Thon rings from amorphous ice and implications of beam-induced Brownian motion in single particle electron cryo-microscopy

Energy Technology Data Exchange (ETDEWEB)

McMullan, G., E-mail: gm2@mrc-lmb.cam.ac.uk; Vinothkumar, K.R.; Henderson, R.

2015-11-15

We have recorded dose-fractionated electron cryo-microscope images of thin films of pure flash-frozen amorphous ice and pre-irradiated amorphous carbon on a Falcon II direct electron detector using 300 keV electrons. We observe Thon rings [1] in both the power spectrum of the summed frames and the sum of power spectra from the individual frames. The Thon rings from amorphous carbon images are always more visible in the power spectrum of the summed frames whereas those of amorphous ice are more visible in the sum of power spectra from the individual frames. This difference indicates that while pre-irradiated carbon behaves like a solid during the exposure, amorphous ice behaves like a fluid with the individual water molecules undergoing beam-induced motion. Using the measured variation in the power spectra amplitude with number of electrons per image we deduce that water molecules are randomly displaced by a mean squared distance of ∼1.1 Å{sup 2} for every incident 300 keV e{sup −}/Å{sup 2}. The induced motion leads to an optimal exposure with 300 keV electrons of 4.0 e{sup −}/Å{sup 2} per image with which to observe Thon rings centred around the strong 3.7 Å scattering peak from amorphous ice. The beam-induced movement of the water molecules generates pseudo-Brownian motion of embedded macromolecules. The resulting blurring of single particle images contributes an additional term, on top of that from radiation damage, to the minimum achievable B-factor for macromolecular structure determination. - Highlights: • Thon rings can be seen from amorphous ice. • Radiation damage to amorphous ice randomly displaces water molecules. • Each incident 300 keV e{sup −}/Å{sup 2} displaces water molecules on average by ∼1 Å. • Macromolecules embedded in amorphous ice undergo beam induced Brownian motion.

Cryo-electron microscopy and three-dimensional reconstructions of hepatitis C virus particles

International Nuclear Information System (INIS)

Yu Xuekui; Qiao Ming; Atanasov, Ivo; Hu Zongyi; Kato, Takanobu; Liang, T. Jake; Zhou, Z. Hong

2007-01-01

The structural details of hepatitis C virus (HCV) have been elusive because of the lack of a robust tissue culture system for producing an adequate amount of virions from infectious sources for in-depth three-dimensional (3D) structural analysis. Using both negative-stain and cryo-electron microscopy (cryoEM), we show that HCV virions isolated from cell culture have a rather uniform size of 500 A in diameter and that recombinantly expressed HCV-like particles (HCV-LPs) have similar morphologic, biophysical and antigenic features in spite of the varying sizes of the particles. 3D reconstructions were obtained from HCV-LPs with the same size as the HCV virions in the presence and absence of monoclonal antibodies bound to the E1 glycoprotein. The 3D reconstruction of HCV-LP reveals a multilayered architecture, with smooth outer-layer densities arranged in a 'fishbone' configuration. Reconstruction of the particles in complex with anti-E1 antibodies shows that sites of the E1 epitope are exposed and surround the 5-, 3- and 2-fold axes. The binding pattern of the anti-E1 antibody and the fitting of the structure of the dengue virus E glycoprotein into our 3D reconstructions further suggest that the HCV-LP E1 and E2 proteins form a tetramer (or dimer of heterodimers) that corresponds morphologically and functionally to the flavivirus E homodimer. This first 3D structural analysis of HCV particles offers important insights into the elusive mechanisms of HCV assembly and maturation

Correlated cryo-fluorescence and cryo-electron microscopy with high spatial precision and improved sensitivity

International Nuclear Information System (INIS)

Schorb, Martin; Briggs, John A.G.

2014-01-01

Performing fluorescence microscopy and electron microscopy on the same sample allows fluorescent signals to be used to identify and locate features of interest for subsequent imaging by electron microscopy. To carry out such correlative microscopy on vitrified samples appropriate for structural cryo-electron microscopy it is necessary to perform fluorescence microscopy at liquid-nitrogen temperatures. Here we describe an adaptation of a cryo-light microscopy stage to permit use of high-numerical aperture objectives. This allows high-sensitivity and high-resolution fluorescence microscopy of vitrified samples. We describe and apply a correlative cryo-fluorescence and cryo-electron microscopy workflow together with a fiducial bead-based image correlation procedure. This procedure allows us to locate fluorescent bacteriophages in cryo-electron microscopy images with an accuracy on the order of 50 nm, based on their fluorescent signal. It will allow the user to precisely and unambiguously identify and locate objects and events for subsequent high-resolution structural study, based on fluorescent signals. - Highlights: • Workflow for correlated cryo-fluorescence and cryo-electron microscopy. • Cryo-fluorescence microscopy setup incorporating a high numerical aperture objective. • Fluorescent signals located in cryo-electron micrographs with 50 nm spatial precision

Correlated cryo-fluorescence and cryo-electron microscopy with high spatial precision and improved sensitivity

Energy Technology Data Exchange (ETDEWEB)

Schorb, Martin [Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg (Germany); Briggs, John A.G., E-mail: john.briggs@embl.de [Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg (Germany); Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg (Germany)

2014-08-01

Performing fluorescence microscopy and electron microscopy on the same sample allows fluorescent signals to be used to identify and locate features of interest for subsequent imaging by electron microscopy. To carry out such correlative microscopy on vitrified samples appropriate for structural cryo-electron microscopy it is necessary to perform fluorescence microscopy at liquid-nitrogen temperatures. Here we describe an adaptation of a cryo-light microscopy stage to permit use of high-numerical aperture objectives. This allows high-sensitivity and high-resolution fluorescence microscopy of vitrified samples. We describe and apply a correlative cryo-fluorescence and cryo-electron microscopy workflow together with a fiducial bead-based image correlation procedure. This procedure allows us to locate fluorescent bacteriophages in cryo-electron microscopy images with an accuracy on the order of 50 nm, based on their fluorescent signal. It will allow the user to precisely and unambiguously identify and locate objects and events for subsequent high-resolution structural study, based on fluorescent signals. - Highlights: • Workflow for correlated cryo-fluorescence and cryo-electron microscopy. • Cryo-fluorescence microscopy setup incorporating a high numerical aperture objective. • Fluorescent signals located in cryo-electron micrographs with 50 nm spatial precision.

Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm.

Science.gov (United States)

Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

2016-01-01

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.

Component tree analysis of cystovirus φ6 nucleocapsid Cryo-EM single particle reconstructions.

Directory of Open Access Journals (Sweden)

Lucas M Oliveira

Full Text Available The 3-dimensional structure of the nucleocapsid (NC of bacteriophage φ6 is described utilizing component tree analysis, a topological and geometric image descriptor. The component trees are derived from density maps of cryo-electron microscopy single particle reconstructions. Analysis determines position and occupancy of structure elements responsible for RNA packaging and transcription. Occupancy of the hexameric nucleotide triphosphorylase (P4 and RNA polymerase (P2 are found to be essentially complete in the NC. The P8 protein lattice likely fixes P4 and P2 in place during maturation. We propose that the viral procapsid (PC is a dynamic structural intermediate where the P4 and P2 can attach and detach until held in place in mature NCs. During packaging, the PC expands to accommodate the RNA, and P2 translates from its original site near the inner 3-fold axis (20 sites to the inner 5-fold axis (12 sites with excess P2 positioned inside the central region of the NC.

Cryo-electron tomography investigation of serum albumin-camouflaged tobacco mosaic virus nanoparticles.

Science.gov (United States)

Gulati, Neetu M; Pitek, Andrzej S; Steinmetz, Nicole F; Stewart, Phoebe L

2017-03-09

Nanoparticles offer great potential in drug delivery and imaging, but shielding strategies are necessary to increase circulation time and performance. Structure-function studies are required to define the design rules to achieve effective shielding. With several formulations reaching clinical testing and approval, the ability to assess and detail nanoparticle formulations at the single particle level is becoming increasingly important. To address this need, we use cryo-electron tomography (cryo-ET) to investigate stealth-coated nanoparticles. As a model system, we studied the soft matter nanotubes formed by tobacco mosaic virus (TMV) coated with human serum albumin (SA) stealth proteins. Cryo-ET and subtomogram averaging allow for visualization of individual SA molecules and determination of their orientations relative to the TMV surface, and also for measurement of the surface coverage provided by added stealth proteins. This information fills a critical gap in the understanding of the structural morphology of stealth-coated nanoparticles, and therefore cryo-ET may play an important role in guiding the development of future nanoparticle-based therapeutics.

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

Energy Technology Data Exchange (ETDEWEB)

Brown, Alan; Long, Fei; Nicholls, Robert A.; Toots, Jaan; Emsley, Paul; Murshudov, Garib, E-mail: garib@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (United Kingdom)

2015-01-01

A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions. The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

International Nuclear Information System (INIS)

Brown, Alan; Long, Fei; Nicholls, Robert A.; Toots, Jaan; Emsley, Paul; Murshudov, Garib

2015-01-01

A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions. The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC

Cryo-electron microscopy and single molecule fluorescent microscopy detect CD4 receptor induced HIV size expansion prior to cell entry

International Nuclear Information System (INIS)

Pham, Son; Tabarin, Thibault; Garvey, Megan; Pade, Corinna; Rossy, Jérémie; Monaghan, Paul; Hyatt, Alex; Böcking, Till; Leis, Andrew; Gaus, Katharina; Mak, Johnson

2015-01-01

Viruses are often thought to have static structure, and they only remodel after the viruses have entered target cells. Here, we detected a size expansion of virus particles prior to viral entry using cryo-electron microscopy (cryo-EM) and single molecule fluorescence imaging. HIV expanded both under cell-free conditions with soluble receptor CD4 (sCD4) targeting the CD4 binding site on the HIV-1 envelope protein (Env) and when HIV binds to receptor on cellular membrane. We have shown that the HIV Env is needed to facilitate receptor induced virus size expansions, showing that the ‘lynchpin’ for size expansion is highly specific. We demonstrate that the size expansion required maturation of HIV and an internal capsid core with wild type stability, suggesting that different HIV compartments are linked and are involved in remodelling. Our work reveals a previously unknown event in HIV entry, and we propose that this pre-entry priming process enables HIV particles to facilitate the subsequent steps in infection. - Highlights: • Cell free viruses are able to receive external trigger that leads to apparent size expansion. • Virus envelope and CD4 receptor engagement is the lynchpin of virus size expansion. • Internal capsid organisation can influence receptor mediated virus size expansion. • Pre-existing virus-associated lipid membrane in cell free virus can accommodate the receptor mediated virus size expansion.

Cryo-electron microscopy and single molecule fluorescent microscopy detect CD4 receptor induced HIV size expansion prior to cell entry

Energy Technology Data Exchange (ETDEWEB)

Pham, Son [Deakin University, Victoria 3216 (Australia); CSIRO Australian Animal Health Laboratory, Victoria 3220 (Australia); Tabarin, Thibault [ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220 (Australia); Garvey, Megan; Pade, Corinna [Deakin University, Victoria 3216 (Australia); CSIRO Australian Animal Health Laboratory, Victoria 3220 (Australia); Rossy, Jérémie [ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220 (Australia); Monaghan, Paul; Hyatt, Alex [CSIRO Australian Animal Health Laboratory, Victoria 3220 (Australia); Böcking, Till [ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220 (Australia); Leis, Andrew [CSIRO Australian Animal Health Laboratory, Victoria 3220 (Australia); Gaus, Katharina, E-mail: k.gaus@unsw.edu.au [ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220 (Australia); Mak, Johnson, E-mail: j.mak@deakin.edu.au [Deakin University, Victoria 3216 (Australia); CSIRO Australian Animal Health Laboratory, Victoria 3220 (Australia)

2015-12-15

Viruses are often thought to have static structure, and they only remodel after the viruses have entered target cells. Here, we detected a size expansion of virus particles prior to viral entry using cryo-electron microscopy (cryo-EM) and single molecule fluorescence imaging. HIV expanded both under cell-free conditions with soluble receptor CD4 (sCD4) targeting the CD4 binding site on the HIV-1 envelope protein (Env) and when HIV binds to receptor on cellular membrane. We have shown that the HIV Env is needed to facilitate receptor induced virus size expansions, showing that the ‘lynchpin’ for size expansion is highly specific. We demonstrate that the size expansion required maturation of HIV and an internal capsid core with wild type stability, suggesting that different HIV compartments are linked and are involved in remodelling. Our work reveals a previously unknown event in HIV entry, and we propose that this pre-entry priming process enables HIV particles to facilitate the subsequent steps in infection. - Highlights: • Cell free viruses are able to receive external trigger that leads to apparent size expansion. • Virus envelope and CD4 receptor engagement is the lynchpin of virus size expansion. • Internal capsid organisation can influence receptor mediated virus size expansion. • Pre-existing virus-associated lipid membrane in cell free virus can accommodate the receptor mediated virus size expansion.

Cryo-transmission electron microscopy of Ag nanoparticles grown on an ionic liquid substrate

KAUST Repository

Anjum, Dalaver H.

2010-07-01

We report a novel method of growing silver nanostructures by cathodic sputtering onto an ionic liquid (IL) and our visualization by transmission cryo-electron microscopy to avoid beam-induced motion of the nanoparticles. By freezing the IL suspension and controlling electron dose, we can assess properties of particle size, morphology, crystallinity, and aggregation in situ and at high detail. We observed round silver nanoparticles with a well-defined diameter of 7.0 ± 1.5 nm that are faceted with crystalline cubic structures and ∼80% of the particles have multiply twinned faults. We also applied cryo-electron tomography to investigate the structure of the nanoparticles and to directly visualize the IL wetting around them. In addition to particles, we observed nanorods that appear to have assembled from individual nanoparticles. Reexamination of the samples after 4-5 days from initial preparation showed significant changes in morphology, and potential mechanisms for this are discussed. © 2010 Materials Research Society.

Collaborative Computational Project for Electron cryo-Microscopy

Energy Technology Data Exchange (ETDEWEB)

Wood, Chris; Burnley, Tom [Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA (United Kingdom); Patwardhan, Ardan [European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom); Scheres, Sjors [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Topf, Maya [University of London, Malet Street, London WC1E 7HX (United Kingdom); Roseman, Alan [University of Manchester, Oxford Road, Manchester M13 9PT (United Kingdom); Winn, Martyn, E-mail: martyn.winn@stfc.ac.uk [Science and Technology Facilities Council, Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA (United Kingdom)

2015-01-01

The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. Progress in supporting the users and developers of cryoEM software is reported. The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has recently been established. The aims of the project are threefold: to build a coherent cryoEM community which will provide support for individual scientists and will act as a focal point for liaising with other communities, to support practising scientists in their use of cryoEM software and finally to support software developers in producing and disseminating robust and user-friendly programs. The project is closely modelled on CCP4 for macromolecular crystallography, and areas of common interest such as model fitting, underlying software libraries and tools for building program packages are being exploited. Nevertheless, cryoEM includes a number of techniques covering a large range of resolutions and a distinct project is required. In this article, progress so far is reported and future plans are discussed.

Collaborative Computational Project for Electron cryo-Microscopy

International Nuclear Information System (INIS)

Wood, Chris; Burnley, Tom; Patwardhan, Ardan; Scheres, Sjors; Topf, Maya; Roseman, Alan; Winn, Martyn

2015-01-01

The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. Progress in supporting the users and developers of cryoEM software is reported. The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has recently been established. The aims of the project are threefold: to build a coherent cryoEM community which will provide support for individual scientists and will act as a focal point for liaising with other communities, to support practising scientists in their use of cryoEM software and finally to support software developers in producing and disseminating robust and user-friendly programs. The project is closely modelled on CCP4 for macromolecular crystallography, and areas of common interest such as model fitting, underlying software libraries and tools for building program packages are being exploited. Nevertheless, cryoEM includes a number of techniques covering a large range of resolutions and a distinct project is required. In this article, progress so far is reported and future plans are discussed

A national facility for biological cryo-electron microscopy

International Nuclear Information System (INIS)

Saibil, Helen R.; Grünewald, Kay; Stuart, David I.

2015-01-01

This review provides a brief update on the use of cryo-electron microscopy for integrated structural biology, along with an overview of the plans for the UK national facility for electron microscopy being built at the Diamond synchrotron. Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback

Advances in cryo-electron tomography for biology and medicine.

Science.gov (United States)

Koning, Roman I; Koster, Abraham J; Sharp, Thomas H

2018-05-01

Cryo-electron tomography (CET) utilizes a combination of specimen cryo-fixation and multi-angle electron microscopy imaging to produce three-dimensional (3D) volume reconstructions of native-state macromolecular and subcellular biological structures with nanometer-scale resolution. In recent years, cryo-electron microscopy (cryoEM) has experienced a dramatic increase in the attainable resolution of 3D reconstructions, resulting from technical improvements of electron microscopes, improved detector sensitivity, the implementation of phase plates, automated data acquisition schemes, and improved image reconstruction software and hardware. These developments also greatly increased the usability and applicability of CET as a diagnostic and research tool, which is now enabling structural biologists to determine the structure of proteins in their native cellular environment to sub-nanometer resolution. These recent technical developments have stimulated us to update on our previous review (Koning, R.I., Koster, A.J., 2009. Cryo-electron tomography in biology and medicine. Ann Anat 191, 427-445) in which we described the fundamentals of CET. In this follow-up, we extend this basic description in order to explain the aforementioned recent advances, and describe related 3D techniques that can be applied to the anatomy of biological systems that are relevant for medicine. Copyright © 2018 Elsevier GmbH. All rights reserved.

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

International Nuclear Information System (INIS)

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R.; Murshudov, Garib N.; Short, Judith M.; Scheres, Sjors H.W.; Henderson, Richard

2013-01-01

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

Energy Technology Data Exchange (ETDEWEB)

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R.; Murshudov, Garib N.; Short, Judith M.; Scheres, Sjors H.W.; Henderson, Richard, E-mail: rh15@mrc-lmb.cam.ac.uk

2013-12-15

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

Modeling of Image Formation in Cryo-Electron Microscopy

NARCIS (Netherlands)

Vulovic, M.

2013-01-01

Knowledge of the structure of biological specimens is crucial for understanding life. Cryo-electron microscopy (cryo-EM) permits structural studies of biological specimen at their near-native state. The research performed in this thesis represents one of two subprojects of the FOM industrial

Cryo-electron microscopy of membrane proteins.

Science.gov (United States)

Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning

2014-01-01

Electron crystallography is used to study membrane proteins in the form of planar, two-dimensional (2D) crystals, or other crystalline arrays such as tubular crystals. This method has been used to determine the atomic resolution structures of bacteriorhodopsin, tubulin, aquaporins, and several other membrane proteins. In addition, a large number of membrane protein structures were studied at a slightly lower resolution, whereby at least secondary structure motifs could be identified.In order to conserve the structural details of delicate crystalline arrays, cryo-electron microscopy (cryo-EM) allows imaging and/or electron diffraction of membrane proteins in their close-to-native state within a lipid bilayer membrane.To achieve ultimate high-resolution structural information of 2D crystals, meticulous sample preparation for electron crystallography is of outmost importance. Beam-induced specimen drift and lack of specimen flatness can severely affect the attainable resolution of images for tilted samples. Sample preparations that sandwich the 2D crystals between symmetrical carbon films reduce the beam-induced specimen drift, and the flatness of the preparations can be optimized by the choice of the grid material and the preparation protocol.Data collection in the cryo-electron microscope using either the imaging or the electron diffraction mode has to be performed applying low-dose procedures. Spot-scanning further reduces the effects of beam-induced drift. Data collection using automated acquisition schemes, along with improved and user-friendlier data processing software, is increasingly being used and is likely to bring the technique to a wider user base.

Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM)

International Nuclear Information System (INIS)

Duke, Elizabeth M.H.; Razi, Minoo; Weston, Anne; Guttmann, Peter; Werner, Stephan; Henzler, Katja; Schneider, Gerd; Tooze, Sharon A.; Collinson, Lucy M.

2014-01-01

Cryo-soft X-ray tomography (cryo-SXT) is a powerful imaging technique that can extract ultrastructural information from whole, unstained mammalian cells as close to the living state as possible. Subcellular organelles including the nucleus, the Golgi apparatus and mitochondria have been identified by morphology alone, due to the similarity in contrast to transmission electron micrographs. In this study, we used cryo-SXT to image endosomes and autophagosomes, organelles that are particularly susceptible to chemical fixation artefacts during sample preparation for electron microscopy. We used two approaches to identify these compartments. For early and recycling endosomes, which are accessible to externally-loaded markers, we used an anti-transferrin receptor antibody conjugated to 10 nm gold particles. For autophagosomes, which are not accessible to externally-applied markers, we developed a correlative cryo-fluorescence and cryo-SXT workflow (cryo-CLXM) to localise GFP-LC3 and RFP-Atg9. We used a stand-alone cryo-fluorescence stage in the home laboratory to localise the cloned fluorophores, followed by cryo-soft X-ray tomography at the synchrotron to analyse cellular ultrastructure. We mapped the 3D ultrastructure of the endocytic and autophagic structures, and discovered clusters of omegasomes arising from ‘hotspots’ on the ER. Thus, immunogold markers and cryo-CLXM can be used to analyse cellular processes that are inaccessible using other imaging modalities. - Highlights: • We image whole, unstained mammalian cells using cryo-soft X-ray tomography. • Endosomes are identified using a gold marker for the transferrin receptor. • A new workflow for correlative cryo-fluorescence and cryo-SXT is used to locate early autophagosomes. • Interactions between endosomes, endoplasmic reticulum and forming autophagosomes are mapped in 3D. • Multiple omegasomes are shown to form at ‘hotspots’ on the endoplasmic reticulum

Nano, Queensland and cryo-electron microscopy

International Nuclear Information System (INIS)

McDowall, A.W.

2002-01-01

Full text: In a recent review the authors, Wolfgang Baumeister and Alasdair Steven wrote, '....there is immense opportunity for Cryo-EM, especially as boosted by merging crystallographic structures of individual subunits into moderate resolution Cryo-EM density maps of whole complexes. Electron tomography has now advanced to the point where it is a realistic goal to glimpse molecular machines operating inside cells....' This statement gives testament to the advances made over the past 25 years by many labs around the world to the area of microscopy referred to as Cryo-EM and related 3-D computing technologies. Australian scientific societies have been eager followers of this progress and heard first hand of the new developments in the field at the 1984 ACEM-8 (2). Since those early days the ACEM and other Australian/NZ societies have sponsored numerous researchers and workshops in the field of Cryo-EM to their conferences, Helin Sabil, Wah Chiu, Ron Milligan, Richard Henderson and Werner Kuhlbrandt to name only a few. These visits have stimulated a desire from Australian/NZ researchers to establish collaborations and access to prominent labs in the USA and Europe, where the means and knowledge to provide Cryo EM and 3D reconstruction technology for studying macromolecular complexes is well established. However, Australia has not been backward in seeking to provide its home research community with access to a base in biological molecular microscopy and electron crystallography technology. Since the last ACEM we have seen the emergence of a number of crucial factors, which will make the establishment of a national research facility in this field an operational reality in early 2003. Well publicized is the development of Australia's newest and perhaps most unique research institute, the institute for Molecular Bioscience (IMB) to open at the University of Queensland (UQ) in 2002. The IMB will be the platform for a new research group in advanced computational 3D

Robust w-Estimators for Cryo-EM Class Means

Science.gov (United States)

Huang, Chenxi; Tagare, Hemant D.

2016-01-01

A critical step in cryogenic electron microscopy (cryo-EM) image analysis is to calculate the average of all images aligned to a projection direction. This average, called the “class mean”, improves the signal-to-noise ratio in single particle reconstruction (SPR). The averaging step is often compromised because of outlier images of ice, contaminants, and particle fragments. Outlier detection and rejection in the majority of current cryo-EM methods is done using cross-correlation with a manually determined threshold. Empirical assessment shows that the performance of these methods is very sensitive to the threshold. This paper proposes an alternative: a “w-estimator” of the average image, which is robust to outliers and which does not use a threshold. Various properties of the estimator, such as consistency and influence function are investigated. An extension of the estimator to images with different contrast transfer functions (CTFs) is also provided. Experiments with simulated and real cryo-EM images show that the proposed estimator performs quite well in the presence of outliers. PMID:26841397

3D Mapping of the SPRY2 domain of ryanodine receptor 1 by single-particle cryo-EM.

Directory of Open Access Journals (Sweden)

Alex Perálvarez-Marín

Full Text Available The type 1 skeletal muscle ryanodine receptor (RyR1 is principally responsible for Ca(2+ release from the sarcoplasmic reticulum and for the subsequent muscle contraction. The RyR1 contains three SPRY domains. SPRY domains are generally known to mediate protein-protein interactions, however the location of the three SPRY domains in the 3D structure of the RyR1 is not known. Combining immunolabeling and single-particle cryo-electron microscopy we have mapped the SPRY2 domain (S1085-V1208 in the 3D structure of RyR1 using three different antibodies against the SPRY2 domain. Two obstacles for the image processing procedure; limited amount of data and signal dilution introduced by the multiple orientations of the antibody bound in the tetrameric RyR1, were overcome by modifying the 3D reconstruction scheme. This approach enabled us to ascertain that the three antibodies bind to the same region, to obtain a 3D reconstruction of RyR1 with the antibody bound, and to map SPRY2 to the periphery of the cytoplasmic domain of RyR1. We report here the first 3D localization of a SPRY2 domain in any known RyR isoform.

CTF determination and correction in electron cryotomography

International Nuclear Information System (INIS)

Fernandez, J.J.; Li, S.; Crowther, R.A.

2006-01-01

Electron cryotomography (cryoET) has the potential to elucidate the structure of complex biological specimens at molecular resolution but technical and computational improvements are still needed. This work addresses the determination and correction of the contrast transfer function (CTF) of the electron microscope in cryoET. Our approach to CTF detection and defocus determination depends on strip-based periodogram averaging, extended throughout the tilt series to overcome the low contrast conditions found in cryoET. A method for CTF correction that deals with the defocus gradient in images of tilted specimens is also proposed. These approaches to CTF determination and correction have been applied here to several examples of cryoET of pleomorphic specimens and of single particles. CTF correction is essential for improving the resolution, particularly in those studies that combine cryoET with single particle averaging techniques

Quantum ballistic transistor and low noise HEMT for cryo-electronics lower than 4.2 K

International Nuclear Information System (INIS)

Gremion, E.

2008-01-01

Next generations of cryo-detectors, widely used in physics of particles and physics of universe, will need in the future high-performance cryo-electronics less noisy and closer to the detector. Within this context, this work investigates properties of two dimensional electron gas GaAlAs/GaAs by studying two components, quantum point contact (QPC) and high electron mobility transistor (HEMT). Thanks to quantized conductance steps in QPC, we have realized a quantum ballistic transistor (voltage gain higher than 1), a new component useful for cryo-electronics thanks to its operating temperature and weak power consumption (about 1 nW). Moreover, the very low capacity of this component leads to promising performances for multiplexing low temperature bolometer dedicated to millimetric astronomy. The second study focused on HEMT with very high quality 2DEG. At 4.2 K, a voltage gain higher than 20 can be obtained with a very low power dissipation of less than 100 μW. Under the above experimental conditions, an equivalent input voltage noise of 1.2 nV/√(Hz) at 1 kHz and 0.12 nV/√(Hz) at 100 kHz has been reached. According to the Hooge formula, these noise performances are get by increasing gate capacity estimated to 60 pF. (author)

Automated data collection in single particle electron microscopy

Science.gov (United States)

Tan, Yong Zi; Cheng, Anchi; Potter, Clinton S.; Carragher, Bridget

2016-01-01

Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed. PMID:26671944

Coordinate transformation based cryo-correlative methods for electron tomography and focused ion beam milling

International Nuclear Information System (INIS)

Fukuda, Yoshiyuki; Schrod, Nikolas; Schaffer, Miroslava; Feng, Li Rebekah; Baumeister, Wolfgang; Lucic, Vladan

2014-01-01

Correlative microscopy allows imaging of the same feature over multiple length scales, combining light microscopy with high resolution information provided by electron microscopy. We demonstrate two procedures for coordinate transformation based correlative microscopy of vitrified biological samples applicable to different imaging modes. The first procedure aims at navigating cryo-electron tomography to cellular regions identified by fluorescent labels. The second procedure, allowing navigation of focused ion beam milling to fluorescently labeled molecules, is based on the introduction of an intermediate scanning electron microscopy imaging step to overcome the large difference between cryo-light microscopy and focused ion beam imaging modes. These methods make it possible to image fluorescently labeled macromolecular complexes in their natural environments by cryo-electron tomography, while minimizing exposure to the electron beam during the search for features of interest. - Highlights: • Correlative light microscopy and focused ion beam milling of vitrified samples. • Coordinate transformation based cryo-correlative method. • Improved correlative light microscopy and cryo-electron tomography

Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter

Science.gov (United States)

Sindelar, Charles V.; Grigorieff, Nikolaus

2012-01-01

The high noise level found in single-particle electron cryo-microscopy (cryo-EM) image data presents a special challenge for three-dimensional (3D) reconstruction of the imaged molecules. The spectral signal-to-noise ratio (SSNR) and related Fourier shell correlation (FSC) functions are commonly used to assess and mitigate the noise-generated error in the reconstruction. Calculation of the SSNR and FSC usually includes the noise in the solvent region surrounding the particle and therefore does not accurately reflect the signal in the particle density itself. Here we show that the SSNR in a reconstructed 3D particle map is linearly proportional to the fractional volume occupied by the particle. Using this relationship, we devise a novel filter (the “single-particle Wiener filter”) to minimize the error in a reconstructed particle map, if the particle volume is known. Moreover, we show how to approximate this filter even when the volume of the particle is not known, by optimizing the signal within a representative interior region of the particle. We show that the new filter improves on previously proposed error-reduction schemes, including the conventional Wiener filter as well as figure-of-merit weighting, and quantify the relationship between all of these methods by theoretical analysis as well as numeric evaluation of both simulated and experimentally collected data. The single-particle Wiener filter is applicable across a broad range of existing 3D reconstruction techniques, but is particularly well suited to the Fourier inversion method, leading to an efficient and accurate implementation. PMID:22613568

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

Science.gov (United States)

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.

Preservation of high resolution protein structure by cryo-electron microscopy of vitreous sections

International Nuclear Information System (INIS)

Sader, Kasim; Studer, Daniel; Zuber, Benoit; Gnaegi, Helmut; Trinick, John

2009-01-01

We have quantitated the degree of structural preservation in cryo-sections of a vitrified biological specimen. Previous studies have used sections of periodic specimens to assess the resolution present, but preservation before sectioning was not assessed and so the damage due particularly to cutting was not clear. In this study large single crystals of lysozyme were vitrified and from these X-ray diffraction patterns extending to better than 2.1 A were obtained. The crystals were high pressure frozen in 30% dextran, and cryo-sectioned using a diamond knife. In the best case, preservation to a resolution of 7.9 A was shown by electron diffraction, the first observation of sub-nanometre structural preservation in a vitreous section.

Energetic particle induced desorption of water vapor cryo-condensate

International Nuclear Information System (INIS)

Menon, M.M.; Owen, L.W.; Simpkins, J.E.; Uckan, T.; Mioduszewski, P.K.

1990-01-01

An in-vessel cryo-condensation pump is being designed for the Advanced Divertor configuration of the DIII-D tokamak. To assess the importance of possible desorption of water vapor from the cryogenic surfaces of the pump due to impingement of energetic particles from the plasma, a 77 K surface on which a thin layer of water vapor was condensed was exposed to a tenuous plasma (density = 2 x 10 10 cm -3 , electron temperature = 3 eV). Significant desorption of the condensate occurred, suggesting that impingement of energeticparticles (10 eV) at flux levels of ∼10 16 cm 2 s -1 on cryogenic surfaces could potentially induce impurity problems in the tokamak plasma. A pumping configuration is presented in which this problem is minimized without sacrificing the pumping speed

Parainfluenza virus type 5 (PIV-5) morphology revealed by cryo-electron microscopy.

Science.gov (United States)

Terrier, Olivier; Rolland, Jean-Paul; Rosa-Calatrava, Manuel; Lina, Bruno; Thomas, Daniel; Moules, Vincent

2009-06-01

The knowledge of parainfluenza type 5 (PIV-5) virion morphology is essentially based on the observation of negatively stained preparations in conventional transmission electron microscopy (CTEM). In this study, the ultrastructure of frozen-hydrated intact PIV-5 was examined by cryo-electron microscopy (cryo-EM). Cryo-EM revealed a majority of spherical virions (70%), with a lower pleiomorphy than originally observed in CTEM. Phospholipid bilayer thickness, spike length and glycoprotein spikes density were measured. About 2000 glycoprotein spikes were present in an average-sized spherical virion. Altogether, these data depict a more precise view of PIV-5 morphology.

Zernike phase contrast cryo-electron tomography of whole bacterial cells.

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Guerrero-Ferreira, Ricardo C; Wright, Elizabeth R

2014-01-01

Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challenge for high-quality tomograms. We show that Zernike phase-contrast imaging allows the electron dose to be reduced. This limits movement of gold fiducials during the tilt series, which leads to better alignment and a higher-resolution reconstruction. Contrast is also enhanced, improving visibility of weak features. The reduced electron dose also means that more images at more tilt angles could be recorded, further increasing resolution. Copyright © 2013 Elsevier Inc. All rights reserved.

Best practices for managing large CryoEM facilities.

Science.gov (United States)

Alewijnse, Bart; Ashton, Alun W; Chambers, Melissa G; Chen, Songye; Cheng, Anchi; Ebrahim, Mark; Eng, Edward T; Hagen, Wim J H; Koster, Abraham J; López, Claudia S; Lukoyanova, Natalya; Ortega, Joaquin; Renault, Ludovic; Reyntjens, Steve; Rice, William J; Scapin, Giovanna; Schrijver, Raymond; Siebert, Alistair; Stagg, Scott M; Grum-Tokars, Valerie; Wright, Elizabeth R; Wu, Shenping; Yu, Zhiheng; Zhou, Z Hong; Carragher, Bridget; Potter, Clinton S

2017-09-01

This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6-7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Cryo-SEM studies of latex/ceramic nanoparticle coating microstructure development.

Science.gov (United States)

Luo, Hui; Scriven, L E; Francis, Lorraine F

2007-12-15

Cryogenic scanning electron microscopy (cryo-SEM) was used to investigate microstructure development of composite coatings prepared from dispersions of antimony-doped tin oxide (ATO) nanoparticles (approximately 30 nm) or indium tin oxide (ITO) nanoparticles (approximately 40 nm) and latex particles (polydisperse, D(v): approximately 300 nm). Cryo-SEM images of ATO/latex dispersions as-frozen show small clusters of ATO and individual latex particles homogeneously distribute in a frozen water matrix. In contrast, cryo-SEM images of ITO/latex dispersions as-frozen show ITO particles adsorb onto latex particle surfaces. Electrostatic repulsion between negatively charged ATO and negatively charged latex particles stabilizes the ATO/latex dispersion, whereas in ITO/latex dispersion, positively charged ITO particles are attracted onto surfaces of negatively charged latex particles. These results are consistent with calculations of interaction potentials from past research. Cryo-SEM images of frozen and fractured coatings reveal that both ceramic nanoparticles and latex become more concentrated as drying proceeds; larger latex particles consolidate with ceramic nanoparticles in the interstitial spaces. With more drying, compaction flattens the latex-latex particle contacts and shrinks the voids between them. Thus, ceramic nanoparticles are forced to pack closely in the interstitial spaces, forming an interconnected network. Finally, latex particles partially coalesce at their flattened contacts, thereby yielding a coherent coating. The research reveals how nanoparticles segregate and interconnect among latex particles during drying.

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Big data in cryoEM: automated collection, processing and accessibility of EM data.

Science.gov (United States)

Baldwin, Philip R; Tan, Yong Zi; Eng, Edward T; Rice, William J; Noble, Alex J; Negro, Carl J; Cianfrocco, Michael A; Potter, Clinton S; Carragher, Bridget

2018-06-01

The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing. Copyright © 2017 Elsevier Ltd. All rights reserved.

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.

Science.gov (United States)

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R; Murshudov, Garib N; Short, Judith M; Scheres, Sjors H W; Henderson, Richard

2013-12-01

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

National Cryo-Electron Microscopy Facility

Science.gov (United States)

Information about the National Cryo-EM Facility at NCI, created to provide researchers access to the latest cryo-EM technology for high resolution imaging. Includes timeline for installation and how to access the facility.

Direct imaging electron microscopy (EM) methods in modern structural biology: overview and comparison with X-ray crystallography and single-particle cryo-EM reconstruction in the studies of large macromolecules.

Science.gov (United States)

Miyaguchi, Katsuyuki

2014-10-01

Determining the structure of macromolecules is important for understanding their function. The fine structure of large macromolecules is currently studied primarily by X-ray crystallography and single-particle cryo-electron microscopy (EM) reconstruction. Before the development of these techniques, macromolecular structure was often examined by negative-staining, rotary-shadowing and freeze-etching EM, which are categorised here as 'direct imaging EM methods'. In this review, the results are summarised by each of the above techniques and compared with respect to four macromolecules: the ryanodine receptor, cadherin, rhodopsin and the ribosome-translocon complex (RTC). The results of structural analysis of the ryanodine receptor and cadherin are consistent between each technique. The results obtained for rhodopsin vary to some extent within each technique and between the different techniques. Finally, the results for RTC are inconsistent between direct imaging EM and other analytical techniques, especially with respect to the space within RTC, the reasons for which are discussed. Then, the role of direct imaging EM methods in modern structural biology is discussed. Direct imaging methods should support and verify the results obtained by other analytical methods capable of solving three-dimensional molecular architecture, and they should still be used as a primary tool for studying macromolecule structure in vivo. © 2014 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography.

Science.gov (United States)

Bharat, Tanmay A M; Noda, Takeshi; Riches, James D; Kraehling, Verena; Kolesnikova, Larissa; Becker, Stephan; Kawaoka, Yoshihiro; Briggs, John A G

2012-03-13

Ebola virus is a highly pathogenic filovirus causing severe hemorrhagic fever with high mortality rates. It assembles heterogenous, filamentous, enveloped virus particles containing a negative-sense, single-stranded RNA genome packaged within a helical nucleocapsid (NC). We have used cryo-electron microscopy and tomography to visualize Ebola virus particles, as well as Ebola virus-like particles, in three dimensions in a near-native state. The NC within the virion forms a left-handed helix with an inner nucleoprotein layer decorated with protruding arms composed of VP24 and VP35. A comparison with the closely related Marburg virus shows that the N-terminal region of nucleoprotein defines the inner diameter of the Ebola virus NC, whereas the RNA genome defines its length. Binding of the nucleoprotein to RNA can assemble a loosely coiled NC-like structure; the loose coil can be condensed by binding of the viral matrix protein VP40 to the C terminus of the nucleoprotein, and rigidified by binding of VP24 and VP35 to alternate copies of the nucleoprotein. Four proteins (NP, VP24, VP35, and VP40) are necessary and sufficient to mediate assembly of an NC with structure, symmetry, variability, and flexibility indistinguishable from that in Ebola virus particles released from infected cells. Together these data provide a structural and architectural description of Ebola virus and define the roles of viral proteins in its structure and assembly.

Spatial and temporal resolution in cryo-electron microscopy : a scope for nano-chemistry

NARCIS (Netherlands)

Frederik, P.M.; Sommerdijk, N.A.J.M.

2005-01-01

Cryo-electron microscopy has evolved in an established approach to study the structure of bio-colloids. Recent developments in instrumentation and automation, often demanded by life sciences, made cryo-EM a general tool in colloid chemistry. Recently improved instrumentation for vitrification has

A cylindrical specimen holder for electron cryo-tomography

International Nuclear Information System (INIS)

Palmer, Colin M.; Löwe, Jan

2014-01-01

The use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. This leads to the “missing wedge” problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. Cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. Such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but never for frozen-hydrated specimens. Here, we demonstrate the use of thin-walled carbon tubes as specimen holders, allowing the preparation of cylindrical frozen-hydrated samples of ribosomes, liposomes and whole bacterial cells. Images acquired from these cylinders have equal quality at all viewing angles, and the accessible tilt range is restricted only by the physical limits of the microscope. Tomographic reconstructions of these specimens demonstrate that the effects of the missing wedge are substantially reduced, and could be completely eliminated if a full tilt range was used. The overall quality of these tomograms is still lower than that obtained by existing methods, but improvements are likely in future. - Highlights: • The missing wedge is a serious problem for electron cryo-tomography. • Cylindrical specimens allow the missing wedge to be eliminated. • Carbon nanopipettes can be used as cylindrical holders for tomography of frozen-hydrated specimens. • Cryo-tomography of cylindrical biological samples demonstrates a reduction of deleterious effects associated with the missing wedge

Spatial Localization of the Ebola Virus Glycoprotein Mucin-Like Domain Determined by Cryo-Electron Tomography

OpenAIRE

Tran, Erin E. H.; Simmons, James A.; Bartesaghi, Alberto; Shoemaker, Charles J.; Nelson, Elizabeth; White, Judith M.; Subramaniam, Sriram

2014-01-01

The Ebola virus glycoprotein mucin-like domain (MLD) is implicated in Ebola virus cell entry and immune evasion. Using cryo-electron tomography of Ebola virus-like particles, we determined a three-dimensional structure for the full-length glycoprotein in a near-native state and compared it to that of a glycoprotein lacking the MLD. Our results, which show that the MLD is located at the apex and the sides of each glycoprotein monomer, provide a structural template for analysis of MLD function.

A simple cryo-holder facilitates specimen observation under a conventional scanning electron microscope.

Science.gov (United States)

Tang, Chih-Yuan; Huang, Rong-Nan; Kuo-Huang, Ling-Long; Kuo, Tai-Chih; Yang, Ya-Yun; Lin, Ching-Yeh; Jane, Wann-Neng; Chen, Shiang-Jiuun

2012-02-01

A pre-cryogenic holder (cryo-holder) facilitating cryo-specimen observation under a conventional scanning electron microscope (SEM) is described. This cryo-holder includes a specimen-holding unit (the stub) and a cryogenic energy-storing unit (a composite of three cylinders assembled with a screw). After cooling, the cryo-holder can continue supplying cryogenic energy to extend the observation time for the specimen in a conventional SEM. Moreover, the cryogenic energy-storing unit could retain appropriate liquid nitrogen that can evaporate to prevent frost deposition on the surface of the specimen. This device is proved feasible for various tissues and cells, and can be applied to the fields of both biology and material science. We have employed this novel cryo-holder for observation of yeast cells, trichome, and epidermal cells in the leaf of Arabidopsis thaliana, compound eyes of insects, red blood cells, filiform papillae on the surface of rat tongue, agar medium, water molecules, penicillium, etc. All results suggested that the newly designed cryo-holder is applicable for cryo-specimen observation under a conventional SEM without cooling system. Most importantly, the design of this cryo-holder is simple and easy to operate and could adapt a conventional SEM to a plain type cryo-SEM affordable for most laboratories. Copyright © 2011 Wiley Periodicals, Inc.

Biological applications of phase-contrast electron microscopy.

Science.gov (United States)

Nagayama, Kuniaki

2014-01-01

Here, I review the principles and applications of phase-contrast electron microscopy using phase plates. First, I develop the principle of phase contrast based on a minimal model of microscopy, introducing a double Fourier-transform process to mathematically formulate the image formation. Next, I explain four phase-contrast (PC) schemes, defocus PC, Zernike PC, Hilbert differential contrast, and schlieren optics, as image-filtering processes in the context of the minimal model, with particular emphases on the Zernike PC and corresponding Zernike phase plates. Finally, I review applications of Zernike PC cryo-electron microscopy to biological systems such as protein molecules, virus particles, and cells, including single-particle analysis to delineate three-dimensional (3D) structures of protein and virus particles and cryo-electron tomography to reconstruct 3D images of complex protein systems and cells.

3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

Science.gov (United States)

Ishikawa, Takashi

2013-01-01

Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex.

Spatial localization of the Ebola virus glycoprotein mucin-like domain determined by cryo-electron tomography.

Science.gov (United States)

Tran, Erin E H; Simmons, James A; Bartesaghi, Alberto; Shoemaker, Charles J; Nelson, Elizabeth; White, Judith M; Subramaniam, Sriram

2014-09-01

The Ebola virus glycoprotein mucin-like domain (MLD) is implicated in Ebola virus cell entry and immune evasion. Using cryo-electron tomography of Ebola virus-like particles, we determined a three-dimensional structure for the full-length glycoprotein in a near-native state and compared it to that of a glycoprotein lacking the MLD. Our results, which show that the MLD is located at the apex and the sides of each glycoprotein monomer, provide a structural template for analysis of MLD function. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Single-particle electron microscopy in the study of membrane protein structure.

Science.gov (United States)

De Zorzi, Rita; Mi, Wei; Liao, Maofu; Walz, Thomas

2016-02-01

Single-particle electron microscopy (EM) provides the great advantage that protein structure can be studied without the need to grow crystals. However, due to technical limitations, this approach played only a minor role in the study of membrane protein structure. This situation has recently changed dramatically with the introduction of direct electron detection device cameras, which allow images of unprecedented quality to be recorded, also making software algorithms, such as three-dimensional classification and structure refinement, much more powerful. The enhanced potential of single-particle EM was impressively demonstrated by delivering the first long-sought atomic model of a member of the biomedically important transient receptor potential channel family. Structures of several more membrane proteins followed in short order. This review recounts the history of single-particle EM in the study of membrane proteins, describes the technical advances that now allow this approach to generate atomic models of membrane proteins and provides a brief overview of some of the membrane protein structures that have been studied by single-particle EM to date. © 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.

Three-dimensional structural analysis of eukaryotic flagella/cilia by electron cryo-tomography

International Nuclear Information System (INIS)

Bui, Khanh Huy; Pigino, Gaia; Ishikawa, Takashi

2011-01-01

Based on the molecular architecture revealed by electron cryo-tomography, the mechanism of the bending motion of eukaryotic flagella/cilia is discussed. Electron cryo-tomography is a potential approach to analyzing the three-dimensional conformation of frozen hydrated biological macromolecules using electron microscopy. Since projections of each individual object illuminated from different orientations are merged, electron tomography is capable of structural analysis of such heterogeneous environments as in vivo or with polymorphism, although radiation damage and the missing wedge are severe problems. Here, recent results on the structure of eukaryotic flagella, which is an ATP-driven bending organelle, from green algae Chlamydomonas are presented. Tomographic analysis reveals asymmetric molecular arrangements, especially that of the dynein motor proteins, in flagella, giving insight into the mechanism of planar asymmetric bending motion. Methodological challenges to obtaining higher-resolution structures from this technique are also discussed

New insights into the structural organization of eukaryotic and prokaryotic cytoskeletons using cryo-electron tomography

International Nuclear Information System (INIS)

Kuerner, Julia; Medalia, Ohad; Linaroudis, Alexandros A.; Baumeister, Wolfgang

2004-01-01

Cryo-electron tomography (cryo-ET) is an emerging imaging technology that combines the potential of three-dimensional (3-D) imaging at molecular resolution (<5 nm) with a close-to-life preservation of the specimen. In conjunction with pattern recognition techniques, it enables us to map the molecular landscape inside cells. The application of cryo-ET to intact cells provides novel insights into the structure and the spatial organization of the cytoskeleton in prokaryotic and eukaryotic cells

Shell structure of natural rubber particles: evidence of chemical stratification by electrokinetics and cryo-TEM.

Science.gov (United States)

Rochette, Christophe N; Crassous, Jérôme J; Drechsler, Markus; Gaboriaud, Fabien; Eloy, Marie; de Gaudemaris, Benoît; Duval, Jérôme F L

2013-11-26

The interfacial structure of natural rubber (NR) colloids is investigated by means of cryogenic transmission electron microscopy (cryo-TEM) and electrokinetics over a broad range of KNO3 electrolyte concentrations (4-300 mM) and pH values (1-8). The asymptotic plateau value reached by NR electrophoretic mobility (μ) in the thin double layer limit supports the presence of a soft (ion- and water-permeable) polyelectrolytic type of layer located at the periphery of the NR particles. This property is confirmed by the analysis of the electron density profile obtained from cryo-TEM that evidences a ∼2-4 nm thick corona surrounding the NR polyisoprene core. The dependence of μ on pH and salt concentration is further marked by a dramatic decrease of the point of zero electrophoretic mobility (PZM) from 3.6 to 0.8 with increasing electrolyte concentration in the range 4-300 mM. Using a recent theory for electrohydrodynamics of soft multilayered particles, this "anomalous" dependence of the PZM on electrolyte concentration is shown to be consistent with a radial organization of anionic and cationic groups across the peripheral NR structure. The NR electrokinetic response in the pH range 1-8 is indeed found to be equivalent to that of particles surrounded by a positively charged ∼3.5 nm thick layer (mean dissociation pK ∼ 4.2) supporting a thin and negatively charged outermost layer (0.6 nm in thickness, pK ∼ 0.7). Altogether, the strong dependence of the PZM on electrolyte concentration suggests that the electrostatic properties of the outer peripheral region of the NR shell are mediated by lipidic residues protruding from a shell containing a significant amount of protein-like charges. This proposed NR shell interfacial structure questions previously reported NR representations according to which the shell consists of either a fully mixed lipid-protein layer, or a layer of phospholipids residing exclusively beneath an outer proteic film.

Atomic Resolution Structures of Human Bufaviruses Determined by Cryo-Electron Microscopy

Directory of Open Access Journals (Sweden)

Maria Ilyas

2018-01-01

Full Text Available Bufavirus strain 1 (BuV1, a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 Å, respectively. The BuVs, 65–73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core β-barrel (βB-βI, α-helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses.

Single Electron Tunneling

International Nuclear Information System (INIS)

Ruggiero, Steven T.

2005-01-01

Financial support for this project has led to advances in the science of single-electron phenomena. Our group reported the first observation of the so-called ''Coulomb Staircase'', which was produced by tunneling into ultra-small metal particles. This work showed well-defined tunneling voltage steps of width e/C and height e/RC, demonstrating tunneling quantized on the single-electron level. This work was published in a now well-cited Physical Review Letter. Single-electron physics is now a major sub-field of condensed-matter physics, and fundamental work in the area continues to be conducted by tunneling in ultra-small metal particles. In addition, there are now single-electron transistors that add a controlling gate to modulate the charge on ultra-small photolithographically defined capacitive elements. Single-electron transistors are now at the heart of at least one experimental quantum-computer element, and single-electron transistor pumps may soon be used to define fundamental quantities such as the farad (capacitance) and the ampere (current). Novel computer technology based on single-electron quantum dots is also being developed. In related work, our group played the leading role in the explanation of experimental results observed during the initial phases of tunneling experiments with the high-temperature superconductors. When so-called ''multiple-gap'' tunneling was reported, the phenomenon was correctly identified by our group as single-electron tunneling in small grains in the material. The main focus throughout this project has been to explore single electron phenomena both in traditional tunneling formats of the type metal/insulator/particles/insulator/metal and using scanning tunneling microscopy to probe few-particle systems. This has been done under varying conditions of temperature, applied magnetic field, and with different materials systems. These have included metals, semi-metals, and superconductors. Amongst a number of results, we have

Fine structure of granal thylakoid membrane organization using cryo electron tomography

NARCIS (Netherlands)

Kouril, Roman; Oostergetel, Gert T.; Boekema, Egbert J.

The architecture of grana membranes from spinach chloroplasts was studied by cryo electron tomography. Tomographic reconstructions of ice-embedded isolated grana stacks enabled to resolve features of photosystem II (PSII) in the native membrane and to assign the absolute orientation of individual

Phasing of the Triatoma virus diffraction data using a cryo-electron microscopy reconstruction

International Nuclear Information System (INIS)

Estrozi, L.F.; Neumann, E.; Squires, G.; Rozas-Dennis, G.; Costabel, M.; Rey, F.A.; Guerin, D.M.A.; Navaza, J.

2008-01-01

The blood-sucking reduviid bug Triatoma infestans, one of the most important vector of American human trypanosomiasis (Chagas disease) is infected by the Triatoma virus (TrV). TrV has been classified as a member of the Cripavirus genus (type cricket paralysis virus) in the Dicistroviridae family. This work presents the three-dimensional cryo-electron microscopy (cryo-EM) reconstruction of the TrV capsid at about 25 A resolution and its use as a template for phasing the available crystallographic data by the molecular replacement method. The main structural differences between the cryo-EM reconstruction of TrV and other two viruses, one from the same family, the cricket paralysis virus (CrPV) and the human rhinovirus 16 from the Picornaviridae family are presented and discussed

Evaluating the pitch bias of CryoSat exploiting stacks of single look ehoes

Science.gov (United States)

Scagliola, Michele; Tagliani, Nicolas; Fornari, Marco; Bouzinac, Catherine; Parrinello, Tommaso

2014-05-01

CryoSat was launched on the 8th April 2010 and it is the first European ice mission dedicated to monitoring precise changes in the thickness of polar ice sheets and floating sea ice over a 3-year period. CryoSat carries an innovative radar altimeter called the Synthetic Aperture Interferometric Altimeter (SIRAL), that transmits pulses at a high pulse repetition frequency thus making the received echoes phase coherent and suitable for azimuth processing. The attitude information of the spacecraft is provided by star trackers, that have an internal accuracy of few arc-seconds. By analysis of the CryoSat products, two different studies [1, 2] verified the existence of a bias between the pitch reported by the star trackers and the actual pitch of CryoSat during its flight. However those studies, that use two different methods to evaluate the actual pitch, provided different values for the pitch bias. This poster is aimed at describing a further method to estimated the pitch with which the satellite is actually flying by analysis of the stacks of the single look echoes that are accumulated for a given location of sea surface during the Level1 processing. In fact, over ocean the power of the single look echoes for a given point is shaped by the along-track antenna pattern. As a consequence, estimating the angular direction of pointing of the antenna from the stack, an estimate of the pitch can be obtained. Finally, the bias evaluated starting from the pitch measured with the proposed method is compared with the pitch bias measured in [1, 2]. [1] Galin,N. and Wingham, D., Estimating Pitch Angle of CryoSat-2 using the Power Distribution of the Synthetic Aperture, presented at SAR Altimetry Expert Group Meeting, Southampton UK, June 25-27, 2013. [2] Smith, W.H.F. and Scharroo, R., Retracking range, SWH, sigma-naught, and attitude in CryoSat conventional ocean data. In proceedings of Ocean Surface Topography Science Team Meeting. San Diego, October 19-21, 2011.

Removal of Vesicle Structures from Transmission Electron Microscope Images

DEFF Research Database (Denmark)

Jensen, Katrine Hommelhoff; Sigworth, Fred; Brandt, Sami Sebastian

2015-01-01

In this paper, we address the problem of imaging membrane proteins for single-particle cryo-electron microscopy reconstruction of the isolated protein structure. More precisely, we propose a method for learning and removing the interfering vesicle signals from the micrograph, prior to reconstruct...

Cryo-imaging of fluorescently labeled single cells in a mouse

Science.gov (United States)

Steyer, Grant J.; Roy, Debashish; Salvado, Olivier; Stone, Meredith E.; Wilson, David L.

2009-02-01

We developed a cryo-imaging system to provide single-cell detection of fluorescently labeled cells in mouse, with particular applicability to stem cells and metastatic cancer. The Case cryoimaging system consists of a fluorescence microscope, robotic imaging positioner, customized cryostat, PC-based control system, and visualization/analysis software. The system alternates between sectioning (10-40 μm) and imaging, collecting color brightfield and fluorescent blockface image volumes >60GB. In mouse experiments, we imaged quantum-dot labeled stem cells, GFP-labeled cancer and stem cells, and cell-size fluorescent microspheres. To remove subsurface fluorescence, we used a simplified model of light-tissue interaction whereby the next image was scaled, blurred, and subtracted from the current image. We estimated scaling and blurring parameters by minimizing entropy of subtracted images. Tissue specific attenuation parameters were found [uT : heart (267 +/- 47.6 μm), liver (218 +/- 27.1 μm), brain (161 +/- 27.4 μm)] to be within the range of estimates in the literature. "Next image" processing removed subsurface fluorescence equally well across multiple tissues (brain, kidney, liver, adipose tissue, etc.), and analysis of 200 microsphere images in the brain gave 97+/-2% reduction of subsurface fluorescence. Fluorescent signals were determined to arise from single cells based upon geometric and integrated intensity measurements. Next image processing greatly improved axial resolution, enabled high quality 3D volume renderings, and improved enumeration of single cells with connected component analysis by up to 24%. Analysis of image volumes identified metastatic cancer sites, found homing of stem cells to injury sites, and showed microsphere distribution correlated with blood flow patterns. We developed and evaluated cryo-imaging to provide single-cell detection of fluorescently labeled cells in mouse. Our cryo-imaging system provides extreme (>60GB), micron

Cryo-transmission electron tomography of native casein micelles from bovine milk

Science.gov (United States)

Trejo, R.; Dokland, T.; Jurat-Fuentes, J.; Harte, F.

2013-01-01

Caseins are the principal protein components in milk and an important ingredient in the food industry. In liquid milk, caseins are found as micelles of casein proteins and colloidal calcium nanoclusters. Casein micelles were isolated from raw skim milk by size exclusion chromatography and suspended in milk protein-free serum produced by ultrafiltration (molecular weight cut-off of 3 kDa) of raw skim milk. The micelles were imaged by cryo-electron microscopy and subjected to tomographic reconstruction methods to visualize the 3-dimensional and internal organization of native casein micelles. This provided new insights into the internal architecture of the casein micelle that had not been apparent from prior cryo-transmission electron microscopy studies. This analysis demonstrated the presence of water-filled cavities (~20 to 30 nm in diameter), channels (diameter greater than ~5 nm), and several hundred high-density nanoclusters (6 to 12 nm in diameter) within the interior of the micelles. No spherical protein submicellar structures were observed. PMID:22118067

Development of superconducting cryo-electron microscope and its applications

International Nuclear Information System (INIS)

Iwatsuki, Masashi

1988-01-01

Recently, a superconducting cryo-electron microscope in which specimens are cooled to the liquid helium temperature (4.2 K) has been developed. The main components and functional features of this new microscope are reported together with application data on polyethylene, poly (4-methyl-1-pentene), valonia cellulose, rock salt, ice crystallites and ceramic superconductor. The resistance to electron radiation damage, of beam-sensitive specimens including polymers has been increased more than ten times. Thus, the microscope has made it possible to take high resolution images and to analyze the crystal-structure of micro-areas. (orig.) [de

Electron correlations in single-electron capture from helium by fast protons and α particles

International Nuclear Information System (INIS)

Mancev, Ivan; Milojevic, Nenad

2010-01-01

Single-electron capture from heliumlike atomic systems by bare projectiles is investigated by means of the four-body boundary-corrected first Born approximation (CB1-4B). The effect of the dynamic electron correlation is explicitly taken into account through the complete perturbation potential. The quantum-mechanical post and prior transition amplitudes for single charge exchange encompassing symmetric and/or asymmetric collisions are derived in terms of two-dimensional real integrals in the case of the prior form and five-dimensional quadratures for the post form. An illustrative computation is performed for single-electron capture from helium by protons and α particles at intermediate and high impact energies. The role of dynamic correlations is examined as a function of increased projectile energy. The validity and utility of the proposed CB1-4B method is critically assessed in comparison with the existing experimental data for total cross sections, and excellent agreement is obtained.

Pleomorphism and Viability of the Lyme Disease Pathogen Borrelia burgdorferi Exposed to Physiological Stress Conditions: A Correlative Cryo-Fluorescence and Cryo-Scanning Electron Microscopy Study

Czech Academy of Sciences Publication Activity Database

Vancová, Marie; Rudenko, Natalia; Vaněček, Jiří; Golovchenko, Maryna; Strnad, Martin; Rego, Ryan O. M.; Tichá, Lucie; Grubhoffer, Libor; Nebesářová, Jana

2017-01-01

Roč. 8, 11 April (2017), č. článku 596. ISSN 1664-302X R&D Projects: GA TA ČR(CZ) TE01020118; GA MŠk(CZ) LM2015062 EU Projects: European Commission(XE) 278976 - ANTIGONE Institutional support: RVO:60077344 Keywords : cryo-fluorescence * cryo-scanning electron microscopy * Borrelia burgdorferi * Lyme disease * round body * pleomorphism * viability staining Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: 2.11 Other engineering and technologies Impact factor: 4.076, year: 2016

Cryo-transmission electron microscopy of Ag nanoparticles grown on an ionic liquid substrate

KAUST Repository

Anjum, Dalaver H.; Stiger, Rebecca M.; Finley, James J.; Conway, James F.

2010-01-01

We report a novel method of growing silver nanostructures by cathodic sputtering onto an ionic liquid (IL) and our visualization by transmission cryo-electron microscopy to avoid beam-induced motion of the nanoparticles. By freezing the IL

Single-particle characterization of 'Asian Dust' certified reference materials using low-Z particle electron probe X-ray microanalysis

International Nuclear Information System (INIS)

Hwang, Hee Jin; Ro, Chul-Un

2006-01-01

In order to clearly elucidate whether Asian Dust particles experience chemical modification during long-range transport, it is necessary to characterize soil particles where Asian Dust particles originate. If chemical compositions of source soil particles are well characterized, then chemical compositions of Asian Dust particles collected outside source regions can be compared with those of source soil particles in order to find out the occurrence of chemical modification. Asian Dust particles are chemically and morphologically heterogeneous, and thus the average composition and the average aerodynamic diameter (obtainable by bulk analysis) are not much relevant if the chemical modifications of the particles must be followed. The major elemental composition and abundance of the particle types that are potential subjects of chemical modification can only be obtained using single-particle analysis. A single particle analytical technique, named low-Z particle electron probe X-ray microanalysis (low-Z particle EPMA), was applied to characterize two certified reference materials (CRMs) for Asian Dust particles, which were collected from a loess plateau area and a desert of China. The CRMs were defined by bulk analyses to provide certified concentrations for 13 chemical elements. Using the low-Z particle EPMA technique, the concentrations of major chemical species such as aluminosilicates, SiO 2 , CaCO 3 , and carbonaceous species were obtained. Elemental concentrations obtained by the low-Z particle EPMA are close to the certified values, with considering that the single particle and bulk analyses employ very different approaches. There are still some discrepancies between those concentration values, resulting from analyses of particles with different sizes, different sample amounts analyzed, and uncertainties involved in the single particle analysis

Single particle analysis based on Zernike phase contrast transmission electron microscopy.

Science.gov (United States)

Danev, Radostin; Nagayama, Kuniaki

2008-02-01

We present the first application of Zernike phase-contrast transmission electron microscopy to single-particle 3D reconstruction of a protein, using GroEL chaperonin as the test specimen. We evaluated the performance of the technique by comparing 3D models derived from Zernike phase contrast imaging, with models from conventional underfocus phase contrast imaging. The same resolution, about 12A, was achieved by both imaging methods. The reconstruction based on Zernike phase contrast data required about 30% fewer particles. The advantages and prospects of each technique are discussed.

Heparin binding sites on Ross River virus revealed by electron cryo-microscopy

International Nuclear Information System (INIS)

Zhang Wei; Heil, Marintha; Kuhn, Richard J.; Baker, Timothy S.

2005-01-01

Cell surface glycosaminoglycans play important roles in cell adhesion and viral entry. Laboratory strains of two alphaviruses, Sindbis and Semliki Forest virus, have been shown to utilize heparan sulfate as an attachment receptor, whereas Ross River virus (RRV) does not significantly interact with it. However, a single amino acid substitution at residue 218 in the RRV E2 glycoprotein adapts the virus to heparan sulfate binding and expands the host range of the virus into chicken embryo fibroblasts. Structures of the RRV mutant, E2 N218R, and its complex with heparin were determined through the use of electron cryo-microscopy and image reconstruction methods. Heparin was found to bind at the distal end of the RRV spikes, in a region of the E2 glycoprotein that has been previously implicated in cell-receptor recognition and antibody binding

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

Science.gov (United States)

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.

Quantum ballistic transistor and low noise HEMT for cryo-electronics lower than 4.2 K; Transistor balistique quantique et HEMT bas-bruit pour la cryoelectronique inferieure a 4.2 K

Energy Technology Data Exchange (ETDEWEB)

Gremion, E

2008-01-15

Next generations of cryo-detectors, widely used in physics of particles and physics of universe, will need in the future high-performance cryo-electronics less noisy and closer to the detector. Within this context, this work investigates properties of two dimensional electron gas GaAlAs/GaAs by studying two components, quantum point contact (QPC) and high electron mobility transistor (HEMT). Thanks to quantized conductance steps in QPC, we have realized a quantum ballistic transistor (voltage gain higher than 1), a new component useful for cryo-electronics thanks to its operating temperature and weak power consumption (about 1 nW). Moreover, the very low capacity of this component leads to promising performances for multiplexing low temperature bolometer dedicated to millimetric astronomy. The second study focused on HEMT with very high quality 2DEG. At 4.2 K, a voltage gain higher than 20 can be obtained with a very low power dissipation of less than 100 {mu}W. Under the above experimental conditions, an equivalent input voltage noise of 1.2 nV/{radical}(Hz) at 1 kHz and 0.12 nV/{radical}(Hz) at 100 kHz has been reached. According to the Hooge formula, these noise performances are get by increasing gate capacity estimated to 60 pF. (author)

Never at rest: insights into the conformational dynamics of ion channels from cryo-electron microscopy.

Science.gov (United States)

Lau, Carus; Hunter, Mark J; Stewart, Alastair; Perozo, Eduardo; Vandenberg, Jamie I

2018-04-01

The tightly regulated opening and closure of ion channels underlies the electrical signals that are vital for a wide range of physiological processes. Two decades ago the first atomic level view of ion channel structures led to a detailed understanding of ion selectivity and conduction. In recent years, spectacular developments in the field of cryo-electron microscopy have resulted in cryo-EM superseding crystallography as the technique of choice for determining near-atomic resolution structures of ion channels. Here, we will review the recent developments in cryo-EM and its specific application to the study of ion channel gating. We will highlight the advantages and disadvantages of the current technology and where the field is likely to head in the next few years. © 2018 The Authors. The Journal of Physiology © 2018 The Physiological Society.

Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

Science.gov (United States)

Fromm, S A; Sachse, C

2016-01-01

Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

Design and properties of silicon charged-particle detectors developed at the Institute of Electron Technology (ITE)

Science.gov (United States)

Wegrzecki, Maciej; Bar, Jan; Budzyński, Tadeusz; CieŻ, Michal; Grabiec, Piotr; Kozłowski, Roman; Kulawik, Jan; Panas, Andrzej; Sarnecki, Jerzy; Słysz, Wojciech; Szmigiel, Dariusz; Wegrzecka, Iwona; Wielunski, Marek; Witek, Krzysztof; Yakushev, Alexander; Zaborowski, Michał

2013-07-01

The paper discusses the design of charged-particle detectors commissioned and developed at the Institute of Electron Technology (ITE) in collaboration with foreign partners, used in international research on transactinide elements and to build personal radiation protection devices in Germany. Properties of these detectors and the results obtained using the devices are also presented. The design of the following epiplanar detector structures is discussed: ♢ 64-element chromatographic arrays for the COMPACT (Cryo On-line Multidetector for Physics And Chemistry of Transactinides) detection system used at the GSI Helmholtzzentrum für Schwerionenforschung in Darmstadt (GSI) for research on Hassium, Copernicium and Flerovium, as well as elements 119 and 120, ♢ 2-element flow detectors for the COLD (Cryo On-Line Detector) system used for research on Copernicium and Flerovium at the Joint Institute for Nuclear Research, Dubna, ♢ detectors for a radon exposimeter and sensors for a neutron dosimeter developed at the Institut für Strahlenschutz, Helmholtz Zentrum München. The design of planar detectors - single-sided and double-sided strip detectors for the Focal Plane Detector Box used at GSI for research on Flerovium and elements 119 and 120 is also discussed.

3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography

Science.gov (United States)

Nicastro, Daniela; McIntosh, J. Richard; Baumeister, Wolfgang

2005-01-01

We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

The fabrication and single electron transport of Au nano-particles placed between Nb nanogap electrodes

International Nuclear Information System (INIS)

Nishino, T; Negishi, R; Ishibashi, K; Kawao, M; Nagata, T; Ozawa, H

2010-01-01

We have fabricated Nb nanogap electrodes using a combination of molecular lithography and electron beam lithography. Au nano-particles with anchor molecules were placed in the gap, the width of which could be controlled on a molecular scale (∼2 nm). Three different anchor molecules which connect the Au nano-particles and the electrodes were tested to investigate their contact resistance, and a local gate was fabricated underneath the Au nano-particles. The electrical transport measurements at liquid helium temperatures indicated single electron transistor (SET) characteristics with a charging energy of about ∼ 5 meV, and a clear indication of the effect of superconducting electrodes was not observed, possibly due to the large tunnel resistance.

Cryo-EM structures of the TMEM16A calcium-activated chloride channel.

Science.gov (United States)

Dang, Shangyu; Feng, Shengjie; Tien, Jason; Peters, Christian J; Bulkley, David; Lolicato, Marco; Zhao, Jianhua; Zuberbühler, Kathrin; Ye, Wenlei; Qi, Lijun; Chen, Tingxu; Craik, Charles S; Jan, Yuh Nung; Minor, Daniel L; Cheng, Yifan; Jan, Lily Yeh

2017-12-21

Calcium-activated chloride channels (CaCCs) encoded by TMEM16A control neuronal signalling, smooth muscle contraction, airway and exocrine gland secretion, and rhythmic movements of the gastrointestinal system. To understand how CaCCs mediate and control anion permeation to fulfil these physiological functions, knowledge of the mammalian TMEM16A structure and identification of its pore-lining residues are essential. TMEM16A forms a dimer with two pores. Previous CaCC structural analyses have relied on homology modelling of a homologue (nhTMEM16) from the fungus Nectria haematococca that functions primarily as a lipid scramblase, as well as subnanometre-resolution electron cryo-microscopy. Here we present de novo atomic structures of the transmembrane domains of mouse TMEM16A in nanodiscs and in lauryl maltose neopentyl glycol as determined by single-particle electron cryo-microscopy. These structures reveal the ion permeation pore and represent different functional states. The structure in lauryl maltose neopentyl glycol has one Ca 2+ ion resolved within each monomer with a constricted pore; this is likely to correspond to a closed state, because a CaCC with a single Ca 2+ occupancy requires membrane depolarization in order to open (C.J.P. et al., manuscript submitted). The structure in nanodiscs has two Ca 2+ ions per monomer and its pore is in a closed conformation; this probably reflects channel rundown, which is the gradual loss of channel activity that follows prolonged CaCC activation in 1 mM Ca 2+ . Our mutagenesis and electrophysiological studies, prompted by analyses of the structures, identified ten residues distributed along the pore that interact with permeant anions and affect anion selectivity, as well as seven pore-lining residues that cluster near pore constrictions and regulate channel gating. Together, these results clarify the basis of CaCC anion conduction.

Cdc6-Induced Conformational Changes in ORC Bound to Origin DNA Revealed by Cryo-Electron Microscopy

Energy Technology Data Exchange (ETDEWEB)

Sun J.; Li H.; Kawakami, H.; Zech, J.; Speck, C.; Stillman, B.

2012-03-07

The eukaryotic origin recognition complex (ORC) interacts with and remodels origins of DNA replication prior to initiation in S phase. Here, we report a single-particle cryo-EM-derived structure of the supramolecular assembly comprising Saccharomyces cerevisiae ORC, the replication initiation factor Cdc6, and double-stranded ARS1 origin DNA in the presence of ATP{gamma}S. The six subunits of ORC are arranged as Orc1:Orc4:Orc5:Orc2:Orc3, with Orc6 binding to Orc2. Cdc6 binding changes the conformation of ORC, in particular reorienting the Orc1 N-terminal BAH domain. Segmentation of the 3D map of ORC-Cdc6 on DNA and docking with the crystal structure of the homologous archaeal Orc1/Cdc6 protein suggest an origin DNA binding model in which the DNA tracks along the interior surface of the crescent-like ORC. Thus, ORC bends and wraps the DNA. This model is consistent with the observation that binding of a single Cdc6 extends the ORC footprint on origin DNA from both ends.

Single-particle coherent diffractive imaging with a soft x-ray free electron laser: towards soot aerosol morphology

Science.gov (United States)

Bogan, Michael J.; Starodub, Dmitri; Hampton, Christina Y.; Sierra, Raymond G.

2010-10-01

The first of its kind, the Free electron LASer facility in Hamburg, FLASH, produces soft x-ray pulses with unprecedented properties (10 fs, 6.8-47 nm, 1012 photons per pulse, 20 µm diameter). One of the seminal FLASH experiments is single-pulse coherent x-ray diffractive imaging (CXDI). CXDI utilizes the ultrafast and ultrabright pulses to overcome resolution limitations in x-ray microscopy imposed by x-ray-induced damage to the sample by 'diffracting before destroying' the sample on sub-picosecond timescales. For many lensless imaging algorithms used for CXDI it is convenient when the data satisfy an oversampling constraint that requires the sample to be an isolated object, i.e. an individual 'free-standing' portion of disordered matter delivered to the centre of the x-ray focus. By definition, this type of matter is an aerosol. This paper will describe the role of aerosol science methodologies used for the validation of the 'diffract before destroy' hypothesis and the execution of the first single-particle CXDI experiments being developed for biological imaging. FLASH CXDI now enables the highest resolution imaging of single micron-sized or smaller airborne particulate matter to date while preserving the native substrate-free state of the aerosol. Electron microscopy offers higher resolution for single-particle analysis but the aerosol must be captured on a substrate, potentially modifying the particle morphology. Thus, FLASH is poised to contribute significant advancements in our knowledge of aerosol morphology and dynamics. As an example, we simulate CXDI of combustion particle (soot) morphology and introduce the concept of extracting radius of gyration of fractal aggregates from single-pulse x-ray diffraction data. Future upgrades to FLASH will enable higher spatially and temporally resolved single-particle aerosol dynamics studies, filling a critical technological need in aerosol science and nanotechnology. Many of the methodologies described for FLASH will

Single-particle coherent diffractive imaging with a soft x-ray free electron laser: towards soot aerosol morphology

International Nuclear Information System (INIS)

Bogan, Michael J; Starodub, Dmitri; Hampton, Christina Y; Sierra, Raymond G

2010-01-01

The first of its kind, the Free electron LASer facility in Hamburg, FLASH, produces soft x-ray pulses with unprecedented properties (10 fs, 6.8-47 nm, 10 12 photons per pulse, 20 μm diameter). One of the seminal FLASH experiments is single-pulse coherent x-ray diffractive imaging (CXDI). CXDI utilizes the ultrafast and ultrabright pulses to overcome resolution limitations in x-ray microscopy imposed by x-ray-induced damage to the sample by 'diffracting before destroying' the sample on sub-picosecond timescales. For many lensless imaging algorithms used for CXDI it is convenient when the data satisfy an oversampling constraint that requires the sample to be an isolated object, i.e. an individual 'free-standing' portion of disordered matter delivered to the centre of the x-ray focus. By definition, this type of matter is an aerosol. This paper will describe the role of aerosol science methodologies used for the validation of the 'diffract before destroy' hypothesis and the execution of the first single-particle CXDI experiments being developed for biological imaging. FLASH CXDI now enables the highest resolution imaging of single micron-sized or smaller airborne particulate matter to date while preserving the native substrate-free state of the aerosol. Electron microscopy offers higher resolution for single-particle analysis but the aerosol must be captured on a substrate, potentially modifying the particle morphology. Thus, FLASH is poised to contribute significant advancements in our knowledge of aerosol morphology and dynamics. As an example, we simulate CXDI of combustion particle (soot) morphology and introduce the concept of extracting radius of gyration of fractal aggregates from single-pulse x-ray diffraction data. Future upgrades to FLASH will enable higher spatially and temporally resolved single-particle aerosol dynamics studies, filling a critical technological need in aerosol science and nanotechnology. Many of the methodologies described for FLASH will

CryoEM at IUCrJ: a new era

Directory of Open Access Journals (Sweden)

Sriram Subramaniam

2016-01-01

Full Text Available In this overview, we briefly outline recent advances in electron cryomicroscopy (cryoEM and explain why the journal IUCrJ, published by the International Union of Crystallography, could provide a natural home for publications covering many present and future developments in the cryoEM field.

Single-particle characterization of urban aerosol particles collected in three Korean cites using low-Z electron probe X-ray microanalysis.

Science.gov (United States)

Ro, Chul-Un; Kim, HyeKyeong; Oh, Keun-Young; Yea, Sun Kyung; Lee, Chong Bum; Jang, Meongdo; Van Grieken, René

2002-11-15

A recently developed single-particle analytical technique, called low-Z electron probe X-ray microanalysis (low-Z EPMA), was applied to characterize urban aerosol particles collected in three cities of Korea (Seoul, CheongJu, and ChunCheon) on single days in the winter of 1999. In this study, it is clearly demonstrated that the low-Z EPMA technique can provide detailed and quantitative information on the chemical composition of particles in the urban atmosphere. The collected aerosol particles were analyzed and classified on the basis of their chemical species. Various types of particles were identified, such as soil-derived, carbonaceous, marine-originated, and anthropogenic particles. In the sample collected in Seoul, carbonaceous, aluminosilicates, silicon dioxide, and calcium carbonate aerosol particles were abundantly encountered. In the CheongJu and ChunCheon samples, carbonaceous, aluminosilicates, reacted sea salts, and ammonium sulfate aerosol particles were often seen. However, in the CheongJu sample, ammonium sulfate particles were the most abundant in the fine fraction. Also, calcium sulfate and nitrate particles were significantly observed. In the ChunCheon sample, organic particles were the most abundant in the fine fraction. Also, sodium nitrate particles were seen at high levels. The ChunCheon sample seemed to be strongly influenced by sea-salt aerosols originating from the Yellow Sea, which is located about 115 km away from the city.

Commissioning result of the KSTAR in-vessel cryo-pump

Energy Technology Data Exchange (ETDEWEB)

Chang, Y. B.; Lee, H. J.; Park, Y.M. [National Fusion Research Institute, Daejeon (Korea, Republic of); and others

2013-12-15

KSTAR in-vessel cryo-pump has been installed in the vacuum vessel top and bottom side with up-down symmetry for the better plasma density control in the D-shape H-mode. The cryogenic helium lines of the in-vessel cryo-pump are located at the vertical positions from the vacuum vessel torus center 2,000 mm. The inductive electrical potential has been optimized to reduce risk of electrical breakdown during plasma disruption. In-vessel cryo-pump consists of three parts of coaxial circular shape components; cryo-panel, thermal shield and particle shield. The cryo-panel is cooled down to below 4.5 K. The cryo-panel and thermal shields were made by Inconel 625 tube for higher mechanical strength. The thermal shields and their cooling tubes were annealed in air environment to improve the thermal radiation emissivity on the surface. Surface of cryo-panel was electro-polished to minimize the thermal radiation heat load. The in-vessel cryo-pump was pre-assembled on a test bed in 180 degree segment base. The leak test was carried out after the thermal shock between room temperature to LN2 one before installing them into vacuum vessel. Two segments were welded together in the vacuum vessel and final leak test was performed after the thermal shock. Commissioning of the in-vessel cryo-pump was carried out using a temporary liquid helium supply system.

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

Science.gov (United States)

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.

Electron cryo-tomographic structure of cystovirus phi 12.

Science.gov (United States)

Hu, Guo-Bin; Wei, Hui; Rice, William J; Stokes, David L; Gottlieb, Paul

2008-03-01

Bacteriophage phi 12 is a member of the Cystoviridae virus family and contains a genome consisting of three segments of double-stranded RNA (dsRNA). This virus family contains eight identified members, of which four have been classified in regard to their complete genomic sequence and encoded viral proteins. A phospholipid envelope that contains the integral proteins P6, P9, P10, and P13 surrounds the viral particles. In species phi 6, host infection requires binding of a multimeric P3 complex to type IV pili. In species varphi8, phi 12, and phi 13, the attachment apparatus is a heteromeric protein assembly that utilizes the rough lipopolysaccharide (rlps) as a receptor. In phi 8 the protein components are designated P3a and P3b while in species phi 12 proteins P3a and P3c have been identified in the complex. The phospholipid envelope of the cystoviruses surrounds a nucleocapsid (NC) composed of two shells. The outer shell is composed of protein P8 with a T=13 icosahedral lattice while the primary component of the inner shell is a dodecahedral frame composed of dimeric protein P1. For the current study, the 3D architecture of the intact phi 12 virus was obtained by electron cryo-tomography. The nucleocapsid appears to be centered within the membrane envelope and possibly attached to it by bridging structures. Two types of densities were observed protruding from the membrane envelope. The densities of the first type were elongated, running parallel, and closely associated to the envelope outer surface. In contrast, the second density was positioned about 12 nm above the envelope connected to it by a flexible low-density stem. This second structure formed a torroidal structure termed "the donut" and appears to inhibit BHT-induced viral envelope fusion.

Electron cryo-tomographic structure of cystovirus φ12

International Nuclear Information System (INIS)

Hu Guobin; Wei Hui; Rice, William J.; Stokes, David L.; Gottlieb, Paul

2008-01-01

Bacteriophage φ12 is a member of the Cystoviridae virus family and contains a genome consisting of three segments of double-stranded RNA (dsRNA). This virus family contains eight identified members, of which four have been classified in regard to their complete genomic sequence and encoded viral proteins. A phospholipid envelope that contains the integral proteins P6, P9, P10, and P13 surrounds the viral particles. In species φ6, host infection requires binding of a multimeric P3 complex to type IV pili. In species φ8, φ12, and φ13, the attachment apparatus is a heteromeric protein assembly that utilizes the rough lipopolysaccharide (rlps) as a receptor. In φ8 the protein components are designated P3a and P3b while in species φ12 proteins P3a and P3c have been identified in the complex. The phospholipid envelope of the cystoviruses surrounds a nucleocapsid (NC) composed of two shells. The outer shell is composed of protein P8 with a T = 13 icosahedral lattice while the primary component of the inner shell is a dodecahedral frame composed of dimeric protein P1. For the current study, the 3D architecture of the intact φ12 virus was obtained by electron cryo-tomography. The nucleocapsid appears to be centered within the membrane envelope and possibly attached to it by bridging structures. Two types of densities were observed protruding from the membrane envelope. The densities of the first type were elongated, running parallel, and closely associated to the envelope outer surface. In contrast, the second density was positioned about 12 nm above the envelope connected to it by a flexible low-density stem. This second structure formed a torroidal structure termed 'the donut' and appears to inhibit BHT-induced viral envelope fusion

Single-electron charging effects

International Nuclear Information System (INIS)

Ruggiero, S.T.

1991-01-01

The status of our project on single-electron tunneling is, again, excellent. As outlined in our original proposal, a key goal for this project has been the development of a scanning tunneling instrument for the purpose of imaging individual particles and tunneling into these particles at high magnetic fields. Further progress is discussed in this report

The 2017 Nobel Prize in Chemistry: cryo-EM comes of age.

Science.gov (United States)

Shen, Peter S

2018-03-01

The 2017 Nobel Prize in Chemistry was awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson for "developing cryo-electron microscopy (cryo-EM) for the high-resolution structure determination of biomolecules in solution." This feature article summarizes some of the major achievements leading to the development of cryo-EM and recent technological breakthroughs that have transformed the method into a mainstream tool for structure determination.

Characterization of intact subcellular bodies in whole bacteria by cryo-electron tomography and spectroscopic imaging.

Science.gov (United States)

Comolli, L R; Kundmann, M; Downing, K H

2006-07-01

We illustrate the combined use of cryo-electron tomography and spectroscopic difference imaging in the study of subcellular structure and subcellular bodies in whole bacteria. We limited our goal and focus to bodies with a distinct elemental composition that was in a sufficiently high concentration to provide the necessary signal-to-noise level at the relatively large sample thicknesses of the intact cell. This combination proved very powerful, as demonstrated by the identification of a phosphorus-rich body in Caulobacter crescentus. We also confirmed the presence of a body rich in carbon, demonstrated that these two types of bodies are readily recognized and distinguished from each other, and provided, for the first time to our knowledge, structural information about them in their intact state. In addition, we also showed the presence of a similar type of phosphorus-rich body in Deinococcus grandis, a member of a completely unrelated bacteria genus. Cryo-electron microscopy and tomography allowed the study of the biogenesis and morphology of these bodies at resolutions better than 10 nm, whereas spectroscopic difference imaging provided a direct identification of their chemical composition.

The enterovirus 71 A-particle forms a gateway to allow genome release: a cryoEM study of picornavirus uncoating.

Directory of Open Access Journals (Sweden)

Kristin L Shingler

2013-03-01

Full Text Available Since its discovery in 1969, enterovirus 71 (EV71 has emerged as a serious worldwide health threat. This human pathogen of the picornavirus family causes hand, foot, and mouth disease, and also has the capacity to invade the central nervous system to cause severe disease and death. Upon binding to a host receptor on the cell surface, the virus begins a two-step uncoating process, first forming an expanded, altered "A-particle", which is primed for genome release. In a second step after endocytosis, an unknown trigger leads to RNA expulsion, generating an intact, empty capsid. Cryo-electron microscopy reconstructions of these two capsid states provide insight into the mechanics of genome release. The EV71 A-particle capsid interacts with the genome near the icosahedral two-fold axis of symmetry, which opens to the external environment via a channel ∼10 Å in diameter that is lined with patches of negatively charged residues. After the EV71 genome has been released, the two-fold channel shrinks, though the overall capsid dimensions are conserved. These structural characteristics identify the two-fold channel as the site where a gateway forms and regulates the process of genome release.

A national facility for biological cryo-electron microscopy.

Science.gov (United States)

Saibil, Helen R; Grünewald, Kay; Stuart, David I

2015-01-01

Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback.

Recent advances in cryo-TEM imaging of soft lipid nanoparticles

DEFF Research Database (Denmark)

Helvig, Shen Yu; Mat Azmi, Intan Diana Binti; Moghimi, Seyed Moien

2015-01-01

Cryo-transmission electron microscopy (Cryo-TEM), and its technological variations thereof, have become a powerful tool for detailed morphological characterization and 3D tomography of soft lipid and polymeric nanoparticles as well as biological materials such as viruses and DNA without chemical...... fixation. Here, we review and discuss recent advances in Cryo-TEM analysis of lipid-based drug nanocarriers with particular emphasis on morphological and internal nanostructure characterization of lyotropic liquid crystalline nanoparticles such as cubosomes and hexosomes....

Classification using diffraction patterns for single-particle analysis

International Nuclear Information System (INIS)

Hu, Hongli; Zhang, Kaiming; Meng, Xing

2016-01-01

An alternative method has been assessed; diffraction patterns derived from the single particle data set were used to perform the first round of classification in creating the initial averages for proteins data with symmetrical morphology. The test protein set was a collection of Caenorhabditis elegans small heat shock protein 17 obtained by Cryo EM, which has a tetrahedral (12-fold) symmetry. It is demonstrated that the initial classification on diffraction patterns is workable as well as the real-space classification that is based on the phase contrast. The test results show that the information from diffraction patterns has the enough details to make the initial model faithful. The potential advantage using the alternative method is twofold, the ability to handle the sets with poor signal/noise or/and that break the symmetry properties. - Highlights: • New classification method. • Create the accurate initial model. • Better in handling noisy data.

Classification using diffraction patterns for single-particle analysis

Energy Technology Data Exchange (ETDEWEB)

Hu, Hongli; Zhang, Kaiming [Department of Biophysics, the Health Science Centre, Peking University, Beijing 100191 (China); Meng, Xing, E-mail: xmeng101@gmail.com [Wadsworth Centre, New York State Department of Health, Albany, New York 12201 (United States)

2016-05-15

An alternative method has been assessed; diffraction patterns derived from the single particle data set were used to perform the first round of classification in creating the initial averages for proteins data with symmetrical morphology. The test protein set was a collection of Caenorhabditis elegans small heat shock protein 17 obtained by Cryo EM, which has a tetrahedral (12-fold) symmetry. It is demonstrated that the initial classification on diffraction patterns is workable as well as the real-space classification that is based on the phase contrast. The test results show that the information from diffraction patterns has the enough details to make the initial model faithful. The potential advantage using the alternative method is twofold, the ability to handle the sets with poor signal/noise or/and that break the symmetry properties. - Highlights: • New classification method. • Create the accurate initial model. • Better in handling noisy data.

Zernike Phase Contrast Electron Cryo-Tomography Applied to Marine Cyanobacteria Infected with Cyanophages

Science.gov (United States)

Dai, Wei; Fu, Caroline; Khant, Htet A.; Ludtke, Steven J.; Schmid, Michael F.; Chiu, Wah

2015-01-01

Advances in electron cryo-tomography have provided a new opportunity to visualize the internal 3D structures of a bacterium. An electron microscope equipped with Zernike phase contrast optics produces images with dramatically increased contrast compared to images obtained by conventional electron microscopy. Here we describe a protocol to apply Zernike phase plate technology for acquiring electron tomographic tilt series of cyanophage-infected cyanobacterial cells embedded in ice, without staining or chemical fixation. We detail the procedures for aligning and assessing phase plates for data collection, and methods to obtain 3D structures of cyanophage assembly intermediates in the host, by subtomogram alignment, classification and averaging. Acquiring three to four tomographic tilt series takes approximately 12 h on a JEM2200FS electron microscope. We expect this time requirement to decrease substantially as the technique matures. Time required for annotation and subtomogram averaging varies widely depending on the project goals and data volume. PMID:25321408

Biophysical analysis of HTLV-1 particles reveals novel insights into particle morphology and Gag stochiometry

Directory of Open Access Journals (Sweden)

Fogarty Keir H

2010-09-01

Full Text Available Abstract Background Human T-lymphotropic virus type 1 (HTLV-1 is an important human retrovirus that is a cause of adult T-cell leukemia/lymphoma. While an important human pathogen, the details regarding virus replication cycle, including the nature of HTLV-1 particles, remain largely unknown due to the difficulties in propagating the virus in tissue culture. In this study, we created a codon-optimized HTLV-1 Gag fused to an EYFP reporter as a model system to quantitatively analyze HTLV-1 particles released from producer cells. Results The codon-optimized Gag led to a dramatic and highly robust level of Gag expression as well as virus-like particle (VLP production. The robust level of particle production overcomes previous technical difficulties with authentic particles and allowed for detailed analysis of particle architecture using two novel methodologies. We quantitatively measured the diameter and morphology of HTLV-1 VLPs in their native, hydrated state using cryo-transmission electron microscopy (cryo-TEM. Furthermore, we were able to determine HTLV-1 Gag stoichiometry as well as particle size with the novel biophysical technique of fluorescence fluctuation spectroscopy (FFS. The average HTLV-1 particle diameter determined by cryo-TEM and FFS was 71 ± 20 nm and 75 ± 4 nm, respectively. These values are significantly smaller than previous estimates made of HTLV-1 particles by negative staining TEM. Furthermore, cryo-TEM reveals that the majority of HTLV-1 VLPs lacks an ordered structure of the Gag lattice, suggesting that the HTLV-1 Gag shell is very likely to be organized differently compared to that observed with HIV-1 Gag in immature particles. This conclusion is supported by our observation that the average copy number of HTLV-1 Gag per particle is estimated to be 510 based on FFS, which is significantly lower than that found for HIV-1 immature virions. Conclusions In summary, our studies represent the first quantitative biophysical

Electron microscopy of atmospheric particles

Science.gov (United States)

Huang, Po-Fu

Electron microscopy coupled with energy dispersive spectrometry (EM/EDS) is a powerful tool for single particle analysis. However, the accuracy with which atmospheric particle compositions can be quantitatively determined by EDS is often hampered by substrate-particle interactions, volatilization losses in the low pressure microscope chamber, electron beam irradiation and use of inaccurate quantitation factors. A pseudo-analytical solution was derived to calculate the temperature rise due to the dissipation of the electron energy on a particle-substrate system. Evaporative mass loss for a spherical cap-shaped sulfuric acid particle resting on a thin film supported by a TEM grid during electron beam impingement has been studied. Measured volatilization rates were found to be in very good agreement with theoretical predictions. The method proposed can also be used to estimate the vapor pressure of a species by measuring the decay of X-ray intensities. Several types of substrates were studied. We found that silver-coated silicon monoxide substrates give carbon detection limits comparable to commercially available substrates. An advantage of these substrates is that the high thermal conductivity of the silver reduces heating due to electron beam impingement. In addition, exposure of sulfuric acid samples to ammonia overnight substantially reduces sulfur loss in the electron beam. Use of size-dependent k-factors determined from particles of known compositions shows promise for improving the accuracy of atmospheric particle compositions measured by EM/EDS. Knowledge accumulated during the course of this thesis has been used to analyze atmospheric particles (Minneapolis, MN) selected by the TDMA and collected by an aerodynamic focusing impactor. 'Less' hygroscopic particles, which do not grow to any measurable extent when humidified to ~90% relative humidity, included chain agglomerates, spheres, flakes, and irregular shapes. Carbon was the predominant element detected in

Two-particle approach to the electronic structure of solids

International Nuclear Information System (INIS)

Gonis, A.

2007-01-01

Based on an extension of Hubbard's treatment of the electronic structure of correlated electrons in matter we propose a methodology that incorporates the scattering off the Coulomb interaction through the determination of a two-particle propagator. The Green function equations of motion are then used to obtain single-particle Green functions and related properties such as densities of states. The solutions of the equations of motion in two- and single-particle spaces are accomplished through applications of the coherent potential approximation. The formalism is illustrated by means of calculations for a single-band model system representing a linear arrangement of sites with nearest neighbor hopping and an one-site repulsion when two electrons of opposite spin occupy the same site in the lattice in the manner described by the so-called Hubbard Hamiltonian

Exploring an optimal wavelet-based filter for cryo-ET imaging.

Science.gov (United States)

Huang, Xinrui; Li, Sha; Gao, Song

2018-02-07

Cryo-electron tomography (cryo-ET) is one of the most advanced technologies for the in situ visualization of molecular machines by producing three-dimensional (3D) biological structures. However, cryo-ET imaging has two serious disadvantages-low dose and low image contrast-which result in high-resolution information being obscured by noise and image quality being degraded, and this causes errors in biological interpretation. The purpose of this research is to explore an optimal wavelet denoising technique to reduce noise in cryo-ET images. We perform tests using simulation data and design a filter using the optimum selected wavelet parameters (three-level decomposition, level-1 zeroed out, subband-dependent threshold, a soft-thresholding and spline-based discrete dyadic wavelet transform (DDWT)), which we call a modified wavelet shrinkage filter; this filter is suitable for noisy cryo-ET data. When testing using real cryo-ET experiment data, higher quality images and more accurate measures of a biological structure can be obtained with the modified wavelet shrinkage filter processing compared with conventional processing. Because the proposed method provides an inherent advantage when dealing with cryo-ET images, it can therefore extend the current state-of-the-art technology in assisting all aspects of cryo-ET studies: visualization, reconstruction, structural analysis, and interpretation.

CryoVEx 2011-12 Airborne Campaigns for CryoSat Validation

DEFF Research Database (Denmark)

Skourup, Henriette; Hvidegaard, Sine Munk; Forsberg, René

2013-01-01

After the successful launch of CryoSat-2 in April 2010, the first direct validation campaign of the satellite was carried out in the April-May 2011. Part of this was repeated in Spring 2012. DTU Space has been involved in ESA’s CryoSat Validation Experiment (CryoVEx) with airborne activities since...... 2003. To validate the performance of the CryoSat-2 radar altimeter (SIRAL), the aircraft is equipped with an airborne version of the SIRAL altimeter (ASIRAS) together with a laser scanner. Of particular interest is to study the penetration depth of SIRAL into both land- and sea ice. This can be done...... of Alert and sea ice around Svalbard in the Fram Strait. Selected tracks were planned to match CryoSat-2 passes and a few of them were flown in formation flight with the AlfredWegener Institute (AWI) Polar- 5 carrying an EM induction sounder. The paper presents an overview of the 2011-12 airborne campaigns...

Thermo-mechanical design methodology for ITER cryo-distribution cold boxes

International Nuclear Information System (INIS)

Shukla, Vinit; Patel, Pratik; Vaghela, Hiten; Das, Jotirmoy; Shah, Nitin; Bhattacharya, Ritendra; Sarkar, Biswanath; Chang, Hyun-sik

2015-01-01

The ITER cryo-distribution system is in charge of the proper distribution of the cryogen at required mass flow rate, pressure and temperature level to the users namely; the superconducting magnets and cryopumps. The cryo-distribution also acts as a thermal buffer in order to run the cryo-plant as much as possible at a steady state condition. A typical cryo-distribution cold box is equipped with mainly liquid helium bath with heat exchangers, cryogenic valves, cold circulating pump and cold compressor. During the intended operation life of ITER, several loads on the cryo-distribution system are envisaged, these are, gravity/assembly loads, nominal pressure/temperature, test pressure/temperature, purge pressure, thermo-mechanical loads due to break of insulation vacuum, transport acceleration and seismic loads. Single loads or combinations of them can act on the cryo-distribution system and its components; therefore, it is very important to analyze the behavior of the system and components under the influence of these loads or combinations. Possible load combinations for the cryo-distribution system will be analyzed and will lead to the basis of the design. This paper will focus on the understanding of the nature of the loads and their combinations for the ITER cryo-distribution as well as their impacts on the design. A representative model of a cold box is considered on which the load combinations have been applied in order to understand their impacts on the design of the cryo-distribution. Also the worst-impact loads or their combination which drive the design of cryo-distribution cold boxes will be derived. (author)

X-ray analysis of a single aerosol particle with combination of scanning electron microscope and synchrotron radiation X-ray microscope

International Nuclear Information System (INIS)

Toyoda, Masatoshi; Kaibuchi, Kazuki; Nagasono, Mitsuru; Terada, Yasuko; Tanabe, Teruo; Hayakawa, Shinjiro; Kawai, Jun

2004-01-01

We developed a microscope by a combination of synchrotron radiation X-ray fluorescence (SR-XRF) microscope and scanning electron microscope (SEM) with an energy dispersive X-ray spectrometer (EDX). SR-XRF is appropriate to detect trace and micro amount of elements and sensitive to heavy elements in an analyte but it cannot observe the real time image. SEM-EDX can observe the secondary electron image of a single particle in real time and is appropriate to detect lighter elements. This combination microscope can ensure the identification of the XRF spectrum to the SEM image without transferring the sample. For aerosol analysis, it is important to analyze each particle. The present method makes feasible to analyze not only the average elemental composition as the total particles but also elemental composition of each particle, which is dependent on the particle shape and size. The microscope was applied to an individual aerosol particle study. The X-ray spectra were different among the particles, but also different between SR-XRF and SEM-EDX for the same particle, due to the difference in fluorescence yields between X-ray excitation and electron excitation

Cryo-scanning electron microscopy discloses differences in dehydration of frozen boar semen stored in large containers.

Science.gov (United States)

Ekwall, H

2009-02-01

In general, freezing in flat plastic polyethylene terephthalate (PET) bags (FlatPacks) at 50 degrees C/min gives better post-thaw viability, in terms of sperm motility and membrane integrity, than does freezing in plastic maxi-straws, probably owing to differences in cryobiology. To test the hypothesis that this better survival post-thaw relates to the degree of sperm dehydration during freezing, the present study investigated the structure of boar semen in a frozen state using cryo-scanning electron microscopy (cryo-SEM) to compare two different packages (FlatPacks and maxi-straws) for single artificial insemination (AI) doses, and three different freezing rates. The semen was split-sample frozen in maxi-straws or FlatPacks (both holding 5 ml) using 3% glycerol as cryoprotectant. Three freezing rates were applied from -5 degrees C to -100 degrees C, namely 2 degrees C/min, 50 degrees C/min and 1200 degrees C/min, the lattermost by plunging the samples into liquid nitrogen (LN(2)). The samples were thereafter fractured into LN(2) and larger areas of extra-cellular, unbound frozen water ('ice lakes') were measured to determine the degree of dehydration of the spermatozoa. These areas decreased in size with an increase in cooling rate, the differences in size being more dramatic for maxi-straws than for FlatPacks. Size of ice lakes was also influenced by location within package in relation to cooling rate, the central values being always smaller in maxi-straws than in Flatpacks (p < 0.05 at 2 degrees C/min and 50 degrees C/min) but not at 1200 degrees C/min, which suggested the FlatPack allows for more homogenous freezing of boar semen.

The mechanism of DNA ejection in the Bacillus anthracis spore-binding phage 8a revealed by cryo-electron tomography

Energy Technology Data Exchange (ETDEWEB)

Fu, Xiaofeng [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States); Walter, Michael H. [Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614 (United States); Paredes, Angel [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States); Morais, Marc C., E-mail: mcmorais@utmb.edu [Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555 (United States); Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Liu, Jun, E-mail: Jun.Liu.1@uth.tmc.edu [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States)

2011-12-20

The structure of the Bacillus anthracis spore-binding phage 8a was determined by cryo-electron tomography. The phage capsid forms a T = 16 icosahedron attached to a contractile tail via a head-tail connector protein. The tail consists of a six-start helical sheath surrounding a central tail tube, and a structurally novel baseplate at the distal end of the tail that recognizes and attaches to host cells. The parameters of the icosahedral capsid lattice and the helical tail sheath suggest protein folds for the capsid and tail-sheath proteins, respectively, and indicate evolutionary relationships to other dsDNA viruses. Analysis of 2518 intact phage particles show four distinct conformations that likely correspond to four sequential states of the DNA ejection process during infection. Comparison of the four observed conformations suggests a mechanism for DNA ejection, including the molecular basis underlying coordination of tail sheath contraction and genome release from the capsid.

Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor

Science.gov (United States)

Estrozi, Leandro F.; Boehringer, Daniel; Shan, Shu-ou; Ban, Nenad; Schaffitzel, Christiane

2013-01-01

We report the early conformation of the E. coli signal recognition particle (SRP) and its receptor FtsY bound to the translating ribosome by cryo-electron microscopy. FtsY binds to the tetraloop of the SRP RNA whereas the NG-domains of the SRP protein and FtsY interact weakly in this conformation. Our results suggest that optimal positioning of the SRP RNA tetraloop and the Ffh NG-domain leads to FtsY recruitment. PMID:21151118

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

Science.gov (United States)

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.

Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

Science.gov (United States)

Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

2018-05-01

The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

Investigations in space-related molecular biology. [cryo-electron microscopic and diffraction studies on terrestrial and extraterrestrial specimens

Science.gov (United States)

Fernandez-Moran, H.; Pritzker, A. N.

1974-01-01

Improved instrumentation and preparation techniques for high resolution, high voltage cryo-electron microscopic and diffraction studies on terrestrial and extraterrestrial specimens are reported. Computer correlated ultrastructural and biochemical work on hydrated and dried cell membranes and related biological systems provided information on membrane organization, ice crystal formation and ordered water, RNA virus linked to cancer, lunar rock samples, and organometallic superconducting compounds. Apollo 11, 12, 14, and 15 specimens were analyzed

(CryoTransmission Electron Microscopy of Phospholipid Model Membranes Interacting with Amphiphilic and Polyphilic Molecules

Directory of Open Access Journals (Sweden)

Annette Meister

2017-10-01

Full Text Available Lipid membranes can incorporate amphiphilic or polyphilic molecules leading to specific functionalities and to adaptable properties of the lipid bilayer host. The insertion of guest molecules into membranes frequently induces changes in the shape of the lipid matrix that can be visualized by transmission electron microscopy (TEM techniques. Here, we review the use of stained and vitrified specimens in (cryoTEM to characterize the morphology of amphiphilic and polyphilic molecules upon insertion into phospholipid model membranes. Special emphasis is placed on the impact of novel synthetic amphiphilic and polyphilic bolalipids and polymers on membrane integrity and shape stability.

A comparative analysis of the sea ice freeboard from CryoSat. CryoVEx and IceBridge

DEFF Research Database (Denmark)

Kildegaard Rose, Stine; Connor, Laurence N.; Farrell, Sinead L.

The CryoSat Validation Experiment (CryoVEx) has been conducted by ESA, to examine the uncertainties in the satellite measurement of e.g. sea ice thickness. In this study, we aim to estimate the sea ice freeboard from CryoSat-2, and compare it with the high-resolution Airborne Laser Scanner (ALS......) measurements collected along CryoSat-2 ground tracks from the CryoVEx 2012 campaign, together with NASA’s Operation IceBridge data. We will use the CryoSat SAR data level 1b (L1b) to discriminate the leads and from this, estimate the sea ice freeboard. Furthermore, we are looking at the CryoSat level 2 (L2...

A search for single electron production in electron positron annihilation at E = 29 GeV

International Nuclear Information System (INIS)

Steele, T.R.

1989-09-01

This thesis presents experimental results from the ASP detector which took data on e + e - interactions in the PEP storage ring at SLAC. Its design was particularly suitable for searching for production of supersymmetric particles. The motivations for and phenomenology of Supersymmetry are discussed. In particular, the production of a single supersymmetric electron (''selectron'', e) in combination with a supersymmetric photon (''photino'', γ) would result in events in which a single electron and no other particles are observed in the detector at an e + e - collider such as PEP, provided the masses of these particles are not too large. Such events would also result from the production of a single supersymmetric W-boson (''wino'', W) in combination with a supersymmetric neutrino (''sneutrino'', ν). These processes make it possible to search for electrons and winos with masses greater than the beam energy. Observation of these unusual events would distinctly indicate the production of new particles. The ASP detector was designed to be hermetic and to provide efficient event reconstruction for low multiplicity events. The detector is described and its performance is evaluated; it is found to be well-suited to this study. The data sample collected with the detector was thoroughly analyzed for evidence of single-electron events. The various possible background processes are considered and Monte Carlo calculations of the distributions from single selectron and single wino production are presented. Using this information an efficient off-line event selection process was developed, and it is described in detail. 82 refs., 41 figs., 4 tabs

Label-free visualization of ultrastructural features of artificial synapses via cryo-EM.

Science.gov (United States)

Gopalakrishnan, Gopakumar; Yam, Patricia T; Madwar, Carolin; Bostina, Mihnea; Rouiller, Isabelle; Colman, David R; Lennox, R Bruce

2011-12-21

The ultrastructural details of presynapses formed between artificial substrates of submicrometer silica beads and hippocampal neurons are visualized via cryo-electron microscopy (cryo-EM). The silica beads are derivatized by poly-d-lysine or lipid bilayers. Molecular features known to exist at presynapses are clearly present at these artificial synapses, as visualized by cryo-EM. Key synaptic features such as the membrane contact area at synaptic junctions, the presynaptic bouton containing presynaptic vesicles, as well as microtubular structures can be identified. This is the first report of the direct, label-free observation of ultrastructural details of artificial synapses.

Single-particle energies and density of states in density functional theory

Science.gov (United States)

van Aggelen, H.; Chan, G. K.-L.

2015-07-01

Time-dependent density functional theory (TD-DFT) is commonly used as the foundation to obtain neutral excited states and transition weights in DFT, but does not allow direct access to density of states and single-particle energies, i.e. ionisation energies and electron affinities. Here we show that by extending TD-DFT to a superfluid formulation, which involves operators that break particle-number symmetry, we can obtain the density of states and single-particle energies from the poles of an appropriate superfluid response function. The standard Kohn- Sham eigenvalues emerge as the adiabatic limit of the superfluid response under the assumption that the exchange- correlation functional has no dependence on the superfluid density. The Kohn- Sham eigenvalues can thus be interpreted as approximations to the ionisation energies and electron affinities. Beyond this approximation, the formalism provides an incentive for creating a new class of density functionals specifically targeted at accurate single-particle eigenvalues and bandgaps.

Inequivalence of single-particle and population lifetimes in a cuprate superconductor

Energy Technology Data Exchange (ETDEWEB)

Yang, Shuolong [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Sobota, J. A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Leuenberger, D. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); He, Y. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Hashimoto, M. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Lu, D. H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Eisaki, H. [National Institute of Advanced Industrial Science and Technology, Ibaraki (Japan); Kirchmann, P. S. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Shen, Z. -X. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States)

2015-06-15

We study optimally doped Bi-2212 (T_c=96 K) using femtosecond time- and angle-resolved photoelectron spectroscopy. Energy-resolved population lifetimes are extracted and compared with single-particle lifetimes measured by equilibrium photoemission. The population lifetimes deviate from the single-particle lifetimes in the low excitation limit by 1–2 orders of magnitude. Fundamental considerations of electron scattering unveil that these two lifetimes are in general distinct, yet for systems with only electron-phonon scattering they should converge in the low-temperature, low-fluence limit. As a result, the qualitative disparity in our data, even in this limit, suggests that scattering channels beyond electron-phonon interactions play a significant role in the electron dynamics of cuprate superconductors.

3D Micro-topography of Transferred Laboratory and Natural Ice Crystal Surfaces Imaged by Cryo and Environmental Scanning Electron Microscopy

Science.gov (United States)

Magee, N. B.; Boaggio, K.; Bancroft, L.; Bandamede, M.

2015-12-01

Recent work has highlighted micro-scale roughness on the surfaces of ice crystals grown and imaged in-situ within the chambers of environmental scanning electron microscopes (ESEM). These observations appear to align with theoretical and satellite observations that suggest a prevalence of rough ice in cirrus clouds. However, the atmospheric application of the lab observations are indeterminate because the observations have been based only on crystals grown on substrates and in pure-water vapor environments. In this work, we present details and results from the development of a transfer technique which allows natural and lab-grown ice and snow crystals to be captured, preserved, and transferred into the ESEM for 3D imaging. Ice crystals were gathered from 1) natural snow, 2) a balloon-borne cirrus particle capture device, and 3) lab-grown ice crystals from a diffusion chamber. Ice crystals were captured in a pre-conditioned small-volume (~1 cm3) cryo-containment cell. The cell was then sealed closed and transferred to a specially-designed cryogenic dewer (filled with liquid nitrogen or crushed dry ice) for transport to a new Hitachi Field Emission, Variable Pressure SEM (SU-5000). The cryo-cell was then removed from the dewer and quickly placed onto the pre-conditioned cryo transfer stage attached to the ESEM (Quorum 3010T). Quantitative 3D topographical digital elevation models of ice surfaces are reported from SEM for the first time, including a variety of objective measures of statistical surface roughness. The surfaces of the transported crystals clearly exhibit signatures of mesoscopic roughening that are similar to examples of roughness seen in ESEM-grown crystals. For most transported crystals, the habits and crystal edges are more intricate that those observed for ice grown directly on substrates within the ESEM chamber. Portions of some crystals do appear smooth even at magnification greater than 1000x, a rare observation in our ESEM-grown crystals. The

Electron tomography of cryo-immobilized plant tissue: a novel approach to studying 3D macromolecular architecture of mature plant cell walls in situ.

Directory of Open Access Journals (Sweden)

Purbasha Sarkar

Full Text Available Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼ 2 nm, and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF, cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we

Molecular architecture of axonemal microtubule doublets revealedby cryo-electron tomography

Energy Technology Data Exchange (ETDEWEB)

Sui, Haixin; Downing, Kenneth H.

2006-05-22

The axoneme, which forms the core of eukaryotic flagella and cilia, is one of the largest macromolecular machines with a structure that is largely conserved from protists to mammals. Microtubule doublets are structural components of axonemes containing a number of proteins besides tubulin, and are usually found in arrays of nine doublets arranged around two singlet microtubules. Coordinated sliding of adjacent doublets, which involves a host of other proteins in the axoneme, produces periodic beating movements of the axoneme. We have obtained a 3D density map of intact microtubule doublets using cryo-electron tomography and image averaging. Our map, with a resolution of about 3 nm, provides insights into locations of particular proteins within the doublets and the structural features of the doublets that define their mechanical properties. We identify likely candidates for several of these non-tubulin components of the doublets. This work offers novel insight on how tubulin protofilaments and accessory proteins attach together to form the doublets and provides a structural basis for understanding doublet function in axonemes.

"Size-Independent" Single-Electron Tunneling.

Science.gov (United States)

Zhao, Jianli; Sun, Shasha; Swartz, Logan; Riechers, Shawn; Hu, Peiguang; Chen, Shaowei; Zheng, Jie; Liu, Gang-Yu

2015-12-17

Incorporating single-electron tunneling (SET) of metallic nanoparticles (NPs) into modern electronic devices offers great promise to enable new properties; however, it is technically very challenging due to the necessity to integrate ultrasmall (<10 nm) particles into the devices. The nanosize requirements are intrinsic for NPs to exhibit quantum or SET behaviors, for example, 10 nm or smaller, at room temperature. This work represents the first observation of SET that defies the well-known size restriction. Using polycrystalline Au NPs synthesized via our newly developed solid-state glycine matrices method, a Coulomb Blockade was observed for particles as large as tens of nanometers, and the blockade voltage exhibited little dependence on the size of the NPs. These observations are counterintuitive at first glance. Further investigations reveal that each observed SET arises from the ultrasmall single crystalline grain(s) within the polycrystal NP, which is (are) sufficiently isolated from the nearest neighbor grains. This work demonstrates the concept and feasibility to overcome orthodox spatial confinement requirements to achieve quantum effects.

Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy.

Science.gov (United States)

Yeung, Heidi O; Förster, Andreas; Bebeacua, Cecilia; Niwa, Hajime; Ewens, Caroline; McKeown, Ciarán; Zhang, Xiaodong; Freemont, Paul S

2014-03-05

The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. These activities are at least in part regulated by the ubiquitin system, in which p97 is thought to target ubiquitylated protein substrates within macromolecular complexes and assist in their extraction or disassembly. Although ATPase activity is essential for p97 function, little is known about how ATP binding or hydrolysis is coupled with p97 conformational changes and substrate remodelling. Here, we have used single-particle electron cryomicroscopy (cryo-EM) to study the effect of nucleotides on p97 conformation. We have identified conformational heterogeneity within the cryo-EM datasets from which we have resolved two major p97 conformations. A comparison of conformations reveals inter-ring rotations upon nucleotide binding and hydrolysis that may be linked to the remodelling of target protein complexes.

Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins.

Science.gov (United States)

Schaffer, Miroslava; Mahamid, Julia; Engel, Benjamin D; Laugks, Tim; Baumeister, Wolfgang; Plitzko, Jürgen M

2017-02-01

While cryo-electron tomography (cryo-ET) can reveal biological structures in their native state within the cellular environment, it requires the production of high-quality frozen-hydrated sections that are thinner than 300nm. Sample requirements are even more stringent for the visualization of membrane-bound protein complexes within dense cellular regions. Focused ion beam (FIB) sample preparation for transmission electron microscopy (TEM) is a well-established technique in material science, but there are only few examples of biological samples exhibiting sufficient quality for high-resolution in situ investigation by cryo-ET. In this work, we present a comprehensive description of a cryo-sample preparation workflow incorporating additional conductive-coating procedures. These coating steps eliminate the adverse effects of sample charging on imaging with the Volta phase plate, allowing data acquisition with improved contrast. We discuss optimized FIB milling strategies adapted from material science and each critical step required to produce homogeneously thin, non-charging FIB lamellas that make large areas of unperturbed HeLa and Chlamydomonas cells accessible for cryo-ET at molecular resolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation.

Science.gov (United States)

Lundborg, Magnus; Narangifard, Ali; Wennberg, Christian L; Lindahl, Erik; Daneholt, Bertil; Norlén, Lars

2018-04-24

In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems. Copyright © 2018. Published by Elsevier Inc.

The cryo-electron microscopy structure of huntingtin

Science.gov (United States)

Guo, Qiang; Bin Huang; Cheng, Jingdong; Seefelder, Manuel; Engler, Tatjana; Pfeifer, Günter; Oeckl, Patrick; Otto, Markus; Moser, Franziska; Maurer, Melanie; Pautsch, Alexander; Baumeister, Wolfgang; Fernández-Busnadiego, Rubén; Kochanek, Stefan

2018-03-01

Huntingtin (HTT) is a large (348 kDa) protein that is essential for embryonic development and is involved in diverse cellular activities such as vesicular transport, endocytosis, autophagy and the regulation of transcription. Although an integrative understanding of the biological functions of HTT is lacking, the large number of identified HTT interactors suggests that it serves as a protein-protein interaction hub. Furthermore, Huntington’s disease is caused by a mutation in the HTT gene, resulting in a pathogenic expansion of a polyglutamine repeat at the amino terminus of HTT. However, only limited structural information regarding HTT is currently available. Here we use cryo-electron microscopy to determine the structure of full-length human HTT in a complex with HTT-associated protein 40 (HAP40; encoded by three F8A genes in humans) to an overall resolution of 4 Å. HTT is largely α-helical and consists of three major domains. The amino- and carboxy-terminal domains contain multiple HEAT (huntingtin, elongation factor 3, protein phosphatase 2A and lipid kinase TOR) repeats arranged in a solenoid fashion. These domains are connected by a smaller bridge domain containing different types of tandem repeats. HAP40 is also largely α-helical and has a tetratricopeptide repeat-like organization. HAP40 binds in a cleft and contacts the three HTT domains by hydrophobic and electrostatic interactions, thereby stabilizing the conformation of HTT. These data rationalize previous biochemical results and pave the way for improved understanding of the diverse cellular functions of HTT.

Single-Molecule Interfacial Electron Transfer

Energy Technology Data Exchange (ETDEWEB)

Lu, H. Peter [Bowling Green State Univ., Bowling Green, OH (United States). Dept. of Chemistry and Center for Photochemical Sciences

2017-11-28

This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static and dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO₂ and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO₂ nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO₂ nanoparticle surfaces by using ultrafast single

Miniaturizing EM Sample Preparation: Opportunities, Challenges, and "Visual Proteomics".

Science.gov (United States)

Arnold, Stefan A; Müller, Shirley A; Schmidli, Claudio; Syntychaki, Anastasia; Rima, Luca; Chami, Mohamed; Stahlberg, Henning; Goldie, Kenneth N; Braun, Thomas

2018-03-01

This review compares and discusses conventional versus miniaturized specimen preparation methods for transmission electron microscopy (TEM). The progress brought by direct electron detector cameras, software developments and automation have transformed transmission cryo-electron microscopy (cryo-EM) and made it an invaluable high-resolution structural analysis tool. In contrast, EM specimen preparation has seen very little progress in the last decades and is now one of the main bottlenecks in cryo-EM. Here, we discuss the challenges faced by specimen preparation for single particle EM, highlight current developments, and show the opportunities resulting from the advanced miniaturized and microfluidic sample grid preparation methods described, such as visual proteomics and time-resolved cryo-EM studies. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single Molecule Spectroscopy of Electron Transfer

International Nuclear Information System (INIS)

Holman, Michael; Zang, Ling; Liu, Ruchuan; Adams, David M.

2009-01-01

The objectives of this research are threefold: (1) to develop methods for the study electron transfer processes at the single molecule level, (2) to develop a series of modifiable and structurally well defined molecular and nanoparticle systems suitable for detailed single molecule/particle and bulk spectroscopic investigation, (3) to relate experiment to theory in order to elucidate the dependence of electron transfer processes on molecular and electronic structure, coupling and reorganization energies. We have begun the systematic development of single molecule spectroscopy (SMS) of electron transfer and summaries of recent studies are shown. There is a tremendous need for experiments designed to probe the discrete electronic and molecular dynamic fluctuations of single molecules near electrodes and at nanoparticle surfaces. Single molecule spectroscopy (SMS) has emerged as a powerful method to measure properties of individual molecules which would normally be obscured in ensemble-averaged measurement. Fluctuations in the fluorescence time trajectories contain detailed molecular level statistical and dynamical information of the system. The full distribution of a molecular property is revealed in the stochastic fluctuations, giving information about the range of possible behaviors that lead to the ensemble average. In the case of electron transfer, this level of understanding is particularly important to the field of molecular and nanoscale electronics: from a device-design standpoint, understanding and controlling this picture of the overall range of possible behaviors will likely prove to be as important as designing ia the ideal behavior of any given molecule.

Retrofit implementation of Zernike phase plate imaging for cryo-TEM.

Science.gov (United States)

Marko, Michael; Leith, Ardean; Hsieh, Chyongere; Danev, Radostin

2011-05-01

In-focus phase-plate imaging is particularly beneficial for cryo-TEM because it offers a substantial overall increase in image contrast, without an electron dose penalty, and it simplifies image interpretation. We show how phase-plate cryo-TEM can be implemented with an appropriate existing TEM, and provide a basic practical introduction to use of thin-film (carbon) phase plates. We point out potential pitfalls of phase-plate operation, and discuss solutions. We provide information on evaluating a particular TEM for its suitability. Copyright © 2011 Elsevier Inc. All rights reserved.

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.

Science.gov (United States)

Fischer, Niels; Konevega, Andrey L; Wintermeyer, Wolfgang; Rodnina, Marina V; Stark, Holger

2010-07-15

The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.

Probing Single Nanometer-scale Particles with Scanning Tunneling Microscopy and Spectroscopies

International Nuclear Information System (INIS)

McCarty, G.S.; Love, J.C.; Kushmerick, J.G.; Charles, L.F.; Keating, C.D.; Toleno, B.J.; Lyn, M.E.; Castleman, A.W.; Natan, M.J.; Weiss, P.S.

1999-01-01

Scanning tunneling microscopy can be used to isolate single particles on surfaces for further study. Local optical and electronic properties coupled with topographic information collected by the scanning tunneling microscope (STM) give insight into the intrinsic properties of the species under study. Since each spectroscopic measurement is done on a single particle, each sample is 'monodisperse', regardless of the degree of heterogeneity of the original preparation. We illustrate this with three example systems - a metal cluster of known atomic structure, metal nanoparticles dispersed from colloid suspensions, and metallocarbohedrenes (Met-Cars) deposited with other reaction products. Au and Ag nanoparticles were imaged using a photon emission STM. The threshold voltage, the lowest bias voltage at which photons are produced, was determined for Au nanoparticles. Electronic spectra of small clusters of Ni atoms on MoS 2 were recorded. Preliminary images of Zr-based Met-Car-containing soot were obtained on Au and MoS 2 substrates and partial electronic spectra were recorded of these possible Met-Car particles

Single particle detecting telescope system

International Nuclear Information System (INIS)

Yamamoto, I.; Tomiyama, T.; Iga, Y.; Komatsubara, T.; Kanada, M.; Yamashita, Y.; Wada, T.; Furukawa, S.

1981-01-01

We constructed the single particle detecting telescope system for detecting a fractionally charged particle. The telescope consists of position detecting counters, wall-less multi-cell chambers, single detecting circuits and microcomputer system as data I/0 processor. Especially, a frequency of double particle is compared the case of the single particle detecting with the case of an ordinary measurement

Single particle dynamics of many-body systems described by Vlasov-Fokker-Planck equations

International Nuclear Information System (INIS)

Frank, T.D.

2003-01-01

Using Langevin equations we describe the random walk of single particles that belong to particle systems satisfying Vlasov-Fokker-Planck equations. In doing so, we show that Haissinski distributions of bunched particles in electron storage rings can be derived from a particle dynamics model

A comparative analysis of the cryo-compression and cryo-adsorption hydrogen storage methods

Energy Technology Data Exchange (ETDEWEB)

Petitpas, G [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Benard, P [Universite du Quebec a Trois-Rivieres (Canada); Klebanoff, L E [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Xiao, J [Universite du Quebec a Trois-Rivieres (Canada); Aceves, S M [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2014-07-01

While conventional low-pressure LH₂ dewars have existed for decades, advanced methods of cryogenic hydrogen storage have recently been developed. These advanced methods are cryo-compression and cryo-adsorption hydrogen storage, which operate best in the temperature range 30–100 K. We present a comparative analysis of both approaches for cryogenic hydrogen storage, examining how pressure and/or sorbent materials are used to effectively increase onboard H₂ density and dormancy. We start by reviewing some basic aspects of LH₂ properties and conventional means of storing it. From there we describe the cryo-compression and cryo-adsorption hydrogen storage methods, and then explore the relationship between them, clarifying the materials science and physics of the two approaches in trying to solve the same hydrogen storage task (~5–8 kg H₂, typical of light duty vehicles). Assuming that the balance of plant and the available volume for the storage system in the vehicle are identical for both approaches, the comparison focuses on how the respective storage capacities, vessel weight and dormancy vary as a function of temperature, pressure and type of cryo-adsorption material (especially, powder MOF-5 and MIL-101). By performing a comparative analysis, we clarify the science of each approach individually, identify the regimes where the attributes of each can be maximized, elucidate the properties of these systems during refueling, and probe the possible benefits of a combined “hybrid” system with both cryo-adsorption and cryo-compression phenomena operating at the same time. In addition the relationships found between onboard H₂ capacity, pressure vessel and/or sorbent mass and dormancy as a function of rated pressure, type of sorbent material and fueling conditions are useful as general designing guidelines in future engineering efforts using these two hydrogen storage approaches.

CryoSat Land Ice Product Validation within the CryoVal-LI project

DEFF Research Database (Denmark)

Sørensen, Louise Sandberg; Baker, Steven; Csatho, Bea

The main objective of the ESA funded CryoVal-LI project has been to identify and quantify the error sources for the CryoSat-2 mission over land ice. This has been undertaken through the careful documentation of the possible error sources, the identification of suitable validation sites...

Long helical filaments are not seen encircling cells in electron cryotomograms of rod-shaped bacteria

International Nuclear Information System (INIS)

Swulius, Matthew T.; Chen, Songye; Jane Ding, H.; Li, Zhuo; Briegel, Ariane; Pilhofer, Martin; Tocheva, Elitza I.; Lybarger, Suzanne R.; Johnson, Tanya L.; Sandkvist, Maria; Jensen, Grant J.

2011-01-01

Highlights: → No long helical filaments are seen near or along rod-shaped bacterial inner membranes by electron cryo-tomography. → Electron cryo-tomography has the resolution to detect single filaments in vivo. -- Abstract: How rod-shaped bacteria form and maintain their shape is an important question in bacterial cell biology. Results from fluorescent light microscopy have led many to believe that the actin homolog MreB and a number of other proteins form long helical filaments along the inner membrane of the cell. Here we show using electron cryotomography of six different rod-shaped bacterial species, at macromolecular resolution, that no long (>80 nm) helical filaments exist near or along either surface of the inner membrane. We also use correlated cryo-fluorescent light microscopy (cryo-fLM) and electron cryo-tomography (ECT) to identify cytoplasmic bundles of MreB, showing that MreB filaments are detectable by ECT. In light of these results, the structure and function of MreB must be reconsidered: instead of acting as a large, rigid scaffold that localizes cell-wall synthetic machinery, moving MreB complexes may apply tension to growing peptidoglycan strands to ensure their orderly, linear insertion.

Self-Assembled Colloidal Particle Clusters from In Situ Pickering-Like Emulsion Polymerization via Single Electron Transfer Mechanism.

Science.gov (United States)

Yuan, Jinfeng; Zhao, Weiting; Pan, Mingwang; Zhu, Lei

2016-08-01

A simple route is reported to synthesize colloidal particle clusters (CPCs) from self-assembly of in situ poly(vinylidene fluoride)/poly(styrene-co-tert-butyl acrylate) [PVDF/P(St-co-tBA)] Janus particles through one-pot seeded emulsion single electron transfer radical polymerization. In the in situ Pickering-like emulsion polymerization, the tBA/St/PVDF feed ratio and polymerization temperature are important for the formation of well-defined CPCs. When the tBA/St/PVDF feed ratio is 0.75 g/2.5 g/0.5 g and the reaction temperature is 35 °C, relatively uniform raspberry-like CPCs are obtained. The hydrophobicity of the P(St-co-tBA) domains and the affinity of PVDF to the aqueous environment are considered to be the driving force for the self-assembly of the in situ formed PVDF/P(St-co-tBA) Janus particles. The resultant raspberry-like CPCs with PVDF particles protruding outward may be promising for superhydrophobic smart coatings. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cryo-CMOS Circuits and Systems for Quantum Computing Applications

NARCIS (Netherlands)

Patra, B; Incandela, R.M.; van Dijk, J.P.G.; Homulle, H.A.R.; Song, Lin; Shahmohammadi, M.; Staszewski, R.B.; Vladimirescu, A.; Babaie, M.; Sebastiano, F.; Charbon, E.E.E.

2018-01-01

A fault-tolerant quantum computer with millions of quantum bits (qubits) requires massive yet very precise control electronics for the manipulation and readout of individual qubits. CMOS operating at cryogenic temperatures down to 4 K (cryo-CMOS) allows for closer system integration, thus promising

Application of CTOF method to detect secondly charged particle from 2 GeV electron

International Nuclear Information System (INIS)

Takahashi, Kazutoshi; Sanami, Toshiya; Ban, Syuichi; Lee, Hee-Seok; Sato, Tatsuhiko

2002-01-01

To design a shield and evaluate leakage radiation at high energy electron accelerators, the energy and angular data of secondary particle from the reaction of electrons with structural materials are required. Secondly neutron spectrum from structural materials has been measured by using electron accelerator in PAL (Pohang Accelerator Laboratory). In the neutron measurement, the electronics with Multi-hit TDC (MHTDC) was adopted to measure Time of Flight of every particles (TOFs) emitted from the reactions by each single electron bunch. The measurements are extended to secondly charged particles. For the charged particles measurement, the pulse height data for every particles are indispensable to distinguish charged particles by Δ E-E method. A new system which can measure pulse height for every particle is required instead of the MHTDC system. For this requirement, the method which can take output current from detectors was developed by using digital storage oscilloscope system is named ''Current Time of Flight method'' (CTOF). The CTOF method is able to measure pulse height and TOF for every particles produced by single electron bunch. Electrons are accelerated to 2.04 GeV and the repetition rate is 10 Hz. These electrons bombard thin disk samples of Cu 1mm, Al 4 mm and W 0.5 mm. Secondly charged particles, proton and deuteron, are produced in the samples by photonuclear reaction. Two dimensional of Δ E-E spectrum for each the samples measured by CTOF shows separation between proton and deuteron perfectly. Thus, proton and deuteron spectrum are obtained from this data. (M. Suetake)

Common lines modeling for reference free Ab-initio reconstruction in cryo-EM.

Science.gov (United States)

Greenberg, Ido; Shkolnisky, Yoel

2017-11-01

We consider the problem of estimating an unbiased and reference-free ab initio model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all images. The contribution of each common line to the estimated orientations is weighted according to a statistical model for common lines' detection errors. The key property of the proposed algorithm is that it finds the global optimum for the orientations given the common lines. In particular, any local optima in the common lines energy landscape do not affect the proposed algorithm. As a result, it is applicable to thousands of images at once, very robust to noise, completely reference free, and not biased towards any initial model. A byproduct of the algorithm is a set of measures that allow to asses the reliability of the obtained ab initio model. We demonstrate the algorithm using class averages from two experimental data sets, resulting in ab initio models with resolutions of 20Å or better, even from class averages consisting of as few as three raw images per class. Copyright © 2017 Elsevier Inc. All rights reserved.

Solving protein nanocrystals by cryo-EM diffraction: Multiple scattering artifacts

Energy Technology Data Exchange (ETDEWEB)

Subramanian, Ganesh [Department of Materials Science and Engineering, Arizona State University, Tempe, AZ (United States); Basu, Shibom [Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ (United States); Liu, Haiguang [Department of Physics, Arizona State University, Tempe, AZ 85287-1504 (United States); Zuo, Jian-Min [Department of Materials Science and Engineering, University of Illinois, Urbana, IL (United States); Spence, John C.H., E-mail: spence@asu.edu [Department of Physics, Arizona State University, Tempe, AZ 85287-1504 (United States)

2015-01-15

The maximum thickness permissible within the single-scattering approximation for the determination of the structure of perfectly ordered protein microcrystals by transmission electron diffraction is estimated for tetragonal hen-egg lysozyme protein crystals using several approaches. Multislice simulations are performed for many diffraction conditions and beam energies to determine the validity domain of the required single-scattering approximation and hence the limit on crystal thickness. The effects of erroneous experimental structure factor amplitudes on the charge density map for lysozyme are noted and their threshold limits calculated. The maximum thickness of lysozyme permissible under the single-scattering approximation is also estimated using R-factor analysis. Successful reconstruction of density maps is found to result mainly from the use of the phase information provided by modeling based on the protein data base through molecular replacement (MR), which dominates the effect of poor quality electron diffraction data at thicknesses larger than about 200 Å. For perfectly ordered protein nanocrystals, a maximum thickness of about 1000 Å is predicted at 200 keV if MR can be used, using R-factor analysis performed over a subset of the simulated diffracted beams. The effects of crystal bending, mosaicity (which has recently been directly imaged by cryo-EM) and secondary scattering are discussed. Structure-independent tests for single-scattering and new microfluidic methods for growing and sorting nanocrystals by size are reviewed. - Highlights: • Validity domain of single-scattering approximation for protein electron diffraction is assessed • Electron Diffraction for tetragonal hen-egg lysozyme is simulated using multislice. • Bias from the use of phase information in modeling by molecular replacement (MR) is evaluated. • We find an approximate upper thickness limit, if MR is used, of 100 nm. • A 35% error in structure factor magnitudes may be

Single particle dynamics

International Nuclear Information System (INIS)

Siemens, P.J.; Jensen, A.S.

1985-01-01

It is shown that the opening of the 3-quasiparticle continuum at 3Δ sets the energy scale for the enhancement of the effective mass near the Fermi surface of nuclei. The authors argue that the spreading width of single-particle states due to coupling with low-lying collective modes is qualitatively different from the two-body collision mechanism, and contributes little to the single-particle lifetime in the sense of the optical model. (orig.)

A new stage of nuclear electronics-particle electronics

International Nuclear Information System (INIS)

Xi Deming

1987-01-01

The rapid development of high energy physics experiments has pushed the nuclear electronics to a new stage, i.e. the particle electronics. In this paper the background, main features and recent trends of the particle electronics are expounded

Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy

Directory of Open Access Journals (Sweden)

Kristin N. Parent

2018-02-01

Full Text Available The majority of viruses on Earth form capsids built by multiple copies of one or more types of a coat protein arranged with 532 symmetry, generating an icosahedral shell. This highly repetitive structure is ideal to closely pack identical protein subunits and to enclose the nucleic acid genomes. However, the icosahedral capsid is not merely a passive cage but undergoes dynamic events to promote packaging, maturation and the transfer of the viral genome into the host. These essential processes are often mediated by proteinaceous complexes that interrupt the shell’s icosahedral symmetry, providing a gateway through the capsid. In this review, we take an inventory of molecular structures observed either internally, or at the 5-fold vertices of icosahedral DNA viruses that infect bacteria, archea and eukaryotes. Taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM and building upon a wealth of crystallographic structures of individual components, we review the design principles of non-icosahedral structural components that interrupt icosahedral symmetry and discuss how these macromolecules play vital roles in genome packaging, ejection and host receptor-binding.

Development of a dielectric barrier discharge (DBD) cryo-microplasma: generation and diagnostics

International Nuclear Information System (INIS)

Ishihara, Daisuke; Noma, Yuri; Stauss, Sven; Sai, Masaki; Tomai, Takaaki; Terashima, Kazuo

2008-01-01

We developed a cryo-microplasma, which can continuously control gas temperature below room temperature and below the freezing point of water. To develop the cryo-microplasma, we first developed an atmospheric-pressure low-temperature microplasma that can suppress the increase in its gas temperature. Helium gas was employed, which was generated in open air. The average estimated electron density and temperature were 10 8 -10 9 cm -3 and 4-5 eV, respectively, independent of the applied voltage. Then, helium gas, which was the working gas of the atmospheric-pressure low-temperature microplasma, was cooled by liquid nitrogen to generate an atmospheric-pressure cryo-microplasma in open air. We observed the generation of frost around the quartz tube in which the plasma was generated and an increase in atomic oxygen emission by optical emission spectroscopy. Finally, to avoid the generation of frost, a cryo-microplasma was generated in a reactor chamber separated from open air. Helium, nitrogen and oxygen were employed as working gases. Using thermocouples and by estimation from the nitrogen rotational temperature, we verified that the gas temperature of the cryo-microplasma was much lower (T g ∼ 180-300 K) than that of the conventional atmospheric-pressure low-temperature plasma (above 300 K).

Development of a dielectric barrier discharge (DBD) cryo-microplasma: generation and diagnostics

Science.gov (United States)

Ishihara, Daisuke; Noma, Yuri; Stauss, Sven; Sai, Masaki; Tomai, Takaaki; Terashima, Kazuo

2008-08-01

We developed a cryo-microplasma, which can continuously control gas temperature below room temperature and below the freezing point of water. To develop the cryo-microplasma, we first developed an atmospheric-pressure low-temperature microplasma that can suppress the increase in its gas temperature. Helium gas was employed, which was generated in open air. The average estimated electron density and temperature were 108-109 cm-3 and 4-5 eV, respectively, independent of the applied voltage. Then, helium gas, which was the working gas of the atmospheric-pressure low-temperature microplasma, was cooled by liquid nitrogen to generate an atmospheric-pressure cryo-microplasma in open air. We observed the generation of frost around the quartz tube in which the plasma was generated and an increase in atomic oxygen emission by optical emission spectroscopy. Finally, to avoid the generation of frost, a cryo-microplasma was generated in a reactor chamber separated from open air. Helium, nitrogen and oxygen were employed as working gases. Using thermocouples and by estimation from the nitrogen rotational temperature, we verified that the gas temperature of the cryo-microplasma was much lower (Tg ≈ 180-300 K) than that of the conventional atmospheric-pressure low-temperature plasma (above 300 K).

Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases

Science.gov (United States)

Mazhab-Jafari, Mohammad T.; Rubinstein, John L.

2016-01-01

Electron cryomicroscopy (cryo-EM) has significantly advanced our understanding of molecular structure in biology. Recent innovations in both hardware and software have made cryo-EM a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Cryo-EM has even become the method of choice in some situations where x-ray crystallography and NMR spectroscopy are possible but where cryo-EM can determine structures at higher resolution or with less time or effort. Rotary adenosine triphosphatases (ATPases) are crucial to the maintenance of cellular homeostasis. These enzymes couple the synthesis or hydrolysis of adenosine triphosphate to the use or production of a transmembrane electrochemical ion gradient, respectively. However, the membrane-embedded nature and conformational heterogeneity of intact rotary ATPases have prevented their high-resolution structural analysis to date. Recent application of cryo-EM methods to the different types of rotary ATPase has led to sudden advances in understanding the structure and function of these enzymes, revealing significant conformational heterogeneity and characteristic transmembrane α helices that are highly tilted with respect to the membrane. In this Review, we will discuss what has been learned recently about rotary ATPase structure and function, with a particular focus on the vacuolar-type ATPases. PMID:27532044

Time-resolved GISAXS and cryo-microscopy characterization of block copolymer membrane formation

KAUST Repository

Marques, Debora S.; Dorin, Rachel Mika; Wiesner, Ulrich B.; Smilgies, Detlef Matthias; Behzad, Ali Reza; Vainio, Ulla; Peinemann, Klaus-Viktor; Nunes, Suzana Pereira

2014-01-01

Time-resolved grazing-incidence small-angle X-ray scattering (GISAXS) and cryo-microscopy were used for the first time to understand the pore evolution by copolymer assembly, leading to the formation of isoporous membranes with exceptional porosity and regularity. The formation of copolymer micelle strings in solution (in DMF/DOX/THF and DMF/DOX) was confirmed by cryo field emission scanning electron microscopy (cryo-FESEM) with a distance of 72 nm between centers of micelles placed in different strings. SAXS measurement of block copolymer solutions in DMF/DOX indicated hexagonal assembly with micelle-to-micelle distance of 84-87 nm for 14-20 wt% copolymer solutions. GISAXS in-plane peaks were detected, revealing order close to hexagonal. The d-spacing corresponding to the first peak in this case was 100-130 nm (lattice constant 115-150 nm) for 17 wt% copolymer solutions evaporating up to 100 s. Time-resolved cryo-FESEM showed the formation of incipient pores on the film surface after 4 s copolymer solution casting with distances between void centers of 125 nm. © 2014 Elsevier Ltd. All rights reserved.

Time-resolved GISAXS and cryo-microscopy characterization of block copolymer membrane formation

KAUST Repository

Marques, Debora S.

2014-03-01

Time-resolved grazing-incidence small-angle X-ray scattering (GISAXS) and cryo-microscopy were used for the first time to understand the pore evolution by copolymer assembly, leading to the formation of isoporous membranes with exceptional porosity and regularity. The formation of copolymer micelle strings in solution (in DMF/DOX/THF and DMF/DOX) was confirmed by cryo field emission scanning electron microscopy (cryo-FESEM) with a distance of 72 nm between centers of micelles placed in different strings. SAXS measurement of block copolymer solutions in DMF/DOX indicated hexagonal assembly with micelle-to-micelle distance of 84-87 nm for 14-20 wt% copolymer solutions. GISAXS in-plane peaks were detected, revealing order close to hexagonal. The d-spacing corresponding to the first peak in this case was 100-130 nm (lattice constant 115-150 nm) for 17 wt% copolymer solutions evaporating up to 100 s. Time-resolved cryo-FESEM showed the formation of incipient pores on the film surface after 4 s copolymer solution casting with distances between void centers of 125 nm. © 2014 Elsevier Ltd. All rights reserved.

Correlative Cryo-Tem Cryo-Stxm and Cryo-Shxm Investigation of Selenium Bioreduction in a Contaminated Aquifer

Science.gov (United States)

Fakra, S.; Luef, B.; Tyliszczak, T.; Castelle, C. J.; Mullin, S. W.; Hug, L. A.; Williams, K. H.; Marcus, M.; Banfield, J. F.

2015-12-01

Accurate mapping of the composition and ultrastructure of minerals and cells is key to understanding biogeochemical process in contaminated environments. Here we developed two apparatus that allow correlation of cryogenic transmission electron microscopy (TEM), synchrotron hard X-ray microprobe (SHXM) and scanning transmission X-ray microscopy (STXM) datasets. These cryogenic methods enabled precise determination of the distribution, valence state and structure of selenium in intact biofilms sampled during a biostimulation experiment in a contaminated aquifer near Rifle, CO, USA. Results were replicated in the laboratory via anaerobic selenate-reducing enrichment cultures. 16S rRNA analyses of field-derived biofilm indicated the dominance of Betaproteobacteria from the Comamonadaceae family, and uncultivated members of the Simplicispira genus. The major product in field and culture-derived biofilms consists of ~25-300 nm red amorphous Se0 aggregates of colloidal nanoparticles. Correlative analyses of the cultures provided direct evidence for microbial dissimilatory reduction of Se(VI) to Se(IV) to Se0. X-ray diffraction and Se K-edge extended X-ray absorption fine structure spectroscopy revealed red amorphous Se0 with a first shell Se-Se interatomic distance of 2.339 ± 0.003 Å. STXM showed that these aggregates are strongly associated with a protein-rich biofilm matrix containing acidic polysaccharides. From Rifle groundwater, we isolated a strain that shares 98.9% 16S rRNA gene sequence identity with Dechloromonas aromatica RCB and grows anaerobically by oxidizing acetate and reducing selenate. We refer to this isolate as Dechloromonas selenatis strain RGW99. 3D cryo-electron tomography showed that Se0 particles do not form inside the cytoplasm but rather originate in the cell membrane. The end product of selenate reduction by D. selenatis is 240 ± 66 nm diameter red amorphous Se0 colloidal aggregates. This product was found to be stable for months. Overall

Processing a Biological Tissue from Cryo-SEM to Replica

Czech Academy of Sciences Publication Activity Database

Vaškovicová, Naděžda; Hrubanová, Kamila; Krzyžánek, Vladislav

2016-01-01

Roč. 22, S3 (2016), s. 236-237 ISSN 1431-9276 R&D Projects: GA MŠk(CZ) LO1212; GA MŠk ED0017/01/01 Institutional support: RVO:68081731 Keywords : Cryo-SEM * ACE600 Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.891, year: 2016

Single-Electron and Single-Photon Sensitivity with a Silicon Skipper CCD

Science.gov (United States)

Tiffenberg, Javier; Sofo-Haro, Miguel; Drlica-Wagner, Alex; Essig, Rouven; Guardincerri, Yann; Holland, Steve; Volansky, Tomer; Yu, Tien-Tien

2017-09-01

We have developed ultralow-noise electronics in combination with repetitive, nondestructive readout of a thick, fully depleted charge-coupled device (CCD) to achieve an unprecedented noise level of 0.068 e- rms /pixel . This is the first time that discrete subelectron readout noise has been achieved reproducible over millions of pixels on a stable, large-area detector. This enables the contemporaneous, discrete, and quantized measurement of charge in pixels, irrespective of whether they contain zero electrons or thousands of electrons. Thus, the resulting CCD detector is an ultra-sensitive calorimeter. It is also capable of counting single photons in the optical and near-infrared regime. Implementing this innovative non-destructive readout system has a negligible impact on CCD design and fabrication, and there are nearly immediate scientific applications. As a particle detector, this CCD will have unprecedented sensitivity to low-mass dark matter particles and coherent neutrino-nucleus scattering, while future astronomical applications may include direct imaging and spectroscopy of exoplanets.

Hybrid fluorescence and electron cryo-microscopy for simultaneous electron and photon imaging.

Science.gov (United States)

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.

Pathogen–host reorganization during Chlamydia invasion revealed by cryo-electron tomography

Science.gov (United States)

Nans, Andrea; Saibil, Helen R; Hayward, Richard D

2014-01-01

Invasion of host cells is a key early event during bacterial infection, but the underlying pathogen–host interactions are yet to be fully visualized in three-dimensional detail. We have captured snapshots of the early stages of bacterial-mediated endocytosis in situ by exploiting the small size of chlamydial elementary bodies (EBs) for whole-cell cryo-electron tomography. Chlamydiae are obligate intracellular bacteria that infect eukaryotic cells and cause sexually transmitted infections and trachoma, the leading cause of preventable blindness. We demonstrate that Chlamydia trachomatis LGV2 EBs are intrinsically polarized. One pole is characterized by a tubular inner membrane invagination, while the other exhibits asymmetric periplasmic expansion to accommodate an array of type III secretion systems (T3SSs). Strikingly, EBs orient with their T3SS-containing pole facing target cells, enabling the T3SSs to directly contact the cellular plasma membrane. This contact induces enveloping macropinosomes, actin-rich filopodia and phagocytic cups to zipper tightly around the internalizing bacteria. Once encapsulated into tight early vacuoles, EB polarity and the T3SSs are lost. Our findings reveal previously undescribed structural transitions in both pathogen and host during the initial steps of chlamydial invasion. PMID:24809274

Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3.

Science.gov (United States)

Hirschi, Marscha; Herzik, Mark A; Wie, Jinhong; Suo, Yang; Borschel, William F; Ren, Dejian; Lander, Gabriel C; Lee, Seok-Yong

2017-10-19

The modulation of ion channel activity by lipids is increasingly recognized as a fundamental component of cellular signalling. The transient receptor potential mucolipin (TRPML) channel family belongs to the TRP superfamily and is composed of three members: TRPML1-TRPML3. TRPMLs are the major Ca 2+ -permeable channels on late endosomes and lysosomes (LEL). They regulate the release of Ca 2+ from organelles, which is important for various physiological processes, including organelle trafficking and fusion. Loss-of-function mutations in the MCOLN1 gene, which encodes TRPML1, cause the neurodegenerative lysosomal storage disorder mucolipidosis type IV, and a gain-of-function mutation (Ala419Pro) in TRPML3 gives rise to the varitint-waddler (Va) mouse phenotype. Notably, TRPML channels are activated by the low-abundance and LEL-enriched signalling lipid phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P 2 ), whereas other phosphoinositides such as PtdIns(4,5)P 2 , which is enriched in plasma membranes, inhibit TRPMLs. Conserved basic residues at the N terminus of the channel are important for activation by PtdIns(3,5)P 2 and inhibition by PtdIns(4,5)P 2 . However, owing to a lack of structural information, the mechanism by which TRPML channels recognize PtdIns(3,5)P 2 and increase their Ca 2+ conductance remains unclear. Here we present the cryo-electron microscopy (cryo-EM) structure of a full-length TRPML3 channel from the common marmoset (Callithrix jacchus) at an overall resolution of 2.9 Å. Our structure reveals not only the molecular basis of ion conduction but also the unique architecture of TRPMLs, wherein the voltage sensor-like domain is linked to the pore via a cytosolic domain that we term the mucolipin domain. Combined with functional studies, these data suggest that the mucolipin domain is responsible for PtdIns(3,5)P 2 binding and subsequent channel activation, and that it acts as a 'gating pulley' for lipid-dependent TRPML gating.

CryoSat-2 Validation using CryoVEX 2011-12 Airborne Campaigns

DEFF Research Database (Denmark)

Skourup, Henriette; Forsberg, René; Kildegaard Rose, Stine

Sat-2 by comparison to airborne and ground measurements. This is possible only through a major effort involving a large group of international partners. DTU Space has been involved in the CryoVEx campaigns with airborne activities since 2003. To validate the performance of the CryoSat-2 radar altimeter...... (SIRAL), the aircraft is equipped with an airborne version of the SIRAL altimeter (ASIRAS) together with a laser scanner. The campaigns are focused on five main validation sites: Devon ice cap (Canada), Austfonna ice cap (Svalbard), the EGIG line crossing the Greenland Ice Sheet, as well as the sea ice...... north of Alert and sea ice around Svalbard in the Fram Strait. Selected tracks were planned to match CryoSat-2 passes and a few of them were flown in formation flight with the Alfred Wegener Institute (AWI) Polar-5 carrying an EM-bird. This presentation summarizes the 2011-12 airborne campaigns...

Diversity of extracellular vesicles in human ejaculates revealed by cryo-electron microscopy

Directory of Open Access Journals (Sweden)

Johanna L. Höög

2015-11-01

Full Text Available Human ejaculates contain extracellular vesicles (EVs, that to a large extent are considered to originate from the prostate gland, and are often denominated “prostasomes.” These EVs are important for human fertility, for example by promoting sperm motility and by inducing immune tolerance of the female immune system to the spermatozoa. So far, the EVs present in human ejaculate have not been studied in their native state, inside the seminal fluid without prior purification and isolation procedures. Using cryo-electron microscopy and tomography, we performed a comprehensive inventory of human ejaculate EVs. The sample was neither centrifuged, fixed, filtered or sectioned, nor were heavy metals added. Approximately 1,500 extracellular structures were imaged and categorized. The extracellular environment of human ejaculate was found to be diverse, with 5 major subcategories of EVs and 6 subcategories of extracellular membrane compartments, including lamellar bodies. Furthermore, 3 morphological features, including electron density, double membrane bilayers and coated surface, are described in all subcategories. This study reveals that the extracellular environment in human ejaculate is multifaceted. Several novel morphological EV subcategories are identified and clues to their cellular origin may be found in their morphology. This inventory is therefore important for developing future experimental approaches, and to interpret previously published data to understand the role of EVs for human male fertility.

Structure of the TRPV1 ion channel determined by electron cryo-microscopy.

Science.gov (United States)

Liao, Maofu; Cao, Erhu; Julius, David; Cheng, Yifan

2013-12-05

Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4 Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane segments 5-6 (S5-S6) and the intervening pore loop, which is flanked by S1-S4 voltage-sensor-like domains. TRPV1 has a wide extracellular 'mouth' with a short selectivity filter. The conserved 'TRP domain' interacts with the S4-S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including amino-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function.

Single Particle Entropy in Heated Nuclei

International Nuclear Information System (INIS)

Guttormsen, M.; Chankova, R.; Hjorth-Jensen, M.; Rekstad, J.; Siem, S.; Sunde, A. C.; Syed, N. U. H.; Agvaanluvsan, U.; Schiller, A.; Voinov, A.

2006-01-01

The thermal motion of single particles represents the largest contribution to level density (or entropy) in atomic nuclei. The concept of single particle entropy is presented and shown to be an approximate extensive (additive) quantity for mid-shell nuclei. A few applications of single particle entropy are demonstrated

Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy

Science.gov (United States)

Sborgi, Lorenzo; Ravotti, Francesco; Dandey, Venkata P.; Dick, Mathias S.; Mazur, Adam; Reckel, Sina; Chami, Mohamed; Scherer, Sebastian; Huber, Matthias; Böckmann, Anja; Egelman, Edward H.; Stahlberg, Henning; Broz, Petr; Meier, Beat H.; Hiller, Sebastian

2015-01-01

Inflammasomes are multiprotein complexes that control the innate immune response by activating caspase-1, thus promoting the secretion of cytokines in response to invading pathogens and endogenous triggers. Assembly of inflammasomes is induced by activation of a receptor protein. Many inflammasome receptors require the adapter protein ASC [apoptosis-associated speck-like protein containing a caspase-recruitment domain (CARD)], which consists of two domains, the N-terminal pyrin domain (PYD) and the C-terminal CARD. Upon activation, ASC forms large oligomeric filaments, which facilitate procaspase-1 recruitment. Here, we characterize the structure and filament formation of mouse ASC in vitro at atomic resolution. Information from cryo-electron microscopy and solid-state NMR spectroscopy is combined in a single structure calculation to obtain the atomic-resolution structure of the ASC filament. Perturbations of NMR resonances upon filament formation monitor the specific binding interfaces of ASC-PYD association. Importantly, NMR experiments show the rigidity of the PYD forming the core of the filament as well as the high mobility of the CARD relative to this core. The findings are validated by structure-based mutagenesis experiments in cultured macrophages. The 3D structure of the mouse ASC-PYD filament is highly similar to the recently determined human ASC-PYD filament, suggesting evolutionary conservation of ASC-dependent inflammasome mechanisms. PMID:26464513

Challenges and opportunities in the high-resolution cryo-EM visualization of microtubules and their binding partners.

Science.gov (United States)

Nogales, Eva; Kellogg, Elizabeth H

2017-10-01

As non-crystallizable polymers, microtubules have been the target of cryo-electron microscopy (cryo-EM) studies since the technique was first established. Over the years, image processing strategies have been developed that take care of the unique, pseudo-helical symmetry of the microtubule. With recent progress in data quality and data processing, cryo-EM reconstructions are now reaching resolutions that allow the generation of atomic models of microtubules and the factors that bind them. These include cellular partners that contribute to microtubule cellular functions, or small ligands that interfere with those functions in the treatment of cancer. The stage is set to generate a family portrait for all identified microtubule interacting proteins and to use cryo-EM as a drug development tool in the targeting of tubulin. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

CryoVex 2008

DEFF Research Database (Denmark)

Hvidegaard, Sine Munk; Forsberg, René; Skourup, Henriette

2009-01-01

Air Greenland. The main purpose was to collect coincident ASIRAS and laser elevation data form validation sites on land and sea ice and in addition offer logistical support to ground teams. Overflights of corner reflectors were done at main validation sites in order to calibrate the ASIRAS data....... The datasets from this campaign will be important for understanding the CryoSat-2 radar signals. The airborne part of CryoVEx 2008 was successfully carried out between April 15 and May 8 and the datasets have been stored and secured at DTU Space and Alfred Wegener Institute (AWI). Afterwards extensive data...

Two-particle versus three-particle interactions in single ionization of helium by ion impact

International Nuclear Information System (INIS)

Schulz, M; Moshammer, R; Fischer, D; Ullrich, J

2004-01-01

We have performed kinematically complete experiments on single ionization of He by 100 MeV amu -1 C 6+ and 3.6 MeV amu -1 Au 24,53+ impact. By analysing doubly differential cross sections (DDCS) as a function of the momenta of all two-particle sub-systems we studied the importance of two-particle interactions. Furthermore, presenting the squared momenta of all three collision fragments simultaneously in a Dalitz plot, we evaluated the role of three-particle interactions. Finally, both for the DDCS and the Dalitz plots the corresponding correlation function was analysed. While the absolute cross sections confirm that ionization predominantly leads to a momentum exchange between the electron and the recoil-ion, the correlation function reveals strong correlations between the particles of any two-particle sub-system. Three-particle correlations, which are not accounted for by perturbative calculations, are quite significant as well, at least for certain kinematic conditions

Electrostatic deposition of a micro solder particle using a single probe by applying a single rectangular pulse

International Nuclear Information System (INIS)

Nakabayashi, Daizo; Sawai, Kenji; Saito, Shigeki; Takahashi, Kunio

2012-01-01

Recently, micromanipulation techniques have been in high demand. A technique to deposit a metal microparticle onto a metal substrate by using a single metal probe has been proposed as one of the techniques. A solder particle with a diameter of 20–30 µm, initially adhering to the probe tip, is detached and deposited onto a substrate. The success rate of the particle deposition was 44% in the previous research, and is insufficient for industrial applications. In this paper, a technique of particle deposition by applying a single rectangular pulse is proposed, and the mechanism of the deposition is described. In the mechanism, an electric discharge between the probe and the particle when the particle reaches the substrate plays an important role in the particle deposition. Moreover, the mechanism of the proposed technique is verified by experiments of particle deposition, which are observed using a high-speed camera, a scanning electron microscope (SEM) and an oscilloscope. The success rate of the particle deposition has increased to 93% by the proposed technique. Furthermore, the damage to the particle by the electric discharge is evaluated using an RC circuit model, and the applicability of the proposed technique is discussed. (paper)

HIE-ISOLDE CRYO-MODULE Assembly - Superconducting Solenoid

CERN Multimedia

Leclercq, Yann

2016-01-01

Assembly of the cryo-module components in SM18 cleanroom. The superconducting solenoid (housed inside its helium vessel) is cleaned, prepared then installed on the supporting frame of the cryo-module and connected to the helium tank, prior to the assembly of the RF cavities on the structure. The completed first 2 cryo-modules installed inside the HIE-ISOLDE-LINAC ready for beam operation is also shown.

Single-particle properties of the Hubbard model in a novel three-pole approximation

Science.gov (United States)

Di Ciolo, Andrea; Avella, Adolfo

2018-05-01

We study the 2D Hubbard model using the Composite Operator Method within a novel three-pole approximation. Motivated by the long-standing experimental puzzle of the single-particle properties of the underdoped cuprates, we include in the operatorial basis, together with the usual Hubbard operators, a field describing the electronic transitions dressed by the nearest-neighbor spin fluctuations, which play a crucial role in the unconventional behavior of the Fermi surface and of the electronic dispersion. Then, we adopt this approximation to study the single-particle properties in the strong coupling regime and find an unexpected behavior of the van Hove singularity that can be seen as a precursor of a pseudogap regime.

Charging of Single Micron Sized Dust Grains by Secondary Electron Emission: A Laboratory Study

Science.gov (United States)

Spann, James F., Jr.; Venturini, Catherine C.; Comfort, R. H.

1998-01-01

We present the details of a new laboratory study whose objective is to experimentally study the interaction of micron sized particles with plasmas and electromagnetic radiation. Specifically, to investigate under what conditions and to what extent do particles of various compositions and sizes become charged, or discharged, while exposed to an electron beam and ultraviolet radiation environment The emphasis is the study of the two charging mechanisms, secondary emission of electrons and photoelectric effect. The experiment uses a technique known as electrodynamic suspension of particles. With this technique, a single charged particle is electrodynamically levitated and then exposed to a controlled environment. Its charge to mass ratio is directly measured. Viscous drag measurements and the light scattering measurements characterize its size and optical characteristics. The environment to which the particle is expose may consist of room temperature and pressure or a rarefied atmosphere where only one major gaseous constituent is present, or, as in this case, a vacuum environment under electron bombardment or UV radiation . In addition, the environment can be cycled as part of the experiment. Therefore, using this technique, a single particle can be repeatedly exposed to a controlled environment and its response measured, or a single particle can be exposed to similar environments with minor differences and its response measured as a function of only the changed environmental conditions.

Deblurring of class-averaged images in single-particle electron microscopy

International Nuclear Information System (INIS)

Park, Wooram; Chirikjian, Gregory S; Madden, Dean R; Rockmore, Daniel N

2010-01-01

This paper proposes a method for the deblurring of class-averaged images in single-particle electron microscopy (EM). Since EM images of biological samples are very noisy, the images which are nominally identical projection images are often grouped, aligned and averaged in order to cancel or reduce the background noise. However, the noise in the individual EM images generates errors in the alignment process, which creates an inherent limit on the accuracy of the resulting class averages. This inaccurate class average due to the alignment errors can be viewed as the result of a convolution of an underlying clear image with a blurring function. In this work, we develop a deconvolution method that gives an estimate for the underlying clear image from a blurred class-averaged image using precomputed statistics of misalignment. Since this convolution is over the group of rigid-body motions of the plane, SE(2), we use the Fourier transform for SE(2) in order to convert the convolution into a matrix multiplication in the corresponding Fourier space. For practical implementation we use a Hermite-function-based image modeling technique, because Hermite expansions enable lossless Cartesian-polar coordinate conversion using the Laguerre–Fourier expansions, and Hermite expansion and Laguerre–Fourier expansion retain their structures under the Fourier transform. Based on these mathematical properties, we can obtain the deconvolution of the blurred class average using simple matrix multiplication. Tests of the proposed deconvolution method using synthetic and experimental EM images confirm the performance of our method

Reconstructing an icosahedral virus from single-particle diffraction experiments

Science.gov (United States)

Saldin, D. K.; Poon, H.-C.; Schwander, P.; Uddin, M.; Schmidt, M.

2011-08-01

The first experimental data from single-particle scattering experiments from free electron lasers (FELs) are now becoming available. The first such experiments are being performed on relatively large objects such as viruses, which produce relatively low-resolution, low-noise diffraction patterns in so-called ``diffract-and-destroy'' experiments. We describe a very simple test on the angular correlations of measured diffraction data to determine if the scattering is from an icosahedral particle. If this is confirmed, the efficient algorithm proposed can then combine diffraction data from multiple shots of particles in random unknown orientations to generate a full 3D image of the icosahedral particle. We demonstrate this with a simulation for the satellite tobacco necrosis virus (STNV), the atomic coordinates of whose asymmetric unit is given in Protein Data Bank entry 2BUK.

Cryo-electron microscopy of vitrified SV40 minichromosomes: the liquid drop model.

Science.gov (United States)

Dubochet, J; Adrian, M; Schultz, P; Oudet, P

1986-03-01

The structure of SV40 minichromosomes has been studied by cryo-electron microscopy of vitrified thin layers of solution. In high-salt buffer (130 mM NaCl), freshly prepared minichromosomes are condensed into globules 30 nm or more in diameter. On the micrograph, they appear to be formed by the close packing of 10 nm granules which give rise to a 10 nm reflection in the optical diffractogram. The globules can adopt many different conformations. At high concentration, they fuse into a homogeneous 'sea' of closely packed 10 nm granules. In low-salt buffer (less than 10 mM NaCl), the globules open, first into 10 nm filaments, and then into nucleosome-strings. The 'liquid drop' model is proposed to explain the condensed structure of the minichromosome in high-salt buffer: nucleosomes stack specifically on top of one another, thus forming the 10 nm filaments. 10 nm filaments in turn, tend to aggregate laterally. Optimizing both these interactions results in the condensation of 10 nm filaments or portions thereof into a structure similar to that of a liquid. Some implications of this model for the structure of cellular chromatin are discussed.

ESA CryoVEx 2014 - Airborne ASIRAS radar and laser scanner measurements during 2014 CryoVEx campaign in the Arctic

DEFF Research Database (Denmark)

Hvidegaard, S. M.; Nielsen, J. E.; Sørensen, L. Sandberg

the penetration depth of the ASIRAS radar. An opportunity site on the Greenland Ice Sheet was surveyed near Jakobshavn Isbræ. No other ground experiments were coordinated with the CryoVEx campaing on the Greenland Ice Sheet. The CryoVEx 2014 campaign was a success and the processed data is of high quality......This report outlines the airborne field operations with the ESA airborne Ku‐band interferometric radar (ASIRAS), coincident airborne laser scanner (ALS) and vertical photography to acquire data over sea‐ and land ice along validation sites and CryoSat‐2 ground tracks. The airborne campaign...... in the Beaufort Sea lead by US office of Naval Research (ONR) and north of Greenland as a dedicated ESA CryoVEx initiative. In addition, selected CryoSat‐2 ground tracks were under‐flown in the Lincoln Sea from CFS Alert, North of Greenland and Svalbard from St. Nord and Longyearbyen. Several of the flights...

Preparation of glibenclamide nanocrystals by a simple laboratory scale ultra cryo-milling

Energy Technology Data Exchange (ETDEWEB)

Martena, Valentina; Censi, Roberta [University of Camerino, School of Pharmacy (Italy); Hoti, Ela; Malaj, Ledjan [University of Tirana, Department of Pharmacy (Albania); Martino, Piera Di, E-mail: piera.dimartino@unicam.it [University of Camerino, School of Pharmacy (Italy)

2013-06-15

The objective of this study is to evaluate the ability to reduce the particle size of glibenclamide (GBC) to the nanometric scale through a very simple and well-known laboratory scale method, the laboratory scale ultra cryo-milling. The effect of milling on GBC crystalline properties and dissolution behaviour was deliberately evaluated in the absence of any surfactants as stabilizers. The milling procedure consisted in adding particles to liquid nitrogen and milling them by hand in a mortar with a pestle for different time intervals (15, 30, 40 min). For comparison, the same milling procedure was also applied without liquid nitrogen. The particle size reduction was evaluated for the coarsest samples (>3 {mu}m) by measuring the particle Ferret's diameter through scanning electron microscopy, while for the smallest one (<3 {mu}m) by dynamic light scattering. A time grinding of 40 min in the presence of liquid nitrogen was revealed highly efficacious to obtain particles of nanodimensions, with a geometric mean particle size of 0.55 {+-} 0.23 {mu}m and more than the 80 % of particles lower than 1,000 nm. Interestingly, non-agglomerated particles were obtained. Differential scanning calorimetry and X-ray powder diffractometry allowed to assess that under mechanical treatment no polymorphic transitions were observed, while a decrease in crystallinity degree occurred depending on the milling procedure (presence or absence of liquid nitrogen) and the milling time (crystallinity decreases at increasing milling time from 15 to 40 min). A comparison of the intrinsic dissolution rate and the dissolution from particles revealed an interesting improvement of particle dissolution particularly for particles milled in the presence of liquid nitrogen due to an increase in particle surface area and concentration gradient, according to the Noyes-Whitney equation.

Morphology of single inhalable particle inside public transit biodiesel fueled bus.

Science.gov (United States)

Shandilya, Kaushik K; Kumar, Ashok

2010-01-01

In an urban-transit bus, fueled by biodiesel in Toledo, Ohio, single inhalable particle samples in October 2008 were collected and detected by scanning electron microscopy and energy dispersive X-ray spectrometry (SEM/EDS). Particle size analysis found bimodal distribution at 0.2 and 0.5 microm. The particle morphology was characterized by 14 different shape clusters: square, pentagon, hexagon, heptagon, octagon, nonagon, decagon, agglomerate, sphere, triangle, oblong, strip, line or stick, and unknown, by quantitative order. The square particles were common in the samples. Round and triangle particles are more, and pentagon, hexagon, heptagon, octagon, nonagon, decagon, strip, line or sticks are less. Agglomerate particles were found in abundance. The surface of most particles was coarse with a fractal edge that can provide a suitable chemical reaction bed in the polluted atmospheric environment. The three sorts of surface patterns of squares were smooth, semi-smooth, and coarse. The three sorts of square surface patterns represented the morphological characteristics of single inhalable particles in the air inside the bus in Toledo. The size and shape distribution results were compared to those obtained for a bus using ultra low sulfur diesel.

Considerations of particle vaporization and analyte diffusion in single-particle inductively coupled plasma-mass spectrometry

International Nuclear Information System (INIS)

Ho, Koon-Sing; Lui, Kwok-On; Lee, Kin-Ho; Chan, Wing-Tat

2013-01-01

The intensity of individual gold nanoparticles with nominal diameters of 80, 100, 150, and 200 nm was measured using single-particle inductively coupled plasma-mass spectrometry (ICP-MS). Since the particles are not perfectly monodisperse, a distribution of ICP-MS intensity was obtained for each nominal diameter. The distribution of particle mass was determined from the transmission electron microscopy (TEM) image of the particles. The distribution of ICP-MS intensity and the distribution of particle mass for each nominal diameter were correlated to give a calibration curve. The calibration curves are linear, but the slope decreases as the nominal diameter increases. The reduced slope is probably due to a smaller degree of vaporization of the large particles. In addition to the degree of particle vaporization, the rate of analyte diffusion in the ICP is an important factor that determines the measured ICP-MS intensity. Simulated ICP-MS intensity versus particle size was calculated using a simple computer program that accounts for the vaporization rate of the gold nanoparticles and the diffusion rate and degree of ionization of the gold atoms. The curvature of the simulated calibration curves changes with sampling depth because the effects of particle vaporization and analyte diffusion on the ICP-MS intensity are dependent on the residence time of the particle in the ICP. Calibration curves of four hypothetical particles representing the four combinations of high and low boiling points (2000 and 4000 K) and high and low analyte diffusion rates (atomic masses of 10 and 200 Da) were calculated to further illustrate the relative effects of particle vaporization and analyte diffusion. The simulated calibration curves show that the sensitivity of single-particle ICP-MS is smaller than that of the ICP-MS measurement of continuous flow of standard solutions by a factor of 2 or more. Calibration using continuous flow of standard solution is semi-quantitative at best. An

Observation of ionomer in catalyst ink of polymer electrolyte fuel cell using cryogenic transmission electron microscopy

International Nuclear Information System (INIS)

Takahashi, Shinichi; Shimanuki, Junichi; Mashio, Tetsuya; Ohma, Atsushi; Tohma, Hajime; Ishihara, Ayumi; Ito, Yoshiko; Nishino, Yuri; Miyazawa, Atsuo

2017-01-01

Optimizing the catalyst layer structure is one of the key issues for improving performance despite lower platinum loading. The catalyst ink, consisting of platinum-loaded carbon particles and ionomer dispersed in an aqueous solvent, is a key factor for controlling the structure of the catalyst layer because the catalyst layer is prepared in a wet coating process. For that purpose, we visualized the nanostructure of the ionomer in the catalyst ink by cryogenic electron microscopy, especially cryogenic transmission electron microscopy (cryo-TEM). By cryo-TEM, it was revealed that ionomer molecules formed rod-like aggregates macro-homogeneously in the solvent, and a similar morphology was observed in a carbon-particle-containing solvent. In contrast, ionomer aggregates in the catalyst ink containing platinum nanoparticles loaded on carbon particles were denser in the vicinity of the platinum-loaded carbon particles. That can be attributed to strong interaction between platinum nanoparticles and sulfonic acid groups in the ionomer. It also implies that a good understanding of ionomer morphology in the catalyst ink can play an important role in controlling the catalyst layer microstructure for reducing platinum loading.

CryoSat product quality and evolutions

Science.gov (United States)

Bouffard, Jérome; Parrinello, Tommaso; Féménias, Pierre

2017-04-01

The main CryoSat mission objectives are to measure the regional and basin-scale changes in the thickness of the sea-ice and, in the elevation of the ice sheets and mountain glaciers. Beside its ice-monitoring objective, CryoSat also provides valuable observations for the oceanographic community. The CryoSat data are processed by ESA both over the ocean and ice surfaces with two independent processors. These data need to be routinely Quality-Controlled and thoroughly Validated (QCV). Based on the QCV outcomes from ESA multi-national partners and the feedback from the scientific community, the data products continuously evolve in order to accommodate a wide range of users over the Sea ice, the Land Ice and the Ocean domains. The main objectives of this paper are to give an overview of main CryoSat QCV results and product improvements; as well as to present the processing algorithm upgrades being implemented for future ice and ocean Baselines.

Delivery of single accelerated particles

International Nuclear Information System (INIS)

McNulty, P.J.; Pease, V.P.; Bond, V.P.; Schimmerling, W.; Vosburgh, K.G.; Crebbin, K.; Everette, W.; Howard, J.

1978-01-01

It is desirable for certain experiments involving accelerators to have the capability of delivering just a single beam particle to the target area. The essential features of such a one-at-a-time facility are discussed. Two such facilities are described which were implemented at high-energy heavy ion accelerators without having to make major structural changes in the existing beam lines or substantially interfering with other accelerator uses. Two accelerator facilities are described which had the capability of delivering a single beam particle to the target area. This feature is necessary in certain experiments investigating visual phenomena induced by charged particles, other single particle interactions in biology, and other experiments in which the low intensities of cosmic rays need to be simulated. Both facilities were implemented without having to make structural changes in the existing beam lines or substantially interfering with other accelerator uses. (Auth.)

Crystallization and preliminary X-ray diffraction analysis of recombinant hepatitis E virus-like particle

International Nuclear Information System (INIS)

Wang, Che-Yen; Miyazaki, Naoyuki; Yamashita, Tetsuo; Higashiura, Akifumi; Nakagawa, Atsushi; Li, Tian-Cheng; Takeda, Naokazu; Xing, Li; Hjalmarsson, Erik; Friberg, Claes; Liou, Der-Ming; Sung, Yen-Jen; Tsukihara, Tomitake; Matsuura, Yoshiharu; Miyamura, Tatsuo; Cheng, R. Holland

2008-01-01

A recombinant virus-like particle that is a potential oral hepatitis E vaccine was crystallized. Diffraction data were collected to 8.3 Å resolution and the X-ray structure was phased with the aid of a low-resolution density map determined using cryo-electron microscopy data. Hepatitis E virus (HEV) accounts for the majority of enterically transmitted hepatitis infections worldwide. Currently, there is no specific treatment for or vaccine against HEV. The major structural protein is derived from open reading frame (ORF) 2 of the viral genome. A potential oral vaccine is provided by the virus-like particles formed by a protein construct of partial ORF3 protein (residue 70–123) fused to the N-terminus of the ORF2 protein (residues 112–608). Single crystals obtained by the hanging-drop vapour-diffusion method at 293 K diffract X-rays to 8.3 Å resolution. The crystals belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 337, b = 343, c = 346 Å, α = β = γ = 90°, and contain one particle per asymmetric unit

Metal-nanoparticle single-electron transistors fabricated using electromigration

DEFF Research Database (Denmark)

Bolotin, K I; Kuemmeth, Ferdinand; Pasupathy, A N

2004-01-01

We have fabricated single-electron transistors from individual metal nanoparticles using a geometry that provides improved coupling between the particle and the gate electrode. This is accomplished by incorporating a nanoparticle into a gap created between two electrodes using electromigration, all...... on top of an oxidized aluminum gate. We achieve sufficient gate coupling to access more than ten charge states of individual gold nanoparticles (5–15 nm in diameter). The devices are sufficiently stable to permit spectroscopic studies of the electron-in-a-box level spectra within the nanoparticle as its...

Single-particle dispersion in compressible turbulence

Science.gov (United States)

Zhang, Qingqing; Xiao, Zuoli

2018-04-01

Single-particle dispersion statistics in compressible box turbulence are studied using direct numerical simulation. Focus is placed on the detailed discussion of effects of the particle Stokes number and turbulent Mach number, as well as the forcing type. When solenoidal forcing is adopted, it is found that the single-particle dispersion undergoes a transition from the ballistic regime at short times to the diffusive regime at long times, in agreement with Taylor's particle dispersion argument. The strongest dispersion of heavy particles is announced when the Stokes number is of order 1, which is similar to the scenario in incompressible turbulence. The dispersion tends to be suppressed as the Mach number increases. When hybrid solenoidal and compressive forcing at a ratio of 1/2 is employed, the flow field shows apparent anisotropic property, characterized by the appearance of large shock wave structures. Accordingly, the single-particle dispersion shows extremely different behavior from the solenoidal forcing case.

Imaging of Norway spruce early somatic embryos with the ESEM, Cryo-SEM and laser scanning microscope.

Science.gov (United States)

Neděla, Vilém; Hřib, Jiří; Havel, Ladislav; Hudec, Jiří; Runštuk, Jiří

2016-05-01

This article describes the surface structure of Norway spruce early somatic embryos (ESEs) as a typical culture with asynchronous development. The microstructure of extracellular matrix covering ESEs were observed using the environmental scanning electron microscope as a primary tool and using the scanning electron microscope with cryo attachment and laser electron microscope as a complementary tool allowing our results to be proven independently. The fresh samples were observed in conditions of the air environment of the environmental scanning electron microscope (ESEM) with the pressure from 550Pa to 690Pa and the low temperature of the sample from -18°C to -22°C. The samples were studied using two different types of detector to allow studying either the thin surface structure or material composition. The scanning electron microscope with cryo attachment was used for imaging frozen extracellular matrix microstructure with higher resolution. The combination of both electron microscopy methods was suitable for observation of "native" plant samples, allowing correct evaluation of our results, free of error and artifacts. Copyright © 2016 Elsevier Ltd. All rights reserved.

New design for a space cryo-mechanism

Science.gov (United States)

Durand, Gilles; Amiaux, Jérôme; Augueres, Jean-Louis; Carty, Michael; Barrière, Jean Christophe; Bouzat, Marylène; Duboué, Bruno; Lagage, Pierre Olivier; Lebeuf, Didier; Lepage, Erwan; Lemer, Isabelle; Marlaguey, Nathalie Peydrol; Poupar, Sébastien

2008-07-01

Based on its experience of space application instrument and its development of cryomechanism for astronomical ground based instrument VLT / VISIR, CEA Saclay is proposing a new concept of Space Cryomechanism. This design is based on VLT/VISIR cryo-mechanism design adapted to space requirements taking into account all the specification of space environment (vibrations at launch, cryogenic vacuum, materials, radiations, ...). The original concept of the design is based on the association of the key elements: a dog-clutch with Hirth teeth jaws coupled to a step-by-step space qualified cryo-motor, a bellows that allows for separation of indexing and rotating functions, and enlarged bearings design in "O" arrangement that increase robustness to vibration. The actuator has 360 steady positions that can be reached within les than a second with repeatability of 5 arcsec peak to peak. After a presentation of the details of the concept and of its benefits to robustness to space environment, the paper describes the thoroughly qualification program of the cryo-mechanism with respect to space requirements (cryo-cycling, indexing accuracy, power consumption, heat dissipation, motorisation margins, vibrations). This cryo-mechanism may be built in 3 different sizes for wheels up to 10 kg.

Cryo-balloon catheter localization in fluoroscopic images

Science.gov (United States)

Kurzendorfer, Tanja; Brost, Alexander; Jakob, Carolin; Mewes, Philip W.; Bourier, Felix; Koch, Martin; Kurzidim, Klaus; Hornegger, Joachim; Strobel, Norbert

2013-03-01

Minimally invasive catheter ablation has become the preferred treatment option for atrial fibrillation. Although the standard ablation procedure involves ablation points set by radio-frequency catheters, cryo-balloon catheters have even been reported to be more advantageous in certain cases. As electro-anatomical mapping systems do not support cryo-balloon ablation procedures, X-ray guidance is needed. However, current methods to provide support for cryo-balloon catheters in fluoroscopically guided ablation procedures rely heavily on manual user interaction. To improve this, we propose a first method for automatic cryo-balloon catheter localization in fluoroscopic images based on a blob detection algorithm. Our method is evaluated on 24 clinical images from 17 patients. The method successfully detected the cryoballoon in 22 out of 24 images, yielding a success rate of 91.6 %. The successful localization achieved an accuracy of 1.00 mm +/- 0.44 mm. Even though our methods currently fails in 8.4 % of the images available, it still offers a significant improvement over manual methods. Furthermore, detecting a landmark point along the cryo-balloon catheter can be a very important step for additional post-processing operations.

Single-particle potential from resummed ladder diagrams

International Nuclear Information System (INIS)

Kaiser, N.

2013-01-01

A recent work on the resummation of fermionic in-medium ladder diagrams to all orders is extended by calculating the complex single-particle potential U(p, k f ) + i W(p, k f ) p > k f . The on-shell single-particle potential is constructed by means of a complex-valued in-medium loop that includes corrections from a test particle of momentum vector p added to the filled Fermi sea. The single-particle potential U(k f , k f ) at the Fermi surface as obtained from the resummation of the combined particle and hole ladder diagrams is shown to satisfy the Hugenholtz-Van-Hove theorem. The perturbative contributions at various orders a n in the scattering length are deduced and checked against the known analytical results at order a 1 and a 2 . The limit a → ∞ is studied as a special case and a strong momentum dependence of the real (and imaginary) single-particle potential is found. This feature indicates an instability against a phase transition to a state with an empty shell inside the Fermi sphere such that the density gets reduced by about 5%. The imaginary single-particle potential vanishes linearly at the Fermi surface. For comparison, the same analysis is performed for the resummed particle-particle ladder diagrams alone. In this truncation an instability for hole excitations near the Fermi surface is found at strong coupling. For the set of particle-hole ring diagrams the single-particle potential is calculated as well. Furthermore, the resummation of in-medium ladder diagrams to all orders is studied for a two-dimensional Fermi gas with a short-range two-body contact interaction. (orig.)

Single particle distributions, ch.2

International Nuclear Information System (INIS)

Blokzijl, R.

1977-01-01

A survey of inclusive single particle distributions is given for various particles. A comparison of particle cross-sections measured in K - p experiments at different center of mass energies shows that some of these cross-sections remain almost constant over a wide range of incoming K - momenta

Plasmon excitation in single wall carbon nanotubes by penetrating charged particles

International Nuclear Information System (INIS)

Segui, Silvina; Gervasoni, Juana L; Arista, Néstor R; Mowbray, Duncan J; Mišković, Zoran L

2012-01-01

In this work we study the excitation of plasmons due to the incidence of a charged particle passing through a single wall carbon nanotube. We use a quantized hydrodynamic, in which the σ and π electrons characteristic of these carbonaceous structures are depicted as two interacting 2-dimensional fluids, to calculate the average number of plasmons excited. We analyze the contribution of the different plasmon modes in a variety of configurations, and study the energy lost by the incident particle.

Novel ultra-cryo milling and co-grinding technique in liquid nitrogen to produce dissolution-enhanced nanoparticles for poorly water-soluble drugs.

Science.gov (United States)

Sugimoto, Shohei; Niwa, Toshiyuki; Nakanishi, Yasuo; Danjo, Kazumi

2012-01-01

A novel ultra-cryo milling micronization technique for pharmaceutical powders using liquid nitrogen (LN2 milling) was used to grind phenytoin, a poorly water-soluble drug, to improve its dissolution rate. LN2 milling produced particles that were much finer and more uniform in size and shape than particles produced by jet milling. However, the dissolution rate of LN2-milled phenytoin was the same as that of unground phenytoin due to agglomeration of the submicron particles. To overcome this, phenytoin was co-ground with polyvinylpyrrolidone (PVP). The dissolution rate of co-ground phenytoin was much higher than that of original phenytoin, single-ground phenytoin, a physical mixture of phenytoin and PVP, or jet-milled phenytoin. X-Ray diffraction showed that the crystalline state of mixtures co-ground by LN2 milling remained unchanged. The equivalent improvement in dissolution, whether phenytoin was co-ground or separately ground and then mixed with PVP, suggested that even when co-ground, the grinding of PVP and phenytoin occurs essentially independently. Mixing original PVP with ground phenytoin provided a slight improvement in dissolution, indicating that the particle size of PVP is important for improving dissolution. When mixed with ground phenytoin, PVP ground by LN2 milling aided the wettability and dispersion of phenytoin, enhancing utilization of the large surface area of ground phenytoin. Co-grinding phenytoin with other excipients such as Eudragit L100, hypromellose, hypromellose acetate-succinate, microcrystalline cellulose, hydroxypropylcellulose and carboxymethyl cellulose also improved the dissolution profile, indicating an ultra-cryo milling and co-grinding technique in liquid nitrogen has a broad applicability of the dissolution enhancement of phenytoin.

The innovation of cryo-SEM freeze-fracturing methodology demonstrated on high pressure frozen biofilm.

Science.gov (United States)

Hrubanova, Kamila; Nebesarova, Jana; Ruzicka, Filip; Krzyzanek, Vladislav

2018-04-22

In this study we present an innovative method for the preparation of fully hydrated samples of microbial biofilms of cultures Staphylococcus epidermidis, Candida parapsilosis and Candida albicans. Cryo-scanning electron microscopy (cryo-SEM) and high-pressure freezing (HPF) rank among cutting edge techniques in the electron microscopy of hydrated samples such as biofilms. However, the combination of these techniques is not always easily applicable. Therefore, we present a method of combining high-pressure freezing using EM PACT2 (Leica Microsystems), which fixes hydrated samples on small sapphire discs, with a high resolution SEM equipped with the widely used cryo-preparation system ALTO 2500 (Gatan). Using a holder developed in house, a freeze-fracturing technique was applied to image and investigate microbial cultures cultivated on the sapphire discs. In our experiments, we focused on the ultrastructure of the extracellular matrix produced during cultivation and the relationships among microbial cells in the biofilm. The main goal of our investigations was the detailed visualization of areas of the biofilm where the microbial cells adhere to the substrate/surface. We show the feasibility of this technique, which is clearly demonstrated in experiments with various freeze-etching times. Copyright © 2018 Elsevier Ltd. All rights reserved.

Cryo-immunogold electron microscopy for prions: toward identification of a conversion site.

Science.gov (United States)

Godsave, Susan F; Wille, Holger; Kujala, Pekka; Latawiec, Diane; DeArmond, Stephen J; Serban, Ana; Prusiner, Stanley B; Peters, Peter J

2008-11-19

Prion diseases are caused by accumulation of an abnormally folded isoform (PrP(Sc)) of the cellular prion protein (PrP(C)). The subcellular distribution of PrP(Sc) and the site of its formation in brain are still unclear. We performed quantitative cryo-immunogold electron microscopy on hippocampal sections from mice infected with the Rocky Mountain Laboratory strain of prions. Two antibodies were used: R2, which recognizes both PrP(C) and PrP(Sc); and F4-31, which only detects PrP(C) in undenatured sections. At a late subclinical stage of prion infection, both PrP(C) and PrP(Sc) were detected principally on neuronal plasma membranes and on vesicles resembling early endocytic or recycling vesicles in the neuropil. The R2 labeling was approximately six times higher in the infected than the uninfected hippocampus and gold clusters were only evident in infected tissue. The biggest increase in labeling density (24-fold) was found on the early/recycling endosome-like vesicles of small-diameter neurites, suggesting these as possible sites of conversion. Trypsin digestion of infected hippocampal sections resulted in a reduction in R2 labeling of >85%, which suggests that a high proportion of PrP(Sc) may be oligomeric, protease-sensitive PrP(Sc).

Cryo-EM structures of two bovine adenovirus type 3 intermediates

International Nuclear Information System (INIS)

Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin; Xiong, Wei; Sun, Wei; Yang, Chongwen; Zhang, Kai; Wang, Ying; Liu, Hongrong; Huang, Xiaojun; Ji, Gang; Sun, Fei; Zheng, Congyi; Zhu, Ping

2014-01-01

Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure represents a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process

Cryo-EM structures of two bovine adenovirus type 3 intermediates

Energy Technology Data Exchange (ETDEWEB)

Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Xiong, Wei [State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Luo-jia-shan, Wuhan, Hubei 430072 (China); Sun, Wei; Yang, Chongwen; Zhang, Kai; Wang, Ying [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Liu, Hongrong [College of Physics and Information Science, Hunan Normal University, Changsha, Hunan 410081 (China); Huang, Xiaojun; Ji, Gang; Sun, Fei [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Zheng, Congyi, E-mail: cctcc202@whu.edu.cn [State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Luo-jia-shan, Wuhan, Hubei 430072 (China); Zhu, Ping, E-mail: zhup@ibp.ac.cn [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

2014-02-15

Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure represents a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process.

Process optimization of helium cryo plant operation for SST-1 superconducting magnet system

Science.gov (United States)

Panchal, P.; Panchal, R.; Patel, R.; Mahesuriya, G.; Sonara, D.; Srikanth G, L. N.; Garg, A.; Christian, D.; Bairagi, N.; Sharma, R.; Patel, K.; Shah, P.; Nimavat, H.; Purwar, G.; Patel, J.; Tanna, V.; Pradhan, S.

2017-02-01

Several plasma discharge campaigns have been carried out in steady state superconducting tokamak (SST-1). SST-1 has toroidal field (TF) and poloidal field (PF) superconducting magnet system (SCMS). The TF coils system is cooled to 4.5 - 4.8 K at 1.5 - 1.7 bar(a) under two phase flow condition using 1.3 kW helium cryo plant. Experience revealed that the PF coils demand higher pressure heads even at lower temperatures in comparison to TF coils because of its longer hydraulic path lengths. Thermal run away are observed within PF coils because of single common control valve for all PF coils in distribution system having non-uniform lengths. Thus it is routine practice to stop the cooling of PF path and continue only TF cooling at SCMS inlet temperature of ˜ 14 K. In order to achieve uniform cool down, different control logic is adopted to make cryo stable system. In adopted control logic, the SCMS are cooled down to 80 K at constant inlet pressure of 9 bar(a). After authorization of turbine A/B, the SCMS inlet pressure is gradually controlled by refrigeration J-T valve to achieve stable operation window for cryo system. This paper presents process optimization for cryo plant operation for SST-1 SCMS.

Development of forage cryo minced fish technology

Directory of Open Access Journals (Sweden)

Titova S. A.

2017-11-01

Full Text Available The technology of grinding the frozen fish raw material using the useful model of a piston-type extrusion plant with cold working bodies for fodder minced fish (cryo minced fish feed by the method of cryoextrusion has been developed. The possibility of replacing the standard manufacturing operations (defrosting and subsequent grinding of raw materials to the one (cryoextrusion has been substantiated. The optimal shape of holes of the die for forcing the raw material has been determined in the form of "hourglass", the hole diameter is 7 mm, the length of the process of pushing is 40 s. It has been established that the finished product (cryo minced fish feed has a homogeneous grinding, juicy, crumbly texture, the temperature in the thickness of the product is equal to the temperature of the raw material before processing (–18 °C. The technological scheme of producing the minced fish feed by the method of cryoextrusion has been developed. Researching the chemical composition of fish and feed of mince produced by the traditional and developed methods it has been established that protein content in the cryo minced fish feed remains unchanged. The amino acid composition of cryo minced fish feed has been determined, the amount of essential amino acids is 365.6 mg/g of protein. In the proteins of the cryo minced fish feed methionine has been contained in the minimum quantity (10.0 mg/g protein and in the maximum – serine (155.3 mg/g protein. In the protein of the cryo minced fish feed the only limiting amino acid is methionine. The coefficient of rationality of the cryo minced fish feed whiting is equal to 0.33. The product is not toxic, is not subject to contamination with dangerous microorganisms, has high biological value, contains necessary in animal nutrition mineral elements, the energy value per 100 g of the product is 87 kcal. The combination of the processes of cryoextrusion and lyophilization allows to obtain a new food product with high

Determining Complex Structures using Docking Method with Single Particle Scattering Data

Directory of Open Access Journals (Sweden)

Haiguang Liu

2017-04-01

Full Text Available Protein complexes are critical for many molecular functions. Due to intrinsic flexibility and dynamics of complexes, their structures are more difficult to determine using conventional experimental methods, in contrast to individual subunits. One of the major challenges is the crystallization of protein complexes. Using X-ray free electron lasers (XFELs, it is possible to collect scattering signals from non-crystalline protein complexes, but data interpretation is more difficult because of unknown orientations. Here, we propose a hybrid approach to determine protein complex structures by combining XFEL single particle scattering data with computational docking methods. Using simulations data, we demonstrate that a small set of single particle scattering data collected at random orientations can be used to distinguish the native complex structure from the decoys generated using docking algorithms. The results also indicate that a small set of single particle scattering data is superior to spherically averaged intensity profile in distinguishing complex structures. Given the fact that XFEL experimental data are difficult to acquire and at low abundance, this hybrid approach should find wide applications in data interpretations.

Microscopic validation of whole mouse micro-metastatic tumor imaging agents using cryo-imaging and sliding organ image registration

OpenAIRE

Liu, Yiqiao; Zhou, Bo; Qutaish, Mohammed; Wilson, David L.

2016-01-01

We created a metastasis imaging, analysis platform consisting of software and multi-spectral cryo-imaging system suitable for evaluating emerging imaging agents targeting micro-metastatic tumor. We analyzed CREKA-Gd in MRI, followed by cryo-imaging which repeatedly sectioned and tiled microscope images of the tissue block face, providing anatomical bright field and molecular fluorescence, enabling 3D microscopic imaging of the entire mouse with single metastatic cell sensitivity. To register ...

Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms.

Science.gov (United States)

Xu, Min; Chai, Xiaoqi; Muthakana, Hariank; Liang, Xiaodan; Yang, Ge; Zeev-Ben-Mordehai, Tzviya; Xing, Eric P

2017-07-15

Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and their spatial organizations inside single cells. However, high degree of structural complexity together with practical imaging limitations makes the systematic de novo discovery of structures within cells challenging. It would likely require averaging and classifying millions of subtomograms potentially containing hundreds of highly heterogeneous structural classes. Although it is no longer difficult to acquire CECT data containing such amount of subtomograms due to advances in data acquisition automation, existing computational approaches have very limited scalability or discrimination ability, making them incapable of processing such amount of data. To complement existing approaches, in this article we propose a new approach for subdividing subtomograms into smaller but relatively homogeneous subsets. The structures in these subsets can then be separately recovered using existing computation intensive methods. Our approach is based on supervised structural feature extraction using deep learning, in combination with unsupervised clustering and reference-free classification. Our experiments show that, compared with existing unsupervised rotation invariant feature and pose-normalization based approaches, our new approach achieves significant improvements in both discrimination ability and scalability. More importantly, our new approach is able to discover new structural classes and recover structures that do not exist in training data. Source code freely available at http://www.cs.cmu.edu/∼mxu1/software . mxu1@cs.cmu.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Airborne campaigns for CryoSat pre-launch calibration and validation

DEFF Research Database (Denmark)

Hvidegaard, Sine Munk; Forsberg, René; Skourup, Henriette

2010-01-01

From 2003 to 2008 DTU Space together with ESA and several international partners carried out airborne and ground field campaigns in preparation for CryoSat validation; called CryoVEx: CryoSat Validation Experiments covering the main ice caps in Greenland, Canada and Svalbard and sea ice in the Ar......From 2003 to 2008 DTU Space together with ESA and several international partners carried out airborne and ground field campaigns in preparation for CryoSat validation; called CryoVEx: CryoSat Validation Experiments covering the main ice caps in Greenland, Canada and Svalbard and sea ice...... in the Arctic Ocean. The main goal of the airborne surveys was to acquire coincident scanning laser and CryoSat type radar elevation measurements of the surface; either sea ice or land ice. Selected lines have been surveyed along with detailed mapping of validation sites coordinated with insitu field work...... and helicopter electromagnetic surveying. This paper summarises the pre-launch campaigns and presents some of the result from the coincident measurement from airborne and ground observations....

Preparation and Characterization of Stable α-Synuclein Lipoprotein Particles.

Science.gov (United States)

Eichmann, Cédric; Campioni, Silvia; Kowal, Julia; Maslennikov, Innokentiy; Gerez, Juan; Liu, Xiaoxia; Verasdonck, Joeri; Nespovitaya, Nadezhda; Choe, Senyon; Meier, Beat H; Picotti, Paola; Rizo, Josep; Stahlberg, Henning; Riek, Roland

2016-04-15

Multiple neurodegenerative diseases are caused by the aggregation of the human α-Synuclein (α-Syn) protein. α-Syn possesses high structural plasticity and the capability of interacting with membranes. Both features are not only essential for its physiological function but also play a role in the aggregation process. Recently it has been proposed that α-Syn is able to form lipid-protein particles reminiscent of high-density lipoproteins. Here, we present a method to obtain a stable and homogeneous population of nanometer-sized particles composed of α-Syn and anionic phospholipids. These particles are called α-Syn lipoprotein (nano)particles to indicate their relationship to high-density lipoproteins formed by human apolipoproteins in vivo and of in vitro self-assembling phospholipid bilayer nanodiscs. Structural investigations of the α-Syn lipoprotein particles by circular dichroism (CD) and magic angle solid-state nuclear magnetic resonance (MAS SS-NMR) spectroscopy establish that α-Syn adopts a helical secondary structure within these particles. Based on cryo-electron microscopy (cryo-EM) and dynamic light scattering (DLS) α-Syn lipoprotein particles have a defined size with a diameter of ∼23 nm. Chemical cross-linking in combination with solution-state NMR and multiangle static light scattering (MALS) of α-Syn particles reveal a high-order protein-lipid entity composed of ∼8-10 α-Syn molecules. The close resemblance in size between cross-linked in vitro-derived α-Syn lipoprotein particles and a cross-linked species of endogenous α-Syn from SH-SY5Y human neuroblastoma cells indicates a potential functional relevance of α-Syn lipoprotein nanoparticles. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

From structure of the complex to understanding of the biology

Energy Technology Data Exchange (ETDEWEB)

Rossmann, Michael G., E-mail: mr@purdue.edu [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Arisaka, Fumio [Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Kanamaru, Shuji [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Kostyuchenko, Victor A. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Mesyanzhinov, Vadim V.; Shneider, Mikhail M. [Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, 117997 (Russian Federation); Morais, Marc C.; Leiman, Petr G. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Palermo, Laura M.; Parrish, Colin R. [James A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (United States); Xiao, Chuan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States)

2007-01-01

The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.

From structure of the complex to understanding of the biology

International Nuclear Information System (INIS)

Rossmann, Michael G.; Arisaka, Fumio; Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan; Kanamaru, Shuji; Kostyuchenko, Victor A.; Mesyanzhinov, Vadim V.; Shneider, Mikhail M.; Morais, Marc C.; Leiman, Petr G.; Palermo, Laura M.; Parrish, Colin R.; Xiao, Chuan

2007-01-01

The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle

Electron cooling and elementary particle physics

International Nuclear Information System (INIS)

Budker, G.I.; Skrinskij, A.N.

1978-01-01

This review is devoted to a new method in experimental physics - the electron cooling. This method opens possibilities in storing the intense and highly monochromatic beams of heavy particles and allows to carry out a wide series of experiments of a high luminocity and resolution. The method is based on the beam cooling by an accompanying flux of electrons. The cooling is due to Coulomb collisions of the beam particles with electrons. In the first part the theoretical aspects of the method are considered shortly. The layout of the NAP-M installation with electron cooling and results of successful experiments on cooling the proton beam are given. In the second part the new possibilities are discussed which appear due to application of electron cooling: storing the intense antiproton beams and realization of the proton - antiproton colliding beams, carrying out experiments with the super fine targets in storage rings, experiments with particles and antiparticles at ultimately low energies, storing the polarized antiprotons and other particles, production of antiatoms, antideuton storing, experiments with ion beams

Compact femtosecond electron diffractometer with 100 keV electron bunches approaching the single-electron pulse duration limit

International Nuclear Information System (INIS)

Waldecker, Lutz; Bertoni, Roman; Ernstorfer, Ralph

2015-01-01

We present the design and implementation of a highly compact femtosecond electron diffractometer working at electron energies up to 100 keV. We use a multi-body particle tracing code to simulate electron bunch propagation through the setup and to calculate pulse durations at the sample position. Our simulations show that electron bunches containing few thousands of electrons per bunch are only weakly broadened by space-charge effects and their pulse duration is thus close to the one of a single-electron wavepacket. With our compact setup, we can create electron bunches containing up to 5000 electrons with a pulse duration below 100 fs on the sample. We use the diffractometer to track the energy transfer from photoexcited electrons to the lattice in a thin film of titanium. This process takes place on the timescale of few-hundred femtoseconds and a fully equilibrated state is reached within 1 ps

The New Electron Microscopy: Cells and Molecules in Three Dimensions | Poster

Science.gov (United States)

NCI recently announced the launch of the new National Cryo-Electron Microscopy Facility (NCEF) at the Frederick National Laboratory for Cancer Research (FNLCR). The launch comes while cryo-electron microscopy (cryo-EM) is enjoying the spotlight as a newly emerging, rapidly evolving technology with the potential to revolutionize the field of structural biology. Read more...

An Electron is the God Particle

Science.gov (United States)

Wolff, Milo

2001-04-01

Philosophers, Clifford, Mach, Einstein, Wyle, Dirac & Schroedinger, believed that only a wave structure of particles could satisfy experiment and fulfill reality. A quantum Wave Structure of Matter is described here. It predicts the natural laws more accurately and completely than classic laws. Einstein reasoned that the universe depends on particles which are "spherically, spatially extended in space." and "Hence a discrete material particle has no place as a fundamental concept in a field theory." Thus the discrete point particle was wrong. He deduced the true electron is primal because its force range is infinite. Now, it is found the electron's wave structure contains the laws of Nature that rule the universe. The electron plays the role of creator - the God particle. Electron structure is a pair of spherical outward/inward quantum waves, convergent to a center in 3D space. This wave pair creates a h/4pi quantum spin when the in-wave spherically rotates to become the out-wave. Both waves form a spinor satisfying the Dirac Equation. Thus, the universe is binary like a computer. Reference: http://members.tripod.com/mwolff

Big Bang Day: 5 Particles - 1. The Electron

CERN Multimedia

Simon Singh

2008-01-01

Simon Singh looks at the stories behind the discovery of 5 of the universe's most significant subatomic particles: the Electron, the Quark, the Anti-particle, the Neutrino and the "next particle". 1. The Electron Just over a century ago, British physicist J.J. Thompson experimenting with electric currents and charged particles inside empty glass tubes, showed that atoms are divisible into indivisible elementary particles. But how could atoms be built up of these so called "corpuscles"? An exciting 30 year race ensued, to grasp the planetary model of the atom with its orbiting electrons, and the view inside the atom was born. Whilst the number of electrons around the nucleus of an atom determines their the chemistry of all elements, the power of electrons themselves have been harnessed for everyday use: electron beams for welding,cathode ray tubes and radiation therapy.

Saha equation, single and two particle states

International Nuclear Information System (INIS)

Kraeft, W.D.; Girardeau, M.D.; Strege, B.

1990-01-01

Single and two particle porperties in dense plasma are discussed in connection with their role in the mass action law for a partially ionized plasma. The two particle bound states are nearly density independent, while the continuum is essentially shifted. The single particle states are damped, and their energy has a negative shift and a parabolic behaviour for small momenta. (orig.)

Stack Characterization in CryoSat Level1b SAR/SARin Baseline C

Science.gov (United States)

Scagliola, Michele; Fornari, Marco; Di Giacinto, Andrea; Bouffard, Jerome; Féménias, Pierre; Parrinello, Tommaso

2015-04-01

CryoSat was launched on the 8th April 2010 and is the first European ice mission dedicated to the monitoring of precise changes in the thickness of polar ice sheets and floating sea ice. CryoSat is the first altimetry mission operating in SAR mode and it carries an innovative radar altimeter called the Synthetic Aperture Interferometric Altimeter (SIRAL), that transmits pulses at a high pulse repetition frequency thus making the received echoes phase coherent and suitable for azimuth processing. The current CryoSat IPF (Instrument Processing Facility), Baseline B, was released in operation in February 2012. After more than 2 years of development, the release in operations of the Baseline C is expected in the first half of 2015. It is worth recalling here that the CryoSat SAR/SARin IPF1 generates 20Hz waveforms in correspondence of an approximately equally spaced set of ground locations on the Earth surface, i.e. surface samples, and that a surface sample gathers a collection of single-look echoes coming from the processed bursts during the time of visibility. Thus, for a given surface sample, the stack can be defined as the collection of all the single-look echoes pointing to the current surface sample, after applying all the necessary range corrections. The L1B product contains the power average of all the single-look echoes in the stack: the multi-looked L1B waveform. This reduces the data volume, while removing some information contained in the single looks, useful for characterizing the surface and modelling the L1B waveform. To recover such information, a set of parameters has been added to the L1B product: the stack characterization or beam behaviour parameters. The stack characterization, already included in previous Baselines, has been reviewed and expanded in Baseline C. This poster describes all the stack characterization parameters, detailing what they represent and how they have been computed. In details, such parameters can be summarized in: - Stack

Experiments in electron microscopy: from metals to nerves

International Nuclear Information System (INIS)

Unwin, Nigel

2015-01-01

Electron microscopy has advanced remarkably as a tool for biological structure research since the development of methods to examine radiation-sensitive unstained specimens and the introduction of cryo-techniques. Structures of biological molecules at near-atomic resolution can now be obtained from images of single particles as well as crystalline arrays. It has also become possible to analyze structures of molecules in their functional context, i.e. in their natural membrane or cellular setting, and in an ionic environment like that in living tissue. Electron microscopy is thus opening ways to answer definitively questions about physiological mechanisms. Here I recall a number of experiments contributing to, and benefiting from the technical advances that have taken place. I begin—in the spirit of this crystallography series—with some biographical background, and then sketch the path to an analysis by time-resolved microscopy of the opening mechanism of an ion channel (nicotinic acetylcholine receptor). This analysis illustrates how electron imaging can be combined with freeze-trapping to illuminate a transient biological event: in our case, chemical-to-electrical transduction at the nerve-muscle synapse. (invited comment)

Detecting single-electron events in TEM using low-cost electronics and a silicon strip sensor.

Science.gov (United States)

Gontard, Lionel C; Moldovan, Grigore; Carmona-Galán, Ricardo; Lin, Chao; Kirkland, Angus I

2014-04-01

There is great interest in developing novel position-sensitive direct detectors for transmission electron microscopy (TEM) that do not rely in the conversion of electrons into photons. Direct imaging improves contrast and efficiency and allows the operation of the microscope at lower energies and at lower doses without loss in resolution, which is especially important for studying soft materials and biological samples. We investigate the feasibility of employing a silicon strip detector as an imaging detector for TEM. This device, routinely used in high-energy particle physics, can detect small variations in electric current associated with the impact of a single charged particle. The main advantages of using this type of sensor for direct imaging in TEM are its intrinsic radiation hardness and large detection area. Here, we detail design, simulation, fabrication and tests in a TEM of the front-end electronics developed using low-cost discrete components and discuss the limitations and applications of this technology for TEM.

Chemical compositions of subway particles in Seoul, Korea determined by a quantitative single particle analysis.

Science.gov (United States)

Kang, Sunni; Hwang, HeeJin; Park, YooMyung; Kim, HyeKyoung; Ro, Chul-Un

2008-12-15

A novel single particle analytical technique, low-Z particle electron probe X-ray microanalysis, was applied to characterize seasonal subway samples collected at a subway station in Seoul, Korea. For all 8 samples collected twice in each season, 4 major types of subway particles, based on their chemical compositions, are significantly encountered: Fe-containing; soil-derived; carbonaceous; and secondary nitrate and/or sulfate particles. Fe-containing particles are generated indoors from wear processes at rail-wheel-brake interfaces while the others may be introduced mostly from the outdoor urban atmosphere. Fe-containing particles are the most frequently encountered with relative abundances in the range of 61-79%. In this study, it is shown that Fe-containing subway particles almost always exist either as partially or fully oxidized forms in underground subway microenvironments. Their relative abundances of Fe-containing particles increase as particle sizes decrease. Relative abundances of Fe-containing particles are higher in morning samples than in afternoon samples because of heavier train traffic in the morning. In the summertime samples, Fe-containing particles are the most abundantly encountered, whereas soil-derived and nitrate/sulfate particles are the least encountered, indicating the air-exchange between indoor and outdoor environments is limited in the summer, owing to the air-conditioning in the subway system. In our work, it was observed that the relative abundances of the particles of outdoor origin vary somewhat among seasonal samples to a lesser degree, reflecting that indoor emission sources predominate.

Electron Bio-Imaging Centre (eBIC): the UK national research facility for biological electron microscopy.

Science.gov (United States)

Clare, Daniel K; Siebert, C Alistair; Hecksel, Corey; Hagen, Christoph; Mordhorst, Valerie; Grange, Michael; Ashton, Alun W; Walsh, Martin A; Grünewald, Kay; Saibil, Helen R; Stuart, David I; Zhang, Peijun

2017-06-01

The recent resolution revolution in cryo-EM has led to a massive increase in demand for both time on high-end cryo-electron microscopes and access to cryo-electron microscopy expertise. In anticipation of this demand, eBIC was set up at Diamond Light Source in collaboration with Birkbeck College London and the University of Oxford, and funded by the Wellcome Trust, the UK Medical Research Council (MRC) and the Biotechnology and Biological Sciences Research Council (BBSRC) to provide access to high-end equipment through peer review. eBIC is currently in its start-up phase and began by offering time on a single FEI Titan Krios microscope equipped with the latest generation of direct electron detectors from two manufacturers. Here, the current status and modes of access for potential users of eBIC are outlined. In the first year of operation, 222 d of microscope time were delivered to external research groups, with 95 visits in total, of which 53 were from unique groups. The data collected have generated multiple high- to intermediate-resolution structures (2.8-8 Å), ten of which have been published. A second Krios microscope is now in operation, with two more due to come online in 2017. In the next phase of growth of eBIC, in addition to more microscope time, new data-collection strategies and sample-preparation techniques will be made available to external user groups. Finally, all raw data are archived, and a metadata catalogue and automated pipelines for data analysis are being developed.

Single-particle Glauber matrix elements

International Nuclear Information System (INIS)

Oset, E.; Strottman, D.

1983-01-01

The single-particle matrix elements of the Glauber profile function are tabulated for harmonic oscillator single-particle wave functions. The tables are presented in such a manner as to be applicable if the hadron--nucleon elementary scattering amplitude is specified by either a partial wave expansion or a Gaussian in momentum transfer squared. The table is complete through the 1 g/sub 9/2/ orbital and contains entries for the 3s/sub 1/2/ orbital for use if realistic wave functions are expanded in terms of harmonic oscillator functions

Frontend electronics for high-precision single photo-electron timing using FPGA-TDCs

Energy Technology Data Exchange (ETDEWEB)

Cardinali, M., E-mail: cardinal@kph.uni-mainz.de [Institut für Kernphysik, Johannes Gutenberg-University Mainz, Mainz (Germany); Helmholtz Institut Mainz, Mainz (Germany); Dzyhgadlo, R.; Gerhardt, A.; Götzen, K.; Hohler, R.; Kalicy, G.; Kumawat, H.; Lehmann, D.; Lewandowski, B.; Patsyuk, M.; Peters, K.; Schepers, G.; Schmitt, L.; Schwarz, C.; Schwiening, J.; Traxler, M.; Ugur, C.; Zühlsdorf, M. [GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt (Germany); Dodokhov, V.Kh. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Britting, A. [Friedrich Alexander-University of Erlangen-Nuremberg, Erlangen (Germany); and others

2014-12-01

The next generation of high-luminosity experiments requires excellent particle identification detectors which calls for Imaging Cherenkov counters with fast electronics to cope with the expected hit rates. A Barrel DIRC will be used in the central region of the Target Spectrometer of the planned PANDA experiment at FAIR. A single photo-electron timing resolution of better than 100 ps is required by the Barrel DIRC to disentangle the complicated patterns created on the image plane. R and D studies have been performed to provide a design based on the TRB3 readout using FPGA-TDCs with a precision better than 20 ps RMS and custom frontend electronics with high-bandwidth pre-amplifiers and fast discriminators. The discriminators also provide time-over-threshold information thus enabling walk corrections to improve the timing resolution. Two types of frontend electronics cards optimised for reading out 64-channel PHOTONIS Planacon MCP-PMTs were tested: one based on the NINO ASIC and the other, called PADIWA, on FPGA discriminators. Promising results were obtained in a full characterisation using a fast laser setup and in a test experiment at MAMI, Mainz, with a small scale DIRC prototype. - Highlights: • Frontend electronics for Cherenkov detectors have been developed. • FPGA-TDCs have been used for high precision timing. • Time over threshold has been utilised for walk correction. • Single photo-electron timing resolution less than 100 ps has been achieved.

Single-particle Schroedinger fluid. I. Formulation

International Nuclear Information System (INIS)

Kan, K.K.; Griffin, J.J.

1976-01-01

The problem of a single quantal particle moving in a time-dependent external potential well is formulated specifically to emphasize and develop the fluid dynamical aspects of the matter flow. This idealized problem, the single-particle Schroedinger fluid, is shown to exhibit already a remarkably rich variety of fluid dynamical features, including compressible flow and line vortices. It provides also a sufficient framework to encompass simultaneously various simplified fluidic models for nuclei which have earlier been postulated on an ad hoc basis, and to illuminate their underlying restrictions. Explicit solutions of the single-particle Schroedinger fluid problem are studied in the adiabatic limit for their mathematical and physical implications (especially regarding the collective kinetic energy). The basic generalizations for extension of the treatment to the many-body Schroedinger fluid are set forth

Methods for forming particles from single source precursors

Science.gov (United States)

Fox, Robert V [Idaho Falls, ID; Rodriguez, Rene G [Pocatello, ID; Pak, Joshua [Pocatello, ID

2011-08-23

Single source precursors are subjected to carbon dioxide to form particles of material. The carbon dioxide may be in a supercritical state. Single source precursors also may be subjected to supercritical fluids other than supercritical carbon dioxide to form particles of material. The methods may be used to form nanoparticles. In some embodiments, the methods are used to form chalcopyrite materials. Devices such as, for example, semiconductor devices may be fabricated that include such particles. Methods of forming semiconductor devices include subjecting single source precursors to carbon dioxide to form particles of semiconductor material, and establishing electrical contact between the particles and an electrode.

Single-particle motion in large-amplitude quadrupole shape transition

International Nuclear Information System (INIS)

Yamada, Kazuya

1991-01-01

The microscopic structure of the single-particle motion for the spherical-deformed transitional nuclei is analysed by using the self-consistent collective-coordinate method (SCC method). The single-particle motion in the moving-frame of reference called the collective vibrating coordinate frame is introduced by the generalized Bogoliubov transformation depending on the collective coordinate. The numerical calculations of the single-particle (quasi-particle) energy level diagrams and their occupation probabilities for the static deformation are carried out for the Sm isotopes. A clear change of the single-particle distribution structure appears in the course of deformation. (author)

Electron beam driven disordering in small particles

International Nuclear Information System (INIS)

Vanfleet, R.R.; Mochel, J.

1997-01-01

Small metal particles in the range of a few nanometers in diameter are seen to progressively disorder when the 100 keV electron beam of a Scanning Transmission Electron Microscope (STEM) is held stationary on the particle. The diffraction pattern of the individual particle is seen to progress from an initial array of indexable diffraction spots to a mixture of diffraction spots and amorphous-like rings and finally to rings with no persistent diffraction spots. After the electron beam is removed, the particles will recrystallize after minutes or hours. Only particles below a critical size are seen to fully disorder. The authors have observed this in platinum, palladium, rhodium, and iridium and based on the model of disordering process believe it is a universal effect. It has also been observed with a platinum ruthenium alloy. They discuss the mechanism of this disordering and the structure of the resulting disordering particle for the case of platinum clusters

4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.

Science.gov (United States)

Cong, Yao; Baker, Matthew L; Jakana, Joanita; Woolford, David; Miller, Erik J; Reissmann, Stefanie; Kumar, Ramya N; Redding-Johanson, Alyssa M; Batth, Tanveer S; Mukhopadhyay, Aindrila; Ludtke, Steven J; Frydman, Judith; Chiu, Wah

2010-03-16

The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of approximately 5-10% of the cellular proteome. Many TRiC substrates cannot be folded by other chaperonins from prokaryotes or archaea. These unique folding properties are likely linked to TRiC's unique heterooligomeric subunit organization, whereby each ring consists of eight different paralogous subunits in an arrangement that remains uncertain. Using single particle cryo-EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7-A resolution. This revealed the existence of a 2-fold axis between its two rings resulting in two homotypic subunit interactions across the rings. A subsequent 2-fold symmetrized map yielded a 4.0-A resolution structure that evinces the densities of a large fraction of side chains, loops, and insertions. These features permitted unambiguous identification of all eight individual subunits, despite their sequence similarity. Independent biochemical near-neighbor analysis supports our cryo-EM derived TRiC subunit arrangement. We obtained a Calpha backbone model for each subunit from an initial homology model refined against the cryo-EM density. A subsequently optimized atomic model for a subunit showed approximately 95% of the main chain dihedral angles in the allowable regions of the Ramachandran plot. The determination of the TRiC subunit arrangement opens the way to understand its unique function and mechanism. In particular, an unevenly distributed positively charged wall lining the closed folding chamber of TRiC differs strikingly from that of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity.

Transmission electron microscopy of amyloid fibrils.

Science.gov (United States)

Gras, Sally L; Waddington, Lynne J; Goldie, Kenneth N

2011-01-01

Transmission Electron Microscopy of negatively stained and cryo-prepared specimens allows amyloid fibrils to be visualised at high resolution in a dried or a hydrated state, and is an essential method for characterising the morphology of fibrils and pre-fibrillar species. We outline the key steps involved in the preparation and observation of samples using negative staining and cryo-electron preservation. We also discuss methods to measure fibril characteristics, such as fibril width, from electron micrographs.

The single scattering properties of the aerosol particles as aggregated spheres

International Nuclear Information System (INIS)

Wu, Y.; Gu, X.; Cheng, T.; Xie, D.; Yu, T.; Chen, H.; Guo, J.

2012-01-01

The light scattering and absorption properties of anthropogenic aerosol particles such as soot aggregates are complicated in the temporal and spatial distribution, which introduce uncertainty of radiative forcing on global climate change. In order to study the single scattering properties of anthorpogenic aerosol particles, the structures of these aerosols such as soot paticles and soot-containing mixtures with the sulfate or organic matter, are simulated using the parallel diffusion limited aggregation algorithm (DLA) based on the transmission electron microscope images (TEM). Then, the single scattering properties of randomly oriented aerosols, such as scattering matrix, single scattering albedo (SSA), and asymmetry parameter (AP), are computed using the superposition T-matrix method. The comparisons of the single scattering properties of these specific types of clusters with different morphological and chemical factors such as fractal parameters, aspect ratio, monomer radius, mixture mode and refractive index, indicate that these different impact factors can respectively generate the significant influences on the single scattering properties of these aerosols. The results show that aspect ratio of circumscribed shape has relatively small effect on single scattering properties, for both differences of SSA and AP are less than 0.1. However, mixture modes of soot clusters with larger sulfate particles have remarkably important effects on the scattering and absorption properties of aggregated spheres, and SSA of those soot-containing mixtures are increased in proportion to the ratio of larger weakly absorbing attachments. Therefore, these complex aerosols come from man made pollution cannot be neglected in the aerosol retrievals. The study of the single scattering properties on these kinds of aggregated spheres is important and helpful in remote sensing observations and atmospheric radiation balance computations.

Scanning electron microscopy-energy dispersive X-ray spectrometry (SEM-EDX) and aerosol time-of-flight mass spectrometry (ATOFMS) single particle analysis of metallurgy plant emissions.

Science.gov (United States)

Arndt, J; Deboudt, K; Anderson, A; Blondel, A; Eliet, S; Flament, P; Fourmentin, M; Healy, R M; Savary, V; Setyan, A; Wenger, J C

2016-03-01

The chemical composition of single particles deposited on industrial filters located in three different chimneys of an iron-manganese (Fe-Mn) alloy manufacturing plant have been compared using aerosol time-of-flight mass spectrometry (ATOFMS) and scanning electron microscopy-energy dispersive X-ray spectrometry (SEM-EDX). Very similar types of particles were observed using both analytical techniques. Calcium-containing particles dominated in the firing area of the sintering unit, Mn and/or Al-bearing particles were observed at the cooling area of the sintering unit, while Mn-containing particles were dominant at the smelting unit. SEM-EDX analysis of particles collected downstream of the industrial filters showed that the composition of the particles emitted from the chimneys is very similar to those collected on the filters. ATOFMS analysis of ore samples was also performed to identify particulate emissions that could be generated by wind erosion and manual activities. Specific particle types have been identified for each emission source (chimneys and ore piles) and can be used as tracers for source apportionment of ambient PM measured in the vicinity of the industrial site. Copyright © 2015 Elsevier Ltd. All rights reserved.

Single particle dynamics in circular accelerators

International Nuclear Information System (INIS)

Ruth, R.D.

1986-10-01

The purpose of this paper is to introduce the reader to the theory associated with the transverse dynamics of single particle, in circular accelerators. The discussion begins with a review of Hamiltonian dynamics and canonical transformations. The case of a single particle in a circular accelerator is considered with a discussion of non-linear terms and chromaticity. The canonical perturbation theory is presented and nonlinear resonances are considered. Finally, the concept of renormalization and residue criterion are examined. (FI)

Simple convergent-nozzle aerosol injector for single-particle diffractive imaging with X-ray free-electron lasers

Directory of Open Access Journals (Sweden)

R. A. Kirian

2015-07-01

Full Text Available A major challenge in high-resolution x-ray free-electron laser-based coherent diffractive imaging is the development of aerosol injectors that can efficiently deliver particles to the peak intensity of the focused X-ray beam. Here, we consider the use of a simple convergent-orifice nozzle for producing tightly focused beams of particles. Through optical imaging we show that 0.5 μm particles can be focused to a full-width at half maximum diameter of 4.2 μm, and we demonstrate the use of such a nozzle for injecting viruses into a micro-focused soft-X-ray FEL beam.

Fundamental study of single biomass particle combustion

Energy Technology Data Exchange (ETDEWEB)

Momeni, M.

2013-06-01

This thesis is a comprehensive study of single biomass particle combustion. The effect of particle shape and size and operating conditions on biomass conversion characteristics were investigated experimentally and theoretically. The experimental samples were divided in two groups: particles with regular shapes (spheres and cylinders) and particles with irregular shapes (almost flake-like). A CAMSIZER analyser (Retsch Technology GMBH) was used to determine the size and shape of the particles via Dynamical Digital Image Processing. The experiments were performed in a single particle reactor under well-defined conditions, and the complete combustion processes were recorded as video sequences by a CCD camera installed in the set-up. One of the project objectives is to simulate conditions reasonably close to the conditions in a power plant boiler, i.e., reasonably high temperatures (up to 1600 deg. C) and varying oxygen concentrations in the 5 to 20% range. A one-dimensional mathematical model was used to simulate all the intraparticle conversion processes (drying, recondensation, devolatilisation, char gasification/oxidation and heat/mass/momentum transfer) within single particles of different shapes and size under various conditions. The model also predicts the flame layer domain of a single particle. The model was validated by experimental results under different conditions; good agreement between the model predictions and the experimental data was observed. Both the experimental and modelling results showed that cylindrical particles lose mass faster than spherical particles of a similar volume (mass) and that the burnout time is reduced by increasing the particle aspect ratio (surface area to volume ratio). Very similar conversion times were observed for cylindrical particles with nearly identical surface area to volume ratios. Similar conversion times were also observed for two size classes of pulverised particles (with irregular shapes) made from the same type of

Markov random field based automatic image alignment for electron tomography.

Science.gov (United States)

Amat, Fernando; Moussavi, Farshid; Comolli, Luis R; Elidan, Gal; Downing, Kenneth H; Horowitz, Mark

2008-03-01

We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

Structural characterization and gas reactions of small metal particles by high resolution in-situ TEM (Transmission Electron Microscopy) and TED (Transmission Electron Diffraction)

Science.gov (United States)

Heinemann, K.

1987-01-01

The detection and size analysis of small metal particles supported on amorphous substrates becomes increasingly difficult when the particle size approaches that of the phase contrast background structures of the support. An approach of digital image analysis, involving Fourier transformation of the original image, filtering, and image reconstruction was studied with respect to the likelihood of unambiguously detecting particles of less than 1 nm diameter on amorphous substrates from a single electron micrograph.

Single particle aerosol mass spectrometry of coal combustion particles associated with high lung cancer rates in Xuanwei and Fuyuan, China.

Science.gov (United States)

Lu, Senlin; Tan, Zhengying; Liu, Pinwei; Zhao, Hui; Liu, Dingyu; Yu, Shang; Cheng, Ping; Win, Myat Sandar; Hu, Jiwen; Tian, Linwei; Wu, Minghong; Yonemochi, Shinich; Wang, Qingyue

2017-11-01

Coal combustion particles (CCPs) are linked to the high incidence of lung cancer in Xuanwei and in Fuyuan, China, but studies on the chemical composition of the CCPs are still limited. Single particle aerosol mass spectrometry (SPAMS) was recently developed to measure the chemical composition and size of single particles in real-time. In this study, SPAMS was used to measure individual combustion particles emitted from Xuanwei and Fuyuan coal samples and the results were compared with those by ICP-MS and transmission electron microscopy (TEM). The total of 38,372 particles mass-analyzed by SPAMS can be divided into 9 groups based on their chemical composition and their number percentages: carbonaceous, Na-rich, K-rich, Al-rich, Fe-rich, Si-rich, Ca-rich, heavy metal-bearing, and PAH-bearing particles. The carbonaceous and PAH-bearing particles are enriched in the size range below 0.56 μm, Fe-bearing particles range from 0.56 to 1.0 μm in size, and heavy metals such as Ti, V, Cr, Cu, Zn, and Pb have diameters below 1 μm. The TEM results show that the particles from Xuanwei and Fuyuan coal combustion can be classified into soot aggregates, Fe-rich particles, heavy metal containing particles, and mineral particles. Non-volatile particles detected by SPAMS could also be observed with TEM. The number percentages by SPAMS also correlate with the mass concentrations measured by ICP-MS. Our results could provide valuable insight for understanding high lung cancer incidence in the area. Copyright © 2017 Elsevier Ltd. All rights reserved.

Distribution of lead in single atmospheric particles

Science.gov (United States)

Murphy, D. M.; Hudson, P. K.; Cziczo, D. J.; Gallavardin, S.; Froyd, K. D.; Johnston, M. V.; Middlebrook, A. M.; Reinard, M. S.; Thomson, D. S.; Thornberry, T.; Wexler, A. S.

2007-06-01

Three independent single particle mass spectrometers measured Pb in individual aerosol particles. These data provide unprecedented sensitivity and statistical significance for the measurement of Pb in single particles. This paper explores the reasons for the frequency of Pb in fine particles now that most gasoline is unleaded. Trace amounts of Pb were found in 5 to 25% of 250 to 3000 nm diameter particles sampled by both aircraft and surface instruments in the eastern and western United States. Over 5% of particles at a mountain site in Switzerland contained Pb. Particles smaller than 100 nm with high Pb content were also observed by an instrument that was only operated in urban areas. Lead was found on all types of particles, including Pb present on biomass burning particles from remote fires. Less common particles with high Pb contents contributed a majority of the total amount of Pb. Single particles with high Pb content often also contained alkali metals, Zn, Cu, Sn, As, and Sb. The association of Pb with Zn and other metals is also found in IMPROVE network filter data from surface sites. Sources of airborne Pb in the United States are reviewed for consistency with these data. The frequent appearance of trace Pb is consistent with widespread emissions of fine Pb particles from combustion sources followed by coagulation with larger particles during long-range transport. Industrial sources that directly emit Pb-rich particles also contribute to the observations. Clean regions of the western United States show some transport of Pb from Asia but most Pb over the United States comes from North American sources. Resuspension of Pb from soil contaminated by the years of leaded gasoline was not directly apparent.

Distribution of lead in single atmospheric particles

Directory of Open Access Journals (Sweden)

D. M. Murphy

2007-06-01

Full Text Available Three independent single particle mass spectrometers measured Pb in individual aerosol particles. These data provide unprecedented sensitivity and statistical significance for the measurement of Pb in single particles. This paper explores the reasons for the frequency of Pb in fine particles now that most gasoline is unleaded. Trace amounts of Pb were found in 5 to 25% of 250 to 3000 nm diameter particles sampled by both aircraft and surface instruments in the eastern and western United States. Over 5% of particles at a mountain site in Switzerland contained Pb. Particles smaller than 100 nm with high Pb content were also observed by an instrument that was only operated in urban areas. Lead was found on all types of particles, including Pb present on biomass burning particles from remote fires. Less common particles with high Pb contents contributed a majority of the total amount of Pb. Single particles with high Pb content often also contained alkali metals, Zn, Cu, Sn, As, and Sb. The association of Pb with Zn and other metals is also found in IMPROVE network filter data from surface sites. Sources of airborne Pb in the United States are reviewed for consistency with these data. The frequent appearance of trace Pb is consistent with widespread emissions of fine Pb particles from combustion sources followed by coagulation with larger particles during long-range transport. Industrial sources that directly emit Pb-rich particles also contribute to the observations. Clean regions of the western United States show some transport of Pb from Asia but most Pb over the United States comes from North American sources. Resuspension of Pb from soil contaminated by the years of leaded gasoline was not directly apparent.

Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy.

Science.gov (United States)

Zhao, Haiyan; Li, Kunpeng; Lynn, Anna Y; Aron, Keith E; Yu, Guimei; Jiang, Wen; Tang, Liang

2017-04-04

The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon-like intercapsomer joints, and abundant β-sheet-like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α-helix-to-β-strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses.

Electron tomography and cryo-SEM characterization reveals novel ultrastructural features of host-parasite interaction during Chlamydia abortus infection.

Science.gov (United States)

Wilkat, M; Herdoiza, E; Forsbach-Birk, V; Walther, P; Essig, A

2014-08-01

Chlamydia (C.) abortus is a widely spread pathogen among ruminants that can be transmitted to women during pregnancy leading to severe systemic infection with consecutive abortion. As a member of the Chlamydiaceae, C. abortus shares the characteristic feature of an obligate intracellular biphasic developmental cycle with two morphological forms including elementary bodies (EBs) and reticulate bodies (RBs). In contrast to other chlamydial species, C. abortus ultrastructure has not been investigated yet. To do so, samples were fixed by high-pressure freezing and processed by different electron microscopic methods. Freeze-substituted samples were analysed by transmission electron microscopy, scanning transmission electron microscopical tomography and immuno-electron microscopy, and freeze-fractured samples were analysed by cryo-scanning electron microscopy. Here, we present three ultrastructural features of C. abortus that have not been reported up to now. Firstly, the morphological evidence that C. abortus is equipped with the type three secretion system. Secondly, the accumulation and even coating of whole inclusion bodies by membrane complexes consisting of multiple closely adjacent membranes which seems to be a C. abortus specific feature. Thirdly, the formation of small vesicles in the periplasmic space of RBs in the second half of the developmental cycle. Concerning the time point of their formation and the fact that they harbour chlamydial components, these vesicles might be morphological correlates of an intermediate step during the process of redifferentiation of RBs into EBs. As this feature has also been shown for C. trachomatis and C. pneumoniae, it might be a common characteristic of the family of Chlamydiaceae.

Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring.

Science.gov (United States)

Mountassif, Driss; Fabre, Lucien; Zaid, Younes; Halawani, Dalia; Rouiller, Isabelle

2015-12-25

Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. Copyright © 2015 Elsevier Inc. All rights reserved.

CryoSat Level1b SAR/SARin: quality improvements towards BaselineC

Science.gov (United States)

Scagliola, Michele; Fornari, Marco; Bouzinac, Catherine; Tagliani, Nicolas; Parrinello, Tommaso

2014-05-01

CryoSat was launched on the 8th April 2010 and it is the first European ice mission dedicated to monitoring precise changes in the thickness of polar ice sheets and floating sea ice over a 3-year period. Cryosat carries an innovative radar altimeter called the Synthetic Aperture Interferometric Altimeter (SIRAL), that transmits pulses at a high pulse repetition frequency thus making the received echoes phase coherent and suitable for azimuth processing. This allows to reach a significantly improved along track resolution with respect to traditional pulse-width limited altimeters. CryoSat is the first altimetry mission operating in SAR mode and continuous improvement in the Level1 Instrument Processing Facility (IPF1) are being identified, tested and validated in order to improve the quality of the Level1b products. Towards the release of the BaselineC of the CryoSat Level1b SAR/SARin products, that is expected during 2014, several improvements have been identified: • a datation bias of about -0.5195 ms will be corrected • a range bias of about -0.6730 m will be corrected • the waveform length in the Level1b product will be doubled with respect to BaselineB • improved processing for 1Hz echoes to have sharper waveforms • surface sample stack weighting to filter out the single look echoes acquired at highest look angle, that results in a sharpening of the 20Hz waveforms This poster details the main improvements that are foreseen to be included in the CryoSat Level1b SAR/SARin products in BaselineC.

Retrocausation acting in the single-electron double-slit interference experiment

Science.gov (United States)

Hokkyo, Noboru

The single electron double-slit interference experiment is given a time-symmetric interpretation and visualization in terms of the intermediate amplitude of transition between the particle source and the detection point. It is seen that the retarded (causal) amplitude of the electron wave expanding from the source shows an advanced (retrocausal) bifurcation and merging in passing through the double-slit and converges towards the detection point as if guided by the advanced (retrocausal) wave from the detected electron. An experiment is proposed to confirm the causation-retrocausation symmetry of the electron behavior by observing the insensitivity of the interference pattern to non-magnetic obstacles placed in the shadows of the retarded and advanced waves appearing on the rear and front sides of the double-slit.

Electronic properties of excited states in single InAs quantum dots

International Nuclear Information System (INIS)

Warming, Till

2009-01-01

The application of quantum-mechanical effects in semiconductor nanostructures enables the realization of novel opto-electronic devices. Examples are given by single-photon emitters and emitters of entangled photon pairs, both being essential for quantum cryptography, or for qubit systems as needed for quantum computing. InAs/GaAs quantum dots are one of the most promising candidates for such applications. A detailed knowledge of the electronic properties of quantum dots is a prerequisite for this development. The aim of this work is an experimental access to the detailed electronic structure of the excited states in single InAs/GaAs quantum dots including few-particle effects and in particular exchange interaction. The experimental approach is micro photoluminescence excitation spectroscopy (μPLE). One of the main difficulties using μPLE to probe single QDs is the unambiguous assignment of the observed resonances in the spectrum to specific transitions. By comparing micro photoluminescence (μPL) and μPLE spectra, the identification of the main resonances becomes possible. The key is given by the fine structure of the hot trion. Excitation spectroscopy on single charged QDs enables for the first time the complete observation of a non-trivial fine structure of an excitonic complex in a QD, the hot trion. Modelling based on eight-band k.p theory in combination with a configuration interaction scheme is in excellent agreement. Therewith the simulation also enables realistic predictions on the fine structure of the ground-state exciton which is of large importance for single quantum dot devices. Theory concludes from the observed transitions that the structural symmetry of the QDs is broken. Micro photoluminescence excitation spectroscopy combined with resonantly excited micro photoluminescence enables an optical access to the single particle states of the hole without the influence of few-particle coulomb interactions. Based on this knowledge the exciton binding

Zernike phase contrast cryo-electron tomography of sodium-driven flagellar hook-basal bodies from Vibrio alginolyticus.

Science.gov (United States)

Hosogi, Naoki; Shigematsu, Hideki; Terashima, Hiroyuki; Homma, Michio; Nagayama, Kuniaki

2011-01-01

Vibrio alginolyticus use flagella to swim. A flagellum consists of a filament, hook and basal body. The basal body is made up of a rod and several ring structures. This study investigates the structure of the T ring which is a unique component of the V. alginolyticus sodium ion-driven flagellar basal body. Using Zernike phase contrast (ZPC) cryo-electron tomography, we compared the 3D structures of purified hook-basal bodies (HBB) from a wild-type strain (KK148) and a deletion mutant lacking MotX and MotY (TH3), which are thought to form the T ring. ZPC images of HBBs had highly improved signal-to-noise ratio compared to conventional phase contrast images. We observed the outline of the HBBs from strains KK148 and TH3, and the TH3 mutant was missing its T ring. In the wild-type strain, the T ring was beneath the LP ring and seemed to form a ring shape with diameter of 32 nm. Copyright © 2010 Elsevier Inc. All rights reserved.

Single-electron charging effects

International Nuclear Information System (INIS)

Ruggiero, S.T.

1990-01-01

The status of our project on single-electron tunneling is at this point excellent. As outlined in our original proposal, a key goal in the development of this project was the demonstration and exploration of the microwave properties of single-electron systems. As discussed here, such work has to date been carried out

Fingerprint-based structure retrieval using electron density.

Science.gov (United States)

Yin, Shuangye; Dokholyan, Nikolay V

2011-03-01

We present a computational approach that can quickly search a large protein structural database to identify structures that fit a given electron density, such as determined by cryo-electron microscopy. We use geometric invariants (fingerprints) constructed using 3D Zernike moments to describe the electron density, and reduce the problem of fitting of the structure to the electron density to simple fingerprint comparison. Using this approach, we are able to screen the entire Protein Data Bank and identify structures that fit two experimental electron densities determined by cryo-electron microscopy. Copyright © 2010 Wiley-Liss, Inc.

Navigation for fluoroscopy-guided cryo-balloon ablation procedures of atrial fibrillation

Science.gov (United States)

Bourier, Felix; Brost, Alexander; Kleinoeder, Andreas; Kurzendorfer, Tanja; Koch, Martin; Kiraly, Attila; Schneider, Hans-Juergen; Hornegger, Joachim; Strobel, Norbert; Kurzidim, Klaus

2012-02-01

Atrial fibrillation (AFib), the most common arrhythmia, has been identified as a major cause of stroke. The current standard in interventional treatment of AFib is the pulmonary vein isolation (PVI). PVI is guided by fluoroscopy or non-fluoroscopic electro-anatomic mapping systems (EAMS). Either classic point-to-point radio-frequency (RF)- catheter ablation or so-called single-shot-devices like cryo-balloons are used to achieve electrically isolation of the pulmonary veins and the left atrium (LA). Fluoroscopy-based systems render overlay images from pre-operative 3-D data sets which are then merged with fluoroscopic imaging, thereby adding detailed 3-D information to conventional fluoroscopy. EAMS provide tracking and visualization of RF catheters by means of electro-magnetic tracking. Unfortunately, current navigation systems, fluoroscopy-based or EAMS, do not provide tools to localize and visualize single shot devices like cryo-balloon catheters in 3-D. We present a prototype software for fluoroscopy-guided ablation procedures that is capable of superimposing 3-D datasets as well as reconstructing cyro-balloon catheters in 3-D. The 3-D cyro-balloon reconstruction was evaluated on 9 clinical data sets, yielded a reprojected 2-D error of 1.72 mm +/- 1.02 mm.

Single particle measurements and two particle interferometry results from CERN experiment NA44

International Nuclear Information System (INIS)

Simon-Gillo, J.

1994-01-01

CERN experiment NA44 is optimized for the study of identified single and multiple particle distributions to p T = 0 near mid-rapidity. We measure π +- , K +- , p, bar p, d and bar d, in p + A and A + A collisions at 450 and 20OGeV/u, respectively. Two-particle intensity interferometry results from π + π + , K + K + , and K - K - measurements and single particle distributions are presented

Integrated Transmission Electron and Single-Molecule Fluorescence Microscopy Correlates Reactivity with Ultrastructure in a Single Catalyst Particle

OpenAIRE

Hendriks, Frank C.; Mohammadian, Sajjad; Ristanovic, Zoran; Kalirai, Samanbir; Meirer, Florian; Vogt, Eelco T. C.; Bruijnincx, Pieter C. A.; Gerritsen, Hans; Weckhuysen, Bert M.

2018-01-01

Establishing structure–activity relationships in complex, hierarchically structured nanomaterials, such as fluid catalytic cracking (FCC) catalysts, requires characterization with complementary, correlated analysis techniques. An integrated setup has been developed to perform transmission electron microscopy (TEM) and single-molecule fluorescence (SMF) microscopy on such nanostructured samples. Correlated structure–reactivity information was obtained for 100 nm thin, microtomed sections of a ...

Towards single particle imaging of human chromosomes at SACLA

International Nuclear Information System (INIS)

Robinson, Ian; Schwenke, Joerg; Yusuf, Mohammed; Estandarte, Ana; Zhang, Fucai; Chen, Bo; Clark, Jesse; Song, Changyong; Nam, Daewoong; Joti, Yasumasa; Tono, Kensuke; Yabashi, Makina; Ratnasari, Gina; Kaneyoshi, Kohei; Takata, Hideaki; Fukui, Kiichi

2015-01-01

Single particle imaging (SPI) is one of the front-page opportunities which were used to motivate the construction of the first x-ray free electron lasers (XFELs). SPI’s big advantage is that it avoids radiation damage to biological samples because the diffraction takes place in femtosecond single shots before any atomic motion can take place in the sample, hence before the onset of radiation damage. This is the ‘diffract before destruction’ theme, destruction being assured from the high x-ray doses used. This article reports our collaboration’s first attempt at SPI using the SACLA XFEL facility in June 2015. The report is limited to experience with the instrumentation and examples of data because we have not yet had time to invert them to images. (paper)

MRPC prototypes for NeuLAND tested using the single electron mode of ELBE/Dresden

Energy Technology Data Exchange (ETDEWEB)

Yakorev, Dmitry; Bemmerer, Daniel; Elekes, Zoltan; Kempe, Mathias; Stach, Daniel; Wagner, Andreas [Forschungszentrum Dresden-Rossendorf (FZD), Dresden (Germany); Aumann, Tom; Boretzky, Konstanze; Caesar, Christoph; Ciobanu, Mircea; Hehner, Joerg; Heil, Michael; Nusair, Omar; Reifarth, Rene; Simon, Haik [GSI, Darmstadt (Germany); Elvers, Michael; Maroussov, Vassili; Zilges, Andreas [Universitaet Koeln (Germany); Zuber, Kai [TU Dresden (Germany)

2010-07-01

The NeuLAND detector at the R{sup 3}B experiment at the future FAIR facility in Darmstadt aims to detect fast neutrons (0.2-1.0 GeV) with high time and spatial resolutions ({sigma}{sub t}<100 ps, {sigma}{sub x,y,z}<1 cm). Prototypes for the NeuLAND detector have been built at FZD and GSI and then studied using the 32 MeV pulsed electron beam at the superconducting electron accelerator ELBE in Dresden, Germany. Owing to the new, single-electron per bunch mode of operation, a rapid validation of the design criteria ({>=}90% efficiency for minimum ionizing particles, {sigma} {<=} 100 ps time resolution) was possible. Tested properties of the prototypes include glass thickness, spacing of the central anode, and a comparison of single-ended and differential readout. Tested frontend electronics schemes include FOPI (single-ended), PADI-based (both single-ended and differential mode tested), and ALICE (differential).

Single-electron charging effects

International Nuclear Information System (INIS)

Ruggiero, S.T.

1991-01-01

The status of our project on single-electron tunneling is, again, excellent. As outlined in our original proposal, a key goal in the development of this project was the demonstration and exploration of the microwave properties of single-electron system. As discussed in this paper such work has to data been carried out. Also as discussed in our previous progress report, the next step in the experimental evolution of the project will be to use lithographically-defined small dots as capacitors as outlined in our proposal. At this point we have made such microdotsdots as will be discussed. We have also continued our work with metal droplets to form single-electron tunnel systems

Airborne campaigns for CryoSat prelaunch calibration and validation

DEFF Research Database (Denmark)

Skourup, Henriette; Hanson, Susanne; Hvidegaard, Sine Munk

2011-01-01

After the successful launch of CryoSat-2 in April 2010, the first direct validation campaign of the satellite is planned for spring 2011. DTU Space has been involved in ESA’s CryoSat Validation Experiment (CryoVEx) with airborne activities since 2003. To validate the prelaunch performance...... of the CryoSat radar altimeter (SIRAL), an airborne version of the SIRAL altimeter (ASIRAS) has been flown together with a laser scanner in 2006 and 2008. Of particular interest is to study the penetration depth of the radar altimeter over both land- and sea ice. This can be done by comparing the radar...... and laser measurements with in situ observations. Here, an overview of the prelaunch airborne campaigns is given, together with results of the ASIRAS performance over land- and sea ice. The observations, used in this study, are obtained from the Greenland ice sheet and from both multiyear and first year sea...

CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast.

Science.gov (United States)

Nguyen, Thi Hoang Duong; Galej, Wojciech P; Fica, Sebastian M; Lin, Pei-Chun; Newman, Andrew J; Nagai, Kiyoshi

2016-02-01

The spliceosome is formed on pre-mRNA substrates from five small nuclear ribonucleoprotein particles (U1, U2, U4/U6 and U5 snRNPs), and numerous non-snRNP factors. Saccharomyces cerevisiae U4/U6.U5 tri-snRNP comprises U5 snRNA, U4/U6 snRNA duplex and approximately 30 proteins and represents a substantial part of the spliceosome before activation. Schizosaccharomyces pombe U2.U6.U5 spliceosomal complex is a post-catalytic intron lariat spliceosome containing U2 and U5 snRNPs, NTC (nineteen complex), NTC-related proteins (NTR), U6 snRNA, and an RNA intron lariat. Two recent papers describe near-complete atomic structures of these complexes based on cryoEM single-particle analysis. The U4/U6.U5 tri-snRNP structure provides crucial insight into the activation mechanism of the spliceosome. The U2.U6.U5 complex reveals the striking architecture of NTC and NTR and important features of the group II intron-like catalytic RNA core remaining after spliced mRNA is released. These two structures greatly advance our understanding of the mechanism of pre-mRNA splicing. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Sensing single electrons with single molecules

International Nuclear Information System (INIS)

Plakhotnik, Taras

2007-01-01

We propose a new methodology for probing transport of just one electron, a process of great importance both in nature and in artificial devices. Our idea for locating a single electron is analogues to the conventional GPS where signals from several satellites are used to locate a macro object. Using fluorescent molecules as tiny sensors, it is possible to determine 3D displacement vector of an electron

Development of CRID [Cerenkov Ring Imaging Detector] single electron wire detector

International Nuclear Information System (INIS)

Aston, D.; Bean, A.; Bienz, T.

1989-02-01

We describe the R and D effort to define the design parameters, method of construction and experimental results from the single electron wire detectors. These detectors will be used for particle identification using the Cerenkov Ring Imaging techniques in the SLD experiment at SLAC. We present measurements of pulse heights for several gases as a function of gas gain, charge division performance on a single electron signal using both 7 μm and 33 μm diameter carbon wires, photon feedback in TMAE laden gas, average pulse shape, and its comparison with the predicted shape and cross-talk. In addition, we present results of wire aging tests, and other tests associated with construction of this unusual type of wire chamber. 12 refs., 9 figs

Monitoring of Multilayered Bacterial Biofilm Morphology by Cryo-SEM for Raman Spectroscopy Measurements

Czech Academy of Sciences Publication Activity Database

Hrubanová, Kamila; Bernatová, Silvie; Samek, Ota; Šerý, Mojmír; Zemánek, Pavel; Nebesářová, Jana; Růžička, F.; Krzyžánek, Vladislav

2015-01-01

Roč. 21, S3 (2015), s. 187-188 ISSN 1431-9276 R&D Projects: GA MŠk(CZ) LO1212; GA MŠk ED0017/01/01; GA ČR(CZ) GA14-20012S Institutional support: RVO:68081731 ; RVO:60077344 Keywords : multilayered bacterial biofilm * morphology by Cryo-SEM * Raman spectroscopy Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.730, year: 2015

A surface-gated InSb quantum well single electron transistor

International Nuclear Information System (INIS)

Orr, J M S; Buckle, P D; Fearn, M; Storey, C J; Buckle, L; Ashley, T

2007-01-01

Single electron charging effects in a surface-gated InSb/AlInSb QW structure are reported. This material, due to its large g-factor and light effective mass, offers considerable advantages over more commonly used materials, such as GaAs, for quantum information processing devices. However, differences in material and device technology result in significant processing challenges. Simple Coulomb blockade and quantized confinement models are considered to explain the observation of conductance oscillations in these structures. The charging energy (e 2 /C) is found to be comparable with the energy spectrum for single particle states (ΔE)

Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids

NARCIS (Netherlands)

van Zundert, G. C P; Bonvin, A. M J J

Cryo-electron microscopy provides fascinating structural insight into large macromolecular machines at increasing detail. Despite significant advances in the field, the resolution of the resulting three-dimensional images is still typically insufficient for . de novo model building. To bridge the

Mechanism of enhancement of controllable secondary-electron emission from fast single electrons

International Nuclear Information System (INIS)

Lorikyan, M.P.; Kavalov, R.L.; Trofimchuk, N.N.; Arvanov, A.N.; Gavalyan, V.G.

For porous KCl films (density approximately 2 percent, thickness 50-400 μm), the controllable secondary electron emission (CSEE) from fast single electrons with energies of 0.7-2 MeV was studied. An electric field E of approximately 10 4 -10 5 V/cm was set up inside the porous films and the emission curves anti sigma = f(E) and the energy spectra of the secondary electrons were measured. The mean emission coefficient anti sigma increases with increasing E, reaching a value of anti sigma approximately equal to 230. Internal enhancement of CSEE under the action of the E field is explained by a process similar to the Townsend semi-self-maintained discharge in gases. The mean free path L/sub e/ of the secondary electrons estimated on the basis of this mechanism of CSEE enhancement is in good agreement with the L/sub e/ value obtained independently from the energy spectra of the secondary electrons. The report examines the effect of the first critical potential U/sub il/ and of the electron affinity of the dielectric α on the formation of CSEE from a porous dielectric film. The possibility of using such films in particle detectors is discussed

Single Molecule Electronics and Devices

Science.gov (United States)

Tsutsui, Makusu; Taniguchi, Masateru

2012-01-01

The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

Safety of information in electronic equipment influenced by the charged space particles

Directory of Open Access Journals (Sweden)

Ksenia Gennad’evna Sizova

2016-10-01

Full Text Available A version of the existing evaluation method of electronic equipment to the influence of charged space particles causing single event effects for the purpose of improving the accuracy of calculation in the field of information safety is suggested. On the basis of the existing and modified methods radiation tolerance of real payload spacecraft responsible for the security of transmitted information are defined. The results of comparison are introduced. Significant differences not only in quantitative but also in qualitative character of tolerance indicators are revealed. It is demonstrated that the modified method allows to take into account the functional complexity of the hardware and the application efficiency of the sophisticated single event effects protection tools. To confirm the applicability of the modified method of equipment tolerance evaluation method to the influence of charged space particles causing single event effects proposals to the procedure of ground tests of the payload and the space experiment are developed.

Smart Energy Cryo-refrigerator Technology for the next generation Very Large Array

Science.gov (United States)

Spagna, Stefano

2018-01-01

We describe a “smart energy” cryocooler technology architecture for the next generation Very Large Array that makes use of multiple variable frequency cold heads driven from a single variable speed air cooled compressor. Preliminary experiments indicate that the compressor variable flow control, advanced diagnostics, and the cryo-refrigerator low vibration, provide a unique energy efficient capability for the very large number of antennas that will be employed in this array.

Observation and applications of single-electron charge signals in the XENON100 experiment

NARCIS (Netherlands)

Aprile, E.; et al., [Unknown; Alfonsi, M.; Colijn, A.P.; Decowski, M.P.

2014-01-01

The XENON100 dark matter experiment uses liquid xenon in a time projection chamber (TPC) to measure xenon nuclear recoils resulting from the scattering of dark matter weakly interacting massive particles (WIMPs). In this paper, we report the observation of single-electron charge signals which are

Single-particle Analyses of Compositions, Morphology, and Viscosity of Aerosol Particles Collected During GoAmazon2014

Science.gov (United States)

Adachi, K.; Gong, Z.; Bateman, A. P.; Martin, S. T.; Cirino, G. G.; Artaxo, P.; Sedlacek, A. J., III; Buseck, P. R.

2014-12-01

Single-particle analysis using transmission electron microscopy (TEM) shows composition and morphology of individual aerosol particles collected during the GoAmazon2014 campaign. These TEM results indicate aerosol types and mixing states, both of which are important for evaluating particle optical properties and cloud condensation nuclei activity. The samples were collected at the T3 site, which is located in the Amazon forest with influences from the urban pollution plume from Manaus. Samples were also collected from the T0 site, which is in the middle of the jungle with minimal to no influences of anthropogenic sources. The aerosol particles mainly originated from 1) anthropogenic pollution (e.g., nanosphere soot, sulfate), 2) biogenic emissions (e.g., primary biogenic particles, organic aerosols), and 3) long-range transport (e.g., sea salts). We found that the biogenic organic aerosol particles contain homogeneously distributed potassium. Particle viscosity is important for evaluating gas-particle interactions and atmospheric chemistry for the particles. Viscosity can be estimated from the rebounding behavior at controlled relative humidities, i.e., highly viscous particles display less rebound on a plate than low-viscosity particles. We collected 1) aerosol particles from a plate (non-rebounded), 2) those that had rebounded from the plate and were then captured onto an adjacent sampling plate, and 3) particles from ambient air using a separate impactor sampler. Preliminary results show that more than 90% of non-rebounded particles consisted of nanosphere soot with or without coatings. The coatings mostly consisted of organic matter. Although rebounded particles also contain nanosphere soot (number fraction 64-69%), they were mostly internally mixed with sulfate, organic matter, or their mixtures. TEM tilted images suggested that the rebounded particles were less deformed on the substrate, whereas the non-rebounded particles were more deformed, which could

Practical aspects of Boersch phase contrast electron microscopy of biological specimens

Energy Technology Data Exchange (ETDEWEB)

Walter, Andreas [Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60439 Frankfurt (Germany); Muzik, Heiko; Vieker, Henning; Turchanin, Andrey; Beyer, Andre; Goelzhaeuser, Armin [University of Bielefeld, Physics of Supramolecular Systems and Surfaces, Universitaetsstr. 25, D-33615 Bielefeld (Germany); Lacher, Manfred; Steltenkamp, Siegfried; Schmitz, Sam; Holik, Peter [Caesar Research Center, Ludwig-Erhard-Allee 2, D-53175 Bonn (Germany); Kuehlbrandt, Werner [Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60439 Frankfurt (Germany); Rhinow, Daniel, E-mail: daniel.rhinow@biophys.mpg.de [Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60439 Frankfurt (Germany)

2012-05-15

Implementation of physical phase plates into transmission electron microscopes to achieve in-focus contrast for ice-embedded biological specimens poses several technological challenges. During the last decade several phase plates designs have been introduced and tested for electron cryo-microscopy (cryoEM), including thin film (Zernike) phase plates and electrostatic devices. Boersch phase plates (BPPs) are electrostatic einzel lenses shifting the phase of the unscattered beam by an arbitrary angle. Adjusting the phase shift to 90 Degree-Sign achieves the maximum contrast transfer for phase objects such as biomolecules. Recently, we reported the implementation of a BPP into a dedicated phase contrast aberration-corrected electron microscope (PACEM) and demonstrated its use to generate in-focus contrast of frozen-hydrated specimens. However, a number of obstacles need to be overcome before BPPs can be used routinely, mostly related to the phase plate devices themselves. CryoEM with a physical phase plate is affected by electrostatic charging, obliteration of low spatial frequencies, and mechanical drift. Furthermore, BPPs introduce single sideband contrast (SSB), due to the obstruction of Friedel mates in the diffraction pattern. In this study we address the technical obstacles in detail and show how they may be overcome. We use X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES) to identify contaminants responsible for electrostatic charging, which occurs with most phase plates. We demonstrate that obstruction of low-resolution features is significantly reduced by lowering the acceleration voltage of the microscope. Finally, we present computational approaches to correct BPP images for SSB contrast and to compensate for mechanical drift of the BPP. -- Highlights: Black-Right-Pointing-Pointer Various obstacles need to be overcome before Boersch phase plates can be used routinely. Black-Right-Pointing-Pointer Technical problems include

Practical aspects of Boersch phase contrast electron microscopy of biological specimens

International Nuclear Information System (INIS)

Walter, Andreas; Muzik, Heiko; Vieker, Henning; Turchanin, Andrey; Beyer, André; Gölzhäuser, Armin; Lacher, Manfred; Steltenkamp, Siegfried; Schmitz, Sam; Holik, Peter; Kühlbrandt, Werner; Rhinow, Daniel

2012-01-01

Implementation of physical phase plates into transmission electron microscopes to achieve in-focus contrast for ice-embedded biological specimens poses several technological challenges. During the last decade several phase plates designs have been introduced and tested for electron cryo-microscopy (cryoEM), including thin film (Zernike) phase plates and electrostatic devices. Boersch phase plates (BPPs) are electrostatic einzel lenses shifting the phase of the unscattered beam by an arbitrary angle. Adjusting the phase shift to 90° achieves the maximum contrast transfer for phase objects such as biomolecules. Recently, we reported the implementation of a BPP into a dedicated phase contrast aberration-corrected electron microscope (PACEM) and demonstrated its use to generate in-focus contrast of frozen–hydrated specimens. However, a number of obstacles need to be overcome before BPPs can be used routinely, mostly related to the phase plate devices themselves. CryoEM with a physical phase plate is affected by electrostatic charging, obliteration of low spatial frequencies, and mechanical drift. Furthermore, BPPs introduce single sideband contrast (SSB), due to the obstruction of Friedel mates in the diffraction pattern. In this study we address the technical obstacles in detail and show how they may be overcome. We use X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES) to identify contaminants responsible for electrostatic charging, which occurs with most phase plates. We demonstrate that obstruction of low-resolution features is significantly reduced by lowering the acceleration voltage of the microscope. Finally, we present computational approaches to correct BPP images for SSB contrast and to compensate for mechanical drift of the BPP. -- Highlights: ► Various obstacles need to be overcome before Boersch phase plates can be used routinely. ► Technical problems include electrostatic charging, mechanical drift, and image artefacts. �

Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State.

Science.gov (United States)

Strauss, Mike; Schotte, Lise; Karunatilaka, Krishanthi S; Filman, David J; Hogle, James M

2017-02-01

By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion. When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events. Copyright © 2017 American Society for Microbiology.

CryoSat Data Quality Overview

Science.gov (United States)

Bouzinac, Catherine; Fornari, Marco; Mannan, Rubinder; Parrinello, Tommaso

2013-09-01

The main objective of CryoSat mission is the observation of ice thickness with SAR interferometry. CryoSat data are routinely controlled by ESA-ESRIN- SPPA office with various tools and with the support of the IDEAS industrial consortium. This presentation introduces to the different instrumental modes and processing levels, the available quality tools (Quality Checks and Monitoring Facility) and visualisation tools, and shows the main statistical results from the data acquired and processed with the new processing version (since February 2012). A major data quality improvement is obtained from this new release of the specialized processors for all instrument modes. These new processors are also used this year for a full reprocessing campaign. This presentation also details the main improvements expected from the next release of the specialized processors in 2013.

Scanning electron microscopy-energy dispersive X-ray spectrometry (SEM-EDX) and aerosol time-of-flight mass spectrometry (ATOFMS) single particle analysis of metallurgy plant emissions

International Nuclear Information System (INIS)

Arndt, J.; Deboudt, K.; Anderson, A.; Blondel, A.; Eliet, S.; Flament, P.; Fourmentin, M.; Healy, R.M.; Savary, V.; Setyan, A.; Wenger, J.C.

2016-01-01

The chemical composition of single particles deposited on industrial filters located in three different chimneys of an iron-manganese (Fe–Mn) alloy manufacturing plant have been compared using aerosol time-of-flight mass spectrometry (ATOFMS) and scanning electron microscopy–energy dispersive X-ray spectrometry (SEM-EDX). Very similar types of particles were observed using both analytical techniques. Calcium-containing particles dominated in the firing area of the sintering unit, Mn and/or Al-bearing particles were observed at the cooling area of the sintering unit, while Mn-containing particles were dominant at the smelting unit. SEM-EDX analysis of particles collected downstream of the industrial filters showed that the composition of the particles emitted from the chimneys is very similar to those collected on the filters. ATOFMS analysis of ore samples was also performed to identify particulate emissions that could be generated by wind erosion and manual activities. Specific particle types have been identified for each emission source (chimneys and ore piles) and can be used as tracers for source apportionment of ambient PM measured in the vicinity of the industrial site. - Highlights: • Similar composition for emitted particles as those collected on the chimney filters. • Emitted particles dominated by Ca-, Mn and/or Al-containing particles. • Identification of specific particle types emitted by the different process units. - The particles emitted by metallurgy activities are fully described by ATOFMS and SEM-EDX, enabling the identification of specific particle types from the different units of the process.

Photon emission by electrons and positrons traversing thin single crystal

International Nuclear Information System (INIS)

Ol'chak, A.S.

1984-01-01

Radiation emission by planar channeled particles (electrons, positrons) in a thin single crystal of thickness L is considered. It is shown that for L approximately πb/THETAsub(L) (b is the lattice constant, THETA sub(L) the Lindhard angle) besides the main spontaneous channeling maxima there exist auxiliary interference maxima, the positions of all the maxima depending on L. The dependence of the radiation spectral intensity on crystal thickness is discussed

New apparatus of single particle trap system for aerosol visualization

Science.gov (United States)

Higashi, Hidenori; Fujioka, Tomomi; Endo, Tetsuo; Kitayama, Chiho; Seto, Takafumi; Otani, Yoshio

2014-08-01

Control of transport and deposition of charged aerosol particles is important in various manufacturing processes. Aerosol visualization is an effective method to directly observe light scattering signal from laser-irradiated single aerosol particle trapped in a visualization cell. New single particle trap system triggered by light scattering pulse signal was developed in this study. The performance of the device was evaluated experimentally. Experimental setup consisted of an aerosol generator, a differential mobility analyzer (DMA), an optical particle counter (OPC) and the single particle trap system. Polystylene latex standard (PSL) particles (0.5, 1.0 and 2.0 μm) were generated and classified according to the charge by the DMA. Singly charged 0.5 and 1.0 μm particles and doubly charged 2.0 μm particles were used as test particles. The single particle trap system was composed of a light scattering signal detector and a visualization cell. When the particle passed through the detector, trigger signal with a given delay time sent to the solenoid valves upstream and downstream of the visualization cell for trapping the particle in the visualization cell. The motion of particle in the visualization cell was monitored by CCD camera and the gravitational settling velocity and the electrostatic migration velocity were measured from the video image. The aerodynamic diameter obtained from the settling velocity was in good agreement with Stokes diameter calculated from the electrostatic migration velocity for individual particles. It was also found that the aerodynamic diameter obtained from the settling velocity was a one-to-one function of the scattered light intensity of individual particles. The applicability of this system will be discussed.

Frontend electronics for high-precision single photo-electron timing using FPGA-TDCs

Science.gov (United States)

Cardinali, M.; Dzyhgadlo, R.; Gerhardt, A.; Götzen, K.; Hohler, R.; Kalicy, G.; Kumawat, H.; Lehmann, D.; Lewandowski, B.; Patsyuk, M.; Peters, K.; Schepers, G.; Schmitt, L.; Schwarz, C.; Schwiening, J.; Traxler, M.; Ugur, C.; Zühlsdorf, M.; Dodokhov, V. Kh.; Britting, A.; Eyrich, W.; Lehmann, A.; Uhlig, F.; Düren, M.; Föhl, K.; Hayrapetyan, A.; Kröck, B.; Merle, O.; Rieke, J.; Cowie, E.; Keri, T.; Montgomery, R.; Rosner, G.; Achenbach, P.; Corell, O.; Ferretti Bondy, M. I.; Hoek, M.; Lauth, W.; Rosner, C.; Sfienti, C.; Thiel, M.; Bühler, P.; Gruber, L.; Marton, J.; Suzuki, K.

2014-12-01

The next generation of high-luminosity experiments requires excellent particle identification detectors which calls for Imaging Cherenkov counters with fast electronics to cope with the expected hit rates. A Barrel DIRC will be used in the central region of the Target Spectrometer of the planned PANDA experiment at FAIR. A single photo-electron timing resolution of better than 100 ps is required by the Barrel DIRC to disentangle the complicated patterns created on the image plane. R&D studies have been performed to provide a design based on the TRB3 readout using FPGA-TDCs with a precision better than 20 ps RMS and custom frontend electronics with high-bandwidth pre-amplifiers and fast discriminators. The discriminators also provide time-over-threshold information thus enabling walk corrections to improve the timing resolution. Two types of frontend electronics cards optimised for reading out 64-channel PHOTONIS Planacon MCP-PMTs were tested: one based on the NINO ASIC and the other, called PADIWA, on FPGA discriminators. Promising results were obtained in a full characterisation using a fast laser setup and in a test experiment at MAMI, Mainz, with a small scale DIRC prototype.

Building the Nanoplasmonics Toolbox Through Shape Modeling and Single Particle Optical Studies

Science.gov (United States)

Ringe, Emilie

Interest in nanotechnology is driven by unprecedented properties tailorability, achievable by controlling particle structure and composition. Unlike bulk components, minute changes in size and shape affect the optical and electronic properties of nanoparticles. Characterization of such structure-function relationships and better understanding of structure control mechanisms is crucial to the development of applications such as plasmonic sensors and devices. The objective of the current research is thus twofold: to theoretically predict and understand how shape is controlled by synthesis conditions, and to experimentally unravel, through single particle studies, how shape, composition, size, and surrounding environment affect plasmonic properties in noble metal particles. Quantitative, predictive rules and fundamental knowledge obtained from this research contributes to the "nanoplasmonics toolbox", a library designed to provide scientists and engineers the tools to create and optimize novel nanotechnology applications. In this dissertation, single particle approaches are developed and used to unravel the effects of size, shape, substrate, aggregation state and surrounding environment on the optical response of metallic nanoparticles. Ag and Au nanocubes on different substrates are first presented, followed by the discussion of the concept of plasmon length, a universal parameter to describe plasmon energy for a variety of particle shapes and plasmon modes. Plasmonic sensing (both refractive index sensing and surface-enhanced Raman spectroscopy) and polarization effects are then studied at the single particle level. In the last two Chapters, analytical shape models based on the Wulff construction provide unique modeling tools for alloy and kinetically grown nanoparticles. The former reveals a size-dependence of the shape of small alloy particles (such as those used in catalysis) because of surface segregation, while the latter uniquely models the shape of many

Analysis of individual environmental particles using modern methods of electron microscopy and X-ray microanalysis

International Nuclear Information System (INIS)

Laskin, A.; Cowin, J.P.; Iedema, M.J.

2006-01-01

Understanding the composition of particles in the atmosphere is critical because of their health effects and their direct and indirect effects on radiative forcing, and hence on climate. In this manuscript, we demonstrate the utility of single particle off-line analysis to investigate the chemistry of individual atmospheric particles using modern, state-of-the-art electron microscopy and time-of-flight secondary ionization mass spectrometry techniques. We show that these methods provide specific, detailed data on particle composition, chemistry, morphology, phase and internal structure. This information is crucial for evaluating hygroscopic properties of aerosols, understanding aerosol aging and reactivity, and correlating the characteristics of aerosols with their optical properties. The manuscript presents a number of analytical advances in methods of electron probe particle analysis along with a brief review of a number of the research projects carried out in the authors' laboratory on the chemical characterization of environmental particles. The obtained data offers a rich set of qualitative and quantitative information on the particle chemistry, composition and the mechanisms of gas-particle interactions which are of high importance to atmospheric processes involving particulate matter and air pollution

A different approach to obtain Mayer’s extension to stationary single particle Wigner distribution

International Nuclear Information System (INIS)

Bose, Anirban; Janaki, M. S.

2012-01-01

It is shown that the stationary collisionless single-particle Wigner equation in one dimension containing quantum corrections at the lowest order is satisfied by a distribution function that is similar in form to the Maxwellian distribution with an effective mass and a generalized potential. The distribution is used to study quantum corrections to electron hole solutions.

ESA CryoVEx 2012

DEFF Research Database (Denmark)

Skourup, Henriette; Einarsson, Indriði; Forsberg, René

Institute (AWI) with fixed‐wing airplane (Polar‐5, Basler BT‐67). The airborne systems are described in detail, together with campaign implementation plan, data processing and data quality analysis. The CryoVEx 2012 campaign was a success and the processed data is of high quality. The data set includes 16...

Single-particle density matrix of liquid 4He

International Nuclear Information System (INIS)

Vakarchuk, I.A.

2008-01-01

The density single-particle matrix in the coordinate notation was calculated based on the expression for the interacting Bose-particle N system density matrix. Under the low temperatures the mentioned matrix in the first approximation enables to reproduce the Bogoliubov theory results. In the classical terms the mentioned theory enables to reproduce the results of the theory of the classical fluids in the approximation of the chaotic phases. On the basis of the density single-particle matrix one managed to obtain the function of the pulse distribution of the particles, the Bose-liquid average kinetic energy, and to study the Bose-Einstein condensation phenomenon [ru

Nuclear charge and magnetization densities of single particle states

International Nuclear Information System (INIS)

Frois, B.

1985-01-01

High energy electron scattering data have recently determined the spatial distributions of nucleons in the center of nuclei with amazing accuracy. For the first time we have access to the structure of the nuclear interior throughout the periodic table. The spatial resolution achieved by high momentum transfer measurements is now sufficient to define clearly the present limits of nuclear theory. The experimental situation is briefly reviewed and the results interpreted in the framework of self-consistent field theory. The shapes of single particle distributions in the nuclear interior are found to be in surprisingly good agreement with the predictions of mean field theory. The effects of correlations are discussed. (orig.)

Nuclear charge and magnetization densities of single particle states

International Nuclear Information System (INIS)

Frois, B.

1985-05-01

High energy electron scattering data have recently determined the spatial distributions of nucleons in the center of nuclei with amazing accuracy. For the first time we have access to the structure of the nuclear interior throughout the periodic table. The spatial resolution achieved by high momentum transfer measurements is now sufficient to define clearly the present limits of nuclear theory. The experimental situation is briefly reviewed and the results interpreted in the framework of self-consistent field theory. The shapes of single particle distributions in the nuclear interior are found to be in surprisingly good agreement with the predictions of mean field theory. The effects of correlations are discussed

Particles and waves in electron optics and microscopy

CERN Document Server

Pozzi, Giulio

2016-01-01

Advances in Imaging and Electron Physics merges two long-running serials, Advances in Electronics and Electron Physics and Advances in Optical and Electron Microscopy. The series features extended articles on the physics of electron devices (especially semiconductor devices), particle optics at high and low energies, microlithography, image science, digital image processing, electromagnetic wave propagation, electron microscopy, and the computing methods used in all these domains. * Contains contributions from leading authorities on the subject matter* Informs and updates all the latest developments in the field of imaging and electron physics* Provides practitioners interested in microscopy, optics, image processing, mathematical morphology, electromagnetic fields, electron, and ion emission with a valuable resource* Features extended articles on the physics of electron devices (especially semiconductor devices), particle optics at high and low energies, microlithography, image science, and digital image pro...

Single particle tracking and single molecule energy transfer

CERN Document Server

Bräuchle, Christoph; Michaelis, Jens

2009-01-01

Closing a gap in the literature, this handbook gathers all the information on single particle tracking and single molecule energy transfer. It covers all aspects of this hot and modern topic, from detecting virus entry to membrane diffusion, and from protein folding using spFRET to coupled dye systems, as well recent achievements in the field. Throughout, the first-class editors and top international authors present content of the highest quality, making this a must-have for physical chemists, spectroscopists, molecular physicists and biochemists.

Cryo-EM image alignment based on nonuniform fast Fourier transform

International Nuclear Information System (INIS)

Yang Zhengfan; Penczek, Pawel A.

2008-01-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis

Cryo-EM image alignment based on nonuniform fast Fourier transform.

Science.gov (United States)

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.

Single mimivirus particles intercepted and imaged with an X-ray laser

Science.gov (United States)

Seibert, M. Marvin; Ekeberg, Tomas; Maia, Filipe R. N. C.; Svenda, Martin; Andreasson, Jakob; Jönsson, Olof; Odić, Duško; Iwan, Bianca; Rocker, Andrea; Westphal, Daniel; Hantke, Max; DePonte, Daniel P.; Barty, Anton; Schulz, Joachim; Gumprecht, Lars; Coppola, Nicola; Aquila, Andrew; Liang, Mengning; White, Thomas A.; Martin, Andrew; Caleman, Carl; Stern, Stephan; Abergel, Chantal; Seltzer, Virginie; Claverie, Jean-Michel; Bostedt, Christoph; Bozek, John D.; Boutet, Sébastien; Miahnahri, A. Alan; Messerschmidt, Marc; Krzywinski, Jacek; Williams, Garth; Hodgson, Keith O.; Bogan, Michael J.; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Andersson, Inger; Bajt, Saša; Barthelmess, Miriam; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Kirian, Richard; Hunter, Mark; Doak, R. Bruce; Marchesini, Stefano; Hau-Riege, Stefan P.; Frank, Matthias; Shoeman, Robert L.; Lomb, Lukas; Epp, Sascha W.; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Schmidt, Carlo; Foucar, Lutz; Kimmel, Nils; Holl, Peter; Rudek, Benedikt; Erk, Benjamin; Hömke, André; Reich, Christian; Pietschner, Daniel; Weidenspointner, Georg; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Schlichting, Ilme; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Chapman, Henry N.; Hajdu, Janos

2014-01-01

X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions1–4. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma1. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval2. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source5. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies. PMID:21293374

Imaging of Norway spruce early somatic embryos with the ESEM, Cryo-SEM and laser scanning microscope

Czech Academy of Sciences Publication Activity Database

Neděla, Vilém; Hřib, Jiří; Havel, L.; Hudec, Jiří; Runštuk, Jiří

2016-01-01

Roč. 84, May 2016 (2016), s. 67-71 ISSN 0968-4328 R&D Projects: GA ČR(CZ) GA14-22777S Institutional support: RVO:68081731 Keywords : ESEM * Cryo-SEM * bright field/dark field microscopy * extracellular matrix * Picea abies * somatic embryogenesis Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.980, year: 2016

A novel storage system for cryoEM samples.

Science.gov (United States)

Scapin, Giovanna; Prosise, Winifred W; Wismer, Michael K; Strickland, Corey

2017-07-01

We present here a new CryoEM grid boxes storage system designed to simplify sample labeling, tracking and retrieval. The system is based on the crystal pucks widely used by the X-ray crystallographic community for storage and shipping of crystals. This system is suitable for any cryoEM laboratory, but especially for large facilities that will need accurate tracking of large numbers of samples coming from different sources. Copyright © 2017. Published by Elsevier Inc.

Single particle irradiation effect of digital signal processor

International Nuclear Information System (INIS)

Fan Si'an; Chen Kenan

2010-01-01

The single particle irradiation effect of high energy neutron on digital signal processor TMS320P25 in dynamic working condition has been studied. The influence of the single particle on the device has been explored through the acquired waveform and working current of TMS320P25. Analysis results, test data and test methods have also been presented. (authors)

Effective particle magnetic moment of multi-core particles

Energy Technology Data Exchange (ETDEWEB)

Ahrentorp, Fredrik; Astalan, Andrea; Blomgren, Jakob; Jonasson, Christian [Acreo Swedish ICT AB, Arvid Hedvalls backe 4, SE-411 33 Göteborg (Sweden); Wetterskog, Erik; Svedlindh, Peter [Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala (Sweden); Lak, Aidin; Ludwig, Frank [Institute of Electrical Measurement and Fundamental Electrical Engineering, TU Braunschweig, D‐38106 Braunschweig Germany (Germany); IJzendoorn, Leo J. van [Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven (Netherlands); Westphal, Fritz; Grüttner, Cordula [Micromod Partikeltechnologie GmbH, D ‐18119 Rostock (Germany); Gehrke, Nicole [nanoPET Pharma GmbH, D ‐10115 Berlin Germany (Germany); Gustafsson, Stefan; Olsson, Eva [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg (Sweden); Johansson, Christer, E-mail: christer.johansson@acreo.se [Acreo Swedish ICT AB, Arvid Hedvalls backe 4, SE-411 33 Göteborg (Sweden)

2015-04-15

In this study we investigate the magnetic behavior of magnetic multi-core particles and the differences in the magnetic properties of multi-core and single-core nanoparticles and correlate the results with the nanostructure of the different particles as determined from transmission electron microscopy (TEM). We also investigate how the effective particle magnetic moment is coupled to the individual moments of the single-domain nanocrystals by using different measurement techniques: DC magnetometry, AC susceptometry, dynamic light scattering and TEM. We have studied two magnetic multi-core particle systems – BNF Starch from Micromod with a median particle diameter of 100 nm and FeraSpin R from nanoPET with a median particle diameter of 70 nm – and one single-core particle system – SHP25 from Ocean NanoTech with a median particle core diameter of 25 nm.

Effective particle magnetic moment of multi-core particles

International Nuclear Information System (INIS)

Ahrentorp, Fredrik; Astalan, Andrea; Blomgren, Jakob; Jonasson, Christian; Wetterskog, Erik; Svedlindh, Peter; Lak, Aidin; Ludwig, Frank; IJzendoorn, Leo J. van; Westphal, Fritz; Grüttner, Cordula; Gehrke, Nicole; Gustafsson, Stefan; Olsson, Eva; Johansson, Christer

2015-01-01

In this study we investigate the magnetic behavior of magnetic multi-core particles and the differences in the magnetic properties of multi-core and single-core nanoparticles and correlate the results with the nanostructure of the different particles as determined from transmission electron microscopy (TEM). We also investigate how the effective particle magnetic moment is coupled to the individual moments of the single-domain nanocrystals by using different measurement techniques: DC magnetometry, AC susceptometry, dynamic light scattering and TEM. We have studied two magnetic multi-core particle systems – BNF Starch from Micromod with a median particle diameter of 100 nm and FeraSpin R from nanoPET with a median particle diameter of 70 nm – and one single-core particle system – SHP25 from Ocean NanoTech with a median particle core diameter of 25 nm

Effective particle magnetic moment of multi-core particles

Science.gov (United States)

Ahrentorp, Fredrik; Astalan, Andrea; Blomgren, Jakob; Jonasson, Christian; Wetterskog, Erik; Svedlindh, Peter; Lak, Aidin; Ludwig, Frank; van IJzendoorn, Leo J.; Westphal, Fritz; Grüttner, Cordula; Gehrke, Nicole; Gustafsson, Stefan; Olsson, Eva; Johansson, Christer

2015-04-01

In this study we investigate the magnetic behavior of magnetic multi-core particles and the differences in the magnetic properties of multi-core and single-core nanoparticles and correlate the results with the nanostructure of the different particles as determined from transmission electron microscopy (TEM). We also investigate how the effective particle magnetic moment is coupled to the individual moments of the single-domain nanocrystals by using different measurement techniques: DC magnetometry, AC susceptometry, dynamic light scattering and TEM. We have studied two magnetic multi-core particle systems - BNF Starch from Micromod with a median particle diameter of 100 nm and FeraSpin R from nanoPET with a median particle diameter of 70 nm - and one single-core particle system - SHP25 from Ocean NanoTech with a median particle core diameter of 25 nm.

Structural analysis of respiratory syncytial virus reveals the position of M2-1 between the matrix protein and the ribonucleoprotein complex.

Science.gov (United States)

Kiss, Gabriella; Holl, Jens M; Williams, Grant M; Alonas, Eric; Vanover, Daryll; Lifland, Aaron W; Gudheti, Manasa; Guerrero-Ferreira, Ricardo C; Nair, Vinod; Yi, Hong; Graham, Barney S; Santangelo, Philip J; Wright, Elizabeth R

2014-07-01

Respiratory syncytial virus (RSV), a member of the Paramyxoviridae family of nonsegmented, negative-sense, single-stranded RNA genome viruses, is a leading cause of lower respiratory tract infections in infants, young children, and the elderly or immunocompromised. There are many open questions regarding the processes that regulate human RSV (hRSV) assembly and budding. Here, using cryo-electron tomography, we identified virus particles that were spherical, filamentous, and asymmetric in structure, all within the same virus preparation. The three particle morphologies maintained a similar organization of the surface glycoproteins, matrix protein (M), M2-1, and the ribonucleoprotein (RNP). RNP filaments were traced in three dimensions (3D), and their total length was calculated. The measurements revealed the inclusion of multiple full-length genome copies per particle. RNP was associated with the membrane whenever the M layer was present. The amount of M coverage ranged from 24% to 86% in the different morphologies. Using fluorescence light microscopy (fLM), direct stochastic optical reconstruction microscopy (dSTORM), and a proximity ligation assay (PLA), we provide evidence illustrating that M2-1 is located between RNP and M in isolated viral particles. In addition, regular spacing of the M2-1 densities was resolved when hRSV viruses were imaged using Zernike phase contrast (ZPC) cryo-electron tomography. Our studies provide a more complete characterization of the hRSV virion structure and substantiation that M and M2-1 regulate virus organization. hRSV is a leading cause of lower respiratory tract infections in infants and young children as well as elderly or immunocompromised individuals. We used cryo-electron tomography and Zernike phase contrast cryo-electron tomography to visualize populations of purified hRSV in 3D. We observed the three distinct morphologies, spherical, filamentous, and asymmetric, which maintained comparable organizational profiles

Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels.

Science.gov (United States)

Si, Dong; He, Jing

2014-01-01

Electron cryo-microscopy (Cryo-EM) technique produces 3-dimensional (3D) density images of proteins. When resolution of the images is not high enough to resolve the molecular details, it is challenging for image processing methods to enhance the molecular features. β-barrel is a particular structure feature that is formed by multiple β-strands in a barrel shape. There is no existing method to derive β-strands from the 3D image of a β-barrel at medium resolutions. We propose a new method, StrandRoller, to generate a small set of possible β-traces from the density images at medium resolutions of 5-10Å. StrandRoller has been tested using eleven β-barrel images simulated to 10Å resolution and one image isolated from the experimentally derived cryo-EM density image at 6.7Å resolution. StrandRoller was able to detect 81.84% of the β-strands with an overall 1.5Å 2-way distance between the detected and the observed β-traces, if the best of fifteen detections is considered. Our results suggest that it is possible to derive a small set of possible β-traces from the β-barrel cryo-EM image at medium resolutions even when no separation of the β-strands is visible in the images.

Electrons and kaons in charmed particle decays

International Nuclear Information System (INIS)

Feller, J.M.

1979-05-01

Inclusive studies of the electron content, kaon content, and associated electron-kaon content of the decays of D mesons and other charmed particles produced in electron-positron annihilation are presented. At the psi(3772) resonance the following inclusive branching ratios for D meson decays to charged kaons were measured. Also at the psi(3772) resonance the average semileptonic branching ratio for D 0 and D + decays to electrons has been measured to be .076 +- .028. The average semileptonic branching ratio of charmed particles produced in e + e - annihilation at center-of-mass energies from 3.9 to 7.4 GeV is found to be equal within errors to that of the D's. At all energies the electron momentum spectra are consistent with a combination of the decays D → Ke nu and D → K*e nu. 84 references

Single-particle states vs. collective modes: friends or enemies ?

Science.gov (United States)

Otsuka, T.; Tsunoda, Y.; Togashi, T.; Shimizu, N.; Abe, T.

2018-05-01

The quantum self-organization is introduced as one of the major underlying mechanisms of the quantum many-body systems. In the case of atomic nuclei as an example, two types of the motion of nucleons, single-particle states and collective modes, dominate the structure of the nucleus. The collective mode arises as the balance between the effect of the mode-driving force (e.g., quadrupole force for the ellipsoidal deformation) and the resistance power against it. The single-particle energies are one of the sources to produce such resistance power: a coherent collective motion is more hindered by larger spacings between relevant single particle states. Thus, the single-particle state and the collective mode are "enemies" against each other. However, the nuclear forces are rich enough so as to enhance relevant collective mode by reducing the resistance power by changing single-particle energies for each eigenstate through monopole interactions. This will be verified with the concrete example taken from Zr isotopes. Thus, the quantum self-organization occurs: single-particle energies can be self-organized by (i) two quantum liquids, e.g., protons and neutrons, (ii) monopole interaction (to control resistance). In other words, atomic nuclei are not necessarily like simple rigid vases containing almost free nucleons, in contrast to the naïve Fermi liquid picture. Type II shell evolution is considered to be a simple visible case involving excitations across a (sub)magic gap. The quantum self-organization becomes more important in heavier nuclei where the number of active orbits and the number of active nucleons are larger.

Ionization of xenon by electrons: Partial cross sections for single, double, and triple ionization

International Nuclear Information System (INIS)

Mathur, D.; Badrinathan, C.

1987-01-01

High-sensitivity measurements of relative partial cross sections for single, double, and triple ionization of Xe by electron impact have been carried out in the energy region from threshold to 100 eV using a crossed-beam apparatus incorporating a quadrupole mass spectrometer. The weighted sum of the relative partial cross sections at 50 eV are normalized to the total ionization cross section of Rapp and Englander-Golden to yield absolute cross-section functions. Shapes of the partial cross sections for single and double ionization are difficult to account for within a single-particle picture. Comparison of the Xe + data with 4d partial photoionization cross-section measurements indicates the important role played by many-body effects in describing electron-impact ionization of high-Z atoms

Effect of two-step aging on spatial distribution of γ-phase particles and mechanical properties of Ni-14at.% Al single crystals

International Nuclear Information System (INIS)

Tyapkin, Yu.D.; Travina, N.T.; Ugarova, E.V.

1977-01-01

Electron microscope images were processed by statistical methods to investigate the space distribution of particles of the γ'-phase (formation of ''quasiperiodic micro-lattices'') after various conditions of single- and double-stage aging of the Ni-14 at.% Al alloy. Mechanical properties in uniaxial tension of single crystals were studied. Parameters of the space distribution of particles have been correlated with the mechanical properties

Dual color single particle tracking via nanobodies

International Nuclear Information System (INIS)

Albrecht, David; Winterflood, Christian M; Ewers, Helge

2015-01-01

Single particle tracking is a powerful tool to investigate the function of biological molecules by following their motion in space. However, the simultaneous tracking of two different species of molecules is still difficult to realize without compromising the length or density of trajectories, the localization accuracy or the simplicity of the assay. Here, we demonstrate a simple dual color single particle tracking assay using small, bright, high-affinity labeling via nanobodies of accessible targets with widely available instrumentation. We furthermore apply a ratiometric step-size analysis method to visualize differences in apparent membrane viscosity. (paper)

Cryogenic transmission electron microscopy nanostructural study of shed microparticles.

Directory of Open Access Journals (Sweden)

Liron Issman

Full Text Available Microparticles (MPs are sub-micron membrane vesicles (100-1000 nm shed from normal and pathologic cells due to stimulation or apoptosis. MPs can be found in the peripheral blood circulation of healthy individuals, whereas elevated concentrations are found in pregnancy and in a variety of diseases. Also, MPs participate in physiological processes, e.g., coagulation, inflammation, and angiogenesis. Since their clinical properties are important, we have developed a new methodology based on nano-imaging that provides significant new data on MPs nanostructure, their composition and function. We are among the first to characterize by direct-imaging cryogenic transmitting electron microscopy (cryo-TEM the near-to-native nanostructure of MP systems isolated from different cell types and stimulation procedures. We found that there are no major differences between the MP systems we have studied, as most particles were spherical, with diameters from 200 to 400 nm. However, each MP population is very heterogeneous, showing diverse morphologies. We investigated by cryo-TEM the effects of standard techniques used to isolate and store MPs, and found that either high-g centrifugation of MPs for isolation purposes, or slow freezing to -80 °C for storage introduce morphological artifacts, which can influence MP nanostructure, and thus affect the efficiency of these particles as future diagnostic tools.

The Cryogenic Anti-Coincidence detector for ATHENA X-IFU: pulse analysis of the AC-S7 single pixel prototype

Science.gov (United States)

D'Andrea, M.; Argan, A.; Lotti, S.; Macculi, C.; Piro, L.; Biasotti, M.; Corsini, D.; Gatti, F.; Torrioli, G.

2016-07-01

The ATHENA observatory is the second large-class mission in ESA Cosmic Vision 2015-2025, with a launch foreseen in 2028 towards the L2 orbit. The mission addresses the science theme "The Hot and Energetic Universe", by coupling a high-performance X-ray Telescope with two complementary focal-plane instruments. One of these is the X-ray Integral Field Unit (X-IFU): it is a TES based kilo-pixel order array able to provide spatially resolved high-resolution spectroscopy (2.5 eV at 6 keV) over a 5 arcmin FoV. The X-IFU sensitivity is degraded by the particles background expected at L2 orbit, which is induced by primary protons of both galactic and solar origin, and mostly by secondary electrons. To reduce the background level and enable the mission science goals, a Cryogenic Anticoincidence (CryoAC) detector is placed address the final design of the CryoAC. It will verify some representative requirements at single-pixel level, especially the detector operation at 50 mK thermal bath and the threshold energy at 20 keV. To reach the final DM design we have developed and tested the AC-S7 prototype, with 1 cm2 absorber area sensed by 65 Ir TESes. Here we will discuss the pulse analysis of this detector, which has been illuminated by the 60 keV line from a 241Am source. First, we will present the analysis performed to investigate pulses timings and spectrum, and to disentangle the athermal component of the pulses from the thermal one. Furthermore, we will show the application to our dataset of an alternative method of pulse processing, based upon Principal Component Analysis (PCA). This kind of analysis allow us to recover better energy spectra than achievable with traditional methods, improving the evaluation of the detector threshold energy, a fundamental parameter characterizing the CryoAC particle rejection efficiency.

Study on the fragmentation of granite due to the impact of single particle and double particles

Directory of Open Access Journals (Sweden)

Yuchun Kuang

2016-09-01

Full Text Available Particle Impact Drilling (PID is a novel method to improve the rate of penetration (ROP. In order to further improve the performance of PID, an investigation into the effect of single and double particles: (1 diameter; (2 initial velocity; (3 distance; and (4 angle of incidence was undertaken to investigate their effects on broken volume and penetration depth into hard brittle rock. For this purpose, the laboratory experiment of single particle impact rock was employed. Meanwhile, based on the LS-DYNA, a new finite element (FE simulation of the PID, including single and double particles impact rock, has been presented. The 3-dimensional (3D, aix-symmetric, dynamic-explicit, Lagrangian model has been considered in this simulation. And the Elastic and Holmquist Johnson Cook (HJC material behaviors have been used for particles and rocks, respectively. The FE simulation results of single particle impacting rock are good agreement with experimental data. Furthermore, in this article the optimal impact parameters, including diameter, initial velocity, distance and the angle of incidence, are obtained in PID.

Irradiation of single cells with individual high-LET particles

International Nuclear Information System (INIS)

Nelson, J.M.; Braby, L.A.

1993-01-01

The dose-limiting normal tissue of concern when irradiating head and neck lesions is often the vascular endothelium within the treatment field. Consequently, the response of capillary endothelial cells exposed to moderate doses of high LET particles is essential for establishing exposure limits for neutron-capture therapy. In an effort to characterize the high-LET radiation biology of cultured endothelial cells, the authors are attempting to measure cellular response to single particles. The single-particle irradiation apparatus, described below, allows them to expose individual cells to known numbers of high-LET particles and follow these cells for extended periods, in order to assess the impact of individual particles on cell growth kinetics. Preliminary cell irradiation experiments have revealed complications related to the smooth and efficient operation of the equipment; these are being resolved. Therefore, the following paragraphs deal primarily with the manner by which high LET particles deposit energy, the requirements for single-cell irradiation, construction and assembly of such apparatus, and testing of experimental procedures, rather than with the radiation biology of endothelial cells

Controlled assembly and single electron charging of monolayer protected Au144 clusters: an electrochemistry and scanning tunneling spectroscopy study

Science.gov (United States)

Bodappa, Nataraju; Fluch, Ulrike; Fu, Yongchun; Mayor, Marcel; Moreno-García, Pavel; Siegenthaler, Hans; Wandlowski, Thomas

2014-11-01

Single gold particles may serve as room temperature single electron memory units because of their size dependent electronic level spacing. Here, we present a proof-of-concept study by electrochemically controlled scanning probe experiments performed on tailor-made Au particles of narrow dispersity. In particular, the charge transport characteristics through chemically synthesized hexane-1-thiol and 4-pyridylbenzene-1-thiol mixed monolayer protected Au144 clusters (MPCs) by differential pulse voltammetry (DPV) and electrochemical scanning tunneling spectroscopy (EC-STS) are reported. The pyridyl groups exposed by the Au-MPCs enable their immobilization on Pt(111) substrates. By varying the humidity during their deposition, samples coated by stacks of compact monolayers of Au-MPCs or decorated with individual, laterally separated Au-MPCs are obtained. DPV experiments with stacked monolayers of Au144-MPCs and EC-STS experiments with laterally separated individual Au144-MPCs are performed both in aqueous and ionic liquid electrolytes. Lower capacitance values were observed for individual clusters compared to ensemble clusters. This trend remains the same irrespective of the composition of the electrolyte surrounding the Au144-MPC. However, the resolution of the energy level spacing of the single clusters is strongly affected by the proximity of neighboring particles.Single gold particles may serve as room temperature single electron memory units because of their size dependent electronic level spacing. Here, we present a proof-of-concept study by electrochemically controlled scanning probe experiments performed on tailor-made Au particles of narrow dispersity. In particular, the charge transport characteristics through chemically synthesized hexane-1-thiol and 4-pyridylbenzene-1-thiol mixed monolayer protected Au144 clusters (MPCs) by differential pulse voltammetry (DPV) and electrochemical scanning tunneling spectroscopy (EC-STS) are reported. The pyridyl groups

Conceptual Design of the Superconducting Proton Linac Short Cryo-module

CERN Document Server

Bourcey, N; Capatina, O; Azevedo, P; Montesinos, E; Parma, V; Renaglia, T; Vande Craen, A; Williams, L R; Weingarten, W; Rousselot, S; Duthil, P; Duchesne, P; Reynet, D; Dambre, P

2012-01-01

The Superconducting Proton Linac (SPL) is an R&amp;amp;D effort conducted by CERN in partnership with other international laboratories, aimed at developing key technologies for the construction of a multi-megawatt proton linac based on state-of-the-art Superconducting Radio Frequency technology, which would serve as a driver for new physics facilities such as neutrinos and radioactive ion beams. Amongst the main objectives of this effort, are the development of 704 MHz bulk niobium b=1 elliptical cavities, operating at 2 K and providing an accelerating field of 25 MV/m, and testing of a string of cavities integrated in a machine-type cryo-module. In an initial phase only four out of the eight cavities of an SPL cryo-module will be tested in a ½ length cryo-module developed for this purpose, and therefore called the Short Cryo-module. This paper presents the conceptual design of the SC, highlighting its innovative principles in terms of cavity supporting and alignment, and describes the integratio...

Test particle modeling of wave-induced energetic electron precipitation

International Nuclear Information System (INIS)

Chang, H.C.; Inan, U.S.

1985-01-01

A test particle computer model of the precipitation of radiation belt electrons is extended to compute the dynamic energy spectrum of transient electron fluxes induced by short-duration VLF wave packets traveling along the geomagnetic field lines. The model is adapted to estimate the count rate and associated spectrum of precipitated electrons that would be observed by satellite-based particle detectors with given geometric factor and orientation with respect to the magnetic field. A constant-frequency wave pulse and a lightning-induced whistler wave packet are used as examples of the stimulating wave signals. The effects of asymmetry of particle mirror heights in the two hemispheres and the atmospheric backscatter of loss cone particles on the computed precipitated fluxes are discussed

Mass loss of Greenland from GRACE, IceSat and CryoSat

DEFF Research Database (Denmark)

Forsberg, René; Sørensen, Louise Sandberg; Fredenslund Levinsen, Joanna

2013-01-01

CryoSat data over the Greenland Ice Sheet are used to continue elevation height change data over the Greenland ice sheet, following a decade of detailed monitoring of ice sheet changes with GRACE and IceSat. The combination and validation of the different data for measuring changes is quantified...... by using available airborne lidar data from IceBridge and CryoVEx. There is a special challenge of using CryoSat as fill-in between EnviSat and Sentinel-3 for the longterm measurements of surface elevation changes, a key essential climate variable in the ESA Climate Change Initiative. Another challenge...... is the joint utilization of both altimetry and gravity field change measurements for consistent estimates of regional change patterns. In the paper we analyze GRACE, IceSat and CryoSat data since 2003, and present consistent estimates of overall mass changes with average values around -220 GT/year, showing...

Combining Envisat and CryoSat-2 altimetry to inform hydrodynamic models

DEFF Research Database (Denmark)

Schneider, Raphael; Nygaard Godiksen, Peter; Ridler, Marc-Etienne

2016-01-01

fitted to the CryoSat-2 data: In a first step, the average simulated water levels along the river were calibrated to the CryoSat-2 data by adapting the hydrodynamic cross section datums. Subsequently the simulated water level amplitudes were fitted to those obtained from Envisat virtual station time......Remote sensing provides valuable data for parameterization and updating of hydrological models, for example water level measurements of inland water bodies from satellite radar altimeters. Many studies have used satellite altimetry data from repeat-orbit missions such as Envisat, ERS or Jason...... on Sentinel-3. CryoSat-2 SARIn level 2 data is used to improve a 1D hydrodynamic model of the Brahmaputra river basin in South Asia set up in the DHI MIKE 11 software. CryoSat-2 water levels were extracted over river masks derived from Landsat imagery. After discharge calibration, simulated water levels were...

Improved cryo-resistors with low temperature coefficients

International Nuclear Information System (INIS)

Warnecke, P.; Braun, E.

1989-01-01

A new type of 10- and 12.9κΩ cryo-resistors operating in a liquid helium bath with small temperature coefficient of resistivity have been built. Details for the fabrication of these improved cryo-resistors are reported. Experimental evidence of their drift rates are on the order of a few parts in 10 9 per day. A reduction of the mean pressure of 98.7 kPa in the helium dewar to 86.1 kPa, corresponding to a temperature decrease from 4.19 to 4.07 Κ, did not change the resistance value by more than the experimental resolution of 4 parts in 10 8

Dragonfly : an implementation of the expand–maximize–compress algorithm for single-particle imaging

OpenAIRE

Ayyer, Kartik; Lan, Ti-Yen; Elser, Veit; Loh, N. Duane

2016-01-01

Single-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map...

Report of the working group on single-particle nonlinear dynamics

International Nuclear Information System (INIS)

Bazzani, A.; Bongini, L.; Corbett, J.; Dome, G.; Fedorova, A.; Freguglia, P.; Ng, K.; Ohmi, K.; Owen, H.; Papaphilippou, Y.; Robin, D.; Safranek, J.; Scandale, W.; Terebilo, A.; Turchetti, G.; Todesco, E.; Warnock, R.; Zeitlin, M.

1999-01-01

The Working Group on single-particle nonlinear dynamics has developed a set of tools to study nonlinear dynamics in a particle accelerator. The design of rings with large dynamic apertures is still far from automatic. The Working Group has concluded that nonlinear single-particle dynamics limits the performance of accelerators. (AIP) copyright 1999 American Institute of Physics

Effective particle magnetic moment of multi-core particles

NARCIS (Netherlands)

Ahrentorp, F.; Astalan, A.; Blomgren, J.; Jonasson, C.; Wetterskog, E.; Svedlindh, P.; Lak, A.; Ludwig, F.; Van IJzendoorn, L.J.; Westphal, F.; Grüttner, C.; Gehrke, N.; Gustafsson, S.; Olsson, E.; Johansson, C.

2015-01-01

In this study we investigate the magnetic behavior of magnetic multi-core particles and the differences in the magnetic properties of multi-core and single-core nanoparticles and correlate the results with the nanostructure of the different particles as determined from transmission electron

Transport and installation of the LHC cryo-magnets

CERN Document Server

Artoos, K; Capatina, O; Chevalley, JM; Foraz, K; Guinchard, M; Hauviller, Claude; Kershaw, K; Prodon, S; Rühl, Ingo; Trinquart, G; Weisz, S; Ponsot, P

2007-01-01

Eleven years have passed between the beginning of transport and handling studies in 1996 and the completion of the LHC cryo-magnets installation in 2007. More than 1700 heavy, long and fragile cryo-magnets had to be transported and installed in the 27 km long LHC tunnel with very restricted available space. The size and complexity of the project involved challenges in the field of equipment design and manufacturing, maintenance, training and follow-up of operators and logistics. The paper presents the milestones, problems to be overcome and lessons learned during this project.

Coastal Sea Level from CryoSat-2 SARIn Altimetry in Norway

DEFF Research Database (Denmark)

Idžanović, Martina; Ophaug, Vegard; Andersen, Ole Baltazar

2017-01-01

Conventional (pulse-limited) altimeters determine the sea surface height with an accuracy of a few centimeters over the open ocean. Sea surface heights and tide-gauge sea level serve as each other’s buddy check. However, in coastal areas, altimetry suffers from numerous effects, which degrade its...... conventional altimeters. In this study, we explore the potential of CryoSat-2 to provide valid observations in the Norwegian coastal zone. We do this by comparing time series of CryoSat-2 sea level anomalies with time series of in situ sea level at 22 tide gauges, where the CryoSat-2 sea level anomalies...... are averaged in a 45-km area around each tide gauge. For all tide gauges, CryoSat-2 shows standard deviations of differences and correlations of 16 cm and 61%, respectively. We further identify the ocean tide and inverted barometer geophysical corrections as the most crucial, and note that a large amount...

Evolution of single-particle structure of silicon isotopes

Science.gov (United States)

Bespalova, O. V.; Fedorov, N. A.; Klimochkina, A. A.; Markova, M. L.; Spasskaya, T. I.; Tretyakova, T. Yu.

2018-01-01

New data on proton and neutron single-particle energies E_{nlj} of Si isotopes with neutron number N from 12 to 28 as well as occupation probabilities N_{nlj} of single-particle states of stable isotopes 28, 30Si near the Fermi energy were obtained by the joint evaluation of the stripping and pick-up reaction data and excited state decay schemes of neighboring nuclei. The evaluated data indicate the following features of single-particle structure evolution: persistence of Z = 14 subshell closure with N increase, the new magicity of the number N = 16, and the conservation of the magic properties of the number N = 20 in Si isotopic chain. The features were described by the dispersive optical model. The calculation also predicts the weakening of N = 28 shell closure and demonstrates evolution of a bubble-like structure of the proton density distributions in neutron-rich Si isotopes.

Preliminary Understanding of Surface Plasmon-Enhanced Circular Dichroism Spectroscopy by Single Particle Imaging

Science.gov (United States)

Zhan, Kangshu

Monitoring chiral optical signals of biomolecules as their conformation changes is an important means to study their structures, properties, and functions. Most measurements, however, are ensemble measurements because chiral optical signals from a single biomolecule is often too weak to be detected. In this dissertation, I present my early attempts to study conformational changes of adsorbed proteins by taking advantage of the enhanced electromagnetic (EM) field around a well-designed plasmonic nanofeature. In particular, I discuss the detection of protein adsorption and denaturation on metallic nanoparticles using single particle scattering and CD spectroscopic imaging. Particles of two distinctively different sizes were compared and two different sample protein molecules were studied. A combination of experimental and computational tools was used to simulate and interpret the collected scattering and CD results. The first chapter provides a brief overview of the state-of-art research in CD spectroscopic studies at the single particle level. Three different means to make particles capable of chiral detection are discussed. Various applications beyond single particle imaging are presented to showcase the potential of the described research project, beyond our immediate goals. The second chapter describes my initial characterization of large, metallic, anisotropic nanorods and the establishment of experimental procedures used later for spectrum reconstruction, data visualization and analysis. The physical shape and structure of the particles were imaged by scanning electron microscopy (SEM), the chemical composition by energy dispersive X-ray Spectroscopy (EDS), and the optical properties by darkfield microscopy. An experimental protocol was developed to connect information collected from separate techniques for the same particle, with the aims of discovering any possible structural-property correlation. The reproducibility of the single particle imaging method was

Microfluidic CODES: a scalable multiplexed electronic sensor for orthogonal detection of particles in microfluidic channels.

Science.gov (United States)

Liu, Ruxiu; Wang, Ningquan; Kamili, Farhan; Sarioglu, A Fatih

2016-04-21

Numerous biophysical and biochemical assays rely on spatial manipulation of particles/cells as they are processed on lab-on-a-chip devices. Analysis of spatially distributed particles on these devices typically requires microscopy negating the cost and size advantages of microfluidic assays. In this paper, we introduce a scalable electronic sensor technology, called microfluidic CODES, that utilizes resistive pulse sensing to orthogonally detect particles in multiple microfluidic channels from a single electrical output. Combining the techniques from telecommunications and microfluidics, we route three coplanar electrodes on a glass substrate to create multiple Coulter counters producing distinct orthogonal digital codes when they detect particles. We specifically design a digital code set using the mathematical principles of Code Division Multiple Access (CDMA) telecommunication networks and can decode signals from different microfluidic channels with >90% accuracy through computation even if these signals overlap. As a proof of principle, we use this technology to detect human ovarian cancer cells in four different microfluidic channels fabricated using soft lithography. Microfluidic CODES offers a simple, all-electronic interface that is well suited to create integrated, low-cost lab-on-a-chip devices for cell- or particle-based assays in resource-limited settings.

Picosecond, single pulse electron linear accelerator

International Nuclear Information System (INIS)

Kikuchi, Riichi; Kawanishi, Masaharu

1979-01-01

The picosecond, single pulse electron linear accelerators, are described, which were installed in the Nuclear Engineering Laboratory of the University of Tokyo and in the Nuclear Radiation Laboratory of the Osaka University. The purpose of the picosecond, single pulse electron linear accelerators is to investigate the very short time reaction of the substances, into which gamma ray or electron beam enters. When the electrons in substances receive radiation energy, the electrons get high kinetic energy, and the energy and the electric charge shift, at last to the quasi-stable state. This transient state can be experimented with these special accelerators very accurately, during picoseconds, raising the accuracy of the time of incidence of radiation and also raising the accuracy of observation time. The outline of these picosecond, single pulse electron linear accelerators of the University of Tokyo and the Osaka University, including the history, the systems and components and the output beam characteristics, are explained. For example, the maximum energy 30 -- 35 MeV, the peak current 1 -- 8 n C, the pulse width 18 -- 40 ps, the pulse repetition rate 200 -- 720 pps, the energy spectrum 1 -- 1.8% and the output beam diameter 2 -- 5 mm are shown as the output beam characteristics of the accelerators in both universities. The investigations utilizing the picosecond single pulse electron linear accelerators, such as the investigation of short life excitation state by pulsed radiation, the dosimetry study of pulsed radiation, and the investigation of the transforming mechanism and the development of the transforming technology from picosecond, single pulse electron beam to X ray, vacuum ultraviolet ray and visual ray, are described. (Nakai, Y.)

High quality single shot diffraction patterns using ultrashort megaelectron volt electron beams from a radio frequency photoinjector

Energy Technology Data Exchange (ETDEWEB)

Musumeci, P.; Moody, J. T.; Scoby, C. M.; Gutierrez, M. S. [Department of Physics and Astronomy, UCLA, Los Angeles, California 90095 (United States); Bender, H. A.; Wilcox, N. S. [National Security Technologies, LLC, Los Alamos Operations, Los Alamos, New Mexico 87544 (United States)

2010-01-15

Single shot diffraction patterns using a 250-fs-long electron beam have been obtained at the UCLA Pegasus laboratory. High quality images with spatial resolution sufficient to distinguish closely spaced peaks in the Debye-Scherrer ring pattern have been recorded by scattering the 1.6 pC 3.5 MeV electron beam generated in the rf photoinjector off a 100-nm-thick Au foil. Dark current and high emittance particles are removed from the beam before sending it onto the diffraction target using a 1 mm diameter collimating hole. These results open the door to the study of irreversible phase transformations by single shot MeV electron diffraction.

High quality single shot diffraction patterns using ultrashort megaelectron volt electron beams from a radio frequency photoinjector.

Science.gov (United States)

Musumeci, P; Moody, J T; Scoby, C M; Gutierrez, M S; Bender, H A; Wilcox, N S

2010-01-01

Single shot diffraction patterns using a 250-fs-long electron beam have been obtained at the UCLA Pegasus laboratory. High quality images with spatial resolution sufficient to distinguish closely spaced peaks in the Debye-Scherrer ring pattern have been recorded by scattering the 1.6 pC 3.5 MeV electron beam generated in the rf photoinjector off a 100-nm-thick Au foil. Dark current and high emittance particles are removed from the beam before sending it onto the diffraction target using a 1 mm diameter collimating hole. These results open the door to the study of irreversible phase transformations by single shot MeV electron diffraction.

High quality single shot diffraction patterns using ultrashort megaelectron volt electron beams from a radio frequency photoinjector

International Nuclear Information System (INIS)

Musumeci, P.; Moody, J. T.; Scoby, C. M.; Gutierrez, M. S.; Bender, H. A.; Wilcox, N. S.

2010-01-01

Single shot diffraction patterns using a 250-fs-long electron beam have been obtained at the UCLA Pegasus laboratory. High quality images with spatial resolution sufficient to distinguish closely spaced peaks in the Debye-Scherrer ring pattern have been recorded by scattering the 1.6 pC 3.5 MeV electron beam generated in the rf photoinjector off a 100-nm-thick Au foil. Dark current and high emittance particles are removed from the beam before sending it onto the diffraction target using a 1 mm diameter collimating hole. These results open the door to the study of irreversible phase transformations by single shot MeV electron diffraction.

Crystallographic and single-particle analyses of native- and nucleotide-bound forms of the cystic fibrosis transmembrane conductance regulator (CFTR) protein.

Science.gov (United States)

Awayn, N H; Rosenberg, M F; Kamis, A B; Aleksandrov, L A; Riordan, J R; Ford, R C

2005-11-01

Cystic fibrosis, one of the major human inherited diseases, is caused by defects in the CFTR (cystic fibrosis transmembrane conductance regulator), a cell-membrane protein. CFTR acts as a chloride channel which can be opened by ATP. Low-resolution structural studies of purified recombinant human CFTR are described in the present paper. Localization of the C-terminal decahistidine tag in CFTR was achieved by Ni2+-nitriloacetate nanogold labelling, followed by electron microscopy and single-particle analysis. The presence of the gold label appears to improve the single-particle-alignment procedure. Projection structures of CFTR from two-dimensional crystals analysed by electron crystallography displayed two alternative conformational states in the presence of nucleotide and nanogold, but only one form of the protein was observed in the quiescent (nucleotide-free) state.

Evolution of single-particle structure of silicon isotopes

Energy Technology Data Exchange (ETDEWEB)

Bespalova, O.V.; Klimochkina, A.A.; Spasskaya, T.I.; Tretyakova, T.Yu. [Lomonosov Moscow State University, Skobeltsyn Institute of Nuclear Physics, Moscow (Russian Federation); Fedorov, N.A.; Markova, M.L. [Lomonosov Moscow State University, Faculty of Physics, Moscow (Russian Federation)

2018-01-15

New data on proton and neutron single-particle energies E{sub nlj} of Si isotopes with neutron number N from 12 to 28 as well as occupation probabilities N{sub nlj} of single-particle states of stable isotopes {sup 28,30}Si near the Fermi energy were obtained by the joint evaluation of the stripping and pick-up reaction data and excited state decay schemes of neighboring nuclei. The evaluated data indicate the following features of single-particle structure evolution: persistence of Z = 14 subshell closure with N increase, the new magicity of the number N = 16, and the conservation of the magic properties of the number N = 20 in Si isotopic chain. The features were described by the dispersive optical model. The calculation also predicts the weakening of N = 28 shell closure and demonstrates evolution of a bubble-like structure of the proton density distributions in neutron-rich Si isotopes. (orig.)

Fragmentation of single-particle states in deformed nuclei

International Nuclear Information System (INIS)

Malov, L.A.; Soloviev, V.G.

1975-01-01

Fragmentation of single-particle states on levels of deformed nuclei is studied on the example of 239 U and 169 Er nuclei in the framework of the model taking into consideration the interaction of quasiparticles with phonons. The dependence of fragmentation on the Fermi surface is considered from the viewpoint of single-particle levels. It is shown that in the distribution of single-particle strength functions a second maximum appears together with the large asymmetry maximum at high-energy excitation, and the distribution has a long ''tail''. A semimicroscopic approach is proposed for calculating the neutron strength functions. The following values of the strength functions are obtained: for sub(239)U-Ssub(0)sup(cal)=1.2x10sup(-4), Ssub(1)sup(cal)=2.7x10sub(-4) and for sub(169)Er-Ssub(0)sup(cal)=1.10sup(-4), Ssub(1)sup(cal)=1.2x10sup(-4)

Modeling of calcination of single kaolinitic clay particle

DEFF Research Database (Denmark)

Gebremariam, Abraham Teklay; Yin, Chungen; Rosendahl, Lasse

The present work aims at modeling of the calcination (dehydroxylation) process of clay particles, specifically kaolinite, and its thermal transformation. For such purpose, 1D single particle calcination model was developed based on the concept of shrinking core model to assess the dehydroxylation...

Semiempirical formulas for single-particle energies of neutrons and protons

International Nuclear Information System (INIS)

Lodhi, M.A.K.; Waak, B.T.

1978-01-01

The stepwise multiple linear regression technique has been used to analyze the single-particle energies of neutrons and protons in nuclei along the line of beta stability. Their regular and systematic trends lead to semiempirical model-independent formulas for single-particle energies of neutrons and protons in the bound nuclei as functions of nuclear parameters A and Z for given states specified by nl/sub j/. These formulas are almost as convenient as the harmonic oscillator energy formulas to use. The single-particle energies computed from these formulas have been compared with the experimental data and are found in reasonable agreement

Characterisation of colloidal drug delivery systems from the naked eye to Cryo-FESEM

DEFF Research Database (Denmark)

Krauel, Karen; Girvan, Liz; Hook, Sarah

2007-01-01

Poly(ethylcyanoacrylate) nanoparticles prepared by interfacial polymerisation on the basis of microemulsions were prepared in this study and both colloidal systems, nanoparticles and microemulsions, were analysed by visual observation and several microscopic techniques. Phase boundaries...... for the microemulsions of the two pseudoternary systems ethyloleate, polyoxyethylene 20 sorbitan mono-oleate/sorbitan monolaurate and water with and without butanol as a cosurfactant were determined by visual observation of the samples. Microemulsions containing liquid crystals were determined by polarisation light...... microscopy. Using freeze-fracture transmission electron microscopy and Cryo-field emission scanning electron microscopy the type of microemulsion (w/o droplet, bicontinuous, solution) was characterised. Nanoparticles prepared from the different types of microemulsion were additionally observed...

Experiments and modeling of single plastic particle conversion in suspension

DEFF Research Database (Denmark)

Nakhaei, Mohammadhadi; Wu, Hao; Grévain, Damien

2018-01-01

Conversion of single high density polyethylene (PE) particles has been studied by experiments and modeling. The experiments were carried out in a single particle combustor for five different shapes and masses of particles at temperature conditions of 900 and 1100°C. Each experiment was recorded...... against the experiments as well as literature data. Furthermore, a simplified isothermal model appropriate for CFD applications was developed, in order to model the combustion of plastic particles in cement calciners. By comparing predictions with the isothermal and the non–isothermal models under typical...

Single particle composition measurements of artificial Calcium Carbonate aerosols

Science.gov (United States)

Zorn, S. R.; Mentel, T. F.; Schwinger, T.; Croteau, P. L.; Jayne, J.; Worsnop, D. R.; Trimborn, A.

2012-12-01

Mineral dust, with an estimated total source from natural and anthropogenic emissions of up to 2800 Tg/yr, is one of the two largest contributors to total aerosol mass, with only Sea salt having a similar source strength (up to 2600 Tg/yr). The composition of dust particles varies strongly depending on the production process and, most importantly, the source location. Therefore, the composition of single dust particles can be used both to trace source regions of air masses as well as to identify chemical aging processes. Here we present results of laboratory studies on generating artificial calcium carbonate (CaCO3) particles, a model compound for carbonaceous mineral dust particles. Particles were generated by atomizing an aqueous hydrogen carbonate solution. Water was removed using a silica diffusion dryer., then the particles were processed in an oven at temperatures up to 900°C, converting the hydrogen carbonate to its anhydrous form. The resulting aerosol was analyzed using an on-line single particle laser ablation aerosol particle time-of-flight mass spectrometer (LAAPTOF). The results confirm the conversion to calcium carbonate, and validate that the produced particles indeed can be used as a model compound for carbonaceous dust aerosols.

Non-linear phenomena in electronic systems consisting of coupled single-electron oscillators

International Nuclear Information System (INIS)

Kikombo, Andrew Kilinga; Hirose, Tetsuya; Asai, Tetsuya; Amemiya, Yoshihito

2008-01-01

This paper describes non-linear dynamics of electronic systems consisting of single-electron oscillators. A single-electron oscillator is a circuit made up of a tunneling junction and a resistor, and produces simple relaxation oscillation. Coupled with another, single electron oscillators exhibit complex behavior described by a combination of continuous differential equations and discrete difference equations. Computer simulation shows that a double-oscillator system consisting of two coupled oscillators produces multi-periodic oscillation with a single attractor, and that a quadruple-oscillator system consisting of four oscillators also produces multi-periodic oscillation but has a number of possible attractors and takes one of them determined by initial conditions

Cryo-EM structure of isomeric molluscan hemocyanin triggered by viral infection.

Directory of Open Access Journals (Sweden)

Hongtao Zhu

Full Text Available Hemocyanins (Hcs of arthropods and mollusks function not only as oxygen transporters, but also as phenoloxidases (POs. In invertebrates, PO is an important component in the innate immune cascade, where it functions as the initiator of melanin synthesis, a pigment involved in encapsulating and killing of pathogenic microbes. Although structures of Hc from several species of invertebrates have been reported, the structural basis for how PO activity is triggered by structural changes of Hc in vivo remains poorly understood. Here, we report a 6.8 Å cryo-electron microscopy (cryo-EM structure of the isomeric form of hemocyanin, which was isolated from Abalone Shriveling syndrome-associated Virus (AbSV infected abalone (Halitotis diversicolor, and build a pseudoatomic model of isomeric H. diversicolor hemocyanin 1 (HdH1. Our results show that, compared with native form of HdH1, the architecture of isomeric HdH1 turns into a more relaxed form. The interactions between certain functional units (FUs present in the native form of Hc either decreased or were totally abolished in the isomeric form of Hc. As a result of that, native state Hc switches to its isomeric form, enabling it to play its role in innate immune responses against invading pathogens.

Fundamental Study of Single Biomass Particle Combustion

DEFF Research Database (Denmark)

Momenikouchaksaraei, Maryam

This thesis is a comprehensive study of single biomass particle combustion. The effect of particle shape and size and operating conditions on biomass conversion characteristics were investigated experimentally and theoretically. The experimental samples were divided in two groups: particles...... well-defined conditions, and the complete combustion processes were recorded as video sequences by a CCD camera installed in the set-up. One of the project objectives is to simulate conditions reasonably close to the conditions in a power plant boiler, i.e., reasonably high temperatures (up to 1600°C...

Hierarchical Ag mesostructures for single particle SERS substrate

Energy Technology Data Exchange (ETDEWEB)

Xu, Minwei, E-mail: xuminwei@xjtu.edu.cn; Zhang, Yin

2017-01-30

Highlights: • Hierarchical Ag mesostructures with the size of 250, 360 and 500 nm are synthesized via a seed-mediated approach. • The Ag mesostructures present the tailorable size and highly roughened surfaces. • The average enhancement factors for individual Ag mesostructures were estimated to be as high as 10{sup 6}. - Abstract: Hierarchical Ag mesostructures with highly rough surface morphology have been synthesized at room temperature through a simple seed-mediated approach. Electron microscopy characterizations indicate that the obtained Ag mesostructures exhibit a textured surface morphology with the flower-like architecture. Moreover, the particle size can be tailored easily in the range of 250–500 nm. For the growth process of the hierarchical Ag mesostructures, it is believed that the self-assembly mechanism is more reasonable rather than the epitaxial overgrowth of Ag seed. The oriented attachment of nanoparticles is revealed during the formation of Ag mesostructures. Single particle surface enhanced Raman spectra (sp-SERS) of crystal violet adsorbed on the hierarchical Ag mesostructures were measured. Results reveal that the hierarchical Ag mesostructures can be highly sensitive sp-SERS substrates with good reproducibility. The average enhancement factors for individual Ag mesostructures are estimated to be about 10{sup 6}.

Burnout of pulverized biomass particles in large scale boiler - Single particle model approach

Energy Technology Data Exchange (ETDEWEB)

Saastamoinen, Jaakko; Aho, Martti; Moilanen, Antero [VTT Technical Research Centre of Finland, Box 1603, 40101 Jyvaeskylae (Finland); Soerensen, Lasse Holst [ReaTech/ReAddit, Frederiksborgsveij 399, Niels Bohr, DK-4000 Roskilde (Denmark); Clausen, Soennik [Risoe National Laboratory, DK-4000 Roskilde (Denmark); Berg, Mogens [ENERGI E2 A/S, A.C. Meyers Vaenge 9, DK-2450 Copenhagen SV (Denmark)

2010-05-15

Burning of coal and biomass particles are studied and compared by measurements in an entrained flow reactor and by modelling. The results are applied to study the burning of pulverized biomass in a large scale utility boiler originally planned for coal. A simplified single particle approach, where the particle combustion model is coupled with one-dimensional equation of motion of the particle, is applied for the calculation of the burnout in the boiler. The particle size of biomass can be much larger than that of coal to reach complete burnout due to lower density and greater reactivity. The burner location and the trajectories of the particles might be optimised to maximise the residence time and burnout. (author)

Pseudo LRM waveforms from CryoSat SARin acquisition

Science.gov (United States)

Scagliola, Michele; Fornari, Marco; Bouffard, Jerome; Parrinello, Tommaso; Féménias, Pierre

2016-04-01

CryoSat was launched on the 8th April 2010 and is the first European ice mission dedicated to the monitoring of precise changes in the thickness of polar ice sheets and floating sea ice. The main payload of CryoSat is a Ku-band pulsewidth limited radar altimeter, called SIRAL (Synthetic interferometric radar altimeter). When commanded in SARIn (synthetic aperture radar interferometry) mode, through coherent along-track processing of the returns received from two antennas, the interferometric phase related to the first arrival of the echo is used to retrieve the angle of arrival of the scattering in the across-track direction. When SIRAL operates in SAR or SARin mode, the obtained waveforms have an along-track resolution and a speckle reduction which is increased with respect to the pulse-limited waveforms. Anyway, in order to analyze the continuity of the geophysical retrieved parameters among different acquisition modes, techniques to transform SARin mode data to pseudo-LRM mode data are welcome. The transformation process is known as SAR reduction and it is worth recalling here that only approximate pseudo-LRM waveforms can be obtained in case of closed burst acquisitions, as SIRAL operates. A SAR reduction processing scheme has been developed to obtain pseudo-LRM waveforms from CryoSat SARin acquisition. As a trade-off between the along-track length on Earth surface contributing to one SARin pseudo-LRM waveform and the noisiness of the waveform itself, it has been chosen a SAR reduction approach based on the averaging of all the SARin echoes received each 20Hz, resulting in one pseudo-LRM waveform for each SARin burst given the SARin burst repetition period. SARin pseudo-LRM waveforms have been produced for CryoSat acquisition both on ice and sea surfaces, aiming at verifying the continuity of the retracked surface height over the ellipsoid between genuine LRM products and pseudo-LRM products. Moreover, the retracked height from the SARin pseudo-LRM has been

A study on the electric properties of single-junction GaAs solar cells under the combined radiation of low-energy protons and electrons

International Nuclear Information System (INIS)

Zhao Huijie; Wu Yiyong; Xiao Jingdong; He Shiyu; Yang Dezhuang; Sun Yanzheng; Sun Qiang; Lv Wei; Xiao Zhibin; Huang Caiyong

2008-01-01

Displacement damage induced by charged particle radiation is the main cause of degradation of orbital-service solar cells, while the radiation-induced ionization shows no permanent damage effect on their electrical properties. It is reported that in single crystal silicon solar cells, low-energy electron radiation does not exert permanent degradation of their properties, but the fluence of electron radiation exerts an influence on the damage magnitude under the combined radiation of protons and electrons. The electrical properties of the single-junction GaAs/Ge solar cells were investigated after irradiation by sequential and synchronous electron and proton beams. Low-energy electron radiation showed no effects on the change of the solar cell properties during sequential or synchronous irradiation, implying ionization during particle radiation could not exert influence on the displacement damage process to the solar cells under the experimental conditions

Transmission electron microscopy of polyhydroxybutyrate-co-valerate (PHBV)/nanocrystalline cellulose (NCC) bio-nanocomposite prepared using cryo-ultramicrotomy

Science.gov (United States)

Ismarul, N. I.; Engku, A. H. E. U.; Siti, N. K.; Tay, K. Y.

2017-12-01

Environmental issues on disposal and end-of-life for product made from synthetic petroleum-derived polymers have gained increasing attention from materials scientist to search for new materials with similar physical and mechanical properties but environmental friendly in a way that they are renewable and biodegradable as well. This work is to study the effect of nanocrystalline cellulose in improving the thermal stability of polyhydroxybutyrate-co-valerate biopolymer for high temperature processing of packaging material. 10 % w/w PHBV-NCC bio-nanocomposite feedstock pellet prepared using RONDOL minilab compounder was used as the sample for the preparation of Transmission Electron Microscopy (TEM) sample. RMC Cryo-Ultramicrotomy equipment was used to prepare the ultra-thin slice of the bio-nanocomposite pellet under liquid nitrogen at - 60 °C. Diamond knife was used to slice off about 80-100 nm ultra-thin bio-nanocomposite films and was transferred into the lacey carbon film coated grid using cooled sugar solution. A few drops of phosphotungstic acid was used as negative stain to improve the contrast during the TEM analysis. HITACHI TEM systems was used to obtain the TEM micrograph of PHBV-NCC bio-nanocomposite using 80kV accelerating voltage. A well dispersed NCC in PHBV matrix, ranging from 5 to 25 nm in width was observed.

New particles produced in electron--positron annihilation

International Nuclear Information System (INIS)

Perl, M.L.

1975-01-01

The main properties of the new particles produced in e + e - annihilation are reviewed. Included are properties of the continuum region, the 4.1-GeV enhancement, the psi and psi', radiative decays of the psi and psi', singly charmed particle searches in e + - e - annihilation, and the e/sub μ/ events

Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states.

Science.gov (United States)

Zhou, Xiaoyuan; Li, Minghui; Su, Deyuan; Jia, Qi; Li, Huan; Li, Xueming; Yang, Jian

2017-12-01

TRPML3 channels are mainly localized to endolysosomes and play a critical role in the endocytic pathway. Their dysfunction causes deafness and pigmentation defects in mice. TRPML3 activity is inhibited by low endolysosomal pH. Here we present cryo-electron microscopy (cryo-EM) structures of human TRPML3 in the closed, agonist-activated, and low-pH-inhibited states, with resolutions of 4.06, 3.62, and 4.65 Å, respectively. The agonist ML-SA1 lodges between S5 and S6 and opens an S6 gate. A polycystin-mucolipin domain (PMD) forms a luminal cap. S1 extends into this cap, forming a 'gating rod' that connects directly to a luminal pore loop, which undergoes dramatic conformational changes in response to low pH. S2 extends intracellularly and interacts with several intracellular regions to form a 'gating knob'. These unique structural features, combined with the results of electrophysiological studies, indicate a new mechanism by which luminal pH and other physiological modulators such as PIP 2 regulate TRPML3 by changing S1 and S2 conformations.

A Validation Dataset for CryoSat Sea Ice Investigators

DEFF Research Database (Denmark)

Julia, Gaudelli,; Baker, Steve; Haas, Christian

Since its launch in April 2010 Cryosat has been collecting valuable sea ice data over the Arctic region. Over the same period ESA’s CryoVEx and NASA IceBridge validation campaigns have been collecting a unique set of coincident airborne measurements in the Arctic. The CryoVal-SI project has...... community. In this talk we will describe the composition of the validation dataset, summarising how it was processed and how to understand the content and format of the data. We will also explain how to access the data and the supporting documentation....

Synthesis of Monodispersed Spherical Single Crystalline Silver Particles by Wet Chemical Process; Shisshiki kagakuho ni yoru tanbunsankyujo tankesshoginryushi no gose

Energy Technology Data Exchange (ETDEWEB)

Ueyama, Ryousuke.; Harada, Masahiro.; Ueyama, Tamotsu.; Harada, Akio. [Daiken Chemistry Industry Corporation, Osaka (Japan); Yamamoto, Takashi. [National Defence Academy, Kanagawa (Japan). Dept. of Electrical Engineering; Shiosaki, Tadashi. [Nara Institute of Science and Technology, Nara (Japan). Graduate School of Materials Science; Kuribayashi, Kiyoshi. [Teikyo University of Science and Technology, Yamanashi (Japan). Dept. of Materials

1999-01-01

Ultrafine silver monodispersed particle were prepared by wet chemical process. To decrease the reduction speed, an important factor in generating monodispersed particles is to control the following three factors: synthesis temperature, concentration of aggregation-relaxing agent added, and concentration of silver nitrate solution. Synthesis of monodispersed spherical Ag particles, used as metal powders for electrode, became possible using the nucleus grouwth reaction method. This process also allowed the control of the diameter of the powder particles. The silver particles were distributed in ta narrow particle diameter range with on average of 0.5 {mu}m. Transmission electron microscopy (TEM) revealed that single-crystalline silver particles were prepared by the present method. (author)

A high efficiency superconducting nanowire single electron detector

NARCIS (Netherlands)

Rosticher, M.; Ladan, F.R.; Maneval, J.P.; Dorenbos, S.N.; Zijlstra, T.; Klapwijk, T.M.; Zwiller, V.; Lupa?cu, A.; Nogues, G.

2010-01-01

We report the detection of single electrons using a Nb0.7Ti0.3N superconducting wire deposited on an oxidized silicon substrate. While it is known that this device is sensitive to single photons, we show that it also detects single electrons with kilo-electron-volt energy emitted from the cathode of

CryoCart Restoration and Vacuum Pipe Construction

Science.gov (United States)

Chaidez, Mariana

2016-01-01

first completed at the component level. During this process, the igniter of the main engine and the RCS thrusters will be tested under a vacuum. To complete the testing of the components, the test setup first needed to be finalized. The CryoCart is being used to feed the propellants to the test article. The CryoCart is a movable test set-up that was developed in 2009 to provide a mobile platform for testing oxygen/methane systems with hot-fire capability up to 100 lbf. The CryoCart consists of three different systems: Oxygen, Methane, and liquid Nitrogen. The Oxygen and Methane systems are placed into two different carts while the liquid nitrogen system is mainly located in the methane cart. Over the years, the CryoCart has been utilized for different projects and has undergone deterioration. For this reason, a new phase has been developed to rebuild it to working conditions once again. During my internship, I was aiding in the construction and restoration of the CryoCart. In the initial stages of the process, I updated the fluid and electrical schematics for the oxygen, methane, and test article systems. The original CryoCart consisted of an electrical panel that utilized electromechanical relays and a terminal to drive the igniter power and signal, as well as the main fuel and oxygen valves. This electrical panel connected to the CryoCart through various wire harnesses that could be found exiting from the CryoCart. First, it was determined how these harnesses connected to the electromechanical relays so that they worked correctly. Once the electrical system was understood, an alternative for the electromechanical relays and the Molex connectors used throughout the system was sought since these components can often prove to be unreliable. Solid State relays and MIL connectors were purchased to serve as replacements. Upon arrival of the parts, crimping and wiring was completed to install the new solid state relays and MIL connectors. During the replacement of the relays

Nonlinear ion-mixing-mode particle transport in the dissipative trapped electron regime

International Nuclear Information System (INIS)

Ware, A.S.; Terry, P.W.

1993-09-01

The nonlinear particle transport arising from the convection of nonadiabatic electron density by ion temperature gradient driven turbulence is examined for trapped electron collisionality regimes. The renormalized dissipative nonadiabatic trapped electron phase space density response is derived and used to calculate the nonlinear particle flux along with an ansatz for the turbulently broadened frequency spectrum. In the lower temperature end of this regime, trapped electrons are collisional and all components of the quasilinear particle flux are outward (i.e., in the direction of the gradients). Nonlinear effects can alter the phase between the nonadiabatic trapped electron phase space density and the electrostatic potential, producing inward components in the particle flux. Specifically, both turbulent shifting of the peak of the frequency spectrum and nonlinear source terms in the trapped electron response can give rise to inward components. However, in the dissipative regime these terms are small and the trapped electron response remains dominantly laminar. When the trapped electrons are collisionless, there is a temperature threshold above which the electron temperature gradient driven component of the quasilinear particle flux changes sign and becomes inward. For finite amplitude turbulence, however, turbulent broadening of both the electron collisional resonance and the frequency spectrum removes tills threshold., and the temperature gradient driven component remains outward

Laboratory Measurements of Single-Particle Polarimetric Spectrum

Science.gov (United States)

Gritsevich, M.; Penttila, A.; Maconi, G.; Kassamakov, I.; Helander, P.; Puranen, T.; Salmi, A.; Hæggström, E.; Muinonen, K.

2017-12-01

Measuring scattering properties of different targets is important for material characterization, remote sensing applications, and for verifying theoretical results. Furthermore, there are usually simplifications made when we model targets and compute the scattering properties, e.g., ideal shape or constant optical parameters throughout the target material. Experimental studies help in understanding the link between the observed properties and computed results. Experimentally derived Mueller matrices of studied particles can be used as input for larger-scale scattering simulations, e.g., radiative transfer computations. This method allows to bypass the problem of using an idealized model for single-particle optical properties. While existing approaches offer ensemble- and orientation-averaged particle properties, our aim is to measure individual particles with controlled or known orientation. With the newly developed scatterometer, we aim to offer novel possibility to measure single, small (down to μm-scale) targets and their polarimetric spectra. This work presents an experimental setup that measures light scattered by a fixed small particle with dimensions ranging between micrometer and millimeter sizes. The goal of our setup is nondestructive characterization of such particles by measuring light of multiple wavelengths scattered in 360° in a horizontal plane by an ultrasonically levitating sample, whilst simultaneously controlling its 3D position and orientation. We describe the principles and design of our instrument and its calibration. We also present example measurements of real samples. This study was conducted under the support from the European Research Council, in the frame of the Advanced Grant project No. 320773 `Scattering and Absorption of Electromagnetic Waves in Particulate Media' (SAEMPL).

Electronic properties of single crystal CVD diamond and its suitability for particle detection in hadron physics experiments

Energy Technology Data Exchange (ETDEWEB)

Pomorski, Michal

2008-08-07

This work presents the study on the suitability of single-crystal CVD diamond for particle-detection systems in present and future hadron physics experiments. Different characterization methods of the electrical and the structural properties were applied to gain a deeper understanding of the crystal quality and the charge transport properties of this novel semiconductor material. First measurements regarding the radiation tolerance of diamond were performed with sensors heavily irradiated with protons and neutrons. Finally, detector prototypes were fabricated and successfully tested in various experiments as time detectors for minimum ionizing particles as well as for spectroscopy of heavy ions at the energy ranges available at the SIS and the UNILAC facilities of GSI. (orig.)

Electronic properties of single crystal CVD diamond and its suitability for particle detection in hadron physics experiments

International Nuclear Information System (INIS)

Pomorski, Michal

2008-01-01

This work presents the study on the suitability of single-crystal CVD diamond for particle-detection systems in present and future hadron physics experiments. Different characterization methods of the electrical and the structural properties were applied to gain a deeper understanding of the crystal quality and the charge transport properties of this novel semiconductor material. First measurements regarding the radiation tolerance of diamond were performed with sensors heavily irradiated with protons and neutrons. Finally, detector prototypes were fabricated and successfully tested in various experiments as time detectors for minimum ionizing particles as well as for spectroscopy of heavy ions at the energy ranges available at the SIS and the UNILAC facilities of GSI. (orig.)

Reversible electron heating vs. wave-particle interactions in quasi-perpendicular shocks

Science.gov (United States)

Veltri, P.; Mangeney, A.; Scudder, J. D.

1992-01-01

The energy necessary to explain the electron heating in quasi-perpendicular collisionless shocks can be derived either from the electron acceleration in the d.c. cross shock electric potential, or by the interactions between the electrons and the waves existing in the shock. A Monte Carlo simulation has been performed to study the electron distribution function evolution through the shock structure, with and without particle diffusion on waves. This simulation has allowed us to clarify the relative importance of the two possible energy sources; in particular it has been shown that the electron parallel temperature is determined by the d.c. electromagnetic field and not by any wave-particle-induced heating. Wave particle interactions are effective in smoothing out the large gradients in phase space produced by the 'reversible' motion of the electrons, thus producing a 'cooling' of the electrons.

Performance analysis of a large-scale helium Brayton cryo-refrigerator with static gas bearing turboexpander

International Nuclear Information System (INIS)

Zhang, Yu; Li, Qiang; Wu, Jihao; Li, Qing; Lu, Wenhai; Xiong, Lianyou; Liu, Liqiang; Xu, Xiangdong; Sun, Lijia; Sun, Yu; Xie, Xiujuan; Wang, Bingming; Qiu, Yinan; Zhang, Peng

2015-01-01

Highlights: • A 2 kW at 20.0 K helium Brayton cryo-refrigerator is built in China. • A series of tests have been systematically conducted to investigate the performance of the cryo-refrigerator. • Maximum heat conductance proportion (90.7%) appears in the heat exchangers of cold box rather than those of heat reservoirs. • A model of helium Brayton cryo-refrigerator/cycle is presented according to finite-time thermodynamics. - Abstract: Large-scale helium cryo-refrigerator is widely used in superconducting systems, nuclear fusion engineering, and scientific researches, etc., however, its energy efficiency is quite low. First, a 2 kW at 20.0 K helium Brayton cryo-refrigerator is built, and a series of tests have been systematically conducted to investigate the performance of the cryo-refrigerator. It is found that maximum heat conductance proportion (90.7%) appears in the heat exchangers of cold box rather than those of heat reservoirs, which is the main characteristic of the helium Brayton cryo-refrigerator/cycle different from the air Brayton refrigerator/cycle. Other three characteristics also lie in the configuration of refrigerant helium bypass, internal purifier and non-linearity of specific heat of helium. Second, a model of helium Brayton cryo-refrigerator/cycle is presented according to finite-time thermodynamics. The assumption named internal purification temperature depth (PTD) is introduced, and the heat capacity rate of whole cycle is divided into three different regions in accordance with the PTD: room temperature region, upper internal purification temperature region and lower one. Analytical expressions of cooling capacity and COP are obtained, and we found that the expressions are piecewise functions. Further, comparison between the model and the experimental results for cooling capacity of the helium cryo-refrigerator shows that error is less than 7.6%. The PTD not only helps to achieve the analytical formulae and indicates the working

Light-induced electronic non-equilibrium in plasmonic particles.

Science.gov (United States)

Kornbluth, Mordechai; Nitzan, Abraham; Seideman, Tamar

2013-05-07

We consider the transient non-equilibrium electronic distribution that is created in a metal nanoparticle upon plasmon excitation. Following light absorption, the created plasmons decohere within a few femtoseconds, producing uncorrelated electron-hole pairs. The corresponding non-thermal electronic distribution evolves in response to the photo-exciting pulse and to subsequent relaxation processes. First, on the femtosecond timescale, the electronic subsystem relaxes to a Fermi-Dirac distribution characterized by an electronic temperature. Next, within picoseconds, thermalization with the underlying lattice phonons leads to a hot particle in internal equilibrium that subsequently equilibrates with the environment. Here we focus on the early stage of this multistep relaxation process, and on the properties of the ensuing non-equilibrium electronic distribution. We consider the form of this distribution as derived from the balance between the optical absorption and the subsequent relaxation processes, and discuss its implication for (a) heating of illuminated plasmonic particles, (b) the possibility to optically induce current in junctions, and (c) the prospect for experimental observation of such light-driven transport phenomena.

CryoSat Mission over Polar Region: Data quality status and product evolutions

Science.gov (United States)

Bouffard, J.; Parrinello, T.; Féménias, P.; Fornari, M.; Scagliola, M.; Baker, S.; Brockley, D.; Mannan, R.; Hall, A.; Webb, E.; Garcia-Mondéjar, A.; Roca, M.; Mantovani, P. L.

2015-12-01

Over the past 20 years, satellite radar altimetry has shown its ability to revolutionize our understanding of the ocean and climate. These advances were mainly limited to ice-free regions, leaving aside large portions of Polar Regions. Launched in 2010, the polar-orbiting CryoSat Satellite was designed to measure the changes in the thickness of polar sea ice and the elevation of the ice sheets and mountain glaciers. To reach this goal, the CryoSat products have to meet the highest performance, through constant improvements of the associated Instrument Processing Facility. Since April 2015, the CryoSat ice products are generated with the Baseline C; which represents a major processor upgrade. Several improvements have been implemented belong this new Baseline, such as SAR retracker optimized for Freeboard retrieval and a coarse slant correction, which is applied directly on the stack data in conjunction with the window delay alignment. The resulting waveforms show more power and the trailing edge is modified, leading to improved L2 geophysical parameters. This paper provides an overview of the CryoSat data characteristics, assessment and exploitation over Polar Regions. In this respect, new science-oriented diagnostics have been implemented to thoroughly understand the signatures within the altimeter signals over sea-ice and land ice areas, to validate the data and therefore propose potential way of improvements for next CryoSat processing Baselines.

Single particle analysis with a 3600 light scattering photometer

International Nuclear Information System (INIS)

Bartholdi, M.F.

1979-06-01

Light scattering by single spherical homogeneous particles in the diameter range 1 to 20 μm and relative refractive index 1.20 is measured. Particle size of narrowly dispersed populations is determined and a multi-modal dispersion of five components is completely analyzed. A 360 0 light scattering photometer for analysis of single particles has been designed and developed. A fluid stream containing single particles intersects a focused laser beam at the primary focal point of an ellipsoidal reflector ring. The light scattered at angles theta = 2.5 0 to 177.5 0 at phi = 0 0 and 180 0 is reflected onto a circular array of photodiodes. The ellipsoidal reflector is situated in a chamber filled with fluid matching that of the stream to minimize refracting and reflecting interfaces. The detector array consists of 60 photodiodes each subtending 3 0 in scattering angle on 6 0 centers around 360 0 . 32 measurements on individual particles can be acquired at rates of 500 particles per second. The intensity and angular distribution of light scattered by spherical particles are indicative of size and relative refractive index. Calculations, using Lorenz--Mie theory, of differential scattering patterns integrated over angle corresponding to the detector geometry determined the instrument response to particle size. From this the expected resolution and experimental procedures are determined.Ultimately, the photometer will be utilized for identification and discrimination of biological cells based on the sensitivity of light scattering to size, shape, refractive index differences, internal granularity, and other internal morphology. This study has demonstrated the utility of the photometer and indicates potential for application to light scattering studies of biological cells

Electron, proton, neutron as spheroidical particles

International Nuclear Information System (INIS)

Bagge, E.R.

1993-01-01

It is shown that it is possible to describe the electron and the proton at rest within the framework of Dirac's relativistic theory of particles as electro-magnetic stable, spheroidal particles like balloons with very thin envelopes. Their properties, especially their spins and their magnetic momenta, are exactly those, which have been measured at first and later on derived by Dirac. In this picture the neutron plays the role of a system of two concentric and synchronically rotating balloons with a small distance between them at a positive energetic minimum of balance at 1.26 MeV. The magnetic moment of this particle has a negative sign and is of the correct size. (orig.)

Single-particle basis and translational invariance in microscopic nuclear calculations

International Nuclear Information System (INIS)

Ehfros, V.D.

1977-01-01

The approach to the few-body problem is considered which allows to use the simple single-particle basis without violation of the translation invariance. A method is proposed to solve the nuclear reaction problems in the single-particle basis. The method satisfies the Pauli principle and the translation invariance. Calculation of the matrix elements of operators is treated

Particle Beam Tests of the Calorimetric Electron Telescope

CERN Document Server

Tamura, Tadahisa

The Calorimetric Electron Telescope (CALET) is a new mission addressing outstanding astrophysics questions including the nature of dark matter, the sources of high-energy particles and photons, and the details of particle acceleration and transport in the galaxy by measuring the high-energy spectra of electrons, nuclei, and gamma-rays. It will launch on HTV-5 (H-II Transfer Vehicle 5) in 2014 for installation on the Japanese Experiment Module–Exposed Facility (JEM-EF) of the International Space Station. The CALET collaboration is led by JAXA and includes researchers from Japan, the U.S. and Italy. The CALET Main Telescope uses a plastic scintillator charge detector followed by a 30 radiation-length (X0) deep particle calorimeter divided into a 3 X0 imaging calorimeter, with scintillating optical fibers interleaved with thin tungsten sheets, and a 27 X0 fully-active total-absorption calorimeter made of lead tungstate scintillators. CALET prototypes were tested at the CERN (European Laboratory for Particle Ph...

Factors Influencing the Ignition and Burnout of a Single Biomass Particle

DEFF Research Database (Denmark)

Momenikouchaksaraei, Maryam; Kær, Søren Knudsen; Yin, Chungen

2011-01-01

Ignition and burnout of a single biomass particle were studied numerically. A one-dimensional particle combustion model was developed which is capable to simulate all the intraparticle conversion processes (drying, recondensation, devolatilization, char gasification/oxidation and heat/mass/moment......Ignition and burnout of a single biomass particle were studied numerically. A one-dimensional particle combustion model was developed which is capable to simulate all the intraparticle conversion processes (drying, recondensation, devolatilization, char gasification/oxidation and heat...... concentration were not very significant. The influences of these factors on particle burnout were much more remarkable than ignition behaviour....

Two-Way Communication with a Single Quantum Particle

Science.gov (United States)

Del Santo, Flavio; Dakić, Borivoje

2018-02-01

In this Letter we show that communication when restricted to a single information carrier (i.e., single particle) and finite speed of propagation is fundamentally limited for classical systems. On the other hand, quantum systems can surpass this limitation. We show that communication bounded to the exchange of a single quantum particle (in superposition of different spatial locations) can result in "two-way signaling," which is impossible in classical physics. We quantify the discrepancy between classical and quantum scenarios by the probability of winning a game played by distant players. We generalize our result to an arbitrary number of parties and we show that the probability of success is asymptotically decreasing to zero as the number of parties grows, for all classical strategies. In contrast, quantum strategy allows players to win the game with certainty.

Snow particles extracted from X-ray computed microtomography imagery and their single-scattering properties

Science.gov (United States)

Ishimoto, Hiroshi; Adachi, Satoru; Yamaguchi, Satoru; Tanikawa, Tomonori; Aoki, Teruo; Masuda, Kazuhiko

2018-04-01

Sizes and shapes of snow particles were determined from X-ray computed microtomography (micro-CT) images, and their single-scattering properties were calculated at visible and near-infrared wavelengths using a Geometrical Optics Method (GOM). We analyzed seven snow samples including fresh and aged artificial snow and natural snow obtained from field samples. Individual snow particles were numerically extracted, and the shape of each snow particle was defined by applying a rendering method. The size distribution and specific surface area distribution were estimated from the geometrical properties of the snow particles, and an effective particle radius was derived for each snow sample. The GOM calculations at wavelengths of 0.532 and 1.242 μm revealed that the realistic snow particles had similar scattering phase functions as those of previously modeled irregular shaped particles. Furthermore, distinct dendritic particles had a characteristic scattering phase function and asymmetry factor. The single-scattering properties of particles of effective radius reff were compared with the size-averaged single-scattering properties. We found that the particles of reff could be used as representative particles for calculating the average single-scattering properties of the snow. Furthermore, the single-scattering properties of the micro-CT particles were compared to those of particle shape models using our current snow retrieval algorithm. For the single-scattering phase function, the results of the micro-CT particles were consistent with those of a conceptual two-shape model. However, the particle size dependence differed for the single-scattering albedo and asymmetry factor.

Single-electron tunneling in InP nanowires

NARCIS (Netherlands)

Franceschi, De S.; Dam, Van J.A.; Bakkers, E.P.A.M.; Feiner, L.F.; Gurevich, L.; Kouwenhoven, L.P.

2003-01-01

A study was performed on single-electron tunneling in InP nanowires. The contact resistances as low as ~10 k¿, with minor temperature dependence were obtained. The Coulomb-blockade behavior was shown with single-electron charging energies of ~1 meV.

Measuring Density Profiles of Electrons and Heavy Particles in a Stable Axially Blown Arc

Science.gov (United States)

Carstensen, J.; Stoller, P.; Galletti, B.; Doiron, C. B.; Sokolov, A.

2017-08-01

Two-color spatial carrier wave interferometry employing pulsed 532- and 671-nm lasers is used to measure the electron-density and heavy-particle-density profiles in the stagnation point of a stable, axially blown arc in argon for currents of 50 to 200 A and stagnation point pressures of 0.2 to 16 bar. This technique takes advantage of the fact that the free-electron contribution to the refractive index depends strongly on the wavelength, while that of the heavy particles does not. The high spatial resolution achieved allows the hot core of the arc to be readily distinguished from the surrounding boundary layer. A custom-built test device is used to ensure flow conditions that lead to a stable, axisymmetric arc; this permits the reconstruction of the density and temperature profiles using a single projection (interferometric image) of the refractive-index distribution through the arc (at two wavelengths). The arc radius determined from the heavy-particle density decreases with increasing stagnation pressure and increases with the current. These measurements are in good agreement with a simple axially blown arc model taking into account Ohmic heating, radiation losses, and enthalpy flow for core temperatures of approximately 16 500 K. The measured electron density at the center of the arc agrees well with a prediction based on local thermodynamic equilibrium.

Mass spectra features of biomass burning boiler and coal burning boiler emitted particles by single particle aerosol mass spectrometer.

Science.gov (United States)

Xu, Jiao; Li, Mei; Shi, Guoliang; Wang, Haiting; Ma, Xian; Wu, Jianhui; Shi, Xurong; Feng, Yinchang

2017-11-15

In this study, single particle mass spectra signatures of both coal burning boiler and biomass burning boiler emitted particles were studied. Particle samples were suspended in clean Resuspension Chamber, and analyzed by ELPI and SPAMS simultaneously. The size distribution of BBB (biomass burning boiler sample) and CBB (coal burning boiler sample) are different, as BBB peaks at smaller size, and CBB peaks at larger size. Mass spectra signatures of two samples were studied by analyzing the average mass spectrum of each particle cluster extracted by ART-2a in different size ranges. In conclusion, BBB sample mostly consists of OC and EC containing particles, and a small fraction of K-rich particles in the size range of 0.2-0.5μm. In 0.5-1.0μm, BBB sample consists of EC, OC, K-rich and Al_Silicate containing particles; CBB sample consists of EC, ECOC containing particles, while Al_Silicate (including Al_Ca_Ti_Silicate, Al_Ti_Silicate, Al_Silicate) containing particles got higher fractions as size increase. The similarity of single particle mass spectrum signatures between two samples were studied by analyzing the dot product, results indicated that part of the single particle mass spectra of two samples in the same size range are similar, which bring challenge to the future source apportionment activity by using single particle aerosol mass spectrometer. Results of this study will provide physicochemical information of important sources which contribute to particle pollution, and will support source apportionment activities. Copyright © 2017. Published by Elsevier B.V.

Single-electron quantum tomography in quantum Hall edge channels

International Nuclear Information System (INIS)

Grenier, Ch; Degiovanni, P; Herve, R; Bocquillon, E; Parmentier, F D; Placais, B; Berroir, J M; Feve, G

2011-01-01

We propose a quantum tomography protocol to measure single-electron coherence in quantum Hall edge channels, and therefore access for the first time the wavefunction of single-electron excitations propagating in ballistic quantum conductors. Its implementation would open the way to quantitative studies of single-electron decoherence and would provide a quantitative tool for analyzing single- to few-electron sources. We show how this protocol could be implemented using ultrahigh-sensitivity noise measurement schemes.

A multi-parametric particle-pairing algorithm for particle tracking in single and multiphase flows

International Nuclear Information System (INIS)

Cardwell, Nicholas D; Vlachos, Pavlos P; Thole, Karen A

2011-01-01

Multiphase flows (MPFs) offer a rich area of fundamental study with many practical applications. Examples of such flows range from the ingestion of foreign particulates in gas turbines to transport of particles within the human body. Experimental investigation of MPFs, however, is challenging, and requires techniques that simultaneously resolve both the carrier and discrete phases present in the flowfield. This paper presents a new multi-parametric particle-pairing algorithm for particle tracking velocimetry (MP3-PTV) in MPFs. MP3-PTV improves upon previous particle tracking algorithms by employing a novel variable pair-matching algorithm which utilizes displacement preconditioning in combination with estimated particle size and intensity to more effectively and accurately match particle pairs between successive images. To improve the method's efficiency, a new particle identification and segmentation routine was also developed. Validation of the new method was initially performed on two artificial data sets: a traditional single-phase flow published by the Visualization Society of Japan (VSJ) and an in-house generated MPF data set having a bi-modal distribution of particles diameters. Metrics of the measurement yield, reliability and overall tracking efficiency were used for method comparison. On the VSJ data set, the newly presented segmentation routine delivered a twofold improvement in identifying particles when compared to other published methods. For the simulated MPF data set, measurement efficiency of the carrier phases improved from 9% to 41% for MP3-PTV as compared to a traditional hybrid PTV. When employed on experimental data of a gas–solid flow, the MP3-PTV effectively identified the two particle populations and reported a vector efficiency and velocity measurement error comparable to measurements for the single-phase flow images. Simultaneous measurement of the dispersed particle and the carrier flowfield velocities allowed for the calculation of

Giant current fluctuations in an overheated single-electron transistor

NARCIS (Netherlands)

Laakso, M.A.; Heikkilä, T.T.; Nazarov, Y.V.

2010-01-01

Interplay of cotunneling and single-electron tunneling in a thermally isolated single-electron transistor leads to peculiar overheating effects. In particular, there is an interesting crossover interval where the competition between cotunneling and single-electron tunneling changes to the dominance

Multi-photon creation and single-photon annihilation of electron-positron pairs

Energy Technology Data Exchange (ETDEWEB)

Hu, Huayu

2011-04-27

In this thesis we study multi-photon e{sup +}e{sup -} pair production in a trident process, and singlephoton e{sup +}e{sup -} pair annihilation in a triple interaction. The pair production is considered in the collision of a relativistic electron with a strong laser beam, and calculated within the theory of laser-dressed quantum electrodynamics. A regularization method is developed systematically for the resonance problem arising in the multi-photon process. Total production rates, positron spectra, and relative contributions of different reaction channels are obtained in various interaction regimes. Our calculation shows good agreement with existing experimental data from SLAC, and adds further insights into the experimental findings. Besides, we study the process in a manifestly nonperturbative domain, whose accessibility to future all-optical experiments based on laser acceleration is shown. In the single-photon e{sup +}e{sup -} pair annihilation, the recoil momentum is absorbed by a spectator particle. Various kinematic configurations of the three incoming particles are examined. Under certain conditions, the emitted photon exhibits distinct angular and polarization distributions which could facilitate the detection of the process. Considering an equilibrium relativistic e{sup +}e{sup -} plasma, it is found that the single-photon process becomes the dominant annihilation channel for plasma temperatures above 3 MeV. Multi-particle correlation effects are therefore essential for the e{sup +}e{sup -} dynamics at very high density. (orig.)

Multi-photon creation and single-photon annihilation of electron-positron pairs

International Nuclear Information System (INIS)

Hu, Huayu

2011-01-01

In this thesis we study multi-photon e + e - pair production in a trident process, and singlephoton e + e - pair annihilation in a triple interaction. The pair production is considered in the collision of a relativistic electron with a strong laser beam, and calculated within the theory of laser-dressed quantum electrodynamics. A regularization method is developed systematically for the resonance problem arising in the multi-photon process. Total production rates, positron spectra, and relative contributions of different reaction channels are obtained in various interaction regimes. Our calculation shows good agreement with existing experimental data from SLAC, and adds further insights into the experimental findings. Besides, we study the process in a manifestly nonperturbative domain, whose accessibility to future all-optical experiments based on laser acceleration is shown. In the single-photon e + e - pair annihilation, the recoil momentum is absorbed by a spectator particle. Various kinematic configurations of the three incoming particles are examined. Under certain conditions, the emitted photon exhibits distinct angular and polarization distributions which could facilitate the detection of the process. Considering an equilibrium relativistic e + e - plasma, it is found that the single-photon process becomes the dominant annihilation channel for plasma temperatures above 3 MeV. Multi-particle correlation effects are therefore essential for the e + e - dynamics at very high density. (orig.)

Momentum spectra for single and double electron ionization of He in relativistic collisions

International Nuclear Information System (INIS)

Wood, C.J.; Olson, R.E.

1997-08-01

The complete momentum spectra for single and double ionization of He by 1GeV/u (β=0.88) U 92+ have been investigated using a classical trajectory Monte Carlo method corrected for the relativistic projectile. The 1/r 12 electron-electron interaction has been included in the post-collision region for double ionization to incorporate the effects of both the nuclear-electron and electron-electron ionizing interactions, and to access the effects of electron correlation in the electron spectra. Experimental measurements were able to determine the longitudinal momentum spectra for single ionization; these observations are in accordance with the theoretical predictions for the three-body momentum balance between projectile, recoil ion, and ionized electron. In particular, the Lorentz contraction of the Coulomb interaction of the projectile manifests itself in the decrease of the post-collision interaction of the projectile with the electron and recoil ion, causing them to recoil back-to-back as in the case for a short electromagnetic pulse. This feature is clearly displayed in both the theoretical and experimental longitudinal momentum spectra, and by comparing to calculations that are performed at the same collision speed but do not include the relativistic potentials. Moreover, collision plane spectra of the three particles demonstrate that the momenta of the recoil ion and ionized electron are preferentially equal, and opposite, to each other. The electron spectra for double ionization show that the inclusion of the electron-electron interaction in the post-collision regime partitions the combined ionization momentum of the electrons so that the electrons are preferentially emitted in opposite azimuthal angles to one another. This is in contrast to calculations made assuming independent electrons. (orig.)

New Insights into HTLV-1 Particle Structure, Assembly, and Gag-Gag Interactions in Living Cells

Directory of Open Access Journals (Sweden)

Jolene L. Johnson

2011-06-01

Full Text Available Human T-cell leukemia virus type 1 (HTLV-1 has a reputation for being extremely difficult to study in cell culture. The challenges in propagating HTLV-1 has prevented a rigorous analysis of how these viruses replicate in cells, including the detailed steps involved in virus assembly. The details for how retrovirus particle assembly occurs are poorly understood, even for other more tractable retroviral systems. Recent studies on HTLV-1 using state-of-the-art cryo-electron microscopy and fluorescence-based biophysical approaches explored questions related to HTLV-1 particle size, Gag stoichiometry in virions, and Gag-Gag interactions in living cells. These results provided new and exciting insights into fundamental aspects of HTLV-1 particle assembly—which are distinct from those of other retroviruses, including HIV-1. The application of these and other novel biophysical approaches promise to provide exciting new insights into HTLV-1 replication.

D0 Cryo System Control System Autodialer

Energy Technology Data Exchange (ETDEWEB)

Urbin, J.; /Fermilab

1990-04-17

The DO cryogenic system is controlled by a TI565-PLC based control system. This allows the system to be unmanned when in steady state operation. System experts will need to be contacted when system parameters exceed normal operating points and reach alarm setpoints. The labwide FIRUS system provides one alarm monitor and communication link. An autodialer provides a second and more flexible alarm monitor and communication link. The autodialer monitors contact points in the control system and after receiving indication of an alarm accesses a list of experts which it calls until it receives an acknowledgement. There are several manufacturers and distributors of autodialer systems. This EN explains the search process the DO cryo group used to fmd an autodialer system that fit the cryo system's needs and includes information and specs for the unit we chose.

The measurement of single particle temperature in plasma sprays

International Nuclear Information System (INIS)

Fincke, J.R.; Swank, W.D.; Bolsaitis, P.P.; Elliott, J.F.

1990-01-01

A measurement technique for simultaneously obtaining the size, velocity, temperature, and relative number density of particles entrained in high temperature flow fields is described. In determining the particle temperature from a two-color pyrometery technique, assumptions about the relative spectral emissivity of the particle are required. For situations in which the particle surface undergoes chemical reactions the assumption of grey body behavior is shown to introduce large Temperature measurement uncertainties. Results from isolated, laser heated, single particle measurements and in-flight data from the plasma spraying of WC-Co are presented. 10 refs., 5 figs

Aerosol particle charger and an SO2 reactor using energetic electrons

International Nuclear Information System (INIS)

Davis, R.H.

1984-01-01

Two properties of energetic electrons in gas, their high specific ionization and their production of radicals and other chemically active specie, have promising applications to the cleanup of flue gas from coal combustion. The copious ionization has been used in a test particle charger to electrically charge 1 and 3 μm particles for subsequent removal by electrostatic precipitation. Particle charge greater than 5 times the theoretical ionic charging value for 1 μm particles have been observed in a bi-electrode electron beam precharger in which the beam energy is matched with the electrode spacing. In another test device, pulsed streamer coronas have been used to release and to energize electrons which promote gas phase chemical reactions and remote sulfur dioxide from humid air with high efficiency. The energized electrons produce oxidant radicals and chemically active specie which convert the SO 2 into sulfuric acid mist. While reported separately here, the two applications of energetic electrons may be amenable to combination in an integrated system for the combined treatment of flue gas

Macroscopic charge quantization in single-electron devices

NARCIS (Netherlands)

Burmistrov, I.S.; Pruisken, A.M.M.

2010-01-01

In a recent paper by the authors [I. S. Burmistrov and A. M. M. Pruisken, Phys. Rev. Lett. 101, 056801 (2008)] it was shown that single-electron devices (single-electron transistor or SET) display "macroscopic charge quantization" which is completely analogous to the quantum Hall effect observed on

Tagged particle in single-file diffusion with arbitrary initial conditions

Science.gov (United States)

Cividini, J.; Kundu, A.

2017-08-01

We compute the full probability distribution of the positions of a tagged particle exactly for the given arbitrary initial positions of the particles, and for general single-particle propagators. We consider the thermodynamic limit of our exact expressions in quenched and annealed settings. For a particular class of single-particle propagators, the exact formula is expressed in a simple integral form in the quenched case whereas in the annealed case, it is expressed as a simple combination of Bessel functions. In particular, we focus on the step and the power-law initial configurations. In the former case, a drift is induced even when the one-particle propagators are symmetric. On the other hand, in the later case the scaling of the cumulants of the position of the tracer differs from the uniform case. We provide numerical verifications of our results.

Tomograms and the quest for single particle nonlocality

International Nuclear Information System (INIS)

Anisimov, M A; Caponigro, M; Mancini, S; Man'ko, V I

2007-01-01

By using a tomographic approach to quantum states, we rise the problem of nonlocality within a single particle (single degree of freedom). We propose a possible way to look for such effects on a qubit. Although a conclusive answer is far from being reached, we provide some reflections on the foundational ground

Many-particle correlations in quasi-two-dimensional electron-hole systems

International Nuclear Information System (INIS)

Nikolaev, Valentin

2002-01-01

This thesis reports a theoretical investigation of many-particle correlation effects in semiconductor heterostructures containing quantum wells. Particular attention is paid towards quasi-particle pair correlations. Using the Green's function technique and the ladder approximation as a basis, the generalized mass action law, which describes the redistribution of particles between correlated and uncorrelated states in quasi-two-dimensional systems for different temperatures and total densities, is derived. The expression is valid beyond the low-density limit, which allows us to investigate the transition of the system from a dilute exciton gas to a dense electron-hole plasma. A generalized Levinson theorem, which takes k-space filling into account, is formulated. Screening in quasi-two-dimensional systems is analyzed rigorously. Firstly, the qualitatively new mechanism of static local screening by indirect excitons is studied using the simple Thomas-Fermi approximation. Then, a detailed many-body description suitable for a proper account of dynamic screening by a quasi-2D electron-hole plasma, and consistent with the previously derived mass action law, is provided. The generalized Lindhard approximation and excitonic plasmon-pole approximations are also derived. The theory is applied to single and double quantum wells. A self-consistent procedure is developed for numerical investigation of the ionization degree of an electron-hole plasma at different values of temperature/exciton Rydberg ratios. This procedure accounts for screening, k-space filling (exciton bleaching), and the formation of excitons. An abrupt jump in the value of the ionization degree that happens with an increase of the carrier density or temperature (Mott transition) is found in a certain density-temperature region. It has been found that the critical density of the Mott transition for indirect excitons may be much smaller than that for direct excitons. A suggestion has been made that some of the

Electronically shielded solid state charged particle detector

International Nuclear Information System (INIS)

Balmer, D.K.; Haverty, T.W.; Nordin, C.W.; Tyree, W.H.

1996-01-01

An electronically shielded solid state charged particle detector system having enhanced radio frequency interference immunity includes a detector housing with a detector entrance opening for receiving the charged particles. A charged particle detector having an active surface is disposed within the housing. The active surface faces toward the detector entrance opening for providing electrical signals representative of the received charged particles when the received charged particles are applied to the active surface. A conductive layer is disposed upon the active surface. In a preferred embodiment, a nonconductive layer is disposed between the conductive layer and the active surface. The conductive layer is electrically coupled to the detector housing to provide a substantially continuous conductive electrical shield surrounding the active surface. The inner surface of the detector housing is supplemented with a radio frequency absorbing material such as ferrite. 1 fig

Single-particle motion in rapidly rotating nuclei

International Nuclear Information System (INIS)

Bengtsson, R.; Frisk, H.

1985-01-01

The motion of particles belonging to a single-j shell is described in terms of classical orbitals. The effects of rapid rotation and pairing correlations are discussed and the results are compared with the quantum mechanical orbitals. (orig.)

Damping of unbound single-particle modes

International Nuclear Information System (INIS)

Fortier, S.; Beaumel, D.; Gales, S.; Guillot, J.; Langevin-Joliot, H.; Laurent, H.; Maison, J.M.

1995-07-01

The (α, 3 He-n) reaction has been investigated at 120 MeV incident energy on 64 Ni, 90 Zr and 120 Sn target nuclei. Neutrons in coincidence with 3 He particles emitted at 0 deg were detected, in order to get information about the decay of single-particle states embedded in the (α, 3 He) continuum. Neutron angular correlations, multiplicity values and branching ratios to low-lying states of the final nuclei have been compared with the predictions of the statistical decay model. Direct branching ratios in 91 Zr deduced from this analysis are compared with the predictions of two nuclear structure models. (author)

Strong reduction of spectral heterogeneity in gold bipyramids for single-particle and single-molecule plasmon sensing.

Science.gov (United States)

Peters, S M E; Verheijen, M A; Prins, M W J; Zijlstra, P

2016-01-15

Single metal nanoparticles are attractive biomolecular sensors. Binding of analyte to a functional particle results in a plasmon shift that can be conveniently monitored in a far-field optical microscope. Heterogeneities in spectral properties of individual particles in an ensemble affect the reliability of a single-particle plasmon sensor, especially when plasmon shifts are monitored in real-time using a fixed irradiation wavelength. We compare the spectral heterogeneity of different plasmon sensor geometries (gold nanospheres, nanorods, and bipyramids) and correlate this to their size and aspect-ratio dispersion. We show that gold bipyramids exhibit a strongly reduced heterogeneity in aspect ratio and plasmon wavelength compared to commonly used gold nanorods. We show that this translates into a significantly improved homogeneity of the response to molecular binding without compromising single-molecule sensitivity.

Physical and chemical study of single aerosol particles using optical trapping cavity ringdown spectroscopy

Science.gov (United States)

2016-08-30

scope that views the trapped particle walking through the ringdown beam step by step. (b) An image that shows the traces of the particle (MWCNT... walking through the RD beam . 5 a b c Fig.3 The OT-CRDS single particle scope views oscillations of a trapped particle. (a) Image of a trapped...and walking single carbon- nanotube particles of ?50 µm in size and viewing those properties via changes of ringdown time. This single- aerosol

New instrument for tribocharge measurement due to single particle impacts

International Nuclear Information System (INIS)

Watanabe, Hideo; Ghadiri, Mojtaba; Matsuyama, Tatsushi; Ding Yulong; Pitt, Kendal G.

2007-01-01

During particulate solid processing, particle-particle and particle-wall collisions can generate electrostatic charges. This may lead to a variety of problems ranging from fire and explosion hazards to segregation, caking, and blocking. A fundamental understanding of the particle charging in such situations is therefore essential. For this purpose we have developed a new device that can measure charge transfer due to impact between a single particle and a metal plate. The device consists of an impact test system and two sets of Faraday cage and preamplifier for charge measurement. With current amplifiers, high-resolution measurements of particle charges of approximately 1 and 10 fC have been achieved before and after the impact, respectively. The device allows charge measurements of single particles with a size as small as ∼100 μm impacting on the target at different incident angles with a velocity up to about 80 m/s. Further analyses of the charge transfer as a function of particle initial charge define an equilibrium charge, i.e., an initial charge level prior to impact for which no net charge transfer would occur as a result of impact

Noise bias in the refinement of structures derived from single particles

International Nuclear Information System (INIS)

Stewart, Alex; Grigorieff, Nikolaus

2004-01-01

One of the main goals in the determination of three-dimensional macromolecular structures from electron microscope images of individual molecules and complexes (single particles) is a sufficiently high spatial resolution, about 4 A, at which the interpretation with an atomic model becomes possible. To reach high resolution, an iterative refinement procedure using an expectation maximization algorithm is often used that leads to a more accurate alignment of the positional and orientational parameters for each particle. We show here the results of refinement algorithms that use a phase residual, a linear correlation coefficient, or a weighted correlation coefficient to align individual particles. The algorithms were applied to computer-generated data sets that contained projections from model structures, as well as noise. The algorithms show different degrees of over-fitting, especially at high resolution where the signal is weak. We demonstrate that the degree of over-fitting is reduced with a weighting scheme that depends on the signal-to-noise ratio in the data. The weighting also improves the accuracy of resolution measurement by the commonly used Fourier shell correlation. The performance of the refinement algorithms is compared to that using a maximum likelihood approach. The weighted correlation coefficient was implemented in the computer program FREALIGN

Momentum spectra for single and double electron ionization of He in relativistic collisions

International Nuclear Information System (INIS)

Anon.

1997-01-01

The complete momentum spectra for single and double ionization of He by 1-GeV/u (β=0.88) U 92+ have been investigated using a classical trajectory Monte Carlo method corrected for the relativistic projectile. The 1/r 12 electron-electron interaction has been included in the post-collision region for double ionization to incorporate the effects of both the nuclear-electron and electron-electron ionizing interactions, and to access the effects of electron correlation in the electron spectra. Experimental measurements were able to determine the longitudinal momentum spectra for single ionization; these observations are in accordance with the theoretical predictions for the three-body momentum balance between projectile, recoil ion, and ionized electron. In particular, the Lorentz contraction of the Coulomb interaction of the projectile manifests itself in the decrease of the post-collision interaction of the projectile with the electron and recoil ion, causing them to recoil back-to-back as in the case for a short electromagnetic pulse. This feature is clearly displayed in both the theoretical and experimental longitudinal momentum spectra, and by comparing to calculations that are performed at the same collision speed but do not include the relativistic potentials. Moreover, collision plane spectra of the three particles demonstrate that the momenta of the recoil ion and ionized electron are preferentially equal, and opposite, to each other. The electron spectra for double ionization show that the inclusion of the electron-electron interaction in the post-collision regime partitions the combined ionization momentum of the electrons so that the electrons are preferentially emitted in opposite azimuthal angles to one another. This is in contrast to calculations made assuming independent electrons. copyright 1997 The American Physical Society

Influence of Torrefaction on Single Particle Combustion of Wood

DEFF Research Database (Denmark)

Lu, Zhimin; Jian, Jie; Jensen, Peter Arendt

2016-01-01

This study focuses on the influence of torrefaction on the char reactivity, char yield, and combustion time of 3-5 mm spherical wood particles in a single particle combustion reactor (SPC) operating at a nominal temperature of 1231 °C. The devolatilization times were reduced and the char burnout...

Pairing fluctuation effects on the single-particle spectra for the superconducting state

International Nuclear Information System (INIS)

Pieri, P.; Pisani, L.; Strinati, G.C.

2004-01-01

Single-particle spectra are calculated in the superconducting state for a fermionic system with an attractive interaction, as functions of temperature and coupling strength from weak to strong. The fermionic system is described by a single-particle self-energy that includes pairing-fluctuation effects in the superconducting state. The theory reduces to the ordinary BCS approximation in weak coupling and to the Bogoliubov approximation for the composite bosons in strong coupling. Several features of the single-particle spectral function are shown to compare favorably with experimental data for cuprate superconductors

A transient single particle model under FCI conditions

Institute of Scientific and Technical Information of China (English)

LI Xiao-Yan; SHANG Zhi; XU Ji-Jun

2005-01-01

The paper is focused on the coupling effect between film boiling heat transfer and evaporation drag around a hot-particle in cold liquid. Based on the continuity, momentum and energy equations of the vapor film, a transient two-dimensional single particle model has been established. This paper contains a detailed description of HPMC (High-temperature Particle Moving in Coolant) model for studying some aspects of the premixing stage of fuel-coolant interactions (FCIs). The transient process of high-temperature particles moving in coolant can be simulated. Comparisons between the experiment results and the calculations using HPMC model demonstrate that HPMC model achieves a good agreement in predicting the time-varying characteristic of high-temperature spheres moving in coolant.

Optimization of magnetic switches for single particle and cell transport

Energy Technology Data Exchange (ETDEWEB)

Abedini-Nassab, Roozbeh; Yellen, Benjamin B., E-mail: yellen@duke.edu [Department of Mechanical Engineering and Materials Science, Duke University, Box 90300 Hudson Hall, Durham, North Carolina 27708 (United States); Joint Institute, University of Michigan—Shanghai Jiao Tong University, Shanghai Jiao Tong University, Shanghai 200240 (China); Murdoch, David M. [Department of Medicine, Duke University, Durham, North Carolina 27708 (United States); Kim, CheolGi [Department of Emerging Materials Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 711-873 (Korea, Republic of)

2014-06-28

The ability to manipulate an ensemble of single particles and cells is a key aim of lab-on-a-chip research; however, the control mechanisms must be optimized for minimal power consumption to enable future large-scale implementation. Recently, we demonstrated a matter transport platform, which uses overlaid patterns of magnetic films and metallic current lines to control magnetic particles and magnetic-nanoparticle-labeled cells; however, we have made no prior attempts to optimize the device geometry and power consumption. Here, we provide an optimization analysis of particle-switching devices based on stochastic variation in the particle's size and magnetic content. These results are immediately applicable to the design of robust, multiplexed platforms capable of transporting, sorting, and storing single cells in large arrays with low power and high efficiency.

Emissions from Ethanol-Gasoline Blends: A Single Particle Perspective

Directory of Open Access Journals (Sweden)

Peter H. McMurry

2011-06-01

Full Text Available Due to its agricultural origin and function as a fuel oxygenate, ethanol is being promoted as an alternative biomass-based fuel for use in spark ignition engines, with mandates for its use at state and regional levels. While it has been established that the addition of ethanol to a fuel reduces the particulate mass concentration in the exhaust, little attention has been paid to changes in the physicochemical properties of the emitted particles. In this work, a dynamometer-mounted GM Quad-4 spark ignition engine run without aftertreatment at 1,500 RPM and 100% load was used with four different fuel blends, containing 0, 20, 40 and 85 percent ethanol in gasoline. This allowed the effects of the fuel composition to be isolated from other effects. Instrumentation employed included two Aerosol Time-of-Flight Mass Spectrometers covering different size ranges for analysis of single particle composition, an Aethalometer for black carbon, a Scanning Mobility Particle Sizer for particle size distributions, a Photoelectric Aerosol Sensor for particle-bound polycyclic aromatic hydrocarbon (PAH species and gravimetric filter measurements for particulate mass concentrations. It was found that, under the conditions investigated here, additional ethanol content in the fuel changes the particle size distribution, especially in the accumulation mode, and decreases the black carbon and total particulate mass concentrations. The molecular weight distribution of the PAHs was found to decrease with added ethanol. However, PAHs produced from higher ethanol-content fuels are associated with NO2− (m/z—46 in the single-particle mass spectra, indicating the presence of nitro-PAHs. Compounds associated with the gasoline (e.g., sulfur-containing species are diminished due to dilution as ethanol is added to the fuel relative to those associated with the lubricating oil (e.g., calcium, zinc, phosphate in the single particle spectra. These changes have potential

The coastal mean dynamic topography in Norway observed by CryoSat-2 and GOCE

DEFF Research Database (Denmark)

Idžanović, Martina; Ophaug, Vegard; Andersen, Ole Baltazar

2017-01-01

New-generation synthetic aperture radar altimetry, as implemented on CryoSat-2, observes sea surface heights in coastal areas that were previously not monitored by conventional altimetry. Therefore,CryoSat-2 is expected to improve the coastal mean dynamic topography (MDT). However, the MDT remains...

Studies of the neutron single-particle structure of exotic nuclei at the HRIBF

International Nuclear Information System (INIS)

Thomas, J.S.; Bardayan, D.W.; Blackmon, J.C.; Cizewski, J.A.; Greife, U.; Gross, C.J.; Johnson, M.S.; Jones, K.L.; Kozub, R.L.; Liang, J.F.; Livesay, R.J.; Ma, Z.; Moazen, B.H.; Nesaraja, C.D.; Shapira, D.; Smith, M.S.

2004-01-01

The study of neutron single-particle strengths in neutron-rich nuclei is of interest for nuclear structure and nuclear astrophysics. The distribution of single-particle strengths constrains the effective Hamiltonian and pairing interactions and determines neutron interaction rates that are crucial for understanding the synthesis of heavy nuclei in supernovae via the rapid neutron capture process. Particularly important are the neutron single-particle levels in nuclei near closed neutron shells. Radioactive ion beams from the Holifield Radioactive Ion Beam Facility have been used to study (d,p) reactions in inverse kinematics in order to probe neutron single-particle states in exotic nuclei. The results of a measurement with a 82 Ge beam will be presented

Hard photon emission from high energy electrons and positrons in single crystals

International Nuclear Information System (INIS)

Bajer, V.N.; Katkov, V.M.; Strakhovenko, V.M.

1991-01-01

A radiation of electrons and positrons in single crystals in coherent bremsstrahlung (CBS) region has been considered for the case when CBS has the most hard spectrum. Under this condition a particle moves near a crystalline plane (in fcc(d) crystal for axis (001) this is the plane (110)) and influence of the continuous plane potential should be taken into account. This potential gives additional contribution in soft part of the spectrum and affects on hard photon emission. Observation of this phenomena at high energy is discussed. 14 refs.; 5 figs.; 1 tab

An experimental study of electron transfer and emission during particle-surface interactions

International Nuclear Information System (INIS)

McGrath, C.T.

2000-09-01

A new coincidence technique has been developed and used to study the secondary electron emission that arises during the interaction of ions with surfaces. This coincidence technique allows the secondary electron emission statistics due to the impact of singly, doubly and multiply charged ions on surfaces to be measured in coincidence with reflected particles, in specific charge states and with specific post-collision trajectories. This system has been used to study the impact of 8 keV H + ions on polycrystalline copper and aluminium targets. Under these conditions the potential emission contribution is negligible and the electron emission is almost entirely due to kinetic emission processes. The sub-surface contribution to the observed electron emission has been isolated using two newly developed models. These models provide valuable information about the depth and amount of surface penetration and on the probability for subsequent electron transport to the surface. The impact of 2 - 100 keV Xe q+ (q = 1 - 10) ions on polycrystalline copper has also been studied using this system. From the subsequent data the potential and kinetic contributions to secondary electron emission have been separated using a previously established model for potential emission. The resulting kinetic emission yield increases with increasing ion impact energy, consistent with current concepts on quasimolecular ionisation. For ions impacting at large incident angles evidence for sub-surface emission has also been observed. The degree of penetration increases with ion impact energy, consistent with current concepts on this effect. The formation of H - ions from incident H + ions has also been studied by measuring the secondary electron emission statistics in coincidence with reflected particles in specific final charge states. This preliminary data is consistent with a two-step process of Auger neutralisation followed by resonant electron capture to the affinity level. However this mechanism

Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring

Energy Technology Data Exchange (ETDEWEB)

Mountassif, Driss; Fabre, Lucien [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada); Zaid, Younes [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada); Current address: Laboratory of Thrombosis and Hemostasis, Montreal Heart Institute, Montreal, Quebec (Canada); Halawani, Dalia [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada); Current address: Department of Cell Biology, Lerner Research Institute, 9500 Euclid Avenue NC10, Cleveland, OH 44195 (United States); Rouiller, Isabelle, E-mail: isabelle.rouiller@mcgill.ca [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada)

2015-12-25

Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. - Highlights: • p97{sub R155P} and p97{sub A232E} decrease the ability of p97 to bind to its co-factor Npl4. • p97{sub R155P} has a different isoelectric point than that of p97{sub R95G}, p97{sub A232E} and p97{sub WT}. • Mutation R155P changes principally the conformation of the D2 ring. • Mutation R155P modifies the interface between two protomers within the D2 ring.

Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring

International Nuclear Information System (INIS)

Mountassif, Driss; Fabre, Lucien; Zaid, Younes; Halawani, Dalia; Rouiller, Isabelle

2015-01-01

Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. - Highlights: • p97 R155P and p97 A232E decrease the ability of p97 to bind to its co-factor Npl4. • p97 R155P has a different isoelectric point than that of p97 R95G , p97 A232E and p97 WT . • Mutation R155P changes principally the conformation of the D2 ring. • Mutation R155P modifies the interface between two protomers within the D2 ring.

Electro-optical detection of charged particles

International Nuclear Information System (INIS)

Semertzidis, Y.K.; Castillo, V.; Kowalski, L.; Kraus, D.E.; Larsen, R.; Lazarus, D.M.; Magurno, B.; Nikas, D.; Ozben, C.; Srinivasan-Rao, T.; Tsang, T.

2000-01-01

We have made the first observation of a charged particle beam by means of its electro-optical effect on the polarization of laser light in a LiNbO 3 crystal. The modulation of the laser light during the passage of a pulsed electron beam was observed using a fast photodiode and a digital oscilloscope. The fastest rise time measured, 120 ps, was obtained in the single shot mode and was limited by the bandwidth of the oscilloscope and the associated electronics. This technology holds good for detectors of greatly improved spatial and temporal resolution for single relativistic charged particles as well as particle beams

Electro-optical detection of charged particles

CERN Document Server

Semertzidis, Y K; Kowalski, L A; Kraus, D E; Larsen, R; Lazarus, D M; Magurno, B; Nikas, D; Ozben, C; Srinivasan-Rao, T; Tsang, Thomas

2000-01-01

We have made the first observation of a charged particle beam by means of its electro-optical effect on the polarization of laser light in a LiNbO sub 3 crystal. The modulation of the laser light during the passage of a pulsed electron beam was observed using a fast photodiode and a digital oscilloscope. The fastest rise time measured, 120 ps, was obtained in the single shot mode and was limited by the bandwidth of the oscilloscope and the associated electronics. This technology holds good for detectors of greatly improved spatial and temporal resolution for single relativistic charged particles as well as particle beams.

Electro-optical detection of charged particles

Energy Technology Data Exchange (ETDEWEB)

Semertzidis, Y.K.; Castillo, V.; Kowalski, L.; Kraus, D.E.; Larsen, R.; Lazarus, D.M. E-mail: lazarus@sun2.bnl.gov; Magurno, B.; Nikas, D.; Ozben, C.; Srinivasan-Rao, T.; Tsang, T

2000-10-01

We have made the first observation of a charged particle beam by means of its electro-optical effect on the polarization of laser light in a LiNbO{sub 3} crystal. The modulation of the laser light during the passage of a pulsed electron beam was observed using a fast photodiode and a digital oscilloscope. The fastest rise time measured, 120 ps, was obtained in the single shot mode and was limited by the bandwidth of the oscilloscope and the associated electronics. This technology holds good for detectors of greatly improved spatial and temporal resolution for single relativistic charged particles as well as particle beams.

Frontend electronics for high-precision single photo-electron timing using FPGA-TDCs

Energy Technology Data Exchange (ETDEWEB)

Cardinali, Matteo [Helmholtz Institut Mainz (Germany); Collaboration: PANDA Cherenkov-Collaboration

2014-07-01

The next generation of high-luminosity experiments requires excellent Particle Identification (PID) detectors which calls for Imaging Cherenkov counters with fast electronics to cope with the expected data rates. The planned PANDA experiment at FAIR expects average interaction rates of 20 MHz. A Barrel DIRC will provide PID in the central region of the Target Spectrometer. A single photo-electron timing resolution of better than 100 ps is projected for the Barrel DIRC to disentangle the complicated patterns created by the focusing optics on the image plane. The typically large amount of readout channels (approx 15,000 in case of the PANDA Barrel DIRC) places non-negligible limits on size and power consumption of the Front-End Electronics (FEE). The proposed design is based on the TRBv3 readout using FPGA-TDCs with a precision better than 20 ps RMS and custom FEE with high-bandwidth pre-amplifiers and fast discriminators. Two types of FEE cards optimised for reading out 64-channel Photonis Planacon MCP-PMTs were tested: one based on the NINO ASIC developed for the ALICE RPC readout and the other, called PaDiWa, using FPGA-based discriminators. Both types of FEE cards were tested with a small DIRC prototype comprising a radiator bar with focusing lens and an oil-filled expansion volume instrumented with 6 Planacon 64-channel MCP-PMTs. In the presentation the result of a test experiment performed at MAMI B, Mainz, are addressed.

Cryo-EM structures of the mammalian endo-lysosomal TRPML1 channel elucidate the combined regulation mechanism

Directory of Open Access Journals (Sweden)

Sensen Zhang

2017-09-01

Full Text Available Abstract TRPML1 channel is a non-selective group-2 transient receptor potential (TRP channel with Ca2+ permeability. Located mainly in late endosome and lysosome of all mammalian cell types, TRPML1 is indispensable in the processes of endocytosis, membrane trafficking, and lysosome biogenesis. Mutations of TRPML1 cause a severe lysosomal storage disorder called mucolipidosis type IV (MLIV. In the present study, we determined the cryo-electron microscopy (cryo-EM structures of Mus musculus TRPML1 (mTRPML1 in lipid nanodiscs and Amphipols. Two distinct states of mTRPML1 in Amphipols are added to the closed state, on which could represent two different confirmations upon activation and regulation. The polycystin-mucolipin domain (PMD may sense the luminal/extracellular stimuli and undergo a “move upward” motion during endocytosis, thus triggering the overall conformational change in TRPML1. Based on the structural comparisons, we propose TRPML1 is regulated by pH, Ca2+, and phosphoinositides in a combined manner so as to accommodate the dynamic endocytosis process.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

Energy Technology Data Exchange (ETDEWEB)

Genderen, E. van; Clabbers, M. T. B. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel (Switzerland); Das, P. P. [Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium); Stewart, A. [Department of Physics and Energy, Materials and Surface Science Institute (MSSI), University of Limerick, Limerick (Ireland); Nederlof, I. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Amsterdam Scientific Instruments, Postbus 41882, 1009 DB Amsterdam (Netherlands); Barentsen, K. C. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Portillo, Q. [Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium); Centres Científics i Tecnològics de la Universitat de Barcelona, University of Barcelona, Carrer de Lluís Solé i Sabaris, 1-3, Barcelona (Spain); Pannu, N. S. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Nicolopoulos, S. [Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium); Gruene, T., E-mail: tim.gruene@psi.ch [Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen (Switzerland); Abrahams, J. P., E-mail: tim.gruene@psi.ch [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel (Switzerland); Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen (Switzerland)

2016-02-05

A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)

Development of Xi'an-CI package – applying the hole–particle symmetry in multi-reference electronic correlation calculations

Science.gov (United States)

Suo, Bingbing; Lei, Yibo; Han, Huixian; Wang, Yubin

2018-04-01

This mini-review introduces our works on the Xi'an-CI (configuration interaction) package using graphical unitary group approach (GUGA). Taking advantage of the hole-particle symmetry in GUGA, the Galfand states used to span the CI space are classified into CI subspaces according to the number of holes and particles, and the coupling coefficients used to calculate Hamiltonian matrix elements could be factorised into the segment factors in the hole, active and external spaces. An efficient multi-reference CI with single and double excitations (MRCISD) algorithm is thus developed that reduces the storage requirement and increases the number of correlated electrons significantly. The hole-particle symmetry also gives rise to a doubly contracted MRCISD approach. Moreover, the internally contracted Gelfand states are defined within the CI subspace arising from the hole-particle symmetry, which makes the implementation of internally contracted MRCISD in the framework of GUGA possible. In addition to MRCISD, the development of multi-reference second-order perturbation theory (MRPT2) also benefits from the hole-particle symmetry. A configuration-based MRPT2 algorithm is proposed and extended to the multi-state n-electron valence-state second-order perturbation theory.

Single-particle behaviour in circulating fluidized beds

DEFF Research Database (Denmark)

Erik Weinell, Claus; Dam-Johansen, Kim; Johnsson, Jan Erik

1997-01-01

This paper describes an experimental investigation of single-particle behaviour in a cold pilot-scale model of a circulating fluidized bed combustor (CFBC). In the system, sand is recirculated by means of air. Pressure measurements along the riser are used to determine the suspension density...

CryoSat Level1b SAR/SARin BaselineC: Product Format and Algorithm Improvements

Science.gov (United States)

Scagliola, Michele; Fornari, Marco; Di Giacinto, Andrea; Bouffard, Jerome; Féménias, Pierre; Parrinello, Tommaso

2015-04-01

CryoSat was launched on the 8th April 2010 and is the first European ice mission dedicated to the monitoring of precise changes in the thickness of polar ice sheets and floating sea ice. Cryosat carries an innovative radar altimeter called the Synthetic Aperture Interferometric Altimeter (SIRAL), that transmits pulses at a high pulse repetition frequency thus making the received echoes phase coherent and suitable for azimuth processing. This allows to reach a significantly improved along track resolution with respect to traditional pulse-width limited altimeters. CryoSat is the first altimetry mission operating in SAR mode and continuous improvements in the Level1 Instrument Processing Facility (IPF1) are being identified, tested and validated in order to improve the quality of the Level1b products. The current IPF, Baseline B, was released in operation in February 2012. A reprocessing campaign followed, in order to reprocess the data since July 2010. After more than 2 years of development, the release in operations of Baseline C is expected in the first half of 2015. BaselineC Level1b products will be distributed in an updated format, including for example the attitude information (roll, pitch and yaw) and, for SAR/SARIN, the waveform length doubled with respect to Baseline B. Moreveor, various algorithm improvements have been identified: • a datation bias of about -0.5195 ms will be corrected (SAR/SARIn) • a range bias of about 0.6730 m will be corrected (SAR/SARIn) • a roll bias of 0.1062 deg and a pitch bias of 0.0520 deg • Surface sample stack weighting to filter out the single look echoes acquired at highest look angle, that results in a sharpening of the 20Hz waveforms With the operational release of BaselineC, the second CryoSat reprocessing campaign will be initiated, taking benefit of the upgrade implemented in the IPF1 processing chain but also at IPF2 level. The reprocessing campaign will cover the full Cryosat mission starting on 16th July 2010

Gyrokinetic Electron and Fully Kinetic Ion Particle Simulation of Collisionless Plasma Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu Lin; Xueyi Wang; Liu Chen; Zhihong Lin

2009-08-11

Fully kinetic-particle simulations and hybrid simulations have been utilized for decades to investigate various fundamental plasma processes, such as magnetic reconnection, fast compressional waves, and wave-particle interaction. Nevertheless, due to disparate temporal and spatial scales between electrons and ions, existing fully kinetic-particle codes have to employ either unrealistically high electron-to-ion mass ratio, me/mi, or simulation domain limited to a few or a few ten's of the ion Larmor radii, or/and time much less than the global Alfven time scale in order to accommodate available computing resources. On the other hand, in the hybrid simulation, the ions are treated as fully kinetic particles but the electrons are treated as a massless fluid. The electron kinetic effects, e.g., wave-particle resonances and finite electron Larmor radius effects, are completely missing. Important physics, such as the electron transit time damping of fast compressional waves or the triggering mechanism of magnetic reconnection in collisionless plasmas is absent in the hybrid codes. Motivated by these considerations and noting that dynamics of interest to us has frequencies lower than the electron gyrofrequency, we planned to develop an innovative particle simulation model, gyrokinetic (GK) electrons and fully kinetic (FK) ions. In the GK-electron and FK-ion (GKe/FKi) particle simulation model, the rapid electron cyclotron motion is removed, while keeping finite electron Larmor radii, realistic me/mi ratio, wave-particle interactions, and off-diagonal components of electron pressure tensor. The computation power can thus be significantly improved over that of the full-particle codes. As planned in the project DE-FG02-05ER54826, we have finished the development of the new GK-electron and FK-ion scheme, finished its benchmark for a uniform plasma in 1-D, 2-D, and 3-D systems against linear waves obtained from analytical theories, and carried out a further convergence

Gyrokinetic Electron and Fully Kinetic Ion Particle Simulation of Collisionless Plasma Dynamics

International Nuclear Information System (INIS)

Lin, Yu; Wang, Xueyi; Chen, Liu; Lin, Zhihong

2009-01-01

Fully kinetic-particle simulations and hybrid simulations have been utilized for decades to investigate various fundamental plasma processes, such as magnetic reconnection, fast compressional waves, and wave-particle interaction. Nevertheless, due to disparate temporal and spatial scales between electrons and ions, existing fully kinetic-particle codes have to employ either unrealistically high electron-to-ion mass ratio, me/mi, or simulation domain limited to a few or a few ten's of the ion Larmor radii, or/and time much less than the global Alfven time scale in order to accommodate available computing resources. On the other hand, in the hybrid simulation, the ions are treated as fully kinetic particles but the electrons are treated as a massless fluid. The electron kinetic effects, e.g., wave-particle resonances and finite electron Larmor radius effects, are completely missing. Important physics, such as the electron transit time damping of fast compressional waves or the triggering mechanism of magnetic reconnection in collisionless plasmas is absent in the hybrid codes. Motivated by these considerations and noting that dynamics of interest to us has frequencies lower than the electron gyrofrequency, we planned to develop an innovative particle simulation model, gyrokinetic (GK) electrons and fully kinetic (FK) ions. In the GK-electron and FK-ion (GKe/FKi) particle simulation model, the rapid electron cyclotron motion is removed, while keeping finite electron Larmor radii, realistic me/mi ratio, wave-particle interactions, and off-diagonal components of electron pressure tensor. The computation power can thus be significantly improved over that of the full-particle codes. As planned in the project DE-FG02-05ER54826, we have finished the development of the new GK-electron and FK-ion scheme, finished its benchmark for a uniform plasma in 1-D, 2-D, and 3-D systems against linear waves obtained from analytical theories, and carried out a further convergence test

Coherent control of single electrons: a review of current progress

Science.gov (United States)

Bäuerle, Christopher; Glattli, D. Christian; Meunier, Tristan; Portier, Fabien; Roche, Patrice; Roulleau, Preden; Takada, Shintaro; Waintal, Xavier

2018-05-01

In this report we review the present state of the art of the control of propagating quantum states at the single-electron level and its potential application to quantum information processing. We give an overview of the different approaches that have been developed over the last few years in order to gain full control over a propagating single-electron in a solid-state system. After a brief introduction of the basic concepts, we present experiments on flying qubit circuits for ensemble of electrons measured in the low frequency (DC) limit. We then present the basic ingredients necessary to realise such experiments at the single-electron level. This includes a review of the various single-electron sources that have been developed over the last years and which are compatible with integrated single-electron circuits. This is followed by a review of recent key experiments on electron quantum optics with single electrons. Finally we will present recent developments in the new physics that has emerged using ultrashort voltage pulses. We conclude our review with an outlook and future challenges in the field.

Direct single electron detection with a CMOS detector for electron microscopy

International Nuclear Information System (INIS)

Faruqi, A.R.; Henderson, R.; Pryddetch, M.; Allport, P.; Evans, A.

2005-01-01

We report the results of an investigation into the use of a monolithic active pixel sensor (MAPS) for electron microscopy. MAPS, designed originally for astronomers at the Rutherford Appleton Laboratories, was installed in a 120 kV electron microscope (Philips CM12) at the MRC Laboratory in Cambridge for tests which included recording single electrons at 40 and 120 keV, and measuring signal-to-noise ratio (SNR), spatial resolution and radiation sensitivity. Our results show that, due to the excellent SNR and resolution, it is possible to register single electrons. The radiation damage to the detector is apparent with low doses and gets progressively greater so that its lifetime is limited to 600,000-900,000 electrons/pixel (very approximately 10-15 krad). Provided this detector can be radiation hardened to reduce its radiation sensitivity several hundred fold and increased in size, it will provide excellent performance for all types of electron microscopy

CryoSat-2 radar altimetry for monitoring freshwater resources of China

DEFF Research Database (Denmark)

Jiang, Liguang; Nielsen, Karina; Andersen, Ole Baltazar

2017-01-01

, the Northeast China Plain, and the central Yangtze River basin. Estimated changes in volume indicate that surface water variation contributes significantly to terrestrial storage variation, especially in the Qaidam Basin and the Tibetan Plateau. CryoSat-2 is capable of measuring regional-scale river level....... Comparatively, accuracy is much lower over the Yangtze and Pearl Rivers (RMSE ~ 2.6 m and ~ 3.3 m), probably due to intensive inland waterway navigation. CryoSat-2 shows great potential for monitoring surface water at national scale in China....

CryoSat-2: A new perspective on the Cryosphere

Science.gov (United States)

Shepherd, A.; Armitage, T.; Briggs, K.; Flament, T.; Hogg, A. E.; McMillan, M.; Muir, A.; Ridout, A.; Sundal, A.; Tilling, R.; Wingham, D.

2014-12-01

CryoSat-2 is ESA's first satellite mission dedicated to measuring changes in the polar land ice and sea ice cover. Following its launch in April 2010, we have examined the performance of the instrument over the continental ice sheets of Antarctica and Greenland, the Artic Ocean, and, for the purposes of calibration, over the oceans. We have confirmed the engineering performance at system level of the interferometer demonstrating that it measures across-track surface slopes with a precision of 25 micro-radians and an accuracy of 10 micro-radians, greatly exceeding the pre-launch specifications (100 micro-radians). Over the polar ice sheets, we have examined the performance of the range estimation, and determined the range precision to be 19 cm RMS at 20 Hz. We have examined the retrieval of the phase information over the ice sheets, and found the phase estimates to be robust and little affected by the uncertain ice sheet topography. Based on the calibration of the interferometer, the contribution of the across track slope error is, at 0.4 mm, negligible. Over marine sea ice, we have verified the discrimination of sea ice and ocean lead returns using contemporaneous SAR imagery from ENVISAT, and we have estimated the precision of individual (20 Hz) measurements to be 2 cm. In summary, with the corrected data products, we are able to confirm that the system performance of CryoSat-2 will meet or exceed its specification over the continental and marine ice sheets. This presenetation sumamrises the key outcomes of the mission performance, and presents a series of example case studies where CryoSat-2 data have been applied to study changes in Earth's land and sea ice cover. We show that in 4 years CryoSat has been able to detect changes in the mass of the Antarctic and Greenland ice sheets with an accuracy comparable to that of the past 20 years of conventional satellite altimetry and that important changes have occured in these regions, we show that CryoSat has been able

Single particle train ordering in microchannel based on inertial and vortex effects

Science.gov (United States)

Fan, Liang-Liang; Yan, Qing; Zhe, Jiang; Zhao, Liang

2018-06-01

A new microfluidic device for microparticle focusing and ordering in a single particle train is reported. The particle focusing and ordering are based on inertial and vortex effects in a microchannel with a series of suddenly contracted and widely expanded structures on one side. In the suddenly contracted regions, particles located near the contracted structures are subjected to a strong wall-effect lift force and momentum-change-induced inertial force due to the highly curved trajectory, migrating to the straight wall. A horizontal vortex is generated downstream of the contracted structure, which prevents the particle from getting close to the wall. In the widely expanded regions, the streamline is curved and no vortex is generated. The shear-gradient lift force and the momentum-change-induced inertial force are dominant for particle lateral migration, driving particles towards the wall of the expanded structures. Eventually, particles are focused and ordered in a single particle train by the combination effects of the inertial forces and the vortex. In comparison with other single-stream particle focusing methods, this device requires no sheath flow, is easy for fabrication and operation, and can work over a wide range of Reynolds numbers from 19.1–142.9. The highly ordered particle chain could be potentially utilized in a variety of lab-chip applications, including micro-flow cytometer, imaging and droplet-based cell entrapment.

Highly efficient electron gun with a single-atom electron source

International Nuclear Information System (INIS)

Ishikawa, Tsuyoshi; Urata, Tomohiro; Cho, Boklae; Rokuta, Eiji; Oshima, Chuhei; Terui, Yoshinori; Saito, Hidekazu; Yonezawa, Akira; Tsong, Tien T.

2007-01-01

The authors have demonstrated highly collimated electron-beam emission from a practical electron gun with a single-atom electron source; ∼80% of the total emission current entered the electron optics. This ratio was two or three orders of magnitude higher than those of the conventional electron sources such as a cold field emission gun and a Zr/O/W Schottky gun. At the pressure of less than 1x10 -9 Pa, the authors observed stable emission of 20 nA, which generates the specimen current of 5 pA required for scanning electron microscopes

Characteristics of trapped electrons and electron traps in single crystals

International Nuclear Information System (INIS)

Budzinski, E.E.; Potter, W.R.; Potienko, G.; Box, H.C.

1979-01-01

Two additional carbohydrates are reported whose crystal structures trap electrons intermolecularly in single crystals x irradiated at low temperature, namely sucrose and rhamnose. Five carbohydrate and polyhydroxy compounds are now known which exhibit this phenomenon. The following characteristics of the phenomenon were investigated: (1) the hyperfine couplings of the electron with protons of the polarized hydroxy groups forming the trap; (2) the distances between these protons and the trapped electron; (3) the spin density of the electron at the protons and (4) the relative stabilities of the electron trapped in various crystal structures

Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit

NARCIS (Netherlands)

C.p.van Zundert, Gydo; M.j.j. Bonvin, Alexandre

2015-01-01

Cryo-EM is a rapidly developing method to investigate the three dimensional structure of large macromolecular complexes. In spite of all the advances in the field, the resolution of most cryo-EM density maps is too low for de novo model building. Therefore, the data are often complemented by fitting

OMNY—A tOMography Nano crYo stage

Science.gov (United States)

Holler, M.; Raabe, J.; Diaz, A.; Guizar-Sicairos, M.; Wepf, R.; Odstrcil, M.; Shaik, F. R.; Panneels, V.; Menzel, A.; Sarafimov, B.; Maag, S.; Wang, X.; Thominet, V.; Walther, H.; Lachat, T.; Vitins, M.; Bunk, O.

2018-04-01

For many scientific questions gaining three-dimensional insight into a specimen can provide valuable information. We here present an instrument called "tOMography Nano crYo (OMNY)," dedicated to high resolution 3D scanning x-ray microscopy at cryogenic conditions via hard X-ray ptychography. Ptychography is a lens-less imaging method requiring accurate sample positioning. In OMNY, this in achieved via dedicated laser interferometry and closed-loop position control reaching sub-10 nm positioning accuracy. Cryogenic sample conditions are maintained via conductive cooling. 90 K can be reached when using liquid nitrogen as coolant, and 10 K is possible with liquid helium. A cryogenic sample-change mechanism permits measurements of cryogenically fixed specimens. We compare images obtained with OMNY with older measurements performed using a nitrogen gas cryo-jet of stained, epoxy-embedded retina tissue and of frozen-hydrated Chlamydomonas cells.

Electron-vibron coupling effects on electron transport via a single-molecule magnet

Science.gov (United States)

McCaskey, Alexander; Yamamoto, Yoh; Warnock, Michael; Burzurí, Enrique; van der Zant, Herre S. J.; Park, Kyungwha

2015-03-01

We investigate how the electron-vibron coupling influences electron transport via an anisotropic magnetic molecule, such as a single-molecule magnet (SMM) Fe4, by using a model Hamiltonian with parameter values obtained from density-functional theory (DFT). The magnetic anisotropy parameters, vibrational energies, and electron-vibron coupling strengths of the Fe4 are computed using DFT. A giant spin model is applied to the Fe4 with only two charge states, specifically a neutral state with a total spin S =5 and a singly charged state with S =9 /2 , which is consistent with our DFT result and experiments on Fe4 single-molecule transistors. In sequential electron tunneling, we find that the magnetic anisotropy gives rise to new features in the conductance peaks arising from vibrational excitations. In particular, the peak height shows a strong, unusual dependence on the direction as well as magnitude of applied B field. The magnetic anisotropy also introduces vibrational satellite peaks whose position and height are modified with the direction and magnitude of applied B field. Furthermore, when multiple vibrational modes with considerable electron-vibron coupling have energies close to one another, a low-bias current is suppressed, independently of gate voltage and applied B field, although that is not the case for a single mode with a similar electron-vibron coupling. In the former case, the conductance peaks reveal a stronger B -field dependence than in the latter case. The new features appear because the magnetic anisotropy barrier is of the same order of magnitude as the energies of vibrational modes with significant electron-vibron coupling. Our findings clearly show the interesting interplay between magnetic anisotropy and electron-vibron coupling in electron transport via the Fe4. Similar behavior can be observed in transport via other anisotropic magnetic molecules.