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“Real-time electrochemical screening of cocaine in lab and field settings with automatic result generation”. de Jong M, Van Echelpoel R, Langley AR, Eliaerts J, van den Berg J, De Wilde M, Somers N, Samyn N, De Wael K, Drug testing and analysis 14, 1471 (2022). http://doi.org/10.1002/DTA.3276
Abstract: This work presents the results of a novel application for the fast on-site screening of cocaine and its main cutting agents in suspicious and confiscated samples. The methodology behind the novel application consists of portable electrochemical detection coupled with a peak-recognition algorithm for automated result output generation, validated both in laboratory and field settings. Currently used field tests, predominantly colorimetric tests, are lacking accuracy, often giving false positive or negative results. This presses the need for alternative approaches to field testing. By combining portable electrochemical approaches with peak-recognition algorithms, an accuracy of 98.4% concerning the detection of cocaine was achieved on a set of 374 powder samples. In addition, the approach was tested on multiple 'smuggled', colored cocaine powders and cocaine mixtures in solid and liquid states, typically in matrices such as charcoal, syrup and clothing. Despite these attempts to hide cocaine, our approach succeeded in detecting cocaine during on-site screening scenarios. This feature presents an advantage over colorimetric and optical detection techniques, which can fail with colored sample matrices. This enhanced accuracy on smuggled samples will lead to increased efficiency in confiscation procedures in the field, thus significantly reducing societal economic and safety concerns and highlighting the potential for electrochemical approaches in on-the-spot identification of drugs of abuse.
Keywords: A1 Journal article; Pharmacology. Therapy; Engineering sciences. Technology; Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab)
DOI: 10.1002/DTA.3276
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“Real-time atomic scale imaging of nanostructural evolution in aluminum alloys”. Malladi SK, Xu Q, van Huis MA, Tichelaar FD, Batenburg KJ, Yucelen E, Dubiel B, Czyrska-Filemonowicz A, Zandbergen HW, Nano Letters 14, 384 (2014). http://doi.org/10.1021/nl404565j
Abstract: We present a new approach to study the three-dimensional compositional and structural evolution of metal alloys during heat treatments such as commonly used for improving overall material properties. It relies on in situ heating in a high-resolution scanning transmission electron microscope (STEM). The approach is demonstrated using a commercial Al alloy AA2024 at 100-240 degrees C, showing in unparalleled detail where and how precipitates nucleate, grow,or dissolve. The observed size evolution of individual precipitates enables a separation between nucleation and growth phenomena, necessary for the development of refined growth models. We conclude that the in situ heating STEM approach opens a route to a much faster determination of the interplay between local compositions, heat treatments, microstructure, and mechanical properties of new alloys.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 12.712
Times cited: 12
DOI: 10.1021/nl404565j
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“Real-space simulations of spin-polarized electronic transitions in iron”. Schattschneider P, Verbeeck J, Mauchamp V, Jaouen M, Hamon A-L, Physical review : B : condensed matter and materials physics 82, 144418 (2010). http://doi.org/10.1103/PhysRevB.82.144418
Abstract: After the advent of energy-loss magnetic chiral dichroism (EMCD) in 2006, rapid progress in theoretical understanding and in experimental performance was achieved, recently demonstrating a spatial resolution of better than 2 nm. Similar to the x-ray magnetic circular dichroism technique, EMCD is used to study atom specific magnetic moments. The latest generation of electron microscopes opens the road to the mapping of spin moments on the atomic scale with this method. Here the theoretical background to reach this challenging aim is elaborated. Numerical simulations of the L3 transition in an Fe specimen, based on a combination of the density-matrix approach for inelastic electron scattering with the propagation of the probe electron in the lattice potential indicate the feasibility of single spin mapping in the electron microscope.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.836
Times cited: 11
DOI: 10.1103/PhysRevB.82.144418
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“Real-space multiple scattering method for angle-resolved photoemission and valence-band photoelectron diffraction and its application to Cu(111)”. Krüger P, da Pieve F, Osterwalder J, Physical review : B : condensed matter and materials physics 83, 115437 (2011). http://doi.org/10.1103/PhysRevB.83.115437
Abstract: A computational method is presented for angle-resolved photoemission spectra (ARPES) and photoelectron diffraction (PED) in the ultraviolet regime. The one-step model is employed and both initial valence and final continuum states are calculated using the finite-cluster, real-space multiple scattering method. Thereby the approach is versatile and provides a natural link to core-level PED. The method is applied to the Cu(111) valence band and good agreement with experiment is found for both ARPES spectra and PED patterns. When the PED patterns are integrated over a filled band of a single-orbital symmetry, such as Cu-3d, we show, both numerically and analytically, that the exact theory with delocalized initial states can be replaced by the much simpler, core-level-type theory where the initial states are taken as localized.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.836
Times cited: 17
DOI: 10.1103/PhysRevB.83.115437
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“Real-space mapping of electronic orbitals”. Stefan Löffler, Matthieu Bugnet, Nicolas Gauquelin, Sorin Lazar, Elias Assmann, Karsten Held, Gianluigi A Botton, Peter Schattschneider, Ultramicroscopy 177, 26 (2017). http://doi.org/10.1016/j.ultramic.2017.01.018
Abstract: Electronic states are responsible for most material properties, including chemical bonds, electrical and thermal conductivity, as well as optical and magnetic properties. Experimentally, however, they remain mostly elusive. Here, we report the real-space mapping of selected transitions between p and d states on the Ångström scale in bulk rutile (TiO2) using electron energy-loss spectrometry (EELS), revealing information on individual bonds between atoms. On the one hand, this enables the experimental verification of theoretical predictions about electronic states. On the other hand, it paves the way for directly investigating electronic states under conditions that are at the limit of the current capabilities of numerical simulations such as, e.g., the electronic states at defects, interfaces, and quantum dots.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
DOI: 10.1016/j.ultramic.2017.01.018
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“Real-space characterization of short-range order in Cu-Pd alloys”. Rodewald M, Rodewald K, De Meulenaere P, Van Tendeloo G, Physical review : B : condensed matter and materials physics 55, 14173 (1997). http://doi.org/10.1103/PhysRevB.55.14173
Abstract: Cu-Pd alloys containing 10, 20, 30, 40, and 50 at. % Pd and quenched from a temperature just above the ordering temperature T-c are investigated by electron diffraction and high-resolution electron microscopy (HREM). The results show diffuse electron diffraction intensities at {100} and {110} positions for the alloy with 10 at. % Pd, but with a characteristic twofold and fourfold splitting for the alloys with more than 10 at. % Pd. High-resolution images show the formation of microdomains best developed between 20 and 30 at. % Pd. A real-space characterization has been performed by applying videographic real-structure simulations revealing that the splitting of the diffuse maxima depends on the average distance between microdomains of Cu3Au type in antiphase with each other. By applying image processing routines on the HREM images, correlation vectors are identified which correspond to correlations between microdomains.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.836
Times cited: 15
DOI: 10.1103/PhysRevB.55.14173
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“Real-space calculation of the conductivity tensor for disordered topological matter”. Garcia JH, Covaci L, Rappoport TG, Physical review letters 114, 116602 (2015). http://doi.org/10.1103/PhysRevLett.114.116602
Abstract: We describe an efficient numerical approach to calculate the longitudinal and transverse Kubo conductivities of large systems using Bastin's formulation. We expand the Green's functions in terms of Chebyshev polynomials and compute the conductivity tensor for any temperature and chemical potential in a single step. To illustrate the power and generality of the approach, we calculate the conductivity tensor for the quantum Hall effect in disordered graphene and analyze the effect of the disorder in a Chern insulator in Haldane's model on a honeycomb lattice.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 8.462
Times cited: 69
DOI: 10.1103/PhysRevLett.114.116602
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“Real space maps of magnetic moments on the atomic scale: theory and feasibility”. Schattschneider P, Ennen I, Stoger-Pollach M, Verbeeck J, Mauchamp V, Jaouen M, Ultramicroscopy 110, 1038 (2010). http://doi.org/10.1016/j.ultramic.2009.11.020
Abstract: The recently discovered EMCD technique (energy loss magnetic chiral dichroism) can detect atom specific magnetic moments with nanometer resolution, exploiting the spin selectivity of electronic transitions in energy loss spectroscopy. Yet, direct imaging of magnetic moments on the atomic scale is not possible. In this paper we present an extension of EMCD that can overcome this limit. As a model system we chose bcc Fe. We present image simulations of the L3 white line signal, based on the kinetic equation for the density matrix of the 200 kV probe electron. With actual progress in instrumentation (high brightness sources, aberration corrected lenses) this technique should allow direct imaging of spin moments on the atomic scale.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 10
DOI: 10.1016/j.ultramic.2009.11.020
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“Real space maps of atomic transitions”. Schattschneider P, Verbeeck J, Hamon AL, Ultramicroscopy 109, 781 (2009). http://doi.org/10.1016/j.ultramic.2009.01.016
Abstract: Considering the rapid technical development of transmission electron microscopes, we investigate the possibility to map electronic transitions in real space on the atomic scale. To this purpose, we analyse the information carried by the scatterer's initial and final state wave functions and the role of the different atomic transition channels for the inelastic scattering cross section. It is shown that the change in the magnetic quantum number in the transition can be mapped. Two experimental set-ups are proposed, one blocking half the diffraction plane, the other one using a cylinder lens for imaging. Both methods break the conventional circular symmetry in the electron microscope making it possible to detect the handedness of electronic transitions as an asymmetry in the image intensity. This finding is of important for atomic resolution energy-loss magnetic chiral dichroism (EMCD), allowing to obtain the magnetic moments of single atoms.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 10
DOI: 10.1016/j.ultramic.2009.01.016
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“Reactivity and stability of plasma-generated oxygen and nitrogen species in buffered water solution: a computational study”. Heirman P, Van Boxem W, Bogaerts A, Physical chemistry, chemical physics 21, 12881 (2019). http://doi.org/10.1039/C9CP00647H
Abstract: Plasma-treated liquids have great potential for biomedical applications. However, insight into the underlying mechanisms and the exact chemistry is still scarce. In this study, we present the combination of a 0D chemical kinetics and a 2D fluid dynamics model to investigate the plasma treatment of a buffered water solution with the kINPen (R) plasma jet. Using this model, we calculated the gas and liquid flow profiles and the transport and chemistry of all species in the gas and the liquid phase. Moreover, we evaluated the stability of the reactive oxygen and nitrogen species after plasma treatment. We found that of all species, only H2O2, HNO2/NO2-, and HNO3/NO3- are stable in the buffered solution after plasma treatment. This is because both their production and loss processes in the liquid phase are dependent on short-lived radicals (e.g. OH, NO, and NO2). Apart from some discrepancy in the absolute values of the concentrations, which can be explained by the model, all general trends and observations in our model are in qualitative agreement with experimental data and literature.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 7
DOI: 10.1039/C9CP00647H
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“Reactive sputter deposition of TiNx films, simulated with a particle-in-cell/Monte Carlo collisions model”. Bultinck E, Mahieu S, Depla D, Bogaerts A, New journal of physics 11, 023039 (2009). http://doi.org/10.1088/1367-2630/11/2/023039
Abstract: The physical processes in an Ar/N2 magnetron discharge used for the reactive sputter deposition of TiNx thin films were simulated with a 2d3v particle-in-cell/Monte Carlo collisions (PIC/MCC) model. Cathode currents and voltages were calculated self-consistently and compared with experiments. Also, ion fractions were calculated and validated with mass spectrometric measurements. With this PIC/MCC model, the influence of N2/Ar gas ratio on the particle densities and fluxes was investigated, taking into account the effect of the poisoned state of the target.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.786
Times cited: 23
DOI: 10.1088/1367-2630/11/2/023039
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“Reactive plasma cleaning and restoration of transition metal dichalcogenide monolayers”. Marinov D, de Marneffe J-F, Smets Q, Arutchelvan G, Bal KM, Voronina E, Rakhimova T, Mankelevich Y, El Kazzi S, Nalin Mehta A, Wyndaele P-J, Heyne MH, Zhang J, With PC, Banerjee S, Neyts EC, Asselberghs I, Lin D, De Gendt S, npj 2D Materials and Applications 5, 17 (2021). http://doi.org/10.1038/s41699-020-00197-7
Abstract: The cleaning of two-dimensional (2D) materials is an essential step in the fabrication of future devices, leveraging their unique physical, optical, and chemical properties. Part of these emerging 2D materials are transition metal dichalcogenides (TMDs). So far there is limited understanding of the cleaning of “monolayer” TMD materials. In this study, we report on the use of downstream H<sub>2</sub>plasma to clean the surface of monolayer WS<sub>2</sub>grown by MOCVD. We demonstrate that high-temperature processing is essential, allowing to maximize the removal rate of polymers and to mitigate damage caused to the WS<sub>2</sub>in the form of sulfur vacancies. We show that low temperature in situ carbonyl sulfide (OCS) soak is an efficient way to resulfurize the material, besides high-temperature H<sub>2</sub>S annealing. The cleaning processes and mechanisms elucidated in this work are tested on back-gated field-effect transistors, confirming that transport properties of WS<sub>2</sub>devices can be maintained by the combination of H<sub>2</sub>plasma cleaning and OCS restoration. The low-damage plasma cleaning based on H<sub>2</sub>and OCS is very reproducible, fast (completed in a few minutes) and uses a 300 mm industrial plasma etch system qualified for standard semiconductor pilot production. This process is, therefore, expected to enable the industrial scale-up of 2D-based devices, co-integrated with silicon technology.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
DOI: 10.1038/s41699-020-00197-7
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“Reactive molecular dynamics simulations on SiO2-coated ultra-small Si-nanowires”. Khalilov U, Pourtois G, Bogaerts A, van Duin ACT, Neyts EC, Nanoscale 5, 719 (2013). http://doi.org/10.1039/c2nr32387g
Abstract: The application of coreshell SiSiO2 nanowires as nanoelectronic devices strongly depends on their structure, which is difficult to tune precisely. In this work, we investigate the formation of the coreshell nanowires at the atomic scale, by reactive molecular dynamics simulations. The occurrence of two temperature-dependent oxidation mechanisms of ultra-small diameter Si-NWs is demonstrated. We found that control over the Si-core radius and the SiOx (x ≤ 2) oxide shell is possible by tuning the growth temperature and the initial Si-NW diameter. Two different structures were obtained, i.e., ultrathin SiO2 silica nanowires at high temperature and Si core|ultrathin SiO2 silica nanowires at low temperature. The transition temperature is found to linearly decrease with the nanowire curvature. Finally, the interfacial stress is found to be responsible for self-limiting oxidation, depending on both the initial Si-NW radius and the oxide growth temperature. These novel insights allow us to gain control over the exact morphology and structure of the wires, as is needed for their application in nanoelectronics.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.367
Times cited: 17
DOI: 10.1039/c2nr32387g
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“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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“Reactive molecular dynamics simulations for a better insight in plasma medicine”. Bogaerts A, Yusupov M, Van der Paal J, Verlackt CCW, Neyts EC, Plasma processes and polymers 11, 1156 (2014). http://doi.org/10.1002/ppap.201400084
Abstract: In this review paper, we present several examples of reactive molecular dynamics simulations, which contribute to a better understanding of the underlying mechanisms in plasma medicine on the atomic scale. This includes the interaction of important reactive oxygen plasma species with the outer cell wall of both gram-positive and gram-negative bacteria, and with lipids present in human skin. Moreover, as most biomolecules are surrounded by a liquid biofilm, the behavior of these plasma species in a liquid (water) layer is presented as well. Finally, a perspective for future atomic scale modeling studies is given, in the field of plasma medicine in general, and for cancer treatment in particular.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 22
DOI: 10.1002/ppap.201400084
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“Reactivation of microbial strains and synthetic communities after a spaceflight to the International Space Station : corroborating the feasibility of essential conversions in the MELiSSA Loop”. Ilgrande C, Mastroleo F, Christiaens MER, Lindeboom REF, Prat D, Van Hoey O, Ambrozova I, Coninx I, Heylen W, Pommerening-Roser A, Spieck E, Boon N, Vlaeminck SE, Leys N, Clauwaert P, Astrobiology 19, 1167 (2019). http://doi.org/10.1089/AST.2018.1973
Abstract: To sustain human deep space exploration or extra-terrestrial settlements where no resupply from the Earth or other planets is possible, technologies for in situ food production, water, air, and waste recovery need to be developed. The Micro-Ecological Life Support System Alternative (MELiSSA) is such a Regenerative Life Support System (RLSS) and it builds on several bacterial bioprocesses. However, alterations in gravity, temperature, and radiation associated with the space environment can affect survival and functionality of the microorganisms. In this study, representative strains of different carbon and nitrogen metabolisms with application in the MELiSSA were selected for launch and Low Earth Orbit (LEO) exposure. An edible photoautotrophic strain (Arthrospira sp. PCC 8005), a photoheterotrophic strain (Rhodospirillum rubrum S1H), a ureolytic heterotrophic strain (Cupriavidus pinatubonensis 1245), and combinations of C. pinatubonensis 1245 and autotrophic ammonia and nitrite oxidizing strains (Nitrosomonas europaea ATCC19718, Nitrosomonas ureae Nm10, and Nitrobacter winogradskyi Nb255) were sent to the International Space Station (ISS) for 7 days. There, the samples were exposed to 2.8 mGy, a dose 140 times higher than on the Earth, and a temperature of 22 degrees C +/- 1 degrees C. On return to the Earth, the cultures were reactivated and their growth and activity were compared with terrestrial controls stored under refrigerated (5 degrees C +/- 2 degrees C) or room temperature (22 degrees C +/- 1 degrees C and 21 degrees C +/- 0 degrees C) conditions. Overall, no difference was observed between terrestrial and ISS samples. Most cultures presented lower cell viability after the test, regardless of the type of exposure, indicating a harsher effect of the storage and sample preparation than the spaceflight itself. Postmission analysis revealed the successful survival and proliferation of all cultures except for Arthrospira, which suffered from the premission depressurization test. These observations validate the possibility of launching, storing, and reactivating bacteria with essential functionalities for microbial bioprocesses in RLSS.
Keywords: A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1089/AST.2018.1973
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“Reaction pathways of biomedically active species in an Ar plasma jet”. Van Gaens W, Bogaerts A, Plasma sources science and technology 23, 035015 (2014). http://doi.org/10.1088/0963-0252/23/3/035015
Abstract: In this paper we analyse the gas phase production and loss pathways for several biomedically active species, i.e. N2(A), O, O3, O2(a), N, H, HO2, OH, NO, NO2, N2O5, H2O2, HNO2 and HNO3, in an argon plasma jet flowing into an open humid air atmosphere. For this purpose, we employ a zero-dimensional reaction kinetics model to mimic the typical experimental conditions by fitting several parameters to experimentally measured values. These include ambient air diffusion, the gas temperature profile and power deposition along the jet effluent. We focus in detail on how the pathways of the biomedically active species change as a function of the position in the effluent, i.e. inside the discharge device, active plasma jet effluent and afterglow region far from the nozzle. Moreover, we demonstrate how the reaction kinetics and species production are affected by different ambient air humidities, total deposited power into the plasma and gas temperature along the jet. It is shown that the dominant pathways can drastically change as a function of the distance from the nozzle exit or experimental conditions.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 34
DOI: 10.1088/0963-0252/23/3/035015
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“Reaction of chloride anion with atomic oxygen in aqueous solutions: can cold plasma help in chemistry research?”.Gorbanev Y, Van der Paal J, Van Boxem W, Dewilde S, Bogaerts A, Physical chemistry, chemical physics 21, 4117 (2019). http://doi.org/10.1039/C8CP07550F
Abstract: Cold atmospheric plasma in contact with solutions has many applications, but its chemistry contains many unknowns such as the undescribed reactions with solutes. By combining experiments and modelling, we report the first direct demonstration of the reaction of chloride with oxygen atoms in aqueous solutions exposed to cold plasma.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 4
DOI: 10.1039/C8CP07550F
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“Reaction mechanisms of low-kinetic energy hydrocarbon radicals on typical hydrogenated amorphous carbon (a-C:H) sites: a molecular dynamics study”. Neyts E, Tacq M, Bogaerts A, Diamond and related materials 15, 1663 (2006). http://doi.org/10.1016/j.diamond.2006.02.003
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.561
Times cited: 18
DOI: 10.1016/j.diamond.2006.02.003
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“Reaction mechanisms of C(3PJ) and C+(2PJ) with benzene in the interstellar medium from quantum mechanical molecular dynamics simulations”. Izadi ME, Bal KM, Maghari A, Neyts EC, Physical Chemistry Chemical Physics 23, 4205 (2021). http://doi.org/10.1039/D0CP04542J
Abstract: While spectroscopic data on small hydrocarbons in interstellar media in combination with crossed molecular beam (CMB) experiments have provided a wealth of information on astrochemically relevant species, much of the underlying mechanistic pathways of their formation remain elusive. Therefore, in this work, the chemical reaction mechanisms of C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>and C<sup>+</sup>(<sup>2</sup>P) + C<sub>6</sub>H<sub>6</sub>systems using the quantum mechanical molecular dynamics (QMMD) technique at the PBE0-D3(BJ) level of theory is investigated, mimicking a CMB experiment. Both the dynamics of the reactions as well as the electronic structure for the purpose of the reaction network are evaluated. The method is validated for the first reaction by comparison to the available experimental data. The reaction scheme for the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system covers the literature data,<italic>e.g.</italic>the major products are the 1,2-didehydrocycloheptatrienyl radical (C<sub>7</sub>H<sub>5</sub>) and benzocyclopropenyl radical (C<sub>6</sub>H<sub>5</sub>–CH), and it reveals the existence of less common pathways for the first time. The chemistry of the C<sup>+</sup>(<sup>2</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system is found to be much richer, and we have found that this is because of more exothermic reactions in this system in comparison to those in the C(<sup>3</sup>P<sub>J</sub>) + C<sub>6</sub>H<sub>6</sub>system. Moreover, using the QMMD simulation, a number of reaction paths have been revealed that produce three distinct classes of reaction products with different ring sizes. All in all, at all the collision energies and orientations, the major product is the heptagon molecular ion for the ionic system. It is also revealed that the collision orientation has a dominant effect on the reaction products in both systems, while the collision energy mostly affects the charged system. These simulations both prove the applicability of this approach to simulate crossed molecular beams, and provide fundamental information on reactions relevant for the interstellar medium.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
DOI: 10.1039/D0CP04542J
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“Reaction mechanisms for atomic layer deposition of aluminum oxide on semiconductor substrates”. Delabie A, Sioncke S, Rip J, Van Elshocht S, Pourtois G, Mueller M, Beckhoff B, Pierloot K, Journal of vacuum science and technology: A: vacuum surfaces and films 30, 01a127 (2012). http://doi.org/10.1116/1.3664090
Abstract: In this work, we have studied the TMA/H(2)O (TMA Al(CH(3))(3)) atomic layer deposition (ALD) of Al(2)O(3) on hydroxyl (OH) and thiol (SH) terminated semiconductor substrates. Total reflection x-ray fluorescence reveals a complex growth-per-cycle evolution during the early ALD reaction cycles. OH and SH terminated surfaces demonstrate growth inhibition from the second reaction cycle on. Theoretical calculations, based on density functional theory, are performed on cluster models to investigate the first TMA/H(2)O reaction cycle. Based on the theoretical results, we discuss possible mechanisms for the growth inhibition from the second reaction cycle on. In addition, our calculations show that AlCH(3) groups are hydrolyzed by a H(2)O molecule adsorbed on a neighboring Al atom, independent of the type of backbonds (Si-O, Ge-O, or Ge-S) of AlCH(3). The coordination of Al remains four-fold after the first TMA/H(2)O reaction cycle. (C) 2012 American Vacuum Society. [DOI: 10.1116/1.3664090]
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.374
Times cited: 41
DOI: 10.1116/1.3664090
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“Reaction mechanisms and thin a-C:H film growth from low energy hydrocarbon radicals”. Neyts E, Bogaerts A, van de Sanden MCM, Journal of physics : conference series 86, 12020 (2007). http://doi.org/10.1088/1742-6596/86/1/012020
Abstract: Molecular dynamics simulations using the Brenner potential have been performed to investigate reaction mechanisms of various hydrocarbon radicals with low kinetic energies on amorphous hydrogenated carbon (a-C:H) surfaces and to simulate thin a-C:H film growth. Experimental data from an expanding thermal plasma setup were used as input for the simulations. The hydrocarbon reaction mechanisms were studied both during growth of the films and on a set of surface sites specific for a-C:H surfaces. Thin film growth was studied using experimentally detected growth species. It is found that the reaction mechanisms and sticking coefficients are dependent on the specific surface sites, and the structural properties of the growth radicals. Furthermore, it is found that thin a-C:H films can be densified using an additional H-flux towards the substrate.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Times cited: 22
DOI: 10.1088/1742-6596/86/1/012020
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“Re-entrant pinning of Wigner molecules in a magnetic field due to a Coulomb impurity”. Szafran B, Peeters FM, Europhysics letters 66, 701 (2004). http://doi.org/10.1209/epl/i2003-10250-8
Abstract: Pinning of magnetic-field-induced Wigner molecules (WMs) confined in parabolic two-dimensional quantum dots by a charged defect is studied by an exact diagonalization approach. We found a re-entrant pinning of the WMs as a function of the magnetic field, a magnetic-field-induced re-orientation of the WMs and a qualitatively different pinning behaviour in the presence of a positive and negative Coulomb impurity.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 11
DOI: 10.1209/epl/i2003-10250-8
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“Rayleigh instability of confined vortex droplets in critical superconductors”. Lukyanchuk I, Vinokur VM, Rydh A, Xie R, Milošević, MV, Welp U, Zach M, Xiao ZL, Crabtree GW, Bending SJ, Peeters FM, Kwok WK, Nature physics 11, 21 (2015). http://doi.org/10.1038/NPHYS3146
Abstract: Depending on the Ginzburg-Landau parameter kappa, superconductors can either be fully diamagnetic if kappa < 1/root 2 (type I superconductors) or allow magnetic flux to penetrate through Abrikosov vortices if kappa > 1/root 2 (type II superconductors; refs 1,2). At the Bogomolny critical point, kappa = kappa(c) = 1/root 2, a state that is infinitely degenerate with respect to vortex spatial configurations arises(3,4). Despite in-depth investigations of conventional type I and type II superconductors, a thorough understanding of the magnetic behaviour in the near-Bogomolny critical regime at kappa similar to kappa(c) remains lacking. Here we report that in confined systems the critical regime expands over a finite interval of kappa forming a critical superconducting state. We show that in this state, in a sample with dimensions comparable to the vortex core size, vortices merge into a multi-quanta droplet, which undergoes Rayleigh instability(5) on increasing kappa and decays by emitting single vortices. Superconducting vortices realize Nielsen-Olesen singular solutions of the Abelian Higgs model, which is pervasive in phenomena ranging from quantum electrodynamics to cosmology(6-9). Our study of the transient dynamics of Abrikosov-Nielsen-Olesen vortices in systems with boundaries promises access to non-trivial effects in quantum field theory by means of bench-top laboratory experiments.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 22.806
Times cited: 20
DOI: 10.1038/NPHYS3146
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“Raw materials for medieval to post-medieval Tuscan glassmaking : new insight from LA-ICP-MS analyses”. Cagno S, Mendera M, Jeffries T, Janssens K, Journal of archaeological science 37, 3030 (2010). http://doi.org/10.1016/J.JAS.2010.06.030
Abstract: LA-ICP-MS analyses were performed on a set of Tuscan (post) medieval archaeological glass finds dated to the 1316th century in order to quantitatively determine the trace element contents. The results are used for defining and distinguishing several compositional groups. The trace element data are consistent with the distinctions obtained by considering the major element data determined via quantitative SEM-EDX, but allow to obtain new insights into the nature and quality of the silica sources employed and the presumed method of ash purification.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 2.602
Times cited: 38
DOI: 10.1016/J.JAS.2010.06.030
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“Rationalizing the influence of the Mn(IV)/Mn(III) red-Ox transition on the electrocatalytic activity of manganese oxides in the oxygen reduction reaction”. Ryabova AS, Napolskiy FS, Poux T, Istomin SY, Bonnefont A, Antipin DM, Baranchikov AY, Levin EE, Abakumov AM, Kéranguéven G, Antipov EV, Tsirlina GA, Savinova ER;, Electrochimica acta 187, 161 (2016). http://doi.org/10.1016/j.electacta.2015.11.012
Abstract: Knowledge on the mechanisms of oxygen reduction reaction (ORR) and descriptors linking the catalytic activity to the structural and electronic properties of transition metal oxides enable rational design of more efficient catalysts. In this work ORR electrocatalysis was studied on a set of single and complex Mn (III) oxides with a rotating disc electrode method and cyclic voltammetry. We discovered an exponential increase of the specific electrocatalytic activity with the potential of the surface Mn(IV)/Mn(III) red-ox couple, suggesting the latter as a new descriptor for the ORR electrocatalysis. The observed dependence is rationalized using a simple mean-field kinetic model considering availability of the Mn( III) centers and adsorbate-adsorbate interactions. We demonstrate an unprecedented activity of Mn2O3, ca. 40 times exceeding that of MnOOH and correlate the catalytic activity of Mn oxides to their crystal structure. (C) 2015 Elsevier Ltd. All rights reserved.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 4.798
Times cited: 51
DOI: 10.1016/j.electacta.2015.11.012
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“Rational synthesis of F-doped iron oxides on Al2O3(0001) single crystals”. Carraro G, Gasparotto A, Maccato C, Bontempi E, Lebedev OI, Sada C, Turner S, Van Tendeloo G, Barreca D, Rsc Advances , 52140 (2014). http://doi.org/10.1039/C4RA09021G
Abstract: A plasma enhanced-chemical vapor deposition (PE-CVD) route to Fe2O3-based materials on Al2O3(0001) single crystals at moderate growth temperatures (200400 °C) is reported. The use of the fluorinated Fe(hfa)2TMEDA (hfa = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionate; TMEDA = N,N,N′,N′-tetramethylethylenediamine) molecular precursor in Ar/O2 plasmas enabled an in situ F-doping of iron oxide matrices, with a fluorine content tunable as a function of the adopted preparative conditions. Variations of the thermal energy supply enabled control of the system phase composition, resulting in γ-Fe2O3 at 200 °C and α-Fe2O3 nanostructures at higher deposition temperatures. Notably, at 400 °C the formation of highly oriented α-Fe2O3 nanocolumns characterized by an epitaxial relation with the Al2O3(0001) substrate was observed. Beside fluorine content, phase composition and nano-organization, even the system optical properties and, in particular, energy gap values, could be tailored by proper modifications of processing parameters.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.108
Times cited: 4
DOI: 10.1039/C4RA09021G
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“Rational synthesis of F-doped iron oxides on Al2O3(0001) single crystals”. Carraro G, Gasparotto A, Maccato C, Bontempi E, Lebedev OI, Sada C, Turner S, Van Tendeloo G, Barreca D, RSC advances 4, 52140 (2014). http://doi.org/10.1039/c4ra09021g
Abstract: A plasma enhanced-chemical vapor deposition (PE-CVD) route to Fe2O3-based materials on Al2O3(0001) single crystals at moderate growth temperatures (200-400 degrees C) is reported. The use of the fluorinated Fe(hfa)(2)TMEDA (hfa = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionate; TMEDA = N,N,N',N'-tetramethylethylenediamine) molecular precursor in Ar/O-2 plasmas enabled an in situ F-doping of iron oxide matrices, with a fluorine content tunable as a function of the adopted preparative conditions. Variations of the thermal energy supply enabled control of the system phase composition, resulting in gamma-Fe2O3 at 200 degrees C and alpha-Fe2O3 nanostructures at higher deposition temperatures. Notably, at 400 degrees C the formation of highly oriented alpha-Fe2O3 nanocolumns characterized by an epitaxial relation with the Al2O3(0001) substrate was observed. Beside fluorine content, phase composition and nano-organization, even the system optical properties and, in particular, energy gap values, could be tailored by proper modifications of processing parameters.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.108
Times cited: 4
DOI: 10.1039/c4ra09021g
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“Rational synthesis of a nanocrystalline calcium phosphate cement exhibiting rapid conversion to hydroxyapatite”. Neira IS, Kolen'ko YV, Lebedev OI, Van Tendeloo G, Gupta HS, Matsushita N, Yoshimura M, Guitian F, Materials science and engineering: part C: biomimetic materials 29, 2124 (2009). http://doi.org/10.1016/j.msec.2009.04.011
Abstract: The rational synthesis, comprehensive characterization, and mechanical and micromechanical properties of a calcium phosphate cement are presented. Hydroxyapatite cement biomaterial was synthesized from reactive sub-micrometer-sized dicalcium phosphate dihydrate and tetracalcium phosphate via a dissolution-precipitation reaction using water as the liquid phase. As a result nanostructured, Ca-deficient and carbonated B-type hydroxyapatite is formed. The cement shows good processibility, sets in 22 ± 2 min and entirely transforms to the end product after 6 h of setting reaction, one of the highest conversion rates among previously reported for calcium phosphate cements based on dicalcium and tetracalcium phosphates. The combination of all elucidated physical-chemical traits leads to an essential bioactivity and biocompatibility of the cement, as revealed by in vitro acellular simulated body fluid and cell culture studies. The compressive strength of the produced cement biomaterial was established to be 25 ± 3 MPa. Furthermore, nanoindentation tests were performed directly on the cement to probe its local elasticity and plasticity at sub-micrometer/micrometer level. The measured elastic modulus and hardness were established to be Es = 23 ± 3.5 and H = 0.7 ± 0.2 GPa, respectively. These values are in close agreement with those reported in literature for trabecular and cortical bones, reflecting good elastic and plastic coherence between synthesized cement biomaterial and human bones.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 4.164
Times cited: 18
DOI: 10.1016/j.msec.2009.04.011
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“Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins”. Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro VB, Lescrinier E, Nucleic acids research 47, 7130 (2019). http://doi.org/10.1093/nar/gkz551
Abstract: Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 10.162
Times cited: 1
DOI: 10.1093/nar/gkz551
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