Cryogenic Electron Microscopy and Tomography on Radiation Sensitive Crystalline Materials

Cryogenic Electron Microscopy and Tomography on Radiation Sensitive Crystalline Materials

Author: Weijiang Zhou

Publisher:

Published: 2022

Total Pages:

ISBN-13:

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Cryogenic electron microscopy (Cryo-EM) has been one of the most exciting technology advancements in biological field in recent years. The idea of freezing samples in liquid nitrogen temperature provides a unique advantage to preserve and observe the object of interest in their native state. The improvements in both electron microscopy related hardware and data processing software enable the retrieval of structural information to atomic details. However, many technical features in electron microscope have not been fully explored for cryo-EM and many other sample systems other than biological specimens could utilize cryo-EM to accelerate their structural characterization research. This dissertation focuses on developing a new cryo-EM based experimental and data processing pipeline to further extend the applications of cryo-EM to broader research fields, where the samples of interest are normally not amenable to conventional electron microscopy methods. There are two common features across the specimens aforementioned: first, they are crystalline materials, meaning they are either single crystals or contain certain degree of periodic structures; second, they are sensitive to electron radiation, thus conventional transmission electron microscopy is not suitable to study such materials due to its high electron radiation damage. To investigate those specimens using cryo-EM, we developed several new methods: customized freezing protocol to preserve the samples from ambient environment; cryogenic focused ion beam milling to prepare electron transparent samples; continuous tilting electron diffraction to solve the atomic structure from single crystals; electron diffraction and high resolution low dose electron imaging to acquire the sub-nanometer structural information in both real-space and Fourier space; electron tomography and automated annotation to recover the morphology of non-biological samples in 3D. Those lead to many unprecedented findings in those representative specimens, which will be described in this dissertation. We anticipate those new technical developments will facilitate the usage of cryo-EM in structural biology, chemical biology, organic chemistry and material science in the near future.


Advances in Scanning Transmission Electron Microscopy for Materials Discovery and Innovation

Advances in Scanning Transmission Electron Microscopy for Materials Discovery and Innovation

Author: Berit Hansen Goodge

Publisher:

Published: 2022

Total Pages: 0

ISBN-13:

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Subtle interplay between structure, charge, and spin in the atomic lattice is the fundamental driver of the functional properties in crystalline quantum materials. These effects can be so subtle that in many cases just a few misplaced atoms are enough to change or suppress the desired material properties entirely. Probing these materials with quantitative detail at the atomic scale therefore offers key insights to the close link between material form and function. The scanning transmission electron microscope (STEM) is a powerful tool which grants access to detailed, quantitative measurements of such properties at the atomic scale. Here, a combination of high spatial-resolution imaging and high energy-resolution electron energy loss spectroscopy (EELS) is harnessed to probe local effects in a variety of quantum materials and these insights are further leveraged for the strategic design of new, tunable materials. Atomic-resolution imaging and spectroscopy rely on certain strict prerequisites ranging from sample suitability to environmental stability of the laboratory.Furthermore, the spatially localized measurements which are critical to understanding the fundamental physics at play in quantum systems can be limited by the practical realities of a material's robustness to measurement. Many quantum materials, however, are sensitive to radiation doses typically applied by the STEM probe, and the exotic phenomena they host exist only at cryogenic temperatures. These considerations have traditionally limited both the materials and the conditions which are studied, confined mostly to robust crystalline materials and ambient temperatures. Accessing exotic states in the STEM therefore necessitates significant advances in experimental capabilities, which are realized here through detector, sample stage, and electron source improvements. Together, these advances open the door to exploring both new materials and new phases in the STEM. Unconventional superconductivity is perhaps one of the most widely-studied phenomena in condensed matter physics, yet in many aspects remains one of the most mysterious. Here we study a subset of superconducting oxides exemplifies a few of the key questions in this field. Copper-based compounds are the prototypical "high-temperature'' superconductors, exhibiting remarkably robust superconductivity with critical temperatures reaching well over 100 K. Early theoretical predictions that nickel-based compounds with similar crystal and electronic structure could host similar properties were finally offered a platform for experimental validation with the discovery of superconducting infinite-layer nickelate thin films in 2019. Despite the nominal similarities between cuprates and nickelates, however, our STEM-EELS measurements reveals notable differences in the electronic landscape of these materials. These local measurements are key to disentangling which properties of the nickelate system reflect challenges of materials synthesis and which reflect the fundamental physics at work. But not all oxide superconductors are so closely related: in stark contrast to the cuprates, superconductivity in Sr2RuO4 is extremely sensitive to crystalline disorder. Local STEM-EELS measurements or Sr2RuO4thin films are used here to extract and characterize different types of disorder in the atomic lattice, thereby illustrating their distinct impacts on superconductivity. The STEM provides unique access to understanding the atomic-scale structures and interactions which impart functional or exotic properties to quantum materials. Detailed quantitative studies of oxide interfaces here inspire new approaches for symmetry templating oxide monolayers. Leveraging the insights of atomic-resolution STEM across a breadth of systems thus inspires and informs new methods for tunably controlling electronic properties in designer compounds.


The Resolution Revolution: Recent Advances In cryoEM

The Resolution Revolution: Recent Advances In cryoEM

Author:

Publisher: Academic Press

Published: 2016-08-26

Total Pages: 488

ISBN-13: 0128054352

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cryoEM, a new volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods and new developments in recording images, the creation, evaluation and validation of 3D maps from the images, model building into maps and refinement of the resulting atomic structures, and applications of essentially single particle methods to helical structures and to sub-tomogram averaging. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods that determine the structures of biological molecules, a vital step for understanding their function Contains the technical developments underpinning the advances of cryoEM and captures the exciting insights that have resulted


Electron Crystallography

Electron Crystallography

Author: Devinder Singh

Publisher: BoD – Books on Demand

Published: 2020-07-22

Total Pages: 116

ISBN-13: 1838801898

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In the quantitative determination of new structures, micro-/nano-crystalline materials pose significant challenges. The different properties of materials are structure-dependent. Traditionally, X-ray crystallography has been used for the analysis of these materials. Electron diffraction is a technique that complements other techniques; for example, single crystal X-ray diffraction and powder X-ray diffraction for determination of structure. Electron diffraction plays a very important role when crystals are very small using single crystal X-ray diffraction or very complex for structure solution by powder X-ray diffraction. With the introduction of advanced methodologies, important methods for crystal structural analysis in the field of electron crystallography have been discovered, such as rotation electron diffraction (RED) and automated electron diffraction tomography (ADT). In recent years, large numbers of crystal structures have been solved using electron crystallography.


Handbook of Nanoscopy

Handbook of Nanoscopy

Author: Gustaaf van Tendeloo

Publisher: John Wiley & Sons

Published: 2012-12-21

Total Pages: 1484

ISBN-13: 3527641874

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This completely revised successor to the Handbook of Microscopy supplies in-depth coverage of all imaging technologies from the optical to the electron and scanning techniques. Adopting a twofold approach, the book firstly presents the various technologies as such, before going on to cover the materials class by class, analyzing how the different imaging methods can be successfully applied. It covers the latest developments in techniques, such as in-situ TEM, 3D imaging in TEM and SEM, as well as a broad range of material types, including metals, alloys, ceramics, polymers, semiconductors, minerals, quasicrystals, amorphous solids, among others. The volumes are divided between methods and applications, making this both a reliable reference and handbook for chemists, physicists, biologists, materials scientists and engineers, as well as graduate students and their lecturers.


Characterisation of Radiation Damage by Transmission Electron Microscopy

Characterisation of Radiation Damage by Transmission Electron Microscopy

Author: M.L Jenkins

Publisher: CRC Press

Published: 2000-11-21

Total Pages: 233

ISBN-13: 1420034642

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Characterization of Radiation Damage by Transmission Electron Microscopy details the electron microscopy methods used to investigate complex and fine-scale microstructures, such as those produced by fast-particle irradiation of metals or ion implantation of semiconductors. The book focuses on the methods used to characterize small point-defect clus


Transmission Electron Microscopy

Transmission Electron Microscopy

Author: David B. Williams

Publisher: Springer Science & Business Media

Published: 2013-03-09

Total Pages: 708

ISBN-13: 1475725191

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Electron microscopy has revolutionized our understanding the extraordinary intellectual demands required of the mi of materials by completing the processing-structure-prop croscopist in order to do the job properly: crystallography, erties links down to atomistic levels. It now is even possible diffraction, image contrast, inelastic scattering events, and to tailor the microstructure (and meso structure ) of materials spectroscopy. Remember, these used to be fields in them to achieve specific sets of properties; the extraordinary abili selves. Today, one has to understand the fundamentals ties of modem transmission electron microscopy-TEM of all of these areas before one can hope to tackle signifi instruments to provide almost all of the structural, phase, cant problems in materials science. TEM is a technique of and crystallographic data allow us to accomplish this feat. characterizing materials down to the atomic limits. It must Therefore, it is obvious that any curriculum in modem mate be used with care and attention, in many cases involving rials education must include suitable courses in electron mi teams of experts from different venues. The fundamentals croscopy. It is also essential that suitable texts be available are, of course, based in physics, so aspiring materials sci for the preparation of the students and researchers who must entists would be well advised to have prior exposure to, for carry out electron microscopy properly and quantitatively.


Single-particle Cryo-electron Microscopy

Single-particle Cryo-electron Microscopy

Author: Joachim Frank

Publisher: World Scientific Publishing Company

Published: 2017-12-31

Total Pages: 0

ISBN-13: 9789813234857

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The book reproduces 55 of more than 300 articles written by the author, representing milestones in methods development of single-particle cryo-EM as well as important results obtained by this technique in the study of biological macromolecules and their interactions. Importantly, neither symmetries nor ordered arrangements (as in two-dimensional crystals, helical assemblies, icosahedral viruses) are required. Although the biological applications are mainly in the area of ribosome structure and function, the elucidation of membrane channel structures and their activation and gating mechanisms are represented, as well. The book is introduced by a commentary that explains the original development of concepts, describes the contributions of the author's colleagues and students, and shows how challenges were overcome as the technique matured. Along the way, the ribosome served as an example for a macromolecule with intricate structure and conformational dynamics that pose challenges for three-dimensional visualization. Toward the end of the book -- bringing us to the present time -- molecular structures with near-atomic resolution are presented, and a novel type of computational analysis, manifold embedding, is introduced. Single-particle cryo-EM is currently revolutionizing structural biology, presenting a powerful alternative to X-ray crystallography as a means to solve the structure of biological macromolecules. The book presents in one place a number of articles containing key advances in mathematical and computational methods leading up to the present time. Secondly, the development of the technique over the years is reflected by ever-expanding discoveries in the field of ribosome structure and function. Thirdly, as all histories of ideas, the history of concepts pertaining to this new method of visualization is fascinating all in itself.