bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electron Microscopy of Negatively Stained and Frozen-Hydrated Bacteriophage Φ29
Authors: Olson N. H. , Xu W. , Grochulski W. D. , Andersont D. L. , Baker T. S. 
Published: June 2020

Bacteriophage Φ29 is a complex-shaped, double-stranded DNA virus that infects Bacillus subtilis . Mature Φ29 particles contain six major structural proteins which give rise to several distinctive features: a prolate-shaped head (gp8), fibers (gp8.5) which radiate from the head, a connector-collar region (gp10 and gp11), collar appendages (gp12*) and a tail (gp9). Although much is known about Φ29 biochemistry, genetics and assembly, relatively little is known about its detailed structure. Three-dimensional reconstructions of the collar demonstrated that it contains two structurally distinct features: an upper portion (proximal to the head) with 12-fold axial symmetry (gp10) and a lower protion with 6-fold symmetry (possibly both gp10 and gp11). The capsid is believed to be organized with two apical regions with trimeric aggregates of gp8 dimers arranged on a T=l icosahedral lattice separated by 10 additional trimers in the equatorial region. Φ29 proheads are assembly intermediates that contain only gp8, gp8.5, gp10 and the scaffolding protein (gp7) which is released upon DNA encapsidation. We have imaged Φ29 with conventional negative-staining and the recently developed cryo-microscopy techniques with the goal of examining the structural basis for Φ29 morphogenesis.Vitrified Φ29 proheads display distinct outlines with one end pointed and the other somewhat flattened and they often orient with their long axes in the plane of the vitreous water (Fig. 1). Occasional end-on views with a circular profile are also observed. Proheads show a tendency to associate in pairs with the closest contact between the flattened ends (Fig. 1, arrow-head). Longer morphological variants are also occassionally observed (Fig. 1, arrow). The morphology of proheads is dramatically distorted in negative-stain preparations indicating significantly poorer preservation using this technique (Fig. 2). Proheads are also permeable to stain.
Three-Dimensional Image Reconstruction of the 50S Subunit from

Escherichia Coli

Ribosomes Lacking 5S-rRNA
Authors: Radermacher Michael , Nowotny Volker , Grassucci Robert , Frank Joachim 
Published: June 2020

In earlier studies the structure of the 50S ribosomal subunit from E. coli has been determined from electron micrographs, using the single exposure random conical reconstruction technique. For the understanding of the function of ribosomes the single proteins and ribosomal RNAs need to be located within the ribosome structure. For localization of most proteins immunoelectron microscopy and neutron scattering data are available. The current study’s goal is the localization of the 5S rRNA from a comparison of the structures of complete 50S subunits with that of subunits reconstituted omitting the 5S rRNA.By Phenol extraction of purified 50S subunits the rRNA fraction was separated form the total protein fraction (TP50). This rRNA fraction was separated into 23S rRNA and 5S rRNA via HPLC on a DEAE-column. The total reconstitution of 23S rRNA and the equivalent amount of TP50 resulted in particles lacking the 5S rRNA. For electron microscopy the subunits were prepared in a negative stain sandwich preparation.Twenty tilt pairs at 50° tilt and 0° were recorded, with an electron dose of approximately 10el/A2 and a magnification of 49,000. A total of 983 particles were selected from these data. The 0° images were aligned using the procedure described in.
A Simple Scanning Tunneling Microscope with Very Wide Scanning Range
Authors: Yao J.E. , Shang G.Y. 
Published: June 2020

Scanning Tunneling Microscope (STM) has been a powerful tool for study of surfaces in the range of about 1 micrometer. The small field of view is enough for imaging homogeneous surfaces with atomic or near-atomic resolution. If, however, integrated circuits, gratings and other small “man-made” structures have to be observed, a STM with very wide scan range, for example, 10 to 100 micrometers is needed. In most of the STMs currently in use, three-dimensional scanner are fabricated from piezoceramic stacks, tubes and beams. The maximum scanning range is restricted to about a micrometer because of the maximum allowable control voltage and piezo element dimensions. Recently, Takashima Koshi has constructed a x/y scan stage for observation of grating(1). In a similar point of view, We have designed and built a simple scanner (Fig.1), which includes a base B, a mechanical amplifying device (consisting of a spring lever S and a metal tube M), x/y driving elements D, z control piezo tube P and tip T. The relation between the displacement dx(dy) and applied voltage V for the scanner is described by the equation:dx(dy)=KV(2L+l)/2d. Where, K is the voltage sensitivity in nm/v; L and l are the lengths of M and S respectively; d is the distance between the axis of S and that of D. When L=30mm, l =8mm, d=5mm, k=60nm/v, a scan range of 120μm will be obtained.
Scanning Tunneling Microscopy of Amorphous Carbon Films
Authors: Fotino Mircea , Parks D.C. 
Published: June 2020

In the last few years scanning tunneling microscopy (STM) has made it possible and easily accessible to visualize surfaces of conducting specimens at the atomic scale. Such performance allows the detailed characterization of surface morphology in an increasing spectrum of applications in a wide variety of fields. Because the basic imaging process in STM differs fundamentally from its equivalent in other well-established microscopies, good understanding of the imaging mechanism in STM enables one to grasp the correct information content in STM images. It thus appears appropriate to explore by STM the structure of amorphous carbon films because they are used in many applications, in particular in the investigation of delicate biological specimens that may be altered through the preparation procedures.All STM images in the present study were obtained with the commercial instrument Nanoscope II (Digital Instruments, Inc., Santa Barbara, California). Since the importance of the scanning tip for image optimization and artifact reduction cannot be sufficiently emphasized, as stressed by early analyses of STM image formation, great attention has been directed toward adopting the most satisfactory tip geometry. The tips used here consisted either of mechanically sheared Pt/Ir wire (90:10, 0.010" diameter) or of etched W wire (0.030" diameter). The latter were eventually preferred after a two-step procedure for etching in NaOH was found to produce routinely tips with one or more short whiskers that are essentially rigid, uniform and sharp (Fig. 1) . Under these circumstances, atomic-resolution images of cleaved highly-ordered pyro-lytic graphite (HOPG) were reproducibly and readily attained as a standard criterion for easily recognizable and satisfactory performance (Fig. 2).
Development of the UHV-STM
Authors: Iwatsuki M. , Kitamura S. , Mogami A. 
Published: June 2020

Since Binnig, Rohrer and associates observed real-space topographic images of Si(111)-7×7 and invented the scanning tunneling microscope (STM),1) the STM has been accepted as a powerful surface science instrument.Recently, many application areas for the STM have been opened up, such as atomic force microscopy (AFM), magnetic force microscopy (MFM) and others. So, the STM technology holds a great promise for the future.The great advantages of the STM are its high spatial resolution in the lateral and vertical directions on the atomic scale. However, the STM has difficulty in identifying atomic images in a desired area because it uses piezoelectric (PZT) elements as a scanner.On the other hand, the demand to observe specimens under UHV condition has grown, along with the advent of the STM technology. The requirment of UHV-STM is especially very high in to study of surface construction of semiconductors and superconducting materials on the atomic scale. In order to improve the STM image quality by keeping the specimen and tip surfaces clean, we have built a new UHV-STM (JSTM-4000XV) system which is provided with other surface analysis capability.
Construction Of UHV-REM-PEEM for Surface Studies
Authors: Kondo Y. , Yagi K. , Kobayashi K. , Kobayashi H. , Yanaka Y. 
Published: June 2020

Recent development of ultra-high vacuum electron microscopy (UHV-EM) is very rapid. This is due to the fact that it can be applied to variety of surface science fields.There are various types of surface imaging in UHV condition; low energy electron microscopy (LEEM) [1], transmission (TEM) and reflection electron microscopy (REM) [2] using conventional transmission electron microscopes (CTEM) (including scanning TEM and REM)), scanning electron microscopy, photoemission electron microscopy (PEEM) [3] and scanning tunneling microscopy (STM including related techniques such as scanning tunneling spectroscopy (STS), atom force microscopy and magnetic force microscopy)[4]. These methods can be classified roughly into two; in one group image contrast is mainly determined by surface atomic structure and in the other it is determined by surface electronic structure. Information obtained by two groups of surface microscopy is complementary with each other. A combination of the two methods may give images of surface crystallography and surface electronic structure. STM-STS[4] and LEEM-PEEM [3] so far developed are typical examples.In the present work a combination of REM(TEM) and PEEM (Fig. 1) was planned with use of a UHV CTEM. Several new designs were made for the new microscope.
Advances in Stem Instrumentation for Biology
Authors: Wall J. S. 
Published: June 2020

The forte of the Scanning transmission Electron Microscope (STEM) is high resolution imaging with high contrast on thin specimens, as demonstrated by visualization of single heavy atoms. of equal importance for biology is the efficient utilization of all available signals, permitting low dose imaging of unstained single molecules such as DNA.Our work at Brookhaven has concentrated on: 1) design and construction of instruments optimized for a narrow range of biological applications and 2) use of such instruments in a very active user/collaborator program. Therefore our program is highly interactive with a strong emphasis on producing results which are interpretable with a high level of confidence.The major challenge we face at the moment is specimen preparation. The resolution of the STEM is better than 2.5 A, but measurements of resolution vs. dose level off at a resolution of 20 A at a dose of 10 el/A2 on a well-behaved biological specimen such as TMV (tobacco mosaic virus). To track down this problem we are examining all aspects of specimen preparation: purification of biological material, deposition on the thin film substrate, washing, fast freezing and freeze drying. As we attempt to improve our equipment/technique, we use image analysis of TMV internal controls included in all STEM samples as a monitor sensitive enough to detect even a few percent improvement. For delicate specimens, carbon films can be very harsh-leading to disruption of the sample. Therefore we are developing conducting polymer films as alternative substrates, as described elsewhere in these Proceedings. For specimen preparation studies, we have identified (from our user/collaborator program ) a variety of “canary” specimens, each uniquely sensitive to one particular aspect of sample preparation, so we can attempt to separate the variables involved.
Novel Approaches to Low-Voltage Scanning Electron Microscopy
Authors: Jones Arthur V. 
Published: June 2020

In comparison with the developers of other forms of instrumentation, scanning electron microscope manufacturers are among the most conservative of people. New concepts usually must wait many years before being exploited commercially. The field emission gun, developed by Albert Crewe and his coworkers in 1968 is only now becoming widely available in commercial instruments, while the innovative lens designs of Mulvey are still waiting to be commercially exploited. The associated electronics is still in general based on operating procedures which have changed little since the original microscopes of Oatley and his co-workers.The current interest in low-voltage scanning electron microscopy will, if sub-nanometer resolution is to be obtained in a useable instrument, lead to fundamental changes in the design of the electron optics. Perhaps this is an opportune time to consider other fundamental changes in scanning electron microscopy instrumentation.
Secondary Electron Imaging of Liquid Water Films in the Environmental Scanning Electron Microscope
Authors: Peters Klaus-Ruediger 
Published: June 2020

High gas pressure scanning electron microscopy is now routinely possible with new microscopes operating between 0.1 and 20 torr gas pressure. Since the specimen chamber is separated from the electron optical column by pressure-limiting apertures, high gas pressures present at the level of the specimen do not affect the high vacuum in the column. The use of a single PLA underneath the last probe-forming lens allows maintainance of ∼0.1 torr. Twenty torr can be stabilized with two PLA, forming two differentially pumped pressure zones which may be incorporated into the last probe-forming lens.One of the most important new features of high gas pressure microscopy is the possibility to alter the type of gas and its pressure over a large range. High gas pressures (>1 torr) are required for charge neutralization on rugged insulators and for gas amplification of the SE signal. Additionally, using water vapors, liquid water can be stabilized. However, the aqueous environment is only one example among many possibilities.The secondary electron imaging of liquid water is a fascinating new aspect of scanning electron microscopy. At saturated water vapor pressures, water is stable indefinitely. Increasing or decreasing the vapor pressure allows condensation or evaporation of water and provides means to generate water films. As can be seer from Fig. 1, the stabilizing pressure for water at 20°C is 17.5 torr. Such a pressure would require a very short working distance for SE imaing. Therefore, it is preferable to reduce the specimen temperature and to establish vapor saturation at lower pressures. However, liquid water can only be stabilized at pressures greater than ∼4.5 torr.
New Configurations of Single - Crystal Scintillator Detectors in SEM
Authors: Autrata R. 
Published: June 2020

There are two reasons for designing special geometrical configurations of detectors of signal electrons in EM.1. For some traditional shapes of scintillators (discs) the quantum efficiency of single crystal YAG or YAP scintillators amounting to 5% - 7% is not fully utilized for achieving the maximum light output signal propagated in the desired. The reason is the small critical angle given by the high index of refraction of both single crystal materials. The shaping of single crystal scintillators and treating of surfaces by making use of the laws of geometrical optics lead to an increase of the value of the light output signal propagated in the desired direction.2. Different kinds of information carried by signal electrons (especially BSEs) of different types must be collected by a detector of a specific geometrical shape placed in a suitable position with regard to the specimen.Non-traditional geometrical configurations and optical modifications of detectors have been designed to solve the problem of a more
efficient propagation of light towards the photocathode of PMT, considering different types of signal electrons.
Condition of Energy and Incident Angle of Primary Beam for Voltage Contrast Observation Over Passivated Devices
Authors: Kodama T. , Koyama N. , Uchikawa Y. 
Published: June 2020

Inspection of passivated micro devices using the scanning electron microscope (SEM) at a low primary electron energy has been increasingly studied. Under an appropriate condition of energy Ep and incident angle Φp of the primary beam, the voltage contrasts follow regular and reversible variations, corresponding to the device electrode voltage under the passivation; i.e., the capacitive coupling voltage contrasts (CCVC). In our previous papers, we reported an empirical formula for conditions under which SEM observations over the passivation layer can be made without serious charging disturbances. In the present work we investigate the charging free conditions of PSG, SiN and Si3N4 passivated devices and the storage time of the voltage contrast is measured for various values of Ep and Φp.There exist a clear threshold of imaging conditions of CCVC with respect to Ep and Φp. Below the threshold, while continued imaging, the observed voltage contrasts follow regular and reversible variations. Above the threshold serious charging occurs and appears as bright and unclear contrast which never disappears throughout the observation. The two kinds of contrasts can be readily distinguished, since the charging contrast does not change its polarity whereas CCVC dose, when the applied voltages to the device electrodes are turned on and off. As was done in our previous works, the threshold values are determined by observing whether or not the observed voltage contrast follows reversible variation. The specimen used are PSG (1.2μm thick), SiN (1.1μm thick) and Si3N4 (0.8μm thick) passivated devices. Table 1 shows the threshold values of Ep for eachΦ p. The value of product Ep· cos2 Φp for each material becomes practically constant (= Ec). The value of Ec does not depend on the other imaging parameters such as magnification, primary beam current and scanning time per frame.
Low-Voltage Diffraction-Limited Probe Current: Limits Due to e-e Interactions in Intermediate Cross-Over
Authors: Barth J.E. , Jansen G.H. , Kruit P. 
Published: June 2020

The minimum diameter of an electron probe is limited by diffraction to the FWHM of the Airy disc, δa≃ λ/2α where the objective aperture semi-angle will be limited by aberrations. For probe voltages Vp less than 10 kV, the relative energy spread ε will cause a to be limited by chromatic aberration to about (λ/Ccε)1/2. The total probe diameter is then δp = Kλ/2α:, K=1. Thus δp = (Ccε;)1/2, which is proportional to V −3/4. Altho the diameter of the diffraction limited probe depends on the voltage, energy spread and the quality of the optics, the current depends (very nearly) only on the voltage independent reduced brightness Br of the e-source.The current into a probe that contains the gaussian image dg of an electron source of reduced brightness Br is Ip = BrVp(π/2 dgα)2. Since a probe without current is not very useful, dg must be greater than zero for sources of less than infinite brightness. The diameter of the probe will not dramatically increase until dg≃δp≃δa. Thus the current into a diffraction limited probe can be as much as Ip = BrVp(π/2 λ/2α α)2 = Brπ2/32 h2/me = Br 10−18 A.
The Determination of Spatial Homogeneity in Multiphase Mixtures
Authors: Misirli Zülal , Altan Burhanettin S. , Yörücü Hüseyin 
Published: June 2020

The modifications of the properties of composite materials by controlling the ratio, size, shape, orientation and spatial distribution of the second phase particles is a well known phenomena. Although there are technique available for the quantifying of most of these parameters, there is no established technique for the determination of the spatial homogeneity; yet this property is also highly influental on the behavior of the material. The aim of this paper is to introduce a fully automated technique to determine the spatial homogeneity of second phase particles.The technique presented in this paper was based on the technique reported by Eisenkolb and Lange and Hirlinger. In this technique the image area was divided by a grid having equal size squares (Fig.1). In a homogeneous mixture the proportion of the second phase would be the same in each square. However, because of the finite size and the agglomeration of particles, the proportion of the second phase varies. This variation is best represented by Relative Standard Deviation, Srel, which is defined as the standard deviation divided by the average. As finer grid sizes are used Srel would naturally increase. It was assumed that for a random dispersion Srel increases linearly as the size of the grid squares becomes smaller. In this study it was shown mathematically that this increase becomes faster when agglomerations are present.
User Interface Design Concepts of the Philips XL-Series Scanning Electron Microscopes
Authors: Peeters Marc H. 
Published: June 2020

Recent developments in Scanning Electron Microscopy have been technology driven. Major improvements have been made in information exchange, image processing technology, mechanical precision devices such as specimen stages, detector design, field emision guns, etc. In this process of automation and refining , the SEM became a rather complicated instrument to handle up to its full capabilities. When designing a user interface for such an instrument, considerable care must be taken that the instrument can be operated in an easy, straightforward way without losing functionality due to oversimplified automation.In the Philips XL SEM series, the user interface provides functional control over the microscope, where a function is defined by what the user wants to achieve, rather than by the individual hardware parts that have to be addressed in order to achieve the result. Such a function-based user interface can be realised by emploing a three-layered machine structure.The first layer consists of a mix of hardware parts such as an electron gun, lenses, a scan generator, an image processor, etc. In a second layer automation and compensation routines are performed by dedicated computers linked within a distributed intelligence network. Thus any of the primary parameters can be changed and the effect can be observed immediately as the related parameters are automatically readjusted. The third, outer layer is the actual user interface, implemented as customer-defined application programs running in an MS-DOS (MICROSOFT™) Windows environment on a personal computer. Simple mouse control provides fast access to a variety of application programs such as microscope setup, imaging, specimen survey, EDX analysis, linewidth measurement, image analysis and image database management. The window applications are overlaid on the microscope image, since the image is the essence of microscopy.
Development of an Ultrahigh-Vacuum Ultrahigh-Resolution Scanning Electron Microscope
Authors: Tomita T. , Kokubo Y. , Harada Y. , Daimon H. , Ino S. 
Published: June 2020

An ultrahigh-vacuum (UHV) ultrahigh-resolution (UHR) 100kV scanning electron microscope with a UHV specimen preparation chamber has been developed for in situ observation of clean specimen surfaces. The measured vacuum in the specmen area was about 2.2 × 10-8 Pa, and a 0.14nm lattice image of Au (220) was observed.Field emission scanning electron microscopes have been developed for the past ten years for sub-nanometer analysis. However, in recent analytical electron microscopy of so-called “new materials” such as ceramics and semiconductors, half nanometer analysis in UHV has become extremely important for materials characterization.Figure 1 shows an external view of the microscope. The microscope column and it’s control console are shown at the left and right, respectively. The seales of microscope column are only metal 0 rings and Cu-gaskets, and automatic bake-out is carried out at about 160°C.Figure 2 shows the electron optics of the system. A thermal assisted field emission gun (TFEG) with a W (100) emitter was used as a high-brightness gun, thus ensuring a brightness of 2 × 108 A/cm2 · str at 100 kV.