| |
Records |
Links  |
|
Author |
Şentürk, D.G.; De Backer, A.; Van Aert, S. |
|
| |
Title |
Element specific atom counting for heterogeneous nanostructures: Combining multiple ADF STEM images for simultaneous thickness and composition determination |
Type |
A1 Journal Article |
| |
Year |
2024 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
259 |
Issue |
|
Pages |
113941 |
|
| |
Keywords |
A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ; |
|
| |
Abstract |
In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
|
Publication Date |
2024-02-19 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record |
|
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N, GOA7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). |
Approved |
Most recent IF: 2.2; 2024 IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @c:irua:204353 |
Serial |
8996 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Şentürk, DG.; Yu, CP.; De Backer, A.; Van Aert, S. |
|
| |
Title |
Atom counting from a combination of two ADF STEM images |
Type |
A1 Journal article |
| |
Year |
2024 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
255 |
Issue |
|
Pages |
113859 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
To understand the structure–property relationship of nanostructures, reliably quantifying parameters, such as the number of atoms along the projection direction, is important. Advanced statistical methodologies have made it possible to count the number of atoms for monotype crystalline nanoparticles from a single ADF STEM image. Recent developments enable one to simultaneously acquire multiple ADF STEM images. Here, we present an extended statistics-based method for atom counting from a combination of multiple statistically independent ADF STEM images reconstructed from non-overlapping annular detector collection regions which improves the accuracy and allows one to retrieve precise atom-counts, especially for images acquired with low electron doses and multiple element structures. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
001089064200001 |
Publication Date |
2023-09-23 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N, G0A7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). |
Approved |
Most recent IF: 2.2; 2024 IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @c:irua:201008 |
Serial |
8964 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Lobato, I.; De Backer, A.; Van Aert, S. |
|
| |
Title |
Real-time simulations of ADF STEM probe position-integrated scattering cross-sections for single element fcc crystals in zone axis orientation using a densely connected neural network |
Type |
A1 Journal article |
| |
Year |
2023 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
251 |
Issue |
|
Pages |
113769 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms
of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In
order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for
a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such
simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently
parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most
research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will
only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and
present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as
a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag,
Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope
parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS
values for a wide range of input parameters that are commonly used for aberration-corrected transmission
electron microscopes. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
001011617200001 |
Publication Date |
2023-06-01 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
|
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N and G0A7723N) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF), Belgium. |
Approved |
Most recent IF: 2.2; 2023 IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @c:irua:197275 |
Serial |
8812 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
De Backer, A.; Bals, S.; Van Aert, S. |
|
| |
Title |
A decade of atom-counting in STEM: From the first results toward reliable 3D atomic models from a single projection |
Type |
A1 Journal article |
| |
Year |
2023 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
|
|
| |
Volume |
|
Issue |
|
Pages |
113702 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
Quantitative structure determination is needed in order to study and understand nanomaterials at the atomic scale. Materials characterisation resulting in precise structural information is a crucial point to understand the structure–property relation of materials. Counting the number of atoms and retrieving the 3D atomic structure of nanoparticles plays an important role here. In this paper, an overview will be given of the atom-counting methodology and its applications over the past decade. The procedure to count the number of atoms will be discussed in detail and it will be shown how the performance of the method can be further improved. Furthermore, advances toward mixed element nanostructures, 3D atomic modelling based on the atom-counting results, and quantifying the nanoparticle dynamics will be highlighted. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000953765800001 |
Publication Date |
2023-02-10 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.2 |
Times cited |
3 |
Open Access |
OpenAccess |
|
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert, Grant 815128 REALNANO to S. Bals, and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N, and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF) . The authors also thank the colleagues who have contributed to this work over the years, including T. Altantzis, E. Arslan Irmak, K.J. Batenburg, E. Bladt, A. De wael, R. Erni, C. Faes, B. Goris, L. Jones, L.M. Liz-Marzán, I. Lobato, G.T. Martinez, P.D. Nellist, M.D. Rosell, A. Rosenauer, K.H.W. van den Bos, A. Varambhia, and Z. Zhang.; esteem3reported; esteem3JRA |
Approved |
Most recent IF: 2.2; 2023 IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @c:irua:195896 |
Serial |
7236 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Zhang, Z.; Lobato, I.; De Backer, A.; Van Aert, S.; Nellist, P. |
|
| |
Title |
Fast generation of calculated ADF-EDX scattering cross-sections under channelling conditions |
Type |
A1 Journal article |
| |
Year |
2023 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
|
|
| |
Volume |
246 |
Issue |
|
Pages |
113671 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
Advanced materials often consist of multiple elements which are arranged in a complicated structure. Quantitative scanning transmission electron microscopy is useful to determine the composition and thickness of nanostructures at the atomic scale. However, significant difficulties remain to quantify mixed columns by comparing the resulting atomic resolution images and spectroscopy data with multislice simulations where dynamic scattering needs to be taken into account. The combination of the computationally intensive nature of these simulations and the enormous amount of possible mixed column configurations for a given composition indeed severely hamper the quantification process. To overcome these challenges, we here report the development of an incoherent non-linear method for the fast prediction of ADF-EDX scattering cross-sections of mixed columns under channelling conditions. We first explain the origin of the ADF and EDX incoherence from scattering physics suggesting a linear dependence between those two signals in the case of a high-angle ADF detector. Taking EDX as a perfect incoherent reference mode, we quantitatively examine the ADF longitudinal incoherence under different microscope conditions using multislice simulations. Based on incoherent imaging, the atomic lensing model previously developed for ADF is now expanded to EDX, which yields ADF-EDX scattering cross-section predictions in good agreement with multislice simulations for mixed columns in a core–shell nanoparticle and a high entropy alloy. The fast and accurate prediction of ADF-EDX scattering cross-sections opens up new opportunities to explore the wide range of ordering possibilities of heterogeneous materials with multiple elements. |
|
| |
Address |
|
|
| |
Corporate Author |
Zezhong Zhang |
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000995063900001 |
Publication Date |
2022-12-28 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
European Research Council 770887 PICOMETRICS; Fonds Wetenschappelijk Onderzoek No.G.0502.18N; Horizon 2020, 770887 ; Horizon 2020 Framework Programme; European Research Council, 823717 ESTEEM3 ; esteem3reported; esteem3JRa |
Approved |
Most recent IF: 2.2; 2023 IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @c:irua:195890 |
Serial |
7251 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Sentürk, D.G.; De Backer, A.; Friedrich, T.; Van Aert, S. |
|
| |
Title |
Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors |
Type |
A1 Journal article |
| |
Year |
2022 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
242 |
Issue |
|
Pages |
113626 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In
addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000873778100001 |
Publication Date |
0000-00-00 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).; esteem3reported; esteem3jra |
Approved |
Most recent IF: 2.2 |
|
| |
Call Number |
EMAT @ emat @c:irua:190925 |
Serial |
7118 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
De wael, A.; De Backer, A.; Lobato, I.; Van Aert, S. |
|
| |
Title |
Modelling ADF STEM images using elliptical Gaussian peaks and its effects on the quantification of structure parameters in the presence of sample tilt |
Type |
A1 Journal article |
| |
Year |
2021 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
|
Issue |
|
Pages |
113391 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
A small sample tilt away from a main zone axis orientation results in an elongation of the atomic columns in ADF STEM images. An often posed research question is therefore whether the ADF STEM image intensities of tilted nanomaterials should be quantified using a parametric imaging model consisting of elliptical rather than the currently used symmetrical peaks. To this purpose, simulated ADF STEM images corresponding to different amounts of sample tilt are studied using a parametric imaging model that consists of superimposed 2D elliptical Gaussian peaks on the one hand and symmetrical Gaussian peaks on the other hand. We investigate the quantification of structural parameters such as atomic column positions and scattering cross sections using both parametric imaging models. In this manner, we quantitatively study what can be gained from this elliptical model for quantitative ADF STEM, despite the increased parameter space and computational effort. Although a qualitative improvement can be achieved, no significant quantitative improvement in the estimated structure parameters is achieved by the elliptical model as compared to the symmetrical model. The decrease in scattering cross sections with increasing sample tilt is even identical for both types of parametric imaging models. This impedes direct comparison with zone axis image simulations. Nonetheless, we demonstrate how reliable atom-counting can still be achieved in the presence of small sample tilt. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000704334200001 |
Publication Date |
2021-09-24 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
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.; esteem3JRA; esteem3reported |
Approved |
Most recent IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @c:irua:181462 |
Serial |
6810 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
De wael, A.; De Backer, A.; Van Aert, S. |
|
| |
Title |
Hidden Markov model for atom-counting from sequential ADF STEM images: Methodology, possibilities and limitations |
Type |
A1 Journal article |
| |
Year |
2020 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
219 |
Issue |
|
Pages |
113131 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
We present a quantitative method which allows us to reliably measure dynamic changes in the atomic structure of monatomic crystalline nanomaterials from a time series of atomic resolution annular dark field scanning transmission electron microscopy images. The approach is based on the so-called hidden Markov model and estimates the number of atoms in each atomic column of the nanomaterial in each frame of the time series. We discuss the origin of the improved performance for time series atom-counting as compared to the current state-of-the-art atom-counting procedures, and show that the so-called transition probabilities that describe the probability for an atomic column to lose or gain one or more atoms from frame to frame are particularly important. Using these transition probabilities, we show that the method can also be used to estimate the probability and cross section related to structural changes. Furthermore, we explore the possibilities for applying the method to time series recorded under variable environmental conditions. The method is shown to be promising for a reliable quantitative analysis of dynamic processes such as surface diffusion, adatom dynamics, beam effects, or in situ experiments. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000594770500003 |
Publication Date |
2020-10-03 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
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 and EOS 30489208. |
Approved |
Most recent IF: 2.2; 2020 IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @c:irua:172449 |
Serial |
6417 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
van den Bos, K.H.W.; Janssens, L.; De Backer, A.; Nellist, P.D.; Van Aert, S. |
|
| |
Title |
The atomic lensing model: new opportunities for atom-by-atom metrology of heterogeneous nanomaterials |
Type |
A1 Journal article |
| |
Year |
2019 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
203 |
Issue |
|
Pages |
155 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
The atomic lensing model has been proposed as a promising method facilitating atom-counting in heterogeneous nanocrystals [1]. Here, image simulations will validate the model, which describes dynamical diffraction as a superposition of individual atoms focussing the incident electrons. It will be demonstrated that the model is reliable in the annular dark field regime for crystals having columns containing dozens of atoms. By using the principles of statistical detection theory, it will be shown that this model gives new opportunities for detecting compositional differences. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000465021000020 |
Publication Date |
2018-12-06 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
4 |
Open Access |
OpenAccess |
|
| |
Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0369.15N, G.0502.18N and WO.010.16N), and by personal grants to K.H.W. van den Bos and A. De Backer. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (grant agreement No. 770887). |
Approved |
Most recent IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @UA @ admin @ c:irua:155721 |
Serial |
5074 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
De wael, A.; De Backer, A.; Jones, L.; Nellist, P.D.; Van Aert, S. |
|
| |
Title |
Hybrid statistics-simulations based method for atom-counting from ADF STEM images |
Type |
A1 Journal article |
| |
Year |
2017 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
177 |
Issue |
177 |
Pages |
69-77 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000401219800010 |
Publication Date |
2017-01-25 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
8 |
Open Access |
OpenAccess |
|
| |
Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0368.15N, G.0369.15N, and WO.010.16N), and a postdoctoral research Grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). The authors are grateful to G.T. Martinez for providing image simulations. |
Approved |
Most recent IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @ c:irua:141718 |
Serial |
4486 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Schryvers, D.; Salje, E.K.H.; Nishida, M.; De Backer, A.; Idrissi, H.; Van Aert, S. |
|
| |
Title |
Quantification by aberration corrected (S)TEM of boundaries formed by symmetry breaking phase transformations |
Type |
A1 Journal article |
| |
Year |
2017 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
176 |
Issue |
|
Pages |
194-199 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
The present contribution gives a review of recent quantification work of atom displacements, atom site occupations and level of crystallinity in various systems and based on aberration corrected HR(S)TEM images. Depending on the case studied, picometer range precisions for individual distances can be obtained, boundary widths at the unit cell level determined or statistical evolutions of fractions of the ordered areas calculated. In all of these cases, these quantitative measures imply new routes for the applications of the respective materials. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000403992200026 |
Publication Date |
2017-01-09 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
1 |
Open Access |
OpenAccess |
|
| |
Notes |
The authors acknowledge financial support from the Fund for Scientific Research-Flanders (G.0064.10N, G.0393.11N, G.0374.13N, G.0368.15N, G.0369.15N) and the Flemish Hercules 3 program for large infrastructure as well as financial support from the European Union Seventh Framework Programme (FP7/2007 – 2013) under Grant agreement no. 312483 (ESTEEM2). EKHS thanks EPSRC (EP/ K009702/1) and the Leverhulme trust (EM-2016-004) for support. DS and MN acknowledge financial support from the Japan Society for the Promotion of Science (JSPS, Japan) through the Grant-in-Aid for Scientific Research (A: No. 26249090) and the Strategic Young Researcher Overseas Visits Program for Accelerating Brain Circulation (R2408). |
Approved |
Most recent IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @c:irua:149654 |
Serial |
4914 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Alania, M.; De Backer, A.; Lobato, I.; Krause, F.F.; Van Dyck, D.; Rosenauer, A.; Van Aert, S. |
|
| |
Title |
How precise can atoms of a nanocluster be located in 3D using a tilt series of scanning transmission electron microscopy images? |
Type |
A1 Journal article |
| |
Year |
2017 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
181 |
Issue |
181 |
Pages |
134-143 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
|
| |
Abstract |
In this paper, we investigate how precise atoms of a small nanocluster can ultimately be located in three dimensions (3D) from a tilt series of images acquired using annular dark field (ADF) scanning transmission electron microscopy (STEM). Therefore, we derive an expression for the statistical precision with which the 3D atomic position coordinates can be estimated in a quantitative analysis. Evaluating this statistical precision as a function of the microscope settings also allows us to derive the optimal experimental design. In this manner, the optimal angular tilt range, required electron dose, optimal detector angles, and number of projection images can be determined. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000411170800016 |
Publication Date |
2016-12-15 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
3 |
Open Access |
OpenAccess |
|
| |
Notes |
The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N, G.0368.15N, and WO.010.16N) and a post-doctoral grant to A. De Backer, and from the DFG under contract No. RO-2057/4-2. |
Approved |
Most recent IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @ c:irua:144432 |
Serial |
4618 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Alania, M.; Altantzis, T.; De Backer, A.; Lobato, I.; Bals, S.; Van Aert, S. |
|
| |
Title |
Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
177 |
Issue |
177 |
Pages |
36-42 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely. In this manner, the morphology of a nanoparticle can be reconstructed in three dimensions. This will be demonstrated using simulations and experimental data of a gold nanorod. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000401219800006 |
Publication Date |
2016-11-09 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
13 |
Open Access |
OpenAccess |
|
| |
Notes |
The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. S. Bals acknowledges funding from the European Research Council (Starting Grant No. COLOURATOMS 335078). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N and G.0368.15N) and a post-doctoral grant to A. De Backer and T. Altantzis. The authors are grateful to Professor Luis M. Liz-Marzán for providing the sample.; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); |
Approved |
Most recent IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @ c:irua:138015UA @ admin @ c:irua:138015 |
Serial |
4316 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S. |
|
| |
Title |
Atom-counting in High Resolution Electron Microscopy: TEM or STEM – that's the question |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
174 |
Issue |
174 |
Pages |
112-120 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
|
| |
Abstract |
In this work, a recently developed quantitative approach based on the principles of detection theory is used in order to determine the possibilities and limitations of High Resolution Scanning Transmission Electron Microscopy (HR STEM) and HR TEM for atom-counting. So far, HR STEM has been shown to be an appropriate imaging mode to count the number of atoms in a projected atomic column. Recently, it has been demonstrated that HR TEM, when using negative spherical aberration imaging, is suitable for atom-counting as well. The capabilities of both imaging techniques are investigated and compared using the probability of error as a criterion. It is shown that for the same incoming electron dose, HR STEM outperforms HR TEM under common practice standards, i.e. when the decision is based on the probability function of the peak intensities in HR TEM and of the scattering cross-sections in HR STEM. If the atom-counting decision is based on the joint probability function of the image pixel values, the dependence of all image pixel intensities as a function of thickness should be known accurately. Under this assumption, the probability of error may decrease significantly for atom-counting in HR TEM and may, in theory, become lower as compared to HR STEM under the predicted optimal experimental settings. However, the commonly used standard for atom-counting in HR STEM leads to a high performance and has been shown to work in practice. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000403342200013 |
Publication Date |
2016-10-27 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
2 |
Open Access |
|
|
| |
Notes |
The authors gratefully acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15N, G.0369.15N, G.0374.13N, and WO.010.16N) and a postdoctoral grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). |
Approved |
Most recent IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @ c:irua:137102 |
Serial |
4315 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
De Backer, A.; van den Bos, K.H.W.; Van den Broek, W.; Sijbers, J.; Van Aert, S. |
|
| |
Title |
StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
171 |
Issue |
171 |
Pages |
104-116 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
|
| |
Abstract |
An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000389106200014 |
Publication Date |
2016-09-09 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
43 |
Open Access |
|
|
| |
Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0393.11, G.0064.10 and G.0374.13), a Ph.D. research grant to K.H.W. van den Bos, and a postdoctoral research grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). A. Rosenauer is acknowledged for providing the STEMsim program.; esteem2_jra2 |
Approved |
Most recent IF: 2.843 |
|
| |
Call Number |
EMAT @ emat @ c:irua:135516 |
Serial |
4280 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S. |
|
| |
Title |
Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
170 |
Issue |
170 |
Pages |
128-138 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
|
| |
Abstract |
In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramer-Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms. |
|
| |
Address |
Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium. Electronic address: sandra.vanaert@uantwerpen.be |
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
English |
Wos |
000386925500014 |
Publication Date |
2016-07-26 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
6 |
Open Access |
|
|
| |
Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15, G.0369.15 and G.0374.13) and a postdoctoral research grant to A. De Backer. The research leading to these results has also received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). The authors would also like to thank A. Rosenauer for providing access to the STEMsim software and Gerardo T. Martinez for fruitful discussions.; esteem2_jra2 |
Approved |
Most recent IF: 2.843 |
|
| |
Call Number |
c:irua:135337 c:irua:135337 |
Serial |
4128 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Martinez, G.T.; Jones, L.; de Backer, A.; Béché, A.; Verbeeck, J.; Van Aert, S.; Nellist, P.D. |
|
| |
Title |
Quantitative STEM normalisation : the importance of the electron flux |
Type |
A1 Journal article |
| |
Year |
2015 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
159 |
Issue |
159 |
Pages |
46-58 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
Annular dark-field (ADF) scanning transmission electron microscopy (STEM) has become widely used in quantitative studies based on the opportunity to directly compare experimental and simulated images. This comparison merely requires the experimental data to be normalised and expressed in units of fractional beam-current. However, inhomogeneities in the response of electron detectors can complicate this normalisation. The quantification procedure becomes both experiment and instrument specific, requiring new simulations for the particular response of each instrument's detector, and for every camera-length used. This not only impedes the comparison between different instruments and research groups, but can also be computationally very time consuming. Furthermore, not all image simulation methods allow for the inclusion of an inhomogeneous detector response. In this work, we propose an alternative method for normalising experimental data in order to compare these with simulations that consider a homogeneous detector response. To achieve this, we determine the electron flux distribution reaching the detector by means of a camera-length series or a so-called atomic column cross-section averaged convergent beam electron diffraction (XSACBED) pattern. The result is then used to determine the relative weighting of the detector response. Here we show that the results obtained by this new electron flux weighted (EFW) method are comparable to the currently used method, while considerably simplifying the needed simulation libraries. The proposed method also allows one to obtain a metric that describes the quality of the detector response in comparison with the ideal detector response. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
|
| |
Language |
|
Wos |
000366220000006 |
Publication Date |
2015-08-01 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
27 |
Open Access |
|
|
| |
Notes |
246791 Countatoms; 278510 Vortex; 312483 Esteem2; Fwo G036815; G036915; G037413; G004413; esteem2ta ECASJO; |
Approved |
Most recent IF: 2.843; 2015 IF: 2.436 |
|
| |
Call Number |
c:irua:127293 c:irua:127293UA @ admin @ c:irua:127293 |
Serial |
2762 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
de Backer, A.; Martinez, G.T.; MacArthur, K.E.; Jones, L.; Béché, A.; Nellist, P.D.; Van Aert, S. |
|
| |
Title |
Dose limited reliability of quantitative annular dark field scanning transmission electron microscopy for nano-particle atom-counting |
Type |
A1 Journal article |
| |
Year |
2015 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
151 |
Issue |
151 |
Pages |
56-61 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
Quantitative annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique to characterise nano-particles on an atomic scale. Because of their limited size and beam sensitivity, the atomic structure of such particles may become extremely challenging to determine. Therefore keeping the incoming electron dose to a minimum is important. However, this may reduce the reliability of quantitative ADF STEM which will here be demonstrated for nano-particle atom-counting. Based on experimental ADF STEM images of a real industrial catalyst, we discuss the limits for counting the number of atoms in a projected atomic column with single atom sensitivity. We diagnose these limits by combining a thorough statistical method and detailed image simulations. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
|
| |
Language |
|
Wos |
000351237800008 |
Publication Date |
2014-12-03 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
29 |
Open Access |
|
|
| |
Notes |
312483 Esteem2; 278510 Vortex; Fwo G039311; G006410; G037413; esteem2ta; ECASJO; |
Approved |
Most recent IF: 2.843; 2015 IF: 2.436 |
|
| |
Call Number |
c:irua:123927 c:irua:123927 |
Serial |
753 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
de Backer, A.; De wael, A.; Gonnissen, J.; Van Aert, S. |
|
| |
Title |
Optimal experimental design for nano-particle atom-counting from high-resolution STEM images |
Type |
A1 Journal article |
| |
Year |
2015 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
151 |
Issue |
151 |
Pages |
46-55 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
In the present paper, the principles of detection theory are used to quantify the probability of error for atom-counting from high resolution scanning transmission electron microscopy (HR STEM) images. Binary and multiple hypothesis testing have been investigated in order to determine the limits to the precision with which the number of atoms in a projected atomic column can be estimated. The probability of error has been calculated when using STEM images, scattering cross-sections or peak intensities as a criterion to count atoms. Based on this analysis, we conclude that scattering cross-sections perform almost equally well as images and perform better than peak intensities. Furthermore, the optimal STEM detector design can be derived for atom-counting using the expression for the probability of error. We show that for very thin objects LAADF is optimal and that for thicker objects the optimal inner detector angle increases. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
|
| |
Language |
|
Wos |
000351237800007 |
Publication Date |
2014-11-11 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
24 |
Open Access |
|
|
| |
Notes |
312483 Esteem2; Fwo G039311; G037413; esteem2_jra2 |
Approved |
Most recent IF: 2.843; 2015 IF: 2.436 |
|
| |
Call Number |
c:irua:123926 c:irua:123926 |
Serial |
2481 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
de Backer, A.; Martinez, G.T.; Rosenauer, A.; Van Aert, S. |
|
| |
Title |
Atom counting in HAADF STEM using a statistical model-based approach : methodology, possibilities, and inherent limitations |
Type |
A1 Journal article |
| |
Year |
2013 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
134 |
Issue |
|
Pages |
23-33 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
In the present paper, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. In order to count the number of atoms, it is assumed that the total scattered intensity scales with the number of atoms per atom column. These intensities are quantitatively determined using model-based statistical parameter estimation theory. The distribution describing the probability that intensity values are generated by atomic columns containing a specific number of atoms is inferred on the basis of the experimental scattered intensities. Finally, the number of atoms per atom column is quantified using this estimated probability distribution. The number of atom columns available in the observed STEM image, the number of components in the estimated probability distribution, the width of the components of the probability distribution, and the typical shape of a criterion to assess the number of components in the probability distribution directly affect the accuracy and precision with which the number of atoms in a particular atom column can be estimated. It is shown that single atom sensitivity is feasible taking the latter aspects into consideration. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
|
| |
Language |
|
Wos |
000324474900005 |
Publication Date |
2013-05-17 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
48 |
Open Access |
|
|
| |
Notes |
FWO; Esteem2; FP 2007-2013; esteem2_jra2 |
Approved |
Most recent IF: 2.843; 2013 IF: 2.745 |
|
| |
Call Number |
UA @ lucian @ c:irua:109916 |
Serial |
162 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
de Backer, A.; Van Aert, S.; van Dyck, D. |
|
| |
Title |
High precision measurements of atom column positions using model-based exit wave reconstruction |
Type |
A1 Journal article |
| |
Year |
2011 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
| |
Volume |
111 |
Issue |
9/10 |
Pages |
1475-1482 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
|
| |
Abstract |
In this paper, it has been investigated how to measure atom column positions as accurately and precisely as possible using a focal series of images. In theory, it is expected that the precision would considerably improve using a maximum likelihood estimator based on the full series of focal images. As such, the theoretical lower bound on the variances of the unknown atom column positions can be attained. However, this approach is numerically demanding. Therefore, maximum likelihood estimation has been compared with the results obtained by fitting a model to a reconstructed exit wave rather than to the full series of focal images. Hence, a real space model-based exit wave reconstruction technique based on the channelling theory is introduced. Simulations show that the reconstructed complex exit wave contains the same amount of information concerning the atom column positions as the full series of focal images. Only for thin samples, which act as weak phase objects, this information can be retrieved from the phase of the reconstructed complex exit wave. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
|
| |
Language |
|
Wos |
000300461200004 |
Publication Date |
2011-07-28 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.843 |
Times cited |
8 |
Open Access |
|
|
| |
Notes |
Fwo |
Approved |
Most recent IF: 2.843; 2011 IF: 2.471 |
|
| |
Call Number |
UA @ lucian @ c:irua:91879 |
Serial |
1438 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
De Backer, J.; Lin, A.; Berghe, W.V.; Bogaerts, A.; Hoogewijs, D. |
|
| |
Title |
Cytoglobin inhibits non-thermal plasma-induced apoptosis in melanoma cells through regulation of the NRF2-mediated antioxidant response |
Type |
A1 Journal article |
| |
Year |
2022 |
Publication |
Redox Biology |
Abbreviated Journal |
Redox Biol |
|
| |
Volume |
55 |
Issue |
|
Pages |
102399 |
|
| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES) |
|
| |
Abstract |
Melanoma arises from pigment-producing cells called melanocytes located in the basal layers of the epidermis of the skin. Cytoglobin (CYGB) is a ubiquitously expressed hexacoordinated globin that is highly enriched in melanocytes and frequently downregulated during melanomagenesis. Previously, we showed that non-thermal plasma (NTP)-produced reactive oxygen and nitrogen species (RONS) lead to the formation of an intra molecular disulfide bridge that would allow CYGB to function as a redox-sensitive protein. Here, we investigate the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels, and we explore the role of CYGB in determining treatment outcome. Our findings are consistent with previous studies supporting that NTP cytotoxicity is mediated through the production of RONS and leads to apoptotic cell death in melanoma cells. Furthermore, we show that NTP-treated solutions elicit an antioxidant response through the activation of nuclear factor erythroid 2–related factor 2 (NRF2). The knock down and overexpression of CYGB respectively sensitizes and protects melanoma cells from RONS-induced apoptotic cell death. The presence of CYGB enhances heme-oxygenase 1 (HO-1) and NRF2 protein expression levels, whereas the absence impairs their expression. Moreover, analysis of the CYGB-dependent transcriptome demonstrates the tumor suppressor long non-coding RNA maternally expressed 3 (MEG3) as a hitherto unde scribed link between CYGB and NRF2. Thus, the presence of CYGB, at least in melanoma cells, seems to play a central role in determining the therapeutic outcome of RONS-inducing anticancer therapies, like NTP-treated solutions, possessing both tumor-suppressive and oncogenic features. Hence, CYGB expression could be of in terest either as a biomarker or as a candidate for future targeted therapies in melanoma. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000844595100002 |
Publication Date |
0000-00-00 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
2213-2317 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
11.4 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work include: 12S9221 N (Abraham Lin) and G044420 N (Abraham Lin and Annemie Bogaerts). Joey De Backer acknowledges a visiting fellowship from the University of Fribourg. David Hoogewijs acknowledges support by the Swiss National Science Foundation (grants 31003A173000 and 310030207460). |
Approved |
Most recent IF: 11.4 |
|
| |
Call Number |
PLASMANT @ plasmant @c:irua:190635 |
Serial |
7101 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
De Backer, J.; Razzokov, J.; Hammerschmid, D.; Mensch, C.; Hafideddine, Z.; Kumar, N.; van Raemdonck, G.; Yusupov, M.; Van Doorslaer, S.; Johannessen, C.; Sobott, F.; Bogaerts, A.; Dewilde, S. |
|
| |
Title |
The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor |
Type |
A1 Journal article |
| |
Year |
2018 |
Publication |
Redox Biology |
Abbreviated Journal |
Redox Biol |
|
| |
Volume |
19 |
Issue |
|
Pages |
1-10 |
|
| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec) |
|
| |
Abstract |
Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000449722100002 |
Publication Date |
2018-07-24 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
2213-2317 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
6.337 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
M.Y. and N.K. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grant nos. 1200216N and 12J5617N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI). C.M acknowledges the financial support provided by the Flemish Community and the University of Antwerp (BOF-NOI) for the pre-doctoral scholarship is under grant number/project ID: 28465. S.V.D., S. D. and Z.H. acknowledge the FWO (Grant G.0687.13) and the GOA-BOF UA 2013–2016 (project-ID 28312) for funding. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI. |
Approved |
Most recent IF: 6.337 |
|
| |
Call Number |
PLASMANT @ plasmant @c:irua:152818 |
Serial |
5006 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Martinez, G.T.; de Backer, A.; Rosenauer, A.; Verbeeck, J.; Van Aert, S. |
|
| |
Title |
The effect of probe inaccuracies on the quantitative model-based analysis of high angle annular dark field scanning transmission electron microscopy images |
Type |
A1 Journal article |
| |
Year |
2014 |
Publication |
Micron |
Abbreviated Journal |
Micron |
|
| |
Volume |
63 |
Issue |
|
Pages |
57-63 |
|
| |
Keywords |
A1 Journal article; Engineering Management (ENM); Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
Quantitative structural and chemical information can be obtained from high angle annular dark field scanning transmission electron microscopy (HAADF STEM) images when using statistical parameter estimation theory. In this approach, we assume an empirical parameterized imaging model for which the total scattered intensities of the atomic columns are estimated. These intensities can be related to the material structure or composition. Since the experimental probe profile is assumed to be known in the description of the imaging model, we will explore how the uncertainties in the probe profile affect the estimation of the total scattered intensities. Using multislice image simulations, we analyze this effect for Cs corrected and non-Cs corrected microscopes as a function of inaccuracies in cylindrically symmetric aberrations, such as defocus and spherical aberration of third and fifth order, and non-cylindrically symmetric aberrations, such as 2-fold and 3-fold astigmatism and coma. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
Oxford |
Editor |
|
|
| |
Language |
|
Wos |
000338402500011 |
Publication Date |
2014-01-02 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0968-4328; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
1.98 |
Times cited |
25 |
Open Access |
|
|
| |
Notes |
FWO (G.0393.11; G.0064.10; G.0374.13; G.0044.13); European Research Council under the 7th Framework Program (FP7); ERC GrantNo. 246791-COUNTATOMS and ERC Starting Grant No. 278510-VORTEX. A.R. thanks the DFG under contract number RO2057/8-1.The research leading to these results has received funding fromthe European Union 7th Framework Programme [FP7/2007-2013]under grant agreement no. 312483 (ESTEEM2).; esteem2ta ECASJO; |
Approved |
Most recent IF: 1.98; 2014 IF: 1.988 |
|
| |
Call Number |
UA @ lucian @ c:irua:113857UA @ admin @ c:irua:113857 |
Serial |
831 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Vingerhoets, R.; Spiller, M.; De Backer, J.; Adriaens, A.; Vlaeminck, S.E.; Meers, E. |
|
| |
Title |
Detailed nitrogen and phosphorus flow analysis, nutrient use efficiency and circularity in the agri-food system of a livestock-intensive region |
Type |
A1 Journal article |
| |
Year |
2023 |
Publication |
Journal of cleaner production |
Abbreviated Journal |
|
|
| |
Volume |
410 |
Issue |
|
Pages |
137278-13 |
|
| |
Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
|
| |
Abstract |
The agri-food value chain is a major cause of nitrogen (N) and phosphorus (P) emissions and associated environmental and health impacts. The EU's farm-to-fork strategy (F2F) demands an agri-food value chain approach to reduce nutrient emissions by 50% and fertilizer use by 20%. Substance flow analysis (SFA) is a method that can be applied to study complex systems such as the agri-food chain. A review of 60 SFA studies shows that they often lack detail by not sufficiently distinguishing between nodes, products and types of emissions. The present study aims to assess the added value of detail in SFAs and to illustrate that valuable indicators can be derived from detailed assessments. This aim will be attained by presenting a highly-detailed SFA for the livestock-intensive region of Flanders, Belgium. The SFA distinguishes 40 nodes and 1827 flows that are classified into eight different categories (e.g. by-products, point source emissions) following life cycle methods. Eight novel indicators were calculated, including indicators that assess the N and P recovery potential. Flanders has a low overall nutrient use efficiency (11% N, 18% P). About 55% of the N and 56% of the P embedded in recoverable streams are reused providing 35% and 37% of the total N and P input. Optimized nutrient recycling could replace 45% of N and 48% of P of the external nutrient input, exceeding the target set by the F2F strategy. Detailed accounting for N and P flows and nodes leads to the identification of more recoverable streams and larger N and P flows. More detailed flow accounting is a prerequisite for the quantification of technological intervention options. Future research should focus on including concentration and quality as a parameter in SFAs. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000991013600001 |
Publication Date |
2023-04-21 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0959-6526 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
11.1 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
|
Approved |
Most recent IF: 11.1; 2023 IF: 5.715 |
|
| |
Call Number |
UA @ admin @ c:irua:196227 |
Serial |
7770 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Attri, P.; Kaushik, N.K.; Kaushik, N.; Hammerschmid, D.; Privat-Maldonado, A.; De Backer, J.; Shiratani, M.; Choi, E.H.; Bogaerts, A. |
|
| |
Title |
Plasma treatment causes structural modifications in lysozyme, and increases cytotoxicity towards cancer cells |
Type |
A1 Journal Article |
| |
Year |
2021 |
Publication |
International Journal Of Biological Macromolecules |
Abbreviated Journal |
Int J Biol Macromol |
|
| |
Volume |
182 |
Issue |
|
Pages |
1724-1736 |
|
| |
Keywords |
A1 Journal Article; Lysozyme; Cold atmospheric plasma; Cancer cell death; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
|
| |
Abstract |
Bacterial and mammalian proteins, such as lysozyme, are gaining increasing interest as anticancer drugs. This study aims to modify the lysozyme structure using cold atmospheric plasma to boost its cancer cell killing effect. We investigated the structure at acidic and neutral pH using various experimental techniques (circular dichroism, fluorescence, and mass spectrometry) and molecular dynamics simulations. The controlled structural modification of lysozyme at neutral pH enhances its activity, while the activity was lost at acidic pH at the same treatment conditions. Indeed, a larger number of amino acids were oxidized at acidic pH after plasma treatment, which results in a greater distortion of the lysozyme structure, whereas only limited structural changes were observed in lysozyme after plasma treatment at neutral pH. We found that the plasma-treated lysozyme significantly induced apoptosis to the cancer cells. Our results reveal that plasma-treated lysozyme could have potential as a new cancer cell killing drug. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000675794700005 |
Publication Date |
2021-05-27 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0141-8130 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
3.671 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
Japan Society for the Promotion of Science; We gratefully acknowledge the European H2020 Marie SkłodowskaCurie Actions Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. NK thanks to National Research Foundation of Korea under Ministry of Science and ICT (NRF2021R1C1C1013875) of Korean Government. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. |
Approved |
Most recent IF: 3.671 |
|
| |
Call Number |
PLASMANT @ plasmant @c:irua:178813 |
Serial |
6792 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Attri, P.; Park, J.-H.; De Backer, J.; Kim, M.; Yun, J.-H.; Heo, Y.; Dewilde, S.; Shiratani, M.; Choi, E.H.; Lee, W.; Bogaerts, A. |
|
| |
Title |
Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study |
Type |
A1 Journal article |
| |
Year |
2020 |
Publication |
International Journal Of Biological Macromolecules |
Abbreviated Journal |
Int J Biol Macromol |
|
| |
Volume |
163 |
Issue |
|
Pages |
2405-2414 |
|
| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
| |
Abstract |
NADPH oxidases 1 (NOX1) derived reactive oxygen species (ROS) play an important role in the progression of cancer through signaling pathways. Therefore, in this paper, we demonstrate the effect of cold atmospheric plasma (CAP) on the structural changes of Noxa1 SH3 protein, one of the regulatory subunits of NOX1. For this purpose, firstly we purified the Noxa1 SH3 protein and analyzed the structure using X-ray crystallography, and subsequently, we treated the protein with two types of CAP reactors such as pulsed dielectric barrier discharge (DBD) and Soft Jet for different time intervals. The structural deformation of Noxa1 SH3 protein was analyzed by various experimental methods (circular dichroism, fluorescence, and NMR spectroscopy) and by MD simulations. Additionally, we demonstrate the effect of CAP (DBD and Soft Jet) on the viability and expression of NOX1 in A375 cancer cells. Our results are useful to understand the structural modification/oxidation occur in protein due to reactive oxygen and nitrogen (RONS) species generated by CAP. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000579839600233 |
Publication Date |
2020-09-19 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0141-8130 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
8.2 |
Times cited |
|
Open Access |
|
|
| |
Notes |
European Marie Skłodowska-Curie Individual Fellowship, 743546 ; JSPS, 20K14454 ; National Research Foundation of Korea, 2019M3A9F6021810 NRF-2017M3A9F6029753 NRF-2019M3E5D6063903 NRF-2016R1A6A3A04010213 ; Brain Korea 21; MSIT, NRF-2016K1A4A3914113 ; Hercules Foundation; Flemish Government; UA; We gratefully acknowledge the European Marie SkłodowskaCurie Individual Fellowship “Anticancer-PAM” within Horizon 2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. Additionally, work was supported by several grants (2019M3A9F6021810, NRF2017M3A9F6029753, NRF-2019M3E5D6063903 to W. Lee), Basic Science Research Program (NRF-2016R1A6A3A04010213 to J.H. Yun) through the National Research Foundation of Korea and in part by the Brain Korea 21 (BK21) PLUS program (J.H.P.). EHC is thankful to National Research Foundation (NRF) of Korea, funded by the Korea government (MSIT) under the grant number (NRF2016K1A4A3914113). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. |
Approved |
Most recent IF: 8.2; 2020 IF: 3.671 |
|
| |
Call Number |
PLASMANT @ plasmant @c:irua:172451 |
Serial |
6419 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Lin, A.; Sahun, M.; Biscop, E.; Verswyvel, H.; De Waele, J.; De Backer, J.; Theys, C.; Cuypers, B.; Laukens, K.; Berghe, W.V.; Smits, E.; Bogaerts, A. |
|
| |
Title |
Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma |
Type |
A1 Journal article |
| |
Year |
2023 |
Publication |
Drug resistance updates |
Abbreviated Journal |
|
|
| |
Volume |
67 |
Issue |
|
Pages |
100914 |
|
| |
Keywords |
A1 Journal article; Pharmacology. Therapy; ADReM Data Lab (ADReM); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
| |
Abstract |
To gain insights into the underlying mechanisms of NTP therapy sensitivity and resistance, using the firstever
NTP-resistant cell line derived from sensitive melanoma cells (A375).
Methods: Melanoma cells were exposed to NTP and re-cultured for 12 consecutive weeks before evaluation
against the parental control cells. Whole transcriptome sequencing analysis was performed to identify differentially
expressed genes and enriched molecular pathways. Glucose uptake, extracellular lactate, media acidification,
and mitochondrial respiration was analyzed to determine metabolic changes. Cell death inhibitors were
used to assess the NTP-induced cell death mechanisms, and apoptosis and ferroptosis was further validated via
Annexin V, Caspase 3/7, and lipid peroxidation analysis.
Results: Cells continuously exposed to NTP became 10 times more resistant to NTP compared to the parental cell
line of the same passage, based on their half-maximal inhibitory concentration (IC50). Sequencing and metabolic
analysis indicated that NTP-resistant cells had a preference towards aerobic glycolysis, while cell death analysis
revealed that NTP-resistant cells exhibited less apoptosis but were more vulnerable to lipid peroxidation and
ferroptosis.
Conclusions: A preference towards aerobic glycolysis and ferroptotic cell death are key physiological changes in
NTP-resistance cells, which opens new avenues for further, in-depth research into other cancer types. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000925156500001 |
Publication Date |
2022-12-29 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
1368-7646 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
24.3 |
Times cited |
|
Open Access |
OpenAccess |
|
| |
Notes |
The authors would like to thank Dr. Christophe Deben and Ms. Hannah Zaryouh (Center for Oncological Research, University of Antwerp) for the use and their help with the D300e Digital Dispenser and Spark® Cyto, as well as Ms. Rapha¨elle Corremans (Laboratory Pathophysiology, University of Antwerp) for the use of their lactate meter. The authors would also like to acknowledge the help from Ms. Tias Verhezen and Mr. Cyrus Akbari, who was involved at the start of the project but could not continue due to the COVID-19 pandemic. The authors also acknowledge the resources and services provided by the VSC (Flemish Supercomputer Center). This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaerts), and 1S67621N (Hanne Verswyvel). We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr. Willy Floren, and the Vereycken family. We would also like to acknowledge the support from the European Cooperation in Science & Technology (COST) Action on Therapeutical applications of Cold Plasmas (CA20114; PlasTHER). |
Approved |
Most recent IF: 24.3; 2023 IF: 10.906 |
|
| |
Call Number |
PLASMANT @ plasmant @c:irua:193167 |
Serial |
7240 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
De Backer, A.; Zhang, Z.; van den Bos, K.H.W.; Bladt, E.; Sánchez‐Iglesias, A.; Liz‐Marzán, L.M.; Nellist, P.D.; Bals, S.; Van Aert, S. |
|
| |
Title |
Element Specific Atom Counting at the Atomic Scale by Combining High Angle Annular Dark Field Scanning Transmission Electron Microscopy and Energy Dispersive X‐ray Spectroscopy |
Type |
A1 Journal article |
| |
Year |
2022 |
Publication |
Small methods |
Abbreviated Journal |
Small Methods |
|
| |
Volume |
|
Issue |
|
Pages |
2200875 |
|
| |
Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
A new methodology is presented to count the number of atoms in multimetallic nanocrystals by combining energy dispersive X-ray spectroscopy (EDX) and high angle annular dark field scanning transmission electron microscopy (HAADF STEM). For this purpose, the existence of a linear relationship between the incoherent HAADF STEM and EDX images is exploited. Next to the number of atoms for each element in the atomic columns, the method also allows quantification of the error in the obtained number of atoms, which is of importance given the noisy nature of the acquired EDX signals. Using experimental images of an Au@Ag core–shell nanorod, it is demonstrated that 3D structural information can be extracted at the atomic scale. Furthermore, simulated data of an Au@Pt core–shell nanorod show the prospect to characterize heterogeneous nanostructures with adjacent atomic numbers. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000862072700001 |
Publication Date |
2022-09-30 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
2366-9608 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
12.4 |
Times cited |
5 |
Open Access |
OpenAccess |
|
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A., Grant 815128 REALNANO to S.B., and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N) and a postdoctoral grant to A.D.B.; esteem3reported; esteem3JRA |
Approved |
Most recent IF: 12.4 |
|
| |
Call Number |
EMAT @ emat @c:irua:191570 |
Serial |
7109 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Hudry, D.; De Backer, A.; Popescu, R.; Busko, D.; Howard, I.A.; Bals, S.; Zhang, Y.; Pedrazo‐Tardajos, A.; Van Aert, S.; Gerthsen, D.; Altantzis, T.; Richards, B.S. |
|
| |
Title |
Interface Pattern Engineering in Core‐Shell Upconverting Nanocrystals: Shedding Light on Critical Parameters and Consequences for the Photoluminescence Properties |
Type |
A1 Journal article |
| |
Year |
2021 |
Publication |
Small |
Abbreviated Journal |
Small |
|
| |
Volume |
|
Issue |
|
Pages |
2104441 |
|
| |
Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT) |
|
| |
Abstract |
Advances in controlling energy migration pathways in core-shell lanthanide (Ln)-based hetero-nanocrystals (HNCs) have relied heavily on assumptions about how optically active centers are distributed within individual HNCs. In this article, it is demonstrated that different types of interface patterns can be formed depending on shell growth conditions. Such interface patterns are not only identified but also characterized with spatial resolution ranging from the nanometer- to the atomic-scale. In the most favorable cases, atomic-scale resolved maps of individual particles are obtained. It is also demonstrated that, for the same type of core-shell architecture, the interface pattern can be engineered with thicknesses of just 1 nm up to several tens of nanometers. Total alloying between the core and shell domains is also possible when using ultra-small particles as seeds. Finally, with different types of interface patterns (same architecture and chemical composition of the core and shell domains) it is possible to modify the output color (yellow, red, and green-yellow) or change (improvement or degradation) the absolute upconversion quantum yield. The results presented in this article introduce an important paradigm shift and pave the way toward the emergence of a new generation of core-shell Ln-based HNCs with better control over their atomic-scale organization. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000710758000001 |
Publication Date |
2021-10-25 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
1613-6810 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
8.643 |
Times cited |
17 |
Open Access |
OpenAccess |
|
| |
Notes |
The authors would like to acknowledge the financial support provided by the Helmholtz Recruitment Initiative Fellowship (B.S.R.) and the Helmholtz Association's Research Field Energy (Materials and Technologies for the Energy Transition program, Topic 1 Photovoltaics and Wind Energy). The authors would like to thank the Karlsruhe Nano Micro Facility (KNMF) for STEM access. 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 PICOMETRICS to S.V.A. and Grant agreement no. 815128 REALNANO to S.B.). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through Projects no. G.0502.18N, G.0267.18N, and a postdoctoral grant to A.D.B. T.A. acknowledges funding from the University of Antwerp Research fund (BOF). This project had received funding (EUSMI proposal #E181100205) from the European Union's Horizon 2020 Research and Innovation Programme under Grant agreement no 731019 (EUSMI). D.H. would like to thank “CGFigures” for helpful tutorials on 3D graphics with Blender.; sygmaSB |
Approved |
Most recent IF: 8.643 |
|
| |
Call Number |
EMAT @ emat @c:irua:183285 |
Serial |
6817 |
|
| Permanent link to this record |
