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“Ab initio calculation of the energy-loss near-edge structure of some carbon allotropes: comparison with n-diamond”. Dadsetani M, Titantah JT, Lamoen D, Diamond and related materials 19, 73 (2010). http://doi.org/10.1016/j.diamond.2009.11.004
Abstract: The energy-loss near-edge structure (ELNES) spectra of several carbon allotropes (non-hydrogenated and hydrogenated face-centered cubic (FCC) carbon, rhombohedral carbon, glitter, hexagonite and lonsdaleite) are calculated within the supercell-core-excited density functional theory approach. In particular an experimental ELNES spectrum of new diamond (n-diamond) [Konyashin et al., Diamond Relat. Mater. 10, (2001) 99102] is compared with the ELNES spectra of FCC carbon, rhombohedral carbon and the so-called glitter structure. Our calculations show that the ELNES spectrum considered in that publication cannot be that of FCC carbon.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.561
Times cited: 11
DOI: 10.1016/j.diamond.2009.11.004
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Daems E, Bassini S, Marië,n L, Op de Beeck H, Stratulat A, Zwaenepoel K, Vandamme T, op de Beeck K, Koljenovic S, Peeters M, Van Camp G, De Wael K (2023) Singlet oxygen-based photoelectrochemical detection of single-point mutations in the KRAS oncogene. 115957–7
Abstract: Single nucleotide point mutations in the KRAS oncogene occur frequently in human cancers, rendering them intriguing targets for diagnosis, early detection and personalized treatment. Current detection methods are based on polymerase chain reaction, sometimes combined with next-generation sequencing, which can be expensive, complex and have limited availability. Here, we propose a novel singlet oxygen (1O2)-based photoelectrochemical detection methodology for single-point mutations, using KRAS mutations as a case study. This detection method combines the use of a sandwich assay, magnetic beads and robust chemical photosensitizers, that need only air and light to produce 1O2, to ensure high specificity and sensitivity. We demonstrate that hybridization of the sandwich hybrid at high temperatures enables discrimination between mutated and wild-type sequences with a detection rate of up to 93.9%. Additionally, the presence of background DNA sequences derived from human cell-line DNA, not containing the mutation of interest, did not result in a signal, highlighting the specificity of the methodology. A limit of detection as low as 112 pM (1.25 ng/mL) was achieved without employing any amplification techniques. The developed 1O2-based photoelectrochemical methodology exhibits unique features, including rapidity, ease of use, and affordability, highlighting its immense potential in the field of nucleic acid-based diagnostics.
Keywords: University Hospital Antwerp; A1 Journal article; Center for Oncological Research (CORE); Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab); Medical Genetics (MEDGEN)
Impact Factor: 12.6
DOI: 10.1016/J.BIOS.2023.115957
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“Native mass spectrometry for the design and selection of protein bioreceptors for perfluorinated compounds”. Daems E, Moro G, Berghmans H, Moretto LM, Dewilde S, Angelini A, Sobott F, De Wael K, Analyst 146, 2065 (2021). http://doi.org/10.1039/D0AN02005B
Abstract: Biosensing platforms are answering the increasing demand for analytical tools for environmental monitoring of small molecules, such as per- and polyfluoroalkyl substances (PFAS). By transferring toxicological findings in bioreceptor design we can develop innovative pathways for biosensor design. Indeed, toxicological studies provide fundamental information about PFAS-biomolecule complexes that can help evaluate the applicability of the latter as bioreceptors. The toolbox of native mass spectrometry (MS) can support this evaluation, as shown by the two case studies reported in this work. The analysis of model proteins’ (i.e. albumin, haemoglobin, cytochrome c and neuroglobin) interactions with well-known PFAS, such as perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), demonstrated the potential of this native MS screening approach. In the first case study, untreated albumin and delipidated albumin were compared in the presence and absence of PFOA confirming that the delipidation step increases albumin affinity for PFOA without affecting protein stability. In the second case study, the applicability of our methodology to identify potential bioreceptors for PFOS/PFOA was extended to other proteins. Structurally related haemoglobin and neuroglobin revealed a 1 : 1 complex, whereas no binding was observed for cytochrome c. These studies have value as a proof-of-concept for a general application of native MS to identify bioreceptors for toxic compounds.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 3.885
DOI: 10.1039/D0AN02005B
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“Pd-zeolites as heterogeneous catalysts in heck chemistry”. Dams M, Drijkoningen L, Pauwels B, Van Tendeloo G, de Vos DE, Jacobs PA, Journal of catalysis 209, 225 (2002). http://doi.org/10.1006/jcat.2002.3630
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 6.844
Times cited: 157
DOI: 10.1006/jcat.2002.3630
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“Low-dimensional confining structures on the surface of helium films suspended on designed cavities”. Dantas DS, Chaves A, Farias GA, Ramos ACA, Peeters FM, Journal of low temperature physics 173, 207 (2013). http://doi.org/10.1007/s10909-013-0895-5
Abstract: We investigate the formation of quantum confined structures on the surface of a liquid helium film suspended on a nanostructured substrate. We show theoretically that, by nanostructuring the substrate, it is possible to change the geometry of the liquid helium surface, opening the possibility of designing and controlling the formation of valleys with different shapes. By applying an external electric field perpendicular to the substrate plane, surface electrons can be trapped into these valleys, as in a quantum dot. We investigate how the external parameters, such as the electric field strength and the height of the liquid helium bath, can be tuned to control the energy spectrum of the trapped surface electrons.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.3
Times cited: 1
DOI: 10.1007/s10909-013-0895-5
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“Bound vortex states and exotic lattices in multicomponent Bose-Einstein condensates : the role of vortex-vortex interaction”. Dantas DS, Lima ARP, Chaves A, Almeida CAS, Farias GA, Milošević, MV, Physical review : A : atomic, molecular and optical physics 91, 023630 (2015). http://doi.org/10.1103/PhysRevA.91.023630
Abstract: We numerically study the vortex-vortex interaction in multicomponent homogeneous Bose-Einstein condensates within the realm of the Gross-Pitaevskii theory. We provide strong evidence that pairwise vortex interaction captures the underlying mechanisms which determine the geometric configuration of the vortices, such as different lattices in many-vortex states, as well as the bound vortex states with two (dimer) or three (trimer) vortices. Specifically, we discuss and apply our theoretical approach to investigate intra- and intercomponent vortex-vortex interactions in two- and three-component Bose-Einstein condensates, thereby shedding light on the formation of the exotic vortex configurations. These results correlate with current experimental efforts in multicomponent Bose-Einstein condensates and the understanding of the role of vortex interactions in multiband superconductors.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.925
Times cited: 12
DOI: 10.1103/PhysRevA.91.023630
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“Valorization of thermal treatment residues in enhanced landfill mining : environmental and economic evaluation”. Danthurebandara M, Van Passel S, Machiels L, Van Acker K, Journal Of Cleaner Production 99, 275 (2015). http://doi.org/10.1016/J.JCLEPRO.2015.03.021
Abstract: Enhanced Landfill Mining is an innovative concept which allows the recovery of land, re-introduction of materials to the material cycles and recovery of energy from a considerably large stock of resources held in landfills. Plasma gasification is a viable candidate for combined energy and material valorization in the framework of Enhanced landfill Mining. Besides energy production, plasma gasification also delivers an environmentally stable vitrified residue called plasmastone, which can be converted into building materials. This paper presents an environmental and economic evaluation of the valorization of thermal treatment residues (plasmastone) in the context of Enhanced Landfill Mining. The most common valorization route, that is, the treatment of plasmastone via production of aggregates, is compared with two other possible, higher added value applications, which are inorganic polymer production and blended cement production. The evaluation is based on life cycle assessment and life cycle costing. The study suggests that the environmental and economic performances of the valorization routes depend mainly on the quality and quantity of the final products produced from a certain amount of plasmastone. The materials with the greatest contribution to potential global warming and to the net present value of the valorization scenarios are the process input materials of sodium silicate, sodium hydroxide and cement. The study concludes that the plasmastone valorization via inorganic polymer production yields higher environmental benefits, while the blended cement production provides higher economic profits. Plasmastone valorization via aggregates production does not yield economic or environmental benefits. Given the trade-off between environmental and economic performances, we conclude that the decisions regarding the selection of appropriate valorization routes should be made cautiously to obtain optimal environmental benefits and economic profits. (C) 2015 Elsevier Ltd. All rights reserved.
Keywords: A1 Journal article; Economics; Engineering sciences. Technology; Engineering Management (ENM)
Impact Factor: 5.715
Times cited: 17
DOI: 10.1016/J.JCLEPRO.2015.03.021
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“Environmental and economic performance of plasma gasification in Enhanced Landfill Mining”. Danthurebandara M, Van Passel S, Vanderreydt I, Van Acker K, Waste Management 45, 458 (2015). http://doi.org/10.1016/J.WASMAN.2015.06.022
Abstract: This paper describes an environmental and economic assessment of plasma gasification, one of the viable candidates for the valorisation of refuse derived fuel from Enhanced Landfill Mining. The study is based on life cycle assessment and life cycle costing. Plasma gasification is benchmarked against conventional incineration, and the study indicates that the process could have significant impact on climate change, human toxicity, particulate matter formation, metal depletion and fossil depletion. Flue gas emission, oxygen usage and disposal of residues (plasmastone) are the major environmental burdens, while electricity production and metal recovery represent the major benefits. Reductions in burdens and improvements in benefits are found when the plasmastone is valorised in building materials instead of landfilling. The study indicates that the overall environmental performance of plasma gasification is better than incineration. The study confirms a trade-off between the environmental and economic performance of the discussed scenarios. Net electrical efficiency and investment cost of the plasma gasification process and the selling price of the products are the major economic drivers.
Keywords: A1 Journal article; Economics; Engineering sciences. Technology; Engineering Management (ENM)
Impact Factor: 4.03
Times cited: 12
DOI: 10.1016/J.WASMAN.2015.06.022
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“Assessment of environmental and economic feasibility of Enhanced Landfill Mining”. Danthurebandara M, Van Passel S, Vanderreydt I, Van Acker K, Waste Management 45, 434 (2015). http://doi.org/10.1016/J.WASMAN.2015.01.041
Abstract: This paper addresses the environmental and economic performance of Enhanced Landfill Mining (ELFM). Based on life cycle assessment and life cycle costing, a detailed model is developed and is applied to a case study, i.e. the first ELFM project in Belgium. The environmental and economic analysis is performed in order to study the valorisation of different waste types in the landfill, such as municipal solid waste, industrial waste and total waste. We found that ELFM is promising for the case study landfill as greater environmental benefits are foreseen in several impact categories compared to the landfills current situation (the Do-nothing scenario). Among the considered processes, the thermal treatment process dominates both the environmental and economic performances of ELFM. Improvements in the electrical efficiency of thermal treatment process, the calorific value of refuse derived fuel and recovery efficiencies of different waste fractions lead the performance of ELFM towards an environmentally sustainable and economically feasible direction. Although the environmental and economic profiles of ELFM will differ from case to case, the results of this analysis can be used as a benchmark for future ELFM projects.
Keywords: A1 Journal article; Economics; Engineering Management (ENM)
Impact Factor: 4.03
Times cited: 30
DOI: 10.1016/J.WASMAN.2015.01.041
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“Composition of prehistoric rock-painting pigments from Egypt (Gilf Kébir area)”. Darchuk L, Gatto Rotondo G, Swaenen M, Worobiec A, Tsybrii Z, Makarovska Y, Van Grieken R, Spectrochimica acta: part A: molecular and biomolecular spectroscopy 83, 34 (2011). http://doi.org/10.1016/J.SAA.2011.06.054
Abstract: The composition of rock-painting pigments from Egypt (Gilf Kebia area) has been analyzed by means of molecular spectroscopy such as Fourier transform infrared and micro-Raman spectroscopy and scanning electron microscopy coupled to an energy dispersive X-ray spectrometer and X-ray fluorescence analysis. Red and yellow pigments were recognized as red and yellow ochre with additional rutile.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1016/J.SAA.2011.06.054
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“Composition of pigments on human bones found in excavations in Argentina studied with micro-Raman spectrometry and scanning electron microscopy”. Darchuk L, Stefaniak EA, Vázquez C, Palacios OM, Worobiec A, Van Grieken R, e-Preservation Science 6, 112 (2009)
Abstract: Results on analysis of prehistoric pigments from excavations and pigments on coloured child bones from North Patagonia, Argentina, are reported. To analyze their composition we used two micro-analytical techniques: micro- Raman spectrometry (MRS) and scanning electron microscopy coupled with X-ray micro-analysis (SEM/EDX). Most investigated excavated pigments show red or yellow ochres consistent with reddish or yellow minerals, such as á- and ã-goethite, haematite, erdite, haapalaite and jarosite. Raman spectra show also evidence of calcium oxalate monohydrate and calcite indicating lichen activity. Pigments covering human bones were identified as hematite and magnetite. This study allows us to infer that pigments found in excavation were employed for burial ceremonies, even though distances between excavated pigment archaeological site and buried remains are quite far, more than 50 km in a straight line.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
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“Argentinean prehistoric pigments' study by combined SEM/EDX and molecular spectroscopy”. Darchuk L, Tsybrii Z, Worobiec A, Vázquez C, Palacios OM, Stefaniak EA, Gatto Rotondo G, Sizov F, Van Grieken R, Spectrochimica acta: part A: molecular and biomolecular spectroscopy 75, 1398 (2010). http://doi.org/10.1016/J.SAA.2010.01.006
Abstract: Composition of the prehistoric pigments (from Carriqueo rock shelter, Rio Negro province, Argentina) has been analysed by means of molecular spectroscopy (Fourier transform infrared (FTIR) and micro-Raman) and scanning electron microscopy (SEM) coupled to an energy-dispersive X-ray spectrometer (EDS). Red and yellow pigments were recognized as red and yellow ochre. The matrix of the pigments is composed of one or more substances. According to the matrix composition yellow and red pigments were also divided into two groupsi.e. those containing kaolinite or sulphates. Green pigment was detected as green earth, made up of celadonite as a chromophore.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1016/J.SAA.2010.01.006
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“Influence of the morphology on the magneto-transport properties of laser-ablated ultrathin La0.7Ba0.3MnO3 films”. Das A, Gordon I, Wagner P, Cannaerts M, Moshchalkov VV, Bruynseraede Y, Schuddinck W, Van Tendeloo G, Borghs G, Journal of applied physics 90, 1429 (2001). http://doi.org/10.1063/1.1380217
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.068
Times cited: 2
DOI: 10.1063/1.1380217
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“The elemental chemistry of sediments in the Nainital lake, Kumaun Himalaya, India”. Das BK, Singh M, Van Grieken R, The science of the total environment 168, 85 (1995). http://doi.org/10.1016/0048-9697(95)04242-S
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/0048-9697(95)04242-S
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“Direct observation of nanometer-scale pinning sites in (Nd0.33Eu0.20Gd0.47)Ba2Cu3O7-\delta single crystals”. Das P, Koblischka MR, Turner S, Van Tendeloo G, Wolf T, Jirsa M, Hartmann U, Europhysics letters 83, 37005 (2008). http://doi.org/10.1209/0295-5075/83/37005
Abstract: We report on the observation of self-organized stripe-like structures on the as-grown surface and in the bulk of (Nd,Eu,Gd)Ba2Cu3Oy single crystals. The periodicity of the stripes on the surface lies between 500800 nm. These are possibly the growth steps of the crystal. Transmission electron microscopy investigations revealed stripes of periodicity in the range of 2040 nm in the bulk. From electron back scattered diffraction investigations, no crystallographic misorientation due to the nanostripes has been found. Scanning tunneling spectroscopic experiments revealed nonsuperconducting regions, running along twin directions, which presumably constitute strong pinning sites.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 1.957
Times cited: 5
DOI: 10.1209/0295-5075/83/37005
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“Low-field switching of noncollinear spin texture at La0.7Sr0.3MnO3-SrRuO3interfaces”. Das S, Rata AD, Maznichenko I V, Agrestini IS, Pippel E, Gauquelin N, Verbeeck J, Chen K, Valvidares SM, Vasili HB, Herrero-Martin J, Pellegrin E, Nenkov K, Herklotz A, Ernst A, Mertig I, Hu Z, Doerr K, Physical review B 99, 024416 (2019). http://doi.org/10.1103/PHYSREVB.99.024416
Abstract: Interfaces of ferroic oxides can show complex magnetic textures which have strong impact on spintronics devices. This has been demonstrated recently for interfaces with insulating antiferromagnets such as BiFeO3. Here, noncollinear spin textures which can be switched in very low magnetic field are reported for conducting ferromagnetic bilayers of La0.7Sr0.3MnO3-SrRuO3 (LSMO-SRO). The magnetic order and switching are fundamentally different for bilayers coherently grown in reversed stacking sequence. The SRO top layer forms a persistent exchange spring which is antiferromagnetically coupled to LSMO and drives switching in low fields of a few milliteslas. Density functional theory reveals the crucial impact of the interface termination on the strength of Mn-Ru exchange coupling across the interface. The observation of an exchange spring agrees with ultrastrong coupling for the MnO2/SrO termination. Our results demonstrate low-field switching of noncollinear spin textures at an interface between conducting oxides, opening a pathway for manipulating and utilizing electron transport phenomena in controlled spin textures at oxide interfaces.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.836
Times cited: 19
DOI: 10.1103/PHYSREVB.99.024416
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“Dynamic phases of vortex-antivortex molecules in a Corbino disk with magnetic dipole on top”. de Aquino BRCHT, Cabral LRE, de Souza Silva CC, Albino Aguiar J, Milošević, MV, Peeters FM, Physica: C : superconductivity 479, 115 (2012). http://doi.org/10.1016/j.physc.2012.12.016
Abstract: We performed a molecular dynamics study of vortex-antivortex motion in a superconducting disk with a magnetic dot on top, in the Corbino disk geometry. In this system, vortices and antivortices are forced to move in opposite azimuthal directions by a radially applied current. The dot is magnetized out of plane in order to stabilize composite vortex-antivortex configurations, with vortices closer to the center of the disk and antivortices near to the disk edge. We observe that the interplay between the spatially inhomogeneous current distribution, the screening currents induced by the dipole, and the attractive vortex-antivortex (v-av) interaction result in different dynamical phases. At low current values, antivortices which are distributed at outer rings – remain bounded to vortices at inner rings and the whole configuration rotates rigidly. Above a threshold current, vortices and antivortices unbind and move at different angular velocities in a highly correlated way. Finally, at very strong drive, vortex-antivortex attraction is overhelmed by the external current Lorentz force, causing them to move in opposite directions. (C) 2011 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.404
DOI: 10.1016/j.physc.2012.12.016
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“Electrostrictive behavior of confined water subjected to GPa pressure”. de Aquino BRH, Ghorbanfekr-Kalashami H, Neek-Amal M, Peeters FM, Physical review B 97, 144111 (2018). http://doi.org/10.1103/PHYSREVB.97.144111
Abstract: Water inside a nanocapillary exhibits unconventional structural and dynamical behavior due to its ordered structure. The confining walls, density, and lateral pressures control profoundly the microscopic structure of trapped water. Here we study the electrostriction of confined water subjected to pressures of the order of GPa for two different setups: (i) a graphene nanochannel containing a constant number of water molecules independent of the height of the channel, (ii) an open nanochannel where water molecules can be exchanged with those in a reservoir. For the former case, a square-rhombic structure of confined water is formed when the height of the channel is d = 6.5 angstrom having a density of rho = 1.42 g cm(-3). By increasing the height of the channel, a transition from a flat to a buckled state occurs, whereas the density rapidly decreases and reaches the bulk density for d congruent to 8.5 angstrom. When a perpendicular electric field is applied, the water structure and the lateral pressure change. For strong electric fields (similar to 1 V/angstrom), the square-rhombic structure is destroyed. For an open setup, a solid phase of confined water consisting of an imperfect square-rhombic structure is formed. By applying a perpendicular field, the density and phase of confined water change. However, the density and pressure inside the channel decrease as compared to the first setup. Our study is closely related to recent experiments on confined water, and it reveals the sensitivity of the microscopic structure of confined water to the size of the channel, the external electric field, and the experimental setup.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.836
Times cited: 6
DOI: 10.1103/PHYSREVB.97.144111
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“Ionized water confined in graphene nanochannels”. de Aquino BRH, Ghorbanfekr-Kalashami H, Neek-Amal M, Peeters FM, Physical chemistry, chemical physics 21, 9285 (2019). http://doi.org/10.1039/C9CP00075E
Abstract: When confined between graphene layers, water behaves differently from the bulk and exhibits unusual properties such as fast water flow and ordering into a crystal. The hydrogen-bonded network is affected by the limited space and by the characteristics of the confining walls. The presence of an extraordinary number of hydronium and hydroxide ions in narrow channels has the following effects: (i) they affect water permeation through the channel, (ii) they may interact with functional groups on the graphene oxide surface and on the edges, and (iii) they change the thermochemistry of water, which are fundamentally important to understand, especially when confined water is subjected to an external electric field. Here we study the physical properties of water when confined between two graphene sheets and containing hydronium and hydroxide. We found that: (i) there is a disruption in the solvation structure of the ions, which is also affected by the layered structure of confined water, (ii) hydronium and hydroxide occupy specific regions inside the nanochannel, with a prevalence of hydronium (hydroxide) ions at the edges (interior), and (iii) ions recombine more slowly in confined systems than in bulk water, with the recombination process depending on the channel height and commensurability between the size of the molecules and the nanochannel height – a decay of 20% (40%) in the number of ions in 8 ps is observed for a channel height of h = 7 angstrom (bulk water). Our work reveals distinctive properties of water confined in a nanocapillary in the presence of additional hydronium and hydroxide ions.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 10
DOI: 10.1039/C9CP00075E
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“Unconventional two-dimensional vibrations of a decorated carbon nanotube under electric field : linking actuation to advanced sensing ability”. de Aquino BRH, Neek-Amal M, Milošević, MV, Scientific reports 7, 13481 (2017). http://doi.org/10.1038/S41598-017-12647-2
Abstract: We show that a carbon nanotube decorated with different types of charged metallic nanoparticles exhibits unusual two-dimensional vibrations when actuated by applied electric field. Such vibrations and diverse possible trajectories are not only fundamentally important but also have minimum two characteristic frequencies that can be directly linked back to the properties of the constituents in the considered nanoresonator. Namely, those frequencies and the maximal deflection during vibrations are very distinctively dependent on the geometry of the nanotube, the shape, element, mass and charge of the nanoparticle, and are vastly tunable by the applied electric field, revealing the unique sensing ability of devices made of molecular filaments and metallic nanoparticles.
Keywords: A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT)
Impact Factor: 4.259
Times cited: 1
DOI: 10.1038/S41598-017-12647-2
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“Structure and reentrant percolation in an inverse patchy colloidal system”. de Araujo JLB, Munarin FF, Farias GA, Peeters FM, Ferreira WP, Physical Review E 95, 062606 (2017). http://doi.org/10.1103/PHYSREVE.95.062606
Abstract: Two-dimensional systems of inverse patchy colloids modeled as disks with a central charge and having their surface decorated with oppositely pointlike charged patches are investigated using molecular dynamics simulations. The self-assembly of the patchy colloids leads to diverse ground state configurations ranging from crystalline arrangements of monomers to linear clusters, ramified linear clusters and to percolated configurations. Two structural phase diagrams are constructed: (1) as a function of the net charge and area fraction, and (2) as a function of the net charge and the range of the pair interaction potential. An interesting reentrant percolation transition is obtained as a function of the net charge of the colloids. We identify distinct mechanisms that lead to the percolation transition.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Times cited: 5
DOI: 10.1103/PHYSREVE.95.062606
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“Element Specific Atom Counting at the Atomic Scale by Combining High Angle Annular Dark Field Scanning Transmission Electron Microscopy and Energy Dispersive X‐ray Spectroscopy”. De Backer A, Zhang Z, van den Bos KHW, Bladt E, Sánchez‐Iglesias A, Liz‐Marzán LM, Nellist PD, Bals S, Van Aert S, Small methods , 2200875 (2022). http://doi.org/10.1002/smtd.202200875
Abstract: A new methodology is presented to count the number of atoms in multimetallic nanocrystals by combining energy dispersive X-ray spectroscopy (EDX) and high angle annular dark field scanning transmission electron microscopy (HAADF STEM). For this purpose, the existence of a linear relationship between the incoherent HAADF STEM and EDX images is exploited. Next to the number of atoms for each element in the atomic columns, the method also allows quantification of the error in the obtained number of atoms, which is of importance given the noisy nature of the acquired EDX signals. Using experimental images of an Au@Ag core–shell nanorod, it is demonstrated that 3D structural information can be extracted at the atomic scale. Furthermore, simulated data of an Au@Pt core–shell nanorod show the prospect to characterize heterogeneous nanostructures with adjacent atomic numbers.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 12.4
Times cited: 5
DOI: 10.1002/smtd.202200875
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“The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor”. De Backer J, Razzokov J, Hammerschmid D, Mensch C, Hafideddine Z, Kumar N, van Raemdonck G, Yusupov M, Van Doorslaer S, Johannessen C, Sobott F, Bogaerts A, Dewilde S, Redox Biology 19, 1 (2018). http://doi.org/10.1016/j.redox.2018.07.019
Abstract: Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec)
Impact Factor: 6.337
DOI: 10.1016/j.redox.2018.07.019
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“Effect of high-dose N-acetylcysteine on airway geometry, inflammation, and oxidative stress in COPD patients”. de Backer J, Vos W, Van Holsbeke C, Vinchurkar S, Claes R, Parizel PM, de Backer W, International Journal Of Chronic Obstructive Pulmonary Disease 8, 569 (2013). http://doi.org/10.2147/COPD.S49307
Abstract: Background: Previous studies have demonstrated the potential beneficial effect of N-acetylcysteine (NAC) in chronic obstructive pulmonary disease (COPD). However, the required dose and responder phenotype remain unclear. The current study investigated the effect of high-dose NAC on airway geometry, inflammation, and oxidative stress in COPD patients. Novel functional respiratory imaging methods combining multislice computed tomography images and computer-based flow simulations were used with high sensitivity for detecting changes induced by the therapy. Methods: Twelve patients with Global Initiative for Chronic Obstructive Lung Disease stage II COPD were randomized to receive NAC 1800 mg or placebo daily for 3 months and were then crossed over to the alternative treatment for a further 3 months. Results: Significant correlations were found between image-based resistance values and glutathione levels after treatment with NAC (P = 0.011) and glutathione peroxidase at baseline (P = 0.036). Image-based resistance values appeared to be a good predictor for glutathione peroxidase levels after NAC (P = 0.02), changes in glutathione peroxidase levels (P = 0.035), and reduction in lobar functional residual capacity levels (P = 0.00084). In the limited set of responders to NAC therapy, the changes in airway resistance were in the same order as changes induced by budesonide/formoterol. Conclusion: A combination of glutathione, glutathione peroxidase, and imaging parameters could potentially be used to phenotype COPD patients who would benefit from addition of NAC to their current therapy. The findings of this small pilot study need to be confirmed in a larger pivotal trial.
Keywords: A1 Journal article; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
Impact Factor: 3.157
Times cited: 21
DOI: 10.2147/COPD.S49307
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“Functional imaging using computational fluid dynamics to predict treatment success of mandibular advancement devices in sleep-disordered breathing”. de Backer JW, Vanderveken OM, Vos WG, Devolder A, Verhulst SL, Verbraecken JA, Parizel PM, Braem MJ, van de Heyning PH, de Backer WA, Journal of biomechanics 40, 3708 (2007). http://doi.org/10.1016/j.jbiomech.2007.06.022
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
Impact Factor: 2.664
Times cited: 66
DOI: 10.1016/j.jbiomech.2007.06.022
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“Computational fluid dynamics can detect changes in airway resistance in asthmatics after acute bronchodilation”. de Backer JW, Vos WG, Devolder A, Verhulst SL, Germonpré, P, Wuyts FL, Parizel PM, de Backer W, Journal of biomechanics 41, 106 (2008). http://doi.org/10.1016/j.jbiomech.2007.07.009
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
Impact Factor: 2.664
Times cited: 53
DOI: 10.1016/j.jbiomech.2007.07.009
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“Clinical applications of image-based airway computational fluid dynamics: assessment of inhalation medication and endobronchial devices”. de Backer JW, Vos WG, Germonpré, P, Salgado R, Parizel PM, de Backer W, Proceedings of the Society of Photo-optical Instrumentation Engineers 7262, 72621p (2009). http://doi.org/10.1117/12.811476
Abstract: Computational fluid dynamics (CFD) is a technique that is used increasingly in the biomedical field. Solving the flow equations numerically provides a convenient way to assess the efficiency of therapies and devices, ranging from cardiovascular stents and heart valves to hemodialysis workflows. Also in the respiratory field CFD has gained increasing interest, especially through the combination of three dimensional image reconstruction which results in highend patient-specific models. This paper provides an overview of clinical applications of CFD through image based modeling, resulting from recent studies performed in our center. We focused on two applications: assessment of the efficiency of inhalation medication and analysis of endobronchial valve placement. In the first application we assessed the mode of action of a novel bronchodilator in 10 treated patients and 4 controls. We assessed the local volume increase and resistance change based on the combination of imaging and CFD. We found a good correlation between the changes in volume and resistance coming from the CFD results and the clinical tests. In the second application we assessed the placement and effect of one way endobronchial valves on respiratory function in 6 patients. We found a strong patientspecific result of the therapy where in some patients the therapy resulted in complete atelectasis of the target lobe while in others the lobe remained inflated. We concluded from these applications that CFD can provide a better insight into clinically relevant therapies.
Keywords: A3 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1117/12.811476
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“Flow analyses in the lower airways: patient-specific model and boundary conditions”. de Backer JW, Vos WG, Gorlé, CD, Germonpré, P, Partoens B, Wuyts FL, Parizel PM, de Backer W, Medical engineering and physics 30, 872 (2008). http://doi.org/10.1016/j.medengphy.2007.11.002
Abstract: Computational fluid dynamics (CFD) is increasingly applied in the respiratory domain. The ability to simulate the flow through a bifurcating tubular system has increased the insight into the internal flow dynamics and the particular characteristics of respiratory flows such as secondary motions and inertial effects. The next step in the evolution is to apply the technique to patient-specific cases, in order to provide more information about pathological airways. This study presents a patient-specific approach where both the geometry and the boundary conditions (BC) are based on individual imaging methods using computed tomography (CT). The internal flow distribution of a 73-year-old female suffering from chronic obstructive pulmonary disease (COPD) is assessed. The validation is performed through the comparison of lung ventilation with gamma scintigraphy. The results show that in order to obtain agreement within the accuracy limits of the gamma scintigraphy scan, both the patient-specific geometry and the BC (driving pressure) play a crucial role. A minimal invasive test (CT scan) supplied enough information to perform an accurate CFD analysis. In the end it was possible to capture the pathological features of the respiratory system using the imaging and computational fluid dynamics techniques. This brings the introduction of this new technique in the clinical practice one step closer.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
Impact Factor: 1.819
Times cited: 82
DOI: 10.1016/j.medengphy.2007.11.002
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“Validation of computational fluid dynamics in CT-based airway models with SPECT/CT1”. de Backer JW, Vos WG, Vinchurkar SC, Claes R, Drollmann A, Wulfrank D, Parizel PM, Germonpré, P, de Backer W, Radiology 257, 854 (2010). http://doi.org/10.1148/radiol.10100322
Abstract: Purpose: To compare the results obtained by using numerical flow simulations with the results of combined single photon emission computed tomography (SPECT) and computed tomography (CT) and to demonstrate the importance of correct boundary conditions for the numerical methods to account for the large amount of interpatient variability in airway geometry. Materials and Methods: This study was approved by all relevant institutional review boards. All patients gave their signed informed consent. In this study, six patients with mild asthma (three men; three women; overall mean age, 46 years ± 17 [standard deviation]) underwent CT at functional residual capacity and total lung capacity, as well as SPECT/CT. CT data were used for segmentation and computational fluid dynamics (CFD) simulations. A comparison was made between airflow distribution, as derived with (a) SPECT/CT through tracer concentration analysis, (b) CT through lobar expansion measurement, and (c) CFD through flow computer simulation. Also, the heterogeneity of the ventilation was examined. Results: Good agreement was found between SPECT/CT, CT, and CFD in terms of airflow distribution and hot spot detection. The average difference for the internal airflow distribution was less than 3% for CFD and CT versus SPECT/CT. Heterogeneity in ventilation patterns could be detected with SPECT/CT and CFD. Conclusion: This results of this study show that patient-specific computer simulations with appropriate boundary conditions yield information that is similar to that obtained with functional imaging tools, such as SPECT/CT.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Vision lab; Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
Impact Factor: 7.296
Times cited: 100
DOI: 10.1148/radiol.10100322
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de Backer W, Vos W, Van Holsbeke C, Vinchurkar S, Claes R, Hufkens A, Parizel PM, Bedert L, de Backer J (2014) The effect of roflumilast in addition to LABA/LAMA/ICS treatment in COPD patients. Copenhagen, 527–529
Keywords: L1 Letter to the editor; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
Impact Factor: 10.569
Times cited: 26
DOI: 10.1183/09031936.00011714
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