“Reactive molecular dynamics simulations of oxygen species in a liquid water layer of interest for plasma medicine”. Yusupov M, Neyts EC, Simon P, Berdiyorov G, Snoeckx R, van Duin ACT, Bogaerts A, Journal of physics: D: applied physics 47, 025205 (2014). http://doi.org/10.1088/0022-3727/47/2/025205
Abstract: The application of atmospheric pressure plasmas in medicine is increasingly gaining attention in recent years, although very little is currently known about the plasma-induced processes occurring on the surface of living organisms. It is known that most bio-organisms, including bacteria, are coated by a liquid film surrounding them, and there might be many interactions between plasma species and the liquid layer before the plasma species reach the surface of the bio-organisms. Therefore, it is essential to study the behaviour of the reactive species in a liquid film, in order to determine whether these species can travel through this layer and reach the biomolecules, or whether new species are formed along the way. In this work, we investigate the interaction of reactive oxygen species (i.e. O, OH, HO2 and H2O2) with water, which is assumed as a simple model system for the liquid layer surrounding biomolecules. Our computational investigations show that OH, HO2 and H2O2 can travel deep into the liquid layer and are hence in principle able to reach the bio-organism. Furthermore, O, OH and HO2 radicals react with water molecules through hydrogen-abstraction reactions, whereas no H-abstraction reaction takes place in the case of H2O2. This study is important to gain insight into the fundamental operating mechanisms in plasma medicine, in general, and the interaction mechanisms of plasma species with a liquid film, in particular.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 51
DOI: 10.1088/0022-3727/47/2/025205
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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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“Combined first-principles and experimental study on the microstructure and mechanical characteristics of the multicomponent additive-manufactured Ti-35Nb-7Zr-5Ta alloy”. Grubova IY, Surmenev RA, Neyts EC, Koptyug AV, Volkova AP, Surmeneva MA, ACS Omega 8, 27519 (2023). http://doi.org/10.1021/ACSOMEGA.3C03157
Abstract: New & beta;-stabilizedTi-based alloys are highly promising forbone implants, thanks in part to their low elasticity. The natureof this elasticity, however, is as yet unknown. We here present combinedfirst-principles DFT calculations and experiments on the microstructure,structural stability, mechanical characteristics, and electronic structureto elucidate this origin. Our results suggest that the studied & beta;Ti-35Nb-7Zr-5Ta wt % (TNZT) alloy manufacturedby the electron-beam powder bed fusion (E-PBF) method has homogeneousmechanical properties (H = 2.01 & PLUSMN; 0.22 GPa and E = 69.48 & PLUSMN; 0.03 GPa) along the building direction,which is dictated by the crystallographic texture and microstructuremorphologies. The analysis of the structural and electronic properties,as the main factors dominating the chemical bonding mechanism, indicatesthat TNZT has a mixture of strong metallic and weak covalent bonding.Our calculations demonstrate that the softening in the Cauchy pressure(C & PRIME; = 98.00 GPa) and elastic constant C ̅ ( 44 ) = 23.84 GPa is the originof the low elasticity of TNZT. Moreover, the nature of this softeningphenomenon can be related to the weakness of the second and thirdneighbor bonds in comparison with the first neighbor bonds in theTNZT. Thus, the obtained results indicate that a carefully designedTNZT alloy can be an excellent candidate for the manufacturing oforthopedic internal fixation devices. In addition, the current findingscan be used as guidance not only for predicting the mechanical propertiesbut also the nature of elastic characteristics of the newly developedalloys with yet unknown properties.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.1
DOI: 10.1021/ACSOMEGA.3C03157
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“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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“Fluorinesilicon surface reactions during cryogenic and near room temperature etching”. Tinck S, Neyts EC, Bogaerts A, The journal of physical chemistry: C : nanomaterials and interfaces 118, 30315 (2014). http://doi.org/10.1021/jp5108872
Abstract: Cyrogenic etching of silicon is envisaged to enable better control over plasma processing in the microelectronics industry, albeit little is known about the fundamental differences compared to the room temperature process. We here present molecular dynamics simulations carried out to obtain sticking probabilities, thermal desorption rates, surface diffusion speeds, and sputter yields of F, F2, Si, SiF, SiF2, SiF3, SiF4, and the corresponding ions on Si(100) and on SiF13 surfaces, both at cryogenic and near room temperature. The different surface behavior during conventional etching and cryoetching is discussed. F2 is found to be relatively reactive compared to other species like SiF03. Thermal desorption occurs at a significantly lower rate under cryogenic conditions, which results in an accumulation of physisorbed species. Moreover, ion incorporation is often observed for ions with energies of 30400 eV, which results in a relatively low net sputter yield. The obtained results suggest that the actual etching of Si, under both cryogenic and near room temperature conditions, is based on the complete conversion of the Si surface to physisorbed SiF4, followed by subsequent sputtering of these molecules, instead of direct sputtering of the SiF03 surface.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 11
DOI: 10.1021/jp5108872
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“PECVD growth of carbon nanotubes : from experiment to simulation”. Neyts EC, Journal of vacuum science and technology: B: micro-electronics processing and phenomena 30, 030803 (2012). http://doi.org/10.1116/1.3702806
Abstract: Nanostructured carbon materials show a tremendous variety in atomic structure, morphology, properties, and applications. As all properties are ultimately determined by the structure of the material, a thorough understanding of the growth mechanisms that give rise to the particular structure is critical. On many occasions, it has been shown that plasma enhanced growth can be strongly beneficial. This review will describe the authors current understanding of plasma enhanced growth of carbon nanotubes, the prototypical example of nanostructured carbon materials, as obtained from experiments, simulations, and modeling. Specific emphasis is put on where experiments and computational approaches correspond, and where they differ. Also, the current status on simulating PECVD growth of some other carbon nanomaterials is reviewed, including amorphous carbon, graphene, and metallofullerenes. Finally, computational challenges with respect to the simulation of PECVD growth are identified.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Times cited: 42
DOI: 10.1116/1.3702806
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“On the reaction behaviour of hydrocarbon species at diamond (1 0 0) and (1 1 1) surfaces: a molecular dynamics investigation”. Eckert M, Neyts E, Bogaerts A, Journal of physics: D: applied physics 41, 032006 (2008). http://doi.org/10.1088/0022-3727/41/3/032006
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 17
DOI: 10.1088/0022-3727/41/3/032006
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“Cation-controlled permeation of charged polymers through nanocapillaries”. Faraji F, Neek-Amal M, Neyts EC, Peeters FM, Physical review E 107, 034501 (2023). http://doi.org/10.1103/PHYSREVE.107.034501
Abstract: Molecular dynamics simulations are used to study the effects of different cations on the permeation of charged polymers through flat capillaries with heights below 2 nm. Interestingly, we found that, despite being monovalent, Li+ , Na+ , and K+ cations have different effects on polymer permeation, which consequently affects their transmission speed throughout those capillaries. We attribute this phenomenon to the interplay of the cations' hydration free energies and the hydrodynamic drag in front of the polymer when it enters the capillary. Different alkali cations exhibit different surface versus bulk preferences in small clusters of water under the influence of an external electric field. This paper presents a tool to control the speed of charged polymers in confined spaces using cations.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.4
Times cited: 1
DOI: 10.1103/PHYSREVE.107.034501
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“Arresting aqueous swelling of layered graphene-oxide membranes with H3O+ and OH- ions”. Gogoi A, Neyts EC, Milošević, MV, Peeters FM, ACS applied materials and interfaces 14, 34946 (2022). http://doi.org/10.1021/ACSAMI.2C05926
Abstract: Over the past decade, graphene oxide (GO) has emerged as a promising membrane material with superior separation performance and intriguing mechanical/chemical stability. However, its practical implementation remains very challenging primarily because of its undesirable swelling in an aqueous environment. Here, we demonstrated that dissociation of water molecules into H3O+ and OH- ions inside the interlayer gallery of a layered GO membrane can strongly affect its stability and performance. We reveal that H3O+ and OH- ions form clusters inside the GO laminates that impede the permeance of water and salt ions through the membrane. Dynamics of those clusters is sensitive to an external ac electric field, which can be used to tailor the membrane performance. The presence of H3O+ and OH- ions also leads to increased stability of the hydrogen bond (H-bond) network among the water molecules and the GO layers, which further reduces water permeance through the membrane, while crucially imparting stability to the layered GO membrane against undesirable swelling. KEYWORDS: layered graphene-oxide membrane, aqueous stability, H3O+ and OH- ions, external electric field, molecular dynamics
Keywords: A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.5
Times cited: 9
DOI: 10.1021/ACSAMI.2C05926
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“A route towards the fabrication of 2D heterostructures using atomic layer etching combined with selective conversion”. Heyne MH, Marinov D, Braithwaite N, Goodyear A, de Marneffe J-F, Cooke M, Radu I, Neyts EC, De Gendt S, 2D materials 6, 035030 (2019). http://doi.org/10.1088/2053-1583/AB1BA7
Abstract: Heterostructures of low-dimensional semiconducting materials, such as transition metal dichalcogenides (MX2), are promising building blocks for future electronic and optoelectronic devices. The patterning of one MX2 material on top of another one is challenging due to their structural similarity. This prevents an intrinsic etch stop when conventional anisotropic dry etching processes are used. An alternative approach consist in a two-step process, where a sacrificial silicon layer is pre-patterned with a low damage plasma process, stopping on the underlying MoS2 film. The pre-patterned layer is used as sacrificial template for the formation of the top WS2 film. This study describes the optimization of a cyclic Ar/Cl-2 atomic layer etch process applied to etch silicon on top of MoS2, with minimal damage, followed by a selective conversion of the patterned Si into WS2. The impact of the Si atomic layer etch towards the MoS2 is evaluated: in the ion energy range used for this study, MoS2 removal occurs in the over-etch step over 1-2 layers, leading to the appearance of MoOx but without significant lattice distortions to the remaining layers. The combination of Si atomic layer etch, on top of MoS2, and subsequent Si-to-WS2 selective conversion, allows to create a WS2/MoS2 heterostructure, with clear Raman signals and horizontal lattice alignment. These results demonstrate a scalable, transfer free method to achieve horizontally individually patterned heterostacks and open the route towards wafer-level processing of 2D materials.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.937
DOI: 10.1088/2053-1583/AB1BA7
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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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“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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“Plasma–liquid interactions: a review and roadmap”. Bruggeman PJ, Kushner MJ, Locke BR, Gardeniers JGE, Graham WG, Graves DB, Hofman-Caris RCHM, Maric D, Reid JP, Ceriani E, Fernandez Rivas D, Foster JE, Garrick SC, Gorbanev Y, Hamaguchi S, Iza F, Jablonowski H, Klimova E, Kolb J, Krcma F, Lukes P, Machala Z, Marinov I, Mariotti D, Mededovic Thagard S, Minakata D, Neyts EC, Pawlat J, Petrovic ZL, Pflieger R, Reuter S, Schram DC, Schröter S, Shiraiwa M, Tarabová, B, Tsai PA, Verlet JRR, von Woedtke T, Wilson KR, Yasui K, Zvereva G, Plasma sources science and technology 25, 053002 (2016). http://doi.org/10.1088/0963-0252/25/5/053002
Abstract: Plasma–liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on nonequilibrium plasmas.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 460
DOI: 10.1088/0963-0252/25/5/053002
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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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“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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“Enhancement of plasma generation in catalyst pores with different shapes”. Zhang Y-R, Neyts EC, Bogaerts A, Plasma sources science and technology 27, 055008 (2018). http://doi.org/10.1088/1361-6595/aac0e4
Abstract: Plasma generation inside catalyst pores is of utmost importance for plasma catalysis, as the existence of plasma species inside the pores affects the active surface area of the catalyst available to the plasma species for catalytic reactions. In this paper, the electric field enhancement, and thus the plasma production inside catalyst pores with different pore shapes is studied with a two-dimensional fluid model. The results indicate that the electric field will be significantly enhanced near tip-like structures. In a conical pore with small opening, the strongest electric field appears at the opening and bottom corners of the pore, giving rise to a prominent ionization rate throughout the pore. For a cylindrical pore, the electric field is only enhanced at the bottom corners of the pore, with lower absolute value, and thus the ionization rate inside the pore is only slightly enhanced. Finally, in a conical pore with large opening, the electric field is characterized by a maximum at the bottom of the pore, yielding a similar behavior for the ionization rate. These results demonstrate that the shape of the pore has a significantly influence on the electric field enhancement, and thus modifies the plasma properties.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 11
DOI: 10.1088/1361-6595/aac0e4
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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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“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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“Atomic-scale insight into the interactions between hydroxyl radicals and DNA in solution using the ReaxFF reactive force field”. Verlackt CCW, Neyts EC, Jacob T, Fantauzzi D, Golkaram M, Shin Y-K, van Duin ACT, Bogaerts A, New journal of physics 17, 103005 (2015). http://doi.org/10.1088/1367-2630/17/10/103005
Abstract: Cold atmospheric pressure plasmas have proven to provide an alternative treatment of cancer by targeting tumorous cells while leaving their healthy counterparts unharmed. However, the underlying mechanisms of the plasma–cell interactions are not yet fully understood. Reactive oxygen species, and in particular hydroxyl radicals (OH), are known to play a crucial role in plasma driven apoptosis of
malignant cells. In this paper we investigate the interaction of OH radicals, as well as H2O2 molecules and HO2 radicals, with DNA by means of reactive molecular dynamics simulations using the ReaxFF force field. Our results provide atomic-scale insight into the dynamics of oxidative stress on DNA caused by the OH radicals, while H2O2 molecules appear not reactive within the considered timescale. Among the observed processes are the formation of 8-OH-adduct radicals, forming the first stages towards the formation of 8-oxoGua and 8-oxoAde, H-abstraction reactions of the amines, and the partial opening of loose DNA ends in aqueous solution.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.786
Times cited: 18
DOI: 10.1088/1367-2630/17/10/103005
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“Enhanced piezoresponse and surface electric potential of hybrid biodegradable polyhydroxybutyrate scaffolds functionalized with reduced graphene oxide for tissue engineering”. Chernozem R V, Romanyuk KN, Grubova I, Chernozem P V, Surmeneva MA, Mukhortova YR, Wilhelm M, Ludwig T, Mathur S, Kholkin AL, Neyts E, Parakhonskiy B, Skirtach AG, Surmenev RA, Nano Energy 89, 106473 (2021). http://doi.org/10.1016/J.NANOEN.2021.106473
Abstract: Piezoelectricity is considered to be one of the key functionalities in biomaterials to boost bone tissue regeneration, however, integrating biocompatibility, biodegradability and 3D structure with pronounced piezoresponse remains a material challenge. Herein, novel hybrid biocompatible 3D scaffolds based on biodegradable poly(3-hydroxybutyrate) (PHB) and reduced graphene oxide (rGO) flakes have been developed. Nanoscale insights revealed a more homogenous distribution and superior surface potential values of PHB fibers (33 +/- 29 mV) with increasing rGO content up to 1.0 wt% (314 +/- 31 mV). The maximum effective piezoresponse was detected at 0.7 wt% rGO content, demonstrating 2.5 and 1.7 times higher out-of-plane and in-plane values, respectively, than that for pure PHB fibers. The rGO addition led to enhanced zigzag chain formation between paired lamellae in PHB fibers. In contrast, a further increase in rGO content reduced the alpha-crystal size and prevented zigzag chain conformation. A corresponding model explaining structural and molecular changes caused by rGO addition in electrospun PHB fibers is proposed. In addition, finite element analysis revealed a negligible vertical piezoresponse compared to lateral piezoresponse in uniaxially oriented PHB fibers based on alpha-phase (P2(1)2(1)2(1) space group). Thus, the present study demonstrates promising results for the development of biodegradable hybrid 3D scaffolds with an enhanced piezoresponse for various tissue engineering applications.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 12.343
DOI: 10.1016/J.NANOEN.2021.106473
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“Accelerated molecular dynamics simulation of large systems with parallel collective variable-driven hyperdynamics”. Fukuhara S, Bal KM, Neyts EC, Shibuta Y, Computational Materials Science 177, 109581 (2020). http://doi.org/10.1016/j.commatsci.2020.109581
Abstract: The limitation in time and length scale is a major issue of molecular dynamics (MD) simulation. Although several methods have been developed to extend the MD time scale, their performance usually deteriorates with increasing system size. Therefore, an acceleration method which is applicable to large systems is required to bridge the gap between the MD simulations and target phenomena. In this study, an accelerated MD method for large system is developed based on the collective variable-driven hyperdynamics (CVHD) method [K.M. Bal and E.C. Neyts, 2015]. The key idea is to run CVHD in parallel with rate control and accelerate multiple possible events simultaneously. Using this novel method, carbon diffusion in bcc-iron bicrystal with grain boundary is examined as an application for practical materials. Carbon atoms reaching at the grain boundary are trapped whereas carbon atoms in the bulk region diffuse randomly, and both dynamic regimes can be simultaneously accelerated with the parallel CVHD technique.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.3
DOI: 10.1016/j.commatsci.2020.109581
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“Molecular dynamics simulations of Cl+ etching on a Si(100) surface”. Gou F, Neyts E, Eckert M, Tinck S, Bogaerts A, Journal of applied physics 107, 113305 (2010). http://doi.org/10.1063/1.3361038
Abstract: Molecular dynamics simulations using improved TersoffBrenner potential parameters were performed to investigate Cl+ etching of a {2×1} reconstructed Si(100) surface. Steady-state Si etching accompanying the Cl coverage of the surface is observed. Furthermore, a steady-state chlorinated reaction layer is formed. The thickness of this reaction layer is found to increase with increasing energy. The stoichiometry of SiClx species in the reaction layer is found to be SiCl:SiCl2:SiCl3 = 1.0:0.14:0.008 at 50 eV. These results are in excellent agreement with available experimental data. While elemental Si products are created by physical sputtering, most SiClx (0<x<4) etch products are produced by chemical-enhanced physical sputtering.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.068
Times cited: 15
DOI: 10.1063/1.3361038
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“Free energy barriers from biased molecular dynamics simulations”. Bal KM, Fukuhara S, Shibuta Y, Neyts EC, Journal Of Chemical Physics 153, 114118 (2020). http://doi.org/10.1063/5.0020240
Abstract: Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.4
DOI: 10.1063/5.0020240
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“Comment on “Misinterpretation of the Shuttleworth equation””. Faraji F, Neyts EC, Milošević, MV, Peeters FM, Scripta Materialia 250, 116186 (2024). http://doi.org/10.1016/j.scriptamat.2024.116186
Keywords: A1 Journal Article; CMT
Impact Factor: 6
DOI: 10.1016/j.scriptamat.2024.116186
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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 natural deep eutectic solvents of non-eutectic compositions on enzyme stability”. Kovács A, Yusupov M, Cornet I, Billen P, Neyts EC, Journal Of Molecular Liquids 366, 120180 (2022). http://doi.org/10.1016/J.MOLLIQ.2022.120180
Abstract: Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; 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: 6
DOI: 10.1016/J.MOLLIQ.2022.120180
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“Numerical simulation of hydrocarbon plasmas for nanoparticle formation and the growth of nanostructured thin films”. Neyts E, Eckert M, Mao M, Bogaerts A, Plasma physics and controlled fusion 51, 124034 (2009). http://doi.org/10.1088/0741-3335/51/12/124034
Abstract: This paper outlines two different numerical simulation approaches, carried out by our group, used for describing hydrocarbon plasmas in their applications for either nanoparticle formation in the plasma or the growth of nanostructured thin films, such as nanocrystalline diamond (NCD). A plasma model based on the fluid approach is utilized to study the initial mechanisms giving rise to nanoparticle formation in an acetylene plasma. The growth of NCD is investigated by molecular dynamics simulations, describing the interaction of the hydrocarbon species with a substrate.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.392
Times cited: 2
DOI: 10.1088/0741-3335/51/12/124034
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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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“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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“Direct methane conversion to methanol on M and MN4 embedded graphene (M = Ni and Si): a comparative DFT study”. Nematollahi P, Neyts EC, Applied surface science 496, 143618 (2019). http://doi.org/10.1016/J.APSUSC.2019.143618
Abstract: The ever increasing global production and dispersion of methane requires novel chemistry to transform it into easily condensable energy carriers that can be integrated into the chemical infrastructure. In this context, single atom catalysts have attracted considerable interest due to their outstanding catalytic activity. We here use density functional theory (DFT) computations to compare the reaction and activation energies of M and MN4 embedded graphene (M = Ni and Si) on the methane-to-methanol conversion near room temperature. Thermodynamically, conversion of methane to methanol is energetically favorable at ambient conditions. Both singlet and triplet spin state of the studied systems are considered in all of the calculations. The DFT results show that the barriers are significantly lower when the complexes are in the triplet state than in the singlet state. In particular, Si-G with the preferred spin multiplicity of triplet seems to be viable catalysts for methane oxidation thanks to the corresponding lower energy barriers and higher stability of the obtained configurations. Our results provide insights into the nature of methane conversion and may serve as guidance for fabricating cost-effective graphene-based single atom catalysts.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.387
Times cited: 2
DOI: 10.1016/J.APSUSC.2019.143618
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