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“Hierarchical zeolite single-crystal reactor for excellent catalytic efficiency”. Sun M-H, Zhou J, Hu Z-Y, Chen L-H, Li L-Y, Wang Y-D, Xie Z-K, Turner S, Van Tendeloo G, Hasan T, Su B-L, Matter 3, 1226 (2020). http://doi.org/10.1016/J.MATT.2020.07.016
Abstract: As a size- and shape-selective catalyst, zeolites are widely used in petroleum and fine-chemicals processing. However, their small micropores severely hinder molecular diffusion and are sensitive to coke formation. Hierarchically porous zeolite single crystals with fully interconnected, ordered, and tunable multimodal porosity at macro-, meso-, and microlength scale, like in leaves, offer the ideal solution. However, their synthesis remains highly challenging. Here, we report a versatile confined zeolite crystallization process to achieve these superior properties. Such zeolite single crystals lead to significantly improved mass transport properties by shortening the diffusion length while maintaining shape-selective properties, endowing them with a high efficiency of zeolite crystals, enhanced catalytic activities and lifetime, highly reduced coke formation, and reduced deactivation rate in bulky-molecule reactions and methanol-to-olefins process. Their industrial utilization can lead to the design of innovative and intensified reactors and processes with highly enhanced efficiency and minimum energy consumption.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
DOI: 10.1016/J.MATT.2020.07.016
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“Nanoscale phase separation in the oxide layer at GeTe (111) surfaces”. Frolov AS, Callaert C, Batuk M, Hadermann J, Volykhov AA, Sirotina AP, Amati M, Gregoratti L, Yashina LV, Nanoscale 14, 12918 (2022). http://doi.org/10.1039/D2NR02261C
Abstract: As a semiconductor ferroelectric, GeTe has become a focus of renewed attention due to the recent discovery of giant Rashba splitting. It already has a wide range of applications, from thermoelectricity to data storage. Its stability in ambient air, as well as the structure and properties of an oxide layer, define the processing media for device production and operation. Here, we studied a reaction between the GeTe (111) surface and molecular oxygen for crystals having solely inversion domains. We evaluated the reaction kinetics both ex situ and in situ using NAP XPS. The structure of the oxide layer is extensively discussed, where, according to HAADF-STEM and STEM-EDX, nanoscale phase separation of GeO2 and Te is observed, which is unusual for semiconductors. We believe that such behaviour is closely related to the ferroelectric properties and the domain structure of GeTe.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 6.7
DOI: 10.1039/D2NR02261C
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“Urban green infrastructure: A review on valuation toolkits from an urban planning perspective”. Van Oijstaeijen W, Van Passel S, Cools J, Journal Of Environmental Management 267, 110603 (2020). http://doi.org/10.1016/j.jenvman.2020.110603
Abstract: As a response to increasing urbanization and changing weather and climatic patterns, urban green infrastructure (UGI) emerged as a concept to increase resilience within the urban boundaries. Given that implementing these (semi-) natural solutions in practice requires a clear overview of the costs and benefits, valuation becomes ever important. A range of decision-support tools for green infrastructure and ecosystem services exist, developed for various purposes. This paper reviews the potential of 10 shortlisted and existing valuation tools to support investment decisions of urban green infrastructure. In the assessment, the functionality is regarded specifically from the urban planning and decision-making viewpoint. The toolkits were evaluated on 12 different criteria. After analyzing the toolkits on these criteria, the findings are evaluated on the (mis)match with specific requirements in the urban planning and management context. Secondly, recommendations and guidelines are formulated to support the design of simple valuation tools, tailored to support the development of green infrastructure in urban areas. Approaching the valuation toolkits biophysically and (socio-)economically provides an integral overview of the challenges and opportunities of the capacities of each framework. It was found that most tools are not designed for the peculiarities of the urban context. Several elements contribute to the hampering uptake of GI valuation tools. Firstly, the limited effort in the economic case for green infrastructure remains a burden to use toolkits to compare grey and green alternatives. Secondly, tools are currently seldom designed for the peculiarities of cities: urban ecosystem (dis)services, multi-scalability, life-span assessments of co-benefits and the importance of social benefits. Thirdly, toolkits should be the result of co-development between the scientific community and local authorities in order to create toolkits that are tailor made to the specific needs in the urban planning process. It can be concluded that current tools, are not readily applicable to support decision making as such. However, if applied cautiously, they can have an indicative role to pinpoint further targeted and in-depth analyses.
Keywords: A1 Journal Article; Engineering Management (ENM) ;
Impact Factor: 8.7
DOI: 10.1016/j.jenvman.2020.110603
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“Aerosol characteristics and sources for the Amazon Basin during the wet season”. Artaxo P, Maenhaut W, Storms H, Van Grieken R, Journal of geophysical research 95, 16971 (1990). http://doi.org/10.1029/JD095ID10P16971
Abstract: As a part of the NASA Global Tropospheric Experiment (GTE), aerosols were sampled in the tropical rain forest of the Amazon Basin during the Amazon Boundary Layer Experiment (ABLE 2B) in April and May 1987, in the wet season, when no forest burning occurs. Fine (dp < 2.0 μm) and coarse (2.0 < dp < 15 μm) aerosol fractions were collected using stacked filter units, at three sites under the forest canopy and at three levels of a tower inside the jungle. Particle-induced X ray emission (PIXE) was used to measure concentrations of 22 elements (Na, Mg, Al, Si, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, Br, Rb, Sr, Zr, and Pb). Morphological and trace element measurements of individual particles were carried out by automated electron probe X ray microanalysis. Gravimetric analysis was performed to obtain the fine and coarse aerosol mass concentration. Absolute factor analysis was used to interpret the large data set of the trace element concentrations and to obtain elemental source profiles. Hierarchical cluster analysis was used to derive groups of individual particles. The concentrations of soil dust related elements (Al, Si, Ti, Fe, Mn) were 5 times larger in the wet season compared to the 1985 ABLE 2A dry season experiment. Biogenic aerosol related elements in the fine fraction showed lower concentrations in the wet season. Fine aerosol mass concentration averaged only 2.1±0.7 μg m−3, while the average coarse mass concentration was 6.1±1.8 μg m −3. Sulphur concentrations averaged 76±14 ng m −3 in the fine fraction and 37±9 ng m −3 in the coarse fraction. Biogenic aerosol-related elements were dominant under the forest canopy, while soil dust dominated at the top of the forest canopy. Only two factors explained about 90% of the data variability for the fine and coarse aerosol fractions. These were soil dust (represented mainly by Al, Si, Ti, Mn, and Fe) and biogenic aerosol (represented by K, P, Cl, S, Zn, and the aerosol mass concentration). Source profiles showed a homogeneous aerosol distribution with similar elemental compositions at the different sampling sites. Enrichment factor calculations revealed a soil dust elemental profile similar to the average bulk soil composition, and a biogenic component similar to the plant bulk elemental composition. Total aerosol mass source apportionment showed that biogenic particles account for 5595% of the airborne concentrations. The analysis of individual aerosol particles showed that the biogenic particles consist of leaf fragments, pollen grains, fungi, algae, and other types of particles. Several groups of particles with K, Cl, P, S, and Ca as minor elements could easily be identified as biogenic particles on the basis of their morphology. Considering the vast area of tropical rain forests and the concentrations measured in this work, it is possible that biogenic particles can play an important role in the global aerosol budget and in the global biogeochemical cycles of various elements.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1029/JD095ID10P16971
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“Evaluation of airborne particles at the Alhambra monument in Granada, Spain”. Horemans B, Cardell C, Bencs L, Kontozova-Deutsch V, De Wael K, Van Grieken R, Microchemical journal 99, 429 (2011). http://doi.org/10.1016/J.MICROC.2011.06.018
Abstract: As a part of an ongoing investigation regarding the air quality at the Alhambra monument (UNESCO World Cultural Heritage), indoor and outdoor atmospheric aerosols (PM1 and PM10-1) and pollutant gases (O3, NO2, SO2 and NH3) were studied during summer and winter. Bulk elements, ionic compounds and black carbon (BC) in aerosols were analyzed with X-ray fluorescence spectrometry, ion chromatography and aethalometry/reflectometry, respectively. Natural PM10-1 aerosols, such as carbonate-rich soil and sea salts, reacted with a typical urban atmosphere, producing a mixture of particulates with diverse chemical composition. The content/formation of secondary inorganic aerosols depended on the air temperature and absolute humidity. Ratios of typical mineral elements (i.e., Ti/Fe and Si/Fe) showed that Saharan dust events contribute to the composition of the observed mineral aerosol content. BC, V and Ni originated from diesel exhaust, while Cu, Cr, Pb and Zn came mainly from non-exhaust vehicular emissions. Weathering phenomena, such as blackening and pigment discoloration, which could arise from gradual aerosol deposition indoors, are discussed.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 3.034
Times cited: 39
DOI: 10.1016/J.MICROC.2011.06.018
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“Investigation of heterogeneous reactions of PAH's on particle surfaces using laser microprobe mass analysis”. Niessner R, Klockow D, Bruynseels F, Van Grieken R, International journal of environmental analytical chemistry 22, 281 (1985). http://doi.org/10.1080/03067318508076427
Abstract: Artificially generated NaCl particles were coated with PAH's by using a condensation technique. These particles were exposed to reactive gases like ozone, bromine and nitrogen dioxide. The original as well as the exposed particles were investigated by fluorimetric analysis and by LAMMA (Laser Microprobe Mass Analysis) in the desorption mode, which allows the evaporation and characterization of surfaces of single particles. The results are interpreted in terms of possible heterogeneous atmospheric reactions. The reactivity of the considered PAH's towards nitrogen dioxide was found to be negligible. The structure of the reaction products formed with ozone was partially elucidated.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1080/03067318508076427
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“Photochemical production of hydrogen peroxide by digging pro-superoxide radical carbon vacancies in carbon nitride”. Ding Y, Maitra S, Arenas Esteban D, Bals S, Vrielinck H, Barakat T, Roy S, Van Tendeloo G, Liu J, Li Y, Vlad A, Su B-L, Cell reports physical science 3, 100874 (2022). http://doi.org/10.1016/J.XCRP.2022.100874
Abstract: Artificial photosynthesis of H2O2, an environmentally friendly oxidant and a clean fuel, holds great promise. However, improving its efficiency and stability for industrial implementation remains highly challenging. Here, we report the visible-light H2O2 artificial photosynthesis by digging pro-superoxide radical carbon vacancies in three-dimensional hierarchical porous g-C3N4 through a simple hydrolysis-freeze-drying-thermal treatment. A significant electronic structure change is revealed upon the implantation of carbon vacancies, broadening visible-light absorption and facilitating the photogenerated charge separation. The strong electron affinity of the carbon vacancies promotes superoxide radical (O-center dot(2)-) formation, significantly boosting the H2O2 photocatalytic production. The developed photocatalyst shows an H2O2 evolution rate of 6287.5 mM g(-1) h(-1) under visible-light irradiation with a long cycling stability being the best-performing photocatalyst among all reported g-C3N4-based systems. Our work provides fundamental insight into highly active and stable photocatalysts with great potential for safe industrial H2O2 production.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Times cited: 12
DOI: 10.1016/J.XCRP.2022.100874
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“Double quantum dots defined in bilayer graphene”. Zebrowski DP, Peeters FM, Szafran B, Physical review B 96, 035434 (2017). http://doi.org/10.1103/PHYSREVB.96.035434
Abstract: Artificial molecular states of double quantum dots defined in bilayer graphene are studied with the atomistic tight-binding method and its low-energy continuum approximation. We indicate that the extended electron wave functions have opposite parities on sublattices of the layers and that the ground-state wave-function components change from bonding to antibonding with the interdot distance. In the weak-coupling limit, the one most relevant for quantum dots defined electrostatically, the signatures of the interdot coupling include, for the two-electron ground state, formation of states with symmetric or antisymmetric spatial wave functions split by the exchange energy. In the high-energy part of the spectrum the states with both electrons in the same dot are found with the splitting of energy levels corresponding to simultaneous tunneling of the electron pair from one dot to the other.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.836
Times cited: 6
DOI: 10.1103/PHYSREVB.96.035434
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“DNA binding by the antimalarial compound artemisinin”. Slavkovic S, Shoara AA, Churcher ZR, Daems E, De Wael K, Sobott F, Johnson PE, Scientific reports 12, 133 (2022). http://doi.org/10.1038/S41598-021-03958-6
Abstract: Artemisinin (ART) is a vital medicinal compound that is used alone or as part of a combination therapy against malaria. ART is thought to function by attaching to heme covalently and alkylating a range of proteins. Using a combination of biophysical methods, we demonstrate that ART is bound by three-way junction and duplex containing DNA molecules. Binding of ART by DNA is first shown for the cocaine-binding DNA aptamer and extensively studied using this DNA molecule. Isothermal titration calorimetry methods show that the binding of ART is both entropically and enthalpically driven at physiological NaCl concentration. Native mass spectrometry methods confirm DNA binding and show that a non-covalent complex is formed. Nuclear magnetic resonance spectroscopy shows that ART binds at the three-way junction of the cocaine-binding aptamer, and that binding results in the folding of the structure-switching variant of this aptamer. This structure-switching ability was exploited using the photochrome aptamer switch assay to demonstrate that ART can be detected using this biosensing assay. This study is the first to demonstrate the DNA binding ability of ART and should lay the foundation for further work to study implications of DNA binding for the antimalarial activity of ART.
Keywords: A1 Journal article; Pharmacology. Therapy; Engineering sciences. Technology; Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab)
DOI: 10.1038/S41598-021-03958-6
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“Optical spectroscopy as a rapid and low-cost tool for the first-line analysis of glass artefacts : a step-by-step plan for Roman green glass”. Meulebroeck W, Cosyns P, Baert K, Wouters H, Cagno S, Janssens K, Terryn H, Nys K, Thienpont H, Journal of archaeological science 38, 2387 (2011). http://doi.org/10.1016/J.JAS.2011.04.023
Abstract: Archaeometric research on glass artefacts is continuously evolving and is converging towards a multidisciplinary research domain where different types of techniques are applied depending on the questions asked and the circumstances involved. The technique described in this work is optical spectroscopy. The benefit of this technique being the possibility of building up a knowledge database for a large amount of material in a relatively short period of time and with a relatively limited budget. This is of particular interest for the investigation of extensive and/or unexplored glass collections where a first-line analysis of artefacts could facilitate the selection of material needing further and more detailed examination. This publication explores the extent to which optical spectroscopy can be used for a first-line analysis of green coloured glass artefacts from the Roman period. It is shown that the colour coordinates calculated from the measured transmission spectrum could reveal information about the fragment under study. In particular it is shown that 1) based on the position of the calculated colour values on the colour diagram (CIE1931) one could easily know whether the artefact was coloured using only iron or if copper oxides were also present. In the case of the artefact owing its colour solely to the presence of iron, the distance between the measured colour values and the colour diagrams white point can roughly indicate the iron concentration of the sample; 2) artefacts that were fabricated under similar furnace conditions can also be identified on the colour diagram; 3) samples with identical compositions and fabrication conditions but with different sample thickness, gave rise to a variation in the colour coordinates, thus allowing optical spectroscopy to help identify fragments which might belong to the same object.
Keywords: A1 Journal article; Engineering sciences. Technology; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 2.602
Times cited: 18
DOI: 10.1016/J.JAS.2011.04.023
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“Arc plasma reactor modification for enhancing performance of dry reforming of methane”. Dinh DK, Trenchev G, Lee DH, Bogaerts A, Journal Of Co2 Utilization 42, 101352 (2020). http://doi.org/10.1016/j.jcou.2020.101352
Abstract: Arc plasma technology is gaining increasing interest for a variety of chemical reaction applications. In this study, we demonstrate how modifying the reactor geometry can significantly enhance the chemical reaction performance. Using dry reforming of methane as a model reaction, we studied different rotating arc reactors (conventional rotating arc reactor and nozzle-type rotating arc reactor) to evaluate the effect of attaching a downstream nozzle. The nozzle structure focuses the heat to a confined reaction volume, resulting in enhanced heat transfer from the arc into gas activation and reduced heat losses to the reactor walls. Compared to the conventional rotating arc reactor, this yields much higher CH4 and CO2 conversion (i.e., 74% and 49%, respectively, versus 40% and 28% in the conventional reactor, at 5 kJ/L) as well as energy efficiency (i.e., 53% versus 36%). The different performance in both reactors was explained by both experiments (measurements of temperature and oscillogram of current and voltage) and numerical modelling of the gas flow dynamics, heat transfer and fluid plasma of the reactor chambers. The results provide important insights for design optimization of arc plasma reactors for various chemical reactions.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.7
DOI: 10.1016/j.jcou.2020.101352
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“Transport of Reactive Oxygen and Nitrogen Species across Aquaporin: A Molecular Level Picture”. Yusupov M, Razzokov J, Cordeiro RM, Bogaerts A, Oxidative medicine and cellular longevity 2019, 1 (2019). http://doi.org/10.1155/2019/2930504
Abstract: Aquaporins (AQPs) are transmembrane proteins that conduct not only water molecules across the cell membrane but also other solutes, such as reactive oxygen and nitrogen species (RONS), produced (among others) by cold atmospheric plasma (CAP). These RONS may induce oxidative stress in the cell interior, which plays a role in cancer treatment. The underlying mechanisms of the transport of RONS across AQPs, however, still remain obscure. We apply molecular dynamics simulations to investigate the permeation of both hydrophilic (H<sub>2</sub>O<sub>2</sub>and OH) and hydrophobic (NO<sub>2</sub>and NO) RONS through AQP1. Our simulations show that these RONS can all penetrate across the pores of AQP1. The permeation free energy barrier of OH and NO is lower than that of H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>, indicating that these radicals may have easier access to the pore interior and interact with the amino acid residues of AQP1. We also study the effect of RONS-induced oxidation of both the phospholipids and AQP1 (i.e., sulfenylation of Cys<sub>191</sub>) on the transport of the above-mentioned RONS across AQP1. Both lipid and protein oxidation seem to slightly increase the free energy barrier for H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>permeation, while for OH and NO, we do not observe a strong effect of oxidation. The simulation results help to gain insight in the underlying mechanisms of the noticeable rise of CAP-induced RONS in cancer cells, thereby improving our understanding on the role of AQPs in the selective anticancer capacity of CAP.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.593
Times cited: 5
DOI: 10.1155/2019/2930504
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“Purple bacteria as added-value protein ingredient in shrimp feed : Penaeus vannamei growth performance, and tolerance against Vibrio and ammonia stress”. Alloul A, Wille M, Lucenti P, Bossier P, Van Stappen G, Vlaeminck SE, Aquaculture 530, 735788 (2021). http://doi.org/10.1016/J.AQUACULTURE.2020.735788
Abstract: Aquafeeds contain protein ingredients such as fishmeal and soybean meal, yet their production puts pressure on the environment. Finding novel protein sources such as dried microbial biomass produced on recovered or renewable resources, so-called single-cell protein or microbial protein, can contribute to a more sustainable aquaculture industry. New microbial protein sources are emerging with photoheterotrophic grown purple non‑sulfur bacteria (PNSB) showing high potential, yet research of PNSB as added-value protein ingredient is limited. This research studied their use as a protein source for the white leg shrimp (Penaeus vannamei) and investigated the shrimp's tolerance against Vibrio and ammonia stress. A 28-day shrimp feeding trial was performed with a commercial formulation without PNSB as experimental control (diet i), two pure PNSB species, namely Rhodopseudomonas palustris (diets ii-iii), Rhodobacter capsulatus (diets iv-v) at two protein inclusion levels of 5 and 11 g PNSBprotein 100 g−1 feedprotein and a PNSB enriched culture at a protein inclusion level of 11 g PNSBprotein 100 g−1 feedprotein (diet vi). For the shrimp fed with Rb. capsulatus, 5–25% higher individual weights (p < .05) and better feed conversion ratios were observed relative to the commercial diet (1.3–1.4 vs. control 1.7 g feed g−1 biomass; p < .05). The diet containing Rps. palustris at 5 g PNSBprotein 100 g−1 feedprotein inclusion also showed higher individual weights (26%, p < .05) and a better feed conversion ratio compared to the commercial feed (1.3 vs. control 1.7 g feed g−1 biomass; p < .05). The challenge test subsequent to the feeding trial showed a higher tolerance against ammonia (3 mg N L−1) for shrimp fed with Rps. palustris (survival 63–75% vs. 8% commercial diet; p < .05). For a post-feeding challenge test with Vibrio parahaemolyticus TW01, mortality rates were equal among all treatments. Yet, in vitro tests in 96-Well plates and agar spot assays showed that the PNSB species (i) Rps. palustris, (ii) Rb. capsulatus, (iii) Rb. sphaeroides, (iv) Rhodospirillum rubrum and (v) Afifella marina suppressed the pathogens V. parahaemolyticus TW01 and V. campbellii LMG 21363. Overall, this study demonstrated the potential of PNSB as an added-value protein ingredient in shrimp nursery feed. This can contribute to a circular economy, as PNSB can be cultivated on recovered or renewable resources (e.g. wastewater).
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 2.57
DOI: 10.1016/J.AQUACULTURE.2020.735788
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“Aptamers in biomedicine : selection strategies and recent advances”. Stefan G, Hosu O, De Wael K, Jesus Lobo-Castanon M, Cristea C, Electrochimica Acta 376, 137994 (2021). http://doi.org/10.1016/J.ELECTACTA.2021.137994
Abstract: Aptamers have come in the spotlight as bio-mimetic molecular recognition elements in the field of biomedicine due to various applications in diagnostics, drug delivery, therapeutics, and pharmaceutical analysis. Aptamers are composed of nucleic acid strands (DNA or RNA) that can specifically interact in a three-dimensional tailored design with the target molecule. The basic method to generate aptamers is Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Recent technological advances in aptamer selection allow for faster and cheaper production of a new generation of high-affinity aptamers compared to the traditional SELEX, which can last up to several months. Rigorous characterization performed by multiple research groups endorsed several well-defined aptamer sequences. Binding affinity, nature of the biomolecular interactions and structural characterization are of paramount importance for aptamer screening and development of applications. However, remarkable challenges still need to be dealt with before the aptamers can make great contributions to the biomedical field. Poor specificity and sensitivity, questionable clinical use, low drug loading, in vivo stability and toxicity are only some of the identified challenges. This review accounts for the 30th celebration of the SELEX technology underlining the most important aptamers' achievements in the biomedical field within mostly the past five years. Aptamers' advantages over antibodies are discussed. Because of potential clinical translational utility, insights of remarkable developments in aptamer-based methods for diagnosis and monitoring of disease biomarkers and pharmaceuticals are discussed focusing on the recent studies (2015-2020). The current challenges and promising opportunities for aptamers for therapeutic and theragnostic purposes are also presented. (C) 2021 Elsevier Ltd. All rights reserved.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 4.798
DOI: 10.1016/J.ELECTACTA.2021.137994
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Daems E (2021) Shaping up oligonucleotides : aptamer-target recognition investigated by native mass spectrometry. 235 p
Abstract: Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application.
Keywords: Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions”. Daems E, Moro G, Campos R, De Wael K, Trac-Trends In Analytical Chemistry 142, 116311 (2021). http://doi.org/10.1016/J.TRAC.2021.116311
Abstract: Aptamers are promising biorecognition elements with a wide applicability from therapeutics to bio-sensing. However, to successfully use these biomolecules, a complete characterisation of their bindingperformance in the presence of the target is crucial. Several multi-analytical approaches have been re-ported including techniques to describe kinetic and thermodynamic aspects of the aptamer-targetinteraction, and techniques which allow an in-depth understanding of the aptamer-target structures.Recent literature shows the need of a critical data interpretation, a combination of characterisationtechniques and suggests the key role of the characterisation protocol design. Indeed, thefinal applicationof the aptamer should be considered before choosing the characterisation method. All the limitations andcapabilities of the analytical tools in use for aptamer characterisation should be taken into account. Here,we present a critical overview of the current methods and multi-analytical approaches to study aptamer-target binding, aiming to provide researchers with guidelines for the design of characterisation protocols.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 8.442
DOI: 10.1016/J.TRAC.2021.116311
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“Undoing the development army : a paradigm shift from transfer of technology to agricultural innovation system in Ethiopian extension”. Gebremariam YA, Dessein J, Wondimagegnhu BA, Breusers M, Lenaerts L, Adgo E, Van Passel S, Minale AS, Nyssen J, Environment, development and sustainability , 1 (2023). http://doi.org/10.1007/S10668-023-04136-6
Abstract: Appropriate use of agricultural technologies and diversifying the farming activities is critical to addressing food security problems in Africa, including Ethiopia. The country is experimenting with the new Agricultural Innovation System (AIS) approach alongside the well-established Transfer of Technology (ToT) approach. This paper analyzes the gaps between policy discourses (as reflected in policy documents and strategic orientation documents) and extension practices (as reflected in the daily exchanges between farmers and the frontline staff of the Ethiopian extension system). It provides insights into the challenges faced and emphasizes the need for better coordination between policy formulation and implementation to enhance extension services. Policymakers, practitioners, and researchers can benefit from the valuable perspectives the findings offer. The study contributes to understanding the relationship between policy discourses and extension practices, and its implications can inform policy design and implementation in similar contexts. A qualitative research approach was deployed to analyze policy discourse and practice. Data were collected in Fogera, a district in Northwest Ethiopia, between August 2018 and February 2019. The data for the paper were obtained from 23 Focus Group Discussions conducted with men and women. 13 Informant Interviews (KIIs) were also carried out with personnel at different levels of government agricultural services and departments. Transcripts of recordings of the Focus Group Discussions (FGDs) and Key Informant Interviews (KIIs) were analyzed using a deductive approach. The study focuses on rice crops in the Fogera district, which are crucial for food security and reducing poverty. Although the geographic area is limited, the results can be used to improve the extension system in other areas facing similar challenges. Specifically, the study suggests switching from the traditional transfer of technology approach to the agricultural innovation system approach. Furthermore, the study's techniques, such as qualitative interviews, may have limitations and not fully capture the intricacies of policy and extension practices. The findings demonstrate that, although the policy documents strongly adhere to agricultural innovation system principles, top-down transfer of technology approaches continues to dominate in practice. Moreover, we have found potential discrepancies between the training content delivered and the specific needs of smallholder farmers. Practically, prescriptive systems are still used because agricultural innovation system approaches are not well understood by the Extension Agents. To realize a genuine agricultural innovation system, Ethiopia's extension apparatus should move forward with building committed and robust relationships between farmers, extension agents, researchers, private sectors, and non-governmental organizations. To this end, more research, enhanced training, and improved institutions are needed on what genuine agricultural innovation system could look like at the grass-roots level. This also includes understanding the roles that different actors within Ethiopia's development army should assume how a multi-actor policy dialogue can be organized.
Keywords: A1 Journal article; Engineering sciences. Technology; Engineering Management (ENM)
Impact Factor: 4.9
DOI: 10.1007/S10668-023-04136-6
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“Sustainable value assessment of farms using frontier efficiency benchmarks”. Van Passel S, Van Huylenbroeck G, Lauwers L, Mathijs E, Journal Of Environmental Management 90, 3057 (2009). http://doi.org/10.1016/J.JENVMAN.2009.04.009
Abstract: Appropriate assessment of firm sustainability facilitates actor-driven processes towards sustainable development. The methodology in this paper builds further on two proven methodologies for the assessment of sustainability performance: it combines the sustainable value approach with frontier efficiency benchmarks. The sustainable value methodology tries to relate firm performance to the use of different resources. This approach assesses contributions to corporate sustainability by comparing firm resource productivity with the resource productivity of a benchmark, and this for all resources considered. The efficiency is calculated by estimating the production frontier indicating the maximum feasible production possibilities. In this research, the sustainable value approach is combined with efficiency analysis methods to benchmark sustainability assessment. In this way, the production theoretical underpinnings of efficiency analysis enrich the sustainable value approach. The methodology is presented using two different functional forms: the CobbDouglas and the translog functional forms. The simplicity of the CobbDouglas functional form as benchmark is very attractive but it lacks flexibility. The translog functional form is more flexible but has the disadvantage that it requires a lot of data to avoid estimation problems. Using frontier methods for deriving firm specific benchmarks has the advantage that the particular situation of each company is taken into account when assessing sustainability. Finally, we showed that the methodology can be used as an integrative sustainability assessment tool for policy measures.
Keywords: A1 Journal article; Economics
Impact Factor: 4.01
Times cited: 41
DOI: 10.1016/J.JENVMAN.2009.04.009
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“Dynamic transitions between metastable states in a superconducting ring”. Vodolazov DI, Peeters FM, Physical review : B : condensed matter and materials physics 66, 054537 (2002). http://doi.org/10.1103/PhysRevB.66.054537
Abstract: Applying the time-dependent Ginzburg-Landau equations, transitions between metastable states of a superconducting ring are investigated in the presence of an external magnetic field. It is shown that if the ring exhibits several metastable states at a particular magnetic field, the transition from one metastable state to another one is governed by both the relaxation time of the absolute value of the order parameter tau(\psi\) and the relaxation time of the phase of the order parameter tau(phi). We found that the larger the ratio tau(\psi\)/tau(phi), the closer the final state will be to the absolute minimum of the free energy, i.e., the thermodynamic equilibrium. The transition to the final state occurs through a subsequent set of single phase slips at a particular point along the ring.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.836
Times cited: 34
DOI: 10.1103/PhysRevB.66.054537
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“Extended homologous series of Sn–O layered systems: A first-principles study”. Govaerts K, Partoens B, Lamoen D, Solid state communications 243, 36 (2016). http://doi.org/10.1016/j.ssc.2016.06.006
Abstract: Apart from the most studied tin-oxide compounds, SnO and SnO2, intermediate states have been claimed to exist for more than a hundred years. In addition to the known homologous series (Seko et al., Phys. Rev. Lett. 100, 045702 (2008)), we here predict the existence of several new compounds with an O concentration between 50 % (SnO) and 67 % (SnO2). All these intermediate compounds are constructed from removing one or more (101) oxygen layers of SnO2. Since the van der Waals (vdW) interaction is known to be important for the Sn-Sn interlayer distances, we use a vdW-corrected functional, and compare these results with results obtained with PBE and hybrid functionals. We present the electronic properties of the intermediate structures and we observe a decrease of the band gap when (i) the O concentration increases and (ii) more SnO-like units are present for a given concentration. The contribution of the different atoms to the valence and conduction band is also investigated.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT)
Impact Factor: 1.554
Times cited: 10
DOI: 10.1016/j.ssc.2016.06.006
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“Strongly Exchange Coupled Core|Shell Nanoparticles with High Magnetic Anisotropy: A Strategy toward Rare-Earth-Free Permanent Magnets”. Lottini E, López-Ortega A, Bertoni G, Turner S, Meledina M, Van Tendeloo G, de Julián Fernández C, Sangregorio C, Chemistry of materials 28, 4214 (2016). http://doi.org/10.1021/acs.chemmater.6b00623
Abstract: Antiferromagnetic(AFM)|ferrimagnetic(FiM) core|shell (CS) nanoparticles (NPs) of formula Co0.3Fe0.7O|Co0.6Fe2.4O4 with mean diameter from 6 to 18 nm have been synthesized through a one-pot thermal decomposition process. The CS structure has been generated by topotaxial oxidation of the core region, leading to the formation of a highly monodisperse single inverted AFM|FiM CS system with variable AFM-core diameter and constant FiM-shell thickness (~2 nm). The sharp interface, the high structural matching between both phases and the good crystallinity of the AFM material have been structurally demonstrated and are corroborated by the robust exchange-coupling between AFM and FiM phases, which gives rise to one among the largest exchange bias (HE) values ever reported for CS NPs (8.6 kOe) and to a strongly enhanced coercive field (HC). In addition, the investigation of the magnetic properties as a function of the AFM-core size (dAFM), revealed a non-monotonous trend of both HC and HE, which display a maximum value for dAFM = 5 nm (19.3 and 8.6 kOe, respectively). These properties induce a huge improvement of the capability of storing energy of the material, a result which suggests that the combination of highly anisotropic AFM|FiM materials can be an efficient strategy towards the realization of novel Rare Earth-free permanent magnets.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 9.466
Times cited: 48
DOI: 10.1021/acs.chemmater.6b00623
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“Modelling cometabolic biotransformation of sulfamethoxazole by an enriched ammonia oxidizing bacteria culture”. Peng L, Kassotaki E, Liu Y, Sun J, Dai X, Pijuan M, Rodriguez-Roda I, Buttiglieri G, Ni B-J, Chemical engineering science 173, 465 (2017). http://doi.org/10.1016/J.CES.2017.08.015
Abstract: Antibiotics such as sulfamethoxazole (SFX) are environmentally hazardous after being released into the aquatic environment and challenges remain in the development of engineered prevention strategies. In this work, a mathematical model was developed to describe and evaluate cometabolic biotransformation of SFX and its transformation products (TPs) in an enriched ammonia oxidizing bacteria (AOB) culture. The growth-linked cometabolic biodegradation by AOB, non-growth transformation by AOB and nongrowth transformation by heterotrophs were considered in the model framework. The production of major TPs comprising 4-Nitro-SFX, Desamino-SFX and N-4-Acetyl-SFX was also specifically modelled. The validity of the model was demonstrated through testing against literature reported data from extensive batch tests, as well as from long-term experiments in a partial nitritation sequencing batch reactor (SBR) and in a combined SBR + membrane aerated biofilm reactor performing nitrification/denitrification. Modelling results revealed that the removal efficiency of SFX increased with the increase of influent ammonium concentration, whereas the influent organic matter, hydraulic retention time and solid retention time exerted a limited effect on SFX biodegradation with the removal efficiencies varying in a narrow range. The variation of influent SFX concentration had no impact on SFX removal efficiency. The established model framework enables interpretation of a range of experimental observations on SFX biodegradation and helps to identify the optimal conditions for efficient removal. (C) 2017 Elsevier Ltd. All rights reserved.
Keywords: A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1016/J.CES.2017.08.015
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“Effect of plasma-induced oxidative stress on the glycolysis pathway of Escherichia coli”. Ranjbar S, Shahmansouri M, Attri P, Bogaerts A, Computers In Biology And Medicine 127, 104064 (2020). http://doi.org/10.1016/j.compbiomed.2020.104064
Abstract: Antibiotic resistance is one of the world’s most urgent public health problems. Due to its antibacterial properties, cold atmospheric plasma (CAP) may serve as an alternative method to antibiotics. It is claimed that oxidative stress caused by CAP is the main reason of bacteria inactivation. In this work, we computationally investigated the effect of plasma-induced oxidation on various glycolysis metabolites, by monitoring the production of the biomass. We observed that in addition to the significant reduction in biomass production, the rate of some reactions has increased. These reactions produce anti-oxidant products, showing the bacterial defense mechanism to escape the oxidative damage. Nevertheless, the simulations show that the plasma-induced oxidation effect is much stronger than the defense mechanism, causing killing of the bacteria.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.7
DOI: 10.1016/j.compbiomed.2020.104064
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“Determination of the atomic width of an APB in ordered CoPt using quantified HAADF-STEM”. Akamine H, Van den Bos KHW, Gauquelin N, Farjami S, Van Aert S, Schryvers D, Nishida M, Journal of alloys and compounds 644, 570 (2015). http://doi.org/10.1016/j.jallcom.2015.04.205
Abstract: Anti-phase boundaries (APBs) in an ordered CoPt alloy are planar defects which disturb the ordered structure in their vicinity and decrease the magnetic properties. However, it has not yet been clarified to what extend the APBs disturb the ordering. In this study, high-resolution HAADF-STEM images are statistically analysed based on the image intensities estimated by the statistical parameter estimation theory. In the procedure, averaging intensities, fitting the intensity profiles to specific functions, and assessment based on a statistical test are performed. As a result, the APBs in the stable CoPt are found to be characterised by two atomic planes, and a contrast transition range as well as the centre of an inclined APB is determined. These results show that the APBs are quite sharp and therefore may have no notable effect on the net magnetic properties due to their small volume fraction. (C) 2015 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 3.133
Times cited: 12
DOI: 10.1016/j.jallcom.2015.04.205
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“Second generation of vortex-antivortex states in mesoscopic superconductors: stabilization by artificial pinning”. Geurts R, Milošević, MV, Peeters FM, Physical review : B : solid state 79, 174508 (2009). http://doi.org/10.1103/PhysRevB.79.174508
Abstract: Antagonistic symmetries of superconducting polygons and their induced multivortex states in a homogeneous magnetic field may lead to the appearance of antivortices in the vicinity of the superconducting/normal-state boundary (where mesoscopic confinement is particularly strong). Resulting vortex-antivortex (V-Av) molecules match the sample symmetry but are extremely sensitive to defects and fluctuations and remain undetected experimentally. Here we show that V-Av states can reappear deep in the superconducting state due to an array of perforations in a polygonal setting, surrounding a central hole. Such states are no longer caused by the symmetry of the sample but rather by pinning itself, which prevents the vortex-antivortex annihilation. As a result, even micron size, clearly spaced V-Av molecules can be stabilized in large mesoscopic samples.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.836
Times cited: 17
DOI: 10.1103/PhysRevB.79.174508
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“Annular dark field imaging in a TEM”. Bals S, Kabius B, Haider M, Radmilovic V, Kisielowski C, Solid state communications 130, 675 (2004). http://doi.org/10.1016/j.ssc.2004.03.035
Abstract: Annular objective apertures are fabricated for a CM300 transmission electron microscope using a focused ion beam system. A central beam stop in the back focal plane of the objective lens of the microscope blocks all electrons scattered up to a semi-angle of approximately 20 mrad. In this manner, contributions to the image from Bragg scattering are largely reduced and the image contrast is sensitive to the atomic number Z. Experimentally, we find that single atom scattering cross sections measured with this technique are close to Rutherford scattering values. A comparison between this new method and STEM-HAADF shows that both techniques result in qualitatively similar images although the resolution of ADF-TEM is limited by contrast delocalization caused by the spherical aberration of the objective lens. This problem can be overcome by using an aberration corrected microscope.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 1.554
Times cited: 43
DOI: 10.1016/j.ssc.2004.03.035
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“A new approach for electron tomography: annular dark-field transmission electron microscopy”. Bals S, Van Tendeloo G, Kisielowski C, Advanced materials 18, 892 (2006). http://doi.org/10.1002/adma.200502201
Abstract: Annular dark-field transmission electron microscopy uses an annular objective aperture that blocks the central beam and all electrons scattered up to a certain serniangle. A contrast suitable for electron tomography is generated and 3D reconstructions of CdTe tetrapods and C nanotubes (see figure) are successfully obtained. With short exposure times and high contrast, the technique could be useful not only for materials science, but also for biological applications.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 19.791
Times cited: 53
DOI: 10.1002/adma.200502201
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“Quantitative STEM normalisation : the importance of the electron flux”. Martinez GT, Jones L, de Backer A, Béché, A, Verbeeck J, Van Aert S, Nellist PD, Ultramicroscopy 159, 46 (2015). http://doi.org/10.1016/j.ultramic.2015.07.010
Abstract: Annular dark-field (ADF) scanning transmission electron microscopy (STEM) has become widely used in quantitative studies based on the opportunity to directly compare experimental and simulated images. This comparison merely requires the experimental data to be normalised and expressed in units of fractional beam-current. However, inhomogeneities in the response of electron detectors can complicate this normalisation. The quantification procedure becomes both experiment and instrument specific, requiring new simulations for the particular response of each instrument's detector, and for every camera-length used. This not only impedes the comparison between different instruments and research groups, but can also be computationally very time consuming. Furthermore, not all image simulation methods allow for the inclusion of an inhomogeneous detector response. In this work, we propose an alternative method for normalising experimental data in order to compare these with simulations that consider a homogeneous detector response. To achieve this, we determine the electron flux distribution reaching the detector by means of a camera-length series or a so-called atomic column cross-section averaged convergent beam electron diffraction (XSACBED) pattern. The result is then used to determine the relative weighting of the detector response. Here we show that the results obtained by this new electron flux weighted (EFW) method are comparable to the currently used method, while considerably simplifying the needed simulation libraries. The proposed method also allows one to obtain a metric that describes the quality of the detector response in comparison with the ideal detector response.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 27
DOI: 10.1016/j.ultramic.2015.07.010
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“Nonlinear imaging using annular dark field TEM”. Bals S, Kilaas R, Kisielowski C, Ultramicroscopy 104, 281 (2005). http://doi.org/10.1016/j.ultramic.2005.05.004
Abstract: Annular dark field TEM images exhibit a dominant mass-thickness contrast that can be quantified to extract single atom scattering cross sections. On top of this incoherent background, additional lattice fringes appear with a nonlinear information limit of 1.2 angstrom at 150 kV. The formation of these fringes is described by coherent nonlinear imaging theory and good agreement is found between experimental and simulated images. Calculations furthermore predict that the use of aberration corrected microscopes will improve the image quality dramatically. (c) 2005 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 15
DOI: 10.1016/j.ultramic.2005.05.004
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“Quantitative 3D Characterization of Elemental Diffusion Dynamics in Individual Ag@Au Nanoparticles with Different Shapes”. Skorikov A, Albrecht W, Bladt E, Xie X, van der Hoeven JES, van Blaaderen A, Van Aert S, Bals S, ACS nano 13, 13421 (2019). http://doi.org/10.1021/acsnano.9b06848
Abstract: Anisotropic bimetallic nanoparticles are promising candidates for plasmonic and catalytic applications. Their catalytic performance and plasmonic properties are closely linked to the distribution of the two metals, which can change during applications in which the particles are exposed to heat. Due to this fact, correlating the thermal stability of complex heterogeneous nanoparticles to their microstructural properties is of high interest for the practical applications of such materials. Here, we employ quantitative electron tomography in high-angle annular dark-field scanning transmission electron microscopy (HAADFSTEM) mode to measure the 3D elemental diffusion dynamics in individual anisotropic Au−Ag nanoparticles upon heating in situ. This approach allows us to study the elemental redistribution in complex, asymmetric nanoparticles on a single particle level, which has been inaccessible to other techniques so far. In this work, we apply the proposed method to compare the alloying dynamics of Au−Ag nanoparticles with different shapes and compositions and find that the shape of the nanoparticle does not exhibit a significant effect on the alloying speed whereas the composition does. Finally, comparing the experimental results to diffusion simulations allows us to estimate the diffusion coefficients of the metals for individual nanoparticles.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 13.942
Times cited: 29
DOI: 10.1021/acsnano.9b06848
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