bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D Reconstruction of Proteasomes Using Random Conical Tilting
Authors: Hegerl R. , Pfeifer G. , Dahlmann B. , Baumeister W. 
Published: June 2020

Proteasomes isolated from the archaebacterium Thermoplasma acidophilum and negatively stained with ammonium molybdate appear in two preferred orientations on electron micrographs. Describing the particle roughly as cylinder-shaped, the orientations "end-on" and "side-on" are defined by the cylinder axis being normal and parallel to the specimen support, respectively. Two-dimensional averages are available from both views. The complexity of the particle, however, prevents an intuitive deduction of a three-dimensional model from these two views. Due to the occurence of two preferred orientations, the object is, in principle, well suited for a 3D reconstruction based on random conical tilting. The side-on view was used for 3D reconstruction for two reasons: First, two-dimensional averages led us to suppose that the particles do not suffer from rotations around their cylinder axis, and second, parallelism of the long cylinder axis and the specimen support promises to give a stable object inclination.The proteasomes were isolated and prepared for electron microscopy as described previously. Many pairs of micrographs were taken in a Philips EM 420 at a magnification of 36000 and an electron dose of about 2000 e/nm2. The first exposure of each pair shows the specimen with a tilt angle of about 60 deg, the second one is untilted (Fig. 1). Several image pairs were selected for computer processing using a favourable distribution of particles and acceptable focus conditions as selection criteria. After digitizing corresponding areas (2048 by 2048 pixels, pixel size 15 μm = 0.42 nm at object level) in each pair using an Eikonix 1412 camera, small images of single particles were extracted from the untilted image and aligned with respect to translation and rotation. Knowing the tilt angle and tilt axis azimuth, position and rotation parameters of the particles could be transferred to the tilted image thus enabling the extraction of a set 227 of projections ready for a three-dimensional back projection (Fig. 2). All computation was done with the EM-system.
Conducting Polymer Films as EM Substrates
Authors: Simon M. N. , Lin B. Y. , Lee H. S. , Skotheim T. A. , Wall J. S. 
Published: June 2020

The developing field of electroactive polymers, when the polymers are manipulated into thin film forms, offers potentially ideal materials for EM substrates. Mechanically, they are strong, flat, thin, and stable in the electron beam. For biological specimens, they are hydrophilic and their chemistry can be adapted to the particular specimen so the attachment can be gentle with no denaturation. They have the excellent electron optical properties of low Z, little grain, good electrical conductivity, and no observable radiation damage in the electron beam. Such films can be made fresh just prior to use to avoid contamination.Up to now, thin C films have been the best EM substrates for direct deposition of biological materials. With high vacuum evaporation of C, 20A thick films with >90% coverage of 4u windows in a holey film can be obtained. However, these films rapidly become hydrophobic by absorbing contaminants from the air and so need something like the wet-film technique or glow discharge to keep them hydrophilic. Even so, there are often hot spots of irreversible attachment of biological molecules causing distortion and even denaturation. Also, C films show a significant phase grain, presumably from C60 microcrystals.
Surface Morphology Studies by Low-Energy Electron Microscopy (LEEM)
Authors: Bauer Ernst , Mundschau Michael , Swiech Waclaw , Telieps Wolfgang 
Published: June 2020

The morphology of a surface determines to a large extent its physical and chemical properties. In order to understand these properties it is frequently sufficient to image the surface with a resolution in the 10 nm range, provided that the relevant surface features show sufficient contrast, as is the case in LEEM. The talk discusses the morphology information which can be obtained with LEEM and illustrates it with various examples.Point defects, e.g. emergence points of screw dislocations, or point-like defects such as small impurity clusters cannot be resolved in LEEM but nevertheless imaged by decorating them (screw dislocations) or by their influence on surface processes (pinning centers in sublimation). Line defects, e.g. sublimation steps, growth steps or glide lines, may be imaged directly down to atomic height by geometric phase contrast or indirectly by decoration. If a step separates regions with different structures (e.g. domain orientations), then ordinary diffraction contrast will reveal the shape and location of the step. Planar defects can also be imaged by diffraction contrast but three-dimensional defects such as large sublimation hillocks frequently cause also topographic contrast.
Rem Study of Current Effect on the Structure of Clean Si(111) Surface
Authors: Yamanaka A. , Ohse H. , Yagi K. 
Published: June 2020

Recently current effects on clean and metal adsorbate surfaces have attracted much attention not only because of interesting phenomena but also because of practically importance in treatingclean and metal adsorbate surfaces [1-6]. In the former case, metals deposited migrate on the deposit depending on the current direction and a patch of the deposit expands on the clean surface [1]. The migration is closely related to the adsorbate structures and substrate structures including their anisotropy [2,7]. In the latter case, configurations of surface atomic steps depends on the current direction. In the case of Si(001) surface equally spaced array of monatom high steps along the [110] direction produces the 2x1 and 1x2 terraces. However, a relative terrace width of the two domain depends on the current direction; a step-up current widen terraces on which dimers are parallel to the current, while a step-down current widen the other terraces [3]. On (111) surface, a step-down current produces step bunching at temperatures between 1250-1350°C, while a step-up current produces step bunching at temperatures between 1050-1250°C [5].In the present paper, our REM observations on a current induced step bunching, started independently, are described.Our results are summarized as follows.(1) Above around 1000°C a step-up current induces step bunching. The phenomenon reverses around 1200 C; a step-down current induces step bunching. The observations agree with the previous reports [5].
High-Resolution Backscattered Electron Imaging of GaAs/Ga1-xAlxAs Superlattice Structures with a Scanning Electron Microscope
Authors: Franchi S. , Merli P.G. , Migliori A. , Ogura K. , Ono A. 
Published: June 2020

It has been shown that using a Scanning Electron Microscope (SEM), equipped with a Field Emission Gun (FEG) and in-lens specimen position (ultrahigh resolution SEM), operating in the backscattered electron (BSE) mode, it is possible to obtain correct characterization of a superlattice with an image contrast related to the atomic number variation (1).In order to check the performance of a JEOL JSM 890 SEM in the BSE imaging mode, a GaAs/ Ga1-xAlxAs superlattice structure, whose cross section is reported in Fig. 1, has been characterized. On the top there are layers with a fixed value of the mole fraction of Al (x =0.3) and thickness variable between 1 and 20 nm. Below, all the layers are 5 nm thick and the Al mole fraction varies in the range 0.05<x<0.40. Observations at different accelerating voltages show that the image contrast decreases by increasing the electron energy, whereas the resolution is improved. According to our experiments, in these specimen, the best compromise between resolution and contrast is in the energy range 10 - 15 kV. Fig. 2 shows the BSE image, taken at 13 kV, of the top superlattice structure; the GaAs layers appear bright and those of Ga0.7Al0.3As are dark. The resolution obtained on this structure, where the mean atomic number varies by ΔZ=2.7 from layer to layer (corresponding to a contrast C= 4.4% ), is 2 nm. A better evidence of this resolution is given by Fig. 3, which shows a superstructure of 2 nm AlAs / 2nm GaAs, ( ΔZ = 9, C=16%). The image of fig. 4 refers to the superlattice on the bottom of Fig. 1 and allows to specify the minimum detectable ΔZ for a fixed resolution of 5nm. The fringe contrast drops linearly, as well known, with the mean atomic number variation between the layers. As the number of visible fringes is 7, we deduce that the minimum detectable mean atomic number variation is 0.8, (C = 1.3 %).
Development of an Ultra - High - Resolution Low Voltage(LV) SEM with an Optimized “in-lens” Design
Authors: Nagatani Takashi , Sato Mitsugu , OSUMI Masako 
Published: June 2020

An “in-lens” type FESEM, Hitachi S-900, developed as an ultra high resolution SEM having 0.7nm resolution at 30kV(Nagatani et al 1986), was modified for better performance at low beam energy(about 5kV or below) with small aberrations of ths objective lens and dual specimen position design. This is in responce to the recent upsurge of interest in using the LVSEM, which enables us hopefully to observe the surface topography of uncoated samples directly with maximum fidelity(Pawley 1987).The actual visibility of the minute topographical details depends upon not anly the spot size of the scanning beam but also physics of interaction between impinging electrons and solid sample(Joy 1989). However, the resolution can never be better than the spot size. Then, it would seem logical to specify the spot size first when designing a high resolution SEM. As discussed earlier(Crewe 1985; Nagatani et al 1987), the spot size of the beam is mainly limited by spherical aberration of the objective lens and diffraction at high voltage(about 10 kV and above). On the other hand, chromatic aberration and diffraction are the dominant factors at low voltages(about 5kV or below). Source size of a cold field emission is so small that we could neglect it for simplicity.In general, chromatic aberration can be smaller at higher excitation of a narrow gap objective pole-piece, which also made the working distance short. Therefore, some compromise is necessary among minimized aberrations, required specimen size, stage traverse and tilting angle etc. In practice, tolerable distortion of the image at low magnification and collection efficiency of the secondary electrons are another factors to be considered in designing the instrument. By taking these factors in simulation, an optimized objective lens was designed as shown in Table 1.
Secondary Electron Counting Images in SEM
Authors: Yamada S. , Ito T. , Gouhara K. , Uchikawa Y. 
Published: June 2020

The conventional method of image recording in scanning electron microscopy is photographic recording of the images displayed on a monitor screen of CRT installed with the SEM. An increasing number of works related to the development of computerized systems for digital recording and processing of the image data have been reported But a serious problem exists that the digiatal image data are acquired by discretizing the analogue output of the conventional detector system. In actuality, proportionality between the analogue output and the number of detected electrons is not ensured because of various kinds of noises and nonlinearity which are parasitic with the electronic circuitry. As a solution, we proposed a detection system to measure directly the number of signal electrons. In this paper, we describe electron counting for secondary electron detection in SEM, and show that the electron counting can provide a far better image quality than the analogue output.I. Images by Counting Method and by Analogue MethodThe signal obtained by the counting method is the electron number reaching the detector. This means that the method can eliminate the thermal noise and the fluctuation of the amplification which are parasitically generated during amplification of any type of secondary electron detectors including Everhart-Thornley detector and semiconductor detectors. In addition, noises caused by electronic circuits connected to the detector can be reduced. As shown in Fig.1, even when a primary electron current is lowered to the level less than 1 pA, we could obtain clear images by the counting method as compared with those by the analogue method. It is clear that the electron counting possesses remarkable advantages, as the secondary electron signal becomes weak.
Observation of GaAs/AlAs Superlattice Structures in both Secondary and Backscattcred Electron Imaging Modes with an Ultrahigh Resolution Scanning Electron Microscope
Authors: Ogura K. , Ono A. , Franchi S. , Merli P.G. , Migliori A. 
Published: June 2020

In the last few years the development of Scanning Electron Microscopes (SEM), equipped with a Field Emission Gun (FEG) and using in-lens specimen position, has allowed a significant improvement of the instrumental resolution . This is a result of the fine and bright probe provided by the FEG and by the reduced aberration coefficients of the strongly excited objective lens. The smaller specimen size required by in-lens instruments (about 1 cm, in comparison to 15 or 20 cm of a conventional SEM) doesn’t represent a serious limitation in the evaluation of semiconductor process techniques, where the demand of high resolution is continuosly increasing. In this field one of the more interesting applications, already described (1), is the observation of superlattice structures.In this note we report a comparison between secondary electron (SE) and backscattered electron (BSE) images of a GaAs / AlAs superlattice structure, whose cross section is reported in fig. 1. The structure consist of a 3 nm GaAs layer and 10 pairs of 7 nm GaAs / 15 nm AlAs layers grown on GaAs substrate. Fig. 2, 3 and 4 are SE images of this structure made with a JEOL JSM 890 SEM operating at an accelerating voltage of 3, 15 and 25 kV respectively. Fig. 5 is a 25 kV BSE image of the same specimen. It can be noticed that the 3nm layer is always visible and that the 3 kV SE image, in spite of the poorer resolution, shows the same contrast of the BSE image. In the SE mode, an increase of the accelerating voltage produces a contrast inversion. On the contrary, when observed with BSE, the layers of GaAs are always brighter than the AlAs ones , independently of the beam energy.
A metal- coating Chamber for High-Resolution Cryo-SEM
Authors: Sheehan John G. 
Published: June 2020

Improvements in particulate coatings for printable paper require understanding mechanisms of colloidal interactions in paper coating suspensions. One way to deduce colloidal interactions is to mage particle spacings and orientations at high resolution with cryo-SEM. Recent improvements in cryo-SEM technique have increased resolution enough to image particles in coating paints,vhich are sometimes smaller than 100 nm. In this report, a metal-coating chamber is described for preparation of colloidal suspensions for cryo-SEM at resolution down to 20 nm. It was found that etching is not necessary to achieve this resolution.A 120 K cryo-SEM sample will remain in an SEM for hours without noticeable condensation of imorphous ice. This is due to the high vapor pressure of vapor-condensed amorphous ice, measured by Kouchi. However, clean vacuum is required to coat samples with the thinnest possible continuous metal films which are required for high magnification SEM. Vapor contaminants, especially hrydrocarbons, are known to interfere with thin-film nucleation and growth so that more metal is needed to form continuous films, and resolution is decreased. That is why the metal-coating chamber in fig. 1 is designed for the cleanest possible vacuum. Feedthroughs for the manipulator md the shutter, which are operated during metal coating, are sealed with leak-proof stainless-steel Dellows. The transfer rod slides through a baseplate feedthrough that is double o-ring sealed.
Molecular Views of Ice-Embedded Lumbricus Terrestris Erythrocruorin Obtained By Invariant Classification
Authors: schatz Michael , Jäger Joachim , Heel Marin van 
Published: June 2020

Lumbricus terrestris erythrocruorin is a giant oxygen-transporting macromolecule in the blood of the common earth worm (worm "hemoglobin"). In our current study, we use specimens (kindly provided by Drs W.E. Royer and W.A. Hendrickson) embedded in vitreous ice (1) to avoid artefacts encountered with the negative stain preparation technigue used in previous studies (2-4).Although the molecular structure is well preserved in vitreous ice, the low contrast and high noise level in the micrographs represent a serious problem in image interpretation. Moreover, the molecules can exhibit many different orientations relative to the object plane of the microscope in this type of preparation. Existing techniques of analysis requiring alignment of the molecular views relative to one or more reference images often thus yield unsatisfactory results.We use a new method in which first rotation-, translation- and mirror invariant functions (5) are derived from the large set of input images, which functions are subsequently classified automatically using multivariate statistical techniques (6). The different molecular views in the data set can therewith be found unbiasedly (5). Within each class, all images are aligned relative to that member of the class which contributes least to the classes′ internal variance (6). This reference image is thus the most typical member of the class. Finally the aligned images from each class are averaged resulting in molecular views with enhanced statistical resolution.
Correction of Spherical Aberration using Defocus Modulation Technique
Authors: Taniguchi Yoshifumi , Shimizu Ryuichi , Chaya Michio , Ikuta Takashi 
Published: June 2020

In the electron optical system of transmission electron microscopes, there essentially exists a spherical aberration in the objective lens. A novel method to correct the spherical aberration based on the defocus modulation technique by the image integration with bipolar weighting functions have been proposed by one of the authors (T. I.). Because a coherent optical system is assumed in this method, this technique can be extended to the transmission electron microscopy.This paper presents the experimental confirmation of the usefulness of this method for the electron microscopy by off-line image integration of the series of though-focus images recorded on a video tape.A thermal field emission type electron microscope (JEM-100CFEG) was used in this experiment. The accelerating voltage was 80 kV and the spherical aberration coefficient of the objective lens was 6.1 mm. The sample was amorphous carbon film of 2 nm thick. Small particles of gold were evaporated onto the film in a Bell-jar. The image filing consists of 125 images as a through-focus series by step of 13.64 nm. Because of the residual asymmetry of the objective pole piece, it was unable to coincide the current center with the voltage center which is true optical axis of the electron microscope. The misalignment of the current center was corrected by shifting the image data itself in a computer after making the image data filing of the through-focus series. The image integration to reconstruct the aberration free images was performed with the corrected image data under appropriate bipolar weighting functions for real and imaginary terms.
Ordered Arrays of Type B Botulinum Toxin On Phospholipid Vesicles
Authors: Schmid F. , DasGupta B. R. , Robinson J. P. 
Published: June 2020

Botulinum neurotoxins comprise a family of potent toxins produced by the bacterium Clostridium botulinum. There are seven serologically distinct types of botulinum neurotoxins and they act near the neuromuscular junction, producing a flaccid paralysis. These neurotoxins are synthesized as single polypeptide chains which may be cleaved artificially or by endogenous proteases to more active dichain forms which are covalently held by disulfide linkage. The carboxy terminal 2/3 of the molecule is designated the heavy (H) chain, the rest is referred to as the light (L) chain. The neurotoxins have a molecular weight of approximately 150kD (for general review, Simpson, 1986)Simpson (1986) has proposed, by analogy to other bacterial toxins and viral infection models that the mode of action of these toxins proceed in three stages: binding to the surface of a cell, internalization and an enzymatic action. These functions can be separated biochemically; for example, the chains bind to the the cell surface and internalize. The enzymatic activity probably involves the L chain. This enzymatic poisoning step in neural cells is not known.
Recent Progress In High-Resolution Shadowing For Biological Transmission Electron Microscopy
Authors: Gross Heinz , Krusche Katarina , Tittmann Peter 
Published: June 2020

Freeze-drying followed by heavy metal shadowing is a long established and straight forward approach to routinely study the structure of dehydrated macromolecules. Very thin specimens such as isolated membranes or single macromolecules are directly adsorbed on C-coated grids. After rapid freezing the grids are transferred into a suitable vacuum equipment for freeze-drying and heavy metal shadowing.To improve the resolution power of shadowing films we introduced shadowing at very low specimen temperature (−250°C). To routinely do that without the danger of contamination we developed in collaboration with Balzers an UHV (p≤10-9 mbar) machine (BAF500K, Fig.2). It should be mentioned here that at −250°C the specimen surface acts as effective cryopump for practically all impinging residual gas molecules from the residual gas atmosphere.Common high resolution shadowing films (Pt/C, Ta/W) have to be protected from alterations due to air contact by a relatively thick C-backing layer, when transferred via atmospheric conditions into the TEM. Such an additional C-coat contributes disturbingly to the contrast at high resolution.