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Author |
Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R. |
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Title |
Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Journal Of Chemical Information And Modeling |
Abbreviated Journal |
J Chem Inf Model |
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Volume |
62 |
Issue |
1 |
Pages |
129-141 |
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Keywords |
A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. |
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Wos |
000740019000001 |
Publication Date |
2022-01-10 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1549-9596 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.6 |
Times cited |
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Open Access |
Not_Open_Access |
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Notes |
Fonds Wetenschappelijk Onderzoek, 1200219N ; Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. |
Approved |
Most recent IF: 5.6 |
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Call Number |
PLASMANT @ plasmant @c:irua:185485 |
Serial |
7050 |
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Author |
Neven, L.; Thiruvottriyur Shanmugam, S.; Rahemi, V.; Trashin, S.; Sleegers, N.; Carrion, E.N.; Gorun, S.M.; De Wael, K. |
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Title |
Optimized photoelectrochemical detection of essential drugs bearing phenolic groups |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Analytical chemistry |
Abbreviated Journal |
Anal Chem |
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Volume |
91 |
Issue |
15 |
Pages |
9962-9969 |
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Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
The World Health Organization (WHO) model “List of Essential Medicines” includes among indispensable medicines antibacterials and pain and migraine relievers. Monitoring their concentration in the environment, while challenging, is important in the context of antibiotic resistance as well as their production of highly toxic compounds via hydrolysis. Traditional detection methods such as high-performance liquid chromatography (HPLC) or LC combined with tandem mass spectrometry or UV-vis spectroscopy are time-consuming, have a high cost, require skilled operators and are difficult to adapt for field operations. In contrast, (electrochemical) sensors have elicited interest because of their rapid response, high selectivity, and sensitivity as well as potential for on-site detection. Previously, we reported a novel sensor system based on a type II photosensitizer, which combines the advantages of enzymatic sensors (high sensitivity) and photoelectrochemical sensors (easy baseline subtraction). Under red-light illumination, the photosensitizer produces singlet oxygen which oxidizes phenolic compounds present in the sample. The subsequent reduction of the oxidized phenolic compounds at the electrode surface gives rise to a quantifiable photocurrent and leads to the generation of a redox cycle. Herein we report the optimization in terms of pH and applied potential of the photoelectrochemical detection of the hydrolysis product of paracetamol, i.e., 4-aminophenol (4-AP), and two antibacterials, namely, cefadroxil (CFD, beta-lactam antibiotic) and doxycycline (DXC, tetracycline antibiotic). The optimized conditions resulted in a detection limit of 0.2 mu mol L-1 for DXC, but in a 10 times higher sensitivity, 20 nmol L-1, for CFD. An even higher sensitivity, 7 nmol L-1, was noted for 4-AP. |
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Wos |
000480499200086 |
Publication Date |
2019-06-25 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0003-2700; 5206-882x |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
6.32 |
Times cited |
2 |
Open Access |
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Notes |
; FWO and UA-BOF are acknowledged for financial support. The Center for Functional Materials of Seton Hall University is thanked for support (S.M.G. and E.N.C.). Joren Van Loon is thanked for the graphical abstract. This research was supported by the medium scale research infrastructure funding Hercules funding (SEM). ; |
Approved |
Most recent IF: 6.32 |
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Call Number |
UA @ admin @ c:irua:161831 |
Serial |
5763 |
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Author |
De wael, A.; De Backer, A.; Yu, C.-P.; Sentürk, D.G.; Lobato, I.; Faes, C.; Van Aert, S. |
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Title |
Three Approaches for Representing the Statistical Uncertainty on Atom-Counting Results in Quantitative ADF STEM |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
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Issue |
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Pages |
1-9 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
A decade ago, a statistics-based method was introduced to count the number of atoms from annular dark-field scanning transmission electron microscopy (ADF STEM) images. In the past years, this method was successfully applied to nanocrystals of arbitrary shape, size, and composition (and its high accuracy and precision has been demonstrated). However, the counting results obtained from this statistical framework are so far presented without a visualization of the actual uncertainty about this estimate. In this paper, we present three approaches that can be used to represent counting results together with their statistical error, and discuss which approach is most suited for further use based on simulations and an experimental ADF STEM image. |
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Wos |
000854930500001 |
Publication Date |
2022-09-19 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276 |
ISBN |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
2.8 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N, G.0267.18N, and EOS 30489208. S.V.A. acknowledges TOP BOF funding from the University of Antwerp. The authors are grateful to L.M. Liz-Marzán (CIC biomaGUNE and Ikerbasque) for providing the samples. esteem3reported; esteem3jra |
Approved |
Most recent IF: 2.8 |
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Call Number |
EMAT @ emat @c:irua:190585 |
Serial |
7119 |
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Author |
Vega Ibañez, F.; Béché, A.; Verbeeck, J. |
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Title |
Can a programmable phase plate serve as an aberration corrector in the transmission electron microscope (TEM)? |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
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Issue |
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Pages |
Pii S1431927622012260-10 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
Current progress in programmable electrostatic phase plates raises questions about their usefulness for specific applications. Here, we explore different designs for such phase plates with the specific goal of correcting spherical aberration in the transmission electron microscope (TEM). We numerically investigate whether a phase plate could provide down to 1 angstrom ngstrom spatial resolution on a conventional uncorrected TEM. Different design aspects (fill factor, pixel pattern, symmetry) were evaluated to understand their effect on the electron probe size and current density. Some proposed designs show a probe size () down to 0.66 angstrom, proving that it should be possible to correct spherical aberration well past the 1 angstrom limit using a programmable phase plate consisting of an array of electrostatic phase-shifting elements. |
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Wos |
000849975400001 |
Publication Date |
2022-09-21 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.8 |
Times cited |
3 |
Open Access |
OpenAccess |
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Notes |
All authors acknowledge funding from the Flemish Research Fund under contract G042820N “Exploring adaptive optics in transmission electron microscopy”. J.V. acknowledges funding from the European Union’s Horizon 2020 Research Infrastructure – Integrating Activities for Advanced Communities under grant agreement No 823717 – ESTEEM3 and from the University of Antwerp through a TOP BOF project.; esteem3reported; esteem3jra |
Approved |
Most recent IF: 2.8 |
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Call Number |
UA @ admin @ c:irua:190627 |
Serial |
7134 |
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Author |
Yu, C.-P.; Friedrich, T.; Jannis, D.; Van Aert, S.; Verbeeck, J. |
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Title |
Real-Time Integration Center of Mass (riCOM) Reconstruction for 4D STEM |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
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Issue |
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Pages |
1-12 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
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Abstract |
A real-time image reconstruction method for scanning transmission electron microscopy (STEM) is proposed. With an algorithm requiring only the center of mass of the diffraction pattern at one probe position at a time, it is able to update the resulting image each time a new probe position is visited without storing any intermediate diffraction patterns. The results show clear features at high spatial frequency, such as atomic column positions. It is also demonstrated that some common post-processing methods, such as band-pass filtering, can be directly integrated in the real-time processing flow. Compared with other reconstruction methods, the proposed method produces high-quality reconstructions with good noise robustness at extremely low memory and computational requirements. An efficient, interactive open source implementation of the concept is further presented, which is compatible with frame-based, as well as event-based camera/file types. This method provides the attractive feature of immediate feedback that microscope operators have become used to, for example, conventional high-angle annular dark field STEM imaging, allowing for rapid decision-making and fine-tuning to obtain the best possible images for beam-sensitive samples at the lowest possible dose. |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Language |
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Wos |
000792176100001 |
Publication Date |
2022-04-25 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.8 |
Times cited |
7 |
Open Access |
OpenAccess |
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Notes |
Bijzonder Onderzoeksfonds UGent; H2020 European Research Council, 770887 ; H2020 European Research Council, 823717 ; H2020 European Research Council, ESTEEM3 / 823717 ; H2020 European Research Council, PICOMETRICS / 770887 ; Fonds Wetenschappelijk Onderzoek, 30489208 ; Herculesstichting; esteem3reported; esteem3jra |
Approved |
Most recent IF: 2.8 |
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Call Number |
EMAT @ emat @c:irua:188538 |
Serial |
7068 |
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Author |
Ning, S.; Xu, W.; Ma, Y.; Loh, L.; Pennycook, T.J.; Zhou, W.; Zhang, F.; Bosman, M.; Pennycook, S.J.; He, Q.; Loh, N.D. |
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Title |
Accurate and Robust Calibration of the Uniform Affine Transformation Between Scan-Camera Coordinates for Atom-Resolved In-Focus 4D-STEM Datasets |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
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Issue |
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Pages |
1-11 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
Accurate geometrical calibration between the scan coordinates and the camera coordinates is critical in four-dimensional scanning transmission electron microscopy (4D-STEM) for both quantitative imaging and ptychographic reconstructions. For atomic-resolved, in-focus 4D-STEM datasets, we propose a hybrid method incorporating two sub-routines, namely a J-matrix method and a Fourier method, which can calibrate the uniform affine transformation between the scan-camera coordinates using raw data, without a priori knowledge about the crystal structure of the specimen. The hybrid method is found robust against scan distortions and residual probe aberrations. It is also effective even when defects are present in the specimen, or the specimen becomes relatively thick. We will demonstrate that a successful geometrical calibration with the hybrid method will lead to a more reliable recovery of both the specimen and the electron probe in a ptychographic reconstruction. We will also show that, although the elimination of local scan position errors still requires an iterative approach, the rate of convergence can be improved, and the residual errors can be further reduced if the hybrid method can be firstly applied for initial calibration. The code is made available as a simple-to-use tool to correct affine transformations of the scan-camera coordinates in 4D-STEM experiments. |
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Corporate Author |
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Publisher |
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Place of Publication |
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Wos |
000767045700001 |
Publication Date |
2022-03-09 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.8 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
N. D. Loh kindly acknowledges support from NUS Early Career Research Award (R-154-000-B35-133), MOE’s AcRF Tier 1 grant nr. R-284-000-172-114 and NRF CRP grant number NRF-CRP16-2015-05. Q. He would also like to acknowledge the support of the National Research Foundation (NRF) Singapore, under its NRF Fellowship (NRF-NRFF11-2019-0002). W. Zhou acknowledges the support from Beijing Outstanding Young Scientist Program (BJJWZYJH01201914430039). F. Zhang acknowledges the support of the National Natural Science Foundation of China (11775105, 12074167). T. J. Pennycook acknowledges funding under the European Union’s Horizon 2020 research and innovation programme from the European Research Council (ERC) Grant agreement No. 802123-HDEM. |
Approved |
Most recent IF: 2.8 |
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Call Number |
EMAT @ emat @c:irua:186958 |
Serial |
6957 |
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Author |
Esteban, D.A.; Vanrompay, H.; Skorikov, A.; Béché, A.; Verbeeck, J.; Freitag, B.; Bals, S. |
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Title |
Fast electron low dose tomography for beam sensitive materials |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Microscopy And Microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
27 |
Issue |
S1 |
Pages |
2116-2118 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
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Place of Publication |
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Wos |
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Publication Date |
2021-07-30 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276 |
ISBN |
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Additional Links |
UA library record |
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Impact Factor |
1.891 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 1.891 |
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Call Number |
EMAT @ emat @c:irua:183278 |
Serial |
6813 |
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Author |
MacArthur, K.E.; Yankovich, A.B.; Béché, A.; Luysberg, M.; Brown, H.G.; Findlay, S.D.; Heggen, M.; Allen, L.J. |
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Title |
Optimizing Experimental Conditions for Accurate Quantitative Energy-Dispersive X-ray Analysis of Interfaces at the Atomic Scale |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Microscopy And Microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
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Issue |
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Pages |
1-15 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
The invention of silicon drift detectors has resulted in an unprecedented improvement in detection efficiency for energy-dispersive X-ray (EDX) spectroscopy in the scanning transmission electron microscope. The result is numerous beautiful atomic-scale maps, which provide insights into the internal structure of a variety of materials. However, the task still remains to understand exactly where the X-ray signal comes from and how accurately it can be quantified. Unfortunately, when crystals are aligned with a low-order zone axis parallel to the incident beam direction, as is necessary for atomic-resolution imaging, the electron beam channels. When the beam becomes localized in this way, the relationship between the concentration of a particular element and its spectroscopic X-ray signal is generally nonlinear. Here, we discuss the combined effect of both spatial integration and sample tilt for ameliorating the effects of channeling and improving the accuracy of EDX quantification. Both simulations and experimental results will be presented for a perovskite-based oxide interface. We examine how the scattering and spreading of the electron beam can lead to erroneous interpretation of interface compositions, and what approaches can be made to improve our understanding of the underlying atomic structure. |
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Wos |
000664532400007 |
Publication Date |
2021-04-12 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
1.891 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
The authors would like to thank Jürgen Schubert for helping to supply the sample and valuable discussions on the topic. K. E. MacArthur and M. Heggen acknowledge the Helmholtz Funding agency and the DFG (grant number HE 7192/1-2) for their financial support of this work. L. J. Allen acknowledges the support of the Alexander von Humboldt Foundation. This research was supported under the Discovery Projects funding scheme of the Australian Research Council (Projects DP140102538 and FT190100619). K.E. MacArthur, A.B. Yankovich and A. Béché acknowledge support from the European Union’s Horizon 2020 research innovation program under grant agreement No. 823717 – ESTEEM3. A.B. Yankovich also acknowledges support from the Materials Science Area of Advance at Chalmers and the Swedish Research Council (VR, under grant No: 2020-04986).; esteem3TA; esteem3reported |
Approved |
Most recent IF: 1.891 |
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Call Number |
EMAT @ emat @c:irua:178129 |
Serial |
6760 |
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Author |
Paterson, G.W.; Webster, R.W.H.; Ross, A.; Paton, K.A.; Macgregor, T.A.; McGrouther, D.; MacLaren, I.; Nord, M. |
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Title |
Fast pixelated detectors in scanning transmission electron microscopy. part II : post-acquisition data processing, visualization, and structural characterization |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Microscopy And Microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
26 |
Issue |
5 |
Pages |
944-963 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
Fast pixelated detectors incorporating direct electron detection (DED) technology are increasingly being regarded as universal detectors for scanning transmission electron microscopy (STEM), capable of imaging under multiple modes of operation. However, several issues remain around the post-acquisition processing and visualization of the often very large multidimensional STEM datasets produced by them. We discuss these issues and present open source software libraries to enable efficient processing and visualization of such datasets. Throughout, we provide examples of the analysis methodologies presented, utilizing data from a 256 x 256 pixel Medipix3 hybrid DED detector, with a particular focus on the STEM characterization of the structural properties of materials. These include the techniques of virtual detector imaging; higher-order Laue zone analysis; nanobeam electron diffraction; and scanning precession electron diffraction. In the latter, we demonstrate a nanoscale lattice parameter mapping with a fractional precision <= 6 x 10(-4) (0.06%). |
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Place of Publication |
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Wos |
000576859800011 |
Publication Date |
2020-09-04 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.8 |
Times cited |
3 |
Open Access |
OpenAccess |
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Notes |
; G.W.P. and M.N. were the principal authors of the fpd and pixStem libraries reported herein (details of all contributions are documented in the repositories) and have made all of these available under open source licence GPLv3 for the benefit of the community. R.W.H.W., A.R., and K.A.P. have also made contributions to the source codes in these libraries. G.W.P and M.N. have led the data acquisition and analysis, and the drafting of this manuscript. The performance of this work was mainly supported by Engineering and Physical Sciences Research Council (EPSRC) of the UK via the project “Fast Pixel Detectors: a paradigm shift in STEM imaging” (Grant No. EP/M009963/1). G.W.P. received additional support from the EPSRC under Grant No. EP/M024423/1. M.N. received additional support for this work from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 838001. R.W.H.W., A.R., K.A.P., T.A.M., D.McG., and I.M. have all contributed either through acquisition and analysis of data or through participation in the revision of the manuscript. The studentships of R.W.H.W. and T.A.M. were supported by the EPSRC Doctoral Training Partnership Grant No. EP/N509668/1. I.M. and D.McG. were supported by EPSRC Grant No. EP/M009963/1. The studentship of K.A.P. was funded entirely by the UK Science and Technology Facilities Council (STFC) Industrial CASE studentship “Next2 TEM Detection” (No. ST/ P002471/1) with Quantum Detectors Ltd. as the industrial partner. As an inventor of intellectual property related to the MERLIN detector hardware, D.McG. is a beneficiary of the license agreement between the University of Glasgow and Quantum Detectors Ltd. We thank Diamond Quantum Detectors Ltd. for Medipix3 detector support; Dr. Bruno Humbel from Okinawa Institute of Science and Technology; and Dr. Caroline Kizilyaprak from the University of Lausanne for providing the liver sample; Dr. Ingrid Hallsteinsen and Prof. Thomas Tybell from the Norwegian University of Science and Technology (NTNU) for providing the La0.7Sr0.3MnO3/LaFeO3/SrTiO3 sample shown in Figure 4; and NanoMEGAS for the loan of the DigiSTAR precession system and TopSpin acquisition software. The development of the integration of TopSpin with the Merlin readout of the Medipix3 camera has been performed with the aid of financial assistance from the EPSRC under Grant No. EP/R511705/1 and through direct collaboration between NanoMEGAS and Quantum Detectors Ltd. ; |
Approved |
Most recent IF: 2.8; 2020 IF: 1.891 |
|
| |
Call Number |
UA @ admin @ c:irua:172695 |
Serial |
6519 |
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| Permanent link to this record |
| |
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| |
|
Author |
Nord, M.; Webster, R.W.H.; Paton, K.A.; McVitie, S.; McGrouther, D.; MacLaren, I.; Paterson, G.W. |
|
| |
Title |
Fast pixelated detectors in scanning transmission electron microscopy. Part I: data acquisition, live processing, and storage |
Type |
A1 Journal article |
| |
Year |
2020 |
Publication |
Microscopy And Microanalysis |
Abbreviated Journal |
Microsc Microanal |
|
| |
Volume |
26 |
Issue |
4 |
Pages |
Pii S1431927620001713-666 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
The use of fast pixelated detectors and direct electron detection technology is revolutionizing many aspects of scanning transmission electron microscopy (STEM). The widespread adoption of these new technologies is impeded by the technical challenges associated with them. These include issues related to hardware control, and the acquisition, real-time processing and visualization, and storage of data from such detectors. We discuss these problems and present software solutions for them, with a view to making the benefits of new detectors in the context of STEM more accessible. Throughout, we provide examples of the application of the technologies presented, using data from a Medipix3 direct electron detector. Most of our software are available under an open source licence, permitting transparency of the implemented algorithms, and allowing the community to freely use and further improve upon them. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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| |
Language |
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Wos |
000555537900004 |
Publication Date |
2020-07-06 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
1431-9276 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.8 |
Times cited |
4 |
Open Access |
OpenAccess |
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| |
Notes |
; The performance of this work was mainly supported by the Engineering and Physical Sciences Research Council (EPSRC) of the UK via the project “Fast Pixel Detectors: a paradigm shift in STEM imaging” (grant no. EP/M009963/1). G.W.P. received additional support from the EPSRC under grant no. EP/M024423/1. M.N. received additional support for this work from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 838001. The studentship of R.W.H.W. was supported by the EPSRC Doctoral Training Partnership grant no. EP/N509668/1. S.McV. was supported by EPSRC grant no. EP/M024423/1. I.M. was supported by EPSRC grant no. EP/M009963/1. The studentship of K.A.P. was funded entirely by the UK Science and Technology Facilities Council (STFC) Industrial CASE studentship “Next2 TEM Detection” (no. ST/P002471/1) with Quantum Detectors Ltd. as the industrial partner. D.McG. was also supported by EPSRC grant no. EP/M009963/1. As an inventor of intellectual property related to the MERLIN detector hardware, he is a beneficiary of the license agreement between the University of Glasgow and Quantum Detectors Ltd. The development of the integration of TopSpin with the Merlin readout of the Medipix3 camera has been performed with the aid of financial assistance from the EPSRC under grant no. EP/R511705/1 and through direct collaboration between NanoMEGAS and Quantum Detectors Ltd. ; |
Approved |
Most recent IF: 2.8; 2020 IF: 1.891 |
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| |
Call Number |
UA @ admin @ c:irua:171185 |
Serial |
6518 |
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| Permanent link to this record |
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| |
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Author |
Goris, B.; Freitag, B.; Zanaga, D.; Bladt, E.; Altantzis, T.; Ringnalda, J.; Bals, S. |
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| |
Title |
Towards quantitative EDX results in 3 dimensions |
Type |
A1 Journal article |
| |
Year |
2014 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
|
| |
Volume |
20 |
Issue |
S:3 |
Pages |
766-767 |
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| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Cambridge, Mass. |
Editor |
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Language |
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Wos |
|
Publication Date |
2014-08-27 |
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| |
Series Editor |
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Series Title |
|
Abbreviated Series Title |
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| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
1431-9276;1435-8115; |
ISBN |
|
Additional Links |
UA library record |
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| |
Impact Factor |
1.891 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
335078 Colouratom; Fwo; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); |
Approved |
Most recent IF: 1.891; 2014 IF: 1.877 |
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| |
Call Number |
UA @ lucian @ c:irua:125381 |
Serial |
3687 |
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| Permanent link to this record |
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| |
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Author |
Masenelli-Varlot, K.; Malchere, A.; Ferreira, J.; Heidari Mezerji, H.; Bals, S.; Messaoudi, C.; Garrido, S.M. |
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| |
Title |
Wet-STEM tomography : principles, potentialities and limitations |
Type |
A1 Journal article |
| |
Year |
2014 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
|
| |
Volume |
20 |
Issue |
2 |
Pages |
366-375 |
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| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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| |
Abstract |
The characterization of biological and inorganic materials by determining their three-dimensional structure in conditions closer to their native state is a major challenge of technological research. Environmental scanning electron microscopy (ESEM) provides access to the observation of hydrated samples in water environments. Here, we present a specific device for ESEM in the scanning transmission electron microscopy mode, allowing the acquisition of tilt-series suitable for tomographic reconstructions. The resolution which can be obtained with this device is first determined. Then, we demonstrate the feasibility of tomography on wet materials. The example studied here is hydrophilic mesoporous silica (MCM-41). Finally, the minimum thickness of water which can be detected is calculated from Monte Carlo simulations and compared with the resolution expected in the tomograms. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Cambridge, Mass. |
Editor |
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Language |
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Wos |
000337304700005 |
Publication Date |
2014-02-26 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
|
Edition |
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| |
ISSN |
1431-9276;1435-8115; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
1.891 |
Times cited |
9 |
Open Access |
OpenAccess |
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| |
Notes |
IAP-PAI; European Research Council under the 7th Framework Program (FP7); ERC grant no. 335078-COLOURATOMS.; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); |
Approved |
Most recent IF: 1.891; 2014 IF: 1.877 |
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| |
Call Number |
UA @ lucian @ c:irua:118411 |
Serial |
3915 |
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| Permanent link to this record |
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| |
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Author |
Batenburg, K.J.; Bals, S.; Van Aert, S.; Roelandts, T.; Sijbers, J. |
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| |
Title |
Ultra-high resolution electron tomography for materials science : a roadmap |
Type |
A1 Journal article |
| |
Year |
2011 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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| |
Volume |
17 |
Issue |
S:2 |
Pages |
934-935 |
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| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Cambridge, Mass. |
Editor |
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Language |
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Wos |
|
Publication Date |
2011-10-07 |
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| |
Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
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| |
ISSN |
1431-9276;1435-8115; |
ISBN |
|
Additional Links |
UA library record |
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| |
Impact Factor |
1.891 |
Times cited |
|
Open Access |
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Notes |
|
Approved |
Most recent IF: 1.891; 2011 IF: 3.007 |
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| |
Call Number |
UA @ lucian @ c:irua:96554 |
Serial |
3792 |
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| Permanent link to this record |
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Author |
Verbeeck, J.; Van Aert, S.; Zhang, L.; Haiyan, T.; Schattschneider, P.; Rosenauer, A. |
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Title |
Computational aspects in quantitative EELS |
Type |
A1 Journal article |
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Year |
2010 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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| |
Volume |
16 |
Issue |
S:2 |
Pages |
240-241 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Cambridge, Mass. |
Editor |
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Language |
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Wos |
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Publication Date |
2010-08-26 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276;1435-8115; |
ISBN |
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Additional Links |
UA library record |
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Impact Factor |
1.891 |
Times cited |
|
Open Access |
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Notes |
|
Approved |
Most recent IF: 1.891; 2010 IF: 3.259 |
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| |
Call Number |
UA @ lucian @ c:irua:96556UA @ admin @ c:irua:96556 |
Serial |
454 |
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| Permanent link to this record |
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| |
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Author |
Van Aert, S.; Verbeeck, J.; Bals, S.; Erni, R.; van Dyck, D.; Van Tendeloo, G. |
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| |
Title |
Atomic resolution mapping using quantitative high-angle annular dark field scanning transmission electron microscopy |
Type |
A1 Journal article |
| |
Year |
2009 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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| |
Volume |
15 |
Issue |
S:2 |
Pages |
464-465 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Cambridge, Mass. |
Editor |
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Language |
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Wos |
000208119100230 |
Publication Date |
2009-07-27 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276;1435-8115; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
1.891 |
Times cited |
1 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 1.891; 2009 IF: 3.035 |
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| |
Call Number |
UA @ lucian @ c:irua:96555UA @ admin @ c:irua:96555 |
Serial |
178 |
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| Permanent link to this record |
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Author |
Tian, H.; Schryvers, D.; Shabalovskaya, S.; van Humbeeck, J. |
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Title |
Microstructure of surface and subsurface layers of a Ni-Ti shape memory microwire |
Type |
A1 Journal article |
| |
Year |
2009 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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| |
Volume |
15 |
Issue |
|
Pages |
62-70 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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| |
Abstract |
The microstructure of a 55 Êm diameter, cold-worked Ni-Ti microwire is investigated by different transmission electron microscopy techniques. The surface consists of a few hundred nanometer thick oxide layer composed of TiO and TiO2 with a small fraction of inhomogeneously distributed Ni. The interior of the wire has a core-shell structure with primarily B2 grains in the 1 Êm thick shell, and heavily twinned B19 martensite in the core. This core-shell structure can be explained by a concentration gradient of the alloying elements resulting in a structure separation due to the strong temperature dependence of the martensitic start temperature. Moreover, in between the B2 part of the metallic core-shell and the oxide layer, a Ni3Ti interfacial layer is detected. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Cambridge, Mass. |
Editor |
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Language |
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Wos |
000262912700009 |
Publication Date |
2009-01-15 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276;1435-8115; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
1.891 |
Times cited |
15 |
Open Access |
|
|
| |
Notes |
FWO G.0465.05; Multimat |
Approved |
Most recent IF: 1.891; 2009 IF: 3.035 |
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| |
Call Number |
UA @ lucian @ c:irua:72319 |
Serial |
2074 |
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| Permanent link to this record |
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Author |
Pennycook, T.J.; Martinez, G.T.; O'Leary, C.M.; Yang, H.; Nellist, P.D. |
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Title |
Efficient Phase Contrast Imaging via Electron Ptychography, a Tutorial |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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| |
Volume |
25 |
Issue |
S2 |
Pages |
2684-2685 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
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Publication Date |
2019-08-06 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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| |
ISSN |
1431-9276 |
ISBN |
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Additional Links |
UA library record |
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| |
Impact Factor |
|
Times cited |
|
Open Access |
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| |
Notes |
|
Approved |
no |
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Call Number |
EMAT @ emat @c:irua:172444 |
Serial |
6424 |
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| Permanent link to this record |
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Author |
Tafuri, F.; Granozio, F.M.; Carillo, F.; Lombardi, F.; Di Uccio, U.S.; Verbist, K.; Lebedev, O.; Van Tendeloo, G. |
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Title |
Josephson phenomenology and microstructure of YBaCuO artificial grain boundaries characterized by misalignment of the c-axes |
Type |
A1 Journal article |
| |
Year |
1999 |
Publication |
Physica: C : superconductivity |
Abbreviated Journal |
Physica C |
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| |
Volume |
327 |
Issue |
|
Pages |
63-71 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
YBa(2)Cu(3)O(7-delta) (YBCO) grain boundaries characterized by a misalignment of the c-axes (45 degrees c-axis tilt or 45 degrees c-axis twist) have been obtained by employing a recently implemented biepitaxial technique. Junctions based on these grain boundaries exhibit good Josephson properties useful for applications. High values of the I(C)R(N) product and a Fraunhofer-like dependence of the critical current on the magnetic field, differently from traditional biepitaxial junctions, have been obtained. The correlation between transport properties and microstructure has been investigated by Transmission Electron Microscopy (TEM), which was also performed on previously measured junctions. The presence of atomically clean basal plane (BP) faced tilt boundaries, among other types of interfaces, has been shown. The possibility of selecting these kinds of boundaries by controlling film growth, and their possible advantages in terms of reproducibility and uniformity of the junction properties an discussed. The possibility of employing these junctions to explore the symmetry of the order parameter is also discussed. (C) 1999 Elsevier Science B.V. All rights reserved. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000084325700008 |
Publication Date |
2002-07-25 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
|
| |
ISSN |
0921-4534; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
1.404 |
Times cited |
7 |
Open Access |
|
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| |
Notes |
|
Approved |
Most recent IF: 1.404; 1999 IF: 1.114 |
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| |
Call Number |
UA @ lucian @ c:irua:95180 |
Serial |
1752 |
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| Permanent link to this record |
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Author |
Yu, R.; Zeng, W.; Zhou, L.; Van Tendeloo, G.; Mai, L.; Yao, Z.; Wu, J. |
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| |
Title |
Layer-by-layer delithiation during lattice collapse as the origin of planar gliding and microcracking in Ni-rich cathodes |
Type |
A1 Journal article |
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Year |
2023 |
Publication |
Cell reports physical science |
Abbreviated Journal |
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Volume |
4 |
Issue |
7 |
Pages |
101480-14 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
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Abstract |
High-energy-density nickel (Ni)-rich cathode materials are used in commercial lithium (Li)-ion batteries for electric vehicles, but they suffer from severe structural degradation upon cycling. Planar gliding and microcracking are seeds for fatal mechanical fracture, but their origin remains unclear. Herein, we show that “layer-by -layer delithiation”is activated at high voltages during the charge process when the “lattice collapse”(a characteristic high-voltage lattice evolution in Ni-rich cathodes) occurs. Layer-by-layer deli-thiation is evidenced by direct observation of the consecutive lattice collapse using in situ scanning transmission electron micro-scopy (STEM). The collapsing of the lattice initiates in the expanded planes and consecutively extends to the whole crystal. Localized strain will be induced at lattice-collapsing interface where planar gliding and intragranular microcracks are generated to release this strain. Our study reveals that layer-by-layer delithia-tion during lattice collapse is the fundamental origin of the mechanical instability in single-crystalline Ni-rich cathodes. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
001048074500001 |
Publication Date |
2023-06-30 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
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ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
|
Times cited |
|
Open Access |
OpenAccess |
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| |
Notes |
|
Approved |
Most recent IF: NA |
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| |
Call Number |
UA @ admin @ c:irua:198299 |
Serial |
8893 |
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| Permanent link to this record |
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Author |
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. |
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Title |
Photochemical production of hydrogen peroxide by digging pro-superoxide radical carbon vacancies in carbon nitride |
Type |
A1 Journal article |
| |
Year |
2022 |
Publication |
Cell reports physical science |
Abbreviated Journal |
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| |
Volume |
3 |
Issue |
5 |
Pages |
100874-17 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
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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. |
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Wos |
000805830100006 |
Publication Date |
2022-04-28 |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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ISSN |
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ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
12 |
Open Access |
OpenAccess |
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Notes |
Y.D. thanks the China Scholarship Council (201808310127) for financial support. This work is financially supported by the National Natural Science Foundation of China (U1663225) , Program for Changjiang Scholars and Innovative Research Team in University (IRT_15R52) of the Chinese Ministry of Education, Program of Introducing Talents of Discipline to Universities-Plan 111 (grant no. B20002) from the Ministry of Science and Technology and the Ministry of Education of China, and the National Key R&D Program of China (2016YFA0202602) . This research was also supported by the European Commission Interreg V France-Wallonie-Vlaanderen project “DepollutAir”. |
Approved |
Most recent IF: NA |
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| |
Call Number |
UA @ admin @ c:irua:189706 |
Serial |
7090 |
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| Permanent link to this record |
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Author |
Sun, C.; Liao, X.; Peng, H.; Zhang, C.; Van Tendeloo, G.; Zhao, Y.; Wu, J. |
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Title |
Interfacial gliding-driven lattice oxygen release in layered cathodes |
Type |
A1 Journal article |
| |
Year |
2022 |
Publication |
Cell reports physical science |
Abbreviated Journal |
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| |
Volume |
3 |
Issue |
1 |
Pages |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
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Abstract |
The oxygen release of layered cathodes causes many battery failures, but the underlying mechanism in an actual working cathode is still elusive as it involves secondary agglomerates that introduce complicated boundary structures. Here, we report a general structure instability on the mismatch boundaries driven by interfacial gliding-it introduces a shear stress causing a distortion of the metal-oxygen octahedra framework that reduces its kinetic stability. The migration of cations and diffusion of oxygen vacancies continue to degrade the whole particle from the boundary to the interior, followed by the formation of nano-sized cracks on the fast-degrading interfaces. This work reveals a robust chemical and mechanical interplay on the oxygen release inherent to the intergranular boundaries of layered cathodes. It also suggests that radially patterned columnar grains with low-angle planar boundaries would be an efficient approach to mitigate the boundary oxygen release. |
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Place of Publication |
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Wos |
000745659500012 |
Publication Date |
2021-12-20 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
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ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:186420 |
Serial |
6961 |
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| Permanent link to this record |
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Author |
Faust, V.; van Alen, T.A.; Op den Camp, H.J.M.; Vlaeminck, S.E.; Ganigué, R.; Boon, N.; Udert, K.M. |
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Title |
Ammonia oxidation by novel “Candidatus Nitrosacidococcus urinae” is sensitive to process disturbances at low pH and to iron limitation at neutral pH |
Type |
A1 Journal article |
| |
Year |
2022 |
Publication |
Water Research X |
Abbreviated Journal |
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| |
Volume |
17 |
Issue |
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Pages |
100157-11 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Acid-tolerant ammonia-oxidizing bacteria (AOB) can open the door to new applications, such as partial nitritation at low pH. However, they can also be problematic because chemical nitrite oxidation occurs at low pH, leading to the release of harmful nitrogen oxide gases. In this publication, the role of acid-tolerant AOB in urine treatment was explored. On the one hand, the technical feasibility of ammonia oxidation under acidic conditions for source-separated urine with total nitrogen concentrations up to 3.5 g-N L−1 was investigated. On the other hand, the abundance and growth of acid-tolerant AOB at more neutral pH was explored. Under acidic conditions (pH of 5), ammonia oxidation rates of 500 mg-N L−1 d−1 and 10 g-N g-VSS-1 d-1 were observed, despite high concentrations of 15 mg-N L−1 of the AOB-inhibiting compound nitrous acid and low concentration of 0.04 mg-N L−1 of the substrate ammonia. However, ammonia oxidation under acidic conditions was very sensitive to process disturbances. Even short periods of less than 12 h without oxygen or without influent resulted in a complete cessation of ammonia oxidation with a recovery time of up to two months, which is a problem for low maintenance applications such as decentralized treatment. Furthermore, undesirable nitrogen losses of about 10% were observed. Under acidic conditions, a novel AOB strain was enriched with a relative abundance of up to 80%, for which the name “Candidatus (Ca.) Nitrosacidococcus urinae” is proposed. While Nitrosacidococcus members were present only to a small extent (0.004%) in urine nitrification reactors operated at pH values between 5.8 and 7, acid-tolerant AOB were always enriched during long periods without influent, resulting in an uncontrolled drop in pH to as low as 2.5. Long-term experiments at different pH values showed that the activity of “Ca. Nitrosacidococcus urinae” decreased strongly at a pH of 7, where they were also outcompeted by the acid-sensitive AOB Nitrosomonas halophila. The experiment results showed that the decreased activity of “Ca. Nitrosacidococcus urinae” correlated with the limited availability of dissolved iron at neutral pH. |
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Corporate Author |
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Place of Publication |
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Wos |
000877925500001 |
Publication Date |
2022-10-04 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
2589-9147 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
|
Times cited |
|
Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:190944 |
Serial |
7124 |
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| Permanent link to this record |
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Author |
Agrawal, S.; Weissbrodt, D.G.; Annavajhala, M.; Jensen, M.M.; Arroyo, J.M.C.; Wells, G.; Chandran, K.; Vlaeminck, S.E.; Terada, A.; Smets, B.F.; Lackner, S. |
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Title |
Time to act–assessing variations in qPCR analyses in biological nitrogen removal with examples from partial nitritation/anammox systems |
Type |
A1 Journal article |
| |
Year |
2021 |
Publication |
Water Research |
Abbreviated Journal |
Water Res |
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| |
Volume |
190 |
Issue |
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Pages |
116604 |
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Keywords |
A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Quantitative PCR (qPCR) is broadly used as the gold standard to quantify microbial community fractions in environmental microbiology and biotechnology. Benchmarking efforts to ensure the comparability of qPCR data for environmental bioprocesses are still scarce. Also, for partial nitritation/anammox (PN/A) systems systematic investigations are still missing, rendering meta-analysis of reported trends and generic insights potentially precarious. We report a baseline investigation of the variability of qPCR-based analyses for microbial communities applied to PN/A systems. Round-robin testing was performed for three PN/A biomass samples in six laboratories, using the respective in-house DNA extraction and qPCR protocols. The concentration of extracted DNA was significantly different between labs, ranged between 2.7 and 328 ng mg−1 wet biomass. The variability among the qPCR abundance data of different labs was very high (1−7 log fold) but differed for different target microbial guilds. DNA extraction caused maximum variation (3–7 log fold), followed by the primers (1–3 log fold). These insights will guide environmental scientists and engineers as well as treatment plant operators in the interpretation of qPCR data. |
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Place of Publication |
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Wos |
000632807700001 |
Publication Date |
2020-11-05 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0043-1354; 1879-2448 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
6.942 |
Times cited |
|
Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 6.942 |
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Call Number |
UA @ admin @ c:irua:173838 |
Serial |
8672 |
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Author |
Geerts, R.; Vandermoere, F.; Van Winckel, T.; Halet, D.; Joos, P.; Van Den Steen, K.; Van Meenen, E.; Blust, R.; Borregán-Ochando, E.; Vlaeminck, S.E. |
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Title |
Bottle or tap? Toward an integrated approach to water type consumption |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Water Research |
Abbreviated Journal |
Water Res |
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Volume |
173 |
Issue |
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Pages |
115578-10 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL); Centre for Research on Environmental and Social Change |
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Abstract |
While in many countries, people have access to cheap and safe potable tap water, the global consumption of bottled water is rising. Flanders, Belgium, where this study is located, has an exceptionally high consumption of bottled water per capita. However, in the interest of resource efficiency and global environmental challenges, the consumption of tap water is preferable. To our knowledge, an integrated analysis of the main reasons why people consume tap and bottled water is absent in Flanders, Belgium. Using Flemish survey data (N = 2309), we first compared tap and bottled water consumers through bivariate correlation analysis. Subsequently, path modelling techniques were used to further investigate these correlations. Our results show that bottled water consumption in Flanders is widespread despite environmental and financial considerations. For a large part, this is caused by negative perceptions about tap water. Many consumers consider it unhealthy, unsafe and prefer the taste of bottled water. Furthermore, we found that the broader social context often inhibits the consumption of tap water. On the one hand, improper infrastructures (e.g. lead piping) can limit access to potable tap water. On the other hand, social norms exist that promote bottled water. Lastly, results suggest that the consumption of bottled water is most common among men, older people and less educated groups. We conclude that future research and policy measures will benefit from an approach that integrates all behavioural aspects associated with water type consumption. This will enable both governments and tap water companies to devise more effective policies to manage and support tap water supply networks. |
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Corporate Author |
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Place of Publication |
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Wos |
000523569000012 |
Publication Date |
2020-01-31 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0043-1354 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
12.8 |
Times cited |
2 |
Open Access |
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Notes |
; This was supported by a grant from Water-link. ; |
Approved |
Most recent IF: 12.8; 2020 IF: 6.942 |
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Call Number |
UA @ admin @ c:irua:165873 |
Serial |
6464 |
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| Permanent link to this record |
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Author |
Vandekerckhove, T.G.L.; Props, R.; Carvajal-Arroyo, J.M.; Boon, N.; Vlaeminck, S.E. |
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Title |
Adaptation and characterization of thermophilic anammox in bioreactors |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Water Research |
Abbreviated Journal |
Water Res |
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Volume |
172 |
Issue |
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Pages |
115462 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Anammox, the oxidation of ammonium with nitrite, is a key microbial process in the nitrogen cycle. Under mesophilic conditions (below 40 °C), it is widely implemented to remove nitrogen from wastewaters lacking organic carbon. Despite evidence of the presence of anammox bacteria in high-temperature environments, reports on the cultivation of thermophilic anammox bacteria are limited to a short-term experiment of 2 weeks. This study showcases the adaptation of a mesophilic inoculum to thermophilic conditions, and its characterization. First, an attached growth technology was chosen to obtain the process. In an anoxic fixed-bed biofilm bioreactor (FBBR), a slow linear temperature increase from 38 to over 48 °C (0.05–0.07 °C d−1) was imposed to the community over 220 days, after which the reactor was operated at 48 °C for over 200 days. Maximum total nitrogen removal rates reached up to 0.62 g N L−1 d−1. Given this promising performance, a suspended growth system was tested. The obtained enrichment culture served as inoculum for membrane bioreactors (MBR) operated at 50 °C, reaching a maximum total nitrogen removal rate of 1.7 g N L−1 d−1 after 35 days. The biomass in the MBR had a maximum specific anammox activity of 1.1 ± 0.1 g NH4+-N g−1 VSS d−1, and the growth rate was estimated at 0.075–0.19 d−1. The thermophilic cultures displayed nitrogen stoichiometry ratios typical for mesophilic anammox: 0.93–1.42 g NO2--Nremoved g−1 NH4+-Nremoved and 0.16–0.35 g NO3--Nproduced g−1 NH4+-Nremoved. Amplicon and Sanger sequencing of the 16S rRNA genes revealed a disappearance of the original “Ca. Brocadia” and “Ca. Jettenia” taxa, yielding Planctomycetes members with only 94–95% similarity to “Ca. Brocadia anammoxidans” and “Ca. B. caroliniensis”, accounting for 45% of the bacterial FBBR community. The long-term operation of thermophilic anammox reactors and snapshot views on the nitrogen stoichiometry, kinetics and microbial community open up the development path of thermophilic partial nitritation/anammox. A first economic assessment highlighted that treatment of sludge reject water from thermophilic anaerobic digestion of sewage sludge may become attractive. |
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Place of Publication |
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Wos |
000517663600014 |
Publication Date |
2020-01-10 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0043-1354 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
12.8 |
Times cited |
5 |
Open Access |
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Notes |
; The authors acknowledge (i) the Agency for Innovation by Science and Technology (IWT Flanders) [grant number SB-141205] for funding T.G.L.V., (ii) Ghent University (BOFDOC2015000601) and the Belgian Nuclear Research Centre (SCK.CEN) for funding R.P., (iii) Bart De Gusseme from Farys/UGent for providing the hollow fiber membranes, (iv) Tim Lacoere for performing the DNA extraction and data processing of the Sanger sequencing and 16S rRNA gene amplicon sequencing data, (v) Tim Hendrickx from Paques BV for providing the inoculum, (vi) Bert Bundervoet and Wim Groen in 't Woud from Colsen for the valuable input on the economic assessment and (vii) Joop Colsen, Stijn Van Hulle, Mark Van Loosdrecht, Erik Smolders and Leen De Gelder for their constructive discussions on this work. ; |
Approved |
Most recent IF: 12.8; 2020 IF: 6.942 |
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Call Number |
UA @ admin @ c:irua:165392 |
Serial |
6449 |
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Author |
Spiller, M.; Muys, M.; Papini, G.; Sakarika, M.; Buyle, M.; Vlaeminck, S.E. |
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Title |
Environmental impact of microbial protein from potato wastewater as feed ingredient : comparative consequential life cycle assessment of three production systems and soybean meal |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Water Research |
Abbreviated Journal |
Water Res |
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Volume |
171 |
Issue |
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Pages |
115406 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL); Energy and Materials in Infrastructure and Buildings (EMIB) |
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Abstract |
Livestock production is utilizing large amounts of protein-rich feed ingredients such as soybean meal. The proven negative environmental impacts of soybean meal production incentivize the search for alternative protein sources. One promising alternative is Microbial Protein (MP), i.e. dried microbial biomass. To date, only few life cycle assessments (LCAs) for MP have been carried out, none of which has used a consequential modelling approach nor has been investigating the production of MP on food and beverage wastewater. Therefore, the objective of this study is to evaluate the environmental impact of MP production on a food and beverage effluent as a substitute for soybean meal using a consequential modelling approach. Three different types of MP production were analysed, namely consortia containing Aerobic Heterotrophic Bacteria (AHB), Microalgae and AHB (MaB), and Purple Non-Sulfur Bacteria (PNSB). The production of MP was modelled for high-strength potato wastewater (COD = 10 kg/m3) at a flow rate of 1,000 m3/day. LCA results were compared against soybean meal production for the endpoint impact categories human health, ecosystems, and resources. Soybean meal showed up to 52% higher impact on human health and up to 87% higher impact on ecosystems than MP. However, energy-related aspects resulted in an 8–88% higher resource exploitation for MP. A comparison between the MP production systems showed that MaB performed best when considering ecosystems (between 13 and 14% better) and resource (between 71 and 80% better) impact categories, while AHB and PNSB had lower values for the impact category human health (8–12%). The sensitivity analysis suggests that the conclusions drawn are robust as in the majority of 1,000 Monte Carlo runs the initial results are confirmed. In conclusion, it is suggested that MP is an alternative protein source of comparatively low environmental impact that should play a role in the future protein transition, in particular when further process improvements can be implemented and more renewable or waste energy sources will be used. |
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Place of Publication |
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Wos |
000514748900032 |
Publication Date |
2019-12-18 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0043-1354 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
12.8 |
Times cited |
10 |
Open Access |
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Notes |
; The authors would like to thank (i) the MIP i-Cleantech Flanders (Milieu innovatieplatform; Environment innovation platform) project Microbial Nutrients on Demand (MicroNOD; 150360) for financial support, (ii) the Research Foundation Flanders (FWO-Vlaanderen) for supporting Gustavo Papini with a doctoral fellowship (strategic basic research; 1S38917N), (iii) Research Foundation Flanders (FWO-Vlaanderen) for supporting Matthias Buyle with a post-doctoral fellowship (Postdoctoral Fellow junior; 1207520N), and (iv) Bo Weidema, Abbas Alloul, Yixing Sui and Tim Van Winckel for their insightful discussions. ; |
Approved |
Most recent IF: 12.8; 2020 IF: 6.942 |
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Call Number |
UA @ admin @ c:irua:164944 |
Serial |
6509 |
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Author |
Vanderkerckhove, T.G.L.; Kerckhof, F.-M.; De Mulder, C.; Vlaeminck, S.E.; Boon, N. |
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Title |
Determining stoichiometry and kinetics of two thermophilic nitrifying communities as a crucial step in the development of thermophilic nitrogen removal |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Water research |
Abbreviated Journal |
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Volume |
156 |
Issue |
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Pages |
34-45 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Nitrification and denitrification, the key biological processes for thermophilic nitrogen removal, have separately been established in bioreactors at 50 °C. A well-characterized set of kinetic parameters is essential to integrate these processes while safeguarding the autotrophs performing nitrification. Knowledge on thermophilic nitrifying kinetics is restricted to isolated or highly enriched batch cultures, which do not represent bioreactor conditions. This study characterized the stoichiometry and kinetics of two thermophilic (50 °C) nitrifying communities. The most abundant ammonia oxidizing archaea (AOA) were related to the Nitrososphaera genus, clustering relatively far from known species Nitrososphaera gargensis (95.5% 16S rRNA gene sequence identity). The most abundant nitrite oxidizing bacteria (NOB) were related to Nitrospira calida (97% 16S rRNA gene sequence identity). The nitrification biomass yield was 0.200.24 g VSS g−1 N, resulting mainly from a high AOA yield (0.160.20 g VSS g−1 N), which was reflected in a high AOA abundance in the community (5776%) compared to NOB (511%). Batch-wise determination of decay rates (AOA: 0.230.29 d−1; NOB: 0.320.43 d−1) rendered an overestimation compared to in situ estimations of overall decay rate (0.0260.078 d−1). Possibly, the inactivation rate rather than the actual decay rate was determined in batch experiments. Maximum growth rates of AOA and NOB were 0.120.15 d−1 and 0.130.33 d−1 respectively. NOB were susceptible to nitrite, opening up opportunities for shortcut nitrogen removal. However, NOB had a similar growth rate and oxygen affinity (0.150.55 mg O2 L−1) as AOA and were resilient towards free ammonia (IC50 > 16 mg NH3-N L−1). This might complicate NOB outselection using common practices to establish shortcut nitrogen removal (SRT control; aeration control; free ammonia shocks). Overall, the obtained insights can assist in integrating thermophilic conversions and facilitate single-sludge nitrification/denitrification. |
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Wos |
000466618400004 |
Publication Date |
2019-03-14 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0043-1354; 1879-2448 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
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Open Access |
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Notes |
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Approved |
no |
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Call Number |
UA @ admin @ c:irua:158226 |
Serial |
7798 |
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| Permanent link to this record |
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Author |
Alloul, A.; Wuyts, S.; Lebeer, S.; Vlaeminck, S.E. |
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Title |
Volatile fatty acids impacting phototrophic growth kinetics of purple bacteria : paving the way for protein production on fermented wastewater |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Water research |
Abbreviated Journal |
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Volume |
152 |
Issue |
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Pages |
138-147 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Nutrient losses in our food chain severely surpass our planetary boundaries. Resource recovery can contribute to mitigation, for instance through converting wastewater resources to microbial protein for animal feed. Wastewater typically holds a complex mixture of organics, posing a challenge to selectively produce heterotrophic biomass. Ensuring the product's quality could be achieved by anaerobic generation of volatile fatty acids (VFAs) followed by photoheterotrophic production of purple non-sulfur bacteria (PNSB) with infrared light. This study aimed to determine the most suitable PNSB culture for VFA conversion and map the effect of acetate, propionate, butyrate and a VFA mixture on growth and biomass yield. Six cultures were screened in batch: (i) Rhodopseudomonas palustris, (ii) Rhodobacter sphaeroides, (iii) Rhodospirillum rubrum, (iv) a 3-species synthetic community (i+ii+iii), (v) a community enriched on VFA holding Rb. capsulatus, and (vi) Rb. capsulatus (isolate v). The VFA mixture elevated growth rates with a factor 1.32.5 compared to individual VFA. Rb. capsulatus showed the highest growth rates: 1.82.2 d−1 (enriched) and 2.33.8 d−1 (isolated). In a photobioreactor (PBR) inoculated with the Rb. capsulatus enrichment, decreasing sludge retention time (SRT) yielded lower biomass concentrations, yet increased productivities, reaching 1.7 g dry weight (DW) L−1 d−1, the highest phototrophic rate reported thus far, and a growth rate of up to 5 d−1. PNSB represented 2657% of the community and the diversity index was low (37), with a dominance of Rhodopseudomonas at long SRT and Rhodobacter at short SRT. The biomass yield for all cultures, in batch and reactor cultivation, approached 1 g CODBiomass g−1 CODRemoved. An economic estimation for a two-stage approach on brewery wastewater (load 2427 kg COD d−1) showed that 0.5 d SRT allowed for the lowest production cost ( 10 kg−1 DW; equal shares for capex and opex). The findings strengthen the potential for a novel two-stage approach for resource recovery from industrial wastewater, enabling high-rate PNSB production. |
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000458223900013 |
Publication Date |
2018-12-27 |
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0043-1354; 1879-2448 |
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UA library record; WoS full record; WoS citing articles |
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Call Number |
UA @ admin @ c:irua:156462 |
Serial |
8739 |
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Author |
Seuntjens, D.; Carvajal-Arroyo, J.M.; Ruopp, M.; Bunse, P.; De Mulder, C.P.; Lochmatter, S.; Agrawal, S.; Boon, N.; Lackner, S.; Vlaeminck, S.E. |
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Title |
High-resolution mapping and modeling of anammox recovery from recurrent oxygen exposure |
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A1 Journal article |
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2018 |
Publication |
Water research |
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144 |
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522-531 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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Oxygen inhibits anammox, a bioconversion executed by anoxic ammonium oxidizing bacteria (AnAOB). Nonetheless, oxygen is mostly found in the proximity of AnAOB in nitrogen removal applications, being a substrate for nitritation. The experiments performed to date were mostly limited to batch activity tests where AnAOB activity is estimated during oxygen exposure. However, little attention has been paid to the recovery and reversibility of activity following aerobic conditions, of direct relevance for bioreactor operation. In this work, anoxic and autotrophic reactor cultivation at 20 degrees C yielded an enriched microbial community in AnAOB, consisting for 75% of a member of the genus Brocadia. High-resolution kinetic data were obtained with online ammonium measurements and further processed with a newly developed Python data pipeline. The experimentally obtained AnAOB response showed complete inhibition until micro-aerobic conditions were reached again (<0.02 mg O-2 L-1). After oxygen inhibition, AnAOB recovered gradually, with recovery times of 5-37 h to reach a steady-state activity, dependent on the perceived inhibition. The recovery immediately after inhibition was lowest when exposed to higher oxygen concentrations (range: 0.5-8 mg O-2 L-1) with long contact times (range: 9-24 h). The experimental data did not fit well with a conventional 'instant recovery' Monod-type inhibition model. Yet, the fit greatly improved by incorporating a dynamic growth rate formula accurately describing gradual activity recovery. With the upgraded model, long-term kinetic simulations for partial nitritation/anammox (PN/A) with intermittent aeration showed a decrease in growth rate compared to the instant recovery mode. These results indicate that recovery of AnAOB after oxygen exposure was previously overlooked. It is recommended to account for this effect in the intensification of partial nitritation/anammox. (C) 2018 Elsevier Ltd. All rights reserved. |
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000447569300051 |
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2018-07-11 |
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0043-1354; 1879-2448 |
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UA @ admin @ c:irua:152910 |
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8037 |
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De Paepe, J.; Lindeboom, R.E.F.; Vanoppen, M.; De Paepe, K.; Demey, D.; Coessens, W.; Lamaze, B.; Verliefde, A.R.D.; Clauwaert, P.; Vlaeminck, S.E. |
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Refinery and concentration of nutrients from urine with electrodialysis enabled by upstream precipitation and nitrification |
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A1 Journal article |
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Year |
2018 |
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Water research |
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144 |
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76-86 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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Human urine is a valuable resource for nutrient recovery, given its high levels of nitrogen, phosphorus and potassium, but the compositional complexity of urine presents a challenge for an energy-efficient concentration and refinery of nutrients. In this study, a pilot installation combining precipitation, nitrification and electrodialysis (ED), designed for one person equivalent (1.2 L-urine d(-l)), was continuously operated for similar to 7 months. First, NaOH addition yielded calcium and magnesium precipitation, preventing scaling in ED. Second, a moving bed biofilm reactor oxidized organics, preventing downstream biofouling, and yielded complete nitrification on diluted urine (20-40%, i.e. dilution factors 5 and 2.5) at an average loading rate of 215 mg N L-1 d(-1). Batch tests demonstrated the halotolerance of the nitrifying community, with nitrification rates not affected up to an electrical conductivity of 40 mS cm(-1) and gradually decreasing, yet ongoing, activity up to 96 mS cm(-1) at 18% of the maximum rate. Next-generation 16S rRNA gene amplicon sequencing revealed that switching from a synthetic influent to real urine induced a profound shift in microbial community and that the AOB community was dominated by halophilic species closely related to Nitrosomonas aestuarii and Nitrosomonas marina. Third, nitrate, phosphate and potassium in the filtered (0.1 mu m) bioreactor effluent were concentrated by factors 43, 2.6 and 4.6, respectively, with ED. Doubling the urine concentration from 20% to 40% further increased the ED recovery efficiency by similar to 10%. Batch experiments at pH 6, 7 and 8 indicated a more efficient phosphate transport to the concentrate at pH 7. The newly proposed three-stage strategy opens up opportunities for energy- and chemical-efficient nutrient recovery from urine. Precipitation and nitrification enabled the long-term continuous operation of ED on fresh urine requiring minimal maintenance, which has, to the best of our knowledge, never been achieved before. (C) 2018 Elsevier Ltd. All rights reserved. |
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000447569300008 |
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2018-07-07 |
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0043-1354; 1879-2448 |
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UA library record; WoS full record; WoS citing articles |
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Call Number |
UA @ admin @ c:irua:152907 |
Serial |
8468 |
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