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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 (down) 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
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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 (down) 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
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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 (down) 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
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Author De Backer, A.; De Wael, A.; Gonnissen, J.; Martinez, G.T.; Béché, A.; MacArthur, K.E.; Jones, L.; Nellist, P.D.; Van Aert, S.
Title Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting: What are the limits? Type P1 Proceeding
Year 2015 Publication Journal of physics : conference series Abbreviated Journal
Volume 644 Issue 644 Pages 012034
Keywords P1 Proceeding; Electron microscopy for materials research (EMAT)
Abstract Quantitative atomic resolution annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique for nanoparticle atom-counting. However, a lot of nanoparticles provide a severe characterisation challenge because of their limited size and beam sensitivity. Therefore, quantitative ADF STEM may greatly benefit from statistical detection theory in order to optimise the instrumental microscope settings such that the incoming electron dose can be kept as low as possible whilst still retaining single-atom precision. The principles of detection theory are used to quantify the probability of error for atom-counting. This enables us to decide between different image performance measures and to optimise the experimental detector settings for atom-counting in ADF STEM in an objective manner. To demonstrate this, ADF STEM imaging of an industrial catalyst has been conducted using the near-optimal detector settings. For this experiment, we discussed the limits for atom-counting diagnosed by combining a thorough statistical method and detailed image simulations.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000366826200034 Publication Date 2015-10-13
Series Editor Series Title Abbreviated Series Title Electron Microscopy and Analysis Group Conference (EMAG), JUN 02-JUL 02, 2015, Manchester, ENGLAND
Series Volume Series Issue Edition
ISSN 1742-6588 ISBN Additional Links UA library record; WoS full record
Impact Factor Times cited Open Access
Notes (down) The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0368.15N, G.0369.15N, and G.0374.15N) and a PhD 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), ERC Starting Grant 278510 Vortex, and the UK Engineering and Physical Sciences Research Council (EP/K032518/1). The authors acknowledge Johnson-Matthey for providing the sample and PhD funding to K E MacArthur. A Rosenauer is acknowledged for providing the STEMsim program.; esteem2jra2; ECASJO; Approved Most recent IF: NA
Call Number c:irua:130314 c:irua:130314 Serial 4050
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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 (down) 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
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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 (down) 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
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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 (down) 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
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Author De Backer, A.; van den Bos, K.H.W.; Van den Broek, W.; Sijbers, J.; Van Aert, S.
Title StatSTEM: An efficient program for accurate and precise model-based quantification of atomic resolution electron microscopy images Type P1 Proceeding
Year 2017 Publication Journal of physics : conference series T2 – Electron Microscopy and Analysis Group Conference 2017 (EMAG2017), 3-6 July 2017, Manchester, UK Abbreviated Journal J. Phys.: Conf. Ser.
Volume 902 Issue Pages 012013
Keywords P1 Proceeding; Electron microscopy for materials research (EMAT); Vision lab
Abstract An efficient model-based estimation algorithm is introduced in order 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 the 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, is investigated. The highest attainable precision is reached even for low dose images. Furthermore, advantages of the model- based approach taking into account overlap between neighbouring columns are highlighted. 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 000416370700013 Publication Date 2017-10-16
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1742-6588 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor Times cited 1 Open Access OpenAccess
Notes (down) The authors acknowledge nancial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0374.13N, G.0368.15N, G.0369.15N, WO.010.16N) and a PhD 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. Approved Most recent IF: NA
Call Number EMAT @ emat @c:irua:147188 Serial 4764
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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 (down) 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
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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 (down) 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
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Author Martinez, G.T.; Rosenauer, A.; de Backer, A.; Verbeeck, J.; Van Aert, S.
Title Quantitative composition determination at the atomic level using model-based high-angle annular dark field scanning transmission electron microscopy Type A1 Journal article
Year 2014 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
Volume 137 Issue Pages 12-19
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000331092200003 Publication Date 2013-11-09
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 74 Open Access
Notes (down) FWO; FP7; ERC Countatoms; ESTEEM2; esteem2_ta Approved Most recent IF: 2.843; 2014 IF: 2.436
Call Number UA @ lucian @ c:irua:111579UA @ admin @ c:irua:111579 Serial 2749
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Author den Dekker, A.J.; Gonnissen, J.; de Backer, A.; Sijbers, J.; Van Aert, S.
Title Estimation of unknown structure parameters from high-resolution (S)TEM images : what are the limits? Type A1 Journal article
Year 2013 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
Volume 134 Issue Pages 34-43
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Abstract Statistical parameter estimation theory is proposed as a quantitative method to measure unknown structure parameters from electron microscopy images. Images are then purely considered as data planes from which structure parameters have to be determined as accurately and precisely as possible using a parametric statistical model of the observations. For this purpose, an efficient algorithm is proposed for the estimation of atomic column positions and intensities from high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. Furthermore, the so-called CramérRao lower bound (CRLB) is reviewed to determine the limits to the precision with which continuous parameters such as atomic column positions and intensities can be estimated. Since this lower bound can only be derived for continuous parameters, alternative measures using the principles of detection theory are introduced for problems concerning the estimation of discrete parameters such as atomic numbers. An experimental case study is presented to show the practical use of these measures for the optimization of the experiment design if the purpose is to decide between the presence of specific atom types using STEM images.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000324474900006 Publication Date 2013-06-01
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0304-3991; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.843 Times cited 31 Open Access
Notes (down) FWO; FP 2007-2013; Esteem2; esteem2_jra2 Approved Most recent IF: 2.843; 2013 IF: 2.745
Call Number UA @ lucian @ c:irua:109240 Serial 1083
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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 (down) 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
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Author Klingstedt, M.; Sundberg, M.; Eriksson, L.; Haigh, S.; Kirkland, A.; Grüner, D.; de Backer, A.; Van Aert, S.; Tarasaki, O.
Title Exit wave reconstruction from focal series of HRTEM images, single crystal XRD and total energy studies on SbxWO3+y (x\sim0.11) Type A1 Journal article
Year 2012 Publication Zeitschrift für Kristallographie Abbreviated Journal Z Krist-Cryst Mater
Volume 227 Issue 6 Pages 341-349
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract A new tungsten bronze in the SbWO system has been prepared in a solid state reaction from Sb2O3, WO3 and W metal powder. The average structure was determined by single crystal X-ray diffraction. SbxWO3+y (x ∼ 0.11) crystallizes in the orthorhombic space group Pm21n (no. 31), a = 27.8135(9) Å, b = 7.3659(2) Å and c = 3.8672(1) Å. The structure belongs to the (n)-ITB class of intergrowth tungsten bronzes. It contains slabs of hexagonal channels formed by six WO6 octahedra. These slabs are separated by three layers of WO6 octahedra that are arranged in a WO3-type fashion. The WO6 octahedra share all vertices to build up a three-dimensional framework. The hexagonal channels are filled with Sb atoms to ∼80% and additional O atoms. The atoms are shifted out of the center of the channels. Exit-wave reconstruction of focal series of high resolution-transmission-electron-microscope (HRTEM) images combined with statistical paramäeter estimation techniques allowed to study local ordering in the channels. Sb atoms in neighbouring channels tend to be displaced in the same direction, which is in agreement with total energy calculations on ordered structure models, but the ratio of the occupation of the two possible Sb sites varies from channel to channel. The structure of SbxWO3+y exhibits pronounced local modulations.
Address
Corporate Author Thesis
Publisher Place of Publication München Editor
Language Wos 000307314200003 Publication Date 2012-06-06
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2194-4946; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.179 Times cited 4 Open Access
Notes (down) Fwo; Esteem 026019 Approved Most recent IF: 3.179; 2012 IF: NA
Call Number UA @ lucian @ c:irua:101218 Serial 1131
Permanent link to this record
 
 
Author Goris, B.; de Beenhouwer, J.; de Backer, A.; Zanaga, D.; Batenburg, K.J.; Sánchez-Iglesias, A.; Liz-Marzán, L.M.; Van Aert, S.; Bals, S.; Sijbers, J.; Van Tendeloo, G.
Title Measuring lattice strain in three dimensions through electron microscopy Type A1 Journal article
Year 2015 Publication Nano letters Abbreviated Journal Nano Lett
Volume 15 Issue 15 Pages 6996-7001
Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Vision lab
Abstract The three-dimensional (3D) atomic structure of nanomaterials, including strain, is crucial to understand their properties. Here, we investigate lattice strain in Au nanodecahedra using electron tomography. Although different electron tomography techniques enabled 3D characterizations of nanostructures at the atomic level, a reliable determination of lattice strain is not straightforward. We therefore propose a novel model-based approach from which atomic coordinates are measured. Our findings demonstrate the importance of investigating lattice strain in 3D.
Address
Corporate Author Thesis
Publisher Place of Publication Washington Editor
Language Wos 000363003100108 Publication Date 2015-09-04
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1530-6984;1530-6992; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 12.712 Times cited 87 Open Access OpenAccess
Notes (down) Fwo; 335078 Colouratom; 267867 Plasmaquo; 312483 Esteem2; 262348 Esmi; esteem2jra4; ECASSara; (ROMEO:white; preprint:; postprint:restricted 12 months embargo; pdfversion:cannot); Approved Most recent IF: 12.712; 2015 IF: 13.592
Call Number c:irua:127639 c:irua:127639 Serial 1965
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Author Van Aert, S.; de Backer, A.; Martinez, G.T.; Goris, B.; Bals, S.; Van Tendeloo, G.; Rosenauer, A.
Title Procedure to count atoms with trustworthy single-atom sensitivity Type A1 Journal article
Year 2013 Publication Physical review : B : condensed matter and materials physics Abbreviated Journal Phys Rev B
Volume 87 Issue 6 Pages 064107-6
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract We report a method to reliably count the number of atoms from high-angle annular dark field scanning transmission electron microscopy images. A model-based analysis of the experimental images is used to measure scattering cross sections at the atomic level. The high sensitivity of these measurements in combination with a thorough statistical analysis enables us to count atoms with single-atom sensitivity. The validity of the results is confirmed by means of detailed image simulations. We will show that the method can be applied to nanocrystals of arbitrary shape, size, and atom type without the need for a priori knowledge about the atomic structure.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000315144700006 Publication Date 2013-02-20
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1098-0121;1550-235X; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.836 Times cited 106 Open Access
Notes (down) FWO; 262348 ESMI; 312483 ESTEEM2;246791 COUNTATOMS; Hercules 3; esteem2_jra2 Approved Most recent IF: 3.836; 2013 IF: 3.664
Call Number UA @ lucian @ c:irua:105674 Serial 2718
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Author Goris, B.; de Backer, A.; Van Aert, S.; Gómez-Graña, S.; Liz-Marzán, L.M.; Van Tendeloo, G.; Bals, S.
Title Three-dimensional elemental mapping at the atomic scale in bimetallic nanocrystals Type A1 Journal article
Year 2013 Publication Nano letters Abbreviated Journal Nano Lett
Volume 13 Issue 9 Pages 4236-4241
Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Abstract A thorough understanding of the three-dimensional (3D) atomic structure and composition of coreshell nanostructures is indispensable to obtain a deeper insight on their physical behavior. Such 3D information can be reconstructed from two-dimensional (2D) projection images using electron tomography. Recently, different electron tomography techniques have enabled the 3D characterization of a variety of nanostructures down to the atomic level. However, these methods have all focused on the investigation of nanomaterials containing only one type of chemical element. Here, we combine statistical parameter estimation theory with compressive sensing based tomography to determine the positions and atom type of each atom in heteronanostructures. The approach is applied here to investigate the interface in coreshell Au@Ag nanorods but it is of great interest in the investigation of a broad range of nanostructures.
Address
Corporate Author Thesis
Publisher Place of Publication Washington Editor
Language Wos 000330158900043 Publication Date 2013-08-16
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1530-6984;1530-6992; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 12.712 Times cited 90 Open Access
Notes (down) FWO; 246791 COUNTATOMS; 267867 PLASMAQUO; 262348 ESMI; 312483 ESTEEM2; Hercules 3; esteem2_jra4 Approved Most recent IF: 12.712; 2013 IF: 12.940
Call Number UA @ lucian @ c:irua:110036 Serial 3650
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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 (down) 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
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Author Gonnissen, J.; de Backer, A.; den Dekker, A.J.; Martinez, G.T.; Rosenauer, A.; Sijbers, J.; Van Aert, S.
Title Optimal experimental design for the detection of light atoms from high-resolution scanning transmission electron microscopy images Type A1 Journal article
Year 2014 Publication Applied physics letters Abbreviated Journal Appl Phys Lett
Volume 105 Issue 6 Pages 063116
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Abstract We report an innovative method to explore the optimal experimental settings to detect light atoms from scanning transmission electron microscopy (STEM) images. Since light elements play a key role in many technologically important materials, such as lithium-battery devices or hydrogen storage applications, much effort has been made to optimize the STEM technique in order to detect light elements. Therefore, classical performance criteria, such as contrast or signal-to-noise ratio, are often discussed hereby aiming at improvements of the direct visual interpretability. However, when images are interpreted quantitatively, one needs an alternative criterion, which we derive based on statistical detection theory. Using realistic simulations of technologically important materials, we demonstrate the benefits of the proposed method and compare the results with existing approaches.
Address
Corporate Author Thesis
Publisher American Institute of Physics Place of Publication New York, N.Y. Editor
Language Wos 000341188700073 Publication Date 2014-08-14
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-6951;1077-3118; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.411 Times cited 12 Open Access
Notes (down) FWO (G.0393.11; G.0064.10; and G.0374.13); European Union Seventh Framework Programme [FP7/2007-2013] under Grant Agreement No. 312483 (ESTEEM2); esteem2_jra2 Approved Most recent IF: 3.411; 2014 IF: 3.302
Call Number UA @ lucian @ c:irua:118333 Serial 2482
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 (down) Fwo Approved Most recent IF: 2.843; 2011 IF: 2.471
Call Number UA @ lucian @ c:irua:91879 Serial 1438
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Author Agrawal, H.; Patra, B.K.; Altantzis, T.; De Backer, A.; Garnett, E.C.
Title Quantifying Strain and Dislocation Density at Nanocube Interfaces after Assembly and Epitaxy Type A1 Journal article
Year 2020 Publication Acs Applied Materials & Interfaces Abbreviated Journal Acs Appl Mater Inter
Volume 12 Issue 7 Pages 8788-8794
Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT)
Abstract Nanoparticle self-assembly and epitaxy are utilized extensively to make 1D and 2D structures with complex shapes. High-resolution transmission electron microscopy (HRTEM) has shown that single-crystalline interfaces can form, but little is known about the strain and dislocations at these interfaces. Such information is critically important for applications: drastically reducing

dislocation density was the key breakthrough enabling widespread implementation of light-emitting diodes, while strain engineering has been fundamental to modern high-performance transistors, solar cells, and thermoelectrics. In this work, the interfacial defect and strain formation after selfassembly and room temperature epitaxy of 7 nm Pd nanocubes capped with polyvinylpyrrolidone (PVP) is examined. It is observed that, during ligand removal, the cubes move over large distances on the substrate, leading to both spontaneous self-assembly and epitaxy to form single crystals. Subsequently, atomically resolved images are used to quantify the strain and dislocation density at the epitaxial interfaces between cubes with different lateral and angular misorientations. It is shown that dislocation- and strain-free interfaces form when the nanocubes align parallel to each other. Angular misalignment between adjacent cubes does not necessarily lead to grain boundaries but does cause dislocations, with higher densities associated with larger rotations.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000515214300101 Publication Date 2020-02-19
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1944-8244 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 9.5 Times cited Open Access OpenAccess
Notes (down) Fonds Wetenschappelijk Onderzoek; H2020 Research Infrastructures, 731019 ; Nederlandse Organisatie voor Wetenschappelijk Onderzoek, 14846 ; The work at AMOLF is part of the research program of the “Nederlandse Organisatie voor Wetenschappelijk Onderzoek” (NWO). This work was supported by the NWO VIDI grant (project no. 14846). The authors would like to thank Reinout Jaarsma and Dr. Sven Askes for helping with the XPS measurements. A.D.B. acknowledges a postdoctoral grant from the research foundation Flanders (FWO). The authors acknowledge financial support from the European Commission under the Horizon 2020 Programme by means of the grant agreement no. 731019 EUSMI. Approved Most recent IF: 9.5; 2020 IF: 7.504
Call Number EMAT @ emat @c:irua:167770 Serial 6398
Permanent link to this record
 
 
Author Guzzinati, G.; Altantzis, T.; Batuk, M.; De Backer, A.; Lumbeeck, G.; Samaee, V.; Batuk, D.; Idrissi, H.; Hadermann, J.; Van Aert, S.; Schryvers, D.; Verbeeck, J.; Bals, S.
Title Recent Advances in Transmission Electron Microscopy for Materials Science at the EMAT Lab of the University of Antwerp Type A1 Journal article
Year 2018 Publication Materials Abbreviated Journal Materials
Volume 11 Issue 11 Pages 1304
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract The rapid progress in materials science that enables the design of materials down to the nanoscale also demands characterization techniques able to analyze the materials down to the same scale, such as transmission electron microscopy. As Belgium’s foremost electron microscopy group, among the largest in the world, EMAT is continuously contributing to the development of TEM techniques, such as high-resolution imaging, diffraction, electron tomography, and spectroscopies, with an emphasis on quantification and reproducibility, as well as employing TEM methodology at the highest level to solve real-world materials science problems. The lab’s recent contributions are presented here together with specific case studies in order to highlight the usefulness of TEM to the advancement of materials science.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000444112800041 Publication Date 2018-07-28
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1996-1944 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.654 Times cited 15 Open Access OpenAccess
Notes (down) Fonds Wetenschappelijk Onderzoek, G.0502.18N, G.0267.18N, G.0120.12N, G.0365.15N, G.0934.17N, S.0100.18N AUHA13009 ; European Research Council, COLOURATOM 335078 ; Universiteit Antwerpen, GOA Solarpaint ; G. Guzzinati, T. Altantzis and A. De Backer have been supported by postdoctoral fellowship grants from the Research Foundation Flanders (FWO). Funding was also received from the European Research Council (starting grant no. COLOURATOM 335078), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 770887), the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0502.18N, G.0267.18N, G.0120.12N, G.0365.15N, G.0934.17N, S.0100.18N, G.0401.16N) and from the University of Antwerp through GOA project Solarpaint. Funding for the TopSPIN precession system under grant AUHA13009, as well as for the Qu-Ant-EM microscope, is acknowledged from the HERCULES Foundation. H. Idrissi is mandated by the Belgian National Fund for Scientific Research (F.R.S.-FNRS). (ROMEO:green; preprint:; postprint:can ; pdfversion:can); saraecas; ECAS_Sara; Approved Most recent IF: 2.654
Call Number EMAT @ emat @c:irua:153737UA @ admin @ c:irua:153737 Serial 5064
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 (down) 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
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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 (down) 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
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Author van den Broek, W.; Verbeeck, J.; Schryvers, D.; de Backer, S.; Scheunders, P.
Title Tomographic spectroscopic imaging; an experimental proof of concept Type A1 Journal article
Year 2009 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
Volume 109 Issue 4 Pages 296-303
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Abstract Recording the electron energy loss spectroscopy data cube with a series of energy filtered images is a dose inefficient process because the energy slit blocks most of the electrons. When recording the data cube by scanning an electron probe over the sample, perfect dose efficiency is attained; but due to the low current in nanoprobes, this often is slower, with a smaller field of view. In W. Van den Broek et al. [Ultramicroscopy, 106 (2006) 269], we proposed a new method to record the data cube, which is more dose efficient than an energy filtered series. It produces a set of projections of the data cube and then tomographically reconstructs it. In this article, we demonstrate these projections in practice, we present a simple geometrical model that allows for quantification of the projection angles and we present the first successful experimental reconstruction, all on a standard post-column instrument.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000265345400003 Publication Date 2008-12-10
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 2.843 Times cited 1 Open Access
Notes (down) Esteem 026019 Approved Most recent IF: 2.843; 2009 IF: 2.067
Call Number UA @ lucian @ c:irua:77271 Serial 3671
Permanent link to this record
 
 
Author Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S.
Title Atom column detection Type H2 Book chapter
Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
Volume Issue Pages 177-214
Keywords H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
Abstract By combining statistical parameter estimation and model-order selection using a Bayesian framework, the maximum a posteriori (MAP) probability rule is proposed in this chapter as an objective and quantitative method to detect atom columns from high-resolution scanning transmission electron microscopy (HRSTEM) images. The validity and usefulness of this approach is demonstrated to both simulated and experimental annular dark-field (ADF) STEM images, but also to simultaneously acquired annular bright-field (ABF) and ADF STEM image data.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos Publication Date 2021-03-06
Series Editor Series Title Abbreviated Series Title
Series Volume 217 Series Issue Edition
ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
Impact Factor Times cited Open Access Not_Open_Access
Notes (down) ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
Call Number UA @ admin @ c:irua:177531 Serial 6775
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
Title Atom counting Type H2 Book chapter
Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
Volume Issue Pages 91-144
Keywords H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
Abstract In this chapter, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high-resolution annular dark-field (ADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. We show that this method can be applied to nanocrystals of arbitrary shape, size, and atom type. The validity of the atom-counting results is confirmed by means of detailed image simulations and it is shown that the high sensitivity of our method enables us to count atoms with single atom sensitivity.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos Publication Date 2021-03-06
Series Editor Series Title Abbreviated Series Title
Series Volume 217 Series Issue Edition
ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
Impact Factor Times cited Open Access Not_Open_Access
Notes (down) ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
Call Number UA @ admin @ c:irua:177529 Serial 6776
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
Title Efficient fitting algorithm Type H2 Book chapter
Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
Volume Issue Pages 73-90
Keywords H2 Book chapter; Electron microscopy for materials research (EMAT)
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 neighboring columns, enabling the analysis of a large field of view. To provide end-users with this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. In this chapter, this efficient algorithm is applied to three different nanostructures for which the analysis of a large field of view is required.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos Publication Date 2021-03-06
Series Editor Series Title Abbreviated Series Title
Series Volume 217 Series Issue Edition
ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
Impact Factor Times cited Open Access Not_Open_Access
Notes (down) ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
Call Number UA @ admin @ c:irua:177528 Serial 6778
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
Title General conclusions and future perspectives Type H2 Book chapter
Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
Volume Issue Pages 243-253
Keywords H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
Abstract This chapter provides an overview of statistical and quantitative methodologies that have pushed (scanning) transmission electron microscopy ((S)TEM) toward accurate and precise measurements of unknown structure parameters for understanding the relation between the structure of a material and its properties. Hereby, statistical parameter estimation theory has extensively been used which enabled not only measuring atomic column positions, but also quantifying the number of atoms, and detecting atomic columns as accurately and precisely as possible from experimental images. As a general conclusion, it can be stated that advanced statistical techniques are ideal tools to perform quantitative electron microscopy at the atomic scale. In the future, statistical methods will continue to be developed and novel quantification procedures will open up new possibilities for studying material structures at the atomic scale.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos Publication Date 2021-03-06
Series Editor Series Title Abbreviated Series Title
Series Volume 217 Series Issue Edition
ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
Impact Factor Times cited Open Access Not_Open_Access
Notes (down) ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
Call Number UA @ admin @ c:irua:177533 Serial 6781
Permanent link to this record
 
 
Author Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S.
Title Image-quality evaluation and model selection with maximum a posteriori probability Type H2 Book chapter
Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
Volume Issue Pages 215-242
Keywords H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
Abstract The maximum a posteriori (MAP) probability rule for atom column detection can also be used as a tool to evaluate the relation between scanning transmission electron microscopy (STEM) image quality and atom detectability. In this chapter, a new image-quality measure is proposed that correlates well with atom detectability, namely the integrated contrast-to-noise ratio (ICNR). Furthermore, the working principle of the MAP probability rule is described in detail showing a close relation to the principles of model-selection methods.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos Publication Date 2021-03-06
Series Editor Series Title Abbreviated Series Title
Series Volume 217 Series Issue Edition
ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
Impact Factor Times cited Open Access Not_Open_Access
Notes (down) ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
Call Number UA @ admin @ c:irua:177532 Serial 6782
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