bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can the Number of D Electrons in Transition Metals be Measured from White Lines?
Authors: Rez P 
Published: July 2020

Abstract
Sharp peaks at threshold are a prominent feature of the L23 electron energy loss edges of both first and second row transition elements. Their intensity decreases monotonically as the atomic number increases across the period. It would therefore seem likely that the number of d electrons at a transition metal atom site and any variation with alloying could be measured from the L23 electron energy loss spectrum. Pearson measured the white line intensities for a series of both 3d and 4d transition metals. He normalised the white line intensity to the intensity in a continuum region 50eV wide starting 50eV above threshold. When this normalised intensity was plotted against the number of d electrons assumed for each elements he obtained a monotonie but non linear variation. The energy loss spectrum is given by

which is a product of p&lt;,the density of d states, and the matrix elements for transitions between 2p and d states.
High Resolution X-Ray Microanalysis of Nb/Al Multilayer Thin Films
Authors: Lucadamo G , Watanabe M , Barmak K , Williams D B 
Published: July 2020

Abstract
A study of reactive phase formation in thin films requires the understanding of the thermodynamics and kinetics of the reactions. Previous investigations of phase formation in Nb/Al multilayers using calorimetry and x-ray diffraction have observed that despite the presence of rather large driving forces for phase formation, a pronounced nucleation event occurs. This behavior has been reported in other systems including Ti/Al and Ni/Al. The initial nature of the interface can affect the nucleation, therefore careful studies of the structure and composition of the initial interfacial region may explain the reason for a kinetically separated nucleation and lateral growth step preceding normal phase growth. In addition, examination of the interface may also lend insight into the effects of different deposition processes and can provide evidence for the formation of solid solutions or compounds that can lower driving forces available for phase formation. Finally, the cross-sectional multilayer sample provides a means of characterizing spatial resolution and isolating specimen preparation artifacts.
Detection of small amounts of Fe and Nb in Zr-2.5wt%Nb pressure tubes
Authors: Müllejans H , Thomas J , Kienzle O , Griffiths M , Rühle M 
Published: July 2020

Abstract
The distribution of Nb and Fe in Zr-2.5wt%Nb pressure tube alloys has been of interest, in particular the effects of neutron irradiation. Both Fe in the β-phase and Nb in the α-phase are present in levels below lwt% and fluctuations of these elements in different parts of a specimen or between different specimens are of interest. In EDS quantification the signal-to-noise ratio and hence the detection limit is determined by the signals but depends also on the data analysis, in particular the background subtraction procedure. Here we compare the noise as given by the commercial analysis software to a simple estimate based on counting statistics. We used a VG HB 501 UX equipped with a thin window HP Ge detector, digital pulse processor and Voyager 3105 data acquisition and analysis system (Noran).In the past artefacts of Fe, Ni and Cu had been observed in EDS spectra, even for materials which did not contain any impurities of these elements.
Imaging of Metallic Nano-Particles Using PlasmOn/Valence Energy Loss Electrons
Authors: Hunt EM , Wang ZL , Evans ND , Hampikian JM 
Published: July 2020

Abstract
Although crystal lattices can be determined reasonably well using high-resolution electron microscopy, determination of local chemistry at high spatial-resolution remains a challenge. An energy-filtering system has made it possible to perform chemically sensitive imaging in a transmission electron microscope (TEM). This type of imaging usually relies on the signal of the inner shell ionization edge, the intensity of which is affected by the threshold energy-loss and the ionization cross-section of the edge. Therefore, the spatial resolution of a core loss image image is strongly affected by the signal-to-noise ratio. In this respect, lower loss electrons from the plasmon or valence region of the energy loss spectrum (10-100 eV) are favorable for chemically sensitive imaging due to the much higher signal intensity, provided any delocalization effects are small in comparison to the required spatial resolution. Compositionally sensitive imaging using the aluminum plasmon energy-loss electrons has been shown to produce ∼2nm resolution for an atomically sharp Al/Ti interface.
Computer-Aided Analysis of Oriented Crystallites by Diffraction Pattern Simulation and Tilt-Stage Control in a TEM
Authors: Thomas LE , Chariot LA , Stanley JT 
Published: July 2020

Abstract
Electron diffraction patterns taken in the transmission electron microscope (TEM) provide information about crystal structures and orientations in small sample areas. Extracting this information and manipulating local crystal orientations has become a great deal easier with the availability of desktop computer programs that allow simulation matching of experimental patterns and crystallographic control of sample tilting in the TEM. This presentation will illustrate an application of computer-aided crystallography for analyzing oriented crystallites in an experimentally complex material.
The surface corrosion films that form on reactive metals such as hafnium or zirconium in hot water provided our example. Cross-sectional examinations of the corrosion films revealed a columnar microstructure of monoclinic HfO2/ZrO2 grains extending normal to the metal/corrosion-film interface.The columnar grains were only about 50 nm in width, and thus were too small to analyze individually by selected-area diffraction. Local strains in the films smeared the diffraction fine structure so there was little hope for analysis by convergent-beam diffraction methods.
Is it Really that Easy to Solve Surface Structures Using Direct Methods?
Authors: Marks L D 
Published: July 2020

Abstract
A basic problem in surface science is that, unlike bulk materials, very few of the atomic scale structures are known despite many years of effort. Even the advent of STM has not helped that much since it is difficult to impossible to interpret images without a-priori information. Transmission electron diffraction (or x-ray diffraction) data from surfaces represent a unique opportunity for the application of Direct Methods to solve surface structures, opening up new avenues for science. Diffraction from a surface when the bulk is only weakly dynamical is at least 90% kinematical, but it may be the case that strong (surface) scattering is buried under bulk reflections including the lxl or “surface forbidden bulk-allowed” reflections. In addition, further out in the diffraction pattern subsurface relaxation effects become very important, and these cannot be considered using conventional Direct Methods; instead of sharp atomic-features the true exit wave will have small positive/negative dipoles.
The Pseudo-Atom Approximation in Direct Phase Determination of Protein Structures.
Authors: Dorset Douglas L 
Published: July 2020

Abstract
In principle, the availability of high-resolution micrographs in electron crystallography is a direct solution of the phase problem that has been used to great advantage for the study of proteins. However, as the resolution of the determination increases, the Fourier transform of the micrograph becomes a less accurate phase source. Hence, alternative direct methods for phase determination have been evaluated, if only to extend the resolution of most reliable lower resolution phases to the limit of the electron diffraction pattern. The first demonstration of its feasibility was published in a study of bacteriorhodopsin extending 15 Å image phases to beyond 3 Å by maximum entropy and likelihood procedures i. Later studies demonstrated that convolutional methods also can be effective.
In protein crystallography, there is always an interest in carrying out a true ab initio determinations, if only because of the challenge to traditional direct methods that become statistically less reliable as the number of atoms in the unit cell increases.
New Strategy for Crystallographic Reconstruction of Biological Bundle-Like Structures
Authors: Sherman MB , Jakana J , Sunt S , Matsudaira p , Chiu W , Schmid MF 
Published: July 2020

Abstract
The acrosomal bundle is an intracellular quasi-crystalline organelle in the head of the sperm of Limulus polyphemus. It is a long (up to 60 μm) straight bundle ∼1000 Å in diameter1 consisting of two major proteins in a 1:1 stoichiometric ratio: actin (42 kDa) and scruin (102 kDa) with a minor calmodulin-like protein (14 kDa) presumably bound to scruin molecule. Previous helical reconstructions of single filaments in the bundle showed actin-scruin interactions. We recorded tilt series from single bundles in a 400 kV cryomicroscope and have developed a novel crystallographic technique to reconstruct a unit cell from the bundle as a whole to reveal interfilament interactions.
Acrosomal bundles were purified as described elsewhere and embedded in vitreous ice over holes on a holey carbon film. Tilt series images were collected in a JEOL 4000EX electron cryo-microscope at 400 kV using 10,000x microscope magnification. Total dose was ∼16-18 electrons/Å per series covering a tilt range of ± 60° with 5° angular increment.
Demonstration of Solid State Electron Optical Devices: Pixelated Fresnel Phase Lenses
Authors: Ito Y , Bleloch AL , Brown LM 
Published: July 2020

Abstract
The ability to produce features of nanometer scale offers the possibility of phase manipulation of electron waves. The first conclusive results of phase manipulation by nanometer-scale diffraction gratings directly cut by the finely focused electron beam in a scanning transmission electron microscope (STEM) have already been demonstrated. This was achieved by using a grating with a “wedge” profile. This produced an asymmetrical diffraction pattern (in violation of Friedel's law). This violation is expected only if the grating acts mostly as a strong phase object. In this paper, a demonstration of solid state Pixelated Fresnel Phase (PFP) lenses for electrons will be presented. An array of these electron lenses can be easily formed and may be utilized, for example, as compact electron-beam forming lenses for parallel electron beam lithography.
In general, an incident plane wave traveling along the optic axis of a lens experiences a phase shift. A conventional Fresnel phase lens, consisting of concentric zones with a modulo of 2π phase structure, focuses an incoming electron plane wave to its focal point.
Determination of Tilt Parameters in Electron Diffraction Patterns of 3D-Microcrystals
Authors: Dimmeler E , Holmes KC , Schröder RR 
Published: July 2020

Abstract
Electron crystallography of thin three-dimensional (3D) protein crystals requires very exact determination of tilt angles and spot profiles to obtain correct merging of diffraction spot amplitudes. The reciprocal lattice of 3D microcrystals consists of ellipsoidal spot profiles which are very extended in the direction normal to the crystal face (z*). To extrapolate from the intensity measured in a section to the total spot intensity, two features need to be known very exactly: 1. the orientation of reciprocal lattice relative to the Ewald sphere, 2. the 3D-shape of the spot cloud.
Fig. 1 shows a tilt series of one frozen hydrated catalase crystal, in the order of recording. The third diffraction pattern gives the highest resolution because it is untilted and therefore the electrons have the shortest path length. In the current experimental data taken at 120 keV electron energy inelastic scattering within the crystal leads to a dramatic loss of elastic information in highly tilted patterns.
Determination of Atomic Positions in SiC 4H Using Quantitative Convergent Beam Refinements
Authors: Holmestad R , Morniroli J-P , Zuo JM , Spence JCH 
Published: July 2020

Abstract
Silicon carbide (SiC) is a widely used ceramic material, with many structural and electronic applications. It exists in many polytypes, differing from one another only by the stacking sequence of close packed double layers of Si and C atoms. The polytype called 4H has the hexagonal structure shown in figure 1. The double layers here have a stacking sequence of ABACABAC.. The distance z between the Si and the C layers (shown in figure 1) is an adjustable parameter, which is not exactly known. The aim of this work is to determine the atomic positions in the c-direction by quantitative convergent beam electron diffraction (QCBED). The goal is to develop a general refinement approach for structure determination by electron diffraction. Many newly synthesized materials are available in only very small quantities in the single crystal form and/or mixed with other phases, making X-ray diffraction methods difficult. SiC is often full of stacking faults. For these types of materials, the CBED method is ideal because of the small probe that can be used; areas of less than 100 Å can be studied.
(Under)Graduate Teaching Using Internet Access to Electron Microscopes
Authors: Voelkl E , Allard LF , Bruley J , Williams D B 
Published: July 2020

Abstract
The Lehigh University is presently offering direct access to top of the line electron microscopes at ORNL via the Internet for one graduate and one undergraduate course (Advanced TEM, Electron Microscopy & Microanalysis). The students at Lehigh have the opportunity to themselves control the Hitach HF-2000 FEG TEM. The controls presently include change of magnification and focus, moving the sample and correction for astigmatism. In this way, the students can collect high resolution lattice images of various materials and study e.g., the effects of changing focus on lattice images (contrast reversal). While the students at Lehigh can sit in the class room and run the instrument in broad daylight and communicate freely without disturbing the instrument by phonics, the instrument itself is protected from misuse through several layers of hardware and software.
This new way of teaching EM courses has become possible through recent advances in computer hardware (live-time Fourier transforms (FFTs)) and software. A commercial software package TimbuktuPro provides remote access to the computer at the HF-2000 at ORNL which controls the instrument as well as the slow-scan CCD-cameras (Gatan, model 794) attached to the instrument.
Database of Electron Microscope Images on the World Wide Web
Authors: Taniyama A , Shindo D , Hiraga K , Oikawa T , Kersker M 
Published: July 2020

Abstract
Recently, new recording devices, such as the Imaging Plate and a slow scan CCD camera, have come into wide use for digitally recording and storing transmission electron microscope images. A digital image has advantages of transferring, sharing and storing data. Furthermore the improvement of world wide computer network systems, for example, Internet makes it easier to transfer and share digital data among researchers. We have studied the processing and a quantitative analysis of digital high-resolution transmission electron microscope (HREM) images by means of a standard EWS and an SX-3 super-computer on the intelligent computer network system in Tohoku University, which is called Super TAINS (Fig. 1). With the increase of digital HREM images, we are in need of tools to help us store and quickly search these data.
A web site called “EMILIA (Electron Microscope Image Library and Archive)” was established in October 1996 as a database of HREM images. EMILIA is implemented by a WWW server on Super TAINS and HTML documents. Figure 2 shows sample pages from EMILIA.
Computational Methods for High Resolution Analysis of Cryo-Electron Micrographs of Hepatitis B Virus Capsids
Authors: Conway JF , Cheng N , Zlotnick A , Wingfield PT , Stahl SJ , Steven AC 
Published: July 2020

Abstract
Cryo-electron microscopy allows high resolution structural studies of macromolecules or macro-molecular complexes. As structural analyses extend to higher resolutions, several major compu-tational problems arise in analyzing cryo-electron micrographs. One is the acute sensitivity of the sample to radiation damage, requiring that images be acquired at a low electron dose with conse-quently low signal-to-noise ratio (SNR), especially at higher spatial frequencies. Secondly, as the size of each digitized image grows, the duration of the computational procedures lengthen consider-ably. A third problem is the complex distortion imposed upon the images by the contrast transfer function (CTF) of the electron microscope. We have addressed these issues in the context of solving the Hepatitis B Virus (HBV) capsid structure, and have succeeded in improving the resolution of our model from 17À[4] to 9À[1] (Fig.l). This is sufficient to define part of the molecular structure, including a 4-helix bundle at the dimer interface which constitutes the protruding ‘spike’ domains seen on the surface of the capsid, as well as other helices elsewhere in the molecule.
Computational Advances and Enabling Technologies for 3D Microscopies in Biology
Authors: Sosinsky Gina , Ellisman Mark 
Published: July 2020

Abstract
Approaches for exploration of biological structures with modern 3D microscopy techniques are expanding rapidly. These technological advances include not only the imaging of structures, but also the computational reconstruction methods for calculating three-dimensional structures. The computational techniques used to investigate the three-dimensional structure of macromolecular complexes, organelles or cells include crystallographic reconstruction, helical reconstruction, icosahedral reconstruction, single particle reconstruction, electron tomography and serial section reconstruction. These techniques have particularly useful in determining structures which are too small for light microscopy or too large for NMR or X-Ray structure determination or structures for which crystals are not available or order in the crystals is limited.
Advances in microscopes and associated computational capabilities have been substantial over the last few years. In this session, presentations will examine technical aspects and methods for three-dimensional reconstruction of biological structures from images acquired by electron microscopy and analyzed using the computational reconstruction techniques listed above.
Image Reconstruction from the Oversampled Diffraction Pattern
Authors: Bailey GW , Dimlich RVW , Alexander KB , McCarthy JJ , Pretlow TP , Miao J , Chapman H , Sayre D 
Published: July 2020

Abstract
In recording the intensity of the diffraction pattern from an arbitrary object, the phase is lost. This gives rise to the “phase problem”in reconstructing the object in crystallography, where the pattern is sampled at the Bragg peaks. It was shown by Bates and by Hayes that sampling at twice crystallographic density (2x oversampling) in each dimension is sufficient in principle to obtain a full reconstruction of the object. It was pointed out by Sayre in 1991 that the diffraction pattern of a non-crystalline object is continuous, therefore the pattern may be sampled on a finer scale, providing the additional information for the image reconstruction.
The loss of phase corresponds to a loss of half the information. It seems therefore that 2x oversampling in each dimension (8x in three dimension) may be unnecessary. We find that oversampling 1.67x in each dimension is sufficient to obtain a reconstruction, even in the presence of noise. However our algorithm fails when we reduce the oversampling factor to 1.58x.
TEMTUTOR - a Teaching Multimedia Program for TEM
Authors: Kuokkala V-T , Lepistö TK 
Published: July 2020

Abstract
Teaching of transmission electron microscopy usually includes both lectures on the contrast theories, electron diffraction, etc., and practical hands-on operation of the microscope. The number of students attending the lectures is normally unlimited, but at the microscope, only a few persons can work at the same time. Since the microscopes are expensive, it would be of a great help if cheaper 'training' microscopes with basic imaging and diffraction capabilities were available. These functions, in fact, can quite easily be realized with fast personal computers and work stations, where the simulation of transmission electron micrographs and related diffraction patterns can help the student better understand the image formation processes. Adding text, audio and video help capabilities to the program, it can be made an efficient supplemental teaching tool.
TemTutor for Windows is based on microScope for Windows, which is a BF/DF TEM micrograph simulation program for dislocations and stacking faults.
Towards Sub-À Resolution Through Incoherent Imaging
Authors: Pennycook SJ , Chisholm MF , Nellist PD 
Published: July 2020

Abstract
As first pointed out by Lord Rayleigh a century ago, incoherent imaging offers a substantial resolution enhancement compared to coherent imaging, together with freedom from phase contrast interference effects and contrast oscillations. In the STEM configuration, with a high angle annular detector to provide the transverse incoherence, the image also shows strong Z-contrast, sufficient in the case of a 300 kV STEM to image single Pt and Rh atoms on a γ-alumina support. The annular detector provides incoherence by virtue of its large central hole, which is equivalent by Babinet's principle of complementarity to a bright field detector of the same size. For weakly scattering specimens, it shows greater contrast than the incoherent bright field image, and also facilitates EELS analysis at atomic resolution, using the Z-contrast image to locate the probe with sub-À precision. The inner radius of the annular detector can be chosen to reduce the transverse coherence length to well below the spacings needed to resolve the object, a significant advantage compared to light microscopy.
The Resolution of the SEM
Authors: Joy David C 
Published: July 2020

Abstract
The resolution of any microscope is usually taken as the benchmark of its quality. When thinking about the scanning electron microscope(SEM) a comparison of its resolution to the resolutions quot-ed for other comparable instruments such as the transmission EM or the scanning tunneling micro-scope has unfortunately led some users to the view that the SEM is only a second best choice. In fact the spatial resolution that can be anticipated for an optimized SEM is highly competitive with its peers making it clearly the microscopy of choice.
The resolution of the SEM depends on two classes of factors; those which are inherent to the use of electrons as an imaging tool, and those which relate to the performance of the instrumentation (and possibly of the operator) used to perform the microscopy. The use of electrons as the scanning probe, and the choice of secondary electrons as the usual imaging mode, potentially affects the achievable resolution in three ways.