Image Restoration in Cryo-electron Microscopy

PubMed Central

Penczek, Pawel A.

2011-01-01

Image restoration techniques are used to obtain, given experimental measurements, the best possible approximation of the original object within the limits imposed by instrumental conditions and noise level in the data. In molecular electron microscopy, we are mainly interested in linear methods that preserve the respective relationships between mass densities within the restored map. Here, we describe the methodology of image restoration in structural electron microscopy, and more specifically, we will focus on the problem of the optimum recovery of Fourier amplitudes given electron microscope data collected under various defocus settings. We discuss in detail two classes of commonly used linear methods, the first of which consists of methods based on pseudoinverse restoration, and which is further subdivided into mean-square error, chi-square error, and constrained based restorations, where the methods in the latter two subclasses explicitly incorporates non-white distribution of noise in the data. The second class of methods is based on the Wiener filtration approach. We show that the Wiener filter-based methodology can be used to obtain a solution to the problem of amplitude correction (or “sharpening”) of the electron microscopy map that makes it visually comparable to maps determined by X-ray crystallography, and thus amenable to comparable interpretation. Finally, we present a semi-heuristic Wiener filter-based solution to the problem of image restoration given sets of heterogeneous solutions. We conclude the chapter with a discussion of image restoration protocols implemented in commonly used single particle software packages. PMID:20888957

Effect of screw threading dislocations and inverse domain boundaries in GaN on the shape of reciprocal-space maps.

PubMed

Barchuk, Mykhailo; Motylenko, Mykhaylo; Lukin, Gleb; Pätzold, Olf; Rafaja, David

2017-04-01

The microstructure of polar GaN layers, grown by upgraded high-temperature vapour phase epitaxy on [001]-oriented sapphire substrates, was studied by means of high-resolution X-ray diffraction and transmission electron microscopy. Systematic differences between reciprocal-space maps measured by X-ray diffraction and those which were simulated for different densities of threading dislocations revealed that threading dislocations are not the only microstructure defect in these GaN layers. Conventional dark-field transmission electron microscopy and convergent-beam electron diffraction detected vertical inversion domains as an additional microstructure feature. On a series of polar GaN layers with different proportions of threading dislocations and inversion domain boundaries, this contribution illustrates the capability and limitations of coplanar reciprocal-space mapping by X-ray diffraction to distinguish between these microstructure features.

Detection, mapping, and quantification of single walled carbon nanotubes in histological specimens with photoacoustic microscopy.

PubMed

Avti, Pramod K; Hu, Song; Favazza, Christopher; Mikos, Antonios G; Jansen, John A; Shroyer, Kenneth R; Wang, Lihong V; Sitharaman, Balaji

2012-01-01

In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM) was investigated to detect, map, and quantify trace amounts [nanograms (ng) to micrograms (µg)] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds). Optical-resolution (OR) and acoustic-resolution (AR)--Photoacoustic microscopy (PAM) was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR) fluorescence microscopy). Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections. The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs.

Neuroanatomy from Mesoscopic to Nanoscopic Scales: An Improved Method for the Observation of Semithin Sections by High-Resolution Scanning Electron Microscopy

PubMed Central

Rodríguez, José-Rodrigo; Turégano-López, Marta; DeFelipe, Javier; Merchán-Pérez, Angel

2018-01-01

Semithin sections are commonly used to examine large areas of tissue with an optical microscope, in order to locate and trim the regions that will later be studied with the electron microscope. Ideally, the observation of semithin sections would be from mesoscopic to nanoscopic scales directly, instead of using light microscopy and then electron microscopy (EM). Here we propose a method that makes it possible to obtain high-resolution scanning EM images of large areas of the brain in the millimeter to nanometer range. Since our method is compatible with light microscopy, it is also feasible to generate hybrid light and electron microscopic maps. Additionally, the same tissue blocks that have been used to obtain semithin sections can later be used, if necessary, for transmission EM, or for focused ion beam milling and scanning electron microscopy (FIB-SEM). PMID:29568263

Neuroanatomy from Mesoscopic to Nanoscopic Scales: An Improved Method for the Observation of Semithin Sections by High-Resolution Scanning Electron Microscopy.

PubMed

Rodríguez, José-Rodrigo; Turégano-López, Marta; DeFelipe, Javier; Merchán-Pérez, Angel

2018-01-01

Semithin sections are commonly used to examine large areas of tissue with an optical microscope, in order to locate and trim the regions that will later be studied with the electron microscope. Ideally, the observation of semithin sections would be from mesoscopic to nanoscopic scales directly, instead of using light microscopy and then electron microscopy (EM). Here we propose a method that makes it possible to obtain high-resolution scanning EM images of large areas of the brain in the millimeter to nanometer range. Since our method is compatible with light microscopy, it is also feasible to generate hybrid light and electron microscopic maps. Additionally, the same tissue blocks that have been used to obtain semithin sections can later be used, if necessary, for transmission EM, or for focused ion beam milling and scanning electron microscopy (FIB-SEM).

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

PubMed

Sanchez Sorzano, Carlos Oscar; Alvarez-Cabrera, Ana Lucia; Kazemi, Mohsen; Carazo, Jose María; Jonić, Slavica

2016-04-26

Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Microscopy and microanalysis 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bailey, G.W.; Corbett, J.M.; Dimlich, R.V.W.

1996-12-31

The Proceedings of this Annual Meeting contain paper of members from the three societies. These proceedings emphasizes the common research interests and attempts to eliminate some unwanted overlap. Topics covered are: microscopic analysis of animals with altered gene expression and in-situ gene and antibody localizations, high-resolution elemental mapping of nucleoprofein interactions, plant biology and pathology, quantitative HREM analysis of perfect and defected materials, computational methods for TEM image analysis, high-resolution FESM in materials research, frontiers in polymer microscopy and microanalysis, oxidation and corrosion, micro XRD and XRF, molecular microspectroscopy and spectral imaging, advances in confocal and multidimensional light microscopy, analyticalmore » electron microscopy in biology, correlative microscopy in biological sciences, grain-boundary microengineering, surfaces and interfaces, telepresence microscopy in education and research, MSA educational outreach, quantitative electron probe microanalysis, frontiers of analytical electron microscopy, critical issues in ceramic microstructures, dynamic organization of the cell, pathology, microbiology, high-resolution biological and cryo SEM, and scanning-probe microscopy.« less

Simultaneous Correlative Scanning Electron and High-NA Fluorescence Microscopy

PubMed Central

Liv, Nalan; Zonnevylle, A. Christiaan; Narvaez, Angela C.; Effting, Andries P. J.; Voorneveld, Philip W.; Lucas, Miriam S.; Hardwick, James C.; Wepf, Roger A.; Kruit, Pieter; Hoogenboom, Jacob P.

2013-01-01

Correlative light and electron microscopy (CLEM) is a unique method for investigating biological structure-function relations. With CLEM protein distributions visualized in fluorescence can be mapped onto the cellular ultrastructure measured with electron microscopy. Widespread application of correlative microscopy is hampered by elaborate experimental procedures related foremost to retrieving regions of interest in both modalities and/or compromises in integrated approaches. We present a novel approach to correlative microscopy, in which a high numerical aperture epi-fluorescence microscope and a scanning electron microscope illuminate the same area of a sample at the same time. This removes the need for retrieval of regions of interest leading to a drastic reduction of inspection times and the possibility for quantitative investigations of large areas and datasets with correlative microscopy. We demonstrate Simultaneous CLEM (SCLEM) analyzing cell-cell connections and membrane protrusions in whole uncoated colon adenocarcinoma cell line cells stained for actin and cortactin with AlexaFluor488. SCLEM imaging of coverglass-mounted tissue sections with both electron-dense and fluorescence staining is also shown. PMID:23409024

Nano-fEM: protein localization using photo-activated localization microscopy and electron microscopy.

PubMed

Watanabe, Shigeki; Richards, Jackson; Hollopeter, Gunther; Hobson, Robert J; Davis, Wayne M; Jorgensen, Erik M

2012-12-03

Mapping the distribution of proteins is essential for understanding the function of proteins in a cell. Fluorescence microscopy is extensively used for protein localization, but subcellular context is often absent in fluorescence images. Immuno-electron microscopy, on the other hand, can localize proteins, but the technique is limited by a lack of compatible antibodies, poor preservation of morphology and because most antigens are not exposed to the specimen surface. Correlative approaches can acquire the fluorescence image from a whole cell first, either from immuno-fluorescence or genetically tagged proteins. The sample is then fixed and embedded for electron microscopy, and the images are correlated (1-3). However, the low-resolution fluorescence image and the lack of fiducial markers preclude the precise localization of proteins. Alternatively, fluorescence imaging can be done after preserving the specimen in plastic. In this approach, the block is sectioned, and fluorescence images and electron micrographs of the same section are correlated (4-7). However, the diffraction limit of light in the correlated image obscures the locations of individual molecules, and the fluorescence often extends beyond the boundary of the cell. Nano-resolution fluorescence electron microscopy (nano-fEM) is designed to localize proteins at nano-scale by imaging the same sections using photo-activated localization microscopy (PALM) and electron microscopy. PALM overcomes the diffraction limit by imaging individual fluorescent proteins and subsequently mapping the centroid of each fluorescent spot (8-10). We outline the nano-fEM technique in five steps. First, the sample is fixed and embedded using conditions that preserve the fluorescence of tagged proteins. Second, the resin blocks are sectioned into ultrathin segments (70-80 nm) that are mounted on a cover glass. Third, fluorescence is imaged in these sections using the Zeiss PALM microscope. Fourth, electron dense structures are imaged in these same sections using a scanning electron microscope. Fifth, the fluorescence and electron micrographs are aligned using gold particles as fiducial markers. In summary, the subcellular localization of fluorescently tagged proteins can be determined at nanometer resolution in approximately one week.

[application of the analytical transmission electron microscopy techniques for detection, identification and visualization of localization of nanoparticles of titanium and cerium oxides in mammalian cells].

PubMed

Shebanova, A S; Bogdanov, A G; Ismagulova, T T; Feofanov, A V; Semenyuk, P I; Muronets, V I; Erokhina, M V; Onishchenko, G E; Kirpichnikov, M P; Shaitan, K V

2014-01-01

This work represents the results of the study on applicability of the modern methods of analytical transmission electron microscopy for detection, identification and visualization of localization of nanoparticles of titanium and cerium oxides in A549 cell, human lung adenocarcinoma cell line. A comparative analysis of images of the nanoparticles in the cells obtained in the bright field mode of transmission electron microscopy, under dark-field scanning transmission electron microscopy and high-angle annular dark field scanning transmission electron was performed. For identification of nanoparticles in the cells the analytical techniques, energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy, were compared when used in the mode of obtaining energy spectrum from different particles and element mapping. It was shown that the method for electron tomography is applicable to confirm that nanoparticles are localized in the sample but not coated by contamination. The possibilities and fields of utilizing different techniques for analytical transmission electron microscopy for detection, visualization and identification of nanoparticles in the biological samples are discussed.

Collection efficiency and acceptance maps of electron detectors for understanding signal detection on modern scanning electron microscopy.

PubMed

Agemura, Toshihide; Sekiguchi, Takashi

2018-02-01

Collection efficiency and acceptance maps of typical detectors in modern scanning electron microscopes (SEMs) were investigated. Secondary and backscattered electron trajectories from a specimen to through-the-lens and under-the-lens detectors placed on an electron optical axis and an Everhart-Thornley detector mounted on a specimen chamber were simulated three-dimensionally. The acceptance maps were drawn as the relationship between the energy and angle of collected electrons under different working distances. The collection efficiency considering the detector sensitivity was also estimated for the various working distances. These data indicated that the acceptance maps and collection efficiency are keys to understand the detection mechanism and image contrast for each detector in the modern SEMs. Furthermore, the working distance is the dominant parameter because electron trajectories are drastically changed with the working distance.

Detection, Mapping, and Quantification of Single Walled Carbon Nanotubes in Histological Specimens with Photoacoustic Microscopy

PubMed Central

Mikos, Antonios G.; Jansen, John A.; Shroyer, Kenneth R.; Wang, Lihong V.; Sitharaman, Balaji

2012-01-01

Aims In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM) was investigated to detect, map, and quantify trace amounts [nanograms (ng) to micrograms (µg)] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds). Materials and Methods Optical-resolution (OR) and acoustic-resolution (AR) - Photoacoustic microscopy (PAM) was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR) fluorescence microscopy). Results Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections. Conclusions The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs. PMID:22496892

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

PubMed

DiMaio, F; Chiu, W

2016-01-01

Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

High-resolution mapping of molecules in an ionic liquid via scanning transmission electron microscopy.

PubMed

Miyata, Tomohiro; Mizoguchi, Teruyasu

2018-03-01

Understanding structures and spatial distributions of molecules in liquid phases is crucial for the control of liquid properties and to develop efficient liquid-phase processes. Here, real-space mapping of molecular distributions in a liquid was performed. Specifically, the ionic liquid 1-Ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (C2mimTFSI) was imaged using atomic-resolution scanning transmission electron microscopy. Simulations revealed network-like bright regions in the images that were attributed to the TFSI- anion, with minimal contributions from the C2mim+ cation. Simple visualization of the TFSI- distribution in the liquid sample was achieved by binarizing the experimental image.

Correlative fractography: combining scanning electron microscopy and light microscopes for qualitative and quantitative analysis of fracture surfaces.

PubMed

Hein, Luis Rogerio de Oliveira; de Oliveira, José Alberto; de Campos, Kamila Amato

2013-04-01

Correlative fractography is a new expression proposed here to describe a new method for the association between scanning electron microscopy (SEM) and light microscopy (LM) for the qualitative and quantitative analysis of fracture surfaces. This article presents a new method involving the fusion of one elevation map obtained by extended depth from focus reconstruction from LM with exactly the same area by SEM and associated techniques, as X-ray mapping. The true topographic information is perfectly associated to local fracture mechanisms with this new technique, presented here as an alternative to stereo-pair reconstruction for the investigation of fractured components. The great advantage of this technique resides in the possibility of combining any imaging methods associated with LM and SEM for the same observed field from fracture surface.

Nanometres-resolution Kikuchi patterns from materials science specimens with transmission electron forward scatter diffraction in the scanning electron microscope.

PubMed

Brodusch, N; Demers, H; Gauvin, R

2013-04-01

A charge-coupled device camera of an electron backscattered diffraction system in a scanning electron microscope was positioned below a thin specimen and transmission Kikuchi patterns were collected. Contrary to electron backscattered diffraction, transmission electron forward scatter diffraction provides phase identification and orientation mapping at the nanoscale. The minimum Pd particle size for which a Kikuchi diffraction pattern was detected and indexed reliably was 5.6 nm. An orientation mapping resolution of 5 nm was measured at 30 kV. The resolution obtained with transmission electron forward scatter diffraction was of the same order of magnitude than that reported in electron nanodiffraction in the transmission electron microscope. An energy dispersive spectrometer X-ray map and a transmission electron forward scatter diffraction orientation map were acquired simultaneously. The high-resolution chemical, phase and orientation maps provided at once information on the chemical form, orientation and coherency of precipitates in an aluminium-lithium 2099 alloy. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

Electron microscopic studies of bacteriophage M13 DNA replication. [Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allison, D.P.; Ganesan, A.T.; Olson, A.C.

Intracellular forms of M13 phage DNA isolated after infection of Escherichia coli with wild-type phage have been studied by electron microscopy and ultracentrifugation. The data indicate the involvement of rolling-circle intermediates in single-stranded DNA synthesis. In addition to single-stranded, circular DNA, we observed covalently closed and nicked replicative-form (RF) DNAs, dimer RF DNAs, concatenated RF DNAs, RF DNAs with single-stranded tails (sigma, rolling circles), and, occasionally, RF DNAs with theta structures. The tails in sigma molecules are always single stranded and are never longer than the DNA from mature phage; the proportion of sigma to other RF molecules does notmore » change significantly with time after infection. The origin of single-stranded DNA synthesis has been mapped by electron microscopy at a unique location on RF DNA by use of partial denaturation mapping and restriction endonuclease digestion. This location is between gene IV and gene II, and synthesis proceeds in a counterclockwise direction on the conventional genetic map.« less

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

PubMed Central

Otón, J.; Vilas, J. L.; Kazemi, M.; Melero, R.; del Caño, L.; Cuenca, J.; Conesa, P.; Gómez-Blanco, J.; Marabini, R.; Carazo, J. M.

2017-01-01

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET). PMID:29312997

Achromatic elemental mapping beyond the nanoscale in the transmission electron microscope.

PubMed

Urban, K W; Mayer, J; Jinschek, J R; Neish, M J; Lugg, N R; Allen, L J

2013-05-03

Newly developed achromatic electron optics allows the use of wide energy windows and makes feasible energy-filtered transmission electron microscopy (EFTEM) at atomic resolution. In this Letter we present EFTEM images formed using electrons that have undergone a silicon L(2,3) core-shell energy loss, exhibiting a resolution in EFTEM of 1.35 Å. This permits elemental mapping beyond the nanoscale provided that quantum mechanical calculations from first principles are done in tandem with the experiment to understand the physical information encoded in the images.

Attosecond electron pulse trains and quantum state reconstruction in ultrafast transmission electron microscopy

NASA Astrophysics Data System (ADS)

Priebe, Katharina E.; Rathje, Christopher; Yalunin, Sergey V.; Hohage, Thorsten; Feist, Armin; Schäfer, Sascha; Ropers, Claus

2017-12-01

Ultrafast electron and X-ray imaging and spectroscopy are the basis for an ongoing revolution in the understanding of dynamical atomic-scale processes in matter. The underlying technology relies heavily on laser science for the generation and characterization of ever shorter pulses. Recent findings suggest that ultrafast electron microscopy with attosecond-structured wavefunctions may be feasible. However, such future technologies call for means to both prepare and fully analyse the corresponding free-electron quantum states. Here, we introduce a framework for the preparation, coherent manipulation and characterization of free-electron quantum states, experimentally demonstrating attosecond electron pulse trains. Phase-locked optical fields coherently control the electron wavefunction along the beam direction. We establish a new variant of quantum state tomography—`SQUIRRELS'—for free-electron ensembles. The ability to tailor and quantitatively map electron quantum states will promote the nanoscale study of electron-matter entanglement and new forms of ultrafast electron microscopy down to the attosecond regime.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kulawik, K., E-mail: kulawik@agh.edu.pl; Buffat, P.A., E-mail: philippe.buffat@epfl.ch; Ecole Polytechnique Fédérale de Lausanne, CIME, Station 12, CH-1015 Lausanne Switzerland

Microstructural characterization of Inconel 718 superalloy after three different heat treatment variants was performed by electron microscopy and electron tomography techniques, taking advantage of recent development in quantitative electron microscopy. Distribution maps of the chemical elements, collected by ChemiSTEM™ EDX system, offer a clear contrast between γ′, γ″, and the γ matrix. It was found that the γ′ phase contains mainly Ni, Al, and Ti, while the γ″ phase contains Ni, Nb, and Ti. Thus application of the Al and Nb STEM–EDX elemental maps enables identification and size measurements of γ′ and γ″ nanoparticles. 3D morphology of γ′ and γ″more » precipitates was examined by electron microscopy and FIB–SEM tomography. Employed methods revealed that in all three heat treatment variants the γ′ particles are almost spheroidal while the γ″ precipitates are mainly elongated-disc shaped. However, the precipitate sizes differed for each variant contributing to differences in the yield strength. Tomographic images were used for estimation of the volume fraction of the both strengthening phases. - Highlights: • ChemiSTEM™ EDX elemental maps bring a fast mean to differentiate γ′ and γ″ particles. • Such maps enable for the explicit size measurements of γ′ and γ″ nanoparticles. • Explicit γ′ and γ″ phases total volume fraction was measured employing FIB–SEM. • γ′/γ″ co-precipitates and sandwich-like γ′/γ″/γ′ particles were present. • HRSTEM-HAADF imaging revealed atomic columns of the γ′/γ″ co-precipitates.« less

Two-dimensional mapping of polarizations of rhombohedral nanostructures in the orthorhombic phase of KNbO3 by the combined use of scanning transmission electron microscopy and convergent-beam electron diffraction

NASA Astrophysics Data System (ADS)

Tsuda, Kenji; Tanaka, Michiyoshi

2015-08-01

Rhombohedral nanostructures previously found in the orthorhombic phase of KNbO3, by convergent-beam electron diffraction [Tsuda et al., Appl. Phys. Lett. 102, 051913 (2013)], have been investigated by the combined use of scanning transmission electron microscopy and convergent-beam electron diffraction. Two-dimensional distributions of the rhombohedral nanostructures, or nanometer-scale spatial fluctuations of polarization clusters, have been successfully visualized. The correlation length of the observed spatial fluctuations of local polarizations is related to the cpc/apc ratio and the transition entropy.

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.

PubMed

Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan; Stone, John E; Zhao, Jianhua; Schulten, Klaus

2016-07-07

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

Nanoparticle discrimination based on wavelength and lifetime-multiplexed cathodoluminescence microscopy.

PubMed

Garming, Mathijs W H; Weppelman, I Gerward C; de Boer, Pascal; Martínez, Felipe Perona; Schirhagl, Romana; Hoogenboom, Jacob P; Moerland, Robert J

2017-08-31

Nanomaterials can be identified in high-resolution electron microscopy images using spectrally-selective cathodoluminescence. Capabilities for multiplex detection can however be limited, e.g., due to spectral overlap or availability of filters. Also, the available photon flux may be limited due to degradation under electron irradiation. Here, we demonstrate single-pass cathodoluminescence-lifetime based discrimination of different nanoparticles, using a pulsed electron beam. We also show that cathodoluminescence lifetime is a robust parameter even when the nanoparticle cathodoluminescence intensity decays over an order of magnitude. We create lifetime maps, where the lifetime of the cathodoluminescence emission is correlated with the emission intensity and secondary-electron images. The consistency of lifetime-based discrimination is verified by also correlating the emission wavelength and the lifetime of nanoparticles. Our results show how cathodoluminescence lifetime provides an additional channel of information in electron microscopy.

Obtaining 3D Chemical Maps by Energy Filtered Transmission Electron Microscopy Tomography.

PubMed

Roiban, Lucian; Sorbier, Loïc; Hirlimann, Charles; Ersen, Ovidiu

2018-06-09

Energy filtered transmission electron microscopy tomography (EFTEM tomography) can provide three-dimensional (3D) chemical maps of materials at a nanometric scale. EFTEM tomography can separate chemical elements that are very difficult to distinguish using other imaging techniques. The experimental protocol described here shows how to create 3D chemical maps to understand the chemical distribution and morphology of a material. Sample preparation steps for data segmentation are presented. This protocol permits the 3D distribution analysis of chemical elements in a nanometric sample. However, it should be noted that currently, the 3D chemical maps can only be generated for samples that are not beam sensitive, since the recording of filtered images requires long exposure times to an intense electron beam. The protocol was applied to quantify the chemical distribution of the components of two different heterogeneous catalyst supports. In the first study, the chemical distribution of aluminum and titanium in titania-alumina supports was analyzed. The samples were prepared using the swing-pH method. In the second, the chemical distribution of aluminum and silicon in silica-alumina supports that were prepared using the sol-powder and mechanical mixture methods was examined.

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

PubMed

Lagerstedt, Ingvar; Moore, William J; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R; Kleywegt, Gerard J

2013-11-01

The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Fractional CO₂ Laser Pretreatment Facilitates Transdermal Delivery of Two Vitamin C Derivatives.

PubMed

Hsiao, Chien-Yu; Sung, Hsin-Ching; Hu, Sindy; Huang, Yau-Li; Huang, Chun-Hsun

2016-11-16

Topical vitamin C derivatives have been used to treat melasma and used as a skin whitener. The aim of this study was to compare skin histology and permeation of l-ascorbic acid 2-phosphate sesquimagnesium salt (MAP-1) and magnesium l-ascorbic acid-2-phosphate (MAP-2) after fractional CO₂ laser pretreatment. The effect of fractional laser treatment on porcine skin was examined by scanning electron microscopy and confocal laser scanning electron microscopy. The effect of fractional CO₂ laser treatment of different fluencies and pass numbers on transdermal flux of the two vitamin C derivatives through porcine skin was examined in vitro using a Franz diffusion chamber. Fluxes of MAP-1 and MAP-2 across fractional CO₂ laser-treated (5 W) skin were eight- to 13-fold, and 20- to 22-fold higher, respectively, than the fluxes of these compounds across intact skin. Fluxes of MAP-1 and MAP-2 across fractional CO₂ laser-treated (9 W) skin were 14- to 19-fold, and 30- to 42-fold higher, respectively, than their fluxes across intact skin. Fractional CO₂ laser treatment is an effective way of delivering vitamin C derivatives into the skin.

Atomic-Scale Characterization of Oxide Interfaces and Superlattices Using Scanning Transmission Electron Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spurgeon, Steven R.; Chambers, Scott A.

Scanning transmission electron microscopy (STEM) has become one of the fundamental tools to characterize oxide interfaces and superlattices. Atomic-scale structure, chemistry, and composition mapping can now be conducted on a wide variety of materials systems thanks to the development of aberration-correctors and advanced detectors. STEM imaging and diffraction, coupled with electron energy loss (EELS) and energy-dispersive X-ray (EDS) spectroscopies, offer unparalleled, high-resolution analysis of structure-property relationships. In this chapter we highlight investigations into key phenomena, including interfacial conductivity in oxide superlattices, charge screening effects in magnetoelectric heterostructures, the design of high-quality iron oxide interfaces, and the complex physics governing atomic-scalemore » chemical mapping. These studies illustrate how unique insights from STEM characterization can be integrated with other techniques and first-principles calculations to develop better models for the behavior of functional oxides.« less

Synthesis of zirconia (ZrO2) nanowires via chemical vapor deposition

NASA Astrophysics Data System (ADS)

Baek, M. K.; Park, S. J.; Choi, D. J.

2017-02-01

Monoclinic zirconia nanowires were synthesized by chemical vapor deposition using ZrCl4 powder as a starting material at 1200 °C and 760 Torr. Graphite was employed as a substrate, and an Au thin film was pre-deposited on the graphite as a catalyst. The zirconia nanostructure morphology was observed through scanning electron microscopy and transmission electron microscopy. Based on X-ray diffraction, selected area electron diffraction, and Raman spectroscopy data, the resulting crystal structure was found to be single crystalline monoclinic zirconia. The homogeneous distributions of Zr, O and Au were studied by scanning transmission electron microscopy with energy dispersive X-ray spectroscopy mapping, and there was no metal droplet at the nanowire tips despite the use of an Au metal catalyst. This result is apart from that of conventional metal catalyzed nanowires.

Imaging interfacial electrical transport in graphene–MoS{sub 2} heterostructures with electron-beam-induced-currents

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, E. R., E-mail: ewhite@physics.ucla.edu; Kerelsky, Alexander; Hubbard, William A.

2015-11-30

Heterostructure devices with specific and extraordinary properties can be fabricated by stacking two-dimensional crystals. Cleanliness at the inter-crystal interfaces within a heterostructure is crucial for maximizing device performance. However, because these interfaces are buried, characterizing their impact on device function is challenging. Here, we show that electron-beam induced current (EBIC) mapping can be used to image interfacial contamination and to characterize the quality of buried heterostructure interfaces with nanometer-scale spatial resolution. We applied EBIC and photocurrent imaging to map photo-sensitive graphene-MoS{sub 2} heterostructures. The EBIC maps, together with concurrently acquired scanning transmission electron microscopy images, reveal how a device's photocurrentmore » collection efficiency is adversely affected by nanoscale debris invisible to optical-resolution photocurrent mapping.« less

Scanning electron microscopy coupled with energy-dispersive X-ray spectrometry for quick detection of sulfur-oxidizing bacteria in environmental water samples

NASA Astrophysics Data System (ADS)

Sun, Chengjun; Jiang, Fenghua; Gao, Wei; Li, Xiaoyun; Yu, Yanzhen; Yin, Xiaofei; Wang, Yong; Ding, Haibing

2017-01-01

Detection of sulfur-oxidizing bacteria has largely been dependent on targeted gene sequencing technology or traditional cell cultivation, which usually takes from days to months to carry out. This clearly does not meet the requirements of analysis for time-sensitive samples and/or complicated environmental samples. Since energy-dispersive X-ray spectrometry (EDS) can be used to simultaneously detect multiple elements in a sample, including sulfur, with minimal sample treatment, this technology was applied to detect sulfur-oxidizing bacteria using their high sulfur content within the cell. This article describes the application of scanning electron microscopy imaging coupled with EDS mapping for quick detection of sulfur oxidizers in contaminated environmental water samples, with minimal sample handling. Scanning electron microscopy imaging revealed the existence of dense granules within the bacterial cells, while EDS identified large amounts of sulfur within them. EDS mapping localized the sulfur to these granules. Subsequent 16S rRNA gene sequencing showed that the bacteria detected in our samples belonged to the genus Chromatium, which are sulfur oxidizers. Thus, EDS mapping made it possible to identify sulfur oxidizers in environmental samples based on localized sulfur within their cells, within a short time (within 24 h of sampling). This technique has wide ranging applications for detection of sulfur bacteria in environmental water samples.

Cryo-Scanning Electron Microscopy (SEM) and Scanning Transmission Electron Microscopy (STEM)-in-SEM for Bio- and Organo-Mineral Interface Characterization in the Environment.

PubMed

Wille, Guillaume; Hellal, Jennifer; Ollivier, Patrick; Richard, Annie; Burel, Agnes; Jolly, Louis; Crampon, Marc; Michel, Caroline

2017-12-01

Understanding biofilm interactions with surrounding substratum and pollutants/particles can benefit from the application of existing microscopy tools. Using the example of biofilm interactions with zero-valent iron nanoparticles (nZVI), this study aims to apply various approaches in biofilm preparation and labeling for fluorescent or electron microscopy and energy dispersive X-ray spectrometry (EDS) microanalysis for accurate observations. According to the targeted microscopy method, biofilms were sampled as flocs or attached biofilm, submitted to labeling using 4',6-diamidino-2-phenylindol, lectins PNA and ConA coupled to fluorescent dye or gold nanoparticles, and prepared for observation (fixation, cross-section, freezing, ultramicrotomy). Fluorescent microscopy revealed that nZVI were embedded in the biofilm structure as aggregates but the resolution was insufficient to observe individual nZVI. Cryo-scanning electron microscopy (SEM) observations showed nZVI aggregates close to bacteria, but it was not possible to confirm direct interactions between nZVI and cell membranes. Scanning transmission electron microscopy in the SEM (STEM-in-SEM) showed that nZVI aggregates could enter the biofilm to a depth of 7-11 µm. Bacteria were surrounded by a ring of extracellular polymeric substances (EPS) preventing direct nZVI/membrane interactions. STEM/EDS mapping revealed a co-localization of nZVI aggregates with lectins suggesting a potential role of EPS in nZVI embedding. Thus, the combination of divergent microscopy approaches is a good approach to better understand and characterize biofilm/metal interactions.

Orientation and phase mapping in the transmission electron microscope using precession-assisted diffraction spot recognition: state-of-the-art results.

PubMed

Viladot, D; Véron, M; Gemmi, M; Peiró, F; Portillo, J; Estradé, S; Mendoza, J; Llorca-Isern, N; Nicolopoulos, S

2013-10-01

A recently developed technique based on the transmission electron microscope, which makes use of electron beam precession together with spot diffraction pattern recognition now offers the possibility to acquire reliable orientation/phase maps with a spatial resolution down to 2 nm on a field emission gun transmission electron microscope. The technique may be described as precession-assisted crystal orientation mapping in the transmission electron microscope, precession-assisted crystal orientation mapping technique-transmission electron microscope, also known by its product name, ASTAR, and consists in scanning the precessed electron beam in nanoprobe mode over the specimen area, thus producing a collection of precession electron diffraction spot patterns, to be thereafter indexed automatically through template matching. We present a review on several application examples relative to the characterization of microstructure/microtexture of nanocrystalline metals, ceramics, nanoparticles, minerals and organics. The strengths and limitations of the technique are also discussed using several application examples. ©2013 The Authors. Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.

Spatially-resolved mapping of history-dependent coupled electrochemical and electronical behaviors of electroresistive NiO

DOE PAGES

Sugiyama, Issei; Kim, Yunseok; Jesse, Stephen; ...

2014-10-22

Bias-induced oxygen ion dynamics underpins a broad spectrum of electroresistive and memristive phenomena in oxide materials. Although widely studied by device-level and local voltage-current spectroscopies, the relationship between electroresistive phenomena, local electrochemical behaviors, and microstructures remains elusive. Here, the interplay between history-dependent electronic transport and electrochemical phenomena in a NiO single crystalline thin film with a number of well-defined defect types is explored on the nanometer scale using an atomic force microscopy-based technique. A variety of electrochemically-active regions were observed and spatially resolved relationship between the electronic and electrochemical phenomena was revealed. The regions with pronounced electroresistive activity were furthermore » correlated with defects identified by scanning transmission electron microscopy. Using fully coupled mechanical-electrochemical modeling, we illustrate that the spatial distribution of strain plays an important role in electrochemical and electroresistive phenomena. In conclusion, these studies illustrate an approach for simultaneous mapping of the electronic and ionic transport on a single defective structure level such as dislocations or interfaces, and pave the way for creating libraries of defect-specific electrochemical responses.« less

Dipole-like electrostatic asymmetry of gold nanorods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Ji -Young; Han, Myung -Geun; Lien, Miao -Bin

The symmetry of metallic nanocolloids, typically envisaged as simple geometrical shapes, is rarely questioned. However, the symmetry considerations are so essential for understanding their electronic structure, optical properties, and biological effects that it is important to reexamine these foundational assumptions for nanocolloids. Gold nanorods (AuNRs) are generally presumed to have nearly perfect geometry of a cylinder and therefore are centrosymmetric. We show that AuNRs, in fact, have a built-in electrostatic potential gradient on their surface and behave as noncentrosymmetric particles. The electrostatic potential gradient of 0.11 to 0.07 V/nm along the long axes of nanorods is observed by off-axis electronmore » holography. Kelvin probe microscopy, secondary electron imaging, energy-filtered transmission electron microscopy, and plasmon mapping reveal that the axial asymmetry is associated with a consistently unequal number of cetyltrimethylammonium bromide moieties capping the two ends of the AuNRs. Electrostatic field maps simulated for the AuNR surface reproduce the holography images. The dipole-like surface potential gradient explains previously puzzling discrepancies in nonlinear optical effects originating from the noncentrosymmetric nature of AuNRs. Furthermore, similar considerations of symmetry breaking are applicable to other nanoscale structures for which the property-governing symmetry of the organic shell may differ from the apparent symmetry of inorganic core observed in standard electron microscopy images.« less

Dipole-like electrostatic asymmetry of gold nanorods

DOE PAGES

Kim, Ji -Young; Han, Myung -Geun; Lien, Miao -Bin; ...

2018-02-09

The symmetry of metallic nanocolloids, typically envisaged as simple geometrical shapes, is rarely questioned. However, the symmetry considerations are so essential for understanding their electronic structure, optical properties, and biological effects that it is important to reexamine these foundational assumptions for nanocolloids. Gold nanorods (AuNRs) are generally presumed to have nearly perfect geometry of a cylinder and therefore are centrosymmetric. We show that AuNRs, in fact, have a built-in electrostatic potential gradient on their surface and behave as noncentrosymmetric particles. The electrostatic potential gradient of 0.11 to 0.07 V/nm along the long axes of nanorods is observed by off-axis electronmore » holography. Kelvin probe microscopy, secondary electron imaging, energy-filtered transmission electron microscopy, and plasmon mapping reveal that the axial asymmetry is associated with a consistently unequal number of cetyltrimethylammonium bromide moieties capping the two ends of the AuNRs. Electrostatic field maps simulated for the AuNR surface reproduce the holography images. The dipole-like surface potential gradient explains previously puzzling discrepancies in nonlinear optical effects originating from the noncentrosymmetric nature of AuNRs. Furthermore, similar considerations of symmetry breaking are applicable to other nanoscale structures for which the property-governing symmetry of the organic shell may differ from the apparent symmetry of inorganic core observed in standard electron microscopy images.« less

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

PubMed Central

Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan; Stone, John E; Zhao, Jianhua; Schulten, Klaus

2016-01-01

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services. DOI: http://dx.doi.org/10.7554/eLife.16105.001 PMID:27383269

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.

PubMed

Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy; He, Jing

2017-01-01

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4-7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map-model pairs.

The significance of Bragg's law in electron diffraction and microscopy, and Bragg's second law.

PubMed

Humphreys, C J

2013-01-01

Bragg's second law, which deserves to be more widely known, is recounted. The significance of Bragg's law in electron diffraction and microscopy is then discussed, with particular emphasis on differences between X-ray and electron diffraction. As an example of such differences, the critical voltage effect in electron diffraction is described. It is then shown that the lattice imaging of crystals in high-resolution electron microscopy directly reveals the Bragg planes used for the imaging process, exactly as visualized by Bragg in his real-space law. Finally, it is shown how in 2012, for the first time, on the centennial anniversary of Bragg's law, single atoms have been identified in an electron microscope using X-rays emitted from the specimen. Hence atomic resolution X-ray maps of a crystal in real space can be formed which give the positions and identities of the different atoms in the crystal, or of a single impurity atom in the crystal.

7A projection map of the S-layer protein sbpA obtained with trehalose-embedded monolayer crystals.

PubMed

Norville, Julie E; Kelly, Deborah F; Knight, Thomas F; Belcher, Angela M; Walz, Thomas

2007-12-01

Two-dimensional crystallization on lipid monolayers is a versatile tool to obtain structural information of proteins by electron microscopy. An inherent problem with this approach is to prepare samples in a way that preserves the crystalline order of the protein array and produces specimens that are sufficiently flat for high-resolution data collection at high tilt angles. As a test specimen to optimize the preparation of lipid monolayer crystals for electron microscopy imaging, we used the S-layer protein sbpA, a protein with potential for designing arrays of both biological and inorganic materials with engineered properties for a variety of nanotechnology applications. Sugar embedding is currently considered the best method to prepare two-dimensional crystals of membrane proteins reconstituted into lipid bilayers. We found that using a loop to transfer lipid monolayer crystals to an electron microscopy grid followed by embedding in trehalose and quick-freezing in liquid ethane also yielded the highest resolution images for sbpA lipid monolayer crystals. Using images of specimens prepared in this way we could calculate a projection map of sbpA at 7A resolution, one of the highest resolution projection structures obtained with lipid monolayer crystals to date.

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.

PubMed

Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila

2016-10-01

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

Real-Space Mapping of Surface Trap States in CIGSe Nanocrystals Using 4D Electron Microscopy.

PubMed

Bose, Riya; Bera, Ashok; Parida, Manas R; Adhikari, Aniruddha; Shaheen, Basamat S; Alarousu, Erkki; Sun, Jingya; Wu, Tom; Bakr, Osman M; Mohammed, Omar F

2016-07-13

Surface trap states in copper indium gallium selenide semiconductor nanocrystals (NCs), which serve as undesirable channels for nonradiative carrier recombination, remain a great challenge impeding the development of solar and optoelectronics devices based on these NCs. In order to design efficient passivation techniques to minimize these trap states, a precise knowledge about the charge carrier dynamics on the NCs surface is essential. However, selective mapping of surface traps requires capabilities beyond the reach of conventional laser spectroscopy and static electron microscopy; it can only be accessed by using a one-of-a-kind, second-generation four-dimensional scanning ultrafast electron microscope (4D S-UEM) with subpicosecond temporal and nanometer spatial resolutions. Here, we precisely map the collective surface charge carrier dynamics of copper indium gallium selenide NCs as a function of the surface trap states before and after surface passivation in real space and time using S-UEM. The time-resolved snapshots clearly demonstrate that the density of the trap states is significantly reduced after zinc sulfide (ZnS) shelling. Furthermore, the removal of trap states and elongation of carrier lifetime are confirmed by the increased photocurrent of the self-biased photodetector fabricated using the shelled NCs.

Rapid, all-optical crystal orientation imaging of two-dimensional transition metal dichalcogenide monolayers

DOE Office of Scientific and Technical Information (OSTI.GOV)

David, Sabrina N.; Zhai, Yao; van der Zande, Arend M.

Two-dimensional (2D) atomic materials such as graphene and transition metal dichalcogenides (TMDCs) have attracted significant research and industrial interest for their electronic, optical, mechanical, and thermal properties. While large-area crystal growth techniques such as chemical vapor deposition have been demonstrated, the presence of grain boundaries and orientation of grains arising in such growths substantially affect the physical properties of the materials. There is currently no scalable characterization method for determining these boundaries and orientations over a large sample area. We here present a second-harmonic generation based microscopy technique for rapidly mapping grain orientations and boundaries of 2D TMDCs. We experimentallymore » demonstrate the capability to map large samples to an angular resolution of ±1° with minimal sample preparation and without involved analysis. A direct comparison of the all-optical grain orientation maps against results obtained by diffraction-filtered dark-field transmission electron microscopy plus selected-area electron diffraction on identical TMDC samples is provided. This rapid and accurate tool should enable large-area characterization of TMDC samples for expedited studies of grain boundary effects and the efficient characterization of industrial-scale production techniques.« less

Application of high-angle annular dark field scanning transmission electron microscopy, scanning transmission electron microscopy-energy dispersive X-ray spectrometry, and energy-filtered transmission electron microscopy to the characterization of nanoparticles in the environment.

PubMed

Utsunomiya, Satoshi; Ewing, Rodney C

2003-02-15

A major challenge to the development of a fundamental understanding of transport and retardation mechanisms of trace metal contaminants (<10 ppm) is their identification and characterization at the nanoscale. Atomic-scale techniques, such as conventional transmission electron microscopy, although powerful, are limited by the extremely small amounts of material that are examined. However, recent advances in electron microscopy provide a number of new analytical techniques that expand its application in environmental studies, particularly those concerning heavy metals on airborne particulates or water-borne colloids. High-angle annular dark field scanning transmission electron microscopy (HAADF-STEM), STEM-energy-dispersive X-ray spectrometry (EDX), and energy-filtered TEM (EFTEM) can be effectively used to identify and characterize nanoparticles. The image contrast in HAADF-STEM is strongly correlated to the atomic mass: heavier elements contribute to brighter contrast. Gold nanocrystals in pyrite and uranium nanocrystals in atmospheric aerosols have been identified by HAADF-STEM and STEM-EDX mapping and subsequently characterized by high-resolution TEM (HRTEM). EFTEM was used to identify U and Fe nanocrystals embedded in an aluminosilicate. A rare, As-bearing nanophase, westerveldite (FeAs), was identified by STEM-EDX and HRTEM. The combined use of these techniques greatly expands the effective application of electron microscopy in environmental studies, especially when applied to metals of very low concentrations. This paper describes examples of how these electron microbeam techniques can be used in combination to characterize a low concentration of heavy metals (a few ppm) on nanoscale particles.

Phosphorus detection in vitrified bacteria by cryo-STEM annular dark-field analysis.

PubMed

Wolf, Sharon Grayer; Rez, Peter; Elbaum, Michael

2015-11-01

Bacterial cells often contain dense granules. Among these, polyphosphate bodies (PPBs) store inorganic phosphate for a variety of essential functions. Identification of PPBs has until now been accomplished by analytical methods that required drying or chemically fixing the cells. These methods entail large electron doses that are incompatible with low-dose imaging of cryogenic specimens. We show here that Scanning Transmission Electron Microscopy (STEM) of fully hydrated, intact, vitrified bacteria provides a simple means for mapping of phosphorus-containing dense granules based on quantitative sensitivity of the electron scattering to atomic number. A coarse resolution of the scattering angles distinguishes phosphorus from the abundant lighter atoms: carbon, nitrogen and oxygen. The theoretical basis is similar to Z contrast of materials science. EDX provides a positive identification of phosphorus, but importantly, the method need not involve a more severe electron dose than that required for imaging. The approach should prove useful in general for mapping of heavy elements in cryopreserved specimens when the element identity is known from the biological context. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Imaging electronic trap states in perovskite thin films with combined fluorescence and femtosecond transient absorption microscopy

DOE PAGES

Xiao, Kai; Ma, Ying -Zhong; Simpson, Mary Jane; ...

2016-04-22

Charge carrier trapping degrades the performance of organometallic halide perovskite solar cells. To characterize the locations of electronic trap states in a heterogeneous photoactive layer, a spatially resolved approach is essential. Here, we report a comparative study on methylammonium lead tri-iodide perovskite thin films subject to different thermal annealing times using a combined photoluminescence (PL) and femtosecond transient absorption microscopy (TAM) approach to spatially map trap states. This approach coregisters the initially populated electronic excited states with the regions that recombine radiatively. Although the TAM images are relatively homogeneous for both samples, the corresponding PL images are highly structured. Themore » remarkable variation in the PL intensities as compared to transient absorption signal amplitude suggests spatially dependent PL quantum efficiency, indicative of trapping events. Furthermore, detailed analysis enables identification of two trapping regimes: a densely packed trapping region and a sparse trapping area that appear as unique spatial features in scaled PL maps.« less

Atom probe trajectory mapping using experimental tip shape measurements.

PubMed

Haley, D; Petersen, T; Ringer, S P; Smith, G D W

2011-11-01

Atom probe tomography is an accurate analytical and imaging technique which can reconstruct the complex structure and composition of a specimen in three dimensions. Despite providing locally high spatial resolution, atom probe tomography suffers from global distortions due to a complex projection function between the specimen and detector which is different for each experiment and can change during a single run. To aid characterization of this projection function, this work demonstrates a method for the reverse projection of ions from an arbitrary projection surface in 3D space back to an atom probe tomography specimen surface. Experimental data from transmission electron microscopy tilt tomography are combined with point cloud surface reconstruction algorithms and finite element modelling to generate a mapping back to the original tip surface in a physically and experimentally motivated manner. As a case study, aluminium tips are imaged using transmission electron microscopy before and after atom probe tomography, and the specimen profiles used as input in surface reconstruction methods. This reconstruction method is a general procedure that can be used to generate mappings between a selected surface and a known tip shape using numerical solutions to the electrostatic equation, with quantitative solutions to the projection problem readily achievable in tens of minutes on a contemporary workstation. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Four-Dimensional Ultrafast Electron Microscopy: Insights into an Emerging Technique.

PubMed

Adhikari, Aniruddha; Eliason, Jeffrey K; Sun, Jingya; Bose, Riya; Flannigan, David J; Mohammed, Omar F

2017-01-11

Four-dimensional ultrafast electron microscopy (4D-UEM) is a novel analytical technique that aims to fulfill the long-held dream of researchers to investigate materials at extremely short spatial and temporal resolutions by integrating the excellent spatial resolution of electron microscopes with the temporal resolution of ultrafast femtosecond laser-based spectroscopy. The ingenious use of pulsed photoelectrons to probe surfaces and volumes of materials enables time-resolved snapshots of the dynamics to be captured in a way hitherto impossible by other conventional techniques. The flexibility of 4D-UEM lies in the fact that it can be used in both the scanning (S-UEM) and transmission (UEM) modes depending upon the type of electron microscope involved. While UEM can be employed to monitor elementary structural changes and phase transitions in samples using real-space mapping, diffraction, electron energy-loss spectroscopy, and tomography, S-UEM is well suited to map ultrafast dynamical events on materials surfaces in space and time. This review provides an overview of the unique features that distinguish these techniques and also illustrates the applications of both S-UEM and UEM to a multitude of problems relevant to materials science and chemistry.

Gold Nanoparticle Quantitation by Whole Cell Tomography.

PubMed

Sanders, Aric W; Jeerage, Kavita M; Schwartz, Cindi L; Curtin, Alexandra E; Chiaramonti, Ann N

2015-12-22

Many proposed biomedical applications for engineered gold nanoparticles require their incorporation by mammalian cells in specific numbers and locations. Here, the number of gold nanoparticles inside of individual mammalian stem cells was characterized using fast focused ion beam-scanning electron microscopy based tomography. Enhanced optical microscopy was used to provide a multiscale map of the in vitro sample, which allows cells of interest to be identified within their local environment. Cells were then serially sectioned using a gallium ion beam and imaged using a scanning electron beam. To confirm the accuracy of single cross sections, nanoparticles in similar cross sections were imaged using transmission electron microscopy and scanning helium ion microscopy. Complete tomographic series were then used to count the nanoparticles inside of each cell and measure their spatial distribution. We investigated the influence of slice thickness on counting single particles and clusters as well as nanoparticle packing within clusters. For 60 nm citrate stabilized particles, the nanoparticle cluster packing volume is 2.15 ± 0.20 times the volume of the bare gold nanoparticles.

Towards 3D crystal orientation reconstruction using automated crystal orientation mapping transmission electron microscopy (ACOM-TEM).

PubMed

Kobler, Aaron; Kübel, Christian

2018-01-01

To relate the internal structure of a volume (crystallite and phase boundaries) to properties (electrical, magnetic, mechanical, thermal), a full 3D reconstruction in combination with in situ testing is desirable. In situ testing allows the crystallographic changes in a material to be followed by tracking and comparing the individual crystals and phases. Standard transmission electron microscopy (TEM) delivers a projection image through the 3D volume of an electron-transparent TEM sample lamella. Only with the help of a dedicated TEM tomography sample holder is an accurate 3D reconstruction of the TEM lamella currently possible. 2D crystal orientation mapping has become a standard method for crystal orientation and phase determination while 3D crystal orientation mapping have been reported only a few times. The combination of in situ testing with 3D crystal orientation mapping remains a challenge in terms of stability and accuracy. Here, we outline a method to 3D reconstruct the crystal orientation from a superimposed diffraction pattern of overlapping crystals without sample tilt. Avoiding the typically required tilt series for 3D reconstruction enables not only faster in situ tests but also opens the possibility for more stable and more accurate in situ mechanical testing. The approach laid out here should serve as an inspiration for further research and does not make a claim to be complete.

Direct observation of dopant distribution in GaAs compound semiconductors using phase-shifting electron holography and Lorentz microscopy.

PubMed

Sasaki, Hirokazu; Otomo, Shinya; Minato, Ryuichiro; Yamamoto, Kazuo; Hirayama, Tsukasa

2014-06-01

Phase-shifting electron holography and Lorentz microscopy were used to map dopant distributions in GaAs compound semiconductors with step-like dopant concentration. Transmission electron microscope specimens were prepared using a triple beam focused ion beam (FIB) system, which combines a Ga ion beam, a scanning electron microscope, and an Ar ion beam to remove the FIB damaged layers. The p-n junctions were clearly observed in both under-focused and over-focused Lorentz microscopy images. A phase image was obtained by using a phase-shifting reconstruction method to simultaneously achieve high sensitivity and high spatial resolution. Differences in dopant concentrations between 1 × 10(19) cm(-3) and 1 × 10(18) cm(-3) regions were clearly observed by using phase-shifting electron holography. We also interpreted phase profiles quantitatively by considering inactive layers induced by ion implantation during the FIB process. The thickness of an inactive layer at different dopant concentration area can be measured from the phase image. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix

PubMed Central

Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy

2017-01-01

Abstract Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4–7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map–model pairs. PMID:27936925

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

DOE PAGES

Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; ...

2015-07-30

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

Atomic force microscopy imaging of fragments from the Martian meteorite ALH84001

NASA Technical Reports Server (NTRS)

Steele, A.; Goddard, D.; Beech, I. B.; Tapper, R. C.; Stapleton, D.; Smith, J. R.

1998-01-01

A combination of scanning electron microscopy (SEM) and environmental scanning electron microscopy (ESEM) techniques, as well as atomic force microscopy (AFM) methods has been used to study fragments of the Martian meteorite ALH84001. Images of the same areas on the meteorite were obtained prior to and following gold/palladium coating by mapping the surface of the fragment using ESEM coupled with energy-dispersive X-ray analysis. Viewing of the fragments demonstrated the presence of structures, previously described as nanofossils by McKay et al. (Search for past life on Mars--possible relic biogenic activity in martian meteorite ALH84001. Science, 1996, pp. 924-930) of NASA who used SEM imaging of gold-coated meteorite samples. Careful imaging of the fragments revealed that the observed structures were not an artefact introduced by the coating procedure.

Observation of nanoscale magnetic fields using twisted electron beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grillo, Vincenzo; Harvey, Tyler R.; Venturi, Federico

Electron waves give an unprecedented enhancement to the field of microscopy by providing higher resolving power compared to their optical counterpart. Further information about a specimen, such as electric and magnetic features, can be revealed in electron microscopy because electrons possess both a magnetic moment and charge. In-plane magnetic structures in materials can be studied experimentally using the effect of the Lorentz force. On the other hand, full mapping of the magnetic field has hitherto remained challenging. Here we measure a nanoscale out-of-plane magnetic field by interfering a highly twisted electron vortex beam with a reference wave. We implement amore » recently developed holographic technique to manipulate the electron wavefunction, which gives free electrons an additional unbounded quantized magnetic moment along their propagation direction. Our finding demonstrates that full reconstruction of all three components of nanoscale magnetic fields is possible without tilting the specimen.« less

Observation of nanoscale magnetic fields using twisted electron beams

DOE PAGES

Grillo, Vincenzo; Harvey, Tyler R.; Venturi, Federico; ...

2017-09-25

Electron waves give an unprecedented enhancement to the field of microscopy by providing higher resolving power compared to their optical counterpart. Further information about a specimen, such as electric and magnetic features, can be revealed in electron microscopy because electrons possess both a magnetic moment and charge. In-plane magnetic structures in materials can be studied experimentally using the effect of the Lorentz force. On the other hand, full mapping of the magnetic field has hitherto remained challenging. Here we measure a nanoscale out-of-plane magnetic field by interfering a highly twisted electron vortex beam with a reference wave. We implement amore » recently developed holographic technique to manipulate the electron wavefunction, which gives free electrons an additional unbounded quantized magnetic moment along their propagation direction. Our finding demonstrates that full reconstruction of all three components of nanoscale magnetic fields is possible without tilting the specimen.« less

Evaluation of bioreactor-cultivated bone by magnetic resonance microscopy and FTIR microspectroscopy.

PubMed

Chesnick, Ingrid E; Avallone, Francis A; Leapman, Richard D; Landis, William J; Eidelman, Naomi; Potter, Kimberlee

2007-04-01

We present a three-dimensional mineralizing model based on a hollow fiber bioreactor (HFBR) inoculated with primary osteoblasts isolated from embryonic chick calvaria. Using non-invasive magnetic resonance microscopy (MRM), the growth and development of the mineralized tissue around the individual fibers were monitored over a period of 9 weeks. Spatial maps of the water proton MRM properties of the intact tissue, with 78 microm resolution, were used to determine changes in tissue composition with development. Unique changes in the mineral and collagen content of the tissue were detected with high specificity by proton density (PD) and magnetization transfer ratio (MTR) maps, respectively. At the end of the growth period, the presence of a bone-like tissue was verified by histology and the formation of poorly crystalline apatite was verified by selected area electron diffraction and electron probe X-ray microanalysis. FTIR microspectroscopy confirmed the heterogeneous nature of the bone-like tissue formed. FTIR-derived phosphate maps confirmed that those locations with the lowest PD values contained the most mineral, and FTIR-derived collagen maps confirmed that bright pixels on MTR maps corresponded to regions of high collagen content. In conclusion, the spatial mapping of tissue constituents by FTIR microspectroscopy corroborated the findings of non-invasive MRM measurements and supported the role of MRM in monitoring the bone formation process in vitro.

Evaluation of Bioreactor-Cultivated Bone by Magnetic Resonance Microscopy and FTIR Microspectroscopy

PubMed Central

Chesnick, Ingrid E.; Avallone, Frank; Leapman, Richard D.; Landis, William J.; Eidelman, Naomi; Potter, Kimberlee

2007-01-01

We present a three-dimensional mineralizing model based on a hollow fiber bioreactor (HFBR) inoculated with primary osteoblasts isolated from embryonic chick calvaria. Using non-invasive magnetic resonance microscopy (MRM), the growth and development of the mineralized tissue around the individual fibers were monitored over a period of nine weeks. Spatial maps of the water proton MRM properties of the intact tissue, with 78 μm resolution, were used to determine changes in tissue composition with development. Unique changes in the mineral and collagen content of the tissue were detected with high specificity by proton density (PD) and magnetization transfer ratio (MTR) maps, respectively. At the end of the growth period, the presence of a bone-like tissue was verified by histology and the formation of poorly crystalline apatite was verified by selected area electron diffraction and electron probe X-ray microanalysis. FTIR microspectroscopy confirmed the heterogeneous nature of the bone-like tissue formed. FTIR-derived phosphate maps confirmed that those locations with the lowest PD values contained the most mineral, and FTIR-derived collagen maps confirmed that bright pixels on MTR maps corresponded to regions of high collagen content. In conclusion, the spatial mapping of tissue constituents by FTIR microspectroscopy corroborated the findings of non-invasive MRM measurements and supported the role of MRM in monitoring the bone formation process in vitro. PMID:17174620

Manipulation of partially oriented hydroxyapatite building blocks to form flowerlike bundles without acid-base regulation.

PubMed

Wen, Zhenliang; Wang, Zihao; Chen, Jingdi; Zhong, Shengnan; Hu, Yimin; Wang, Jianhua; Zhang, Qiqing

2016-06-01

The application of hydroxyapatite (HAP) in different fields depends greatly on its morphology, composition and structure. Besides, the main inorganic building blocks of human bones and teeth are also HAP. Therefore, accurate shape and aggregation control and of hydroxyapatite particles will be of great interest. Herein, oriented bundles of flowerlike HAP nanorods were successfully prepared through hydrothermal treatment without acid-base regulation, with the mono-alkyl phosphate (MAP) and sodium citrate as surfactant and chelating agent, respectively. The prepared samples were characterized by the X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM) and zeta potential, the pH value and conductivity value of suspension were characterized by pH meter and conductivity measurement. The results showed that the MAP and citrate play an important role in assembly of HAP nanorods without acid-base regulation. Citrate calcium complex could decompose slowly and release citrate ions at hydrothermal conditions. Besides, the further decomposition of citrate ions could release aconitic acid as the reaction time prolongs. Moreover, the possible scheme for the formation process was discussed in detail. Copyright © 2016 Elsevier B.V. All rights reserved.

Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER.

PubMed

Han, Xusi; Wei, Qing; Kihara, Daisuke

2017-12-08

With the rapid growth in the number of solved protein structures stored in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), it is essential to develop tools to perform real-time structure similarity searches against the entire structure database. Since conventional structure alignment methods need to sample different orientations of proteins in the three-dimensional space, they are time consuming and unsuitable for rapid, real-time database searches. To this end, we have developed 3D-SURFER and EM-SURFER, which utilize 3D Zernike descriptors (3DZD) to conduct high-throughput protein structure comparison, visualization, and analysis. Taking an atomic structure or an electron microscopy map of a protein or a protein complex as input, the 3DZD of a query protein is computed and compared with the 3DZD of all other proteins in PDB or EMDB. In addition, local geometrical characteristics of a query protein can be analyzed using VisGrid and LIGSITE CSC in 3D-SURFER. This article describes how to use 3D-SURFER and EM-SURFER to carry out protein surface shape similarity searches, local geometric feature analysis, and interpretation of the search results. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Holographic maps of quasiparticle interference

NASA Astrophysics Data System (ADS)

Dalla Torre, Emanuele G.; He, Yang; Demler, Eugene

2016-11-01

The analysis of Fourier-transformed scanning tunnelling microscopy images with subatomic resolution is a common tool for studying the properties of quasiparticle excitations in strongly correlated materials. Although Fourier amplitudes are generally complex valued, earlier analysis primarily focused on their absolute values. Their complex phases were often deemed random, and thus irrelevant, due to the unknown positions of the impurities in the sample. Here we show how to factor out these random phases by analysing overlaps between Fourier amplitudes that differ by reciprocal lattice vectors. The resulting holographic maps provide important and previously unknown information about the electronic structures. When applied to superconducting cuprates, our method solves a long-standing puzzle of the dichotomy between equivalent wavevectors. We show that d-wave Wannier functions of the conduction band provide a natural explanation for experimental results that were interpreted as evidence for competing unconventional charge modulations. Our work opens a new pathway to identify the nature of electronic states in scanning tunnelling microscopy.

Quantitative nanoscopy: Tackling sampling limitations in (S)TEM imaging of polymers and composites.

PubMed

Gnanasekaran, Karthikeyan; Snel, Roderick; de With, Gijsbertus; Friedrich, Heiner

2016-01-01

Sampling limitations in electron microscopy questions whether the analysis of a bulk material is representative, especially while analyzing hierarchical morphologies that extend over multiple length scales. We tackled this problem by automatically acquiring a large series of partially overlapping (S)TEM images with sufficient resolution, subsequently stitched together to generate a large-area map using an in-house developed acquisition toolbox (TU/e Acquisition ToolBox) and stitching module (TU/e Stitcher). In addition, we show that quantitative image analysis of the large scale maps provides representative information that can be related to the synthesis and process conditions of hierarchical materials, which moves electron microscopy analysis towards becoming a bulk characterization tool. We demonstrate the power of such an analysis by examining two different multi-phase materials that are structured over multiple length scales. Copyright © 2015 Elsevier B.V. All rights reserved.

Identification of Metal Oxide Nanoparticles in Histological Samples by Enhanced Darkfield Microscopy and Hyperspectral Mapping.

PubMed

Roth, Gary A; Sosa Peña, Maria del Pilar; Neu-Baker, Nicole M; Tahiliani, Sahil; Brenner, Sara A

2015-12-08

Nanomaterials are increasingly prevalent throughout industry, manufacturing, and biomedical research. The need for tools and techniques that aid in the identification, localization, and characterization of nanoscale materials in biological samples is on the rise. Currently available methods, such as electron microscopy, tend to be resource-intensive, making their use prohibitive for much of the research community. Enhanced darkfield microscopy complemented with a hyperspectral imaging system may provide a solution to this bottleneck by enabling rapid and less expensive characterization of nanoparticles in histological samples. This method allows for high-contrast nanoscale imaging as well as nanomaterial identification. For this technique, histological tissue samples are prepared as they would be for light-based microscopy. First, positive control samples are analyzed to generate the reference spectra that will enable the detection of a material of interest in the sample. Negative controls without the material of interest are also analyzed in order to improve specificity (reduce false positives). Samples can then be imaged and analyzed using methods and software for hyperspectral microscopy or matched against these reference spectra in order to provide maps of the location of materials of interest in a sample. The technique is particularly well-suited for materials with highly unique reflectance spectra, such as noble metals, but is also applicable to other materials, such as semi-metallic oxides. This technique provides information that is difficult to acquire from histological samples without the use of electron microscopy techniques, which may provide higher sensitivity and resolution, but are vastly more resource-intensive and time-consuming than light microscopy.

Magnetic mapping of iron in rodent spleen

PubMed Central

Blissett, Angela R.; Ollander, Brooke; Penn, Brittany; McTigue, Dana M.; Agarwal, Gunjan

2016-01-01

Evaluation of iron distribution and density in biological tissues is important to understand the pathogenesis of a variety of diseases and the fate of exogenously administered iron-based carriers and contrast agents. Iron distribution in tissues is typically characterized via histochemical (Perl’s) stains or immunohistochemistry for ferritin, the major iron storage protein. A more accurate mapping of iron can be achieved via ultrastructural transmission electron microscopy (TEM) based techniques, which involve stringent sample preparation conditions. In this study, we elucidate the capability of magnetic force microscopy (MFM) as a label-free technique to map iron at the nanoscale level in rodent spleen tissue. We complemented and compared our MFM results with those obtained using Perl’s staining and TEM. Our results show how MFM mapping corresponded to sizes of iron-rich lysosomes at a resolution comparable to that of TEM. In addition MFM is compatible with tissue sections commonly prepared for routine histology. PMID:27890658

Correlating Intravital Multi-Photon Microscopy to 3D Electron Microscopy of Invading Tumor Cells Using Anatomical Reference Points

PubMed Central

Karreman, Matthia A.; Mercier, Luc; Schieber, Nicole L.; Shibue, Tsukasa; Schwab, Yannick; Goetz, Jacky G.

2014-01-01

Correlative microscopy combines the advantages of both light and electron microscopy to enable imaging of rare and transient events at high resolution. Performing correlative microscopy in complex and bulky samples such as an entire living organism is a time-consuming and error-prone task. Here, we investigate correlative methods that rely on the use of artificial and endogenous structural features of the sample as reference points for correlating intravital fluorescence microscopy and electron microscopy. To investigate tumor cell behavior in vivo with ultrastructural accuracy, a reliable approach is needed to retrieve single tumor cells imaged deep within the tissue. For this purpose, fluorescently labeled tumor cells were subcutaneously injected into a mouse ear and imaged using two-photon-excitation microscopy. Using near-infrared branding, the position of the imaged area within the sample was labeled at the skin level, allowing for its precise recollection. Following sample preparation for electron microscopy, concerted usage of the artificial branding and anatomical landmarks enables targeting and approaching the cells of interest while serial sectioning through the specimen. We describe here three procedures showing how three-dimensional (3D) mapping of structural features in the tissue can be exploited to accurately correlate between the two imaging modalities, without having to rely on the use of artificially introduced markers of the region of interest. The methods employed here facilitate the link between intravital and nanoscale imaging of invasive tumor cells, enabling correlating function to structure in the study of tumor invasion and metastasis. PMID:25479106

Fabrication and characterization of CNT-based smart tips for synchrotron assisted STM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Hui; Cummings, Marvin; Camino, Fernando

Determination of chemical composition along with imaging at the atomic level provides critical information towards fundamental understanding of the surface of materials and, hence, yields the capability to design new materials by tailoring their ultimate functionalities. Synchrotron X-ray assisted scanning tunneling microscopy (SX-STM) is a promising new technique to achieve real space chemically specific atomic mapping. Chemical sensitivity of SX-STM relies on excitation of core electrons by incident X-rays when their energy is tuned to an absorption edge of a particular element. However, along with core-level electrons, photoelectrons are also excited, which yield additional current and interfere with the tunnelingmore » current. To reduce the background photoelectron current and to improve ultimate resolution of SX-STM, we have developed and fabricated multiwalled carbon nanotubes (MWCNT) based “smart tips” using plasma enhanced chemical vapor deposition and focused ion beam milling. As a result, the newly developed CNT-based smart tips, characterized step by step by scanning electron microscopy (SEM) during the fabrication process, demonstrate good performance and provide opportunity for realizing atomic chemical mapping.« less

Effect of Welding Heat Input on Microstructure and Texture of Inconel 625 Weld Overlay Studied Using the Electron Backscatter Diffraction Method

NASA Astrophysics Data System (ADS)

Kim, Joon-Suk; Lee, Hae-Woo

2016-12-01

The grain size and the texture of three specimens prepared at different heat inputs were determined using optical microscopy and the electron backscatter diffraction method of scanning electron microscopy. Each specimen was equally divided into fusion line zone (FLZ), columnar dendrite zone (CDZ), and surface zone (SZ), according to the location of the weld. Fine dendrites were observed in the FLZ, coarse dendrites in the CDZ, and dendrites grew perpendicular to the FLZ and CDZ. As the heat input increased, the melted zone in the vicinity of the FLZ widened due to the higher Fe content. A lower image quality value was observed for the FLZ compared to the other zones. The results of grain size measurement in each zone showed that the grain size of the SZ became larger as the heat input increased. From the inverse pole figure (IPF) map in the normal direction (ND) and the rolling direction (RD), as the heat input increased, a specific orientation was formed. However, a dominant [001] direction was observed in the RD IPF map.

Fabrication and characterization of CNT-based smart tips for synchrotron assisted STM

DOE PAGES

Yan, Hui; Cummings, Marvin; Camino, Fernando; ...

2015-08-05

Determination of chemical composition along with imaging at the atomic level provides critical information towards fundamental understanding of the surface of materials and, hence, yields the capability to design new materials by tailoring their ultimate functionalities. Synchrotron X-ray assisted scanning tunneling microscopy (SX-STM) is a promising new technique to achieve real space chemically specific atomic mapping. Chemical sensitivity of SX-STM relies on excitation of core electrons by incident X-rays when their energy is tuned to an absorption edge of a particular element. However, along with core-level electrons, photoelectrons are also excited, which yield additional current and interfere with the tunnelingmore » current. To reduce the background photoelectron current and to improve ultimate resolution of SX-STM, we have developed and fabricated multiwalled carbon nanotubes (MWCNT) based “smart tips” using plasma enhanced chemical vapor deposition and focused ion beam milling. As a result, the newly developed CNT-based smart tips, characterized step by step by scanning electron microscopy (SEM) during the fabrication process, demonstrate good performance and provide opportunity for realizing atomic chemical mapping.« less

Stress in recrystallized quartz by electron backscatter diffraction mapping

NASA Astrophysics Data System (ADS)

Llana-Fúnez, S.

2017-07-01

The long-term state of stress at middle and lower crustal depths can be estimated through the study of the microstructure of exhumed rocks from active and/or ancient shear zones. Constitutive equations for deformation mechanisms in experimentally deformed rocks relate differential stress to the size of recrystallized grains. Cross et al. (2017) take advantage of electron backscatter diffraction mapping to systematically separate new recrystallized grains from host grains on the basis of the measurable lattice distorsion within the grains. They produce the first calibrated piezometer for quartz with this technique, reproducing within error a previous calibration based on optical microscopy.

Nanowires: Enhanced Optoelectronic Performance of a Passivated Nanowire-Based Device: Key Information from Real-Space Imaging Using 4D Electron Microscopy (Small 17/2016).

PubMed

Khan, Jafar I; Adhikari, Aniruddha; Sun, Jingya; Priante, Davide; Bose, Riya; Shaheen, Basamat S; Ng, Tien Khee; Zhao, Chao; Bakr, Osman M; Ooi, Boon S; Mohammed, Omar F

2016-05-01

Selective mapping of surface charge carrier dynamics of InGaN nanowires before and after surface passivation with octadecylthiol (ODT) is reported by O. F. Mohammed and co-workers on page 2313, using scanning ultrafast electron microscopy. In a typical experiment, the 343 nm output of the laser beam is used to excite the microscope tip to generate pulsed electrons for probing, and the 515 nm output is used as a clocking excitation pulse to initiate dynamics. Time-resolved images demonstrate clearly that carrier recombination is significantly slowed after ODT treatment, which supports the efficient removal of surface trap states. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detection of local chemical states of lithium and their spatial mapping by scanning transmission electron microscopy, electron energy-loss spectroscopy and hyperspectral image analysis.

PubMed

Muto, Shunsuke; Tatsumi, Kazuyoshi

2017-02-08

Advancements in the field of renewable energy resources have led to a growing demand for the analysis of light elements at the nanometer scale. Detection of lithium is one of the key issues to be resolved for providing guiding principles for the synthesis of cathode active materials, and degradation analysis after repeated use of those materials. We have reviewed the different techniques currently used for the characterization of light elements such as high-resolution transmission electron microscopy, scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS). In the present study, we have introduced a methodology to detect lithium in solid materials, particularly for cathode active materials used in lithium-ion battery. The chemical states of lithium were isolated and analyzed from the overlapping multiple spectral profiles, using a suite of STEM, EELS and hyperspectral image analysis. The method was successfully applied in the chemical state analyses of hetero-phases near the surface and grain boundary regions of the active material particles formed by chemical reactions between the electrolyte and the active materials. © The Author 2016. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Correlating Atom Probe Tomography with Atomic-Resolved Scanning Transmission Electron Microscopy: Example of Segregation at Silicon Grain Boundaries.

PubMed

Stoffers, Andreas; Barthel, Juri; Liebscher, Christian H; Gault, Baptiste; Cojocaru-Mirédin, Oana; Scheu, Christina; Raabe, Dierk

2017-04-01

In the course of a thorough investigation of the performance-structure-chemistry interdependency at silicon grain boundaries, we successfully developed a method to systematically correlate aberration-corrected scanning transmission electron microscopy and atom probe tomography. The correlative approach is conducted on individual APT and TEM specimens, with the option to perform both investigations on the same specimen in the future. In the present case of a Σ9 grain boundary, joint mapping of the atomistic details of the grain boundary topology, in conjunction with chemical decoration, enables a deeper understanding of the segregation of impurities observed at such grain boundaries.

Measurement Error in Atomic-Scale Scanning Transmission Electron Microscopy-Energy-Dispersive X-Ray Spectroscopy (STEM-EDS) Mapping of a Model Oxide Interface.

PubMed

Spurgeon, Steven R; Du, Yingge; Chambers, Scott A

2017-06-01

With the development of affordable aberration correctors, analytical scanning transmission electron microscopy (STEM) studies of complex interfaces can now be conducted at high spatial resolution at laboratories worldwide. Energy-dispersive X-ray spectroscopy (EDS) in particular has grown in popularity, as it enables elemental mapping over a wide range of ionization energies. However, the interpretation of atomically resolved data is greatly complicated by beam-sample interactions that are often overlooked by novice users. Here we describe the practical factors-namely, sample thickness and the choice of ionization edge-that affect the quantification of a model perovskite oxide interface. Our measurements of the same sample, in regions of different thickness, indicate that interface profiles can vary by as much as 2-5 unit cells, depending on the spectral feature. This finding is supported by multislice simulations, which reveal that on-axis maps of even perfectly abrupt interfaces exhibit significant delocalization. Quantification of thicker samples is further complicated by channeling to heavier sites across the interface, as well as an increased signal background. We show that extreme care must be taken to prepare samples to minimize channeling effects and argue that it may not be possible to extract atomically resolved information from many chemical maps.

Direct observation and analysis of york-shell materials using low-voltage high-resolution scanning electron microscopy: Nanometal-particles encapsulated in metal-oxide, carbon, and polymer

NASA Astrophysics Data System (ADS)

Asahina, Shunsuke; Suga, Mitsuo; Takahashi, Hideyuki; Young Jeong, Hu; Galeano, Carolina; Schüth, Ferdi; Terasaki, Osamu

2014-11-01

Nanometal particles show characteristic features in chemical and physical properties depending on their sizes and shapes. For keeping and further enhancing their features, the particles should be protected from coalescence or degradation. One approach is to encapsulate the nanometal particles inside pores with chemically inert or functional materials, such as carbon, polymer, and metal oxides, which contain mesopores to allow permeation of only chemicals not the nanometal particles. Recently developed low-voltage high-resolution scanning electron microscopy was applied to the study of structural, chemical, and electron state of both nanometal particles and encapsulating materials in yolk-shell materials of Au@C, Ru/Pt@C, Au@TiO2, and Pt@Polymer. Progresses in the following categories were shown for the yolk-shell materials: (i) resolution of topographic image contrast by secondary electrons, of atomic-number contrast by back-scattered electrons, and of elemental mapping by X-ray energy dispersive spectroscopy; (ii) sample preparation for observing internal structures; and (iii) X-ray spectroscopy such as soft X-ray emission spectroscopy. Transmission electron microscopy was also used for characterization of Au@C.

Imaging electron wave functions inside open quantum rings.

PubMed

Martins, F; Hackens, B; Pala, M G; Ouisse, T; Sellier, H; Wallart, X; Bollaert, S; Cappy, A; Chevrier, J; Bayot, V; Huant, S

2007-09-28

Combining scanning gate microscopy (SGM) experiments and simulations, we demonstrate low temperature imaging of the electron probability density |Psi|(2)(x,y) in embedded mesoscopic quantum rings. The tip-induced conductance modulations share the same temperature dependence as the Aharonov-Bohm effect, indicating that they originate from electron wave function interferences. Simulations of both |Psi|(2)(x,y) and SGM conductance maps reproduce the main experimental observations and link fringes in SGM images to |Psi|(2)(x,y).

Microwave-accelerated cytochemical stains for the image analysis and the electron microscopic examination of light microscopy diagnostic slides.

PubMed

Hanker, J; Giammara, B

1993-01-01

Recent studies in our laboratories have shown how microwave (MW) irradiation can accelerate a number of tissue-processing techniques, especially staining, to aid in the preparation of single specimens on glass microscope slides or coverslips for examination by light microscopy (and electron microscopy, if required) for diagnostic purposes. Techniques have been developed, which give permanently stained preparations, that can be studied initially by light microscopy, their areas of interest mapped, and computer-automated image analysis performed to obtain quantitative information. This is readily performed after MW-accelerated staining with silver methenamine by the Giammara-Hanker PATS or PATS-TS reaction. This variation of the PAS reaction gives excellent markers for specific infectious agents such as lipopolysaccharides for gram-negative bacteria or mannans for fungi. It is also an excellent stain for glycogen and basement membranes and an excellent marker for type III collagen or reticulin in the endoneurium or perineurium of peripheral nerve or in the capillary walls. Our improved MW-accelerated Feulgen reaction with silver methenamine for nuclear DNA is useful to show the nuclei of bacteria and fungi as well as of cells they are infecting. Improved coating and penetration of tissue surfaces by thiocarbohydrazide bridging of ruthenium red, applied under MW-acceleration, render biologic specimens sufficiently conductive for SEM so that sputter coating with gold is unnecessary. The specimens treated with these highly visible electron-opaque stains can be screened with the light microscope after mounting in polyethylene glycol (PEG) and the structures or areas selected for EM study are mapped with a Micro-Locator slide. After removal of the water soluble PEG the specimens are remounted in the usual EM media for scanning electron microscopy (SEM) or transmission electron microscopy (TEM) study of the mapped areas. By comparing duplicate smears from areas of infection, such as two coverslips of buffy coat smears of blood from a patient with septicemia, the microorganisms responsible can occasionally be classified for antimicrobial therapy long before culture results are available; gram-negative bacteria are positive with the Giammara-Hanker PATS-TS stain, and gram-positive bacteria are positive with the SIGMA HT40 Gram stain. The gram-positive as well as gram-negative bacteria are both initially stained by the crystal violet component of the Gram stain. The crystal violet stain is readily removed from the gram-negative (but not the gram-positive) bacteria when the specimens are rinsed with alcohol/acetone. If this rinse step is omitted, the crystal violet remains attached to both gram-negative and gram-positive bacteria. It can then be rendered insoluble, electron-opaque, and conductive by treatment with silver methenamine solution under MW-irradiation. This metallized crystal violet is a more effective silver stain than the PATS-TS stain for a number of gram-negative spirochetes such as Treponema pallidum, the microbe that causes syphilis.

Correlative two-photon and serial block face scanning electron microscopy in neuronal tissue using 3D near-infrared branding maps.

PubMed

Lees, Robert M; Peddie, Christopher J; Collinson, Lucy M; Ashby, Michael C; Verkade, Paul

2017-01-01

Linking cellular structure and function has always been a key goal of microscopy, but obtaining high resolution spatial and temporal information from the same specimen is a fundamental challenge. Two-photon (2P) microscopy allows imaging deep inside intact tissue, bringing great insight into the structural and functional dynamics of cells in their physiological environment. At the nanoscale, the complex ultrastructure of a cell's environment in tissue can be reconstructed in three dimensions (3D) using serial block face scanning electron microscopy (SBF-SEM). This provides a snapshot of high resolution structural information pertaining to the shape, organization, and localization of multiple subcellular structures at the same time. The pairing of these two imaging modalities in the same specimen provides key information to relate cellular dynamics to the ultrastructural environment. Until recently, approaches to relocate a region of interest (ROI) in tissue from 2P microscopy for SBF-SEM have been inefficient or unreliable. However, near-infrared branding (NIRB) overcomes this by using the laser from a multiphoton microscope to create fiducial markers for accurate correlation of 2P and electron microscopy (EM) imaging volumes. The process is quick and can be user defined for each sample. Here, to increase the efficiency of ROI relocation, multiple NIRB marks are used in 3D to target ultramicrotomy. A workflow is described and discussed to obtain a data set for 3D correlated light and electron microscopy, using three different preparations of brain tissue as examples. Copyright © 2017 Elsevier Inc. All rights reserved.

Co-axial Electrospun Polyacrylonitrile-Poly(methylmethacrylate) Nanofibers: Atomic Force Microscopy and Compositional Characterization

PubMed Central

Zander, N.E.; Strawhecker, K.E.; Orlicki, J.A.; Rawlett, A.M.; Beebe, T.P.

2011-01-01

Poly(methylmethacrylate) (PMMA)- Polyacrylonitrile (PAN) fibers were prepared using a conventional single-nozzle electrospinning technique. The as-spun fibers exhibited core-shell morphology as verified by transmission electron microscopy (TEM) and atomic force microscopy (AFM). AFM-phase and modulus mapping images of the fiber cross-section and x-ray photoelectron spectroscopy (XPS) analysis indicated PAN formed the shell and PMMA the core material. XPS, thermal gravimetric analysis (TGA), and elemental analysis were used to determine fiber compositional information. Soaking the fibers in solvent demonstrated removal of the core material, generating hollow PAN fibers. PMID:21928836

Mapping Ionic Currents and Reactivity on the Nanoscale: Electrochemical Strain Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalinin, S.V.

2010-10-19

Solid-state electrochemical processes in oxides underpin a broad spectrum of energy and information storage devices, ranging from Li-ion and Li-air batteries, to solid oxide fuel cells (SOFC) to electroresistive and memristive systems. These functionalities are controlled by the bias-driven diffusive and electromigration transport of mobile ionic species, as well as intricate a set of electrochemical and defect-controlled reactions at interfaces and in bulk. Despite the wealth of device-level and atomistic studies, little is known on the mesoscopic mechanisms of ion diffusion and electronic transport on the level of grain clusters, individual grains, and extended defects. The development of the capabilitymore » for probing ion transport on the nanometer scale is a key to deciphering complex interplay between structure, functionality, and performance in these systems. Here we introduce Electrochemical Strain Microscopy, a scanning probe microscopy technique based on strong strain-bias coupling in the systems in which local ion concentrations are changed by electrical fields. The imaging capability, as well as time- and voltage spectroscopies analogous to traditional current based electrochemical characterization methods are developed. The reversible intercalation of Li and mapping electrochemical activity in LiCoO2 is demonstrated, illustrating higher Li diffusivity at non-basal planes and grain boundaries. In Si-anode device structure, the direct mapping of Li diffusion at extended defects and evolution of Li-activity with charge state is explored. The electrical field-dependence of Li mobility is studied to determine the critical bias required for the onset of electrochemical transformation, allowing reaction and diffusion processes in the battery system to be separated at each location. Finally, the applicability of ESM for probing oxygen vacancy diffusion and oxygen reduction/evolution reactions is illustrated, and the high resolution ESM maps are correlated with aberration corrected scanning transmission electron microscopy imaging. The future potential for deciphering mechanisms of electrochemical transformations on an atomically-defined single-defect level is discussed.« less

Ion Microscopy on Diamond

NASA Astrophysics Data System (ADS)

Manfredotti, Claudio

Because of its physical properties (strong radiation hardness, wide energy gap with a consequent extremely low dark current, very large electron and hole mobility) diamond is a very good candidate for nuclear particle detection, particularly in harsh environments or in conditions of strong radiation damage. Being commonly polycrystalline, diamond samples obtained by chemical vapour deposition (CVD) are not homogeneous, not only from the morphological point of view, but also from the electronic one. As a consequence, as it was indicated quite early starting from 1995, charge collection properties such as charge collection efficiency (cce) are not uniform, but they are depending on the site hit by incoming particle. Moreover, these properties are influenced by previous irradiations which are used in order to improve them and, finally, they are also dependent on the thickness of the sample, since the electronic non uniformity extends also in depth by affecting the profile of the electrical field from top to bottom electrode of the nuclear detector in the standard "sandwich" arrangement. By the use of focussed ion beams, it is possible to investigate these non uniformities by the aid of techniques like IBIC (Ion Beam Induced Charge) and IBIL (Ion Beam Induced Luminescence) with a space resolution of the order of 1 m. This relatively new kind of microscopy, which is called "ion microscopy", is capable not only to give 2D maps of cce, which can be quite precisely compared with morphological images obtained by Scanning Electron Microscopy (generally the grains display a much better cce than intergrain regions), but also to give the electric field profile from one electrode to the other one in a "lateral" arrangement of the ion beam. IBIL, by supplying 2D maps of luminescence intensity at different wavelength, can give information about the presence of specific radiative recombination centers and their distribution in the material. Finally, a new technique called XBIC (X-ray Beam Induced Charge), which makes use of very collimated (to 0.1 m) x-ray beams from high energy electron synchrotrons, opens new ways to map cce with a less damaging radiation and with a better energy resolution. In this paper we resume recent and less recent work carried out by our group by using these techniques, a work that has been undertaken afterwards also by other research groups in the world. In particular, topics such as the better homogeneity obtained by "priming" and the effects of "light priming", together with a certain "complementarity" between IBIC and IBIL maps, giving evidence that radiative recombination centers along the grain boundaries or in damaged regions are important in affecting cce, will be presented and discussed in some details. The conclusion is that ion microscopy is a powerful and essentially unique method for the investigation of diamond and other semiconductor materials proposed for nuclear detection.

Reduced graphene oxide-induced recrystallization of NiS nanorods to nanosheets and the improved Na-storage properties.

PubMed

Pan, Qin; Xie, Jian; Zhu, Tiejun; Cao, Gaoshao; Zhao, Xinbing; Zhang, Shichao

2014-04-07

Preparation of two-dimensional (2D) graphene-like materials is currently an emerging field in materials science since the discovery of single-atom-thick graphene prepared by mechanical cleavage. In this work, we proposed a new method to prepare 2D NiS, where reduced graphene oxide (rGO) was found to induce the recrystallization of NiS from nanorods to nanosheets in a hydrothermal process. The process and mechanism of recrystallization have been clarified by various characterization techniques, including scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS) mapping, and X-ray photoelectron spectroscopy (XPS). The characterization of ex situ NiS/rGO products by SEM and EDS mapping indicates that the recrystallization of NiS from nanorods to nanosheets is realized actually through an exfoliation process, while the characterization of in situ NiS/rGO products by SEM, TEM, and EDS mapping reveals the exfoliation process. The XPS result demonstrates that hydrothermally assisted chemical bonding occurs between NiS and rGO, which induces the exfoliation of NiS nanorods into nanosheets. The obtained NiS/rGO composite shows promising Na-storage properties.

Self-consistent modelling of electrochemical strain microscopy in mixed ionic-electronic conductors: Nonlinear and dynamic regimes

DOE PAGES

Varenyk, O. V.; Silibin, M. V.; Kiselev, Dmitri A.; ...

2015-08-19

The frequency dependent Electrochemical Strain Microscopy (ESM) response of mixed ionic-electronic conductors is analyzed within the framework of Fermi-Dirac statistics and the Vegard law, accounting for steric effects from mobile donors. The emergence of dynamic charge waves and nonlinear deformation of the surface in response to bias applied to the tip-surface junction is numerically explored. The 2D maps of the strain and concentration distributions across the mixed ionic-electronic conductor and bias-induced surface displacements are calculated. Furthermore, the obtained numerical results can be applied to quantify the ESM response of Li-based solid electrolytes, materials with resistive switching, and electroactive ferroelectric polymers,more » which are of potential interest for flexible and high-density non-volatile memory devices.« less

Self-consistent modelling of electrochemical strain microscopy in mixed ionic-electronic conductors: Nonlinear and dynamic regimes

NASA Astrophysics Data System (ADS)

Varenyk, O. V.; Silibin, M. V.; Kiselev, D. A.; Eliseev, E. A.; Kalinin, S. V.; Morozovska, A. N.

2015-08-01

The frequency dependent Electrochemical Strain Microscopy (ESM) response of mixed ionic-electronic conductors is analyzed within the framework of Fermi-Dirac statistics and the Vegard law, accounting for steric effects from mobile donors. The emergence of dynamic charge waves and nonlinear deformation of the surface in response to bias applied to the tip-surface junction is numerically explored. The 2D maps of the strain and concentration distributions across the mixed ionic-electronic conductor and bias-induced surface displacements are calculated. The obtained numerical results can be applied to quantify the ESM response of Li-based solid electrolytes, materials with resistive switching, and electroactive ferroelectric polymers, which are of potential interest for flexible and high-density non-volatile memory devices.

Separating strain from composition in unit cell parameter maps obtained from aberration corrected high resolution transmission electron microscopy imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schulz, T.; Remmele, T.; Korytov, M.

2014-01-21

Based on the evaluation of lattice parameter maps in aberration corrected high resolution transmission electron microscopy images, we propose a simple method that allows quantifying the composition and disorder of a semiconductor alloy at the unit cell scale with high accuracy. This is realized by considering, next to the out-of-plane, also the in-plane lattice parameter component allowing to separate the chemical composition from the strain field. Considering only the out-of-plane lattice parameter component not only yields large deviations from the true local alloy content but also carries the risk of identifying false ordering phenomena like formations of chains or platelets.more » Our method is demonstrated on image simulations of relaxed supercells, as well as on experimental images of an In{sub 0.20}Ga{sub 0.80}N quantum well. Principally, our approach is applicable to all epitaxially strained compounds in the form of quantum wells, free standing islands, quantum dots, or wires.« less

Mediator structure and rearrangements required for holoenzyme formation.

PubMed

Tsai, Kuang-Lei; Yu, Xiaodi; Gopalan, Sneha; Chao, Ti-Chun; Zhang, Ying; Florens, Laurence; Washburn, Michael P; Murakami, Kenji; Conaway, Ronald C; Conaway, Joan W; Asturias, Francisco J

2017-04-13

The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.

Flat ion milling: a powerful tool for preparation of cross-sections of lead-silver alloys.

PubMed

Brodusch, Nicolas; Boisvert, Sophie; Gauvin, Raynald

2013-06-01

While conventional mechanical and chemical polishing results in stress, deformation and polishing particles embedded on the surface, flat milling with Ar+ ions erodes the material with no mechanical artefacts. This flat milling process is presented as an alternative method to prepare a Pb-Ag alloy cross-section for scanning electron microscopy. The resulting surface is free of scratches with very little to no stress induced, so that electron diffraction and channelling contrast are possible. The results have shown that energy dispersive spectrometer (EDS) mapping, electron channelling contrast imaging and electron backscatter diffraction can be conducted with only one sample preparation step. Electron diffraction patterns acquired at 5 keV possessed very good pattern quality, highlighting an excellent surface condition. An orientation map was acquired at 20 keV with an indexing rate of 90.1%. An EDS map was performed at 5 keV, and Pb-Ag precipitates of sizes lower than 100 nm were observed. However, the drawback of the method is the generation of a noticeable surface topography resulting from the interaction of the ion beam with a polycrystalline and biphasic sample.

Simplification of femtosecond transient absorption microscopy data from CH 3NH 3PbI 3 perovskite thin films into decay associated amplitude maps

DOE PAGES

Doughty, Benjamin; Simpson, Mary Jane; Yang, Bin; ...

2016-02-16

Our work aims to simplify multi-dimensional femtosecond transient absorption microscopy (TAM) data into decay associated amplitude maps that describe the spatial distributions of dynamical processes occurring on various characteristic timescales. Application of this method to TAM data obtained from a model methyl-ammonium lead iodide (CH 3NH 3PbI 3) perovskite thin film allows us to simplify the dataset consisting of a 68 time-resolved images into 4 decay associated amplitude maps. Furthermore, these maps provide a simple means to visualize the complex electronic excited-state dynamics in this system by separating distinct dynamical processes evolving on characteristic timescales into individual spatial images. Thismore » approach provides new insight into subtle aspects of ultrafast relaxation dynamics associated with excitons and charge carriers in the perovskite thin film, which have recently been found to coexist at spatially distinct locations.« less

EBSD as a tool to identify and quantify bainite and ferrite in low-alloyed Al-TRIP steels.

PubMed

Zaefferer, S; Romano, P; Friedel, F

2008-06-01

Bainite is thought to play an important role for the chemical and mechanical stabilization of metastable austenite in low-alloyed TRIP steels. Therefore, in order to understand and improve the material properties, it is important to locate and quantify the bainitic phase. To this aim, electron backscatter diffraction-based orientation microscopy has been employed. The main difficulty herewith is to distinguish bainitic ferrite from ferrite because both have bcc crystal structure. The most important difference between them is the occurrence of transformation induced geometrically necessary dislocations in the bainitic phase. To determine the areas with larger geometrically necessary dislocation density, the following orientation microscopy maps were explored: pattern quality maps, grain reference orientation deviation maps and kernel average misorientation maps. We show that only the latter allow a reliable separation of the bainitic and ferritic phase. The kernel average misorientation threshold value that separates both constituents is determined by an algorithm that searches for the smoothness of the boundaries between them.

Simplification of femtosecond transient absorption microscopy data from CH3NH3PbI3 perovskite thin films into decay associated amplitude maps

NASA Astrophysics Data System (ADS)

Doughty, Benjamin; Simpson, Mary Jane; Yang, Bin; Xiao, Kai; Ma, Ying-Zhong

2016-03-01

This work aims to simplify multi-dimensional femtosecond transient absorption microscopy (TAM) data into decay associated amplitude maps (DAAMs) that describe the spatial distributions of dynamical processes occurring on various characteristic timescales. Application of this method to TAM data obtained from a model methyl-ammonium lead iodide (CH3NH3PbI3) perovskite thin film allows us to simplify the data set comprising 68 time-resolved images into four DAAMs. These maps offer a simple means to visualize the complex electronic excited-state dynamics in this system by separating distinct dynamical processes evolving on characteristic timescales into individual spatial images. This approach provides new insight into subtle aspects of ultrafast relaxation dynamics associated with excitons and charge carriers in the perovskite thin film, which have recently been found to coexist at spatially distinct locations.

Inner- and outer-wall sorting of double-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Li, Han; Gordeev, Georgy; Wasserroth, Sören; Chakravadhanula, Venkata Sai Kiran; Neelakandhan, Shyam Kumar Chethala; Hennrich, Frank; Jorio, Ado; Reich, Stephanie; Krupke, Ralph; Flavel, Benjamin Scott

2017-12-01

Double-walled carbon nanotubes (DWCNTs) consist of two coaxially aligned single-walled carbon nanotubes (SWCNTs), and previous sorting methods only achieved outer-wall electronic-type selectivity. Here, a separation technique capable of sorting DWCNTs by semiconducting (S) or metallic (M) inner- and outer-wall electronic type is presented. Electronic coupling between the inner and outer wall is used to alter the surfactant coating around each of the DWCNT types, and aqueous gel permeation is used to separate them. Aqueous methods are used to remove SWCNT species from the raw material and prepare enriched DWCNT fractions. The enriched DWCNT fractions are then transferred into either chlorobenzene or toluene using the copolymer PFO-BPy to yield the four inner@outer combinations of M@M, M@S, S@M and S@S. The high purity of the resulting fractions is verified by absorption measurements, transmission electron microscopy, atomic force microscopy, resonance Raman mapping and high-density field-effect transistor devices.

Inner- and outer-wall sorting of double-walled carbon nanotubes.

PubMed

Li, Han; Gordeev, Georgy; Wasserroth, Sören; Chakravadhanula, Venkata Sai Kiran; Neelakandhan, Shyam Kumar Chethala; Hennrich, Frank; Jorio, Ado; Reich, Stephanie; Krupke, Ralph; Flavel, Benjamin Scott

2017-12-01

Double-walled carbon nanotubes (DWCNTs) consist of two coaxially aligned single-walled carbon nanotubes (SWCNTs), and previous sorting methods only achieved outer-wall electronic-type selectivity. Here, a separation technique capable of sorting DWCNTs by semiconducting (S) or metallic (M) inner- and outer-wall electronic type is presented. Electronic coupling between the inner and outer wall is used to alter the surfactant coating around each of the DWCNT types, and aqueous gel permeation is used to separate them. Aqueous methods are used to remove SWCNT species from the raw material and prepare enriched DWCNT fractions. The enriched DWCNT fractions are then transferred into either chlorobenzene or toluene using the copolymer PFO-BPy to yield the four inner@outer combinations of M@M, M@S, S@M and S@S. The high purity of the resulting fractions is verified by absorption measurements, transmission electron microscopy, atomic force microscopy, resonance Raman mapping and high-density field-effect transistor devices.

Wave-function description of conductance mapping for a quantum Hall electron interferometer

NASA Astrophysics Data System (ADS)

Kolasiński, K.; Szafran, B.

2014-04-01

Scanning gate microscopy of quantum point contacts (QPC) in the integer quantum Hall regime is considered in terms of the scattering wave functions with a finite-difference implementation of the quantum transmitting boundary approach. Conductance (G) maps for a clean QPC as well as for a system including an antidot within the QPC constriction are evaluated. The steplike locally flat G maps for clean QPCs turn into circular resonances that are reentrant in an external magnetic field when the antidot is introduced to the constriction. The current circulation around the antidot and the spacing of the resonances at the magnetic field scale react to the probe approaching the QPC. The calculated G maps with a rigid but soft antidot potential reproduce the features detected recently in the electron interferometer [F. Martins et al., Sci. Rep. 3, 1416 (2013), 10.1038/srep01416].

Improved Serial Sectioning Techniques for Correlative Light-Electron Microscopy Mapping of Human Langerhans Islets

PubMed Central

Saitoh, Sei; Ohno, Nobuhiko; Saitoh, Yurika; Terada, Nobuo; Shimo, Satoshi; Aida, Kaoru; Fujii, Hideki; Kobayashi, Tetsuro; Ohno, Shinichi

2018-01-01

Combined analysis of immunostaining for various biological molecules coupled with investigations of ultrastructural features of individual cells is a powerful approach for studies of cellular functions in normal and pathological conditions. However, weak antigenicity of tissues fixed by conventional methods poses a problem for immunoassays. This study introduces a method of correlative light and electron microscopy imaging of the same endocrine cells of compact and diffuse islets from human pancreatic tissue specimens. The method utilizes serial sections obtained from Epon-embedded specimens fixed with glutaraldehyde and osmium tetroxide. Double-immunofluorescence staining of thick Epon sections for endocrine hormones (insulin and glucagon) and regenerating islet-derived gene 1 α (REG1α) was performed following the removal of Epoxy resin with sodium ethoxide, antigen retrieval by autoclaving, and de-osmification treatment with hydrogen peroxide. The immunofluorescence images of endocrine cells were superimposed with the electron microscopy images of the same cells obtained from serial ultrathin sections. Immunofluorescence images showed well-preserved secretory granules in endocrine cells, whereas electron microscopy observations demonstrated corresponding secretory granules and intracellular organelles in the same cells. In conclusion, the correlative imaging approach developed by us may be useful for examining ultrastructural features in combination with immunolocalisation of endocrine hormones in the same human pancreatic islets. PMID:29622846

Challenges of microtome‐based serial block‐face scanning electron microscopy in neuroscience

PubMed Central

WANNER, A. A.; KIRSCHMANN, M. A.

2015-01-01

Summary Serial block‐face scanning electron microscopy (SBEM) is becoming increasingly popular for a wide range of applications in many disciplines from biology to material sciences. This review focuses on applications for circuit reconstruction in neuroscience, which is one of the major driving forces advancing SBEM. Neuronal circuit reconstruction poses exceptional challenges to volume EM in terms of resolution, field of view, acquisition time and sample preparation. Mapping the connections between neurons in the brain is crucial for understanding information flow and information processing in the brain. However, information on the connectivity between hundreds or even thousands of neurons densely packed in neuronal microcircuits is still largely missing. Volume EM techniques such as serial section TEM, automated tape‐collecting ultramicrotome, focused ion‐beam scanning electron microscopy and SBEM (microtome serial block‐face scanning electron microscopy) are the techniques that provide sufficient resolution to resolve ultrastructural details such as synapses and provides sufficient field of view for dense reconstruction of neuronal circuits. While volume EM techniques are advancing, they are generating large data sets on the terabyte scale that require new image processing workflows and analysis tools. In this review, we present the recent advances in SBEM for circuit reconstruction in neuroscience and an overview of existing image processing and analysis pipelines. PMID:25907464

Lorentz microscopy sheds light on the role of dipolar interactions in magnetic hyperthermia

NASA Astrophysics Data System (ADS)

Campanini, M.; Ciprian, R.; Bedogni, E.; Mega, A.; Chiesi, V.; Casoli, F.; de Julián Fernández, C.; Rotunno, E.; Rossi, F.; Secchi, A.; Bigi, F.; Salviati, G.; Magén, C.; Grillo, V.; Albertini, F.

2015-04-01

Monodispersed Fe3O4 nanoparticles with comparable size distributions have been synthesized by two different synthesis routes, co-precipitation and thermal decomposition. Thanks to the different steric stabilizations, the described samples can be considered as a model system to investigate the effects of magnetic dipolar interactions on the aggregation states of the nanoparticles. Moreover, the presence of magnetic dipolar interactions can strongly affect the nanoparticle efficiency as a hyperthermic mediator. In this paper, we present a novel way to visualize and map the magnetic dipolar interactions in different kinds of nanoparticle aggregates by the use of Lorentz microscopy, an easy and reliable in-line electron holographic technique. By exploiting Lorentz microscopy, which is complementary to the magnetic measurements, it is possible to correlate the interaction degrees of magnetic nanoparticles with their magnetic behaviors. In particular, we demonstrate that Lorentz microscopy is successful in visualizing the magnetic configurations stabilized by dipolar interactions, thus paving the way to the comprehension of the power loss mechanisms for different nanoparticle aggregates.Monodispersed Fe3O4 nanoparticles with comparable size distributions have been synthesized by two different synthesis routes, co-precipitation and thermal decomposition. Thanks to the different steric stabilizations, the described samples can be considered as a model system to investigate the effects of magnetic dipolar interactions on the aggregation states of the nanoparticles. Moreover, the presence of magnetic dipolar interactions can strongly affect the nanoparticle efficiency as a hyperthermic mediator. In this paper, we present a novel way to visualize and map the magnetic dipolar interactions in different kinds of nanoparticle aggregates by the use of Lorentz microscopy, an easy and reliable in-line electron holographic technique. By exploiting Lorentz microscopy, which is complementary to the magnetic measurements, it is possible to correlate the interaction degrees of magnetic nanoparticles with their magnetic behaviors. In particular, we demonstrate that Lorentz microscopy is successful in visualizing the magnetic configurations stabilized by dipolar interactions, thus paving the way to the comprehension of the power loss mechanisms for different nanoparticle aggregates. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00273g

The connectomics challenge

PubMed Central

Silvestri, Ludovico; Sacconi, Leonardo; Pavone, Francesco Saverio

Summary One of the most fascinating challenges in neuroscience is the reconstruction of the connectivity map of the brain. Recent years have seen a rapid expansion in the field of connectomics, whose aim is to trace this map and understand its relationship with neural computation. Many different approaches, ranging from electron and optical microscopy to magnetic resonance imaging, have been proposed to address the connectomics challenge on various spatial scales and in different species. Here, we review the main technological advances in the microscopy techniques applied to connectomics, highlighting the potential and limitations of the different methods. Finally, we briefly discuss the role of connectomics in the Human Brain Project, the Future and Emerging Technologies (FET) Flagship recently approved by the European Commission. PMID:24139653

Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix

PubMed Central

He, Jing; Zeil, Stephanie; Hallak, Hussam; McKaig, Kele; Kovacs, Julio; Wriggers, Willy

2016-01-01

Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices. PMID:27280059

3D imaging and quantitative analysis of small solubilized membrane proteins and their complexes by transmission electron microscopy

PubMed Central

Vahedi-Faridi, Ardeschir; Jastrzebska, Beata; Palczewski, Krzysztof; Engel, Andreas

2013-01-01

Inherently unstable, detergent-solubilized membrane protein complexes can often not be crystallized. For complexes that have a mass of >300 kDa, cryo-electron microscopy (EM) allows their three-dimensional (3D) structure to be assessed to a resolution that makes secondary structure elements visible in the best case. However, many interesting complexes exist whose mass is below 300 kDa and thus need alternative approaches. Two methods are reviewed: (i) Mass measurement in a scanning transmission electron microscope, which has provided important information on the stoichiometry of membrane protein complexes. This technique is applicable to particulate, filamentous and sheet-like structures. (ii) 3D-EM of negatively stained samples, which determines the molecular envelope of small membrane protein complexes. Staining and dehydration artifacts may corrupt the quality of the 3D map. Staining conditions thus need to be optimized. 3D maps of plant aquaporin SoPIP2;1 tetramers solubilized in different detergents illustrate that the flattening artifact can be partially prevented and that the detergent itself contributes significantly. Another example discussed is the complex of G protein-coupled receptor rhodopsin with its cognate G protein transducin. PMID:23267047

Visualization of Current and Mapping of Elements in Quantum Dot Solar Cells

DOE PAGES

Niezgoda, J. Scott; Ng, Amy; Poplawsky, Jonathan D.; ...

2015-12-17

The delicate influence of properties such as high surface state density and organic-inorganic boundaries on the individual quantum dot electronic structure complicates pursuits toward forming quantitative models of quantum dot thin films ab initio. Our report describes the application of electron beam-induced current (EBIC) microscopy to depleted-heterojunction colloidal quantum dot photovoltaics (DH-CQD PVs), a technique which affords one a map of current production within the active layer of a PV device. The effects of QD sample size polydispersity as well as layer thickness in CQD active layers as they pertain to current production within these PVs are imaged and explained.more » The results from these experiments compare well with previous estimations, and confirm the ability of EBIC to function as a valuable empirical tool for the design and betterment of DH-CQD PVs. Lastly, extensive and unexpected PbS QD penetration into the mesoporous TiO 2 layer is observed through imaging of device cross sections by energy-dispersive X-ray spectroscopy combined with scanning transmission electron microscopy. Finally, the effects of this finding are discussed and corroborated with the EBIC studies on similar devices.« less

Characterization of 3D interconnected microstructural network in mixed ionic and electronic conducting ceramic composites

NASA Astrophysics Data System (ADS)

Harris, William M.; Brinkman, Kyle S.; Lin, Ye; Su, Dong; Cocco, Alex P.; Nakajo, Arata; Degostin, Matthew B.; Chen-Wiegart, Yu-Chen Karen; Wang, Jun; Chen, Fanglin; Chu, Yong S.; Chiu, Wilson K. S.

2014-04-01

The microstructure and connectivity of the ionic and electronic conductive phases in composite ceramic membranes are directly related to device performance. Transmission electron microscopy (TEM) including chemical mapping combined with X-ray nanotomography (XNT) have been used to characterize the composition and 3-D microstructure of a MIEC composite model system consisting of a Ce0.8Gd0.2O2 (GDC) oxygen ion conductive phase and a CoFe2O4 (CFO) electronic conductive phase. The microstructural data is discussed, including the composition and distribution of an emergent phase which takes the form of isolated and distinct regions. Performance implications are considered with regards to the design of new material systems which evolve under non-equilibrium operating conditions.The microstructure and connectivity of the ionic and electronic conductive phases in composite ceramic membranes are directly related to device performance. Transmission electron microscopy (TEM) including chemical mapping combined with X-ray nanotomography (XNT) have been used to characterize the composition and 3-D microstructure of a MIEC composite model system consisting of a Ce0.8Gd0.2O2 (GDC) oxygen ion conductive phase and a CoFe2O4 (CFO) electronic conductive phase. The microstructural data is discussed, including the composition and distribution of an emergent phase which takes the form of isolated and distinct regions. Performance implications are considered with regards to the design of new material systems which evolve under non-equilibrium operating conditions. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr06684c

Advanced electron microscopy methods for the analysis of MgB2 superconductor

NASA Astrophysics Data System (ADS)

Birajdar, B.; Peranio, N.; Eibl, O.

2008-02-01

Advanced electron microscopy methods used for the analysis of superconducting MgB2 wires and tapes are described. The wires and tapes were prepared by the powder in tube method using different processing technologies and thoroughly characterised for their superconducting properties within the HIPERMAG project. Microstructure analysis on μm to nm length scales is necessary to understand the superconducting properties of MgB2. For the MgB2 phase analysis on μm scale an analytical SEM, and for the analysis on nm scale a energy-filtered STEM is used. Both the microscopes were equipped with EDX detector and field emission gun. Electron microscopy and spectroscopy of MgB2 is challenging because of the boron analysis, carbon and oxygen contamination, and the presence of large number of secondary phases. Advanced electron microscopy involves, combined SEM, EPMA and TEM analysis with artefact free sample preparation, elemental mapping and chemical quantification of point spectra. Details of the acquisition conditions and achieved accuracy are presented. Ex-situ wires show oxygen-free MgB2 colonies (a colony is a dense arrangement of several MgB2 grains) embedded in a porous and oxygen-rich matrix, introducing structural granularity. In comparison, in-situ wires are generally more dense, but show inhibited MgB2 phase formation with significantly higher fraction of B-rich secondary phases. SiC additives in the in-situ wires forms Mg2Si secondary phases. The advanced electron microscopy has been used to extract the microstructure parameters like colony size, B-rich secondary phase fraction, O mole fraction and MgB2 grain size, and establish a microstructure-critical current density model [1]. In summary, conventional secondary electron imaging in SEM and diffraction contrast imaging in the TEM are by far not sufficient and advanced electron microscopy methods are essential for the analysis of superconducting MgB2 wires and tapes.

Scanning electron microscopy/energy dispersive spectrometry fixedbeam or overscan x-ray microanalysis of particles can miss the real structure: x-ray spectrum image mapping reveals the true nature

NASA Astrophysics Data System (ADS)

Newbury, Dale E.; Ritchie, Nicholas W. M.

2013-05-01

The typical strategy for analysis of a microscopic particle by scanning electron microscopy/energy dispersive spectrometry x-ray microanalysis (SEM/EDS) is to use a fixed beam placed at the particle center or to continuously overscan to gather an "averaged" x-ray spectrum. While useful, such strategies inevitably concede any possibility of recognizing microstructure within the particle, and such fine scale structure is often critical for understanding the origins, behavior, and fate of particles. Elemental imaging by x-ray mapping has been a mainstay of SEM/EDS analytical practice for many years, but the time penalty associated with mapping with older EDS technology has discouraged its general use and reserved it more for detailed studies that justified the time investment. The emergence of the high throughput, high peak stability silicon drift detector (SDD-EDS) has enabled a more effective particle mapping strategy: "flash" x-ray spectrum image maps can now be recorded in seconds that capture the spatial distribution of major (concentration, C > 0.1 mass fraction) and minor (0.01 <= C <= 0.1) constituents. New SEM/SDD-EDS instrument configurations feature multiple SDDs that view the specimen from widely spaced azimuthal angles. Multiple, simultaneous measurements from different angles enable x-ray spectrometry and mapping that can minimize the strong geometric effects of particles. The NIST DTSA-II software engine is a powerful aid for quantitatively analyzing EDS spectra measured individually as well as for mapping information (available free for Java platforms at: http://www.cstl.nist.gov/div837/837.02/epq/dtsa2/index.html).

Probing low-energy hyperbolic polaritons in van der Waals crystals with an electron microscope.

PubMed

Govyadinov, Alexander A; Konečná, Andrea; Chuvilin, Andrey; Vélez, Saül; Dolado, Irene; Nikitin, Alexey Y; Lopatin, Sergei; Casanova, Fèlix; Hueso, Luis E; Aizpurua, Javier; Hillenbrand, Rainer

2017-07-21

Van der Waals materials exhibit intriguing structural, electronic, and photonic properties. Electron energy loss spectroscopy within scanning transmission electron microscopy allows for nanoscale mapping of such properties. However, its detection is typically limited to energy losses in the eV range-too large for probing low-energy excitations such as phonons or mid-infrared plasmons. Here, we adapt a conventional instrument to probe energy loss down to 100 meV, and map phononic states in hexagonal boron nitride, a representative van der Waals material. The boron nitride spectra depend on the flake thickness and on the distance of the electron beam to the flake edges. To explain these observations, we developed a classical response theory that describes the interaction of fast electrons with (anisotropic) van der Waals slabs, revealing that the electron energy loss is dominated by excitation of hyperbolic phonon polaritons, and not of bulk phonons as often reported. Thus, our work is of fundamental importance for interpreting future low-energy loss spectra of van der Waals materials.Here the authors adapt a STEM-EELS system to probe energy loss down to 100 meV, and apply it to map phononic states in hexagonal boron nitride, revealing that the electron loss is dominated by hyperbolic phonon polaritons.

Single Particulate SEM-EDX Analysis of Iron-Containing Coarse Particulate Matter in an Urban Environment: Sources and Distribution of Iron within Cleveland, Ohio

EPA Science Inventory

The physicochemical properties of coarse-mode, iron-containing particles, and their temporal and spatial distributions are poorly understood. Single particle analysis combining x-ray elemental mapping and computer-controlled scanning electron microscopy (CCSEM-EDX) of passively ...

Strain distributions and their influence on electronic structures of WSe2-MoS2 laterally strained heterojunctions

NASA Astrophysics Data System (ADS)

Zhang, Chendong; Li, Ming-Yang; Tersoff, Jerry; Han, Yimo; Su, Yushan; Li, Lain-Jong; Muller, David A.; Shih, Chih-Kang

2018-02-01

Monolayer transition metal dichalcogenide heterojunctions, including vertical and lateral p-n junctions, have attracted considerable attention due to their potential applications in electronics and optoelectronics. Lattice-misfit strain in atomically abrupt lateral heterojunctions, such as WSe2-MoS2, offers a new band-engineering strategy for tailoring their electronic properties. However, this approach requires an understanding of the strain distribution and its effect on band alignment. Here, we study a WSe2-MoS2 lateral heterojunction using scanning tunnelling microscopy and image its moiré pattern to map the full two-dimensional strain tensor with high spatial resolution. Using scanning tunnelling spectroscopy, we measure both the strain and the band alignment of the WSe2-MoS2 lateral heterojunction. We find that the misfit strain induces type II to type I band alignment transformation. Scanning transmission electron microscopy reveals the dislocations at the interface that partially relieve the strain. Finally, we observe a distinctive electronic structure at the interface due to hetero-bonding.

A Shear Strain Route Dependency of Martensite Formation in 316L Stainless Steel.

PubMed

Kang, Suk Hoon; Kim, Tae Kyu; Jang, Jinsung; Oh, Kyu Hwan

2015-06-01

In this study, the effect of simple shearing on microstructure evolution and mechanical properties of 316L austenitic stainless steel were investigated. Two different shear strain routes were obtained by twisting cylindrical specimens in the forward and backward directions. The strain-induced martensite phase was effectively obtained by alteration of the routes. Formation of the martensite phase clearly resulted in significant hardening of the steel. Grain-size reduction and strain-induced martensitic transformation within the deformed structures of the strained specimens were characterized by scanning electron microscopy - electron back-scattered diffraction, X-ray diffraction, and the TEM-ASTAR (transmission electron microscopy - analytical scanning transmission atomic resolution, automatic crystal orientation/phase mapping for TEM) system. Significant numbers of twin networks were formed by alteration of the shear strain routes, and the martensite phases were nucleated at the twin interfaces.

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.

PubMed

Caulfield, Thomas R; Devkota, Batsal; Rollins, Geoffrey C

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

Assessing Strain Mapping by Electron Backscatter Diffraction and Confocal Raman Microscopy Using Wedge-indented Si

PubMed Central

Friedman, Lawrence H.; Vaudin, Mark D.; Stranick, Stephan J.; Stan, Gheorghe; Gerbig, Yvonne B.; Osborn, William; Cook, Robert F.

2016-01-01

The accuracy of electron backscatter diffraction (EBSD) and confocal Raman microscopy (CRM) for small-scale strain mapping are assessed using the multi-axial strain field surrounding a wedge indentation in Si as a test vehicle. The strain field is modeled using finite element analysis (FEA) that is adapted to the near-indentation surface profile measured by atomic force microscopy (AFM). The assessment consists of (1) direct experimental comparisons of strain and deformation and (2) comparisons in which the modeled strain field is used as an intermediate step. Direct experimental methods (1) consist of comparisons of surface elevation and gradient measured by AFM and EBSD and of Raman shifts measured and predicted by CRM and EBSD, respectively. Comparisons that utilize the combined FEA-AFM model (2) consist of predictions of distortion, strain, and rotation for comparison with EBSD measurements and predictions of Raman shift for comparison with CRM measurements. For both EBSD and CRM, convolution of measurements in depth-varying strain fields is considered. The interconnected comparisons suggest that EBSD was able to provide an accurate assessment of the wedge indentation deformation field to within the precision of the measurements, approximately 2 × 10−4 in strain. CRM was similarly precise, but was limited in accuracy to several times this value. PMID:26939030

Pump-probe Kelvin-probe force microscopy: Principle of operation and resolution limits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murawski, J.; Graupner, T.; Milde, P., E-mail: peter.milde@tu-dresden.de

Knowledge on surface potential dynamics is crucial for understanding the performance of modern-type nanoscale devices. We describe an electrical pump-probe approach in Kelvin-probe force microscopy that enables a quantitative measurement of dynamic surface potentials at nanosecond-time and nanometer-length scales. Also, we investigate the performance of pump-probe Kelvin-probe force microscopy with respect to the relevant experimental parameters. We exemplify a measurement on an organic field effect transistor that verifies the undisturbed functionality of our pump-probe approach in terms of simultaneous and quantitative mapping of topographic and electronic information at a high lateral and temporal resolution.

Mapping the magnetic and crystal structure in cobalt nanowires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cantu-Valle, Jesus; Betancourt, Israel; Sanchez, John E.

2015-07-14

Using off-axis electron holography under Lorentz microscopy conditions to experimentally determine the magnetization distribution in individual cobalt (Co) nanowires, and scanning precession-electron diffraction to obtain their crystalline orientation phase map, allowed us to directly visualize with high accuracy the effect of crystallographic texture on the magnetization of nanowires. The influence of grain boundaries and disorientations on the magnetic structure is correlated on the basis of micromagnetic analysis in order to establish the detailed relationship between magnetic and crystalline structure. This approach demonstrates the applicability of the method employed and provides further understanding on the effect of crystalline structure on magneticmore » properties at the nanometric scale.« less

Atomic Resolution Cryo-EM Structure of β-Galactosidase.

PubMed

Bartesaghi, Alberto; Aguerrebere, Cecilia; Falconieri, Veronica; Banerjee, Soojay; Earl, Lesley A; Zhu, Xing; Grigorieff, Nikolaus; Milne, Jacqueline L S; Sapiro, Guillermo; Wu, Xiongwu; Subramaniam, Sriram

2018-05-10

The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at ∼ 1.5 Å resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design. Published by Elsevier Ltd.

Towards quantitative off-axis electron holographic mapping of the electric field around the tip of a sharp biased metallic needle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beleggia, M.; Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin; Kasama, T.

We apply off-axis electron holography and Lorentz microscopy in the transmission electron microscope to map the electric field generated by a sharp biased metallic tip. A combination of experimental data and modelling provides quantitative information about the potential and the field around the tip. Close to the tip apex, we measure a maximum field intensity of 82 MV/m, corresponding to a field k factor of 2.5, in excellent agreement with theory. In order to verify the validity of the measurements, we use the inferred charge density distribution in the tip region to generate simulated phase maps and Fresnel (out-of-focus) imagesmore » for comparison with experimental measurements. While the overall agreement is excellent, the simulations also highlight the presence of an unexpected astigmatic contribution to the intensity in a highly defocused Fresnel image, which is thought to result from the geometry of the applied field.« less

Rapid quantitative chemical mapping of surfaces with sub-2 nm resolution

NASA Astrophysics Data System (ADS)

Lai, Chia-Yun; Perri, Saverio; Santos, Sergio; Garcia, Ricardo; Chiesa, Matteo

2016-05-01

We present a theory that exploits four observables in bimodal atomic force microscopy to produce maps of the Hamaker constant H. The quantitative H maps may be employed by the broader community to directly interpret the high resolution of standard bimodal AFM images as chemical maps while simultaneously quantifying chemistry in the non-contact regime. We further provide a simple methodology to optimize a range of operational parameters for which H is in the closest agreement with the Lifshitz theory in order to (1) simplify data acquisition and (2) generalize the methodology to any set of cantilever-sample systems.We present a theory that exploits four observables in bimodal atomic force microscopy to produce maps of the Hamaker constant H. The quantitative H maps may be employed by the broader community to directly interpret the high resolution of standard bimodal AFM images as chemical maps while simultaneously quantifying chemistry in the non-contact regime. We further provide a simple methodology to optimize a range of operational parameters for which H is in the closest agreement with the Lifshitz theory in order to (1) simplify data acquisition and (2) generalize the methodology to any set of cantilever-sample systems. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr00496b

Spatially Resolved Nano-Scale Characterization of Electronic States in SrTiO3(001) Surfaces by STM/STS

NASA Astrophysics Data System (ADS)

Iwaya, Katsuya; Ohsawa, Takeo; Shimizu, Ryota; Hashizume, Tomihiro; Hitosugi, Taro

2012-02-01

We have performed low temperature scanning tunneling microscopy/spectroscopy (STM/STS) measurements on TiO2-terminated SrTiO3(001) thin film surfaces. The conductance map exhibited electronic modulations that were completely different from the surface structure. We also found that the electronic modulations were strongly dependent on temperature and the density of atomic defects associated with oxygen vacancies. These results suggest the existence of strongly correlated two-dimensional electronic states near the SrTiO3 surface, implying the importance of electron correlation at the interfaces of SrTiO3-related heterostructures.

Scanning Electron Microscopy (SEM) Procedure for HE Powders on a Zeiss Sigma HD VP SEM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaka, F.

This method describes the characterization of inert and HE materials by the Zeiss Sigma HD VP field emission Scanning Electron Microscope (SEM). The SEM uses an accelerated electron beam to generate high-magnification images of explosives and other materials. It is fitted with five detectors (SE, Inlens, STEM, VPSE, HDBSD) to enable imaging of the sample via different secondary electron signatures, angles, and energies. In addition to imaging through electron detection, the microscope is also fitted with two Oxford Instrument Energy Dispersive Spectrometer (EDS) 80 mm detectors to generate elemental constituent spectra and two-dimensional maps of the material being scanned.

Determination of the mean inner potential of cadmium telluride via electron holography

NASA Astrophysics Data System (ADS)

Cassidy, C.; Dhar, A.; Shintake, T.

2017-04-01

Mean inner potential is a fundamental material parameter in solid state physics and electron microscopy and has been experimentally measured in CdTe, a technologically important semiconductor. As a first step, the inelastic mean free path for electron scattering in CdTe was determined, using electron energy loss spectroscopy, to enable precise thickness mapping of thin CdTe lamellae. The obtained value was λi(CdTe, 300 kV) = 192 ± 10 nm. This value is relatively large, given the high density of the material, and is discussed in the text. Next, electron diffraction and specimen tilting were employed to identify weakly diffracting lattice orientations, to enable the straightforward measurement of the electron phase shift. Finally, electron holography was utilized to quantitatively map the phase shift experienced by electron waves passing through a CdTe crystal, with several different propagation vectors. Utilization of both thickness and phase data allowed computation of mean inner potential as V0 (CdTe) = 14.0 ± 0.9 V, within the range of previous theoretical estimates.

Cathodoluminescence study of one-dimensional free-standing widegap-semiconductor nanostructures: GaN nanotubes, Si3N4 nanobelts and ZnS/Si nanowires.

PubMed

Sekiguchi, Takashi; Hu, Junqing; Bando, Yoshio

2004-01-01

Luminescence properties of one-dimensional free-standing widegap-semiconductor nanostructures were characterized by means of cathodoluminescence (CL). GaN nanopipes, alpha-Si3N4 nanobelts and ZnS/Si nanowires were fabricated by a catalyst-free method, namely grown in an induction furnace from powders. After the observation of morphology by scanning electron microscopy as well as the confirmation of their crystal structures by transmission electron microscopy, their CL spectra and images were observed. The CL spectra mapping as well as the monochromatic CL imaging revealed the variation of the luminescence spectra of different nanowires as well as that along a single wire. These results revealed the optical features of nanostructures.

Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling

NASA Astrophysics Data System (ADS)

Jahn, Martin T.; Markert, Sebastian M.; Ryu, Taewoo; Ravasi, Timothy; Stigloher, Christian; Hentschel, Ute; Moitinho-Silva, Lucas

2016-10-01

Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We observed high transcriptional activity for proteins related to bacterial microcompartments (BMC) and we resolved their subcellular localisation by combining FISH-CLEM with immunohistochemistry (IHC) on ultra-thin sponge tissue sections. In terms of functional relevance, we propose that the BMC-A region may be involved in 1,2-propanediol degradation. The FISH-IHC-CLEM approach was proven an effective toolkit to combine -omics approaches with functional studies and it should be widely applicable in environmental microbiology.

High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy

NASA Astrophysics Data System (ADS)

Demers, Jean-Philippe; Habenstein, Birgit; Loquet, Antoine; Kumar Vasa, Suresh; Giller, Karin; Becker, Stefan; Baker, David; Lange, Adam; Sgourakis, Nikolaos G.

2014-09-01

We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information. Combining a 7.7-Å cryo-EM density map and 996 ssNMR distance constraints, the structure of the type-III secretion system needle of Shigella flexneri is determined to a precision of 0.4 Å. The calculated structures are cross-validated using an independent data set of 691 ssNMR constraints and scanning transmission electron microscopy measurements. The hybrid model resolves the conformation of the non-conserved N terminus, which occupies a protrusion in the cryo-EM density, and reveals conserved pore residues forming a continuous pattern of electrostatic interactions, thereby suggesting a mechanism for effector protein translocation.

Scanning tunneling microscopy of atomically precise graphene nanoribbons exfoliated onto H:Si(100)

NASA Astrophysics Data System (ADS)

Radocea, Adrian; Mehdi Pour, Mohammad; Vo, Timothy; Shekhirev, Mikhail; Sinitskii, Alexander; Lyding, Joseph

Atomically precise graphene nanoribbons (GNRs) are promising materials for next generation transistors due to their well-controlled bandgaps and the high thermal conductivity of graphene. The solution synthesis of graphene nanoribbons offers a pathway towards scalable manufacturing. While scanning tunneling microscopy (STM) can access size scales required for characterization, solvent residue increases experimental difficulty and precludes band-gap determination via scanning tunneling spectroscopy (STS). Our work addresses this challenge through a dry contact transfer method that cleanly transfers solution-synthesized GNRs onto H:Si(100) under UHV using a fiberglass applicator. The semiconducting silicon surface avoids problems with image charge screening enabling intrinsic bandgap measurements. We characterize the nanoribbons using STM and STS. For chevron GNRs, we find a 1.6 eV bandgap, in agreement with computational modeling, and map the electronic structure spatially with detailed spectra lines and current imaging tunneling spectroscopy. Mapping the electronic structure of graphene nanoribbons is an important step towards taking advantage of the ability to form atomically precise nanoribbons and finely tune their properties.

A simple method for detection of gunshot residue particles from hands, hair, face, and clothing using scanning electron microscopy/wavelength dispersive X-ray (SEM/WDX).

PubMed

Kage, S; Kudo, K; Kaizoji, A; Ryumoto, J; Ikeda, H; Ikeda, N

2001-07-01

We devised a simple and rapid method for detection of gunshot residue (GSR) particles, using scanning electron microscopy/wavelength dispersive X-ray (SEM/WDX) analysis. Experiments were done on samples containing GSR particles obtained from hands, hair, face, and clothing, using double-sided adhesive coated aluminum stubs (tape-lift method). SEM/WDX analyses for GSR were carried out in three steps: the first step was map analysis for barium (Ba) to search for GSR particles from lead styphnate primed ammunition, or tin (Sn) to search for GSR particles from mercury fulminate primed ammunition. The second step was determination of the location of GSR particles by X-ray imaging of Ba or Sn at a magnification of x 1000-2000 in the SEM, using data of map analysis, and the third step was identification of GSR particles, using WDX spectrometers. Analysis of samples from each primer of a stub took about 3 h. Practical applications were shown for utility of this method.

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

NASA Astrophysics Data System (ADS)

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang

2016-03-01

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ~2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy.

PubMed

Mainprize, Iain L; Beniac, Daniel R; Falkovskaia, Elena; Cleverley, Robert M; Gierasch, Lila M; Ottensmeyer, F Peter; Andrews, David W

2006-12-01

Structural studies on various domains of the ribonucleoprotein signal recognition particle (SRP) have not converged on a single complete structure of bacterial SRP consistent with the biochemistry of the particle. We obtained a three-dimensional structure for Escherichia coli SRP by cryoscanning transmission electron microscopy and mapped the internal RNA by electron spectroscopic imaging. Crystallographic data were fit into the SRP reconstruction, and although the resulting model differed from previous models, they could be rationalized by movement through an interdomain linker of Ffh, the protein component of SRP. Fluorescence resonance energy transfer experiments determined interdomain distances that were consistent with our model of SRP. Docking our model onto the bacterial ribosome suggests a mechanism for signal recognition involving interdomain movement of Ffh into and out of the nascent chain exit site and suggests how SRP could interact and/or compete with the ribosome-bound chaperone, trigger factor, for a nascent chain during translation.

Imaging electronic states on topological semimetals using scanning tunneling microscopy

DOE PAGES

Gyenis, András; Inoue, Hiroyuki; Jeon, Sangjun; ...

2016-10-18

Following the intense studies on topological insulators, significant efforts have recently been devoted to the search for gapless topological systems. These materials not only broaden the topological classification of matter but also provide a condensed matter realization of various relativistic particles and phenomena previously discussed mainly in high energy physics. Weyl semimetals host massless, chiral, low-energy excitations in the bulk electronic band structure, whereas a symmetry protected pair of Weyl fermions gives rise to massless Dirac fermions.Weemployed scanning tunneling microscopy/spectroscopy to explore the behavior of electronic states both on the surface and in the bulk of topological semimetal phases. Bymore » mapping the quasiparticle interference (QPI) and emerging Landau levels at high magnetic field in Dirac semimetals Cd 3As 2 and Na 3Bi, we observed extended Dirac-like bulk electronic bands. QPI imaged on Weyl semimetal TaAs demonstrated the predicted momentum dependent delocalization of Fermi arc surface states in the vicinity of the surface projected Weyl nodes.« less

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Imaging quantum transport using scanning gate microscopy

NASA Astrophysics Data System (ADS)

Hackens, Benoit

2014-03-01

Quantum transport in nanodevices is usually probed thanks to measurements of the electrical resistance or conductance, which lack the spatial resolution necessary to probe electron behaviour inside the devices. In this talk, we will show that scanning gate microscopy (SGM) yields real-space images of quantum transport phenomena inside archetypal mesoscopic devices such as quantum point contacts and quantum rings. We will first discuss the SGM technique, which is based on mapping the electrical conductance of a device as an electrically-biased sharp metallic tip scans in its vicinity. With SGM, we demonstrated low temperature imaging of the electron probability density and interferences in embedded mesoscopic quantum rings [B. Hackens et al., Nat. Phys. 2, 826 (2006)]. At high magnetic field, thanks to the SGM conductance maps, one can decrypt complex transport phenomena such as tunneling between quantum Hall edge state, either direct or through localized states [B. Hackens et al., Nat. Comm. 1, 39 (2010)]. Moreover, the technique also allows to perform local spectroscopy of electron transport through selected localized states [F. Martins et al., New J. of Phys. 15, 013049 (2013); F. Martins et al., Sci. Rep. 3, 1416 (2013)]. Overall, these examples show that scanning gate microscopy is a powerful tool for imaging charge carrier behavior inside devices fabricated from a variety of materials, and opens the way towards a more intimate manipulation of charge and quasiparticle transport. This work was performed in collaboration with F. Martins, S. Faniel, B. Brun, M. Pala, X. Wallart, L. Desplanque, B. Rosenow, T. Ouisse, H. Sellier, S. Huant and V. Bayot.

Failure analysis of explanted sternal wires.

PubMed

Shih, Chun-Ming; Su, Yea-Yang; Lin, Shing-Jong; Shih, Chun-Che

2005-05-01

To classify and understand the mechanisms of surface damages and fracture mechanisms of sternal wires, explanted stainless steel sternal wires were collected from patients with sternal dehiscence following open-heart surgery. Surface alterations and fractured ends of sternal wires were examined and analyzed. Eighty fractured wires extracted from 25 patients from January 1999 to December 2003, with mean implantation interval of 55+/-149 days (range 5-729 days) after cardiac surgery, were studied by various techniques. The extracted wires were cleaned and the fibrotic tissues were removed. Irregularities and fractured ends were assayed by a scanning electron microscopy. After stereomicroscopy and documentation, the explants were cleaned with 1% sodium hypochlorite to remove the blood and tissues and was followed by cleaned with deionized water and alcohol. The explants were examined by stereomicroscopy, and irregularities on surface and fracture surfaces of sternal wires were assayed by scanning electron microscopy, energy dispersive X-ray analysis (EDAX) and X-ray mapping. The explants with surrounding fibrotic tissue were stained and examined with stereomicroscopy and transmission electronic microscopy. Corrosion pits were found on the surface of explanted sternal wires. EDAX and X-ray mapping examinations revealed diminution of nickel concentration in the severely corroded pits on sternal wires. A feature of transgranular cracking was observed for stress corrosion cracking and striation character for typical corrosion fatigue was also identified. TEM examination of tissue showed the metallic particles in phagolysosomes of macrophages inside the surrounding sternal tissue. The synergic effect of hostile environment and the stress could be the precursors of failures for sternal wires.

Growth of single-layer graphene on Ge (1 0 0) by chemical vapor deposition

NASA Astrophysics Data System (ADS)

Mendoza, C. D.; Caldas, P. G.; Freire, F. L.; Maia da Costa, M. E. H.

2018-07-01

The integration of graphene into nanoelectronic devices is dependent on the availability of direct deposition processes, which can provide uniform, large-area and high-quality graphene on semiconductor substrates such as Ge or Si. In this work, we synthesised graphene directly on p-type Ge (1 0 0) substrates by chemical vapour deposition. The influence of the CH4:H2 flow ratio on the graphene growth was investigated. Raman Spectroscopy, Raman mapping, Scanning Electron Microscopy, Atomic Force Microscopy and Scanning Tunnelling Microscopy/Scanning Tunnelling Spectroscopy results showed that good quality and homogeneous monolayer graphene over a large area can be achieved on Ge substrates directly with optimal growth conditions.

Scanning Electron Microscope Mapping System Developed for Detecting Surface Defects in Fatigue Specimens

NASA Technical Reports Server (NTRS)

Bonacuse, Peter J.; Kantzos, Peter T.

2002-01-01

An automated two-degree-of-freedom specimen positioning stage has been developed at the NASA Glenn Research Center to map and monitor defects in fatigue specimens. This system expedites the examination of the entire gauge section of fatigue specimens so that defects can be found using scanning electron microscopy (SEM). Translation and rotation stages are driven by microprocessor-based controllers that are, in turn, interfaced to a computer running custom-designed software. This system is currently being used to find and record the location of ceramic inclusions in powder metallurgy materials. The mapped inclusions are periodically examined during interrupted fatigue experiments. The number of cycles to initiate cracks from these inclusions and the rate of growth of initiated cracks can then be quantified. This information is necessary to quantify the effect of this type of defect on the durability of powder metallurgy materials. This system was developed with support of the Ultra Safe program.

Role of the charge state of interface defects in electronic inhomogeneity evolution with gate voltage in graphene

NASA Astrophysics Data System (ADS)

Singh, Anil Kumar; Gupta, Anjan K.

2018-05-01

Evolution of electronic inhomogeneities with back-gate voltage in graphene on SiO2 was studied using room temperature scanning tunneling microscopy and spectroscopy. Reversal of contrast in some places in the conductance maps and sharp changes in cross correlations between topographic and conductance maps, when graphene Fermi energy approaches its Dirac point, are attributed to the change in charge state of interface defects. The spatial correlations in the conductance maps, described by two length scales, and their growth during approach to Dirac point, show a qualitative agreement with the predictions of the screening theory of graphene. Thus a sharp change in the two length scales close to the Dirac point, seen in our experiments, is interpreted in terms of the change in charge state of some of the interface defects. A systematic understanding and control of the charge state of defects can help in memory applications of graphene.

Atomic resolved phase map of monolayer MoS2 retrieved by spherical aberration-corrected transport of intensity equation.

PubMed

Zhang, Xiaobin; Oshima, Yoshifumi

2016-10-01

An atomic resolution phase map, which enables us to observe charge distribution or magnetic properties at an atomic scale, has been pointed out to be retrieved by transport of intensity equation (TIE) when taking two atomic-resolved transmission electron microscope (TEM) images of small defocus difference. In this work, we firstly obtained the atomic-resolved phase maps of an exfoliated molybdenum disulfide sheet using spherical aberration-corrected transmission electron microscope. We successfully observed 60° grain boundary of mechanically exfoliated monolayer molybdenum disulfide sheet. The relative phase shift of a single molybdenum atomic column to the column consisting of two sulfur atoms was obtained to be about 0.01 rad on average, which was about half lower than the simulated TIE phase map, indicating that the individual atomic sites can be distinguished qualitatively. The appropriate condition for retrieving atomic-resolved TIE phase maps was briefly discussed. © The Author 2016. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Quantitative Phase Fraction Detection in Organic Photovoltaic Materials through EELS Imaging

DOE PAGES

Dyck, Ondrej; Hu, Sheng; Das, Sanjib; ...

2015-11-24

Organic photovoltaic materials have recently seen intense interest from the research community. Improvements in device performance are occurring at an impressive rate; however, visualization of the active layer phase separation still remains a challenge. Our paper outlines the application of two electron energy-loss spectroscopic (EELS) imaging techniques that can complement and enhance current phase detection techniques. Specifically, the bulk plasmon peak position, often used to produce contrast between phases in energy filtered transmission electron microscopy (EFTEM), is quantitatively mapped across a sample cross section. One complementary spectrum image capturing the carbon and sulfur core loss edges is compared with themore » plasmon peak map and found to agree quite well, indicating that carbon and sulfur density differences between the two phases also allows phase discrimination. Additionally, an analytical technique for determining absolute atomic areal density is used to produce an absolute carbon and sulfur areal density map. We also show how these maps may be re-interpreted as a phase ratio map, giving quantitative information about the purity of the phases within the junction.« less

Nanoscale investigation of the degradation mechanism of a historical chrome yellow paint by quantitative electron energy loss spectroscopy mapping of chromium species.

PubMed

Tan, Haiyan; Tian, He; Verbeeck, Jo; Monico, Letizia; Janssens, Koen; Van Tendeloo, Gustaaf

2013-10-18

Getting the picture: The investigation of 100 year old chrome yellow paint by transmission electron microscopy and spectroscopy has led to the identification of four types of core-shell particles. This nanoscale investigation has allowed a mechanism to be proposed for the darkening of some bright yellow colors in Van Gogh's paintings (e.g. in Falling leaves (Les Alyscamps), 1888). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transmission Kikuchi diffraction and transmission electron forescatter imaging of electropolished and FIB manufactured TEM specimens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zieliński, W., E-mail: wiziel@inmat.pw.edu.pl; Płociński, T.; Kurzydłowski, K.J.

2015-06-15

We present a study of the efficiency of the utility of scanning electron microscope (SEM)-based transmission methods for characterizing grain structure in thinned bulk metals. Foils of type 316 stainless steel were prepared by two methods commonly used for transmission electron microscopy — double-jet electropolishing and focused ion beam milling. A customized holder allowed positioning of the foils in a configuration appropriate for both transmission electron forward scatter diffraction, and for transmission imaging by the use of a forescatter detector with two diodes. We found that both crystallographic orientation maps and dark-field transmitted images could be obtained for specimens preparedmore » by either method. However, for both methods, preparation-induced artifacts may affect the quality or accuracy of transmission SEM data, especially those acquired by the use of transmission Kikuchi diffraction. Generally, the quality of orientation data was better for specimens prepared by electropolishing, due to the absence of ion-induced damage. - Highlights: • The transmission imaging and diffraction techniques are emerging in scanning electron microscopy (SEM) as promising new field of materials characterization. • The manuscript titled: “Transmission Kikuchi Diffraction and Transmission Electron Forescatter Imaging of Electropolished and FIB Manufactured TEM Specimens” documents how different specimen thinning procedures can effect efficiency of transmission Kikuchi diffraction and transmission electron forescatter imaging. • The abilities to make precision crystallographic orientation maps and dark-field images in transmission was studied on electropolished versus focus ion beam manufactured TEM specimens. • Depending on the need, electropolished and focused ion beam technique may produce suitable specimens for transmission imaging and diffraction in SEM.« less

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

PubMed Central

Caulfield, Thomas R.; Devkota, Batsal; Rollins, Geoffrey C.

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16. PMID:21716650

Raman microscopy of freeze-dried mouse eyeball-slice in conjunction with the "in vivo cryotechnique".

PubMed

Terada, Nobuo; Ohno, Nobuhiko; Saitoh, Sei; Fujii, Yasuhisa; Ohguro, Hiroshi; Ohno, Shinichi

2007-07-01

The wavelength of Raman-scattered light depends on the molecular composition of the substance. This is the first attempt to acquire Raman spectra of a mouse eyeball removed from a living mouse, in which the eyeball was preserved using the "in vivo cryotechnique" followed by freeze-drying. Eyeballs were cryofixed using a rapid freezing cryotechnique, and then sliced in the cryostat machine. The slices were sandwiched between glass slides, freeze-dried, and analyzed with confocal Raman microscopy. Important areas including various eyeball tissue layers were selected using bright-field microscopy, and then the Raman spectra were obtained at 240 locations. Four typical patterns of Raman spectra were electronically mapped on the specimen images obtained by the bright-field microscopy. Tissue organization was confirmed by embedding the same eyeball slice used for Raman spectra into epoxy resin and the thick sections were prepared with the inverted capsule method. Each Raman spectral pattern represents a different histological layer in the eyeball which was mapped by comparing the images of toluidine blue staining and Raman mapping with different colors. In the choroid and pigment cell layer, the Raman spectrum had two peaks, corresponding to melanin. Some of the peaks of the Raman spectra obtained from the blood vessels in sclera and the photoreceptor layer were similar to those obtained from the purified hemoglobin and rhodopsin proteins, respectively. Our experimental protocol can distinguish different tissue components with Raman microscopy; therefore, this method can be very useful for examining the distribution of a biological structures and/or chemical components in rapidly frozen freeze-dried tissue.

X-Ray Absorption Microspectroscopy with Electrostatic Force Microscopy and its Application to Chemical States Mapping

NASA Astrophysics Data System (ADS)

Ishii, M.; Rigopoulos, N.; Poolton, N. R. J.; Hamilton, B.

2007-02-01

A new technique named X-EFM that measures the x-ray absorption fine structure (XAFS) of nanometer objects was developed. In X-EFM, electrostatic force microscopy (EFM) is used as an x-ray absorption detector, and photoionization induced by x-ray absorption of surface electron trapping sites is detected by EFM. An EFM signal with respect to x-ray photon energy provides the XAFS spectra of the trapping sites. We adopted X-EFM to observe Si oxide thin films. An edge jump shift intrinsic to the X-EFM spectrum was found, and it was explained with a model where an electric field between the trapping site and probe deepens the energy level of the inner-shell. A scanning probe under x-rays with fixed photon energy provided the chemical state mapping on the surface.

Field emission scanning electron microscopy (FE-SEM) as an approach for nanoparticle detection inside cells.

PubMed

Havrdova, M; Polakova, K; Skopalik, J; Vujtek, M; Mokdad, A; Homolkova, M; Tucek, J; Nebesarova, J; Zboril, R

2014-12-01

When developing new nanoparticles for bio-applications, it is important to fully characterize the nanoparticle's behavior in biological systems. The most common techniques employed for mapping nanoparticles inside cells include transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). These techniques entail passing an electron beam through a thin specimen. STEM or TEM imaging is often used for the detection of nanoparticles inside cellular organelles. However, lengthy sample preparation is required (i.e., fixation, dehydration, drying, resin embedding, and cutting). In the present work, a new matrix (FTO glass) for biological samples was used and characterized by field emission scanning electron microscopy (FE-SEM) to generate images comparable to those obtained by TEM. Using FE-SEM, nanoparticle images were acquired inside endo/lysosomes without disruption of the cellular shape. Furthermore, the initial steps of nanoparticle incorporation into the cells were captured. In addition, the conductive FTO glass endowed the sample with high stability under the required accelerating voltage. Owing to these features of the sample, further analyses could be performed (material contrast and energy-dispersive X-ray spectroscopy (EDS)), which confirmed the presence of nanoparticles inside the cells. The results showed that FE-SEM can enable detailed characterization of nanoparticles in endosomes without the need for contrast staining or metal coating of the sample. Images showing the intracellular distribution of nanoparticles together with cellular morphology can give important information on the biocompatibility and demonstrate the potential of nanoparticle utilization in medicine. Copyright © 2014 Elsevier Ltd. All rights reserved.

RAPID COMMUNICATION: Study of superstructure II in multiferroic BiMnO3

NASA Astrophysics Data System (ADS)

Ge, Bing-Hui; Li, Fang-Hua; Li, Xue-Ming; Wang, Yu-Mei; Chi, Zhen-Hua; Jin, Chang-Qing

2008-09-01

The crystal structure of the minor phase, named superstructure II, existing in multiferroic compound BiMnO3 has been studied by electron diffraction and high-resolution transmission electron microscopy. Domains of major and minor phases coexisting in BiMnO3 were observed in high-resolution electron microscope images. The unit cell of minor phase was determined to be triclinic with the size 4×4×4 times as large as the distorted perovskite subcell. The [111] and [10bar 1] projected structure maps of the minor phase have been derived from the corresponding images by means of the image processing. A possible rough three-dimensional (3D) structure model was proposed based on the 3D structural information extracted from the two projected structure maps. Since there is no inversion centre in the proposed model, the minor phase may contribute to the ferroelectric property of BiMnO3.

Determination of the five parameter grain boundary character distribution of nanocrystalline alpha-zirconium thin films using transmission electron microscopy

DOE PAGES

Ghamarian, I.; Samani, P.; Rohrer, G. S.; ...

2017-03-24

Grain boundary engineering and other fundamental materials science problems (e.g., phase transformations and physical properties) require an improvement in the understanding of the type and population of grain boundaries in a given system – yet, databases are limited in number and spare in detail, including for hcp crystals such as zirconium. One way to rapidly obtain databases to analyze is to use small-grained materials and high spatial resolution orientation microscopy techniques, such as ASTAR™/precession electron diffraction. To demonstrate this, a study of grain boundary character distributions was conducted for α-zirconium deposited at room temperature on fused silica substrates using physicalmore » vapor deposition. The orientation maps of the nanocrystalline thin films were acquired by the ASTARα/precession electron diffraction technique, a new transmission electron microscope based orientation microscopy method. The reconstructed grain boundaries were classified as pure tilt, pure twist, 180°-twist and 180°-tilt grain boundaries based on the distribution of grain boundary planes with respect to the angle/axis of misorientation associated with grain boundaries. The results of the current study were compared to the results of a similar study on α-titanium and the molecular dynamics results of grain boundary energy for α-titanium.« less

A pseudo-tetragonal tungsten bronze superstructure: a combined solution of the crystal structure of K6.4(Nb,Ta)(36.3)O94 with advanced transmission electron microscopy and neutron diffraction.

PubMed

Paria Sena, Robert; Babaryk, Artem A; Khainakov, Sergiy; Garcia-Granda, Santiago; Slobodyanik, Nikolay S; Van Tendeloo, Gustaaf; Abakumov, Artem M; Hadermann, Joke

2016-01-21

The crystal structure of the K6.4Nb28.2Ta8.1O94 pseudo-tetragonal tungsten bronze-type oxide was determined using a combination of X-ray powder diffraction, neutron diffraction and transmission electron microscopy techniques, including electron diffraction, high angle annular dark field scanning transmission electron microscopy (HAADF-STEM), annular bright field STEM (ABF-STEM) and energy-dispersive X-ray compositional mapping (STEM-EDX). The compound crystallizes in the space group Pbam with unit cell parameters a = 37.468(9) Å, b = 12.493(3) Å, c = 3.95333(15) Å. The structure consists of corner sharing (Nb,Ta)O6 octahedra forming trigonal, tetragonal and pentagonal tunnels. All tetragonal tunnels are occupied by K(+) ions, while 1/3 of the pentagonal tunnels are preferentially occupied by Nb(5+)/Ta(5+) and 2/3 are occupied by K(+) in a regular pattern. A fractional substitution of K(+) in the pentagonal tunnels by Nb(5+)/Ta(5+) is suggested by the analysis of the HAADF-STEM images. In contrast to similar structures, such as K2Nb8O21, also parts of the trigonal tunnels are fractionally occupied by K(+) cations.

Three-dimensional locations of gold-labeled proteins in a whole mount eukaryotic cell obtained with 3nm precision using aberration-corrected scanning transmission electron microscopy.

PubMed

Dukes, Madeline J; Ramachandra, Ranjan; Baudoin, Jean-Pierre; Gray Jerome, W; de Jonge, Niels

2011-06-01

Three-dimensional (3D) maps of proteins within the context of whole cells are important for investigating cellular function. However, 3D reconstructions of whole cells are challenging to obtain using conventional transmission electron microscopy (TEM). We describe a methodology to determine the 3D locations of proteins labeled with gold nanoparticles on whole eukaryotic cells. The epidermal growth factor receptors on COS7 cells were labeled with gold nanoparticles, and critical-point dried whole-mount cell samples were prepared. 3D focal series were obtained with aberration-corrected scanning transmission electron microscopy (STEM), without tilting the specimen. The axial resolution was improved with deconvolution. The vertical locations of the nanoparticles in a whole-mount cell were determined with a precision of 3nm. From the analysis of the variation of the axial positions of the labels we concluded that the cellular surface was ruffled. To achieve sufficient stability of the sample under electron beam irradiation during the recording of the focal series, the sample was carbon coated. A quantitative method was developed to analyze the stability of the ultrastructure after electron beam irradiation using TEM. The results of this study demonstrate the feasibility of using aberration-corrected STEM to study the 3D nanoparticle distribution in whole cells. Copyright © 2011 Elsevier Inc. All rights reserved.

Atomic-scale mapping of electronic structures across heterointerfaces by cross-sectional scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Chiu, Ya-Ping; Huang, Bo-Chao; Shih, Min-Chuan; Huang, Po-Cheng; Chen, Chun-Wei

2015-09-01

Interfacial science has received much attention recently based on the development of state-of-the-art analytical tools that can create and manipulate the charge, spin, orbital, and lattice degrees of freedom at interfaces. Motivated by the importance of nanoscale interfacial science that governs device operation, we present a technique to probe the electronic characteristics of heterointerfaces with atomic resolution. In this work, the interfacial characteristics of heteroepitaxial structures are investigated and the fundamental mechanisms that pertain in these systems are elucidated through cross-sectional scanning tunneling microscopy (XSTM). The XSTM technique is employed here to directly observe epitaxial interfacial structures and probe local electronic properties with atomic-level capability. Scanning tunneling microscopy and spectroscopy experiments with atomic precision provide insight into the origin and spatial distribution of electronic properties across heterointerfaces. The first part of this report provides a brief description of the cleavage technique and spectroscopy analysis in XSTM measurements. The second part addresses interfacial electronic structures of several model heterostructures in current condensed matter research using XSTM. Topics to be discussed include high-κ‘s/III-V’s semiconductors, polymer heterojunctions, and complex oxide heterostructures, which are all material systems whose investigation using this technique is expected to benefit the research community. Finally, practical aspects and perspectives of using XSTM in interface science are presented.

Three-dimensional locations of gold-labeled proteins in a whole mount eukaryotic cell obtained with 3 nm precision using aberration-corrected scanning transmission electron microscopy

PubMed Central

Dukes, Madeline J.; Ramachandra, Ranjan; Baudoin, Jean-Pierre; Jerome, W. Gray; de Jonge, Niels

2011-01-01

Three-dimensional (3D) maps of proteins within the context of whole cells are important for investigating cellular function. However, 3D reconstructions of whole cells are challenging to obtain using conventional transmission electron microscopy (TEM). We describe a methodology to determine the 3D locations of proteins labeled with gold nanoparticles on whole eukaryotic cells. The epidermal growth factor receptors on COS7 cells were labeled with gold nanoparticles, and critical-point dried whole-mount cell samples were prepared. 3D focal series were obtained with aberration-corrected scanning transmission electron microscopy (STEM), without tilting the specimen. The axial resolution was improved with deconvolution. The vertical locations of the nanoparticles in a whole-mount cell were determined with a precision of 3 nm. From the analysis of the variation of the axial positions of the labels we concluded that the cellular surface was ruffled. To achieve sufficient stability of the sample under the electron beam irradiation during the recording of the focal series, the sample was carbon coated. A quantitative method was developed to analyze the stability of the ultrastructure after electron beam irradiation using TEM. The results of this study demonstrate the feasibility of using aberration-corrected STEM to study the 3D nanoparticle distribution in whole cells. PMID:21440635

High-Resolution Structural and Electronic Properties of Epitaxial Topological Crystalline Insulator Films

NASA Astrophysics Data System (ADS)

Dagdeviren, Omur; Zhou, Chao; Zou, Ke; Simon, Georg; Albright, Stephen; Mandal, Subhasish; Morales-Acosta, Mayra; Zhu, Xiaodong; Ismail-Beigi, Sohrab; Walker, Frederick; Ahn, Charles; Schwarz, Udo; Altman, Eric

Revealing the local electronic properties of surfaces and their link to structural properties is an important problem for topological crystalline insulators (TCI) in which metallic surface states are protected by crystal symmetry. The microstructure and electronic properties of TCI SnTe film surfaces grown by molecular beam epitaxy were characterized using scanning probe microscopy. These results reveal the influence of various defects on the electronic properties: tilt boundaries leading to dislocation arrays that serve as periodic nucleation sites for pit growth; screw dislocations, and point defects. These features have varying length scale and display variations in the electronic structure of the surface, which are mapped with scanning tunneling microscopy images as standing waves superimposed on atomic scale images of the surface topography that consequently shape the wave patterns. Since the growth process results in symmetry breaking defects that patterns the topological states, we propose that the scanning probe tip can pattern the surface and electronic structure and enable the fabrication of topological devices on the SnTe surface. Financial support from the National Science Foundation through the Yale Materials Research Science and Engineering Center (Grant No. MRSEC DMR-1119826) and FAME.

Analysis of acute brain slices by electron microscopy: a correlative light-electron microscopy workflow based on Tokuyasu cryo-sectioning.

PubMed

Loussert Fonta, Celine; Leis, Andrew; Mathisen, Cliff; Bouvier, David S; Blanchard, Willy; Volterra, Andrea; Lich, Ben; Humbel, Bruno M

2015-01-01

Acute brain slices are slices of brain tissue that are kept vital in vitro for further recordings and analyses. This tool is of major importance in neurobiology and allows the study of brain cells such as microglia, astrocytes, neurons and their inter/intracellular communications via ion channels or transporters. In combination with light/fluorescence microscopies, acute brain slices enable the ex vivo analysis of specific cells or groups of cells inside the slice, e.g. astrocytes. To bridge ex vivo knowledge of a cell with its ultrastructure, we developed a correlative microscopy approach for acute brain slices. The workflow begins with sampling of the tissue and precise trimming of a region of interest, which contains GFP-tagged astrocytes that can be visualised by fluorescence microscopy of ultrathin sections. The astrocytes and their surroundings are then analysed by high resolution scanning transmission electron microscopy (STEM). An important aspect of this workflow is the modification of a commercial cryo-ultramicrotome to observe the fluorescent GFP signal during the trimming process. It ensured that sections contained at least one GFP astrocyte. After cryo-sectioning, a map of the GFP-expressing astrocytes is established and transferred to correlation software installed on a focused ion beam scanning electron microscope equipped with a STEM detector. Next, the areas displaying fluorescence are selected for high resolution STEM imaging. An overview area (e.g. a whole mesh of the grid) is imaged with an automated tiling and stitching process. In the final stitched image, the local organisation of the brain tissue can be surveyed or areas of interest can be magnified to observe fine details, e.g. vesicles or gold labels on specific proteins. The robustness of this workflow is contingent on the quality of sample preparation, based on Tokuyasu's protocol. This method results in a reasonable compromise between preservation of morphology and maintenance of antigenicity. Finally, an important feature of this approach is that the fluorescence of the GFP signal is preserved throughout the entire preparation process until the last step before electron microscopy. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Investigating Antibacterial Effects of Garlic (Allium sativum) Concentrate and Garlic-Derived Organosulfur Compounds on Campylobacter jejuni by Using Fourier Transform Infrared Spectroscopy, Raman Spectroscopy, and Electron Microscopy ▿ †

PubMed Central

Lu, Xiaonan; Rasco, Barbara A.; Jabal, Jamie M. F.; Aston, D. Eric; Lin, Mengshi; Konkel, Michael E.

2011-01-01

Fourier transform infrared (FT-IR) spectroscopy and Raman spectroscopy were used to study the cell injury and inactivation of Campylobacter jejuni from exposure to antioxidants from garlic. C. jejuni was treated with various concentrations of garlic concentrate and garlic-derived organosulfur compounds in growth media and saline at 4, 22, and 35°C. The antimicrobial activities of the diallyl sulfides increased with the number of sulfur atoms (diallyl sulfide < diallyl disulfide < diallyl trisulfide). FT-IR spectroscopy confirmed that organosulfur compounds are responsible for the substantial antimicrobial activity of garlic, much greater than those of garlic phenolic compounds, as indicated by changes in the spectral features of proteins, lipids, and polysaccharides in the bacterial cell membranes. Confocal Raman microscopy (532-nm-gold-particle substrate) and Raman mapping of a single bacterium confirmed the intracellular uptake of sulfur and phenolic components. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed to verify cell damage. Principal-component analysis (PCA), discriminant function analysis (DFA), and soft independent modeling of class analogs (SIMCA) were performed, and results were cross validated to differentiate bacteria based upon the degree of cell injury. Partial least-squares regression (PLSR) was employed to quantify and predict actual numbers of healthy and injured bacterial cells remaining following treatment. PLSR-based loading plots were investigated to further verify the changes in the cell membrane of C. jejuni treated with organosulfur compounds. We demonstrated that bacterial injury and inactivation could be accurately investigated by complementary infrared and Raman spectroscopies using a chemical-based, “whole-organism fingerprint” with the aid of chemometrics and electron microscopy. PMID:21642409

Improving Signal-to-Noise Ratio in Scanning Transmission Electron Microscopy Energy-Dispersive X-Ray (STEM-EDX) Spectrum Images Using Single-Atomic-Column Cross-Correlation Averaging.

PubMed

Jeong, Jong Seok; Mkhoyan, K Andre

2016-06-01

Acquiring an atomic-resolution compositional map of crystalline specimens has become routine practice, thus opening possibilities for extracting subatomic information from such maps. A key challenge for achieving subatomic precision is the improvement of signal-to-noise ratio (SNR) of compositional maps. Here, we report a simple and reliable solution for achieving high-SNR energy-dispersive X-ray (EDX) spectroscopy spectrum images for individual atomic columns. The method is based on standard cross-correlation aided by averaging of single-column EDX maps with modifications in the reference image. It produces EDX maps with minimal specimen drift, beam drift, and scan distortions. Step-by-step procedures to determine a self-consistent reference map with a discussion on the reliability, stability, and limitations of the method are presented here.

PVP-Assisted Synthesis of Uniform Carbon Coated Li2S/CB for High-Performance Lithium-Sulfur Batteries.

PubMed

Chen, Lin; Liu, Yuzi; Zhang, Fan; Liu, Caihong; Shaw, Leon L

2015-11-25

The lithium-sulfur (Li-S) battery is a great alternative to the state-of-the-art lithium ion batteries due to its high energy density. However, low utilization of active materials, the insulating nature of sulfur or lithium sulfide (Li2S), and polysulfide dissolution in organic liquid electrolyte lead to low initial capacity and fast performance degradation. Herein, we propose a facile and viable approach to address these issues. This new approach entails synthesis of Li2S/carbon black (Li2S/CB) cores encapsulated by a nitrogen-doped carbon shell with polyvinylpyrrolidone (PVP) assistance. Combining energy-filtered transmission electron microscopy (EFTEM) elemental mappings, XPS and FTIR measurements, it is confirmed that the as-synthesized material has a structure of a Li2S/CB core with a nitrogen-doped carbon shell (denoted as Li2S/CB@NC). The Li2S/CB@NC cathode yields an exceptionally high initial capacity of 1020 mAh/g based on Li2S mass at 0.1 C with stable Coulombic efficiency of 99.7% over 200 cycles. Also, cycling performance shows the capacity decay per cycle as small as 0.17%. Most importantly, to further understand the materials for battery applications, field emission transmission electron microscopy (FETEM) and elemental mapping tests without exposure to air for Li2S samples in cycled cells are reported. Along with the first ever FETEM and field emission scanning electron microscopy (FESEM) investigations of cycled batteries, Li2S/CB@NC cathode demonstrates the capability of robust core-shell nanostructures for different rates and improved capacity retention, revealing Li2S/CB@NC designed here as an outstanding system for high-performance lithium-sulfur batteries.

Conventions and workflows for using Situs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wriggers, Willy, E-mail: wriggers@biomachina.org

2012-04-01

Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described. Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs tomore » be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed.« less

HRTEMFringeAnalyzer a free python module for an automated analysis of fringe pattern in transmission electron micrographs.

PubMed

Alxneit, Ivo

2018-03-30

A python module (HRTEMFringeAnalyzer) is reported to evaluate the local crystallinity of samples from high-resolution transmission electron microscopy images in a mostly automated fashion. The user only selects the size of a square analyser window and a step size which translates the window in the micrograph. Together they define the resolution of the results obtained. Regions where fringe patterns are visible are identified and their lattice spacing d and direction ϕ as well as the corresponding mean errors σ determined. 1/σd is proportional to the coherence length of the structure, whereas σφ is a measure of how well the direction of the fringes is defined. Maps of these four indicators are computed. The performance of the program is demonstrated on two very different samples: ill-crystalline carbon deposits on a coked Ni/LFNO (reduced LaFe 0.8 Ni 0.2 O3±δ) catalyst and well-crystallized nanoparticles of zinc doped ceria. In the latter case, the automatic segmentation of large aggregates into individual crystalline domains is achieved by ϕ maps. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

DOE PAGES

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; ...

2016-03-30

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtainmore » 14 density maps at ~ 2-nm resolution . Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.« less

Mapping carrier diffusion in single silicon core-shell nanowires with ultrafast optical microscopy.

PubMed

Seo, M A; Yoo, J; Dayeh, S A; Picraux, S T; Taylor, A J; Prasankumar, R P

2012-12-12

Recent success in the fabrication of axial and radial core-shell heterostructures, composed of one or more layers with different properties, on semiconductor nanowires (NWs) has enabled greater control of NW-based device operation for various applications. (1-3) However, further progress toward significant performance enhancements in a given application is hindered by the limited knowledge of carrier dynamics in these structures. In particular, the strong influence of interfaces between different layers in NWs on transport makes it especially important to understand carrier dynamics in these quasi-one-dimensional systems. Here, we use ultrafast optical microscopy (4) to directly examine carrier relaxation and diffusion in single silicon core-only and Si/SiO(2) core-shell NWs with high temporal and spatial resolution in a noncontact manner. This enables us to reveal strong coherent phonon oscillations and experimentally map electron and hole diffusion currents in individual semiconductor NWs for the first time.

Nanoscale elasticity mappings of micro-constituents of abalone shell by band excitation-contact resonance force microscopy

NASA Astrophysics Data System (ADS)

Li, Tao; Zeng, Kaiyang

2014-01-01

The macroscopic mechanical properties of the abalone shell have been studied extensively in the literature, but the in situ nanoscale elasticity of various micro-constituents in the shell have not been characterized and reported yet. In this study, the nanoscale elasticity mappings including different micro-constituents in abalone shell were observed by using the Contact Resonance Force Microscopy (CR-FM) technique. CR-FM is one of the advanced scanning probe microscopy techniques that is able to quantify the local elastic moduli of various materials in a non-destructive manner. Instead of an average value, an elasticity mapping that reveals the nanoscale variations of elastic moduli with location can be extracted and correlated with the topography of the structure. Therefore in this study, by adopting the CR-FM technique that is incorporated with the band excitation technique, the elasticity variations of the abalone shell caused by different micro-constituents and crystal orientations are reported, and the elasticity values of the aragonite and calcite nanograins are quantified.The macroscopic mechanical properties of the abalone shell have been studied extensively in the literature, but the in situ nanoscale elasticity of various micro-constituents in the shell have not been characterized and reported yet. In this study, the nanoscale elasticity mappings including different micro-constituents in abalone shell were observed by using the Contact Resonance Force Microscopy (CR-FM) technique. CR-FM is one of the advanced scanning probe microscopy techniques that is able to quantify the local elastic moduli of various materials in a non-destructive manner. Instead of an average value, an elasticity mapping that reveals the nanoscale variations of elastic moduli with location can be extracted and correlated with the topography of the structure. Therefore in this study, by adopting the CR-FM technique that is incorporated with the band excitation technique, the elasticity variations of the abalone shell caused by different micro-constituents and crystal orientations are reported, and the elasticity values of the aragonite and calcite nanograins are quantified. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr05292c

Correlation mapping microscopy

NASA Astrophysics Data System (ADS)

McGrath, James; Alexandrov, Sergey; Owens, Peter; Subhash, Hrebesh M.; Leahy, Martin J.

2015-03-01

Changes in the microcirculation are associated with conditions such as Raynauds disease. Current modalities used to assess the microcirculation such as nailfold capillaroscopy are limited due to their depth ambiguity. A correlation mapping technique was recently developed to extend the capabilities of Optical Coherence Tomography to generate depth resolved images of the microcirculation. Here we present the extension of this technique to microscopy modalities, including confocal microscopy. It is shown that this correlation mapping microscopy technique can extend the capabilities of conventional microscopy to enable mapping of vascular networks in vivo with high spatial resolution.

Using Synchrotron Radiation and Electron Microscopy to Map the Huge Structural Changes that Occur in Viruses During Their Life Cycle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rossman, Michael

2011-09-07

The crystallographic techniques for structure determination of proteins and neucleic acids at near atomic resolution using synchrotron X-radiation has become almost automatic. However the limits of this procedure are determined by the availability of crystals. As the size and complexity of the molecular assemblies being studied increases, the likelihood of growing useful crystals diminishes. Cryo electron microscopy and tomography have extended the range of biological objects that can be determined at near atomic resolution. Furthermore it is now becoming apparent that the function of the molecular assemblies most often requires very large conformational changes that could never be contained withinmore » a crystal, Examples will be presented of the structural changes that occur in viruses as they assembly and prepare to infect new cells.« less

Tem Observation of Precipitates in Ag-Added Al-Mg-Si Alloys

NASA Astrophysics Data System (ADS)

Nagai, Takeshi; Matsuda, Kenji; Nakamura, Junya; Kawabata, Tokimasa; Marioara, Calin; Andersen, Sigmund J.; Holmestad, Randi; Hirosawa, Shoichi; Horita, Zenji; Terada, Daisuke; Ikeno, Susumu

The influence of addition of the small amount of transition metals to Al-Mg-Si alloy had reported by many researchers. In the previous our work, β' phase in alloys Al — 1.0 mass% Mg2Si -0.5 mass% Ag (Ag-addition) and Al -1.0 mass% Mg2Si (base) were investigated by high resolution transmission electron microscopy (HRTEM) and selected area electron diffraction (SAED), in order to understand the effect of Ag. In addition, the distribution of Ag was investigated by energy filtered mapping and high annular angular dark field scanning transmission electron microscopy (HAADF-STEM). One Ag-containing atomic column was observed per β' unit cell, and the unit cell symmetry is slightly changed as compared with the Ag-free β'. In this work, the microstructure of G.P. zone and β'' phase was investigated by TEM observation, which were formed before β' phase. The deformed sample by high pressure torsion (HPT) technique before aging was also investigated to understand its effect for aging in this alloy.

Challenges in quantitative crystallographic characterization of 3D thin films by ACOM-TEM.

PubMed

Kobler, A; Kübel, C

2017-02-01

Automated crystal orientation mapping for transmission electron microscopy (ACOM-TEM) has become an easy to use method for the investigation of crystalline materials and complements other TEM methods by adding local crystallographic information over large areas. It fills the gap between high resolution electron microscopy and electron back scatter diffraction in terms of spatial resolution. Recent investigations showed that spot diffraction ACOM-TEM is a quantitative method with respect to sample parameters like grain size, twin density, orientation density and others. It can even be used in combination with in-situ tensile or thermal testing. However, there are limitations of the current method. In this paper we discuss some of the challenges and discuss solutions, e.g. we present an ambiguity filter that reduces the number of pixels with a '180° ambiguity problem'. For that an ACOM-TEM tilt series of nanocrystalline Pd thin films with overlapping crystallites was acquired and analyzed. Copyright © 2017. Published by Elsevier B.V.

Visible cathodoluminescence of Er ions in β-Ga(2)O(3) nanowires and microwires.

PubMed

Nogales, E; Méndez, B; Piqueras, J

2008-01-23

Erbium doped β-Ga(2)O(3) nanowires and microwires have been obtained by a vapour-solid process from an initial mixture of Ga(2)O(3) and Er(2)O(3) powders. X-ray diffraction (XRD) analysis reveals the presence of erbium gallium garnet as well as β-Ga(2)O(3) phases in the microwires. Scanning electron microscopy (SEM) images show that the larger microwires have a nearly rectangular cross-section. Transmission electron microscopy (TEM) and high-resolution TEM (HRTEM) analysis show good crystal quality of the β-Ga(2)O(3) nanowires. The nanostructures have been studied by means of the cathodoluminescence technique in the scanning electron microscope. Er intraionic blue, green and red emission lines are observed in luminescence spectra even at room temperature, which confirms the optical activity of the rare earth ions in the grown structures. Mapping of the main 555 nm emission intensity shows a non-homogeneous distribution of Er ions in the microstructures.

Determination of domain wall chirality using in situ Lorentz transmission electron microscopy

DOE PAGES

Chess, Jordan J.; Montoya, Sergio A.; Fullerton, Eric E.; ...

2017-02-23

Controlling domain wall chirality is increasingly seen in non-centrosymmetric materials. Mapping chiral magnetic domains requires knowledge about all the vector components of the magnetization, which poses a problem for conventional Lorentz transmission electron microscopy (LTEM) that is only sensitive to magnetic fields perpendicular to the electron beams direction of travel. The standard approach in LTEM for determining the third component of the magnetization is to tilt the sample to some angle and record a second image. Furthermore, this presents a problem for any domain structures that are stabilized by an applied external magnetic field (e.g. skyrmions), because the standard LTEMmore » setup does not allow independent control of the angle of an applied magnetic field, and sample tilt angle. Here we show that applying a modified transport of intensity equation analysis to LTEM images collected during an applied field sweep, we can determine the domain wall chirality of labyrinth domains in a perpendicularly magnetized material, avoiding the need to tilt the sample.« less

Determination of domain wall chirality using in situ Lorentz transmission electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chess, Jordan J.; Montoya, Sergio A.; Fullerton, Eric E.

Controlling domain wall chirality is increasingly seen in non-centrosymmetric materials. Mapping chiral magnetic domains requires knowledge about all the vector components of the magnetization, which poses a problem for conventional Lorentz transmission electron microscopy (LTEM) that is only sensitive to magnetic fields perpendicular to the electron beams direction of travel. The standard approach in LTEM for determining the third component of the magnetization is to tilt the sample to some angle and record a second image. Furthermore, this presents a problem for any domain structures that are stabilized by an applied external magnetic field (e.g. skyrmions), because the standard LTEMmore » setup does not allow independent control of the angle of an applied magnetic field, and sample tilt angle. Here we show that applying a modified transport of intensity equation analysis to LTEM images collected during an applied field sweep, we can determine the domain wall chirality of labyrinth domains in a perpendicularly magnetized material, avoiding the need to tilt the sample.« less

Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography

DOE PAGES

Lei, Dongsheng; Marras, Alexander E.; Liu, Jianfang; ...

2018-02-09

Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. In this paper, we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~6-14 nm resolution. The statisticalmore » analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.« less

Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lei, Dongsheng; Marras, Alexander E.; Liu, Jianfang

Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. In this paper, we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~6-14 nm resolution. The statisticalmore » analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.« less

Nanoscale imaging of whole cells using a liquid enclosure and a scanning transmission electron microscope.

PubMed

Peckys, Diana B; Veith, Gabriel M; Joy, David C; de Jonge, Niels

2009-12-14

Nanoscale imaging techniques are needed to investigate cellular function at the level of individual proteins and to study the interaction of nanomaterials with biological systems. We imaged whole fixed cells in liquid state with a scanning transmission electron microscope (STEM) using a micrometer-sized liquid enclosure with electron transparent windows providing a wet specimen environment. Wet-STEM images were obtained of fixed E. coli bacteria labeled with gold nanoparticles attached to surface membrane proteins. Mammalian cells (COS7) were incubated with gold-tagged epidermal growth factor and fixed. STEM imaging of these cells resulted in a resolution of 3 nm for the gold nanoparticles. The wet-STEM method has several advantages over conventional imaging techniques. Most important is the capability to image whole fixed cells in a wet environment with nanometer resolution, which can be used, e.g., to map individual protein distributions in/on whole cells. The sample preparation is compatible with that used for fluorescent microscopy on fixed cells for experiments involving nanoparticles. Thirdly, the system is rather simple and involves only minimal new equipment in an electron microscopy (EM) laboratory.

An investigation into the surface heterogeneity of nitric acid oxidized carbon fiber

NASA Astrophysics Data System (ADS)

Woodhead, Andrea L.; de Souza, Mandy L.; Church, Jeffrey S.

2017-04-01

The carbon fiber surface plays a critical role in the performance of carbon fiber composite materials and, thus it is important to have a thorough understanding of the fiber surface. A series of nitric acid treated intermediate modulus carbon fibers with increasing treatment level was prepared and characterized using a range of surface sensitive techniques including Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), X-ray Photoelectron Spectroscopy (XPS) and Raman spectroscopy. The results, which were found to be consistent with increasing treatment levels, were compared to the literature. Raman spectral mapping has been used to investigate the heterogeneity of the carbon fiber surface after nitric acid oxidation. The mapping enabled the effects of surface treatment on carbon fiber to be investigated at a spatial resolution unattainable by XPS and provided chemical structure information not provided by SEM or AFM. The highest level of treatment resulted in the most heterogeneous surface. Raman mapping, while time consuming, can provide valuable information which can lead to an enhanced understanding of the heterogeneity of the carbon fiber surface.

Surface compositional profiles of self-assembled InAs/GaAs quantum rings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magri, Rita; Heun, Stefan; Biasiol, Giorgio

2010-01-04

The surface composition profiles of self-assembled InAs/GaAs quantum rings (QR) are studied both experimentally and theoretically. By using X-ray Photoemission Electron Microscopy (XPEEM) we obtain a 2D composition mapping of unburied rings, which can be directly related to the QR topography measured by Atomic Force Microscopy (AFM). Top-surface composition mapping allows us to obtain information on structures which cannot be directly accessed with cross-sectional studies since overgrowing the QRs with a thick GaAs film alters both their morphology and composition. The 2D surface maps reveal a non-uniform distribution across the rings with an In richer InGaAs alloy in the centralmore » hole regions. Elastic energy calculations via a Valence Force Field (VFF) approach show that, for a given shape of the rings and a fixed total number of Ga and In atoms, an In enrichment of the alloy in the central hole region, together with an In enrichment of the surface layers, leads to a lowering of the total strain energy.« less

Mapping of Heavy Metal Ion Sorption to Cell-Extracellular Polymeric Substance-Mineral Aggregates by Using Metal-Selective Fluorescent Probes and Confocal Laser Scanning Microscopy

PubMed Central

Li, Jianli; Kappler, Andreas; Obst, Martin

2013-01-01

Biofilms, organic matter, iron/aluminum oxides, and clay minerals bind toxic heavy metal ions and control their fate and bioavailability in the environment. The spatial relationship of metal ions to biomacromolecules such as extracellular polymeric substances (EPS) in biofilms with microbial cells and biogenic minerals is complex and occurs at the micro- and submicrometer scale. Here, we review the application of highly selective and sensitive metal fluorescent probes for confocal laser scanning microscopy (CLSM) that were originally developed for use in life sciences and propose their suitability as a powerful tool for mapping heavy metals in environmental biofilms and cell-EPS-mineral aggregates (CEMAs). The benefit of using metal fluorescent dyes in combination with CLSM imaging over other techniques such as electron microscopy is that environmental samples can be analyzed in their natural hydrated state, avoiding artifacts such as aggregation from drying that is necessary for analytical electron microscopy. In this minireview, we present data for a group of sensitive fluorescent probes highly specific for Fe3+, Cu2+, Zn2+, and Hg2+, illustrating the potential of their application in environmental science. We evaluate their application in combination with other fluorescent probes that label constituents of CEMAs such as DNA or polysaccharides and provide selection guidelines for potential combinations of fluorescent probes. Correlation analysis of spatially resolved heavy metal distributions with EPS and biogenic minerals in their natural, hydrated state will further our understanding of the behavior of metals in environmental systems since it allows for identifying bonding sites in complex, heterogeneous systems. PMID:23974141

Investigation of AlGaN/GaN high electron mobility transistor structures on 200-mm silicon (111) substrates employing different buffer layer configurations.

PubMed

Lee, H-P; Perozek, J; Rosario, L D; Bayram, C

2016-11-21

AlGaN/GaN high electron mobility transistor (HEMT) structures are grown on 200-mm diameter Si(111) substrates by using three different buffer layer configurations: (a) Thick-GaN/3 × {Al x Ga 1-x N}/AlN, (b) Thin-GaN/3 × {Al x Ga 1-x N}/AlN, and (c) Thin-GaN/AlN, so as to have crack-free and low-bow (<50 μm) wafer. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, high resolution-cross section transmission electron microscopy, optical microscopy, atomic-force microscopy, cathodoluminescence, Raman spectroscopy, X-ray diffraction (ω/2θ scan and symmetric/asymmetric ω scan (rocking curve scan), reciprocal space mapping) and Hall effect measurements are employed to study the structural, optical, and electrical properties of these AlGaN/GaN HEMT structures. The effects of buffer layer stacks (i.e. thickness and content) on defectivity, stress, and two-dimensional electron gas (2DEG) mobility and 2DEG concentration are reported. It is shown that 2DEG characteristics are heavily affected by the employed buffer layers between AlGaN/GaN HEMT structures and Si(111) substrates. Particularly, we report that in-plane stress in the GaN layer affects the 2DEG mobility and 2DEG carrier concentration significantly. Buffer layer engineering is shown to be essential for achieving high 2DEG mobility (>1800 cm 2 /V∙s) and 2DEG carrier concentration (>1.0 × 10 13  cm -2 ) on Si(111) substrates.

Investigation of AlGaN/GaN high electron mobility transistor structures on 200-mm silicon (111) substrates employing different buffer layer configurations

PubMed Central

Lee, H.-P.; Perozek, J.; Rosario, L. D.; Bayram, C.

2016-01-01

AlGaN/GaN high electron mobility transistor (HEMT) structures are grown on 200-mm diameter Si(111) substrates by using three different buffer layer configurations: (a) Thick-GaN/3 × {AlxGa1−xN}/AlN, (b) Thin-GaN/3 × {AlxGa1−xN}/AlN, and (c) Thin-GaN/AlN, so as to have crack-free and low-bow (<50 μm) wafer. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, high resolution-cross section transmission electron microscopy, optical microscopy, atomic-force microscopy, cathodoluminescence, Raman spectroscopy, X-ray diffraction (ω/2θ scan and symmetric/asymmetric ω scan (rocking curve scan), reciprocal space mapping) and Hall effect measurements are employed to study the structural, optical, and electrical properties of these AlGaN/GaN HEMT structures. The effects of buffer layer stacks (i.e. thickness and content) on defectivity, stress, and two-dimensional electron gas (2DEG) mobility and 2DEG concentration are reported. It is shown that 2DEG characteristics are heavily affected by the employed buffer layers between AlGaN/GaN HEMT structures and Si(111) substrates. Particularly, we report that in-plane stress in the GaN layer affects the 2DEG mobility and 2DEG carrier concentration significantly. Buffer layer engineering is shown to be essential for achieving high 2DEG mobility (>1800 cm2/V∙s) and 2DEG carrier concentration (>1.0 × 1013 cm−2) on Si(111) substrates. PMID:27869222

Icosahedral stereographic projections in three dimensions for use in dark field TEM.

PubMed

Bourdillon, Antony J

2013-08-01

Thermodynamics require that rapidly cooled crystals and quasicrystals are relatively defective. Yet, without convenient 3-dimensional indexation both at crystal poles and in diffraction planes, or Kikuchi maps, it is difficult to identify the defects by dark field transmission electron microscopy. For two phase Al6Mn, these maps are derived. They relate i-Al6Mn to the standard face centered cubic, matrix crystals. An example of their usefulness in determining interfacial characteristics is described. Indices are integral powers on an irrational number. Copyright © 2013 Elsevier Ltd. All rights reserved.

FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.

PubMed

Saha, Mitul; Morais, Marc C

2012-12-15

Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.

Kelvin probe microscopy and electronic transport measurements in reduced graphene oxide chemical sensors

NASA Astrophysics Data System (ADS)

Kehayias, Christopher E.; MacNaughton, Samuel; Sonkusale, Sameer; Staii, Cristian

2013-06-01

Reduced graphene oxide (RGO) is an electronically hybrid material that displays remarkable chemical sensing properties. Here, we present a quantitative analysis of the chemical gating effects in RGO-based chemical sensors. The gas sensing devices are patterned in a field-effect transistor geometry, by dielectrophoretic assembly of RGO platelets between gold electrodes deposited on SiO2/Si substrates. We show that these sensors display highly selective and reversible responses to the measured analytes, as well as fast response and recovery times (tens of seconds). We use combined electronic transport/Kelvin probe microscopy measurements to quantify the amount of charge transferred to RGO due to chemical doping when the device is exposed to electron-acceptor (acetone) and electron-donor (ammonia) analytes. We demonstrate that this method allows us to obtain high-resolution maps of the surface potential and local charge distribution both before and after chemical doping, to identify local gate-susceptible areas on the RGO surface, and to directly extract the contact resistance between the RGO and the metallic electrodes. The method presented is general, suggesting that these results have important implications for building graphene and other nanomaterial-based chemical sensors.

Kelvin probe microscopy and electronic transport measurements in reduced graphene oxide chemical sensors.

PubMed

Kehayias, Christopher E; MacNaughton, Samuel; Sonkusale, Sameer; Staii, Cristian

2013-06-21

Reduced graphene oxide (RGO) is an electronically hybrid material that displays remarkable chemical sensing properties. Here, we present a quantitative analysis of the chemical gating effects in RGO-based chemical sensors. The gas sensing devices are patterned in a field-effect transistor geometry, by dielectrophoretic assembly of RGO platelets between gold electrodes deposited on SiO2/Si substrates. We show that these sensors display highly selective and reversible responses to the measured analytes, as well as fast response and recovery times (tens of seconds). We use combined electronic transport/Kelvin probe microscopy measurements to quantify the amount of charge transferred to RGO due to chemical doping when the device is exposed to electron-acceptor (acetone) and electron-donor (ammonia) analytes. We demonstrate that this method allows us to obtain high-resolution maps of the surface potential and local charge distribution both before and after chemical doping, to identify local gate-susceptible areas on the RGO surface, and to directly extract the contact resistance between the RGO and the metallic electrodes. The method presented is general, suggesting that these results have important implications for building graphene and other nanomaterial-based chemical sensors.

Synchrotron X-ray imaging of nanomagnetism in meteoritic metal (Invited)

NASA Astrophysics Data System (ADS)

Bryson, J. F.; Herrero Albillos, J.; Kronast, F.; Tyliszczak, T.; Redfern, S. A.; van der Laan, G.; Harrison, R. J.

2013-12-01

It is becoming increasingly apparent that a wealth of paleomagnetic information is stored at the nanoscale within natural samples. To date, this nanopaleomagetism has been investigated using high resolution magnetic microscopies, such as electron holography. Although unparalleled in its spatial resolution, electron holography produces images that are indirectly related to the magnetisation state of the sample, introducing ambiguity when interpreting magnetisation information. Holography also requires extensive off-line processing, making it unsuitable for studying dynamic processes, and the sample preparation negates the study of natural remanences. Here we demonstrate the capabilities of a new generation of nanomagnetic imaging methods using synchrotron X-ray radiation. X-rays tuned to an elemental absorption edge can display differing excitation probabilities depending on the orientation of an electron's magnetic moment relative to that of the X-ray beam. This is achieved by introducing an angular momentum to the photon through circular polarisation, resulting in an absorption signal that is proportional to the projection of the magnetic moment on to the X-ray beam direction. We introduce and compare two experimental set-ups capable of spatially resolving these signals to form a high-resolution magnetisation map: photoemission electron microscopy and scanning transmission electron microscopy. Both techniques provide measurements of magnetisation with 30-50nm resolution and elemental specificity. Photoemission electron microscopy can be used also to create maps of all three of the spatial components of magnetisation and investigate dynamic magnetic switching processes. The full capabilities of X-ray imaging are demonstrated through the application of both of these techniques to meteoritic metal. We show that the 'cloudy zone' within iron meteorites contains nanoscale islands of tetrataenite (FeNi) that are populated equally by all three possible magnetic easy axes, suggesting that there were no stray fields (either magnetic or stress) effecting the magnetisation during cloudy zone formation. This observation allows for dynamo field information to be extracted from X-ray nanomagnetic images of the cloudy zone in metallic inclusions within certain chondritic meteorites, as it implies that any deviation from the randomly populated easy axis distribution can be assigned to an external dynamo field. As the cloudy zone forms over 10-100 Ma, this observation suggests that X-ray imaging of the nanopaleomagentism in these meteorites could provide an elegant and concise relative measure of asteroid dynamo field direction and strength over this entire time period, revolutionising our understanding of dynamo processes and planetary formation.

Revealing the Crystalline Integrity of Wafer-Scale Graphene on SiO2/Si: An Azimuthal RHEED Approach.

PubMed

Lu, Zonghuan; Sun, Xin; Xiang, Yu; Washington, Morris A; Wang, Gwo-Ching; Lu, Toh-Ming

2017-07-12

The symmetry of graphene is usually determined by a low-energy electron diffraction (LEED) method when the graphene is on the conductive substrates, but LEED cannot handle graphene transferred to SiO 2 /Si substrates due to the charging effect. While transmission electron microscopy can generate electron diffraction on post-transferred graphene, this method is too localized. Herein, we employed an azimuthal reflection high-energy electron diffraction (RHEED) method to construct the reciprocal space mapping and determine the symmetry of wafer-size graphene both pre- and post-transfer. In this work, single-crystalline Cu(111) films were prepared on sapphire(0001) and spinel(111) substrates with sputtering. Then the graphene was epitaxially grown on single-crystalline Cu(111) films with a low pressure chemical vapor deposition. The reciprocal space mapping using azimuthal RHEED confirmed that the graphene grown on Cu(111) films was single-crystalline, no matter the form of the monolayer or multilayer structure. While the Cu(111) film grown on sapphire(0001) may occasionally consist of 60° in-plane rotational twinning, the reciprocal space mapping revealed that the in-plane orientation of graphene grown atop was not affected. The proposed method for checking the crystalline integrity of the post-transferred graphene sheets is an important step in the realization of the graphene as a platform to fabricate electronic and optoelectronic devices.

In situ electrical and thermal monitoring of printed electronics by two-photon mapping.

PubMed

Pastorelli, Francesco; Accanto, Nicolò; Jørgensen, Mikkel; van Hulst, Niek F; Krebs, Frederik C

2017-06-19

Printed electronics is emerging as a new, large scale and cost effective technology that will be disruptive in fields such as energy harvesting, consumer electronics and medical sensors. The performance of printed electronic devices relies principally on the carrier mobility and molecular packing of the polymer semiconductor material. Unfortunately, the analysis of such materials is generally performed with destructive techniques, which are hard to make compatible with in situ measurements, and pose a great obstacle for the mass production of printed electronics devices. A rapid, in situ, non-destructive and low-cost testing method is needed. In this study, we demonstrate that nonlinear optical microscopy is a promising technique to achieve this goal. Using ultrashort laser pulses we stimulate two-photon absorption in a roll coated polymer semiconductor and map the resulting two-photon induced photoluminescence and second harmonic response. We show that, in our experimental conditions, it is possible to relate the total amount of photoluminescence detected to important material properties such as the charge carrier density and the molecular packing of the printed polymer material, all with a spatial resolution of 400 nm. Importantly, this technique can be extended to the real time mapping of the polymer semiconductor film, even during the printing process, in which the high printing speed poses the need for equally high acquisition rates.

Characterization of ELISA Antibody-Antigen Interaction using Footprinting-Mass Spectrometry and Negative Staining Transmission Electron Microscopy

NASA Astrophysics Data System (ADS)

Lin, Margaret; Krawitz, Denise; Callahan, Matthew D.; Deperalta, Galahad; Wecksler, Aaron T.

2018-05-01

We describe epitope mapping data using multiple covalent labeling footprinting-mass spectrometry (MS) techniques coupled with negative stain transmission electron microscopy (TEM) data to analyze the antibody-antigen interactions in a sandwich enzyme-linked immunosorbant assay (ELISA). Our hydroxyl radical footprinting-MS data using fast photochemical oxidation of proteins (FPOP) indicates suppression of labeling across the antigen upon binding either of the monoclonal antibodies (mAbs) utilized in the ELISA. Combining these data with Western blot analysis enabled the identification of the putative epitopes that appeared to span regions containing N-linked glycans. An additional structural mapping technique, carboxyl group footprinting-mass spectrometry using glycine ethyl ester (GEE) labeling, was used to confirm the epitopes. Deglycosylation of the antigen resulted in loss of potency in the ELISA, supporting the FPOP and GEE labeling data by indicating N-linked glycans are necessary for antigen binding. Finally, mapping of the epitopes onto the antigen crystal structure revealed an approximate 90° relative spatial orientation, optimal for a noncompetitive binding ELISA. TEM data shows both linear and diamond antibody-antigen complexes with a similar binding orientation as predicted from the two footprinting-MS techniques. This study is the first of its kind to utilize multiple bottom-up footprinting-MS techniques and TEM visualization to characterize the monoclonal antibody-antigen binding interactions of critical reagents used in a quality control (QC) lot-release ELISA. [Figure not available: see fulltext.

Characterization of ELISA Antibody-Antigen Interaction using Footprinting-Mass Spectrometry and Negative Staining Transmission Electron Microscopy.

PubMed

Lin, Margaret; Krawitz, Denise; Callahan, Matthew D; Deperalta, Galahad; Wecksler, Aaron T

2018-05-01

We describe epitope mapping data using multiple covalent labeling footprinting-mass spectrometry (MS) techniques coupled with negative stain transmission electron microscopy (TEM) data to analyze the antibody-antigen interactions in a sandwich enzyme-linked immunosorbant assay (ELISA). Our hydroxyl radical footprinting-MS data using fast photochemical oxidation of proteins (FPOP) indicates suppression of labeling across the antigen upon binding either of the monoclonal antibodies (mAbs) utilized in the ELISA. Combining these data with Western blot analysis enabled the identification of the putative epitopes that appeared to span regions containing N-linked glycans. An additional structural mapping technique, carboxyl group footprinting-mass spectrometry using glycine ethyl ester (GEE) labeling, was used to confirm the epitopes. Deglycosylation of the antigen resulted in loss of potency in the ELISA, supporting the FPOP and GEE labeling data by indicating N-linked glycans are necessary for antigen binding. Finally, mapping of the epitopes onto the antigen crystal structure revealed an approximate 90° relative spatial orientation, optimal for a noncompetitive binding ELISA. TEM data shows both linear and diamond antibody-antigen complexes with a similar binding orientation as predicted from the two footprinting-MS techniques. This study is the first of its kind to utilize multiple bottom-up footprinting-MS techniques and TEM visualization to characterize the monoclonal antibody-antigen binding interactions of critical reagents used in a quality control (QC) lot-release ELISA. Graphical Abstract ᅟ.

Characterization of ELISA Antibody-Antigen Interaction using Footprinting-Mass Spectrometry and Negative Staining Transmission Electron Microscopy

NASA Astrophysics Data System (ADS)

Lin, Margaret; Krawitz, Denise; Callahan, Matthew D.; Deperalta, Galahad; Wecksler, Aaron T.

2018-03-01

We describe epitope mapping data using multiple covalent labeling footprinting-mass spectrometry (MS) techniques coupled with negative stain transmission electron microscopy (TEM) data to analyze the antibody-antigen interactions in a sandwich enzyme-linked immunosorbant assay (ELISA). Our hydroxyl radical footprinting-MS data using fast photochemical oxidation of proteins (FPOP) indicates suppression of labeling across the antigen upon binding either of the monoclonal antibodies (mAbs) utilized in the ELISA. Combining these data with Western blot analysis enabled the identification of the putative epitopes that appeared to span regions containing N-linked glycans. An additional structural mapping technique, carboxyl group footprinting-mass spectrometry using glycine ethyl ester (GEE) labeling, was used to confirm the epitopes. Deglycosylation of the antigen resulted in loss of potency in the ELISA, supporting the FPOP and GEE labeling data by indicating N-linked glycans are necessary for antigen binding. Finally, mapping of the epitopes onto the antigen crystal structure revealed an approximate 90° relative spatial orientation, optimal for a noncompetitive binding ELISA. TEM data shows both linear and diamond antibody-antigen complexes with a similar binding orientation as predicted from the two footprinting-MS techniques. This study is the first of its kind to utilize multiple bottom-up footprinting-MS techniques and TEM visualization to characterize the monoclonal antibody-antigen binding interactions of critical reagents used in a quality control (QC) lot-release ELISA. [Figure not available: see fulltext.

In vivo correlation mapping microscopy

NASA Astrophysics Data System (ADS)

McGrath, James; Alexandrov, Sergey; Owens, Peter; Subhash, Hrebesh; Leahy, Martin

2016-04-01

To facilitate regular assessment of the microcirculation in vivo, noninvasive imaging techniques such as nailfold capillaroscopy are required in clinics. Recently, a correlation mapping technique has been applied to optical coherence tomography (OCT), which extends the capabilities of OCT to microcirculation morphology imaging. This technique, known as correlation mapping optical coherence tomography, has been shown to extract parameters, such as capillary density and vessel diameter, and key clinical markers associated with early changes in microvascular diseases. However, OCT has limited spatial resolution in both the transverse and depth directions. Here, we extend this correlation mapping technique to other microscopy modalities, including confocal microscopy, and take advantage of the higher spatial resolution offered by these modalities. The technique is achieved as a processing step on microscopy images and does not require any modification to the microscope hardware. Results are presented which show that this correlation mapping microscopy technique can extend the capabilities of conventional microscopy to enable mapping of vascular networks in vivo with high spatial resolution in both the transverse and depth directions.

Photoionization microscopy: Hydrogenic theory in semiparabolic coordinates and comparison with experimental results

NASA Astrophysics Data System (ADS)

Kalaitzis, P.; Danakas, S.; Lépine, F.; Bordas, C.; Cohen, S.

2018-05-01

Photoionization microscopy (PM) is an experimental method allowing for high-resolution measurements of the electron current probability density in the case of photoionization of an atom in an external uniform static electric field. PM is based on high-resolution velocity-map imaging and offers the unique opportunity to observe the quantum oscillatory spatial structure of the outgoing electron flux. We present the basic elements of the quantum-mechanical theoretical framework of PM for hydrogenic systems near threshold. Our development is based on the computationally more convenient semiparabolic coordinate system. Theoretical results are first subjected to a quantitative comparison with hydrogenic images corresponding to quasibound states and a qualitative comparison with nonresonant images of multielectron atoms. Subsequently, particular attention is paid on the structure of the electron's momentum distribution transversely to the static field (i.e., of the angularly integrated differential cross-section as a function of electron energy and radius of impact on the detector). Such 2D maps provide at a glance a complete picture of the peculiarities of the differential cross-section over the entire near-threshold energy range. Hydrogenic transverse momentum distributions are computed for the cases of the ground and excited initial states and single- and two-photon ionization schemes. Their characteristics of general nature are identified by comparing the hydrogenic distributions among themselves, as well as with a presently recorded experimental distribution concerning the magnesium atom. Finally, specificities attributed to different target atoms, initial states, and excitation scenarios are also discussed, along with directions of further work.

Study of Etching Pits in a Large-grain Single Cell Bulk Niobium Cavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Xin; Ciovati, Gianluigi; Reece, Charles E.

2009-11-01

Performance of SRF cavities are limited by non-linear localized effects. The variation of local material characters between "hot" and "cold" spots is thus of intense interest. Such locations were identified in a BCP-etched large-grain single-cell cavity and removed for examination by high resolution electron microscopy (SEM), electron-back scattering diffraction microscopy (EBSD), optical microscopy, and 3D profilometry. Pits with clearly discernable crystal facets were observed in both "hotspot" and "coldspot" specimens. The pits were found in-grain, at bi-crystal boundaries, and on tri-crystal junctions. They are interpreted as etch pits induced by surface crystal defects (e.g. dislocations). All "coldspots" examined had qualitativelymore » low density of etching pits or very shallow tri-crystal boundary junction. EBSD revealed crystal structure surrounding the pits via crystal phase orientation mapping, while 3D profilometry gave information on the depth and size of the pits. In addition, a survey of the samples by energy dispersive X-ray analysis (EDX) did not show any significant contamination of the samples surface.« less

Enhanced dispersion of multiwall carbon nanotubes in natural rubber latex nanocomposites by surfactants bearing phenyl groups.

PubMed

Mohamed, Azmi; Anas, Argo Khoirul; Bakar, Suriani Abu; Ardyani, Tretya; Zin, Wan Manshol W; Ibrahim, Sofian; Sagisaka, Masanobu; Brown, Paul; Eastoe, Julian

2015-10-01

Here is presented a systematic study of the dispersibility of multiwall carbon nanotubes (MWCNTs) in natural rubber latex (NR-latex) assisted by a series of single-, double-, and triple-sulfosuccinate anionic surfactants containing phenyl ring moieties. Optical polarising microscopy, field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), and Raman spectroscopy have been performed to obtain the dispersion-level profiles of the MWCNTs in the nanocomposites. Interestingly, a triple-chain, phenyl-containing surfactant, namely sodium 1,5-dioxo-1,5-bis(3-phenylpropoxy)-3-((3-phenylpropoxy)carbonyl) pentane-2-sulfonate (TCPh), has a greater capacity the stabilisation of MWCNTs than a commercially available single-chain sodium dodecylbenzenesulfonate (SDBS) surfactant. TCPh provides significant enhancements in the electrical conductivity of nanocomposites, up to ∼10(-2) S cm(-1), as measured by a four-point probe instrument. These results have allowed compilation of a road map for the design of surfactant architectures capable of providing the homogeneous dispersion of MWCNTs required for the next generation of polymer-carbon-nanotube materials, specifically those used in aerospace technology. Copyright © 2015 Elsevier Inc. All rights reserved.

Orientation-dependent imaging of electronically excited quantum dots

NASA Astrophysics Data System (ADS)

Nguyen, Duc; Goings, Joshua J.; Nguyen, Huy A.; Lyding, Joseph; Li, Xiaosong; Gruebele, Martin

2018-02-01

We previously demonstrated that we can image electronic excitations of quantum dots by single-molecule absorption scanning tunneling microscopy (SMA-STM). With this technique, a modulated laser beam periodically saturates an electronic transition of a single nanoparticle, and the resulting tunneling current modulation ΔI(x0, y0) maps out the SMA-STM image. In this paper, we first derive the basic theory to calculate ΔI(x0, y0) in the one-electron approximation. For near-resonant tunneling through an empty orbital "i" of the nanostructure, the SMA-STM signal is approximately proportional to the electron density |φi) (x0,y0)|

Orientation-dependent imaging of electronically excited quantum dots.

PubMed

Nguyen, Duc; Goings, Joshua J; Nguyen, Huy A; Lyding, Joseph; Li, Xiaosong; Gruebele, Martin

2018-02-14

We previously demonstrated that we can image electronic excitations of quantum dots by single-molecule absorption scanning tunneling microscopy (SMA-STM). With this technique, a modulated laser beam periodically saturates an electronic transition of a single nanoparticle, and the resulting tunneling current modulation ΔI(x 0 , y 0 ) maps out the SMA-STM image. In this paper, we first derive the basic theory to calculate ΔI(x 0 , y 0 ) in the one-electron approximation. For near-resonant tunneling through an empty orbital "i" of the nanostructure, the SMA-STM signal is approximately proportional to the electron density φ i x 0 ,y 0 2 of the excited orbital in the tunneling region. Thus, the SMA-STM signal is approximated by an orbital density map (ODM) of the resonantly excited orbital at energy E i . The situation is more complex for correlated electron motion, but either way a slice through the excited electronic state structure in the tunneling region is imaged. We then show experimentally that we can nudge quantum dots on the surface and roll them, thus imaging excited state electronic structure of a single quantum dot at different orientations. We use density functional theory to model ODMs at various orientations, for qualitative comparison with the SMA-STM experiment. The model demonstrates that our experimentally observed signal monitors excited states, localized by defects near the surface of an individual quantum dot. The sub-nanometer super-resolution imaging technique demonstrated here could become useful for mapping out the three-dimensional structure of excited states localized by defects within nanomaterials.

EMDataBank unified data resource for 3DEM.

PubMed

Lawson, Catherine L; Patwardhan, Ardan; Baker, Matthew L; Hryc, Corey; Garcia, Eduardo Sanz; Hudson, Brian P; Lagerstedt, Ingvar; Ludtke, Steven J; Pintilie, Grigore; Sala, Raul; Westbrook, John D; Berman, Helen M; Kleywegt, Gerard J; Chiu, Wah

2016-01-04

Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata (emdatabank.org). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Real-space visualization of conformation-independent oligothiophene electronic structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taber, Benjamen N.; Kislitsyn, Dmitry A.; Gervasi, Christian F.

2016-05-21

We present scanning tunneling microscopy and spectroscopy (STM/STS) investigations of the electronic structures of different alkyl-substituted oligothiophenes on the Au(111) surface. STM imaging showed that on Au(111), oligothiophenes adopted distinct straight and bent conformations. By combining STS maps with STM images, we visualize, in real space, particle-in-a-box-like oligothiophene molecular orbitals. We demonstrate that different planar conformers with significant geometrical distortions of oligothiophene backbones surprisingly exhibit very similar electronic structures, indicating a low degree of conformation-induced electronic disorder. The agreement of these results with gas-phase density functional theory calculations implies that the oligothiophene interaction with the Au(111) surface is generally insensitivemore » to molecular conformation.« less

Comparative microstructures and cytotoxicity assays for ballistic aerosols composed of micrometals and nanometals: respiratory health implications

PubMed Central

Machado, Brenda I; Suro, Raquel M; Garza, Kristine M; Murr, Lawrence E

2011-01-01

Aerosol particulates collected on filters from ballistic penetration and erosion events for W–Ni–Co and W–Ni–Fe kinetic energy rod projectiles penetrating steel target plates were observed to be highly cytotoxic to human epithelial A549 lung cells in culture after 48 hours of exposure. The aerosol consisted of micron-sized Fe particulates and nanoparticulate aggregates consisting of W, Ni or W, Co, and some Fe, characterized by scanning electron microscopy and transmission electron microscopy, and using energy-dispersive (X-ray) spectrometry for elemental analysis and mapping. Cytotoxic assays of manufactured micron-sized and nanosized metal particulates of W, Ni, Fe, and Co demonstrated that, consistent with many studies in the literature, only the nanoparticulate elements demonstrated measurable cytotoxicity. These results suggest the potential for very severe, short-term, human toxicity, in particular to the respiratory system on inhaling ballistic aerosols. PMID:21499416

GePb Alloy Growth Using Layer Inversion Method

NASA Astrophysics Data System (ADS)

Alahmad, Hakimah; Mosleh, Aboozar; Alher, Murtadha; Banihashemian, Seyedeh Fahimeh; Ghetmiri, Seyed Amir; Al-Kabi, Sattar; Du, Wei; Li, Bauhoa; Yu, Shui-Qing; Naseem, Hameed A.

2018-04-01

Germanium-lead films have been investigated as a new direct-bandgap group IV alloy. GePb films were deposited on Si via thermal evaporation of Ge and Pb solid sources using the layer inversion metal-induced crystallization method for comparison with the current laser-induced recrystallization method. Material characterization of the films using x-ray diffraction analysis revealed highly oriented crystallinity and Pb incorporation as high as 13.5% before and 5.2% after annealing. Transmission electron microscopy, scanning electron microscopy, and energy-dispersive x-ray mapping of the samples revealed uniform incorporation of elements and complete layer inversion. Optical characterization of the GePb films by Raman spectroscopy and photoluminescence techniques showed that annealing the samples resulted in higher crystalline quality as well as bandgap reduction. The bandgap reduction from 0.67 eV to 0.547 eV observed for the highest-quality material confirms the achievement of a direct-bandgap material.

GePb Alloy Growth Using Layer Inversion Method

NASA Astrophysics Data System (ADS)

Alahmad, Hakimah; Mosleh, Aboozar; Alher, Murtadha; Banihashemian, Seyedeh Fahimeh; Ghetmiri, Seyed Amir; Al-Kabi, Sattar; Du, Wei; Li, Bauhoa; Yu, Shui-Qing; Naseem, Hameed A.

2018-07-01

Germanium-lead films have been investigated as a new direct-bandgap group IV alloy. GePb films were deposited on Si via thermal evaporation of Ge and Pb solid sources using the layer inversion metal-induced crystallization method for comparison with the current laser-induced recrystallization method. Material characterization of the films using x-ray diffraction analysis revealed highly oriented crystallinity and Pb incorporation as high as 13.5% before and 5.2% after annealing. Transmission electron microscopy, scanning electron microscopy, and energy-dispersive x-ray mapping of the samples revealed uniform incorporation of elements and complete layer inversion. Optical characterization of the GePb films by Raman spectroscopy and photoluminescence techniques showed that annealing the samples resulted in higher crystalline quality as well as bandgap reduction. The bandgap reduction from 0.67 eV to 0.547 eV observed for the highest-quality material confirms the achievement of a direct-bandgap material.

Reduced electron exposure for energy-dispersive spectroscopy using dynamic sampling

DOE PAGES

Zhang, Yan; Godaliyadda, G. M. Dilshan; Ferrier, Nicola; ...

2017-10-23

Analytical electron microscopy and spectroscopy of biological specimens, polymers, and other beam sensitive materials has been a challenging area due to irradiation damage. There is a pressing need to develop novel imaging and spectroscopic imaging methods that will minimize such sample damage as well as reduce the data acquisition time. The latter is useful for high-throughput analysis of materials structure and chemistry. Here, in this work, we present a novel machine learning based method for dynamic sparse sampling of EDS data using a scanning electron microscope. Our method, based on the supervised learning approach for dynamic sampling algorithm and neuralmore » networks based classification of EDS data, allows a dramatic reduction in the total sampling of up to 90%, while maintaining the fidelity of the reconstructed elemental maps and spectroscopic data. In conclusion, we believe this approach will enable imaging and elemental mapping of materials that would otherwise be inaccessible to these analysis techniques.« less

Mapping Thermal Expansion Coefficients in Freestanding 2D Materials at the Nanometer Scale

NASA Astrophysics Data System (ADS)

Hu, Xuan; Yasaei, Poya; Jokisaari, Jacob; Öǧüt, Serdar; Salehi-Khojin, Amin; Klie, Robert F.

2018-02-01

Two-dimensional materials, including graphene, transition metal dichalcogenides and their heterostructures, exhibit great potential for a variety of applications, such as transistors, spintronics, and photovoltaics. While the miniaturization offers remarkable improvements in electrical performance, heat dissipation and thermal mismatch can be a problem in designing electronic devices based on two-dimensional materials. Quantifying the thermal expansion coefficient of 2D materials requires temperature measurements at nanometer scale. Here, we introduce a novel nanometer-scale thermometry approach to measure temperature and quantify the thermal expansion coefficients in 2D materials based on scanning transmission electron microscopy combined with electron energy-loss spectroscopy to determine the energy shift of the plasmon resonance peak of 2D materials as a function of sample temperature. By combining these measurements with first-principles modeling, the thermal expansion coefficients (TECs) of single-layer and freestanding graphene and bulk, as well as monolayer MoS2 , MoSe2 , WS2 , or WSe2 , are directly determined and mapped.

Mapping Thermal Expansion Coefficients in Freestanding 2D Materials at the Nanometer Scale.

PubMed

Hu, Xuan; Yasaei, Poya; Jokisaari, Jacob; Öğüt, Serdar; Salehi-Khojin, Amin; Klie, Robert F

2018-02-02

Two-dimensional materials, including graphene, transition metal dichalcogenides and their heterostructures, exhibit great potential for a variety of applications, such as transistors, spintronics, and photovoltaics. While the miniaturization offers remarkable improvements in electrical performance, heat dissipation and thermal mismatch can be a problem in designing electronic devices based on two-dimensional materials. Quantifying the thermal expansion coefficient of 2D materials requires temperature measurements at nanometer scale. Here, we introduce a novel nanometer-scale thermometry approach to measure temperature and quantify the thermal expansion coefficients in 2D materials based on scanning transmission electron microscopy combined with electron energy-loss spectroscopy to determine the energy shift of the plasmon resonance peak of 2D materials as a function of sample temperature. By combining these measurements with first-principles modeling, the thermal expansion coefficients (TECs) of single-layer and freestanding graphene and bulk, as well as monolayer MoS_{2}, MoSe_{2}, WS_{2}, or WSe_{2}, are directly determined and mapped.

Mapping bright and dark modes in gold nanoparticle chains using electron energy loss spectroscopy.

PubMed

Barrow, Steven J; Rossouw, David; Funston, Alison M; Botton, Gianluigi A; Mulvaney, Paul

2014-07-09

We present a scanning transmission electron microscopy-electron energy loss spectroscopy (STEM-EELS) investigation of gold nanosphere chains with lengths varying from 1 to 5 particles. We show localized EELS signals from the chains and identify energy-loss peaks arising due to l = 1, 2, 3, 4, and 5 plasmon modes through the use of EELS mapping. We also show the evolution of the energy of these modes as the length of a given chain increases, and we find that a chain containing N particles can accommodate at least N experimentally observable modes, in addition to the transverse mode. As the chain length is increased by the addition of one more gold particle to the chain, the new N + 1 mode becomes the highest energy mode, while the existing modes lower their energy and eventually asymptote as they delocalize along the chain. We also show that modes become increasingly difficult to detect with the EELS technique as l approaches N. The data are compared to numerical simulations.

PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

PubMed

Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

2015-10-01

There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps

PubMed Central

Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

2015-01-01

There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF2 fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF2 fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

X-ray elemental mapping techniques for elucidating the ecophysiology of hyperaccumulator plants.

PubMed

van der Ent, Antony; Przybyłowicz, Wojciech J; de Jonge, Martin D; Harris, Hugh H; Ryan, Chris G; Tylko, Grzegorz; Paterson, David J; Barnabas, Alban D; Kopittke, Peter M; Mesjasz-Przybyłowicz, Jolanta

2018-04-01

Contents Summary 432 I. Introduction 433 II. Preparation of plant samples for X-ray micro-analysis 433 III. X-ray elemental mapping techniques 438 IV. X-ray data analysis 442 V. Case studies 443 VI. Conclusions 446 Acknowledgements 449 Author contributions 449 References 449 SUMMARY: Hyperaccumulators are attractive models for studying metal(loid) homeostasis, and probing the spatial distribution and coordination chemistry of metal(loid)s in their tissues is important for advancing our understanding of their ecophysiology. X-ray elemental mapping techniques are unique in providing in situ information, and with appropriate sample preparation offer results true to biological conditions of the living plant. The common platform of these techniques is a reliance on characteristic X-rays of elements present in a sample, excited either by electrons (scanning/transmission electron microscopy), protons (proton-induced X-ray emission) or X-rays (X-ray fluorescence microscopy). Elucidating the cellular and tissue-level distribution of metal(loid)s is inherently challenging and accurate X-ray analysis places strict demands on sample collection, preparation and analytical conditions, to avoid elemental redistribution, chemical modification or ultrastructural alterations. We compare the merits and limitations of the individual techniques, and focus on the optimal field of applications for inferring ecophysiological processes in hyperaccumulator plants. X-ray elemental mapping techniques can play a key role in answering questions at every level of metal(loid) homeostasis in plants, from the rhizosphere interface, to uptake pathways in the roots and shoots. Further improvements in technological capabilities offer exciting perspectives for the study of hyperaccumulator plants into the future. © 2017 University of Queensland. New Phytologist © 2017 New Phytologist Trust.

Self-assembly preparation of SiO2@Ni-Al layered double hydroxide composites and their enhanced electrorheological characteristics

PubMed Central

Ji, Xuqiang; Zhang, Wenling; Shan, Lei; Tian, Yu; Liu, Jingquan

2015-01-01

The core-shell structured SiO2@Ni-Al layered double hydroxide (LDH) composites were prepared via self-assembly of Ni-Al LDH on the surface of SiO2 spheres. Only coating a layer of ultrathin Ni-Al LDH sheet, the resulting SiO2@Ni-Al LDH composites exhibit significantly enhanced electrorheological (ER) characteristics compared to conventional bare SiO2 spheres. The monodispersed SiO2 spheres with average diameters of 260 nm were synthesized by the hydrolysis of tetraethyl orthosilicate (TEOS), while the shell part, Ni-Al LDH sheet was prepared by the hydrothermal procedure. The morphology of the samples was investigated via scanning transmission electron microscopy (STEM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The structure of the samples was characterized by X-ray diffraction (XRD). The species and distribution of elements in samples were confirmed by X-ray photoelectron spectroscopy (XPS), Energy dispersive analysis of X-ray (EDX) and elemental mapping in STEM. Subsequently, the ER characteristics of the composites dispersed in insulating oil were characterized by a rotational rheometer. The electric field-stimulated rheological performances (yield stress, viscosity, modulus, etc.) were observed under an external electric field, which is different from the Newtonian state in the free electric field. PMID:26670467

Self-assembly preparation of SiO2@Ni-Al layered double hydroxide composites and their enhanced electrorheological characteristics

NASA Astrophysics Data System (ADS)

Ji, Xuqiang; Zhang, Wenling; Shan, Lei; Tian, Yu; Liu, Jingquan

2015-12-01

The core-shell structured SiO2@Ni-Al layered double hydroxide (LDH) composites were prepared via self-assembly of Ni-Al LDH on the surface of SiO2 spheres. Only coating a layer of ultrathin Ni-Al LDH sheet, the resulting SiO2@Ni-Al LDH composites exhibit significantly enhanced electrorheological (ER) characteristics compared to conventional bare SiO2 spheres. The monodispersed SiO2 spheres with average diameters of 260 nm were synthesized by the hydrolysis of tetraethyl orthosilicate (TEOS), while the shell part, Ni-Al LDH sheet was prepared by the hydrothermal procedure. The morphology of the samples was investigated via scanning transmission electron microscopy (STEM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The structure of the samples was characterized by X-ray diffraction (XRD). The species and distribution of elements in samples were confirmed by X-ray photoelectron spectroscopy (XPS), Energy dispersive analysis of X-ray (EDX) and elemental mapping in STEM. Subsequently, the ER characteristics of the composites dispersed in insulating oil were characterized by a rotational rheometer. The electric field-stimulated rheological performances (yield stress, viscosity, modulus, etc.) were observed under an external electric field, which is different from the Newtonian state in the free electric field.

Synthesis of mesoporous Mn/TiO2 nanocomposites and investigating the photocatalytic properties in aqueous systems.

PubMed

Oseghe, Ekemena Oghenovoh; Ndungu, Patrick Gathura; Jonnalagadda, Sreekanth Babu

2015-01-01

Mesoporous 20 wt% Mn/TiO2 nanocomposites were synthesized adopting modified sol-gel method at different pH (pH = 2, 7 and 11) conditions and calcined at 400 °C. Based on the characteristics of the 20 wt% Mn/TiO2 nanocomposites synthesized at pH 11, same procedure was adopted for the synthesis of different wt% Mn/TiO2. The nanocomposite samples and their surface properties were characterized by X-ray powder diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), high resolution transmission electron microscopy (HRTEM), mapping, inductively coupled plasma optical emission spectrometry (ICP-OES), Fourier transform infrared (FTIR), and fluorescence spectrometry. The nanocomposites existed in the anatase phase of TiO2 with no peak assigned to Mn on the diffractogram. The photocatalytic activities of the materials were evaluated by monitoring degradation of a model dye (methylene blue (MB)) in presence of visible light and ozone. The nanocomposite synthesized under neutral condition (pH = 7) exhibited the best photocatalytic activity resulting from its relatively smaller crystal size (5.98 nm) and larger pore volume (0.30 cm(3)/g). One percentage of weight Mn/TiO2 showed 100% decolouration of MB in the presence of O3 after 100 min.

Atomic photoionization processes under magnification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lepine, F.; Bordas, Ch.; Nicole, C.

2004-09-01

Recently, classical simulations of threshold photoionization in the presence of an electric field have shown that a clear distinction between direct and indirect trajectories followed by the outgoing electron can be observed in the patterns of electron impacts on a two-dimensional detector. Subsequently, slow photoelectron imaging experiments have been reported where this distinction could be observed in atomic xenon. Furthermore, using a magnifying electrostatic lens to improve the velocity-map imaging technique, oscillatory patterns were observed modulating the classical envelope that was measured in the experiments of Nicole et al. [Phys. Rev. Lett. 88, 133001 (2002)]. This extension of slow photoelectronmore » imaging, called photoionization microscopy, relies on the existence of interferences between various trajectories by which the electron moves from the atom to the plane of observation. In this article we present the main experimental results obtained both in slow photoelectron imaging and in photoionization microscopy. The formation of the interference pattern is discussed in the framework of a semiclassical model that is described in detail elsewhere. The qualitative information that can be drawn from the experiments is discussed, and the potential applications of photoionization microscopy are considered. Particular attention is paid to the role of continuum Stark resonances that appear between the saddle point in the Coulomb+dc field potential and the field-free ionization limit.« less

Nanoscale investigation of the piezoelectric properties of perovskite ferroelectrics and III-nitrides

NASA Astrophysics Data System (ADS)

Rodriguez, Brian Joseph

Nanoscale characterization of the piezoelectric and polarization related properties of III-Nitrides by piezoresponse force microscopy (PFM), electrostatic force microscopy (EFM) and scanning Kelvin probe microscopy (SKPM) resulted in the measurement of piezoelectric constants, surface charge and surface potential. Photo-electron emission microscopy (PEEM) was used to determine the local electronic band structure of a GaN-based lateral polarity heterostructure (GaN-LPH). Nanoscale characterization of the imprint and switching behavior of ferroelectric thin films by PFM resulted in the observation of domain pinning, while nanoscale characterization of the spatial variations in the imprint and switching behavior of integrated (111)-oriented PZT-based ferroelectric random access memory (FRAM) capacitors by PFM have revealed a significant difference in imprint and switching behavior between the inner and outer parts of capacitors. The inner regions of the capacitors are typically negatively imprinted and consequently tend to switch back after being poled by a positive bias, while regions at the edge of the capacitors tend to exhibit more symmetric hysteresis behavior. Evidence was obtained indicating that mechanical stress conditions in the central regions of the capacitors can lead to incomplete switching. A combination of vertical and lateral piezoresponse force microscopy (VPFM and LPFM, respectively) has been used to map the out-of-plane and in-plane polarization distribution, respectively, of integrated (111)-oriented PZT-based capacitors, which revealed poled capacitors are in a polydomain state.

Structure, Electronic Properties, and Electrochemical Behavior of a Boron-Doped Diamond/Quartz Optically Transparent Electrode.

PubMed

Wächter, Naihara; Munson, Catherine; Jarošová, Romana; Berkun, Isil; Hogan, Timothy; Rocha-Filho, Romeu C; Swain, Greg M

2016-10-26

The morphology, microstructure, chemistry, electronic properties, and electrochemical behavior of a boron-doped nanocrystalline diamond (BDD) thin film grown on quartz were evaluated. Diamond optically transparent electrodes (OTEs) are useful for transmission spectroelectrochemical measurements, offering excellent stability during anodic and cathodic polarization and exposure to a variety of chemical environments. We report on the characterization of a BDD OTE by atomic force microscopy, optical spectroscopy, Raman spectroscopic mapping, alternating-current Hall effect measurements, X-ray photoelectron spectroscopy, and electrochemical methods. The results reported herein provide the first comprehensive study of the relationship between the physical and chemical structure and electronic properties of a diamond OTE and the electrode's electrochemical activity.

Coexistence of two electronic nano-phases on a CH 3NH 3PbI 3–xCl x surface observed in STM measurements

DOE PAGES

Yost, Andrew J.; Pimachev, Artem; Ho, Chun -Chih; ...

2016-10-10

Scanning tunneling microscopy is utilized to investigate the local density of states of a CH 3NH 3PbI 3-xCl x perovskite in cross-sectional geometry. Two electronic phases, 10-20 nm in size, with different electronic properties inside the CH 3NH 3PbI 3-xCl x perovskite layer are observed by the dI/ dV mapping and point spectra. A power law dependence of the dI/dV point spectra is revealed. In addition, the distinct electronic phases are found to have preferential orientations close to the normal direction of the film surface. Density functional theory calculations indicate that the observed electronic phases are associated with local deviationmore » of I/Cl ratio, rather than different orientations of the electric dipole moments in the ferroelectric phases. Furthermore, by comparing the calculated results with experimental data we conclude that phase A (lower contrast in dI/dV mapping at -2.0 V bias) contains a lower I/Cl ratio than that in phase B (higher contrast in dI/dV).« less

2D strain mapping using scanning transmission electron microscopy Moiré interferometry and geometrical phase analysis.

PubMed

Pofelski, A; Woo, S Y; Le, B H; Liu, X; Zhao, S; Mi, Z; Löffler, S; Botton, G A

2018-04-01

A strain characterization technique based on Moiré interferometry in a scanning transmission electron microscope (STEM) and geometrical phase analysis (GPA) method is demonstrated. The deformation field is first captured in a single STEM Moiré hologram composed of multiple sets of periodic fringes (Moiré patterns) generated from the interference between the periodic scanning grating, fixing the positions of the electron probe on the sample, and the crystal structure. Applying basic principles from sampling theory, the Moiré patterns arrangement is then simulated using a STEM electron micrograph reference to convert the experimental STEM Moiré hologram into information related to the crystal lattice periodicities. The GPA method is finally applied to extract the 2D relative strain and rotation fields. The STEM Moiré interferometry enables the local information to be de-magnified to a large length scale, comparable to what can be achieved in dark-field electron holography. The STEM Moiré GPA method thus extends the conventional high-resolution STEM GPA capabilities by providing comparable quantitative 2D strain mapping with a larger field of view (up to a few microns). Copyright © 2017 Elsevier B.V. All rights reserved.

Compressed Sensing and Electron Microscopy

DTIC Science & Technology

2010-01-01

dimensional space IRn and so there is a lot of collapsing of information. For example, any vector η in the null space N = N (Φ) of Φ is mapped...assignment of the pixel intensity f̂P in the image. Thus, the pixels size is the same as the grid spacing h and we can ( with only a slight abuse of notation...offers a fresh view of signal/image acquisition and reconstruction.

Mapping Strain Gradients in the FIB-Structured InGaN/GaN Multilayered Films with 3D X-ray Microbeam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barabash, Rozaliya; Gao, Yanfei; Ice, Gene E

2010-01-01

This research presents a combined experimental-modeling study of lattice rotations and deviatoric strain gradients induced by focused-ion beam (FIB) milling in nitride heterostructures. 3D X-ray polychromatic microdiffraction (PXM) is used to map the local lattice orientation distribution in FIB-structured areas. Results are discussed in connection with microphotoluminescence ({mu}-PL), fluorescent analysis, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) data. It is demonstrated that FIB-milling causes both direct and indirect damage to the InGaN/GaN layers. In films subjected to direct ion beam impact, a narrow amorphidized top layer is formed. Near the milling area, FIB-induced stress relaxation and formation ofmore » complicated 3D strain fields are observed. The resulting lattice orientation changes are found to correlate with a decrease and/or loss of PL intensity, and agree well with finite element simulations of the three-dimensional strain fields near the relaxed trenches. Experimentally, it is found that the lattice surface normal has an in-plane rotation, which only appears in simulations when the GaN-substrate lattice mismatch annihilates the InGaN-substrate mismatch. This behavior further supports the notion that the film/substrate interface is incoherent.« less

Mapping strain gradients in the FIB-structured InGaN/GaN multilayered films with 3D x-ray microbeam.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barabash, R. I.; Gao, Y. F.; Ice, G. E.

2010-11-25

This research presents a combined experimental-modeling study of lattice rotations and deviatoric strain gradients induced by focused-ion beam (FIB) milling in nitride heterostructures. 3D X-ray polychromatic microdiffraction (PXM) is used to map the local lattice orientation distribution in FIB-structured areas. Results are discussed in connection with microphotoluminescence ({mu}-PL), fluorescent analysis, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) data. It is demonstrated that FIB-milling causes both direct and indirect damage to the InGaN/GaN layers. In films subjected to direct ion beam impact, a narrow amorphidized top layer is formed. Near the milling area, FIB-induced stress relaxation and formation ofmore » complicated 3D strain fields are observed. The resulting lattice orientation changes are found to correlate with a decrease and/or loss of PL intensity, and agree well with finite element simulations of the three-dimensional strain fields near the relaxed trenches. Experimentally, it is found that the lattice surface normal has an in-plane rotation, which only appears in simulations when the GaN-substrate lattice mismatch annihilates the InGaN-substrate mismatch. This behavior further supports the notion that the film/substrate interface is incoherent.« less

Multiwalled carbon nanotubes in alfalfa and wheat: toxicology and uptake.

PubMed

Miralles, Pola; Johnson, Errin; Church, Tamara L; Harris, Andrew T

2012-12-07

Data on the bioavailability and toxicity of carbon nanotubes (CNTs) in the environment, and, in particular, on their interactions with vascular plants, are limited. We investigated the effects of industrial-grade multiwalled CNTs (75 wt% CNTs) and their impurities on alfalfa and wheat. Phytotoxicity assays were performed during both seed germination and seedling growth. The germinations of both species were tolerant of up to 2560 mg l(-1) CNTs, and root elongation was enhanced in alfalfa and wheat seedlings exposed to CNTs. Remarkably, catalyst impurities also enhanced root elongation in alfalfa seedlings as well as wheat germination. Thus the impurities, not solely the CNTs, impacted the plants. CNT internalization by plants was investigated using electron microscopy and two-dimensional Raman mapping. The latter showed that CNTs were adsorbed onto the root surfaces of alfalfa and wheat without significant uptake or translocation. Electron microscopy investigations of internalization were inconclusive owing to poor contrast, so Fe(3)O(4)-functionalized CNTs were prepared and studied using energy-filter mapping of Fe(3)O(4). CNTs bearing Fe(3)O(4) nanoparticles were detected in the epidermis of one wheat root tip only, suggesting that internalization was possible but unusual. Thus, alfalfa and wheat tolerated high concentrations of industrial-grade multiwalled CNTs, which adsorbed onto their roots but were rarely taken up.

Multiwalled carbon nanotubes in alfalfa and wheat: toxicology and uptake

PubMed Central

Miralles, Pola; Johnson, Errin; Church, Tamara L.; Harris, Andrew T.

2012-01-01

Data on the bioavailability and toxicity of carbon nanotubes (CNTs) in the environment, and, in particular, on their interactions with vascular plants, are limited. We investigated the effects of industrial-grade multiwalled CNTs (75 wt% CNTs) and their impurities on alfalfa and wheat. Phytotoxicity assays were performed during both seed germination and seedling growth. The germinations of both species were tolerant of up to 2560 mg l−1 CNTs, and root elongation was enhanced in alfalfa and wheat seedlings exposed to CNTs. Remarkably, catalyst impurities also enhanced root elongation in alfalfa seedlings as well as wheat germination. Thus the impurities, not solely the CNTs, impacted the plants. CNT internalization by plants was investigated using electron microscopy and two-dimensional Raman mapping. The latter showed that CNTs were adsorbed onto the root surfaces of alfalfa and wheat without significant uptake or translocation. Electron microscopy investigations of internalization were inconclusive owing to poor contrast, so Fe3O4-functionalized CNTs were prepared and studied using energy-filter mapping of Fe3O4. CNTs bearing Fe3O4 nanoparticles were detected in the epidermis of one wheat root tip only, suggesting that internalization was possible but unusual. Thus, alfalfa and wheat tolerated high concentrations of industrial-grade multiwalled CNTs, which adsorbed onto their roots but were rarely taken up. PMID:22977097

Ion-induced electron emission microscopy

DOEpatents

Doyle, Barney L.; Vizkelethy, Gyorgy; Weller, Robert A.

2001-01-01

An ion beam analysis system that creates multidimensional maps of the effects of high energy ions from an unfocussed source upon a sample by correlating the exact entry point of an ion into a sample by projection imaging of the secondary electrons emitted at that point with a signal from a detector that measures the interaction of that ion within the sample. The emitted secondary electrons are collected in a strong electric field perpendicular to the sample surface and (optionally) projected and refocused by the electron lenses found in a photon emission electron microscope, amplified by microchannel plates and then their exact position is sensed by a very sensitive X Y position detector. Position signals from this secondary electron detector are then correlated in time with nuclear, atomic or electrical effects, including the malfunction of digital circuits, detected within the sample that were caused by the individual ion that created these secondary electrons in the fit place.

Molecules to maps: tools for visualization and interaction in support of computational biology.

PubMed

Kraemer, E T; Ferrin, T E

1998-01-01

The volume of data produced by genome projects, X-ray crystallography, NMR spectroscopy, and electron and confocal microscopy present the bioinformatics community with new challenges for analyzing, understanding, and exchanging this data. At the 1998 Pacific Symposium on Biocomputing, a track entitled 'Molecules to Maps: Tools for Visualization and Interaction in Computational Biology' provided tool developers and users with the opportunity to discuss advances in tools and techniques to assist scientists in evaluating, absorbing, navigating, and correlating this sea of information, through visualization and user interaction. In this paper we present these advances and discuss some of the challenges that remain to be solved.

When will Low-Contrast Features be Visible in a STEM X-Ray Spectrum Image?

PubMed

Parish, Chad M

2015-06-01

When will a small or low-contrast feature, such as an embedded second-phase particle, be visible in a scanning transmission electron microscopy (STEM) X-ray map? This work illustrates a computationally inexpensive method to simulate X-ray maps and spectrum images (SIs), based upon the equations of X-ray generation and detection. To particularize the general procedure, an example of nanostructured ferritic alloy (NFA) containing nm-sized Y2Ti2O7 embedded precipitates in ferritic stainless steel matrix is chosen. The proposed model produces physically appearing simulated SI data sets, which can either be reduced to X-ray dot maps or analyzed via multivariate statistical analysis. Comparison to NFA X-ray maps acquired using three different STEM instruments match the generated simulations quite well, despite the large number of simplifying assumptions used. A figure of merit of electron dose multiplied by X-ray collection solid angle is proposed to compare feature detectability from one data set (simulated or experimental) to another. The proposed method can scope experiments that are feasible under specific analysis conditions on a given microscope. Future applications, such as spallation proton-neutron irradiations, core-shell nanoparticles, or dopants in polycrystalline photovoltaic solar cells, are proposed.

Magnetic and Structural characterization of Co nanowires using advanced electron microscopy techniques

NASA Astrophysics Data System (ADS)

Cantu-Valle, Jesus; Ruiz-Zepeda, Francisco; Sanchez, John Eder; Mendoza-Santoyo, Fernando; Ponnce, Arturo; UTSA Team

2015-03-01

We report the magnetic imaging and crystalline structure of high aspect ratio cobalt nanowires. Experimental results of magnetization reversal in cobalt nanowires are presented to illustrate the functionality of the in situ magnetization process through the manipulation of the objective lens. By making use of this applicability, we measure the magnetization and show experimental evidence of the magnetic flux distribution in polycrystalline cobalt nanowires using off-axis electron holography. The retrieved phase map can distinguishes the magnetic contribution from the crystalline contribution with high accuracy. To determine the size and orientation of the grains within the Co nanowires, PED-assisted orientation mapping was performed. Finally, the magnetic analysis performed at individual nanowires was correlated with the crystalline orientation map, obtained by PED-assisted crystal phase orientation mapping. The large shape anisotropy determines the mayor magnetization direction rather than the magneto-crystalline anisotropy in the studied nanowires. The combination of the two techniques allowed us to directly visualize the effects of the crystallographic texture on the magnetization of the nanowire. The authors would like to acknowledge Dr. B.J.H. Stadler for providing the samples and financial support from NSF PREM #DMR 0934218, CONACYT, #215762 and Department of Defense #64756-RT-REP.

Characterization of twin boundaries in an Fe–17.5Mn–0.56C twinning induced plasticity steel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patterson, Erin E., E-mail: erin.diedrich@yahoo.com; Field, David P., E-mail: dfield@wsu.edu; Zhang, Yudong, E-mail: yudong.zhang@univ-metz.fr

2013-11-15

A twinning-induced plasticity steel of composition Fe–17.5 wt.% Mn–0.56 wt.% C–1.39 wt.% Al–0.24 wt.% Si was analyzed for the purpose of characterizing the relationship between tensile strain and deformation twinning. Tensile samples achieved a maximum of 0.46 true strain at failure, and a maximum ultimate tensile strength of 1599 MPa. Electron backscatter diffraction (EBSD) analysis showed that the grain orientation rotated heavily to < 111 > parallel to the tensile axis above 0.3 true strain. Sigma 3 misorientations, as identified by EBSD orientation measurements, and using the image quality maps were used to quantify the number of twins present inmore » the scanned areas of the samples. The image quality method yielded a distinct positive correlation between the twin area density and deformation, but the orientation measurements were unreliable in quantifying twin density in these structures. Quantitative analysis of the twin fraction is limited from orientation information because of the poor spatial resolution of EBSD in relation to the twin thickness. The EBSD orientation maps created for a thin foil sample showed some improvement in the resolution of the twins, but not enough to be significant. Measurements of the twins in the transmission electron microscopy micrographs yielded an average thickness of 23 nm, which is near the resolution capabilities of EBSD on this material for the instrumentation used. Electron channeling contrast imaging performed on one bulk tensile specimen of 0.34 true strain, using a method of controlled diffraction, yielded several images of twinning, dislocation structures and strain fields. A twin thickness of 66 nm was measured by the same method used for the transmission electron microscopy measurement. It is apparent that the results obtain by electron channeling contrast imaging were better than those by EBSD but did not capture all information on the twin boundaries such as was observed by transmission electron microscopy. - Highlights: • Performed tensile tests to assess mechanical performance of TWIP alloy • Analyzed tensile specimens using EBSD, TEM, and ECCI • EBSD showed that most twinning occurred at or near the < 111 >//TA orientation. • EBSD, TEM and ECCI were used to measure average twin density. • Compared spatial resolution of EBSD, ECCI and TEM for the instrumentation used.« less

Correlation between electron work functions of multiphase Cu-8Mn-8Al and de-alloying corrosion

NASA Astrophysics Data System (ADS)

Punburi, P.; Tareelap, N.; Srisukhumbowornchai, N.; Euaruksakul, C.; Yordsri, V.

2018-05-01

Low energy electron emission microscopy (LEEM) was used to measure local transition energy that was directly correlated to electron work function (EWF) of multiphase manganese-aluminum bronze alloys. We developed color mapping to distinguish the EWF of multiple phases and clarified that the EWF were in the following order: EWF of α > EWF of β > EWF of κ (EWFα > EWFβ > EWFκ). De-alloying corrosion took place due to the micro-galvanic cell at grain boundaries before it propagated into the β phase that had lower EWF than the α phase. The α phase was a stable phase because it contained high Cu while the β phase contained high Al and Mn. In addition, XRD analysis showed that the texture coefficient of the β phase revealed that almost all of the grains had (2 2 0) orientation, the lowest EWF compared to (1 1 1) and (2 0 0). Furthermore, transmission electron microscopy illustrated that there were fine Cu3Mn2Al precipitates in the Cu2MnAl matrix of the β phase. These precipitates formed micro-galvanic cells which played an important role in accelerating de-alloying corrosion.

Energy filtering transmission electron microscopy immunocytochemistry and antigen retrieval of surface layer proteins from Tannerella forsythensis using microwave or autoclave heating with citraconic anhydride

PubMed Central

2012-01-01

Tannerella forsythensis (Bacteroides forsythus), an anaerobic Gram-negative species of bacteria that plays a role in the progression of periodontal disease, has a unique bacterial protein profile. It is characterized by two unique protein bands with molecular weights of more than 200 kDa. It also is known to have a typical surface layer (S-layer) consisting of regularly arrayed subunits outside the outer membrane. We examined the relationship between high molecular weight proteins and the S-layer using electron microscopic immunolabeling with chemical fixation and an antigen retrieval procedure consisting of heating in a microwave oven or autoclave with citraconic anhydride. Immunogold particles were localized clearly at the outermost cell surface. We also used energy-filtering transmission electron microscopy (EFTEM) to visualize 3, 3′-diaminobenzidine tetrahydrochloride (DAB) reaction products after microwave antigen retrieval with 1% citraconic anhydride. The three-window method for electron spectroscopic images (ESI) of nitrogen by the EFTEM reflected the presence of moieties demonstrated by the DAB reaction with horseradish peroxidase (HRP)-conjugated secondary antibodies instead of immunogold particles. The mapping patterns of net nitrogen were restricted to the outermost cell surface. PMID:22984898

Energy filtering transmission electron microscopy immunocytochemistry and antigen retrieval of surface layer proteins from Tannerella forsythensis using microwave or autoclave heating with citraconic anhydride.

PubMed

Moriguchi, K; Mitamura, Y; Iwami, J; Hasegawa, Y; Higuchi, N; Murakami, Y; Maeda, H; Yoshimura, F; Nakamura, H; Ohno, N

2012-11-01

Tannerella forsythensis (Bacteroides forsythus), an anaerobic Gram-negative species of bacteria that plays a role in the progression of periodontal disease, has a unique bacterial protein profile. It is characterized by two unique protein bands with molecular weights of more than 200 kDa. It also is known to have a typical surface layer (S-layer) consisting of regularly arrayed subunits outside the outer membrane. We examined the relationship between high molecular weight proteins and the S-layer using electron microscopic immunolabeling with chemical fixation and an antigen retrieval procedure consisting of heating in a microwave oven or autoclave with citraconic anhydride. Immunogold particles were localized clearly at the outermost cell surface. We also used energy-filtering transmission electron microscopy (EFTEM) to visualize 3, 3'-diaminobenzidine tetrahydrochloride (DAB) reaction products after microwave antigen retrieval with 1% citraconic anhydride. The three-window method for electron spectroscopic images (ESI) of nitrogen by the EFTEM reflected the presence of moieties demonstrated by the DAB reaction with horseradish peroxidase (HRP)-conjugated secondary antibodies instead of immunogold particles. The mapping patterns of net nitrogen were restricted to the outermost cell surface.

Nanoscale Imaging of Whole Cells Using a Liquid Enclosure and a Scanning Transmission Electron Microscope

PubMed Central

Peckys, Diana B.; Veith, Gabriel M.; Joy, David C.; de Jonge, Niels

2009-01-01

Nanoscale imaging techniques are needed to investigate cellular function at the level of individual proteins and to study the interaction of nanomaterials with biological systems. We imaged whole fixed cells in liquid state with a scanning transmission electron microscope (STEM) using a micrometer-sized liquid enclosure with electron transparent windows providing a wet specimen environment. Wet-STEM images were obtained of fixed E. coli bacteria labeled with gold nanoparticles attached to surface membrane proteins. Mammalian cells (COS7) were incubated with gold-tagged epidermal growth factor and fixed. STEM imaging of these cells resulted in a resolution of 3 nm for the gold nanoparticles. The wet-STEM method has several advantages over conventional imaging techniques. Most important is the capability to image whole fixed cells in a wet environment with nanometer resolution, which can be used, e.g., to map individual protein distributions in/on whole cells. The sample preparation is compatible with that used for fluorescent microscopy on fixed cells for experiments involving nanoparticles. Thirdly, the system is rather simple and involves only minimal new equipment in an electron microscopy (EM) laboratory. PMID:20020038

Large-scale Scanning Transmission Electron Microscopy (Nanotomy) of Healthy and Injured Zebrafish Brain.

PubMed

Kuipers, Jeroen; Kalicharan, Ruby D; Wolters, Anouk H G; van Ham, Tjakko J; Giepmans, Ben N G

2016-05-25

Large-scale 2D electron microscopy (EM), or nanotomy, is the tissue-wide application of nanoscale resolution electron microscopy. Others and we previously applied large scale EM to human skin pancreatic islets, tissue culture and whole zebrafish larvae(1-7). Here we describe a universally applicable method for tissue-scale scanning EM for unbiased detection of sub-cellular and molecular features. Nanotomy was applied to investigate the healthy and a neurodegenerative zebrafish brain. Our method is based on standardized EM sample preparation protocols: Fixation with glutaraldehyde and osmium, followed by epoxy-resin embedding, ultrathin sectioning and mounting of ultrathin-sections on one-hole grids, followed by post staining with uranyl and lead. Large-scale 2D EM mosaic images are acquired using a scanning EM connected to an external large area scan generator using scanning transmission EM (STEM). Large scale EM images are typically ~ 5 - 50 G pixels in size, and best viewed using zoomable HTML files, which can be opened in any web browser, similar to online geographical HTML maps. This method can be applied to (human) tissue, cross sections of whole animals as well as tissue culture(1-5). Here, zebrafish brains were analyzed in a non-invasive neuronal ablation model. We visualize within a single dataset tissue, cellular and subcellular changes which can be quantified in various cell types including neurons and microglia, the brain's macrophages. In addition, nanotomy facilitates the correlation of EM with light microscopy (CLEM)(8) on the same tissue, as large surface areas previously imaged using fluorescent microscopy, can subsequently be subjected to large area EM, resulting in the nano-anatomy (nanotomy) of tissues. In all, nanotomy allows unbiased detection of features at EM level in a tissue-wide quantifiable manner.

Large-scale Scanning Transmission Electron Microscopy (Nanotomy) of Healthy and Injured Zebrafish Brain

PubMed Central

Kuipers, Jeroen; Kalicharan, Ruby D.; Wolters, Anouk H. G.

2016-01-01

Large-scale 2D electron microscopy (EM), or nanotomy, is the tissue-wide application of nanoscale resolution electron microscopy. Others and we previously applied large scale EM to human skin pancreatic islets, tissue culture and whole zebrafish larvae1-7. Here we describe a universally applicable method for tissue-scale scanning EM for unbiased detection of sub-cellular and molecular features. Nanotomy was applied to investigate the healthy and a neurodegenerative zebrafish brain. Our method is based on standardized EM sample preparation protocols: Fixation with glutaraldehyde and osmium, followed by epoxy-resin embedding, ultrathin sectioning and mounting of ultrathin-sections on one-hole grids, followed by post staining with uranyl and lead. Large-scale 2D EM mosaic images are acquired using a scanning EM connected to an external large area scan generator using scanning transmission EM (STEM). Large scale EM images are typically ~ 5 - 50 G pixels in size, and best viewed using zoomable HTML files, which can be opened in any web browser, similar to online geographical HTML maps. This method can be applied to (human) tissue, cross sections of whole animals as well as tissue culture1-5. Here, zebrafish brains were analyzed in a non-invasive neuronal ablation model. We visualize within a single dataset tissue, cellular and subcellular changes which can be quantified in various cell types including neurons and microglia, the brain's macrophages. In addition, nanotomy facilitates the correlation of EM with light microscopy (CLEM)8 on the same tissue, as large surface areas previously imaged using fluorescent microscopy, can subsequently be subjected to large area EM, resulting in the nano-anatomy (nanotomy) of tissues. In all, nanotomy allows unbiased detection of features at EM level in a tissue-wide quantifiable manner. PMID:27285162

Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.

2014-12-15

Fertilization of a mammalian egg initiates a series of 'zinc sparks' that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each ofmore » which contains, on average, 10(6) zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes« less

Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks.

PubMed

Que, Emily L; Bleher, Reiner; Duncan, Francesca E; Kong, Betty Y; Gleber, Sophie C; Vogt, Stefan; Chen, Si; Garwin, Seth A; Bayer, Amanda R; Dravid, Vinayak P; Woodruff, Teresa K; O'Halloran, Thomas V

2015-02-01

Fertilization of a mammalian egg initiates a series of 'zinc sparks' that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 10(6) zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes.

Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

PubMed Central

Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak; Woodruff, Teresa K.; O’Halloran, Thomas V.

2015-01-01

Fertilization of a mammalian egg induces a series of ‘zinc sparks’ that are necessary for inducing the egg-to-embryo transition. Despite the importance of these zinc efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches to resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy dispersive spectroscopy, X-ray fluorescence microscopy, and 3D elemental tomography for high resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 106 zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes. PMID:25615666

Locating a silane coupling agent in silica-filled rubber composites by EFTEM.

PubMed

Dohi, Hidehiko; Horiuchi, Shin

2007-11-20

A silane coupling agent (SA) was added to silica/rubber composites at different mixing temperatures and the formation of a coupling layer at the silica/rubber interface was investigated by energy-filtering transmission electron microscopy. Bis(triethoxysilypropyl)tetrasulfane (TESPT), which was used as the SA, reacted with the silanol groups on the silica surface and with styrene-butadiene rubber to form an interfacial coupling layer. The silicon and sulfur elemental distributions were analyzed by electron energy loss spectroscopy (EELS) and elemental mapping. The amount of TESPT trapped in the rubber matrix could be qualitatively estimated by EELS, and the in situ formed coupling layer could be characterized by elemental mapping. The result indicated that the formation of the coupling layer was affected by the mixing temperature. The technique described here will contribute to the study of interface-property relationships and the evaluation of the role of SAs in polymeric composites.

Photogrammetry of the three-dimensional shape and texture of a nanoscale particle using scanning electron microscopy and free software.

PubMed

Gontard, Lionel C; Schierholz, Roland; Yu, Shicheng; Cintas, Jesús; Dunin-Borkowski, Rafal E

2016-10-01

We apply photogrammetry in a scanning electron microscope (SEM) to study the three-dimensional shape and surface texture of a nanoscale LiTi2(PO4)3 particle. We highlight the fact that the technique can be applied non-invasively in any SEM using free software (freeware) and does not require special sample preparation. Three-dimensional information is obtained in the form of a surface mesh, with the texture of the sample stored as a separate two-dimensional image (referred to as a UV Map). The mesh can be used to measure parameters such as surface area, volume, moment of inertia and center of mass, while the UV map can be used to study the surface texture using conventional image processing techniques. We also illustrate the use of 3D printing to visualize the reconstructed model. Copyright © 2016 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Kai; Ma, Ying -Zhong; Simpson, Mary Jane

Charge carrier trapping degrades the performance of organometallic halide perovskite solar cells. To characterize the locations of electronic trap states in a heterogeneous photoactive layer, a spatially resolved approach is essential. Here, we report a comparative study on methylammonium lead tri-iodide perovskite thin films subject to different thermal annealing times using a combined photoluminescence (PL) and femtosecond transient absorption microscopy (TAM) approach to spatially map trap states. This approach coregisters the initially populated electronic excited states with the regions that recombine radiatively. Although the TAM images are relatively homogeneous for both samples, the corresponding PL images are highly structured. Themore » remarkable variation in the PL intensities as compared to transient absorption signal amplitude suggests spatially dependent PL quantum efficiency, indicative of trapping events. Furthermore, detailed analysis enables identification of two trapping regimes: a densely packed trapping region and a sparse trapping area that appear as unique spatial features in scaled PL maps.« less

Molecular architecture of the yeast Mediator complex

PubMed Central

Robinson, Philip J; Trnka, Michael J; Pellarin, Riccardo; Greenberg, Charles H; Bushnell, David A; Davis, Ralph; Burlingame, Alma L; Sali, Andrej; Kornberg, Roger D

2015-01-01

The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI: http://dx.doi.org/10.7554/eLife.08719.001 PMID:26402457

Microstructural investigation of nickel silicide thin films and the silicide-silicon interface using transmission electron microscopy.

PubMed

Bhaskaran, M; Sriram, S; Mitchell, D R G; Short, K T; Holland, A S; Mitchell, A

2009-01-01

This article discusses the results of transmission electron microscopy (TEM)-based investigation of nickel silicide (NiSi) thin films grown on silicon. Nickel silicide is currently used as the CMOS technology standard for local interconnects and in electrical contacts. Films were characterized with a range of TEM-based techniques along with glancing angle X-ray diffraction. The nickel silicide thin films were formed by vacuum annealing thin films of nickel (50 nm) deposited on (100) silicon. The cross-sectional samples indicated a final silicide thickness of about 110 nm. This investigation studied and reports on three aspects of the thermally formed thin films: the uniformity in composition of the film using jump ratio maps; the nature of the interface using high resolution imaging; and the crystalline orientation of the thin films using selected-area electron diffraction (SAED). The analysis highlighted uniform composition in the thin films, which was also substantiated by spectroscopy techniques; an interface exhibiting the desired abrupt transition from silicide to silicon; and desired and preferential crystalline orientation corresponding to stoichiometric NiSi, supported by glancing angle X-ray diffraction results.

Spatially Resolved Imaging on Photocarrier Generations and Band Alignments at Perovskite/PbI2 Heterointerfaces of Perovskite Solar Cells by Light-Modulated Scanning Tunneling Microscopy.

PubMed

Shih, Min-Chuan; Li, Shao-Sian; Hsieh, Cheng-Hua; Wang, Ying-Chiao; Yang, Hung-Duen; Chiu, Ya-Ping; Chang, Chia-Seng; Chen, Chun-Wei

2017-02-08

The presence of the PbI 2 passivation layers at perovskite crystal grains has been found to considerably affect the charge carrier transport behaviors and device performance of perovskite solar cells. This work demonstrates the application of a novel light-modulated scanning tunneling microscopy (LM-STM) technique to reveal the interfacial electronic structures at the heterointerfaces between CH 3 NH 3 PbI 3 perovskite crystals and PbI 2 passivation layers of individual perovskite grains under light illumination. Most importantly, this technique enabled the first observation of spatially resolved mapping images of photoinduced interfacial band bending of valence bands and conduction bands and the photogenerated electron and hole carriers at the heterointerfaces of perovskite crystal grains. By systematically exploring the interfacial electronic structures of individual perovskite grains, enhanced charge separation and reduced back recombination were observed when an optimal design of interfacial PbI 2 passivation layers consisting of a thickness less than 20 nm at perovskite crystal grains was applied.

Effective reduction of p-nitrophenol by silver nanoparticle loaded on magnetic Fe3O4/ATO nano-composite

NASA Astrophysics Data System (ADS)

Karki, Hem Prakash; Ojha, Devi Prashad; Joshi, Mahesh Kumar; Kim, Han Joo

2018-03-01

A silver loaded hematite (Fe3O4) and antimony doped tin oxide (ATO) magnetic nano-composite (Ag-Fe3O4/ATO) was successfully synthesized by in situ one pot green and facile hydrothermal process. The formation of nano-composite, its structure, morphology, and stability were characterized by field emission scanning electron microscopy (FE-SEM), high resolution transmission electron microscopy (HRTEM), electron diffraction spectroscopy (EDS), elemental mapping by high resolution scanning transmission electron microscopy (STEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Fourier transform infra-red spectroscopy (FTIR). UV-vis spectroscopy was used to monitor the catalytic reduction of p-nitrophenol (PNP) into p-aminophenol (PAP) in presence of Ag-Fe3O4/ATO nano-composite with excess of sodium borohydride (NaBH4). The pseudo-first order kinetic equation could describe the reduction of p-nitrophenol with excess of NaBH4. For the first time, ATO surface was used for hydrothermal growth of silver and iron oxide magnetic nanoparticles. The in situ growth of these nanoparticles provided an effective bonding of components of the nano-composite over the surface of ATO nanoparticles. This nano-composite exhibited easy synthesis, high stability, cost effective and rapid separation using external magnet. The excellent catalytic and anti-bacterial activity of as-synthesized silver nano-composite makes it potential nano-catalyst for waste water treatment as well as biomedical application.

Creating and Steering Highly Directional Electron Beams in Graphene.

PubMed

Liu, Ming-Hao; Gorini, Cosimo; Richter, Klaus

2017-02-10

We put forward a concept to create highly collimated, nondispersive electron beams in pseudorelativistic Dirac materials such as graphene or topological insulator surfaces. Combining negative refraction and Klein collimation at a parabolic pn junction, the proposed lens generates beams, as narrow as the focal length, that stay focused over scales of several microns and can be steered by a magnetic field without losing collimation. We demonstrate the lens capabilities by applying it to two paradigmatic settings of graphene electron optics: We propose a setup for observing high-resolution angle-dependent Klein tunneling, and, exploiting the intimate quantum-to-classical correspondence of these focused electron waves, we consider high-fidelity transverse magnetic focusing accompanied by simulations for current mapping through scanning gate microscopy. Our proposal opens up new perspectives for next-generation graphene electron optics experiments.

Creating and Steering Highly Directional Electron Beams in Graphene

NASA Astrophysics Data System (ADS)

Liu, Ming-Hao; Gorini, Cosimo; Richter, Klaus

2017-02-01

We put forward a concept to create highly collimated, nondispersive electron beams in pseudorelativistic Dirac materials such as graphene or topological insulator surfaces. Combining negative refraction and Klein collimation at a parabolic p n junction, the proposed lens generates beams, as narrow as the focal length, that stay focused over scales of several microns and can be steered by a magnetic field without losing collimation. We demonstrate the lens capabilities by applying it to two paradigmatic settings of graphene electron optics: We propose a setup for observing high-resolution angle-dependent Klein tunneling, and, exploiting the intimate quantum-to-classical correspondence of these focused electron waves, we consider high-fidelity transverse magnetic focusing accompanied by simulations for current mapping through scanning gate microscopy. Our proposal opens up new perspectives for next-generation graphene electron optics experiments.

Investigation of TiO2 nanoparticles translocation through a Caco-2 monolayer

NASA Astrophysics Data System (ADS)

Brun, E.; Jugan, M.-L.; Herlin-Boime, N.; Jaillard, D.; Fayard, B.; Flank, A.-M.; Mabondzo, A.; Carrière, M.

2011-07-01

Nanoparticles (NPs) are introduced in a growing number of commercial products, including food and beverage but their effects on gastrointestinal tract are poorly investigated. Here we focused on the translocation of TiO2 NPs through Caco-2 monolayers exposed to anatase and rutile NPs up to 24 h. Internalization was followed by transmission electronic microscopy and μ-XRF elemental mapping, coupled to XAS analysis of Ti atoms environment. This innovative technique is among the best techniques to get insights on NP fate after internalization. The originality of this project relies on the panel of microscopy techniques implemented to investigate digestive barrier translocation, bringing together biologists, chemists and physicists in a pluridisciplinary research program.

Ferroelectric Polarization-Modulated Interfacial Fine Structures Involving Two-Dimensional Electron Gases in Pb(Zr,Ti)O3/LaAlO3/SrTiO3 Heterostructures.

PubMed

Wang, Shuangbao; Bai, Yuhang; Xie, Lin; Li, Chen; Key, Julian D; Wu, Di; Wang, Peng; Pan, Xiaoqing

2018-01-10

Interfacial fine structures of bare LaAlO 3 /SrTiO 3 (LAO/STO) heterostructures are compared with those of LAO/STO heterostructures capped with upward-polarized Pb(Zr 0.1 ,Ti 0.9 )O 3 (PZT up ) or downward-polarized Pb(Zr 0.5 ,Ti 0.5 )O 3 (PZT down ) overlayers by aberration-corrected scanning transmission electron microscopy experiments. By combining the acquired electron energy-loss spectroscopy mapping, we are able to directly observe electron transfer from Ti 4+ to Ti 3+ and ionic displacements at the interface of bare LAO/STO and PZT down /LAO/STO heterostructure unit cell by unit cell. No evidence of Ti 3+ is observed at the interface of the PZT up /LAO/STO samples. Furthermore, the confinement of the two-dimensional electron gas (2DEG) at the interface is determined by atomic-column spatial resolution. Compared with the bare LAO/STO interface, the 2DEG density at the LAO/STO interface is enhanced or depressed by the PZT down or PZT up overlayer, respectively. Our microscopy studies shed light on the mechanism of ferroelectric modulation of interfacial transport at polar/nonpolar oxide heterointerfaces, which may facilitate applications of these materials as nonvolatile memory.

Microstructural characterization of weld joints of 9Cr reduced activation ferritic martensitic steel fabricated by different joining methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas Paul, V.; Saroja, S.; Albert, S.K.

This paper presents a detailed electron microscopy study on the microstructure of various regions of weldment fabricated by three welding methods namely tungsten inert gas welding, electron beam welding and laser beam welding in an indigenously developed 9Cr reduced activation ferritic/martensitic steel. Electron back scatter diffraction studies showed a random micro-texture in all the three welds. Microstructural changes during thermal exposures were studied and corroborated with hardness and optimized conditions for the post weld heat treatment have been identified for this steel. Hollomon–Jaffe parameter has been used to estimate the extent of tempering. The activation energy for the tempering processmore » has been evaluated and found to be corresponding to interstitial diffusion of carbon in ferrite matrix. The type and microchemistry of secondary phases in different regions of the weldment have been identified by analytical transmission electron microscopy. - Highlights: • Comparison of microstructural parameters in TIG, electron beam and laser welds of RAFM steel • EBSD studies to illustrate the absence of preferred orientation and identification of prior austenite grain size using phase identification map • Optimization of PWHT conditions for indigenous RAFM steel • Study of kinetics of tempering and estimation of apparent activation energy of the process.« less

FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.

PubMed

Tiemann, Johanna K S; Rose, Alexander S; Ismer, Jochen; Darvish, Mitra D; Hilal, Tarek; Spahn, Christian M T; Hildebrand, Peter W

2018-05-21

Cryo-electron microscopy (cryo-EM) is a standard method to determine the three-dimensional structures of molecular complexes. However, easy to use tools for modeling of protein segments into cryo-EM maps are sparse. Here, we present the FragFit web-application, a web server for interactive modeling of segments of up to 35 amino acids length into cryo-EM density maps. The fragments are provided by a regularly updated database containing at the moment about 1 billion entries extracted from PDB structures and can be readily integrated into a protein structure. Fragments are selected based on geometric criteria, sequence similarity and fit into a given cryo-EM density map. Web-based molecular visualization with the NGL Viewer allows interactive selection of fragments. The FragFit web-application, accessible at http://proteinformatics.de/FragFit, is free and open to all users, without any login requirements.

Measurement of atomic electric fields and charge densities from average momentum transfers using scanning transmission electron microscopy.

PubMed

Müller-Caspary, Knut; Krause, Florian F; Grieb, Tim; Löffler, Stefan; Schowalter, Marco; Béché, Armand; Galioit, Vincent; Marquardt, Dennis; Zweck, Josef; Schattschneider, Peter; Verbeeck, Johan; Rosenauer, Andreas

2017-07-01

This study sheds light on the prerequisites, possibilities, limitations and interpretation of high-resolution differential phase contrast (DPC) imaging in scanning transmission electron microscopy (STEM). We draw particular attention to the well-established DPC technique based on segmented annular detectors and its relation to recent developments based on pixelated detectors. These employ the expectation value of the momentum transfer as a reliable measure of the angular deflection of the STEM beam induced by an electric field in the specimen. The influence of scattering and propagation of electrons within the specimen is initially discussed separately and then treated in terms of a two-state channeling theory. A detailed simulation study of GaN is presented as a function of specimen thickness and bonding. It is found that bonding effects are rather detectable implicitly, e.g., by characteristics of the momentum flux in areas between the atoms than by directly mapping electric fields and charge densities. For strontium titanate, experimental charge densities are compared with simulations and discussed with respect to experimental artifacts such as scan noise. Finally, we consider practical issues such as figures of merit for spatial and momentum resolution, minimum electron dose, and the mapping of larger-scale, built-in electric fields by virtue of data averaged over a crystal unit cell. We find that the latter is possible for crystals with an inversion center. Concerning the optimal detector design, this study indicates that a sampling of 5mrad per pixel is sufficient in typical applications, corresponding to approximately 10×10 available pixels. Copyright © 2016 Elsevier B.V. All rights reserved.

In situ identification and X-ray imaging of microorganisms distribution on the Tatahouine meteorite

NASA Astrophysics Data System (ADS)

Lemelle, L.; Salomé, M.; Fialin, M.; Simionovici, A.; Gillet, Ph.

2004-10-01

Microorganisms were searched for among the complex microstructures observed on the surface of a fragment of the Tatahouine meteorite inherited from the Tunisian soil in which they were buried. In this view, the chemical compositions, particularly the nitrogen, phosphorus, and sulphur compositions, including the sulphur speciation, were investigated using scanning electron microscopy (SEM), electron probe microanalysis (EPMA) mapping, and scanning X-ray microscopy (SXM). A few 2-μm-thick filaments, partly covered by patches of calcite ensuring they were not deposited by a laboratory contamination, were observed by SEM. The EPMA maps show that the portions free of calcite of the filaments have low but constant contents of nitrogen, sulphur, and phosphorus. The SXM maps were recorded at 2473.5, 2478, and 2482.2 eV, which are respectively characteristic for amino acid linked sulphur, sulphite (SO32-), and sulphate (SO42-). The portions of the filaments detected by EPMA are also those that are enriched in amino acid linked sulphur. The calculated (N/S) elemental ratio is consistent with the one of the dehydrated Escherichia coli matter, contrary to the much lower (P/S) elemental ratio. In living cells, the bulk N and S elements are mainly located in large polymers by covalent bonds, whereas a significant amount of P belongs to small and reactive molecules. We thus can propose that the observed microstructures are dehydrated microorganisms, in which most of the elements that were composing the polymers were retained, whereas the small electrolytes and molecules were removed.

Ion microprobe, electron microprobe and cathodoluminescence data for Allende inclusions with emphasis on plagioclase chemistry

NASA Technical Reports Server (NTRS)

Hutcheon, I. D.; Steele, I. M.; Smith, J. V.; Clayton, R. N.

1978-01-01

Three Type B inclusions from the Allende meteorite have been analyzed. A grain-to-grain characterization of mineral chemistry and isotopic content was made possible by the use of a range of techniques, including luminescence and scanning electron microscopy and electron and ion microprobe analysis. Cathodoluminescence was used in fine-grained, optically opaque regions to distinguish between sub-micrometer phases, such as garnet and Si-rich material, subsequently identified by electron probe and scanning electron microscope analyses. Four types of luminescence patterns, due to twinning, primary sector zoning, alteration of boundaries and fractures, and shock effects, were identified in Allende plagioclase. Luminescence color exhibited a strong correlation with Mg content and provided a guide for an electron probe quantitative map of Mg and Na distributions. Ion microprobe studies of individual grains revealed large excesses of Mg-26.

Effective absorption correction for energy dispersive X-ray mapping in a scanning transmission electron microscope: analysing the local indium distribution in rough samples of InGaN alloy layers.

PubMed

Wang, X; Chauvat, M-P; Ruterana, P; Walther, T

2017-12-01

We have applied our previous method of self-consistent k*-factors for absorption correction in energy-dispersive X-ray spectroscopy to quantify the indium content in X-ray maps of thick compound InGaN layers. The method allows us to quantify the indium concentration without measuring the sample thickness, density or beam current, and works even if there is a drastic local thickness change due to sample roughness or preferential thinning. The method is shown to select, point-by-point in a two-dimensional spectrum image or map, the k*-factor from the local Ga K/L intensity ratio that is most appropriate for the corresponding sample geometry, demonstrating it is not the sample thickness measured along the electron beam direction but the optical path length the X-rays have to travel through the sample that is relevant for the absorption correction. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

MapA, an iron-regulated, cytoplasmic membrane protein in the cyanobacterium Synechococcus sp. strain PCC7942.

PubMed

Webb, R; Troyan, T; Sherman, D; Sherman, L A

1994-08-01

Growth of Synechococcus sp. strain PCC 7942 in iron-deficient media leads to the accumulation of an approximately 34-kDa protein. The gene encoding this protein, mapA (membrane-associated protein A), has been cloned and sequenced (GenBank accession number, L01621). The mapA transcript is not detectable in normally grown cultures but is stably accumulated by cells grown in iron-deficient media. However, the promoter sequence for this gene does not resemble other bacterial iron-regulated promoters described to date. The carboxyl-terminal region of the derived amino acid sequence of MapA resembles bacterial proteins involved in iron acquisition, whereas the amino-terminal end of MapA has a high degree of amino acid identity with the abundant, chloroplast envelope protein E37. An approach employing improved cellular fractionation techniques as well as electron microscopy and immunocytochemistry was essential in localizing MapA protein to the cytoplasmic membrane of Synechococcus sp. strain PCC 7942. When these cells were grown under iron-deficient conditions, a significant fraction of MapA could also be localized to the thylakoid membranes.

Gap junctions on hippocampal mossy fiber axons demonstrated by thin-section electron microscopy and freeze–fracture replica immunogold labeling

PubMed Central

Hamzei-Sichani, Farid; Kamasawa, Naomi; Janssen, William G. M.; Yasumura, Thomas; Davidson, Kimberly G. V.; Hof, Patrick R.; Wearne, Susan L.; Stewart, Mark G.; Young, Steven R.; Whittington, Miles A.; Rash, John E.; Traub, Roger D.

2007-01-01

Gap junctions have been postulated to exist between the axons of excitatory cortical neurons based on electrophysiological, modeling, and dye-coupling data. Here, we provide ultrastructural evidence for axoaxonic gap junctions in dentate granule cells. Using combined confocal laser scanning microscopy, thin-section transmission electron microscopy, and grid-mapped freeze–fracture replica immunogold labeling, 10 close appositions revealing axoaxonic gap junctions (≈30–70 nm in diameter) were found between pairs of mossy fiber axons (≈100–200 nm in diameter) in the stratum lucidum of the CA3b field of the rat ventral hippocampus, and one axonal gap junction (≈100 connexons) was found on a mossy fiber axon in the CA3c field of the rat dorsal hippocampus. Immunogold labeling with two sizes of gold beads revealed that connexin36 was present in that axonal gap junction. These ultrastructural data support computer modeling and in vitro electrophysiological data suggesting that axoaxonic gap junctions play an important role in the generation of very fast (>70 Hz) network oscillations and in the hypersynchronous electrical activity of epilepsy. PMID:17640909

Growth characteristics of primary M7C3 carbide in hypereutectic Fe-Cr-C alloy.

PubMed

Liu, Sha; Zhou, Yefei; Xing, Xiaolei; Wang, Jibo; Ren, Xuejun; Yang, Qingxiang

2016-09-06

The microstructure of the hypereutectic Fe-Cr-C alloy is observed by optical microscopy (OM). The initial growth morphology, the crystallographic structure, the semi-molten morphology and the stacking faults of the primary M7C3 carbide are observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The in-suit growth process of the primary M7C3 carbide was observed by confocal laser microscope (CLM). It is found that the primary M7C3 carbide in hypereutectic Fe-Cr-C alloy is irregular polygonal shape with several hollows in the center and gaps on the edge. Some primary M7C3 carbides are formed by layers of shell or/and consist of multiple parts. In the initial growth period, the primary M7C3 carbide forms protrusion parallel to {} crystal planes. The extending and revolving protrusion forms the carbide shell. The electron backscattered diffraction (EBSD) maps show that the primary M7C3 carbide consists of multiple parts. The semi-molten M7C3 carbide contains unmelted shell and several small-scale carbides inside, which further proves that the primary M7C3 carbide is not an overall block. It is believed that the coalescence of the primary M7C3 carbides is ascribed to the growing condition of the protrusion and the gap filling process.

Growth characteristics of primary M7C3 carbide in hypereutectic Fe-Cr-C alloy

PubMed Central

Liu, Sha; Zhou, Yefei; Xing, Xiaolei; Wang, Jibo; Ren, Xuejun; Yang, Qingxiang

2016-01-01

The microstructure of the hypereutectic Fe-Cr-C alloy is observed by optical microscopy (OM). The initial growth morphology, the crystallographic structure, the semi-molten morphology and the stacking faults of the primary M7C3 carbide are observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The in-suit growth process of the primary M7C3 carbide was observed by confocal laser microscope (CLM). It is found that the primary M7C3 carbide in hypereutectic Fe-Cr-C alloy is irregular polygonal shape with several hollows in the center and gaps on the edge. Some primary M7C3 carbides are formed by layers of shell or/and consist of multiple parts. In the initial growth period, the primary M7C3 carbide forms protrusion parallel to {} crystal planes. The extending and revolving protrusion forms the carbide shell. The electron backscattered diffraction (EBSD) maps show that the primary M7C3 carbide consists of multiple parts. The semi-molten M7C3 carbide contains unmelted shell and several small-scale carbides inside, which further proves that the primary M7C3 carbide is not an overall block. It is believed that the coalescence of the primary M7C3 carbides is ascribed to the growing condition of the protrusion and the gap filling process. PMID:27596718

Observation of FeGe skyrmions by electron phase microscopy with hole-free phase plate

NASA Astrophysics Data System (ADS)

Kotani, Atsuhiro; Harada, Ken; Malac, Marek; Salomons, Mark; Hayashida, Misa; Mori, Shigeo

2018-05-01

We report application of hole-free phase plate (HFPP) to imaging of magnetic skyrmion lattices. Using HFPP imaging, we observed skyrmions in FeGe, and succeeded in obtaining phase contrast images that reflect the sample magnetization distribution. According to the Aharonov-Bohm effect, the electron phase is shifted by the magnetic flux due to sample magnetization. The differential processing of the intensity in a HFPP image allows us to successfully reconstruct the magnetization map of the skyrmion lattice. Furthermore, the calculated phase shift due to the magnetization of the thin film was consistent with that measured by electron holography experiment, which demonstrates that HFPP imaging can be utilized for analysis of magnetic fields and electrostatic potential distribution at the nanoscale.

Biomedical Applications of Nanodiamonds: An Overview.

PubMed

Passeri, D; Rinaldi, F; Ingallina, C; Carafa, M; Rossi, M; Terranova, M L; Marianecci, C

2015-02-01

Nanodiamonds are a novel class of nanomaterials which have raised much attention for application in biomedical field, as they combine the possibility of being produced on large scale using relatively inexpensive synthetic processes, of being fluorescent as a consequence of the presence of nitrogen vacancies, of having their surfaces functionalized, and of having good biocompatibility. Among other applications, we mainly focus on drug delivery, including cell interaction, targeting, cancer therapy, gene and protein delivery. In addition, nanodiamonds for bone and dental implants and for antibacterial use is discussed. Techniques for detection and imaging of nanodiamonds in biological tissues are also reviewed, including electron microscopy, fluorescence microscopy, Raman mapping, atomic force microscopy, thermal imaging, magnetic resonance imaging, and positron emission tomography, either in vitro, in vivo, or ex vivo. Toxicological aspects related to the use of nanodiamonds are also discussed. Finally, patents, preclinical and clinical trials based on the use of nanodiamonds for biomedical applications are reviewed.

Macromolecular refinement by model morphing using non-atomic parameterizations.

PubMed

Cowtan, Kevin; Agirre, Jon

2018-02-01

Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.

Building the atomic model of a boreal lake virus of unknown fold in a 3.9 Å cryo-EM map.

PubMed

De Colibus, Luigi; Stuart, David I

2018-04-01

We report here the protocol adopted to build the atomic model of the newly discovered virus FLiP (Flavobacterium infecting, lipid-containing phage) into 3.9 Å cryo-electron microscopy (cryo-EM) maps. In particular, this report discusses the combination of density modification procedures, automatic model building and bioinformatics tools applied to guide the tracing of the major capsid protein (MCP) of this virus. The protocol outlined here may serve as a reference for future structural determination by cryo-EM of viruses lacking detectable structural homologues. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Selective Capture of Histidine-tagged Proteins from Cell Lysates Using TEM grids Modified with NTA-Graphene Oxide

NASA Astrophysics Data System (ADS)

Benjamin, Christopher J.; Wright, Kyle J.; Bolton, Scott C.; Hyun, Seok-Hee; Krynski, Kyle; Grover, Mahima; Yu, Guimei; Guo, Fei; Kinzer-Ursem, Tamara L.; Jiang, Wen; Thompson, David H.

2016-10-01

We report the fabrication of transmission electron microscopy (TEM) grids bearing graphene oxide (GO) sheets that have been modified with Nα, Nα-dicarboxymethyllysine (NTA) and deactivating agents to block non-selective binding between GO-NTA sheets and non-target proteins. The resulting GO-NTA-coated grids with these improved antifouling properties were then used to isolate His6-T7 bacteriophage and His6-GroEL directly from cell lysates. To demonstrate the utility and simplified workflow enabled by these grids, we performed cryo-electron microscopy (cryo-EM) of His6-GroEL obtained from clarified E. coli lysates. Single particle analysis produced a 3D map with a gold standard resolution of 8.1 Å. We infer from these findings that TEM grids modified with GO-NTA are a useful tool that reduces background and improves both the speed and simplicity of biological sample preparation for high-resolution structure elucidation by cryo-EM.

Observation of stable Néel skyrmions in cobalt/palladium multilayers with Lorentz transmission electron microscopy

DOE PAGES

Pollard, Shawn D.; Garlow, Joseph A.; Yu, Jiawei; ...

2017-03-10

Néel skyrmions are of high interest due to their potential applications in a variety of spintronic devices, currently accessible in ultrathin heavy metal/ferromagnetic bilayers and multilayers with a strong Dzyaloshinskii–Moriya interaction. Here in this paper we report on the direct imaging of chiral spin structures including skyrmions in an exchange-coupled cobalt/palladium multilayer at room temperature with Lorentz transmission electron microscopy, a high-resolution technique previously suggested to exhibit no Néel skyrmion contrast. Phase retrieval methods allow us to map the internal spin structure of the skyrmion core, identifying a 25 nm central region of uniform magnetization followed by a larger regionmore » characterized by rotation from in- to out-of-plane. The formation and resolution of the internal spin structure of room temperature skyrmions without a stabilizing out-of-plane field in thick magnetic multilayers opens up a new set of tools and materials to study the physics and device applications associated with chiral ordering and skyrmions.« less

Evidence of sharp and diffuse domain walls in BiFeO3 by means of unit-cell-wise strain and polarization maps obtained with high resolution scanning transmission electron microscopy.

PubMed

Lubk, A; Rossell, M D; Seidel, J; He, Q; Yang, S Y; Chu, Y H; Ramesh, R; Hÿtch, M J; Snoeck, E

2012-07-27

Domain walls (DWs) substantially influence a large number of applications involving ferroelectric materials due to their limited mobility when shifted during polarization switching. The discovery of greatly enhanced conduction at BiFeO(3) DWs has highlighted yet another role of DWs as a local material state with unique properties. However, the lack of precise information on the local atomic structure is still hampering microscopical understanding of DW properties. Here, we examine the atomic structure of BiFeO(3) 109° DWs with pm precision by a combination of high-angle annular dark-field scanning transmission electron microscopy and a dedicated structural analysis. By measuring simultaneously local polarization and strain, we provide direct experimental proof for the straight DW structure predicted by ab initio calculations as well as the recently proposed theory of diffuse DWs, thus resolving a long-standing discrepancy between experimentally measured and theoretically predicted DW mobilities.

Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy

PubMed Central

Liao, Hstau Y.; Hashem, Yaser; Frank, Joachim

2015-01-01

Summary Single-particle cryogenic electron microscopy (cryo-EM) is a powerful tool for the study of macromolecular structures at high resolution. Classification allows multiple structural states to be extracted and reconstructed from the same sample. One classification approach is via the covariance matrix, which captures the correlation between every pair of voxels. Earlier approaches employ computing-intensive resampling and estimate only the eigenvectors of the matrix, which are then used in a separate fast classification step. We propose an iterative scheme to explicitly estimate the covariance matrix in its entirety. In our approach, the flexibility in choosing the solution domain allows us to examine a part of the molecule in greater detail. 3D covariance maps obtained in this way from experimental data (cryo-EM images of the eukaryotic pre-initiation complex) prove to be in excellent agreement with conclusions derived by using traditional approaches, revealing in addition the interdependencies of ligand bindings and structural changes. PMID:25982529

Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy.

PubMed

Liao, Hstau Y; Hashem, Yaser; Frank, Joachim

2015-06-02

Single-particle cryogenic electron microscopy (cryo-EM) is a powerful tool for the study of macromolecular structures at high resolution. Classification allows multiple structural states to be extracted and reconstructed from the same sample. One classification approach is via the covariance matrix, which captures the correlation between every pair of voxels. Earlier approaches employ computing-intensive resampling and estimate only the eigenvectors of the matrix, which are then used in a separate fast classification step. We propose an iterative scheme to explicitly estimate the covariance matrix in its entirety. In our approach, the flexibility in choosing the solution domain allows us to examine a part of the molecule in greater detail. Three-dimensional covariance maps obtained in this way from experimental data (cryo-EM images of the eukaryotic pre-initiation complex) prove to be in excellent agreement with conclusions derived by using traditional approaches, revealing in addition the interdependencies of ligand bindings and structural changes. Copyright © 2015 Elsevier Ltd. All rights reserved.

cisTEM, user-friendly software for single-particle image processing.

PubMed

Grant, Timothy; Rohou, Alexis; Grigorieff, Nikolaus

2018-03-07

We have developed new open-source software called cis TEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cis TEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k - 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cis TEM is available for download from cistem.org. © 2018, Grant et al.

Multi-color electron microscopy by element-guided identification of cells, organelles and molecules.

PubMed

Scotuzzi, Marijke; Kuipers, Jeroen; Wensveen, Dasha I; de Boer, Pascal; Hagen, Kees C W; Hoogenboom, Jacob P; Giepmans, Ben N G

2017-04-07

Cellular complexity is unraveled at nanometer resolution using electron microscopy (EM), but interpretation of macromolecular functionality is hampered by the difficulty in interpreting grey-scale images and the unidentified molecular content. We perform large-scale EM on mammalian tissue complemented with energy-dispersive X-ray analysis (EDX) to allow EM-data analysis based on elemental composition. Endogenous elements, labels (gold and cadmium-based nanoparticles) as well as stains are analyzed at ultrastructural resolution. This provides a wide palette of colors to paint the traditional grey-scale EM images for composition-based interpretation. Our proof-of-principle application of EM-EDX reveals that endocrine and exocrine vesicles exist in single cells in Islets of Langerhans. This highlights how elemental mapping reveals unbiased biomedical relevant information. Broad application of EM-EDX will further allow experimental analysis on large-scale tissue using endogenous elements, multiple stains, and multiple markers and thus brings nanometer-scale 'color-EM' as a promising tool to unravel molecular (de)regulation in biomedicine.

Multi-color electron microscopy by element-guided identification of cells, organelles and molecules

PubMed Central

Scotuzzi, Marijke; Kuipers, Jeroen; Wensveen, Dasha I.; de Boer, Pascal; Hagen, Kees (C.) W.; Hoogenboom, Jacob P.; Giepmans, Ben N. G.

2017-01-01

Cellular complexity is unraveled at nanometer resolution using electron microscopy (EM), but interpretation of macromolecular functionality is hampered by the difficulty in interpreting grey-scale images and the unidentified molecular content. We perform large-scale EM on mammalian tissue complemented with energy-dispersive X-ray analysis (EDX) to allow EM-data analysis based on elemental composition. Endogenous elements, labels (gold and cadmium-based nanoparticles) as well as stains are analyzed at ultrastructural resolution. This provides a wide palette of colors to paint the traditional grey-scale EM images for composition-based interpretation. Our proof-of-principle application of EM-EDX reveals that endocrine and exocrine vesicles exist in single cells in Islets of Langerhans. This highlights how elemental mapping reveals unbiased biomedical relevant information. Broad application of EM-EDX will further allow experimental analysis on large-scale tissue using endogenous elements, multiple stains, and multiple markers and thus brings nanometer-scale ‘color-EM’ as a promising tool to unravel molecular (de)regulation in biomedicine. PMID:28387351

Extended and Point Defects in Diamond Studied with the Aid of Various Forms of Microscopy.

PubMed

Steeds; Charles; Gilmore; Butler

2000-07-01

It is shown that star disclinations can be a significant source of stress in chemical vapor deposited (CVD) diamond. This purely geometrical origin contrasts with other sources of stress that have been proposed previously. The effectiveness is demonstrated of the use of electron irradiation using a transmission electron microscope (TEM) to displace atoms from their equilibrium sites to investigate intrinsic defects and impurities in CVD diamond. After irradiation, the samples are studied by low temperature photoluminescence microscopy using UV or blue laser illumination. Results are given that are interpreted as arising from isolated <100> split self-interstitials and positively charged single vacancies. Negatively charged single vacancies can also be revealed by this technique. Nitrogen and boron impurities may also be studied similarly. In addition, a newly developed liquid gallium source scanned ion beam mass spectrometry (SIMS) instrument has been used to map out the B distribution in B doped CVD diamond specimens. The results are supported by micro-Raman spectroscopy.

Selective Capture of Histidine-tagged Proteins from Cell Lysates Using TEM grids Modified with NTA-Graphene Oxide.

PubMed

Benjamin, Christopher J; Wright, Kyle J; Bolton, Scott C; Hyun, Seok-Hee; Krynski, Kyle; Grover, Mahima; Yu, Guimei; Guo, Fei; Kinzer-Ursem, Tamara L; Jiang, Wen; Thompson, David H

2016-10-17

We report the fabrication of transmission electron microscopy (TEM) grids bearing graphene oxide (GO) sheets that have been modified with N α , N α -dicarboxymethyllysine (NTA) and deactivating agents to block non-selective binding between GO-NTA sheets and non-target proteins. The resulting GO-NTA-coated grids with these improved antifouling properties were then used to isolate His 6 -T7 bacteriophage and His 6 -GroEL directly from cell lysates. To demonstrate the utility and simplified workflow enabled by these grids, we performed cryo-electron microscopy (cryo-EM) of His 6 -GroEL obtained from clarified E. coli lysates. Single particle analysis produced a 3D map with a gold standard resolution of 8.1 Å. We infer from these findings that TEM grids modified with GO-NTA are a useful tool that reduces background and improves both the speed and simplicity of biological sample preparation for high-resolution structure elucidation by cryo-EM.

Calcium copper-titanate thin film growth: tailoring of the operational conditions through nanocharacterization and substrate nature effects.

PubMed

Lo Nigro, Raffaella; Toro, Roberta G; Malandrino, Graziella; Fragalà, Ignazio L; Losurdo, Maria; Giangregorio, Michelaria M; Bruno, Giovanni; Raineri, Vito; Fiorenza, Patrick

2006-09-07

A novel approach based on a molten multicomponent precursor source has been applied for the MOCVD fabrication of high-quality CaCu(3)Ti(4)O(12) (CCTO) thin films on various substrates. The adopted in situ strategy involves a molten mixture consisting of Ca(hfa)(2).tetraglyme, Ti(tmhd)(2)(O-iPr)(2), and Cu(tmhd)(2) [Hhfa = 1,1,1,5,5,5-hexafluoro-2,4-pentanedione; tetraglyme = 2,5,8,11,14-pentaoxapentadecane; Htmhd = 2,2,6,6-tetramethyl-3,5-heptandione; O-iPr = isopropoxide] precursors. Film structural and morphological characterizations have been carried out by several techniques [X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM)], and in particular the energy filtered TEM mapping and X-ray energy dispersive (EDX) analysis in TEM mode provided a suitable correlation between nanostructural properties of CCTO films and deposition conditions and/or the substrate nature. Correlation between the nanostructure and optical/dielectric properties has been investigated exploiting spectroscopic ellipsometry.

cisTEM, user-friendly software for single-particle image processing

PubMed Central

2018-01-01

We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org. PMID:29513216

Nanoscale infrared spectroscopy as a non-destructive probe of extraterrestrial samples.

PubMed

Dominguez, Gerardo; Mcleod, A S; Gainsforth, Zack; Kelly, P; Bechtel, Hans A; Keilmann, Fritz; Westphal, Andrew; Thiemens, Mark; Basov, D N

2014-12-09

Advances in the spatial resolution of modern analytical techniques have tremendously augmented the scientific insight gained from the analysis of natural samples. Yet, while techniques for the elemental and structural characterization of samples have achieved sub-nanometre spatial resolution, infrared spectral mapping of geochemical samples at vibrational 'fingerprint' wavelengths has remained restricted to spatial scales >10 μm. Nevertheless, infrared spectroscopy remains an invaluable contactless probe of chemical structure, details of which offer clues to the formation history of minerals. Here we report on the successful implementation of infrared near-field imaging, spectroscopy and analysis techniques capable of sub-micron scale mineral identification within natural samples, including a chondrule from the Murchison meteorite and a cometary dust grain (Iris) from NASA's Stardust mission. Complementary to scanning electron microscopy, energy-dispersive X-ray spectroscopy and transmission electron microscopy probes, this work evidences a similarity between chondritic and cometary materials, and inaugurates a new era of infrared nano-spectroscopy applied to small and invaluable extraterrestrial samples.

Multifrequency spectrum analysis using fully digital G Mode-Kelvin probe force microscopy.

PubMed

Collins, Liam; Belianinov, Alex; Somnath, Suhas; Rodriguez, Brian J; Balke, Nina; Kalinin, Sergei V; Jesse, Stephen

2016-03-11

Since its inception over two decades ago, Kelvin probe force microscopy (KPFM) has become the standard technique for characterizing electrostatic, electrochemical and electronic properties at the nanoscale. In this work, we present a purely digital, software-based approach to KPFM utilizing big data acquisition and analysis methods. General mode (G-Mode) KPFM works by capturing the entire photodetector data stream, typically at the sampling rate limit, followed by subsequent de-noising, analysis and compression of the cantilever response. We demonstrate that the G-Mode approach allows simultaneous multi-harmonic detection, combined with on-the-fly transfer function correction-required for quantitative CPD mapping. The KPFM approach outlined in this work significantly simplifies the technique by avoiding cumbersome instrumentation optimization steps (i.e. lock in parameters, feedback gains etc), while also retaining the flexibility to be implemented on any atomic force microscopy platform. We demonstrate the added advantages of G-Mode KPFM by allowing simultaneous mapping of CPD and capacitance gradient (C') channels as well as increased flexibility in data exploration across frequency, time, space, and noise domains. G-Mode KPFM is particularly suitable for characterizing voltage sensitive materials or for operation in conductive electrolytes, and will be useful for probing electrodynamics in photovoltaics, liquids and ionic conductors.

Multifrequency spectrum analysis using fully digital G Mode-Kelvin probe force microscopy

DOE PAGES

Collins, Liam F.; Jesse, Stephen; Belianinov, Alex; ...

2016-02-11

Since its inception over two decades ago, Kelvin probe force microscopy (KPFM) has become the standard technique for characterizing electrostatic, electrochemical and electronic properties at the nanoscale. In this work, we present a purely digital, software-based approach to KPFM utilizing big data acquisition and analysis methods. General Mode (G-Mode) KPFM, works by capturing the entire photodetector data stream, typically at the sampling rate limit, followed by subsequent de-noising, analysis and compression of the cantilever response. We demonstrate that the G-Mode approach allows simultaneous multi-harmonic detection, combined with on-the-fly transfer function correction required for quantitative CPD mapping. The KPFM approach outlinedmore » in this work significantly simplifies the technique by avoiding cumbersome instrumentation optimization steps (i.e. lock in parameters, feedback gains etc.), while also retaining the flexibility to be implemented on any atomic force microscopy platform. We demonstrate the added advantages of G-Mode KPFM by allowing simultaneous mapping of CPD and capacitance gradient (C') channels as well as increased flexibility in data exploration across frequency, time, space, and noise domains. As a result, G-Mode KPFM is particularly suitable for characterizing voltage sensitive materials or for operation in conductive electrolytes, and will be useful for probing electrodynamics in photovoltaics, liquids and ionic conductors.« less

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.

PubMed

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S; Subramanian, Hariharan; Dravid, Vinayak P; Backman, Vadim

2017-06-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm

PubMed Central

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A.; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S.; Subramanian, Hariharan; Dravid, Vinayak P.; Backman, Vadim

2018-01-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass–density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass–density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass–density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass–density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass–density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes. PMID:28416035

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

NASA Astrophysics Data System (ADS)

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cullen, David A; Koestner, Roland; Kukreja, Ratan

Improved conditions for imaging and spectroscopic mapping of thin perfluorosulfonic acid (PFSA) ionomer layers in fuel cell electrodes by scanning transmission electron microscopy (STEM) have been investigated. These conditions are first identified on model systems of Nafion ionomer-coated nanostructured thin films and nanoporous Si. The optimized conditions are then applied in a quantitative study of the ionomer through-layer loading for two typical electrode catalyst coatings using electron energy loss and energy dispersive X-ray spectroscopy in the transmission electron microscope. The e-beam induced damage to the perfluorosulfonic acid (PFSA) ionomer is quantified by following the fluorine mass loss with electron exposuremore » and is then mitigated by a few orders of magnitude using cryogenic specimen cooling and a higher incident electron voltage. Multivariate statistical analysis is also applied to the analysis of spectrum images for data denoising and unbiased separation of independent components related to the catalyst, ionomer, and support.« less

Imaging quasiperiodic electronic states in a synthetic Penrose tiling

NASA Astrophysics Data System (ADS)

Collins, Laura C.; Witte, Thomas G.; Silverman, Rochelle; Green, David B.; Gomes, Kenjiro K.

2017-06-01

Quasicrystals possess long-range order but lack the translational symmetry of crystalline solids. In solid state physics, periodicity is one of the fundamental properties that prescribes the electronic band structure in crystals. In the absence of periodicity and the presence of quasicrystalline order, the ways that electronic states change remain a mystery. Scanning tunnelling microscopy and atomic manipulation can be used to assemble a two-dimensional quasicrystalline structure mapped upon the Penrose tiling. Here, carbon monoxide molecules are arranged on the surface of Cu(111) one at a time to form the potential landscape that mimics the ionic potential of atoms in natural materials by constraining the electrons in the two-dimensional surface state of Cu(111). The real-space images reveal the presence of the quasiperiodic order in the electronic wave functions and the Fourier analysis of our results links the energy of the resonant states to the local vertex structure of the quasicrystal.

Imaging quasiperiodic electronic states in a synthetic Penrose tiling.

PubMed

Collins, Laura C; Witte, Thomas G; Silverman, Rochelle; Green, David B; Gomes, Kenjiro K

2017-06-22

Quasicrystals possess long-range order but lack the translational symmetry of crystalline solids. In solid state physics, periodicity is one of the fundamental properties that prescribes the electronic band structure in crystals. In the absence of periodicity and the presence of quasicrystalline order, the ways that electronic states change remain a mystery. Scanning tunnelling microscopy and atomic manipulation can be used to assemble a two-dimensional quasicrystalline structure mapped upon the Penrose tiling. Here, carbon monoxide molecules are arranged on the surface of Cu(111) one at a time to form the potential landscape that mimics the ionic potential of atoms in natural materials by constraining the electrons in the two-dimensional surface state of Cu(111). The real-space images reveal the presence of the quasiperiodic order in the electronic wave functions and the Fourier analysis of our results links the energy of the resonant states to the local vertex structure of the quasicrystal.

Optical magnetic imaging of living cells

PubMed Central

Le Sage, D.; Arai, K.; Glenn, D. R.; DeVience, S. J.; Pham, L. M.; Rahn-Lee, L.; Lukin, M. D.; Yacoby, A.; Komeili, A.; Walsworth, R. L.

2013-01-01

Magnetic imaging is a powerful tool for probing biological and physical systems. However, existing techniques either have poor spatial resolution compared to optical microscopy and are hence not generally applicable to imaging of sub-cellular structure (e.g., magnetic resonance imaging [MRI]1), or entail operating conditions that preclude application to living biological samples while providing sub-micron resolution (e.g., scanning superconducting quantum interference device [SQUID] microscopy2, electron holography3, and magnetic resonance force microscopy [MRFM]4). Here we demonstrate magnetic imaging of living cells (magnetotactic bacteria) under ambient laboratory conditions and with sub-cellular spatial resolution (400 nm), using an optically-detected magnetic field imaging array consisting of a nanoscale layer of nitrogen-vacancy (NV) colour centres implanted at the surface of a diamond chip. With the bacteria placed on the diamond surface, we optically probe the NV quantum spin states and rapidly reconstruct images of the vector components of the magnetic field created by chains of magnetic nanoparticles (magnetosomes) produced in the bacteria, and spatially correlate these magnetic field maps with optical images acquired in the same apparatus. Wide-field sCMOS acquisition allows parallel optical and magnetic imaging of multiple cells in a population with sub-micron resolution and >100 micron field-of-view. Scanning electron microscope (SEM) images of the bacteria confirm that the correlated optical and magnetic images can be used to locate and characterize the magnetosomes in each bacterium. The results provide a new capability for imaging bio-magnetic structures in living cells under ambient conditions with high spatial resolution, and will enable the mapping of a wide range of magnetic signals within cells and cellular networks5, 6. PMID:23619694

Structure and Uncoating of Immature Adenovirus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perez-Berna, A.J.; Mangel, W.; Marabini, R.

2009-09-18

Maturation via proteolytic processing is a common trait in the viral world and is often accompanied by large conformational changes and rearrangements in the capsid. The adenovirus protease has been shown to play a dual role in the viral infectious cycle: (a) in maturation, as viral assembly starts with precursors to several of the structural proteins but ends with proteolytically processed versions in the mature virion, and (b) in entry, because protease-impaired viruses have difficulties in endosome escape and uncoating. Indeed, viruses that have not undergone proteolytic processing are not infectious. We studied the three-dimensional structure of immature adenovirus particlesmore » as represented by the adenovirus type 2 thermosensitive mutant ts1 grown under non-permissive conditions and compared it with the mature capsid. Our three-dimensional electron microscopy maps at subnanometer resolution indicate that adenovirus maturation does not involve large-scale conformational changes in the capsid. Difference maps reveal the locations of unprocessed peptides pIIIa and pVI and help define their role in capsid assembly and maturation. An intriguing difference appears in the core, indicating a more compact organization and increased stability of the immature cores. We have further investigated these properties by in vitro disassembly assays. Fluorescence and electron microscopy experiments reveal differences in the stability and uncoating of immature viruses, both at the capsid and core levels, as well as disassembly intermediates not previously imaged.« less

Immunohistochemistry for the MEPHISTO X-PEEM

NASA Astrophysics Data System (ADS)

Gilbert, B.; Neumann, M.; Steen, S.; Gabel, D.; Andres, R.; Perfetti, P.; Margaritondo, G.; De Stasio, Gelsomina

2000-05-01

Over almost 50 years of its development, the science of immunology has become an indispensable tool for the understanding of the histology of tissues. Antibodies are highly specific probes, so that tissue structure can be interpreted not just by morphological considerations but by association with a wide variety of physiological molecular antigens. The simple concept of an antibody linked to a microscopically dense marker remains constant in each application of the technique, such as the use of fluorescent markers or the incorporation of electron-dense gold colloids for electron microscopy. We describe a new application of immunocytochemistry to x-ray spectromicroscopy: the antibody labeling of tissue structures with nickel precipitates. Regions of positive staining can be seen by the acquisition of nickel distribution maps in the MEPHISTO X-PEEM from the intense Ni L-edge absorption features around 850 eV. The aim of this work is to know the background tissue structures on which the distribution of other relevant elements (such as boron for BNCT) can be mapped. Results are presented showing positive staining by two antibodies in human glioblastoma tissue, anti-Ki-67, a protein found in the nuclei of proliferating cells, and anti-van Willebrandt factor, located in blood vessel endothelia. We show that the criteria for successful staining for optical microscopy are different than for spectroscopic imaging, but useful results can be obtained with careful image treatment.

Accumulation and interparticle connections of triangular Ag-coated Au nanoprisms by oil-coating method for surface-enhanced Raman scattering applications

NASA Astrophysics Data System (ADS)

Noda, Yuta; Asaka, Toru; Fudouzi, Hiroshi; Hayakawa, Tomokatsu

2018-03-01

To examine the optical responses of surface-enhanced Raman scattering (SERS) for tuned plasmonic nanoparticles, triangular Ag-coated Au (Au@Ag) nanoprisms with different sizes were separately synthesized, which were well controlled in their size (edge-length) and localized surface plasmon resonance (LSPR) wavelength (69.0 ± 8.4 to 173.8 ± 25.6 nm in size and 662-943 nm in LSPR wavelength). The mechanism of Ag shell formation on the Au nanoprisms was also studied with scanning transmission electron microscopy-energy dispersive X-ray spectroscopy (STEM-EDS). The Au@Ag nanoprisms were immobilized by covering a colloidal solution containing the nanoprisms with silicone oil and evaporating the solvent in the oil (oil-coating method) so as to form a layer of accumulated plasmonic Au@Ag nanoprisms that had LSPR peak wavelengths tuned from 839 to 1182 nm. The accumulation conditions were analyzed by field-emission scanning electron microscopy (FE-SEM) and a Raman mapping technique. The Au@Ag nanoprisms under excitation at 632.8 nm exhibited higher SERS signals of rhodamine 6G, and SERS-mapped images of the novel immobilized films were obtained at different magnifications. It was concluded that accumulated Au@Ag nanoprisms undergoing tip-planar interconnections could produce enhanced local fields, resulting in higher SERS signals.

Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA

PubMed Central

Kandiah, Eaazhisai; Carriel, Diego; Perard, Julien; Malet, Hélène; Bacia, Maria; Liu, Kaiyin; Chan, Sze W. S.; Houry, Walid A.; Ollagnier de Choudens, Sandrine; Elsen, Sylvie; Gutsche, Irina

2016-01-01

The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role. A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation. Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer. We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity. Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding. Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions. PMID:27080013

Strategy for reliable strain measurement in InAs/GaAs materials from high-resolution Z-contrast STEM images

NASA Astrophysics Data System (ADS)

Vatanparast, Maryam; Vullum, Per Erik; Nord, Magnus; Zuo, Jian-Min; Reenaas, Turid W.; Holmestad, Randi

2017-09-01

Geometric phase analysis (GPA), a fast and simple Fourier space method for strain analysis, can give useful information on accumulated strain and defect propagation in multiple layers of semiconductors, including quantum dot materials. In this work, GPA has been applied to high resolution Z-contrast scanning transmission electron microscopy (STEM) images. Strain maps determined from different g vectors of these images are compared to each other, in order to analyze and assess the GPA technique in terms of accuracy. The SmartAlign tool has been used to improve the STEM image quality getting more reliable results. Strain maps from template matching as a real space approach are compared with strain maps from GPA, and it is discussed that a real space analysis is a better approach than GPA for aberration corrected STEM images.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doughty, Benjamin; Simpson, Mary Jane; Yang, Bin

Our work aims to simplify multi-dimensional femtosecond transient absorption microscopy (TAM) data into decay associated amplitude maps that describe the spatial distributions of dynamical processes occurring on various characteristic timescales. Application of this method to TAM data obtained from a model methyl-ammonium lead iodide (CH 3NH 3PbI 3) perovskite thin film allows us to simplify the dataset consisting of a 68 time-resolved images into 4 decay associated amplitude maps. Furthermore, these maps provide a simple means to visualize the complex electronic excited-state dynamics in this system by separating distinct dynamical processes evolving on characteristic timescales into individual spatial images. Thismore » approach provides new insight into subtle aspects of ultrafast relaxation dynamics associated with excitons and charge carriers in the perovskite thin film, which have recently been found to coexist at spatially distinct locations.« less

Electron Microscope Studies of Cadmium Mercury Telluride

NASA Astrophysics Data System (ADS)

Lyster, Martin

Available from UMI in association with The British Library. Requires signed TDF. Epitaxial layers of Cd_{x }Hg_{(1-x)}Te grown on various substrates by liquid phase epitaxy and metallo-organic vapour phase epitaxy have been studied using transmission and scanning electron microscopy, in a variety of contrast modes. Wavelength-dispersive X-ray microanalysis has been used to study interfaces in epitaxial specimens, and the results are used to derive diffusion coefficients for a range of values of x in Cd_ {x}Hg_{(1-x)} Te. Extensive use has been made of back-scattered electron contrast in the SEM as a means of compositional mapping, and defect structures are imaged by this technique. The back-scattered electron contrast at interfaces has been studied in detail and is modelled using the Monte Carlo approach. The modelling is combined with calculations and practical measurements of the probe size in the SEM instrument used in the work, to arrive at a quantitative explanation of this contrast. The SEM and scintillator detector used allow a spatial resolution of better than 1000A, but it is shown that improvements in this are possible with present technology. Scanning infra-red microscopy (SIRM) and high -resolution transmission electron microscopy (HREM) have been applied to the study of CdTe. SIRM images reveal information about Te precipitation, including particle size and density. HREM images provide results concerning dislocation structures in CdTe. Selected-area diffraction contrast TEM results are presented which illustrate the microstructure of LPE and MOVPE material; and TEM foil preparation techniques are discussed, including the choice of ion species for milling cross-sectional specimens. In view of the results obtained, suggestions are made for future work in this field.

Three-dimensional characterization of ODS ferritic steel using by FIB-SEM serial sectioning method.

PubMed

Endo, T; Sugino, Y; Ohono, N; Ukai, S; Miyazaki, N; Wang, Y; Ohnuki, S

2014-11-01

Considerable attention has been paid to the research of the electron tomography due to determine the three-dimensional (3D) structure of materials [1]. One of the electron tomography techniques, focused ion beam/scanning electron microscopy (FIB-SEM) imaging has advantages of high resolutions (10 nm), large area observation (μm order) and simultaneous energy dispersive x- ray microanalysis (EDS)/ electron backscatter diffraction (EBSD) analysis. The purpose of this study, three-dimensional EBSD analysis of ODS ferritic steel which carried out cold work using FIB-SEM equipment was conducted, and it aimed at analyzing the microstructure obtained there. The zone annealing tests were conducted for ferritic steel [2,3], which were produced through mechanical alloying and hot-extrusion. After zone annealing, specimens were mechanically polished with #400∼4000 emery paper, 1 µm diamond paste and alumina colloidal silica. The serial sectioning and the 3D-electron backscattering diffraction (3D-EBSD) analysis were carried out. We made the micro pillar (30 x 30 x 15 µm). The EBSD measurements were carried out in each layer after serial sectioning at a step size and milling depth was 80 nm with 30 slices. After EBSD analysis, the series of cross-sectional images were aligned according to arbitrarily specified areas and then stacked up to form a volume. Consequently, we obtained the 3D-IPF maps for ODS ferritic steel. In this specimen, the {111} and {001} grains are layered by turns. In addition, the volume fraction value of both plane are similar. The aspect ratio increases with specimen depth. The 3D-EBSD mapping is useful to analysis of the bulk material since this method obtain many microstructure information, such a shape, volume and orientation of the crystal, grain boundary. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Interplay between bulk and edge-bound topological defects in a square micromagnet

DOE PAGES

Sloetjes, Sam D.; Digernes, Einar; Olsen, Fredrik K.; ...

2018-01-22

A field-driven transformation of a domain pattern in a square micromagnet, defined in a thin film of La 0.7Sr 0.3MnO 3, is discussed in terms of creation and annihilation of bulk vortices and edge-bound topological defects with half-integer winding numbers. The evolution of the domain pattern was mapped with soft x-ray photoemission electron microscopy and magnetic force microscopy. Micromagnetic modeling, permitting detailed analysis of the spin texture, accurately reproduces the measured domain state transformation. The simulations also helped stipulate the energy barriers associated with the creation and annihilation of the topological charges and thus to assess the stability of themore » domain states in this magnetic microstructure.« less

Interplay between bulk and edge-bound topological defects in a square micromagnet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sloetjes, Sam D.; Digernes, Einar; Olsen, Fredrik K.

A field-driven transformation of a domain pattern in a square micromagnet, defined in a thin film of La 0.7Sr 0.3MnO 3, is discussed in terms of creation and annihilation of bulk vortices and edge-bound topological defects with half-integer winding numbers. The evolution of the domain pattern was mapped with soft x-ray photoemission electron microscopy and magnetic force microscopy. Micromagnetic modeling, permitting detailed analysis of the spin texture, accurately reproduces the measured domain state transformation. The simulations also helped stipulate the energy barriers associated with the creation and annihilation of the topological charges and thus to assess the stability of themore » domain states in this magnetic microstructure.« less

355, 532, and 1064 nm picosecond laser interaction with grass tissues

NASA Astrophysics Data System (ADS)

Kim, Jaehun; Ki, Hyungson

2012-12-01

In this article, we investigate how 355, 532, and 1064 nm picosecond lasers interact with grass tissues. We have identified five interaction regimes, and based on this classification, interaction maps have been constructed from a systematic experiment. The optical properties of light absorbing grass constituents are studied theoretically in order to understand how and how much light is absorbed by grass tissues. Scanning electron microscopy and optical microscopy are employed for observing morphological and structural changes of grass tissues. To the best of the authors' knowledge, this is the first investigation into laser interaction with plant leaves and reveals some fundamental findings regarding how a laser interacts with grass tissues and how plant leaves can be processed using lasers.

New developments in electron microscopy for serial image acquisition of neuronal profiles.

PubMed

Kubota, Yoshiyuki

2015-02-01

Recent developments in electron microscopy largely automate the continuous acquisition of serial electron micrographs (EMGs), previously achieved by laborious manual serial ultrathin sectioning using an ultramicrotome and ultrastructural image capture process with transmission electron microscopy. The new systems cut thin sections and capture serial EMGs automatically, allowing for acquisition of large data sets in a reasonably short time. The new methods are focused ion beam/scanning electron microscopy, ultramicrotome/serial block-face scanning electron microscopy, automated tape-collection ultramicrotome/scanning electron microscopy and transmission electron microscope camera array. In this review, their positive and negative aspects are discussed. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

High-Resolution AES Mapping and TEM Study of Cu(In,Ga)Se2 Thin Film Growth: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkins, C. L.; Yan, Y.; Jones, K.

2001-10-01

Presented at 2001 NCPV Program Review Meeting: TEM and high-resolution AES mapping data on CIGS samples. The chalcopyrite Cu(In,Ga)Se{sub 2} (CIGS) shows promise as an absorber layer in thin polycrystalline solar cells, however, details of the PVD growth of this complicated material remain in a developing stage. Previous workers have postulated the existence of a thin film of liquid Cu{sub x}Se on the growing CIGS film, and that this layer acts as a reservoir of copper as well as a layer in which rapid mass transport is possible. In this paper we present transmission electron microscopy (TEM) and high resolutionmore » Auger electron spectroscopy (AES) mapping data taken on samples that had their growth interrupted at a stage when Cu{sub x}Se was expected to be present. The AES maps show CIGS grains which are highly enriched in copper relative to the rest of the CIGS film, and that these same areas contain almost no indium, results consistent with the presence of CuxSe. Small-area diffraction analysis and energy dispersive spectroscopy (EDS) performed on these same samples independently confirm the presence of Cu{sub x}Se at the surface of growing CIGS films.« less

When will low-contrast features be visible in a STEM X-ray spectrum image?

DOE PAGES

Parish, Chad M.

2015-04-01

When will a small or low-contrast feature, such as an embedded second-phase particle, be visible in a scanning transmission electron microscopy (STEM) X-ray map? This work illustrates a computationally inexpensive method to simulate X-ray maps and spectrum images (SIs), based upon the equations of X-ray generation and detection. To particularize the general procedure, an example of nanostructured ferritic alloy (NFA) containing nm-sized Y 2Ti 2O 7 embedded precipitates in ferritic stainless steel matrix is chosen. The proposed model produces physically appearing simulated SI data sets, which can either be reduced to X-ray dot maps or analyzed via multivariate statistical analysis.more » Comparison to NFA X-ray maps acquired using three different STEM instruments match the generated simulations quite well, despite the large number of simplifying assumptions used. A figure of merit of electron dose multiplied by X-ray collection solid angle is proposed to compare feature detectability from one data set (simulated or experimental) to another. The proposed method can scope experiments that are feasible under specific analysis conditions on a given microscope. As a result, future applications, such as spallation proton–neutron irradiations, core-shell nanoparticles, or dopants in polycrystalline photovoltaic solar cells, are proposed.« less

Elemental analysis of sunflower cataract in Wilson's disease: a study using scanning transmission electron microscopy and energy dispersive spectroscopy.

PubMed

Jang, Hyo Ju; Kim, Joon Mo; Choi, Chul Young

2014-04-01

Signature ophthalmic characteristics of Wilson's disease (WD) are regarded as diagnostically important manifestations of the disease. Previous studies have proved the common occurrence of copper accumulation in the liver of patients with WD. However, in the case of sunflower cataracts, one of the rare diagnostic signs of WD, no study has demonstrated copper accumulation in the lens capsules of sunflower cataracts in WD patients. To investigate the nanostructure and elemental composition of sunflower cataracts in WD, transmission electron microscopy (TEM) was done on the capsulorhexised anterior lens capsule of sunflower cataracts in WD in order to evaluate anatomical variation and elemental changes. We utilized energy dispersive X-ray spectroscopy (EDS) to investigate the elemental composition of the lens capsule using both point and mapping spectroscopy. Quantitative analysis was performed for relative comparison of the elements. TEM showed the presence of granular deposits of varying size (20-350 nm), appearing mainly in the posterior one third of the anterior capsule. The deposits appeared in linear patterns with scattered dots. There were no electron-dense particles in the epithelial cell layer of the lens. Copper and sulfur peaks were consistently revealed in electron-dense granular deposits. In contrast, copper and sulfur peaks were absent in other tissues, including granule-free lens capsules and epithelial tissue. Most copper was exclusively located in clusters of electron-dense particles, and the copper distribution overlapped with sulfur on mapping spectroscopy. Quantitative analysis presented inconsistent ratios of copper to sulfur in each electron-dense granule. The mean ratio of copper to sulfur was about 3.25 (with a range of 2.39-3.78). This is the first elemental analysis of single electron particles in sunflower cataracts using EDS in the ophthalmic area. Sunflower cataracts with WD are assumed to be the result of accumulation of heterogeneous compounds composed of several materials, including copper, sulfur, and/or copper-binding proteins. Linear patterns of copper and sulfur deposition were detected in various sizes and composition ratios with these elements in cases of WD. Copyright © 2014 Elsevier Ltd. All rights reserved.

Geometry of phase-separated domains in phospholipid bilayers by diffraction-contrast electron microscopy.

PubMed Central

Hui, S W

1981-01-01

The sizes and shapes of solidus (gel) phase domains in the hydrated molecular bilayers of dilauroylphosphatidylcholine/dipalmitoylphasphatidylcholine (DLPC/DPPC) (1:1) and phosphatidylserine (PS)/DPPC (1:2) are visualized directly by low dose diffraction-contrast electron microscopy. The temperature and humidity of the bilayers are controlled by an environmental chamber set in an electron microscope. The contrast between crystalline domains is enhanced by electron optical filtering of the diffraction patterns of the bilayers. The domains are seen as a patchwork in the plane of the bilayer, with an average width of 0.2-0.5 micrometer. The percentage of solidus area measured from diffraction-contrast micrographs at various temperatures agrees in general with those depicted by known phase diagrams. The shape and size of the domains resemble those seen by freeze-fracture in multilamellar vesicles. Temperature-related changes in domain size and in phase boundary per unit area are more pronounced in the less miscible DLPC/DPPC mixture. No significant change in these geometric parameters with temperature is found in the PS/DPPC mixture. Mapping domains by their molecular diffraction signals not only verifies the existance of areas of different molecular packing during phase separation but also provides a quantitative measurement of structural boundaries and defects in lipid bilayers. Images FIGURE 1 FIGURE 3 FIGURE 6 PMID:6894707

On mapping subangstrom electron clouds with force microscopy.

PubMed

Wright, C Alan; Solares, Santiago D

2011-11-09

In 2004 Hembacher et al. (Science 2004, 305, 380-383) reported simultaneous higher-harmonics atomic force mocroscopy (AFM)/scanning tunneling microscopy (STM) images acquired while scanning a graphite surface with a tungsten tip. They interpreted the observed subatomic features in the AFM images as the signature of lobes of increased electron density at the tungsten tip apex. Although these intriguing images have stirred controversy, an in-depth theoretical feasibility study has not yet been produced. Here we report on the development of a method for simulating higher harmonics AFM images and its application to the same system. Our calculations suggest that four lobes of increased electron density are expected to be present at a W(001) tip apex atom and that the corresponding higher harmonics AFM images of graphite can exhibit 4-fold symmetry features. Despite these promising results, open questions remain since the calculated amplitudes of the higher harmonics generated by the short-range forces are on the order of hundredths of picometers, leading to very small corrugations in the theoretical images. Additionally, the complex, intermittent nature of the tip-sample interaction, which causes constant readjustment of the tip and sample orbitals as the tip approaches and retracts from the surface, prevents a direct quantitative connection between the electron density and the AFM image features.

Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells

PubMed Central

Martell, Jeffrey D; Deerinck, Thomas J; Lam, Stephanie S; Ellisman, Mark H; Ting, Alice Y

2018-01-01

Electron microscopy (EM) is the premiere technique for high-resolution imaging of cellular ultrastructure. Unambiguous identification of specific proteins or cellular compartments in electron micrographs, however, remains challenging because of difficulties in delivering electron-dense contrast agents to specific subcellular targets within intact cells. We recently reported enhanced ascorbate peroxidase 2 (APEX2) as a broadly applicable genetic tag that generates EM contrast on a specific protein or subcellular compartment of interest. This protocol provides guidelines for designing and validating APEX2 fusion constructs, along with detailed instructions for cell culture, transfection, fixation, heavy-metal staining, embedding in resin, and EM imaging. Although this protocol focuses on EM in cultured mammalian cells, APEX2 is applicable to many cell types and contexts, including intact tissues and organisms, and is useful for numerous applications beyond EM, including live-cell proteomic mapping. This protocol, which describes procedures for sample preparation from cell monolayers and cell pellets, can be completed in 10 d, including time for APEX2 fusion construct validation, cell growth, and solidification of embedding resins. Notably, the only additional steps required relative to a standard EM sample preparation are cell transfection and a 2- to 45-min staining period with 3,3′-diaminobenzidine (DAB) and hydrogen peroxide (H2O2). PMID:28796234

Ponderomotive Generation and Detection of Attosecond Free-Electron Pulse Trains

NASA Astrophysics Data System (ADS)

Kozák, M.; Schönenberger, N.; Hommelhoff, P.

2018-03-01

Atomic motion dynamics during structural changes or chemical reactions have been visualized by pico- and femtosecond pulsed electron beams via ultrafast electron diffraction and microscopy. Imaging the even faster dynamics of electrons in atoms, molecules, and solids requires electron pulses with subfemtosecond durations. We demonstrate here the all-optical generation of trains of attosecond free-electron pulses. The concept is based on the periodic energy modulation of a pulsed electron beam via an inelastic interaction, with the ponderomotive potential of an optical traveling wave generated by two femtosecond laser pulses at different frequencies in vacuum. The subsequent dispersive propagation leads to a compression of the electrons and the formation of ultrashort pulses. The longitudinal phase space evolution of the electrons after compression is mapped by a second phase-locked interaction. The comparison of measured and calculated spectrograms reveals the attosecond temporal structure of the compressed electron pulse trains with individual pulse durations of less than 300 as. This technique can be utilized for tailoring and initial characterization of suboptical-cycle free-electron pulses at high repetition rates for stroboscopic time-resolved experiments with subfemtosecond time resolution.

Palmitoylethanolamide Ameliorates Hippocampal Damage and Behavioral Dysfunction After Perinatal Asphyxia in the Immature Rat Brain

PubMed Central

Herrera, María I.; Udovin, Lucas D.; Toro-Urrego, Nicolás; Kusnier, Carlos F.; Luaces, Juan P.; Capani, Francisco

2018-01-01

Perinatal asphyxia (PA) is an obstetric complication associated with an impaired gas exchange. This health problem continues to be a determinant of neonatal mortality and neurodevelopmental disorders. Palmitoylethanolamide (PEA) has exerted neuroprotection in several models of brain injury and neurodegeneration. We aimed at evaluating the potential neuroprotective role of PEA in an experimental model, which induces PA in the immature rat brain. PA was induced by placing Sprague Dawley newborn rats in a water bath at 37°C for 19 min. Once their physiological conditions improved, they were given to surrogate mothers that had delivered normally within the last 24 h. The control group was represented by non-fostered vaginally delivered pups, mimicking the clinical situation. Treatment with PEA (10 mg/kg) was administered within the first hour of life. Modifications in the hippocampus were analyzed with conventional electron microscopy, immunohistochemistry (for NeuN, pNF-H/M, MAP-2, and GFAP) and western blot (for pNF H/M, MAP-2, and GFAP). Behavior was also studied throughout Open Field (OF) Test, Passive Avoidance (PA) Task and Elevated Plus Maze (EPM) Test. After 1 month of the PA insult, we observed neuronal nucleus degeneration in CA1 using electron microscopy. Immunohistochemistry revealed a significant increase in pNF-H/M and decrease in MAP-2 in CA1 reactive area. These changes were also observed when analyzing the level of expression of these markers by western blot. Vertical exploration impairments and anxiety-related behaviors were encountered in the OF and EPM tests. PEA treatment attenuated PA-induced hippocampal damage and its corresponding behavioral alterations. These results contribute to the elucidation of PEA neuroprotective role after PA and the future establishment of therapeutic strategies for the developing brain. PMID:29662433

Spectral imaging and passive sampling to investigate particle sources in urban desert regions.

PubMed

Wagner, Jeff; Casuccio, Gary

2014-07-01

Two types of electron microscopy analyses were employed along with geographic information system (GIS) mapping to investigate potential sources of PM2.5 and PM10 (airborne particulate matter smaller than 2.5 and 10 μm, respectively) in two urbanized desert areas known to exhibit PM excursions. Integrated spectral imaging maps were obtained from scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM/EDS) analyses of 13 filters collected in Imperial Valley, California. Seven were from 24 h PM10 Federal Reference Method (FRM) samplers and six were from PM2.5 FRM samplers. This technique enabled extraction of information from particles collected on complex filter matrices, and indicated that all samples exhibited substantial proportions of crustal particles. Six Imperial PM2.5 and PM10 filters selected from unusually high-PM days exhibited more large particles (2.5-15 and 10-30 μm, respectively) than did filters from low-PM days, and were more consistent with soils analyzed from the region. High winds were present on three of the six high-PM days. One of the high-PM2.5 filters also exhibited substantial fine carbonaceous soot PM, suggesting significant contributions from a combustion source. Computer-controlled SEM/EDS (CCSEM/EDS) was conducted on PM collected with UNC Passive samplers from Phoenix, Arizona. The passive samplers showed good agreement with co-located FRM PM10 and PM2.5 measurements (μg m(-3)), and also enabled detailed individual particle analysis. The CCSEM/EDS data revealed mostly crustal particles in both the Phoenix fine and coarse PM10 fractions. GIS maps of multiple dust-related parameters confirm that both Imperial Valley and Phoenix possess favorable conditions for airborne crustal PM from natural and anthropogenic sources.

Hippocampal mutant APP and amyloid beta-induced cognitive decline, dendritic spine loss, defective autophagy, mitophagy and mitochondrial abnormalities in a mouse model of Alzheimer's disease.

PubMed

Manczak, Maria; Kandimalla, Ramesh; Yin, Xiangling; Reddy, P Hemachandra

2018-04-15

The purpose of our study was to determine the toxic effects of hippocampal mutant APP and amyloid beta (Aβ) in 12-month-old APP transgenic mice. Using rotarod and Morris water maze tests, immunoblotting and immunofluorescence, Golgi-cox staining and transmission electron microscopy, we assessed cognitive behavior, protein levels of synaptic, autophagy, mitophagy, mitochondrial dynamics, biogenesis, dendritic protein MAP2 and quantified dendritic spines and mitochondrial number and length in 12-month-old APP mice that express Swedish mutation. Mitochondrial function was assessed by measuring the levels of hydrogen peroxide, lipid peroxidation, cytochrome c oxidase activity and mitochondrial ATP. Morris water maze and rotarod tests revealed that hippocampal learning and memory and motor learning and coordination were impaired in APP mice relative to wild-type (WT) mice. Increased levels of mitochondrial fission proteins, Drp1 and Fis1 and decreased levels of fusion (Mfn1, Mfn2 and Opa1) biogenesis (PGC1α, NRF1, NRF2 and TFAM), autophagy (ATG5 and LC3BI, LC3BII), mitophagy (PINK1 and TERT), synaptic (synaptophysin and PSD95) and dendritic (MAP2) proteins were found in 12-month-old APP mice relative to age-matched non-transgenic WT mice. Golgi-cox staining analysis revealed that dendritic spines are significantly reduced. Transmission electron microscopy revealed significantly increased mitochondrial numbers and reduced mitochondrial length in APP mice. These findings suggest that hippocampal accumulation of mutant APP and Aβ is responsible for abnormal mitochondrial dynamics and defective biogenesis, reduced MAP2, autophagy, mitophagy and synaptic proteins and reduced dendritic spines and hippocampal-based learning and memory impairments, and mitochondrial structural and functional changes in 12-month-old APP mice.

Cancer nanomedicine: gold nanoparticle mediated combined cancer therapy

NASA Astrophysics Data System (ADS)

Yang, C.; Bromma, Kyle; Chithrani, B. D.

2018-02-01

Recent developments in nanotechnology has provided new tools for cancer therapy and diagnosis. Among other nanomaterial systems, gold nanoparticles are being used as radiation dose enhancers and anticancer drug carriers in cancer therapy. Fate of gold nanoparticles within biological tissues can be probed using techniques such as TEM (transmission electron microscopy) and SEM (Scanning Electron Microscopy) due to their high electron density. We have shown for the first time that cancer drug loaded gold nanoparticles can reach the nucleus (or the brain) of cancer cells enhancing the therapeutic effect dramatically. Nucleus of the cancer cells are the most desirable target in cancer therapy. In chemotherapy, smart delivery of highly toxic anticancer drugs through packaging using nanoparticles will reduce the side effects and improve the quality and care of cancer patients. In radiation therapy, use of gold nanoparticles as radiation dose enhancer is very promising due to enhanced localized dose within the cancer tissue. Recent advancement in nanomaterial characterization techniques will facilitate mapping of nanomaterial distribution within biological specimens to correlate the radiobiological effects due to treatment. Hence, gold nanoparticle mediated combined chemoradiation would provide promising tools to achieve personalized and tailored cancer treatments in the near future.

Nature and evolution of incommensurate charge order in manganites visualized with cryogenic scanning transmission electron microscopy

PubMed Central

Savitzky, Benjamin H.; Admasu, Alemayehu S.; Kim, Jaewook; Cheong, Sang-Wook; Hovden, Robert; Kourkoutis, Lena F.

2018-01-01

Incommensurate charge order in hole-doped oxides is intertwined with exotic phenomena such as colossal magnetoresistance, high-temperature superconductivity, and electronic nematicity. Here, we map, at atomic resolution, the nature of incommensurate charge–lattice order in a manganite using scanning transmission electron microscopy at room temperature and cryogenic temperature (∼93 K). In diffraction, the ordering wave vector changes upon cooling, a behavior typically associated with incommensurate order. However, using real space measurements, we discover that the ordered state forms lattice-locked regions over a few wavelengths interspersed with phase defects and changing periodicity. The cations undergo picometer-scale (∼6 pm to 11 pm) transverse displacements, suggesting that charge–lattice coupling is strong. We further unearth phase inhomogeneity in the periodic lattice displacements at room temperature, and emergent phase coherence at 93 K. Such local phase variations govern the long-range correlations of the charge-ordered state and locally change the periodicity of the modulations, resulting in wave vector shifts in reciprocal space. These atomically resolved observations underscore the importance of lattice coupling and phase inhomogeneity, and provide a microscopic explanation for putative “incommensurate” order in hole-doped oxides. PMID:29382750

Insights into electrode/electrolyte interfacial processes and the effect of nanostructured cobalt oxides loading on graphene-based hybrids by scanning electrochemical microscopy

NASA Astrophysics Data System (ADS)

Gupta, Sanju; Carrizosa, Sara B.

2016-12-01

Nanostructured cobalt oxide polymorphs (CoO and Co3O4) deposited via electrodeposition allowed optimal loading on supercapacitive graphene nanosheets producing a set of graphene-based hybrids namely, CoO/GO, CoO/ErGO, Co3O4/GO, Co3O4/rGO, and Co3O4/ErGO, as pseudocapacitive electrochemical electrodes. We gained fundamental insights into the complex physicochemical interfacial processes at electrode surfaces and electrode/electrolyte (or solid/liquid) interfaces by scanning electrochemical microscopy operating in the feedback probe approach and imaging modes while monitoring and mapping the redox probe (re)activity behavior. We determined the various experimental descriptors including diffusion coefficient, electron transfer rate, and electroactive site distribution on electrodes. We emphasize the interplay of (1) heterogeneous basal and edge plane active sites, (2) graphene surface functional moieties (conducting/semiconducting), and (3) crystalline spinel cobalt oxides (semiconducting/insulating) coated graphene, reinforcing the available electron density of states in the vicinity of the Fermi level contributing to higher electroactivity, faster interfacial diffusion, and shorter distances for electron transfer, facilitated through molecular and chemical bridges obtained by electrodeposition as compared with the physical deposition.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghamarian, I.; Samani, P.; Rohrer, G. S.

Grain boundary engineering and other fundamental materials science problems (e.g., phase transformations and physical properties) require an improvement in the understanding of the type and population of grain boundaries in a given system – yet, databases are limited in number and spare in detail, including for hcp crystals such as zirconium. One way to rapidly obtain databases to analyze is to use small-grained materials and high spatial resolution orientation microscopy techniques, such as ASTAR™/precession electron diffraction. To demonstrate this, a study of grain boundary character distributions was conducted for α-zirconium deposited at room temperature on fused silica substrates using physicalmore » vapor deposition. The orientation maps of the nanocrystalline thin films were acquired by the ASTARα/precession electron diffraction technique, a new transmission electron microscope based orientation microscopy method. The reconstructed grain boundaries were classified as pure tilt, pure twist, 180°-twist and 180°-tilt grain boundaries based on the distribution of grain boundary planes with respect to the angle/axis of misorientation associated with grain boundaries. The results of the current study were compared to the results of a similar study on α-titanium and the molecular dynamics results of grain boundary energy for α-titanium.« less

Porous Ni-Mn oxide nanosheets in situ formed on nickel foam as 3D hierarchical monolith de-NOx catalysts

NASA Astrophysics Data System (ADS)

Cai, Sixiang; Zhang, Dengsong; Shi, Liyi; Xu, Jing; Zhang, Lei; Huang, Lei; Li, Hongrui; Zhang, Jianping

2014-06-01

In this work, we successfully in situ decorated nickel foam with porous Ni-Mn oxide nanosheets (3DH-NM/NF) as 3D hierarchical monolith de-NOx catalysts via a simple hydrothermal reaction and calcination process. The catalysts were carefully examined by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, elemental mapping, X-ray photoelectron spectroscopy, H2 temperature-programmed reduction and NH3 temperature-programmed desorption measurements. The results indicated that the nanosheets are composed of a Ni6Mn1O8 spinel and the metal species are uniformly dispersed in bi-metal oxides. As a result, the strong synergistic effects between the Mn and Ni species have been observed. The active oxygen species, reducible species and acidity are enhanced by the in situ formation of the nanosheets on the surface of nickel foam. These desirable features of 3DH-NM/NF catalysts bring about the excellent de-NOx performance. Moreover, the 3DH-NM/NF catalysts also present good stability and H2O resistance. Based on these favorable properties, 3DH-NM/NF could be considered as a promising candidate for the monolith de-NOx catalysts.In this work, we successfully in situ decorated nickel foam with porous Ni-Mn oxide nanosheets (3DH-NM/NF) as 3D hierarchical monolith de-NOx catalysts via a simple hydrothermal reaction and calcination process. The catalysts were carefully examined by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, elemental mapping, X-ray photoelectron spectroscopy, H2 temperature-programmed reduction and NH3 temperature-programmed desorption measurements. The results indicated that the nanosheets are composed of a Ni6Mn1O8 spinel and the metal species are uniformly dispersed in bi-metal oxides. As a result, the strong synergistic effects between the Mn and Ni species have been observed. The active oxygen species, reducible species and acidity are enhanced by the in situ formation of the nanosheets on the surface of nickel foam. These desirable features of 3DH-NM/NF catalysts bring about the excellent de-NOx performance. Moreover, the 3DH-NM/NF catalysts also present good stability and H2O resistance. Based on these favorable properties, 3DH-NM/NF could be considered as a promising candidate for the monolith de-NOx catalysts. Electronic supplementary information (ESI) available: Experimental details and catalytic performance of the NM/cordierite catalysts, SEM image and EDX analysis of the NF and 3DH-N/NF catalysts, N2 selectivity and catalytic performance under different gas hourly space velocities of the 3DH-NM/NF catalysts. See DOI: 10.1039/c4nr00475b

Mapping Free-Carriers in Multijunction Silicon Nanowires Using Infrared Near-Field Optical Microscopy.

PubMed

Ritchie, Earl T; Hill, David J; Mastin, Tucker M; Deguzman, Panfilo C; Cahoon, James F; Atkin, Joanna M

2017-11-08

We report the use of infrared (IR) scattering-type scanning near-field optical microscopy (s-SNOM) as a nondestructive method to map free-carriers in axially modulation-doped silicon nanowires (SiNWs) with nanoscale spatial resolution. Using this technique, we can detect local changes in the electrically active doping concentration based on the infrared free-carrier response in SiNWs grown using the vapor-liquid-solid (VLS) method. We demonstrate that IR s-SNOM is sensitive to both p-type and n-type free-carriers for carrier densities above ∼1 × 10 19 cm -3 . We also resolve subtle changes in local conductivity properties, which can be correlated with growth conditions and surface effects. The use of s-SNOM is especially valuable in low mobility materials such as boron-doped p-type SiNWs, where optimization of growth has been difficult to achieve due to the lack of information on dopant distribution and junction properties. s-SNOM can be widely employed for the nondestructive characterization of nanostructured material synthesis and local electronic properties without the need for contacts or inert atmosphere.

Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

DOE PAGES

Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; ...

2014-12-15

Fertilization of a mammalian egg induces a series of ‘zinc sparks’ that are necessary for inducing the egg-to-embryo transition. Despite the importance of these zinc efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches to resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy dispersive spectroscopy, X-ray fluorescence microscopy, and 3D elemental tomography for high resolution elemental mapping. Here we show that the zinc spark arises from a system of thousands ofmore » zinc-loaded vesicles, each of which contains, on average, 106 zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. We conclude that the discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes.« less

Quantitative high-resolution mapping of phenanthrene sorption to black carbon particles.

PubMed

Obst, Martin; Grathwohl, Peter; Kappler, Andreas; Eibl, Oliver; Peranio, Nicola; Gocht, Tilman

2011-09-01

Sorption of hydrophobic organic contaminants such as polycyclic aromatic hydrocarbons (PAHs) to black carbon (BC) particles has been the focus of numerous studies. Conclusions on sorption mechanisms of PAH on BC were mostly derived from studies of sorption isotherms and sorption kinetics, which are based on batch experiments. However, mechanistic modeling approaches consider processes at the subparticle scale, some including transport within the pore-space or different spatial pore-domains. Direct evidence based on analytical techniques operating at the submicrometer scale for the location of sorption sites and the adsorbed species is lacking. In this work, we identified, quantified, and mapped the sorption of PAHs on different BC particles (activated carbon, charcoal and diesel soot) on a 25-100 nm scale using scanning transmission X-ray microscopy (STXM). In addition, we visualized the pore structure of the particles by transmission electron microscopy (TEM) on the 1-10 nm-scale. The combination of the chemical information from STXM with the physical information from TEM revealed that phenanthrene accumulates in the interconnected pore-system along primary "cracks" in the particles, confirming an adsorption mechanism.

Diffraction contrast as a sensitive indicator of femtosecond sub-nanoscale motion in ultrafast transmission electron microscopy

NASA Astrophysics Data System (ADS)

Cremons, Daniel R.; Schliep, Karl B.; Flannigan, David J.

2013-09-01

With ultrafast transmission electron microscopy (UTEM), access can be gained to the spatiotemporal scales required to directly visualize rapid, non-equilibrium structural dynamics of materials. This is achieved by operating a transmission electron microscope (TEM) in a stroboscopic pump-probe fashion by photoelectrically generating coherent, well-timed electron packets in the gun region of the TEM. These probe photoelectrons are accelerated down the TEM column where they travel through the specimen before reaching a standard, commercially-available CCD detector. A second laser pulse is used to excite (pump) the specimen in situ. Structural changes are visualized by varying the arrival time of the pump laser pulse relative to the probe electron packet at the specimen. Here, we discuss how ultrafast nanoscale motions of crystalline materials can be visualized and precisely quantified using diffraction contrast in UTEM. Because diffraction contrast sensitively depends upon both crystal lattice orientation as well as incoming electron wavevector, minor spatial/directional variations in either will produce dynamic and often complex patterns in real-space images. This is because sections of the crystalline material that satisfy the Laue conditions may be heterogeneously distributed such that electron scattering vectors vary over nanoscale regions. Thus, minor changes in either crystal grain orientation, as occurs during specimen tilting, warping, or anisotropic expansion, or in the electron wavevector result in dramatic changes in the observed diffraction contrast. In this way, dynamic contrast patterns observed in UTEM images can be used as sensitive indicators of ultrafast specimen motion. Further, these motions can be spatiotemporally mapped such that direction and amplitude can be determined.

Final Project Report CFA-14-6357: A New Paradigm for Understanding Multiphase Ceramic Waste Form Performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brinkman, Kyle; Bordia, Rajendra; Reifsnider, Kenneth

This project fabricated model multiphase ceramic waste forms with processing-controlled microstructures followed by advanced characterization with synchrotron and electron microscopy-based 3D tomography to provide elemental and chemical state-specific information resulting in compositional phase maps of ceramic composites. Details of 3D microstructural features were incorporated into computer-based simulations using durability data for individual constituent phases as inputs in order to predict the performance of multiphase waste forms with varying microstructure and phase connectivity.

Development of Biodegradable Polyphosphazene- Nanohydroxyapatite Composite Nanofibers Via Electrospinning

DTIC Science & Technology

2005-01-01

transmission electron microscopy (TEM), gravimetry and energy dispersive X-ray mapping. This study demonstrated the feasibility of developing novel composite...successive precipitations into hexane (3x) and pentane (2x). The product was an off-white fibrous material. 31P NMR: (CDC13), ppm 3 -1.1. ’H NMR (CDC13), ppm...determined by gravimetry . Theoretical loading of 50% (w/w) of the nanofibers showed an actual loading of 59% (w/w) of nHAp in the nanofiber matrix. This

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

3D reconstruction of the magnetic vector potential using model based iterative reconstruction.

PubMed

Prabhat, K C; Aditya Mohan, K; Phatak, Charudatta; Bouman, Charles; De Graef, Marc

2017-11-01

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. A comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach. Copyright © 2017 Elsevier B.V. All rights reserved.

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

DOE PAGES

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta; ...

2017-07-03

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

Effect of Surface Morphology and Magnetic Impurities on the Electronic Structure in Cobalt-Doped BaFe 2 As 2 Superconductors

DOE PAGES

Zou, Qiang; Wu, Zhiming; Fu, Mingming; ...

2017-02-03

Combined scanning tunneling microscopy, spectroscopy, and local barrier height (LBH) studies show that low-temperature-cleaved optimally doped Ba(Fe 1–xCo x) 2As 2 crystals with x = 0.06, with T c = 22 K, have complicated morphologies. Although the cleavage surface and hence the morphologies are variable, the superconducting gap maps show the same gap widths and nanometer size inhomogeneities irrelevant to the morphology. Based on the spectroscopy and LBH maps, the bright patches and dark stripes in the morphologies are identified as Ba- and As-dominated surface terminations, respectively. Magnetic impurities, possibly due to Co or Fe atoms, are believed to createmore » local in-gap state and, in addition, suppress the superconducting coherence peaks. Lastly, this study will clarify the confusion on the cleavage surface terminations of the Fe-based superconductors and its relation with the electronic structures.« less

MapA, an iron-regulated, cytoplasmic membrane protein in the cyanobacterium Synechococcus sp. strain PCC7942.

PubMed Central

Webb, R; Troyan, T; Sherman, D; Sherman, L A

1994-01-01

Growth of Synechococcus sp. strain PCC 7942 in iron-deficient media leads to the accumulation of an approximately 34-kDa protein. The gene encoding this protein, mapA (membrane-associated protein A), has been cloned and sequenced (GenBank accession number, L01621). The mapA transcript is not detectable in normally grown cultures but is stably accumulated by cells grown in iron-deficient media. However, the promoter sequence for this gene does not resemble other bacterial iron-regulated promoters described to date. The carboxyl-terminal region of the derived amino acid sequence of MapA resembles bacterial proteins involved in iron acquisition, whereas the amino-terminal end of MapA has a high degree of amino acid identity with the abundant, chloroplast envelope protein E37. An approach employing improved cellular fractionation techniques as well as electron microscopy and immunocytochemistry was essential in localizing MapA protein to the cytoplasmic membrane of Synechococcus sp. strain PCC 7942. When these cells were grown under iron-deficient conditions, a significant fraction of MapA could also be localized to the thylakoid membranes. Images PMID:8051004

Controllable self-assembly of mesoporous hydroxyapatite.

PubMed

Chen, Jingdi; Wang, Zihao; Wen, Zhenliang; Yang, Shen; Wang, Jianhua; Zhang, Qiqing

2015-03-01

In this paper, mesoporous hydroxyapatite (HAp) of controllable pore size was tailored with the template of a biodegradable mono-alkyl phosphate (MAP) via a simple route by hydrothermal treatment. A serial study of the various experimental parameters on pore size of HAp was investigated. The additive amount of MAP and hydrothermal temperature were important factors for the pore structure and pore size. Powder X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and nitrogen adsorption-desorption (BET, BJH) were used to characterize the structure and composition of the HAp samples. Both XRD and BJH results indicated that regular mesoporous HAp nanoparticles (with a mean pore size of 3.5nm) were successfully produced. As shown in transmission electron microscopy (TEM), orderly uniform pore structure appeared in the HAp particles. Because of the special structure of the MAP and the interaction between ionized MAP and other ions in solution, the product presents uniform mesoporous structure with well-defined pore size. Copyright © 2015 Elsevier B.V. All rights reserved.

Column ratio mapping: a processing technique for atomic resolution high-angle annular dark-field (HAADF) images.

PubMed

Robb, Paul D; Craven, Alan J

2008-12-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [110]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 angstroms-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

Mechanisms of grain refinement in aluminum alloys in the process of severe plastic deformation

NASA Astrophysics Data System (ADS)

Kaibyshev, R. O.; Mazurina, I. A.; Gromov, D. A.

2006-01-01

A study of the mechanisms of grain refinement in the process of severe plastic deformation of two aluminum alloys, i.e., 2219 bearing nanometric particles of Al3Zr and low-alloy Al-3% Cu, is described. The alloys are deformed by the method of equal channel angular pressing at 250°C to a maximum strain degree of about 12. The angles of (sub)grain boundaries in alloy 2219 are determined with the help of transmission electron microscopy by the method of Kikuchi lines. The evolution of the microstructure in alloy Al-3% Cu is studied with the help of grain-boundary maps obtained by the method of electron back-scattered diffraction.

Comprehensive analysis of TEM methods for LiFePO4/FePO4 phase mapping: spectroscopic techniques (EFTEM, STEM-EELS) and STEM diffraction techniques (ACOM-TEM).

PubMed

Mu, X; Kobler, A; Wang, D; Chakravadhanula, V S K; Schlabach, S; Szabó, D V; Norby, P; Kübel, C

2016-11-01

Transmission electron microscopy (TEM) has been used intensively in investigating battery materials, e.g. to obtain phase maps of partially (dis)charged (lithium) iron phosphate (LFP/FP), which is one of the most promising cathode material for next generation lithium ion (Li-ion) batteries. Due to the weak interaction between Li atoms and fast electrons, mapping of the Li distribution is not straightforward. In this work, we revisited the issue of TEM measurements of Li distribution maps for LFP/FP. Different TEM techniques, including spectroscopic techniques (energy filtered (EF)TEM in the energy range from low-loss to core-loss) and a STEM diffraction technique (automated crystal orientation mapping (ACOM)), were applied to map the lithiation of the same location in the same sample. This enabled a direct comparison of the results. The maps obtained by all methods showed excellent agreement with each other. Because of the strong difference in the imaging mechanisms, it proves the reliability of both the spectroscopic and STEM diffraction phase mapping. A comprehensive comparison of all methods is given in terms of information content, dose level, acquisition time and signal quality. The latter three are crucial for the design of in-situ experiments with beam sensitive Li-ion battery materials. Furthermore, we demonstrated the power of STEM diffraction (ACOM-STEM) providing additional crystallographic information, which can be analyzed to gain a deeper understanding of the LFP/FP interface properties such as statistical information on phase boundary orientation and misorientation between domains. Copyright © 2016 Elsevier B.V. All rights reserved.

Electric field imaging of single atoms

PubMed Central

Shibata, Naoya; Seki, Takehito; Sánchez-Santolino, Gabriel; Findlay, Scott D.; Kohno, Yuji; Matsumoto, Takao; Ishikawa, Ryo; Ikuhara, Yuichi

2017-01-01

In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures. PMID:28555629

Elucidating the charge carrier separation and working mechanism of CH3NH3PbI(3-x)Cl(x) perovskite solar cells.

PubMed

Edri, Eran; Kirmayer, Saar; Mukhopadhyay, Sabyasachi; Gartsman, Konstantin; Hodes, Gary; Cahen, David

2014-03-11

Developments in organic-inorganic lead halide-based perovskite solar cells have been meteoric over the last 2 years, with small-area efficiencies surpassing 15%. We address the fundamental issue of how these cells work by applying a scanning electron microscopy-based technique to cell cross-sections. By mapping the variation in efficiency of charge separation and collection in the cross-sections, we show the presence of two prime high efficiency locations, one at/near the absorber/hole-blocking-layer, and the second at/near the absorber/electron-blocking-layer interfaces, with the former more pronounced. This 'twin-peaks' profile is characteristic of a p-i-n solar cell, with a layer of low-doped, high electronic quality semiconductor, between a p- and an n-layer. If the electron blocker is replaced by a gold contact, only a heterojunction at the absorber/hole-blocking interface remains.

[Characteristics of exosomes andmicroparticles discovered in human tears].

PubMed

Grigor'eva, A E; Tamkovich, S N; Eremina, A V; Tupikin, A E; Kabilov, M R; Chernykh, V V; Vlassov, V V; Laktionov, P P; Ryabchikova, E I

2016-01-01

Exosomes represent a sort of extracellular vesicles, which transfer molecular signals in organism and possess markers of producing cells. Our study was aimed at search of exosomes in the tears of healthy humans, confirmation of their nature and examination of exosome morphological and molecular-biological characteristics. The tears (110-340 ml) were collected from 24 healthy donors (aged 46-60 years); individual probes were centrifuged at 20000 g for 15 min to pellet cell debris. The supernatants were examined in electron microscope using negative staining; and they were also used for isolation and purification of the exosomes by filtration (100 nm pore-size) and double ultracentrifugation (90 min at 100000 g, 4°C). The "pellets" were subjected to electron microscopy, immunolabeling. The RNA and DNA were isolated from the samples, and their sizes were evaluated by capillary electrophoresis, the concentration and localization of nucleic acids were determined. Sequencing of DNA was performed using MiSeq ("Illumina", USA), data were analyzed using CLC GW 7.5 ("Qiagen", USA). Sequences were mapped on human genome (hg19). Electron microscopy revealed in supernatants of the tears cell debris, spherical microparticles (20-40 nm), membrane vesicles and macromolecular aggregates. The "pellets" obtained after ultracentrifugation, contained microparticles (17%), spherical and cup-shaped EVs (40-100 nm, 83%), which were positive for CD63, CD9 and CD24 receptors (specific markers of exosomes). Our study showed presence of high amount of exosomes in human tears, and relation of the exosomes with RNA (size less than 200 nt) and DNA (size was 3-9 kb). Sequencing of the DNA showed that about 92% of the reads mapped to human genome.

Mapping stress in polycrystals with sub-10 nm spatial resolution.

PubMed

Polop, C; Vasco, E; Perrino, A P; Garcia, R

2017-09-28

From aircraft to electronic devices, and even in Formula One cars, stress is the main cause of degraded material performance and mechanical failure in applications incorporating thin films and coatings. Over the last two decades, the scientific community has searched for the mechanisms responsible for stress generation in films, with no consensus in sight. The main difficulty is that most current models of stress generation, while atomistic in nature, are based on macroscopic measurements. Here, we demonstrate a novel method for mapping the stress at the surface of polycrystals with sub-10 nm spatial resolution. This method consists of transforming elastic modulus maps measured by atomic force microscopy techniques into stress maps via the local stress-stiffening effect. The validity of this approach is supported by finite element modeling simulations. Our study reveals a strongly heterogeneous distribution of intrinsic stress in polycrystalline Au films, with gradients as high as 100 MPa nm -1 near the grain boundaries. Consequently, our study discloses the limited capacity of macroscopic stress assessments and standard tests to discriminate among models, and the great potential of nanometer-scale stress mapping.

Real-space imaging of fractional quantum Hall liquids

NASA Astrophysics Data System (ADS)

Hayakawa, Junichiro; Muraki, Koji; Yusa, Go

2013-01-01

Electrons in semiconductors usually behave like a gas--as independent particles. However, when confined to two dimensions under a perpendicular magnetic field at low temperatures, they condense into an incompressible quantum liquid. This phenomenon, known as the fractional quantum Hall (FQH) effect, is a quantum-mechanical manifestation of the macroscopic behaviour of correlated electrons that arises when the Landau-level filling factor is a rational fraction. However, the diverse microscopic interactions responsible for its emergence have been hidden by its universality and macroscopic nature. Here, we report real-space imaging of FQH liquids, achieved with polarization-sensitive scanning optical microscopy using trions (charged excitons) as a local probe for electron spin polarization. When the FQH ground state is spin-polarized, the triplet/singlet intensity map exhibits a spatial pattern that mirrors the intrinsic disorder potential, which is interpreted as a mapping of compressible and incompressible electron liquids. In contrast, when FQH ground states with different spin polarization coexist, domain structures with spontaneous quasi-long-range order emerge, which can be reproduced remarkably well from the disorder patterns using a two-dimensional random-field Ising model. Our results constitute the first reported real-space observation of quantum liquids in a class of broken symmetry state known as the quantum Hall ferromagnet.

Platinum replica electron microscopy: Imaging the cytoskeleton globally and locally.

PubMed

Svitkina, Tatyana M

2017-05-01

Structural studies reveal how smaller components of a system work together as a whole. However, combining high resolution of details with full coverage of the whole is challenging. In cell biology, light microscopy can image many cells in their entirety, but at a lower resolution, whereas electron microscopy affords very high resolution, but usually at the expense of the sample size and coverage. Structural analyses of the cytoskeleton are especially demanding, because cytoskeletal networks are unresolvable by light microscopy due to their density and intricacy, whereas their proper preservation is a challenge for electron microscopy. Platinum replica electron microscopy can uniquely bridge the gap between the "comfort zones" of light and electron microscopy by allowing high resolution imaging of the cytoskeleton throughout the entire cell and in many cells in the population. This review describes the principles and applications of platinum replica electron microscopy for studies of the cytoskeleton. Copyright © 2017 Elsevier Ltd. All rights reserved.

Platinum Replica Electron Microscopy: Imaging the Cytoskeleton Globally and Locally

PubMed Central

SVITKINA, Tatyana M.

2017-01-01

Structural studies reveal how smaller components of a system work together as a whole. However, combining high resolution of details with full coverage of the whole is challenging. In cell biology, light microscopy can image many cells in their entirety, but at a lower resolution, whereas electron microscopy affords very high resolution, but usually at the expense of the sample size and coverage. Structural analyses of the cytoskeleton are especially demanding, because cytoskeletal networks are unresolvable by light microscopy due to their density and intricacy, whereas their proper preservation is a challenge for electron microscopy. Platinum replica electron microscopy can uniquely bridge the gap between the “comfort zones” of light and electron microscopy by allowing high resolution imaging of the cytoskeleton throughout the entire cell and in many cells in the population. This review describes the principles and applications of platinum replica electron microscopy for studies of the cytoskeleton. PMID:28323208

Diagnostic pitfalls in newborns and babies with blisters and erosions.

PubMed

Nischler, Elke; Klausegger, Alfred; Hüttner, Clemens; Pohla-Gubo, Gabriele; Diem, Anja; Bauer, Johann W; Hintner, Helmut

2009-01-01

Establishing the correct diagnosis in newborns presenting with blisters and erosions is not always a straightforward process. Many different disease entities including acquired (i.e., infectious, immunobullous, traumatic) and inherited disorders have to be taken into consideration. Similarities in clinical appearance, colonization and/or superinfections of preexisting skin lesions, as well as the absence of late changes in the neonate often pose significant diagnostic challenges. In this paper we discuss by giving examples the process of making an accurate diagnosis of blistering skin diseases in the neonatal period on the basis of a diagnostic algorithm. In addition, we provide an overview of the rational use and the limitations of laboratory procedures such as microbial testing, routine light microscopy, immunofluorescence antigen mapping, transmission electron microscopy, and molecular genetic analysis.

Imaging the surface morphology, chemistry and conductivity of LiNi 1/3 Fe 1/3 Mn 4/3 O 4 crystalline facets using scanning transmission X-ray microscopy

DOE PAGES

Zhou, Jigang; Wang, Jian; Cutler, Jeffrey; ...

2016-07-26

We have employed scanning transmission X-ray microscopy (STXM) using the X-ray fluorescence mode in order to elucidate the chemical structures at Ni, Fe, Mn and O sites from the (111) and (100) facets of micron-sized LiNi 1/3Fe 1/3Mn 4/3O 4 energy material particles. Furthermore, STXM imaging using electron yield mode has mapped out the surface conductivity of the crystalline particles. Our study presents a novel approach that visualizes local element segregation, chemistry and conductivity variation among different crystal facets, which will assist further tailoring of the morphology and surface structure of this high voltage spinel lithium ion battery cathode material.

Silver stain for electron microscopy

NASA Technical Reports Server (NTRS)

Corbett, R. L.

1972-01-01

Ammoniacal silver stain used for light microscopy was adapted advantageously for use with very thin biological sections required for electron microscopy. Silver stain can be performed in short time, has more contrast, and is especially useful for low power electron microscopy.

Correlated Light and Electron Microscopy/Electron Tomography of Mitochondria In Situ

PubMed Central

Perkins, Guy A.; Sun, Mei G.; Frey, Terrence G.

2009-01-01

Three-dimensional light microscopy and three-dimensional electron microscopy (electron tomography) separately provide very powerful tools to study cellular structure and physiology, including the structure and physiology of mitochondria. Fluorescence microscopy allows one to study processes in live cells with specific labels and stains that follow the movement of labeled proteins and changes within cellular compartments but does not have sufficient resolution to define the ultrastructure of intracellular organelles such as mitochondria. Electron microscopy and electron tomography provide the highest resolution currently available to study mitochondrial ultrastructure but cannot follow processes in living cells. We describe the combination of these two techniques in which fluorescence confocal microscopy is used to study structural and physiologic changes in mitochondria within apoptotic HeLa cells to define the apoptotic timeframe. Cells can then be selected at various stages of the apoptotic timeframe for examination at higher resolution by electron microscopy and electron tomography. This is a form of “virtual” 4-dimensional electron microscopy that has revealed interesting structural changes in the mitochondria of HeLa cells during apoptosis. The same techniques can be applied, with modification, to study other dynamic processes within cells in other experimental contexts. PMID:19348881

Tip induced mechanical deformation of epitaxial graphene grown on reconstructed 6H-SiC(0001) surface during scanning tunneling and atomic force microscopy studies.

PubMed

Meza, José Antonio Morán; Lubin, Christophe; Thoyer, François; Cousty, Jacques

2015-01-26

The structural and mechanical properties of an epitaxial graphene (EG) monolayer thermally grown on top of a 6H-SiC(0001) surface were studied by combined dynamic scanning tunneling microscopy (STM) and frequency modulation atomic force microscopy (FM-AFM). Experimental STM, dynamic STM and AFM images of EG on 6H-SiC(0001) show a lattice with a 1.9 nm period corresponding to the (6 × 6) quasi-cell of the SiC surface. The corrugation amplitude of this (6 × 6) quasi-cell, measured from AFM topographies, increases with the setpoint value of the frequency shift Δf (15-20 Hz, repulsive interaction). Excitation variations map obtained simultaneously with the AFM topography shows that larger dissipation values are measured in between the topographical bumps of the (6 × 6) quasi-cell. These results demonstrate that the AFM tip deforms the graphene monolayer. During recording in dynamic STM mode, a frequency shift (Δf) map is obtained in which Δf values range from 41 to 47 Hz (repulsive interaction). As a result, we deduced that the STM tip, also, provokes local mechanical distortions of the graphene monolayer. The origin of these tip-induced distortions is discussed in terms of electronic and mechanical properties of EG on 6H-SiC(0001).

Do's and don'ts of cryo-electron microscopy: a primer on sample preparation and high quality data collection for macromolecular 3D reconstruction.

PubMed

Cabra, Vanessa; Samsó, Montserrat

2015-01-09

Cryo-electron microscopy (cryoEM) entails flash-freezing a thin layer of sample on a support, and then visualizing the sample in its frozen hydrated state by transmission electron microscopy (TEM). This can be achieved with very low quantity of protein and in the buffer of choice, without the use of any stain, which is very useful to determine structure-function correlations of macromolecules. When combined with single-particle image processing, the technique has found widespread usefulness for 3D structural determination of purified macromolecules. The protocol presented here explains how to perform cryoEM and examines the causes of most commonly encountered problems for rational troubleshooting; following all these steps should lead to acquisition of high quality cryoEM images. The technique requires access to the electron microscope instrument and to a vitrification device. Knowledge of the 3D reconstruction concepts and software is also needed for computerized image processing. Importantly, high quality results depend on finding the right purification conditions leading to a uniform population of structurally intact macromolecules. The ability of cryoEM to visualize macromolecules combined with the versatility of single particle image processing has proven very successful for structural determination of large proteins and macromolecular machines in their near-native state, identification of their multiple components by 3D difference mapping, and creation of pseudo-atomic structures by docking of x-ray structures. The relentless development of cryoEM instrumentation and image processing techniques for the last 30 years has resulted in the possibility to generate de novo 3D reconstructions at atomic resolution level.

Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design

PubMed Central

Sharp, Thomas H.; Bruning, Marc; Mantell, Judith; Sessions, Richard B.; Thomson, Andrew R.; Zaccai, Nathan R.; Brady, R. Leo; Verkade, Paul; Woolfson, Derek N.

2012-01-01

Nature presents various protein fibers that bridge the nanometer to micrometer regimes. These structures provide inspiration for the de novo design of biomimetic assemblies, both to address difficulties in studying and understanding natural systems, and to provide routes to new biomaterials with potential applications in nanotechnology and medicine. We have designed a self-assembling fiber system, the SAFs, in which two small α-helical peptides are programmed to form a dimeric coiled coil and assemble in a controlled manner. The resulting fibers are tens of nm wide and tens of μm long, and, therefore, comprise millions of peptides to give gigadalton supramolecular structures. Here, we describe the structure of the SAFs determined to approximately 8 Å resolution using cryotransmission electron microscopy. Individual micrographs show clear ultrastructure that allowed direct interpretation of the packing of individual α-helices within the fibers, and the construction of a 3D electron density map. Furthermore, a model was derived using the cryotransmission electron microscopy data and side chains taken from a 2.3 Å X-ray crystal structure of a peptide building block incapable of forming fibers. This was validated using single-particle analysis techniques, and was stable in prolonged molecular-dynamics simulation, confirming its structural viability. The level of self-assembly and self-organization in the SAFs is unprecedented for a designed peptide-based material, particularly for a system of considerably reduced complexity compared with natural proteins. This structural insight is a unique high-resolution description of how α-helical fibrils pack into larger protein fibers, and provides a basis for the design and engineering of future biomaterials. PMID:22847414

Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM

PubMed Central

Kishchenko, Gregory P.; Danev, Radostin; Fisher, Rebecca; He, Jie; Hsieh, Chyongere; Marko, Michael; Sui, Haixin

2015-01-01

Zernike phase-plate (ZPP) imaging greatly increases contrast in cryo-electron microscopy, however fringe artifacts appear in the images. A computational de-fringing method has been proposed, but it has not been widely employed, perhaps because the importance of de-fringing has not been clearly demonstrated. For testing purposes, we employed Zernike phase-plate imaging in a cryo-electron tomographic study of radial-spoke complexes attached to microtubule doublets. We found that the contrast enhancement by ZPP imaging made nonlinear denoising insensitive to the filtering parameters, such that simple low-frequency band-pass filtering made the same improvement in map quality. We employed sub-tomogram averaging, which compensates for the effect of the “missing wedge” and considerably improves map quality. We found that fringes (caused by the abrupt cut-on of the central hole in the phase plate) can lead to incorrect representation of a structure that is well-known from the literature. The expected structure was restored by amplitude scaling, as proposed in the literature. Our results show that de-fringing is an important part of image-processing for cryo-electron tomography of macromolecular complexes with ZPP imaging. PMID:26210582

Faults and foibles of quantitative scanning electron microscopy/energy dispersive x-ray spectrometry (SEM/EDS)

NASA Astrophysics Data System (ADS)

Newbury, Dale E.; Ritchie, Nicholas W. M.

2012-06-01

Scanning electron microscopy with energy dispersive x-ray spectrometry (SEM/EDS) is a powerful and flexible elemental analysis method that can identify and quantify elements with atomic numbers > 4 (Be) present as major constituents (where the concentration C > 0.1 mass fraction, or 10 weight percent), minor (0.01<= C <= 0.1) and trace (C < 0.01, with a minimum detectable limit of ~+/- 0.0005 - 0.001 under routine measurement conditions, a level which is analyte and matrix dependent ). SEM/EDS can select specimen volumes with linear dimensions from ~ 500 nm to 5 μm depending on composition (masses ranging from ~ 10 pg to 100 pg) and can provide compositional maps that depict lateral elemental distributions. Despite the maturity of SEM/EDS, which has a history of more than 40 years, and the sophistication of modern analytical software, the method is vulnerable to serious shortcomings that can lead to incorrect elemental identifications and quantification errors that significantly exceed reasonable expectations. This paper will describe shortcomings in peak identification procedures, limitations on the accuracy of quantitative analysis due to specimen topography or failures in physical models for matrix corrections, and quantitative artifacts encountered in xray elemental mapping. Effective solutions to these problems are based on understanding the causes and then establishing appropriate measurement science protocols. NIST DTSA II and Lispix are open source analytical software available free at www.nist.gov that can aid the analyst in overcoming significant limitations to SEM/EDS.

Elemental imaging at the nanoscale: NanoSIMS and complementary techniques for element localisation in plants.

PubMed

Moore, Katie L; Lombi, Enzo; Zhao, Fang-Jie; Grovenor, Chris R M

2012-04-01

The ability to locate and quantify elemental distributions in plants is crucial to understanding plant metabolisms, the mechanisms of uptake and transport of minerals and how plants cope with toxic elements or elemental deficiencies. High-resolution secondary ion mass spectrometry (SIMS) is emerging as an important technique for the analysis of biological material at the subcellular scale. This article reviews recent work using the CAMECA NanoSIMS to determine elemental distributions in plants. The NanoSIMS is able to map elemental distributions at high resolution, down to 50 nm, and can detect very low concentrations (milligrams per kilogram) for some elements. It is also capable of mapping almost all elements in the periodic table (from hydrogen to uranium) and can distinguish between stable isotopes, which allows the design of tracer experiments. In this review, particular focus is placed upon studying the same or similar specimens with both the NanoSIMS and a wide range of complementary techniques, showing how the advantages of each technique can be combined to provide a fuller data set to address complex scientific questions. Techniques covered include optical microscopy, synchrotron techniques, including X-ray fluorescence and X-ray absorption spectroscopy, transmission electron microscopy, electron probe microanalysis, particle-induced X-ray emission and inductively coupled plasma mass spectrometry. Some of the challenges associated with sample preparation of plant material for SIMS analysis, the artefacts and limitations of the technique and future trends are also discussed.

Graphene-enabled electron microscopy and correlated super-resolution microscopy of wet cells.

PubMed

Wojcik, Michal; Hauser, Margaret; Li, Wan; Moon, Seonah; Xu, Ke

2015-06-11

The application of electron microscopy to hydrated biological samples has been limited by high-vacuum operating conditions. Traditional methods utilize harsh and laborious sample dehydration procedures, often leading to structural artefacts and creating difficulties for correlating results with high-resolution fluorescence microscopy. Here, we utilize graphene, a single-atom-thick carbon meshwork, as the thinnest possible impermeable and conductive membrane to protect animal cells from vacuum, thus enabling high-resolution electron microscopy of wet and untreated whole cells with exceptional ease. Our approach further allows for facile correlative super-resolution and electron microscopy of wet cells directly on the culturing substrate. In particular, individual cytoskeletal actin filaments are resolved in hydrated samples through electron microscopy and well correlated with super-resolution results.

Mapping the local reaction kinetics by PEEM: CO oxidation on individual (100)-type grains of Pt foil

PubMed Central

Vogel, D.; Spiel, C.; Suchorski, Y.; Urich, A.; Schlögl, R.; Rupprechter, G.

2011-01-01

The locally-resolved reaction kinetics of CO oxidation on individual (100)-type grains of a polycrystalline Pt foil was monitored in situ using photoemission electron microscopy (PEEM). Reaction-induced surface morphology changes were studied by optical differential interference contrast microscopy and atomic force microscopy (AFM). Regions of high catalytic activity, low activity and bistability in a (p,T)-parameter space were determined, allowing to establish a local kinetic phase diagram for CO oxidation on (100) facets of Pt foil. PEEM observations of the reaction front propagation on Pt(100) domains reveal a high degree of propagation anisotropy both for oxygen and CO fronts on the apparently isotropic Pt(100) surface. The anisotropy vanishes for oxygen fronts at temperatures above 465 K, but is maintained for CO fronts at all temperatures studied, i.e. in the range of 417 to 513 K. A change in the front propagation mechanism is proposed to explain the observed effects. PMID:22140277

Label-free volumetric optical imaging of intact murine brains

NASA Astrophysics Data System (ADS)

Ren, Jian; Choi, Heejin; Chung, Kwanghun; Bouma, Brett E.

2017-04-01

A central effort of today’s neuroscience is to study the brain’s ’wiring diagram’. The nervous system is believed to be a network of neurons interacting with each other through synaptic connection between axons and dendrites, therefore the neuronal connectivity map not only depicts the underlying anatomy, but also has important behavioral implications. Different approaches have been utilized to decipher neuronal circuits, including electron microscopy (EM) and light microscopy (LM). However, these approaches typically demand extensive sectioning and reconstruction for a brain sample. Recently, tissue clearing methods have enabled the investigation of a fully assembled biological system with greatly improved light penetration. Yet, most of these implementations, still require either genetic or exogenous contrast labeling for light microscopy. Here we demonstrate a high-speed approach, termed as Clearing Assisted Scattering Tomography (CAST), where intact brains can be imaged at optical resolution without labeling by leveraging tissue clearing and the scattering contrast of optical frequency domain imaging (OFDI).

Contrast in the Photoelectric Effect of Organic and Biochemical Surfaces

PubMed Central

Birrell, G. B.; Burke, C.; Dehlinger, P.; Griffith, O. H.

1973-01-01

The photoelectric effect can provide the physical basis for a new method of mapping organic and biological surfaces. The technique, photoelectron microscopy, is similar to fluorescence microscopy using incident ultraviolet light except that photoejected electrons form the image of the specimen surface. In this work the minimum wavelengths of incident light required to produce an image were determined for the molecules 3,6-bis(dimethylamino)acridine (acridine orange) (I), benzo[a]pyrene (II), N,N,N′,N′-tetraphenylbenzidine (III), and copper phthalocyanine (IV). The photoelectron image thresholds for these compounds are 220 (I), 215 (II), 220 (III), and 240 nm (IV), all ±5 nm. Contrast of I-IV with respect to typical protein, lipid, nucleic acid, and polysaccharide surfaces was examined over the wavelength range 240-180 nm. The low magnification micrographs exhibited bright areas corresponding to I-IV but dark regions for the biochemical surfaces. The high contrast suggests the feasibility of performing extrinsic photoelectron microscopy experiments through selective labeling of sites on biological surfaces. ImagesFIGURE 3 PMID:4704486

Resonant antenna probes for tip-enhanced infrared near-field microscopy.

PubMed

Huth, Florian; Chuvilin, Andrey; Schnell, Martin; Amenabar, Iban; Krutokhvostov, Roman; Lopatin, Sergei; Hillenbrand, Rainer

2013-03-13

We report the development of infrared-resonant antenna probes for tip-enhanced optical microscopy. We employ focused-ion-beam machining to fabricate high-aspect ratio gold cones, which replace the standard tip of a commercial Si-based atomic force microscopy cantilever. Calculations show large field enhancements at the tip apex due to geometrical antenna resonances in the cones, which can be precisely tuned throughout a broad spectral range from visible to terahertz frequencies by adjusting the cone length. Spectroscopic analysis of these probes by electron energy loss spectroscopy, Fourier transform infrared spectroscopy, and Fourier transform infrared near-field spectroscopy corroborates their functionality as resonant antennas and verifies the broad tunability. By employing the novel probes in a scattering-type near-field microscope and imaging a single tobacco mosaic virus (TMV), we experimentally demonstrate high-performance mid-infrared nanoimaging of molecular absorption. Our probes offer excellent perspectives for optical nanoimaging and nanospectroscopy, pushing the detection and resolution limits in many applications, including nanoscale infrared mapping of organic, molecular, and biological materials, nanocomposites, or nanodevices.

Charge density wave order in 1D mirror twin boundaries of single-layer MoSe 2

DOE PAGES

Barja, Sara; Wickenburg, Sebastian; Liu, Zhen-Fei; ...

2016-04-18

Here, We provide direct evidence for the existence of isolated, one-dimensional charge density waves at mirror twin boundaries (MTBs) of single-layer semiconducting MoSe 2. Such MTBs have been previously observed by transmission electron microscopy and have been predicted to be metallic in MoSe 2 and MoS 2. Our low-temperature scanning tunnelling microscopy/spectroscopy measurements revealed a substantial bandgap of 100 meV opening at the Fermi energy in the otherwise metallic one-dimensional structures. We found a periodic modulation in the density of states along the MTB, with a wavelength of approximately three lattice constants. In addition to mapping the energy-dependent densitymore » of states, we determined the atomic structure and bonding of the MTB through simultaneous high-resolution non-contact atomic force microscopy. Density functional theory calculations based on the observed structure reproduced both the gap opening and the spatially resolved density of states.« less

Fast Atomic-Scale Elemental Mapping of Crystalline Materials by STEM Energy-Dispersive X-Ray Spectroscopy Achieved with Thin Specimens.

PubMed

Lu, Ping; Yuan, Renliang; Zuo, Jian Min

2017-02-01

Elemental mapping at the atomic-scale by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) provides a powerful real-space approach to chemical characterization of crystal structures. However, applications of this powerful technique have been limited by inefficient X-ray emission and collection, which require long acquisition times. Recently, using a lattice-vector translation method, we have shown that rapid atomic-scale elemental mapping using STEM-EDS can be achieved. This method provides atomic-scale elemental maps averaged over crystal areas of ~few 10 nm2 with the acquisition time of ~2 s or less. Here we report the details of this method, and, in particular, investigate the experimental conditions necessary for achieving it. It shows, that in addition to usual conditions required for atomic-scale imaging, a thin specimen is essential for the technique to be successful. Phenomenological modeling shows that the localization of X-ray signals to atomic columns is a key reason. The effect of specimen thickness on the signal delocalization is studied by multislice image simulations. The results show that the X-ray localization can be achieved by choosing a thin specimen, and the thickness of less than about 22 nm is preferred for SrTiO3 in [001] projection for 200 keV electrons.

Measurement Error in Atomic-Scale Scanning Transmission Electron Microscopy—Energy-Dispersive X-Ray Spectroscopy (STEM-EDS) Mapping of a Model Oxide Interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spurgeon, Steven R.; Du, Yingge; Chambers, Scott A.

Abstract With the development of affordable aberration correctors, analytical scanning transmission electron microscopy (STEM) studies of complex interfaces can now be conducted at high spatial resolution at laboratories worldwide. Energy-dispersive X-ray spectroscopy (EDS) in particular has grown in popularity, as it enables elemental mapping over a wide range of ionization energies. However, the interpretation of atomically resolved data is greatly complicated by beam–sample interactions that are often overlooked by novice users. Here we describe the practical factors—namely, sample thickness and the choice of ionization edge—that affect the quantification of a model perovskite oxide interface. Our measurements of the same sample,more » in regions of different thickness, indicate that interface profiles can vary by as much as 2–5 unit cells, depending on the spectral feature. This finding is supported by multislice simulations, which reveal that on-axis maps of even perfectly abrupt interfaces exhibit significant delocalization. Quantification of thicker samples is further complicated by channeling to heavier sites across the interface, as well as an increased signal background. We show that extreme care must be taken to prepare samples to minimize channeling effects and argue that it may not be possible to extract atomically resolved information from many chemical maps.« less

Measurement Error in Atomic-Scale Scanning Transmission Electron Microscopy—Energy-Dispersive X-Ray Spectroscopy (STEM-EDS) Mapping of a Model Oxide Interface

DOE PAGES

Spurgeon, Steven R.; Du, Yingge; Chambers, Scott A.

2017-04-05

Abstract With the development of affordable aberration correctors, analytical scanning transmission electron microscopy (STEM) studies of complex interfaces can now be conducted at high spatial resolution at laboratories worldwide. Energy-dispersive X-ray spectroscopy (EDS) in particular has grown in popularity, as it enables elemental mapping over a wide range of ionization energies. However, the interpretation of atomically resolved data is greatly complicated by beam–sample interactions that are often overlooked by novice users. Here we describe the practical factors—namely, sample thickness and the choice of ionization edge—that affect the quantification of a model perovskite oxide interface. Our measurements of the same sample,more » in regions of different thickness, indicate that interface profiles can vary by as much as 2–5 unit cells, depending on the spectral feature. This finding is supported by multislice simulations, which reveal that on-axis maps of even perfectly abrupt interfaces exhibit significant delocalization. Quantification of thicker samples is further complicated by channeling to heavier sites across the interface, as well as an increased signal background. We show that extreme care must be taken to prepare samples to minimize channeling effects and argue that it may not be possible to extract atomically resolved information from many chemical maps.« less

4D electron microscopy: principles and applications.

PubMed

Flannigan, David J; Zewail, Ahmed H

2012-10-16

The transmission electron microscope (TEM) is a powerful tool enabling the visualization of atoms with length scales smaller than the Bohr radius at a factor of only 20 larger than the relativistic electron wavelength of 2.5 pm at 200 keV. The ability to visualize matter at these scales in a TEM is largely due to the efforts made in correcting for the imperfections in the lens systems which introduce aberrations and ultimately limit the achievable spatial resolution. In addition to the progress made in increasing the spatial resolution, the TEM has become an all-in-one characterization tool. Indeed, most of the properties of a material can be directly mapped in the TEM, including the composition, structure, bonding, morphology, and defects. The scope of applications spans essentially all of the physical sciences and includes biology. Until recently, however, high resolution visualization of structural changes occurring on sub-millisecond time scales was not possible. In order to reach the ultrashort temporal domain within which fundamental atomic motions take place, while simultaneously retaining high spatial resolution, an entirely new approach from that of millisecond-limited TEM cameras had to be conceived. As shown below, the approach is also different from that of nanosecond-limited TEM, whose resolution cannot offer the ultrafast regimes of dynamics. For this reason "ultrafast electron microscopy" is reserved for the field which is concerned with femtosecond to picosecond resolution capability of structural dynamics. In conventional TEMs, electrons are produced by heating a source or by applying a strong extraction field. Both methods result in the stochastic emission of electrons, with no control over temporal spacing or relative arrival time at the specimen. The timing issue can be overcome by exploiting the photoelectric effect and using pulsed lasers to generate precisely timed electron packets of ultrashort duration. The spatial and temporal resolutions achievable with short intense pulses containing a large number of electrons, however, are limited to tens of nanometers and nanoseconds, respectively. This is because Coulomb repulsion is significant in such a pulse, and the electrons spread in space and time, thus limiting the beam coherence. It is therefore not possible to image the ultrafast elementary dynamics of complex transformations. The challenge was to retain the high spatial resolution of a conventional TEM while simultaneously enabling the temporal resolution required to visualize atomic-scale motions. In this Account, we discuss the development of four-dimensional ultrafast electron microscopy (4D UEM) and summarize techniques and applications that illustrate the power of the approach. In UEM, images are obtained either stroboscopically with coherent single-electron packets or with a single electron bunch. Coulomb repulsion is absent under the single-electron condition, thus permitting imaging, diffraction, and spectroscopy, all with high spatiotemporal resolution, the atomic scale (sub-nanometer and femtosecond). The time resolution is limited only by the laser pulse duration and energy carried by the electron packets; the CCD camera has no bearing on the temporal resolution. In the regime of single pulses of electrons, the temporal resolution of picoseconds can be attained when hundreds of electrons are in the bunch. The applications given here are selected to highlight phenomena of different length and time scales, from atomic motions during structural dynamics to phase transitions and nanomechanical oscillations. We conclude with a brief discussion of emerging methods, which include scanning ultrafast electron microscopy (S-UEM), scanning transmission ultrafast electron microscopy (ST-UEM) with convergent beams, and time-resolved imaging of biological structures at ambient conditions with environmental cells.

Scanning ultrafast electron microscopy.

PubMed

Yang, Ding-Shyue; Mohammed, Omar F; Zewail, Ahmed H

2010-08-24

Progress has been made in the development of four-dimensional ultrafast electron microscopy, which enables space-time imaging of structural dynamics in the condensed phase. In ultrafast electron microscopy, the electrons are accelerated, typically to 200 keV, and the microscope operates in the transmission mode. Here, we report the development of scanning ultrafast electron microscopy using a field-emission-source configuration. Scanning of pulses is made in the single-electron mode, for which the pulse contains at most one or a few electrons, thus achieving imaging without the space-charge effect between electrons, and still in ten(s) of seconds. For imaging, the secondary electrons from surface structures are detected, as demonstrated here for material surfaces and biological specimens. By recording backscattered electrons, diffraction patterns from single crystals were also obtained. Scanning pulsed-electron microscopy with the acquired spatiotemporal resolutions, and its efficient heat-dissipation feature, is now poised to provide in situ 4D imaging and with environmental capability.

Design of PdAg Hollow Nanoflowers through Galvanic Replacement and Their Application for Ethanol Electrooxidation.

PubMed

Bin, Duan; Yang, Beibei; Zhang, Ke; Wang, Caiqin; Wang, Jin; Zhong, Jiatai; Feng, Yue; Guo, Jun; Du, Yukou

2016-11-07

In this study, galvanic replacement provides a simple route for the synthesis of PdAg hollow nanoflower structures by using the Ag-seeds as sacrificial templates in the presence of l-ascorbic acid (reductant) and CTAC (capping agent). Transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and EDS mapping were used to characterize the as-prepared PdAg hollow nanoflower catalysts, where they were alloyed nanoflower structures with hollow interiors. By maneuvering the Pd/Ag ratio, we found that the as-prepared Pd 1 Ag 3 hollow nanoflower catalysts had the optimized performance for catalytic activity toward ethanol oxidation reaction. Moreover, these as-prepared PdAg hollow nanoflower catalysts exhibited noticeably higher electrocatalytic activity as compared to pure Pd and commercial Pd/C catalysts due to the alloyed Ag-Pd composition as well as the hollow nanoflower structures. It is anticipated that this work provides a rational design of other architecturally controlled bimetallic nanocrystals for application in fuel cells. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unravelling merging behaviors and electrostatic properties of CVD-grown monolayer MoS{sub 2} domains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hao, Song; Yang, Bingchu, E-mail: bingchuyang@csu.edu.cn; Hunan Key Laboratory for Super-Microstructure and Ultrafast Process, Central South University, 932 South Lushan Road, Changsha 410012

The presence of grain boundaries is inevitable for chemical vapor deposition (CVD)-grown MoS{sub 2} domains owing to various merging behaviors, which greatly limits its potential applications in novel electronic and optoelectronic devices. It is therefore of great significance to unravel the merging behaviors of the synthesized polygon shape MoS{sub 2} domains. Here we provide systematic investigations of merging behaviors and electrostatic properties of CVD-grown polycrystalline MoS{sub 2} crystals by multiple means. Morphological results exhibit various polygon shape features, ascribed to polycrystalline crystals merged with triangle shape MoS{sub 2} single crystals. The thickness of triangle and polygon shape MoS{sub 2} crystalsmore » is identical manifested by Raman intensity and peak position mappings. Three merging behaviors are proposed to illustrate the formation mechanisms of observed various polygon shaped MoS{sub 2} crystals. The combined photoemission electron microscopy and kelvin probe force microscopy results reveal that the surface potential of perfect merged crystals is identical, which has an important implication for fabricating MoS{sub 2}-based devices.« less

SAPO-34/AlMCM-41, as a novel hierarchical nanocomposite: preparation, characterization and investigation of synthesis factors using response surface methodology

NASA Astrophysics Data System (ADS)

Roohollahi, Hossein; Halladj, Rouein; Askari, Sima; Yaripour, Fereydoon

2018-06-01

SAPO-34/AlMCM-41, as a new hierarchical nanocomposite was successfully synthesized via hydrothermal and dry-gel conversion. In an experimental and statistical study, effect of five input parameters including synthesis period, drying temperature, NaOH/Si, water/dried-gel and SAPO% were investigated on range-order degree of mesochannels and the relative crystallinity. X-ray diffraction (XRD) patterns were recorded to characterize the ordered AlMCM-41 and crystalline SAPO-34 structures. Nitrogen adsorption-desorption technique, scanning electron microscopy (SEM), field-emission SEM (FESEM) equipped with an energy-dispersive X-ray spectroscopy (EDS-Map) and transmission electron microscopy (TEM) were used to study the textural properties, morphology and surface elemental composition. Two reduced polynomials were fitted to the responses with good precision. Further, based on analysis of variances, SAPO% and time duration of dry-gel conversion were observed as the most effective parameters on the composite structure. The hierarchical porosity, narrow pore size distribution, high external surface area and large specific pore volume were of interesting characteristics for this novel nanocomposite.

Advances in Chemical and Structural Characterization of Concretion with Implications for Modeling Marine Corrosion

NASA Astrophysics Data System (ADS)

Johnson, Donald L.; DeAngelis, Robert J.; Medlin, Dana J.; Carr, James D.; Conlin, David L.

2014-05-01

The Weins number model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selected-area EDS data collection at precise locations is presented in terms of atomic percent. The mechanism of formation and distribution of the iron-bearing mineral species at specific locations will be presented. Based on water retention measurements, porosity in terms of void volume varies from 15 v/o to 30 v/o (vol.%). The void path displayed by scanning electron microscopy imaging illustrates the tortuous path by which oxygen migrates in the water phase within the concretion from seaside to metalside.

A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data.

PubMed

Larivière, Damien; Galindo-Murillo, Rodrigo; Fourmentin, Eric; Hornus, Samuel; Lévy, Bruno; Papillon, Julie; Ménétret, Jean-François; Lamour, Valérie

2017-01-01

The structural modeling of a macromolecular machine is like a "Lego" approach that is challenged when blocks, like proteins imported from the Protein Data Bank, are to be assembled with an element adopting a serpentine shape, such as DNA templates. DNA must then be built ex nihilo, but modeling approaches are either not user-friendly or very long and fastidious. In this method chapter we show how to use GraphiteLifeExplorer, a software with a simple graphical user interface that enables the sketching of free forms of DNA, of any length, at the atomic scale, as fast as drawing a line on a sheet of paper. We took as an example the nucleoprotein complex of DNA gyrase, a bacterial topoisomerase whose structure has been determined using cryo-electron microscopy (Cryo-EM). Using GraphiteLifeExplorer, we could model in one go a 155 bp long and twisted DNA duplex that wraps around DNA gyrase in the cryo-EM map, improving the quality and interpretation of the final model compared to the initially published data.

Studies on microstructure, mechanical and corrosion properties of high nitrogen stainless steel shielded metal arc welds

NASA Astrophysics Data System (ADS)

Mohammed, Raffi; Madhusudhan Reddy, G.; Srinivasa Rao, K.

2018-03-01

The present work is aimed at studying the microstructure, mechanical and corrosion properties of high nitrogen stainless steel shielded metal arc (SMA) welds made with Cromang-N electrode. Basis for selecting this electrode is to increase the solubility of nitrogen in weld metal due to high chromium and manganese content. Microstructures of the welds were characterized using optical microscopy (OM), field emission scanning electron microscopy (FESEM) and electron back scattered diffraction (EBSD) mainly to determine the morphology, phase analysis, grain size and orientation image mapping. Hardness, tensile and ductility bend tests were carried out to determine mechanical properties. Potentio-dynamic polarization testing was carried out to study the pitting corrosion resistance using a GillAC basic electrochemical system. Constant load type testing was carried out to study stress corrosion cracking (SCC) behaviour of welds. The investigation results shown that the selected Cr–Mn–N type electrode resulted in favourable microstructure and completely solidified as single phase coarse austenite. Mechanical properties of SMA welds are found to be inferior when compared to that of base metal and is due to coarse and dendritic structure.

The Structure of Barmah Forest Virus as Revealed by Cryo-Electron Microscopy at a 6-Angstrom Resolution Has Detailed Transmembrane Protein Architecture and Interactions ▿ †

PubMed Central

Kostyuchenko, Victor A.; Jakana, Joanita; Liu, Xiangan; Haddow, Andrew D.; Aung, Myint; Weaver, Scott C.; Chiu, Wah; Lok, Shee-Mei

2011-01-01

Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, with RNA-containing nucleocapsid surrounded by a bilipid membrane anchored with the surface proteins E1 and E2. The map allows details of the transmembrane regions of E1 and E2 to be seen. The C-terminal end of the E2 transmembrane helix binds to the capsid protein. Following the E2 transmembrane helix, a short α-helical endodomain lies on the inner surface of the lipid envelope. The E2 endodomain interacts with E1 transmembrane helix from a neighboring E1-E2 trimeric spike, thereby acting as a spacer and a linker between spikes. In agreement with previous mutagenesis studies, the endodomain plays an important role in recruiting other E1-E2 spikes to the budding site during virus assembly. The E2 endodomain may thus serve as a target for antiviral drug design. PMID:21752915

Virus Particle Detection by Convolutional Neural Network in Transmission Electron Microscopy Images.

PubMed

Ito, Eisuke; Sato, Takaaki; Sano, Daisuke; Utagawa, Etsuko; Kato, Tsuyoshi

2018-06-01

A new computational method for the detection of virus particles in transmission electron microscopy (TEM) images is presented. Our approach is to use a convolutional neural network that transforms a TEM image to a probabilistic map that indicates where virus particles exist in the image. Our proposed approach automatically and simultaneously learns both discriminative features and classifier for virus particle detection by machine learning, in contrast to existing methods that are based on handcrafted features that yield many false positives and require several postprocessing steps. The detection performance of the proposed method was assessed against a dataset of TEM images containing feline calicivirus particles and compared with several existing detection methods, and the state-of-the-art performance of the developed method for detecting virus was demonstrated. Since our method is based on supervised learning that requires both the input images and their corresponding annotations, it is basically used for detection of already-known viruses. However, the method is highly flexible, and the convolutional networks can adapt themselves to any virus particles by learning automatically from an annotated dataset.

Incorporating TiO2 nanotubes with a peptide of D-amino K122-4 (D) for enhanced mechanical and photocatalytic properties

NASA Astrophysics Data System (ADS)

Guo, L. Q.; Hu, Y. W.; Yu, B.; Davis, E.; Irvin, R.; Yan, X. G.; Li, D. Y.

2016-02-01

Titanium dioxide (TiO2) nanotubes are promising for a wide variety of potential applications in energy, biomedical and environmental sectors. However, their low mechanical strength and wide band gap limit their widespread technological use. This article reports our recent efforts to increase the mechanical strength of TiO2 nanotubes with lowered band gap by immobilizing a peptide of D-amino K122-4 (D) onto the nanotubes. Topographies and chemical compositions of the peptide-coated and uncoated TiO2 nanotubular arrays were characterized by scanning electron microscopy and X-ray photoelectron spectroscopy (XPS). Properties of the peptide-coated and uncoated TiO2 nanotubular arrays, including hardness, elastic modulus, electron work function and photocurrent, were evaluated using micromechanical probe, Kelvin Probe and electrochemical system. Effect of the peptide on surface conductivity was also investigated through current mapping and I-V curve analysis with conductive atomic force microscopy. It is demonstrated that the peptide coating simultaneously enhances the mechanical strength, photocatalytic and electrical properties of TiO2 nanotubes.

A Toolbox for Ab Initio 3-D Reconstructions in Single-particle Electron Microscopy

PubMed Central

Voss, Neil R; Lyumkis, Dmitry; Cheng, Anchi; Lau, Pick-Wei; Mulder, Anke; Lander, Gabriel C; Brignole, Edward J; Fellmann, Denis; Irving, Christopher; Jacovetty, Erica L; Leung, Albert; Pulokas, James; Quispe, Joel D; Winkler, Hanspeter; Yoshioka, Craig; Carragher, Bridget; Potter, Clinton S

2010-01-01

Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a “toolbox” of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map. PMID:20018246

Compartmentalization of membrane trafficking, glucose transport, glycolysis, actin, tubulin and the proteasome in the cytoplasmic droplet/Hermes body of epididymal sperm.

PubMed

Au, Catherine E; Hermo, Louis; Byrne, Elliot; Smirle, Jeffrey; Fazel, Ali; Kearney, Robert E; Smith, Charles E; Vali, Hojatollah; Fernandez-Rodriguez, Julia; Simon, Paul H G; Mandato, Craig; Nilsson, Tommy; Bergeron, John J M

2015-08-01

Discovered in 1909 by Retzius and described mainly by morphology, the cytoplasmic droplet of sperm (renamed here the Hermes body) is conserved among all mammalian species but largely undefined at the molecular level. Tandem mass spectrometry of the isolated Hermes body from rat epididymal sperm characterized 1511 proteins, 43 of which were localized to the structure in situ by light microscopy and two by quantitative electron microscopy localization. Glucose transporter 3 (GLUT-3) glycolytic enzymes, selected membrane traffic and cytoskeletal proteins were highly abundant and concentrated in the Hermes body. By electron microscope gold antibody labelling, the Golgi trafficking protein TMED7/p27 localized to unstacked flattened cisternae of the Hermes body, as did GLUT-3, the most abundant protein. Its biogenesis was deduced through the mapping of protein expression for all 43 proteins during male germ cell differentiation in the testis. It is at the terminal step 19 of spermiogenesis that the 43 characteristic proteins accumulated in the nascent Hermes body. © 2015 The Authors.

The interaction of E. coli integration host factor and lambda cos DNA: multiple complex formation and protein-induced bending.

PubMed Central

Kosturko, L D; Daub, E; Murialdo, H

1989-01-01

The interaction of E. coli's integration Host Factor (IHF) with fragments of lambda DNA containing the cos site has been studied by gel-mobility retardation and electron microscopy. The cos fragment used in the mobility assays is 398 bp and spans a region from 48,298 to 194 on the lambda chromosome. Several different complexes of IHF with this fragment can be distinguished by their differential mobility on polyacrylamide gels. Relative band intensities indicate that the formation of a complex between IHF and this DNA fragment has an equilibrium binding constant of the same magnitude as DNA fragments containing lambda's attP site. Gel-mobility retardation and electron microscopy have been employed to show that IHF sharply bends DNA near cos and to map the bending site. The protein-induced bend is near an intrinsic bend due to DNA sequence. The position of the bend suggests that IHF's role in lambda DNA packaging may be the enhancement of terminase binding/cos cutting by manipulating DNA structure. Images PMID:2521383

High-resolution x-ray diffraction and transmission electron microscopy of multiferroic BiFeO3 films

NASA Astrophysics Data System (ADS)

Qi, Xiaoding; Wei, Ming; Lin, Yuan; Jia, Quanxi; Zhi, Dan; Dho, Joonghoe; Blamire, Mark G.; MacManus-Driscoll, Judith L.

2005-02-01

High-resolution x-ray diffraction and transmission electron microscopy (TEM) have been used to study BiFeO3 thin films grown on the bare and SrRuO3 buffered (001) SrTiO3 substrates. Reciprocal space mapping (RSM) around (002) and (103) reflections revealed that BFO films with a thickness of about 200 nm were almost fully relaxed and had a rhombohedral structure. Cross-sectional, high-resolution TEM showed that the films started to relax at a very early stage of growth, which was consistent with the RSM results. A thin intermediate layer of about 2 nm was observed at the interface, which had a smaller lattice than the overgrown film. Twist distortions about the c axis to release the shear strain introduced by the growth of rhombic (001) BiFeO3 on cubic (001) SrTiO3 were also observed. The results indicate that a strained, coherent BiFeO3 film on (001) SrTiO3 is very difficult to maintain and (111) STO substrates are preferable.

Pseudomonas aeruginosa biofilm formation and UV/irradiation exposure change surface and chemical structures of Pre-Production Resin Pellets

NASA Astrophysics Data System (ADS)

Stam, C. N.; Neal, A.; Park, S.; Mielke, R.; Tsapin, A. I.; Bhartia, R.; Salas, E.; Hug, W.; Behar, A. E.; Nadeau, J. L.

2011-12-01

Microbial interactions with synthetic polymers in open ocean is poorly understood. Plastics are a major and persistent contaminant of ocean waters. Many of these plastics are contaminated with toxic and synthetic chemicals that persist in the environment with minimal degradation. The purpose of this study is to look at the effects that microbial biofilm communities have on both surface and chemical structures of pre-production resin pellets (PRPs). Pseudomonas aeruignosa was grown with PRPs under multiple growth and nutrient conditions. These conditions were combined with varying lengths of UV exposures common to ocean environments. Material degradation of the PRPs and the changing surface and chemical structures of these synthetic polymers was evaluated using a combination of Fourier transform infrared spectroscopy, environmental scanning electron microscopy, scanning transmission electron microscopy, X-ray microtomography, and ArcGIS mapping. This study correlates with previous studies conducted on environmental PRP's , collected on the 2009 Project Kaisei expedition in the Subtropical Convergence Zone of the North Pacific Gyre. Further studies are needed to develop a full understanding of degradation rates of synthetic polymers in oceanic environments.

Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

PubMed Central

Walls, Alexandra C.; Tortorici, M. Alejandra; Frenz, Brandon; Snijder, Joost; Li, Wentao; Rey, Félix A.; DiMaio, Frank; Bosch, Berend-Jan; Veesler, David

2017-01-01

The threat of a major coronavirus pandemic urges the development of suitable strategies to combat these pathogens. HCoV-NL63 is an α-coronavirus that can cause severe lower respiratory tract infections requiring hospitalization. We report here the 3.4 Å resolution cryo-electron microscopy reconstruction of the HCoV-NL63 coronavirus spike glycoprotein trimer, which is the conformational machine responsible for entry into host cells and the sole target of neutralizing antibodies during infection. The map resolves the extensive glycan shield obstructing the protein surface and, in combination with mass-spectrometry, provides a structural framework to understand accessibility to antibodies. The structure also reveals a remarkable modular architecture of the receptor-binding subunit and the complete architecture of the fusion machinery including the triggering loop and the C-terminal domains, which contribute to anchoring the trimer to the viral membrane. Our data further suggest that HCoV-NL63 and other coronaviruses use molecular trickery, based on masking of epitopes with glycans and activating conformational changes, to evade the immune system of infected hosts. PMID:27617430

Direct Detection Electron Energy-Loss Spectroscopy: A Method to Push the Limits of Resolution and Sensitivity.

PubMed

Hart, James L; Lang, Andrew C; Leff, Asher C; Longo, Paolo; Trevor, Colin; Twesten, Ray D; Taheri, Mitra L

2017-08-15

In many cases, electron counting with direct detection sensors offers improved resolution, lower noise, and higher pixel density compared to conventional, indirect detection sensors for electron microscopy applications. Direct detection technology has previously been utilized, with great success, for imaging and diffraction, but potential advantages for spectroscopy remain unexplored. Here we compare the performance of a direct detection sensor operated in counting mode and an indirect detection sensor (scintillator/fiber-optic/CCD) for electron energy-loss spectroscopy. Clear improvements in measured detective quantum efficiency and combined energy resolution/energy field-of-view are offered by counting mode direct detection, showing promise for efficient spectrum imaging, low-dose mapping of beam-sensitive specimens, trace element analysis, and time-resolved spectroscopy. Despite the limited counting rate imposed by the readout electronics, we show that both core-loss and low-loss spectral acquisition are practical. These developments will benefit biologists, chemists, physicists, and materials scientists alike.

Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface

PubMed Central

Sun, Ce; Paulauskas, Tadas; Sen, Fatih G.; Lian, Guoda; Wang, Jinguo; Buurma, Christopher; Chan, Maria K. Y.; Klie, Robert F.; Kim, Moon J.

2016-01-01

Extended defects are of considerable importance in determining the electronic properties of semiconductors, especially in photovoltaics (PVs), due to their effects on electron-hole recombination. We employ model systems to study the effects of dislocations in CdTe by constructing grain boundaries using wafer bonding. Atomic-resolution scanning transmission electron microscopy (STEM) of a [1–10]/(110) 4.8° tilt grain boundary reveals that the interface is composed of three distinct types of Lomer dislocations. Geometrical phase analysis is used to map strain fields, while STEM and density functional theory (DFT) modeling determine the atomic structure at the interface. The electronic structure of the dislocation cores calculated using DFT shows significant mid-gap states and different charge-channeling tendencies. Cl-doping is shown to reduce the midgap states, while maintaining the charge separation effects. This report offers novel avenues for exploring grain boundary effects in CdTe-based solar cells by fabricating controlled bicrystal interfaces and systematic atomic-scale analysis. PMID:27255415

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

DOE PAGES

Belianinov, Alex; Panchapakesan, G.; Lin, Wenzhi; ...

2014-12-02

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signaturemore » and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belianinov, Alex, E-mail: belianinova@ornl.gov; Ganesh, Panchapakesan; Lin, Wenzhi

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe{sub 0.55}Se{sub 0.45} (T{sub c} = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe{sub 1−x}Se{sub x} structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified bymore » their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface

DOE PAGES

Sun, Ce; Paulauskas, Tadas; Sen, Fatih G.; ...

2016-06-03

Extended defects are of considerable importance in determining the electronic properties of semiconductors, especially in photovoltaics (PVs), due to their effects on electron-hole recombination. We employ model systems to study the effects of dislocations in CdTe by constructing grain boundaries using wafer bonding. Atomic-resolution scanning transmission electron microscopy (STEM) of a [1–10]/ (110) 4.8° tilt grain boundary reveals that the interface is composed of three distinct types of Lomer dislocations. Geometrical phase analysis is used to map strain fields, while STEM and density functional theory (DFT) modeling determine the atomic structure at the interface. The electronic structure of the dislocationmore » cores calculated using DFT shows significant mid-gap states and different charge-channeling tendencies. Cl-doping is shown to reduce the midgap states, while maintaining the charge separation effects. In conclusion, this report offers novel avenues for exploring grain boundary effects in CdTe-based solar cells by fabricating controlled bicrystal interfaces and systematic atomic-scale analysis.« less

Surfing Silicon Nanofacets for Cold Cathode Electron Emission Sites.

PubMed

Basu, Tanmoy; Kumar, Mohit; Saini, Mahesh; Ghatak, Jay; Satpati, Biswarup; Som, Tapobrata

2017-11-08

Point sources exhibit low threshold electron emission due to local field enhancement at the tip. In the case of silicon, however, the realization of tip emitters has been hampered by unwanted oxidation, limiting the number of emission sites and the overall current. In contrast to this, here, we report the fascinating low threshold (∼0.67 V μm -1 ) cold cathode electron emission from silicon nanofacets (Si-NFs). The ensembles of nanofacets fabricated at different time scales, under low energy ion impacts, yield tunable field emission with a Fowler-Nordheim tunneling field in the range of 0.67-4.75 V μm -1 . The local probe surface microscopy-based tunneling current mapping in conjunction with Kelvin probe force microscopy measurements revealed that the valleys and a part of the sidewalls of the nanofacets contribute more to the field emission process. The observed lowest turn-on field is attributed to the absence of native oxide on the sidewalls of the smallest facets as well as their lowest work function. In addition, first-principle density functional theory-based simulation revealed a crystal orientation-dependent work function of Si, which corroborates well with our experimental observations. The present study demonstrates a novel way to address the origin of the cold cathode electron emission sites from Si-NFs fabricated at room temperature. In principle, the present methodology can be extended to probe the cold cathode electron emission sites from any nanostructured material.

Real-Space Imaging of Carrier Dynamics of Materials Surfaces by Second-Generation Four-Dimensional Scanning Ultrafast Electron Microscopy.

PubMed

Sun, Jingya; Melnikov, Vasily A; Khan, Jafar I; Mohammed, Omar F

2015-10-01

In the fields of photocatalysis and photovoltaics, ultrafast dynamical processes, including carrier trapping and recombination on material surfaces, are among the key factors that determine the overall energy conversion efficiency. A precise knowledge of these dynamical events on the nanometer (nm) and femtosecond (fs) scales was not accessible until recently. The only way to access such fundamental processes fully is to map the surface dynamics selectively in real space and time. In this study, we establish a second generation of four-dimensional scanning ultrafast electron microscopy (4D S-UEM) and demonstrate the ability to record time-resolved images (snapshots) of material surfaces with 650 fs and ∼5 nm temporal and spatial resolutions, respectively. In this method, the surface of a specimen is excited by a clocking optical pulse and imaged using a pulsed primary electron beam as a probe pulse, generating secondary electrons (SEs), which are emitted from the surface of the specimen in a manner that is sensitive to the local electron/hole density. This method provides direct and controllable information regarding surface dynamics. We clearly demonstrate how the surface morphology, grains, defects, and nanostructured features can significantly impact the overall dynamical processes on the surface of photoactive-materials. In addition, the ability to access two regimes of dynamical probing in a single experiment and the energy loss of SEs in semiconductor-nanoscale materials will also be discussed.

Real-time mapping of the corneal sub-basal nerve plexus by in vivo laser scanning confocal microscopy

NASA Astrophysics Data System (ADS)

Guthoff, Rudolf F.; Zhivov, Andrey; Stachs, Oliver

2010-02-01

The aim of the study was to produce two-dimensional reconstruction maps of the living corneal sub-basal nerve plexus by in vivo laser scanning confocal microscopy in real time. CLSM source data (frame rate 30Hz, 384x384 pixel) were used to create large-scale maps of the scanned area by selecting the Automatic Real Time (ART) composite mode. The mapping algorithm is based on an affine transformation. Microscopy of the sub-basal nerve plexus was performed on normal and LASIK eyes as well as on rabbit eyes. Real-time mapping of the sub-basal nerve plexus was performed in large-scale up to a size of 3.2mm x 3.2mm. The developed method enables a real-time in vivo mapping of the sub-basal nerve plexus which is stringently necessary for statistically firmed conclusions about morphometric plexus alterations.

High-Resolution of Electron Microscopy of Montmorillonite and Montmorillonite/Epoxy Nanocomposites

DTIC Science & Technology

2005-01-01

AFRL-ML-WP-TP-2006-464 HIGH-RESOLUTION OF ELECTRON MICROSCOPY OF MONTMORILLONITE AND MONTMORILLONITE /EPOXY NANOCOMPOSITES Lawrence F...HIGH-RESOLUTION OF ELECTRON MICROSCOPY OF MONTMORILLONITE AND MONTMORILLONITE /EPOXY NANOCOMPOSITES 5c. PROGRAM ELEMENT NUMBER 62102F 5d...transmission electron microscopy the structure and morphology of montmorillonite (MMT), a material of current interest for use in polymer nanocomposites, was

Characterization of structural and electrostatic complexity in pentacene thin films by scanning probe microscopy

NASA Astrophysics Data System (ADS)

Puntambekar, Kanan Prakash

The advancement of organic electronics for applications in solar energy conversion, printed circuitry, displays, and solid-state lighting depends upon optimization of structure and properties for a variety of organic semiconductor interfaces. Organic semiconductor/insulator (O/I) and organic-metal (O/M) interfaces, in particular, are critical to the operation of organic thin film transistors (OTFTs) currently being developed for printed flexible electronics. Scanning probe microscopy (SPM) is a powerful tool to isolate and characterize the bottlenecks to charge transport at these interfaces. This thesis establishes a direct correlation between the structural disorder and electrical complexity at these interfaces, using various SPM based methods and discusses the implications of such complexity on device performance. To examine the O/M interfaces, surface potentials of operating pentacene TFTs with two different contact geometries (bottom or top) were mapped by Kelvin probe force microscopy (KFM). The surface potential distribution was used to isolate the potential drops at the source and drain contacts. Simultaneously obtained topography and surface potential maps elucidated the correlation between the morphology and contact resistance at the O/M interface; the bottom contact TFTs were observed to be contact limited at large gate voltages, while the top contact TFTs were not contact limited. A direct correlation between structural defects and electric potential variations at the pentacene and silicon dioxide, a common insulator, is demonstrated. Lateral force microscopy (LFM) generates striking images of the polycrystalline microstructure of a monolayer thick pentacene film, allowing clear visualization of the grain boundary network. Further more, surface potential wells localized at the grain boundaries were observed by KFM, suggesting that the grain boundaries may serve as charge carrier (hole) traps. Line dislocations were also revealed in the second monolayer by chemical etching and SPM and produce strong variations in the surface potential that must affect the interfacial charge conductance. Structural disorder at the O/I and O/M interfaces degrades both injection and transport of charge, and therefore needs to be minimized. Thus both visualization and correlation of structural and electrical complexity at these interfaces have important implications for understanding electrical transport in OTFTs and for defining strategies to improve device performance.

Correlative fluorescence microscopy and scanning transmission electron microscopy of quantum-dot-labeled proteins in whole cells in liquid.

PubMed

Dukes, Madeline J; Peckys, Diana B; de Jonge, Niels

2010-07-27

Correlative fluorescence microscopy and transmission electron microscopy (TEM) is a state-of-the-art microscopy methodology to study cellular function, combining the functionality of light microscopy with the high resolution of electron microscopy. However, this technique involves complex sample preparation procedures due to its need for either thin sections or frozen samples for TEM imaging. Here, we introduce a novel correlative approach capable of imaging whole eukaryotic cells in liquid with fluorescence microscopy and with scanning transmission electron microscopy (STEM); there is no additional sample preparation necessary for the electron microscopy. Quantum dots (QDs) were bound to epidermal growth factor (EGF) receptors of COS7 fibroblast cells. Fixed whole cells in saline water were imaged with fluorescence microscopy and subsequently with STEM. The STEM images were correlated with fluorescence images of the same cellular regions. QDs of dimensions 7x12 nm were visible in a 5 microm thick layer of saline water, consistent with calculations. A spatial resolution of 3 nm was achieved on the QDs.

Correlative Fluorescence Microscopy and Scanning Transmission Electron Microscopy of Quantum Dot Labeled Proteins in Whole Cells in Liquid

PubMed Central

Dukes, Madeline J.; Peckys, Diana B.; de Jonge, Niels

2010-01-01

Correlative fluorescence microscopy and transmission electron microscopy (TEM) is a state-of-the-art microscopy methodology to study cellular function, combining the functionality of light microscopy with the high resolution of electron microscopy. However, this technique involves complex sample preparation procedures due to its need for either thin sections or frozen samples for TEM imaging. Here, we introduce a novel correlative approach capable of imaging whole eukaryotic cells in liquid with fluorescence microscopy and with scanning transmission electron microscopy (STEM); there is no additional sample preparation necessary for the electron microscopy. Quantum dots (QDs) were bound to epidermal growth factor (EGF) receptors of COS7 fibroblast cells. Fixed whole cells in saline water were imaged with fluorescence microscopy and subsequently with STEM. The STEM images were correlated with fluorescence images of the same cellular regions. QDs of dimensions 7 × 12 nm were visible in a 5 μm thick layer of saline water, consistent with calculations. A spatial resolution of 3 nm was achieved on the QDs. PMID:20550177

Mapping the Complex Morphology of Cell Interactions with Nanowire Substrates Using FIB-SEM

PubMed Central

Jensen, Mikkel R. B.; Łopacińska, Joanna; Schmidt, Michael S.; Skolimowski, Maciej; Abeille, Fabien; Qvortrup, Klaus; Mølhave, Kristian

2013-01-01

Using high resolution focused ion beam scanning electron microscopy (FIB-SEM) we study the details of cell-nanostructure interactions using serial block face imaging. 3T3 Fibroblast cellular monolayers are cultured on flat glass as a control surface and on two types of nanostructured scaffold substrates made from silicon black (Nanograss) with low- and high nanowire density. After culturing for 72 hours the cells were fixed, heavy metal stained, embedded in resin, and processed with FIB-SEM block face imaging without removing the substrate. The sample preparation procedure, image acquisition and image post-processing were specifically optimised for cellular monolayers cultured on nanostructured substrates. Cells display a wide range of interactions with the nanostructures depending on the surface morphology, but also greatly varying from one cell to another on the same substrate, illustrating a wide phenotypic variability. Depending on the substrate and cell, we observe that cells could for instance: break the nanowires and engulf them, flatten the nanowires or simply reside on top of them. Given the complexity of interactions, we have categorised our observations and created an overview map. The results demonstrate that detailed nanoscale resolution images are required to begin understanding the wide variety of individual cells’ interactions with a structured substrate. The map will provide a framework for light microscopy studies of such interactions indicating what modes of interactions must be considered. PMID:23326412

Three-dimensional characterization of pigment dispersion in dried paint films using focused ion beam-scanning electron microscopy.

PubMed

Lin, Jui-Ching; Heeschen, William; Reffner, John; Hook, John

2012-04-01

The combination of integrated focused ion beam-scanning electron microscope (FIB-SEM) serial sectioning and imaging techniques with image analysis provided quantitative characterization of three-dimensional (3D) pigment dispersion in dried paint films. The focused ion beam in a FIB-SEM dual beam system enables great control in slicing paints, and the sectioning process can be synchronized with SEM imaging providing high quality serial cross-section images for 3D reconstruction. Application of Euclidean distance map and ultimate eroded points image analysis methods can provide quantitative characterization of 3D particle distribution. It is concluded that 3D measurement of binder distribution in paints is effective to characterize the order of pigment dispersion in dried paint films.

High resolution electron backscatter diffraction (EBSD) data from calcite biominerals in recent gastropod shells.

PubMed

Pérez-Huerta, Alberto; Dauphin, Yannicke; Cuif, Jean Pierre; Cusack, Maggie

2011-04-01

Electron backscatter diffraction (EBSD) is a microscopy technique that reveals in situ crystallographic information. Currently, it is widely used for the characterization of geological materials and in studies of biomineralization. Here, we analyze high resolution EBSD data from biogenic calcite in two mollusk taxa, Concholepas and Haliotis, previously used in the understanding of complex biomineralization and paleoenvironmental studies. Results indicate that Concholepas has less ordered prisms than in Haliotis, and that in Concholepas the level of order is not homogenous in different areas of the shell. Overall, the usefulness of data integration obtained from diffraction intensity and crystallographic orientation maps, and corresponding pole figures, is discussed as well as its application to similar studies. © 2010 Elsevier Ltd. All rights reserved.

In Situ D-periodic Molecular Structure of Type II Collagen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antipova, Olga; Orgel, Joseph P.R.O.

Collagens are essential components of extracellular matrices in multicellular animals. Fibrillar type II collagen is the most prominent component of articular cartilage and other cartilage-like tissues such as notochord. Its in situ macromolecular and packing structures have not been fully characterized, but an understanding of these attributes may help reveal mechanisms of tissue assembly and degradation (as in osteo- and rheumatoid arthritis). In some tissues such as lamprey notochord, the collagen fibrillar organization is naturally crystalline and may be studied by x-ray diffraction. We used diffraction data from native and derivative notochord tissue samples to solve the axial, D-periodic structuremore » of type II collagen via multiple isomorphous replacement. The electron density maps and heavy atom data revealed the conformation of the nonhelical telopeptides and the overall D-periodic structure of collagen type II in native tissues, data that were further supported by structure prediction and transmission electron microscopy. These results help to explain the observed differences in collagen type I and type II fibrillar architecture and indicate the collagen type II cross-link organization, which is crucial for fibrillogenesis. Transmission electron microscopy data show the close relationship between lamprey and mammalian collagen fibrils, even though the respective larger scale tissue architecture differs.« less

Nature and evolution of incommensurate charge order in manganites visualized with cryogenic scanning transmission electron microscopy.

PubMed

El Baggari, Ismail; Savitzky, Benjamin H; Admasu, Alemayehu S; Kim, Jaewook; Cheong, Sang-Wook; Hovden, Robert; Kourkoutis, Lena F

2018-02-13

Incommensurate charge order in hole-doped oxides is intertwined with exotic phenomena such as colossal magnetoresistance, high-temperature superconductivity, and electronic nematicity. Here, we map, at atomic resolution, the nature of incommensurate charge-lattice order in a manganite using scanning transmission electron microscopy at room temperature and cryogenic temperature ([Formula: see text]93 K). In diffraction, the ordering wave vector changes upon cooling, a behavior typically associated with incommensurate order. However, using real space measurements, we discover that the ordered state forms lattice-locked regions over a few wavelengths interspersed with phase defects and changing periodicity. The cations undergo picometer-scale ([Formula: see text]6 pm to 11 pm) transverse displacements, suggesting that charge-lattice coupling is strong. We further unearth phase inhomogeneity in the periodic lattice displacements at room temperature, and emergent phase coherence at 93 K. Such local phase variations govern the long-range correlations of the charge-ordered state and locally change the periodicity of the modulations, resulting in wave vector shifts in reciprocal space. These atomically resolved observations underscore the importance of lattice coupling and phase inhomogeneity, and provide a microscopic explanation for putative "incommensurate" order in hole-doped oxides. Copyright © 2018 the Author(s). Published by PNAS.

Microstructure engineering of Pt-Al alloy thin films through Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Harris, R. A.; Terblans, J. J.; Swart, H. C.

2014-06-01

A kinetic algorithm, based on the regular solution model, was used in conjunction with the Monte Carlo method to simulate the evolution of a micro-scaled thin film system during exposure to a high temperature environment. Pt-Al thin films were prepared via electron beam physical vapor deposition (EB-PVD) with an atomic concentration ratio of Pt63:Al37. These films were heat treated at an annealing temperature of 400 °C for 16 and 49 minutes. Scanning Auger Microscopy (SAM) (PHI 700) was used to obtain elemental maps while sputtering through the thin films. Simulations were run for the same annealing temperatures and thin-film composition. From these simulations theoretical depth profiles and simulated microstructures were obtained. These were compared to the experimentally measured depth profiles and elemental maps.

Variable electronic stripe structures of the parent iron-chalcogenide superconductor Fe1 +dTe observed by STM-STS

NASA Astrophysics Data System (ADS)

Sugimoto, Akira; Ekino, Toshikazu; Gabovich, Alexander M.

2014-12-01

Nanoscale stripe structures of the parent iron-11 superconductor Fe1.033Te were investigated using low-temperature scanning tunnel microscopy-scanning tunnel spectroscopy (STM-STS). STM topographies and d I /d V maps show clear stripe structures with the bias-dependent multiple periods 2 ×a0 and a0, where a0 is the lattice constant ˜0.38 nm. The form of the stripe structures seen on d I /d V maps strongly depends on the bias voltage. Varying stripe structures are apparently driven by magnetic order appearing below the transition temperature Ts˜72 K, that is defined by the noticeable drop in the temperature dependence of resistivity, and are strongly influenced by the underlying excess Fe.

The big data challenges of connectomics.

PubMed

Lichtman, Jeff W; Pfister, Hanspeter; Shavit, Nir

2014-11-01

The structure of the nervous system is extraordinarily complicated because individual neurons are interconnected to hundreds or even thousands of other cells in networks that can extend over large volumes. Mapping such networks at the level of synaptic connections, a field called connectomics, began in the 1970s with a the study of the small nervous system of a worm and has recently garnered general interest thanks to technical and computational advances that automate the collection of electron-microscopy data and offer the possibility of mapping even large mammalian brains. However, modern connectomics produces 'big data', unprecedented quantities of digital information at unprecedented rates, and will require, as with genomics at the time, breakthrough algorithmic and computational solutions. Here we describe some of the key difficulties that may arise and provide suggestions for managing them.

Electron Microscopy.

ERIC Educational Resources Information Center

Beer, Michael

1980-01-01

Reviews technical aspects of structure determination in biological electron microscopy (EM). Discusses low dose EM, low temperature microscopy, electron energy loss spectra, determination of mass or molecular weight, and EM of labeled systems. Cites 34 references. (CS)

Application of a real-space three-dimensional image reconstruction method in the structural analysis of noncrystalline biological macromolecules enveloped by water in coherent x-ray diffraction microscopy.

PubMed

Kodama, Wataru; Nakasako, Masayoshi

2011-08-01

Coherent x-ray diffraction microscopy is a novel technique in the structural analyses of particles that are difficult to crystallize, such as the biological particles composing living cells. As water is indispensable for maintaining particles in functional structures, sufficient hydration of targeted particles is required during sample preparation for diffraction microscopy experiments. However, the water enveloping particles also contributes significantly to the diffraction patterns and reduces the electron-density contrast of the sample particles. In this study, we propose a protocol for the structural analyses of particles in water by applying a three-dimensional reconstruction method in real space for the projection images phase-retrieved from diffraction patterns, together with a developed density modification technique. We examined the feasibility of the protocol through three simulations involving a protein molecule in a vacuum, and enveloped in either a droplet or a cube-shaped water. The simulations were carried out for the diffraction patterns in the reciprocal planes normal to the incident x-ray beam. This assumption and the simulation conditions corresponded to experiments using x-ray wavelengths of shorter than 0.03 Å. The analyses demonstrated that our protocol provided an interpretable electron-density map. Based on the results, we discuss the advantages and limitations of the proposed protocol and its practical application for experimental data. In particular, we examined the influence of Poisson noise in diffraction patterns on the reconstructed three-dimensional electron density in the proposed protocol.

Imaging of endodontic biofilms by combined microscopy (FISH/cLSM - SEM).

PubMed

Schaudinn, C; Carr, G; Gorur, A; Jaramillo, D; Costerton, J W; Webster, P

2009-08-01

Scanning electron microscopy is a useful imaging approach for the visualization of bacterial biofilms in their natural environments including their medical and dental habitats, because it allows for the exploration of large surfaces with excellent resolution of topographic features. Most biofilms in nature, however, are embedded in a thick layer of extracellular matrix that prevents a clear identification of individual bacteria by scanning electron microscopy. The use of confocal laser scanning microscopy on the other hand in combination with fluorescence in situ hybridization enables the visualization of matrix embedded bacteria in multi-layered biofilms. In our study, fluorescence in situ hybridization/confocal laser scanning microscopy and scanning electron microscopy were applied to visualize bacterial biofilm in endodontic root canals. The resulting fluorescence in situ hybridization /confocal laser scanning microscopy and scanning electron microscopy and pictures were subsequently combined into one single image to provide high-resolution information on the location of hidden bacteria. The combined use of scanning electron microscopy and fluorescence in situ hybridization / confocal laser scanning microscopy has the potential to overcome the limits of each single technique.

High-resolution crossover maps for each bivalent of Zea mays using recombination nodules.

PubMed Central

Anderson, Lorinda K; Doyle, Gregory G; Brigham, Brian; Carter, Jenna; Hooker, Kristina D; Lai, Ann; Rice, Mindy; Stack, Stephen M

2003-01-01

Recombination nodules (RNs) are closely correlated with crossing over, and, because they are observed by electron microscopy of synaptonemal complexes (SCs) in extended pachytene chromosomes, RNs provide the highest-resolution cytological marker currently available for defining the frequency and distribution of crossovers along the length of chromosomes. Using the maize inbred line KYS, we prepared an SC karyotype in which each SC was identified by relative length and arm ratio and related to the proper linkage group using inversion heterozygotes. We mapped 4267 RNs on 2080 identified SCs to produce high-resolution maps of RN frequency and distribution on each bivalent. RN frequencies are closely correlated with both chiasma frequencies and SC length. The total length of the RN recombination map is about twofold shorter than that of most maize linkage maps, but there is good correspondence between the relative lengths of the different maps when individual bivalents are considered. Each bivalent has a unique distribution of crossing over, but all bivalents share a high frequency of distal RNs and a severe reduction of RNs at and near kinetochores. The frequency of RNs at knobs is either similar to or higher than the average frequency of RNs along the SCs. These RN maps represent an independent measure of crossing over along maize bivalents. PMID:14573493

Mapping the distribution of emissive molecules in human ocular lipofuscin granules with near-field scanning optical microscopy.

PubMed

Krogmeier, J R; Clancy, C M; Pawlak, A; Rozanowska, M; Sarna, T; Simon, J D; Dunn, R C

2001-05-01

Several high resolution imaging techniques are utilized to probe the structure of human ocular lipofuscin granules. Atomic force microscopy reveals typical granule sizes to be about one micrometre in diameter and hundreds of nanometres in height, in agreement with previous electron microscopy results. For issues concerning the role of lipofuscin in age-related macular degeneration, recent attention has focused on the orange-emitting fluorophore, A2E. Confocal microscopy measurements are presented which reveal the presence of a highly emissive component in the granules, consistent with the presence of A2E. It is shown, however, that the interpretation of these results is complicated by the lack of structural details about the particles. To address these issues, near-field scanning optical microscopy (NSOM) measurements are presented which measure both the lipofuscin fluorescence and topography, simultaneously. These measurements reveal distinct structure in the fluorescence image which do not necessarily correlate with the topography of the granules. Moreover, direct comparison between the NSOM fluorescence and topography measurements suggests that A2E is not the major component in lipofuscin. These measurements illustrate the unique capabilities of NSOM for probing into the microstructure of lipofuscin and uncovering new insights into its phototoxicity.

The MIND PALACE: A Multi-Spectral Imaging and Spectroscopy Database for Planetary Science

NASA Astrophysics Data System (ADS)

Eshelman, E.; Doloboff, I.; Hara, E. K.; Uckert, K.; Sapers, H. M.; Abbey, W.; Beegle, L. W.; Bhartia, R.

2017-12-01

The Multi-Instrument Database (MIND) is the web-based home to a well-characterized set of analytical data collected by a suite of deep-UV fluorescence/Raman instruments built at the Jet Propulsion Laboratory (JPL). Samples derive from a growing body of planetary surface analogs, mineral and microbial standards, meteorites, spacecraft materials, and other astrobiologically relevant materials. In addition to deep-UV spectroscopy, datasets stored in MIND are obtained from a variety of analytical techniques obtained over multiple spatial and spectral scales including electron microscopy, optical microscopy, infrared spectroscopy, X-ray fluorescence, and direct fluorescence imaging. Multivariate statistical analysis techniques, primarily Principal Component Analysis (PCA), are used to guide interpretation of these large multi-analytical spectral datasets. Spatial co-referencing of integrated spectral/visual maps is performed using QGIS (geographic information system software). Georeferencing techniques transform individual instrument data maps into a layered co-registered data cube for analysis across spectral and spatial scales. The body of data in MIND is intended to serve as a permanent, reliable, and expanding database of deep-UV spectroscopy datasets generated by this unique suite of JPL-based instruments on samples of broad planetary science interest.

Adhesive Bioactive Coatings Inspired by Sea Life.

PubMed

Rego, Sónia J; Vale, Ana C; Luz, Gisela M; Mano, João F; Alves, Natália M

2016-01-19

Inspired by nature, in particular by the marine mussels adhesive proteins (MAPs) and by the tough brick-and-mortar nacre-like structure, novel multilayered films are prepared in the present work. Organic-inorganic multilayered films, with an architecture similar to nacre based on bioactive glass nanoparticles (BG), chitosan, and hyaluronic acid modified with catechol groups, which are the main components responsible for the outstanding adhesion in MAPs, are developed for the first time. The biomimetic conjugate is prepared by carbodiimide chemistry and analyzed by ultraviolet-visible spectrophotometry. The buildup of the multilayered films is monitored with a quartz crystal microbalance with dissipation monitoring, and their topography is characterized by atomic force microscopy. The mechanical properties reveal that the films containing catechol groups and BG present an enhanced adhesion. Moreover, the bioactivity of the films upon immersion in a simulated body fluid solution is evaluated by scanning electron microscopy coupled with energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, and X-ray diffraction. It was found that the constructed films promote the formation of bonelike apatite in vitro. Such multifunctional mussel inspired LbL films, which combine enhanced adhesion and bioactivity, could be potentially used as coatings of a variety of implants for orthopedic applications.

The transfer of titanium dioxide nanoparticles from the host plant to butterfly larvae through a food chain

PubMed Central

Kubo-Irie, Miyoko; Yokoyama, Masaaki; Shinkai, Yusuke; Niki, Rikio; Takeda, Ken; Irie, Masaru

2016-01-01

This study aimed to examine the transfer of nanoparticles within a terrestrial food chain. Oviposited eggs of the swallowtail butterfly (Atrophaneura alcinous) were hatched on the leaves of the host plant (Aristolochia debilis), and the root stock and root hairs were submerged in a suspension of 10 μg/ml titanium dioxide nanoparticles (TiO2-NPs) in a 100 ml bottle. The presence of TiO2-NPs in the veins of the leaves was confirmed by X-ray analytical microscopy (X-ray AM). The hatched 1st instar larvae fed on the leaves to moult into 2nd instar larvae. Small agglomerates of TiO2-NPs less than 150 nm in diameter were identified in the vascular tissue of the exposed plant, the midgut and the excreta of the larvae by transmission electron microscopy. The image of Ti elemental mapping by X-ray AM was analysed with the quantitative spatial information mapping (QSIM) technique. The results demonstrated that TiO2-NPs were transferred from the plant to the larvae and they were disseminated throughout the environment via larval excreta. PMID:27030539

Versatile derivatives of carbohydrate-binding modules for imaging of complex carbohydrates approaching the molecular level of resolution.

PubMed

Ding, Shi-You; Xu, Qi; Ali, Mursheda K; Baker, John O; Bayer, Edward A; Barak, Yoav; Lamed, Raphael; Sugiyama, Junji; Rumbles, Garry; Himmel, Michael E

2006-10-01

The innate binding specificity of different carbohydrate-binding modules (CBMs) offers a versatile approach for mapping the chemistry and structure of surfaces that contain complex carbohydrates. We have employed the distinct recognition properties of a double His-tagged recombinant CBM tagged with semiconductor quantum dots for direct imaging of crystalline cellulose at the molecular level of resolution, using transmission and scanning transmission electron microscopy. In addition, three different types of CBMs from families 3, 6, and 20 that exhibit different carbohydrate specificities were each fused with either green fluorescent protein (GFP) or red fluorescent protein (RFP) and employed for double-labeling fluorescence microscopy studies of primary cell walls and various mixtures of complex carbohydrate target molecules. CBM probes can be used for characterizing both native complex carbohydrates and engineered biomaterials.

New hardware and workflows for semi-automated correlative cryo-fluorescence and cryo-electron microscopy/tomography.

PubMed

Schorb, Martin; Gaechter, Leander; Avinoam, Ori; Sieckmann, Frank; Clarke, Mairi; Bebeacua, Cecilia; Bykov, Yury S; Sonnen, Andreas F-P; Lihl, Reinhard; Briggs, John A G

2017-02-01

Correlative light and electron microscopy allows features of interest defined by fluorescence signals to be located in an electron micrograph of the same sample. Rare dynamic events or specific objects can be identified, targeted and imaged by electron microscopy or tomography. To combine it with structural studies using cryo-electron microscopy or tomography, fluorescence microscopy must be performed while maintaining the specimen vitrified at liquid-nitrogen temperatures and in a dry environment during imaging and transfer. Here we present instrumentation, software and an experimental workflow that improves the ease of use, throughput and performance of correlated cryo-fluorescence and cryo-electron microscopy. The new cryo-stage incorporates a specially modified high-numerical aperture objective lens and provides a stable and clean imaging environment. It is combined with a transfer shuttle for contamination-free loading of the specimen. Optimized microscope control software allows automated acquisition of the entire specimen area by cryo-fluorescence microscopy. The software also facilitates direct transfer of the fluorescence image and associated coordinates to the cryo-electron microscope for subsequent fluorescence-guided automated imaging. Here we describe these technological developments and present a detailed workflow, which we applied for automated cryo-electron microscopy and tomography of various specimens. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Scanning ultrafast electron microscopy

PubMed Central

Yang, Ding-Shyue; Mohammed, Omar F.; Zewail, Ahmed H.

2010-01-01

Progress has been made in the development of four-dimensional ultrafast electron microscopy, which enables space-time imaging of structural dynamics in the condensed phase. In ultrafast electron microscopy, the electrons are accelerated, typically to 200 keV, and the microscope operates in the transmission mode. Here, we report the development of scanning ultrafast electron microscopy using a field-emission-source configuration. Scanning of pulses is made in the single-electron mode, for which the pulse contains at most one or a few electrons, thus achieving imaging without the space-charge effect between electrons, and still in ten(s) of seconds. For imaging, the secondary electrons from surface structures are detected, as demonstrated here for material surfaces and biological specimens. By recording backscattered electrons, diffraction patterns from single crystals were also obtained. Scanning pulsed-electron microscopy with the acquired spatiotemporal resolutions, and its efficient heat-dissipation feature, is now poised to provide in situ 4D imaging and with environmental capability. PMID:20696933

Serial block face scanning electron microscopy--the future of cell ultrastructure imaging.

PubMed

Hughes, Louise; Hawes, Chris; Monteith, Sandy; Vaughan, Sue

2014-03-01

One of the major drawbacks in transmission electron microscopy has been the production of three-dimensional views of cells and tissues. Currently, there is no one suitable 3D microscopy technique that answers all questions and serial block face scanning electron microscopy (SEM) fills the gap between 3D imaging using high-end fluorescence microscopy and the high resolution offered by electron tomography. In this review, we discuss the potential of the serial block face SEM technique for studying the three-dimensional organisation of animal, plant and microbial cells.

Compensation of missing wedge effects with sequential statistical reconstruction in electron tomography.

PubMed

Paavolainen, Lassi; Acar, Erman; Tuna, Uygar; Peltonen, Sari; Moriya, Toshio; Soonsawad, Pan; Marjomäki, Varpu; Cheng, R Holland; Ruotsalainen, Ulla

2014-01-01

Electron tomography (ET) of biological samples is used to study the organization and the structure of the whole cell and subcellular complexes in great detail. However, projections cannot be acquired over full tilt angle range with biological samples in electron microscopy. ET image reconstruction can be considered an ill-posed problem because of this missing information. This results in artifacts, seen as the loss of three-dimensional (3D) resolution in the reconstructed images. The goal of this study was to achieve isotropic resolution with a statistical reconstruction method, sequential maximum a posteriori expectation maximization (sMAP-EM), using no prior morphological knowledge about the specimen. The missing wedge effects on sMAP-EM were examined with a synthetic cell phantom to assess the effects of noise. An experimental dataset of a multivesicular body was evaluated with a number of gold particles. An ellipsoid fitting based method was developed to realize the quantitative measures elongation and contrast in an automated, objective, and reliable way. The method statistically evaluates the sub-volumes containing gold particles randomly located in various parts of the whole volume, thus giving information about the robustness of the volume reconstruction. The quantitative results were also compared with reconstructions made with widely-used weighted backprojection and simultaneous iterative reconstruction technique methods. The results showed that the proposed sMAP-EM method significantly suppresses the effects of the missing information producing isotropic resolution. Furthermore, this method improves the contrast ratio, enhancing the applicability of further automatic and semi-automatic analysis. These improvements in ET reconstruction by sMAP-EM enable analysis of subcellular structures with higher three-dimensional resolution and contrast than conventional methods.

Applications of microscopy to genetic therapy of cystic fibrosis and other human diseases.

PubMed

Moninger, Thomas O; Nessler, Randy A; Moore, Kenneth C

2006-01-01

Gene therapy has become an extremely important and active field of biomedical research. Microscopy is an integral component of this effort. This chapter presents an overview of imaging techniques used in our facility in support of cystic fibrosis gene therapy research. Instrumentation used in these studies includes light and confocal microscopy, transmission electron microscopy, and scanning electron microscopy. Techniques outlined include negative staining, cryo-electron microscopy, three-dimentional reconstruction, enzyme cytochemistry, immunocytochemistry, and fluorescence imaging.

Application of environmental scanning electron microscopy to determine biological surface structure.

PubMed

Kirk, S E; Skepper, J N; Donald, A M

2009-02-01

The use of environmental scanning electron microscopy in biology is growing as more becomes understood about the advantages and limitations of the technique. These are discussed and we include new evidence about the effect of environmental scanning electron microscopy imaging on the viability of mammalian cells. We show that although specimen preparation for high-vacuum scanning electron microscopy introduces some artefacts, there are also challenges in the use of environmental scanning electron microscopy, particularly at higher resolutions. This suggests the two technologies are best used in combination. We have used human monocyte-derived macrophages as a test sample, imaging their complicated and delicate membrane ruffles and protrusions. We have also explored the possibility of using environmental scanning electron microscopy for dynamic experiments, finding that mammalian cells cannot be imaged and kept alive in the environmental scanning electron microscopy. The dehydration step in which the cell surface is exposed causes irreversible damage, probably via loss of membrane integrity during liquid removal in the specimen chamber. Therefore, mammalian cells should be imaged after fixation where possible to protect against damage as a result of chamber conditions.

Cross-section imaging and p-type doping assessment of ZnO/ZnO:Sb core-shell nanowires by scanning capacitance microscopy and scanning spreading resistance microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lin, E-mail: lin.wang@insa-lyon.fr; Brémond, Georges; Sallet, Vincent

2016-08-29

ZnO/ZnO:Sb core-shell structured nanowires (NWs) were grown by the metal organic chemical vapor deposition method where the shell was doped with antimony (Sb) in an attempt to achieve ZnO p-type conduction. To directly investigate the Sb doping effect in ZnO, scanning capacitance microscopy (SCM) and scanning spreading resistance microscopy (SSRM) were performed on the NWs' cross-sections mapping their two dimensional (2D) local electrical properties. Although no direct p-type inversion in ZnO was revealed, a lower net electron concentration was pointed out for the Sb-doped ZnO shell layer with respect to the non-intentionally doped ZnO core, indicating an evident compensating effectmore » as a result of the Sb incorporation, which can be ascribed to the formation of Sb-related acceptors. The results demonstrate SCM/SSRM investigation being a direct and effective approach for characterizing radial semiconductor one-dimensional (1D) structures and, particularly, for the doping study on the ZnO nanomaterial towards its p-type realization.« less

Visualization of molecular packing and tilting domains and interface effects in tetracene thin films on H/Si(001)

DOE PAGES

Tersigni, Andrew; Sadowski, Jerzy T.; Qin, Xiao-Rong

2017-03-27

Visualizing molecular crystalline domains and influence of substrate defects are important in understanding the charge transport in organic thin film devices. Vacuum evaporated tetracene films of four monolayers on hydrogen-terminated Si(001)-2x1 substrate, as a prototypical system, have been studied with ex situ atomic force microscopy (AFM), transverse shear microscopy (TSM), friction force microscopy (FFM), and low-energy electron microscopy (LEEM). Two differently oriented in-plane lattice domains are found due to the symmetry of the substrate lattice, with no visible azimuthal twist between adjacent molecular layers in surface islands, indicating significant bulk-like crystallization in the film. Meanwhile, two types of subdomains aremore » observed inside of each in-plane lattice domain. The subdomains are anisotropic in shape, and their sizes and distribution are highly influenced by the substrate atomic steps. TSM and FFM measurements indicate that these subdomains result from molecule-tilt orderings within the bulk-like lattice domains. Lastly, TSM evidently shows a sensitivity to probe vertical molecule-tilt anisotropy for the molecular crystals, in addition to its known ability to map the lateral lattice orientations.« less

Fully Hydrated Yeast Cells Imaged with Electron Microscopy

PubMed Central

Peckys, Diana B.; Mazur, Peter; Gould, Kathleen L.; de Jonge, Niels

2011-01-01

We demonstrate electron microscopy of fully hydrated eukaryotic cells with nanometer resolution. Living Schizosaccaromyces pombe cells were loaded in a microfluidic chamber and imaged in liquid with scanning transmission electron microscopy (STEM). The native intracellular (ultra)structures of wild-type cells and three different mutants were studied without prior labeling, fixation, or staining. The STEM images revealed various intracellular components that were identified on the basis of their shape, size, location, and mass density. The maximal achieved spatial resolution in this initial study was 32 ± 8 nm, an order of magnitude better than achievable with light microscopy on pristine cells. Light-microscopy images of the same samples were correlated with the corresponding electron-microscopy images. Achieving synergy between the capabilities of light and electron microscopy, we anticipate that liquid STEM will be broadly applied to explore the ultrastructure of live cells. PMID:21575587

Fully hydrated yeast cells imaged with electron microscopy.

PubMed

Peckys, Diana B; Mazur, Peter; Gould, Kathleen L; de Jonge, Niels

2011-05-18

We demonstrate electron microscopy of fully hydrated eukaryotic cells with nanometer resolution. Living Schizosaccharomyces pombe cells were loaded in a microfluidic chamber and imaged in liquid with scanning transmission electron microscopy (STEM). The native intracellular (ultra)structures of wild-type cells and three different mutants were studied without prior labeling, fixation, or staining. The STEM images revealed various intracellular components that were identified on the basis of their shape, size, location, and mass density. The maximal achieved spatial resolution in this initial study was 32 ± 8 nm, an order of magnitude better than achievable with light microscopy on pristine cells. Light-microscopy images of the same samples were correlated with the corresponding electron-microscopy images. Achieving synergy between the capabilities of light and electron microscopy, we anticipate that liquid STEM will be broadly applied to explore the ultrastructure of live cells. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A new method for mapping the three-dimensional atomic distribution within nanoparticles by atom probe tomography (APT).

PubMed

Kim, Se-Ho; Kang, Phil Woong; Park, O Ok; Seol, Jae-Bok; Ahn, Jae-Pyoung; Lee, Ji Yeong; Choi, Pyuck-Pa

2018-07-01

We present a new method of preparing needle-shaped specimens for atom probe tomography from freestanding Pd and C-supported Pt nanoparticles. The method consists of two steps, namely electrophoresis of nanoparticles on a flat Cu substrate followed by electrodeposition of a Ni film acting as an embedding matrix for the nanoparticles. Atom probe specimen preparation can be subsequently carried out by means of focused-ion-beam milling. Using this approach, we have been able to perform correlative atom probe tomography and transmission electron microscopy analyses on both nanoparticle systems. Reliable mass spectra and three-dimensional atom maps could be obtained for Pd nanoparticle specimens. In contrast, atom probe samples prepared from C-supported Pt nanoparticles showed uneven field evaporation and hence artifacts in the reconstructed atom maps. Our developed method is a viable means of mapping the three-dimensional atomic distribution within nanoparticles and is expected to contribute to an improved understanding of the structure-composition-property relationships of various nanoparticle systems. Copyright © 2018 Elsevier B.V. All rights reserved.

De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy

PubMed Central

Mills, Deryck J; Vitt, Stella; Strauss, Mike; Shima, Seigo; Vonck, Janet

2013-01-01

Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the cytoplasmic protein and forms a huge complex consisting of FrhABG heterotrimers with each a [NiFe] center, four Fe-S clusters and an FAD. Here, we report the structure determined by near-atomic resolution cryo-EM of Frh with and without bound substrate F420. The polypeptide chains of FrhB, for which there was no homolog, was traced de novo from the EM map. The 1.2-MDa complex contains 12 copies of the heterotrimer, which unexpectedly form a spherical protein shell with a hollow core. The cryo-EM map reveals strong electron density of the chains of metal clusters running parallel to the protein shell, and the F420-binding site is located at the end of the chain near the outside of the spherical structure. DOI: http://dx.doi.org/10.7554/eLife.00218.001 PMID:23483797

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gyenis, András; Inoue, Hiroyuki; Jeon, Sangjun

Following the intense studies on topological insulators, significant efforts have recently been devoted to the search for gapless topological systems. These materials not only broaden the topological classification of matter but also provide a condensed matter realization of various relativistic particles and phenomena previously discussed mainly in high energy physics. Weyl semimetals host massless, chiral, low-energy excitations in the bulk electronic band structure, whereas a symmetry protected pair of Weyl fermions gives rise to massless Dirac fermions.Weemployed scanning tunneling microscopy/spectroscopy to explore the behavior of electronic states both on the surface and in the bulk of topological semimetal phases. Bymore » mapping the quasiparticle interference (QPI) and emerging Landau levels at high magnetic field in Dirac semimetals Cd 3As 2 and Na 3Bi, we observed extended Dirac-like bulk electronic bands. QPI imaged on Weyl semimetal TaAs demonstrated the predicted momentum dependent delocalization of Fermi arc surface states in the vicinity of the surface projected Weyl nodes.« less

Computational prediction of atomic structures of helical membrane proteins aided by EM maps.

PubMed

Kovacs, Julio A; Yeager, Mark; Abagyan, Ruben

2007-09-15

Integral membrane proteins pose a major challenge for protein-structure prediction because only approximately 100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane alpha-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of alpha-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the alpha-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL.

Pressure-temperature dependence of nanowire formation in the arsenic-sulfur system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riley, Brian J.; Johnson, Bradley R.; Sundaram, S. K.

2006-12-01

Nanowire Formation in Arsenic Trisulfide Brian J. Riley, S.K. Sundaram*, Bradley R. Johnson, Mark Engelhard Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99352 * Corresponding author: Phone: 509-373-6665; Fax: 509-376-3108, E-mail: sk.Sundaram@pnl.gov Abstract: Arsenic trisulfide (As2S3) nanowires, nano-droplets, and micro-islands were synthesized on fused silica substrates, using a sublimation-condensation process at reduced pressures (70 mtorr – 70 torr) in a sealed ampoule. Microstructural control of the deposited thin film was achieved by controlling initial pressure, substrate temperature and substrate surface treatment. Microstructures were characterized using scanning electron microscopy (SEM), and energy dispersive spectrometry (EDS). Surface topography and chemistrymore » of the substrates were characterized using x-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). Semi-quantitative image analysis and basic curve-fitting were used to develop empirical models to mathematically describe the variation of microstructure as a function of initial pressure and substrate temperature and map out the regions of different microstructures in P-T space. Thermodyamic properties (available from literature) of this system are also incorporated in this map. Nanowires of an amorphous, transparent in visible-LWIR region, semi-conducting material, like As2S3, provide new opportunities for the development of novel nano-photonic and electronic devices. Additionally, this system provides an excellent opportunity to model (and control) microstructure development from nanometer to micron scales in a physical vapor deposition process, which is of great value to nanoscience and nanotechnology in general.« less

Flow Stress and Processing Map of a PM 8009Al/SiC Particle Reinforced Composite During Hot Compression

NASA Astrophysics Data System (ADS)

Luo, Haibo; Teng, Jie; Chen, Shuang; Wang, Yu; Zhang, Hui

2017-10-01

Hot compression tests of 8009Al alloy reinforced with 15% SiC particles (8009Al/15%SiCp composites) prepared by powder metallurgy (direct hot extrusion methods) were performed on Gleeble-3500 system in the temperature range of 400-550 °C and strain rate range of 0.001-1 s-1. The processing map based on the dynamic material model was established to evaluate the flow instability regime and optimize processing parameters; the associated microstructural changes were studied by the observations of optical metallographic and scanning electron microscopy. The results showed that the flow stress increased initially and reached a plateau after peak stress value with increasing strain. The peak stress increased as the strain rate increased and deformation temperature decreased. The optimum parameters were identified to be deformation temperature range of 500-550 °C and strain rate range of 0.001-0.02 s-1 by combining the processing map with microstructural observation.

Demonstration of transmission high energy electron microscopy

DOE PAGES

Merrill, F. E.; Goett, J.; Gibbs, J. W.; ...

2018-04-06

High energy electrons have been used to investigate an extension of transmission electron microscopy. This technique, transmission high energy electron microscopy (THEEM), provides two additional capabilities to electron microscopy. First, high energy electrons are more penetrating than low energy electrons, and thus, they are able to image through thicker samples. Second, the accelerating mode of a radio-frequency linear accelerator provides fast exposures, down to 1 ps, which are ideal for flash radiography, making THEEM well suited to study the evolution of fast material processes under dynamic conditions. Lastly, initial investigations with static objects and during material processing have been performedmore » to investigate the capabilities of this technique.« less

Introduction: A Symposium in Honor of Professor Sir John Meurig Thomas

NASA Astrophysics Data System (ADS)

Gai, P. L.; Saka, H.; Tomokiyo, Y.; Boyes, E. D.

2002-02-01

This issue is dedicated to Professor Sir John Meurig Thomas for his renowned contributions to electron microscopy in the chemical sciences. It is a collection of peer-reviewed leading articles in electron microscopy, based on the presentations at the Microscopy and Microanalysis (M&M) 2000 symposium, which was held to honor Professor Thomas's exceptional scientific leadership and wide-ranging fundamental contributions in the chemical applications of electron microscopy.The issue contains key papers by leading international researchers on the recent developments and applications of electron microscopy in the solid state and liquid state sciences. They include synthesis and characterization of silicon nitride nanorods, nanostructures of amorphous silica, electron microscopy studies of nanoscale structure and chemistry of Pt-Ru electrocatalysts of interest in direct methanol fuel cells, development of in situ wet-environmental transmission electron microscopy for the first nanoscale studies of dynamic liquid-catalyst reactions, strain analysis of silicon by finite element method and energy filtering convergent beam electron diffraction, applications of chemistry with electron microscopy, bismuth nanowires for applications in nanoelectronics technology, synthesis and characterization of quantum dots for superlattices and in situ electron microscopy at very high temperatures to study the motion of W5Si3 on [alpha][beta]-SiN3 substrates.We thank all the participants, including the invited speakers, contributors, and session chairs, who made the symposium successful. We also thank the authors and reviewers of the papers who worked assiduously towards the publication of this issue.We are very grateful to the Microscopy Society of America (MSA) for providing the opportunity to honor Professor Sir John Meurig Thomas. Organizational support from the MSA is also gratefully acknowledged.We thank Charles E. Lyman, editor in chief of Microscopy and Microanalysis for coordinating the publication of this issue and the entire journal staff for their efforts.

Fast Atomic-Scale Elemental Mapping of Crystalline Materials by STEM Energy-Dispersive X-Ray Spectroscopy Achieved with Thin Specimens [Fast Atomic-Scale Chemical Imaging of Crystalline Materials by STEM Energy-Dispersive X-ray Spectroscopy Achieved with Thin Specimens].

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Ping; Yuan, Renliang; Zuo, Jian Min

Abstract Elemental mapping at the atomic-scale by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) provides a powerful real-space approach to chemical characterization of crystal structures. However, applications of this powerful technique have been limited by inefficient X-ray emission and collection, which require long acquisition times. Recently, using a lattice-vector translation method, we have shown that rapid atomic-scale elemental mapping using STEM-EDS can be achieved. This method provides atomic-scale elemental maps averaged over crystal areas of ~few 10 nm 2with the acquisition time of ~2 s or less. Here we report the details of this method, and, inmore » particular, investigate the experimental conditions necessary for achieving it. It shows, that in addition to usual conditions required for atomic-scale imaging, a thin specimen is essential for the technique to be successful. Phenomenological modeling shows that the localization of X-ray signals to atomic columns is a key reason. The effect of specimen thickness on the signal delocalization is studied by multislice image simulations. The results show that the X-ray localization can be achieved by choosing a thin specimen, and the thickness of less than about 22 nm is preferred for SrTiO 3in [001] projection for 200 keV electrons.« less

Fast Atomic-Scale Elemental Mapping of Crystalline Materials by STEM Energy-Dispersive X-Ray Spectroscopy Achieved with Thin Specimens [Fast Atomic-Scale Chemical Imaging of Crystalline Materials by STEM Energy-Dispersive X-ray Spectroscopy Achieved with Thin Specimens].

DOE PAGES

Lu, Ping; Yuan, Renliang; Zuo, Jian Min

2017-02-23

Abstract Elemental mapping at the atomic-scale by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) provides a powerful real-space approach to chemical characterization of crystal structures. However, applications of this powerful technique have been limited by inefficient X-ray emission and collection, which require long acquisition times. Recently, using a lattice-vector translation method, we have shown that rapid atomic-scale elemental mapping using STEM-EDS can be achieved. This method provides atomic-scale elemental maps averaged over crystal areas of ~few 10 nm 2with the acquisition time of ~2 s or less. Here we report the details of this method, and, inmore » particular, investigate the experimental conditions necessary for achieving it. It shows, that in addition to usual conditions required for atomic-scale imaging, a thin specimen is essential for the technique to be successful. Phenomenological modeling shows that the localization of X-ray signals to atomic columns is a key reason. The effect of specimen thickness on the signal delocalization is studied by multislice image simulations. The results show that the X-ray localization can be achieved by choosing a thin specimen, and the thickness of less than about 22 nm is preferred for SrTiO 3in [001] projection for 200 keV electrons.« less

Mapping owl's eye cells of patients with cytomegalovirus corneal endotheliitis using in vivo laser confocal microscopy.

PubMed

Yokogawa, Hideaki; Kobayashi, Akira; Sugiyama, Kazuhisa

2013-01-01

To produce a two-dimensional reconstruction map of owl's eye cells using in vivo laser confocal microscopy in patients with cytomegalovirus (CMV) corneal endotheliitis, and to demonstrate any association between owl's eye cells and coin-shaped lesions observed with slit-lamp biomicroscopy. Two patients (75- and 77-year-old men) with polymerase chain reaction-proven CMV corneal endotheliitis were evaluated in this study. Slit-lamp biomicroscopy and in vivo laser confocal microscopy were performed. Images of owl's eye cells in the endothelial cell layer were arranged and mapped into subconfluent montages. Montage images of owl's eye cells were then superimposed on a slit-lamp photo of the corresponding coin-shaped lesion. Degree of concordance between the confocal microscopic images and slit-lamp photos was evaluated. In both eyes, a two-dimensional reconstruction map of the owl's eye cells was created by computer software using acquired confocal images; the maps showed circular patterns. Superimposing montage images of owl's eye cells onto the photos of a coin-shaped lesion showed good concordance in the two eyes. This study suggests that there is an association between owl's eye cells observed by confocal microscopy and coin-shaped lesions observed by slit-lamp biomicroscopy in patients with CMV corneal endotheliitis. The use of in vivo laser confocal microscopy may provide clues as to the underlying causes of CMV corneal endotheliitis.

A correlative optical microscopy and scanning electron microscopy approach to locating nanoparticles in brain tumors.

PubMed

Kempen, Paul J; Kircher, Moritz F; de la Zerda, Adam; Zavaleta, Cristina L; Jokerst, Jesse V; Mellinghoff, Ingo K; Gambhir, Sanjiv S; Sinclair, Robert

2015-01-01

The growing use of nanoparticles in biomedical applications, including cancer diagnosis and treatment, demands the capability to exactly locate them within complex biological systems. In this work a correlative optical and scanning electron microscopy technique was developed to locate and observe multi-modal gold core nanoparticle accumulation in brain tumor models. Entire brain sections from mice containing orthotopic brain tumors injected intravenously with nanoparticles were imaged using both optical microscopy to identify the brain tumor, and scanning electron microscopy to identify the individual nanoparticles. Gold-based nanoparticles were readily identified in the scanning electron microscope using backscattered electron imaging as bright spots against a darker background. This information was then correlated to determine the exact location of the nanoparticles within the brain tissue. The nanoparticles were located only in areas that contained tumor cells, and not in the surrounding healthy brain tissue. This correlative technique provides a powerful method to relate the macro- and micro-scale features visible in light microscopy with the nanoscale features resolvable in scanning electron microscopy. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fine Structure in Multi-Phase Zr8Ni21-Zr7Ni10-Zr2Ni7 Alloy Revealed by Transmission Electron Microscope

PubMed Central

Shen, Haoting; Bendersky, Leonid A.; Young, Kwo; Nei, Jean

2015-01-01

The microstructure of an annealed alloy with a Zr8Ni21 composition was studied by both scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The presence of three phases, Zr8Ni21, Zr2Ni7, and Zr7Ni10, was confirmed by SEM/X-ray energy dispersive spectroscopy compositional mapping and TEM electron diffraction. Distribution of the phases and their morphology can be linked to a multi-phase structure formed by a sequence of reactions: (1) L → Zr2Ni7 + L’; (2) peritectic Zr2Ni7 + L’ → Zr2Ni7 + Zr8Ni21 + L”; (3) eutectic L” → Zr8Ni21 + Zr7Ni10. The effect of annealing at 960 °C, which was intended to convert a cast structure into a single-phase Zr8Ni21 structure, was only moderate and the resulting alloy was still multi-phased. TEM and crystallographic analysis of the Zr2Ni7 phase show a high density of planar (001) defects that were explained as low-energy boundaries between rotational variants and stacking faults. The crystallographic features arise from the pseudo-hexagonal structure of Zr2Ni7. This highly defective Zr2Ni7 phase was identified as the source of the broad X-ray diffraction peaks at around 38.4° and 44.6° when a Cu-K was used as the radiation source. PMID:28793460

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buck, E.C.; Dietz, N.L.; Bates, J.K.

Uranium contaminated soils from the Fernald Operation Site, Ohio, have been examined by a combination of optical microscopy, scanning electron microscopy with backscattered electron detection (SEM/BSE), and analytical electron microscopy (AEM). A method is described for preparing of transmission electron microscopy (TEM) thin sections by ultramicrotomy. By using these thin sections, SEM and TEM images can be compared directly. Uranium was found in iron oxides, silicates (soddyite), phosphates (autunites), and fluorite. Little uranium was associated with clays. The distribution of uranium phases was found to be inhomogeneous at the microscopic level.

Electron Microscopy of Ebola Virus-Infected Cells.

PubMed

Noda, Takeshi

2017-01-01

Ebola virus (EBOV) replicates in host cells, where both viral and cellular components show morphological changes during the process of viral replication from entry to budding. These steps in the replication cycle can be studied using electron microscopy (EM), including transmission electron microscopy (TEM) and scanning electron microscopy (SEM), which is one of the most useful methods for visualizing EBOV particles and EBOV-infected cells at the ultrastructural level. This chapter describes conventional methods for EM sample preparation of cultured cells infected with EBOV.

A direct electron detector for time-resolved MeV electron microscopy

DOE PAGES

Vecchione, T.; Denes, P.; Jobe, R. K.; ...

2017-03-15

The introduction of direct electron detectors enabled the structural biology revolution of cryogenic electron microscopy. Direct electron detectors are now expected to have a similarly dramatic impact on time-resolved MeV electron microscopy, particularly by enabling both spatial and temporal jitter correction. Here in this paper, we report on the commissioning of a direct electron detector for time-resolved MeV electron microscopy. The direct electron detector demonstrated MeV single electron sensitivity and is capable of recording megapixel images at 180 Hz. The detector has a 15-bit dynamic range, better than 30-μm spatial resolution and less than 20 analogue-to-digital converter count RMS pixelmore » noise. The unique capabilities of the direct electron detector and the data analysis required to take advantage of these capabilities are presented. The technical challenges associated with generating and processing large amounts of data are also discussed.« less

A direct electron detector for time-resolved MeV electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vecchione, T.; Denes, P.; Jobe, R. K.

The introduction of direct electron detectors enabled the structural biology revolution of cryogenic electron microscopy. Direct electron detectors are now expected to have a similarly dramatic impact on time-resolved MeV electron microscopy, particularly by enabling both spatial and temporal jitter correction. Here we report on the commissioning of a direct electron detector for time-resolved MeV electron microscopy. The direct electron detector demonstrated MeV single electron sensitivity and is capable of recording megapixel images at 180 Hz. The detector has a 15-bit dynamic range, better than 30-μmμm spatial resolution and less than 20 analogue-to-digital converter count RMS pixel noise. The uniquemore » capabilities of the direct electron detector and the data analysis required to take advantage of these capabilities are presented. The technical challenges associated with generating and processing large amounts of data are also discussed.« less

A direct electron detector for time-resolved MeV electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vecchione, T.; Denes, P.; Jobe, R. K.

The introduction of direct electron detectors enabled the structural biology revolution of cryogenic electron microscopy. Direct electron detectors are now expected to have a similarly dramatic impact on time-resolved MeV electron microscopy, particularly by enabling both spatial and temporal jitter correction. Here in this paper, we report on the commissioning of a direct electron detector for time-resolved MeV electron microscopy. The direct electron detector demonstrated MeV single electron sensitivity and is capable of recording megapixel images at 180 Hz. The detector has a 15-bit dynamic range, better than 30-μm spatial resolution and less than 20 analogue-to-digital converter count RMS pixelmore » noise. The unique capabilities of the direct electron detector and the data analysis required to take advantage of these capabilities are presented. The technical challenges associated with generating and processing large amounts of data are also discussed.« less

Infrared vibrational nanocrystallography and nanoimaging

PubMed Central

Muller, Eric A.; Pollard, Benjamin; Bechtel, Hans A.; van Blerkom, Peter; Raschke, Markus B.

2016-01-01

Molecular solids and polymers can form low-symmetry crystal structures that exhibit anisotropic electron and ion mobility in engineered devices or biological systems. The distribution of molecular orientation and disorder then controls the macroscopic material response, yet it is difficult to image with conventional techniques on the nanoscale. We demonstrated a new form of optical nanocrystallography that combines scattering-type scanning near-field optical microscopy with both optical antenna and tip-selective infrared vibrational spectroscopy. From the symmetry-selective probing of molecular bond orientation with nanometer spatial resolution, we determined crystalline phases and orientation in aggregates and films of the organic electronic material perylenetetracarboxylic dianhydride. Mapping disorder within and between individual nanoscale domains, the correlative hybrid imaging of nanoscale heterogeneity provides insight into defect formation and propagation during growth in functional molecular solids. PMID:27730212

Atomic-scale identification of novel planar defect phases in heteroepitaxial YBa2Cu3O7-δ thin films

NASA Astrophysics Data System (ADS)

Gauquelin, Nicolas; Zhang, Hao; Zhu, Guozhen; Wei, John Y. T.; Botton, Gianluigi A.

2018-05-01

We have discovered two novel types of planar defects that appear in heteroepitaxial YBa2Cu3O7-δ (YBCO123) thin films, grown by pulsed-laser deposition (PLD) either with or without a La2/3Ca1/3MnO3 (LCMO) overlayer, using the combination of high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) imaging and electron energy loss spectroscopy (EELS) mapping for unambiguous identification. These planar lattice defects are based on the intergrowth of either a BaO plane between two CuO chains or multiple Y-O layers between two CuO2 planes, resulting in non-stoichiometric layer sequences that could directly impact the high-Tc superconductivity.

Continuous Changes in Structure Mapped by Manifold Embedding of Single-Particle Data in Cryo-EM

PubMed Central

Fran, Joachim; Ourmazd, Abbas

2016-01-01

Cryo-electron microscopy, when combined with single-particle reconstruction, is a powerful method for studying macromolecular structure. Recent developments in detector technology have pushed the resolution into a range comparable to that of X-ray crystallography. However, cryo-EM is able to separate and thus recover the structure of each of several discrete structures present in the sample. For the more general case involving continuous structural changes, a novel technique employing manifold embedding has been recently demonstrated. Potentially, the entire work-cycle of a molecular machine may be observed as it passes through a continuum of states, and its free-energy landscape may be mapped out. This technique will be outlined and discussed in the context of its application to a large single-particle dataset of yeast ribosomes. PMID:26884261

The big data challenges of connectomics

PubMed Central

Lichtman, Jeff W; Pfister, Hanspeter; Shavit, Nir

2015-01-01

The structure of the nervous system is extraordinarily complicated because individual neurons are interconnected to hundreds or even thousands of other cells in networks that can extend over large volumes. Mapping such networks at the level of synaptic connections, a field called connectomics, began in the 1970s with a the study of the small nervous system of a worm and has recently garnered general interest thanks to technical and computational advances that automate the collection of electron-microscopy data and offer the possibility of mapping even large mammalian brains. However, modern connectomics produces ‘big data’, unprecedented quantities of digital information at unprecedented rates, and will require, as with genomics at the time, breakthrough algorithmic and computational solutions. Here we describe some of the key difficulties that may arise and provide suggestions for managing them. PMID:25349911

The big data challenges of connectomics

DOE PAGES

Lichtman, Jeff W.; Pfister, Hanspeter; Shavit, Nir

2014-10-28

The structure of the nervous system is extraordinarily complicated because individual neurons are interconnected to hundreds or even thousands of other cells in networks that can extend over large volumes. Mapping such networks at the level of synaptic connections, a field called connectomics, began in the 1970s with a the study of the small nervous system of a worm and has recently garnered general interest thanks to technical and computational advances that automate the collection of electron-microscopy data and offer the possibility of mapping even large mammalian brains. However, modern connectomics produces ‘big data’, unprecedented quantities of digital information atmore » unprecedented rates, and will require, as with genomics at the time, breakthrough algorithmic and computational solutions. Here in this paper we describe some of the key difficulties that may arise and provide suggestions for managing them.« less

Nano-scale Stripe Structures on FeTe Observed by Low-temperature STM/STS

NASA Astrophysics Data System (ADS)

Sugimoto, A.; Ukita, R.; Ekino, T.

We have investigated the nano-scale stripe structures on a parent compound of the iron chalcogenide superconductor Fe1+dTe (d=0.033) by using low-temperature scanning tunneling microscopy (STM). The STM topographies and the dI/dV maps show clear stripe structures with the period of twice as large as the Te-Te atomic displacement (~0.76 nm = 2a0, a0 is lattice constant), in addition to weak modulation with the same period of lattice constant (~0.38 nm). The bias-voltage dependence of both STM topographies and dI/dV maps show the several kinds of the stripe structures. The 2a0 modulations are similar to the bicollinear spin order of the parent compound FeTe, indicating the possibility of the coupling with spin density wave and electronic structures.

The big data challenges of connectomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lichtman, Jeff W.; Pfister, Hanspeter; Shavit, Nir

The structure of the nervous system is extraordinarily complicated because individual neurons are interconnected to hundreds or even thousands of other cells in networks that can extend over large volumes. Mapping such networks at the level of synaptic connections, a field called connectomics, began in the 1970s with a the study of the small nervous system of a worm and has recently garnered general interest thanks to technical and computational advances that automate the collection of electron-microscopy data and offer the possibility of mapping even large mammalian brains. However, modern connectomics produces ‘big data’, unprecedented quantities of digital information atmore » unprecedented rates, and will require, as with genomics at the time, breakthrough algorithmic and computational solutions. Here in this paper we describe some of the key difficulties that may arise and provide suggestions for managing them.« less

Digital direct electron imaging of energy-filtered electron backscatter diffraction patterns

NASA Astrophysics Data System (ADS)

Vespucci, S.; Winkelmann, A.; Naresh-Kumar, G.; Mingard, K. P.; Maneuski, D.; Edwards, P. R.; Day, A. P.; O'Shea, V.; Trager-Cowan, C.

2015-11-01

Electron backscatter diffraction is a scanning electron microscopy technique used to obtain crystallographic information on materials. It allows the nondestructive mapping of crystal structure, texture, and strain with a lateral and depth resolution on the order of tens of nanometers. Electron backscatter diffraction patterns (EBSPs) are presently acquired using a detector comprising a scintillator coupled to a digital camera, and the crystallographic information obtainable is limited by the conversion of electrons to photons and then back to electrons again. In this article we will report the direct acquisition of energy-filtered EBSPs using a digital complementary metal-oxide-semiconductor hybrid pixel detector, Timepix. We show results from a range of samples with different mass and density, namely diamond, silicon, and GaN. Direct electron detection allows the acquisition of EBSPs at lower (≤5 keV) electron beam energies. This results in a reduction in the depth and lateral extension of the volume of the specimen contributing to the pattern and will lead to a significant improvement in lateral and depth resolution. Direct electron detection together with energy filtering (electrons having energy below a specific value are excluded) also leads to an improvement in spatial resolution but in addition provides an unprecedented increase in the detail in the acquired EBSPs. An increase in contrast and higher-order diffraction features are observed. In addition, excess-deficiency effects appear to be suppressed on energy filtering. This allows the fundamental physics of pattern formation to be interrogated and will enable a step change in the use of electron backscatter diffraction (EBSD) for crystal phase identification and the mapping of strain. The enhancement in the contrast in high-pass energy-filtered EBSD patterns is found to be stronger for lighter, less dense materials. The improved contrast for such materials will enable the application of the EBSD technique to be expanded to materials for which conventional EBSD analysis is not presently practicable.

Optical spectroscopy and microscopy of radiation-induced light-emitting point defects in lithium fluoride crystals and films

NASA Astrophysics Data System (ADS)

Montereali, R. M.; Bonfigli, F.; Menchini, F.; Vincenti, M. A.

2012-08-01

Broad-band light-emitting radiation-induced F2 and F3+ electronic point defects, which are stable and laser-active at room temperature in lithium fluoride crystals and films, are used in dosimeters, tuneable color-center lasers, broad-band miniaturized light sources and novel radiation imaging detectors. A brief review of their photoemission properties is presented, and their behavior at liquid nitrogen temperatures is discussed. Some experimental data from optical spectroscopy and fluorescence microscopy of these radiation-induced point defects in LiF crystals and thin films are used to obtain information about the coloration curves, the efficiency of point defect formation, the effects of photo-bleaching processes, etc. Control of the local formation, stabilization, and transformation of radiation-induced light-emitting defect centers is crucial for the development of optically active micro-components and nanostructures. Some of the advantages of low temperature measurements for novel confocal laser scanning fluorescence microscopy techniques, widely used for spatial mapping of these point defects through the optical reading of their visible photoluminescence, are highlighted.

Surface modification of argon/oxygen plasma treated vulcanized ethylene propylene diene polymethylene surfaces for improved adhesion with natural rubber

NASA Astrophysics Data System (ADS)

Basak, Ganesh C.; Bandyopadhyay, Abhijit; Neogi, Sudarsan; Bhowmick, Anil K.

2011-01-01

Vulcanized ethylene propylene diene polymethylene (EPDM) rubber surface was treated in a radio frequency capacitatively coupled low pressure argon/oxygen plasma to improve adhesion with compounded natural rubber (NR) during co-vulcanization. The plasma modified surfaces were analyzed by means of contact angle measurement, surface energy, attenuated total reflection-infrared spectroscopy, X-ray photoelectron spectroscopy, scanning electron microscopy, energy dispersive X-ray sulfur mapping and atomic force microscopy. Several experimental variables such as plasma power, length of exposure time and composition of the argon-oxygen gas mixture were considered. It was delineated that plasma treatment changed both surface composition and roughness, and consequently increased peel strength. The change in surface composition was mainly ascribed to the formation of C-O and -Cdbnd O functional groups on the vulcanized surfaces. A maximum of 98% improvement in peel strength was observed after plasma treatment.

Local electronic and optical behaviors of a-plane GaN grown via epitaxial lateral overgrowth

NASA Astrophysics Data System (ADS)

Moore, J. C.; Kasliwal, V.; Baski, A. A.; Ni, X.; Özgür, Ü.; Morkoç, H.

2007-01-01

Conductive atomic force microscopy and near-field optical microscopy (NSOM) were used to study the morphology, conduction, and optical properties of a-plane GaN films grown via epitaxial lateral overgrowth (ELO) by metal organic chemical vapor deposition. The AFM images for the coalesced ELO films show undulations, where the window regions appear as depressions with a high density of surface pits. At reverse bias below 12V, very low uniform conduction (2pA) is seen in the window regions. Above 20V, a lower-quality sample shows localized sites inside the window regions with significant leakage, indicating a correlation between the presence of surface pits and leakage sites. Room temperature NSOM studies explicitly showed enhanced optical quality in the wing regions of the overgrown GaN due to a reduced density of dislocations, with the wings and the windows clearly discernible from near-field photoluminescence mapping.

Extracellular space preservation aids the connectomic analysis of neural circuits.

PubMed

Pallotto, Marta; Watkins, Paul V; Fubara, Boma; Singer, Joshua H; Briggman, Kevin L

2015-12-09

Dense connectomic mapping of neuronal circuits is limited by the time and effort required to analyze 3D electron microscopy (EM) datasets. Algorithms designed to automate image segmentation suffer from substantial error rates and require significant manual error correction. Any improvement in segmentation error rates would therefore directly reduce the time required to analyze 3D EM data. We explored preserving extracellular space (ECS) during chemical tissue fixation to improve the ability to segment neurites and to identify synaptic contacts. ECS preserved tissue is easier to segment using machine learning algorithms, leading to significantly reduced error rates. In addition, we observed that electrical synapses are readily identified in ECS preserved tissue. Finally, we determined that antibodies penetrate deep into ECS preserved tissue with only minimal permeabilization, thereby enabling correlated light microscopy (LM) and EM studies. We conclude that preservation of ECS benefits multiple aspects of the connectomic analysis of neural circuits.

Nanoscale chemical imaging by photoinduced force microscopy

PubMed Central

Nowak, Derek; Morrison, William; Wickramasinghe, H. Kumar; Jahng, Junghoon; Potma, Eric; Wan, Lei; Ruiz, Ricardo; Albrecht, Thomas R.; Schmidt, Kristin; Frommer, Jane; Sanders, Daniel P.; Park, Sung

2016-01-01

Correlating spatial chemical information with the morphology of closely packed nanostructures remains a challenge for the scientific community. For example, supramolecular self-assembly, which provides a powerful and low-cost way to create nanoscale patterns and engineered nanostructures, is not easily interrogated in real space via existing nondestructive techniques based on optics or electrons. A novel scanning probe technique called infrared photoinduced force microscopy (IR PiFM) directly measures the photoinduced polarizability of the sample in the near field by detecting the time-integrated force between the tip and the sample. By imaging at multiple IR wavelengths corresponding to absorption peaks of different chemical species, PiFM has demonstrated the ability to spatially map nm-scale patterns of the individual chemical components of two different types of self-assembled block copolymer films. With chemical-specific nanometer-scale imaging, PiFM provides a powerful new analytical method for deepening our understanding of nanomaterials. PMID:27051870

The control of ice crystal growth and effect on porous structure of konjac glucomannan-based aerogels.

PubMed

Ni, Xuewen; Ke, Fan; Xiao, Man; Wu, Kao; Kuang, Ying; Corke, Harold; Jiang, Fatang

2016-11-01

Konjac glucomannan (KGM)-based aerogels were prepared using a combination of sol-gel and freeze-drying methods. Preparation conditions were chosen to control ice crystal growth and aerogel structure formation. The ice crystals formed during pre-freezing were observed by low temperature polarizing microscopy, and images of aerogel pores were obtained by scanning electron microscopy. The size of ice crystals were calculated and size distribution maps were drawn, and similarly for aerogel pores. Results showed that ice crystal growth and aerogel pore sizes may be controlled by varying pre-freezing temperatures, KGM concentration and glyceryl monostearate concentration. The impact of pre-freezing temperatures on ice crystal growth was explained as combining ice crystal growth rate with nucleation rate, while the impacts of KGM and glyceryl monostearate concentration on ice crystal growth were interpreted based on their influences on sol network structure. Copyright © 2016 Elsevier B.V. All rights reserved.

Sub-10 fs Time-Resolved Vibronic Optical Microscopy

PubMed Central

2016-01-01

We introduce femtosecond wide-field transient absorption microscopy combining sub-10 fs pump and probe pulses covering the complete visible (500–650 nm) and near-infrared (650–950 nm) spectrum with diffraction-limited optical resolution. We demonstrate the capabilities of our system by reporting the spatially- and spectrally-resolved transient electronic response of MAPbI3–xClx perovskite films and reveal significant quenching of the transient bleach signal at grain boundaries. The unprecedented temporal resolution enables us to directly observe the formation of band-gap renormalization, completed in 25 fs after photoexcitation. In addition, we acquire hyperspectral Raman maps of TIPS pentacene films with sub-400 nm spatial and sub-15 cm–1 spectral resolution covering the 100–2000 cm–1 window. Our approach opens up the possibility of studying ultrafast dynamics on nanometer length and femtosecond time scales in a variety of two-dimensional and nanoscopic systems. PMID:27934055

Calibrated work function mapping by Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Fernández Garrillo, Pablo A.; Grévin, Benjamin; Chevalier, Nicolas; Borowik, Łukasz

2018-04-01

We propose and demonstrate the implementation of an alternative work function tip calibration procedure for Kelvin probe force microscopy under ultrahigh vacuum, using monocrystalline metallic materials with known crystallographic orientation as reference samples, instead of the often used highly oriented pyrolytic graphite calibration sample. The implementation of this protocol allows the acquisition of absolute and reproducible work function values, with an improved uncertainty with respect to unprepared highly oriented pyrolytic graphite-based protocols. The developed protocol allows the local investigation of absolute work function values over nanostructured samples and can be implemented in electronic structures and devices characterization as demonstrated over a nanostructured semiconductor sample presenting Al0.7Ga0.3As and GaAs layers with variable thickness. Additionally, using our protocol we find that the work function of annealed highly oriented pyrolytic graphite is equal to 4.6 ± 0.03 eV.

Semiclassical description of photoionization microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bordas, Ch.; Lepine, F.; Nicole, C.

2003-07-01

Recently, experiments have been reported where a geometrical interference pattern was observed when photoelectrons ejected in the threshold photoionization of xenon were detected in a velocity-map imaging apparatus [C. Nicole et al., Phys. Rev. Lett. 88, 133001 (2002)]. This technique, called photoionization microscopy, relies on the existence of interferences between various trajectories by which the electron moves from the atom to the plane of observation. Unlike previous predictions relevant to the hydrogenic case, the structure of the interference pattern evolves smoothly with the excess energy above the saddle point and is only weakly affected by the presence of continuum Starkmore » resonances. In this paper, we describe a semiclassical analysis of this process and present numerical simulations in excellent agreement with the experimental results. It is shown that the background contribution dominates in the observations, as opposed to the behavior expected for hydrogenic systems where the interference pattern is qualitatively different on quasidiscrete Stark resonances.« less

Correlative Stochastic Optical Reconstruction Microscopy and Electron Microscopy

PubMed Central

Kim, Doory; Deerinck, Thomas J.; Sigal, Yaron M.; Babcock, Hazen P.; Ellisman, Mark H.; Zhuang, Xiaowei

2015-01-01

Correlative fluorescence light microscopy and electron microscopy allows the imaging of spatial distributions of specific biomolecules in the context of cellular ultrastructure. Recent development of super-resolution fluorescence microscopy allows the location of molecules to be determined with nanometer-scale spatial resolution. However, correlative super-resolution fluorescence microscopy and electron microscopy (EM) still remains challenging because the optimal specimen preparation and imaging conditions for super-resolution fluorescence microscopy and EM are often not compatible. Here, we have developed several experiment protocols for correlative stochastic optical reconstruction microscopy (STORM) and EM methods, both for un-embedded samples by applying EM-specific sample preparations after STORM imaging and for embedded and sectioned samples by optimizing the fluorescence under EM fixation, staining and embedding conditions. We demonstrated these methods using a variety of cellular targets. PMID:25874453

Dark-field transmission electron microscopy and the Debye-Waller factor of graphene

PubMed Central

Hubbard, William A.; White, E. R.; Dawson, Ben; Lodge, M. S.; Ishigami, Masa; Regan, B. C.

2014-01-01

Graphene's structure bears on both the material's electronic properties and fundamental questions about long range order in two-dimensional crystals. We present an analytic calculation of selected area electron diffraction from multi-layer graphene and compare it with data from samples prepared by chemical vapor deposition and mechanical exfoliation. A single layer scatters only 0.5% of the incident electrons, so this kinematical calculation can be considered reliable for five or fewer layers. Dark-field transmission electron micrographs of multi-layer graphene illustrate how knowledge of the diffraction peak intensities can be applied for rapid mapping of thickness, stacking, and grain boundaries. The diffraction peak intensities also depend on the mean-square displacement of atoms from their ideal lattice locations, which is parameterized by a Debye-Waller factor. We measure the Debye-Waller factor of a suspended monolayer of exfoliated graphene and find a result consistent with an estimate based on the Debye model. For laboratory-scale graphene samples, finite size effects are sufficient to stabilize the graphene lattice against melting, indicating that ripples in the third dimension are not necessary. PMID:25242882

Dark-field transmission electron microscopy and the Debye-Waller factor of graphene.

PubMed

Shevitski, Brian; Mecklenburg, Matthew; Hubbard, William A; White, E R; Dawson, Ben; Lodge, M S; Ishigami, Masa; Regan, B C

2013-01-15

Graphene's structure bears on both the material's electronic properties and fundamental questions about long range order in two-dimensional crystals. We present an analytic calculation of selected area electron diffraction from multi-layer graphene and compare it with data from samples prepared by chemical vapor deposition and mechanical exfoliation. A single layer scatters only 0.5% of the incident electrons, so this kinematical calculation can be considered reliable for five or fewer layers. Dark-field transmission electron micrographs of multi-layer graphene illustrate how knowledge of the diffraction peak intensities can be applied for rapid mapping of thickness, stacking, and grain boundaries. The diffraction peak intensities also depend on the mean-square displacement of atoms from their ideal lattice locations, which is parameterized by a Debye-Waller factor. We measure the Debye-Waller factor of a suspended monolayer of exfoliated graphene and find a result consistent with an estimate based on the Debye model. For laboratory-scale graphene samples, finite size effects are sufficient to stabilize the graphene lattice against melting, indicating that ripples in the third dimension are not necessary.

Electronic properties of epitaxial silicene: a LT-STM/STS study

NASA Astrophysics Data System (ADS)

Fleurence, Antoine; Lee, Chi-Cheng; Ozaki, Taisuke; Yamada-Takamura, Yukiko; Yoshida, Yasuo; Hasegawa, Yukio

2013-03-01

The astonishing properties of silicene, the Si-counterpart of graphene, together with pioneering experimental observations, triggered in the very recent years, an exponentially increasing interest for this atom-thick material, both at fundamental level and for applications in high-speed electronic devices. We demonstrated, that the spontaneous segregation of silicon on (0001) surface of zirconium diboride (ZrB2) thin films epitaxied on Si(111) wafers gives rise to a wide-scale uniform two-dimensional silicene sheet. The silicene nature of the honeycomb structure imaged by scanning tunneling microscopy is evidenced by the observation of gap-opened π-electronic bands. The band gap opening is primarily due the specifically imprinted buckling. Here, we present the results of a low-temperature scanning tunneling spectroscopy investigation, which evidences the n-doped nature of silicene. The mapping of the local density of states, together with density functional theory give precious insights into the microscopic origin of the electronic bands of silicene. In particular, it shows the correlation between the degree of sp2 hybridization of different Si atoms in the internal structure and the character of the electronic bands.

Seeing tobacco mosaic virus through direct electron detectors

PubMed Central

Fromm, Simon A.; Bharat, Tanmay A.M.; Jakobi, Arjen J.; Hagen, Wim J.H.; Sachse, Carsten

2015-01-01

With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35 Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2 Å in resolution using cryo-EM. PMID:25528571

Plasmon 3D Electron Tomography and Local Electric-Field Enhancement of Engineered Plasmonic Nanoantennas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Archanjo, B. S.; Vasconcelos, T. L.; Oliveira, B. S.

Plasmonic nano-antennas are pushing the limits of optical imaging resolution capabilities in near-field scanning optical microscopy (NSOM). Accordingly, these techniques are driving the basic understanding of photonic and optoelectronic nanoscale devices with applications in sensing, energy conversion, solid-state lighting and information technology. Imaging the localized surface plasmon resonance (LSPR) at the nanoscale is a key to understanding the optical responses of a given tip geometry in order to engineer better plasmonic nano-antennas for near-field experiments. In recent years the advancement of focused ion beam technology provides the ability to directly modify plasmonic structures with nanometer resolution. Also, scanning transmission electronmore » microscopy (STEM) with electron energy loss spectroscopy (EELS) is an established technique allowing imaging of LSPR. Specifically, the combination of these two techniques provides spectrally sensitive two-dimensional (2D) imaging information to better visualize and understand LSPR on the nanometer scale. This can be combined with electron tomography to provide the three-dimensional LSPR distribution. Here in this paper we demonstrate the fabrication of Au nano-pyramids using helium ion microscopy, and analyze the LSPR in 3D reconstructions produced by total variation (TV)-norm minimization of a set of 2D STEM-EELS maps. Additionally, a boundary element simulation method was used to verify the experimentally observed nanopyramid LSPR modes. Finally, we show that the point-spread-functions (PSF) of LSPR mode hot spots in nanopyramids differ to local electric-field enhancement under optical excitation making direct comparison to NSOM experimental resolution difficult. However, the STEM-EELS results show how LSPR modes are influenced by the tip characteristics, which can inform the development of new nano-antenna designs.« less

Plasmon 3D Electron Tomography and Local Electric-Field Enhancement of Engineered Plasmonic Nanoantennas

DOE PAGES

Archanjo, B. S.; Vasconcelos, T. L.; Oliveira, B. S.; ...

2018-06-01

Plasmonic nano-antennas are pushing the limits of optical imaging resolution capabilities in near-field scanning optical microscopy (NSOM). Accordingly, these techniques are driving the basic understanding of photonic and optoelectronic nanoscale devices with applications in sensing, energy conversion, solid-state lighting and information technology. Imaging the localized surface plasmon resonance (LSPR) at the nanoscale is a key to understanding the optical responses of a given tip geometry in order to engineer better plasmonic nano-antennas for near-field experiments. In recent years the advancement of focused ion beam technology provides the ability to directly modify plasmonic structures with nanometer resolution. Also, scanning transmission electronmore » microscopy (STEM) with electron energy loss spectroscopy (EELS) is an established technique allowing imaging of LSPR. Specifically, the combination of these two techniques provides spectrally sensitive two-dimensional (2D) imaging information to better visualize and understand LSPR on the nanometer scale. This can be combined with electron tomography to provide the three-dimensional LSPR distribution. Here in this paper we demonstrate the fabrication of Au nano-pyramids using helium ion microscopy, and analyze the LSPR in 3D reconstructions produced by total variation (TV)-norm minimization of a set of 2D STEM-EELS maps. Additionally, a boundary element simulation method was used to verify the experimentally observed nanopyramid LSPR modes. Finally, we show that the point-spread-functions (PSF) of LSPR mode hot spots in nanopyramids differ to local electric-field enhancement under optical excitation making direct comparison to NSOM experimental resolution difficult. However, the STEM-EELS results show how LSPR modes are influenced by the tip characteristics, which can inform the development of new nano-antenna designs.« less

Nanoparticle Treated Stainless Steel Filters for Metal Vapor Sequestration

NASA Astrophysics Data System (ADS)

Murph, Simona E. Hunyadi; Larsen, George K.; Korinko, Paul; Coopersmith, Kaitlin J.; Summer, Ansley J.; Lewis, Rebecca

2017-02-01

The ability to sequester vapor phase radioactive compounds during industrial processes reduces the exposure of workers and the environment to dangerous radioactive materials. Nanomaterials have a lot of potential in this area because they typically demonstrate size- and shape-dependent properties with higher reactivity than bulk. This is due to the increased surface area-to-volume ratio and quantum size effects. In this report, we developed a gold nanomaterial-treated stainless steel filter, namely wools and coupons, that can be efficiently used for zinc vapor sequestration. Without nanoparticle modification, stainless steel coupons do not react or alloy with Zn. Gold nanomaterials were grown onto various stainless steel filters using solution chemistry that is amenable to scaling up. Materials were characterized by electron microscopy, inductively coupled plasma mass spectroscopy and dynamic light scattering before and after exposure to zinc vapors. X-ray diffraction, high-resolution transmission electron microscopy, energy dispersive x-ray spectroscopy mapping and ultraviolet-visible spectroscopy confirm the formation of gold-zinc alloys after Zn vapor exposure. The effect of surface topography on nanoparticle morphology, size and loading density were also investigated, and stainless steel surface defects were found to have an impact on the Au NP growth and subsequently Zn sequestration.

Synthesis of phosphorus-doped graphene and its wide potential window in aqueous supercapacitors.

PubMed

Wen, Yangyang; Wang, Bei; Huang, Congcong; Wang, Lianzhou; Hulicova-Jurcakova, Denisa

2015-01-02

Phosphorus-doped (P-doped) graphene with the P doping level of 1.30 at % was synthesized by annealing the mixture of graphene and phosphoric acid. The presence of P was confirmed by elemental mapping and X-ray photoelectron spectroscopy, while the morphology of P-doped graphene was revealed by using scanning electron microscopy and transmission electron microscopy. To investigate the effect of P doping, the electrochemical properties of P-doped graphene were tested as a supercapacitor electrode in an aqueous electrolyte of 1 M H2 SO4. The results showed that doping of P in graphene exhibited significant improvement in terms of specific capacitance and cycling stability, compared with undoped graphene electrode. More interestingly, the P-doped graphene electrode can survive at a wide voltage window of 1.7 V with only 3 % performance degradation after 5000 cycles at a current density of 5 A g(-1), providing a high energy density of 11.64 Wh kg(-1) and a high power density of 831 W kg(-1). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lithium dendrite and solid electrolyte interphase investigation using OsO4

NASA Astrophysics Data System (ADS)

Zier, Martin; Scheiba, Frieder; Oswald, Steffen; Thomas, Jürgen; Goers, Dietrich; Scherer, Torsten; Klose, Markus; Ehrenberg, Helmut; Eckert, Jürgen

2014-11-01

Osmium tetroxide (OsO4) staining, commonly used to enhance scattering contrast in electron microscopy of biologic tissue and polymer blends, has been adopted for studies of graphite anodes in lithium-ion batteries. OsO4 shows a coordinated reaction with components of the solid electrolyte interphase (SEI) and lithium dendrites, thereby increasing material contrast for scanning electron microscopy investigations. Utilizing the high affinity of lithium metal to react with osmium tetroxide it was possible to localize even small lithium deposits on graphite electrodes. In spite of their reaction with the OsO4 fume, the lithium dendrite morphology remains almost untouched by the staining procedure, offering information on the dendrite growth process. Correlating the quantity of osmium detected with the amount of residual ("dead") lithium of a discharged electrode, it was possible to obtain a practical measure for lithium plating and stripping efficiencies. EDX mappings allowed for a localization of electrochemically stripped lithium dendrites by their residual stained SEI shells. Cross sections, prepared by focused ion beam (FIB) of cycled graphite electrodes treated with OsO4, revealed important information about deposition and distribution of metallic lithium and the electrolyte reduction layer across the electrode.

Coating stainless steel plates with Ag/TiO2 for chlorpyrifos decontamination

NASA Astrophysics Data System (ADS)

Abdel Fattah, Wafa I.; Gobara, Mohammed M.; El-Hotaby, Walid; Mostafa, Sherif F. M.; Ali, Ghareib W.

2016-05-01

Spray coatings of either nanosilver (Ag), titanium (TiO2) or nanosilver titanium (Ag/TiO2) on stainless steel substrates prepared by sol-gel process were successfully achieved. The efficiency of the Ag/TiO2 coat onto 316 stainless steel surface towards cloropyrifos degradation as a chemical warfare agent (CWA) was proved. The crystalline structure and morphological characterization, as well as surface roughness measurements, were assessed. X-ray diffraction results proved the crystalline TiO2 anatase phase. The uniform distribution of Ag along with TiO2 nanoparticles was evidenced through transmission electron microscopy and scanning electron microscopy mapping. The hydrophilic nature of individual Ag, TiO2 and Ag/TiO2 coats was proved by contact angle measurements. The loading of Ag nanoparticles influenced positively the Ag/TiO2 coats surface roughness. The photocatalytic cloropyrifos degradation achieved about 50% within one-hour post UV treatment proving, therefore, the promising Ag/TiO2 continued decontamination efficiency. In conclusion, tuning the physical and morphological properties of TiO2 coated on stainless steel surface could be significantly enhanced by Ag nanoparticles incorporation. The developed Ag/TiO2 coat could be conveniently applied as CWA decontaminant.

Measuring surface topography with scanning electron microscopy. I. EZEImage: a program to obtain 3D surface data.

PubMed

Ponz, Ezequiel; Ladaga, Juan Luis; Bonetto, Rita Dominga

2006-04-01

Scanning electron microscopy (SEM) is widely used in the science of materials and different parameters were developed to characterize the surface roughness. In a previous work, we studied the surface topography with fractal dimension at low scale and two parameters at high scale by using the variogram, that is, variance vs. step log-log graph, of a SEM image. Those studies were carried out with the FERImage program, previously developed by us. To verify the previously accepted hypothesis by working with only an image, it is indispensable to have reliable three-dimensional (3D) surface data. In this work, a new program (EZEImage) to characterize 3D surface topography in SEM has been developed. It uses fast cross correlation and dynamic programming to obtain reliable dense height maps in a few seconds which can be displayed as an image where each gray level represents a height value. This image can be used for the FERImage program or any other software to obtain surface topography characteristics. EZEImage also generates anaglyph images as well as characterizes 3D surface topography by means of a parameter set to describe amplitude properties and three functional indices for characterizing bearing and fluid properties.

Stability of Catalyzed Magnesium Hydride Nanocrystalline During Hydrogen Cycling. Part II: Microstructure Evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Chengshang; Fang, Zhigang Zak; Bowman, Robert C.

2015-10-01

In Part I, the cyclic stabilities of the kinetics of catalyzed MgH2 systems including MgH2–TiH2, MgH2–TiMn2, and MgH2–VTiCr were investigated, showing stable kinetics at 300 °C but deteriorations of the hydrogenation kinetics at temperatures below 150 °C. The present Part II describes the characterization of uncycled and cycled catalyzed MgH2 by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS) analysis. XRD analysis shows the crystallite sizes of the Mg and MgH2 significantly increased after the cycling. The mean crystallite sizes of the catalysts (TiH2 and VTiCr) increased moderately after the cycling. SEMmore » and TEM imaging were used to compare the microstructures of uncycled (as-milled) and cycled materials, revealing a drastic change of the microstructure after 100 cycles. In particular, results from energy-dispersive spectroscopy (EDS) mapping show that a change of distribution of the catalyst particles in the Mg and MgH2 phase occurred during the cycling.« less

Optical and structural properties in type-II InAlAs/AlGaAs quantum dots observed by photoluminescence, X-ray diffraction and transmission electron microscopy

NASA Astrophysics Data System (ADS)

Ben Daly, A.; Craciun, D.; Laura Ursu, E.; Lemaître, A.; Maaref, M. A.; Iacomi, F.; Vasile, B. S.; Craciun, V.

2017-10-01

We present the effects of AlGaAs alloy composition on InAlAs quantum dots (QDs) optical and structural properties. Photoluminescence (PL) analysis of samples having a variety of aluminium composition values covering type-II transitions clearly in QDs showed the presence of two transitions X-Sh and X-Ph. High-resolution X-ray diffraction (HRXRD) investigations showed that the layers grew epitaxially on the GaAs substrate, with no relaxation regardless the Al content of AlGaAs layer. From the reciprocal space map (RSM) investigation around (004) and (115) diffraction peaks, it was shown that the InAlAs layer is fully strained, the in-plane lattice parameters (a and b, a = b) being identical to those of GaAs substrate, while the c lattice parameter was dependent on the In and Al concentrations, being larger than that of the substrate. High-resolution transmission electronic microscopy (HRTEM) investigations confirmed that films grew epitaxially on the GaAs substrate with no visible dislocations or other major defects within the InAlAs/GaAlAs QDs structure.

In Situ Analysis of a Silver Nanoparticle-Precipitating Shewanella Biofilm by Surface Enhanced Confocal Raman Microscopy

PubMed Central

Schkolnik, Gal; Schmidt, Matthias; Mazza, Marco G.; Harnisch, Falk; Musat, Niculina

2015-01-01

Shewanella oneidensis MR-1 is an electroactive bacterium, capable of reducing extracellular insoluble electron acceptors, making it important for both nutrient cycling in nature and microbial electrochemical technologies, such as microbial fuel cells and microbial electrosynthesis. When allowed to anaerobically colonize an Ag/AgCl solid interface, S. oneidensis has precipitated silver nanoparticles (AgNp), thus providing the means for a surface enhanced confocal Raman microscopy (SECRaM) investigation of its biofilm. The result is the in-situ chemical mapping of the biofilm as it developed over time, where the distribution of cytochromes, reduced and oxidized flavins, polysaccharides and phosphate in the undisturbed biofilm is monitored. Utilizing AgNp bio-produced by the bacteria colonizing the Ag/AgCl interface, we could perform SECRaM while avoiding the use of a patterned or roughened support or the introduction of noble metal salts and reducing agents. This new method will allow a spatially and temporally resolved chemical investigation not only of Shewanella biofilms at an insoluble electron acceptor, but also of other noble metal nanoparticle-precipitating bacteria in laboratory cultures or in complex microbial communities in their natural habitats. PMID:26709923

Detection of neuron membranes in electron microscopy images using a serial neural network architecture.

PubMed

Jurrus, Elizabeth; Paiva, Antonio R C; Watanabe, Shigeki; Anderson, James R; Jones, Bryan W; Whitaker, Ross T; Jorgensen, Erik M; Marc, Robert E; Tasdizen, Tolga

2010-12-01

Study of nervous systems via the connectome, the map of connectivities of all neurons in that system, is a challenging problem in neuroscience. Towards this goal, neurobiologists are acquiring large electron microscopy datasets. However, the shear volume of these datasets renders manual analysis infeasible. Hence, automated image analysis methods are required for reconstructing the connectome from these very large image collections. Segmentation of neurons in these images, an essential step of the reconstruction pipeline, is challenging because of noise, anisotropic shapes and brightness, and the presence of confounding structures. The method described in this paper uses a series of artificial neural networks (ANNs) in a framework combined with a feature vector that is composed of image intensities sampled over a stencil neighborhood. Several ANNs are applied in series allowing each ANN to use the classification context provided by the previous network to improve detection accuracy. We develop the method of serial ANNs and show that the learned context does improve detection over traditional ANNs. We also demonstrate advantages over previous membrane detection methods. The results are a significant step towards an automated system for the reconstruction of the connectome. Copyright 2010 Elsevier B.V. All rights reserved.

Structure, photoluminescence and thermoluminescence study of a composite ZnTa2O6/ZnGa2O4 compound doped with Pr3+

NASA Astrophysics Data System (ADS)

Noto, L. L.; Shaat, S. K. K.; Poelman, D.; Dhlamini, M. S.; Mothudi, B. M.; Swart, H. C.

2016-05-01

The study of persistent luminescence is interesting for applications related to biological imaging, self-lit roads and security signs. Composite Pr-doped samples were prepared in one pot by solid chemical reaction at 1200 °C for 4 h. The X-ray diffraction patterns of the samples showed mixed phases which correspond to ZnGa2O4 and ZnTa2O6 phases. Interestingly, the secondary electron microscopy images showed that the surface morphology is composed of particles with different shapes: irregular, rhombus and rod shapes. The X-ray maps obtained using field emission scanning electron microscopy, confirmed that the irregular particles correspond to ZnTa2O6, and the rods correspond to ZnGa2O4. Red emission was observed from 1D2 → 3H4, 3P0 → 3H6, 3P0 → 3F2 and 1D2 → 3H5 transitions of Pr3+. The lifetime of the persistent luminescence was measured, and the corresponding trapping centres were investigated using thermoluminescence spectroscopy.

Live cell refractometry using Hilbert phase microscopy and confocal reflectance microscopy.

PubMed

Lue, Niyom; Choi, Wonshik; Popescu, Gabriel; Yaqoob, Zahid; Badizadegan, Kamran; Dasari, Ramachandra R; Feld, Michael S

2009-11-26

Quantitative chemical analysis has served as a useful tool for understanding cellular metabolisms in biology. Among many physical properties used in chemical analysis, refractive index in particular has provided molecular concentration that is an important indicator for biological activities. In this report, we present a method of extracting full-field refractive index maps of live cells in their native states. We first record full-field optical thickness maps of living cells by Hilbert phase microscopy and then acquire physical thickness maps of the same cells using a custom-built confocal reflectance microscope. Full-field and axially averaged refractive index maps are acquired from the ratio of optical thickness to physical thickness. The accuracy of the axially averaged index measurement is 0.002. This approach can provide novel biological assays of label-free living cells in situ.

High-resolution imaging by scanning electron microscopy of semithin sections in correlation with light microscopy.

PubMed

Koga, Daisuke; Kusumi, Satoshi; Shodo, Ryusuke; Dan, Yukari; Ushiki, Tatsuo

2015-12-01

In this study, we introduce scanning electron microscopy (SEM) of semithin resin sections. In this technique, semithin sections were adhered on glass slides, stained with both uranyl acetate and lead citrate, and observed with a backscattered electron detector at a low accelerating voltage. As the specimens are stained in the same manner as conventional transmission electron microscopy (TEM), the contrast of SEM images of semithin sections was similar to TEM images of ultrathin sections. Using this technique, wide areas of semithin sections were also observed by SEM, without the obstruction of grids, which was inevitable for traditional TEM. This study also applied semithin section SEM to correlative light and electron microscopy. Correlative immunofluorescence microscopy and immune-SEM were performed in semithin sections of LR white resin-embedded specimens using a FluoroNanogold-labeled secondary antibody. Because LR white resin is hydrophilic and electron stable, this resin is suitable for immunostaining and SEM observation. Using correlative microscopy, the precise localization of the primary antibody was demonstrated by fluorescence microscopy and SEM. This method has great potential for studies examining the precise localization of molecules, including Golgi- and ER-associated proteins, in correlation with LM and SEM. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Characterisation of mineral deposition systems associated with rock art in the Kimberley region of northwest Australia.

PubMed

Green, Helen; Gleadow, Andrew; Finch, Damien

2017-10-01

This data article contains mineralogical and chemical data from mineral accretions sampled from rock art shelters in the Kimberley region of north west Australia. The accretions were collected both on and off pigment and engraved rock art of varying styles observed in the Kimberley with an aim of providing a thorough understanding of the formation and preservation of such materials in the context of dating [1]. This contribution includes processed powder X-ray Diffraction data, Scanning Electron Microscopy energy dispersive spectroscopy data, and Laser Ablation ICP-MS trace element mapping data.

Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis.

PubMed

Yang, Yu-Jiao; Wang, Shuai; Zhang, Biao; Shen, Hong-Bin

2018-06-25

As a relatively new technology to solve the three-dimensional (3D) structure of a protein or protein complex, single-particle reconstruction (SPR) of cryogenic electron microscopy (cryo-EM) images shows much superiority and is in a rapidly developing stage. Resolution measurement in SPR, which evaluates the quality of a reconstructed 3D density map, plays a critical role in promoting methodology development of SPR and structural biology. Because there is no benchmark map in the generation of a new structure, how to realize the resolution estimation of a new map is still an open problem. Existing approaches try to generate a hypothetical benchmark map by reconstructing two 3D models from two halves of the original 2D images for cross-reference, which may result in a premature estimation with a half-data model. In this paper, we report a new self-reference-based resolution estimation protocol, called SRes, that requires only a single reconstructed 3D map. The core idea of SRes is to perform a multiscale spectral analysis (MSSA) on the map through multiple size-variable masks segmenting the map. The MSSA-derived multiscale spectral signal-to-noise ratios (mSSNRs) reveal that their corresponding estimated resolutions will show a cliff jump phenomenon, indicating a significant change in the SSNR properties. The critical point on the cliff borderline is demonstrated to be the right estimator for the resolution of the map.

On the Progress of Scanning Transmission Electron Microscopy (STEM) Imaging in a Scanning Electron Microscope.

PubMed

Sun, Cheng; Müller, Erich; Meffert, Matthias; Gerthsen, Dagmar

2018-04-01

Transmission electron microscopy (TEM) with low-energy electrons has been recognized as an important addition to the family of electron microscopies as it may avoid knock-on damage and increase the contrast of weakly scattering objects. Scanning electron microscopes (SEMs) are well suited for low-energy electron microscopy with maximum electron energies of 30 keV, but they are mainly used for topography imaging of bulk samples. Implementation of a scanning transmission electron microscopy (STEM) detector and a charge-coupled-device camera for the acquisition of on-axis transmission electron diffraction (TED) patterns, in combination with recent resolution improvements, make SEMs highly interesting for structure analysis of some electron-transparent specimens which are traditionally investigated by TEM. A new aspect is correlative SEM, STEM, and TED imaging from the same specimen region in a SEM which leads to a wealth of information. Simultaneous image acquisition gives information on surface topography, inner structure including crystal defects and qualitative material contrast. Lattice-fringe resolution is obtained in bright-field STEM imaging. The benefits of correlative SEM/STEM/TED imaging in a SEM are exemplified by structure analyses from representative sample classes such as nanoparticulates and bulk materials.

Annealing-Induced Bi Bilayer on Bi2Te3 Investigated via Quasi-Particle-Interference Mapping.

PubMed

Schouteden, Koen; Govaerts, Kirsten; Debehets, Jolien; Thupakula, Umamahesh; Chen, Taishi; Li, Zhe; Netsou, Asteriona; Song, Fengqi; Lamoen, Dirk; Van Haesendonck, Chris; Partoens, Bart; Park, Kyungwha

2016-09-27

Topological insulators (TIs) are renowned for their exotic topological surface states (TSSs) that reside in the top atomic layers, and hence, detailed knowledge of the surface top atomic layers is of utmost importance. Here we present the remarkable morphology changes of Bi2Te3 surfaces, which have been freshly cleaved in air, upon subsequent systematic annealing in ultrahigh vacuum and the resulting effects on the local and area-averaging electronic properties of the surface states, which are investigated by combining scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and Auger electron spectroscopy (AES) experiments with density functional theory (DFT) calculations. Our findings demonstrate that the annealing induces the formation of a Bi bilayer atop the Bi2Te3 surface. The adlayer results in n-type doping, and the atomic defects act as scattering centers of the TSS electrons. We also investigated the annealing-induced Bi bilayer surface on Bi2Te3 via voltage-dependent quasi-particle-interference (QPI) mapping of the surface local density of states and via comparison with the calculated constant-energy contours and QPI patterns. We observed closed hexagonal patterns in the Fourier transform of real-space QPI maps with secondary outer spikes. DFT calculations attribute these complex QPI patterns to the appearance of a "second" cone due to the surface charge transfer between the Bi bilayer and the Bi2Te3. Annealing in ultrahigh vacuum offers a facile route for tuning of the topological properties and may yield similar results for other topological materials.

Mapping of trap densities and hotspots in pentacene thin-film transistors by frequency-resolved scanning photoresponse microscopy.

PubMed

Westermeier, Christian; Fiebig, Matthias; Nickel, Bert

2013-10-25

Frequency-resolved scanning photoresponse microscopy of pentacene thin-film transistors is reported. The photoresponse pattern maps the in-plane distribution of trap states which is superimposed by the level of trap filling adjusted by the gate voltage of the transistor. Local hotspots in the photoresponse map thus indicate areas of high trap densities within the pentacene thin film. © 2013 WILEY-VCH Verlag GmbH 8 Co. KGaA, Weinheim.

Mapping optical path length and image enhancement using quantitative orientation-independent differential interference contrast microscopy

PubMed Central

Shribak, Michael; Larkin, Kieran G.; Biggs, David

2017-01-01

Abstract. We describe the principles of using orientation-independent differential interference contrast (OI-DIC) microscopy for mapping optical path length (OPL). Computation of the scalar two-dimensional OPL map is based on an experimentally received map of the OPL gradient vector field. Two methods of contrast enhancement for the OPL image, which reveal hardly visible structures and organelles, are presented. The results obtained can be used for reconstruction of a volume image. We have confirmed that a standard research grade light microscope equipped with the OI-DIC and 100×/1.3 NA objective lens, which was not specially selected for minimum wavefront and polarization aberrations, provides OPL noise level of ∼0.5  nm and lateral resolution if ∼300  nm at a wavelength of 546 nm. The new technology is the next step in the development of the DIC microscopy. It can replace standard DIC prisms on existing commercial microscope systems without modification. This will allow biological researchers that already have microscopy setups to expand the performance of their systems. PMID:28060991

Electron transparent graphene windows for environmental scanning electron microscopy in liquids and dense gases.

PubMed

Stoll, Joshua D; Kolmakov, Andrei

2012-12-21

Due to its ultrahigh electron transmissivity in a wide electron energy range, molecular impermeability, high electrical conductivity and excellent mechanical stiffness, suspended graphene membranes appear to be a nearly ideal window material for in situ (in vivo) environmental electron microscopy of nano- and mesoscopic objects (including bio-medical samples) immersed in liquids and/or in dense gaseous media. In this paper, taking advantage of a small modification of the graphene transfer protocol onto metallic and SiN supporting orifices, reusable environmental cells with exchangeable graphene windows have been designed. Using colloidal gold nanoparticles (50 nm) dispersed in water as model objects for scanning electron microscopy in liquids as proof of concept, different conditions for imaging through the graphene membrane were tested. Limiting factors for electron microscopy in liquids, such as electron beam induced water radiolysis and damage of the graphene membrane at high electron doses, are discussed.

Ultrafast Science Opportunities with Electron Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Durr, Hermann

X-rays and electrons are two of the most fundamental probes of matter. When the Linac Coherent Light Source (LCLS), the world’s first x-ray free electron laser, began operation in 2009, it transformed ultrafast science with the ability to generate laser-like x-ray pulses from the manipulation of relativistic electron beams. This document describes a similar future transformation. In Transmission Electron Microscopy, ultrafast relativistic (MeV energy) electron pulses can achieve unsurpassed spatial and temporal resolution. Ultrafast temporal resolution will be the next frontier in electron microscopy and can ideally complement ultrafast x-ray science done with free electron lasers. This document describes themore » Grand Challenge science opportunities in chemistry, material science, physics and biology that arise from an MeV ultrafast electron diffraction & microscopy facility, especially when coupled with linac-based intense THz and X-ray pump capabilities.« less

Microstructure of milk

USDA-ARS?s Scientific Manuscript database

The fat and protein in milk may be examined by scanning electron microscopy, transmission electron microscopy, and confocal laser scanning microscopy, and any bacteria present may be viewed by light microscopy. The fat exists as globules, the bulk of the protein is in the form of casein micelles, a...

Fabrication of [001]-oriented tungsten tips for high resolution scanning tunneling microscopy

PubMed Central

Chaika, A. N.; Orlova, N. N.; Semenov, V. N.; Postnova, E. Yu.; Krasnikov, S. A.; Lazarev, M. G.; Chekmazov, S. V.; Aristov, V. Yu.; Glebovsky, V. G.; Bozhko, S. I.; Shvets, I. V.

2014-01-01

The structure of the [001]-oriented single crystalline tungsten probes sharpened in ultra-high vacuum using electron beam heating and ion sputtering has been studied using scanning and transmission electron microscopy. The electron microscopy data prove reproducible fabrication of the single-apex tips with nanoscale pyramids grained by the {011} planes at the apexes. These sharp, [001]-oriented tungsten tips have been successfully utilized in high resolution scanning tunneling microscopy imaging of HOPG(0001), SiC(001) and graphene/SiC(001) surfaces. The electron microscopy characterization performed before and after the high resolution STM experiments provides direct correlation between the tip structure and picoscale spatial resolution achieved in the experiments. PMID:24434734

Towards native-state imaging in biological context in the electron microscope

PubMed Central

Weston, Anne E.; Armer, Hannah E. J.

2009-01-01

Modern cell biology is reliant on light and fluorescence microscopy for analysis of cells, tissues and protein localisation. However, these powerful techniques are ultimately limited in resolution by the wavelength of light. Electron microscopes offer much greater resolution due to the shorter effective wavelength of electrons, allowing direct imaging of sub-cellular architecture. The harsh environment of the electron microscope chamber and the properties of the electron beam have led to complex chemical and mechanical preparation techniques, which distance biological samples from their native state and complicate data interpretation. Here we describe recent advances in sample preparation and instrumentation, which push the boundaries of high-resolution imaging. Cryopreparation, cryoelectron microscopy and environmental scanning electron microscopy strive to image samples in near native state. Advances in correlative microscopy and markers enable high-resolution localisation of proteins. Innovation in microscope design has pushed the boundaries of resolution to atomic scale, whilst automatic acquisition of high-resolution electron microscopy data through large volumes is finally able to place ultrastructure in biological context. PMID:19916039

An overview of state-of-the-art image restoration in electron microscopy.

PubMed

Roels, J; Aelterman, J; Luong, H Q; Lippens, S; Pižurica, A; Saeys, Y; Philips, W

2018-06-08

In Life Science research, electron microscopy (EM) is an essential tool for morphological analysis at the subcellular level as it allows for visualization at nanometer resolution. However, electron micrographs contain image degradations such as noise and blur caused by electromagnetic interference, electron counting errors, magnetic lens imperfections, electron diffraction, etc. These imperfections in raw image quality are inevitable and hamper subsequent image analysis and visualization. In an effort to mitigate these artefacts, many electron microscopy image restoration algorithms have been proposed in the last years. Most of these methods rely on generic assumptions on the image or degradations and are therefore outperformed by advanced methods that are based on more accurate models. Ideally, a method will accurately model the specific degradations that fit the physical acquisition settings. In this overview paper, we discuss different electron microscopy image degradation solutions and demonstrate that dedicated artefact regularisation results in higher quality restoration and is applicable through recently developed probabilistic methods. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Mapping of dendritic lesions in patients with herpes simplex keratitis using in vivo confocal microscopy

PubMed Central

Yokogawa, Hideaki; Kobayashi, Akira; Mori, Natsuko; Sugiyama, Kazuhisa

2015-01-01

Purpose To produce a two-dimensional reconstruction map of dendritic lesions in patients with herpes simplex keratitis (HSK) using in vivo confocal microscopy. Methods Four eyes of four patients (mean 65.8 years) with HSK presenting with a dendritic lesion were enrolled. Slit-lamp biomicroscopy and in vivo laser confocal microscopy were performed. Acquired confocal images at the level of the epithelium were arranged and mapped into subconfluent montages. Changes in the shape and degree of light reflection of abnormal cells and deposits around dendritic lesions as well as other corneal layers were qualitatively evaluated. Results Mapping of dendritic lesion was successful in all cases, and the subconfluent montages clearly showed the larger image of dendritic lesion. In all cases, the dendritic lesion consisted of hyperreflective irregular epithelial cells, and was surrounded by distorted and elongated epithelial cells. In three cases, hyperreflective deposits were noted at the midline of the lesion. The corneal stroma showed a hyperreflective honeycomb pattern. In two cases, inflammatory cells were observed at the level of endothelial cell layer. Conclusion Mapping of dendritic lesions in patients with HSK was successful in all patients using in vivo confocal microscopy. Cellular level observation of dendritic lesion at a relatively larger magnification may help understand the in vivo morphological change of HSK. Further study in more patients with HSK and nonherpetic dendritic lesion is needed to utilize confocal microscopy images in differential diagnosis and follow-up of the epithelial lesions with dendrite. PMID:26445524

Mapping of dendritic lesions in patients with herpes simplex keratitis using in vivo confocal microscopy.

PubMed

Yokogawa, Hideaki; Kobayashi, Akira; Mori, Natsuko; Sugiyama, Kazuhisa

2015-01-01

To produce a two-dimensional reconstruction map of dendritic lesions in patients with herpes simplex keratitis (HSK) using in vivo confocal microscopy. Four eyes of four patients (mean 65.8 years) with HSK presenting with a dendritic lesion were enrolled. Slit-lamp biomicroscopy and in vivo laser confocal microscopy were performed. Acquired confocal images at the level of the epithelium were arranged and mapped into subconfluent montages. Changes in the shape and degree of light reflection of abnormal cells and deposits around dendritic lesions as well as other corneal layers were qualitatively evaluated. Mapping of dendritic lesion was successful in all cases, and the subconfluent montages clearly showed the larger image of dendritic lesion. In all cases, the dendritic lesion consisted of hyperreflective irregular epithelial cells, and was surrounded by distorted and elongated epithelial cells. In three cases, hyperreflective deposits were noted at the midline of the lesion. The corneal stroma showed a hyperreflective honeycomb pattern. In two cases, inflammatory cells were observed at the level of endothelial cell layer. Mapping of dendritic lesions in patients with HSK was successful in all patients using in vivo confocal microscopy. Cellular level observation of dendritic lesion at a relatively larger magnification may help understand the in vivo morphological change of HSK. Further study in more patients with HSK and nonherpetic dendritic lesion is needed to utilize confocal microscopy images in differential diagnosis and follow-up of the epithelial lesions with dendrite.

He-Ion Microscopy as a High-Resolution Probe for Complex Quantum Heterostructures in Core-Shell Nanowires.

PubMed

Pöpsel, Christian; Becker, Jonathan; Jeon, Nari; Döblinger, Markus; Stettner, Thomas; Gottschalk, Yeanitza Trujillo; Loitsch, Bernhard; Matich, Sonja; Altzschner, Marcus; Holleitner, Alexander W; Finley, Jonathan J; Lauhon, Lincoln J; Koblmüller, Gregor

2018-06-13

Core-shell semiconductor nanowires (NW) with internal quantum heterostructures are amongst the most complex nanostructured materials to be explored for assessing the ultimate capabilities of diverse ultrahigh-resolution imaging techniques. To probe the structure and composition of these materials in their native environment with minimal damage and sample preparation calls for high-resolution electron or ion microscopy methods, which have not yet been tested on such classes of ultrasmall quantum nanostructures. Here, we demonstrate that scanning helium ion microscopy (SHeIM) provides a powerful and straightforward method to map quantum heterostructures embedded in complex III-V semiconductor NWs with unique material contrast at ∼1 nm resolution. By probing the cross sections of GaAs-Al(Ga)As core-shell NWs with coaxial GaAs quantum wells as well as short-period GaAs/AlAs superlattice (SL) structures in the shell, the Al-rich and Ga-rich layers are accurately discriminated by their image contrast in excellent agreement with correlated, yet destructive, scanning transmission electron microscopy and atom probe tomography analysis. Most interestingly, quantitative He-ion dose-dependent SHeIM analysis of the ternary AlGaAs shell layers and of compositionally nonuniform GaAs/AlAs SLs reveals distinct alloy composition fluctuations in the form of Al-rich clusters with size distributions between ∼1-10 nm. In the GaAs/AlAs SLs the alloy clustering vanishes with increasing SL-period (>5 nm-GaAs/4 nm-AlAs), providing insights into critical size dimensions for atomic intermixing effects in short-period SLs within a NW geometry. The straightforward SHeIM technique therefore provides unique benefits in imaging the tiniest nanoscale features in topography, structure and composition of a multitude of diverse complex semiconductor nanostructures.

Quantitative FE-EPMA measurement of formation and inhibition of carbon contamination on Fe for trace carbon analysis.

PubMed

Tanaka, Yuji; Yamashita, Takako; Nagoshi, Masayasu

2017-04-01

Hydrocarbon contamination introduced during point, line and map analyses in a field emission electron probe microanalysis (FE-EPMA) was investigated to enable reliable quantitative analysis of trace amounts of carbon in steels. The increment of contamination on pure iron in point analysis is proportional to the number of iterations of beam irradiation, but not to the accumulated irradiation time. A combination of a longer dwell time and single measurement with a liquid nitrogen (LN2) trap as an anti-contamination device (ACD) is sufficient for a quantitative point analysis. However, in line and map analyses, contamination increases with irradiation time in addition to the number of iterations, even though the LN2 trap and a plasma cleaner are used as ACDs. Thus, a shorter dwell time and single measurement are preferred for line and map analyses, although it is difficult to eliminate the influence of contamination. While ring-like contamination around the irradiation point grows during electron-beam irradiation, contamination at the irradiation point increases during blanking time after irradiation. This can explain the increment of contamination in iterative point analysis as well as in line and map analyses. Among the ACDs, which are tested in this study, specimen heating at 373 K has a significant contamination inhibition effect. This technique makes it possible to obtain line and map analysis data with minimum influence of contamination. The above-mentioned FE-EPMA data are presented and discussed in terms of the contamination-formation mechanisms and the preferable experimental conditions for the quantification of trace carbon in steels. © The Author 2016. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Multi-modal Registration for Correlative Microscopy using Image Analogies

PubMed Central

Cao, Tian; Zach, Christopher; Modla, Shannon; Powell, Debbie; Czymmek, Kirk; Niethammer, Marc

2014-01-01

Correlative microscopy is a methodology combining the functionality of light microscopy with the high resolution of electron microscopy and other microscopy technologies for the same biological specimen. In this paper, we propose an image registration method for correlative microscopy, which is challenging due to the distinct appearance of biological structures when imaged with different modalities. Our method is based on image analogies and allows to transform images of a given modality into the appearance-space of another modality. Hence, the registration between two different types of microscopy images can be transformed to a mono-modality image registration. We use a sparse representation model to obtain image analogies. The method makes use of corresponding image training patches of two different imaging modalities to learn a dictionary capturing appearance relations. We test our approach on backscattered electron (BSE) scanning electron microscopy (SEM)/confocal and transmission electron microscopy (TEM)/confocal images. We perform rigid, affine, and deformable registration via B-splines and show improvements over direct registration using both mutual information and sum of squared differences similarity measures to account for differences in image appearance. PMID:24387943

A look inside epitaxial cobalt-on-fluorite nanoparticles with three-dimensional reciprocal space mapping using GIXD, RHEED and GISAXS.

PubMed

Suturin, S M; Fedorov, V V; Korovin, A M; Valkovskiy, G A; Konnikov, S G; Tabuchi, M; Sokolov, N S

2013-08-01

In this work epitaxial growth of cobalt on CaF 2 (111), (110) and (001) surfaces has been extensively studied. It has been shown by atomic force microscopy that at selected growth conditions stand-alone faceted Co nanoparticles are formed on a fluorite surface. Grazing-incidence X-ray diffraction (GIXD) and reflection high-energy electron diffraction (RHEED) studies have revealed that the particles crystallize in the face-centered cubic lattice structure otherwise non-achievable in bulk cobalt under normal conditions. The particles were found to inherit lattice orientation from the underlying CaF 2 layer. Three-dimensional reciprocal space mapping carried out using X-ray and electron diffraction has revealed that there exist long bright 〈111〉 streaks passing through the cobalt Bragg reflections. These streaks are attributed to stacking faults formed in the crystal lattice of larger islands upon coalescence of independently nucleated smaller islands. Distinguished from the stacking fault streaks, crystal truncation rods perpendicular to the {111} and {001} particle facets have been observed. Finally, grazing-incidence small-angle X-ray scattering (GISAXS) has been applied to decouple the shape-related scattering from that induced by the crystal lattice defects. Particle faceting has been verified by modeling the GISAXS patterns. The work demonstrates the importance of three-dimensional reciprocal space mapping in the study of epitaxial nanoparticles.

A look inside epitaxial cobalt-on-fluorite nanoparticles with three-dimensional reciprocal space mapping using GIXD, RHEED and GISAXS

PubMed Central

Suturin, S. M.; Fedorov, V. V.; Korovin, A. M.; Valkovskiy, G. A.; Konnikov, S. G.; Tabuchi, M.; Sokolov, N. S.

2013-01-01

In this work epitaxial growth of cobalt on CaF2(111), (110) and (001) surfaces has been extensively studied. It has been shown by atomic force microscopy that at selected growth conditions stand-alone faceted Co nanoparticles are formed on a fluorite surface. Grazing-incidence X-ray diffraction (GIXD) and reflection high-energy electron diffraction (RHEED) studies have revealed that the particles crystallize in the face-centered cubic lattice structure otherwise non-achievable in bulk cobalt under normal conditions. The particles were found to inherit lattice orientation from the underlying CaF2 layer. Three-dimensional reciprocal space mapping carried out using X-ray and electron diffraction has revealed that there exist long bright 〈111〉 streaks passing through the cobalt Bragg reflections. These streaks are attributed to stacking faults formed in the crystal lattice of larger islands upon coalescence of independently nucleated smaller islands. Distinguished from the stacking fault streaks, crystal truncation rods perpendicular to the {111} and {001} particle facets have been observed. Finally, grazing-incidence small-angle X-ray scattering (GISAXS) has been applied to decouple the shape-related scattering from that induced by the crystal lattice defects. Particle faceting has been verified by modeling the GISAXS patterns. The work demonstrates the importance of three-dimensional reciprocal space mapping in the study of epitaxial nanoparticles. PMID:24046491

Microstructure characterization of the stir zone of submerged friction stir processed aluminum alloy 2219

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Xiuli, E-mail: feng.97@osu.edu; State Key Laboratory of Advanced Welding and Joining, Harbin Institute of Technology, Harbin 150001; Liu, Huijie, E-mail: liuhj@hit.edu.cn

Aluminum alloy 2219-T6 was friction stir processed using a novel submerged processing technique to facilitate cooling. Processing was conducted at a constant tool traverse speed of 200 mm/min and spindle rotation speeds in the range from 600 to 800 rpm. The microstructural characteristics of the base metal and processed zone, including grain structure and precipitation behavior, were studied using optical microscopy (OM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Microhardness maps were constructed on polished cross sections of as-processed samples. The effect of tool rotation speed on the microstructure and hardness of the stir zone was investigated. Themore » average grain size of the stir zone was much smaller than that of the base metal, but the hardness was also lower due to the formation of equilibrium θ precipitates from the base metal θ′ precipitates. Stir zone hardness was found to decrease with increasing rotation speed (heat input). The effect of processing conditions on strength (hardness) was rationalized based on the competition between grain refinement strengthening and softening due to precipitate overaging. - Highlights: • SZ grain size (∼ 1 μm) is reduced by over one order of magnitude relative to the BM. • Hardness in the SZ is lower than that of the precipitation strengthened BM. • Metastable θ′ in the base metal transforms to equilibrium θ in the stir zone. • Softening in the SZ results from a decrease of precipitation strengthening.« less

Characterization of etch pits found on a large-grain bulk niobium superconducting radio-frequency resonant cavity

DOE PAGES

Zhao, Xin; Ciovati, G.; Bieler, T. R.

2010-12-15

The performance of superconducting radio-frequency (SRF) resonant cavities made of bulk niobium is limited by nonlinear localized effects. Surface analysis of regions of higher power dissipation is thus of intense interest. Such areas (referred to as “hotspots”) were identified in a large-grain single-cell cavity that had been buffered-chemical polished and dissected for examination by high resolution electron microscopy, electron backscattered diffraction microscopy (EBSD), and optical microscopy. Pits with clearly discernible crystal facets were observed in both “hotspot” and “coldspot” specimens. The pits were found in-grain, at bicrystal boundaries, and on tricrystal junctions. They are interpreted as etch pits induced bymore » crystal defects (e.g. dislocations). All coldspots examined had a qualitatively lower density of etch pits or relatively smooth tricrystal boundary junctions. EBSD mapping revealed the crystal orientation surrounding the pits. Locations with high pit density are correlated with higher mean values of the local average misorientation angle distributions, indicating a higher geometrically necessary dislocation content. In addition, a survey of the samples by energy dispersive x-ray analysis did not show any significant contamination of the samples’ surface. In conclusion, the local magnetic field enhancement produced by the sharp-edge features observed on the samples is not sufficient to explain the observed degradation of the cavity quality factor, which starts at peak surface magnetic field as low as 20 mT.« less

Sub-micron Hard X-ray Fluorescence Imaging of Synthetic Elements

PubMed Central

Jensen, Mark P.; Aryal, Baikuntha P.; Gorman-Lewis, Drew; Paunesku, Tatjana; Lai, Barry; Vogt, Stefan; Woloschak, Gayle E.

2013-01-01

Synchrotron-based X-ray fluorescence microscopy (SXFM) using hard X-rays focused into sub-micron spots is a powerful technique for elemental quantification and mapping, as well as microspectroscopic measurement such as μ-XANES (X-ray absorption near edge structure). We have used SXFM to image and simultaneously quantify the transuranic element plutonium at the L3 or L2 edge as well as lighter biologically essential elements in individual rat pheochromocytoma (PC12) cells after exposure to the long-lived plutonium isotope 242Pu. Elemental maps reveal that plutonium localizes principally in the cytoplasm of the cells and avoids the cell nucleus, which is marked by the highest concentrations of phosphorus and zinc, under the conditions of our experiments. The minimum detection limit under typical acquisition conditions for an average 202 μm2 cell is 1.4 fg Pu/cell or 2.9 × 10−20 moles Pu/μm2, which is similar to the detection limit of K-edge SXFM of transition metals at 10 keV. Copper electron microscopy grids were used to avoid interference from gold X-ray emissions, but traces of strontium present in naturally occurring calcium can still interfere with plutonium detection using its Lα X-ray emission. PMID:22444530

Hybrid fluorescence and electron cryo-microscopy for simultaneous electron and photon imaging.

PubMed

Iijima, Hirofumi; Fukuda, Yoshiyuki; Arai, Yoshihiro; Terakawa, Susumu; Yamamoto, Naoki; Nagayama, Kuniaki

2014-01-01

Integration of fluorescence light and transmission electron microscopy into the same device would represent an important advance in correlative microscopy, which traditionally involves two separate microscopes for imaging. To achieve such integration, the primary technical challenge that must be solved regards how to arrange two objective lenses used for light and electron microscopy in such a manner that they can properly focus on a single specimen. To address this issue, both lateral displacement of the specimen between two lenses and specimen rotation have been proposed. Such movement of the specimen allows sequential collection of two kinds of microscopic images of a single target, but prevents simultaneous imaging. This shortcoming has been made up by using a simple optical device, a reflection mirror. Here, we present an approach toward the versatile integration of fluorescence and electron microscopy for simultaneous imaging. The potential of simultaneous hybrid microscopy was demonstrated by fluorescence and electron sequential imaging of a fluorescent protein expressed in cells and cathodoluminescence imaging of fluorescent beads. Copyright © 2013 Elsevier Inc. All rights reserved.

In-depth evolution of chemical states and sub-10-nm-resolution crystal orientation mapping of nanograins in Ti(5 nm)/Au(20 nm)/Cr(3 nm) tri-layer thin films

NASA Astrophysics Data System (ADS)

Zhu, Xiaoli; Todeschini, Matteo; Bastos da Silva Fanta, Alice; Liu, Lintao; Jensen, Flemming; Hübner, Jörg; Jansen, Henri; Han, Anpan; Shi, Peixiong; Ming, Anjie; Xie, Changqing

2018-09-01

The applications of Au thin films and their adhesion layers often suffer from a lack of sufficient information about the chemical states of adhesion layers and about the high-lateral-resolution crystallographic morphology of Au nanograins. Here, we demonstrate the in-depth evolution of the chemical states of adhesive layers at the interfaces and the crystal orientation mapping of gold nanograins with a lateral resolution of less than 10 nm in a Ti/Au/Cr tri-layer thin film system. Using transmission electron microscopy, the variation in the interdiffusion at Cr/Au and Ti/Au interfaces was confirmed. From X-ray photoelectron spectroscopy (XPS) depth profiling, the chemical states of Cr, Au and Ti were characterized layer by layer, suggesting the insufficient oxidation of the adhesive layers. At the interfaces the Au 4f peaks shift to higher binding energies and this behavior can be described by a proposed model based on electron reorganization and substrate-induced final-state neutralization in small Au clusters supported by the partially oxidized Ti layer. Utilizing transmission Kikuchi diffraction (TKD) in a scanning electron microscope, the crystal orientation of Au nanograins between two adhesion layers was non-destructively characterized with sub-10 nm spatial resolution. The results provide nanoscale insights into the Ti/Au/Cr thin film system and contribute to our understanding of its behavior in nano-optic and nano-electronic devices.

Analytical SuperSTEM for extraterrestrial materials research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bradley, J P; Dai, Z R

2009-09-08

Electron-beam studies of extraterrestrial materials with significantly improved spatial resolution, energy resolution and sensitivity are enabled using a 300 keV SuperSTEM scanning transmission electron microscope with a monochromator and two spherical aberration correctors. The improved technical capabilities enable analyses previously not possible. Mineral structures can be directly imaged and analyzed with single-atomic-column resolution, liquids and implanted gases can be detected, and UV-VIS optical properties can be measured. Detection limits for minor/trace elements in thin (<100 nm thick) specimens are improved such that quantitative measurements of some extend to the sub-500 ppm level. Electron energy-loss spectroscopy (EELS) can be carried outmore » with 0.10-0.20 eV energy resolution and atomic-scale spatial resolution such that variations in oxidation state from one atomic column to another can be detected. Petrographic mapping is extended down to the atomic scale using energy-dispersive x-ray spectroscopy (EDS) and energy-filtered transmission electron microscopy (EFTEM) imaging. Technical capabilities and examples of the applications of SuperSTEM to extraterrestrial materials are presented, including the UV spectral properties and organic carbon K-edge fine structure of carbonaceous matter in interplanetary dust particles (IDPs), x-ray elemental maps showing the nanometer-scale distribution of carbon within GEMS (glass with embedded metal and sulfides), the first detection and quantification of trace Ti in GEMS using EDS, and detection of molecular H{sub 2}O in vesicles and implanted H{sub 2} and He in irradiated mineral and glass grains.« less

Chemistry Viewed through the Eyes of High-Resolution Microscopy.

ERIC Educational Resources Information Center

Beer, Michael; And Others

1981-01-01

This special report, prepared by several chemists working in the field of electron microscopy, provides information regarding the most recent developments in transmission and scanning electron microscopy that have chemical significance. (CS)

Pulsed and oscillating gradient MRI for assessment of cell size and Extracellular space (POMACE) in mouse gliomas

PubMed Central

Reynaud, Olivier; Winters, Kerryanne Veronica; Hoang, Dung Minh; Wadghiri, Youssef Zaim; Novikov, Dmitry S.; Kim, Sungheon Gene

2016-01-01

Solid tumor microstructure is related to aggressiveness of tumor, interstitial pressure and drug delivery pathways that are closely associated with treatment response, metastatic spread and prognosis. In this study, we introduce a novel diffusion MRI data analysis framework, Pulsed and Oscillating gradient MRI for Assessment of Cell size and Extracellular space (POMACE), and demonstrate its feasibility in a mouse tumor model. In vivo and ex vivo POMACE experiments were performed on mice bearing the GL261 murine glioma model (n=8). Since the complete diffusion time-dependence is in general non-analytical, the tumor microstructure was modeled in an appropriate time/frequency regime by impermeable spheres (radius Rcell, intracellular diffusivity Dics) surrounded by extracellular space (approximated by constant apparent diffusivity Decs in volume fraction ECS). POMACE parametric maps (ECS, Rcell, Dics, Decs) were compared with conventional diffusion weighted imaging metrics, electron microscopy (EM), alternative ECS determination based on effective medium theory (EMT), and optical microscopy performed on the same samples. It was shown that Decs can be approximated by its long-time tortuosity limit in the range [1/(88 Hz) - 31 ms]. ECS estimations (44±7% in vivo and 54±11% ex vivo) were in agreement with EMT-based ECS and literature on brain gliomas. Ex vivo, ECS maps correlated well with optical microscopy. Cell sizes (Rcell=4.8±1.3 in vivo and 4.3±1.4 μm ex vivo) were consistent with EM measurements (4.7±1.8 μm). In conclusion, Rcell and ECS can be quantified and mapped in vivo and ex vivo in brain tumors using the proposed POMACE method. Our experimental results support that POMACE provides a way to interpret the frequency- or time-dependence of the diffusion coefficient in tumors in terms of objective biophysical parameters of neuronal tissue, which can be used for non-invasive monitoring of preclinical cancer studies and treatment efficacy. PMID:27448059

Imaging electronic motions by ultrafast electron diffraction

NASA Astrophysics Data System (ADS)

Shao, Hua-Chieh; Starace, Anthony F.

2017-08-01

Recently ultrafast electron diffraction and microscopy have reached unprecedented temporal resolution, and transient structures with atomic precision have been observed in various reactions. It is anticipated that these extraordinary advances will soon allow direct observation of electronic motions during chemical reactions. We therefore performed a series of theoretical investigations and simulations to investigate the imaging of electronic motions in atoms and molecules by ultrafast electron diffraction. Three prototypical electronic motions were considered for hydrogen atoms. For the case of a breathing mode, the electron density expands and contracts periodically, and we show that the time-resolved scattering intensities reflect such changes of the charge radius. For the case of a wiggling mode, the electron oscillates from one side of the nucleus to the other, and we show that the diffraction images exhibit asymmetric angular distributions. The last case is a hybrid mode that involves both breathing and wiggling motions. Owing to the demonstrated ability of ultrafast electrons to image these motions, we have proposed to image a coherent population transfer in lithium atoms using currently available femtosecond electron pulses. A frequency-swept laser pulse adiabatically drives the valence electron of a lithium atom from the 2s to 2p orbitals, and a time-delayed electron pulse maps such motion. Our simulations show that the diffraction images reflect this motion both in the scattering intensities and the angular distributions.

Correlative scanning-transmission electron microscopy reveals that a chimeric flavivirus is released as individual particles in secretory vesicles.

PubMed

Burlaud-Gaillard, Julien; Sellin, Caroline; Georgeault, Sonia; Uzbekov, Rustem; Lebos, Claude; Guillaume, Jean-Marc; Roingeard, Philippe

2014-01-01

The intracellular morphogenesis of flaviviruses has been well described, but flavivirus release from the host cell remains poorly documented. We took advantage of the optimized production of an attenuated chimeric yellow fever/dengue virus for vaccine purposes to study this phenomenon by microscopic approaches. Scanning electron microscopy (SEM) showed the release of numerous viral particles at the cell surface through a short-lived process. For transmission electron microscopy (TEM) studies of the intracellular ultrastructure of the small number of cells releasing viral particles at a given time, we developed a new correlative microscopy method: CSEMTEM (for correlative scanning electron microscopy - transmission electron microscopy). CSEMTEM analysis suggested that chimeric flavivirus particles were released as individual particles, in small exocytosis vesicles, via a regulated secretory pathway. Our morphological findings provide new insight into interactions between flaviviruses and cells and demonstrate that CSEMTEM is a useful new method, complementary to SEM observations of biological events by intracellular TEM investigations.

Correlative Scanning-Transmission Electron Microscopy Reveals that a Chimeric Flavivirus Is Released as Individual Particles in Secretory Vesicles

PubMed Central

Burlaud-Gaillard, Julien; Sellin, Caroline; Georgeault, Sonia; Uzbekov, Rustem; Lebos, Claude; Guillaume, Jean-Marc; Roingeard, Philippe

2014-01-01

The intracellular morphogenesis of flaviviruses has been well described, but flavivirus release from the host cell remains poorly documented. We took advantage of the optimized production of an attenuated chimeric yellow fever/dengue virus for vaccine purposes to study this phenomenon by microscopic approaches. Scanning electron microscopy (SEM) showed the release of numerous viral particles at the cell surface through a short-lived process. For transmission electron microscopy (TEM) studies of the intracellular ultrastructure of the small number of cells releasing viral particles at a given time, we developed a new correlative microscopy method: CSEMTEM (for correlative scanning electron microscopy - transmission electron microscopy). CSEMTEM analysis suggested that chimeric flavivirus particles were released as individual particles, in small exocytosis vesicles, via a regulated secretory pathway. Our morphological findings provide new insight into interactions between flaviviruses and cells and demonstrate that CSEMTEM is a useful new method, complementary to SEM observations of biological events by intracellular TEM investigations. PMID:24681578

Writing silica structures in liquid with scanning transmission electron microscopy.

PubMed

van de Put, Marcel W P; Carcouët, Camille C M C; Bomans, Paul H H; Friedrich, Heiner; de Jonge, Niels; Sommerdijk, Nico A J M

2015-02-04

Silica nanoparticles are imaged in solution with scanning transmission electron microscopy (STEM) using a liquid cell with silicon nitride (SiN) membrane windows. The STEM images reveal that silica structures are deposited in well-defined patches on the upper SiN membranes upon electron beam irradiation. The thickness of the deposits is linear with the applied electron dose. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) demonstrate that the deposited patches are a result of the merging of the original 20 nm-diameter nanoparticles, and that the related surface roughness depends on the electron dose rate used. Using this approach, sub-micrometer scale structures are written on the SiN in liquid by controlling the electron exposure as function of the lateral position. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.