“Farmers' decision to use drought early warning system in developing countries”. Sharafi L, Zarafshani K, Keshavarz M, Azadi H, Van Passel S, Science Of The Total Environment 758, 142761 (2021). http://doi.org/10.1016/J.SCITOTENV.2020.142761
Abstract: Drought is a persistent, sluggish natural disaster in developing countries that has generated a financial burden and an unstable climate. Farmers should adopt early warning systems (EWS) in their strategies for monitoring drought to reduce its serious consequences. However, farmers in developing countries are reluctant to use EWS as their management strategies. Hence, the aim of this study was to investigate the decision of farmers to use climate knowledge through the model of farming activity in Kermanshah Township, Iran. A surveyor questionnaire was used to gather data from 370 wheat farmers using random sampling methods inmulti-stage clusters. Results revealed that the decision to use climate information is affected by personal factors, attitude towards climate information, objectives of using climate information, and external/physical farming factors. The result of this study has implications for drought management practitioners. To be specific, the results can aid policymakers to design early alert programs to minimize the risk of drought and thus move from conventional to climate smart agriculture. (C) 2020 Elsevier B.V. All rights reserved.
Keywords: A1 Journal article; Engineering Management (ENM)
Impact Factor: 4.9
DOI: 10.1016/J.SCITOTENV.2020.142761
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Shaw P (2021) Dual action of reactive species as signal and stress agents in plasma medicine : combined computational and experimental research. 191 p
Abstract: Reactive oxygen and nitrogen species (RONS) generated by cold atmospheric plasma (CAP) can activate discrete signaling transduction pathways or disrupt redox cellular homeostasis, depending on their concentration. This makes that CAP possesses therapeutic potential towards wound healing, cancer, and other diseases. In order to effectively use CAP in the clinic, a clear understanding of the interaction of RONS with biomolecules (lipids, proteins and nucleic acids) from the atomic to the macro scale, and their biological significance, is needed. In this work, I have therefore studied the dual role of CAP-derived RONS, i.e., (i) in the signaling pathways involved in wound healing, and (ii) in their reaction with biomolecules to cause oxidation-mediated damage. I performed computer simulations to provide fundamental insight about the occurring processes that are difficult or even impossible to obtain experimentally. Furthermore, next to computational studies, I used both 2D and 3D tissue cultures. 3D model allows proliferation in a more physiologically relevant geometry that stimulates the production of extracellular matrix proteins. I investigated the treatment of human gingival fibroblasts with low doses of CAP-generated RONS. This treatment demonstrated that it can inhibit colony formation but does not induce cell death, induce the expression of metalloprotease proteins, induce extracellular matrix degradation, and promote cell migration, which could result in enhanced wound healing. In contrast, at high concentrations, RONS can disrupt the cell membrane integrity and induce cancer cell death through oxidative stress-mediated pathways. I discovered how oxidation of the cell membrane (lipid-peroxidation) can facilitate the access of a drug (Melittin) into cancer cells, and in this way, reduce the required therapeutic dose of Melittin in melanoma and breast cancer cells (demonstrated using in vitro, in ovo and in silico approaches). Furthermore, I studied how excessive lipid-oxidation in chemoresistant pancreatic cancer cells promotes ferroptotic cell death. This was due to the stimulation of the iron-dependent Fenton reaction by targeting a redox specific signaling network. However, upon oxidative stress, cells protect themselves via a sophisticated intracellular antioxidant system that involves the regulation of glutathione/glutathione peroxidase 4 (lipid repair enzyme). Cancer cells exhibited increased levels of intracellular RONS due to their hyper metabolism, leading to high expression of anti-oxidant systems. I therefore focus on the effect of reactive species on the intracellular anti-oxidant system and corresponding DNA damages in both temozolomide-sensitive as well as temozolomide-resistant glioblastoma spheroids, in a 3-dimensional tumor model with a more complex tumor microenvironment than cell monolayers.
Keywords: Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
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“Evaluation of non-thermal effect of microwave radiation and its mode of action in bacterial cell inactivation”. Shaw P, Kumar N, Mumtaz S, Lim JS, Jang JH, Kim D, Sahu BD, Bogaerts A, Choi EH, Scientific Reports 11, 14003 (2021). http://doi.org/10.1038/s41598-021-93274-w
Abstract: A growing body of literature has recognized the non-thermal effect of pulsed microwave radiation (PMR) on bacterial systems. However, its mode of action in deactivating bacteria has not yet been extensively investigated. Nevertheless, it is highly important to advance the applications of PMR from simple to complex biological systems. In this study, we first optimized the conditions of the PMR device and we assessed the results by simulations, using ANSYS HFSS (High Frequency Structure Simulator) and a 3D particle-in-cell code for the electron behavior, to provide a better overview of the bacterial cell exposure to microwave radiation. To determine the sensitivity of PMR,<italic>Escherichia coli</italic> and<italic>Staphylococcus aureus</italic>cultures were exposed to PMR (pulse duration: 60 ns, peak frequency: 3.5 GHz) with power density of 17 kW/cm<sup>2</sup>at the free space of sample position, which would induce electric field of 8.0 kV/cm inside the PBS solution of falcon tube in this experiment at 25 °C. At various discharges (D) of microwaves, the colony forming unit curves were analyzed. The highest ratios of viable count reductions were observed when the doses were increased from 20D to 80D, which resulted in an approximate 6 log reduction in <italic>E. coli</italic>and 4 log reduction in<italic>S. aureus.</italic>Moreover, scanning electron microscopy also revealed surface damage in both bacterial strains after PMR exposure. The bacterial inactivation was attributed to the deactivation of oxidation-regulating genes and DNA damage.
Keywords: A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 4.259
DOI: 10.1038/s41598-021-93274-w
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“Cold Atmospheric Plasma Increases Temozolomide Sensitivity of Three-Dimensional Glioblastoma Spheroids via Oxidative Stress-Mediated DNA Damage”. Shaw P, Kumar N, Privat-Maldonado A, Smits E, Bogaerts A, Cancers 13, 1780 (2021). http://doi.org/10.3390/cancers13081780
Abstract: Glioblastoma multiforme (GBM) is the most frequent and aggressive primary malignant brain tumor in adults. Current standard radiotherapy and adjuvant chemotherapy with the alkylating agent temozolomide (TMZ) yield poor clinical outcome. This is due to the stem-like properties of tumor cells and genetic abnormalities in GBM, which contribute to resistance to TMZ and progression. In this study, we used cold atmospheric plasma (CAP) to enhance the sensitivity to TMZ through inhibition of antioxidant signaling (linked to TMZ resistance). We demonstrate that CAP indeed enhances the cytotoxicity of TMZ by targeting the antioxidant specific glutathione (GSH)/glutathione peroxidase 4 (GPX4) signaling. We optimized the threshold concentration of TMZ on five different GBM cell lines (U251, LN18, LN229, U87-MG and T98G). We combined TMZ with CAP and tested it on both TMZ-sensitive (U251, LN18 and LN229) and TMZ-resistant (U87-MG and T98G) cell lines using two-dimensional cell cultures. Subsequently, we used a three-dimensional spheroid model for the U251 (TMZ-sensitive) and U87-MG and T98G (TMZ-resistant) cells. The sensitivity of TMZ was enhanced, i.e., higher cytotoxicity and spheroid shrinkage was obtained when TMZ and CAP were administered together. We attribute the anticancer properties to the release of intracellular reactive oxygen species, through inhibiting the GSH/GPX4 antioxidant machinery, which can lead to DNA damage. Overall, our findings suggest that the combination of CAP with TMZ is a promising combination therapy to enhance the efficacy of TMZ towards the treatment of GBM spheroids.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
DOI: 10.3390/cancers13081780
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“Can leaf shape be represented by the ratio of leaf width to length? Evidence from nine species of Magnolia and Michelia (Magnoliaceae)”. Shi P, Yu K, Niinemets Ü, Gielis J, Forests 12, 41 (2021). http://doi.org/10.3390/F12010041
Abstract: Leaf shape is closely related to economics of leaf support and leaf functions, including light interception, water use, and CO2 uptake, so correct quantification of leaf shape is helpful for studies of leaf structure/function relationships. There are some extant indices for quantifying leaf shape, including the leaf width/length ratio (W/L), leaf shape fractal dimension (FD), leaf dissection index, leaf roundness index, standardized bilateral symmetrical index, etc. W/L ratio is the simplest to calculate, and recent studies have shown the importance of the W/L ratio in explaining the scaling exponent of leaf dry mass vs. leaf surface area and that of leaf surface area vs. leaf length. Nevertheless, whether the W/L ratio could reflect sufficient geometrical information of leaf shape has been not tested. The FD might be the most accurate measure for the complexity of leaf shape because it can characterize the extent of the self-similarity and other planar geometrical features of leaf shape. However, it is unknown how strongly different indices of leaf shape complexity correlate with each other, especially whether W/L ratio and FD are highly correlated. In this study, the leaves of nine Magnoliaceae species (>140 leaves for each species) were chosen for the study. We calculated the FD value for each leaf using the box-counting approach, and measured leaf fresh mass, surface area, perimeter, length, and width. We found that FD is significantly correlated to the W/L ratio and leaf length. However, the correlation between FD and the W/L ratio was far stronger than that between FD and leaf length for each of the nine species. There were no strong correlations between FD and other leaf characteristics, including leaf area, ratio of leaf perimeter to area, fresh mass, ratio of leaf fresh mass to area, and leaf roundness index. Given the strong correlation between FD and W/L, we suggest that the simpler index, W/L ratio, can provide sufficient information of leaf shape for similarly-shaped leaves. Future studies are needed to characterize the relationships among FD and W/L in leaves with strongly varying shape, e.g., in highly dissected leaves.
Keywords: A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 1.951
DOI: 10.3390/F12010041
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“&alpha, phase growth and branching in titanium alloys”. Shi R, Choudhuri D, Kashiwar A, Dasari S, Wang Y, Banerjee R, Banerjee D, Philosophical magazine (2021). http://doi.org/10.1080/14786435.2021.1998693
Abstract: The morphology and spatial distribution of alpha (α) precipitates have been mapped as a function of Mo content in Ti-Mo binary alloys employing a combinatorial approach. Heat-treatments were carried out on compositionally graded Ti-xMo samples processed using a rapid throughput laser engineered net shape (LENS) process. The composition space spans 1.5 at% to 6 at% Mo with ageing at 750°C, 650°C and 600°C following a β solution treatment. Three distinct regimes of α morphology and distribution were observed. These are colony-dominated microstructures originating from grain boundary α allotriomorphs, bundles of intragranular α laths, and homogeneously distributed individual fine-scale α laths. Branching of the α precipitates was observed in all these domains in a manner reminiscent of solid-state dendritic growth. The phenomenon is particularly apparent at low volume fractions of α. Similar features are present in a wide variety of alloy compositions. 3-dimensional features of such branched structures have been analysed. Simulation of the branching process by phase field methods incorporating anisotropy in the α/β interface energy and elasticity suggests that it can be initiated at growth ledges present at broad faces of the α laths, driven by the enhancement of the diffusion flux at these steps. The dependence of branching on various parameters such as supersaturation and diffusivity, and microstructural features like ledge height and distribution and the presence of adjacent α variants has been evaluated.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 1.505
DOI: 10.1080/14786435.2021.1998693
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“Vibrational properties and thermal transport in quaternary chalcogenides : the case of Te-based compositions”. Shi W, Pandey T, Lindsay L, Woods LM, Physical review materials 5, 045401 (2021). http://doi.org/10.1103/PHYSREVMATERIALS.5.045401
Abstract: Vibrational thermal properties of CuZn2InTe4, AgZn2InTe4, and Cu2CdSnTe4, derived from binary II-VI zinc-blendes, are reported based on first-principles calculations. While the chalcogenide atoms in these materials have the same lattice positions, the cation atom arrangements vary, resulting in different crystal symmetries and subsequent properties. The compositional differences have important effects on the vibrational thermal characteristics of the studied materials, which demonstrate that low-frequency optical phonons hybridize with acoustic phonons and lead to enhanced phonon-phonon scattering and low lattice thermal conductivities. The phonon density of states, mode Gruneisen parameters, and phonon scattering rates are also calculated, enabling deeper insight into the microscopic thermal conduction processes in these materials. Compositional variations drive differences among the three materials considered here; nonetheless, their structural similarities and generally low thermal conductivities (0.5-4 W/mK at room temperature) suggest that other similar II-VI zinc-blende derived materials will also exhibit similarly low values, as also corroborated by experimental data. This, combined with the versatility in designing a variety of motifs on the overall structure, makes quaternary chalcogenides interesting for thermal management and energy conversion applications that require low thermal conductivity.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
DOI: 10.1103/PHYSREVMATERIALS.5.045401
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Skorikov A (2021) Fast approaches for investigating 3D elemental distribution in nanomaterials. 143 p
Keywords: Doctoral thesis; Electron microscopy for materials research (EMAT)
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“Deep learning-based denoising for improved dose efficiency in EDX tomography of nanoparticles”. Skorikov A, Heyvaert W, Albecht W, Pelt DM, Bals S, Nanoscale 13, 12242 (2021). http://doi.org/10.1039/D1NR03232A
Abstract: The combination of energy-dispersive X-ray spectroscopy (EDX) and electron tomography is a powerful approach to retrieve the 3D elemental distribution in nanomaterials, providing an unprecedented level of information for complex, multi-component systems, such as semiconductor devices, as well as catalytic and plasmonic nanoparticles. Unfortunately, the applicability of EDX tomography is severely limited because of extremely long acquisition times and high electron irradiation doses required to obtain 3D EDX reconstructions with an adequate signal-to-noise ratio. One possibility to address this limitation is intelligent denoising of experimental data using prior expectations about the objects of interest. Herein, this approach is followed using the deep learning methodology, which currently demonstrates state-of-the-art performance for an increasing number of data processing problems. Design choices for the denoising approach and training data are discussed with a focus on nanoparticle-like objects and extremely noisy signals typical for EDX experiments. Quantitative analysis of the proposed method demonstrates its significantly enhanced performance in comparison to classical denoising approaches. This allows for improving the tradeoff between the reconstruction quality, acquisition time and radiation dose for EDX tomography. The proposed method is therefore especially beneficial for the 3D EDX investigation of electron beam-sensitive materials and studies of nanoparticle transformations.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 7.367
Times cited: 11
DOI: 10.1039/D1NR03232A
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Skorikov A, Heyvaert W, Albrecht W, Pelt DM, Bals S (2021) EMAT Simulated 3D Nanoparticle Structures Dataset
Abstract: This dataset contains 1000 simulated nanoparticle-like 3D structures and noisy EDX-like elemental maps based on them. These data are intended to be used for quantitative analysis of data processing methods in (EDX) tomography of nanoparticles and training the data-driven approaches for these tasks. The dataset is structured as follows: voxel_data/clean 3D voxel grid representation of the simulated nanoparticles. Voxel intensities are adjusted so that the total intensity equals 103. All 3D structures have unique identifiers in 0..999 range. The data derived from a 3D structure preserves this unique identifier. sinograms/clean Tilt series of projection images obtained from the corresponding 3D structures over an angular range of -75..75 degrees with a tilt step of 10 degrees to simulate a typical tilt series used in EDX tomography. Total intensity in each projection image equals 103. sinograms/noisy Tilt series of projection images corrupted with Poisson noise and an additional spatially uniform background noise. projections/clean Projection images extracted from the clean tilt series at 0 degrees tilt angle. projections/noisy Projection images extracted from the noisy tilt series at 0 degrees tilt angle. images/clean Visualizations of the clean projections as PNG images with the intensity range adjusted to 0..255 images/noisy Visualizations of the noisy projections as PNG images with the intensity range adjusted to 0..255
Keywords: Dataset; Electron microscopy for materials research (EMAT)
DOI: 10.5281/zenodo.4580545
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Sleegers N (2021) Cephalosporin antibiotics : electrochemical fingerprints and redox pathways investigated by mass spectral analysis. 208 p
Keywords: Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab)
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“Electrochemistry of intact versus degraded cephalosporin antibiotics facilitated by LC–MS analysis”. Sleegers N, van Nuijs ALN, van den Berg M, De Wael K, Analytical Chemistry 93, 2394 (2021). http://doi.org/10.1021/ACS.ANALCHEM.0C04286
Abstract: The electrochemical detection of cephalosporins is a promising approach for the monitoring of cephalosporin levels in process waters. However, this class of antibiotics, like penicillins, is composed of chemically active molecules and susceptible to hydrolysis and aminolysis of the four membered β-lactam ring present. In order to develop a smart monitoring strategy for cephalosporins, the influence of degradation (hydrolysis and aminolysis) on the electrochemical fingerprint has to be taken into account. Therefore, an investigation was carried out to understand the changes of the voltammetric fingerprints upon acidic and alkaline degradation. Changes in fingerprints were correlated to the degradation pathways through the combination of square wave voltammetry and liquid chromatography quadrupole time-of-flight analysis. The characteristic electrochemical signals of the β-lactam ring disappeared upon hydrolysis. Additional oxidation signals that appeared after degradation were elucidated and linked to different degradation products, and therefore, enrich the voltammetric fingerprints with information of the state of the cephalosporins. The applicability of the electrochemical monitoring system was explored by the analysis of the intact and degraded industrial process waters containing the key intermediate 7-aminodeacetoxycephalosporanic acid (7-ADCA). Clearly, the intact process samples exhibited the expected core signals of 7-ADCA and could be quantified, while the degraded samples only showed the newly formed degradation products.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Toxicological Centre
Impact Factor: 6.32
DOI: 10.1021/ACS.ANALCHEM.0C04286
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“Cocktail of reactive species generated by cold atmospheric plasma: oral administration induces non-small cell lung cancer cell death”. Song C-H, Attri P, Ku S-K, Han I, Bogaerts A, Choi EH, Journal Of Physics D-Applied Physics 54, 185202 (2021). http://doi.org/10.1088/1361-6463/abdff2
Abstract: Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, with 85% of all lung cancer reported as NSCLC. Moreover, there are no effective treatments in advanced NSCLC. This study shows for the first time that oral administration of plasma-treated water (PTW) can cure advanced NSCLC. The cold plasma in water generates a cocktail of reactive species, and oral administration of this cocktail to mice showed no toxicities even at the highest dose of PTW, after a single dose and repeated doses for 28 d in mice. In vivo studies reveal that PTW showed favorable anticancer effects on chemo-resistant lung cancer, similarly to gefitinib treatment as a reference drug in a chemo-resistant NSCLC model. The anticancer activities of PTW seem to be involved in inhibiting proliferation and angiogenesis and enhancing apoptosis in the cancer cells. Interestingly, the PTW contributes to enhanced immune response and improved cachexia in the model.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
DOI: 10.1088/1361-6463/abdff2
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“Vibrational and optical identification of GeO₂, and GeO single layers : a first-principles study”. Sozen Y, Yagmurcukardes M, Sahin H, Physical Chemistry Chemical Physics 23, 21307 (2021). http://doi.org/10.1039/D1CP02299G
Abstract: In the present work, the identification of two hexagonal phases of germanium oxides (namely GeO2 and GeO) through the vibrational and optical properties is reported using density functional theory calculations. While structural optimizations show that single-layer GeO2 and GeO crystallize in 1T and buckled phases, phonon band dispersions reveal the dynamical stability of each structure. First-order off-resonant Raman spectral predictions demonstrate that each free-standing single-layer possesses characteristic peaks that are representative for the identification of the germanium oxide phase. On the other hand, electronic band dispersion analysis shows the insulating and large-gap semiconducting nature of single-layer GeO2 and GeO, respectively. Moreover, optical absorption, reflectance, and transmittance spectra obtained by means of G(0)W(0)-BSE calculations reveal the existence of tightly bound excitons in each phase, displaying strong optical absorption. Furthermore, the excitonic gaps are found to be at deep UV and visible portions of the spectrum, for GeO2 and GeO crystals, with energies of 6.24 and 3.10 eV, respectively. In addition, at the prominent excitonic resonances, single-layers display high reflectivity with a zero transmittance, which is another indication of the strong light-matter interaction inside the crystal medium.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 4.123
DOI: 10.1039/D1CP02299G
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“Microbial food from light, carbon dioxide and hydrogen gas : kinetic, stoichiometric and nutritional potential of three purple bacteria”. Spanoghe J, Vermeir P, Vlaeminck SE, Bioresource Technology 337, 125364 (2021). http://doi.org/10.1016/J.BIORTECH.2021.125364
Abstract: The urgency for a protein transition towards more sustainable solutions is one of the major societal challenges. Microbial protein is one of the alternative routes, in which land- and fossil-free production should be targeted. The photohydrogenotrophic growth of purple bacteria, which builds on the H2– and CO2-economy, is unexplored for its microbial protein potential. The three tested species (Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas palustris) obtained promising growth rates (2.3–2.7 d−1 at 28°C) and protein productivities (0.09–0.12 g protein L−1 d−1), rendering them likely faster and more productive than microalgae. The achieved protein yields (2.6–2.9 g protein g−1 H2) transcended the ones of aerobic hydrogen oxidizing bacteria. Furthermore, all species provided full dietary protein matches for humans and their fatty acid content was dominated by vaccenic acid (82–86%). Given its kinetic and nutritional performance we recommend to consider Rhodobacter capsulatus as a high-potential sustainable source of microbial food.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 5.651
DOI: 10.1016/J.BIORTECH.2021.125364
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“Power outages and bill savings : a choice experiment on residential demand response acceptability in Delhi”. Srivastava A, Van Passel S, Valkering P, Laes EJW, Renewable &, Sustainable Energy Reviews 143, 110904 (2021). http://doi.org/10.1016/J.RSER.2021.110904
Abstract: This paper conducts a discrete choice experiment among 167 households in the Delhi region in India, to study the acceptability of demand response (DR) programs among upper-income households. Attributes include rate types, rate bands, reductions in power outages, and expected monthly savings. Results indicate a preference for time-of-use pricing over real-time pricing, and a preference for three rate slabs per day over two. Respondents prioritize reductions in power outages and minimizing potential expenses, reflecting the financial sensitivity and energy poverty relative to other countries. Respondents' ages and incomes further affect the value that they attach to reductions in power outages. The paper proposes various structures of DR programs that could achieve high predicted enrollment and concludes by estimating the potential benefits of implementing such programs. Overall, the analysis indicates that a DR program could be feasible in a developing country context, particularly if it is designed keeping in mind local socio-economic considerations. This may be supported through further confirmatory research.
Keywords: A1 Journal article; Engineering sciences. Technology; Engineering Management (ENM)
Impact Factor: 8.05
DOI: 10.1016/J.RSER.2021.110904
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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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“Misfit dislocation structure and thermal boundary conductance of GaN/AlN interfaces”. Sun J, Li Y, Karaaslan Y, Sevik C, Chen Y, Journal Of Applied Physics 130, 035301 (2021). http://doi.org/10.1063/5.0049662
Abstract: The structure and thermal boundary conductance of the wurtzite GaN/AlN (0001) interface are investigated using molecular dynamics simulation. Simulation results with three different empirical interatomic potentials have produced similar misfit dislocation networks and dislocation core structures. Specifically, the misfit dislocation network at the GaN/AlN interface is found to consist of pure edge dislocations with a Burgers vector of 1/3(1 (2) over bar 10) and the misfit dislocation core has an eight-atom ring structure. Although different interatomic potentials lead to different dislocation properties and thermal conductance values, all have demonstrated a significant effect of misfit dislocations on the thermal boundary conductance of the GaN/AlN (0001) interface. Published under an exclusive license by AIP Publishing.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.068
DOI: 10.1063/5.0049662
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“Exponentially selective molecular sieving through angstrom pores”. Sun PZ, Yagmurcukardes M, Zhang R, Kuang WJ, Lozada-Hidalgo M, Liu BL, Cheng H-M, Wang FC, Peeters FM, Grigorieva IV, Geim AK, Nature Communications 12, 7170 (2021). http://doi.org/10.1038/S41467-021-27347-9
Abstract: Two-dimensional crystals with angstrom-scale pores are widely considered as candidates for a next generation of molecular separation technologies aiming to provide extreme, exponentially large selectivity combined with high flow rates. No such pores have been demonstrated experimentally. Here we study gas transport through individual graphene pores created by low intensity exposure to low kV electrons. Helium and hydrogen permeate easily through these pores whereas larger species such as xenon and methane are practically blocked. Permeating gases experience activation barriers that increase quadratically with molecules' kinetic diameter, and the effective diameter of the created pores is estimated as similar to 2 angstroms, about one missing carbon ring. Our work reveals stringent conditions for achieving the long sought-after exponential selectivity using porous two-dimensional membranes and suggests limits on their possible performance. Two-dimensional membranes with angstrom-sized pores are predicted to combine high permeability with exceptional selectivity, but experimental demonstration has been challenging. Here the authors realize angstrom-sized pores in monolayer graphene and demonstrate gas transport with activation barriers increasing quadratically with the molecular kinetic diameter.
Keywords: A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT)
Impact Factor: 12.124
Times cited: 28
DOI: 10.1038/S41467-021-27347-9
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“Tailoring dirac plasmons via anisotropic dielectric environment by design”. Tao ZH, Dong HM, Milošević, MV, Peeters FM, Van Duppen B, Physical Review Applied 16, 054030 (2021). http://doi.org/10.1103/PHYSREVAPPLIED.16.054030
Abstract: Dirac plasmons in a two-dimensional (2D) crystal are strongly affected by the dielectric properties of the environment, due to interaction of their electric field lines with the surrounding medium. Using graphene as a 2D reservoir of free carriers, one can engineer a material configuration that provides an anisotropic environment to the plasmons. In this work, we discuss the physical properties of Dirac plasmons in graphene surrounded by an arbitrary anisotropic dielectric and exemplify how h-BN-based heterostructures can be designed to bear the required anisotropic characteristics. We calculate how dielec-tric anisotropy impacts the spatial propagation of the plasmons and find that an anisotropy-induced plasmon mode emerges, together with a damping pathway, that stem from the out-of-plane off-diagonal elements in the dielectric tensor. Furthermore, we find that one can create hyperbolic plasmons by inher-iting the dielectric hyperbolicity of the designed material environment. Strong control over plasmon propagation patterns can be realized in a similar manner. Finally, we show that in this way one can also control the polarization of the light-matter excitations that constitute the plasmon. Taken together, our results promote the design of the dielectric environment as an effective path to tailor the plasmonic response of graphene on the nanoscopic level.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 4.808
Times cited: 2
DOI: 10.1103/PHYSREVAPPLIED.16.054030
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“Synthesis and characterization of heteroleptic rare earth double-decker complexes involving tetradiazepinoporphyrazine and phthalocyanine macrocycles”. Tarakanova EN, Tarakanov PA, Simakov AO, Furuyama T, Kobayashi N, Konev DV, Goncharova OA, Trashin SA, De Wael K, Sulimenkov IV, Filatov VV, Kozlovskiy VI, Tomilova LG, Stuzhin PA, Pushkarev VE, Dalton Transactions 50, 6245 (2021). http://doi.org/10.1039/D1DT00088H
Abstract: Reaction of (2,3,9,10,16,17,23,24-octabutylphthalocyaninato)lanthanide(iii) acetylacetonates ((Bu)PcLn(acac), 1a-c, Ln = Lu (a), Eu (b), La (c)) with a tetrakis(5,7-bis(4-tert-butylphenyl)-6H-1,4-diazepino)[2,3-b,g,l,q]porphyrazine ligand ((tBuPh)DzPzH(2), 2) produced sandwich compounds ((tBuPh)DzPz)Ln(Pc-Bu) (3a-c), which represent the first heteroleptic double-deckers incorporating both Pc and DzPz decks. A combination of high-resolution mass spectrometry, UV-Vis/NIR, MCD, and H-1 NMR spectroscopy, and square-wave voltammetry provided unambiguous characterization of target complexes 3 indicating that their spectral and electrochemical properties are generally intermediate with respect to their homoleptic relatives. Based on the data of solution-state H-1-H-1 NMR (COSY, NOESY) correlation spectroscopy supported by DFT calculations, a dimerization tendency of compounds 3 proportional to the Ln(iii) ion size was found. The spectroelectrochemical study of 3 and the corresponding homoleptic double-deckers revealed a pronounced tendency to aggregation of the one-electron oxidized forms of DzPz-containing double-decker complexes compared to homoleptic Pc(2)Ln compounds.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 4.029
DOI: 10.1039/D1DT00088H
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“Inventory and assessment of geosites for geotourism development in the eastern and southeastern Lake Tana Region, Ethiopia”. Tessema GA, van der Borg J, Minale AS, Van Rompaey A, Adgo E, Nyssen J, Asrese K, Van Passel S, Poesen J, Geoheritage 13, 43 (2021). http://doi.org/10.1007/S12371-021-00560-0
Abstract: Geotourism is a niche form of sustainable tourism that focuses on the geological and geomorphological features of an area, and the associated culture and biodiversity. Geosites are important resources for geotourism development. The eastern and southeastern Lake Tana region in Ethiopia has several geosites with a potential for geotourism development. Despite the diversity of potential geosites and the strategic location of the area in the Northern Tourist Circuit of Ethiopia, only a few attractions such as Lake Tana and the Blue Nile Falls are currently being visited. The objective of this paper is twofold: to inventory geosites in the eastern and southeastern Lake Tana region and assess their potential for geotourism development; and to propose a geosite inventory and assessment methodology for geotourism purposes with adaptations from previous studies. Several studies were reviewed and finally nine of them used as the main references to prepare the criteria, indicators, and sub-indicators for this study. The indicators used for assessing the potential of geosites relate to scientific, educational, scenic, recreational, protection, functional, and ecological values. This research presents the first inventory of geosites in the Lake Tana basin. A first list of 120 geosites has been inventoried. Further screening and clustering resulted in 61 geosites, of which 17 are viewpoints. Among the major geosites are waterfalls, a lake with islands and island monasteries, a flood plain, caves and cave churches, lava tubes, a mountain (shield volcano), volcanic plugs, volcanic cones, rock-hewn churches, and viewpoints. Quantitative assessment of the geotouristic potential of these geosites revealed that clustered (complex area) geosites received higher scientific, scenic, and recreational value scores.
Keywords: A1 Journal article; Engineering Management (ENM)
Impact Factor: 1.472
DOI: 10.1007/S12371-021-00560-0
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“Towards developing a screening strategy for ecstasy : revealing the electrochemical profile”. Thiruvottriyur Shanmugam S, Van Echelpoel R, Boeye G, Eliaerts J, Samanipour M, Ching HYV, Florea A, Van Doorslaer S, Van Durme F, Samyn N, Parrilla M, De Wael K, Chemelectrochem 8, 4826 (2021). http://doi.org/10.1002/CELC.202101198
Abstract: This article describes the development of an electrochemical screening strategy for 3,4-methylenedioxymethamphetamine (MDMA), the regular psychoactive compound in ecstasy (XTC) pills. We have investigated the specific electrochemical profile of MDMA and its electro-oxidation mechanisms at disposable graphite screen-printed electrodes. We have proved that the formation of a radical cation and subsequent reactions are indeed responsible for the electrode surface passivation, as evidenced by using electron paramagnetic resonance spectroscopy and electrochemistry. Thereafter, pure cutting agents and MDMA as well as simulated binary mixtures of compounds with MDMA were subjected to square wave voltammetry at pH 7 to understand the characteristic electrochemical profile. An additional measurement at pH 12 was able to resolve false positives and negatives occurring at pH 7. Finally, validation of the screening strategy was done by measuring a set of ecstasy street samples. Overall, our proposed electrochemical screening strategy has been demonstrated for the rapid, sensitive, and selective detection of MDMA, resolving most of the false positives and negatives given by the traditional Marquis color tests, thus exhibiting remarkable promises for the on-site screening of MDMA.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Organic synthesis (ORSY); Applied Electrochemistry & Catalysis (ELCAT); Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab)
Impact Factor: 4.136
DOI: 10.1002/CELC.202101198
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“The environmental impact of household's water use: A case study in Flanders assessing various water sources, production methods and consumption patterns”. Thomassen G, Huysveld S, Boone L, Vilain C, Geysen D, Huysman K, Cools B, Dewulf J, Science Of The Total Environment 770, 145398 (2021). http://doi.org/10.1016/j.scitotenv.2021.145398
Abstract: Responsible water use and sustainable consumption and production are high on the agenda of multiple stakeholders. Different water supply sources are available, including tap water, bottled water, domestically harvested rainwater and domestically abstracted groundwater. The extent to which each of these water supply sources is used, differs over consumption patterns in various housing types, being detached houses, semi-detached houses, terraced houses and apartments. To identify the environmental impact of a household's water use and potential environmental impact reduction strategies, a holistic assessment is required. In this paper, the environmental impact of a household's water use in Flanders (Belgium) was assessed including four different water supply sources and four different consumption patterns by means of a life cycle assessment. The outcomes of this study reveal a large difference between the environmental impact of bottled water use, having a global warming impact of 259 kg CO2-eq.·m−3, compared to the other three supply sources. Tap water supply had the lowest global warming impact (0.17 kg CO2-eq.·m−3) and resource footprint (6.51 MJex·m−3) of all water supply sources. The most efficient strategy to reduce the environmental impact of household's water use is to shift the water consumption from bottled to tap water consumption. This would induce a reduction in global warming impact of the water use of an inhabitant in Flanders by on average 80%, saving 0.1 kg CO2-eq.·day−1 in case of groundwater-based tap water. These results provide insights into sustainable water use for multiple consumption patterns and can be used to better frame the environmental benefits of tap water use.
Keywords: A1 Journal Article; Engineering Management (ENM) ;
Impact Factor: 4.9
DOI: 10.1016/j.scitotenv.2021.145398
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“Critical behavior of the ferromagnets CrI₃, CrBr₃, and CrGeTe₃, and the antiferromagnet FeCl₂, : a detailed first-principles study”. Tiwari S, Van de Put ML, Sorée B, Vandenberghe WG, Physical Review B 103, 014432 (2021). http://doi.org/10.1103/PHYSREVB.103.014432
Abstract: We calculate the Curie temperature of layered ferromagnets, chromium tri-iodide (CrI3), chromium tri-bromide (CrBr3), chromium germanium tri-telluride (CrGeTe3), and the Ned temperature of a layered antiferromagnet iron di-chloride (FeCl2), using first-principles density functional theory calculations and Monte Carlo simulations. We develop a computational method to model the magnetic interactions in layered magnetic materials and calculate their critical temperature. We provide a unified method to obtain the magnetic exchange parameters (J) for an effective Heisenberg Hamiltonian from first principles, taking into account both the magnetic ansiotropy as well as the out-of-plane interactions. We obtain the magnetic phase change behavior, in particular the critical temperature, from the susceptibility and the specific-heat, calculated using the three-dimensional Monte Carlo (METROPOLIS) algorithm. The calculated Curie temperatures for ferromagnetic materials (CrI3, CrBr3, and CrGeTe3), match well with experimental values. We show that the interlayer interaction in bulk CrI3 with R (3) over bar stacking is significantly stronger than the C2/m stacking, in line with experimental observations. We show that the strong interlayer interaction in R (3) over bar CrI3 results in a competition between the in-plane and the out-of-plane magnetic easy axes. Finally, we calculate the Ned temperature of FeCl2 to be 47 +/- 8 K and show that the magnetic phase transition in FeCl2 occurs in two steps with a high-temperature intralayer ferromagnetic phase transition and a low-temperature interlayer antiferromagnetic phase transition.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 3.836
DOI: 10.1103/PHYSREVB.103.014432
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“Magnetic order and critical temperature of substitutionally doped transition metal dichalcogenide monolayers”. Tiwari S, Van de Put ML, Sorée B, Vandenberghe WG, npj 2D Materials and Applications 5, 54 (2021). http://doi.org/10.1038/S41699-021-00233-0
Abstract: Using first-principles calculations, we investigate the magnetic order in two-dimensional (2D) transition-metal-dichalcogenide (TMD) monolayers: MoS2, MoSe2, MoTe2, WSe2, and WS2 substitutionally doped with period four transition-metals (Ti, V, Cr, Mn, Fe, Co, Ni). We uncover five distinct magnetically ordered states among the 35 distinct TMD-dopant pairs: the non-magnetic (NM), the ferromagnetic with out-of-plane spin polarization (Z FM), the out-of-plane polarized clustered FMs (clustered Z FM), the in-plane polarized FMs (X-Y FM), and the anti-ferromagnetic (AFM) state. Ni and Ti dopants result in an NM state for all considered TMDs, while Cr dopants result in an anti-ferromagnetically ordered state for all the TMDs. Most remarkably, we find that Fe, Mn, Co, and V result in an FM ordered state for all the TMDs, except for MoTe2. Finally, we show that V-doped MoSe2 and WSe2, and Mn-doped MoS2, are the most suitable candidates for realizing a room-temperature FM at a 16-18% atomic substitution.
Keywords: A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT)
DOI: 10.1038/S41699-021-00233-0
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“Ab initio modeling of few-layer dilute magnetic semiconductors”. Tiwari S, Van de Put ML, Sorée B, Vandenberghe WG, International Conference on Simulation of Semiconductor Processes and Devices : [proceedings]
T2 –, International Conference on Simulation of Semiconductor Processes and, Devices (SISPAD), SEP 27-29, 2021, Dallas, TX , 141 (2021). http://doi.org/10.1109/SISPAD54002.2021.9592535
Abstract: We present a computational model to model the magnetic structure of two-dimensional (2D) dilute-magnetic-semiconductors (DMS) both the monolayers and multilayers using first-principles density functional theory (DFT), as well as their magnetic phase transition as a function of temperature using Monte-Carlo simulations. Using our method, we model the magnetic structure of bulk, bilayer, and monolayer MoS2 substitutionally doped with Fe atoms. We find that the out-of-plane interaction in bilayer MoS2 is weakly ferromagnetic, whereas in bulk MoS2 it is strongly anti-ferromagnetic. Finally, we show that the magnetic order is more robust in bilayer Fe-doped MoS2 compared to the monolayer and results in a room-temperature FM at an atomic substitution of 14-16%.
Keywords: P1 Proceeding; Engineering sciences. Technology; Condensed Matter Theory (CMT)
DOI: 10.1109/SISPAD54002.2021.9592535
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“Computing Curie temperature of two-dimensional ferromagnets in the presence of exchange anisotropy”. Tiwari S, Vanherck J, Van de Put ML, Vandenberghe WG, Sorée B, Physical review research 3, 043024 (2021). http://doi.org/10.1103/PHYSREVRESEARCH.3.043024
Abstract: We compare three first-principles methods of calculating the Curie temperature in two-dimensional (2D) ferromagnetic materials (FM), modeled using the Heisenberg model, and propose a simple formula for estimating the Curie temperature with high accuracy that works for all common 2D lattice types. First, we study the effect of exchange anisotropy on the Curie temperature calculated using the Monte Carlo (MC), the Green's function, and the renormalized spin-wave (RNSW) methods. We find that the Green's function method overestimates the Curie temperature in high-anisotropy regimes compared to the MC method, whereas the RNSW method underestimates the Curie temperature compared to the MC and the Green's function methods. Next, we propose a closed-form formula for calculating the Curie temperature of 2D FMs, which provides an estimate of the Curie temperature that is greatly improved over the mean-field expression for magnetic material screening. We apply the closed-form formula to predict the Curie temperature 2D magnets screened from the C2DB database and discover several high Curie temperature FMs, with Fe2F2 and MoI2 emerging as the most promising 2D ferromagnets. Finally, by comparing to experimental results for CrI3, CrCl3, and CrBr3, we conclude that for small effective anisotropies, the Green's-function-based equations are preferable, while for larger anisotropies, MC-based results are more predictive.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
DOI: 10.1103/PHYSREVRESEARCH.3.043024
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“Nanobody-based immunosensor detection enhanced by photocatalytic-electrochemical redox cycling”. Trashin S, Morales-Yánez F, Thiruvottriyur Shanmugam S, Paredis L, Carrión EN, Sariego I, Muyldermans S, Polman K, Gorun SM, De Wael K, Analytical Chemistry 93, 13606 (2021). http://doi.org/10.1021/ACS.ANALCHEM.1C02876
Abstract: Detection of antigenic biomarkers present in trace amounts is of crucial importance for medical diagnosis. A parasitic disease, human toxocariasis, lacks an adequate diagnostic method despite its worldwide occurrence. The currently used serology tests may stay positive even years after a possibly unnoticed infection, whereas the direct detection of a re-infection or a still active infection remains a diagnostic challenge due to the low concentration of circulating parasitic antigens. We report a time-efficient sandwich immunosensor using small recombinant single-domain antibodies (nanobodies) derived from camelid heavy-chain antibodies specific to Toxocara canis antigens. An enhanced sensitivity to pg/mL levels is achieved by using a redox cycle consisting of a photocatalytic oxidation and electrochemical reduction steps. The photocatalytic oxidation is achieved by a photosensitizer generating singlet oxygen (1O2) that, in turn, readily reacts with p-nitrophenol enzymatically produced under alkaline conditions. The photooxidation produces benzoquinone that is electrochemically reduced to hydroquinone, generating an amperometric response. The light-driven process could be easily separated from the background, thus making amperometric detection more reliable. The proposed method for detection of the toxocariasis antigen marker shows superior performances compared to other detection schemes with the same nanobodies and outperforms by at least two orders of magnitude the assays based on regular antibodies, thus suggesting new opportunities for electrochemical immunoassays of challenging low levels of antigens.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab)
Impact Factor: 6.32
DOI: 10.1021/ACS.ANALCHEM.1C02876
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“Optimal timing of multiple investment decisions in a wood value chain : a real options approach”. Tschulkow M, Compernolle T, Van Passel S, Journal Of Environmental Management 290, 112590 (2021). http://doi.org/10.1016/J.JENVMAN.2021.112590
Abstract: A new reductive catalytic fractionation biorefinery process (RCF) is currently being developed transforming wood into high-value end-products. RCF is considered to be in the pilot stage with a technology readiness level of 5–6. Apart from the RCF-process characteristics, the economic feasibility also depends on the investment decisions that are made upstream and downstream within the wood value chain, increasing the level of uncertainty. Two investment options within the value chain are considered: an option to invest in harvesting equipment and an option to invest in the RCF. To understand the impact of multiple sources of uncertainty on the decision to invest in an innovative RCF-driven wood value chain, an analytical two-factor real options model is presented, accounting for correlated cost and price uncertainties. Two different scenarios, separated and united investments in harvesting equipment and RCF, are analyzed. In both scenarios, market uncertainty postpones investment in comparison to the traditional NPV approach. When both investments are considered separately, the investment in RCF is expected to be earlier than the investment in harvesting equipment. When both investment decisions are united, the probability of investment increases. The study reveals that RCF has the potential to stimulate investments from different investors, –upstream and midstream–, within the wood value chain. Besides, the introduced real options model proofs its ability to assess the economic feasibility of innovative technologies (e.g RCF) individually or within the value chain, taking into account multiple sources of uncertainty.
Keywords: A1 Journal article; Economics; Engineering Management (ENM)
Impact Factor: 4.01
DOI: 10.1016/J.JENVMAN.2021.112590
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