1
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Schwarz TM, Yang J, Aota LS, Woods E, Zhou X, Neugebauer J, Todorova M, McCarroll I, Gault B. Quasi-"In Situ" Analysis of the Reactive Liquid-Solid Interface during Magnesium Corrosion Using Cryo-Atom Probe Tomography. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2401735. [PMID: 38813786 DOI: 10.1002/adma.202401735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/23/2024] [Indexed: 05/31/2024]
Abstract
The early stages of corrosion occurring at liquid-solid interfaces control the evolution of the material's degradation process, yet due to their transient state, their analysis remains a formidable challenge. Here corrosion tests are performed on a MgCa alloy, a candidate material for biodegradable implants using pure water as a model system. The corrosion reaction is suspended by plunge freezing into liquid nitrogen. The evolution of the early-stage corrosion process on the nanoscale by correlating cryo-atom probe tomography (APT) with transmission-electron microscopy (TEM) and spectroscopy, is studied. The outward growth of Mg hydroxide Mg(OH)2 and the inward growth of an intermediate corrosion layer consisting of hydrloxides of different compositions, mostly monohydroxide Mg(OH) instead of the expected MgO layer, are observed. In addition, Ca partitions to these newly formed hydroxides and oxides. Density-functional theory calculations suggest a domain of stability for this previously experimental unreported Mg(OH) phase. This new approach and these new findings advance the understanding of the early stages of magnesium corrosion, and in general reactions and processes at liquid-solid interfaces, which can further facilitate the development of corrosion-resistant materials or better control of the biodegradation rate of future implants.
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Affiliation(s)
- Tim M Schwarz
- Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany
| | - Jing Yang
- Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany
| | - Leonardo S Aota
- Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany
| | - Eric Woods
- Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany
| | - Xuyang Zhou
- Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany
| | - Jörg Neugebauer
- Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany
| | - Mira Todorova
- Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany
| | - Ingrid McCarroll
- Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany
| | - Baptiste Gault
- Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany
- Department of Materials, Imperial College London, London, SW7 2AZ, UK
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2
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Tegg L, McCarroll IE, Kim SH, Dubosq R, Woods EV, El-Zoka AA, Gault B, Cairney JM. Analysis of Water Ice in Nanoporous Copper Needles Using Cryo Atom Probe Tomography. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024:ozae062. [PMID: 39027931 DOI: 10.1093/mam/ozae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/23/2024] [Accepted: 06/23/2024] [Indexed: 07/20/2024]
Abstract
The application of atom probe tomography (APT) to frozen liquids is limited by difficulties in specimen preparation. Here, we report on the use of nanoporous Cu needles as a physical framework to hold water ice for investigation using APT. Nanoporous Cu needles are prepared by electropolishing and dealloying Cu-Mn matchstick precursors. Cryogenic scanning electron microscopy and focused ion beam milling reveal a hierarchical, dendritic, highly wettable microstructure. The atom probe mass spectrum is dominated by peaks of Cu+ and H(H2O)n+ up to n ≤ 3, and the reconstructed volume shows the protrusion of a Cu ligament into an ice-filled pore. The continuous Cu ligament network electrically connects the apex to the cryostage, leading to an enhanced electric field at the apex and increased cooling, both of which simplify the mass spectrum compared to previous reports.
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Affiliation(s)
- Levi Tegg
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Camperdown, New South Wales 2006, Australia
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Ingrid E McCarroll
- Department of Microstructure Physics and Alloy Design,Max-Planck-Institut für Eisenforschung, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Se-Ho Kim
- Department of Microstructure Physics and Alloy Design,Max-Planck-Institut für Eisenforschung, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
- Department of Materials Science and Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Renelle Dubosq
- Department of Microstructure Physics and Alloy Design,Max-Planck-Institut für Eisenforschung, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Eric V Woods
- Department of Microstructure Physics and Alloy Design,Max-Planck-Institut für Eisenforschung, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Ayman A El-Zoka
- Department of Microstructure Physics and Alloy Design,Max-Planck-Institut für Eisenforschung, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Baptiste Gault
- Department of Microstructure Physics and Alloy Design,Max-Planck-Institut für Eisenforschung, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Julie M Cairney
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Camperdown, New South Wales 2006, Australia
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Camperdown, New South Wales 2006, Australia
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3
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Exertier F, Tegg L, Taylor A, Cairney JM, Fu J, Marceau RKW. Nanoscale Analysis of Frozen Water by Atom Probe Tomography Using Graphene Encapsulation and Cryo-Workflows. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024:ozae054. [PMID: 38905154 DOI: 10.1093/mam/ozae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/24/2024] [Accepted: 05/28/2024] [Indexed: 06/23/2024]
Abstract
There has been an increasing interest in atom probe tomography (APT) to characterize hydrated and biological materials. A major benefit of APT compared to microscopy techniques more commonly used in biology is its combination of outstanding three-dimensional (3D) spatial resolution and mass sensitivity. APT has already been successfully used to characterize biominerals, revealing key structural information at the atomic scale, however there are many challenges inherent to the analysis of soft hydrated materials. New preparation protocols, often involving specimen preparation and transfer at cryogenic temperature, enable APT analysis of hydrated materials and have the potential to enable 3D atomic scale characterization of biological materials in the near-native hydrated state. In this study, samples of pure water at the tips of tungsten needle specimens were prepared at room temperature by graphene encapsulation. A comparative study was conducted where specimens were transferred at either room temperature or cryo-temperature and analyzed by APT by varying the flight path and pulsing mode. The differences between the analysis workflows are presented along with recommendations for future studies, and the compatibility between graphene coating and cryogenic workflows is demonstrated.
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Affiliation(s)
- Florant Exertier
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - Levi Tegg
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW 2006, Australia
| | - Adam Taylor
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - Julie M Cairney
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Ross K W Marceau
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
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Woods EV, Saksena A, El-Zoka AA, Stephenson LT, Schwarz TM, Singh MP, Aota LS, Kim SH, Schneider J, Gault B. Nanoporous Gold Thin Films as Substrates to Analyze Liquids by Cryo-atom Probe Tomography. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024:ozae041. [PMID: 38833315 DOI: 10.1093/mam/ozae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/09/2024] [Accepted: 04/24/2024] [Indexed: 06/06/2024]
Abstract
Cryogenic atom probe tomography (cryo-APT) is being developed to enable nanoscale compositional analyses of frozen liquids. Yet, the availability of readily available substrates that allow for the fixation of liquids while providing sufficient strength to their interface is still an issue. Here, we propose the use of 1-2-µm-thick binary alloy film of gold-silver sputtered onto flat silicon, with sufficient adhesion without an additional layer. Through chemical dealloying, we successfully fabricate a nanoporous substrate, with an open-pore structure, which is mounted on a microarray of Si posts by lift-out in the focused-ion beam system, allowing for cryogenic fixation of liquids. We present cryo-APT results obtained after cryogenic sharpening, vacuum cryo-transfer, and analysis of pure water on the top and inside the nanoporous film. We demonstrate that this new substrate has the requisite characteristics for facilitating cryo-APT of frozen liquids, with a relatively lower volume of precious metals. This complete workflow represents an improved approach for frozen liquid analysis, from preparation of the films to the successful fixation of the liquid in the porous network, to cryo-APT.
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Affiliation(s)
- Eric V Woods
- Max-Planck-Institut für Eisenforschung, Mikrostrukturphysik und Legierungsdesign, Max-Planck-Str. 1, Düsseldorf, Germany
| | - Aparna Saksena
- Max-Planck-Institut für Eisenforschung, Mikrostrukturphysik und Legierungsdesign, Max-Planck-Str. 1, Düsseldorf, Germany
| | - Ayman A El-Zoka
- Max-Planck-Institut für Eisenforschung, Mikrostrukturphysik und Legierungsdesign, Max-Planck-Str. 1, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Leigh T Stephenson
- Max-Planck-Institut für Eisenforschung, Mikrostrukturphysik und Legierungsdesign, Max-Planck-Str. 1, Düsseldorf, Germany
| | - Tim M Schwarz
- Max-Planck-Institut für Eisenforschung, Mikrostrukturphysik und Legierungsdesign, Max-Planck-Str. 1, Düsseldorf, Germany
| | - Mahander P Singh
- Max-Planck-Institut für Eisenforschung, Mikrostrukturphysik und Legierungsdesign, Max-Planck-Str. 1, Düsseldorf, Germany
| | - Leonardo S Aota
- Max-Planck-Institut für Eisenforschung, Mikrostrukturphysik und Legierungsdesign, Max-Planck-Str. 1, Düsseldorf, Germany
| | - Se-Ho Kim
- Max-Planck-Institut für Eisenforschung, Mikrostrukturphysik und Legierungsdesign, Max-Planck-Str. 1, Düsseldorf, Germany
| | - Jochen Schneider
- Materials Chemistry, RWTH Aachen University, Kopernikusstrasse. 10, 52074 Aachen, Germany
| | - Baptiste Gault
- Max-Planck-Institut für Eisenforschung, Mikrostrukturphysik und Legierungsdesign, Max-Planck-Str. 1, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
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5
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Vorlaufer N, Josten J, Carl S, Göbel E, Søgaard A, Taccardi N, Spiecker E, Felfer P. Preparation of atom probe tips from (nano)particles in dispersion using (di)electrophoresis and electroplating. Microsc Res Tech 2024; 87:476-483. [PMID: 37921114 DOI: 10.1002/jemt.24448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/15/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
The behavior of catalytic particles depends on their chemical structure and morphology. To reveal this information, the characterization with atom probe tomography has huge potential. Despite progresses and papers proposing various approaches towards the incorporation of particles inside atom probe tips, no single approach has been broadly applicable to date. In this paper, we introduce a workflow that allowed us to prepare atom probe specimens from Ga particles in suspension in the size range of 50 nm up to 2 μm. By combining dielectrophoresis and electrodeposition in a suitable way, we achieve a near-tip shape geometry, without a time-consuming FIB lift-out. This workflow is a simple and quick method to prepare atom probe tips and allows for a high preparation throughput. Also, not using a lift-out allowed us to use a cryo-stage, avoiding melting of the Ga particles, while ensuring a mechanical stable atom probe tip. The specimen prepared by this workflow enable a stable measurement and low fracture rates. RESEARCH HIGHLIGHTS: Enabling cryo-preparation of (nano)particles for the atom probe. Characterization of surface and bulk elemental distribution of GaPt model SCALMS.
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Affiliation(s)
- Nora Vorlaufer
- Institute I, Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jan Josten
- Institute I, Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Simon Carl
- Institute of Micro- and Nanostructure Research (IMN) and Center for Nanoanalysis and Electron Microscopy (CENEM), Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Erik Göbel
- Institute I, Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Alexander Søgaard
- Institute of Chemical Reaction Engineering, Department Chemical and Biological Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- CHEC Research Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicola Taccardi
- Institute of Chemical Reaction Engineering, Department Chemical and Biological Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Erdmann Spiecker
- Institute of Micro- and Nanostructure Research (IMN) and Center for Nanoanalysis and Electron Microscopy (CENEM), Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Peter Felfer
- Institute I, Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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6
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Schwarz TM, Woods E, Singh MP, Chen X, Jung C, Aota LS, Jang K, Krämer M, Kim SH, McCarroll I, Gault B. In Situ Metallic Coating of Atom Probe Specimen for Enhanced Yield, Performance, and Increased Field-of-View. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024:ozae006. [PMID: 38366381 DOI: 10.1093/mam/ozae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
Atom probe tomography requires needle-shaped specimens with a diameter typically below 100 nm, making them both very fragile and reactive, and defects (notches at grain boundaries or precipitates) are known to affect the yield and data quality. The use of a conformal coating directly on the sharpened specimen has been proposed to increase yield and reduce background. However, to date, these coatings have been applied ex situ and mostly are not uniform. Here, we report on the controlled focused-ion beam in situ deposition of a thin metal film on specimens immediately after specimen preparation. Different metallic targets e.g. Cr were attached to a micromanipulator via a conventional lift-out method and sputtered using Ga or Xe ions. We showcase the many advantages of coating specimens from metallic to nonmetallic materials. We have identified an increase in data quality and yield, an improvement of the mass resolution, as well as an increase in the effective field-of-view. This wider field-of-view enables visualization of the entire original specimen, allowing to detect the complete surface oxide layer around the specimen. The ease of implementation of the approach makes it very attractive for generalizing its use across a very wide range of atom probe analyses.
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Affiliation(s)
- Tim M Schwarz
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
| | - Eric Woods
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
| | - Mahander P Singh
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
| | - Xinren Chen
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
| | - Chanwon Jung
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
| | - Leonardo S Aota
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
| | - Kyuseon Jang
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Mathias Krämer
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
| | - Se-Ho Kim
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
| | - Ingrid McCarroll
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
| | - Baptiste Gault
- Department of Microstructure Physics and Alloy Design, Max-Planck-Institut für Eisenforschung, Max-Planck-Str. 1, Düsseldorf 40237, Germany
- Department of Materials, Imperial College London, London SW7 2AZ, UK
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7
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Woods EV, Singh MP, Kim SH, Schwarz TM, Douglas JO, El-Zoka AA, Giulani F, Gault B. A Versatile and Reproducible Cryo-sample Preparation Methodology for Atom Probe Studies. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1992-2003. [PMID: 37856778 DOI: 10.1093/micmic/ozad120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/14/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023]
Abstract
Repeatable and reliable site-specific preparation of specimens for atom probe tomography (APT) at cryogenic temperatures has proven challenging. A generalized workflow is required for cryogenic specimen preparation including lift-out via focused ion beam and in situ deposition of capping layers, to strengthen specimens that will be exposed to high electric field and stresses during field evaporation in APT and protect them from environment during transfer into the atom probe. Here, we build on existing protocols and showcase preparation and analysis of a variety of metals, oxides, and supported frozen liquids and battery materials. We demonstrate reliable in situ deposition of a metallic capping layer that significantly improves the atom probe data quality for challenging material systems, particularly battery cathode materials which are subjected to delithiation during the atom probe analysis itself. Our workflow design is versatile and transferable widely to other instruments.
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Affiliation(s)
- Eric V Woods
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
| | - Mahander P Singh
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
| | - Se-Ho Kim
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
| | - Tim M Schwarz
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
| | - James O Douglas
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Ayman A El-Zoka
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Finn Giulani
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Baptiste Gault
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
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8
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Schiøtz OH, Kaiser CJO, Klumpe S, Morado DR, Poege M, Schneider J, Beck F, Klebl DP, Thompson C, Plitzko JM. Serial Lift-Out: sampling the molecular anatomy of whole organisms. Nat Methods 2023:10.1038/s41592-023-02113-5. [PMID: 38110637 DOI: 10.1038/s41592-023-02113-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/25/2023] [Indexed: 12/20/2023]
Abstract
Cryo-focused ion beam milling of frozen-hydrated cells and subsequent cryo-electron tomography (cryo-ET) has enabled the structural elucidation of macromolecular complexes directly inside cells. Application of the technique to multicellular organisms and tissues, however, is still limited by sample preparation. While high-pressure freezing enables the vitrification of thicker samples, it prolongs subsequent preparation due to increased thinning times and the need for extraction procedures. Additionally, thinning removes large portions of the specimen, restricting the imageable volume to the thickness of the final lamella, typically <300 nm. Here we introduce Serial Lift-Out, an enhanced lift-out technique that increases throughput and obtainable contextual information by preparing multiple sections from single transfers. We apply Serial Lift-Out to Caenorhabditis elegans L1 larvae, yielding a cryo-ET dataset sampling the worm's anterior-posterior axis, and resolve its ribosome structure to 7 Å and a subregion of the 11-protofilament microtubule to 13 Å, illustrating how Serial Lift-Out enables the study of multicellular molecular anatomy.
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Affiliation(s)
- Oda Helene Schiøtz
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christoph J O Kaiser
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sven Klumpe
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Dustin R Morado
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department for Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Matthias Poege
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jonathan Schneider
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Beck
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David P Klebl
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christopher Thompson
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Jürgen M Plitzko
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
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9
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Klumpe S, Schioetz OH, Kaiser C, Luchner M, Brenner J, Plitzko JM. Developments in cryo-FIB Sample Preparation: Targeting in Cryo-Lift-Out Preparation of Tissues and Machine Learning Models for Fully Automated On-Grid Lamella Preparation. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:511-513. [PMID: 37613116 DOI: 10.1093/micmic/ozad067.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Sven Klumpe
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Oda H Schioetz
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | | | - Marina Luchner
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Johann Brenner
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
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10
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Douglas JO, Conroy M, Giuliani F, Gault B. In Situ Sputtering From the Micromanipulator to Enable Cryogenic Preparation of Specimens for Atom Probe Tomography by Focused-Ion Beam. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1009-1017. [PMID: 37749683 DOI: 10.1093/micmic/ozad020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/13/2023] [Accepted: 02/05/2023] [Indexed: 09/27/2023]
Abstract
Workflows have been developed in the past decade to enable atom probe tomography analysis at cryogenic temperatures. The inability to control the local deposition of the metallic precursor from the gas-injection system (GIS) at cryogenic temperatures makes the preparation of site-specific specimens by using lift-out extremely challenging in the focused-ion beam. Schreiber et al. exploited redeposition to weld the lifted-out sample to a support. Here, we build on their approach to attach the region-of-interest and additionally strengthen the interface with locally sputtered metal from the micromanipulator. Following standard focused-ion beam annular milling, we demonstrate atom probe analysis of Si in both laser pulsing and voltage mode, with comparable analytical performance as a presharpened microtip coupon. Our welding approach is versatile, as various metals could be used for sputtering, and allows similar flexibility as the GIS in principle.
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Affiliation(s)
- James O Douglas
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Michele Conroy
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Finn Giuliani
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Baptiste Gault
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Str. 1, 40237 Düsseldorf, Germany
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Schwarz TM, Ott J, Solodenko H, Schmitz G, Stender P. Nanoscale analysis of frozen honey by atom probe tomography. Sci Rep 2022; 12:17786. [PMID: 36273026 PMCID: PMC9587987 DOI: 10.1038/s41598-022-22717-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/18/2022] [Indexed: 01/19/2023] Open
Abstract
Three-dimensional reconstruction of the analysed volume is one of the main goals of atom probe tomography (APT) and can deliver nearly atomic resolution (~ 0.2 nm spatial resolution) and chemical information with a mass sensitivity down to the ppm range. Extending this technique to frozen biological systems would have an enormous impact on the structural analysis of biomolecules. In previous works, we have shown that it is possible to measure frozen liquids with APT. In this paper, we demonstrate the ability of APT to trace nanoscale precipitation in frozen natural honey. While the mass signals of the common sugar fragments CxHy and CxOyHz overlap with (H2O)nH from water, we achieved correct stoichiometric values via different interpretation approaches for the peaks and thus determined the water content reliably. Next, we use honey to investigate the spatial resolution capabilities as a step toward the measurement of biological molecules in solution in 3D with sub-nanometer resolution. This may take analytical techniques to a new level, since methods of chemical characterization for cryogenic samples, especially biological samples, are still limited.
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Affiliation(s)
- Tim M. Schwarz
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Jonas Ott
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Helena Solodenko
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Guido Schmitz
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Patrick Stender
- grid.5719.a0000 0004 1936 9713Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569 Stuttgart, Germany
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12
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Long DM, Singh MK, Small KA, Watt J. Cryo-FIB for TEM investigation of soft matter and beam sensitive energy materials. NANOTECHNOLOGY 2022; 33:503001. [PMID: 36121746 DOI: 10.1088/1361-6528/ac92eb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Abstract
Primarily driven by structural biology, the rapid advances in cryogenic electron microscopy techniques are now being adopted and applied by materials scientists. Samples that inherently have electron transparency can be rapidly frozen (vitrified) in amorphous ice and imaged directly on a cryogenic transmission electron microscopy (cryo-TEM), however this is not the case for many important materials systems, which can consist of layered structures, embedded architectures, or be contained within a device. Cryogenic focused ion beam (cryo-FIB) lift-out procedures have recently been developed to extract intact regions and interfaces of interest, that can then be thinned to electron transparency and transferred to the cryo-TEM for characterization. Several detailed studies have been reported demonstrating the cryo-FIB lift-out procedure, however due to its relative infancy in materials science improvements are still required to ensure the technique becomes more accessible and routinely successful. Here, we review recent results on the preparation of cryo-TEM lamellae using cryo-FIB and show that the technique is broadly applicable to a range of soft matter and beam sensitive energy materials. We then present a tutorial that can guide the materials scientist through the cryo-FIB lift-out process, highlighting recent methodological advances that address the most common failure points of the technique, such as needle attachment, lift-out and transfer, and final thinning.
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Affiliation(s)
- Daniel M Long
- Sandia National Laboratories, Albuquerque, NM 87123, United States of America
| | - Manish Kumar Singh
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Kathryn A Small
- Sandia National Laboratories, Albuquerque, NM 87123, United States of America
| | - John Watt
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
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13
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Zhang S, Gervinskas G, Qiu S, Venugopal H, Marceau RKW, de Marco A, Li J, Fu J. Methods of Preparing Nanoscale Vitreous Ice Needles for High-Resolution Cryogenic Characterization. NANO LETTERS 2022; 22:6501-6508. [PMID: 35926226 DOI: 10.1021/acs.nanolett.2c01495] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
New high-resolution imaging methods for biological samples such as atom probe tomography (APT), facilitated by the invention of laser-pulsed atom probes and cryo-transfer procedures, have recently emerged. However, ensuring the vitreous state of the fabricated aqueous needle-shaped APT samples remains a challenge despite it being crucial for characterizing biomolecules such as proteins and cellular architectures in their near-native state. Our work investigated three potential approaches: (1) open microcapillary (OMC) method, (2) high-pressure freezing method (HPF), and (3) graphene encapsulation method. Diffraction patterns of the needle specimens acquired by cryo-TEM have demonstrated the vitreous state of the ice needles, although limited to the tip regions, has been achieved with the three proposed approaches. With the capability to prepare vitreous ice needles from hydrated samples of up to ∼200 μm thickness (HPF), combined use of the three approaches opens new avenues for future near-atomic imaging of biological cells in their near-native state.
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Affiliation(s)
- Shuo Zhang
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Gediminas Gervinskas
- Ramaciotti Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia
| | - Shi Qiu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Hari Venugopal
- Ramaciotti Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia
| | - Ross K W Marceau
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
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14
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Segreto N, Schwarz TM, Dietrich CA, Stender P, Schuldt R, Schmitz G, Kästner J. Understanding the Underlying Field Evaporation Mechanism of Pure Water Tips in High Electrical Fields. J Phys Chem A 2022; 126:5663-5671. [PMID: 35972399 DOI: 10.1021/acs.jpca.2c04163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the field evaporation process of frozen water in atom probe tomography (APT) by density functional simulations. In previous experiments, a strong tailing effect was observed for peaks caused by the molecular structure (H2O)nH+, in contrast to other peaks. In purely field-induced and thermally assisted evaporation simulations, we found that chains of protonated water molecules were pulled out of the dielectric surface by up to 6 Å, which are stable over a wide range of field strengths. Therefore, the resulting water clusters experience only part of the acceleration after evaporation compared to molecules evaporating directly from the surface and, thus, exhibit an energy deficit, which explains the tailing effect. Our simulations provide new insight into the complex evaporation behavior of water in high electrical fields and reveal possibilities for adapting the existing reconstruction algorithms.
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Affiliation(s)
- Nico Segreto
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Tim M Schwarz
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Carolin A Dietrich
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Patrick Stender
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Robin Schuldt
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guido Schmitz
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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15
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Grandfield K, Micheletti C, Deering J, Arcuri G, Tang T, Langelier B. Atom Probe Tomography for Biomaterials and Biomineralization. Acta Biomater 2022; 148:44-60. [DOI: 10.1016/j.actbio.2022.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/18/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023]
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16
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Molecular Dynamics Simulation and Cryo-Electron Microscopy Investigation of AOT Surfactant Structure at the Hydrated Mica Surface. MINERALS 2022. [DOI: 10.3390/min12040479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Structural properties of the anionic surfactant dioctyl sodium sulfosuccinate (AOT or Aerosol-OT) adsorbed on the mica surface were investigated by molecular dynamics simulation, including the effect of surface loading in the presence of monovalent and divalent cations. The simulations confirmed recent neutron reflectivity experiments that revealed the binding of anionic surfactant to the negatively charged surface via adsorbed cations. At low loading, cylindrical micelles formed on the surface, with sulfate head groups bound to the surface by water molecules or adsorbed cations. Cation bridging was observed in the presence of weakly hydrating monovalent cations, while sulfate groups interacted with strongly hydrating divalent cations through water bridges. The adsorbed micelle structure was confirmed experimentally with cryogenic electronic microscopy, which revealed micelles approximately 2 nm in diameter at the basal surface. At higher AOT loading, the simulations reveal adsorbed bilayers with similar surface binding mechanisms. Adsorbed micelles were slightly thicker (2.2–3.0 nm) than the corresponding bilayers (2.0–2.4 nm). Upon heating the low loading systems from 300 K to 350 K, the adsorbed micelles transformed to a more planar configuration resembling bilayers. The driving force for this transition is an increase in the number of sulfate head groups interacting directly with adsorbed cations.
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17
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Stender P, Gault B, Schwarz TM, Woods EV, Kim SH, Ott J, Stephenson LT, Schmitz G, Freysoldt C, Kästner J, El-Zoka AA. Status and Direction of Atom Probe Analysis of Frozen Liquids. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-18. [PMID: 35039105 DOI: 10.1017/s1431927621013994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Imaging of liquids and cryogenic biological materials by electron microscopy has been recently enabled by innovative approaches for specimen preparation and the fast development of optimized instruments for cryo-enabled electron microscopy (cryo-EM). Yet, cryo-EM typically lacks advanced analytical capabilities, in particular for light elements. With the development of protocols for frozen wet specimen preparation, atom probe tomography (APT) could advantageously complement insights gained by cryo-EM. Here, we report on different approaches that have been recently proposed to enable the analysis of relatively large volumes of frozen liquids from either a flat substrate or the fractured surface of a wire. Both allowed for analyzing water ice layers which are several micrometers thick consisting of pure water, pure heavy water, and aqueous solutions. We discuss the merits of both approaches and prospects for further developments in this area. Preliminary results raise numerous questions, in part concerning the physics underpinning field evaporation. We discuss these aspects and lay out some of the challenges regarding the APT analysis of frozen liquids.
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Affiliation(s)
- Patrick Stender
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | - Baptiste Gault
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
| | - Tim M Schwarz
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | - Eric V Woods
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - Se-Ho Kim
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - Jonas Ott
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | | | - Guido Schmitz
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | | | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569Stuttgart, Germany
| | - Ayman A El-Zoka
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
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18
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Kühbach M, London AJ, Wang J, Schreiber DK, Mendez Martin F, Ghamarian I, Bilal H, Ceguerra AV. Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 28:1-16. [PMID: 34311798 DOI: 10.1017/s1431927621012241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Atom probe tomography, and related methods, probe the composition and the three-dimensional architecture of materials. The software tools which microscopists use, and how these tools are connected into workflows, make a substantial contribution to the accuracy and precision of such material characterization experiments. Typically, we adapt methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. We also realize that improving on research data management is a challenge when it comes to align with the FAIR data stewardship principles. Faced with this global challenge, we are convinced it is useful to join forces. Here, we report the results and challenges with an inter-laboratory call for developing test cases for several types of atom probe microscopy software tools. The results support why defining detailed recipes of software workflows and sharing these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to substantiated results.
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Affiliation(s)
- Markus Kühbach
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, D-40237Düsseldorf, Germany
| | - Andrew J London
- United Kingdom Atomic Energy Authority, Culham Centre for Fusion Energy, Culham Science Centre, Abingdon, OxonOX14 3DB, UK
| | - Jing Wang
- Pacific Northwest National Laboratory, Energy and Environment Directorate, 902 Battelle Boulevard, Richland, WA99352, USA
| | - Daniel K Schreiber
- Pacific Northwest National Laboratory, Energy and Environment Directorate, 902 Battelle Boulevard, Richland, WA99352, USA
| | - Francisca Mendez Martin
- Department of Materials Science, Montanuniversität Leoben, Franz Josef-Straße 18, A-8700Leoben, Austria
| | - Iman Ghamarian
- Department of Materials Science and Engineering, University of Michigan, 2300 Hayward St, Ann Arbor, MI48109-2117, USA
- School of Aerospace and Mechanical Engineering, University of Oklahoma, Norman, OK7019-1052, USA
| | - Huma Bilal
- Australian Centre for Microscopy & Microanalysis, School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW2006, Australia
| | - Anna V Ceguerra
- Australian Centre for Microscopy & Microanalysis, School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW2006, Australia
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19
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Frankel GS, Vienna JD, Lian J, Guo X, Gin S, Kim SH, Du J, Ryan JV, Wang J, Windl W, Taylor CD, Scully JR. Recent Advances in Corrosion Science Applicable To Disposal of High-Level Nuclear Waste. Chem Rev 2021; 121:12327-12383. [PMID: 34259500 DOI: 10.1021/acs.chemrev.0c00990] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-level radioactive waste is accumulating at temporary storage locations around the world and will eventually be placed in deep geological repositories. The waste forms and containers will be constructed from glass, crystalline ceramic, and metallic materials, which will eventually come into contact with water, considering that the period of performance required to allow sufficient decay of dangerous radionuclides is on the order of 105-106 years. Corrosion of the containers and waste forms in the aqueous repository environment is therefore a concern. This Review describes the recent advances of the field of materials corrosion that are relevant to fundamental materials science issues associated with the long-term performance assessment and the design of materials with improved performance, where performance is defined as resistance to aqueous corrosion. Glass, crystalline ceramics, and metals are discussed separately, and the near-field interactions of these different material classes are also briefly addressed. Finally, recommendations for future directions of study are provided.
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Affiliation(s)
- Gerald S Frankel
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - John D Vienna
- Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, Washington 99354, United States
| | - Jie Lian
- Department of Mechanical Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Xiaolei Guo
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Stephane Gin
- CEA, DE2D, University of Montpellier, Marcoule, F-30207 Bagnols sur Cèze, 34000 Montpellier, France
| | - Seong H Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16801, United States
| | - Jincheng Du
- Department of Materials Science and Engineering, University of North Texas, Denton, Texas 76203, United States
| | - Joseph V Ryan
- Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, Washington 99354, United States
| | - Jianwei Wang
- Department of Geology and Geophysics, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Wolfgang Windl
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher D Taylor
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - John R Scully
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
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20
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Schwarz TM, Dietrich CA, Ott J, Weikum EM, Lawitzki R, Solodenko H, Hadjixenophontos E, Gault B, Kästner J, Schmitz G, Stender P. 3D sub-nanometer analysis of glucose in an aqueous solution by cryo-atom probe tomography. Sci Rep 2021; 11:11607. [PMID: 34078953 PMCID: PMC8172843 DOI: 10.1038/s41598-021-90862-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/18/2021] [Indexed: 11/23/2022] Open
Abstract
Atom Probe Tomography (APT) is currently a well-established technique to analyse the composition of solid materials including metals, semiconductors and ceramics with up to near-atomic resolution. Using an aqueous glucose solution, we now extended the technique to frozen solutions. While the mass signals of the common glucose fragments CxHy and CxOyHz overlap with (H2O)nH from water, we achieved stoichiometrically correct values via signal deconvolution. Density functional theory (DFT) calculations were performed to investigate the stability of the detected pyranose fragments. This paper demonstrates APT’s capabilities to achieve sub-nanometre resolution in tracing whole glucose molecules in a frozen solution by using cryogenic workflows. We use a solution of defined concentration to investigate the chemical resolution capabilities as a step toward the measurement of biological molecules. Due to the evaporation of nearly intact glucose molecules, their position within the measured 3D volume of the solution can be determined with sub-nanometre resolution. Our analyses take analytical techniques to a new level, since chemical characterization methods for cryogenically-frozen solutions or biological materials are limited.
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Affiliation(s)
- T M Schwarz
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - C A Dietrich
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - J Ott
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - E M Weikum
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - R Lawitzki
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - H Solodenko
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - E Hadjixenophontos
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - B Gault
- Max-Planck-Institut Für Eisenforschung, Max-Planck-Str. 1, 40237, Düsseldorf, Germany.,Department of Materials, Royal School of Mines, Imperial College, Prince Consort Road, London, SW7 2BP, UK
| | - J Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - G Schmitz
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - P Stender
- Chair of Materials Physics, Institute for Materials Science, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany.
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21
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Gault B, Chiaramonti A, Cojocaru-Mirédin O, Stender P, Dubosq R, Freysoldt C, Makineni SK, Li T, Moody M, Cairney JM. Atom probe tomography. NATURE REVIEWS. METHODS PRIMERS 2021; 1:10.1038/s43586-021-00047-w. [PMID: 37719173 PMCID: PMC10502706 DOI: 10.1038/s43586-021-00047-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 09/19/2023]
Abstract
Atom probe tomography (APT) provides three-dimensional compositional mapping with sub-nanometre resolution. The sensitivity of APT is in the range of parts per million for all elements, including light elements such as hydrogen, carbon or lithium, enabling unique insights into the composition of performance-enhancing or lifetime-limiting microstructural features and making APT ideally suited to complement electron-based or X-ray-based microscopies and spectroscopies. Here, we provide an introductory overview of APT ranging from its inception as an evolution of field ion microscopy to the most recent developments in specimen preparation, including for nanomaterials. We touch on data reconstruction, analysis and various applications, including in the geosciences and the burgeoning biological sciences. We review the underpinnings of APT performance and discuss both strengths and limitations of APT, including how the community can improve on current shortcomings. Finally, we look forwards to true atomic-scale tomography with the ability to measure the isotopic identity and spatial coordinates of every atom in an ever wider range of materials through new specimen preparation routes, novel laser pulsing and detector technologies, and full interoperability with complementary microscopy techniques.
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Affiliation(s)
- Baptiste Gault
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College, London, UK
| | - Ann Chiaramonti
- National Institute of Standards and Technology, Applied Chemicals and Materials Division, Boulder, CO, USA
| | | | - Patrick Stender
- Institute of Materials Science, University of Stuttgart, Stuttgart, Germany
| | - Renelle Dubosq
- Department of Earth and Environmental Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | - Tong Li
- Institute for Materials, Ruhr-Universität Bochum, Bochum, Germany
| | - Michael Moody
- Department of Materials, University of Oxford, Oxford, UK
| | - Julie M. Cairney
- Australian Centre for Microscopy and Microanalysis, University of Sydney, Sydney, New South Wales, Australia
- School of Aerospace, Mechanical and Mechatronic Engineering, University of Sydney, Sydney, New South Wales, Australia
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22
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El-Zoka AA, Kim SH, Deville S, Newman RC, Stephenson LT, Gault B. Enabling near-atomic-scale analysis of frozen water. SCIENCE ADVANCES 2020; 6:6/49/eabd6324. [PMID: 33277259 PMCID: PMC7821902 DOI: 10.1126/sciadv.abd6324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/21/2020] [Indexed: 05/04/2023]
Abstract
Transmission electron microscopy went through a revolution enabling routine cryo-imaging of biological and (bio)chemical systems, in liquid form. Yet, these approaches typically lack advanced analytical capabilities. Here, we used atom probe tomography to analyze frozen liquids in three dimensions with subnanometer resolution. We introduce a specimen preparation strategy using nanoporous gold. We report data on 2- to 3-μm-thick layers of ice formed from both high-purity deuterated water and a solution of 50 mM NaCl in high-purity deuterated water. The analysis of the gold-ice interface reveals a substantial increase in the solute concentrations across the interface. We explore a range of experimental parameters to show that atom probe analyses of bulk aqueous specimens come with their own challenges and discuss physical processes that produce the observed phenomena. Our study demonstrates the viability of using frozen water as a carrier for near-atomic-scale analysis of objects in solution by atom probe tomography.
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Affiliation(s)
- A A El-Zoka
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany.
| | - S-H Kim
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - S Deville
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, 69622 Villeurbanne, France
| | - R C Newman
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Canada
| | - L T Stephenson
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - B Gault
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany.
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
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23
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Schwarz TM, Weikum EM, Meng K, Hadjixenophontos E, Dietrich CA, Kästner J, Stender P, Schmitz G. Field evaporation and atom probe tomography of pure water tips. Sci Rep 2020; 10:20271. [PMID: 33219263 PMCID: PMC7680140 DOI: 10.1038/s41598-020-77130-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/05/2020] [Indexed: 01/12/2023] Open
Abstract
Measuring biological samples by atom probe tomography (APT) in their natural environment, i.e. aqueous solution, would take this analytical method, which is currently well established for metals, semi-conductive materials and non-metals, to a new level. It would give information about the 3D chemical structure of biological systems, which could enable unprecedented insights into biological systems and processes, such as virus protein interactions. For this future aim, we present as a first essential step the APT analysis of pure water (Milli-Q) which is the main component of biological systems. After Cryo-preparation, nanometric water tips are field evaporated with assistance by short laser pulses. The obtained data sets of several tens of millions of atoms reveal a complex evaporation behavior. Understanding the field evaporation process of water is fundamental for the measurement of more complex biological systems. For the identification of the individual signals in the mass spectrum, DFT calculations were performed to prove the stability of the detected molecules.
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Affiliation(s)
- T M Schwarz
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - E M Weikum
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - K Meng
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - E Hadjixenophontos
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - C A Dietrich
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - J Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - P Stender
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany.
| | - G Schmitz
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstr. 3, 70569, Stuttgart, Germany
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24
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Parmenter CD, Nizamudeen ZA. Cryo-FIB-lift-out: practically impossible to practical reality. J Microsc 2020; 281:157-174. [PMID: 32815145 DOI: 10.1111/jmi.12953] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 01/14/2023]
Abstract
In this paper, we explore the development of the Cryo-Lift-Out (cryo-LO) technique as preparation tool for cryogenic transmission electron microscopy (cryo-TEM). What started in early work defying what was considered 'practically impossible' has developed into state-of-the-art practical reality. This paper presents the key hardware, basic principles and key considerations for the practical usage of cryogenic Lift-Out for those new to the field. Detailed protocols and in-depth description of considerations and points for further development are presented. The authors have attempted to formalise everything known about the technique gathered together from their expertise gained in the development of this approach. LAY DESCRIPTION: A major challenge in electron microscopy is the production of suitable samples from hydrated biological and soft-matter materials for subnanometre resolution imaging in a cryo-Transmission Electron Microscope (TEM). A well-known solution for room temperature materials is called (in situ) Lift-Out. It uses a fine needle that picks up a tiny section called a lamella. Lamellae are made by a Focused Ion Beam (FIB). In this paper, we seek to set out the beginnings of Lift-Out sample preparation conducted under cryogenic conditions and the development of this approach as applied to frozen, hydrated biological and soft-matter samples. We discuss the required basic hardware and provide a thorough description of developed protocols. We aim at those new to the field of cryo-Lift-Out to fully educate them in the finer points of hardware setup and practical considerations when attempting to perform cryo-Lift-Out and to demonstrate what has been achieved thus far. We also discuss areas of further improvement and talking points for the future direction of this promising sample preparation technique.
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Affiliation(s)
| | - Zubair Ahmed Nizamudeen
- Nottingham Nanoscale and Microscale Research Centre, University of Nottingham, Nottingham, UK.,Division of Cancer and Stem Cells, Nottingham Biodiscovery Institute, The University of Nottingham, Nottingham, UK
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25
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McCarroll I, Bagot P, Devaraj A, Perea D, Cairney J. New frontiers in atom probe tomography: a review of research enabled by cryo and/or vacuum transfer systems. MATERIALS TODAY. ADVANCES 2020; 7:100090. [PMID: 33103106 PMCID: PMC7581275 DOI: 10.1016/j.mtadv.2020.100090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
There has been a recent surge in the use of cryo and/or vacuum specimen preparation and transfer systems to broaden the scope of research enabled by the microscopy technique of atom probe tomography. This is driven by the fact that, as for many microscopes, the application of atom probes to air- and temperature-sensitive materials or wet biological specimens has previously been limited by transfer through air at room temperature. Here we provide an overview of areas of research that benefit from these new transfer and analysis protocols, as well as a review of current advances in transfer devices, environmental cells, and glove boxes for controlled specimen manipulation. This includes the study of catalysis and corrosion, biological samples, liquid-solid interfaces, natural aging, and the distribution of hydrogen in materials.
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Affiliation(s)
- I.E. McCarroll
- Australian Centre for Microscopy and Microanalysis, University of Sydney, Madsen Building F09, NSW 2006, Australia
| | - P.A.J. Bagot
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, United Kingdom
| | - A. Devaraj
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - D.E. Perea
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, P.O. Box 999 Richland, WA 99352, USA
| | - J.M. Cairney
- Australian Centre for Microscopy and Microanalysis, University of Sydney, Madsen Building F09, NSW 2006, Australia
- School of Aerospace, Mechanical and Mechatronic Engineering, University of Sydney, NSW 2006, Australia
- Corresponding author. (J.M. Cairney)
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26
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Qiu S, Garg V, Zhang S, Chen Y, Li J, Taylor A, Marceau RKW, Fu J. Graphene encapsulation enabled high-throughput atom probe tomography of liquid specimens. Ultramicroscopy 2020; 216:113036. [PMID: 32540722 DOI: 10.1016/j.ultramic.2020.113036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022]
Abstract
A new method for imaging liquid specimens with atom probe tomography (APT) is proposed by introducing graphene encapsulation. By tuning the encapsulation speed and the number of encapsulations, controllable volumes of liquid can be encapsulated on a pre-sharpened specimen tip, with the end radius less than 75 nm to allow field ionization and evaporation. Encapsulation of liquid has been confirmed by using various characterization techniques, including electron microscopy and stimulated emission depletion microscopy. The graphene-encapsulated liquid specimen was then directly frozen at the cryogenic stage inside the atom probe instrument, followed by APT imaging in laser-pulsed mode. Using water as a test example, water-related ions have been identified in the acquired mass spectrum, which are spatially correlated to a reconstructed three-dimensional volume of water on top of the base specimen tip, as clearly revealed in the chemical maps. In addition, the proposed method has also been shown to produce multiple liquid specimens simultaneously on a pre-sharpened silicon micro-tip array for high-throughput APT imaging of liquid specimens. It is expected that the proposed lift-out-free method for preparing APT specimens in their hydrated state will open a new avenue for obtaining insights into various materials at atomic resolution.
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Affiliation(s)
- Shi Qiu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC3800, Australia
| | - Vivek Garg
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC3800, Australia; IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shuo Zhang
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC3800, Australia
| | - Yu Chen
- Monash Centre for Electron Microscopy, Monash University, Clayton, VIC3800, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia; Department of Microbiology, Monash University, Clayton, VIC3800, Australia
| | - Adam Taylor
- Deakin University, Institute for Frontier Materials, Geelong, VIC3216, Australia
| | - Ross K W Marceau
- Deakin University, Institute for Frontier Materials, Geelong, VIC3216, Australia.
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC3800, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC3800, Australia.
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27
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Qiu S, Zheng C, Garg V, Chen Y, Gervinskas G, Li J, Dunstone MA, Marceau RKW, Fu J. Three-Dimensional Chemical Mapping of a Single Protein in the Hydrated State with Atom Probe Tomography. Anal Chem 2020; 92:5168-5177. [DOI: 10.1021/acs.analchem.9b05668] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shi Qiu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Changxi Zheng
- ARC Centre of Excellence for Future Low-Energy Electronics Technologies, Monash University, Clayton, VIC 3800, Australia
- School of Physics and Astronomy, Monash University, Clayton, VIC 3800, Australia
| | - Vivek Garg
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Yu Chen
- Monash Centre for Electron Microscopy, Monash University, Clayton, VIC 3800, Australia
| | - Gediminas Gervinskas
- Monash Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Clayton, VIC 3800, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Michelle A. Dunstone
- Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Ross K. W. Marceau
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
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28
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Abstract
Atom probe tomography is a well-established analytical instrument for imaging the 3D structure and composition of materials with high mass resolution, sub-nanometer spatial resolution and ppm elemental sensitivity. Thanks to recent hardware developments in Atom Probe Tomography (APT), combined with progress on site-specific focused ion beam (FIB)-based sample preparation methods and improved data treatment software, complex materials can now be routinely investigated. From model samples to complex, usable porous structures, there is currently a growing interest in the analysis of catalytic materials. APT is able to probe the end state of atomic-scale processes, providing information needed to improve the synthesis of catalysts and to unravel structure/composition/reactivity relationships. This review focuses on the study of catalytic materials with increasing complexity (tip-sample, unsupported and supported nanoparticles, powders, self-supported catalysts and zeolites), as well as sample preparation methods developed to obtain suitable specimens for APT experiments.
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29
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Sundell G, Hulander M, Pihl A, Andersson M. Atom Probe Tomography for 3D Structural and Chemical Analysis of Individual Proteins. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900316. [PMID: 31058464 DOI: 10.1002/smll.201900316] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/01/2019] [Indexed: 06/09/2023]
Abstract
Determination of the 3D structure of proteins and other biomolecules is a major goal in structural biology, to provide insights to their biological function. Such structures are historically unveiled experimentally by X-ray crystallography or NMR spectroscopy, and in recent years using cryo-electron microscopy. Here, a method for structural analysis of individual proteins on the sub-nanometer scale using atom probe tomography is described. This technique offers a combination of high-resolution analysis of biomolecules in 3D, and the chemical sensitivity of mass spectrometry. As a model protein, the well-characterized antibody IgG is used. IgG is encapsulated in an amorphous solid silica matrix via a sol-gel process to provide the requisite support for atom probe analysis. The silica synthesis is tuned to resemble physiological conditions. The 3D reconstructions show good agreement with the protein databank IgG crystal structure. This suggests that the silica-embedding strategy can open the field of atom probe tomography to the analysis of biological molecules. In addition to high-resolution structural information, the technique may potentially provide chemical information on the atomic scale using isotopic labeling. It is envisaged that this method may constitute a useful complement to existing tools in structural biology, particularly for the examination of proteins with low propensity for crystallization.
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Affiliation(s)
- Gustav Sundell
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, 41296, Sweden
| | - Mats Hulander
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, 41296, Sweden
| | - Astrid Pihl
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, 41296, Sweden
| | - Martin Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, 41296, Sweden
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30
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Ti and its alloys as examples of cryogenic focused ion beam milling of environmentally-sensitive materials. Nat Commun 2019; 10:942. [PMID: 30808943 PMCID: PMC6391424 DOI: 10.1038/s41467-019-08752-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 01/22/2019] [Indexed: 11/09/2022] Open
Abstract
Hydrogen pick-up leading to hydride formation is often observed in commercially pure Ti (CP-Ti) and Ti-based alloys prepared for microscopic observation by conventional methods, such as electro-polishing and room temperature focused ion beam (FIB) milling. Here, we demonstrate that cryogenic FIB milling can effectively prevent undesired hydrogen pick-up. Specimens of CP-Ti and a Ti dual-phase alloy (Ti-6Al-2Sn-4Zr-6Mo, Ti6246, in wt.%) were prepared using a xenon-plasma FIB microscope equipped with a cryogenic stage reaching −135 °C. Transmission electron microscopy (TEM), selected area electron diffraction, and scanning TEM indicated no hydride formation in cryo-milled CP-Ti lamellae. Atom probe tomography further demonstrated that cryo-FIB significantly reduces hydrogen levels within the Ti6246 matrix compared with conventional methods. Supported by molecular dynamics simulations, we show that significantly lowering the thermal activation for H diffusion inhibits undesired environmental hydrogen pick-up during preparation and prevents pre-charged hydrogen from diffusing out of the sample, allowing for hydrogen embrittlement mechanisms of Ti-based alloys to be investigated at the nanoscale. Hydrogen contamination in metals during sample preparation for high-resolution microscopy remains a challenge, especially when hydrogen itself is being investigated. Here, the authors show that using cryogenic milling significantly reduces hydrogen pick-up during sample preparation of titanium and titanium alloys.
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31
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Stephenson LT, Szczepaniak A, Mouton I, Rusitzka KAK, Breen AJ, Tezins U, Sturm A, Vogel D, Chang Y, Kontis P, Rosenthal A, Shepard JD, Maier U, Kelly TF, Raabe D, Gault B. The Laplace Project: An integrated suite for preparing and transferring atom probe samples under cryogenic and UHV conditions. PLoS One 2018; 13:e0209211. [PMID: 30576351 PMCID: PMC6303089 DOI: 10.1371/journal.pone.0209211] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 11/30/2018] [Indexed: 11/22/2022] Open
Abstract
We present sample transfer instrumentation and integrated protocols for the preparation and atom probe characterization of environmentally-sensitive materials. Ultra-high vacuum cryogenic suitcases allow specimen transfer between preparation, processing and several imaging platforms without exposure to atmospheric contamination. For expedient transfers, we installed a fast-docking station equipped with a cryogenic pump upon three systems; two atom probes, a scanning electron microscope / Xe-plasma focused ion beam and a N2-atmosphere glovebox. We also installed a plasma FIB with a solid-state cooling stage to reduce beam damage and contamination, through reducing chemical activity and with the cryogenic components as passive cryogenic traps. We demonstrate the efficacy of the new laboratory protocols by the successful preparation and transfer of two highly contamination- and temperature-sensitive samples—water and ice. Analysing pure magnesium atom probe data, we show that surface oxidation can be effectively suppressed using an entirely cryogenic protocol (during specimen preparation and during transfer). Starting with the cryogenically-cooled plasma FIB, we also prepared and transferred frozen ice samples while avoiding significant melting or sublimation, suggesting that we may be able to measure the nanostructure of other normally-liquid or soft materials. Isolated cryogenic protocols within the N2 glove box demonstrate the absence of ice condensation suggesting that environmental control can commence from fabrication until atom probe analysis.
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Affiliation(s)
- Leigh T Stephenson
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Agnieszka Szczepaniak
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany.,Cameca Instruments Inc., 5470 Nobel Dr, Fitchburg, WI 53711, United States of America
| | - Isabelle Mouton
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Kristiane A K Rusitzka
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Andrew J Breen
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Uwe Tezins
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Andreas Sturm
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Dirk Vogel
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Yanhong Chang
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Paraskevas Kontis
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Alexander Rosenthal
- Microscopy Improvements e.U., Rudolf von Eichthal str. 66/6, 7000 Eisenstadt, Austria
| | - Jeffrey D Shepard
- Cameca Instruments Inc., 5470 Nobel Dr, Fitchburg, WI 53711, United States of America
| | - Urs Maier
- Ferrovac GmbH, Thurgauerstrasse 72, 8050 Zürich, Switzerland
| | - Thomas F Kelly
- Cameca Instruments Inc., 5470 Nobel Dr, Fitchburg, WI 53711, United States of America
| | - Dierk Raabe
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
| | - Baptiste Gault
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany
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