bluuebunny/crossref_metadata_2025 huggingface dataset:
Challenges of three-dimensional reconstruction of ribonucleoprotein complexes from electron spectroscopic images - Reconstructing ribosomal RNA
Authors: Beniac D.R. , Czarnota G.J. , Bartlett T.A. , Ottensmeyer F.P. , Harauz G.
Published: June 2020

Transmission electron microscopy has been dominant in structural studies of the ribosome and its constituent ribonucleic acids and proteins. Ribosomal RNA (rRNA) has central importance in the architecture of this complex and in protein synthesis. Our work has entailed using electron spectroscopic imaging (ESI) to probe the tertiary structure of rRNAin situin a prokaryote (Escherichia coli) and in a eukaryote (Thermomyces lanuginosus). ESI uses only electrons which have lost a specific amount of energy due to specific inner-shell ionisation interactions with the specimen to form an elemental map. In nucleoprotein complexes, a map of the phosphorus distribution represents primarily a projection of the phosphate backbone of the nucleic acid component. The visualisation of rRNAin situin the intact ribosomal subunit by ESI was demonstrated almost a decade ago to be feasible. Our work on quantitative image analysis of ES images ofE. coliandTh. lanuginosusribosomal subunits has presented unique challenges and has resulted in new algorithmic developments generally applicable to such images. These innovations include a singular pretreatment procedure, the use of mutual correlation functions rather than cross correlation functions to reduce the effect of low spatial frequency components, and angular determination using iterative quaternion-assisted angular reconstitution to compute a three-dimensional reconstruction. These investigations have produced direct information regarding ribosomal rRNA localisation in the ribosomal subunits ofE. coliandTh. lanuginosus, and the position of non-conserved sequences.
The structure of myelin basic protein determined by high resolution electron microscopy and molecular modelling
Authors: Beniac D.R. , Ridsdale R.A. , Luckevich M.D. , Tompkins T.A. , Harauz G.
Published: June 2020

Multiple sclerosis (MS) is characterised by the active degradation of the myelin sheath, and is thought to be precipitated by an autoimmune response to one or more of the sheath’s protein components. Myelin basic protein (MBP) is generally considered to be the antigen responsible for autoimmunity and is one of the most abundant proteins of the sheath. Knowledge of the tertiary structure of MBP, and its organisation on lipid layers and within the compacted myelin multilayers, is essential to understanding the organisation of the myelin membrane and the mechanisms of development of autoimmunity in MS. MBP has hitherto not proved crystallisable for structural studies by X-ray diffractometry despite much effort in this area. We have initiated high-resolution electron microscopical analyses of MBP. When imaged as individual particles, a recurring motif is that of a “C” shape in projection, of approximately 2 nm in thickness and 8 nm in length (Figure a – field of view; Figure b – class averages after single particle analysis; Figure c – 3D reconstruction). The total length of this particle is less than would be expected if the polypeptide chain were fully extended. Crystallisation experiments on MBP using monolayers of lipid mixtures (phosphatidylcholine, phosphatidylserine, dioleoyl phosphatidylethanolamine, galactocerebroside) yielded microcrystalline structures with a repeating pattern of packed protein molecules of size 5 nm, with an arm width of 2 nm and total length of 10-11 nm (Figure d). Molecular modelling of MBP based on the schemes proposed by Stoner and Martenson, and using coordinates of the β sheet backbone of bacteriochlorophyll A protein and energy minimisation of intervening segments, yielded a compact structure of size and appearance consistent with the electron microscopical data (Figure e). The bend of the C shape appears due to a natural curvature in the β sheet. These results are fully congruous with MBP having a regular secondary structure and domains that are potentially flexible with respect to one another. Energy minimisation experiments were performed on this model structure after specific post-translational modifications such as phosphorylation of specific sites (e.g., Ser7, Thr98) and conversion of arginine residues to citrullines. These results are consistent with biochemical data on accessibility of these sites to modification, and provide a framework for hypothesising scenarios of myelin sheath degradation in MS.
Stomatal morphology and distribution of Pinus koraiensis
Authors: Ning Zhu Hua , Abdollahi Kamran Ken
Published: June 2020

Stomata are the important channels for the necessary exchange of gases between the plants and the surrounding earth. Stomata open and close in response to environmental and physiological signals, thus helping the plant maintain a balance between its water losses and its oxygen and carbon dioxide requirements. This paper reports the study on stomatal morphology and distribution of Pinus koraiensis, a five needle pine tree with a natural distribution in Northeastern China.

Needle samples were collected from one-year-old seedlings. They were cut into 1mm lengths and fixed overnight at 4°C in 4% glutaraldehyde buffered with 0.07M cacodylate at pH 7.2-7.4. After being rinsed with the same buffer, they were post-fixed for 1 hour in 1 % osmium tetroxide in the same buffer and dehydrated in a graded ethanol series. Afterward, tissues were dried in a DCP-1 critical point dryer and coated in a Hummer II sputter coater. Stomatal morphology and distribution were examined under a Hitachi S-405A scanning electron microscope.
Quantitative determination of imaging parameters and composition from high-resolution transmission electron microscopy lattice images
Authors: Stenkamp D.
Published: June 2020

A quantitative method for the direct determination of defocus Δf, local sample thickness t and local composition x from high-resolution transmission electron microscopy (HRTEM) lattice images of wedge-shaped samples is described. The method is applicable to a wide class of crystalline materials comprising elemental semiconductors, elemental metals and substitutional random alloys composed of these elements. The proposed method relies on the functional dependence of linear and non-linear image Fourier coefficients on the parameters defocus Δf, sample thickness t and composition x. This relationship is analytically derived by application of the Bloch wave formalism and the non-linear imaging theory to the HRTEM imaging process. Influences of inelastic electron scattering and partially coherent illumination conditions are taken into account explicitly.
Characterization of the (0110) α-Ti/γ-TiH Interface Using High-Resolution Transmission Electron Microscopy (TEM) and Electron Energy Loss Spectroscopy (EELS)
Authors: Tsai M. M. , Howe J. M.
Published: June 2020

Precipitation of γ-TiH in α-Ti-H alloys involves a hcp → fct lattice transformation with hydrogen as an interstitial diffusing element Results obtained from a previous TEM study have shown that the lengthening rate of γ-TiH is diffusionally controlled at 25°C, and possibly interfacially controlled at temperatures of 50°C and higher. Therefore, it is essential to ascertain the presence or absence of hydrogen atoms at the interface. TEM foils from a 800 ppm wt.% Ti-H alloy were analyzed using high-resolution TEM and image simulations in order to determine the effects of hydrogen on high-resolution images of the α-Ti/γ-TiH interface, and EELS was used to determine the whether the hydnde structure was fully formed up to the interface.
Energy Filtered Electron Backscattering Images of 10-nm NbC and AIN Precipitates in Steels Computed by Monte Carlo Simulations
Authors: Gauvin Raynald , Drouin Dominique , Hovington Pierre
Published: June 2020

In modern materials science, it is important to improve the resolution of the Scanning Electron Microscope (SEM) because small phases play a crutial role in the properties of materials. The Transmission Electron Microscope (TEM) is the tool of choice for imaging small phases embedded in a given matrix. However, this technique is expensive and also is slow owing to specimen preparation. In this context, it is important to improve spatial resolution of the SEM.

In electron backscattering images, it is well know that the backscattered electrons have an energetic distribution when they escape the specimen.The electrons having loss less energy are those which have travelled less in the specimen and thus escape closer to the electron beam. So, in filtering the energy of the backscattering electron and keeping those which have loss only a small amount of energy to create the image, a significant improvement of the resolution of such images is expected. New detectors are now under development to take advantage of this technique of imaging.
Characterization of schottky depletion zone using EBIC imaging
Authors: Drouin D. , Gauvin R. , Beauvais J. , Hovington P. , Joy D. C.
Published: June 2020

Scanning Electron Microscopy (SEM) has been widely used to characterize semiconductor materials. Approximately one half of all SEMs are used by the electronic industry. The SEM can be used as a local current source that can be scanned over semiconductor device surfaces. This imaging mode is called Electron Beam Induced Current (EBIC).

A depletion zone formed by a Schottky diode is visualized using this technique. This Shottky diode is fabricated by placing a metal contact on a semiconductor surfaces. The work function of the metal and the semiconductor produce an equilibrium contact potential. This potential barrier occurs across a region free of charge carriers and thus an electric field is present. This region is called a depletion zone.
Cross-sectional tem analysis of solvent-cast SBS thin films
Authors: Kim G. , Libera M.
Published: June 2020

Block copolymers can assume a range of microphase-separated morphologies, and the dependence of morphology on temperature and composition is an area of active research. Our work has been studying the morphology of solvent-cast thin films of polystyrene-polybutadiene-polystyrene (SBS) as a function of solvent evaporation rate and post-specimen annealing. This paper describes the analysis of thin film cross-sections to distinguish between possible morphologies. ∼50 nm-0.5 μm thick films were cast from a 0.1 wt% solution of SBS (30 wt%, Mw=105) in toluene. GPC analysis indicates PS/PB diblock and PS homopolymer is present (<5wt% total). 50 μl of solution was deposited on water-polished salt. The solvent evaporation rate was roughly controlled between 200 nl/sec and 0.2 nl/sec. After evaporation, the film was cut, floated from the salt, collected on grids, and exposed to OsO4 vapor (20 min) to stain the PB. After plan view study, some specimens were cross-sectioned. A carbon layer was evaporated on both sides prior to embedding in epoxy and ultramicrotomy(−130°C). Microscopy used a Philips CM3 0ST TEM.
Direct Imaging of Non-Classical Triblock Copolymer Blend and Gel Morphologies in the Dilute Regime
Authors: Laurer Jonathan H. , Spontak Richard J. , Smith Steven D. , Bukovnik Rudy
Published: June 2020

Incorporation of a low-molecular-weight, midblock-selective homopolymer into the microstructure of a microphase-ordered triblock copolymer results in preferential midblock swelling or a morphological transition, depending on the blend concentration and the size of the homopolymer chain relative to that of the host block. Since the blend properties are strongly dependent on the existing microstructure, morphological changes induced by variation in blend composition have attracted considerable interest. Recent efforts have sought to discern the phase stability of both copolymer-rich (concentrated) blends, in which parent homopolymer molecules are contained within their preferred microphase, and homo-polymer-rich (dilute) blends, in which the copolymer molecules micellize to reduce repulsive interactions in a parent homopolymer matrix. Since dilute blends typically consist of spherical copolymer micelles, most morphological studies have focused on concentrated copolymer/homopolymer blends in order to (i) tailor the blend microstructure, and properties, at the molecular level and (ii) examine macromolecular mixing in conformationally constrained nanoscale environments. In this work, we return to the dilute copolymer/homopolymer blend regime and examine the self-assembly of triblock copolymer molecules in the presence of low-molecular-weight parent and nonparent homopolymers and, in some cases, an oil.
A new method for characterization of domain morphology of polymer blends using RuO4 staining and LVSEM
Authors: Brown G. M. , Butler J. H.
Published: June 2020

Ruthenium tetroxide (RuO4) staining for TEM is a well proven technique for the characterization of crystalline polyolefins. Blend morphology has also been studied using RuO4 staining and SEM and low voltage SEM. A new method has been developed which uses RuO4 staining and LVSEM in the characterization of polyolefin blend morphology, specifically blends of polypropylene modified by the addition of elastomers or plastics. This method is often preferred over TEM for the characterization of blends and is applicable to many problems encountered in commercial and industrial laboratories including the analysis of domain morphology in molded parts, extruded films and fibers, failure analysis, and the analysis of layer morphology in certain coextruded films.

Three sample preparation steps are required prior to the LVSEM analysis. (1) The sample face is cryogenically sectioned on a glass knife in the cryomicrotome. (2) This face is stained in RuO4 vapors for 2.5 hours. The staining solution is prepared in situ by a modification of the method of Montezinos.
A molecular yarn: Near-Field optical studies of self-assembled, flexible fluorescent fibers
Authors: Higgins D. A. , Kerimo J. , Bout D. A. Vanden , Barbara P. F.
Published: June 2020

The formation of flexible molecular fibers via the solution-phase self-assembly of the pseudoisocyanine dye (PIC) 1,1’-diethyl-2,2’-cyanine and poly(vinyl sulfate) (PVS) is reported. The physical and electronic properties of these fibers spin coated into thin films on fused-quartz substrates are studied by fluorescence and topographic imaging with near-field scanning optical microscopy (NSOM) and also by atomic force microscopy (AFM). The scanned-probe images demonstrate that fibers with lengths in the hundred micron range, widths of hundreds of nanometers, and thicknesses of a few tens of nanometers, are readily formed in aqueous mixtures of PVS and PIC. Unprecedented flexibility in these fibers is exemplified by the formation of numerous curved and looped structures in the spin-coated thin films. A sandwich-like composite structure of alternating anionic PVS and cationic PIC layers is proposed as a model for the assembly of the dye and polymer in these fibers. The alternating layers in this model are held tightly together via the cooperative “cross-linking” of the PVS and PIC layers by electrostatic dye/polymer interactions, and by hydrophobic van der Waals interactions between the PIC molecules. The intermolecular interactions in the PIC layer result in the formation of a liquid-crystalline-like, well-ordered layer of the PIC, which exhibits the spectral characteristics of J-aggregates. The proposed layered structure apparently possess “reactive” surfaces which link individual fibers into a yam-like assembly. This cross-linking effect is supported by the presence of continuous circular fibers and by the gel-forming ability of the solutions from which these fibers are grown.
XRMF applications of a monolithic, polycapillary, focusing x-ray optic
Authors: Carpenter D. A. , Gao Ning , Havrilla G. J.
Published: June 2020

A monolithic, polycapillary, x-ray optic was adapted to a laboratory-based x-ray microprobe to evaluate the potential of the optic for x-ray micro fluorescence analysis. The polycapillary was capable of collecting x-rays over a 6 degree angle from a point source and focusing them to a spot approximately 40 µm diameter. The high intensities expected from this capillary should be useful for determining and mapping minor to trace elements in materials. Fig. 1 shows a sketch of the capillary with important dimensions.

The microprobe had previously been used with straight and with tapered monocapillaries. Alignment of the monocapillaries with the focal spot was accomplished by electromagnetically scanning the focal spot over the beveled anode. With the polycapillary it was also necessary to manually adjust the distance between the focal spot and the polycapillary.

The focal distance and focal spot diameter of the polycapillary were determined from a series of edge scans.
Molecular Microspectroscopy: Where are we and where are we going ?
Authors: Reffner John A.
Published: June 2020

Molecular microspectroscopy is the application of infrared or Raman spectroscopy, combined with light microscopy, for chemical analysis on the microscopic scale. For over a decade infrared microspectroscopy (IMS) has been an expanding technology both scientifically and commercially. Micro-Raman spectroscopy has a long history of scientific accomplishments with limited commercial success. Both of these techniques give spectral data that can be related to the bonding, crystalline state, isotopic content and molecular orientation of a material, but not its elemental composition. In this regards, molecular microspectroscopy compliments the elemental analyses performed with electron microscopes using x-ray emission spectroscopy. Resolving molecular chemistry of microscopic domains is the essence of molecular microspectroscopy.

Raman spectroscopy is experiencing renewed interest because of several advances in optics and photonics. Near-infrared lasers combined with Fourier transform spectrometers greatly reduced fluorescence interference, making Raman spectroscopy practical for many samples. The development of filters with high rejection of the Rayleigh scattered radiation simplifies the optical design of Raman systems. These filters are playing an important role in micro-Raman. CCD and CID detector technology, lasers, acusto-optical tuned filters (AOTF), liquid-crystal tuned filters (LCTF) and imaging spectrometers are contributing to a proliferation of new micro-Raman systems.
Infrared spectroscopic chemical imaging
Authors: Marcott Curtis , Reeder Robert C.
Published: June 2020

Infrared (IR) spectroscopy is a powerful, widely used technique for identifying materials or chemical compounds. An IR spectrum often provides a specific fingerprint for a given molecular component or species. IR frequencies, intensities, and line widths are also extremely sensitive to environmental perturbations and changes in molecular structure. Infrared spectroscopic images recorded through a Fourier transform infrared (FT-IR) microscope attachment have traditionally been constructed by translating a mapping stage a single pixel at a time through the sample area of interest; this is a very tedious and time-consuming procedure. Recently, a technique for rapidly performing high-fidelity FT-IR imaging spectroscopy using an indium antimonide (InSb) focal-plane array (FPA) detector coupled to an IR microscope and a step-scanning FT-IR spectrometer has been developed. These multichannel IR detectors were originally developed for thermal-imaging applications (mainly in the military), but they have tremendous potential as chemical imaging detectors when used as part of a spectrometer. The multiple detector elements enable images from all pixels to be collected simultaneously for each mirror retardation position of the interferometer. Use of an interferometer allows the entire IR spectrum over some wavelength range to be measured. The combination of a step-scanning FT-IR microscope and an InSb FPA detector provides unprecedented speed and image quality, limited only by the diffraction limit and/or the number of detector elements on the array.
Applications of Wide Field Fluorescence and Confocal Reflectance Microscopy to Bone and Cartilage Studies
Authors: Chestnut M.H. , Ibbotson K.J. , Taiwo Y.O. , Dufresne T.E. , Amburgey J.S. , Ebetino F.H. , Finch J.L.
Published: June 2020

Bisphosphonate Uptake by Living Cells

Bisphosphonates are drugs which inhibit bone resorption and are being pursued as therapies for osteoporosis. The molecular mechanisms by which bisphosphonates exert their biological effects are still unclear. It is generally assumed that uptake of these highly polar molecules by cells is very limited. In order to determine whether bisphosphonates are internalized and therefore may act intracellularly, we have examined the extent of their cellular uptake using a fluorescent naphthalene-dicarboxaldehyde (NDA) derivative of alendronate (ALN).

The distribution of NDA-ALN was examined in Ros 17/2.8 osteoblast-like osteosarcoma cells and freshly isolated neonatal rat osteoclasts by fluorescence microscopy following 0.5-24 hours of treatment in vitro. Data were collected using a Nikon Diaphot 300 equipped with a 60x planapochromat objective and high N.A. DIC optics. Images captured using a Photometries PXL camera were processed using UIC Metamorph software.

Uptake of the bisphosphonate into the cells was rapid and could be detected after 30 minutes of treatment in cells exposed to an external concentration of 10–5M NDA-ALN. Bisphosphonate appeared to accumulate over time within vacuolar, often perinuclear structures similar in appearance to secondary lysosomes (Figure 1). NDA-ALN was retained within cells after washing. These observations are consistent with the uptake of NDA-ALN proceeding via fluid-phase endocytosis. Uptake was greatly reduced when cells were incubated with the bisphosphonate at 20°C rather than 37°C. Freshly isolated osteoclasts also exhibited a noticeable amount of diffuse cytoplasmic staining (Figure 1), possibly indicating the presence of a second path of entry into the cell.
Analysis of Grain-Boundary Structures by Quantitative Hrtem
Authors: Nadarzinski K. , Kienzle O. , Ernst F.
Published: June 2020

HRTEM (high-resolution transmission electron microscopy) constitutes a powerful technique to investigate the atomistic structure of grain boundaries. However, interpreting HRTEM images of grain boundaries in terms of “projected structure” may lead to errors: Near a boundary, the contrast patterns of atom columns may differ from the corresponding patterns in regions of unfaulted crystal. Even worse, dynamic diffraction and lens aberrations may displace the contrast patterns against the actual (projected) positions of the columns. Nevertheless, it is possible to interpret such images safely by comparing them with simulated images of structure models. This method becomes powerful if one compares experimental and simulated images not merely by visual inspection but quantitatively, by means of digital image processing.

For a given HRTEM image of a grain boundary we iterate such quantitative image comparisons to perform an automatic structure refinement, which determines the structure that yields the best-matching simulated image to the experimental image (Fig. 1). While we can refine the positions of atom columns to any numerical precision, the coordinates only have a limited reliability. This arises because it is impossible to simulate HRTEM images perfectly – even if one knew the structure of the specimen. To quantify error limits for the column coordinates we explore how the simulated image of the refined structure changes with small displacements of the columns. It turns out that our method delivers the coordinates of atom columns with a precision in the order of 0.01 nm. The method also accounts for the damage that electron beam irradiation introduces in the specimen. By means of “beam damaging experiments” we estimate the maximum duration of irradiation to be allowed before damaging interferes with determining the structure at a given precision.
Atomic Structure of the (310) Symmetrical TILT Grain Boundary in Strontium Titanate - A Comparison among Experimental Methods and Atomistic Simulations
Authors: Ravikumar V. , Dravid Vinayak. P. , Wolf D.
Published: June 2020

Strontium Titanate is a prototypical perovskite oxide whose macroscopic electroceramic properties, like varistor and grain boundary barrier layer capacitor (GBBLC) behavior, are controlled by grain boundary (GB) phenomena. In this paper, we present a comparative analysis of the results of both experimental and theoretical investigations of the atomic structure of a (310) symmetrical tilt GB (a Σ=5 (310) [001] GB in the CSL notation) in SrTiO3. Bicrystals of SrTiO3 were procured from Shinkosha Ltd., and electron backscatter kikuchi pattern analysis as well as transmission electron diffraction studies confirm that the GB conforms to the Σ =5 misorientation. The atomic structure of this GB has been investigated using high resolution transmission electron microscopy (HRTEM) and associated image simulations, as well as by atomistic simulations using static iterative energy minimization schemes (“lattice-statics”).2
Determining Atomic Structure-Property Relationships at Grain Boundaries
Authors: Browning N. D. , Wallis D. J. , Nellist P. D. , Pennycook S. J.
Published: June 2020

Atomic scale effects at grain boundaries are known to play a dominant role in controlling the bulk properties of many materials. However, a detailed understanding of this role is complicated by the tendency for boundaries to behave in a “non-ideal” manner, i.e. the boundary plane can change on the scale of a few nanometers, altering the number of vacancies and impurities and the presence of second phases. The crucial first step to engineering boundary properties is therefore the ability to observe these changes experimentally with both atomic resolution and sensitivity. Such a capability is provided by the combination of Z-contrast imaging and electron energy loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM).

The Z-contrast technique generates an incoherent, atomic resolution structural image of a grain boundary which can be used to position the electron probe with atomic precision for spectroscopy. As the spectrum has nearly the same resolution as the image for core-losses >100eV, this arrangement has the unique advantage of allowing compositional fluctuations to be correlated directly with structural features in the boundary plane. Furthermore, multiple-scattering (MS) analysis can be utilized to extract 3- dimensional structural information from the spectrum. MS techniques consider the fine-structure of the spectrum to arise from interference effects occurring when a photoelectron created during the energy loss process is reflected from neighboring atoms. The real-space clusters used in this methodology allow the flexibility to determine whether the contributions to the spectrum arise from single or multiple scattering paths and from which atomic neighbors they originate. This allows the different structural relaxations that occur at boundaries, i.e. vacancies or structural disorder, to be distinguished from the spectrum.
EELS Measurement of the Local Electronic Structure of Copper Atoms Segregated to Aluminum Grain Boundaries
Authors: Splinter S.J. , Bruley J. , Batson P.E. , Smith D.A. , Rosenberg R.
Published: June 2020

It has long been known that the addition of Cu to Al interconnects improves the resistance to electromigration failure. It is generally accepted that this improvement is the result of Cu segregation to Al grain boundaries. The exact mechanism by which segregated Cu increases service lifetime is not understood, although it has been suggested that the formation of thin layers of θ-CuA12 (or some metastable substoichiometric precursor, θ’ or θ”) at the boundaries may be necessary. This paper reports measurements of the local electronic structure of Cu atoms segregated to Al grain boundaries using spatially resolved EELS in a UHV STEM. It is shown that segregated Cu exists in a chemical environment similar to that of Cu atoms in bulk θ-phase precipitates.

Films of 100 nm thickness and nominal composition Al-2.5wt%Cu were deposited by sputtering from alloy targets onto NaCl substrates. The samples were solution heat treated at 748K for 30 min and aged at 523K for 4 h to promote equilibrium grain boundary segregation. EELS measurements were made using a Gatan 666 PEELS spectrometer interfaced to a VG HB501 STEM operating at 100 keV. The probe size was estimated to be 1 nm FWHM. Grain boundaries with the narrowest projected
width were chosen for analysis. EDX measurements of Cu segregation were made using a VG HB603 STEM.
AFM as a Tool for Studying Ceramic Surfaces
Authors: Heffelfinger Jason R. , Bench Michael W. , Johnson Matthew T. , Carter C. Barry
Published: June 2020

Atomic-force microscopy (AFM), which is a relatively new technique, has found an invaluable niche in the imaging of insulating surfaces. AFM allows for analysis of topographical details at the atomic level with minimum sample preparation. Unlike scanning electron microscopy (SEM), AFM sample preparation requires no conductive coatings that may cover small surface features. The real power of the AFM lies in its ability to directly measure the heights of various surface features such as surface steps and particulates that measure as small as a few tenths of a nanometer in size. This technique does have limitations, and image artifacts, such as broadening of surface structures and ghost images of the tip, arise from the finite size and shape of the contacting probe. In the present investigation, AFM is used to characterize ceramic surfaces in a variety of experiments which range from surface faceting to solid-state reaction studies.

AFM studies were performed on a multi-mode, Nanoscope III (Digital Instruments, Santa Barbara, CA) using microfabricated Si3N4 cantilevers. The cantilevers were Cr coated to avoid charging effects between the tip and specimen. All images were recorded in air with a nominal applied force of 10-15 nN. AFM samples which were used to study the effect of surface faceting were prepared from polished single crystals. To remove surface damage and create a faceted surface, these sample were annealed at 1400°C for different amounts of time in air. Special precautions were taken to minimize the exposure of the surfaces to any contamination from the furnace environment during annealing. Solid-state reactions experiments were performed by reacting a cleaved {001} MgO surface with a Fe2O3 powder for 6 hours at 1450°C in air.
The Variation of (1 0-1 0) Surfaces of Sapphire between Different Annealing Time and Temperatures[1] Using Reflection Electron Microscopy (REM) [1]
Authors: HSU Tung , SU Guo Hung , Kim Yootaek
Published: June 2020

The (1 0-1 0) surface of sapphire (α-Al2O3), one of the prismatic surfaces, is a high energy surface [2,3]- Therefore, upon annealing, this surface breaks down into two sets of facets of lower energies. The two facets have been indexed and have been found to start developing along defects of the polished (1 0-1 0) surfaces [4, 5]. The goal of this study was to observe the very beginning of the development of these facets under various temperatures. The technique employed was reflection electron microscopy (REM) [6, 7] which is very sensitive to irregularity on crystal surfaces and has been successfully applied to the study of other low index surfaces of sapphire [8-10].

The sapphire specimens used in this experimental were manufactured with the edge-defined film -fed growth (EFG) method by Saphikon, Inc., Milford, NH. Specimen orientation was confirmed with the reflection Laue camera. The specimens were polished by hand to 0.1 µm. Annealing was done in a Lindberg tube furnace, with a heating rate of 200°C/hr and maximum temperatures of 1000°C to 1400°C maintained for 0.1 hr to 40 hr.
Remote On-Line Control of a High-Voltage in situ Transmission Electron Microscope with A Rational User Interface
Authors: O’Keefe M.A. , Taylor J. , Owen D. , Crowley B. , Westmacott K.H. , Johnston W. , Dahmen U.
Published: June 2020

Remote on-line electron microscopy is rapidly becoming more available as improvements continue to be developed in the software and hardware of interfaces and networks. Scanning electron microscopes have been driven remotely across both wide and local area networks. Initial implementations with transmission electron microscopes have targeted unique facilities like an advanced analytical electron microscope, a biological 3-D IVEM and a HVEM capable of in situ materials science applications. As implementations of on-line transmission electron microscopy become more widespread, it is essential that suitable standards be developed and followed. Two such standards have been proposed for a high-level protocol language for on-line access, and we have proposed a rational graphical user interface. The user interface we present here is based on experience gained with a full-function materials science application providing users of the National Center for Electron Microscopy with remote on-line access to a 1.5MeV Kratos EM-1500 in situ high-voltage transmission electron microscope via existing wide area networks. We have developed and implemented, and are continuing to refine, a set of tools, protocols, and interfaces to run the Kratos EM-1500 on-line for collaborative research. Computer tools for capturing and manipulating real-time video signals are integrated into a standardized user interface that may be used for remote access to any transmission electron microscope equipped with a suitable control computer.
Microscopy Outreach Through Shared Technology
Authors: Walsh Rosemary A.
Published: June 2020

Educational Outreach at PSU’s EM Facility for the Life Sciences evolved from the consolidation of multi-user laboratories and a growing demand for hands- on laboratory experiences requested by undergraduates, middle and highschool students and their teachers in central Pennsylvania. The EM lab is one of five such shared technology facilities which primarily provide university researchers with services and training.

The development of educational outreach programs grew from early work on extension projects with faculty and graduate students in the College for Agricultural Sciences. That experience and a new climate of cooperation permitted our laboratory to promote problem-based learning in funded programs such as undergraduate reasearch (independent study /honors projects) and summer institutes for pre-college students in Biology (Howard Hughes Institute) and Agricultural Sciences (Pennsylvania Governor’s School, PGSAS).
Outreach Opportunities Using the Instructional SEM at Iowa State University
Authors: Chumbley L. S. , Meyer M. , Fredrickson K. , Laabs F.C.
Published: June 2020

The development of a scanning electron microscope (SEM) suitable for instructional purposes has created a large number of outreach opportunities for the Materials Science and Engineering (MSE) Department at Iowa State University. Several collaborative efforts are presently underway with local schools and the Department of Curriculum and Instruction (C&I) at ISU to bring SEM technology into the classroom in a near live-time, interactive manner. The SEM laboratory is shown in Figure 1.

Interactions between the laboratory and the classroom use inexpensive digital cameras and shareware called CU-SeeMe, Figure 2. Developed by Cornell University and available over the internet, CUSeeMe provides inexpensive video conferencing capabilities. The software allows video and audio signals from Quikcam™ cameras to be sent and received between computers. A reflector site has been established in the MSE department that allows eight different computers to be interconnected simultaneously. This arrangement allows us to demonstrate SEM principles in the classroom. An Apple Macintosh has been configured to allow the SEM image to be seen using CU-SeeMe.
An Automated Procedure for On-Line Measurement of Spherical-Aberration Coefficient of High-Resolution Electron Microscopes
Authors: Pan M. , Krivanek O.L.
Published: June 2020

Spherical aberration coefficient (Cs) of the objective lens and electron wavelength ultimately determine the point-resolution of a high resolution electron microscope (HREM). Accurate measurement of Cs has become increasingly critical for reconstruction of structural information well beyond the point-resolution by means of either electron holography or focal series methods with a field emission gun (FEG) microscope. There are two main existing procedures for Cs measurement, i.e. (1) using diffractograms from a thin amorphous material, and (2) using beam-tilt-induced image displacement (BID). Since these procedures generally involve intensive data measurement, it is highly desirable to have an automated procedure. With an image pickup system such as CCD camera and appropriate software, we have developed an automated procedure for on-line Cs measurement. The procedure is based on analyzing diffractograms from a thin amorphous material such as amorphous carbon or germanium. The use of CCD camera allows for on-line measurement, and also for magnification to be calibrated with high precision, which is critical in Cs measurement.
True Colour SEM Imaging for Phase Recognition and X-Ray Microanalysis
Authors: Statham Peter J.
Published: June 2020

Secondary (SE) and backscattered electron (BSE) signals in the SEM provide high resolution monochrome images. BSE signal strength is modulated by mean atomic number and “false” colour can be introduced to enhance material contrast. Colour can also be introduced using multiple SE detectors, each with a different sensitivity to topographic and compositional information: by controlling signal mixtures and colours, the operator effectively has access to a powerful “studio” to generate aesthetically pleasing colour images. In both these examples, the correspondence between local elemental content and colour is entirely arbitrary and under subjective control of the operator. Elemental x-ray maps can be acquired and combinations colour coded to reveal phase distributions. For large numbers of maps and images, chemometric techniques such as PCA may be used to discover common relationships and assist the process of colour coding. Images derived from x-ray maps are usually low resolution and the analyst has to decide which elements to include and do a fair amount of data manipulation before any conclusions can be drawn. Furthermore, local topography effects perturb any multivariate statistical analysis. This paper presents a novel imaging technique which addresses these limitations.
Total-Reflection X-Ray Fluorescence Spectrometry (TXRF): Application to Elemental Profiles on Trace Evidence and Microsamples
Authors: Kubic MS, JD Thomas A. , Buscaglia MS JoAnn , Reus Ulrich
Published: June 2020

Total-Reflection X-ray Fluorescence spectrometry has been available as commercial instrumentation for the past few years. Since that time investigations and research has been conducted on the application of the technique particularly to problems involving micro samples such as in conservation and forensic analysis.

Elemental characterization of paint pigments, glass samples, textile fibers and liquid inclusions have been performed.

The EXTRA IIA TXRF spectrometer has inherent potential for the microanalysis. This instrumentation allows for simultaneous multi-element analysis for elements Phosphorus to Uranium with instrument detection levels (IDLs) less than or equal to 10 picograms for 50 of these elements.

Qualitative and semi-quantitative screening are possible with little sample preparation, while dissolved samples result in improved accuracy and precision with a dynamic range of five orders of magnitude without multiple dilutions.

This paper briefly reviews the principal and theory of TXRF, the operation of this instrument and its advantages over other quantitative elemental analysis techniques for these types of samples. Data demonstrating the comparable results obtained with the EXTRA IIA to that of ICP, AA, and NAA methods on samples supplied as proficiency tests will be presented. No difference in the quantitative results was exhibited between the reference and test data at a 95% confidence level.
Corrections for Several Factors that Limit Quantitative Analysis Of 3-D Data Sets Collected using Scanning-Laser Confocal Microscopy
Authors: Kayali S. , Ancin H. , Roysam B. , Szarowski D.H. , Shain W. , Turner J.N.
Published: June 2020

The confocal microscope collects high contrast 2-D images at different depths from thick (≥100 μm) tissues samples, thus providing data for quantitative measurements of 3-D objects. There are several factors that may limit quanititative analysis including photobleaching of fluors, attenuation of measured signal, mismatch in the various refractive indeces of the sample, and the width of the point spread function. We have addressed the first three of these limitations by using acriflavine-stained 100- [im thick sections of rat hippocampus and our 3-D automated analysis software. The laminar structure of the hippocampus provides tissue sections with areas of high and low nuclear density (pyramidal and extra-pyradmidal cell regions, respectively). Corrections for these limitations were made to samples from rat testes where developing spermatogonia provide nuclei of different DNA content.

The contribution of photobleaching to signal degradation was determined by collecting multiple 3-D images (z-series) of the same field. Twenty-one images of 50 planes each were collected (total scans= 1050).
“Standardless”, quantitative electron probe x-ray microanalysis with energy-dispersive spectrometry: What is the distribution of errors?
Authors: Newbury Dale E.
Published: June 2020

Conferences on quantitative electron probe X-ray microanalysis are typically highlighted by presentations which seek to advance the state of analytical science in this field through improvements in knowledge of the fundamentals of electron/X-ray-specimen interactions, inter-element (matrix) corrections, corrections for irregular specimen geometry, etc. However, in light of recent developments in computer-assisted, energy dispersive X-ray spectrometry analytical systems, we need to re-evaluate what is actually taking place in the everyday application of this analytical technique. The central paradigm in quantitative electron probe X-ray microanalysis, as established in the earliest work of Castaing and built upon by generations of contributors, is the measurement of the ratio of the intensity of an element in the unknown to the intensity for the same element in a standard under constant conditions of beam energy, known dose, and spectrometer performance. The set of such “k-values” determined for all constituents in the unknown is then converted into a set of concentrations through the use of matrix correction factors calculated through one of several schemes, e.g., “ZAF”, ϕ(ρz), etc. The great power of electron-excited X-ray microanalysis derives from the simplicity of the standards required.
Fundamental parameters for microanalysis
Authors: Joy David C
Published: June 2020

In order to perform quantitative X-ray microanalysis many parameters, representing the various stages of Xray generation and transport through the specimen at the chosen experimental conditions, must be known for all of the elements that might be encountered. Although ideally quantification is done by reference to standards so that only the functional variation of these parameters is required, in current practice it is increasingly necessary to work in situations where standardization is impossible and consequently where absolute magnitudes must be known. The quality and quantity of data that is now available varies widely.

Ionization cross sections

Although the amount of experimental data is limited, particularly in the energy range between 1 and 20keV, a critical assessment has concluded that for K-shell excitations both the magnitude of the cross-section σ and its variation with energy are adequately well known for overvoltages greater than about 2. For L- and M-shell excitations, however, and in all cases when the operational overvoltage is less than 2, the situation is much less satisfactory.
EDS x-ray microcalorimeters with 13 eV energy resolution
Authors: Wollman D. A. , Hilton G. C. , Irwin K. D. , Martinis J. M.
Published: June 2020

Although Si- and Ge-based Energy Dispersive Spectroscopy (EDS) detectors are by far the most commonly used x-ray spectrometers for microanalysis, they are limited by energy resolutions on the order of 100 eV. This low energy resolution is insufficient to clearly resolve many peak overlaps between Kα x-ray lines of different elements. In addition, many L and M lines of heavier elements fall in the 100 eV to 2 keV energy range, making it difficult in complicated spectra to identify and quantify the presence of technologically important lighter elements. Higher energy resolution and good count rates are necessary to provide improved limits of detectability.

We are developing a cryogenic x-ray microcalorimeter with significantly improved energy resolution and a count rate and detector area suitable for EDS microanalysis. In a calorimeter, the energy of an x-ray is converted to heat, and a measurement of the temperature rise of the detector gives the deposited photon energy. Our microcalorimeter detector consists of a normal-metal x-ray absorber which is in thermal and electrical contact with a superconducting transition-edge sensor (TES).
Lead-phase determination and demonstration of contaminated soil remediation mechanism by scanning electron microscopy and characteristic x-ray imaging
Authors: Vander Wood T. B.
Published: June 2020

The utility of microscopy and microanalysis in the study of contaminated atmospheres is well established. The particulate nature of soils suggests that these methods would be equally useful in the study of contaminated soils and similar materials; however, the focus on bulk contaminant concentrations, solution chemistry and leachability has obscured the role of microanalysis in elucidating the chemistry of contamination and in guiding remediation methods.

A case in point is the study of lead contaminated soils and possible remediation strategies. Ma, et al, recognized that reaction of lead with hydroxyapatite provided a possible remediation method for lead contaminated soils by precipitation of hydroxypyromorphite [Pb10(PO4)6(OH)2], proposing that the mechanism of lead immobilization in contaminated soils is congruent alteration, that is, dissolution of hydroxyapatite [Ca10(PO4)6(OH)2]to give phosphate ion in solution, followed by precipitation of dissolved lead ion as hydroxypyromorphite.
Atomic-resolution eels for composition and 3-D coordination determination at interfaces and defects
Authors: Browning N. D. , Wallis D. J. , Sivananthan S. , Nellist P. D. , Pennycook S. J.
Published: June 2020

Materials properties associated with interfaces and defects are dominated by atomic scale fluctuations in composition, structure and bonding. Although electron energy loss spectroscopy (EELS) provides a powerful tool to probe these features, low signal, lens aberrations, image coherence and specimen drift preclude the use of spectrum imaging and energy filtered imaging for these high-resolution problems. However, by utilizing Z-contrast imaging in conjunction with EELS in the scanning transmission electron microscope (STEM), these limitations are largely overcome and EELS appears capable of providing fudamental 3-D characterization of defect and interface structures with atomic resolution and sensitivity.

The main premise in utilizing these combined techniques is that the properties of defects and interfaces must be associated with structural differences relative to the bulk. If those structural differences can be located, then it is only necessary to perform spectroscopy in their vicinity to understand the structure property relationship. For crystalline materials in zone-axis orientations, the Z-contrast image provides this atomic resolution structural map. As this direct image is generated with only the high-angle scattering, it can be used to position the electron probe with atomic precision and does not interfere with the low-angle scattering for spectroscopy.