energy barriers still remain relatively high. More importantly, oxidation of the lipids results in a drop of the electric field threshold needed for pore formation (i.e., electroporation) in the PLB. The created pores in the membrane facilitate the penetration of reactive plasma species deep into the cell interior, eventually causing oxidative damage.
General significance: This study is of particular interest for plasma medicine, as plasma generates both ROS and electric fields, but it is also of more general interest for applications where strong electric fields and ROS both come into play.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.702
DOI: 10.1016/j.bbagen.2017.01.030
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