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“Position-dependent effect of non-magnetic impurities on superconducting properties of nanowires”. Zhang L-F, Covaci L, Peeters FM, Europhysics letters 109, 17010 (2015). http://doi.org/10.1209/0295-5075/109/17010
Abstract: Anderson's theorem states that non-magnetic impurities do not change the bulk properties of conventional superconductors. However, as the dimensionality is reduced, the effect of impurities becomes more significant. Here we investigate superconducting nanowires with diameter comparable to the Fermi wavelength $\lambda_F$ (which is less than the superconducting coherence length) by using a microscopic description based on the Bogoliubov-de Gennes method. We find that: 1) impurities strongly affect the superconducting properties, 2) the effect is impurity position dependent, and 3) it exhibits opposite behavior for resonant and off-resonant wire widths. We show that this is due to the interplay between the shape resonances of the order parameter and the subband energy spectrum induced by the lateral quantum confinement. These effects can be used to manipulate the Josephson current, filter electrons by subband and investigate the symmetries of the superconducting subband gaps.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 7
DOI: 10.1209/0295-5075/109/17010
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“Gate tunable layer selectivity of transport in bilayer graphene nanostructures”. Abdullah HM, Zarenia M, Bahlouli H, Peeters FM, Van Duppen B, Europhysics letters 113, 17006 (2016). http://doi.org/10.1209/0295-5075/113/17006
Abstract: Recently it was found that bilayer graphene may exhibit regions with and without van der Waals coupling between the two layers. We show that such structures can exhibit a strong layer selectivity when current flows through the coupled region and that this selectivity can be tuned by means of electrostatic gating. Analysing how this effect depends on the type of bilayer stacking, the potential on the gates and the smoothness of the boundary between the coupled and decoupled regions, we show that nearly perfect layer selectivity is achievable in these systems. This effect can be further used to realise a tunable layer switch.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 15
DOI: 10.1209/0295-5075/113/17006
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“Advanced electron tomography of nanoparticle assemblies”. Altantzis T, Zanaga D, Bals S, Europhysics letters 119, 38001 (2017). http://doi.org/10.1209/0295-5075/119/38001
Abstract: Nanoparticle assemblies have attracted enormous scientific interest during the last
years, due to their unique properties compared to those of their building blocks. To understand
the origin of these properties and to establish the connection with their structure, a detailed and
quantitative structural characterization is essential. Transmission electron microscopy has been
widely used to investigate nano-assemblies. However, TEM images only correspond to a twodimensional
projection of a three-dimensional object. Therefore, in order to obtain the necessary
3D structural information electron tomography has to be applied. By means of advanced electron
tomography, both qualitative and quantitative information can be obtained, which can be used
for detailed theoretical studies.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 1.957
Times cited: 8
DOI: 10.1209/0295-5075/119/38001
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“Dynamics of topological defects and the effects of the cooling rate on finite-size two-dimensional screened Coulomb clusters”. Nelissen K, Partoens B, Peeters FM, Europhysics letters 79, 66001 (2007). http://doi.org/10.1209/0295-5075/79/66001
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 9
DOI: 10.1209/0295-5075/79/66001
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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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“Field-enhanced critical parameters in magnetically nanostructured superconductors”. Milošević, MV, Peeters FM, Europhysics letters 70, 670 (2005). http://doi.org/10.1209/epl/i2005-10032-4
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 40
DOI: 10.1209/epl/i2005-10032-4
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“Lorentz-force-induced asymmetry in the Aharonov-Bohm effect in a three-terminal semiconductor quantum ring”. Szafran B, Peeters FM, Europhysics letters 70, 810 (2005). http://doi.org/10.1209/epl/i2005-10049-7
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 28
DOI: 10.1209/epl/i2005-10049-7
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“The break-up of the vortex structure in a mesoscopic wire containing a constriction”. Elmurodov AK, Vodolazov DY, Peeters FM, Europhysics letters 74, 151 (2006). http://doi.org/10.1209/epl/i2005-10496-0
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 11
DOI: 10.1209/epl/i2005-10496-0
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“Superconducting films with antidot arrays: novel behaviour of the critical current”. Berdiyorov GR, Milošević, MV, Peeters FM, Europhysics letters 74, 493 (2006). http://doi.org/10.1209/epl/i2006-10013-1
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 36
DOI: 10.1209/epl/i2006-10013-1
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“Induced order and re-entrant melting in classical two-dimensional binary clusters”. Nelissen K, Partoens B, Schweigert I, Peeters FM, Europhysics letters 74, 1046 (2006). http://doi.org/10.1209/epl/i2006-10044-6
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 17
DOI: 10.1209/epl/i2006-10044-6
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“Microscopic model for multiple flux transitions in mesoscopic superconducting loops”. Vodolazov DY, Peeters FM, Hongisto TT, Arutyunov KY, Europhysics letters 75, 315 (2006). http://doi.org/10.1209/epl/i2006-10112-y
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 1.957
Times cited: 13
DOI: 10.1209/epl/i2006-10112-y
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“Quantum-size effects on T-c in superconducting nanofilms”. Shanenko AA, Croitoru MD, Peeters FM, Europhysics letters 76, 498 (2006). http://doi.org/10.1209/epl/i2006-10274-6
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Electron microscopy for materials research (EMAT)
Impact Factor: 1.957
Times cited: 31
DOI: 10.1209/epl/i2006-10274-6
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“Associations between PM2.5 and heart rate variability are modified by particle composition and beta-blocker use in patients with coronary heart disease”. de Hartog JJ, Lanki T, Timonen KL, Hoek G, Janssen NAH, Ibald-Mulli A, Peters A, Heinrich J, Tarkainen TH, Van Grieken R, van Wijnen JH, Brunekreef B, Pekkanen J, Environmental health perspectives 117, 105 (2009). http://doi.org/10.1289/EHP.11062
Abstract: Background: It has been hypothesized that ambient particulate air pollution is able to modify the autonomic nervous control of the heart, measured as heart rate variability (HRV) . Previously we reported heterogeneous associations between particulate matter with aerodynamic diameter < 2.5 µm (PM2.5) and HRV across three study centers. Objective: We evaluated whether exposure misclassification, effect modification by medication, or differences in particle composition could explain the inconsistencies. Methods: Subjects with coronary heart disease visited clinics biweekly in Amsterdam, the Netherlands ; Erfurt, Germany ; and Helsinki, Finland for 68 months. The standard deviation (SD) of NN intervals on an electrocardiogram (ECG ; SDNN) and high frequency (HF) power of HRV was measured with ambulatory ECG during paced breathing. Outdoor levels of PM2.5 were measured at a central site. In Amsterdam and Helsinki, indoor and personal PM2.5 were measured during the 24 hr preceding the clinic visit. PM2.5 was apportioned between sources using principal component analyses. We analyzed associations of indoor/personal PM2.5, elements of PM2.5, and source-specific PM2.5 with HRV using linear regression. Results: Indoor and personal PM2.5 were not associated with HRV. Increased outdoor PM2.5 was associated with decreased SDNN and HF at lags of 2 and 3 days only among persons not using beta-blocker medication. Traffic-related PM2.5 was associated with decreased SDNN, and long-range transported PM2.5 with decreased SDNN and HF, most strongly among persons not using beta blockers. Indicators for PM2.5 from traffic and long-range transport were also associated with decreased HRV. Conclusions: Our results suggest that differences in the composition of particles, beta-blocker use, and obesity of study subjects may explain some inconsistencies among previous studies on HRV.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1289/EHP.11062
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“Resolution of coherent and incoherent imaging systems reconsidered: classical criteria and a statistical alternative”. Van Aert S, van Dyck D, den Dekker AJ, Optics express 14, 3830 (2006). http://doi.org/10.1364/OE.14.003830
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 3.307
Times cited: 45
DOI: 10.1364/OE.14.003830
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“Preparation and luminescence of bulk oxyfluoride glasses doped with Ag nanoclusters”. Tikhomirov VK, Rodriguez VD, Kutznetsov D, Kirilenko D, Van Tendeloo G, Moshchalkov VV, Optics express 18, 22032 (2010). http://doi.org/10.1364/OE.18.022032
Abstract: Bulk oxyfluoride glasses doped with Ag nanoclusters have been prepared using the melt quenching technique. When pumped in the absorption band of Ag nanoclusters between 300 to 500 nm, these glasses emit a very broad luminescence band covering all the visible range with a weak tail extending into the near infrared. The maximum of the luminescence band and its color shifts to the blue with a shortening of the excitation wavelength and an increasing ratio of oxide to fluoride components, resulting in white color luminescence at a particular ratio of oxide to fluoride; with a quantum yield above 20%.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.307
Times cited: 74
DOI: 10.1364/OE.18.022032
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“Quantum cutting in Li (770 nm) and Yb (1000 nm) co-dopant emission bands by energy transfer from the ZnO nano-crystalline host”. Shestakov MV, Tikhomirov VK, Kirilenko D, Kuznetsov AS, Chibotaru LF, Baranov AN, Van Tendeloo G, Moshchalkov VV, Optics express 19, 15955 (2011). http://doi.org/10.1364/OE.19.015955
Abstract: Li-Yb co-doped nano-crystalline ZnO has been synthesized by a method of thermal growth from the salt mixtures. X-ray diffraction, transmission electron microscopy, atomic absorption spectroscopy and optical spectroscopy confirm the doping and indicate that the dopants may form Li-Li and Yb3+-Li based nanoclusters. When pumped into the conduction and exciton absorption bands of ZnO between 250 to 425 nm, broad emission bands of about 100 nm half-height-width are excited around 770 and 1000 nm, due to Li and Yb dopants, respectively. These emission bands are activated by energy transfer from the ZnO host mostly by quantum cutting processes, which generate pairs of quanta in Li (770 nm) and Yb (1000 nm) emission bands, respectively, out of one quantum absorbed by the ZnO host. These quantum cutting phenomena have great potential for application in the down-conversion layers coupled to the Si solar cells.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.307
Times cited: 19
DOI: 10.1364/OE.19.015955
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“Energy transfer in Eu3+ doped scheelites : use as thermographic phosphor”. Meert KW, Morozov VA, Abakumov AM, Hadermann J, Poelman D, Smet PF, Optics express 22, A961 (2014). http://doi.org/10.1364/OE.22.00A961
Abstract: In this paper the luminescence of the scheelite-based CaGd2(1-x)Eu2x(WO4)4 solid solutions is investigated as a function of the Eu content and temperature. All phosphors show intense red luminescence due to the 5D0 7F2 transition in Eu3+, along with other transitions from the 5D1 and 5D0 excited states. For high Eu3+ concentrations the intensity ratio of the emission originating from the 5D1 and 5D0 levels has a non-conventional temperature dependence, which could be explained by a phonon-assisted cross-relaxation process. It is demonstrated that this intensity ratio can be used as a measure of temperature with high spatial resolution, allowing the use of these scheelites as thermographic phosphor. The main disadvantage of many thermographic phosphors, a decreasing signal for increasing temperature, is absent.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.307
Times cited: 47
DOI: 10.1364/OE.22.00A961
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“Optical enhancement of a printed organic tandem solar cell using diffractive nanostructures”. Mayer JA, Offermans T, Chrapa M, Pfannmöller M, Bals S, Ferrini R, Nisato G, Optics express 26, A240 (2018). http://doi.org/10.1364/OE.26.00A240
Abstract: Solution processable organic tandem solar cells offer a promising approach to achieve cost-effective, lightweight and flexible photovoltaics. In order to further enhance the efficiency of optimized organic tandem cells, diffractive light-management nanostructures were designed for an optimal redistribution of the light as function of both wavelength and propagation angles in both sub-cells. As the fabrication of these optical structures is compatible with roll-to-roll production techniques such as hot-embossing or UV NIL imprinting, they present an optimal cost-effective solution for printed photovoltaics. Tandem cells with power conversion efficiencies of 8-10% were fabricated in the ambient atmosphere by doctor blade coating, selected to approximate the conditions during roll-to-roll manufacturing. Application of the light management structure onto an 8.7% efficient encapsulated tandem cell boosted the conversion efficiency of the cell to 9.5%. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.307
Times cited: 9
DOI: 10.1364/OE.26.00A240
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“Electrical generation of terahertz blackbody radiation from graphene”. Dong HM, Xu W, Peeters FM, Optics express 26, 24621 (2018). http://doi.org/10.1364/OE.26.024621
Abstract: Recent experimental work on the application of graphene for novel illumination motivated us to present a theoretical study of the blackbody radiation emission from a freely suspended graphene driven by a dc electric field. Strong terahertz (THz) emission, with intensity up to mW/cm(2), can be generated with increasing electric field strength due to the heating of electrons in graphene. We show that the intensity of the THz emission generated electrically from graphene depends rather sensitively on the lattice temperature in relatively weak electric fields, whereas it is less sensitive to the lattice temperature in relative strong electric fields. Our study highlights the practical application of graphene as intense THz source where the radiation is generated electrically. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.307
Times cited: 14
DOI: 10.1364/OE.26.024621
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“Linearized radially polarized light for improved precision in strain measurements using micro-Raman spectroscopy”. Prabhakara V, Nuytten T, Bender H, Vandervorst W, Bals S, Verbeeck J, Optics Express 29, 34531 (2021). http://doi.org/10.1364/OE.434726
Abstract: Strain engineering in semiconductor transistor devices has become vital in the semiconductor industry due to the ever-increasing need for performance enhancement at the nanoscale. Raman spectroscopy is a non-invasive measurement technique with high sensitivity to mechanical stress that does not require any special sample preparation procedures in comparison to characterization involving transmission electron microscopy (TEM), making it suitable for inline strain measurement in the semiconductor industry. Indeed, at present, strain measurements using Raman spectroscopy are already routinely carried out in semiconductor devices as it is cost effective, fast and non-destructive. In this paper we explore the usage of linearized radially polarized light as an excitation source, which does provide significantly enhanced accuracy and precision as compared to linearly polarized light for this application. Numerical simulations are done to quantitatively evaluate the electric field intensities that contribute to this enhanced sensitivity. We benchmark the experimental results against TEM diffraction-based techniques like nano-beam diffraction and Bessel diffraction. Differences between both approaches are assigned to strain relaxation due to sample thinning required in TEM setups, demonstrating the benefit of Raman for nondestructive inline testing.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.307
Times cited: 2
DOI: 10.1364/OE.434726
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“Substrate dependent terahertz magneto-optical properties of monolayer WS2”. Dong HM, Tao ZH, Duan YF, Li LL, Huang F, Peeters FM, Optics Letters 46, 4892 (2021). http://doi.org/10.1364/OL.435055
Abstract: Terahertz (THz) magneto-optical (MO) properties of monolayer (ML) tungsten disulfide (WS2), placed on different substrates and subjected to external magnetic fields, are studied using THz time-domain spectroscopy (TDS). We find that the THz MO conductivity exhibits a nearly linear response in a weak magnetic field, while a distinctly nonlinear/oscillating behavior is found in strong magnetic fields owing to strong substrate-induced random impurity scattering and interactions. The THz MO response of ML WS2 depends sensitively on the choice of the substrates, which we trace back to electronic localization and the impact of the substrates on the Landau level (LL) spectrum. Our results provide an in-depth understanding of the THz MO properties of ML WS2/substrate systems, especially the effect of substrates, which can be utilized to realize atomically thin THz MO nano-devices. (C) 2021 Optical Society of America
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.416
Times cited: 2
DOI: 10.1364/OL.435055
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“Preparation, structural and optical characterization of nanocrystalline ZnO doped with luminescent Ag-nanoclusters”. Kuznetsov AS, Lu Y-G, Turner S, Shestakov MV, Tikhomirov VK, Kirilenko D, Verbeeck J, Baranov AN, Moshchalkov VV, Optical materials express 2, 723 (2012). http://doi.org/10.1364/OME.2.000723
Abstract: Nanocrystalline ZnO doped with Ag-nanoclusters has been synthesized by a salt solid state reaction. Three overlapping broad emission bands due to the Ag nanoclusters have been detected at about 570, 750 and 900 nm. These emission bands are excited by an energy transfer from the exciton state of the ZnO host when pumped in the wavelength range from 250 to 400 nm. The 900 nm emission band shows characteristic orbital splitting into three components pointing out that the anisotropic crystalline wurtzite host of ZnO is responsible for this feature. Heat-treatment and temperature dependence studies confirm the origin of these emission bands. An energy level diagram for the emission process and a model for Ag nanoclusters sites are suggested. The emission of nanocrystalline ZnO doped with Ag nanoclusters may be applied for white light generation, displays driven by UV light, down-convertors for solar cells and luminescent lamps.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.591
DOI: 10.1364/OME.2.000723
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“Universal natural shapes : from unifying shape description to simple methods for shape analysis and boundary value problems”. Gielis J, Caratelli D, Fougerolle Y, Ricci PE, Tavkelidze I, Gerats T, PLoS ONE 7, e29324 (2012). http://doi.org/10.1371/JOURNAL.PONE.0029324
Abstract: Gielis curves and surfaces can describe a wide range of natural shapes and they have been used in various studies in biology and physics as descriptive tool. This has stimulated the generalization of widely used computational methods. Here we show that proper normalization of the Levenberg-Marquardt algorithm allows for efficient and robust reconstruction of Gielis curves, including self-intersecting and asymmetric curves, without increasing the overall complexity of the algorithm. Then, we show how complex curves of k-type can be constructed and how solutions to the Dirichlet problem for the Laplace equation on these complex domains can be derived using a semi-Fourier method. In all three methods, descriptive and computational power and efficiency is obtained in a surprisingly simple way.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1371/JOURNAL.PONE.0029324
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“Effect of operating and sampling conditions on the exhaust gas composition of small-scale power generators”. Smits M, Vanpachtenbeke F, Horemans B, De Wael K, Hauchecorne B, Van Langenhove H, Demeestere K, Lenaerts S, PLoS ONE 7, e32825 (2012). http://doi.org/10.1371/JOURNAL.PONE.0032825
Abstract: Small stationary diesel engines, like in generator sets, have limited emission control measures and are therefore responsible for 44% of the particulate matter (PM) emissions in the United States. The diesel exhaust composition depends on operating conditions of the combustion engine. Furthermore, the measurements are influenced by the used sampling method. This study examines the effect of engine loading and exhaust gas dilution on the composition of small-scale power generators. These generators are used in different operating conditions than road-transport vehicles, resulting in different emission characteristics. Experimental data were obtained for gaseous volatile organic compounds (VOC) and PM mass concentration, elemental composition and nitrate content. The exhaust composition depends on load condition because of its effect on fuel consumption, engine wear and combustion temperature. Higher load conditions result in lower PM concentration and sharper edged particles with larger aerodynamic diameters. A positive correlation with load condition was found for K, Ca, Sr, Mn, Cu, Zn and Pb adsorbed on PM, elements that originate from lubricating oil or engine corrosion. The nitrate concentration decreases at higher load conditions, due to enhanced nitrate dissociation to gaseous NO at higher engine temperatures. Dilution on the other hand decreases PM and nitrate concentration and increases gaseous VOC and adsorbed metal content. In conclusion, these data show that operating and sampling conditions have a major effect on the exhaust gas composition of small-scale diesel generators. Therefore, care must be taken when designing new experiments or comparing literature results.
Keywords: A1 Journal article; Engineering sciences. Technology; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 2.806
Times cited: 5
DOI: 10.1371/JOURNAL.PONE.0032825
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“An N-myristoylated globin with a redox-sensing function that regulates the defecation cycle in Caenorhabditis elegans”. Tilleman L, De Henau S, Pauwels M, Nagy N, Pintelon I, Braeckman BP, De Wael K, Van Doorslaer S, Adriaensen D, Timmermans J-P, Moens L, Dewilde S, PLoS ONE 7, e48768 (2012). http://doi.org/10.1371/JOURNAL.PONE.0048768
Abstract: Globins occur in all kingdoms of life where they fulfill a wide variety of functions. In the past they used to be primarily characterized as oxygen transport/storage proteins, but since the discovery of new members of the globin family like neuroglobin and cytoglobin, more diverse and complex functions have been assigned to this heterogeneous family. Here we propose a function for a membrane-bound globin of C. elegans, GLB-26. This globin was predicted to be myristoylated at its N-terminus, a post-translational modification only recently described in the globin family. In vivo, this globin is found in the membrane of the head mesodermal cell and in the tail stomato-intestinal and anal depressor muscle cells. Since GLB-26 is almost directly oxidized when exposed to oxygen, we postulate a possible function as electron transfer protein. Phenotypical studies show that GLB-26 takes part in regulating the length of the defecation cycle in C. elegans under oxidative stress conditions.
Keywords: A1 Journal article; Engineering sciences. Technology; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 2.806
Times cited: 6
DOI: 10.1371/JOURNAL.PONE.0048768
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“Multifractal properties of a closed contour : a peek beyond the shape analysis”. Duarte-Neto P, Stosic B, Stosic T, Lessa R, Milošević, MV, Stanley HE, PLoS ONE 9, e115262 (2014). http://doi.org/10.1371/journal.pone.0115262
Abstract: In recent decades multifractal analysis has been successfully applied to characterize the complex temporal and spatial organization of such diverse natural phenomena as heartbeat dynamics, the dendritic shape of neurons, retinal vessels, rock fractures, and intricately shaped volcanic ash particles. The characterization of multifractal properties of closed contours has remained elusive because applying traditional methods to their quasi-one-dimensional nature yields ambiguous answers. Here we show that multifractal analysis can reveal meaningful and sometimes unexpected information about natural structures with a perimeter well-defined by a closed contour. To this end, we demonstrate how to apply multifractal detrended fluctuation analysis, originally developed for the analysis of time series, to an arbitrary shape of a given study object. In particular, we show the application of the method to fish otoliths, calcareous concretions located in fish's inner ear. Frequently referred to as the fish's “black box”, they contain a wealth of information about the fish's life history and thus have recently attracted increasing attention. As an illustrative example, we show that a multifractal approach can uncover unexpected relationships between otolith contours and size and age of fish at maturity.
Keywords: A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT)
Impact Factor: 2.806
Times cited: 6
DOI: 10.1371/journal.pone.0115262
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“Ion current rectification, limiting and overlimiting conductances in nanopores”. van Oeffelen L, Van Roy W, Idrissi H, Charlier D, Lagae L, Borghs G, PLoS ONE 10, e0124171 (2015). http://doi.org/10.1371/journal.pone.0124171
Abstract: Previous reports on Poisson-Nernst-Planck (PNP) simulations of solid-state nanopores have focused on steady state behaviour under simplified boundary conditions. These are Neumann boundary conditions for the voltage at the pore walls, and in some cases also Donnan equilibrium boundary conditions for concentrations and voltages at both entrances of the nanopore. In this paper, we report time-dependent and steady state PNP simulations under less restrictive boundary conditions, including Neumann boundary conditions applied throughout the membrane relatively far away from the nanopore. We simulated ion currents through cylindrical and conical nanopores with several surface charge configurations, studying the spatial and temporal dependence of the currents contributed by each ion species. This revealed that, due to slow co-diffusion of oppositely charged ions, steady state is generally not reached in simulations or in practice. Furthermore, it is shown that ion concentration polarization is responsible for the observed limiting conductances and ion current rectification in nanopores with asymmetric surface charges or shapes. Hence, after more than a decade of collective research attempting to understand the nature of ion current rectification in solid-state nanopores, a relatively intuitive model is retrieved. Moreover, we measured and simulated current-voltage characteristics of rectifying silicon nitride nanopores presenting overlimiting conductances. The similarity between measurement and simulation shows that overlimiting conductances can result from the increased conductance of the electric double-layer at the membrane surface at the depletion side due to voltage-induced polarization charges.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 2.806
Times cited: 11
DOI: 10.1371/journal.pone.0124171
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“Structure and function of p53-DNA complexes with inactivation and rescue mutations : a molecular dynamics simulation study”. Kamaraj B, Bogaerts A, PLoS ONE 10, e0134638 (2015). http://doi.org/10.1371/journal.pone.0134638
Abstract: The tumor suppressor protein p53 can lose its function upon DNA-contact mutations (R273C and R273H) in the core DNA-binding domain. The activity can be restored by second-site suppressor or rescue mutations (R273CT284R, R273HT284R, and R273HS240R). In this paper, we elucidate the structural and functional consequence of p53 proteins upon DNA-contact mutations and rescue mutations and the underlying mechanisms at the atomic level by means of molecular dynamics simulations. Furthermore, we also apply the docking approach to investigate the binding phenomena between the p53 protein and DNA upon DNA-contact mutations and rescue mutations. This study clearly illustrates that, due to DNA-contact mutants, the p53 structure loses its stability and becomes more rigid than the native protein. This structural loss might affect the p53-DNA interaction and leads to inhibition of the cancer suppression. Rescue mutants (R273CT284R, R273HT284R and R273HS240R) can restore the functional activity of the p53 protein upon DNA-contact mutations and show a good interaction between the p53 protein and a DNA molecule, which may lead to reactivate the cancer suppression function. Understanding the effects of p53 cancer and rescue mutations at the molecular level will be helpful for designing drugs for p53 associated cancer diseases. These drugs should be designed so that they can help to inhibit the abnormal function of the p53 protein and to reactivate the p53 function (cell apoptosis) to treat human cancer.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.806
DOI: 10.1371/journal.pone.0134638
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Mannaerts D, Faes E, Cos P, Briedé, JJ, Gyselaers W, Cornette J, Gorbanev Y, Bogaerts A, Spaanderman M, Van Craenenbroeck E, Jacquemyn Y, Torrens C (2018) Oxidative stress in healthy pregnancy and preeclampsia is linked to chronic inflammation, iron status and vascular function. e0202919
Abstract: Background
During normal pregnancy, placental oxidative stress (OS) is present during all three trimesters and is necessary to obtain normal cell function. However, if OS reaches a certain level, pregnancy complications might arise. In preeclampsia (PE), a dangerous pregnancy specific hypertensive disorder, OS induced in the ischemic placenta causes a systemic inflammatory response and activates maternal endothelial cells. In this study, we aimed to quantify superoxide concentrations (as a measure of systemic OS) using electron paramagnetic resonance (EPR) and correlate them to markers of systemic inflammation, iron status and vascular function.
Methods
Fifty-nine women with a healthy pregnancy (HP), 10 non-pregnant controls (NP) and 28 PE patients (32±3.3weeks) were included. During HP, blood samples for superoxide, neutrophil to lymphocyte ratio (NLR), mean platelet volume (MPV) and iron status were taken at 10, 25 and 39 weeks. Vascular measurements for arterial stiffness (carotid-femoral pulse wave velocity (CF-PWV), augmentation index (AIx), augmentation Pressure (AP)) and microvascular endothelial function (reactive hyperemia index (RHI)) were performed at 35 weeks. In PE, all measurements were performed at diagnosis. CMH (1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine) was used as spin probe for EPR, since the formed CM radical
corresponds to the amount of superoxide.
Results
Superoxide concentration remains stable during pregnancy (p = 0.92), but is significantly higher compared to the NP controls (p<0.0001). At 25 weeks, there is a significant positive correlation between superoxide and ferritin concentration. (p = 0.04) In PE, superoxide, systemic inflammation and iron status are much higher compared to HP (all p<0.001). During HP, superoxide concentrations correlate significantly with arterial stiffness (all p<0.04), while in PE superoxide is significantly correlated to microvascular endothelial function (p = 0.03).
Conclusions
During HP there is an increased but stable oxidative environment, which is correlated to ferritin concentration. If superoxide levels increase, there is an augmentation in arterial stiffness. In PE pregnancies, systemic inflammation and superoxide concentrations are higher and result in a deterioration of endothelial function. Together, these findings support the hypothesis that vascular function is directly linked to the amount of OS and that measurement of OS in combination with vascular function tests might be used in the prediction of PE.
Keywords: University Hospital Antwerp; A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Translational Pathophysiological Research (TPR)
Impact Factor: 2.806
Times cited: 15
DOI: 10.1371/journal.pone.0202919
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“Aerobes and phototrophs as microbial organic fertilizers : exploring mineralization, fertilization and plant protection features”. Wambacq E, Alloul A, Grunert O, Carrette J, Vermeir P, Spanoghe J, Sakarika M, Vlaeminck SE, Haesaert G, PLoS ONE 17, e0262497 (2022). http://doi.org/10.1371/JOURNAL.PONE.0262497
Abstract: Organic fertilizers and especially microbial biomass, also known as microbial fertilizer, can enable a paradigm shift to the conventional fertilizer-to-food chain, particularly when produced on secondary resources. Microbial fertilizers are already common practice (e.g. Bloom® and Synagro); yet microbial fertilizer blends to align the nutrient release profile to the plant’s needs are, thus far, unexplored. Moreover, most research only focuses on direct fertilization effects without considering added value properties, such as disease prevention. This study has explored three promising types of microbial fertilizers, namely dried biomass from a consortium of aerobic heterotrophic bacteria, a microalga (Arthrospira platensis) and a purple non-sulfur bacterium (Rhodobacter sphaeroides). Mineralization and nitrification experiments showed that the nitrogen mineralization profile can be tuned to the plant’s needs by blending microbial fertilizers, without having toxic ammonium peaks. In a pot trial with perennial ryegrass (Lolium perenne L.), the performance of microbial fertilizers was similar to the reference organic fertilizer, with cumulative dry matter yields of 5.6–6.7 g per pot. This was confirmed in a pot trial with tomato (Solanum lycopersicum L.), showing an average total plant length of 90–99 cm after a growing period of 62 days for the reference organic fertilizer and the microbial fertilizers. Moreover, tomato plants artificially infected with powdery mildew (Oidium neolycopersici), a devastating disease for the horticultural industry, showed reduced disease symptoms when A. platensis was present in the growing medium. These findings strengthen the application potential of this novel class of organic fertilizers in the bioeconomy, with a promising match between nutrient mineralization and plant requirements as well as added value in crop protection.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 3.7
DOI: 10.1371/JOURNAL.PONE.0262497
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