Modeling and numerical simulations of growth and morphologies of three dimensional aggregated silver films

NASA Astrophysics Data System (ADS)

Davis, L. J.; Boggess, M.; Kodpuak, E.; Deutsch, M.

2012-11-01

We report on a model for the deposition of three dimensional, aggregated nanocrystalline silver films, and an efficient numerical simulation method developed for visualizing such structures. We compare our results to a model system comprising chemically deposited silver films with morphologies ranging from dilute, uniform distributions of nanoparticles to highly porous aggregated networks. Disordered silver films grown in solution on silica substrates are characterized using digital image analysis of high resolution scanning electron micrographs. While the latter technique provides little volume information, plane-projected (two dimensional) island structure and surface coverage may be reliably determined. Three parameters governing film growth are evaluated using these data and used as inputs for the deposition model, greatly reducing computing requirements while still providing direct access to the complete (bulk) structure of the films throughout the growth process. We also show how valuable three dimensional characteristics of the deposited materials can be extracted using the simulated structures.

Two-photon polymerization of a three dimensional structure using beams with orbital angular momentum

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

Zhang, Shi-Jie; Li, Yan, E-mail: li@pku.edu.cn; Liu, Zhao-Pei

The focus of a beam with orbital angular momentum exhibits internal structure instead of an elliptical intensity distribution of a Gaussian beam, and the superposition of Gauss-Laguerre beams realized by two-dimensional phase modulation can generate a complex three-dimensional (3D) focus. By taking advantage of the flexibility of this 3D focus tailoring, we have fabricated a 3D microstructure with high resolution by two-photon polymerization with a single exposure. Furthermore, we have polymerized an array of double-helix structures that demonstrates optical chirality.

Are X-rays the key to integrated computational materials engineering?

DOE PAGES

Ice, Gene E.

2015-11-01

The ultimate dream of materials science is to predict materials behavior from composition and processing history. Owing to the growing power of computers, this long-time dream has recently found expression through worldwide excitement in a number of computation-based thrusts: integrated computational materials engineering, materials by design, computational materials design, three-dimensional materials physics and mesoscale physics. However, real materials have important crystallographic structures at multiple length scales, which evolve during processing and in service. Moreover, real materials properties can depend on the extreme tails in their structural and chemical distributions. This makes it critical to map structural distributions with sufficient resolutionmore » to resolve small structures and with sufficient statistics to capture the tails of distributions. For two-dimensional materials, there are high-resolution nondestructive probes of surface and near-surface structures with atomic or near-atomic resolution that can provide detailed structural, chemical and functional distributions over important length scales. Furthermore, there are no nondestructive three-dimensional probes with atomic resolution over the multiple length scales needed to understand most materials.« less

Compton imaging tomography technique for NDE of large nonuniform structures

NASA Astrophysics Data System (ADS)

Grubsky, Victor; Romanov, Volodymyr; Patton, Ned; Jannson, Tomasz

2011-09-01

In this paper we describe a new nondestructive evaluation (NDE) technique called Compton Imaging Tomography (CIT) for reconstructing the complete three-dimensional internal structure of an object, based on the registration of multiple two-dimensional Compton-scattered x-ray images of the object. CIT provides high resolution and sensitivity with virtually any material, including lightweight structures and organics, which normally pose problems in conventional x-ray computed tomography because of low contrast. The CIT technique requires only one-sided access to the object, has no limitation on the object's size, and can be applied to high-resolution real-time in situ NDE of large aircraft/spacecraft structures and components. Theoretical and experimental results will be presented.

A High-Resolution, Three-Dimensional Model of Jupiter's Great Red Spot

NASA Technical Reports Server (NTRS)

Cho, James Y.-K.; delaTorreJuarez, Manuel; Ingersoll, Andrew P.; Dritschel, David G.

2001-01-01

The turbulent flow at the periphery of the Great Red Spot (GRS) contains many fine-scale filamentary structures, while the more quiescent core, bounded by a narrow high- velocity ring, exhibits organized, possibly counterrotating, motion. Past studies have neither been able to capture this complexity nor adequately study the effect of vertical stratification L(sub R)(zeta) on the GRS. We present results from a series of high-resolution, three-dimensional simulations that advect the dynamical tracer, potential vorticity. The detailed flow is successfully captured with a characteristic value of L(sub R) approx. equals 2000 km, independent of the precise vertical stratification profile.

A synchrotron radiation microtomography system for the analysis of trabecular bone samples.

PubMed

Salomé, M; Peyrin, F; Cloetens, P; Odet, C; Laval-Jeantet, A M; Baruchel, J; Spanne, P

1999-10-01

X-ray computed microtomography is particularly well suited for studying trabecular bone architecture, which requires three-dimensional (3-D) images with high spatial resolution. For this purpose, we describe a three-dimensional computed microtomography (microCT) system using synchrotron radiation, developed at ESRF. Since synchrotron radiation provides a monochromatic and high photon flux x-ray beam, it allows high resolution and a high signal-to-noise ratio imaging. The principle of the system is based on truly three-dimensional parallel tomographic acquisition. It uses a two-dimensional (2-D) CCD-based detector to record 2-D radiographs of the transmitted beam through the sample under different angles of view. The 3-D tomographic reconstruction, performed by an exact 3-D filtered backprojection algorithm, yields 3-D images with cubic voxels. The spatial resolution of the detector was experimentally measured. For the application to bone investigation, the voxel size was set to 6.65 microm, and the experimental spatial resolution was found to be 11 microm. The reconstructed linear attenuation coefficient was calibrated from hydroxyapatite phantoms. Image processing tools are being developed to extract structural parameters quantifying trabecular bone architecture from the 3-D microCT images. First results on human trabecular bone samples are presented.

High Resolution Crystal Structure of the Catalytic Domain of ADAMTS-5 (Aggrecanase-2)

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

Shieh, Huey-Sheng; Mathis, Karl J.; Williams, Jennifer M.

Aggrecanase-2 (a disintegrin and metalloproteinase with thrombospondin motifs-5 (ADAMTS-5)), a member of the ADAMTS protein family, is critically involved in arthritic diseases because of its direct role in cleaving the cartilage component aggrecan. The catalytic domain of aggrecanase-2 has been refolded, purified, and crystallized, and its three-dimensional structure determined to 1.4{angstrom} resolution in the presence of an inhibitor. A high resolution structure of an ADAMTS/aggrecanase protein provides an opportunity for the development of therapeutics to treat osteoarthritis.

Three dimensional canonical singularity and five dimensional N = 1 SCFT

NASA Astrophysics Data System (ADS)

Xie, Dan; Yau, Shing-Tung

2017-06-01

We conjecture that every three dimensional canonical singularity defines a five dimensional N = 1 SCFT. Flavor symmetry can be found from singularity structure: non-abelian flavor symmetry is read from the singularity type over one dimensional singular locus. The dimension of Coulomb branch is given by the number of compact crepant divisors from a crepant resolution of singularity. The detailed structure of Coulomb branch is described as follows: a) a chamber of Coulomb branch is described by a crepant resolution, and this chamber is given by its Nef cone and the prepotential is computed from triple intersection numbers; b) Crepant resolution is not unique and different resolutions are related by flops; Nef cones from crepant resolutions form a fan which is claimed to be the full Coulomb branch.

Three-dimensional micro/nano-scale structure fabricated by combination of non-volatile polymerizable RTIL and FIB irradiation

PubMed Central

Kuwabata, Susumu; Minamimoto, Hiro; Inoue, Kosuke; Imanishi, Akihito; Hosoya, Ken; Uyama, Hiroshi; Torimoto, Tsukasa; Tsuda, Tetsuya; Seki, Shu

2014-01-01

Room-temperature ionic liquid (RTIL) has been widely investigated as a nonvolatile solvent as well as a unique liquid material because of its interesting features, e.g., negligible vapor pressure and high thermal stability. Here we report that a non-volatile polymerizable RTIL is a useful starting material for the fabrication of micro/nano-scale polymer structures with a focused-ion-beam (FIB) system operated under high-vacuum condition. Gallium-ion beam irradiation to the polymerizable 1-allyl-3-ethylimidazolium bis((trifluoromethane)sulfonyl)amide RTIL layer spread on a Si wafer induced a polymerization reaction without difficulty. What is interesting to note is that we have succeeded in provoking the polymerization reaction anywhere on the Si wafer substrate by using FIB irradiation with a raster scanning mode. By this finding, two- and three-dimensional micro/nano-scale polymer structure fabrications were possible at the resolution of 500,000 dpi. Even intricate three-dimensional micro/nano-figures with overhang and hollow moieties could be constructed at the resolution of approximately 100 nm. PMID:24430465

CLICK: The new USGS center for LIDAR information coordination and knowledge

USGS Publications Warehouse

Stoker, Jason M.; Greenlee, Susan K.; Gesch, Dean B.; Menig, Jordan C.

2006-01-01

Elevation data is rapidly becoming an important tool for the visualization and analysis of geographic information. The creation and display of three-dimensional models representing bare earth, vegetation, and structures have become major requirements for geographic research in the past few years. Light Detection and Ranging (lidar) has been increasingly accepted as an effective and accurate technology for acquiring high-resolution elevation data for bare earth, vegetation, and structures. Lidar is an active remote sensing system that records the distance, or range, of a laser fi red from an airborne or space borne platform such as an airplane, helicopter or satellite to objects or features on the Earth’s surface. By converting lidar data into bare ground topography and vegetation or structural morphologic information, extremely accurate, high-resolution elevation models can be derived to visualize and quantitatively represent scenes in three dimensions. In addition to high-resolution digital elevation models (Evans et al., 2001), other lidar-derived products include quantitative estimates of vegetative features such as canopy height, canopy closure, and biomass (Lefsky et al., 2002), and models of urban areas such as building footprints and three-dimensional city models (Maas, 2001).

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Linking rainforest ecophysiology and microclimate through fusion of airborne LiDAR and hyperspectral imagery

Treesearch

Eben N. Broadbent; Angélica M. Almeyda Zambrano; Gregory P. Asner; Christopher B. Field; Brad E. Rosenheim; Ty Kennedy-Bowdoin; David E. Knapp; David Burke; Christian Giardina; Susan Cordell

2014-01-01

We develop and validate a high-resolution three-dimensional model of light and air temperature for a tropical forest interior in Hawaii along an elevation gradient varying greatly in structure but maintaining a consistent species composition. Our microclimate models integrate high-resolution airborne waveform light detection and ranging data (LiDAR) and hyperspectral...

Confocal Imaging of porous media

NASA Astrophysics Data System (ADS)

Shah, S.; Crawshaw, D.; Boek, D.

2012-12-01

Carbonate rocks, which hold approximately 50% of the world's oil and gas reserves, have a very complicated and heterogeneous structure in comparison with sandstone reservoir rock. We present advances with different techniques to image, reconstruct, and characterize statistically the micro-geometry of carbonate pores. The main goal here is to develop a technique to obtain two dimensional and three dimensional images using Confocal Laser Scanning Microscopy. CLSM is used in epi-fluorescent imaging mode, allowing for the very high optical resolution of features well below 1μm size. Images of pore structures were captured using CLSM imaging where spaces in the carbonate samples were impregnated with a fluorescent, dyed epoxy-resin, and scanned in the x-y plane by a laser probe. We discuss the sample preparation in detail for Confocal Imaging to obtain sub-micron resolution images of heterogeneous carbonate rocks. We also discuss the technical and practical aspects of this imaging technique, including its advantages and limitation. We present several examples of this application, including studying pore geometry in carbonates, characterizing sub-resolution porosity in two dimensional images. We then describe approaches to extract statistical information about porosity using image processing and spatial correlation function. We have managed to obtain very low depth information in z -axis (~ 50μm) to develop three dimensional images of carbonate rocks with the current capabilities and limitation of CLSM technique. Hence, we have planned a novel technique to obtain higher depth information to obtain high three dimensional images with sub-micron resolution possible in the lateral and axial planes.

Three-dimensional inversion recovery manganese-enhanced MRI of mouse brain using super-resolution reconstruction to visualize nuclei involved in higher brain function.

PubMed

Poole, Dana S; Plenge, Esben; Poot, Dirk H J; Lakke, Egbert A J F; Niessen, Wiro J; Meijering, Erik; van der Weerd, Louise

2014-07-01

The visualization of activity in mouse brain using inversion recovery spin echo (IR-SE) manganese-enhanced MRI (MEMRI) provides unique contrast, but suffers from poor resolution in the slice-encoding direction. Super-resolution reconstruction (SRR) is a resolution-enhancing post-processing technique in which multiple low-resolution slice stacks are combined into a single volume of high isotropic resolution using computational methods. In this study, we investigated, first, whether SRR can improve the three-dimensional resolution of IR-SE MEMRI in the slice selection direction, whilst maintaining or improving the contrast-to-noise ratio of the two-dimensional slice stacks. Second, the contrast-to-noise ratio of SRR IR-SE MEMRI was compared with a conventional three-dimensional gradient echo (GE) acquisition. Quantitative experiments were performed on a phantom containing compartments of various manganese concentrations. The results showed that, with comparable scan times, the signal-to-noise ratio of three-dimensional GE acquisition is higher than that of SRR IR-SE MEMRI. However, the contrast-to-noise ratio between different compartments can be superior with SRR IR-SE MEMRI, depending on the chosen inversion time. In vivo experiments were performed in mice receiving manganese using an implanted osmotic pump. The results showed that SRR works well as a resolution-enhancing technique in IR-SE MEMRI experiments. In addition, the SRR image also shows a number of brain structures that are more clearly discernible from the surrounding tissues than in three-dimensional GE acquisition, including a number of nuclei with specific higher brain functions, such as memory, stress, anxiety and reward behavior. Copyright © 2014 John Wiley & Sons, Ltd.

Investigating Hydrocarbon Seep Environments with High-Resolution, Three-Dimensional Geographic Visualizations.

NASA Astrophysics Data System (ADS)

Doolittle, D. F.; Gharib, J. J.; Mitchell, G. A.

2015-12-01

Detailed photographic imagery and bathymetric maps of the seafloor acquired by deep submergence vehicles such as Autonomous Underwater Vehicles (AUV) and Remotely Operated Vehicles (ROV) are expanding how scientists and the public view and ultimately understand the seafloor and the processes that modify it. Several recently acquired optical and acoustic datasets, collected during ECOGIG (Ecosystem Impacts of Oil and Gas Inputs to the Gulf) and other Gulf of Mexico expeditions using the National Institute for Undersea Science Technology (NIUST) Eagle Ray, and Mola Mola AUVs, have been fused with lower resolution data to create unique three-dimensional geovisualizations. Included in these data are multi-scale and multi-resolution visualizations over hydrocarbon seeps and seep related features. Resolution of the data range from 10s of mm to 10s of m. When multi-resolution data is integrated into a single three-dimensional visual environment, new insights into seafloor and seep processes can be obtained from the intuitive nature of three-dimensional data exploration. We provide examples and demonstrate how integration of multibeam bathymetry, seafloor backscatter data, sub-bottom profiler data, textured photomosaics, and hull-mounted multibeam acoustic midwater imagery are made into a series a three-dimensional geovisualizations of actively seeping sites and associated chemosynthetic communities. From these combined and merged datasets, insights on seep community structure, morphology, ecology, fluid migration dynamics, and process geomorphology can be investigated from new spatial perspectives. Such datasets also promote valuable inter-comparisons of sensor resolution and performance.

Magnetic resonance imaging-three-dimensional printing technology fabricates customized scaffolds for brain tissue engineering

PubMed Central

Fu, Feng; Qin, Zhe; Xu, Chao; Chen, Xu-yi; Li, Rui-xin; Wang, Li-na; Peng, Ding-wei; Sun, Hong-tao; Tu, Yue; Chen, Chong; Zhang, Sai; Zhao, Ming-liang; Li, Xiao-hong

2017-01-01

Conventional fabrication methods lack the ability to control both macro- and micro-structures of generated scaffolds. Three-dimensional printing is a solid free-form fabrication method that provides novel ways to create customized scaffolds with high precision and accuracy. In this study, an electrically controlled cortical impactor was used to induce randomized brain tissue defects. The overall shape of scaffolds was designed using rat-specific anatomical data obtained from magnetic resonance imaging, and the internal structure was created by computer-aided design. As the result of limitations arising from insufficient resolution of the manufacturing process, we magnified the size of the cavity model prototype five-fold to successfully fabricate customized collagen-chitosan scaffolds using three-dimensional printing. Results demonstrated that scaffolds have three-dimensional porous structures, high porosity, highly specific surface areas, pore connectivity and good internal characteristics. Neural stem cells co-cultured with scaffolds showed good viability, indicating good biocompatibility and biodegradability. This technique may be a promising new strategy for regenerating complex damaged brain tissues, and helps pave the way toward personalized medicine. PMID:28553343

Development of synchrotron X-ray micro-tomography under extreme conditions of pressure and temperature.

PubMed

Álvarez-Murga, M; Perrillat, J P; Le Godec, Y; Bergame, F; Philippe, J; King, A; Guignot, N; Mezouar, M; Hodeau, J L

2017-01-01

X-ray tomography is a non-destructive three-dimensional imaging/microanalysis technique selective to a wide range of properties such as density, chemical composition, chemical states and crystallographic structure with extremely high sensitivity and spatial resolution. Here the development of in situ high-pressure high-temperature micro-tomography using a rotating module for the Paris-Edinburgh cell combined with synchrotron radiation is described. By rotating the sample chamber by 360°, the limited angular aperture of ordinary high-pressure cells is surmounted. Such a non-destructive high-resolution probe provides three-dimensional insight on the morphological and structural evolution of crystalline as well as amorphous phases during high pressure and temperature treatment. To demonstrate the potentials of this new experimental technique the compression behavior of a basalt glass is investigated by X-ray absorption tomography, and diffraction/scattering tomography imaging of the structural changes during the polymerization of C 60 molecules under pressure is performed. Small size and weight of the loading frame and rotating module means that this apparatus is portable, and can be readily installed on most synchrotron facilities to take advantage of the diversity of three-dimensional imaging techniques available at beamlines. This experimental breakthrough should open new ways for in situ imaging of materials under extreme pressure-temperature-stress conditions, impacting diverse areas in physics, chemistry, geology or materials sciences.

Three Dimensional High-Resolution Reconstruction of the Ionosphere Over the Very Large Array

DTIC Science & Technology

2010-12-15

Watts Progress Report, Dec 10; 1 Final Report: Three Dimensional High-Resolution Reconstruction of the Ionosphere over the Very Large Array...proposed research is reconstruct the three-dimensional regional electron density profile of Earth’s ionosphere with spatial resolution of better than 10 km...10x better sensitivity to total electron content (TEC, or chord integrated density) in the ionosphere that does GPS. The proposal funds the

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

PubMed

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Three-Dimensional Intercalated Porous Graphene on Si(111)

NASA Astrophysics Data System (ADS)

Pham, Trung T.; Sporken, Robert

2018-02-01

Three-dimensional intercalated porous graphene has been formed on Si(111) by electron beam evaporation under appropriate conditions and its structural and electronic properties investigated in detail by reflection high-energy electron diffraction, x-ray photoemission spectroscopy, Raman spectroscopy, high-resolution scanning electron microscopy, atomic force microscopy, and scanning tunneling microscopy. The results show that the crystalline quality of the porous graphene depended not only on the substrate temperature but also on the SiC layer thickness during carbon atom deposition.

Method and apparatus for multiple-projection, dual-energy x-ray absorptiometry scanning

NASA Technical Reports Server (NTRS)

Feldmesser, Howard S. (Inventor); Magee, Thomas C. (Inventor); Charles, Jr., Harry K. (Inventor); Beck, Thomas J. (Inventor)

2007-01-01

Methods and apparatuses for advanced, multiple-projection, dual-energy X-ray absorptiometry scanning systems include combinations of a conical collimator; a high-resolution two-dimensional detector; a portable, power-capped, variable-exposure-time power supply; an exposure-time control element; calibration monitoring; a three-dimensional anti-scatter-grid; and a gantry-gantry base assembly that permits up to seven projection angles for overlapping beams. Such systems are capable of high precision bone structure measurements that can support three dimensional bone modeling and derivations of bone strength, risk of injury, and efficacy of countermeasures among other properties.

Three-dimensional imaging of the brain cavities in human embryos.

PubMed

Blaas, H G; Eik-Nes, S H; Kiserud, T; Berg, S; Angelsen, B; Olstad, B

1995-04-01

A system for high-resolution three-dimensional imaging of small structures has been developed, based on the Vingmed CFM-800 annular array sector scanner with a 7.5-MHz transducer attached to a PC-based TomTec Echo-Scan unit. A stepper motor rotates the transducer 180 degrees and the complete three-dimensional scan consists of 132 two-dimensional images, video-grabbed and scan-converted into a regular volumetric data set by the TomTec unit. Three normal pregnancies with embryos of gestational age 7, 9 and 10 weeks received a transvaginal examination with special attention to the embryonic/fetal brain. In all three cases, it was possible to obtain high-resolution images of the brain cavities. At 7 weeks, both hemispheres and their connection to the third ventricle were delineated. The isthmus rhombencephali could be visualized. At 9 weeks, the continuous development of the brain cavities could be followed and at 11 weeks the dominating size of the hemispheres could be depicted. It is concluded that present ultrasound technology has reached a stage where structures of only a few millimeters can be imaged in vivo in three-dimensions with a quality that resembles the plaster figures used in embryonic laboratories. The method can become an important tool in future embryological research and also in the detection of early developmental disorders of the embryo.

High resolution structural characterization of giant magnetoresistance structures containing a nano-oxide layer

NASA Astrophysics Data System (ADS)

You, C. Y.; Cerezo, A.; Clifton, P. H.; Folks, L.; Carey, M. J.; Petford-Long, A. K.

2007-07-01

The microstructure and chemistry of a current-perpendicular-to-plane giant magnetoresistance structure containing a nano-oxide layer (NOL) have been studied using a combination of high resolution transmission electron microscopy and three-dimensional atom probe analysis. It was found that the morphology of the NOL changes from a planar layer to discrete particles on annealing, indicating the dominance of surface energy on the morphology evolution. Direct evidence was obtained for significant Mn diffusion from the IrMn antiferromagnetic layer and partitioning to the oxide region during annealing.

High-resolution three-dimensional magnetic resonance imaging of mouse lung in situ.

PubMed

Scadeng, Miriam; Rossiter, Harry B; Dubowitz, David J; Breen, Ellen C

2007-01-01

This study establishes a method for high-resolution isotropic magnetic resonance (MR) imaging of mouse lungs using tracheal liquid-instillation to remove MR susceptibility artifacts. C57BL/6J mice were instilled sequentially with perfluorocarbon and phosphate-buffered saline to an airway pressure of 10, 20, or 30 cm H2O. Imaging was performed in a 7T MR scanner using a 2.5-cm Quadrature volume coil and a 3-dimensional (3D) FLASH imaging sequence. Liquid-instillation removed magnetic susceptibility artifacts and allowed lung structure to be viewed at an isotropic resolution of 78-90 microm. Instilled liquid and modeled lung volumes were well correlated (R = 0.92; P < 0.05) and differed by a constant tissue volume (220 +/- 92 microL). 3D image renderings allowed differences in structural dimensions (volumes and areas) to be accurately measured at each inflation pressure. These data demonstrate the efficacy of pulmonary liquid instillation for in situ high-resolution MR imaging of mouse lungs for accurate measurement of pulmonary airway, parenchymal, and vascular structures.

In-line three-dimensional holography of nanocrystalline objects at atomic resolution

PubMed Central

Chen, F.-R.; Van Dyck, D.; Kisielowski, C.

2016-01-01

Resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we report a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose rate electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. We apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1–2 Å, which is smaller than inter-atomic distances. PMID:26887849

Three-Dimensional Unstained Live-Cell Imaging Using Stimulated Parametric Emission Microscopy

NASA Astrophysics Data System (ADS)

Dang, Hieu M.; Kawasumi, Takehito; Omura, Gen; Umano, Toshiyuki; Kajiyama, Shin'ichiro; Ozeki, Yasuyuki; Itoh, Kazuyoshi; Fukui, Kiichi

2009-09-01

The ability to perform high-resolution unstained live imaging is very important to in vivo study of cell structures and functions. Stimulated parametric emission (SPE) microscopy is a nonlinear-optical microscopy based on ultra-fast electronic nonlinear-optical responses. For the first time, we have successfully applied this technique to archive three-dimensional (3D) images of unstained sub-cellular structures, such as, microtubules, nuclei, nucleoli, etc. in live cells. Observation of a complete cell division confirms the ability of SPE microscopy for long time-scale imaging.

High-resolution non-destructive three-dimensional imaging of integrated circuits

NASA Astrophysics Data System (ADS)

Holler, Mirko; Guizar-Sicairos, Manuel; Tsai, Esther H. R.; Dinapoli, Roberto; Müller, Elisabeth; Bunk, Oliver; Raabe, Jörg; Aeppli, Gabriel

2017-03-01

Modern nanoelectronics has advanced to a point at which it is impossible to image entire devices and their interconnections non-destructively because of their small feature sizes and the complex three-dimensional structures resulting from their integration on a chip. This metrology gap implies a lack of direct feedback between design and manufacturing processes, and hampers quality control during production, shipment and use. Here we demonstrate that X-ray ptychography—a high-resolution coherent diffractive imaging technique—can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques. Foreseeable developments in X-ray sources, optics and detectors, as well as adoption of an instrument geometry optimized for planar rather than cylindrical samples, could lead to a thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes.

High-resolution non-destructive three-dimensional imaging of integrated circuits.

PubMed

Holler, Mirko; Guizar-Sicairos, Manuel; Tsai, Esther H R; Dinapoli, Roberto; Müller, Elisabeth; Bunk, Oliver; Raabe, Jörg; Aeppli, Gabriel

2017-03-15

Modern nanoelectronics has advanced to a point at which it is impossible to image entire devices and their interconnections non-destructively because of their small feature sizes and the complex three-dimensional structures resulting from their integration on a chip. This metrology gap implies a lack of direct feedback between design and manufacturing processes, and hampers quality control during production, shipment and use. Here we demonstrate that X-ray ptychography-a high-resolution coherent diffractive imaging technique-can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques. Foreseeable developments in X-ray sources, optics and detectors, as well as adoption of an instrument geometry optimized for planar rather than cylindrical samples, could lead to a thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes.

Numerical viscosity and resolution of high-order weighted essentially nonoscillatory schemes for compressible flows with high Reynolds numbers.

PubMed

Zhang, Yong-Tao; Shi, Jing; Shu, Chi-Wang; Zhou, Ye

2003-10-01

A quantitative study is carried out in this paper to investigate the size of numerical viscosities and the resolution power of high-order weighted essentially nonoscillatory (WENO) schemes for solving one- and two-dimensional Navier-Stokes equations for compressible gas dynamics with high Reynolds numbers. A one-dimensional shock tube problem, a one-dimensional example with parameters motivated by supernova and laser experiments, and a two-dimensional Rayleigh-Taylor instability problem are used as numerical test problems. For the two-dimensional Rayleigh-Taylor instability problem, or similar problems with small-scale structures, the details of the small structures are determined by the physical viscosity (therefore, the Reynolds number) in the Navier-Stokes equations. Thus, to obtain faithful resolution to these small-scale structures, the numerical viscosity inherent in the scheme must be small enough so that the physical viscosity dominates. A careful mesh refinement study is performed to capture the threshold mesh for full resolution, for specific Reynolds numbers, when WENO schemes of different orders of accuracy are used. It is demonstrated that high-order WENO schemes are more CPU time efficient to reach the same resolution, both for the one-dimensional and two-dimensional test problems.

Synthesis and identification of three-dimensional faces from image(s) and three-dimensional generic models

NASA Astrophysics Data System (ADS)

Liu, Zexi; Cohen, Fernand

2017-11-01

We describe an approach for synthesizing a three-dimensional (3-D) face structure from an image or images of a human face taken at a priori unknown poses using gender and ethnicity specific 3-D generic models. The synthesis process starts with a generic model, which is personalized as images of the person become available using preselected landmark points that are tessellated to form a high-resolution triangular mesh. From a single image, two of the three coordinates of the model are reconstructed in accordance with the given image of the person, while the third coordinate is sampled from the generic model, and the appearance is made in accordance with the image. With multiple images, all coordinates and appearance are reconstructed in accordance with the observed images. This method allows for accurate pose estimation as well as face identification in 3-D rendering of a difficult two-dimensional (2-D) face recognition problem into a much simpler 3-D surface matching problem. The estimation of the unknown pose is achieved using the Levenberg-Marquardt optimization process. Encouraging experimental results are obtained in a controlled environment with high-resolution images under a good illumination condition, as well as for images taken in an uncontrolled environment under arbitrary illumination with low-resolution cameras.

3D visualization of middle ear structures

NASA Astrophysics Data System (ADS)

Vogel, Uwe; Schmitt, Thomas

1998-06-01

The achievement of volume geometry data from middle ear structures and surrounding components performs a necessary supposition for the finite element simulation of the vibrational and transfer characteristics of the ossicular chain. So far those models base on generalized figures and size data from anatomy textbooks or particular manual and one- or two-dimensional distance measurements of single ossicles, mostly obtained by light microscopy, respectively. Therefore the goal of this study is to create a procedure for complete three-dimensional imaging of real middle ear structures (tympanic membrane, ossicles, ligaments) in vitro or even in vivo. The main problems are their microscopic size with relevant structures from 10 micrometer to 5 mm, representing various tissue properties (bone, soft tissue). Additionally, these structures are surrounded by the temporal bone, the most solid bone of the human body. Generally there exist several established diagnostic tools for medical imaging that could be used for geometry data acquisition, e.g., X-ray computed tomography and magnetic resonance imaging. Basically they image different tissue parameters, either bony structures (ossicles), or soft tissue (tympanic membrane, ligaments). But considering this application those standard techniques allow low spatial resolution only, usually in the 0.5 - 1mm range, at least in one spatial direction. Thus particular structures of the middle ear region could even be missed completely because of their spatial location. In vitro there is a way out by collecting three complete data sets, each distinguished by 90 degree rotation of a cube-shaped temporal bone specimen. That allows high-resolution imaging in three orthogonal planes, which essentially supports the three-dimensional interpolation of the unknown elements, starting from the regularly set elements of the cubic grid with an edge extension given by the original two-dimensional matrix. A different approach represents the application of a micro- tomographic imaging device. Therefore an X-ray beam focused down to few microns passes the object in a tomographic arrangement. Subsequently the slices become reconstructed. Generally spatial resolution down to 10 micrometer may be obtained by using this procedure. But there exist few devices only, it is not available as standard equipment. The best results concerning spatial resolution should be achieved by applying conventional histologic sectioning techniques. Of course the target will become destroyed during the procedure. It is cut into sections (e.g., 10 micrometer thick), every layer is stained, and the image acquired and stored by a digital still-camera with appropriate resolution (e.g., 2024 X 3036). Three-dimensional reconstruction is done with the computer. The staining allows visual selection of bones and soft tissues, resolutions down to 10 micrometer are possible without target segmentation. But there arise some practical problems. Mainly the geometric context of the layers is affected by the cutting procedure, especially if cutting bone. Another problem performs the adjustment of the -- possibly distorted -- slices to each other. Artificial markers are necessary, which could allow automatic adjustment too. But the introduction and imaging of the markers is difficult inside the temporal bone specimen, that is interspersed by several cavities. Of course the internal target structures must not be destroyed by the marker introduction. Furthermore the embedding compound could disturb the image acquisition, e.g., by optical scattering of paraffin. A related alternative is given by layered ablation/grinding and imaging of the top layer. This saves the geometric consistency, but requires very tricky and time-consuming embedding procedures. Both approaches require considerable expenditures. The possible approaches are evaluated in detail and first results are compared. So far none of the above-mentioned procedures has been established as a standard tool for three-dimensional geometry data acquisition of the middle ear. Otherwise the establishment of a high-resolution imaging technique for those structures, even in vivo, would be of high interest in diagnostics, anatomy and middle ear modeling and research at all.

3D printing from microfocus computed tomography (micro-CT) in human specimens: education and future implications.

PubMed

Shelmerdine, Susan C; Simcock, Ian C; Hutchinson, John Ciaran; Aughwane, Rosalind; Melbourne, Andrew; Nikitichev, Daniil I; Ong, Ju-Ling; Borghi, Alessandro; Cole, Garrard; Kingham, Emilia; Calder, Alistair D; Capelli, Claudio; Akhtar, Aadam; Cook, Andrew C; Schievano, Silvia; David, Anna; Ourselin, Sebastian; Sebire, Neil J; Arthurs, Owen J

2018-06-14

Microfocus CT (micro-CT) is an imaging method that provides three-dimensional digital data sets with comparable resolution to light microscopy. Although it has traditionally been used for non-destructive testing in engineering, aerospace industries and in preclinical animal studies, new applications are rapidly becoming available in the clinical setting including post-mortem fetal imaging and pathological specimen analysis. Printing three-dimensional models from imaging data sets for educational purposes is well established in the medical literature, but typically using low resolution (0.7 mm voxel size) data acquired from CT or MR examinations. With higher resolution imaging (voxel sizes below 1 micron, <0.001 mm) at micro-CT, smaller structures can be better characterised, and data sets post-processed to create accurate anatomical models for review and handling. In this review, we provide examples of how three-dimensional printing of micro-CT imaged specimens can provide insight into craniofacial surgical applications, developmental cardiac anatomy, placental imaging, archaeological remains and high-resolution bone imaging. We conclude with other potential future usages of this emerging technique.

High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

PubMed Central

Zook, James D.; Molugu, Trivikram R.; Jacobsen, Neil E.; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra

2013-01-01

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

Three-dimensional structure of E. Coli purine nucleoside phosphorylase at 0.99 Å resolution

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

Timofeev, V. I., E-mail: tostars@mail.ru; Abramchik, Yu. A., E-mail: ugama@yandex.ru; Zhukhlistova, N. E., E-mail: inna@ns.crys.ras.ru

2016-03-15

Purine nucleoside phosphorylases (PNPs) catalyze the reversible phosphorolysis of nucleosides and are key enzymes involved in nucleotide metabolism. They are essential for normal cell function and can catalyze the transglycosylation. Crystals of E. coli PNP were grown in microgravity by the capillary counterdiffusion method through a gel layer. The three-dimensional structure of the enzyme was determined by the molecular-replacement method at 0.99 Å resolution. The structural features are considered, and the structure of E. coli PNP is compared with the structures of the free enzyme and its complexes with purine base derivatives established earlier. A comparison of the environment ofmore » the purine base in the complex of PNP with formycin A and of the pyrimidine base in the complex of uridine phosphorylase with thymidine revealed the main structural features of the base-binding sites. Coordinates of the atomic model determined with high accuracy were deposited in the Protein Data Bank (PDB-ID: 4RJ2).« less

High-resolution computer-generated reflection holograms with three-dimensional effects written directly on a silicon surface by a femtosecond laser.

PubMed

Wædegaard, Kristian J; Balling, Peter

2011-02-14

An infrared femtosecond laser has been used to write computer-generated holograms directly on a silicon surface. The high resolution offered by short-pulse laser ablation is employed to write highly detailed holograms with resolution up to 111 kpixels/mm2. It is demonstrated how three-dimensional effects can be realized in computer-generated holograms. Three-dimensional effects are visualized as a relative motion between different parts of the holographic reconstruction, when the hologram is moved relative to the reconstructing laser beam. Potential security applications are briefly discussed.

Determination of minority-carrier lifetime and surface recombination velocity with high spacial resolution

NASA Technical Reports Server (NTRS)

Watanabe, M.; Actor, G.; Gatos, H. C.

1977-01-01

Quantitative analysis of the electron beam induced current in conjunction with high-resolution scanning makes it possible to evaluate the minority-carrier lifetime three dimensionally in the bulk and the surface recombination velocity two dimensionally, with a high spacial resolution. The analysis is based on the concept of the effective excitation strength of the carriers which takes into consideration all possible recombination sources. Two-dimensional mapping of the surface recombination velocity of phosphorus-diffused silicon diodes is presented as well as a three-dimensional mapping of the changes in the minority-carrier lifetime in ion-implanted silicon.

Observation of three-dimensional internal structure of steel materials by means of serial sectioning with ultrasonic elliptical vibration cutting.

PubMed

Fujisaki, K; Yokota, H; Nakatsuchi, H; Yamagata, Y; Nishikawa, T; Udagawa, T; Makinouchi, A

2010-01-01

A three-dimensional (3D) internal structure observation system based on serial sectioning was developed from an ultrasonic elliptical vibration cutting device and an optical microscope combined with a high-precision positioning device. For bearing steel samples, the cutting device created mirrored surfaces suitable for optical metallography, even for long-cutting distances during serial sectioning of these ferrous materials. Serial sectioning progressed automatically by means of numerical control. The system was used to observe inclusions in steel materials on a scale of several tens of micrometers. Three specimens containing inclusions were prepared from bearing steels. These inclusions could be detected as two-dimensional (2D) sectional images with resolution better than 1 mum. A three-dimensional (3D) model of each inclusion was reconstructed from the 2D serial images. The microscopic 3D models had sharp edges and complicated surfaces.

Diatom Valve Three-Dimensional Representation: A New Imaging Method Based on Combined Microscopies

PubMed Central

Ferrara, Maria Antonietta; De Tommasi, Edoardo; Coppola, Giuseppe; De Stefano, Luca; Rea, Ilaria; Dardano, Principia

2016-01-01

The frustule of diatoms, unicellular microalgae, shows very interesting photonic features, generally related to its complicated and quasi-periodic micro- and nano-structure. In order to simulate light propagation inside and through this natural structure, it is important to develop three-dimensional (3D) models for synthetic replica with high spatial resolution. In this paper, we present a new method that generates images of microscopic diatoms with high definition, by merging scanning electron microscopy and digital holography microscopy or atomic force microscopy data. Starting from two digital images, both acquired separately with standard characterization procedures, a high spatial resolution (Δz = λ/20, Δx = Δy ≅ 100 nm, at least) 3D model of the object has been generated. Then, the two sets of data have been processed by matrix formalism, using an original mathematical algorithm implemented on a commercially available software. The developed methodology could be also of broad interest in the design and fabrication of micro-opto-electro-mechanical systems. PMID:27690008

Three-dimensional interactions and vortical flows with emphasis on high speeds

NASA Technical Reports Server (NTRS)

Peake, D. J.; Tobak, M.

1980-01-01

Diverse kinds of three-dimensional regions of separation in laminar and turbulent boundary layers are discussed that exist on lifting aerodynamic configurations immersed in flows from subsonic to hypersonic speeds. In all cases of three dimensional flow separation, the assumption of continuous vector fields of skin-friction lines and external-flow streamlines, coupled with simple topology laws, provides a flow grammar whose elemental constituents are the singular points: nodes, foci, and saddles. Adopting these notions enables one to create sequences of plausible flow structures, to deduce mean flow characteristics, expose flow mechanisms, and to aid theory and experiment where lack of resolution in numerical calculations or wind tunnel observation causes imprecision in diagnosing the three dimensional flow features.

Three dimensional imaging detector employing wavelength-shifting optical fibers

DOEpatents

Worstell, William A.

1997-01-01

A novel detector element structure and method for its use is provided. In a preferred embodiment, one or more inorganic scintillating crystals are coupled through wavelength shifting optical fibers (WLSFs) to position sensitive photomultipliers (PS-PMTs). The superior detector configuration in accordance with this invention is designed for an array of applications in high spatial resolution gamma ray sensing with particular application to SPECT, PET and PVI imaging systems. The design provides better position resolution than prior art devices at a lower total cost. By employing wavelength shifting fibers (WLSFs), the sensor configuration of this invention can operate with a significant reduction in the number of photomultipliers and electronics channels, while potentially improving the resolution of the system by allowing three dimensional reconstruction of energy deposition positions.

Three dimensional imaging detector employing wavelength-shifting optical fibers

DOEpatents

Worstell, W.A.

1997-02-04

A novel detector element structure and method for its use is provided. In a preferred embodiment, one or more inorganic scintillating crystals are coupled through wavelength shifting optical fibers (WLSFs) to position sensitive photomultipliers (PS-PMTs). The superior detector configuration in accordance with this invention is designed for an array of applications in high spatial resolution gamma ray sensing with particular application to SPECT, PET and PVI imaging systems. The design provides better position resolution than prior art devices at a lower total cost. By employing wavelength shifting fibers (WLSFs), the sensor configuration of this invention can operate with a significant reduction in the number of photomultipliers and electronics channels, while potentially improving the resolution of the system by allowing three dimensional reconstruction of energy deposition positions. 11 figs.

Three-dimensional confocal microscopy of the living cornea and ocular lens

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1991-07-01

The three-dimensional reconstruction of the optic zone of the cornea and the ocular crystalline lens has been accomplished using confocal microscopy and volume rendering computer techniques. A laser scanning confocal microscope was used in the reflected light mode to obtain the two-dimensional images from the cornea and the ocular lens of a freshly enucleated rabbit eye. The light source was an argon ion laser with a 488 nm wavelength. The microscope objective was a Leitz X25, NA 0.6 water immersion lens. The 400 micron thick cornea was optically sectioned into 133 three micron sections. The semi-transparent cornea and the in-situ ocular lens was visualized as high resolution, high contrast two-dimensional images. The structures observed in the cornea include: superficial epithelial cells and their nuclei, basal epithelial cells and their 'beaded' cell borders, basal lamina, nerve plexus, nerve fibers, nuclei of stromal keratocytes, and endothelial cells. The structures observed in the in- situ ocular lens include: lens capsule, lens epithelial cells, and individual lens fibers. The three-dimensional data sets of the cornea and the ocular lens were reconstructed in the computer using volume rendering techniques. Stereo pairs were also created of the two- dimensional ocular images for visualization. The stack of two-dimensional images was reconstructed into a three-dimensional object using volume rendering techniques. This demonstration of the three-dimensional visualization of the intact, enucleated eye provides an important step toward quantitative three-dimensional morphometry of the eye. The important aspects of three-dimensional reconstruction are discussed.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

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

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identifiedmore » in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.« less

In-line three-dimensional holography of nanocrystalline objects at atomic resolution

DOE PAGES

Chen, F. -R.; Van Dyck, D.; Kisielowski, C.

2016-02-18

We report that resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we show a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose ratemore » electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. Lastly, we apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1–2 Å, which is smaller than inter-atomic distances.« less

High-resolution ab initio three-dimensional x-ray diffraction microscopy

DOE PAGES

Chapman, Henry N.; Barty, Anton; Marchesini, Stefano; ...

2006-01-01

Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatialmore » resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources.« less

High-resolution three-dimensional structural microscopy by single-angle Bragg ptychography

DOE PAGES

Hruszkewycz, S. O.; Allain, M.; Holt, M. V.; ...

2016-11-21

Coherent X-ray microscopy by phase retrieval of Bragg diffraction intensities enables lattice distortions within a crystal to be imaged at nanometre-scale spatial resolutions in three dimensions. While this capability can be used to resolve structure–property relationships at the nanoscale under working conditions, strict data measurement requirements can limit the application of current approaches. Here, in this work, we introduce an efficient method of imaging three-dimensional (3D) nanoscale lattice behaviour and strain fields in crystalline materials with a methodology that we call 3D Bragg projection ptychography (3DBPP). This method enables 3D image reconstruction of a crystal volume from a series ofmore » two-dimensional X-ray Bragg coherent intensity diffraction patterns measured at a single incident beam angle. Structural information about the sample is encoded along two reciprocal-space directions normal to the Bragg diffracted exit beam, and along the third dimension in real space by the scanning beam. Finally, we present our approach with an analytical derivation, a numerical demonstration, and an experimental reconstruction of lattice distortions in a component of a nanoelectronic prototype device.« less

Three-dimensional high-resolution second-harmonic generation imaging of endogenous structural proteins in biological tissues.

PubMed Central

Campagnola, Paul J; Millard, Andrew C; Terasaki, Mark; Hoppe, Pamela E; Malone, Christian J; Mohler, William A

2002-01-01

We find that several key endogenous protein structures give rise to intense second-harmonic generation (SHG)-nonabsorptive frequency doubling of an excitation laser line. Second-harmonic imaging microscopy (SHIM) on a laser-scanning system proves, therefore, to be a powerful and unique tool for high-resolution, high-contrast, three-dimensional studies of live cell and tissue architecture. Unlike fluorescence, SHG suffers no inherent photobleaching or toxicity and does not require exogenous labels. Unlike polarization microscopy, SHIM provides intrinsic confocality and deep sectioning in complex tissues. In this study, we demonstrate the clarity of SHIM optical sectioning within unfixed, unstained thick specimens. SHIM and two-photon excited fluorescence (TPEF) were combined in a dual-mode nonlinear microscopy to elucidate the molecular sources of SHG in live cells and tissues. SHG arose not only from coiled-coil complexes within connective tissues and muscle thick filaments, but also from microtubule arrays within interphase and mitotic cells. Both polarization dependence and a local symmetry cancellation effect of SHG allowed the signal from species generating the second harmonic to be decoded, by ratiometric correlation with TPEF, to yield information on local structure below optical resolution. The physical origin of SHG within these tissues is addressed and is attributed to the laser interaction with dipolar protein structures that is enhanced by the intrinsic chirality of the protein helices. PMID:11751336

[Extraction of buildings three-dimensional information from high-resolution satellite imagery based on Barista software].

PubMed

Zhang, Pei-feng; Hu, Yuan-man; He, Hong-shi

2010-05-01

The demand for accurate and up-to-date spatial information of urban buildings is becoming more and more important for urban planning, environmental protection, and other vocations. Today's commercial high-resolution satellite imagery offers the potential to extract the three-dimensional information of urban buildings. This paper extracted the three-dimensional information of urban buildings from QuickBird imagery, and validated the precision of the extraction based on Barista software. It was shown that the extraction of three-dimensional information of the buildings from high-resolution satellite imagery based on Barista software had the advantages of low professional level demand, powerful universality, simple operation, and high precision. One pixel level of point positioning and height determination accuracy could be achieved if the digital elevation model (DEM) and sensor orientation model had higher precision and the off-Nadir View Angle was relatively perfect.

Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview

PubMed Central

Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized. PMID:24688696

Conformational sampling in template-free protein loop structure modeling: an overview.

PubMed

Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

Three-dimensional electron diffraction of plant light-harvesting complex

PubMed Central

Wang, Da Neng; Kühlbrandt, Werner

1992-01-01

Electron diffraction patterns of two-dimensional crystals of light-harvesting chlorophyll a/b-protein complex (LHC-II) from photosynthetic membranes of pea chloroplasts, tilted at different angles up to 60°, were collected to 3.2 Å resolution at -125°C. The reflection intensities were merged into a three-dimensional data set. The Friedel R-factor and the merging R-factor were 21.8 and 27.6%, respectively. Specimen flatness and crystal size were critical for recording electron diffraction patterns from crystals at high tilts. The principal sources of experimental error were attributed to limitations of the number of unit cells contributing to an electron diffraction pattern, and to the critical electron dose. The distribution of strong diffraction spots indicated that the three-dimensional structure of LHC-II is less regular than that of other known membrane proteins and is not dominated by a particular feature of secondary structure. ImagesFIGURE 1FIGURE 2 PMID:19431817

Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors

PubMed Central

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2012-01-01

A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root mean square deviation of less than 2.5 Å were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases. PMID:22417139

Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.

PubMed

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2012-06-14

A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three-dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root-mean-square deviation of less than 2.5 Å were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases.

Time-efficient high-resolution whole-brain three-dimensional macromolecular proton fraction mapping

PubMed Central

Yarnykh, Vasily L.

2015-01-01

Purpose Macromolecular proton fraction (MPF) mapping is a quantitative MRI method that reconstructs parametric maps of a relative amount of macromolecular protons causing the magnetization transfer (MT) effect and provides a biomarker of myelination in neural tissues. This study aimed to develop a high-resolution whole-brain MPF mapping technique utilizing a minimal possible number of source images for scan time reduction. Methods The described technique is based on replacement of an actually acquired reference image without MT saturation by a synthetic one reconstructed from R1 and proton density maps, thus requiring only three source images. This approach enabled whole-brain three-dimensional MPF mapping with isotropic 1.25×1.25×1.25 mm3 voxel size and scan time of 20 minutes. The synthetic reference method was validated against standard MPF mapping with acquired reference images based on data from 8 healthy subjects. Results Mean MPF values in segmented white and gray matter appeared in close agreement with no significant bias and small within-subject coefficients of variation (<2%). High-resolution MPF maps demonstrated sharp white-gray matter contrast and clear visualization of anatomical details including gray matter structures with high iron content. Conclusions Synthetic reference method improves resolution of MPF mapping and combines accurate MPF measurements with unique neuroanatomical contrast features. PMID:26102097

Microholography of Living Organisms.

ERIC Educational Resources Information Center

Solem, Johndale C.; Baldwin, George C.

1982-01-01

By using intense pulsed coherent x-ray sources it will be possible to obtain magnified three-dimensional images of living elementary biological structures at precisely defined instants. Discussed are sources/geometrics for x-ray holography, x-radiation interactions, factors affecting resolution, recording the hologram, high-intensity holography,…

Accessibility of selenomethionine proteins by total chemical synthesis: structural studies of human herpesvirus-8 MIP-II.

PubMed

Shao, W; Fernandez, E; Wilken, J; Thompson, D A; Siani, M A; West, J; Lolis, E; Schweitzer, B I

1998-12-11

The determination of high resolution three-dimensional structures by X-ray crystallography or nuclear magnetic resonance (NMR) is a time-consuming process. Here we describe an approach to circumvent the cloning and expression of a recombinant protein as well as screening for heavy atom derivatives. The selenomethionine-modified chemokine macrophage inflammatory protein-II (MIP-II) from human herpesvirus-8 has been produced by total chemical synthesis, crystallized, and characterized by NMR. The protein has a secondary structure typical of other chemokines and forms a monomer in solution. These results indicate that total chemical synthesis can be used to accelerate the determination of three-dimensional structures of new proteins identified in genome programs.

Rapid high-resolution four-dimensional NMR spectroscopy using the filter diagonalization method and its advantages for detailed structural elucidation of oligosaccharides.

PubMed

Armstrong, Geoffrey S; Mandelshtam, Vladimir A; Shaka, A J; Bendiak, Brad

2005-03-01

Four-dimensional nuclear magnetic resonance spectroscopy with high resolution of signals in the indirect dimensions is reported as an implementation of the filter diagonalization method (FDM). Using an oligosaccharide derivatized with 13C-labeled acetyl isotags, a four-dimensional constant-time pulse sequence was tailored for conjoint use with the FDM. Results demonstrate that high resolution in all dimensions can be achieved using a relatively short experimental time period (19 h), even though the spectrum is highly congested in the direct and all three indirect dimensions. The combined use of isotags, constant-time pulse sequences, and FDM permits rapid isolation of sugar ring proton spin systems in multiple dimensions and enables all endocyclic J-couplings to be simply measured, the key goal to assigning sugar stereochemistry and anomeric configuration. A general method for rapid, unambiguous elucidation of spin systems in oligosaccharides has been a long-sought goal of carbohydrate NMR, and isotags combined with the FDM now enable this to be easily performed. Additional general advantages of the FDM program for generating high-resolution 2D slices in any dimension from a 4D spectrum are emphasized.

Online service for monitoring the ionosphere based on data from the global navigation satellite system

NASA Astrophysics Data System (ADS)

Aleshin, I. M.; Alpatov, V. V.; Vasil'ev, A. E.; Burguchev, S. S.; Kholodkov, K. I.; Budnikov, P. A.; Molodtsov, D. A.; Koryagin, V. N.; Perederin, F. V.

2014-07-01

A service is described that makes possible the effective construction of a three-dimensional ionospheric model based on the data of ground receivers of signals from global navigation satellite positioning systems (GNSS). The obtained image has a high resolution, mainly because data from the IPG GNSS network of the Federal Service for Hydrometeorology and Environmental Monitoring (Rosgidromet) are used. A specially developed format and its implementation in the form of SQL structures are used to collect, transmit, and store data. The method of high-altitude radio tomography is used to construct the three-dimensional model. The operation of all system components (from registration point organization to the procedure for constructing the electron density three-dimensional distribution and publication of the total electron content map on the Internet) has been described in detail. The three-dimensional image of the ionosphere, obtained automatically, is compared with the ionosonde measurements, calculated using the two-dimensional low-altitude tomography method and averaged by the ionospheric model.

Toward atomic-scale bright-field electron tomography for the study of fullerene-like nanostructures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Wolf, Sharon G; Enyashin, Andrey; Seifert, Gotthard; Tenne, Reshef; Urban, Knut

2008-03-01

We present the advancement of electron tomography for three-dimensional structure reconstruction of fullerene-like particles toward atomic-scale resolution. The three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is achieved by the combination of low voltage operation of the electron microscope with aberration-corrected phase contrast imaging. The method enables the study of defects and irregularities in the three-dimensional structure of individual fullerene-like particles on the scale of 2-3 A. Control over shape, size, and atomic architecture is a key issue in synthesis and design of functional nanoparticles. Transmission electron microscopy (TEM) is the primary technique to characterize materials down to the atomic level, albeit the images are two-dimensional projections of the studied objects. Recent advancements in aberration-corrected TEM have demonstrated single atom sensitivity for light elements at subångström resolution. Yet, the resolution of tomographic schemes for three-dimensional structure reconstruction has not surpassed 1 nm3, preventing it from becoming a powerful tool for characterization in the physical sciences on the atomic scale. Here we demonstrate that negative spherical aberration imaging at low acceleration voltage enables tomography down to the atomic scale at reduced radiation damage. First experimental data on the three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is presented. The method is applicable to the analysis of the atomic architecture of a wide range of nanostructures where strong electron channeling is absent, in particular to carbon fullerenes and inorganic fullerenes.

The Seismic Attenuation Structure of the East Pacific Rise

DTIC Science & Technology

1992-02-27

Kanamori, R. W. Clayton, Three- dimensional attenuation structure of Kilauea -East rift zone, Hawaii , J. Geophys. Res., submitted, 1990. Holt, M., Underwater...and J. J. Zucca, Active high-resolution seismic tomography of compressional wave velocity and attenuation at Medicine Lake volcano , northern California...zones of anomalously high S-wave attenuation in the upper crust near Ruapehu and Ngauruhoe volcanoes , New Zealand, J. Volcanol. Geotherm. Res., 10, 125

High-resolution liquid patterns via three-dimensional droplet shape control.

PubMed

Raj, Rishi; Adera, Solomon; Enright, Ryan; Wang, Evelyn N

2014-09-25

Understanding liquid dynamics on surfaces can provide insight into nature's design and enable fine manipulation capability in biological, manufacturing, microfluidic and thermal management applications. Of particular interest is the ability to control the shape of the droplet contact area on the surface, which is typically circular on a smooth homogeneous surface. Here, we show the ability to tailor various droplet contact area shapes ranging from squares, rectangles, hexagons, octagons, to dodecagons via the design of the structure or chemical heterogeneity on the surface. We simultaneously obtain the necessary physical insights to develop a universal model for the three-dimensional droplet shape by characterizing the droplet side and top profiles. Furthermore, arrays of droplets with controlled shapes and high spatial resolution can be achieved using this approach. This liquid-based patterning strategy promises low-cost fabrication of integrated circuits, conductive patterns and bio-microarrays for high-density information storage and miniaturized biochips and biosensors, among others.

Nightside Structure of the Venusian Ionosphere

NASA Astrophysics Data System (ADS)

Ledvina, S. A.; Brecht, S. H.

2017-12-01

The Pioneer Venus Orbiter, PVO, was the first mission to detect large-scale structure in the nightside region of Venus. This structure is often referred to as "tail rays." Since this discovery, there has been continuous discussion as to the cause of the structure. There have been theoretical attempts to explain the structure but no definitive determination of the mechanism. Typically, the wavelengths of the structure were not always consistent with the theory. Three-dimensional hybrid simulations are reported that produce structure on the nightside of Venus. The structure seems consistent with the data. This paper will present the results of the simulations as well as a variety of numerical tests that offer some insight into the mechanism driving the development of the structure. The tests reveal that the ambipolar electric fields as produced by the gradient of the electron pressure seems to be the root cause of the structure. It will be shown that different realizations of the neutral wind modify the structure. The hybrid simulations are three dimensional with neutral winds included in the simulations. The resolution of the simulation is 50 km/cell and lower. The spherical grid used in the simulations to handle chemistry and collisions has a resolution of 5 km radially and under 50 km in the angular directions. It is these high resolution simulations that produce the structure to be discussed in this paper.

Temporal focusing microscopy combined with three-dimensional structured illumination

NASA Astrophysics Data System (ADS)

Isobe, Keisuke; Toda, Keisuke; Song, Qiyuan; Kannari, Fumihiko; Kawano, Hiroyuki; Miyawaki, Atsushi; Midorikawa, Katsumi

2017-05-01

Temporal focusing microscopy provides the optical sectioning capability in wide-field two-photon fluorescence imaging. Here, we demonstrate temporal focusing microscopy combined with three-dimensional structured illumination, which enables us to enhance the three-dimensional spatial resolution and reject the background fluorescence. Experimentally, the periodic pattern of the illumination was produced not only in the lateral direction but also in the axial direction by the interference between three temporal focusing pulses, which were easily generated using a digital micromirror device. The lateral resolution and optical sectioning capability were successfully enhanced by factors of 1.6 and 3.6, respectively, compared with those of temporal focusing microscopy. In the two-photon fluorescence imaging of a tissue-like phantom, the out-of-focus background fluorescence and the scattered background fluorescence could also be rejected.

The three-dimensional structure of the cellobiohydrolase Cel7A from Aspergillus fumigatus at 1.5 Å resolution

PubMed Central

Moroz, Olga V.; Maranta, Michelle; Shaghasi, Tarana; Harris, Paul V.; Wilson, Keith S.; Davies, Gideon J.

2015-01-01

The enzymatic degradation of plant cell-wall cellulose is central to many industrial processes, including second-generation biofuel production. Key players in this deconstruction are the fungal cellobiohydrolases (CBHs), notably those from family GH7 of the carbohydrate-active enzymes (CAZY) database, which are generally known as CBHI enzymes. Here, three-dimensional structures are reported of the Aspergillus fumigatus CBHI Cel7A solved in uncomplexed and disaccharide-bound forms at resolutions of 1.8 and 1.5 Å, respectively. The product complex with a disaccharide in the +1 and +2 subsites adds to the growing three-dimensional insight into this family of industrially relevant biocatalysts. PMID:25615982

Resolution of ab initio shapes determined from small-angle scattering.

PubMed

Tuukkanen, Anne T; Kleywegt, Gerard J; Svergun, Dmitri I

2016-11-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.

Resolution of ab initio shapes determined from small-angle scattering

PubMed Central

Tuukkanen, Anne T.; Kleywegt, Gerard J.; Svergun, Dmitri I.

2016-01-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models. PMID:27840683

Label-free imaging of the dynamics of cell-to-cell string-like structure bridging in the free-space by low-coherent quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka

2013-03-01

We succeeded in utilizing our low-coherent quantitative phase microscopy (LC-QPM) to achieve label-free and three-dimensional imaging of string-like structures bridging the free-space between live cells. In past studies, three dimensional morphology of the string-like structures between cells had been investigated by electron microscopies and fluorescence microscopies and these structures were called "membrane nanotubes" or "tunneling nanotubes." However, use of electron microscopy inevitably kills these cells and fluorescence microscopy is itself a potentially invasive method. To achieve noninvasive imaging of live cells, we applied our LC-QPM which is a reflection-type, phase resolved and full-field interference microscope employing a low-coherent light source. LC-QPM is able to visualize the three-dimensional morphology of live cells without labeling by means of low-coherence interferometry. The lateral (diffraction limit) and longitudinal (coherence-length) spatial resolution of LC-QPM were respectively 0.49 and 0.93 micrometers and the repeatability of the phase measurement was 0.02 radians (1.0 nm). We successfully obtained three-dimensional morphology of live cultured epithelial cells (cell type: HeLa, derived from cervix cancer) and were able to clearly observe the individual string-like structures interconnecting the cells. When we performed volumetric imaging, a 80 micrometer by 60 micrometer by 6.5 micrometer volume was scanned every 5.67 seconds and 70 frames of a three-dimensional movie were recorded for a duration of 397 seconds. Moreover, the optical phase images gave us detailed information about the three-dimensional morphology of the string-like structure at sub-wavelength resolution. We believe that our LC-QPM will be a useful tool for the study of three-dimensional morphology of live cells.

Three-dimensional high-resolution ultrasonic imaging of the eye

NASA Astrophysics Data System (ADS)

Silverman, Ronald H.; Lizzi, Frederick L.; Kalisz, Andrew; Coleman, D. J.

2000-04-01

Very high frequency (50 MHz) ultrasound provides spatial resolution on the order of 30 microns axially by 60 microns laterally. Our aim was to reconstruct the three-dimensional anatomy of the eye in the full detail permitted by this fine- scale transducer resolution. We scanned the eyes of human subjects and anesthetized rabbits in a sequence of parallel planes 50 microns apart. Within each scan plane, vectors were also spaced 50 microns apart. Radio-frequency data were digitized at a rate of 250 MHz or higher. A series of spectrum analysis and segmentation algorithms was applied to data acquired in each plane; the outputs of these procedures were used to produce color-coded 3-D representations of the sclera, iris and ciliary processes to enhance 3-D volume rendered presentation. We visualized the radial pattern of individual ciliary processes in humans and rabbits and the geodetic web of supporting connections between the ciliary processes and iris that exist only in the rabbit. By acquiring data such that adjacent vectors and planes are separated by less than the transducer's lateral resolution, we were able to visualize structures, such as the ciliary web, that had not been seen before in-vivo. Our techniques offer the possibility of high- precision imaging and measurement of anterior segment structures. This would be relevant in monitoring of glaucoma, tumors, foreign bodies and other clinical conditions.

Cornea and ocular lens visualized with three-dimensional confocal microscopy

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1992-08-01

This paper demonstrates the advantages of three-dimensional reconstruction of the cornea and the ocular crystalline lens by confocal microscopy and volume rendering computer techniques. The advantages of noninvasive observation of ocular structures in living, unstained, unfixed tissue include the following: the tissue is in a natural living state without the artifacts of fixation, mechanical sectioning, and staining; the three-dimensional structure can be observed from any view point and quantitatively analyzed; the dynamics of morphological changes can be studied; and the use of confocal microscopic observation results in a reduction of the number of animals required for ocular morphometric studies. The main advantage is that the dynamic morphology of ocular structures can be investigated in living ocular tissue. A laser scanning confocal microscope was used in the reflected light mode to obtain the two- dimensional images from the cornea and the ocular lens of a freshly enucleated rabbit eye. The light source was an argon ion laser with 488 nm wavelength. The microscope objective was a Leitz 25X, NA 0.6 water immersion lens. The 400 micron thick cornea was optically sectioned into 133, three micron sections. The semi-transparent cornea and the in-situ ocular lens was visualized as high resolution, high contrast two-dimensional images. The under sampling resulted in a three-dimensional visualization rendering in which the corneal thickness (z-axis) is compressed. The structures observed in the cornea include: superficial epithelial cells and their nuclei, basal epithelial cells and their `beaded' cell borders, basal lamina, nerve plexus, nerve fibers, free nerve endings in the basal epithelial cells, nuclei of stromal keratocytes, and endothelial cells. The structures observed in the in-situ ocular lens include: lens capsule, lens epithelial cells, and individual lens fibers.

High-resolution two-dimensional and three-dimensional modeling of wire grid polarizers and micropolarizer arrays

NASA Astrophysics Data System (ADS)

Vorobiev, Dmitry; Ninkov, Zoran

2017-11-01

Recent advances in photolithography allowed the fabrication of high-quality wire grid polarizers for the visible and near-infrared regimes. In turn, micropolarizer arrays (MPAs) based on wire grid polarizers have been developed and used to construct compact, versatile imaging polarimeters. However, the contrast and throughput of these polarimeters are significantly worse than one might expect based on the performance of large area wire grid polarizers or MPAs, alone. We investigate the parameters that affect the performance of wire grid polarizers and MPAs, using high-resolution two-dimensional and three-dimensional (3-D) finite-difference time-domain simulations. We pay special attention to numerical errors and other challenges that arise in models of these and other subwavelength optical devices. Our tests show that simulations of these structures in the visible and near-IR begin to converge numerically when the mesh size is smaller than ˜4 nm. The performance of wire grid polarizers is very sensitive to the shape, spacing, and conductivity of the metal wires. Using 3-D simulations of micropolarizer "superpixels," we directly study the cross talk due to diffraction at the edges of each micropolarizer, which decreases the contrast of MPAs to ˜200∶1.

Puzzle Imaging: Using Large-Scale Dimensionality Reduction Algorithms for Localization.

PubMed

Glaser, Joshua I; Zamft, Bradley M; Church, George M; Kording, Konrad P

2015-01-01

Current high-resolution imaging techniques require an intact sample that preserves spatial relationships. We here present a novel approach, "puzzle imaging," that allows imaging a spatially scrambled sample. This technique takes many spatially disordered samples, and then pieces them back together using local properties embedded within the sample. We show that puzzle imaging can efficiently produce high-resolution images using dimensionality reduction algorithms. We demonstrate the theoretical capabilities of puzzle imaging in three biological scenarios, showing that (1) relatively precise 3-dimensional brain imaging is possible; (2) the physical structure of a neural network can often be recovered based only on the neural connectivity matrix; and (3) a chemical map could be reproduced using bacteria with chemosensitive DNA and conjugative transfer. The ability to reconstruct scrambled images promises to enable imaging based on DNA sequencing of homogenized tissue samples.

Crystallized N-terminal domain of influenza virus matrix protein M1 and method of determining and using same

NASA Technical Reports Server (NTRS)

Luo, Ming (Inventor); Sha, Bingdong (Inventor)

2000-01-01

The matrix protein, M1, of influenza virus strain A/PR/8/34 has been purified from virions and crystallized. The crystals consist of a stable fragment (18 Kd) of the M1 protein. X-ray diffraction studies indicated that the crystals have a space group of P3.sub.t 21 or P3.sub.2 21. Vm calculations showed that there are two monomers in an asymmetric unit. A crystallized N-terminal domain of M1, wherein the N-terminal domain of M1 is crystallized such that the three dimensional structure of the crystallized N-terminal domain of M1 can be determined to a resolution of about 2.1 .ANG. or better, and wherein the three dimensional structure of the uncrystallized N-terminal domain of M1 cannot be determined to a resolution of about 2.1 .ANG. or better. A method of purifying M1 and a method of crystallizing M1. A method of using the three-dimensional crystal structure of M1 to screen for antiviral, influenza virus treating or preventing compounds. A method of using the three-dimensional crystal structure of M1 to screen for improved binding to or inhibition of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the manufacture of an inhibitor of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the screening of candidates for inhibition of influenza virus M1.

Spider-web inspired multi-resolution graphene tactile sensor.

PubMed

Liu, Lu; Huang, Yu; Li, Fengyu; Ma, Ying; Li, Wenbo; Su, Meng; Qian, Xin; Ren, Wanjie; Tang, Kanglai; Song, Yanlin

2018-05-08

Multi-dimensional accurate response and smooth signal transmission are critical challenges in the advancement of multi-resolution recognition and complex environment analysis. Inspired by the structure-activity relationship between discrepant microstructures of the spiral and radial threads in a spider web, we designed and printed graphene with porous and densely-packed microstructures to integrate into a multi-resolution graphene tactile sensor. The three-dimensional (3D) porous graphene structure performs multi-dimensional deformation responses. The laminar densely-packed graphene structure contributes excellent conductivity with flexible stability. The spider-web inspired printed pattern inherits orientational and locational kinesis tracking. The multi-structure construction with homo-graphene material can integrate discrepant electronic properties with remarkable flexibility, which will attract enormous attention for electronic skin, wearable devices and human-machine interactions.

Three-dimensional structure and ligand interactions of the low molecular weight protein tyrosine phosphatase from Campylobacter jejuni.

PubMed

Tolkatchev, Dmitri; Shaykhutdinov, Rustem; Xu, Ping; Plamondon, Josée; Watson, David C; Young, N Martin; Ni, Feng

2006-10-01

A putative low molecular weight protein tyrosine phosphatase (LMW-PTP) was identified in the genome sequence of the bacterial pathogen, Campylobacter jejuni. This novel gene, cj1258, has sequence homology with a distinctive class of phosphatases widely distributed among prokaryotes and eukaryotes. We report here the solution structure of Cj1258 established by high-resolution NMR spectroscopy using NOE-derived distance restraints, hydrogen bond data, and torsion angle restraints. The three-dimensional structure consists of a central four-stranded parallel beta-sheet flanked by five alpha-helices, revealing an overall structural topology similar to those of the eukaryotic LMW-PTPs, such as human HCPTP-A, bovine BPTP, and Saccharomyces cerevisiae LTP1, and to those of the bacterial LMW-PTPs MPtpA from Mycobacterium tuberculosis and YwlE from Bacillus subtilis. The active site of the enzyme is flexible in solution and readily adapts to the binding of ligands, such as the phosphate ion. An NMR-based screen was carried out against a number of potential inhibitors and activators, including phosphonomethylphenylalanine, derivatives of the cinnamic acid, 2-hydroxy-5-nitrobenzaldehyde, cinnamaldehyde, adenine, and hypoxanthine. Despite its bacterial origin, both the three-dimensional structure and ligand-binding properties of Cj1258 suggest that this novel phosphatase may have functional roles close to those of eukaryotic and mammalian tyrosine phosphatases. The three-dimensional structure along with mapping of small-molecule binding will be discussed in the context of developing high-affinity inhibitors of this novel LMW-PTP.

Scanning photoelectron microscope for nanoscale three-dimensional spatial-resolved electron spectroscopy for chemical analysis.

PubMed

Horiba, K; Nakamura, Y; Nagamura, N; Toyoda, S; Kumigashira, H; Oshima, M; Amemiya, K; Senba, Y; Ohashi, H

2011-11-01

In order to achieve nondestructive observation of the three-dimensional spatially resolved electronic structure of solids, we have developed a scanning photoelectron microscope system with the capability of depth profiling in electron spectroscopy for chemical analysis (ESCA). We call this system 3D nano-ESCA. For focusing the x-ray, a Fresnel zone plate with a diameter of 200 μm and an outermost zone width of 35 nm is used. In order to obtain the angular dependence of the photoelectron spectra for the depth-profile analysis without rotating the sample, we adopted a modified VG Scienta R3000 analyzer with an acceptance angle of 60° as a high-resolution angle-resolved electron spectrometer. The system has been installed at the University-of-Tokyo Materials Science Outstation beamline, BL07LSU, at SPring-8. From the results of the line-scan profiles of the poly-Si/high-k gate patterns, we achieved a total spatial resolution better than 70 nm. The capability of our system for pinpoint depth-profile analysis and high-resolution chemical state analysis is demonstrated. © 2011 American Institute of Physics

Biological imaging by soft X-ray diffraction microscopy

NASA Astrophysics Data System (ADS)

Shapiro, David

We have developed a microscope for soft x-ray diffraction imaging of dry or frozen hydrated biological specimens. This lensless imaging system does not suffer from the resolution or specimen thickness limitations that other short wavelength microscopes experience. The microscope, currently situated at beamline 9.0.1 of the Advanced Light Source, can collect diffraction data to 12 nm resolution with 750 eV photons and 17 nm resolution with 520 eV photons. The specimen can be rotated with a precision goniometer through an angle of 160 degrees allowing for the collection of nearly complete three-dimensional diffraction data. The microscope is fully computer controlled through a graphical user interface and a scripting language automates the collection of both two-dimensional and three-dimensional data. Diffraction data from a freeze-dried dwarf yeast cell, Saccharomyces cerevisiae carrying the CLN3-1 mutation, was collected to 12 run resolution from 8 specimen orientations spanning a total rotation of 8 degrees. The diffraction data was phased using the difference map algorithm and the reconstructions provide real space images of the cell to 30 nm resolution from each of the orientations. The agreement of the different reconstructions provides confidence in the recovered, and previously unknown, structure and indicates the three dimensionality of the cell. This work represents the first imaging of the natural complex refractive contrast from a whole unstained cell by the diffraction microscopy method and has achieved a resolution superior to lens based x-ray tomographic reconstructions of similar specimens. Studies of the effects of exposure to large radiation doses were also carried out. It was determined that the freeze-dried cell suffers from an initial collapse, which is followed by a uniform, but slow, shrinkage. This structural damage to the cell is not accompanied by a diminished ability to see small features in the specimen. Preliminary measurements on frozen-hydrated yeast indicate that the frozen specimens do not exhibit these changes even with doses as high as 5 x 109 Gray.

Three-dimensional nanoscale imaging by plasmonic Brownian microscopy

NASA Astrophysics Data System (ADS)

Labno, Anna; Gladden, Christopher; Kim, Jeongmin; Lu, Dylan; Yin, Xiaobo; Wang, Yuan; Liu, Zhaowei; Zhang, Xiang

2017-12-01

Three-dimensional (3D) imaging at the nanoscale is a key to understanding of nanomaterials and complex systems. While scanning probe microscopy (SPM) has been the workhorse of nanoscale metrology, its slow scanning speed by a single probe tip can limit the application of SPM to wide-field imaging of 3D complex nanostructures. Both electron microscopy and optical tomography allow 3D imaging, but are limited to the use in vacuum environment due to electron scattering and to optical resolution in micron scales, respectively. Here we demonstrate plasmonic Brownian microscopy (PBM) as a way to improve the imaging speed of SPM. Unlike photonic force microscopy where a single trapped particle is used for a serial scanning, PBM utilizes a massive number of plasmonic nanoparticles (NPs) under Brownian diffusion in solution to scan in parallel around the unlabeled sample object. The motion of NPs under an evanescent field is three-dimensionally localized to reconstruct the super-resolution topology of 3D dielectric objects. Our method allows high throughput imaging of complex 3D structures over a large field of view, even with internal structures such as cavities that cannot be accessed by conventional mechanical tips in SPM.

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography.

PubMed

Li, Qiong; Gluch, Jürgen; Krüger, Peter; Gall, Martin; Neinhuis, Christoph; Zschech, Ehrenfried

2016-10-14

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have a direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. Copyright © 2016 Elsevier Inc. All rights reserved.

Three-dimensional bio-printing.

PubMed

Gu, Qi; Hao, Jie; Lu, YangJie; Wang, Liu; Wallace, Gordon G; Zhou, Qi

2015-05-01

Three-dimensional (3D) printing technology has been widely used in various manufacturing operations including automotive, defence and space industries. 3D printing has the advantages of personalization, flexibility and high resolution, and is therefore becoming increasingly visible in the high-tech fields. Three-dimensional bio-printing technology also holds promise for future use in medical applications. At present 3D bio-printing is mainly used for simulating and reconstructing some hard tissues or for preparing drug-delivery systems in the medical area. The fabrication of 3D structures with living cells and bioactive moieties spatially distributed throughout will be realisable. Fabrication of complex tissues and organs is still at the exploratory stage. This review summarize the development of 3D bio-printing and its potential in medical applications, as well as discussing the current challenges faced by 3D bio-printing.

Three-dimensional structure of Erwinia carotovora L-asparaginase

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

Kislitsyn, Yu. A.; Kravchenko, O. V.; Nikonov, S. V.

2006-10-15

Three-dimensional structure of Erwinia carotovora L-asparaginase, which has antitumor activity and is used for the treatment of acute lymphoblastic leukemia, was solved at 3 A resolution and refined to R{sub cryst} = 20% and R{sub free} = 28%. Crystals of recombinant Erwinia carotovora L-asparaginase were grown by the hanging-drop vapor-diffusion method from protein solutions in a HEPES buffer (pH 6.5) and PEG MME 5000 solutions in a cacodylate buffer (pH 6.5) as the precipitant. Three-dimensional X-ray diffraction data were collected up to 3 A resolution from one crystal at room temperature. The structure was solved by the molecular replacement methodmore » using the coordinates of Erwinia chrysanthemi L-asparaginase as the starting model. The coordinates refined with the use of the CNS program package were deposited in the Protein Data Bank (PDB code 1ZCF)« less

Retinal Structure of Birds of Prey Revealed by Ultra-High Resolution Spectral-Domain Optical Coherence Tomography

PubMed Central

Ruggeri, Marco; Major, James C.; McKeown, Craig; Knighton, Robert W.; Puliafito, Carmen A.

2010-01-01

Purpose. To reveal three-dimensional (3-D) information about the retinal structures of birds of prey in vivo. Methods. An ultra-high resolution spectral-domain optical coherence tomography (SD-OCT) system was built for in vivo imaging of retinas of birds of prey. The calibrated imaging depth and axial resolution of the system were 3.1 mm and 2.8 μm (in tissue), respectively. 3-D segmentation was performed for calculation of the retinal nerve fiber layer (RNFL) map. Results. High-resolution OCT images were obtained of the retinas of four species of birds of prey: two diurnal hawks (Buteo platypterus and Buteo brachyurus) and two nocturnal owls (Bubo virginianus and Strix varia). These images showed the detailed retinal anatomy, including the retinal layers and the structure of the deep and shallow foveae. The calculated thickness map showed the RNFL distribution. Traumatic injury to one bird's retina was also successfully imaged. Conclusions. Ultra-high resolution SD-OCT provides unprecedented high-quality 2-D and 3-D in vivo visualization of the retinal structures of birds of prey. SD-OCT is a powerful imaging tool for vision research in birds of prey. PMID:20554605

Fabrication of micromechanical and microoptical systems by two-photon polymerization

NASA Astrophysics Data System (ADS)

Reinhardt, Carsten; Ovsianikov, A.; Passinger, Sven; Chichkov, Boris N.

2007-01-01

The recently developed two-photon polymerisation technique is used for the fabrication of two- and three-dimensional structures in photosensitive inorganic-organic hybrid material (ORMOCER), in SU8 , and in positive tone resist with resolutions down to 100nm. In this contribution we present applications of this powerful technology for the realization of micromechanical systems and microoptical components. We will demonstrate results on the fabrication of complex movable three-dimensional micromechanical systems and microfluidic components which cannot be realized by other technologies. This approach of structuring photosensitive materials also provides unique possibilities for the fabrication of different microoptical components such as arbitrary shaped microlenses, microprisms, and 3D-photonic crystals with high optical quality.

Quantitative 3D reconstruction of airway and pulmonary vascular trees using HRCT

NASA Astrophysics Data System (ADS)

Wood, Susan A.; Hoford, John D.; Hoffman, Eric A.; Zerhouni, Elias A.; Mitzner, Wayne A.

1993-07-01

Accurate quantitative measurements of airway and vascular dimensions are essential to evaluate function in the normal and diseased lung. In this report, a novel method is described for three-dimensional extraction and analysis of pulmonary tree structures using data from High Resolution Computed Tomography (HRCT). Serially scanned two-dimensional slices of the lower left lobe of isolated dog lungs were stacked to create a volume of data. Airway and vascular trees were three-dimensionally extracted using a three dimensional seeded region growing algorithm based on difference in CT number between wall and lumen. To obtain quantitative data, we reduced each tree to its central axis. From the central axis, branch length is measured as the distance between two successive branch points, branch angle is measured as the angle produced by two daughter branches, and cross sectional area is measured from a plane perpendicular to the central axis point. Data derived from these methods can be used to localize and quantify structural differences both during changing physiologic conditions and in pathologic lungs.

High-resolution three-dimensional imaging and analysis of rock falls in Yosemite valley, California

USGS Publications Warehouse

Stock, Gregory M.; Bawden, G.W.; Green, J.K.; Hanson, E.; Downing, G.; Collins, B.D.; Bond, S.; Leslar, M.

2011-01-01

We present quantitative analyses of recent large rock falls in Yosemite Valley, California, using integrated high-resolution imaging techniques. Rock falls commonly occur from the glacially sculpted granitic walls of Yosemite Valley, modifying this iconic landscape but also posing signifi cant potential hazards and risks. Two large rock falls occurred from the cliff beneath Glacier Point in eastern Yosemite Valley on 7 and 8 October 2008, causing minor injuries and damaging structures in a developed area. We used a combination of gigapixel photography, airborne laser scanning (ALS) data, and ground-based terrestrial laser scanning (TLS) data to characterize the rock-fall detachment surface and adjacent cliff area, quantify the rock-fall volume, evaluate the geologic structure that contributed to failure, and assess the likely failure mode. We merged the ALS and TLS data to resolve the complex, vertical to overhanging topography of the Glacier Point area in three dimensions, and integrated these data with gigapixel photographs to fully image the cliff face in high resolution. Three-dimensional analysis of repeat TLS data reveals that the cumulative failure consisted of a near-planar rock slab with a maximum length of 69.0 m, a mean thickness of 2.1 m, a detachment surface area of 2750 m2, and a volume of 5663 ?? 36 m3. Failure occurred along a surfaceparallel, vertically oriented sheeting joint in a clear example of granitic exfoliation. Stress concentration at crack tips likely propagated fractures through the partially attached slab, leading to failure. Our results demonstrate the utility of high-resolution imaging techniques for quantifying far-range (>1 km) rock falls occurring from the largely inaccessible, vertical rock faces of Yosemite Valley, and for providing highly accurate and precise data needed for rock-fall hazard assessment. ?? 2011 Geological Society of America.

A three-dimensional stereotaxic MRI brain atlas of the cichlid fish Oreochromis mossambicus.

PubMed

Simões, José M; Teles, Magda C; Oliveira, Rui F; Van der Linden, Annemie; Verhoye, Marleen

2012-01-01

The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system.

High Resolution Three-Dimensional MR Imaging of the Skull Base: Compartments, Boundaries, and Critical Structures.

PubMed

Blitz, Ari Meir; Aygun, Nafi; Herzka, Daniel A; Ishii, Masaru; Gallia, Gary L

2017-01-01

High-resolution 3D MRI of the skull base allows for a more detailed and accurate assessment of normal anatomic structures as well as the location and extent of skull base pathologies than has previously been possible. This article describes the techniques employed for high-resolution skull base MRI including pre- and post-contrast constructive interference in the steady state (CISS) imaging and their utility for evaluation of the many small structures of the skull base, focusing on those regions and concepts most pertinent to localization of cranial nerve palsies and in providing pre-operative guidance and post-operative assessment. The concept of skull base compartments as a means of conceptualizing the various layers of the skull base and their importance in assessment of masses of the skull base is discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Unravelling earth flow dynamics with 3-D time series derived from UAV-SfM models

NASA Astrophysics Data System (ADS)

Clapuyt, François; Vanacker, Veerle; Schlunegger, Fritz; Van Oost, Kristof

2017-12-01

Accurately assessing geo-hazards and quantifying landslide risks in mountainous environments are gaining importance in the context of the ongoing global warming. For an in-depth understanding of slope failure mechanisms, accurate monitoring of the mass movement topography at high spatial and temporal resolutions remains essential. The choice of the acquisition framework for high-resolution topographic reconstructions will mainly result from the trade-off between the spatial resolution needed and the extent of the study area. Recent advances in the development of unmanned aerial vehicle (UAV)-based image acquisition combined with the structure-from-motion (SfM) algorithm for three-dimensional (3-D) reconstruction make the UAV-SfM framework a competitive alternative to other high-resolution topographic techniques. In this study, we aim at gaining in-depth knowledge of the Schimbrig earthflow located in the foothills of the Central Swiss Alps by monitoring ground surface displacements at very high spatial and temporal resolution using the efficiency of the UAV-SfM framework. We produced distinct topographic datasets for three acquisition dates between 2013 and 2015 in order to conduct a comprehensive 3-D analysis of the landslide. Therefore, we computed (1) the sediment budget of the hillslope, and (2) the horizontal and (3) the three-dimensional surface displacements. The multitemporal UAV-SfM based topographic reconstructions allowed us to quantify rates of sediment redistribution and surface movements. Our data show that the Schimbrig earthflow is very active, with mean annual horizontal displacement ranging between 6 and 9 m. Combination and careful interpretation of high-resolution topographic analyses reveal the internal mechanisms of the earthflow and its complex rotational structure. In addition to variation in horizontal surface movements through time, we interestingly showed that the configuration of nested rotational units changes through time. Although there are major changes in the internal structure of the earthflow in the 2013-2015 period, the sediment budget of the drainage basin is nearly in equilibrium. As a consequence, our data show that the time lag between sediment mobilization by landslides and enhanced sediment fluxes in the river network can be considerable.

Uncertainty in peat volume and soil carbon estimated using ground-penetrating radar and probing

Treesearch

Andrew D. Parsekian; Lee Slater; Dimitrios Ntarlagiannis; James Nolan; Stephen D. Sebestyen; Randall K. Kolka; Paul J. Hanson

2012-01-01

Estimating soil C stock in a peatland is highly dependent on accurate measurement of the peat volume. In this study, we evaluated the uncertainty in calculations of peat volume using high-resolution data to resolve the three-dimensional structure of a peat basin based on both direct (push probes) and indirect geophysical (ground-penetrating radar) measurements. We...

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

PubMed

Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

2017-09-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

High-resolution x-ray tomography using laboratory sources

NASA Astrophysics Data System (ADS)

Tkachuk, Andrei; Feser, Michael; Cui, Hongtao; Duewer, Fred; Chang, Hauyee; Yun, Wenbing

2006-08-01

X-ray computed tomography (XCT) is a powerful nondestructive 3D imaging technique, which enables the visualization of the three dimensional structure of complex, optically opaque samples. High resolution XCT using Fresnel zone plate lenses has been confined in the past to synchrotron radiation centers due to the need for a bright and intense source of x-rays. This confinement severely limits the availability and accessibility of x-ray microscopes and the wide proliferation of this methodology. We are describing a sub-50nm resolution XCT system operating at 8 keV in absorption and Zernike phase contrast mode based on a commercially available laboratory x-ray source. The system utilizes high-efficiency Fresnel zone plates with an outermost zone width of 35 nm and 700 nm structure height resulting in a current spatial resolution better than 50 nm. In addition to the technical description of the system and specifications, we present application examples in the semiconductor field.

High resolution three-dimensional photoacoustic imaging of human finger joints in vivo

NASA Astrophysics Data System (ADS)

Xi, Lei; Jiang, Huabei

2015-08-01

We present a method for noninvasively imaging the hand joints using a three-dimensional (3D) photoacoustic imaging (PAI) system. This 3D PAI system utilizes cylindrical scanning in data collection and virtual-detector concept in image reconstruction. The maximum lateral and axial resolutions of the PAI system are 70 μm and 240 μm. The cross-sectional photoacoustic images of a healthy joint clearly exhibited major internal structures including phalanx and tendons, which are not available from the current photoacoustic imaging methods. The in vivo PAI results obtained are comparable with the corresponding 3.0 T MRI images of the finger joint. This study suggests that the proposed method has the potential to be used in early detection of joint diseases such as osteoarthritis.

Data center thermal management

DOEpatents

Hamann, Hendrik F.; Li, Hongfei

2016-02-09

Historical high-spatial-resolution temperature data and dynamic temperature sensor measurement data may be used to predict temperature. A first formulation may be derived based on the historical high-spatial-resolution temperature data for determining a temperature at any point in 3-dimensional space. The dynamic temperature sensor measurement data may be calibrated based on the historical high-spatial-resolution temperature data at a corresponding historical time. Sensor temperature data at a plurality of sensor locations may be predicted for a future time based on the calibrated dynamic temperature sensor measurement data. A three-dimensional temperature spatial distribution associated with the future time may be generated based on the forecasted sensor temperature data and the first formulation. The three-dimensional temperature spatial distribution associated with the future time may be projected to a two-dimensional temperature distribution, and temperature in the future time for a selected space location may be forecasted dynamically based on said two-dimensional temperature distribution.

Three-Dimensional Photoacoustic Endoscopic Imaging of the Rabbit Esophagus

PubMed Central

Yao, Junjie; Chen, Ruimin; Zhou, Qifa; Shung, K. Kirk; Wang, Lihong V.

2015-01-01

We report photoacoustic and ultrasonic endoscopic images of two intact rabbit esophagi. To investigate the esophageal lumen structure and microvasculature, we performed in vivo and ex vivo imaging studies using a 3.8-mm diameter photoacoustic endoscope and correlated the images with histology. Several interesting anatomic structures were newly found in both the in vivo and ex vivo images, which demonstrates the potential clinical utility of this endoscopic imaging modality. In the ex vivo imaging experiment, we acquired high-resolution motion-artifact-free three-dimensional photoacoustic images of the vasculatures distributed in the walls of the esophagi and extending to the neighboring mediastinal regions. Blood vessels with apparent diameters as small as 190 μm were resolved. Moreover, by taking advantage of the dual-mode high-resolution photoacoustic and ultrasound endoscopy, we could better identify and characterize the anatomic structures of the esophageal lumen, such as the mucosal and submucosal layers in the esophageal wall, and an esophageal branch of the thoracic aorta. In this paper, we present the first photoacoustic images showing the vasculature of a vertebrate esophagus and discuss the potential clinical applications and future development of photoacoustic endoscopy. PMID:25874640

Three-dimensional photoacoustic endoscopic imaging of the rabbit esophagus.

PubMed

Yang, Joon Mo; Favazza, Christopher; Yao, Junjie; Chen, Ruimin; Zhou, Qifa; Shung, K Kirk; Wang, Lihong V

2015-01-01

We report photoacoustic and ultrasonic endoscopic images of two intact rabbit esophagi. To investigate the esophageal lumen structure and microvasculature, we performed in vivo and ex vivo imaging studies using a 3.8-mm diameter photoacoustic endoscope and correlated the images with histology. Several interesting anatomic structures were newly found in both the in vivo and ex vivo images, which demonstrates the potential clinical utility of this endoscopic imaging modality. In the ex vivo imaging experiment, we acquired high-resolution motion-artifact-free three-dimensional photoacoustic images of the vasculatures distributed in the walls of the esophagi and extending to the neighboring mediastinal regions. Blood vessels with apparent diameters as small as 190 μm were resolved. Moreover, by taking advantage of the dual-mode high-resolution photoacoustic and ultrasound endoscopy, we could better identify and characterize the anatomic structures of the esophageal lumen, such as the mucosal and submucosal layers in the esophageal wall, and an esophageal branch of the thoracic aorta. In this paper, we present the first photoacoustic images showing the vasculature of a vertebrate esophagus and discuss the potential clinical applications and future development of photoacoustic endoscopy.

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types.

PubMed

van Unen, Vincent; Höllt, Thomas; Pezzotti, Nicola; Li, Na; Reinders, Marcel J T; Eisemann, Elmar; Koning, Frits; Vilanova, Anna; Lelieveldt, Boudewijn P F

2017-11-23

Mass cytometry allows high-resolution dissection of the cellular composition of the immune system. However, the high-dimensionality, large size, and non-linear structure of the data poses considerable challenges for the data analysis. In particular, dimensionality reduction-based techniques like t-SNE offer single-cell resolution but are limited in the number of cells that can be analyzed. Here we introduce Hierarchical Stochastic Neighbor Embedding (HSNE) for the analysis of mass cytometry data sets. HSNE constructs a hierarchy of non-linear similarities that can be interactively explored with a stepwise increase in detail up to the single-cell level. We apply HSNE to a study on gastrointestinal disorders and three other available mass cytometry data sets. We find that HSNE efficiently replicates previous observations and identifies rare cell populations that were previously missed due to downsampling. Thus, HSNE removes the scalability limit of conventional t-SNE analysis, a feature that makes it highly suitable for the analysis of massive high-dimensional data sets.

Puzzle Imaging: Using Large-Scale Dimensionality Reduction Algorithms for Localization

PubMed Central

Glaser, Joshua I.; Zamft, Bradley M.; Church, George M.; Kording, Konrad P.

2015-01-01

Current high-resolution imaging techniques require an intact sample that preserves spatial relationships. We here present a novel approach, “puzzle imaging,” that allows imaging a spatially scrambled sample. This technique takes many spatially disordered samples, and then pieces them back together using local properties embedded within the sample. We show that puzzle imaging can efficiently produce high-resolution images using dimensionality reduction algorithms. We demonstrate the theoretical capabilities of puzzle imaging in three biological scenarios, showing that (1) relatively precise 3-dimensional brain imaging is possible; (2) the physical structure of a neural network can often be recovered based only on the neural connectivity matrix; and (3) a chemical map could be reproduced using bacteria with chemosensitive DNA and conjugative transfer. The ability to reconstruct scrambled images promises to enable imaging based on DNA sequencing of homogenized tissue samples. PMID:26192446

3D printing of high-resolution PLA-based structures by hybrid electrohydrodynamic and fused deposition modeling techniques

NASA Astrophysics Data System (ADS)

Zhang, Bin; Seong, Baekhoon; Nguyen, VuDat; Byun, Doyoung

2016-02-01

Recently, the three-dimensional (3D) printing technique has received much attention for shape forming and manufacturing. The fused deposition modeling (FDM) printer is one of the various 3D printers available and has become widely used due to its simplicity, low-cost, and easy operation. However, the FDM technique has a limitation whereby its patterning resolution is too low at around 200 μm. In this paper, we first present a hybrid mechanism of electrohydrodynamic jet printing with the FDM technique, which we name E-FDM. We then develop a novel high-resolution 3D printer based on the E-FDM process. To determine the optimal condition for structuring, we also investigated the effect of several printing parameters, such as temperature, applied voltage, working height, printing speed, flow-rate, and acceleration on the patterning results. This method was capable of fabricating both high resolution 2D and 3D structures with the use of polylactic acid (PLA). PLA has been used to fabricate scaffold structures for tissue engineering, which has different hierarchical structure sizes. The fabrication speed was up to 40 mm/s and the pattern resolution could be improved to 10 μm.

Isotropic-resolution linear-array-based photoacoustic computed tomography through inverse Radon transform

NASA Astrophysics Data System (ADS)

Li, Guo; Xia, Jun; Li, Lei; Wang, Lidai; Wang, Lihong V.

2015-03-01

Linear transducer arrays are readily available for ultrasonic detection in photoacoustic computed tomography. They offer low cost, hand-held convenience, and conventional ultrasonic imaging. However, the elevational resolution of linear transducer arrays, which is usually determined by the weak focus of the cylindrical acoustic lens, is about one order of magnitude worse than the in-plane axial and lateral spatial resolutions. Therefore, conventional linear scanning along the elevational direction cannot provide high-quality three-dimensional photoacoustic images due to the anisotropic spatial resolutions. Here we propose an innovative method to achieve isotropic resolutions for three-dimensional photoacoustic images through combined linear and rotational scanning. In each scan step, we first elevationally scan the linear transducer array, and then rotate the linear transducer array along its center in small steps, and scan again until 180 degrees have been covered. To reconstruct isotropic three-dimensional images from the multiple-directional scanning dataset, we use the standard inverse Radon transform originating from X-ray CT. We acquired a three-dimensional microsphere phantom image through the inverse Radon transform method and compared it with a single-elevational-scan three-dimensional image. The comparison shows that our method improves the elevational resolution by up to one order of magnitude, approaching the in-plane lateral-direction resolution. In vivo rat images were also acquired.

Method of fabricating free-form, high-aspect ratio components for high-current, high-speed microelectrics

DOEpatents

Maxwell, James L; Rose, Chris R; Black, Marcie R; Springer, Robert W

2014-03-11

Microelectronic structures and devices, and method of fabricating a three-dimensional microelectronic structure is provided, comprising passing a first precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures to enhance formation of a first portion of said three-dimensional microelectronic structure; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said first portion of a selected three-dimensional microelectronic structure is formed from said first precursor material; positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs; passing a second precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures whereby a second portion of said three-dimensional microelectronic structure formation is enhanced; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said second portion of a selected three-dimensional microelectronic structure is formed from said second precursor material; and, positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs.

Novel 16-channel receive coil array for accelerated upper airway MRI at 3 Tesla.

PubMed

Kim, Yoon-Chul; Hayes, Cecil E; Narayanan, Shrikanth S; Nayak, Krishna S

2011-06-01

Upper airway MRI can provide a noninvasive assessment of speech and swallowing disorders and sleep apnea. Recent work has demonstrated the value of high-resolution three-dimensional imaging and dynamic two-dimensional imaging and the importance of further improvements in spatio-temporal resolution. The purpose of the study was to describe a novel 16-channel 3 Tesla receive coil that is highly sensitive to the human upper airway and investigate the performance of accelerated upper airway MRI with the coil. In three-dimensional imaging of the upper airway during static posture, 6-fold acceleration is demonstrated using parallel imaging, potentially leading to capturing a whole three-dimensional vocal tract with 1.25 mm isotropic resolution within 9 sec of sustained sound production. Midsagittal spiral parallel imaging of vocal tract dynamics during natural speech production is demonstrated with 2 × 2 mm(2) in-plane spatial and 84 ms temporal resolution. Copyright © 2010 Wiley-Liss, Inc.

Deep and high-resolution three-dimensional tracking of single particles using nonlinear and multiplexed illumination

NASA Astrophysics Data System (ADS)

Perillo, Evan P.; Liu, Yen-Liang; Huynh, Khang; Liu, Cong; Chou, Chao-Kai; Hung, Mien-Chie; Yeh, Hsin-Chih; Dunn, Andrew K.

2015-07-01

Molecular trafficking within cells, tissues and engineered three-dimensional multicellular models is critical to the understanding of the development and treatment of various diseases including cancer. However, current tracking methods are either confined to two dimensions or limited to an interrogation depth of ~15 μm. Here we present a three-dimensional tracking method capable of quantifying rapid molecular transport dynamics in highly scattering environments at depths up to 200 μm. The system has a response time of 1 ms with a temporal resolution down to 50 μs in high signal-to-noise conditions, and a spatial localization precision as good as 35 nm. Built on spatiotemporally multiplexed two-photon excitation, this approach requires only one detector for three-dimensional particle tracking and allows for two-photon, multicolour imaging. Here we demonstrate three-dimensional tracking of epidermal growth factor receptor complexes at a depth of ~100 μm in tumour spheroids.

X-ray scattering data and structural genomics

NASA Astrophysics Data System (ADS)

Doniach, Sebastian

2003-03-01

High throughput structural genomics has the ambitious goal of determining the structure of all, or a very large number of protein folds using the high-resolution techniques of protein crystallography and NMR. However, the program is facing significant bottlenecks in reaching this goal, which include problems of protein expression and crystallization. In this talk, some preliminary results on how the low-resolution technique of small-angle X-ray solution scattering (SAXS) can help ameliorate some of these bottlenecks will be presented. One of the most significant bottlenecks arises from the difficulty of crystallizing integral membrane proteins, where only a handful of structures are available compared to thousands of structures for soluble proteins. By 3-dimensional reconstruction from SAXS data, the size and shape of detergent-solubilized integral membrane proteins can be characterized. This information can then be used to classify membrane proteins which constitute some 25% of all genomes. SAXS may also be used to study the dependence of interparticle interference scattering on solvent conditions so that regions of the protein solution phase diagram which favor crystallization can be elucidated. As a further application, SAXS may be used to provide physical constraints on computational methods for protein structure prediction based on primary sequence information. This in turn can help in identifying structural homologs of a given protein, which can then give clues to its function. D. Walther, F. Cohen and S. Doniach. "Reconstruction of low resolution three-dimensional density maps from one-dimensional small angle x-ray scattering data for biomolecules." J. Appl. Cryst. 33(2):350-363 (2000). Protein structure prediction constrained by solution X-ray scattering data and structural homology identification Zheng WJ, Doniach S JOURNAL OF MOLECULAR BIOLOGY , v. 316(#1) pp. 173-187 FEB 8, 2002

Intact Imaging of Human Heart Structure Using X-ray Phase-Contrast Tomography.

PubMed

Kaneko, Yukihiro; Shinohara, Gen; Hoshino, Masato; Morishita, Hiroyuki; Morita, Kiyozo; Oshima, Yoshihiro; Takahashi, Masashi; Yagi, Naoto; Okita, Yutaka; Tsukube, Takuro

2017-02-01

Structural examination of human heart specimens at the microscopic level is a prerequisite for understanding congenital heart diseases. It is desirable not to destroy or alter the properties of such specimens because of their scarcity. However, many of the currently available imaging techniques either destroy the specimen through sectioning or alter the chemical and mechanical properties of the specimen through staining and contrast agent injection. As a result, subsequent studies may not be possible. X-ray phase-contrast tomography is an imaging modality for biological soft tissues that does not destroy or alter the properties of the specimen. The feasibility of X-ray phase-contrast tomography for the structural examination of heart specimens was tested using infantile and fetal heart specimens without congenital diseases. X-ray phase-contrast tomography was carried out at the SPring-8 synchrotron radiation facility using the Talbot grating interferometer at the bending magnet beamline BL20B2 to visualize the structure of five non-pretreated whole heart specimens obtained by autopsy. High-resolution, three-dimensional images were obtained for all specimens. The images clearly showed the myocardial structure, coronary vessels, and conduction bundle. X-ray phase-contrast tomography allows high-resolution, three-dimensional imaging of human heart specimens. Intact imaging using X-ray phase-contrast tomography can contribute to further structural investigation of heart specimens with congenital heart diseases.

Intracardiac echocardiography: use during transcatheter device closure of a patent ductus arteriosus in a dog.

PubMed

Chetboul, V; Damoiseaux, C; Behr, L; Morlet, A; Moise, N S; Gouni, V; Lavennes, M; Pouchelon, J-L; Laborde, F; Borenstein, N

2017-06-01

Intracardiac echocardiography (ICE) is used in humans for percutaneous interventional procedures, such as transcatheter device closures. Intracardiac echocardiography provides high-resolution imaging of cardiac structures with two-dimensional, M-mode, Doppler, and also three-dimensional modalities. The present report describes application of ICE during transcatheter occlusion of patent ductus arteriosus using a canine ductal occluder in a dog for which transesophageal echocardiography could not provide an optimal acoustic window. Copyright © 2017 Elsevier B.V. All rights reserved.

Nonlinear structured-illumination enhanced temporal focusing multiphoton excitation microscopy with a digital micromirror device.

PubMed

Cheng, Li-Chung; Lien, Chi-Hsiang; Da Sie, Yong; Hu, Yvonne Yuling; Lin, Chun-Yu; Chien, Fan-Ching; Xu, Chris; Dong, Chen Yuan; Chen, Shean-Jen

2014-08-01

In this study, the light diffraction of temporal focusing multiphoton excitation microscopy (TFMPEM) and the excitation patterning of nonlinear structured-illumination microscopy (NSIM) can be simultaneously and accurately implemented via a single high-resolution digital micromirror device. The lateral and axial spatial resolutions of the TFMPEM are remarkably improved through the second-order NSIM and projected structured light, respectively. The experimental results demonstrate that the lateral and axial resolutions are enhanced from 397 nm to 168 nm (2.4-fold) and from 2.33 μm to 1.22 μm (1.9-fold), respectively, in full width at the half maximum. Furthermore, a three-dimensionally rendered image of a cytoskeleton cell featuring ~25 nm microtubules is improved, with other microtubules at a distance near the lateral resolution of 168 nm also able to be distinguished.

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography

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

Li, Qiong; Gluch, Jürgen; Krüger, Peter

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have amore » direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. - Highlights: • The unstained whole pine pollen was visualized by high-resolution laboratory-based HXRM for the first time. • The comparison study of pollen grains by LM, SEM and high-resolution laboratory-based HXRM. • Phase contrast imaging provides significantly higher contrast of the raw images compared to absorption contrast imaging. • Surface and internal structure of the pine pollen including exine, intine and cellular structures are clearly visualized. • 3D volume data of unstained whole pollen grains are acquired and the specific volumes of the different layer are calculated.« less

Characterization of a detector chain using a FPGA-based time-to-digital converter to reconstruct the three-dimensional coordinates of single particles at high flux

NASA Astrophysics Data System (ADS)

Nogrette, F.; Heurteau, D.; Chang, R.; Bouton, Q.; Westbrook, C. I.; Sellem, R.; Clément, D.

2015-11-01

We report on the development of a novel FPGA-based time-to-digital converter and its implementation in a detection chain that records the coordinates of single particles along three dimensions. The detector is composed of micro-channel plates mounted on top of a cross delay line and connected to fast electronics. We demonstrate continuous recording of the timing signals from the cross delay line at rates up to 4.1 × 106 s-1 and three-dimensional reconstruction of the coordinates up to 3.2 × 106 particles per second. From the imaging of a calibrated structure we measure the in-plane resolution of the detector to be 140(20) μm at a flux of 3 × 105 particles per second. In addition, we analyze a method to estimate the resolution without placing any structure under vacuum, a significant practical improvement. While we use UV photons here, the results of this work apply to the detection of other kinds of particles.

Research on the development of space target detecting system and three-dimensional reconstruction technology

NASA Astrophysics Data System (ADS)

Li, Dong; Wei, Zhen; Song, Dawei; Sun, Wenfeng; Fan, Xiaoyan

2016-11-01

With the development of space technology, the number of spacecrafts and debris are increasing year by year. The demand for detecting and identification of spacecraft is growing strongly, which provides support to the cataloguing, crash warning and protection of aerospace vehicles. The majority of existing approaches for three-dimensional reconstruction is scattering centres correlation, which is based on the radar high resolution range profile (HRRP). This paper proposes a novel method to reconstruct the threedimensional scattering centre structure of target from a sequence of radar ISAR images, which mainly consists of three steps. First is the azimuth scaling of consecutive ISAR images based on fractional Fourier transform (FrFT). The later is the extraction of scattering centres and matching between adjacent ISAR images using grid method. Finally, according to the coordinate matrix of scattering centres, the three-dimensional scattering centre structure is reconstructed using improved factorization method. The three-dimensional structure is featured with stable and intuitive characteristic, which provides a new way to improve the identification probability and reduce the complexity of the model matching library. A satellite model is reconstructed using the proposed method from four consecutive ISAR images. The simulation results prove that the method has gotten a satisfied consistency and accuracy.

Science with a selfie stick: Plant biomass estimation using smartphone based ‘Structure From Motion’ photogrammetry

USDA-ARS?s Scientific Manuscript database

Significant advancements in photogrammetric Structure-from-Motion (SfM) software, coupled with improvements in the quality and resolution of smartphone cameras, has made it possible to create ultra-fine resolution three-dimensional models of physical objects using an ordinary smartphone. Here we pre...

Computational high-resolution optical imaging of the living human retina

NASA Astrophysics Data System (ADS)

Shemonski, Nathan D.; South, Fredrick A.; Liu, Yuan-Zhi; Adie, Steven G.; Scott Carney, P.; Boppart, Stephen A.

2015-07-01

High-resolution in vivo imaging is of great importance for the fields of biology and medicine. The introduction of hardware-based adaptive optics (HAO) has pushed the limits of optical imaging, enabling high-resolution near diffraction-limited imaging of previously unresolvable structures. In ophthalmology, when combined with optical coherence tomography, HAO has enabled a detailed three-dimensional visualization of photoreceptor distributions and individual nerve fibre bundles in the living human retina. However, the introduction of HAO hardware and supporting software adds considerable complexity and cost to an imaging system, limiting the number of researchers and medical professionals who could benefit from the technology. Here we demonstrate a fully automated computational approach that enables high-resolution in vivo ophthalmic imaging without the need for HAO. The results demonstrate that computational methods in coherent microscopy are applicable in highly dynamic living systems.

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

PubMed Central

Kumar, Yadhu; Westram, Ralf; Kipfer, Peter; Meier, Harald; Ludwig, Wolfgang

2006-01-01

Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via . PMID:16672074

Single-shot three-dimensional reconstruction based on structured light line pattern

NASA Astrophysics Data System (ADS)

Wang, ZhenZhou; Yang, YongMing

2018-07-01

Reconstruction of the object by single-shot is of great importance in many applications, in which the object is moving or its shape is non-rigid and changes irregularly. In this paper, we propose a single-shot structured light 3D imaging technique that calculates the phase map from the distorted line pattern. This technique makes use of the image processing techniques to segment and cluster the projected structured light line pattern from one single captured image. The coordinates of the clustered lines are extracted to form a low-resolution phase matrix which is then transformed to full-resolution phase map by spline interpolation. The 3D shape of the object is computed from the full-resolution phase map and the 2D camera coordinates. Experimental results show that the proposed method was able to reconstruct the three-dimensional shape of the object robustly from one single image.

Three-dimensional reconstruction of frozen and thawed plant tissues from microscopic images

USDA-ARS?s Scientific Manuscript database

Histological analysis of frozen and thawed plants has been conducted for many years but the observation of individual sections only provides a 2 dimensional representation of a 3 dimensional phenomenon. Most techniques for viewing internal plant structure in 3 dimensions is either low in resolution...

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

PubMed Central

Marti-Renom, Marc A.; Mirny, Leonid A.

2011-01-01

Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and chromosome conformation capture methods, the availability of experimental data on genome three-dimensional organization has dramatically increased. We now have access to unprecedented details of how genomes organize within the interphase nucleus. Development of new computational approaches to leverage this data has already resulted in the first three-dimensional structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. Our outlook describes computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains. PMID:21779160

Three-dimensional structure of phosphoribosyl pyrophosphate synthetase from E. coli at 2.71 Å resolution

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

Timofeev, V. I., E-mail: inna@ns.crys.ras.ru, E-mail: tostars@mail.ru, E-mail: ugama@yandex.ru; Abramchik, Yu. A.; Zhukhlistova, N. E.

2016-01-15

Phosphoribosyl pyrophosphate synthetase from Escherichia coli was cloned, purified, and crystallized. Single crystals of the enzyme were grown under microgravity. The X-ray diffraction data set was collected at the Spring-8 synchrotron facility and used to determine the three-dimensional structure of the enzyme by the molecular-replacement method at 2.71 Å resolution. The active and regulatory sites in the molecule of E. coli phosphoribosyl pyrophosphate synthetase were revealed by comparison with the homologous protein from Bacillus subtilis, the structure of which was determined in a complex with functional ligands. The conformations of polypeptide-chain fragments surrounding and composing the active and regulatory sitesmore » were shown to be identical in both proteins.« less

Quasi-three-dimensional particle imaging with digital holography.

PubMed

Kemppinen, Osku; Heinson, Yuli; Berg, Matthew

2017-05-01

In this work, approximate three-dimensional structures of microparticles are generated with digital holography using an automated focus method. This is done by stacking a collection of silhouette-like images of a particle reconstructed from a single in-line hologram. The method enables estimation of the particle size in the longitudinal and transverse dimensions. Using the discrete dipole approximation, the method is tested computationally by simulating holograms for a variety of particles and attempting to reconstruct the known three-dimensional structure. It is found that poor longitudinal resolution strongly perturbs the reconstructed structure, yet the method does provide an approximate sense for the structure's longitudinal dimension. The method is then applied to laboratory measurements of holograms of single microparticles and their scattering patterns.

High axial resolution imaging system for large volume tissues using combination of inclined selective plane illumination and mechanical sectioning

PubMed Central

Zhang, Qi; Yang, Xiong; Hu, Qinglei; Bai, Ke; Yin, Fangfang; Li, Ning; Gang, Yadong; Wang, Xiaojun; Zeng, Shaoqun

2017-01-01

To resolve fine structures of biological systems like neurons, it is required to realize microscopic imaging with sufficient spatial resolution in three dimensional systems. With regular optical imaging systems, high lateral resolution is accessible while high axial resolution is hard to achieve in a large volume. We introduce an imaging system for high 3D resolution fluorescence imaging of large volume tissues. Selective plane illumination was adopted to provide high axial resolution. A scientific CMOS working in sub-array mode kept the imaging area in the sample surface, which restrained the adverse effect of aberrations caused by inclined illumination. Plastic embedding and precise mechanical sectioning extended the axial range and eliminated distortion during the whole imaging process. The combination of these techniques enabled 3D high resolution imaging of large tissues. Fluorescent bead imaging showed resolutions of 0.59 μm, 0.47μm, and 0.59 μm in the x, y, and z directions, respectively. Data acquired from the volume sample of brain tissue demonstrated the applicability of this imaging system. Imaging of different depths showed uniform performance where details could be recognized in either the near-soma area or terminal area, and fine structures of neurons could be seen in both the xy and xz sections. PMID:29296503

An Essential Protein Repair Enzyme: Investigation of the Molecular Recognition Mechanism of Methionine Sulfoxide Reductase A

DTIC Science & Technology

2008-05-01

4 ). The three-dimensional spatial orientation of the atoms for these resolved solution structures (Protein Data Bank accession codes: 2gt3...Crystal structure of the Escherichia coli peptide methionine sulphoxide reductase at 1.9 Å resolution . Struct. Fold. Des. 8: 1167 – 1178. 2 . Brot...sources (8). There is a 67% sequence identity between the E.coli and human MsrA ( 2 ). N-terminus C-terminus Figure 2 . Three-dimensional structure

Fabrication of 3D SiO x structures using patterned PMMA sacrificial layer

NASA Astrophysics Data System (ADS)

Li, Zhiqin; Xiang, Quan; Zheng, Mengjie; Bi, Kaixi; Chen, Yiqin; Chen, Keqiu; Duan, Huigao

2018-02-01

Three-dimensional (3D) nanofabrication based on electron-beam lithography (EBL) has drawn wide attention for various applications with its high patterning resolution and design flexibility. In this work, we present a bilayer EBL process to obtain 3D freestanding SiO x structures via the release of the bottom sacrificial layer. This new kind of bilayer process enables us to define various 3D freestanding SiO x structures with high resolution and low edge roughness. As a proof of concept for applications, metal-coated freestanding SiO x microplates with an underlying air gap were fabricated to form asymmetric Fabry-Perot resonators, which can be utilized for colorimetric refractive index sensing and thus also have application potential for biochemical detection, anti-counterfeiting and smart active nano-optical devices.

High resolution imaging and lithography with hard x rays using parabolic compound refractive lenses

NASA Astrophysics Data System (ADS)

Schroer, C. G.; Benner, B.; Günzler, T. F.; Kuhlmann, M.; Zimprich, C.; Lengeler, B.; Rau, C.; Weitkamp, T.; Snigirev, A.; Snigireva, I.; Appenzeller, J.

2002-03-01

Parabolic compound refractive lenses are high quality optical components for hard x rays. They are particularly suited for full field imaging, with applications in microscopy and x-ray lithography. Taking advantage of the large penetration depth of hard x rays, the interior of opaque samples can be imaged with submicrometer resolution. To obtain the three-dimensional structure of a sample, microscopy is combined with tomographic techniques. In a first hard x-ray lithography experiment, parabolic compound refractive lenses have been used to project the reduced image of a lithography mask onto a resist. Future developments are discussed.

A new FIB fabrication method for micropillar specimens for three-dimensional observation using scanning transmission electron microscopy.

PubMed

Fukuda, Muneyuki; Tomimatsu, Satoshi; Nakamura, Kuniyasu; Koguchi, Masanari; Shichi, Hiroyasu; Umemura, Kaoru

2004-01-01

A new method to prepare micropillar specimens with a high aspect ratio that is suitable for three-dimensional scanning transmission electron microscopy (3D-STEM) was developed. The key features of the micropillar fabrication are: first, microsampling to extract a small piece including the structure of interest in an IC chip, and second, an ion-beam with an incident direction of 60 degrees to the pillar's axis that enables the parallel sidewalls of the pillar to be produced with a high aspect ratio. A memory-cell structure (length: 6 microm; width: 300 x 500 nm) was fabricated in the micropillar and observed from various directions with a 3D-STEM. A planiform capacitor covered with granular surfaces and a solid crossing gate and metal lines was successfully observed threedimensionally at a resolution of approximately 5 nm.

Three-dimensional wide-field pump-probe structured illumination microscopy

PubMed Central

Kim, Yang-Hyo; So, Peter T.C.

2017-01-01

We propose a new structured illumination scheme for achieving depth resolved wide-field pump-probe microscopy with sub-diffraction limit resolution. By acquiring coherent pump-probe images using a set of 3D structured light illumination patterns, a 3D super-resolution pump-probe image can be reconstructed. We derive the theoretical framework to describe the coherent image formation and reconstruction scheme for this structured illumination pump-probe imaging system and carry out numerical simulations to investigate its imaging performance. The results demonstrate a lateral resolution improvement by a factor of three and providing 0.5 µm level axial optical sectioning. PMID:28380860

Nonlinear structured-illumination enhanced temporal focusing multiphoton excitation microscopy with a digital micromirror device

PubMed Central

Cheng, Li-Chung; Lien, Chi-Hsiang; Da Sie, Yong; Hu, Yvonne Yuling; Lin, Chun-Yu; Chien, Fan-Ching; Xu, Chris; Dong, Chen Yuan; Chen, Shean-Jen

2014-01-01

In this study, the light diffraction of temporal focusing multiphoton excitation microscopy (TFMPEM) and the excitation patterning of nonlinear structured-illumination microscopy (NSIM) can be simultaneously and accurately implemented via a single high-resolution digital micromirror device. The lateral and axial spatial resolutions of the TFMPEM are remarkably improved through the second-order NSIM and projected structured light, respectively. The experimental results demonstrate that the lateral and axial resolutions are enhanced from 397 nm to 168 nm (2.4-fold) and from 2.33 μm to 1.22 μm (1.9-fold), respectively, in full width at the half maximum. Furthermore, a three-dimensionally rendered image of a cytoskeleton cell featuring ~25 nm microtubules is improved, with other microtubules at a distance near the lateral resolution of 168 nm also able to be distinguished. PMID:25136483

Structure and dynamics of the coronal magnetic field

NASA Technical Reports Server (NTRS)

VanHoven, Gerard; Schnack, Dalton D.

1996-01-01

The last few years have seen a marked increase in the sophistication of models of the solar corona. This has been brought about by a confluence of three key elements. First, the collection of high-resolution observations of the Sun, both in space and time, has grown tremendously. The SOHO (Solar Heliospheric Observatory) mission is providing additional correlated high-resolution magnetic, white-light and spectroscopic observations. Second, the power and availability of supercomputers has made two- and three-dimensional modeling routine. Third, the sophistication of the models themselves, both in their geometrical realism and in the detailed physics that has been included, has improved significantly. The support from our current Space Physics Theory grant has allowed us to exploit this confluence of capabilities. We have carried out direct comparisons between observations and models of the solar corona. The agreement between simulated coronal structure and observations has verified that the models are mature enough for detailed analysis, as we will describe. The development of this capability is especially timely, since observations obtained from three space missions that are underway (Ulysses, WIND and SOHO) offer an opportunity for significant advances in our understanding of the corona and heliosphere. Through this interplay of observations and theory we can improve our understanding of the Sun. Our achievements thus far include progress modeling the large-scale structure of the solar corona, three-dimensional models of active region fields, development of emerging flux and current, formation and evolution of coronal loops, and coronal heating by current filaments.

Three-Axis Distributed Fiber Optic Strain Measurement in 3D Woven Composite Structures

NASA Technical Reports Server (NTRS)

Castellucci, Matt; Klute, Sandra; Lally, Evan M.; Froggatt, Mark E.; Lowry, David

2013-01-01

Recent advancements in composite materials technologies have broken further from traditional designs and require advanced instrumentation and analysis capabilities. Success or failure is highly dependent on design analysis and manufacturing processes. By monitoring smart structures throughout manufacturing and service life, residual and operational stresses can be assessed and structural integrity maintained. Composite smart structures can be manufactured by integrating fiber optic sensors into existing composite materials processes such as ply layup, filament winding and three-dimensional weaving. In this work optical fiber was integrated into 3D woven composite parts at a commercial woven products manufacturing facility. The fiber was then used to monitor the structures during a VARTM manufacturing process, and subsequent static and dynamic testing. Low cost telecommunications-grade optical fiber acts as the sensor using a high resolution commercial Optical Frequency Domain Reflectometer (OFDR) system providing distributed strain measurement at spatial resolutions as low as 2mm. Strain measurements using the optical fiber sensors are correlated to resistive strain gage measurements during static structural loading. Keywords: fiber optic, distributed strain sensing, Rayleigh scatter, optical frequency domain reflectometry

The High Resolution Stereo Camera (HRSC): 10 Years of Imaging Mars

NASA Astrophysics Data System (ADS)

Jaumann, R.; Neukum, G.; Tirsch, D.; Hoffmann, H.

2014-04-01

The HRSC Experiment: Imagery is the major source for our current understanding of the geologic evolution of Mars in qualitative and quantitative terms.Imaging is required to enhance our knowledge of Mars with respect to geological processes occurring on local, regional and global scales and is an essential prerequisite for detailed surface exploration. The High Resolution Stereo Camera (HRSC) of ESA's Mars Express Mission (MEx) is designed to simultaneously map the morphology, topography, structure and geologic context of the surface of Mars as well as atmospheric phenomena [1]. The HRSC directly addresses two of the main scientific goals of the Mars Express mission: (1) High-resolution three-dimensional photogeologic surface exploration and (2) the investigation of surface-atmosphere interactions over time; and significantly supports: (3) the study of atmospheric phenomena by multi-angle coverage and limb sounding as well as (4) multispectral mapping by providing high-resolution threedimensional color context information. In addition, the stereoscopic imagery will especially characterize landing sites and their geologic context [1]. The HRSC surface resolution and the digital terrain models bridge the gap in scales between highest ground resolution images (e.g., HiRISE) and global coverage observations (e.g., Viking). This is also the case with respect to DTMs (e.g., MOLA and local high-resolution DTMs). HRSC is also used as cartographic basis to correlate between panchromatic and multispectral stereo data. The unique multi-angle imaging technique of the HRSC supports its stereo capability by providing not only a stereo triplet but also a stereo quintuplet, making the photogrammetric processing very robust [1, 3]. The capabilities for three dimensional orbital reconnaissance of the Martian surface are ideally met by HRSC making this camera unique in the international Mars exploration effort.

Correlated Light and Electron Microscopy/Electron Tomography of Mitochondria In Situ

PubMed Central

Perkins, Guy A.; Sun, Mei G.; Frey, Terrence G.

2009-01-01

Three-dimensional light microscopy and three-dimensional electron microscopy (electron tomography) separately provide very powerful tools to study cellular structure and physiology, including the structure and physiology of mitochondria. Fluorescence microscopy allows one to study processes in live cells with specific labels and stains that follow the movement of labeled proteins and changes within cellular compartments but does not have sufficient resolution to define the ultrastructure of intracellular organelles such as mitochondria. Electron microscopy and electron tomography provide the highest resolution currently available to study mitochondrial ultrastructure but cannot follow processes in living cells. We describe the combination of these two techniques in which fluorescence confocal microscopy is used to study structural and physiologic changes in mitochondria within apoptotic HeLa cells to define the apoptotic timeframe. Cells can then be selected at various stages of the apoptotic timeframe for examination at higher resolution by electron microscopy and electron tomography. This is a form of “virtual” 4-dimensional electron microscopy that has revealed interesting structural changes in the mitochondria of HeLa cells during apoptosis. The same techniques can be applied, with modification, to study other dynamic processes within cells in other experimental contexts. PMID:19348881

Laboratory-size three-dimensional water-window x-ray microscope with Wolter type I mirror optics

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

Ohsuka, Shinji; The Graduate School for the Creation of New Photonics Industries, 1955-1 Kurematsu-cho, Nishi-ku, Hamamatsu-City, 431-1202; Ohba, Akira

2016-01-28

We constructed a laboratory-size three-dimensional water-window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques. It consists of an electron-impact x-ray source emitting oxygen Kα x-rays, Wolter type I grazing incidence mirror optics, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit better than 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm-scale three-dimensional fine structures were resolved.

Filling the gap: Micro-C accesses the nucleosomal fiber at 100-1000 bp resolution.

PubMed

Mozziconacci, Julien; Koszul, Romain

2015-08-21

The fine three-dimensional structure of the nucleosomal fiber has remained elusive to genome-wide chromosome conformation capture (3C) approaches. A new study mapping contacts at the single nucleosome level (Micro-C) reveals topological interacting domains along budding yeast chromosomes. These domains encompass one to five consecutive genes and are delimited by highly active promoters.

Interaction of a supersonic particle with a three-dimensional complex plasma

NASA Astrophysics Data System (ADS)

Zaehringer, E.; Schwabe, M.; Zhdanov, S.; Mohr, D. P.; Knapek, C. A.; Huber, P.; Semenov, I. L.; Thomas, H. M.

2018-03-01

The influence of a supersonic projectile on a three-dimensional complex plasma is studied. Micron sized particles in a low-temperature plasma formed a large undisturbed system in the new "Zyflex" chamber during microgravity conditions. A supersonic probe particle excited a Mach cone with Mach number M ≈ 1.5-2 and double Mach cone structure in the large weakly damped particle cloud. The speed of sound is measured with different methods and particle charge estimations are compared to the calculations from standard theories. The high image resolution enables the study of Mach cones in microgravity on the single particle level of a three-dimensional complex plasma and gives insight to the dynamics. A heating of the microparticles is discovered behind the supersonic projectile but not in the flanks of the Mach cone.

Three-dimensional Magnetotelluric Characterization of the Xinzhou Geothermal Field, Southeastern China

NASA Astrophysics Data System (ADS)

Han, Q.; Hu, X.; Cai, J.; Wei, W.

2016-12-01

Xinzhou geothermal field is located in the Guangdong province and adjacent to the China South Sea, and its hot springs can reach up to 92 degree Celsius. Yanshanian granite expose widely in the south of this geothermal field and four faults cut across each other over it. A dense grid of 176 magnetotelluric (MT) sites with broadband has been acquired over the Xinzhou geothermal field and its surrounding area. Due to the related electromagnetic (EM) noise one permanent observatory was placed as a remote reference to suppress this cultural EM noise interference. The datasets are processed using the mutual reference technique, static shift correction, and structural strike and dimensionality analysis based on tensor decomposition. Data analysis reveals that the underground conductivity structure has obvious three-dimensional characterization. For the high resolution result ,two and three dimensional inversion are both applied in this area employing the non-linear conjugate gradient method (NLCG).These MT data sets are supposed to detect the deep subsurface resistivity structure correlated to the distribution of geothermal reservoir (such as faults and fractured granite) and investigate the channel of the upwelling magma. The whole and cold granite usually present high resistivity but once it functions as reservoir the resistivity will decrease, sometimes it is hard to separate the reservoir from the cap layer. The 3D inversion results delineate three high resistivity anomalies distributed in different locations. At last we put forward that the large areas of granite form the major thermal source for the study area and discuss whether any melt under these magma intrusions exists.

RAPID COMMUNICATION: Study of superstructure II in multiferroic BiMnO3

NASA Astrophysics Data System (ADS)

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

2008-09-01

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

Insights into Head-Tailed Viruses Infecting Extremely Halophilic Archaea

PubMed Central

Pietilä, Maija K.; Laurinmäki, Pasi; Russell, Daniel A.; Ko, Ching-Chung; Jacobs-Sera, Deborah; Butcher, Sarah J.

2013-01-01

Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date, about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by cryo-electron microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to a ∼10-Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class, but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein into the capsid lattice. PMID:23283946

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization.

PubMed

Szałaj, Przemysław; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Michał; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz

2016-12-01

ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding. This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D models to study structural-functional relationships at multiple length scales, but doing so requires a structural modeling platform. Here, we report the development of 3D-GNOME (3-Dimensional Genome Modeling Engine), a complete computational pipeline for 3D simulation using ChIA-PET data. 3D-GNOME consists of three integrated components: a graph-distance-based heat map normalization tool, a 3D modeling platform, and an interactive 3D visualization tool. Using ChIA-PET and Hi-C data derived from human B-lymphocytes, we demonstrate the effectiveness of 3D-GNOME in building 3D genome models at multiple levels, including the entire genome, individual chromosomes, and specific segments at megabase (Mb) and kilobase (kb) resolutions of single average and ensemble structures. Further incorporation of CTCF-motif orientation and high-resolution looping patterns in 3D simulation provided additional reliability of potential biologically plausible topological structures. © 2016 Szałaj et al.; Published by Cold Spring Harbor Laboratory Press.

Towards microscale electrohydrodynamic three-dimensional printing

NASA Astrophysics Data System (ADS)

He, Jiankang; Xu, Fangyuan; Cao, Yi; Liu, Yaxiong; Li, Dichen

2016-02-01

It is challenging for the existing three-dimensional (3D) printing techniques to fabricate high-resolution 3D microstructures with low costs and high efficiency. In this work we present a solvent-based electrohydrodynamic 3D printing technique that allows fabrication of microscale structures like single walls, crossed walls, lattice and concentric circles. Process parameters were optimized to deposit tiny 3D patterns with a wall width smaller than 10 μm and a high aspect ratio of about 60. Tight bonding among neighbour layers could be achieved with a smooth lateral surface. In comparison with the existing microscale 3D printing techniques, the presented method is low-cost, highly efficient and applicable to multiple polymers. It is envisioned that this simple microscale 3D printing strategy might provide an alternative and innovative way for application in MEMS, biosensor and flexible electronics.

Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region

PubMed Central

Stephenson, James D.; Li, Haitao; Kenyon, Julia C.; Symmons, Martyn; Klenerman, Dave; Lever, Andrew M.L.

2013-01-01

Summary HIV-1 genomic RNA has a noncoding 5′ region containing sequential conserved structural motifs that control many parts of the life cycle. Very limited data exist on their three-dimensional (3D) conformation and, hence, how they work structurally. To assemble a working model, we experimentally reassessed secondary structure elements of a 240-nt region and used single-molecule distances, derived from fluorescence resonance energy transfer, between defined locations in these elements as restraints to drive folding of the secondary structure into a 3D model with an estimated resolution below 10 Å. The folded 3D model satisfying the data is consensual with short nuclear-magnetic-resonance-solved regions and reveals previously unpredicted motifs, offering insight into earlier functional assays. It is a 3D representation of this entire region, with implications for RNA dimerization and protein binding during regulatory steps. The structural information of this highly conserved region of the virus has the potential to reveal promising therapeutic targets. PMID:23685210

High-Resolution Three-Dimensional Structural Data Quantify the Impact of Photoinhibition on Long-Term Carbon Gain in Wheat Canopies in the Field1[OPEN

PubMed Central

Burgess, Alexandra J.; Retkute, Renata; Pound, Michael P.; Foulkes, John; Preston, Simon P.; Jensen, Oliver E.; Pridmore, Tony P.; Murchie, Erik H.

2015-01-01

Photoinhibition reduces photosynthetic productivity; however, it is difficult to quantify accurately in complex canopies partly because of a lack of high-resolution structural data on plant canopy architecture, which determines complex fluctuations of light in space and time. Here, we evaluate the effects of photoinhibition on long-term carbon gain (over 1 d) in three different wheat (Triticum aestivum) lines, which are architecturally diverse. We use a unique method for accurate digital three-dimensional reconstruction of canopies growing in the field. The reconstruction method captures unique architectural differences between lines, such as leaf angle, curvature, and leaf density, thus providing a sensitive method of evaluating the productivity of actual canopy structures that previously were difficult or impossible to obtain. We show that complex data on light distribution can be automatically obtained without conventional manual measurements. We use a mathematical model of photosynthesis parameterized by field data consisting of chlorophyll fluorescence, light response curves of carbon dioxide assimilation, and manual confirmation of canopy architecture and light attenuation. Model simulations show that photoinhibition alone can result in substantial reduction in carbon gain, but this is highly dependent on exact canopy architecture and the diurnal dynamics of photoinhibition. The use of such highly realistic canopy reconstructions also allows us to conclude that even a moderate change in leaf angle in upper layers of the wheat canopy led to a large increase in the number of leaves in a severely light-limited state. PMID:26282240

Three-dimensional reciprocal space x-ray coherent scattering tomography of two-dimensional object.

PubMed

Zhu, Zheyuan; Pang, Shuo

2018-04-01

X-ray coherent scattering tomography is a powerful tool in discriminating biological tissues and bio-compatible materials. Conventional x-ray scattering tomography framework can only resolve isotropic scattering profile under the assumption that the material is amorphous or in powder form, which is not true especially for biological samples with orientation-dependent structure. Previous tomography schemes based on x-ray coherent scattering failed to preserve the scattering pattern from samples with preferred orientations, or required elaborated data acquisition scheme, which could limit its application in practical settings. Here, we demonstrate a simple imaging modality to preserve the anisotropic scattering signal in three-dimensional reciprocal (momentum transfer) space of a two-dimensional sample layer. By incorporating detector movement along the direction of x-ray beam, combined with a tomographic data acquisition scheme, we match the five dimensions of the measurements with the five dimensions (three in momentum transfer domain, and two in spatial domain) of the object. We employed a collimated pencil beam of a table-top copper-anode x-ray tube, along with a panel detector to investigate the feasibility of our method. We have demonstrated x-ray coherent scattering tomographic imaging at a spatial resolution ~2 mm and momentum transfer resolution 0.01 Å -1 for the rotation-invariant scattering direction. For any arbitrary, non-rotation-invariant direction, the same spatial and momentum transfer resolution can be achieved based on the spatial information from the rotation-invariant direction. The reconstructed scattering profile of each pixel from the experiment is consistent with the x-ray diffraction profile of each material. The three-dimensional scattering pattern recovered from the measurement reveals the partially ordered molecular structure of Teflon wrap in our sample. We extend the applicability of conventional x-ray coherent scattering tomography to the reconstruction of two-dimensional samples with anisotropic scattering profile by introducing additional degree of freedom on the detector. The presented method has the potential to achieve low-cost, high-specificity material discrimination based on x-ray coherent scattering. © 2018 American Association of Physicists in Medicine.

Rapid Prototyping Integrated With Nondestructive Evaluation and Finite Element Analysis

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Baaklini, George Y.

2001-01-01

Most reverse engineering approaches involve imaging or digitizing an object then creating a computerized reconstruction that can be integrated, in three dimensions, into a particular design environment. Rapid prototyping (RP) refers to the practical ability to build high-quality physical prototypes directly from computer aided design (CAD) files. Using rapid prototyping, full-scale models or patterns can be built using a variety of materials in a fraction of the time required by more traditional prototyping techniques (refs. 1 and 2). Many software packages have been developed and are being designed to tackle the reverse engineering and rapid prototyping issues just mentioned. For example, image processing and three-dimensional reconstruction visualization software such as Velocity2 (ref. 3) are being used to carry out the construction process of three-dimensional volume models and the subsequent generation of a stereolithography file that is suitable for CAD applications. Producing three-dimensional models of objects from computed tomography (CT) scans is becoming a valuable nondestructive evaluation methodology (ref. 4). Real components can be rendered and subjected to temperature and stress tests using structural engineering software codes. For this to be achieved, accurate high-resolution images have to be obtained via CT scans and then processed, converted into a traditional file format, and translated into finite element models. Prototyping a three-dimensional volume of a composite structure by reading in a series of two-dimensional images generated via CT and by using and integrating commercial software (e.g. Velocity2, MSC/PATRAN (ref. 5), and Hypermesh (ref. 6)) is being applied successfully at the NASA Glenn Research Center. The building process from structural modeling to the analysis level is outlined in reference 7. Subsequently, a stress analysis of a composite cooling panel under combined thermomechanical loading conditions was performed to validate this process.

Erratum: The Effects of Thermal Energetics on Three-dimensional Hydrodynamic Instabilities in Massive Protostellar Disks. II. High-Resolution and Adiabatic Evolutions

NASA Astrophysics Data System (ADS)

Pickett, Brian K.; Cassen, Patrick; Durisen, Richard H.; Link, Robert

2000-02-01

In the paper ``The Effects of Thermal Energetics on Three-dimensional Hydrodynamic Instabilities in Massive Protostellar Disks. II. High-Resolution and Adiabatic Evolutions'' by Brian K. Pickett, Patrick Cassen, Richard H. Durisen, and Robert Link (ApJ, 529, 1034 [2000]), the wrong version of Figure 10 was published as a result of an error at the Press. The correct version of Figure 10 appears below. The Press sincerely regrets this error.

3D structure of individual nanocrystals in solution by electron microscopy

NASA Astrophysics Data System (ADS)

Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

2015-07-01

Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

PubMed Central

Seer-Linnemayr, Charlotte; Ravelli, Raimond B. G.; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V.; Pannu, Navraj S.; Schatz, Michael; van Heel, Marin

2017-01-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the ‘Einstein from random noise’ problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (‘four-dimensional’) cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, ‘random-startup’ three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external ‘starting models’. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive ‘ABC-4D’ pipeline is based on the two-dimensional reference-free ‘alignment by classification’ (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. PMID:28989723

High-throughput isotropic mapping of whole mouse brain using multi-view light-sheet microscopy

NASA Astrophysics Data System (ADS)

Nie, Jun; Li, Yusha; Zhao, Fang; Ping, Junyu; Liu, Sa; Yu, Tingting; Zhu, Dan; Fei, Peng

2018-02-01

Light-sheet fluorescence microscopy (LSFM) uses an additional laser-sheet to illuminate selective planes of the sample, thereby enabling three-dimensional imaging at high spatial-temporal resolution. These advantages make LSFM a promising tool for high-quality brain visualization. However, even by the use of LSFM, the spatial resolution remains insufficient to resolve the neural structures across a mesoscale whole mouse brain in three dimensions. At the same time, the thick-tissue scattering prevents a clear observation from the deep of brain. Here we use multi-view LSFM strategy to solve this challenge, surpassing the resolution limit of standard light-sheet microscope under a large field-of-view (FOV). As demonstrated by the imaging of optically-cleared mouse brain labelled with thy1-GFP, we achieve a brain-wide, isotropic cellular resolution of 3μm. Besides the resolution enhancement, multi-view braining imaging can also recover complete signals from deep tissue scattering and attenuation. The identification of long distance neural projections across encephalic regions can be identified and annotated as a result.

Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals

DOE PAGES

Casadei, Cecilia M.; Tsai, Ching-Ju; Barty, Anton; ...

2018-01-01

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography atmore » X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump–probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.« less

Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals

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

Casadei, Cecilia M.; Tsai, Ching-Ju; Barty, Anton

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography atmore » X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump–probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.« less

THREE-DIMENSIONAL MODEL FOR HYPERTHERMIA CALCULATIONS

EPA Science Inventory

Realistic three-dimensional models that predict temperature distributions with a high degree of spatial resolution in bodies exposed to electromagnetic (EM) fields are required in the application of hyperthermia for cancer treatment. To ascertain the thermophysiologic response of...

Scientific Visualization to Study Flux Transfer Events at the Community Coordinated Modeling Center

NASA Technical Reports Server (NTRS)

Rastatter, Lutz; Kuznetsova, Maria M.; Sibeck, David G.; Berrios, David H.

2011-01-01

In this paper we present results of modeling of reconnection at the dayside magnetopause with subsequent development of flux transfer event signatures. The tools used include new methods that have been added to the suite of visualization methods that are used at the Community Coordinated Modeling Center (CCMC). Flux transfer events result from localized reconnection that connect magnetosheath magnetic field and plasma with magnetospheric fields and plasma and results in flux rope structures that span the dayside magnetopause. The onset of flux rope formation and the three-dimensional structure of flux ropes are studied as they have been modeled by high-resolution magnetohydrodynamic simulations of the dayside magnetosphere of the Earth. We show that flux transfer events are complex three-dimensional structures that require modern visualization and analysis techniques. Two suites of visualization methods are presented and we demonstrate the usefulness of those methods through the CCMC web site to the general science user.

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

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

Three-Dimensional Bioprinting: Toward the Era of Manufacturing Human Organs as Spare Parts for Healthcare and Medicine^.

PubMed

Mir, Tanveer Ahmad; Nakamura, Makoto

2017-06-01

Three-dimensional (3D) printing technology has been used in industrial worlds for decades. Three-dimensional bioprinting has recently received an increasing attention across the globe among researchers, academicians, students, and even the ordinary people. This emerging technique has a great potential to engineer highly organized functional bioconstructs with complex geometries and tailored components for engineering bioartificial tissues/organs for widespread applications, including transplantation, therapeutic investigation, drug development, bioassay, and disease modeling. Although many specialized 3D printers have been developed and applied to print various types of 3D tissue constructs, bioprinting technologies still have several technical challenges, including high resolution distribution of cells, controlled deposition of bioinks, suitable bioink materials, maturation of cells, and effective vascularization and innervation within engineered complex structures. In this brief review, we discuss about bioprinting approach, current limitations, and possibility of future advancements for producing engineered bioconstructs and bioartificial organs with desired functionalities.

Characterization of a detector chain using a FPGA-based time-to-digital converter to reconstruct the three-dimensional coordinates of single particles at high flux

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

Nogrette, F.; Chang, R.; Bouton, Q.

We report on the development of a novel FPGA-based time-to-digital converter and its implementation in a detection chain that records the coordinates of single particles along three dimensions. The detector is composed of micro-channel plates mounted on top of a cross delay line and connected to fast electronics. We demonstrate continuous recording of the timing signals from the cross delay line at rates up to 4.1 × 10{sup 6} s{sup −1} and three-dimensional reconstruction of the coordinates up to 3.2 × 10{sup 6} particles per second. From the imaging of a calibrated structure we measure the in-plane resolution of themore » detector to be 140(20) μm at a flux of 3 × 10{sup 5} particles per second. In addition, we analyze a method to estimate the resolution without placing any structure under vacuum, a significant practical improvement. While we use UV photons here, the results of this work apply to the detection of other kinds of particles.« less

Morphological imaging and quantification of axial xylem tissue in Fraxinus excelsior L. through X-ray micro-computed tomography.

PubMed

Koddenberg, Tim; Militz, Holger

2018-05-05

The popularity of X-ray based imaging methods has continued to increase in research domains. In wood research, X-ray micro-computed tomography (XμCT) is useful for structural studies examining the three-dimensional and complex xylem tissue of trees qualitatively and quantitatively. In this study, XμCT made it possible to visualize and quantify the spatial xylem organization of the angiosperm species Fraxinus excelsior L. on the microscopic level. Through image analysis, it was possible to determine morphological characteristics of the cellular axial tissue (vessel elements, fibers, and axial parenchyma cells) three-dimensionally. X-ray imaging at high resolutions provides very distinct visual insight into the xylem structure. Numerical analyses performed through semi-automatic procedures made it possible to quickly quantify cell characteristics (length, diameter, and volume of cells). Use of various spatial resolutions (0.87-5 μm) revealed boundaries users should be aware of. Nevertheless, our findings, both qualitative and quantitative, demonstrate XμCT to be a valuable tool for studying the spatial cell morphology of F. excelsior. Copyright © 2018. Published by Elsevier Ltd.

Plexus structure imaging with thin slab MR neurography: rotating frames, fly-throughs, and composite projections

NASA Astrophysics Data System (ADS)

Raphael, David T.; McIntee, Diane; Tsuruda, Jay S.; Colletti, Patrick; Tatevossian, Raymond; Frazier, James

2006-03-01

We explored multiple image processing approaches by which to display the segmented adult brachial plexus in a three-dimensional manner. Magnetic resonance neurography (MRN) 1.5-Tesla scans with STIR sequences, which preferentially highlight nerves, were performed in adult volunteers to generate high-resolution raw images. Using multiple software programs, the raw MRN images were then manipulated so as to achieve segmentation of plexus neurovascular structures, which were incorporated into three different visualization schemes: rotating upper thoracic girdle skeletal frames, dynamic fly-throughs parallel to the clavicle, and thin slab volume-rendered composite projections.

Individual tree detection from Unmanned Aerial Vehicle (UAV) derived canopy height model in an open canopy mixed conifer forest

Treesearch

Midhun Mohan; Carlos Alberto Silva; Carine Klauberg; Prahlad Jat; Glenn Catts; Adrian Cardil; Andrew Thomas Hudak; Mahendra Dia

2017-01-01

Advances in Unmanned Aerial Vehicle (UAV) technology and data processing capabilities have made it feasible to obtain high-resolution imagery and three dimensional (3D) data which can be used for forest monitoring and assessing tree attributes. This study evaluates the applicability of low consumer grade cameras attached to UAVs and structure-from-motion (SfM)...

Development of high-resolution x-ray CT system using parallel beam geometry

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

Yoneyama, Akio, E-mail: akio.yoneyama.bu@hitachi.com; Baba, Rika; Hyodo, Kazuyuki

2016-01-28

For fine three-dimensional observations of large biomedical and organic material samples, we developed a high-resolution X-ray CT system. The system consists of a sample positioner, a 5-μm scintillator, microscopy lenses, and a water-cooled sCMOS detector. Parallel beam geometry was adopted to attain a field of view of a few mm square. A fine three-dimensional image of birch branch was obtained using a 9-keV X-ray at BL16XU of SPring-8 in Japan. The spatial resolution estimated from the line profile of a sectional image was about 3 μm.

Transparency-enhancing technology allows three-dimensional assessment of gastrointestinal mucosa: A porcine model.

PubMed

Mizutani, Hiroya; Ono, Satoshi; Ushiku, Tetsuo; Kudo, Yotaro; Ikemura, Masako; Kageyama, Natsuko; Yamamichi, Nobutake; Fujishiro, Mitsuhiro; Someya, Takao; Fukayama, Masashi; Koike, Kazuhiko; Onodera, Hiroshi

2018-02-01

Although high-resolution three-dimensional imaging of endoscopically resected gastrointestinal specimens can help elucidating morphological features of gastrointestinal mucosa or tumor, there are no established methods to achieve this without breaking specimens apart. We evaluated the utility of transparency-enhancing technology for three-dimensional assessment of gastrointestinal mucosa in porcine models. Esophagus, stomach, and colon mucosa samples obtained from a sacrificed swine were formalin-fixed and paraffin-embedded, and subsequently deparaffinized for analysis. The samples were fluorescently stained, optically cleared using transparency-enhancing technology: ilLUmination of Cleared organs to IDentify target molecules method (LUCID), and visualized using laser scanning microscopy. After observation, all specimens were paraffin-embedded again and evaluated by conventional histopathological assessment to measure the impact of transparency-enhancing procedures. As a result, microscopic observation revealed horizontal section views of mucosa at deeper levels and enabled the three-dimensional image reconstruction of glandular and vascular structures. Besides, paraffin-embedded specimens after transparency-enhancing procedures were all assessed appropriately by conventional histopathological staining. These results suggest that transparency-enhancing technology may be feasible for clinical application and enable the three-dimensional structural analysis of endoscopic resected specimen non-destructively. Although there remain many limitations or problems to be solved, this promising technology might represent a novel histopathological method for evaluating gastrointestinal cancers. © 2018 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

Overview of Three-Dimensional Atomic-Resolution Holography and Imaging Techniques: Recent Advances in Local-Structure Science

NASA Astrophysics Data System (ADS)

Daimon, Hiroshi

2018-06-01

Local three-dimensional (3D) atomic arrangements without periodicity have not been able to be studied until recently. Recently, several holographies and related techniques have been developed to reveal the 3D atomic arrangement around specific atoms with no translational symmetry. This review gives an overview of these new local 3D atomic imaging techniques.

Three-dimensional study of the vector potential of magnetic structures.

PubMed

Phatak, Charudatta; Petford-Long, Amanda K; De Graef, Marc

2010-06-25

The vector potential is central to a number of areas of condensed matter physics, such as superconductivity and magnetism. We have used a combination of electron wave phase reconstruction and electron tomographic reconstruction to experimentally measure and visualize the three-dimensional vector potential in and around a magnetic Permalloy structure. The method can probe the vector potential of the patterned structures with a resolution of about 13 nm. A transmission electron microscope operated in the Lorentz mode is used to record four tomographic tilt series. Measurements for a square Permalloy structure with an internal closure domain configuration are presented.

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

PubMed Central

Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J.; Brewster, Aaron S.; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G.; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R.; Miahnahri, Alan; White, William E.; Schafer, Donald W.; Seibert, M. Marvin; Koglin, Jason E.; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J.; Glatzel, Pieter; Zwart, Petrus H.; Grosse-Kunstleve, Ralf W.; Bogan, Michael J.; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K.; Adams, Paul D.; Sauter, Nicholas K.

2014-01-01

X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and free from radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract statistically significant high-resolution signals from fewer diffraction measurements. PMID:24633409

Application of dot-matrix illumination of liquid crystal phase space light modulator in 3D imaging of APD array

NASA Astrophysics Data System (ADS)

Wang, Shuai; Sun, Huayan; Guo, Huichao

2018-01-01

Aiming at the problem of beam scanning in low-resolution APD array in three-dimensional imaging, a method of beam scanning with liquid crystal phase-space optical modulator is proposed to realize high-resolution imaging by low-resolution APD array. First, a liquid crystal phase spatial light modulator is used to generate a beam array and then a beam array is scanned. Since the sub-beam divergence angle in the beam array is smaller than the field angle of a single pixel in the APD array, the APD's pixels respond only to the three-dimensional information of the beam illumination position. Through the scanning of the beam array, a single pixel is used to collect the target three-dimensional information multiple times, thereby improving the resolution of the APD detector. Finally, MATLAB is used to simulate the algorithm in this paper by using two-dimensional scalar diffraction theory, which realizes the splitting and scanning with a resolution of 5 x 5. The feasibility is verified theoretically.

Fabrication of three-dimensional hybrid nanostructure-embedded ITO and its application as a transparent electrode for high-efficiency solution processable organic photovoltaic devices.

PubMed

Kim, Jeong Won; Jeon, Hwan-Jin; Lee, Chang-Lyoul; Ahn, Chi Won

2017-03-02

Well-aligned, high-resolution (10 nm), three-dimensional (3D) hybrid nanostructures consisting of patterned cylinders and Au islands were fabricated on ITO substrates using an ion bombardment process and a tilted deposition process. The fabricated 3D hybrid nanostructure-embedded ITO maintained its excellent electrical and optical properties after applying a surface-structuring process. The solution processable organic photovoltaic device (SP-OPV) employing a 3D hybrid nanostructure-embedded ITO as the anode displayed a 10% enhancement in the photovoltaic performance compared to the photovoltaic device prepared using a flat ITO electrode, due to the improved charge collection (extraction and transport) efficiency as well as light absorbance by the photo-active layer.

Two-Dimensional Micro-/Nanoradian Angle Generator with High Resolution and Repeatability Based on Piezo-Driven Double-Axis Flexure Hinge and Three Capacitive Sensors.

PubMed

Tan, Xinran; Zhu, Fan; Wang, Chao; Yu, Yang; Shi, Jian; Qi, Xue; Yuan, Feng; Tan, Jiubin

2017-11-19

This study presents a two-dimensional micro-/nanoradian angle generator (2D-MNAG) that achieves high angular displacement resolution and repeatability using a piezo-driven flexure hinge for two-dimensional deflections and three capacitive sensors for output angle monitoring and feedback control. The principal error of the capacitive sensor for precision microangle measurement is analyzed and compensated for; so as to achieve a high angle output resolution of 10 nrad (0.002 arcsec) and positioning repeatability of 120 nrad (0.024 arcsec) over a large angular range of ±4363 μrad (±900 arcsec) for the 2D-MNAG. The impact of each error component, together with the synthetic error of the 2D-MNAG after principal error compensation are determined using Monte Carlo simulation for further improvement of the 2D-MNAG.

Two-Dimensional Micro-/Nanoradian Angle Generator with High Resolution and Repeatability Based on Piezo-Driven Double-Axis Flexure Hinge and Three Capacitive Sensors

PubMed Central

Tan, Xinran; Zhu, Fan; Wang, Chao; Yu, Yang; Shi, Jian; Qi, Xue; Yuan, Feng; Tan, Jiubin

2017-01-01

This study presents a two-dimensional micro-/nanoradian angle generator (2D-MNAG) that achieves high angular displacement resolution and repeatability using a piezo-driven flexure hinge for two-dimensional deflections and three capacitive sensors for output angle monitoring and feedback control. The principal error of the capacitive sensor for precision microangle measurement is analyzed and compensated for; so as to achieve a high angle output resolution of 10 nrad (0.002 arcsec) and positioning repeatability of 120 nrad (0.024 arcsec) over a large angular range of ±4363 μrad (±900 arcsec) for the 2D-MNAG. The impact of each error component, together with the synthetic error of the 2D-MNAG after principal error compensation are determined using Monte Carlo simulation for further improvement of the 2D-MNAG. PMID:29156595

Three-dimensional structure of a variant `Termamyl-like' Geobacillus stearothermophilus α-amylase at 1.9 Å resolution.

PubMed

Offen, Wendy A; Viksoe-Nielsen, Anders; Borchert, Torben V; Wilson, Keith S; Davies, Gideon J

2015-01-01

The enzyme-catalysed degradation of starch is central to many industrial processes, including sugar manufacture and first-generation biofuels. Classical biotechnological platforms involve steam explosion of starch followed by the action of endo-acting glycoside hydrolases termed α-amylases and then exo-acting α-glucosidases (glucoamylases) to yield glucose, which is subsequently processed. A key enzymatic player in this pipeline is the `Termamyl' class of bacterial α-amylases and designed/evolved variants thereof. Here, the three-dimensional structure of one such Termamyl α-amylase variant based upon the parent Geobacillus stearothermophilus α-amylase is presented. The structure has been solved at 1.9 Å resolution, revealing the classical three-domain fold stabilized by Ca2+ and a Ca2+-Na+-Ca2+ triad. As expected, the structure is similar to the G. stearothermophilus α-amylase but with main-chain deviations of up to 3 Å in some regions, reflecting both the mutations and differing crystal-packing environments.

High Resolution Global Topography of Eros from NEAR Imaging and LIDAR Data

NASA Technical Reports Server (NTRS)

Gaskell, Robert W.; Konopliv, A.; Barnouin-Jha, O.; Scheeres, D.

2006-01-01

Principal Data Products: Ensemble of L-maps from SPC, Spacecraft state, Asteroid pole and rotation. Secondary Products: Global topography model, inertia tensor, gravity. Composite high resolution topography. Three dimensional image maps.

Three-dimensional scanning transmission electron microscopy of biological specimens.

PubMed

de Jonge, Niels; Sougrat, Rachid; Northan, Brian M; Pennycook, Stephen J

2010-02-01

A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2-3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset.

Three-Dimensional Scanning Transmission Electron Microscopy of Biological Specimens

PubMed Central

de Jonge, Niels; Sougrat, Rachid; Northan, Brian M.; Pennycook, Stephen J.

2010-01-01

A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2–3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset. PMID:20082729

Two-dimensional joint inversion of Magnetotelluric and local earthquake data: Discussion on the contribution to the solution of deep subsurface structures

NASA Astrophysics Data System (ADS)

Demirci, İsmail; Dikmen, Ünal; Candansayar, M. Emin

2018-02-01

Joint inversion of data sets collected by using several geophysical exploration methods has gained importance and associated algorithms have been developed. To explore the deep subsurface structures, Magnetotelluric and local earthquake tomography algorithms are generally used individually. Due to the usage of natural resources in both methods, it is not possible to increase data quality and resolution of model parameters. For this reason, the solution of the deep structures with the individual usage of the methods cannot be fully attained. In this paper, we firstly focused on the effects of both Magnetotelluric and local earthquake data sets on the solution of deep structures and discussed the results on the basis of the resolving power of the methods. The presence of deep-focus seismic sources increase the resolution of deep structures. Moreover, conductivity distribution of relatively shallow structures can be solved with high resolution by using MT algorithm. Therefore, we developed a new joint inversion algorithm based on the cross gradient function in order to jointly invert Magnetotelluric and local earthquake data sets. In the study, we added a new regularization parameter into the second term of the parameter correction vector of Gallardo and Meju (2003). The new regularization parameter is enhancing the stability of the algorithm and controls the contribution of the cross gradient term in the solution. The results show that even in cases where resistivity and velocity boundaries are different, both methods influence each other positively. In addition, the region of common structural boundaries of the models are clearly mapped compared with original models. Furthermore, deep structures are identified satisfactorily even with using the minimum number of seismic sources. In this paper, in order to understand the future studies, we discussed joint inversion of Magnetotelluric and local earthquake data sets only in two-dimensional space. In the light of these results and by means of the acceleration on the three-dimensional modelling and inversion algorithms, it is thought that it may be easier to identify underground structures with high resolution.

Incoherent Diffractive Imaging via Intensity Correlations of Hard X Rays

NASA Astrophysics Data System (ADS)

Classen, Anton; Ayyer, Kartik; Chapman, Henry N.; Röhlsberger, Ralf; von Zanthier, Joachim

2017-08-01

Established x-ray diffraction methods allow for high-resolution structure determination of crystals, crystallized protein structures, or even single molecules. While these techniques rely on coherent scattering, incoherent processes like fluorescence emission—often the predominant scattering mechanism—are generally considered detrimental for imaging applications. Here, we show that intensity correlations of incoherently scattered x-ray radiation can be used to image the full 3D arrangement of the scattering atoms with significantly higher resolution compared to conventional coherent diffraction imaging and crystallography, including additional three-dimensional information in Fourier space for a single sample orientation. We present a number of properties of incoherent diffractive imaging that are conceptually superior to those of coherent methods.

High spatial resolution measurements in a single stage ram accelerator

NASA Technical Reports Server (NTRS)

Hinkey, J. B.; Burnham, E. A.; Bruckner, A. P.

1992-01-01

High spatial resolution experimental tube wall pressure measurements of ram accelerator gas dynamic phenomena are presented in this paper. The ram accelerator is a ramjet-in-tube device which operates in a manner similar to that of a conventional ramjet. The projectile resembles the centerbody of a ramjet and travels supersonically through a tube filled with a combustible gaseous mixture, with the tube acting as the outer cowling. Pressure data are recorded as the projectile passes by sensors mounted in the tube wall at various locations along the tube. Utilization of special highly instrumented sections of tube has allowed the recording of gas dynamic phenomena with high resolution. High spatial resolution tube wall pressure data from the three regimes of propulsion studied to date (subdetonative, transdetonative, and superdetonative) in a single stage gas mixture are presented and reveal the three-dimensional character of the flow field induced by projectile fins and the canting of the fins and the canting of the projectile body relative to the tube wall. Also presented for comparison to the experimental data are calculations made with an inviscid, three-dimensional CFD code. The knowledge gained from these experiments and simulations is useful in understanding the underlying nature of ram accelerator propulsive regimes, as well as assisting in the validation of three-dimensional CFD coded which model unsteady, chemically reactive flows.

Focused ion beam assisted three-dimensional rock imaging at submicron scale

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

Tomutsa, Liviu; Radmilovic, Velimir

2003-05-09

Computation of effective flow properties of fluids in porous media based on three dimensional (3D) pore structure information has become more successful in the last few years, due to both improvements in the input data and the network models. Computed X-ray microtomography has been successful in 3D pore imaging at micron scale, which is adequate for many sandstones. For other rocks of economic interest, such as chalk and diatomite, submicron resolution is needed in order to resolve the 3D-pore structure. To achieve submicron resolution, a new method of sample serial sectioning and imaging using Focused Ion Beam (FIB) technology hasmore » been developed and 3D pore images of the pore system for diatomite and chalk have been obtained. FIB was used in the milling of layers as wide as 50 micrometers and as thin as 100 nanometers by sputtering of atoms from the sample surface. The focused ion beam, consisting of gallium ions (Ga+) accelerated by potentials of up to 30 kV and currents up to 20,000 pA, yields very clean, flat surfaces in which the pore-grain boundaries appear in high contrast. No distortion of the pore boundaries due to the ion milling is apparent. After each milling step, as a new surface is exposed, an image of the surface is generated. Using secondary electrons or ions, resolutions as high as 10 nm can be obtained. Afterwards, the series of 2D images can be stacked in the computer and, using appropriate interpolation and surface rendering algorithms, the 3D pore structure is reconstructed.« less

Probing the atomic structure of metallic nanoclusters with the tip of a scanning tunneling microscope.

PubMed

Schouteden, Koen; Lauwaet, Koen; Janssens, Ewald; Barcaro, Giovanni; Fortunelli, Alessandro; Van Haesendonck, Chris; Lievens, Peter

2014-02-21

Preformed Co clusters with an average diameter of 2.5 nm are produced in the gas phase and are deposited under controlled ultra-high vacuum conditions onto a thin insulating NaCl film on Au(111). Relying on a combined experimental and theoretical investigation, we demonstrate visualization of the three-dimensional atomic structure of the Co clusters by high-resolution scanning tunneling microscopy (STM) using a Cl functionalized STM tip that can be obtained on the NaCl surface. More generally, use of a functionalized STM tip may allow for systematic atomic structure determination with STM of nanoparticles that are deposited on metal surfaces.

A Three-Dimensional Atlas of the Honeybee Neck

PubMed Central

Berry, Richard P.; Ibbotson, Michael R.

2010-01-01

Three-dimensional digital atlases are rapidly becoming indispensible in modern biology. We used serial sectioning combined with manual registration and segmentation of images to develop a comprehensive and detailed three-dimensional atlas of the honeybee head-neck system. This interactive atlas includes skeletal structures of the head and prothorax, the neck musculature, and the nervous system. The scope and resolution of the model exceeds atlases previously developed on similar sized animals, and the interactive nature of the model provides a far more accessible means of interpreting and comprehending insect anatomy and neuroanatomy. PMID:20520729

Wave field restoration using three-dimensional Fourier filtering method.

PubMed

Kawasaki, T; Takai, Y; Ikuta, T; Shimizu, R

2001-11-01

A wave field restoration method in transmission electron microscopy (TEM) was mathematically derived based on a three-dimensional (3D) image formation theory. Wave field restoration using this method together with spherical aberration correction was experimentally confirmed in through-focus images of amorphous tungsten thin film, and the resolution of the reconstructed phase image was successfully improved from the Scherzer resolution limit to the information limit. In an application of this method to a crystalline sample, the surface structure of Au(110) was observed in a profile-imaging mode. The processed phase image showed quantitatively the atomic relaxation of the topmost layer.

Noninvasive assessment of the developing Xenopus cardiovascular system using optical coherence tomography

PubMed Central

Boppart, Stephen A.; Tearney, Gary J.; Bouma, Brett E.; Southern, James F.; Brezinski, Mark E.; Fujimoto, James G.

1997-01-01

Studies investigating normal and abnormal cardiac development are frequently limited by an inability to assess cardiovascular function within the intact organism. In this work, optical coherence tomography (OCT), a new method of micron-scale, noninvasive imaging based on the measurement of backscattered infrared light, was introduced for the high resolution assessment of structure and function in the developing Xenopus laevis cardiovascular system. Microstructural details, such as ventricular size and wall positions, were delineated with OCT at 16-μm resolution and correlated with histology. Three-dimensional representation of the cardiovascular system also was achieved by repeated cross-sectional imaging at intervals of 25 μm. In addition to structural information, OCT provides high speed in vivo axial ranging and imaging, allowing quantitative dynamic activity, such as ventricular ejection fraction, to be assessed. The sensitivity of OCT for dynamic assessment was demonstrated with an inotropic agent that altered cardiac function and dimensions. Optical coherence tomography is an attractive new technology for assessing cardiovascular development because of its high resolution, its ability to image through nontransparent structures, and its inexpensive portable design. In vivo and in vitro imaging are performed at a resolution approaching that of histopathology without the need for animal killing. PMID:9113976

Preparation of wholemount mouse intestine for high-resolution three-dimensional imaging using two-photon microscopy.

PubMed

Appleton, P L; Quyn, A J; Swift, S; Näthke, I

2009-05-01

Visualizing overall tissue architecture in three dimensions is fundamental for validating and integrating biochemical, cell biological and visual data from less complex systems such as cultured cells. Here, we describe a method to generate high-resolution three-dimensional image data of intact mouse gut tissue. Regions of highest interest lie between 50 and 200 mum within this tissue. The quality and usefulness of three-dimensional image data of tissue with such depth is limited owing to problems associated with scattered light, photobleaching and spherical aberration. Furthermore, the highest-quality oil-immersion lenses are designed to work at a maximum distance of

A high-resolution three-dimensional far-infrared thermal and true-color imaging system for medical applications.

PubMed

Cheng, Victor S; Bai, Jinfen; Chen, Yazhu

2009-11-01

As the needs for various kinds of body surface information are wide-ranging, we developed an imaging-sensor integrated system that can synchronously acquire high-resolution three-dimensional (3D) far-infrared (FIR) thermal and true-color images of the body surface. The proposed system integrates one FIR camera and one color camera with a 3D structured light binocular profilometer. To eliminate the emotion disturbance of the inspector caused by the intensive light projection directly into the eye from the LCD projector, we have developed a gray encoding strategy based on the optimum fringe projection layout. A self-heated checkerboard has been employed to perform the calibration of different types of cameras. Then, we have calibrated the structured light emitted by the LCD projector, which is based on the stereo-vision idea and the least-squares quadric surface-fitting algorithm. Afterwards, the precise 3D surface can fuse with undistorted thermal and color images. To enhance medical applications, the region-of-interest (ROI) in the temperature or color image representing the surface area of clinical interest can be located in the corresponding position in the other images through coordinate system transformation. System evaluation demonstrated a mapping error between FIR and visual images of three pixels or less. Experiments show that this work is significantly useful in certain disease diagnoses.

An Assessment of Stream Confluence Flow Dynamics using Large Scale Particle Image Velocimetry Captured from Unmanned Aerial Systems

NASA Astrophysics Data System (ADS)

Lewis, Q. W.; Rhoads, B. L.

2017-12-01

The merging of rivers at confluences results in complex three-dimensional flow patterns that influence sediment transport, bed morphology, downstream mixing, and physical habitat conditions. The capacity to characterize comprehensively flow at confluences using traditional sensors, such as acoustic Doppler velocimeters and profiles, is limited by the restricted spatial resolution of these sensors and difficulties in measuring velocities simultaneously at many locations within a confluence. This study assesses two-dimensional surficial patterns of flow structure at a small stream confluence in Illinois, USA, using large scale particle image velocimetry (LSPIV) derived from videos captured by unmanned aerial systems (UAS). The method captures surface velocity patterns at high spatial and temporal resolution over multiple scales, ranging from the entire confluence to details of flow within the confluence mixing interface. Flow patterns at high momentum ratio are compared to flow patterns when the two incoming flows have nearly equal momentum flux. Mean surface flow patterns during the two types of events provide details on mean patterns of surface flow in different hydrodynamic regions of the confluence and on changes in these patterns with changing momentum flux ratio. LSPIV data derived from the highest resolution imagery also reveal general characteristics of large-scale vortices that form along the shear layer between the flows during the high-momentum ratio event. The results indicate that the use of LSPIV and UAS is well-suited for capturing in detail mean surface patterns of flow at small confluences, but that characterization of evolving turbulent structures is limited by scale considerations related to structure size, image resolution, and camera instability. Complementary methods, including camera platforms mounted at fixed positions close to the water surface, provide opportunities to accurately characterize evolving turbulent flow structures in confluences.

Dual-wavelength optical-resolution photoacoustic microscopy for cells with gold nanoparticle bioconjugates in three-dimensional cultures

NASA Astrophysics Data System (ADS)

Lee, Po-Yi; Liu, Wei-Wen; Chen, Shu-Ching; Li, Pai-Chi

2016-03-01

Three-dimensional (3D) in vitro models bridge the gap between typical two-dimensional cultures and in vivo conditions. However, conventional optical imaging methods such as confocal microscopy and two-photon microscopy cannot accurately depict cellular processing in 3D models due to limited penetration of photons. We developed a dualwavelength optical-resolution photoacoustic microscopy (OR-PAM), which provides sufficient penetration depth and spatial resolution, for studying CD8+ cytotoxic T lymphocytes (CTLs) trafficking in an in vitro 3D tumor microenvironment. CTLs play a cardinal role in host defense against tumor. Efficient trafficking of CTLs to the tumor microenvironment is a critical step for cancer immunotherapy. For the proposed system, gold nanospheres and indocyanine green (ICG) have been remarkable choices for contrast agents for photoacoustic signals due to their excellent biocompatibility and high optical absorption. With distinct absorption spectrums, targeted cells with gold nanospheres and ICG respectively can be identified by switching 523-nm and 800-nm laser irradiation. Moreover, we use an x-y galvanometer scanner to obtain high scanning rate. In the developed system, lateral and axial resolutions were designed at 1.6 μm and 5 μm, respectively. We successfully showed that dual-spectral OR-PAM can map either the distribution of CTLs with gold nanospheres at a visible wavelength of 523 nm or the 3D structure of tumor spheres with ICG in an in vitro 3D microenvironment. Our OR-PAM can provide better biological relevant information in cellular interaction and is potential for preclinical screening of anti-cancer drugs.

3D structure of individual nanocrystals in solution by electron microscopy

DOE PAGES

Park, Jungwok; Elmlund, Hans; Ercius, Peter; ...

2015-07-17

Here, knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unorderedmore » nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.« less

Nanoparticle imaging. 3D structure of individual nanocrystals in solution by electron microscopy.

PubMed

Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A; Zettl, A; Alivisatos, A Paul

2015-07-17

Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale. Copyright © 2015, American Association for the Advancement of Science.

3D structure of individual nanocrystals in solution by electron microscopy

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

Park, Jungwok; Elmlund, Hans; Ercius, Peter

Here, knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unorderedmore » nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.« less

3D Structure Determination of Native Mammalian Cells using Cryo-FIB and Cryo-electron Tomography

PubMed Central

Wang, Ke; Strunk, Korrinn; Zhao, Gongpu; Gray, Jennifer L.; Zhang, Peijun

2012-01-01

Cryo-electron tomography (cryo-ET) has enabled high resolution three-dimensional (3D) structural analysis of virus and host cell interactions and many cell signaling events; these studies, however, have largely been limited to very thin, peripheral regions of eukaryotic cells or to small prokaryotic cells. Recent efforts to make thin, vitreous sections using cryo-ultramicrotomy have been successful, however, this method is technically very challenging and with many artifacts. Here, we report a simple and robust method for creating in situ, frozen-hydrated cell lamellas using a focused ion beam at cryogenic temperature (cryo-FIB), allowing access to any interior cellular regions of interest. We demonstrate the utility of cryo-FIB with high resolution 3D cellular structures from both bacterial cells and large mammalian cells. The method will not only facilitate high-throughput 3D structural analysis of biological specimens, but is also broadly applicable to sample preparation of thin films and surface materials without the need for FIB “lift-out”. PMID:22796867

X-Ray Nanofocus CT: Visualising Of Internal 3D-Structures With Submicrometer Resolution

NASA Astrophysics Data System (ADS)

Weinekoetter, Christian

2008-09-01

High-resolution X-ray Computed Tomography (CT) allows the visualization and failure analysis of the internal micro structure of objects—even if they have complicated 3D-structures where 2D X-ray microscopy would give unclear information. During the past several years, computed tomography has progressed to higher resolution and quicker reconstruction of the 3D-volume. Most recently it even allows a three-dimensional look into the inside of materials with submicron resolution. With the use of nanofocus® tube technology, nanoCT®-systems are pushing forward into application fields that were exclusive to high cost and rare available synchrotron techniques. The study was performed with the new nanotom, a very compact laboratory system which allows the analysis of samples up to 120 mm in diameter and weighing up to 1 kg with exceptional voxel-resolution down to <500 nm (<0.5 microns). It is the first 180 kV nanofocus® computed tomography system in the world which is tailored specifically to the highest-resolution applications in the fields of material science, micro electronics, geology and biology. Therefore it is particularly suitable for nanoCT-examinations e.g. of synthetic materials, metals, ceramics, composite materials, mineral and organic samples. There are a few physical effects influencing the CT quality, such as beam-hardening within the sample or ring-artefacts, which can not be completely avoided. To optimize the quality of high resolution 3D volumes, the nanotom® includes a variety of effective software tools to reduce ring-artefacts and correct beam hardenings or drift effects which occurred during data acquisition. The resulting CT volume data set can be displayed in various ways, for example by virtual slicing and sectional views in any direction of the volume. By the fact that this requires only a mouse click, this technique will substitute destructive mechanical slicing and cutting in many applications. The initial CT results obtained with the nanotom® demonstrate that it is now possible to analyze the three-dimensional micro structure of materials and small objects with submicrometer resolution. Any internal difference in material, density or porosity within a sample can be visualized and data like distances can be measured. NanoCT® widely expands the spectrum of detectable micro-structures. The nanotom® opens a new dimension of 3D-microanalysis and will replace more destructive methods—saving costs and time per sample inspected.

Predicting nucleic acid binding interfaces from structural models of proteins

PubMed Central

Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

2011-01-01

The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared to patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. PMID:22086767

Improved imaging of cochlear nerve hypoplasia using a 3-Tesla variable flip-angle turbo spin-echo sequence and a 7-cm surface coil.

PubMed

Giesemann, Anja M; Raab, Peter; Lyutenski, Stefan; Dettmer, Sabine; Bültmann, Eva; Frömke, Cornelia; Lenarz, Thomas; Lanfermann, Heinrich; Goetz, Friedrich

2014-03-01

Magnetic resonance imaging of the temporal bone has an important role in decision making with regard to cochlea implantation, especially in children with cochlear nerve deficiency. The purpose of this study was to evaluate the usefulness of the combination of an advanced high-resolution T2-weighted sequence with a surface coil in a 3-Tesla magnetic resonance imaging scanner in cases of suspected cochlear nerve aplasia. Prospective study. Seven patients with cochlear nerve hypoplasia or aplasia were prospectively examined using a high-resolution three-dimensional variable flip-angle turbo spin-echo sequence using a surface coil, and the images were compared with the same sequence in standard resolution using a standard head coil. Three neuroradiologists evaluated the magnetic resonance images independently, rating the visibility of the nerves in diagnosing hypoplasia or aplasia. Eight ears in seven patients with hypoplasia or aplasia of the cochlear nerve were examined. The average age was 2.7 years (range, 9 months-5 years). Seven ears had accompanying malformations. The inter-rater reliability in diagnosing hypoplasia or aplasia was greater using the high-resolution three-dimensional variable flip-angle turbo spin-echo sequence (fixed-marginal kappa: 0.64) than with the same sequence in lower resolution (fixed-marginal kappa: 0.06). Examining cases of suspected cochlear nerve aplasia using the high-resolution three-dimensional variable flip-angle turbo spin-echo sequence in combination with a surface coil shows significant improvement over standard methods. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

Three-dimensional hydrogen microscopy using a high-energy proton probe

NASA Astrophysics Data System (ADS)

Dollinger, G.; Reichart, P.; Datzmann, G.; Hauptner, A.; Körner, H.-J.

2003-01-01

It is a challenge to measure two-dimensional or three-dimensional (3D) hydrogen profiles on a micrometer scale. Quantitative hydrogen analyses of micrometer resolution are demonstrated utilizing proton-proton scattering at a high-energy proton microprobe. It has more than an-order-of-magnitude better position resolution and in addition higher sensitivity than any other technique for 3D hydrogen analyses. This type of hydrogen imaging opens plenty room to characterize microstructured materials, and semiconductor devices or objects in microbiology. The first hydrogen image obtained with a 10 MeV proton microprobe shows the hydrogen distribution of the microcapillary system being present in the wing of a mayfly and demonstrates the potential of the method.

A new Lagrangian method for three-dimensional steady supersonic flows

NASA Technical Reports Server (NTRS)

Loh, Ching-Yuen; Liou, Meng-Sing

1993-01-01

In this report, the new Lagrangian method introduced by Loh and Hui is extended for three-dimensional, steady supersonic flow computation. The derivation of the conservation form and the solution of the local Riemann solver using the Godunov and the high-resolution TVD (total variation diminished) scheme is presented. This new approach is accurate and robust, capable of handling complicated geometry and interactions between discontinuous waves. Test problems show that the extended Lagrangian method retains all the advantages of the two-dimensional method (e.g., crisp resolution of a slip-surface (contact discontinuity) and automatic grid generation). In this report, we also suggest a novel three dimensional Riemann problem in which interesting and intricate flow features are present.

Dynamic-focusing microscope objective for optical coherence tomography

NASA Astrophysics Data System (ADS)

Murali, Supraja; Rolland, Jannick

2007-01-01

Optical Coherence Tomography (OCT) is a novel optical imaging technique that has assumed significant importance in bio-medical imaging in the last two decades because it is non-invasive and provides accurate, high resolution images of three dimensional cross-sections of body tissue, exceeding the capabilities of the current predominant imaging technique - ultrasound. In this paper, the application of high resolution OCT, known as optical coherence microscopy (OCM) is investigated for in vivo detection of abnormal skin pathology for the early diagnosis of cancer. A main challenge in OCM is maintaining invariant resolution throughout the sample. The technology presented is based on a dynamic focusing microscope imaging probe conceived for skin imaging and the detection of abnormalities in the epithelium. A novel method for dynamic focusing in the biological sample is presented using variable-focus lens technology to obtain three dimensional images with invariant resolution throughout the cross-section and depth of the sample is presented and discussed. A low coherence broadband source centered at near IR wavelengths is used to illuminate the sample. The design, analysis and predicted performance of the dynamic focusing microscope objective designed for dynamic three dimensional imaging at 5μm resolution for the chosen broadband spectrum is presented.

Multi-slice ptychography with large numerical aperture multilayer Laue lenses

DOE PAGES

Ozturk, Hande; Yan, Hanfei; He, Yan; ...

2018-05-09

Here, the highly convergent x-ray beam focused by multilayer Laue lenses with large numerical apertures is used as a three-dimensional (3D) probe to image layered structures with an axial separation larger than the depth of focus. Instead of collecting weakly scattered high-spatial-frequency signals, the depth-resolving power is provided purely by the intense central cone diverged from the focused beam. Using the multi-slice ptychography method combined with the on-the-fly scan scheme, two layers of nanoparticles separated by 10 μm are successfully reconstructed with 8.1 nm lateral resolution and with a dwell time as low as 0.05 s per scan point. Thismore » approach obtains high-resolution images with extended depth of field, which paves the way for multi-slice ptychography as a high throughput technique for high-resolution 3D imaging of thick samples.« less

Multi-slice ptychography with large numerical aperture multilayer Laue lenses

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

Ozturk, Hande; Yan, Hanfei; He, Yan

Here, the highly convergent x-ray beam focused by multilayer Laue lenses with large numerical apertures is used as a three-dimensional (3D) probe to image layered structures with an axial separation larger than the depth of focus. Instead of collecting weakly scattered high-spatial-frequency signals, the depth-resolving power is provided purely by the intense central cone diverged from the focused beam. Using the multi-slice ptychography method combined with the on-the-fly scan scheme, two layers of nanoparticles separated by 10 μm are successfully reconstructed with 8.1 nm lateral resolution and with a dwell time as low as 0.05 s per scan point. Thismore » approach obtains high-resolution images with extended depth of field, which paves the way for multi-slice ptychography as a high throughput technique for high-resolution 3D imaging of thick samples.« less

S = 1 on a Diamond Lattice in NiRh2O4

NASA Astrophysics Data System (ADS)

Chamorro, Juan; McQueen, Tyrel

An S = 1 system has the potential of rich physics, and has been the subject of intense theoretical work. Extensive work has been done on one-dimensional and two-dimensional S = 1 systems, yet three dimensional systems remain elusive. Experimental realizations of three-dimensional S = 1, however, are limited, and no system to date has been found to genuinely harbor this. Recent theoretical work suggests that S = 1 on a diamond lattice would enable a novel topological paramagnet state, generated by fluctuating Haldane chains within the structure, with topologically protected end states. Here we present data on NiRh2O4, a tetragonal spinel that has a structural phase transition from cubic to tetragonal at T = 380 K. High resolution XRD shows it to have a tetragonally distorted spinel structure, with Ni2+ (d8, S = 1) on the tetrahedral, diamond sublattice site. Magnetic susceptibility and specific heat measurements show that it does not order magnetically down to T = 0.1 K. Nearest neighbor interactions remain the same despite the cubic to tetragonal phase transition. Comparison to theoretical models indicate that this system might fulfill the requirements necessary to have both highly entangled and topological behaviors. IQM Is Funded by US Department of Energy, Office of Basic Energy Sciences, Division of Material Sciences and Engineering, under Grant No. DE-FG02-08ER46544.

Enhancing multi-spot structured illumination microscopy with fluorescence difference

NASA Astrophysics Data System (ADS)

Ward, Edward N.; Torkelsen, Frida H.; Pal, Robert

2018-03-01

Structured illumination microscopy is a super-resolution technique used extensively in biological research. However, this technique is limited in the maximum possible resolution increase. Here we report the results of simulations of a novel enhanced multi-spot structured illumination technique. This method combines the super-resolution technique of difference microscopy with structured illumination deconvolution. Initial results give at minimum a 1.4-fold increase in resolution over conventional structured illumination in a low-noise environment. This new technique also has the potential to be expanded to further enhance axial resolution with three-dimensional difference microscopy. The requirement for precise pattern determination in this technique also led to the development of a new pattern estimation algorithm which proved more efficient and reliable than other methods tested.

Three-dimensional representation of the human cochlea using micro-computed tomography data: presenting an anatomical model for further numerical calculations.

PubMed

Braun, Katharina; Böhnke, Frank; Stark, Thomas

2012-06-01

We present a complete geometric model of the human cochlea, including the segmentation and reconstruction of the fluid-filled chambers scala tympani and scala vestibuli, the lamina spiralis ossea and the vibrating structure (cochlear partition). Future fluid-structure coupled simulations require a reliable geometric model of the cochlea. The aim of this study was to present an anatomical model of the human cochlea, which can be used for further numerical calculations. Using high resolution micro-computed tomography (µCT), we obtained images of a cut human temporal bone with a spatial resolution of 5.9 µm. Images were manually segmented to obtain the three-dimensional reconstruction of the cochlea. Due to the high resolution of the µCT data, a detailed examination of the geometry of the twisted cochlear partition near the oval and the round window as well as the precise illustration of the helicotrema was possible. After reconstruction of the lamina spiralis ossea, the cochlear partition and the curved geometry of the scala vestibuli and the scala tympani were presented. The obtained data sets were exported as standard lithography (stl) files. These files represented a complete framework for future numerical simulations of mechanical (acoustic) wave propagation on the cochlear partition in the form of mathematical mechanical cochlea models. Additional quantitative information concerning heights, lengths and volumes of the scalae was found and compared with previous results.

Three-dimensional digital holographic aperture synthesis for rapid and highly-accurate large-volume metrology

NASA Astrophysics Data System (ADS)

Crouch, Stephen; Kaylor, Brant M.; Barber, Zeb W.; Reibel, Randy R.

2015-09-01

Currently large volume, high accuracy three-dimensional (3D) metrology is dominated by laser trackers, which typically utilize a laser scanner and cooperative reflector to estimate points on a given surface. The dependency upon the placement of cooperative targets dramatically inhibits the speed at which metrology can be conducted. To increase speed, laser scanners or structured illumination systems can be used directly on the surface of interest. Both approaches are restricted in their axial and lateral resolution at longer stand-off distances due to the diffraction limit of the optics used. Holographic aperture ladar (HAL) and synthetic aperture ladar (SAL) can enhance the lateral resolution of an imaging system by synthesizing much larger apertures by digitally combining measurements from multiple smaller apertures. Both of these approaches only produce two-dimensional imagery and are therefore not suitable for large volume 3D metrology. We combined the SAL and HAL approaches to create a swept frequency digital holographic 3D imaging system that provides rapid measurement speed for surface coverage with unprecedented axial and lateral resolution at longer standoff ranges. The technique yields a "data cube" of Fourier domain data, which can be processed with a 3D Fourier transform to reveal a 3D estimate of the surface. In this paper, we provide the theoretical background for the technique and show experimental results based on an ultra-wideband frequency modulated continuous wave (FMCW) chirped heterodyne ranging system showing ~100 micron lateral and axial precisions at >2 m standoff distances.

High-resolution three-dimensional imaging radar

NASA Technical Reports Server (NTRS)

Cooper, Ken B. (Inventor); Chattopadhyay, Goutam (Inventor); Siegel, Peter H. (Inventor); Dengler, Robert J. (Inventor); Schlecht, Erich T. (Inventor); Mehdi, Imran (Inventor); Skalare, Anders J. (Inventor)

2010-01-01

A three-dimensional imaging radar operating at high frequency e.g., 670 GHz, is disclosed. The active target illumination inherent in radar solves the problem of low signal power and narrow-band detection by using submillimeter heterodyne mixer receivers. A submillimeter imaging radar may use low phase-noise synthesizers and a fast chirper to generate a frequency-modulated continuous-wave (FMCW) waveform. Three-dimensional images are generated through range information derived for each pixel scanned over a target. A peak finding algorithm may be used in processing for each pixel to differentiate material layers of the target. Improved focusing is achieved through a compensation signal sampled from a point source calibration target and applied to received signals from active targets prior to FFT-based range compression to extract and display high-resolution target images. Such an imaging radar has particular application in detecting concealed weapons or contraband.

Increasing the electron-transfer ability of Cyanidioschyzon merolae ferredoxin by a one-point mutation – A high resolution and Fe-SAD phasing crystal structure analysis of the Asp58Asn mutant

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

Ueno, Yuko; Matsumoto, Takashi; Yamano, Akihito

2013-07-12

Highlights: •A single amino acid change on the ferredoxin surface affects electron transfer. •Precise positions of amide atoms were located utilizing no prior structural data. •Ultra high resolution and SAD phasing may be used for bias-free model building. -- Abstract: Cyanidioschyzon merolae (Cm) is a single cell red algae that grows in rather thermophilic (40–50 °C) and acidic (pH 1–3) conditions. Ferredoxin (Fd) was purified from this algae and characterized as a plant-type [2Fe–2S] Fd by physicochemical techniques. A high resolution (0.97 Å) three-dimensional structure of the CmFd D58N mutant molecule has been determined using the Fe-SAD phasing method tomore » clarify the precise position of the Asn58 amide, as this substitution increases the electron-transfer ability relative to wild-type CmFd by a factor of 1.5. The crystal structure reveals an electro-positive surface surrounding Asn58 that may interact with ferredoxin NADP{sup +} reductase or cytochrome c.« less

Anisotropic S-wave velocity structure from joint inversion of surface wave group velocity dispersion: A case study from India

NASA Astrophysics Data System (ADS)

Mitra, S.; Dey, S.; Siddartha, G.; Bhattacharya, S.

2016-12-01

We estimate 1-dimensional path average fundamental mode group velocity dispersion curves from regional Rayleigh and Love waves sampling the Indian subcontinent. The path average measurements are combined through a tomographic inversion to obtain 2-dimensional group velocity variation maps between periods of 10 and 80 s. The region of study is parametrised as triangular grids with 1° sides for the tomographic inversion. Rayleigh and Love wave dispersion curves from each node point is subsequently extracted and jointly inverted to obtain a radially anisotropic shear wave velocity model through global optimisation using Genetic Algorithm. The parametrization of the model space is done using three crustal layers and four mantle layers over a half-space with varying VpH , VsV and VsH. The anisotropic parameter (η) is calculated from empirical relations and the density of the layers are taken from PREM. Misfit for the model is calculated as a sum of error-weighted average dispersion curves. The 1-dimensional anisotropic shear wave velocity at each node point is combined using linear interpolation to obtain 3-dimensional structure beneath the region. Synthetic tests are performed to estimate the resolution of the tomographic maps which will be presented with our results. We envision to extend this to a larger dataset in near future to obtain high resolution anisotrpic shear wave velocity structure beneath India, Himalaya and Tibet.

Fractal-like hierarchical organization of bone begins at the nanoscale

NASA Astrophysics Data System (ADS)

Reznikov, Natalie; Bilton, Matthew; Lari, Leonardo; Stevens, Molly M.; Kröger, Roland

2018-05-01

The components of bone assemble hierarchically to provide stiffness and toughness. However, the organization and relationship between bone’s principal components—mineral and collagen—has not been clearly elucidated. Using three-dimensional electron tomography imaging and high-resolution two-dimensional electron microscopy, we demonstrate that bone mineral is hierarchically assembled beginning at the nanoscale: Needle-shaped mineral units merge laterally to form platelets, and these are further organized into stacks of roughly parallel platelets. These stacks coalesce into aggregates that exceed the lateral dimensions of the collagen fibrils and span adjacent fibrils as continuous, cross-fibrillar mineralization. On the basis of these observations, we present a structural model of hierarchy and continuity for the mineral phase, which contributes to the structural integrity of bone.

Three-dimensional imaging of adherent cells using FIB/SEM and STEM.

PubMed

Villinger, Clarissa; Schauflinger, Martin; Gregorius, Heiko; Kranz, Christine; Höhn, Katharina; Nafeey, Soufi; Walther, Paul

2014-01-01

In this chapter we describe three different approaches for three-dimensional imaging of electron microscopic samples: serial sectioning transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM) tomography, and focused ion beam/scanning electron microscopy (FIB/SEM) tomography. With these methods, relatively large volumes of resin-embedded biological structures can be analyzed at resolutions of a few nm within a reasonable expenditure of time. The traditional method is serial sectioning and imaging the same area in all sections. Another method is TEM tomography that involves tilting a section in the electron beam and then reconstruction of the volume by back projection of the images. When the scanning transmission (STEM) mode is used, thicker sections (up to 1 μm) can be analyzed. The third approach presented here is focused ion beam/scanning electron microscopy (FIB/SEM) tomography, in which a sample is repeatedly milled with a focused ion beam (FIB) and each newly produced block face is imaged with the scanning electron microscope (SEM). This process can be repeated ad libitum in arbitrary small increments allowing 3D analysis of relatively large volumes such as eukaryotic cells. We show that resolution of this approach is considerably improved when the secondary electron signal is used. However, the most important prerequisite for three-dimensional imaging is good specimen preparation. For all three imaging methods, cryo-fixed (high-pressure frozen) and freeze-substituted samples have been used.

Three-dimensional nanoscale characterisation of materials by atom probe tomography

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

Devaraj, Arun; Perea, Daniel E.; Liu, Jia

The development of three-dimensional (3D), characterization techniques with high spatial and mass resolution is crucial for understanding and developing advanced materials for many engineering applications as well as for understanding natural materials. In recent decades, atom probe tomography (APT) which combines a point projection microscope and time-of-flight mass spectrometer has evolved to be an excellent characterization technique capable of providing 3D nanoscale characterization of materials with sub-nanometer scale spatial resolution, with equal sensitivity for all elements. This review discusses the current state as of beginning of the year 2016 of APT instrumentation, new developments in sample preparation methods, experimental proceduresmore » for different material classes, reconstruction of APT results, the current status of correlative microscopy, and application of APT for microstructural characterization in established scientific areas like structural materials as well as new applications in semiconducting nanowires, semiconductor devices, battery materials, catalyst materials, geological materials and biological materials. Finally, a brief perspective is given regarding the future of APT.« less

A volumetric three-dimensional digital light photoactivatable dye display

NASA Astrophysics Data System (ADS)

Patel, Shreya K.; Cao, Jian; Lippert, Alexander R.

2017-07-01

Volumetric three-dimensional displays offer spatially accurate representations of images with a 360° view, but have been difficult to implement due to complex fabrication requirements. Herein, a chemically enabled volumetric 3D digital light photoactivatable dye display (3D Light PAD) is reported. The operating principle relies on photoactivatable dyes that become reversibly fluorescent upon illumination with ultraviolet light. Proper tuning of kinetics and emission wavelengths enables the generation of a spatial pattern of fluorescent emission at the intersection of two structured light beams. A first-generation 3D Light PAD was fabricated using the photoactivatable dye N-phenyl spirolactam rhodamine B, a commercial picoprojector, an ultraviolet projector and a custom quartz imaging chamber. The system displays a minimum voxel size of 0.68 mm3, 200 μm resolution and good stability over repeated `on-off' cycles. A range of high-resolution 3D images and animations can be projected, setting the foundation for widely accessible volumetric 3D displays.

A volumetric three-dimensional digital light photoactivatable dye display

PubMed Central

Patel, Shreya K.; Cao, Jian; Lippert, Alexander R.

2017-01-01

Volumetric three-dimensional displays offer spatially accurate representations of images with a 360° view, but have been difficult to implement due to complex fabrication requirements. Herein, a chemically enabled volumetric 3D digital light photoactivatable dye display (3D Light PAD) is reported. The operating principle relies on photoactivatable dyes that become reversibly fluorescent upon illumination with ultraviolet light. Proper tuning of kinetics and emission wavelengths enables the generation of a spatial pattern of fluorescent emission at the intersection of two structured light beams. A first-generation 3D Light PAD was fabricated using the photoactivatable dye N-phenyl spirolactam rhodamine B, a commercial picoprojector, an ultraviolet projector and a custom quartz imaging chamber. The system displays a minimum voxel size of 0.68 mm3, 200 μm resolution and good stability over repeated ‘on-off’ cycles. A range of high-resolution 3D images and animations can be projected, setting the foundation for widely accessible volumetric 3D displays. PMID:28695887

Spectral tailoring of nanoscale EUV and soft x-ray multilayer optics

NASA Astrophysics Data System (ADS)

Huang, Qiushi; Medvedev, Viacheslav; van de Kruijs, Robbert; Yakshin, Andrey; Louis, Eric; Bijkerk, Fred

2017-03-01

Extreme ultraviolet and soft X-ray (XUV) multilayer optics have experienced significant development over the past few years, particularly on controlling the spectral characteristics of light for advanced applications like EUV photolithography, space observation, and accelerator- or lab-based XUV experiments. Both planar and three dimensional multilayer structures have been developed to tailor the spectral response in a wide wavelength range. For the planar multilayer optics, different layered schemes are explored. Stacks of periodic multilayers and capping layers are demonstrated to achieve multi-channel reflection or suppression of the reflective properties. Aperiodic multilayer structures enable broadband reflection both in angles and wavelengths, with the possibility of polarization control. The broad wavelength band multilayer is also used to shape attosecond pulses for the study of ultrafast phenomena. Narrowband multilayer monochromators are delivered to bridge the resolution gap between crystals and regular multilayers. High spectral purity multilayers with innovated anti-reflection structures are shown to select spectrally clean XUV radiation from broadband X-ray sources, especially the plasma sources for EUV lithography. Significant progress is also made in the three dimensional multilayer optics, i.e., combining micro- and nanostructures with multilayers, in order to provide new freedom to tune the spectral response. Several kinds of multilayer gratings, including multilayer coated gratings, sliced multilayer gratings, and lamellar multilayer gratings are being pursued for high resolution and high efficiency XUV spectrometers/monochromators, with their advantages and disadvantages, respectively. Multilayer diffraction optics are also developed for spectral purity enhancement. New structures like gratings, zone plates, and pyramids that obtain full suppression of the unwanted radiation and high XUV reflectance are reviewed. Based on the present achievement of the spectral tailoring multilayer optics, the remaining challenges and opportunities for future researches are discussed.

Retinal Optical Coherence Tomography Imaging

NASA Astrophysics Data System (ADS)

Drexler, Wolfgang; Fujimoto, James G.

The eye is essentially transparent, transmitting light with only minimal optical attenuation and scattering providing easy optical access to the anterior segment as well as the retina. For this reason, ophthalmic and especially retinal imaging has been not only the first but also most successful clinical application for optical coherence tomography (OCT). This chapter focuses on the development of OCT technology for retinal imaging. OCT has significantly improved the potential for early diagnosis, understanding of retinal disease pathogenesis, as well as monitoring disease progression and response to therapy. Development of ultrabroad bandwidth light sources and high-speed detection techniques has enabled significant improvements in ophthalmic OCT imaging performance, demonstrating the potential of three-dimensional, ultrahigh-resolution OCT (UHR OCT) to perform noninvasive optical biopsy of the living human retina, i.e., the in vivo visualization of microstructural, intraretinal morphology in situ approaching the resolution of conventional histopathology. Significant improvements in axial resolution and speed not only enable three-dimensional rendering of retinal volumes but also high-definition, two-dimensional tomograms, topographic thickness maps of all major intraretinal layers, as well as volumetric quantification of pathologic intraretinal changes. These advances in OCT technology have also been successfully applied in several animal models of retinal pathologies. The development of light sources emitting at alternative wavelengths, e.g., around #1,060 nm, not only enabled three-dimensional OCT imaging with enhanced choroidal visualization but also improved OCT performance in cataract patients due to reduced scattering losses in this wavelength region. Adaptive optics using deformable mirror technology, with unique high stroke to correct higher-order ocular aberrations, with specially designed optics to compensate chromatic aberration of the human eye, in combination with three-dimensional UHR OCT, recently enabled in vivo cellular resolution retinal imaging.

High-order ENO schemes applied to two- and three-dimensional compressible flow

NASA Technical Reports Server (NTRS)

Shu, Chi-Wang; Erlebacher, Gordon; Zang, Thomas A.; Whitaker, David; Osher, Stanley

1991-01-01

High order essentially non-oscillatory (ENO) finite difference schemes are applied to the 2-D and 3-D compressible Euler and Navier-Stokes equations. Practical issues, such as vectorization, efficiency of coding, cost comparison with other numerical methods, and accuracy degeneracy effects, are discussed. Numerical examples are provided which are representative of computational problems of current interest in transition and turbulence physics. These require both nonoscillatory shock capturing and high resolution for detailed structures in the smooth regions and demonstrate the advantage of ENO schemes.

Soft Tissue Structure Modelling for Use in Orthopaedic Applications and Musculoskeletal Biomechanics

NASA Astrophysics Data System (ADS)

Audenaert, E. A.; Mahieu, P.; van Hoof, T.; Pattyn, C.

2009-12-01

We present our methodology for the three-dimensional anatomical and geometrical description of soft tissues, relevant for orthopaedic surgical applications and musculoskeletal biomechanics. The technique involves the segmentation and geometrical description of muscles and neurovascular structures from high-resolution computer tomography scanning for the reconstruction of generic anatomical models. These models can be used for quantitative interpretation of anatomical and biomechanical aspects of different soft tissue structures. This approach should allow the use of these data in other application fields, such as musculoskeletal modelling, simulations for radiation therapy, and databases for use in minimally invasive, navigated and robotic surgery.

High resolution structural characterisation of laser-induced defect clusters inside diamond

NASA Astrophysics Data System (ADS)

Salter, Patrick S.; Booth, Martin J.; Courvoisier, Arnaud; Moran, David A. J.; MacLaren, Donald A.

2017-08-01

Laser writing with ultrashort pulses provides a potential route for the manufacture of three-dimensional wires, waveguides, and defects within diamond. We present a transmission electron microscopy study of the intrinsic structure of the laser modifications and reveal a complex distribution of defects. Electron energy loss spectroscopy indicates that the majority of the irradiated region remains as sp3 bonded diamond. Electrically conductive paths are attributed to the formation of multiple nano-scale, sp2-bonded graphitic wires and a network of strain-relieving micro-cracks.

Do Gender-Specific and High-Resolution Three Dimensional Body Charts Facilitate the Communication of Pain for Women? A Quantitative and Qualitative Study

PubMed Central

Egsgaard, Line Lindhardt

2016-01-01

Background Chronic pain is more prevalent among women; however, the majority of standardized pain drawings are often collected using male-like androgynous body representations. Objective The purpose of this study was to assess whether gender-specific and high-resolution three-dimensional (3D) body charts facilitate the communication of pain for women. Methods Using mixed-methods and a cross-over design, female patients with chronic pain were asked to provide detailed drawings of their current pain on masculine and feminine two-dimensional (2D) body schemas (N=41, Part I) or on female 2D and 3D high-resolution body schemas (N=41, Part II) on a computer tablet. The consistency of the drawings between body charts were assessed by intraclass correlation coefficient (ICC) and Bland-Altman plots. Semistructured interviews and a preference questionnaire were then used to obtain qualitative and quantitative responses of the drawing experience. Results The consistency between body charts were high (Part I: ICC=0.980, Part II: ICC=0.994). The preference ratio for the masculine to feminine body schemas were 6:35 and 18:23 for the 2D to 3D female body charts. Patients reported that the 3D body chart enabled a more accurate expression of their pain due to the detailed contours of the musculature and bone structure, however, patients also reported the 3D body chart was too human and believed that skin-like appearance limited ‘deep pain’ expressions. Conclusions Providing gender-specific body charts may facilitate the communication of pain and the level of detail (2D vs 3D body charts) should be used according to patients’ needs. PMID:27440737

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

PubMed

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

2015-06-02

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

Reconstruction of three-dimensional porous media using generative adversarial neural networks

NASA Astrophysics Data System (ADS)

Mosser, Lukas; Dubrule, Olivier; Blunt, Martin J.

2017-10-01

To evaluate the variability of multiphase flow properties of porous media at the pore scale, it is necessary to acquire a number of representative samples of the void-solid structure. While modern x-ray computer tomography has made it possible to extract three-dimensional images of the pore space, assessment of the variability in the inherent material properties is often experimentally not feasible. We present a method to reconstruct the solid-void structure of porous media by applying a generative neural network that allows an implicit description of the probability distribution represented by three-dimensional image data sets. We show, by using an adversarial learning approach for neural networks, that this method of unsupervised learning is able to generate representative samples of porous media that honor their statistics. We successfully compare measures of pore morphology, such as the Euler characteristic, two-point statistics, and directional single-phase permeability of synthetic realizations with the calculated properties of a bead pack, Berea sandstone, and Ketton limestone. Results show that generative adversarial networks can be used to reconstruct high-resolution three-dimensional images of porous media at different scales that are representative of the morphology of the images used to train the neural network. The fully convolutional nature of the trained neural network allows the generation of large samples while maintaining computational efficiency. Compared to classical stochastic methods of image reconstruction, the implicit representation of the learned data distribution can be stored and reused to generate multiple realizations of the pore structure very rapidly.

Parallel Computation and Visualization of Three-dimensional, Time-dependent, Thermal Convective Flows

NASA Technical Reports Server (NTRS)

Wang, P.; Li, P.

1998-01-01

A high-resolution numerical study on parallel systems is reported on three-dimensional, time-dependent, thermal convective flows. A parallel implentation on the finite volume method with a multigrid scheme is discussed, and a parallel visualization systemm is developed on distributed systems for visualizing the flow.

Comparison of propagation-based phase-contrast tomography approaches for the evaluation of dentin microstructure

NASA Astrophysics Data System (ADS)

Deyhle, Hans; Weitkamp, Timm; Lang, Sabrina; Schulz, Georg; Rack, Alexander; Zanette, Irene; Müller, Bert

2012-10-01

The complex hierarchical structure of human tooth hard tissues, enamel and dentin, guarantees function for decades. On the micrometer level the dentin morphology is dominated by the tubules, micrometer-narrow channels extending from the dentin-enamel junction to the pulp chamber. Their structure has been extensively studied, mainly with two-dimensional approaches. Dentin tubules are formed during tooth growth and their orientation is linked to the morphology of the nanometer-sized components, which is of interest for example for the development of bio-inspired dental fillings. Therefore, a method has to be identified that can access the three-dimensional organization of the tubules, e.g. density and orientation. Tomographic setups with pixel sizes in the sub-micrometer range allow for the three-dimensional visualization of tooth dentin tubules both in phase and absorption contrast modes. We compare high-resolution tomographic scans reconstructed with propagation based phase retrieval algorithms as well as reconstructions without phase retrieval concerning spatial and density resolution as well as rendering of the dentin microstructure to determine the approach best suited for dentin tubule imaging. Reasonable results were obtained with a single-distance phase retrieval algorithm and a propagation distance of about 75% of the critical distance of d2/λ, where d is the size of the smallest objects identifiable in the specimen and λ is the X-ray wavelength.

Casting inorganic structures with DNA molds

PubMed Central

Sun, Wei; Boulais, Etienne; Hakobyan, Yera; Wang, Wei Li; Guan, Amy; Bathe, Mark; Yin, Peng

2014-01-01

We report a general strategy for designing and synthesizing inorganic nanostructures with arbitrarily prescribed three-dimensional shapes. Computationally designed DNA strands self-assemble into a stiff “nano-mold” that contains a user-specified three-dimensional cavity and encloses a nucleating gold “seed”. Under mild conditions, this seed grows into a larger cast structure that fills and thus replicates the cavity. We synthesized a variety of nanoparticles with three nanometer resolution: three distinct silver cuboids with three independently tunable dimensions, silver and gold nanoparticles with diverse cross sections, and composite structures with homo-/heterogeneous components. The designer equilateral silver triangular and spherical nanoparticles exhibited plasmonic properties consistent with electromagnetism-based simulations. Our framework is generalizable to more complex geometries and diverse inorganic materials, offering a range of applications in biosensing, photonics, and nanoelectronics. PMID:25301973

High-resolution echocardiography

NASA Technical Reports Server (NTRS)

Nathan, R.

1979-01-01

High resolution computer aided ultrasound system provides two-and three-dimensional images of beating heart from many angles. System provides means for determining whether small blood vessels around the heart are blocked or if heart wall is moving normally without interference of dead and noncontracting muscle tissue.

Enhancing multi-spot structured illumination microscopy with fluorescence difference

PubMed Central

Torkelsen, Frida H.

2018-01-01

Structured illumination microscopy is a super-resolution technique used extensively in biological research. However, this technique is limited in the maximum possible resolution increase. Here we report the results of simulations of a novel enhanced multi-spot structured illumination technique. This method combines the super-resolution technique of difference microscopy with structured illumination deconvolution. Initial results give at minimum a 1.4-fold increase in resolution over conventional structured illumination in a low-noise environment. This new technique also has the potential to be expanded to further enhance axial resolution with three-dimensional difference microscopy. The requirement for precise pattern determination in this technique also led to the development of a new pattern estimation algorithm which proved more efficient and reliable than other methods tested. PMID:29657751

Electron beam enhanced surface modification for making highly resolved structures

DOEpatents

Pitts, John R.

1986-01-01

A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

Electron beam enhanced surface modification for making highly resolved structures

DOEpatents

Pitts, J.R.

1984-10-10

A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

Life in the fast lane for protein crystallization and X-ray crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2005-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Life in the Fast Lane for Protein Crystallization and X-Ray Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2004-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today s high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Contribution of high-resolution correlative imaging techniques in the study of the liver sieve in three-dimensions.

PubMed

Braet, Filip; Wisse, Eddie; Bomans, Paul; Frederik, Peter; Geerts, Willie; Koster, Abraham; Soon, Lilian; Ringer, Simon

2007-03-01

Correlative microscopy has become increasingly important for the analysis of the structure, function, and dynamics of cells. This is largely due to the result of recent advances in light-, probe-, laser- and various electron microscopy techniques that facilitate three-dimensional studies. Furthermore, the improved understanding in the past decade of imaging cell compartments in the third dimension has resulted largely from the availability of powerful computers, fast high-resolution CCD cameras, specifically developed imaging analysis software, and various probes designed for labeling living and or fixed cells. In this paper, we review different correlative high-resolution imaging methodologies and how these microscopy techniques facilitated the accumulation of new insights in the morpho-functional and structural organization of the hepatic sieve. Various aspects of hepatic endothelial fenestrae regarding their structure, origin, dynamics, and formation will be explored throughout this paper by comparing the results of confocal laser scanning-, correlative fluorescence and scanning electron-, atomic force-, and whole-mount electron microscopy. Furthermore, the recent advances of vitrifying cells with the vitrobot in combination with the glove box for the preparation of cells for cryo-electron microscopic investigation will be discussed. Finally, the first transmission electron tomography data of the liver sieve in three-dimensions are presented. The obtained data unambiguously show the involvement of special domains in the de novo formation and disappearance of hepatic fenestrae, and focuses future research into the (supra)molecular structure of the fenestrae-forming center, defenestration center and fenestrae-, and sieve plate cytoskeleton ring by using advanced cryo-electron tomography. (c) 2007 Wiley-Liss, Inc.

Imaging of cardiovascular structures using near-infrared femtosecond multiphoton laser scanning microscopy.

PubMed

Schenke-Layland, Katja; Riemann, Iris; Stock, Ulrich A; König, Karsten

2005-01-01

Multiphoton imaging represents a novel and very promising medical diagnostic technology for the high-resolution analysis of living biological tissues. We performed multiphoton imaging to analyzed structural features of extracellular matrix (ECM) components, e.g., collagen and elastin, of vital pulmonary and aortic heart valves. High-resolution autofluorescence images of collagenous and elastic fibers were demonstrated using multifluorophore, multiphoton excitation at two different wavelengths and optical sectioning, without the requirement of embedding, fixation, or staining. Collagenous structures were selectively imaged by detection of second harmonic generation (SHG). Additionally, routine histology and electron microscopy were integrated to verify the observed results. In comparison with pulmonary tissues, aortic heart valve specimens show very similar matrix formations. The quality of the resulting three-dimensional (3-D) images enabled the differentiation between collagenous and elastic fibers. These experimental results indicate that multiphoton imaging with near-infrared (NIR) femtosecond laser pulses may prove to be a useful tool for the nondestructive monitoring and characterization of cardiovascular structures. Copyright 2005 Society of Photo-Optical Instrumentation Engineers.

Coherent diffraction imaging of nanoscale strain evolution in a single crystal under high pressure

PubMed Central

Yang, Wenge; Huang, Xiaojing; Harder, Ross; Clark, Jesse N.; Robinson, Ian K.; Mao, Ho-kwang

2013-01-01

The evolution of morphology and internal strain under high pressure fundamentally alters the physical property, structural stability, phase transition and deformation mechanism of materials. Until now, only averaged strain distributions have been studied. Bragg coherent X-ray diffraction imaging is highly sensitive to the internal strain distribution of individual crystals but requires coherent illumination, which can be compromised by the complex high-pressure sample environment. Here we report the successful de-convolution of these effects with the recently developed mutual coherent function method to reveal the three-dimensional strain distribution inside a 400 nm gold single crystal during compression within a diamond-anvil cell. The three-dimensional morphology and evolution of the strain under pressures up to 6.4 GPa were obtained with better than 30 nm spatial resolution. In addition to providing a new approach for high-pressure nanotechnology and rheology studies, we draw fundamental conclusions about the origin of the anomalous compressibility of nanocrystals. PMID:23575684

Coherent diffraction imaging of nanoscale strain evolution in a single crystal under high pressure.

PubMed

Yang, Wenge; Huang, Xiaojing; Harder, Ross; Clark, Jesse N; Robinson, Ian K; Mao, Ho-kwang

2013-01-01

The evolution of morphology and internal strain under high pressure fundamentally alters the physical property, structural stability, phase transition and deformation mechanism of materials. Until now, only averaged strain distributions have been studied. Bragg coherent X-ray diffraction imaging is highly sensitive to the internal strain distribution of individual crystals but requires coherent illumination, which can be compromised by the complex high-pressure sample environment. Here we report the successful de-convolution of these effects with the recently developed mutual coherent function method to reveal the three-dimensional strain distribution inside a 400 nm gold single crystal during compression within a diamond-anvil cell. The three-dimensional morphology and evolution of the strain under pressures up to 6.4 GPa were obtained with better than 30 nm spatial resolution. In addition to providing a new approach for high-pressure nanotechnology and rheology studies, we draw fundamental conclusions about the origin of the anomalous compressibility of nanocrystals.

Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.

PubMed

Nannenga, Brent L; Iadanza, Matthew G; Vollmar, Breanna S; Gonen, Tamir

2013-01-01

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

Hubble space telescope observations and geometric models of compact multipolar planetary nebulae

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

Hsia, Chih-Hao; Chau, Wayne; Zhang, Yong

2014-05-20

We report high angular resolution Hubble Space Telescope observations of 10 compact planetary nebulae (PNs). Many interesting internal structures, including multipolar lobes, arcs, two-dimensional rings, tori, and halos, are revealed for the first time. These results suggest that multipolar structures are common among PNs, and these structures develop early in their evolution. From three-dimensional geometric models, we have determined the intrinsic dimensions of the lobes. Assuming the lobes are the result of interactions between later-developed fast winds and previously ejected asymptotic giant branch winds, the geometric structures of these PNs suggest that there are multiple phases of fast winds separatedmore » by temporal variations and/or directional changes. A scenario of evolution from lobe-dominated to cavity-dominated stages is presented. The results reported here will provide serious constraints on any dynamical models of PNs.« less

Atomistic three-dimensional coherent x-ray imaging of nonbiological systems

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

Ho, Phay J.; Knight, Chris; Tegze, Miklos

We computationally study the resolution limits for three-dimensional coherent x-ray diffractive imaging of heavy, nonbiological systems using Ar clusters as a prototype. We treat electronic and nuclear dynamics on an equal footing and remove the frozen-lattice approximation often used in electronic damage studies. We explore the achievable resolution as a function of pulse parameters (fluence level, pulse duration, and photon energy) and particle size. The contribution of combined lattice and electron dynamics is not negligible even for 2 fs pulses, and the Compton scattering is less deleterious than in biological systems for atomic-scale imaging. Although free-electron scattering represents a significantmore » background, we find that recovery of the original structure is in principle possible with 3 angstrom resolution for particles of 11 nm diameter.« less

Atomistic three-dimensional coherent x-ray imaging of nonbiological systems

DOE PAGES

Ho, Phay J.; Knight, Chris; Tegze, Miklos; ...

2016-12-12

We computationally study the resolution limits for three-dimensional coherent x-ray diffractive imaging of heavy, nonbiological systems using Ar clusters as a prototype. We treat electronic and nuclear dynamics on an equal footing and remove the frozen-lattice approximation often used in electronic damage studies. We explore the achievable resolution as a function of pulse parameters (fluence level, pulse duration, and photon energy) and particle size. The contribution of combined lattice and electron dynamics is not negligible even for 2 fs pulses, and the Compton scattering is less deleterious than in biological systems for atomic-scale imaging. Although free-electron scattering represents a significantmore » background, we find that recovery of the original structure is in principle possible with 3 angstrom resolution for particles of 11 nm diameter.« less

Laboratory-size three-dimensional x-ray microscope with Wolter type I mirror optics and an electron-impact water window x-ray source

NASA Astrophysics Data System (ADS)

Ohsuka, Shinji; Ohba, Akira; Onoda, Shinobu; Nakamoto, Katsuhiro; Nakano, Tomoyasu; Miyoshi, Motosuke; Soda, Keita; Hamakubo, Takao

2014-09-01

We constructed a laboratory-size three-dimensional water window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques, and observed bio-medical samples to evaluate its applicability to life science research fields. It consists of a condenser and an objective grazing incidence Wolter type I mirror, an electron-impact type oxygen Kα x-ray source, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit of around 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm scale three-dimensional fine structures were resolved.

Laboratory-size three-dimensional x-ray microscope with Wolter type I mirror optics and an electron-impact water window x-ray source.

PubMed

Ohsuka, Shinji; Ohba, Akira; Onoda, Shinobu; Nakamoto, Katsuhiro; Nakano, Tomoyasu; Miyoshi, Motosuke; Soda, Keita; Hamakubo, Takao

2014-09-01

We constructed a laboratory-size three-dimensional water window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques, and observed bio-medical samples to evaluate its applicability to life science research fields. It consists of a condenser and an objective grazing incidence Wolter type I mirror, an electron-impact type oxygen Kα x-ray source, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit of around 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm scale three-dimensional fine structures were resolved.

Predicting nucleic acid binding interfaces from structural models of proteins.

PubMed

Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

2012-02-01

The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Copyright © 2011 Wiley Periodicals, Inc.

Structural Analysis of MoS2 and other 2D layered materials using LEEM/LEED-I(V) and STM

NASA Astrophysics Data System (ADS)

Grady, Maxwell; Dai, Zhongwei; Jin, Wencan; Dadap, Jerry; Osgood, Richard; Sadowski, Jerzy; Pohl, Karsten

Layered two-dimensional materials, such as molybdenum disulfide, MoS2, are of interest for the development of many types of novel electronic devices. To fully understand the interfaces between these new materials, the atomic reconstructions at their surfaces must be understood. Low Energy Electron Microscopy and Diffraction, LEEM/ μLEED, present a unique method for rapid material characterization in real space and reciprocal space with high resolution. Here we present a study of the surface structure of 2H-MoS2 using μLEED intensity-voltage analysis. To aid this analysis, software is under development to automate the procedure of extracting I(V) curves from LEEM and LEED data. When matched with computational modeling, this data provides information with angstrom level resolution concerning the three dimensional atomic positions. We demonstrate that the surface structure of bulk MoS2 is distinct from the bulk crystal structure and exhibits a smaller surface relaxation at 320K compared to previous results at 95K. Furthermore, suspended monolayer samples exhibit large interlayer relaxations compared to the bulk surface termination. Further techniques for refining layer thickness determination are under development.

A Non-hydrostatic Atmospheric Model for Global High-resolution Simulation

NASA Astrophysics Data System (ADS)

Peng, X.; Li, X.

2017-12-01

A three-dimensional non-hydrostatic atmosphere model, GRAPES_YY, is developed on the spherical Yin-Yang grid system in order to enforce global high-resolution weather simulation or forecasting at the CAMS/CMA. The quasi-uniform grid makes the computation be of high efficiency and free of pole problem. Full representation of the three-dimensional Coriolis force is considered in the governing equations. Under the constraint of third-order boundary interpolation, the model is integrated with the semi-implicit semi-Lagrangian method using the same code on both zones. A static halo region is set to ensure computation of cross-boundary transport and updating Dirichlet-type boundary conditions in the solution process of elliptical equations with the Schwarz method. A series of dynamical test cases, including the solid-body advection, the balanced geostrophic flow, zonal flow over an isolated mountain, development of the Rossby-Haurwitz wave and a baroclinic wave, are carried out, and excellent computational stability and accuracy of the dynamic core has been confirmed. After implementation of the physical processes of long and short-wave radiation, cumulus convection, micro-physical transformation of water substances and the turbulent processes in the planetary boundary layer include surface layer vertical fluxes parameterization, a long-term run of the model is then put forward under an idealized aqua-planet configuration to test the model physics and model ability in both short-term and long-term integrations. In the aqua-planet experiment, the model shows an Earth-like structure of circulation. The time-zonal mean temperature, wind components and humidity illustrate reasonable subtropical zonal westerly jet, meridional three-cell circulation, tropical convection and thermodynamic structures. The specific SST and solar insolation being symmetric about the equator enhance the ITCZ and tropical precipitation, which concentrated in tropical region. Additional analysis and tuning of the model is still going on, and preliminary results have demonstrated the possibility of high-resolution application of the model to global weather prediction and even seasonal climate projection.

Mapping of photoreceptor dysfunction using high resolution three-dimensional spectral optical coherence tomography

NASA Astrophysics Data System (ADS)

Sikorski, B. L.; Szkulmowski, M.; Kałużny, J. J.; Bajraszewski, T.; Kowalczyk, A.; Wojtkowski, M.

2008-02-01

The ability to obtain reliable information on functional status of photoreceptor layer is essential for assessing vision impairment in patients with macular diseases. The reconstruction of three-dimensional retinal structure in vivo using Spectral Optical Coherence Tomography (Spectral OCT) became possible with a recent progress of the OCT field. Three-dimensional data collected by Spectral OCT devices comprise information on light intensity back-reflected from the junction between photoreceptor outer and inner segments (IS/OS) and thus can be used for evaluating photoreceptors impairment. In this paper, we introduced so called Spectral OCT reflectivity maps - a new method of selecting and displaying the spatial distribution of reflectivity of individual retinal layers. We analyzed the reflectivity of the IS/OS layer in various macular diseases. We have measured eyes of 49 patients with photoreceptor dysfunction in course of age-related macular degeneration, macular holes, central serous chorioretinopathy, acute zonal occult outer retinopathy, multiple evanescent white dot syndrome, acute posterior multifocal placoid pigment epitheliopathy, drug-induced retinopathy and congenital disorders.

Resistivity and Seismic Surface Wave Tomography Results for the Nevşehir Kale Region: Cappadocia, Turkey

NASA Astrophysics Data System (ADS)

Coşkun, Nart; Çakır, Özcan; Erduran, Murat; Arif Kutlu, Yusuf

2014-05-01

The Nevşehir Kale region located in the middle of Cappadocia with approximately cone shape is investigated for existence of an underground city using the geophysical methods of electrical resistivity and seismic surface wave tomography together. Underground cities are generally known to exist in Cappadocia. The current study has obtained important clues that there may be another one under the Nevşehir Kale region. Two-dimensional resistivity and seismic profiles approximately 4-km long surrounding the Nevşehir Kale are measured to determine the distribution of electrical resistivities and seismic velocities under the profiles. Several high resistivity anomalies with a depth range 8-20 m are discovered to associate with a systematic void structure beneath the region. Because of the high resolution resistivity measurement system currently employed we were able to isolate the void structure from the embedding structure. Low seismic velocity zones associated with the high resistivity depths are also discovered. Using three-dimensional visualization techniques we show the extension of the void structure under the measured profiles.

Demonstration of arbitrary views based on autostereoscopic three-dimensional display system

NASA Astrophysics Data System (ADS)

Liu, Boyang; Sang, Xinzhu; Yu, Xunbo; Li, Liu; Yang, Le; Yan, Binbin; Wang, Kuiru; Yu, Chongxiu

2017-10-01

A method to realize arbitrary views for the lenticular lens array based on autostereoscopic three-dimensional display system is demonstrated. Normally, the number of views is proportional to pitch of the lenticular lens array. Increasing the number of views will result in reducing resolution and enhancing of granular sensation. 32 dense views can be achieved with one lenticular lens pitch covering 5.333 sub-pixels, which does significantly increases the number of views without affecting the resolution. But the structure of pitch and the number of views are fixed. Here, the 3D display method that the number of views can be changed artificially for most structures of lenticular lens is presented. Compared with the previous 32 views display method, the smoothness of motion parallex and the display depth of field are significantly improved.

[Crystal structure of SMU.2055 protein from Streptococcus mutans and its small molecule inhibitors design and selection].

PubMed

Xiaodan, Chen; Xiurong, Zhan; Xinyu, Wu; Chunyan, Zhao; Wanghong, Zhao

2015-04-01

The aim of this study is to analyze the three-dimensional crystal structure of SMU.2055 protein, a putative acetyltransferase from the major caries pathogen Streptococcus mutans (S. mutans). The design and selection of the structure-based small molecule inhibitors are also studied. The three-dimensional crystal structure of SMU.2055 protein was obtained by structural genomics research methods of gene cloning and expression, protein purification with Ni²⁺-chelating affinity chromatography, crystal screening, and X-ray diffraction data collection. An inhibitor virtual model matching with its target protein structure was set up using computer-aided drug design methods, virtual screening and fine docking, and Libdock and Autodock procedures. The crystal of SMU.2055 protein was obtained, and its three-dimensional crystal structure was analyzed. This crystal was diffracted to a resolution of 0.23 nm. It belongs to orthorhombic space group C222(1), with unit cell parameters of a = 9.20 nm, b = 9.46 nm, and c = 19.39 nm. The asymmetric unit contained four molecules, with a solvent content of 56.7%. Moreover, five small molecule compounds, whose structure matched with that of the target protein in high degree, were designed and selected. Protein crystallography research of S. mutans SMU.2055 helps to understand the structures and functions of proteins from S. mutans at the atomic level. These five compounds may be considered as effective inhibitors to SMU.2055. The virtual model of small molecule inhibitors we built will lay a foundation to the anticaries research based on the crystal structure of proteins.

The three-dimensional genome organization of Drosophila melanogaster through data integration.

PubMed

Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank

2017-07-31

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

Three-dimensional sinus imaging as an adjunct to two-dimensional imaging to accelerate education and improve spatial orientation.

PubMed

Yao, William C; Regone, Rachel M; Huyhn, Nancy; Butler, E Brian; Takashima, Masayoshi

2014-03-01

Develop a novel three-dimensional (3-D) anatomical model to assist in improving spatial knowledge of the skull base, paranasal sinuses, and adjacent structures, and validate the utilization of 3-D reconstruction to augment two-dimensional (2-D) computed tomography (CT) for the training of medical students and otolaryngology-head and neck surgery residents. Prospective study. A study of 18 subjects studying sinus anatomy was conducted at a tertiary academic center during the 2011 to 2012 academic year. An image processing and 3-D modeling program was used to create a color coded 3-D scalable/layerable/rotatable model of key paranasal and skull base structures from a 2-D high-resolution sinus CT scan. Subjects received instruction of the sinus anatomy in two sessions, first through review of a 2-D CT sinus scan, followed by an educational module of the 3-D reconstruction. After each session, subjects rated their knowledge of the sinus and adjacent structures on a self-assessment questionnaire. Significant improvement in the perceived understanding of the anatomy was noted after the 3-D educational module session when compared to the 2-D CT session alone (P < .01). Every subject believed the addition of 3-D imaging accelerated their education of sinus anatomy and recommended its use to others. The impression of the learners was that a 3-D educational module, highlighting key structures, is a highly effective tool to enhance the education of medical students and otolaryngology residents in sinus and skull base anatomy and its adjacent structures, specifically in conceptualizing the spatial orientation of these structures. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

High resolution three-dimensional magnetization mapping in Tokachidake Volcano using low altitude airborne magnetic survey data

NASA Astrophysics Data System (ADS)

Iwata, M.; Mogi, T.; Okuma, S.; Nakatsuka, T.

2016-12-01

Tokachidake Volcano, central Hokkaido, Japan erupted in 1926, 1962 and 1988-1989 in the 20th century from the central part. In recent years, expansions of the edifice of the volcano at shallow depth and increases of the volcanic smoke in the Taisho crater were observed (Meteorological Agency of Japan, 2014). Magnetic changes were observed at the 62-2 crater by repeated magnetic measurements in 2008-2009, implying a demagnetization beneath the crater (Hashimoto at al., 2010). Moreover, a very low resistivity part was found right under the 62-2 crater from an AMT survey (Yamaya et al., 2010). However, since the station numbers of the survey are limited, the area coverage is not sufficient. In this study, we have re-analyzed high-resolution aeromagnetic data to delineate the three-dimensional magnetic structure of the volcano to understand the nature of other craters.A low altitude airborne magnetic survey was conducted in 2014 mainly over the active areas of the volcano by the Ministry of Land, Infrastructure, Transport and Tourism to manage land slide risk in the volcano. The survey was flown at an altitude of 60 m above ground by a helicopter with a Cesium magnetometer in the towed-bird 30m below the helicopter. The low altitude survey enables us to delineate the detailed magnetic structure. We calculated magnetic anomaly distribution on a smooth surface assuming equivalent anomalies below the observation surface. Then the 3D magnetic imaging method (Nakatsuka and Okuma, 2014) was applied to the magnetic anomalies to reveal the three-dimensional magnetic structure.As a result, magnetization highs were seen beneath the Ground crater, Suribachi crater and Kitamuki crater. This implies that magmatic activity occurred in the past at these craters. These magma should have already solidified and acquired strong remanent magnetization. Relative magnetization lows were seen beneath the 62-2 crater and the Taisho crater where fumarolic activity is active. However a magnetization high was seen beneath the Nukkakushi crater where fumarolic activity and hydrothermal alteration had been observed on the ground. Further studies on this interesting distribution is necessary.

The three-dimensional structure of aquaporin-1

NASA Astrophysics Data System (ADS)

Walz, Thomas; Hirai, Teruhisa; Murata, Kazuyoshi; Heymann, J. Bernard; Mitsuoka, Kaoru; Fujiyoshi, Yoshinori; Smith, Barbara L.; Agre, Peter; Engel, Andreas

1997-06-01

The entry and exit of water from cells is a fundamental process of life. Recognition of the high water permeability of red blood cells led to the proposal that specialized water pores exist in the plasma membrane. Expression in Xenopus oocytes and functional studies of an erythrocyte integral membrane protein of relative molecular mass 28,000, identified it as the mercury-sensitive water channel, aquaporin-1 (AQP1). Many related proteins, all belonging to the major intrinsic protein (MIP) family, are found throughout nature. AQP1 is a homotetramer containing four independent aqueous channels. When reconstituted into lipid bilayers, the protein forms two-dimensional lattices with a unit cell containing two tetramers in opposite orientation. Here we present the three-dimensional structure of AQP1 determined at 6Å resolution by cryo-electron microscopy. Each AQP1 monomer has six tilted, bilayer-spanning α-helices which form a right-handed bundle surrounding a central density. These results, together with functional studies, provide a model that identifies the aqueous pore in the AQP1 molecule and indicates the organization of the tetrameric complex in the membrane.

Stretchable ultrasonic transducer arrays for three-dimensional imaging on complex surfaces

PubMed Central

Zhu, Xuan; Li, Xiaoshi; Chen, Zeyu; Chen, Yimu; Lei, Yusheng; Li, Yang; Nomoto, Akihiro; Zhou, Qifa; di Scalea, Francesco Lanza

2018-01-01

Ultrasonic imaging has been implemented as a powerful tool for noninvasive subsurface inspections of both structural and biological media. Current ultrasound probes are rigid and bulky and cannot readily image through nonplanar three-dimensional (3D) surfaces. However, imaging through these complicated surfaces is vital because stress concentrations at geometrical discontinuities render these surfaces highly prone to defects. This study reports a stretchable ultrasound probe that can conform to and detect nonplanar complex surfaces. The probe consists of a 10 × 10 array of piezoelectric transducers that exploit an “island-bridge” layout with multilayer electrodes, encapsulated by thin and compliant silicone elastomers. The stretchable probe shows excellent electromechanical coupling, minimal cross-talk, and more than 50% stretchability. Its performance is demonstrated by reconstructing defects in 3D space with high spatial resolution through flat, concave, and convex surfaces. The results hold great implications for applications of ultrasound that require imaging through complex surfaces. PMID:29740603

Reprocessable thermosets for sustainable three-dimensional printing.

PubMed

Zhang, Biao; Kowsari, Kavin; Serjouei, Ahmad; Dunn, Martin L; Ge, Qi

2018-05-08

Among all three-dimensional (3D) printing materials, thermosetting photopolymers claim almost half of the market, and have been widely used in various fields owing to their superior mechanical stability at high temperatures, excellent chemical resistance as well as good compatibility with high-resolution 3D printing technologies. However, once these thermosetting photopolymers form 3D parts through photopolymerization, the covalent networks are permanent and cannot be reprocessed, i.e., reshaped, repaired, or recycled. Here, we report a two-step polymerization strategy to develop 3D printing reprocessable thermosets (3DPRTs) that allow users to reform a printed 3D structure into a new arbitrary shape, repair a broken part by simply 3D printing new material on the damaged site, and recycle unwanted printed parts so the material can be reused for other applications. These 3DPRTs provide a practical solution to address environmental challenges associated with the rapid increase in consumption of 3D printing materials.

Solar microwave bursts - A review

NASA Technical Reports Server (NTRS)

Kundu, M. R.; Vlahos, L.

1982-01-01

Observational and theoretical results on the physics of microwave bursts that occur in the solar atmosphere are reviewed. Special attention is given to the advances made in burst physics over the last few years with the great improvement in spatial and time resolution, especially with instruments like the NRAO three-element interferometer, the Westerbork Synthesis Radio Telescope, and more recently the Very Large Array. Observations made on the preflare build-up of an active region at centimeter wavelengths are reviewed. Three distinct phases in the evolution of cm bursts, namely the impulsive phase, the post-burst phase, and the gradual rise and fall, are discussed. Attention is also given to the flux density spectra of centimeter bursts. Descriptions are given of observations of fine structures with temporal resolution of 10-100 ms in the intensity profiles of cm-wavelength bursts. High spatial resolution observations are analyzed, with special reference to the one- and two-dimensional maps of cm burst sources.

Three-dimensional laser microvision.

PubMed

Shimotahira, H; Iizuka, K; Chu, S C; Wah, C; Costen, F; Yoshikuni, Y

2001-04-10

A three-dimensional (3-D) optical imaging system offering high resolution in all three dimensions, requiring minimum manipulation and capable of real-time operation, is presented. The system derives its capabilities from use of the superstructure grating laser source in the implementation of a laser step frequency radar for depth information acquisition. A synthetic aperture radar technique was also used to further enhance its lateral resolution as well as extend the depth of focus. High-speed operation was made possible by a dual computer system consisting of a host and a remote microcomputer supported by a dual-channel Small Computer System Interface parallel data transfer system. The system is capable of operating near real time. The 3-D display of a tunneling diode, a microwave integrated circuit, and a see-through image taken by the system operating near real time are included. The depth resolution is 40 mum; lateral resolution with a synthetic aperture approach is a fraction of a micrometer and that without it is approximately 10 mum.

Development of an unstructured solution adaptive method for the quasi-three-dimensional Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Jiang, Yi-Tsann

1993-01-01

A general solution adaptive scheme-based on a remeshing technique is developed for solving the two-dimensional and quasi-three-dimensional Euler and Favre-averaged Navier-Stokes equations. The numerical scheme is formulated on an unstructured triangular mesh utilizing an edge-based pointer system which defines the edge connectivity of the mesh structure. Jameson's four-stage hybrid Runge-Kutta scheme is used to march the solution in time. The convergence rate is enhanced through the use of local time stepping and implicit residual averaging. As the solution evolves, the mesh is regenerated adaptively using flow field information. Mesh adaptation parameters are evaluated such that an estimated local numerical error is equally distributed over the whole domain. For inviscid flows, the present approach generates a complete unstructured triangular mesh using the advancing front method. For turbulent flows, the approach combines a local highly stretched structured triangular mesh in the boundary layer region with an unstructured mesh in the remaining regions to efficiently resolve the important flow features. One-equation and two-equation turbulence models are incorporated into the present unstructured approach. Results are presented for a wide range of flow problems including two-dimensional multi-element airfoils, two-dimensional cascades, and quasi-three-dimensional cascades. This approach is shown to gain flow resolution in the refined regions while achieving a great reduction in the computational effort and storage requirements since solution points are not wasted in regions where they are not required.

Development of an unstructured solution adaptive method for the quasi-three-dimensional Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Jiang, Yi-Tsann; Usab, William J., Jr.

1993-01-01

A general solution adaptive scheme based on a remeshing technique is developed for solving the two-dimensional and quasi-three-dimensional Euler and Favre-averaged Navier-Stokes equations. The numerical scheme is formulated on an unstructured triangular mesh utilizing an edge-based pointer system which defines the edge connectivity of the mesh structure. Jameson's four-stage hybrid Runge-Kutta scheme is used to march the solution in time. The convergence rate is enhanced through the use of local time stepping and implicit residual averaging. As the solution evolves, the mesh is regenerated adaptively using flow field information. Mesh adaptation parameters are evaluated such that an estimated local numerical error is equally distributed over the whole domain. For inviscid flows, the present approach generates a complete unstructured triangular mesh using the advancing front method. For turbulent flows, the approach combines a local highly stretched structured triangular mesh in the boundary layer region with an unstructured mesh in the remaining regions to efficiently resolve the important flow features. One-equation and two-equation turbulence models are incorporated into the present unstructured approach. Results are presented for a wide range of flow problems including two-dimensional multi-element airfoils, two-dimensional cascades, and quasi-three-dimensional cascades. This approach is shown to gain flow resolution in the refined regions while achieving a great reduction in the computational effort and storage requirements since solution points are not wasted in regions where they are not required.

New sesquiterpenes from Euonymus europaeus (Celastraceae).

PubMed

Descoins, Charles; Bazzocchi, Isabel López; Ravelo, Angel Gutiérrez

2002-02-01

A new sesquiterpene evoninate alkaloid (1), and two sesquiterpenes (2, 3) with a dihydro-beta-agarofuran skeleton, along with three known sesquiterpenes (4-6), were isolated from the seeds of Euonymus europaeus. Their structures were elucidated by high resolution mass analysis, and one- and two-dimensional (1D and 2D) NMR spectroscopy, including homonuclear and heteronuclear correlation [correlation spectroscopy (COSY), rotating frame Overhauser enhancement spectroscopy (ROESY), heteronuclear single quantum coherence (HSQC), and heteronuclear multiple bond correlation (HMBC)] experiments.

The three-dimensional crystal structure of cholera toxin

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

Zhang, Rong-Guang; Westbrook, M.L.; Nance, S.

1996-02-01

The clinical manifestations of cholera are largely attributable to the actions of a secreted hexameric AB{sub 5} enterotoxin (choleragen). We have solved the three-dimensional structure of choleragen at 2.5 {Angstrom} resolution and compared the refined coordinates with those of choleragenoid (isolated B pentamer) and the heat-labile enterotoxin from Escherichia coli (LT). The crystalline coordinates provide a detailed view of the stereochemistry implicated in binding to GM1 gangliosides and in carrying out ADP-ribosylation. The A2 chain of choleragen, in contrast to that of LT, is a nearly continuous {alpha}-helix with an interpretable carboxyl tail.

Casting inorganic structures with DNA molds

DOE PAGES

Sun, Wei; Boulais, Etienne; Hakobyan, Yera; ...

2014-10-09

Here we report a general strategy for designing and synthesizing inorganic nanostructures with arbitrarily prescribed three-dimensional shapes. Computationally designed DNA strands self-assemble into a stiff “nano-mold” that contains a user-specified three-dimensional cavity and encloses a nucleating gold “seed”. Under mild conditions, this seed grows into a larger cast structure that fills and thus replicates the cavity. We synthesized a variety of nanoparticles with three nanometer resolution: three distinct silver cuboids with three independently tunable dimensions, silver and gold nanoparticles with diverse cross sections, and composite structures with homo-/heterogeneous components. The designer equilateral silver triangular and spherical nanoparticles exhibited plasmonic propertiesmore » consistent with electromagnetism-based simulations. Our framework is generalizable to more complex geometries and diverse inorganic materials, offering a range of applications in biosensing, photonics, and nanoelectronics.« less

Advanced Reservoir Characterization and Development through High-Resolution 3C3D Seismic and Horizontal Drilling: Eva South Marrow Sand Unit, Texas County, Oklahoma

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

Wheeler,David M.; Miller, William A.; Wilson, Travis C.

2002-03-11

The Eva South Morrow Sand Unit is located in western Texas County, Oklahoma. The field produces from an upper Morrow sandstone, termed the Eva sandstone, deposited in a transgressive valley-fill sequence. The field is defined as a combination structural stratigraphic trap; the reservoir lies in a convex up -dip bend in the valley and is truncated on the west side by the Teepee Creek fault. Although the field has been a successful waterflood since 1993, reservoir heterogeneity and compartmentalization has impeded overall sweep efficiency. A 4.25 square mile high-resolution, three component three-dimensional (3C3D) seismic survey was acquired in order tomore » improve reservoir characterization and pinpoint the optimal location of a new horizontal producing well, the ESU 13-H.« less

High spatial resolution three-dimensional mapping of vegetation spectral dynamics using computer vision and hobbyist unmanned aerial vehicles

NASA Astrophysics Data System (ADS)

Dandois, J. P.; Ellis, E. C.

2013-12-01

High spatial resolution three-dimensional (3D) measurements of vegetation by remote sensing are advancing ecological research and environmental management. However, substantial economic and logistical costs limit this application, especially for observing phenological dynamics in ecosystem structure and spectral traits. Here we demonstrate a new aerial remote sensing system enabling routine and inexpensive aerial 3D measurements of canopy structure and spectral attributes, with properties similar to those of LIDAR, but with RGB (red-green-blue) spectral attributes for each point, enabling high frequency observations within a single growing season. This 'Ecosynth' methodology applies photogrammetric ''Structure from Motion'' computer vision algorithms to large sets of highly overlapping low altitude (< 130 m) aerial photographs acquired using off-the-shelf digital cameras mounted on an inexpensive (< USD$4000), lightweight (< 2 kg), hobbyist-grade unmanned aerial system (UAS). Ecosynth 3D point clouds with densities of 30 - 67 points m-2 were produced using commercial computer vision software from digital photographs acquired repeatedly by UAS over three 6.25 ha (250 m x 250 m) Temperate Deciduous forest sites in Maryland USA. Ecosynth canopy height maps (CHMs) were strong predictors of field-measured tree heights (R2 0.63 to 0.84) and were highly correlated with a LIDAR CHM (R 0.87) acquired 4 days earlier, though Ecosynth-based estimates of aboveground biomass densities included significant errors (31 - 36% of field-based estimates). Repeated scanning of a 0.25 ha forested area at six different times across a 16 month period revealed ecologically significant dynamics in canopy color at different heights and a structural shift upward in canopy density, as demonstrated by changes in vertical height profiles of point density and relative RGB brightness. Changes in canopy relative greenness were highly correlated (R2 = 0.88) with MODIS NDVI time series for the same area and vertical differences in canopy color revealed the early green up of the dominant canopy species, Liriodendron tulipifera, strong evidence that Ecosynth time series measurements capture vegetation structural and spectral dynamics at the spatial scale of individual trees. Observing canopy phenology in 3D at high temporal resolutions represents a breakthrough in forest ecology. Inexpensive user-deployed technologies for multispectral 3D scanning of vegetation at landscape scales (< 1 km2) heralds a new era of participatory remote sensing by field ecologists, community foresters and the interested public.

Highly cytocompatible and flexible three-dimensional graphene/polydimethylsiloxane composite for culture and electrochemical detection of L929 fibroblast cells.

PubMed

Waiwijit, Uraiwan; Maturos, Thitima; Pakapongpan, Saithip; Phokharatkul, Ditsayut; Wisitsoraat, Anurat; Tuantranont, Adisorn

2016-08-01

Recently, three-dimensional graphene interconnected network has attracted great interest as a scaffold structure for tissue engineering due to its high biocompatibility, high electrical conductivity, high specific surface area and high porosity. However, free-standing three-dimensional graphene exhibits poor flexibility and stability due to ease of disintegration during processing. In this work, three-dimensional graphene is composited with polydimethylsiloxane to improve the structural flexibility and stability by a new simple two-step process comprising dip coating of polydimethylsiloxane on chemical vapor deposited graphene/Ni foam and wet etching of nickel foam. Structural characterizations confirmed an interconnected three-dimensional multi-layer graphene structure with thin polydimethylsiloxane scaffold. The composite was employed as a substrate for culture of L929 fibroblast cells and its cytocompatibility was evaluated by cell viability (Alamar blue assay), reactive oxygen species production and vinculin immunofluorescence imaging. The result revealed that cell viability on three-dimensional graphene/polydimethylsiloxane composite increased with increasing culture time and was slightly different from a polystyrene substrate (control). Moreover, cells cultured on three-dimensional graphene/polydimethylsiloxane composite generated less ROS than the control at culture times of 3-6 h. The results of immunofluorescence staining demonstrated that fibroblast cells expressed adhesion protein (vinculin) and adhered well on three-dimensional graphene/polydimethylsiloxane surface. Good cell adhesion could be attributed to suitable surface properties of three-dimensional graphene/polydimethylsiloxane with moderate contact angle and small negative zeta potential in culture solution. The results of electrochemical study by cyclic voltammetry showed that an oxidation current signal with no apparent peak was induced by fibroblast cells and the oxidation current at an oxidation potential of +0.9 V increased linearly with increasing cell number. Therefore, the three-dimensional graphene/polydimethylsiloxane composite exhibits high cytocompatibility and can potentially be used as a conductive substrate for cell-based electrochemical sensing. © The Author(s) 2016.

Micro-Mirrors for Nanoscale Three-Dimensional Microscopy

PubMed Central

Seale, Kevin; Janetopoulos, Chris; Wikswo, John

2013-01-01

A research-grade optical microscope is capable of resolving fine structures in two-dimensional images. However, three-dimensional resolution, or the ability of the microscope to distinguish between objects lying above or below the focal plane from in-focus objects, is not nearly as good as in-plane resolution. In this issue of ACS Nano, McMahon et al. report the use of mirrored pyramidal wells with a conventional microscope for rapid, 3D localization and tracking of nanoparticles. Mirrors have been used in microscopy before, but recent work with MPWs is unique because it enables the rapid determination of the x-, y-, and z-position of freely diffusing nanoparticles and cellular nanostructures with unprecedented speed and spatial accuracy. As inexpensive tools for 3D visualization, mirrored pyramidal wells may prove to be invaluable aids in nanotechnology and engineering of nanomaterials. PMID:19309167

Three-dimensional structure of homodimeric cholesterol esterase-ligand complex at 1.4 Å resolution

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

Pletnev, V.; Addlagatta, A.; Wawrzak, Z.

2010-03-08

The three-dimensional structure of a Candida cylindracea cholesterol esterase (ChE) homodimer (534 x 2 amino acids) in complex with a ligand of proposed formula C{sub 23}H{sub 48}O{sub 2} has been determined at 1.4 {angstrom} resolution in space group P1 using synchrotron low-temperature data. The structure refined to R = 0.136 and R{sub free} = 0.169 and has revealed new stereochemical details in addition to those detected for the apo- and holo-forms at 1.9 and 2.0 {angstrom} resolution, respectively [Ghosh et al. (1995), Structure, 3, 279-288]. The cholesterol esterase structure is a dimer with four spatially separated interfacial contact areas andmore » two symmetry-related pairs of openings to an internal intradimer cavity. Hydrophobic active-site gorges in each subunit face each other across a central interfacial cavity. The ChE subunits have carbohydrate chains attached to their Asn314 and Asn351 residues, with two ordered N-acetyl-D-glucosoamine moieties visible at each site. The side chains of 14 residues have two alternative conformations with occupancy values of 0.5 {+-} 0.2. For each subunit the electron density in the enzyme active-site gorge is well modeled by a C{sub 23}-chain fatty acid.« less

High-frame-rate full-vocal-tract 3D dynamic speech imaging.

PubMed

Fu, Maojing; Barlaz, Marissa S; Holtrop, Joseph L; Perry, Jamie L; Kuehn, David P; Shosted, Ryan K; Liang, Zhi-Pei; Sutton, Bradley P

2017-04-01

To achieve high temporal frame rate, high spatial resolution and full-vocal-tract coverage for three-dimensional dynamic speech MRI by using low-rank modeling and sparse sampling. Three-dimensional dynamic speech MRI is enabled by integrating a novel data acquisition strategy and an image reconstruction method with the partial separability model: (a) a self-navigated sparse sampling strategy that accelerates data acquisition by collecting high-nominal-frame-rate cone navigator sand imaging data within a single repetition time, and (b) are construction method that recovers high-quality speech dynamics from sparse (k,t)-space data by enforcing joint low-rank and spatiotemporal total variation constraints. The proposed method has been evaluated through in vivo experiments. A nominal temporal frame rate of 166 frames per second (defined based on a repetition time of 5.99 ms) was achieved for an imaging volume covering the entire vocal tract with a spatial resolution of 2.2 × 2.2 × 5.0 mm 3 . Practical utility of the proposed method was demonstrated via both validation experiments and a phonetics investigation. Three-dimensional dynamic speech imaging is possible with full-vocal-tract coverage, high spatial resolution and high nominal frame rate to provide dynamic speech data useful for phonetic studies. Magn Reson Med 77:1619-1629, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Structured light optical microscopy for three-dimensional reconstruction of technical surfaces

NASA Astrophysics Data System (ADS)

Kettel, Johannes; Reinecke, Holger; Müller, Claas

2016-04-01

In microsystems technology quality control of micro structured surfaces with different surface properties is playing an ever more important role. The process of quality control incorporates three-dimensional (3D) reconstruction of specularand diffusive reflecting technical surfaces. Due to the demand on high measurement accuracy and data acquisition rates, structured light optical microscopy has become a valuable solution to solve this problem providing high vertical and lateral resolution. However, 3D reconstruction of specular reflecting technical surfaces still remains a challenge to optical measurement principles. In this paper we present a measurement principle based on structured light optical microscopy which enables 3D reconstruction of specular- and diffusive reflecting technical surfaces. It is realized using two light paths of a stereo microscope equipped with different magnification levels. The right optical path of the stereo microscope is used to project structured light onto the object surface. The left optical path is used to capture the structured illuminated object surface with a camera. Structured light patterns are generated by a Digital Light Processing (DLP) device in combination with a high power Light Emitting Diode (LED). Structured light patterns are realized as a matrix of discrete light spots to illuminate defined areas on the object surface. The introduced measurement principle is based on multiple and parallel processed point measurements. Analysis of the measured Point Spread Function (PSF) by pattern recognition and model fitting algorithms enables the precise calculation of 3D coordinates. Using exemplary technical surfaces we demonstrate the successful application of our measurement principle.

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

Structured-illumination reflectance imaging coupled with spiral phase transform for bruise detection and three-dimensional geometry reconstruction of apples

USDA-ARS?s Scientific Manuscript database

Structured-illumination reflectance imaging (SIRI) is a new, promising imaging technique with enhanced, versatile capabilities for quality evaluation of food products. SIRI enables simultaneous acquisition of higher-contrast/resolution and better depth-controlled intensity and phase images for detec...

Using synchrotron-based X-ray micro-computed tomography and high-performance pore-scale simulation to evaluate hydraulic properties in biochar-amended soils

NASA Astrophysics Data System (ADS)

Zhou, H.; Yu, X.; Chen, C.; Zeng, L.; Lu, S.; Wu, L.

2016-12-01

In this research, we combined synchrotron-based X-ray micro-computed tomography (SR-mCT), with three-dimensional lattice Bolzmann (LB) method, to quantify how the change in pore space architecture affected macroscopic hydraulic of two clayey soils amended with biochar. SR-mCT was used to characterize pore structures of the soils before and after biochar addition. The high-resolution soil pore structures were then directly used as internal boundary conditions for three-dimensional water flow simulations with the LB method, which was accelerated by graphics processing unit (GPU) parallel computing. It was shown that, due to the changes in soil pore geometry, the application of biochar increased the soil permeability by at least 1 order of magnitude, and decreased the tortuosity by 20-30%. This work was the first physics based modeling study on the effect of biochar amendment on soil hydraulic properties. The developed theories and techniques have promising potential in understanding the mechanisms of water and nutrient transport in soil at the pore scale.

Three-Dimensional Anisotropic Acoustic and Elastic Full-Waveform Seismic Inversion

NASA Astrophysics Data System (ADS)

Warner, M.; Morgan, J. V.

2013-12-01

Three-dimensional full-waveform inversion is a high-resolution, high-fidelity, quantitative, seismic imaging technique that has advanced rapidly within the oil and gas industry. The method involves the iterative improvement of a starting model using a series of local linearized updates to solve the full non-linear inversion problem. During the inversion, forward modeling employs the full two-way three-dimensional heterogeneous anisotropic acoustic or elastic wave equation to predict the observed raw field data, wiggle-for-wiggle, trace-by-trace. The method is computationally demanding; it is highly parallelized, and runs on large multi-core multi-node clusters. Here, we demonstrate what can be achieved by applying this newly practical technique to several high-density 3D seismic datasets that were acquired to image four contrasting sedimentary targets: a gas cloud above an oil reservoir, a radially faulted dome, buried fluvial channels, and collapse structures overlying an evaporate sequence. We show that the resulting anisotropic p-wave velocity models match in situ measurements in deep boreholes, reproduce detailed structure observed independently on high-resolution seismic reflection sections, accurately predict the raw seismic data, simplify and sharpen reverse-time-migrated reflection images of deeper horizons, and flatten Kirchhoff-migrated common-image gathers. We also show that full-elastic 3D full-waveform inversion of pure pressure data can generate a reasonable shear-wave velocity model for one of these datasets. For two of the four datasets, the inclusion of significant transversely isotropic anisotropy with a vertical axis of symmetry was necessary in order to fit the kinematics of the field data properly. For the faulted dome, the full-waveform-inversion p-wave velocity model recovers the detailed structure of every fault that can be seen on coincident seismic reflection data. Some of the individual faults represent high-velocity zones, some represent low-velocity zones, some have more-complex internal structure, and some are visible merely as offsets between two regions with contrasting velocity. Although this has not yet been demonstrated quantitatively for this dataset, it seems likely that at least some of this fine structure in the recovered velocity model is related to the detailed lithology, strain history and fluid properties within the individual faults. We have here applied this technique to seismic data that were acquired by the extractive industries, however this inversion scheme is immediately scalable and applicable to a much wider range of problems given sufficient quality and density of observed data. Potential targets range from shallow magma chambers beneath active volcanoes, through whole-crustal sections across plate boundaries, to regional and whole-Earth models.

Globular and fibrous structure in barley chromosomes revealed by high-resolution scanning electron microscopy.

PubMed

Iwano, M; Fukui, K; Takaichi, S; Isogai, A

1997-08-01

Barley chromosomes were prepared for high-resolution scanning electron microscopy using a combination of enzyme maceration, treatment in acetic acid and osmium impregnation using thiocarbohydrazide. Using this technique, the three-dimensional ultrastructure of interphase nuclei and mitotic chromosomes was examined. In Interphase, different levels of chromatin condensation were observed, consisting of fibrils 10 nm in diameter, 20- to 40-nm fibres and a higher order complex. In prophase, globular and strand-like structures composed of 20- to 40-nm fibres were dominant. As the cells progressed through the cell cycle and the chromatin condensed, globular and strand-like structures (chromomeres) were coiled and packed to form chromosomes. Chromomeres were observed as globular protuberances on the surface of metaphase chromosomes. These findings indicate that the chromomere is a fundamental substructure of the higher order architecture of the chromosome. In the centromeric region, there were no globular protuberances, but 20- to 40-nm fibres were folded compactly to form a higher level organization surrounding the chromosomal axia.

X-ray phase-contrast tomography for high-spatial-resolution zebrafish muscle imaging

NASA Astrophysics Data System (ADS)

Vågberg, William; Larsson, Daniel H.; Li, Mei; Arner, Anders; Hertz, Hans M.

2015-11-01

Imaging of muscular structure with cellular or subcellular detail in whole-body animal models is of key importance for understanding muscular disease and assessing interventions. Classical histological methods for high-resolution imaging methods require excision, fixation and staining. Here we show that the three-dimensional muscular structure of unstained whole zebrafish can be imaged with sub-5 μm detail with X-ray phase-contrast tomography. Our method relies on a laboratory propagation-based phase-contrast system tailored for detection of low-contrast 4-6 μm subcellular myofibrils. The method is demonstrated on 20 days post fertilization zebrafish larvae and comparative histology confirms that we resolve individual myofibrils in the whole-body animal. X-ray imaging of healthy zebrafish show the expected structured muscle pattern while specimen with a dystrophin deficiency (sapje) displays an unstructured pattern, typical of Duchenne muscular dystrophy. The method opens up for whole-body imaging with sub-cellular detail also of other types of soft tissue and in different animal models.

Ex vivo mouse brain microscopy at 15T with loop-gap RF coil.

PubMed

Cohen, Ouri; Ackerman, Jerome L

2018-04-18

The design of a loop-gap-resonator RF coil optimized for ex vivo mouse brain microscopy at ultra high fields is described and its properties characterized using simulations, phantoms and experimental scans of mouse brains fixed in 10% formalin containing 4 mM Magnevist™. The RF (B 1 ) and magnetic field (B 0 ) homogeneities are experimentally quantified and compared to electromagnetic simulations of the coil. The coil's performance is also compared to a similarly sized surface coil and found to yield double the sensitivity. A three-dimensional gradient-echo (GRE) sequence is used to acquire high resolution mouse brain scans at (47 μm) 3 resolution in 1.8 h and a 20 × 20 × 19 μm 3 resolution in 27 h. The high resolution obtained permitted clear visualization and identification of multiple structures in the ex vivo mouse brain and represents, to our knowledge, the highest resolution ever achieved for a whole mouse brain. Importantly, the coil design is simple and easy to construct. Copyright © 2018 Elsevier Inc. All rights reserved.

BIM-Sim: Interactive Simulation of Broadband Imaging Using Mie Theory

PubMed Central

Berisha, Sebastian; van Dijk, Thomas; Bhargava, Rohit; Carney, P. Scott; Mayerich, David

2017-01-01

Understanding the structure of a scattered electromagnetic (EM) field is critical to improving the imaging process. Mechanisms such as diffraction, scattering, and interference affect an image, limiting the resolution, and potentially introducing artifacts. Simulation and visualization of scattered fields thus plays an important role in imaging science. However, EM fields are high-dimensional, making them time-consuming to simulate, and difficult to visualize. In this paper, we present a framework for interactively computing and visualizing EM fields scattered by micro and nano-particles. Our software uses graphics hardware for evaluating the field both inside and outside of these particles. We then use Monte-Carlo sampling to reconstruct and visualize the three-dimensional structure of the field, spectral profiles at individual points, the structure of the field at the surface of the particle, and the resulting image produced by an optical system. PMID:29170738

Resolution and contrast in Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Jacobs, H. O.; Leuchtmann, P.; Homan, O. J.; Stemmer, A.

1998-08-01

The combination of atomic force microscopy and Kelvin probe technology is a powerful tool to obtain high-resolution maps of the surface potential distribution on conducting and nonconducting samples. However, resolution and contrast transfer of this method have not been fully understood, so far. To obtain a better quantitative understanding, we introduce a model which correlates the measured potential with the actual surface potential distribution, and we compare numerical simulations of the three-dimensional tip-specimen model with experimental data from test structures. The observed potential is a locally weighted average over all potentials present on the sample surface. The model allows us to calculate these weighting factors and, furthermore, leads to the conclusion that good resolution in potential maps is obtained by long and slender but slightly blunt tips on cantilevers of minimal width and surface area.

Three-Dimensional Media Technologies: Potentials for Study in Visual Literacy.

ERIC Educational Resources Information Center

Thwaites, Hal

This paper presents an overview of three-dimensional media technologies (3Dmt). Many of the new 3Dmt are the direct result of interactions of computing, communications, and imaging technologies. Computer graphics are particularly well suited to the creation of 3D images due to the high resolution and programmable nature of the current displays.…

Aligning Microtomography Analysis with Traditional Anatomy for a 3D Understanding of the Host-Parasite Interface – Phoradendron spp. Case Study

PubMed Central

Teixeira-Costa, Luíza; Ceccantini, Gregório C. T.

2016-01-01

The complex endophytic structure formed by parasitic plant species often represents a challenge in the study of the host-parasite interface. Even with the large amounts of anatomical slides, a three-dimensional comprehension of the structure may still be difficult to obtain. In the present study we applied the High Resolution X-ray Computed Tomography (HRXCT) analysis along with usual plant anatomy techniques in order to compare the infestation pattern of two mistletoe species of the genus Phoradendron. Additionally, we tested the use of contrasting solutions in order to improve the detection of the parasite’s endophytic tissue. To our knowledge, this is the first study to show the three-dimensional structure of host-mistletoe interface by using HRXCT technique. Results showed that Phoradendron perrottetii growing on the host Tapirira guianensis forms small woody galls with a restricted endophytic system. The sinkers were short and eventually grouped creating a continuous interface with the host wood. On the other hand, the long sinkers of P. bathyoryctum penetrate deeply into the wood of Cedrela fissilis branching in all directions throughout the woody gall area, forming a spread-out infestation pattern. The results indicate that the HRXCT is indeed a powerful approach to understand the endophytic system of parasitic plants. The combination of three-dimensional models of the infestation with anatomical analysis provided a broader understanding of the host-parasite connection. Unique anatomic features are reported for the sinkes of P. perrottetii, while the endophytic tissue of P. bathyoryctum conformed to general anatomy observed for other species of this genus. These differences are hypothesized to be related to the three-dimensional structure of each endophytic system and the communication stablished with the host. PMID:27630661

Dual-color three-dimensional STED microscopy with a single high-repetition-rate laser

PubMed Central

Han, Kyu Young; Ha, Taekjip

2016-01-01

We describe a dual-color three-dimensional stimulated emission depletion (3D-STED) microscopy employing a single laser source with a repetition rate of 80 MHz. Multiple excitation pulses synchronized with a STED pulse were generated by a photonic crystal fiber and the desired wavelengths were selected by an acousto-optic tunable filter with high spectral purity. Selective excitation at different wavelengths permits simultaneous imaging of two fluorescent markers at a nanoscale resolution in three dimensions. PMID:26030581

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

PubMed Central

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

2011-01-01

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. PMID:21169680

An update on intraoperative three-dimensional transesophageal echocardiography

PubMed Central

2017-01-01

Transesophageal echocardiography (TEE) was first used routinely in the operating rooms in the 1980s to facilitate surgical decision-making. Since then, TEE has evolved from the standard two-dimensional (2D) exam to include focused real-time three-dimensional (RT-3D) imaging both inside and outside the operating rooms. Improved spatial and temporal resolution due to technological advances has expedited surgical interventions in diseased valves. 3D imaging has also emerged as a crucial adjunct in percutaneous interventions for structural heart disease. With continued advancement in software, RT-3D TEE will continue to impact perioperative decisions. PMID:28540070

Three-Dimensional Printing of Bisphenol A-Free Polycarbonates.

PubMed

Zhu, Wei; Pyo, Sang-Hyun; Wang, Pengrui; You, Shangting; Yu, Claire; Alido, Jeffrey; Liu, Justin; Leong, Yew; Chen, Shaochen

2018-02-14

Polycarbonates are widely used in food packages, drink bottles, and various healthcare products such as dental sealants and tooth coatings. However, bisphenol A (BPA) and phosgene used in the production of commercial polycarbonates pose major concerns to public health safety. Here, we report a green pathway to prepare BPA-free polycarbonates (BFPs) by thermal ring-opening polymerization and photopolymerization. Polycarbonates prepared from two cyclic carbonates in different mole ratios demonstrated tunable mechanical stiffness, excellent thermal stability, and high optical transparency. Three-dimensional (3D) printing of the new BFPs was demonstrated using a two-photon laser direct writing system and a rapid 3D optical projection printer to produce structures possessing complex high-resolution geometries. Seeded C3H10T1/2 cells also showed over 95% viability with potential applications in biological studies. By combining biocompatible BFPs with 3D printing, novel safe and high-performance biomedical devices and healthcare products could be developed with broad long-term benefits to society.

Segmenting Brain Tissues from Chinese Visible Human Dataset by Deep-Learned Features with Stacked Autoencoder

PubMed Central

Zhao, Guangjun; Wang, Xuchu; Niu, Yanmin; Tan, Liwen; Zhang, Shao-Xiang

2016-01-01

Cryosection brain images in Chinese Visible Human (CVH) dataset contain rich anatomical structure information of tissues because of its high resolution (e.g., 0.167 mm per pixel). Fast and accurate segmentation of these images into white matter, gray matter, and cerebrospinal fluid plays a critical role in analyzing and measuring the anatomical structures of human brain. However, most existing automated segmentation methods are designed for computed tomography or magnetic resonance imaging data, and they may not be applicable for cryosection images due to the imaging difference. In this paper, we propose a supervised learning-based CVH brain tissues segmentation method that uses stacked autoencoder (SAE) to automatically learn the deep feature representations. Specifically, our model includes two successive parts where two three-layer SAEs take image patches as input to learn the complex anatomical feature representation, and then these features are sent to Softmax classifier for inferring the labels. Experimental results validated the effectiveness of our method and showed that it outperformed four other classical brain tissue detection strategies. Furthermore, we reconstructed three-dimensional surfaces of these tissues, which show their potential in exploring the high-resolution anatomical structures of human brain. PMID:27057543

Segmenting Brain Tissues from Chinese Visible Human Dataset by Deep-Learned Features with Stacked Autoencoder.

PubMed

Zhao, Guangjun; Wang, Xuchu; Niu, Yanmin; Tan, Liwen; Zhang, Shao-Xiang

2016-01-01

Cryosection brain images in Chinese Visible Human (CVH) dataset contain rich anatomical structure information of tissues because of its high resolution (e.g., 0.167 mm per pixel). Fast and accurate segmentation of these images into white matter, gray matter, and cerebrospinal fluid plays a critical role in analyzing and measuring the anatomical structures of human brain. However, most existing automated segmentation methods are designed for computed tomography or magnetic resonance imaging data, and they may not be applicable for cryosection images due to the imaging difference. In this paper, we propose a supervised learning-based CVH brain tissues segmentation method that uses stacked autoencoder (SAE) to automatically learn the deep feature representations. Specifically, our model includes two successive parts where two three-layer SAEs take image patches as input to learn the complex anatomical feature representation, and then these features are sent to Softmax classifier for inferring the labels. Experimental results validated the effectiveness of our method and showed that it outperformed four other classical brain tissue detection strategies. Furthermore, we reconstructed three-dimensional surfaces of these tissues, which show their potential in exploring the high-resolution anatomical structures of human brain.

GRID: a high-resolution protein structure refinement algorithm.

PubMed

Chitsaz, Mohsen; Mayo, Stephen L

2013-03-05

The energy-based refinement of protein structures generated by fold prediction algorithms to atomic-level accuracy remains a major challenge in structural biology. Energy-based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high-resolution refinement algorithm called GRID. It takes a three-dimensional protein structure as input and, using an all-atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side-chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high-resolution (≤ 2.8 Å) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 ± 0.02 Å for GRID versus 0.14 ± 0.04 Å for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms. Copyright © 2012 Wiley Periodicals, Inc.

Optimized 14 + 1 receive coil array and position system for 3D high-resolution MRI of dental and maxillomandibular structures.

PubMed

Sedlacik, Jan; Kutzner, Daniel; Khokale, Arun; Schulze, Dirk; Fiehler, Jens; Celik, Turgay; Gareis, Daniel; Smeets, Ralf; Friedrich, Reinhard E; Heiland, Max; Assaf, Alexandre T

2016-01-01

The purpose of this study was to design, build and test a multielement receive coil array and position system, which is optimized for three-dimensional (3D) high-resolution dental and maxillomandibular MRI with high patient comfort. A 14 + 1 coil array and positioning system, allowing easy handling by the technologists, reproducible positioning of the patients and high patient comfort, was tested with three healthy volunteers using a 3.0-T MRI machine (Siemens Skyra; Siemens Medical Solutions, Erlangen, Germany). High-resolution 3D T1 weighted, water excitation T1 weighted and fat-saturated T2 weighted imaging sequences were scanned, and 3D image data were reformatted in different orientations and curvatures to aid diagnosis. The high number of receiving coils and the comfortable positioning of the coil array close to the patient's face provided a high signal-to-noise ratio and allowed high quality, high resolution, 3D image data to be acquired within reasonable scan times owing to the possibility of parallel image acquisition acceleration. Reformatting the isotropic 3D image data in different views is helpful for diagnosis, e.g. panoramic reconstruction. The visibility of soft tissues such as the mandibular canal, nutritive canals and periodontal ligaments was exquisite. The optimized MRI receive coil array and positioning system for dental and oral-maxillofacial imaging provides a valuable tool for detecting and diagnosing pathologies in dental and oral-maxillofacial structures while avoiding radiation dose. The high patient comfort, as achieved by our design, is very crucial, since image artefacts due to movement or failing to complete the examination jeopardize the diagnostic value of MRI examinations.

NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.

PubMed

Serrano, Pedro; Dutta, Samit K; Proudfoot, Andrew; Mohanty, Biswaranjan; Susac, Lukas; Martin, Bryan; Geralt, Michael; Jaroszewski, Lukasz; Godzik, Adam; Elsliger, Marc; Wilson, Ian A; Wüthrich, Kurt

2016-11-01

For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs. © 2016 Federation of European Biochemical Societies.

Casting inorganic structures with DNA molds.

PubMed

Sun, Wei; Boulais, Etienne; Hakobyan, Yera; Wang, Wei Li; Guan, Amy; Bathe, Mark; Yin, Peng

2014-11-07

We report a general strategy for designing and synthesizing inorganic nanostructures with arbitrarily prescribed three-dimensional shapes. Computationally designed DNA strands self-assemble into a stiff "nanomold" that contains a user-specified three-dimensional cavity and encloses a nucleating gold "seed." Under mild conditions, this seed grows into a larger cast structure that fills and thus replicates the cavity. We synthesized a variety of nanoparticles with 3-nanometer resolution: three distinct silver cuboids with three independently tunable dimensions, silver and gold nanoparticles with diverse cross sections, and composite structures with homo- and heterogeneous components. The designer equilateral silver triangular and spherical nanoparticles exhibited plasmonic properties consistent with electromagnetism-based simulations. Our framework is generalizable to more complex geometries and diverse inorganic materials, offering a range of applications in biosensing, photonics, and nanoelectronics. Copyright © 2014, American Association for the Advancement of Science.

Structural insights into the interaction of human IgG1 with FcγRI: no direct role of glycans in binding

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

Oganesyan, Vaheh, E-mail: oganesyanv@medimmune.com; Mazor, Yariv; Yang, Chunning

In an effort to identify the critical structural features responsible for the high-affinity interaction of IgG1 Fc with FcγRI, the structure of the corresponding complex was solved at a resolution of 2.4 Å. The three-dimensional structure of a human IgG1 Fc fragment bound to wild-type human FcγRI is reported. The structure of the corresponding complex was solved at a resolution of 2.4 Å using molecular replacement; this is the highest resolution achieved for an unmutated FcγRI molecule. This study highlights the critical structural and functional role played by the second extracellular subdomain of FcγRI. It also explains the long-known majormore » energetic contribution of the Fc ‘LLGG’ motif at positions 234–237, and particularly of Leu235, via a ‘lock-and-key’ mechanism. Finally, a previously held belief is corrected and a differing view is offered on the recently proposed direct role of Fc carbohydrates in the corresponding interaction. Structural evidence is provided that such glycan-related effects are strictly indirect.« less

Guide-star-based computational adaptive optics for broadband interferometric tomography

PubMed Central

Adie, Steven G.; Shemonski, Nathan D.; Graf, Benedikt W.; Ahmad, Adeel; Scott Carney, P.; Boppart, Stephen A.

2012-01-01

We present a method for the numerical correction of optical aberrations based on indirect sensing of the scattered wavefront from point-like scatterers (“guide stars”) within a three-dimensional broadband interferometric tomogram. This method enables the correction of high-order monochromatic and chromatic aberrations utilizing guide stars that are revealed after numerical compensation of defocus and low-order aberrations of the optical system. Guide-star-based aberration correction in a silicone phantom with sparse sub-resolution-sized scatterers demonstrates improvement of resolution and signal-to-noise ratio over a large isotome. Results in highly scattering muscle tissue showed improved resolution of fine structure over an extended volume. Guide-star-based computational adaptive optics expands upon the use of image metrics for numerically optimizing the aberration correction in broadband interferometric tomography, and is analogous to phase-conjugation and time-reversal methods for focusing in turbid media. PMID:23284179

Topographic Structure from Motion

NASA Astrophysics Data System (ADS)

Fonstad, M. A.; Dietrich, J. T.; Courville, B. C.; Jensen, J.; Carbonneau, P.

2011-12-01

The production of high-resolution topographic datasets is of increasing concern and application throughout the geomorphic sciences, and river science is no exception. Consequently, a wide range of topographic measurement methods have evolved. Despite the range of available methods, the production of high resolution, high quality digital elevation models (DEMs) generally requires a significant investment in personnel time, hardware and/or software. However, image-based methods such as digital photogrammetry have steadily been decreasing in costs. Initially developed for the purpose of rapid, inexpensive and easy three dimensional surveys of buildings or small objects, the "structure from motion" photogrammetric approach (SfM) is a purely image based method which could deliver a step-change if transferred to river remote sensing, and requires very little training and is extremely inexpensive. Using the online SfM program Microsoft Photosynth, we have created high-resolution digital elevation models (DEM) of rivers from ordinary photographs produced from a multi-step workflow that takes advantage of free and open source software. This process reconstructs real world scenes from SfM algorithms based on the derived positions of the photographs in three-dimensional space. One of the products of the SfM process is a three-dimensional point cloud of features present in the input photographs. This point cloud can be georeferenced from a small number of ground control points collected via GPS in the field. The georeferenced point cloud can then be used to create a variety of digital elevation model products. Among several study sites, we examine the applicability of SfM in the Pedernales River in Texas (USA), where several hundred images taken from a hand-held helikite are used to produce DEMs of the fluvial topographic environment. This test shows that SfM and low-altitude platforms can produce point clouds with point densities considerably better than airborne LiDAR, with horizontal and vertical precision in the centimeter range, and with very low capital and labor costs and low expertise levels. Advanced structure from motion software (such as Bundler and OpenSynther) are currently under development and should increase the density of topographic points rivaling those of terrestrial laser scanning when using images shot from low altitude platforms such as helikites, poles, remote-controlled aircraft and rotocraft, and low-flying manned aircraft. Clearly, the development of this set of inexpensive and low-required-expertise tools has the potential to fundamentally shift the production of digital fluvial topography from a capital-intensive enterprise of a low number of researchers to a low-cost exercise of many river researchers.

A high-resolution probabilistic in vivo atlas of human subcortical brain nuclei

PubMed Central

Pauli, Wolfgang M.; Nili, Amanda N.; Tyszka, J. Michael

2018-01-01

Recent advances in magnetic resonance imaging methods, including data acquisition, pre-processing and analysis, have benefited research on the contributions of subcortical brain nuclei to human cognition and behavior. At the same time, these developments have led to an increasing need for a high-resolution probabilistic in vivo anatomical atlas of subcortical nuclei. In order to address this need, we constructed high spatial resolution, three-dimensional templates, using high-accuracy diffeomorphic registration of T1- and T2- weighted structural images from 168 typical adults between 22 and 35 years old. In these templates, many tissue boundaries are clearly visible, which would otherwise be impossible to delineate in data from individual studies. The resulting delineations of subcortical nuclei complement current histology-based atlases. We further created a companion library of software tools for atlas development, to offer an open and evolving resource for the creation of a crowd-sourced in vivo probabilistic anatomical atlas of the human brain. PMID:29664465

Key issues review: numerical studies of turbulence in stars

NASA Astrophysics Data System (ADS)

Arnett, W. David; Meakin, Casey

2016-10-01

Three major problems of single-star astrophysics are convection, magnetic fields and rotation. Numerical simulations of convection in stars now have sufficient resolution to be truly turbulent, with effective Reynolds numbers of \\text{Re}>{{10}4} , and some turbulent boundary layers have been resolved. Implications of these developments are discussed for stellar structure, evolution and explosion as supernovae. Methods for three-dimensional (3D) simulations of stars are compared and discussed for 3D atmospheres, solar rotation, core-collapse and stellar boundary layers. Reynolds-averaged Navier-Stokes (RANS) analysis of the numerical simulations has been shown to provide a novel and quantitative estimate of resolution errors. Present treatments of stellar boundaries require revision, even for early burning stages (e.g. for mixing regions during He-burning). As stellar core-collapse is approached, asymmetry and fluctuations grow, rendering spherically symmetric models of progenitors more unrealistic. Numerical resolution of several different types of three-dimensional (3D) stellar simulations are compared; it is suggested that core-collapse simulations may be under-resolved. The Rayleigh-Taylor instability in explosions has a deep connection to convection, for which the abundance structure in supernova remnants may provide evidence.

A Jones matrix formalism for simulating three-dimensional polarized light imaging of brain tissue.

PubMed

Menzel, M; Michielsen, K; De Raedt, H; Reckfort, J; Amunts, K; Axer, M

2015-10-06

The neuroimaging technique three-dimensional polarized light imaging (3D-PLI) provides a high-resolution reconstruction of nerve fibres in human post-mortem brains. The orientations of the fibres are derived from birefringence measurements of histological brain sections assuming that the nerve fibres—consisting of an axon and a surrounding myelin sheath—are uniaxial birefringent and that the measured optic axis is oriented in the direction of the nerve fibres (macroscopic model). Although experimental studies support this assumption, the molecular structure of the myelin sheath suggests that the birefringence of a nerve fibre can be described more precisely by multiple optic axes oriented radially around the fibre axis (microscopic model). In this paper, we compare the use of the macroscopic and the microscopic model for simulating 3D-PLI by means of the Jones matrix formalism. The simulations show that the macroscopic model ensures a reliable estimation of the fibre orientations as long as the polarimeter does not resolve structures smaller than the diameter of single fibres. In the case of fibre bundles, polarimeters with even higher resolutions can be used without losing reliability. When taking the myelin density into account, the derived fibre orientations are considerably improved. © 2015 The Author(s).

Direct laser writing of microstructures on optically opaque and reflective surfaces

NASA Astrophysics Data System (ADS)

Rekštytė, S.; Jonavičius, T.; Malinauskas, M.

2014-02-01

Direct laser writing (DLW) based on ultra-localized polymerization is an efficient way to produce three-dimensional (3D) micro/nano-structures for diverse applications in science and industry. It is attractive for its flexibility to materialize CAD models out of wide spectrum of materials on the desired substrates. In case of direct laser lithography, photo-crosslinking can be achieved by tightly focusing ultrashort laser pulses to a photo- or thermo-polymers. Selectively exposing material to laser radiation allows creating fully 3D structures with submicrometer spatial resolution. In this paper we present DLW results of hybrid organic-inorganic material SZ2080 on optically opaque and reflective surfaces, such as silicon and various metals (Cr, Ti, Au). Our studies prove that one can precisely fabricate 2D and 3D structures with lower than 1 μm spatial resolution even on glossy or rough surfaces (surface roughness rms 0.068-0.670 μm) using sample translation velocities of up to 1 mm/s. Using femtosecond high pulse repetition rate laser, sample translation velocity can reach over 1 mm/s ensuring repeatable submicrometer structuring resolution.

Structural basis for the mechanism of inhibition of uridine phosphorylase from Salmonella typhimurium

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

Lashkov, A. A.; Zhukhlistova, N. E.; Sotnichenko, S. E.

2010-01-15

The three-dimensional structures of three complexes of Salmonella typhimurium uridine phosphorylase with the inhibitor 2,2'-anhydrouridine, the substrate PO{sub 4}, and with both the inhibitor 2,2'-anhydrouridine and the substrate PO{sub 4} (a binary complex) were studied in detail by X-ray diffraction. The structures of the complexes were refined at 2.38, 1.5, and 1.75 A resolution, respectively. Changes in the three-dimensional structure of the subunits in different crystal structures are considered depending on the presence or absence of the inhibitor molecule and (or) the phosphate ion in the active site of the enzyme. The presence of the phosphate ion in the phosphate-bindingmore » site was found to substantially change the orientations of the side chains of the amino-acid residues Arg30, Arg91, and Arg48 coordinated to this ion. A comparison showed that the highly flexible loop L9 is unstable. The atomic coordinates of the refined structures of the complexes and the corresponding structure factors were deposited in the Protein Data Bank (their PDB ID codes are 3DD0 and 3C74). The experimental data on the spatial reorganization of the active site caused by changes in its functional state from the unligated to the completely inhibited state suggest the structural basis for the mechanism of inhibition of Salmonella typhimurium uridine phosphorylase.« less

Cerebral cortex three-dimensional profiling in human fetuses by magnetic resonance imaging

PubMed Central

Sbarbati, Andrea; Pizzini, Francesca; Fabene, Paolo F; Nicolato, Elena; Marzola, Pasquina; Calderan, Laura; Simonati, Alessandro; Longo, Laura; Osculati, Antonio; Beltramello, Alberto

2004-01-01

Seven human fetuses of crown/rump length corresponding to gestational ages ranging from the 12th to the 16th week were studied using a paradigm based on three-dimensional reconstruction of the brain obtained by magnetic resonance imaging (MRI). The aim of the study was to evaluate brain morphology in situ and to describe developmental dynamics during an important period of fetal morphogenesis. Three-dimensional MRI showed the increasing degree of maturation of the brains; fronto-occipital distance, bitemporal distance and occipital angle were examined in all the fetuses. The data were interpreted by correlation with the internal structure as visualized using high-spatial-resolution MRI, acquired using a 4.7-T field intensity magnet with a gradient power of 20 G cm−1. The spatial resolution was sufficient for a detailed detection of five layers, and the contrast was optimized using sequences with different degrees of T1 and T2 weighting. Using the latter, it was possible to visualize the subplate and marginal zones. The cortical thickness was mapped on to the hemispheric surface, describing the thickness gradient from the insular cortex to the periphery of the hemispheres. The study demonstrates the utility of MRI for studying brain development. The method provides a quantitative profiling of the brain, which allows the calculation of important morphological parameters, and it provides informative regarding transient features of the developing brain. PMID:15198688

Propagation Diagnostic Simulations Using High-Resolution Equatorial Plasma Bubble Simulations

NASA Astrophysics Data System (ADS)

Rino, C. L.; Carrano, C. S.; Yokoyama, T.

2017-12-01

In a recent paper, under review, equatorial-plasma-bubble (EPB) simulations were used to conduct a comparative analysis of the EPB spectra characteristics with high-resolution in-situ measurements from the C/NOFS satellite. EPB realizations sampled in planes perpendicular to magnetic field lines provided well-defined EPB structure at altitudes penetrating both high and low-density regions. The average C/NOFS structure in highly disturbed regions showed nearly identical two-component inverse-power-law spectral characteristics as the measured EPB structure. This paper describes the results of PWE simulations using the same two-dimensional cross-field EPB realizations. New Irregularity Parameter Estimation (IPE) diagnostics, which are based on two-dimensional equivalent-phase-screen theory [A theory of scintillation for two-component power law irregularity spectra: Overview and numerical results, by Charles Carrano and Charles Rino, DOI: 10.1002/2015RS005903], have been successfully applied to extract two-component inverse-power-law parameters from measured intensity spectra. The EPB simulations [Low and Midlatitude Ionospheric Plasma DensityIrregularities and Their Effects on Geomagnetic Field, by Tatsuhiro Yokoyama and Claudia Stolle, DOI 10.1007/s11214-016-0295-7] have sufficient resolution to populate the structure scales (tens of km to hundreds of meters) that cause strong scintillation at GPS frequencies. The simulations provide an ideal geometry whereby the ramifications of varying structure along the propagation path can be investigated. It is well known path-integrated one-dimensional spectra increase the one-dimensional index by one. The relation requires decorrelation along the propagation path. Correlated structure would be interpreted as stochastic total-electron-content (TEC). The simulations are performed with unmodified structure. Because the EPB structure is confined to the central region of the sample planes, edge effects are minimized. Consequently, the propagated signal phase can be comparted to path-integrated phase for evaluating TEC extraction. Only the frequency dependence of phase scintillation distinguishes phase scintillation. The simulations allow scale-dependent exploration of remote-sensing diagnostics.

Polymerization of room-temperature ionic liquid monomers by electron beam irradiation with the aim of fabricating three-dimensional micropolymer/nanopolymer structures.

PubMed

Minamimoto, H; Irie, H; Uematsu, T; Tsuda, T; Imanishi, A; Seki, S; Kuwabata, S

2015-04-14

A novel method for fabricating microsized and nanosized polymer structures from a room-temperature ionic liquid (RTIL) on a Si substrate was developed by the patterned irradiation of an electron beam (EB). An extremely low vapor pressure of the RTIL, 1-allyl-3-ethylimidazolium bis((trifluoromethane)sulfonyl)amide, allows it to be introduced into the high-vacuum chamber of an electron beam apparatus to conduct a radiation-induced polymerization in the nanoregion. We prepared various three-dimensional (3D) micro/nanopolymer structures having high aspect ratios of up to 5 with a resolution of sub-100 nm. In addition, the effects of the irradiation dose and beam current on the physicochemical properties of the deposited polymers were investigated by recording the FT-IR spectra and Young's modulus. Interestingly, the overall shapes of the obtained structures were different from those prepared in our recent study using a focused ion beam (FIB) even if the samples were irradiated in a similar manner. This may be due to the different transmission between the two types of beams as discussed on the basis of the theoretical calculations of the quantum beam trajectories. Perceptions obtained in this study provide facile preparation procedures for the micro/nanostructures.

High-Resolution Three-Dimensional Computed Tomography for Assessing Complications Related to Intrathecal Drug Delivery.

PubMed

Morgalla, Matthias; Fortunato, Marcos; Azam, Ala; Tatagiba, Marcos; Lepski, Guillherme

2016-07-01

The assessment of the functionality of intrathecal drug delivery (IDD) systems remains difficult and time-consuming. Catheter-related problems are still very common, and sometimes difficult to diagnose. The aim of the present study is to investigate the accuracy of high-resolution three-dimensional computed tomography (CT) in order to detect catheter-related pump dysfunction. An observational, retrospective investigation. Academic medical center in Germany. We used high-resolution three dimensional (3D) computed tomography with volume rendering technique (VRT) or fluoroscopy and conventional axial-CT to assess IDD-related complications in 51 patients from our institution who had IDD systems implanted for the treatment of chronic pain or spasticity. Twelve patients (23.5%) presented a total of 22 complications. The main type of complication in our series was catheter-related (50%), followed by pump failure, infection, and inappropriate refilling. Fluoroscopy and conventional CT were used in 12 cases. High-resolution 3D CT VRT scan was used in 35 instances with suspected yet unclear complications. Using 3D-CT (VRT) the sensitivity was 58.93% - 100% (CI 95%) and the specificity 87.54% - 100% (CI 95%).The positive predictive value was 58.93% - 100% (CI 95%) and the negative predictive value: 87.54% - 100% (CI 95%).Fluoroscopy and axial CT as a combined diagnostic tool had a sensitivity of 8.3% - 91.7% (CI 95%) and a specificity of 62.9% - 100% (CI 95%). The positive predictive value was 19.29% - 100% (CI 95%) and the negative predictive value: 44.43% - 96.89% (CI 95%). This study is limited by its observational design and the small number of cases. High-resolution 3D CT VRT is a non- invasive method that can identify IDD-related complications with more precision than axial CT and fluoroscopy.

MicroCT angiography detects vascular formation and regression in skin wound healing

PubMed Central

Urao, Norifumi; Okonkwo, Uzoagu A.; Fang, Milie M.; Zhuang, Zhen W.; Koh, Timothy J.; DiPietro, Luisa A.

2016-01-01

Properly regulated angiogenesis and arteriogenesis are essential for effective wound healing. Tissue injury induces robust new vessel formation and subsequent vessel maturation, which involves vessel regression and remodeling. Although formation of functional vasculature is essential for healing, alterations in vascular structure over the time course of skin wound healing are not well understood. Here, using high-resolution ex vivo X-ray micro-computed tomography (microCT), we describe the vascular network during healing of skin excisional wounds with highly detailed three-dimensional (3D) reconstructed images and associated quantitative analysis. We found that relative vessel volume, surface area and branching number are significantly decreased in wounds from day 7 to day 14 and 21. Segmentation and skeletonization analysis of selected branches from high-resolution images as small as 2.5 μm voxel size show that branching orders are decreased in the wound vessels during healing. In histological analysis, we found that the contrast agent fills mainly arterioles, but not small capillaries nor large veins. In summary, high-resolution microCT revealed dynamic alterations of vessel structures during wound healing. This technique may be useful as a key tool in the study of the formation and regression of wound vessels. PMID:27009591

Polymorphism in 'L' shaped lipids: structure of N-, O-diacylethanolamines with mixed acyl chains.

PubMed

Tarafdar, Pradip K; Swamy, Musti J

2009-11-01

Although solid state polymorphism in lipids has been established by spectroscopic and calorimetric studies long ago, only in a few cases crystal structures of different polymorphs of the same compound have been reported, possibly due to difficulties in obtaining high quality single crystals of individual polymorphs. Recent studies show that N-, O-diacylethanolamines (DAEs) can be derived by the O-acylation of the stress-related lipids, the N-acylethanolamines under physiological conditions. In this study, two DAEs with mixed acyl chains, namely N-palmitoyl, O-octanoylethanolamine and N-palmitoyl, O-decanoylethanolamine have been synthesized and their three-dimensional structures were determined. Both the compounds were found to adopt 'L' shaped structures and exist in two polymorphic forms, alpha and beta. In the alpha form a mixed-type chain packing has been observed whereas in the beta form the chain packing is symmetric. Similar polymorphic forms are likely to exist in other 'L' shaped lipids such as 1,3-diacylglycerols and ceramides, where polymorphism has been detected earlier, but three-dimensional structures - which can give precise information about the packing at atomic resolution - have not been reported.

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

PubMed Central

Stadler, Michael R; Haines, Jenna E

2017-01-01

High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters. Further, we show a striking correspondence between these elements and the locations of mapped polytene interband regions. We believe it is likely this relationship between insulators, topological boundaries, and polytene interbands extends across the genome, and we therefore propose a model in which decompaction of boundary-insulator-interband regions drives the organization of interphase chromosomes by creating stable physical separation between adjacent domains. PMID:29148971

An adaptive front tracking technique for three-dimensional transient flows

NASA Astrophysics Data System (ADS)

Galaktionov, O. S.; Anderson, P. D.; Peters, G. W. M.; van de Vosse, F. N.

2000-01-01

An adaptive technique, based on both surface stretching and surface curvature analysis for tracking strongly deforming fluid volumes in three-dimensional flows is presented. The efficiency and accuracy of the technique are demonstrated for two- and three-dimensional flow simulations. For the two-dimensional test example, the results are compared with results obtained using a different tracking approach based on the advection of a passive scalar. Although for both techniques roughly the same structures are found, the resolution for the front tracking technique is much higher. In the three-dimensional test example, a spherical blob is tracked in a chaotic mixing flow. For this problem, the accuracy of the adaptive tracking is demonstrated by the volume conservation for the advected blob. Adaptive front tracking is suitable for simulation of the initial stages of fluid mixing, where the interfacial area can grow exponentially with time. The efficiency of the algorithm significantly benefits from parallelization of the code. Copyright

Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison.

PubMed

Wegel, Eva; Göhler, Antonia; Lagerholm, B Christoffer; Wainman, Alan; Uphoff, Stephan; Kaufmann, Rainer; Dobbie, Ian M

2016-06-06

Many biological questions require fluorescence microscopy with a resolution beyond the diffraction limit of light. Super-resolution methods such as Structured Illumination Microscopy (SIM), STimulated Emission Depletion (STED) microscopy and Single Molecule Localisation Microscopy (SMLM) enable an increase in image resolution beyond the classical diffraction-limit. Here, we compare the individual strengths and weaknesses of each technique by imaging a variety of different subcellular structures in fixed cells. We chose examples ranging from well separated vesicles to densely packed three dimensional filaments. We used quantitative and correlative analyses to assess the performance of SIM, STED and SMLM with the aim of establishing a rough guideline regarding the suitability for typical applications and to highlight pitfalls associated with the different techniques.

The three-dimensional shape of serrations at barn owl wings: towards a typical natural serration as a role model for biomimetic applications

PubMed Central

Bachmann, Thomas; Wagner, Hermann

2011-01-01

Barn owl feathers at the leading edge of the wing are equipped with comb-like structures termed serrations on their outer vanes. Each serration is formed by one barb ending that separates and bends upwards. This structure is considered to play a role in air-flow control and noise reduction during flight. Hence, it has considerable potential for engineering applications, particularly in the aviation industry. Several publications have reported possible functions of serrations at artificial airfoils. However, only crude approximations of natural serrations have so far been investigated. We refer to these attempts as zero-order approximations of serrations. It was the goal of this study to present a quantitative three-dimensional characterization of natural serrations as first-order approximations (mean values) and second-order approximations (listed differences depending on the position of the serration along the leading edge). Confocal laser scanning microscopy was used for a three-dimensional reconstruction and investigation with high spatial resolution. Each serration was defined by its length, profile geometry and curvature. Furthermore, the orientation of the serrations at the leading edge was characterized by the inclination angle, the tilt angle and the separation distance of neighboring serrations. These data are discussed with respect to possible applications of serration-like structures for noise suppression and air-flow control. PMID:21507001

Dual-dimensional microscopy: real-time in vivo three-dimensional observation method using high-resolution light-field microscopy and light-field display.

PubMed

Kim, Jonghyun; Moon, Seokil; Jeong, Youngmo; Jang, Changwon; Kim, Youngmin; Lee, Byoungho

2018-06-01

Here, we present dual-dimensional microscopy that captures both two-dimensional (2-D) and light-field images of an in-vivo sample simultaneously, synthesizes an upsampled light-field image in real time, and visualizes it with a computational light-field display system in real time. Compared with conventional light-field microscopy, the additional 2-D image greatly enhances the lateral resolution at the native object plane up to the diffraction limit and compensates for the image degradation at the native object plane. The whole process from capturing to displaying is done in real time with the parallel computation algorithm, which enables the observation of the sample's three-dimensional (3-D) movement and direct interaction with the in-vivo sample. We demonstrate a real-time 3-D interactive experiment with Caenorhabditis elegans. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Electron coherent diffraction tomography of a nanocrystal

NASA Astrophysics Data System (ADS)

Dronyak, Roman; Liang, Keng S.; Tsai, Jin-Sheng; Stetsko, Yuri P.; Lee, Ting-Kuo; Chen, Fu-Rong

2010-05-01

Coherent diffractive imaging (CDI) with electron or x-ray sources is a promising technique for investigating the structure of nanoparticles down to the atomic scale. In electron CDI, a two-dimensional reconstruction is demonstrated using highly coherent illumination from a field-emission gun as a source of electrons. In a three-dimensional (3D) electron CDI, we experimentally determine the morphology of a single MgO nanocrystal using the Bragg diffraction geometry. An iterative algorithm is applied to invert the 3D diffraction pattern about a (200) reflection of the nanoparticle measured at an angular range of 1.8°. The results reveal a 3D image of the sample at ˜8 nm resolution, and agree with a simulation. Our work demonstrates an alternative approach to obtain the 3D structure of nanocrystals with an electron microscope.

Asymmetric three-dimensional topography over mantle plumes.

PubMed

Burov, Evgueni; Gerya, Taras

2014-09-04

The role of mantle-lithosphere interactions in shaping surface topography has long been debated. In general, it is supposed that mantle plumes and vertical mantle flows result in axisymmetric, long-wavelength topography, which strongly differs from the generally asymmetric short-wavelength topography created by intraplate tectonic forces. However, identification of mantle-induced topography is difficult, especially in the continents. It can be argued therefore that complex brittle-ductile rheology and stratification of the continental lithosphere result in short-wavelength modulation and localization of deformation induced by mantle flow. This deformation should also be affected by far-field stresses and, hence, interplay with the 'tectonic' topography (for example, in the 'active/passive' rifting scenario). Testing these ideas requires fully coupled three-dimensional numerical modelling of mantle-lithosphere interactions, which so far has not been possible owing to the conceptual and technical limitations of earlier approaches. Here we present new, ultra-high-resolution, three-dimensional numerical experiments on topography over mantle plumes, incorporating a weakly pre-stressed (ultra-slow spreading), rheologically realistic lithosphere. The results show complex surface evolution, which is very different from the smooth, radially symmetric patterns usually assumed as the canonical surface signature of mantle upwellings. In particular, the topography exhibits strongly asymmetric, small-scale, three-dimensional features, which include narrow and wide rifts, flexural flank uplifts and fault structures. This suggests a dominant role for continental rheological structure and intra-plate stresses in controlling dynamic topography, mantle-lithosphere interactions, and continental break-up processes above mantle plumes.

Three-dimensional nanostructure determination from a large diffraction data set recorded using scanning electron nanodiffraction.

PubMed

Meng, Yifei; Zuo, Jian-Min

2016-09-01

A diffraction-based technique is developed for the determination of three-dimensional nanostructures. The technique employs high-resolution and low-dose scanning electron nanodiffraction (SEND) to acquire three-dimensional diffraction patterns, with the help of a special sample holder for large-angle rotation. Grains are identified in three-dimensional space based on crystal orientation and on reconstructed dark-field images from the recorded diffraction patterns. Application to a nanocrystalline TiN thin film shows that the three-dimensional morphology of columnar TiN grains of tens of nanometres in diameter can be reconstructed using an algebraic iterative algorithm under specified prior conditions, together with their crystallographic orientations. The principles can be extended to multiphase nanocrystalline materials as well. Thus, the tomographic SEND technique provides an effective and adaptive way of determining three-dimensional nanostructures.

Using Synchrotron Radiation Microtomography to Investigate Multi-scale Three-dimensional Microelectronic Packages

DOE PAGES

Carlton, Holly D.; Elmer, John W.; Li, Yan; ...

2016-04-13

For this study synchrotron radiation micro-­tomography, a non-destructive three-dimensional imaging technique, is employed to investigate an entire microelectronic package with a cross-sectional area of 16 x 16 mm. Due to the synchrotron’s high flux and brightness the sample was imaged in just 3 minutes with an 8.7 μm spatial resolution.

High resolution IVEM tomography of biological specimens

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

Sedat, J.W.; Agard, D.A.

Electron tomography is a powerful tool for elucidating the three-dimensional architecture of large biological complexes and subcellular organelles. The introduction of intermediate voltage electron microscopes further extended the technique by providing the means to examine very large and non-symmetrical subcellular organelles, at resolutions beyond what would be possible using light microscopy. Recent studies using electron tomography on a variety of cellular organelles and assemblies such as centrosomes, kinetochores, and chromatin have clearly demonstrated the power of this technique for obtaining 3D structural information on non-symmetric cell components. When combined with biochemical and molecular observations, these 3D reconstructions have provided significantmore » new insights into biological function.« less

Imaging an Active Volcano Edifice at Tenerife Island, Spain

NASA Astrophysics Data System (ADS)

Ibáñez, Jesús M.; Rietbrock, Andreas; García-Yeguas, Araceli

2008-08-01

An active seismic experiment to study the internal structure of Teide volcano is being carried out on Tenerife, a volcanic island in Spain's Canary Islands archipelago. The main objective of the Tomography at Teide Volcano Spain (TOM-TEIDEVS) experiment, begun in January 2007, is to obtain a three-dimensional (3-D) structural image of Teide volcano using seismic tomography and seismic reflection/refraction imaging techniques. At present, knowledge of the deeper structure of Teide and Tenerife is very limited, with proposed structural models based mainly on sparse geophysical and geological data. The multinational experiment-involving institutes from Spain, the United Kingdom, Italy, Ireland, and Mexico-will generate a unique high-resolution structural image of the active volcano edifice and will further our understanding of volcanic processes.

Wide-bandwidth, wide-beamwidth, high-resolution, millimeter-wave imaging for concealed weapon detection

NASA Astrophysics Data System (ADS)

Sheen, David M.; Fernandes, Justin L.; Tedeschi, Jonathan R.; McMakin, Douglas L.; Jones, A. Mark; Lechelt, Wayne M.; Severtsen, Ronald H.

2013-05-01

Active millimeter-wave imaging is currently being used for personnel screening at airports and other high-security facilities. The cylindrical imaging techniques used in the deployed systems are based on licensed technology developed at the Pacific Northwest National Laboratory. The cylindrical and a related planar imaging technique form three-dimensional images by scanning a diverging beam swept frequency transceiver over a two-dimensional aperture and mathematically focusing or reconstructing the data into three-dimensional images of the person being screened. The resolution, clothing penetration, and image illumination quality obtained with these techniques can be significantly enhanced through the selection of the aperture size, antenna beamwidth, center frequency, and bandwidth. The lateral resolution can be improved by increasing the center frequency, or it can be increased with a larger antenna beamwidth. The wide beamwidth approach can significantly improve illumination quality relative to a higher frequency system. Additionally, a wide antenna beamwidth allows for operation at a lower center frequency resulting in less scattering and attenuation from the clothing. The depth resolution of the system can be improved by increasing the bandwidth. Utilization of extremely wide bandwidths of up to 30 GHz can result in depth resolution as fine as 5 mm. This wider bandwidth operation may allow for improved detection techniques based on high range resolution. In this paper, the results of an extensive imaging study that explored the advantages of using extremely wide beamwidth and bandwidth are presented, primarily for 10-40 GHz frequency band.

Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

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

Han,Q.; Robinson, H.; Gao, Y.

Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75{angstrom} high-resolution three-dimensional crystal structure of AGT from themore » mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1{angstrom} resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.« less

A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing.

PubMed

Murakami, Tatsuya C; Mano, Tomoyuki; Saikawa, Shu; Horiguchi, Shuhei A; Shigeta, Daichi; Baba, Kousuke; Sekiya, Hiroshi; Shimizu, Yoshihiro; Tanaka, Kenji F; Kiyonari, Hiroshi; Iino, Masamitsu; Mochizuki, Hideki; Tainaka, Kazuki; Ueda, Hiroki R

2018-04-01

A three-dimensional single-cell-resolution mammalian brain atlas will accelerate systems-level identification and analysis of cellular circuits underlying various brain functions. However, its construction requires efficient subcellular-resolution imaging throughout the entire brain. To address this challenge, we developed a fluorescent-protein-compatible, whole-organ clearing and homogeneous expansion protocol based on an aqueous chemical solution (CUBIC-X). The expanded, well-cleared brain enabled us to construct a point-based mouse brain atlas with single-cell annotation (CUBIC-Atlas). CUBIC-Atlas reflects inhomogeneous whole-brain development, revealing a significant decrease in the cerebral visual and somatosensory cortical areas during postnatal development. Probabilistic activity mapping of pharmacologically stimulated Arc-dVenus reporter mouse brains onto CUBIC-Atlas revealed the existence of distinct functional structures in the hippocampal dentate gyrus. CUBIC-Atlas is shareable by an open-source web-based viewer, providing a new platform for whole-brain cell profiling.

NUMERICAL SIMULATIONS OF CORONAL HEATING THROUGH FOOTPOINT BRAIDING

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

Hansteen, V.; Pontieu, B. De; Carlsson, M.

2015-10-01

Advanced three-dimensional (3D) radiative MHD simulations now reproduce many properties of the outer solar atmosphere. When including a domain from the convection zone into the corona, a hot chromosphere and corona are self-consistently maintained. Here we study two realistic models, with different simulated areas, magnetic field strength and topology, and numerical resolution. These are compared in order to characterize the heating in the 3D-MHD simulations which self-consistently maintains the structure of the atmosphere. We analyze the heating at both large and small scales and find that heating is episodic and highly structured in space, but occurs along loop-shaped structures, andmore » moves along with the magnetic field. On large scales we find that the heating per particle is maximal near the transition region and that widely distributed opposite-polarity field in the photosphere leads to a greater heating scale height in the corona. On smaller scales, heating is concentrated in current sheets, the thicknesses of which are set by the numerical resolution. Some current sheets fragment in time, this process occurring more readily in the higher-resolution model leading to spatially highly intermittent heating. The large-scale heating structures are found to fade in less than about five minutes, while the smaller, local, heating shows timescales of the order of two minutes in one model and one minutes in the other, higher-resolution, model.« less

Three-dimensional imaging of sulfides in silicate rocks at submicron resolution with multiphoton microscopy.

PubMed

Bénard, Antoine; Palle, Sabine; Doucet, Luc Serge; Ionov, Dmitri A

2011-12-01

We report the first application of multiphoton microscopy (MPM) to generate three-dimensional (3D) images of natural minerals (micron-sized sulfides) in thick (∼120 μm) rock sections. First, reflection mode (RM) using confocal laser scanning microscopy (CLSM), combined with differential interference contrast (DIC), was tested on polished sections. Second, two-photon fluorescence (TPF) and second harmonic signal (SHG) images were generated using a femtosecond-laser on the same rock section without impregnation by a fluorescent dye. CSLM results show that the silicate matrix is revealed with DIC and RM, while sulfides can be imaged in 3D at low resolution by RM. Sulfides yield strong autofluorescence from 392 to 715 nm with TPF, while SHG is only produced by the embedding medium. Simultaneous recording of TPF and SHG images enables efficient discrimination between different components of silicate rocks. Image stacks obtained with MPM enable complete reconstruction of the 3D structure of a rock slice and of sulfide morphology at submicron resolution, which has not been previously reported for 3D imaging of minerals. Our work suggests that MPM is a highly efficient tool for 3D studies of microstructures and morphologies of minerals in silicate rocks, which may find other applications in geosciences.

Max CAPR: high-resolution 3D contrast-enhanced MR angiography with acquisition times under 5 seconds.

PubMed

Haider, Clifton R; Borisch, Eric A; Glockner, James F; Mostardi, Petrice M; Rossman, Phillip J; Young, Phillip M; Riederer, Stephen J

2010-10-01

High temporal and spatial resolution is desired in imaging of vascular abnormalities having short arterial-to-venous transit times. Methods that exploit temporal correlation to reduce the observed frame time demonstrate temporal blurring, obfuscating bolus dynamics. Previously, a Cartesian acquisition with projection reconstruction-like (CAPR) sampling method has been demonstrated for three-dimensional contrast-enhanced angiographic imaging of the lower legs using two-dimensional sensitivity-encoding acceleration and partial Fourier acceleration, providing 1mm isotropic resolution of the calves, with 4.9-sec frame time and 17.6-sec temporal footprint. In this work, the CAPR acquisition is further undersampled to provide a net acceleration approaching 40 by eliminating all view sharing. The tradeoff of frame time and temporal footprint in view sharing is presented and characterized in phantom experiments. It is shown that the resultant 4.9-sec acquisition time, three-dimensional images sets have sufficient spatial and temporal resolution to clearly portray arterial and venous phases of contrast passage. It is further hypothesized that these short temporal footprint sequences provide diagnostic quality images. This is tested and shown in a series of nine contrast-enhanced MR angiography patient studies performed with the new method.

Measurement of pO2 and pH in Living Breast Tumor Models with Three-Dimensional Resolution by Multiphoton Microscopy during Combined Therapy with Herceptin

DTIC Science & Technology

2007-04-01

contact with a freshly spin-coated NC–titania pre- polymer , which was transferred to a hot plate to initiate polymerization . The pattern of the PDMS stamp...to quantify pO2 and pH in vivo with high three-dimensional resolution (~1 µm3) and significant depth penetration (up to 400 µm) with MPLSM. The...proposed to develop techniques for measuring in vivo pO2 and pH of HER2-positive and negative primary tumors in murine models of breast cancer using

High-resolution velocimetry in energetic tidal currents using a convergent-beam acoustic Doppler profiler

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

Sellar, Brian; Harding, Samuel F.; Richmond, Marshall C.

An array of convergent acoustic Doppler velocimeters has been developed and tested for the high resolution measurement of three-dimensional tidal flow velocities in an energetic tidal site. This configuration has been developed to increase spatial resolution of velocity measurements in comparison to conventional acoustic Doppler profilers (ADPs) which characteristically use diverging acoustic beams emanating from a single instrument. This is achieved using converging acoustic beams with a sample volume at the focal point of 0.03 m 3. The array is also able to simultaneously measure three-dimensional velocity components in a profile throughout the water column, and as such is referredmore » to herein as a converging-beam acoustic Doppler profiler (CADP). Mid-depth profiling is achieved through integration of the sensor platform with the operational Alstom 1MW DeepGen-IV Tidal Turbine. This proof-of-concept paper outlines system configuration and comparison to measurements provided by co-installed reference instrumentation. Comparison of CADP to standard ADP velocity measurements reveals a mean difference of 8 mm/s, standard deviation of 18 mm/s, and order-of-magnitude reduction in realizable length-scale. CADP focal point measurements compared to a proximal single-beam reference show peak cross-correlation coefficient of 0.96 over 4.0 s averaging period and a 47% reduction in Doppler noise. The dual functionality of the CADP as a profiling instrument with a high resolution focal point make this configuration a unique and valuable advancement in underwater velocimetry enabling improved turbulence, resource and structural loading quantification and validation of numerical simulations. Alternative modes of operation have been implemented including noise-reducing bi-static sampling. Since waves are simultaneously measured it is expected that derivatives of this system will be a powerful tool in wave-current interaction studies.« less

Design, fabrication, and verification of a three-dimensional autocollimator.

PubMed

Yin, Yanhe; Cai, Sheng; Qiao, Yanfeng

2016-12-10

The autocollimator is an optical instrument for noncontact angle measurement with high resolution and a long detection range. It measures two-dimensional angles, i.e., pitch and yaw, but not roll. In this paper, we present a novelly structured autocollimator capable of measuring three-dimensional (3D) angles simultaneously. In this setup, two collimated beams of different wavelengths are projected onto a right-angle prism. One beam is reflected by the hypotenuse of the prism and received by an autocollimation unit for detecting pitch and yaw. The other is reflected by the two legs of the right-angle prism and received by a moiré fringe imaging unit for detecting roll. Furthermore, a prototype is designed and fabricated. Experiments are carried out to evaluate its basic performance. Calibration results show that this prototype has angular RMS errors of less than 5 arcsec in all 3Ds over a range of 1000 arcsec at a working distance of 2 m.

The Three-Dimensional Structure of HH 32 from GMOS IFU Spectroscopy

NASA Astrophysics Data System (ADS)

Beck, Tracy L.; Riera, A.; Raga, A. C.; Aspin, C.

2004-01-01

We present new high-resolution spectroscopic observations of the Herbig-Haro object HH 32 from system verification observations made with the GMOS IFU at Gemini North Observatory. The three-dimensional spectral data cover a 8.7"×5.85" spatial field and 4820-7040 Å spectral region centered on the HH 32 A knot complex. We show the position-dependent line profiles and radial velocity channel maps of the Hα line, as well as line ratio velocity channel maps of [O III] λ5007/Hα, [O I] λ6300/Hα, [N II] λ6583/Hα, [S II] λλ(6716+6730)/Hα, and [S II] λ6716/λ6730. We find that the line emission and the line ratios vary significantly on spatial scales of ~1" and over velocities of ~50 km s-1. A ``3/2-dimensional'' bow shock model is qualitatively successful at reproducing the general features of the radial velocity channel maps, but it does not show the same complexity as the data, and it fails to reproduce the line ratios in our high spatial resolution maps. The observations of HH 32 A show two or three superposed bow shocks with separations of ~3", which we interpret as evidence of a line-of-sight superposition of two or three working surfaces located along the redshifted body of the HH 32 outflow. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the National Science Foundation on behalf of the Gemini partnership: the NSF, the Particle Physics and Astronomy Research Council (United Kingdom), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), CNPq (Brazil), and CONICET (Argentina).

New horizons for study of the cardiopulmonary and circulatory systems. [image reconstruction techniques

NASA Technical Reports Server (NTRS)

Wood, E. H.

1976-01-01

The paper discusses the development of computer-controlled three-dimensional reconstruction techniques designed to determine the dynamic changes in the true shape and dimensions of the epi- and endocardial surfaces of the heart, along with variable time base (stop-action to real-time) displays of the transmural distribution of the coronary microcirculation and the three-dimensional anatomy of the macrovasculature in all regions of the body throughout individual cardiac and/or respiratory cycles. A technique for reconstructing a cross section of the heart from multiplanar videoroentgenograms is outlined. The capability of high spatial and high temporal resolution scanning videodensitometry makes possible measurement of the appearance, mean transit and clearance of roentgen opaque substances in three-dimensional space through the myocardium with a degree of simultaneous anatomic and temporal resolution not obtainable by current isotope techniques. The distribution of a variety of selected chemical elements or biologic materials within a body portion can also be determined.

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

Niemi, Merja, E-mail: merja.niemi@joensuu.fi; Jänis, Janne; Jylhä, Sirpa

The high-resolution mass-spectrometric characterization, crystallization and X-ray diffraction studies of a recombinant IgE Fab fragment in complex with bovine β-lactoglobulin are reported. A D1 Fab fragment containing the allergen-binding variable domains of the IgE antibody was characterized by ESI FT–ICR mass spectrometry and crystallized with bovine β-lactoglobulin (BLG) using the hanging-drop vapour-diffusion method at 293 K. X-ray data suitable for structure determination were collected to 2.8 Å resolution using synchrotron radiation. The crystal belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 67.0, b = 100.6, c = 168.1 Å. The three-dimensional structure ofmore » the D1 Fab fragment–BLG complex will provide the first insight into IgE antibody–allergen interactions at the molecular level.« less

Recovery of permittivity and depth from near-field data as a step toward infrared nanotomography.

PubMed

Govyadinov, Alexander A; Mastel, Stefan; Golmar, Federico; Chuvilin, Andrey; Carney, P Scott; Hillenbrand, Rainer

2014-07-22

The increasing complexity of composite materials structured on the nanometer scale requires highly sensitive analytical tools for nanoscale chemical identification, ideally in three dimensions. While infrared near-field microscopy provides high chemical sensitivity and nanoscopic spatial resolution in two dimensions, the quantitative extraction of material properties of three-dimensionally structured samples has not been achieved yet. Here we introduce a method to perform rapid recovery of the thickness and permittivity of simple 3D structures (such as thin films and nanostructures) from near-field measurements, and provide its first experimental demonstration. This is accomplished via a novel nonlinear invertible model of the imaging process, taking advantage of the near-field data recorded at multiple harmonics of the oscillation frequency of the near-field probe. Our work enables quantitative nanoscale-resolved optical studies of thin films, coatings, and functionalization layers, as well as the structural analysis of multiphase materials, among others. It represents a major step toward the further goal of near-field nanotomography.

Structure of the extracellular domain of matrix protein 2 of influenza A virus in complex with a protective monoclonal antibody.

PubMed

Cho, Ki Joon; Schepens, Bert; Seok, Jong Hyeon; Kim, Sella; Roose, Kenny; Lee, Ji-Hye; Gallardo, Rodrigo; Van Hamme, Evelien; Schymkowitz, Joost; Rousseau, Frederic; Fiers, Walter; Saelens, Xavier; Kim, Kyung Hyun

2015-04-01

The extracellular domain of influenza A virus matrix protein 2 (M2e) is conserved and is being evaluated as a quasiuniversal influenza A vaccine candidate. We describe the crystal structure at 1.6 Å resolution of M2e in complex with the Fab fragment of an M2e-specific monoclonal antibody that protects against influenza A virus challenge. This antibody binds M2 expressed on the surfaces of cells infected with influenza A virus. Five out of six complementary determining regions interact with M2e, and three highly conserved M2e residues are critical for this interaction. In this complex, M2e adopts a compact U-shaped conformation stabilized in the center by the highly conserved tryptophan residue in M2e. This is the first description of the three-dimensional structure of M2e. M2e of influenza A is under investigation as a universal influenza A vaccine, but its three-dimensional structure is unknown. We describe the structure of M2e stabilized with an M2e-specific monoclonal antibody that recognizes natural M2. We found that the conserved tryptophan is positioned in the center of the U-shaped structure of M2e and stabilizes its conformation. The structure also explains why previously reported in vivo escape viruses, selected with a similar monoclonal antibody, carried proline residue substitutions at position 10 in M2. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Cellulose Tailored Anatase TiO2 Nanospindles in Three-Dimensional Graphene Composites for High-Performance Supercapacitors.

PubMed

Ding, Yangbin; Bai, Wei; Sun, Jinhua; Wu, Yu; Memon, Mushtaque A; Wang, Chao; Liu, Chengbin; Huang, Yong; Geng, Jianxin

2016-05-18

The morphologies of transition metal oxides have decisive impact on the performance of their applications. Here, we report a new and facile strategy for in situ preparation of anatase TiO2 nanospindles in three-dimensional reduced graphene oxide (RGO) structure (3D TiO2@RGO) using cellulose as both an intermediate agent eliminating the negative effect of graphene oxide (GO) on the growth of TiO2 crystals and as a structure-directing agent for the shape-controlled synthesis of TiO2 crystals. High-resolution transmission electron microscopy and X-ray diffractometer analysis indicated that the spindle shape of TiO2 crystals was formed through the restriction of the growth of high energy {010} facets due to preferential adsorption of cellulose on these facets. Because of the 3D structure of the composite, the large aspect ratio of the TiO2 nanospindles, and the exposed high-energy {010} facets of the TiO2 crystals, the 3D TiO2@RGO(Ce 1.7) exhibited excellent capacitive performance as an electrode material for supercapacitors, with a high specific capacitance (ca. 397 F g(-1)), a high energy density (55.7 Wh kg(-1)), and a high power density (1327 W kg(-1)) on the basis of the masses of RGO and TiO2. These levels of capacitive performance far exceed those of previously reported TiO2-based composites.

High-Speed, Three Dimensional Object Composition Mapping Technology

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

Ishikawa, M Y

2001-02-14

This document overviews an entirely new approach to determining the composition--the chemical-elemental, isotopic and molecular make-up--of complex, highly structured objects, moreover with microscopic spatial resolution in all 3 dimensions. The front cover depicts the new type of pulsed laser system at the heart of this novel technology under adjustment by Alexis Wynne, and schematically indicates two of its early uses: swiftly analyzing the 3-D composition governed structure of a transistor circuit with both optical and mass-spectrometric detectors, and of fossilized dinosaur and turtle bones high-speed probed by optical detection means. Studying the composition-cued 3-D micro-structures of advanced composite materials andmore » the microscopic scale composition-texture of biological tissues are two near-term examples of the rich spectrum of novel applications enabled by this field-opening analytic tool-set.« less

Discovery of a diamond-based photonic crystal structure in beetle scales.

PubMed

Galusha, Jeremy W; Richey, Lauren R; Gardner, John S; Cha, Jennifer N; Bartl, Michael H

2008-05-01

We investigated the photonic crystal structure inside iridescent scales of the weevil Lamprocyphus augustus. By combining a high-resolution structure analysis technique based on sequential focused ion beam milling and scanning electron microscopy imaging with theoretical modeling and photonic band-structure calculations, we discovered a natural three-dimensional photonic structure with a diamond-based crystal lattice operating at visible wavelengths. Moreover, we found that within individual scales, the diamond-based structure is assembled in the form of differently oriented single-crystalline micrometer-sized pixels with only selected lattice planes facing the scales' top surface. A comparison of results obtained from optical microreflectance measurements with photonic band-structure calculations reveals that it is this sophisticated microassembly of the diamond-based crystal lattice that lends Lamprocyphus augustus its macroscopically near angle-independent green coloration.

Hierarchical classification in high dimensional numerous class cases

NASA Technical Reports Server (NTRS)

Kim, Byungyong; Landgrebe, D. A.

1990-01-01

As progress in new sensor technology continues, increasingly high resolution imaging sensors are being developed. These sensors give more detailed and complex data for each picture element and greatly increase the dimensionality of data over past systems. Three methods for designing a decision tree classifier are discussed: a top down approach, a bottom up approach, and a hybrid approach. Three feature extraction techniques are implemented. Canonical and extended canonical techniques are mainly dependent upon the mean difference between two classes. An autocorrelation technique is dependent upon the correlation differences. The mathematical relationship between sample size, dimensionality, and risk value is derived.

Optimized Deconvolution for Maximum Axial Resolution in Three-Dimensional Aberration-Corrected Scanning Transmission Electron Microscopy

PubMed Central

Ramachandra, Ranjan; de Jonge, Niels

2012-01-01

Three-dimensional (3D) data sets were recorded of gold nanoparticles placed on both sides of silicon nitride membranes using focal series aberration-corrected scanning transmission electron microscopy (STEM). The deconvolution of the 3D datasets was optimized to obtain the highest possible axial resolution. The deconvolution involved two different point spread function (PSF)s, each calculated iteratively via blind deconvolution.. Supporting membranes of different thicknesses were tested to study the effect of beam broadening on the deconvolution. It was found that several iterations of deconvolution was efficient in reducing the imaging noise. With an increasing number of iterations, the axial resolution was increased, and most of the structural information was preserved. Additional iterations improved the axial resolution by maximal a factor of 4 to 6, depending on the particular dataset, and up to 8 nm maximal, but at the cost of a reduction of the lateral size of the nanoparticles in the image. Thus, the deconvolution procedure optimized for highest axial resolution is best suited for applications where one is interested in the 3D locations of nanoparticles only. PMID:22152090

Two-photon polymerization as a structuring technology in production: future or fiction?

NASA Astrophysics Data System (ADS)

Harnisch, Emely Marie; Schmitt, Robert

2017-02-01

Two-photon polymerization (TPP) has become an established generative fabrication technique for individual, up to three-dimensional micro- and nanostructures. Due to its high resolution beyond the diffraction limit, its writing speed is limited and in most cases, very special structures are fabricated in small quantities. With regard to the trends of the optical market towards higher efficiencies, miniaturization and higher functionalities, there is a high demand for so called intelligent light management systems, including also individual optical elements. Here, TPP could offer a fabrication technique, enabling higher complexities of structures than conventional cutting and lithographic technologies do. But how can TPP opened up for production? In the following, some approaches to establish TPP as a mastering technique for molding are presented against this background.

Three-dimensional measurement system for crime scene documentation

NASA Astrophysics Data System (ADS)

Adamczyk, Marcin; Hołowko, Elwira; Lech, Krzysztof; Michoński, Jakub; MÄ czkowski, Grzegorz; Bolewicki, Paweł; Januszkiewicz, Kamil; Sitnik, Robert

2017-10-01

Three dimensional measurements (such as photogrammetry, Time of Flight, Structure from Motion or Structured Light techniques) are becoming a standard in the crime scene documentation process. The usage of 3D measurement techniques provide an opportunity to prepare more insightful investigation and helps to show every trace in the context of the entire crime scene. In this paper we would like to present a hierarchical, three-dimensional measurement system that is designed for crime scenes documentation process. Our system reflects the actual standards in crime scene documentation process - it is designed to perform measurement in two stages. First stage of documentation, the most general, is prepared with a scanner with relatively low spatial resolution but also big measuring volume - it is used for the whole scene documentation. Second stage is much more detailed: high resolution but smaller size of measuring volume for areas that required more detailed approach. The documentation process is supervised by a specialised application CrimeView3D, that is a software platform for measurements management (connecting with scanners and carrying out measurements, automatic or semi-automatic data registration in the real time) and data visualisation (3D visualisation of documented scenes). It also provides a series of useful tools for forensic technicians: virtual measuring tape, searching for sources of blood spatter, virtual walk on the crime scene and many others. In this paper we present our measuring system and the developed software. We also provide an outcome from research on metrological validation of scanners that was performed according to VDI/VDE standard. We present a CrimeView3D - a software-platform that was developed to manage the crime scene documentation process. We also present an outcome from measurement sessions that were conducted on real crime scenes with cooperation with Technicians from Central Forensic Laboratory of Police.

Does Explosive Nuclear Burning Occur in Tidal Disruption Events of White Dwarfs by Intermediate-mass Black Holes?

NASA Astrophysics Data System (ADS)

Tanikawa, Ataru; Sato, Yushi; Nomoto, Ken'ichi; Maeda, Keiichi; Nakasato, Naohito; Hachisu, Izumi

2017-04-01

We investigate nucleosynthesis in tidal disruption events (TDEs) of white dwarfs (WDs) by intermediate-mass black holes. We consider various types of WDs with different masses and compositions by means of three-dimensional (3D) smoothed particle hydrodynamics (SPH) simulations. We model these WDs with different numbers of SPH particles, N, from a few 104 to a few 107 in order to check mass resolution convergence, where SPH simulations with N > 107 (or a space resolution of several 106 cm) have unprecedentedly high resolution in this kind of simulation. We find that nuclear reactions become less active with increasing N and that these nuclear reactions are excited by spurious heating due to low resolution. Moreover, we find no shock wave generation. In order to investigate the reason for the absence of a shock wave, we additionally perform one-dimensional (1D) SPH and mesh-based simulations with a space resolution ranging from 104 to 107 cm, using a characteristic flow structure extracted from the 3D SPH simulations. We find shock waves in these 1D high-resolution simulations, one of which triggers a detonation wave. However, we must be careful of the fact that, if the shock wave emerged in an outer region, it could not trigger the detonation wave due to low density. Note that the 1D initial conditions lack accuracy to precisely determine where a shock wave emerges. We need to perform 3D simulations with ≲106 cm space resolution in order to conclude that WD TDEs become optical transients powered by radioactive nuclei.

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

Meng, Yifei; Zuo, Jian -Min

A diffraction-based technique is developed for the determination of three-dimensional nanostructures. The technique employs high-resolution and low-dose scanning electron nanodiffraction (SEND) to acquire three-dimensional diffraction patterns, with the help of a special sample holder for large-angle rotation. Grains are identified in three-dimensional space based on crystal orientation and on reconstructed dark-field images from the recorded diffraction patterns. Application to a nanocrystalline TiN thin film shows that the three-dimensional morphology of columnar TiN grains of tens of nanometres in diameter can be reconstructed using an algebraic iterative algorithm under specified prior conditions, together with their crystallographic orientations. The principles can bemore » extended to multiphase nanocrystalline materials as well. Furthermore, the tomographic SEND technique provides an effective and adaptive way of determining three-dimensional nanostructures.« less

Electronic band structure of ReS2 by high-resolution angle-resolved photoemission spectroscopy

NASA Astrophysics Data System (ADS)

Webb, James L.; Hart, Lewis S.; Wolverson, Daniel; Chen, Chaoyu; Avila, Jose; Asensio, Maria C.

2017-09-01

The rhenium-based transition metal dichalcogenides (TMDs) are atypical of the TMD family due to their highly anisotropic crystalline structure and are recognized as promising materials for two-dimensional heterostructure devices. The nature of the band gap (direct or indirect) for bulk, few-, and single-layer forms of ReS2 is of particular interest, due to its comparatively weak interplanar interaction. However, the degree of interlayer interaction and the question of whether a transition from indirect to direct gap is observed on reducing thickness (as in other TMDs) are controversial. We present a direct determination of the valence band structure of bulk ReS2 using high-resolution angle-resolved photoemission spectroscopy. We find a clear in-plane anisotropy due to the presence of chains of Re atoms, with a strongly directional effective mass which is larger in the direction orthogonal to the Re chains (2.2 me ) than along them (1.6 me ). An appreciable interplane interaction results in an experimentally measured difference of ≈100 -200 meV between the valence band maxima at the Z point (0,0,1/2 ) and the Γ point (0,0,0) of the three-dimensional Brillouin zone. This leads to a direct gap at Z and a close-lying but larger gap at Γ , implying that bulk ReS2 is marginally indirect. This may account for recent conflicting transport and photoluminescence measurements and the resulting uncertainty about the nature of the band gap in this material.

Dynamic three-dimensional display of common congenital cardiac defects from reconstruction of two-dimensional echocardiographic images.

PubMed

Hsieh, K S; Lin, C C; Liu, W S; Chen, F L

1996-01-01

Two-dimensional echocardiography had long been a standard diagnostic modality for congenital heart disease. Further attempts of three-dimensional reconstruction using two-dimensional echocardiographic images to visualize stereotypic structure of cardiac lesions have been successful only recently. So far only very few studies have been done to display three-dimensional anatomy of the heart through two-dimensional image acquisition because such complex procedures were involved. This study introduced a recently developed image acquisition and processing system for dynamic three-dimensional visualization of various congenital cardiac lesions. From December 1994 to April 1995, 35 cases were selected in the Echo Laboratory here from about 3000 Echo examinations completed. Each image was acquired on-line with specially designed high resolution image grazmber with EKG and respiratory gating technique. Off-line image processing using a window-architectured interactive software package includes construction of 2-D ehcocardiographic pixel to 3-D "voxel" with conversion of orthogonal to rotatory axial system, interpolation, extraction of region of interest, segmentation, shading and, finally, 3D rendering. Three-dimensional anatomy of various congenital cardiac defects was shown, including four cases with ventricular septal defects, two cases with atrial septal defects, and two cases with aortic stenosis. Dynamic reconstruction of a "beating heart" is recorded as vedio tape with video interface. The potential application of 3D display of the reconstruction from 2D echocardiographic images for the diagnosis of various congenital heart defects has been shown. The 3D display was able to improve the diagnostic ability of echocardiography, and clear-cut display of the various congenital cardiac defects and vavular stenosis could be demonstrated. Reinforcement of current techniques will expand future application of 3D display of conventional 2D images.

Assessment of geometry in 2D immune systems using high accuracy laser-based bioprinting techniques (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lauzurica, Sara; Márquez, Andrés.; Molpeceres, Carlos; Notario, Laura; Gómez-Fontela, Miguel; Lauzurica, Pilar

2017-02-01

The immune system is a very complex system that comprises a network of genetic and signaling pathways subtending a network of interacting cells. The location of the cells in a network, along with the gene products they interact with, rules the behavior of the immune system. Therefore, there is a great interest in understanding properly the role of a cell in such networks to increase our knowledge of the immune system response. In order to acquire a better understanding of these processes, cell printing with high spatial resolution emerges as one of the promising approaches to organize cells in two and three-dimensional patterns to enable the study the geometry influence in these interactions. In particular, laser assisted bio-printing techniques using sub-nanosecond laser sources have better characteristics for application in this field, mainly due to its higher spatial resolution, cell viability percentage and process automation. This work presents laser assisted bio-printing of antigen-presenting cells (APCs) in two-dimensional geometries, placing cellular components on a matrix previously generated on demand, permitting to test the molecular interactions between APCs and lymphocytes; as well as the generation of two-dimensional structures designed ad hoc in order to study the mechanisms of mobilization of immune system cells. The use of laser assisted bio-printing, along with APCs and lymphocytes emulate the structure of different niches of the immune system so that we can analyse functional requirement of these interaction.

Hydrogel-Tissue Chemistry: Principles and Applications.

PubMed

Gradinaru, Viviana; Treweek, Jennifer; Overton, Kristin; Deisseroth, Karl

2018-05-20

Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.

Large image microscope array for the compilation of multimodality whole organ image databases.

PubMed

Namati, Eman; De Ryk, Jessica; Thiesse, Jacqueline; Towfic, Zaid; Hoffman, Eric; Mclennan, Geoffrey

2007-11-01

Three-dimensional, structural and functional digital image databases have many applications in education, research, and clinical medicine. However, to date, apart from cryosectioning, there have been no reliable means to obtain whole-organ, spatially conserving histology. Our aim was to generate a system capable of acquiring high-resolution images, featuring microscopic detail that could still be spatially correlated to the whole organ. To fulfill these objectives required the construction of a system physically capable of creating very fine whole-organ sections and collecting high-magnification and resolution digital images. We therefore designed a large image microscope array (LIMA) to serially section and image entire unembedded organs while maintaining the structural integrity of the tissue. The LIMA consists of several integrated components: a novel large-blade vibrating microtome, a 1.3 megapixel peltier cooled charge-coupled device camera, a high-magnification microscope, and a three axis gantry above the microtome. A custom control program was developed to automate the entire sectioning and automated raster-scan imaging sequence. The system is capable of sectioning unembedded soft tissue down to a thickness of 40 microm at specimen dimensions of 200 x 300 mm to a total depth of 350 mm. The LIMA system has been tested on fixed lung from sheep and mice, resulting in large high-quality image data sets, with minimal distinguishable disturbance in the delicate alveolar structures. Copyright 2007 Wiley-Liss, Inc.

Fabrication of three-dimensional scaffolds using precision extrusion deposition with an assisted cooling device.

PubMed

Hamid, Q; Snyder, J; Wang, C; Timmer, M; Hammer, J; Guceri, S; Sun, W

2011-09-01

In the field of biofabrication, tissue engineering and regenerative medicine, there are many methodologies to fabricate a building block (scaffold) which is unique to the target tissue or organ that facilitates cell growth, attachment, proliferation and/or differentiation. Currently, there are many techniques that fabricate three-dimensional scaffolds; however, there are advantages, limitations and specific tissue focuses of each fabrication technique. The focus of this initiative is to utilize an existing technique and expand the library of biomaterials which can be utilized to fabricate three-dimensional scaffolds rather than focusing on a new fabrication technique. An expanded library of biomaterials will enable the precision extrusion deposition (PED) device to construct three-dimensional scaffolds with enhanced biological, chemical and mechanical cues that will benefit tissue generation. Computer-aided motion and extrusion drive the PED to precisely fabricate micro-scaled scaffolds with biologically inspired, porosity, interconnectivity and internal and external architectures. The high printing resolution, precision and controllability of the PED allow for closer mimicry of tissues and organs. The PED expands its library of biopolymers by introducing an assisting cooling (AC) device which increases the working extrusion temperature from 120 to 250 °C. This paper investigates the PED with the integrated AC's capabilities to fabricate three-dimensional scaffolds that support cell growth, attachment and proliferation. Studies carried out in this paper utilized a biopolymer whose melting point is established to be 200 °C. This polymer was selected to illustrate the newly developed device's ability to fabricate three-dimensional scaffolds from a new library of biopolymers. Three-dimensional scaffolds fabricated with the integrated AC device should illustrate structural integrity and ability to support cell attachment and proliferation.

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

DOE PAGES

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

2016-03-30

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

Mechanism of aquaporin-4's fast and highly selective water conduction and proton exclusion.

PubMed

Tani, Kazutoshi; Mitsuma, Tadanori; Hiroaki, Yoko; Kamegawa, Akiko; Nishikawa, Kouki; Tanimura, Yukihiro; Fujiyoshi, Yoshinori

2009-06-19

Members of the aquaporin (AQP) family are expressed in almost every organism, including 13 homologues in humans. Based on the electron crystallographic structure of AQP1, the hydrogen-bond isolation mechanism was proposed to explain why AQPs are impermeable to protons despite their very fast water conduction. The mechanism by which AQPs exclude protons remained controversial, however. Here we present the structure of AQP4 at 2.8 A resolution obtained by electron crystallography of double-layered two-dimensional crystals. The resolution has been improved from the previous 3.2 A, with accompanying improvement in data quality resulting in the ability to identify individual water molecules. Our structure of AQP4, the predominant water channel in the brain, reveals eight water molecules in the channel. The arrangement of the waters provides support for the hydrogen-bond isolation mechanism. Our AQP4 structure also visualizes five lipids, showing that direct interactions of the extracellular surface of AQP4 with three lipids in the adjoining membrane help stabilize the membrane junction.

A Three-Dimensional DOSY HMQC Experiment for the High-Resolution Analysis of Complex Mixtures

NASA Astrophysics Data System (ADS)

Barjat, Hervé; Morris, Gareth A.; Swanson, Alistair G.

1998-03-01

A three-dimensional experiment is described in which NMR signals are separated according to their proton chemical shift,13C chemical shift, and diffusion coefficient. The sequence is built up from a stimulated echo sequence with bipolar field gradient pulses and a conventional decoupled HMQC sequence. Results are presented for a model mixture of quinine, camphene, and geraniol in deuteriomethanol.

Direct Numerical Simulation of Cell Printing

NASA Astrophysics Data System (ADS)

Qiao, Rui; He, Ping

2010-11-01

Structural cell printing, i.e., printing three dimensional (3D) structures of cells held in a tissue matrix, is gaining significant attention in the biomedical community. The key idea is to use desktop printer or similar devices to print cells into 3D patterns with a resolution comparable to the size of mammalian cells, similar to that in living organs. Achieving such a resolution in vitro can lead to breakthroughs in areas such as organ transplantation and understanding of cell-cell interactions in truly 3D spaces. Although the feasibility of cell printing has been demonstrated in the recent years, the printing resolution and cell viability remain to be improved. In this work, we investigate one of the unit operations in cell printing, namely, the impact of a cell-laden droplet into a pool of highly viscous liquids using direct numerical simulations. The dynamics of droplet impact (e.g., crater formation and droplet spreading and penetration) and the evolution of cell shape and internal stress are quantified in details.

Three-dimensional nanostructure determination from a large diffraction data set recorded using scanning electron nanodiffraction

DOE PAGES

Meng, Yifei; Zuo, Jian -Min

2016-07-04

A diffraction-based technique is developed for the determination of three-dimensional nanostructures. The technique employs high-resolution and low-dose scanning electron nanodiffraction (SEND) to acquire three-dimensional diffraction patterns, with the help of a special sample holder for large-angle rotation. Grains are identified in three-dimensional space based on crystal orientation and on reconstructed dark-field images from the recorded diffraction patterns. Application to a nanocrystalline TiN thin film shows that the three-dimensional morphology of columnar TiN grains of tens of nanometres in diameter can be reconstructed using an algebraic iterative algorithm under specified prior conditions, together with their crystallographic orientations. The principles can bemore » extended to multiphase nanocrystalline materials as well. Furthermore, the tomographic SEND technique provides an effective and adaptive way of determining three-dimensional nanostructures.« less

Micro-pixelation and color mixing in biological photonic structures (presentation video)

NASA Astrophysics Data System (ADS)

Bartl, Michael H.; Nagi, Ramneet K.

2014-03-01

The world of insects displays myriad hues of coloration effects produced by elaborate nano-scale architectures built into wings and exoskeleton. For example, we have recently found many weevils possess photonic architectures with cubic lattices. In this talk, we will present high-resolution three-dimensional reconstructions of weevil photonic structures with diamond and gyroid lattices. Moreover, by reconstructing entire scales we found arrays of single-crystalline domains, each oriented such that only selected crystal faces are visible to an observer. This pixel-like arrangement is key to the angle-independent coloration typical of weevils—a strategy that could enable a new generation of coating technologies.

Atomic structure and chemistry of human serum albumin

NASA Technical Reports Server (NTRS)

He, Xiao M.; Carter, Daniel C.

1992-01-01

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

Atomic structure and chemistry of human serum albumin

NASA Astrophysics Data System (ADS)

He, Xiao Min; Carter, Daniel C.

1992-07-01

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 Å. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and IIIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

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

Yap, Thai Leong; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551; Chen, Yen Liang

Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents anmore » interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration.« less

Extinction maps toward the Milky Way bulge: Two-dimensional and three-dimensional tests with apogee

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

Schultheis, M.; Zasowski, G.; Allende Prieto, C.

Galactic interstellar extinction maps are powerful and necessary tools for Milky Way structure and stellar population analyses, particularly toward the heavily reddened bulge and in the midplane. However, due to the difficulty of obtaining reliable extinction measures and distances for a large number of stars that are independent of these maps, tests of their accuracy and systematics have been limited. Our goal is to assess a variety of photometric stellar extinction estimates, including both two-dimensional and three-dimensional extinction maps, using independent extinction measures based on a large spectroscopic sample of stars toward the Milky Way bulge. We employ stellar atmosphericmore » parameters derived from high-resolution H-band Apache Point Observatory Galactic Evolution Experiment (APOGEE) spectra, combined with theoretical stellar isochrones, to calculate line-of-sight extinction and distances for a sample of more than 2400 giants toward the Milky Way bulge. We compare these extinction values to those predicted by individual near-IR and near+mid-IR stellar colors, two-dimensional bulge extinction maps, and three-dimensional extinction maps. The long baseline, near+mid-IR stellar colors are, on average, the most accurate predictors of the APOGEE extinction estimates, and the two-dimensional and three-dimensional extinction maps derived from different stellar populations along different sightlines show varying degrees of reliability. We present the results of all of the comparisons and discuss reasons for the observed discrepancies. We also demonstrate how the particular stellar atmospheric models adopted can have a strong impact on this type of analysis, and discuss related caveats.« less

Anatomically Realistic Three-Dimensional Meshes of the Pelvic Floor & Anal Canal for Finite Element Analysis

PubMed Central

Noakes, Kimberley F.; Bissett, Ian P.; Pullan, Andrew J.; Cheng, Leo K.

2014-01-01

Three anatomically realistic meshes, suitable for finite element analysis, of the pelvic floor and anal canal regions have been developed to provide a framework with which to examine the mechanics, via finite element analysis of normal function within the pelvic floor. Two cadaver-based meshes were produced using the Visible Human Project (male and female) cryosection data sets, and a third mesh was produced based on MR image data from a live subject. The Visible Man (VM) mesh included 10 different pelvic structures while the Visible Woman and MRI meshes contained 14 and 13 structures respectively. Each image set was digitized and then finite element meshes were created using an iterative fitting procedure with smoothing constraints calculated from ‘L’-curves. These weights produced accurate geometric meshes of each pelvic structure with average Root Mean Square (RMS) fitting errors of less than 1.15 mm. The Visible Human cadaveric data provided high resolution images, however, the cadaveric meshes lacked the normal dynamic form of living tissue and suffered from artifacts related to postmortem changes. The lower resolution MRI mesh was able to accurately portray structure of the living subject and paves the way for dynamic, functional modeling. PMID:18317929

Micro-computed tomography: Applications for high-resolution skeletal density determinations: An example using annually banded crustose coralline algae

NASA Astrophysics Data System (ADS)

Chan, P.; Halfar, J.; Norley, C. J. D.; Pollmann, S. I.; Adey, W.; Holdsworth, D. W.

2017-09-01

Warming and acidification of the world's oceans are expected to have widespread consequences for marine biodiversity and ecosystem functioning. However, due to the relatively short record of instrumental observations, one has to rely upon geochemical and physical proxy information stored in biomineralized shells and skeletons of calcareous marine organisms as in situ recorders of past environments. Of particular interest is the response of marine calcifiers to ocean acidification through the examination of structural growth characteristics. Here we demonstrate the application of micro-computed tomography (micro-CT) for three-dimensional visualization and analysis of growth, skeletal density, and calcification in a slow-growing, annually banded crustose coralline alga Clathromorphum nereostratum (increment width ˜380 µm). X-ray images and time series of skeletal density were generated at 20 µm resolution and rebinned to 40, 60, 80, and 100 µm for comparison in a sensitivity analysis. Calcification rates were subsequently calculated as the product of density and growth (linear extension). While both skeletal density and calcification rates do not significantly differ at varying spatial resolutions (the latter being strongly influenced by growth rates), clear visualization of micron-scale growth features and the quantification of structural changes on subannual time scales requires higher scanning resolutions. In the present study, imaging at 20 µm resolution reveals seasonal cycles in density that correspond to summer/winter variations in skeletal structure observed using scanning electron microscopy (SEM). Micro-CT is a fast, nondestructive, and high-resolution technique for structural and morphometric analyses of temporally banded paleoclimate archives, particularly those that exhibit slow or compressed growth or micron-scale structures.

Large-scale three-dimensional phase-field simulations for phase coarsening at ultrahigh volume fraction on high-performance architectures

NASA Astrophysics Data System (ADS)

Yan, Hui; Wang, K. G.; Jones, Jim E.

2016-06-01

A parallel algorithm for large-scale three-dimensional phase-field simulations of phase coarsening is developed and implemented on high-performance architectures. From the large-scale simulations, a new kinetics in phase coarsening in the region of ultrahigh volume fraction is found. The parallel implementation is capable of harnessing the greater computer power available from high-performance architectures. The parallelized code enables increase in three-dimensional simulation system size up to a 5123 grid cube. Through the parallelized code, practical runtime can be achieved for three-dimensional large-scale simulations, and the statistical significance of the results from these high resolution parallel simulations are greatly improved over those obtainable from serial simulations. A detailed performance analysis on speed-up and scalability is presented, showing good scalability which improves with increasing problem size. In addition, a model for prediction of runtime is developed, which shows a good agreement with actual run time from numerical tests.

Three-dimensional evaluation of the facet joints

NASA Astrophysics Data System (ADS)

Folio, Les R.

1990-04-01

Computerized tomography and magnetic resonance imaging nave revolurionalized analysis of vertebral anatomy and pathology. Further advances with 3-dimensional imaging have recently become an important adjunct for diagnosis and treatment in structural abnormalities. Facets are intimately related to their surrounding musculature and malalignment may cause pain directly or indirectly. High resolution 3-dimensional reformations of CT Scans give us new insight on structure and function of facet joints, since their motion and architecture are ever complex. It is well documented in the literature that facet joint biomecnanics is a partial contributor to the myriad at causes of low back The term "facet Joint syndrome" was coined in 1933 by GhorMley.3 The osteopathic lesion complex is well defined by LeRoy and McCole and comparison of roentgenographic findings before and after manipulation has teen described by Long and Lioyd.4,5 since alterations in facet biamechanics are an important aspect of osteopathic manipulative therapy (OT), 3-dimensional hign resolution imaging will prove to be a great asset in osteopathic research. Rotating the spine allows for different viewing perspectives to provide optimal and consistent measurements of the facet joint. Rotations are performed on the X, Y and 7, axis and measurements pre and post-manipulation are performed and compared on matching axis and perspectives. Rotation about the X, Y and Z axis help appreciate the 3-dimensionality of the vertebral column to project to the viewer a feeling that the spine is floating in space before them. This does give the viewer a 3-D understanding of the object however, only at a perspective at a Lime.

In vivo, high-resolution, three-dimensional imaging of port wine stain microvasculature in human skin.

PubMed

Liu, Gangjun; Jia, Wangcun; Nelson, J Stuart; Chen, Zhongping

2013-12-01

Port-wine stain (PWS) is a congenital, progressive vascular malformation of the dermis. The use of optical coherence tomography (OCT) for the characterization of blood vessels in PWS skin has been demonstrated by several groups. In the past few years, advances in OCT technology have greatly increased imaging speed. Sophisticated numerical algorithms have improved the sensitivity of Doppler OCT dramatically. These improvements have enabled the noninvasive, high-resolution, three-dimensional functional imaging of PWS skin. Here, we demonstrate high-resolution, three-dimensional, microvasculature imaging of PWS and normal skin using Doppler OCT technique. The OCT system uses a swept source laser which has a central wavelength of 1,310 nm, an A-line rate of 50 kHz and a total average power of 16 mW. The system uses a handheld imaging probe and has an axial resolution of 9.3 µm in air and a lateral resolution of approximately 15 µm. Images were acquired from PWS subjects at the Beckman Laser Institute and Medical Clinic. Microvasculature of the PWS skin and normal skin were obtained from the PWS subject. High-resolution, three-dimensional microvasculature of PWS and normal skin were obtained. Many enlarged PWS vessels are detected in the dermis down to 1.0 mm below the PWS skin surface. In one subject, the blood vessel diameters range from 40 to 90 µm at the epidermal-dermal junction and increase up to 300-500 µm at deeper regions 700-1,000 µm below skin surface. The blood vessels close to the epidermal-dermal junction are more uniform, in terms of diameter. The more tortuous and dilated PWS blood vessels are located at deeper regions 600-1,000 µm below the skin surface. In another subject example, the PWS skin blood vessels are dilated at very superficial layers at a depth less than 500 µm below the skin surface. The PWS skin vessel diameters range from 60 to 650 µm, with most vessels having a diameter of around 200 µm. OCT can be used to quantitatively image in vivo skin micro-vasculature. Analysis of the PWS and normal skin blood vessels were performed and the results can provide quantitative information to optimize laser treatment on an individual patient basis. © 2013 Wiley Periodicals, Inc.

Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo

PubMed Central

Chen, Chen; Lim, Hong Hwa; Shi, Jian; Tamura, Sachiko; Maeshima, Kazuhiro; Surana, Uttam; Gan, Lu

2016-01-01

Chromatin organization has an important role in the regulation of eukaryotic systems. Although recent studies have refined the three-dimensional models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin—nucleosomes—are positioned in three dimensions in vivo. Here we use electron cryotomography to study chromatin organization in the budding yeast Saccharomyces cerevisiae. Direct visualization of yeast nuclear densities shows no evidence of 30-nm fibers. Aside from preribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an “open” configuration that is conducive to high levels of transcription. From our study and those of others, we propose that yeast can regulate its transcription using local nucleosome–nucleosome associations. PMID:27605704

A Multi-Resolution Data Structure for Two-Dimensional Morse Functions

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

Bremer, P-T; Edelsbrunner, H; Hamann, B

2003-07-30

The efficient construction of simplified models is a central problem in the field of visualization. We combine topological and geometric methods to construct a multi-resolution data structure for functions over two-dimensional domains. Starting with the Morse-Smale complex we build a hierarchy by progressively canceling critical points in pairs. The data structure supports mesh traversal operations similar to traditional multi-resolution representations.

The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays.

PubMed

Dubrovin, E V; Presnova, G V; Rubtsova, M Yu; Egorov, A M; Grigorenko, V G; Yaminsky, I V

2015-01-01

Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles.

Split-ball resonator as a three-dimensional analogue of planar split-rings

NASA Astrophysics Data System (ADS)

Kuznetsov, Arseniy I.; Miroshnichenko, Andrey E.; Hsing Fu, Yuan; Viswanathan, Vignesh; Rahmani, Mohsen; Valuckas, Vytautas; Ying Pan, Zhen; Kivshar, Yuri; Pickard, Daniel S.; Luk'Yanchuk, Boris

2014-01-01

Split-ring resonators are basic elements of metamaterials, which can induce a magnetic response in metallic nanosctructures. Tunability of such response up to the visible frequency range is still a challenge. Here we introduce the concept of the split-ball resonator and demonstrate the strong magnetic response in the visible for both gold and silver spherical plasmonic nanoparticles with nanometre scale cuts. We realize this concept experimentally by employing the laser-induced transfer method to produce near-perfect metallic spheres and helium ion beam milling to make cuts with the clean straight sidewalls and nanometre resolution. The magnetic resonance is observed at 600 nm in gold and at 565 nm in silver nanoparticles. This method can be applied to the structuring of arbitrary three-dimensional features on the surface of nanoscale resonators. It provides new ways for engineering hybrid resonant modes and ultra-high near-field enhancement.

The Two-Dimensional Gabor Function Adapted to Natural Image Statistics: A Model of Simple-Cell Receptive Fields and Sparse Structure in Images.

PubMed

Loxley, P N

2017-10-01

The two-dimensional Gabor function is adapted to natural image statistics, leading to a tractable probabilistic generative model that can be used to model simple cell receptive field profiles, or generate basis functions for sparse coding applications. Learning is found to be most pronounced in three Gabor function parameters representing the size and spatial frequency of the two-dimensional Gabor function and characterized by a nonuniform probability distribution with heavy tails. All three parameters are found to be strongly correlated, resulting in a basis of multiscale Gabor functions with similar aspect ratios and size-dependent spatial frequencies. A key finding is that the distribution of receptive-field sizes is scale invariant over a wide range of values, so there is no characteristic receptive field size selected by natural image statistics. The Gabor function aspect ratio is found to be approximately conserved by the learning rules and is therefore not well determined by natural image statistics. This allows for three distinct solutions: a basis of Gabor functions with sharp orientation resolution at the expense of spatial-frequency resolution, a basis of Gabor functions with sharp spatial-frequency resolution at the expense of orientation resolution, or a basis with unit aspect ratio. Arbitrary mixtures of all three cases are also possible. Two parameters controlling the shape of the marginal distributions in a probabilistic generative model fully account for all three solutions. The best-performing probabilistic generative model for sparse coding applications is found to be a gaussian copula with Pareto marginal probability density functions.

Hyperspectral range imaging for transportation systems evaluation

NASA Astrophysics Data System (ADS)

Bridgelall, Raj; Rafert, J. B.; Atwood, Don; Tolliver, Denver D.

2016-04-01

Transportation agencies expend significant resources to inspect critical infrastructure such as roadways, railways, and pipelines. Regular inspections identify important defects and generate data to forecast maintenance needs. However, cost and practical limitations prevent the scaling of current inspection methods beyond relatively small portions of the network. Consequently, existing approaches fail to discover many high-risk defect formations. Remote sensing techniques offer the potential for more rapid and extensive non-destructive evaluations of the multimodal transportation infrastructure. However, optical occlusions and limitations in the spatial resolution of typical airborne and space-borne platforms limit their applicability. This research proposes hyperspectral image classification to isolate transportation infrastructure targets for high-resolution photogrammetric analysis. A plenoptic swarm of unmanned aircraft systems will capture images with centimeter-scale spatial resolution, large swaths, and polarization diversity. The light field solution will incorporate structure-from-motion techniques to reconstruct three-dimensional details of the isolated targets from sequences of two-dimensional images. A comparative analysis of existing low-power wireless communications standards suggests an application dependent tradeoff in selecting the best-suited link to coordinate swarming operations. This study further produced a taxonomy of specific roadway and railway defects, distress symptoms, and other anomalies that the proposed plenoptic swarm sensing system would identify and characterize to estimate risk levels.

Defect detection on hardwood logs using high resolution three-dimensional laser scan data

Treesearch

Liya Thomas; Lamine Mili; Clifford A. Shaffer; Ed Thomas; Ed Thomas

2004-01-01

The location, type, and severity of external defects on hardwood logs and skills are the primary indicators of overall log quality and value. External defects provide hints about the internal log characteristics. Defect data would improve the sawyer's ability to process logs such that a higher valued product (lumber) is generated. Using a high-resolution laser log...

Visualization of Stereoscopic Anatomic Models of the Paranasal Sinuses and Cervical Vertebrae from the Surgical and Procedural Perspective

ERIC Educational Resources Information Center

Chen, Jian; Smith, Andrew D.; Khan, Majid A.; Sinning, Allan R.; Conway, Marianne L.; Cui, Dongmei

2017-01-01

Recent improvements in three-dimensional (3D) virtual modeling software allows anatomists to generate high-resolution, visually appealing, colored, anatomical 3D models from computed tomography (CT) images. In this study, high-resolution CT images of a cadaver were used to develop clinically relevant anatomic models including facial skull, nasal…

Correcting pervasive errors in RNA crystallography through enumerative structure prediction.

PubMed

Chou, Fang-Chieh; Sripakdeevong, Parin; Dibrov, Sergey M; Hermann, Thomas; Das, Rhiju

2013-01-01

Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by electron density under Rosetta (ERRASER), coupled to Python-based hierarchical environment for integrated 'xtallography' (PHENIX) diffraction-based refinement. On 24 data sets, ERRASER automatically corrects the majority of MolProbity-assessed errors, improves the average R(free) factor, resolves functionally important discrepancies in noncanonical structure and refines low-resolution models to better match higher-resolution models.

Three-Dimensional Terahertz Coded-Aperture Imaging Based on Single Input Multiple Output Technology.

PubMed

Chen, Shuo; Luo, Chenggao; Deng, Bin; Wang, Hongqiang; Cheng, Yongqiang; Zhuang, Zhaowen

2018-01-19

As a promising radar imaging technique, terahertz coded-aperture imaging (TCAI) can achieve high-resolution, forward-looking, and staring imaging by producing spatiotemporal independent signals with coded apertures. In this paper, we propose a three-dimensional (3D) TCAI architecture based on single input multiple output (SIMO) technology, which can reduce the coding and sampling times sharply. The coded aperture applied in the proposed TCAI architecture loads either purposive or random phase modulation factor. In the transmitting process, the purposive phase modulation factor drives the terahertz beam to scan the divided 3D imaging cells. In the receiving process, the random phase modulation factor is adopted to modulate the terahertz wave to be spatiotemporally independent for high resolution. Considering human-scale targets, images of each 3D imaging cell are reconstructed one by one to decompose the global computational complexity, and then are synthesized together to obtain the complete high-resolution image. As for each imaging cell, the multi-resolution imaging method helps to reduce the computational burden on a large-scale reference-signal matrix. The experimental results demonstrate that the proposed architecture can achieve high-resolution imaging with much less time for 3D targets and has great potential in applications such as security screening, nondestructive detection, medical diagnosis, etc.

Fabrication of a biomimetic elastic intervertebral disk scaffold using additive manufacturing.

PubMed

Whatley, Benjamin R; Kuo, Jonathan; Shuai, Cijun; Damon, Brooke J; Wen, Xuejun

2011-03-01

A custom-designed three-dimensional additive manufacturing device was developed to fabricate scaffolds for intervertebral disk (IVD) regeneration. This technique integrated a computer with a device capable of 3D movement allowing for precise motion and control over the polymer scaffold resolution. IVD scaffold structures were designed using computer-aided design to resemble the natural IVD structure. Degradable polyurethane (PU) was used as an elastic scaffold construct to mimic the elastic nature of the native IVD tissue and was deposited at a controlled rate using ultra-fine micropipettes connected to a syringe pump. The elastic PU was extruded directly onto a collecting substrate placed on a freezing stage. The three-dimensional movement of the computer-controlled device combined with the freezing stage enabled precise control of polymer deposition using extrusion. The addition of the freezing stage increased the polymer solution viscosity and hardened the polymer solution as it was extruded out of the micropipette tip. This technique created scaffolds with excellent control over macro- and micro-structure to influence cell behavior, specifically for cell adhesion, proliferation, and alignment. Concentric lamellae were printed at a high resolution to mimic the native shape and structure of the IVD. Seeded cells aligned along the concentric lamellae and acquired cell morphology similar to native tissue in the outer portion of the IVD. The fabricated scaffolds exhibited elastic behavior during compressive and shear testing, proving that the scaffolds could support loads with proper fatigue resistance without permanent deformation. Additionally, the mechanical properties of the scaffolds were comparable to those of native IVD tissue.

3D fluorescence anisotropy imaging using selective plane illumination microscopy.

PubMed

Hedde, Per Niklas; Ranjit, Suman; Gratton, Enrico

2015-08-24

Fluorescence anisotropy imaging is a popular method to visualize changes in organization and conformation of biomolecules within cells and tissues. In such an experiment, depolarization effects resulting from differences in orientation, proximity and rotational mobility of fluorescently labeled molecules are probed with high spatial resolution. Fluorescence anisotropy is typically imaged using laser scanning and epifluorescence-based approaches. Unfortunately, those techniques are limited in either axial resolution, image acquisition speed, or by photobleaching. In the last decade, however, selective plane illumination microscopy has emerged as the preferred choice for three-dimensional time lapse imaging combining axial sectioning capability with fast, camera-based image acquisition, and minimal light exposure. We demonstrate how selective plane illumination microscopy can be utilized for three-dimensional fluorescence anisotropy imaging of live cells. We further examined the formation of focal adhesions by three-dimensional time lapse anisotropy imaging of CHO-K1 cells expressing an EGFP-paxillin fusion protein.

Fractal Dimensionality of Pore and Grain Volume of a Siliciclastic Marine Sand

NASA Astrophysics Data System (ADS)

Reed, A. H.; Pandey, R. B.; Lavoie, D. L.

Three-dimensional (3D) spatial distributions of pore and grain volumes were determined from high-resolution computer tomography (CT) images of resin-impregnated marine sands. Using a linear gradient extrapolation method, cubic three-dimensional samples were constructed from two-dimensional CT images. Image porosity (0.37) was found to be consistent with the estimate of porosity by water weight loss technique (0.36). Scaling of the pore volume (Vp) with the linear size (L), V~LD provides the fractal dimensionalities of the pore volume (D=2.74+/-0.02) and grain volume (D=2.90+/-0.02) typical for sedimentary materials.

Multi-photon microfabrication of three-dimensional capillary-scale vascular networks

NASA Astrophysics Data System (ADS)

Skylar-Scott, Mark A.; Liu, Man-Chi; Wu, Yuelong; Yanik, Mehmet Fatih

2017-02-01

Biomimetic models of microvasculature could enable assays of complex cellular behavior at the capillary-level, and enable efficient nutrient perfusion for the maintenance of tissues. However, existing three-dimensional printing methods for generating perfusable microvasculature with have insufficient resolution to recapitulate the microscale geometry of capillaries. Here, we present a collection of multiphoton microfabrication methods that enable the production of precise, three-dimensional, branched microvascular networks in collagen. When endothelial cells are added to the channels, they form perfusable lumens with diameters as small as 10 μm. Using a similar photochemistry, we also demonstrate the micropatterning of proteins embedded in microfabricated collagen scaffolds, producing hybrid scaffolds with both defined microarchitecture with integrated gradients of chemical cues. We provide examples for how these hybrid microfabricated scaffolds could be used in angiogenesis and cell homing assays. Finally, we describe a new method for increasing the micropatterning speed by synchronous laser and stage scanning. Using these technologies, we are working towards large-scale (>1 cm), high resolution ( 1 μm) scaffolds with both microarchitecture and embedded protein cues, with applications in three-dimensional assays of cellular behavior.

Three-dimensional refractive index and fluorescence tomography using structured illumination (Conference Presentation)

NASA Astrophysics Data System (ADS)

Park, GwangSik; Shin, SeungWoo; Kim, Kyoohyun; Park, YongKeun

2017-02-01

Optical diffraction tomography (ODT) has been an emerging optical technique for label-free imaging of three-dimensional (3-D) refractive index (RI) distribution of biological samples. ODT employs interferometric microscopy for measuring multiple holograms of samples with various incident angles, from which the Fourier diffraction theorem reconstructs the 3-D RI distribution of samples from retrieved complex optical fields. Since the RI value is linearly proportional to the protein concentration of biological samples where the proportional coefficient is called as refractive index increment (RII), reconstructed 3-D RI tomograms provide precise structural and biochemical information of individual biological samples. Because most proteins have similar RII value, however, ODT has limited molecular specificity, especially for imaging eukaryotic cells having various types of proteins and subcellular organelles. Here, we present an ODT system combined with structured illumination microscopy which can measure the 3-D RI distribution of biological samples as well as 3-D super-resolution fluorescent images in the same optical setup. A digital micromirror device (DMD) controls the incident angle of the illumination beam for tomogram reconstruction, and the same DMD modulates the structured illumination pattern of the excitation beam for super-resolution fluorescent imaging. We first validate the proposed method for simultaneous optical diffraction tomographic imaging and super-resolution fluorescent imaging of fluorescent beads. The proposed method is also exploited for various biological samples.

The application of holography as a real-time three-dimensional motion picture camera

NASA Technical Reports Server (NTRS)

Kurtz, R. L.

1973-01-01

A historical introduction to holography is presented, as well as a basic description of sideband holography for stationary objects. A brief theoretical development of both time-dependent and time-independent holography is also provided, along with an analytical and intuitive discussion of a unique holographic arrangement which allows the resolution of front surface detail from an object moving at high speeds. As an application of such a system, a real-time three-dimensional motion picture camera system is discussed and the results of a recent demonstration of the world's first true three-dimensional motion picture are given.

High-resolution absolute position detection using a multiple grating

NASA Astrophysics Data System (ADS)

Schilling, Ulrich; Drabarek, Pawel; Kuehnle, Goetz; Tiziani, Hans J.

1996-08-01

To control electro-mechanical engines, high-resolution linear and rotary encoders are needed. Interferometric methods (grating interferometers) promise a resolution of a few nanometers, but have an ambiguity range of some microns. Incremental encoders increase the absolute measurement range by counting the signal periods starting from a defined initial point. In many applications, however, it is not possible to move to this initial point, so that absolute encoders have to be used. Absolute encoders generally have a scale with two or more tracks placed next to each other. Therefore, they use a two-dimensional grating structure to measure a one-dimensional position. We present a new method, which uses a one-dimensional structure to determine the position in one dimension. It is based on a grating with a large grating period up to some millimeters, having the same diffraction efficiency in several predefined diffraction orders (multiple grating). By combining the phase signals of the different diffraction orders, it is possible to establish the position in an absolute range of the grating period with a resolution like incremental grating interferometers. The principal functionality was demonstrated by applying the multiple grating in a heterodyne grating interferometer. The heterodyne frequency was generated by a frequency modulated laser in an unbalanced interferometer. In experimental measurements an absolute range of 8 mm was obtained while achieving a resolution of 10 nm.

DMD-based LED-illumination super-resolution and optical sectioning microscopy.

PubMed

Dan, Dan; Lei, Ming; Yao, Baoli; Wang, Wen; Winterhalder, Martin; Zumbusch, Andreas; Qi, Yujiao; Xia, Liang; Yan, Shaohui; Yang, Yanlong; Gao, Peng; Ye, Tong; Zhao, Wei

2013-01-01

Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×10(7) pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens.

DMD-based LED-illumination Super-resolution and optical sectioning microscopy

PubMed Central

Dan, Dan; Lei, Ming; Yao, Baoli; Wang, Wen; Winterhalder, Martin; Zumbusch, Andreas; Qi, Yujiao; Xia, Liang; Yan, Shaohui; Yang, Yanlong; Gao, Peng; Ye, Tong; Zhao, Wei

2013-01-01

Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×107 pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens. PMID:23346373

3D printing of preclinical X-ray computed tomographic data sets.

PubMed

Doney, Evan; Krumdick, Lauren A; Diener, Justin M; Wathen, Connor A; Chapman, Sarah E; Stamile, Brian; Scott, Jeremiah E; Ravosa, Matthew J; Van Avermaete, Tony; Leevy, W Matthew

2013-03-22

Three-dimensional printing allows for the production of highly detailed objects through a process known as additive manufacturing. Traditional, mold-injection methods to create models or parts have several limitations, the most important of which is a difficulty in making highly complex products in a timely, cost-effective manner.(1) However, gradual improvements in three-dimensional printing technology have resulted in both high-end and economy instruments that are now available for the facile production of customized models.(2) These printers have the ability to extrude high-resolution objects with enough detail to accurately represent in vivo images generated from a preclinical X-ray CT scanner. With proper data collection, surface rendering, and stereolithographic editing, it is now possible and inexpensive to rapidly produce detailed skeletal and soft tissue structures from X-ray CT data. Even in the early stages of development, the anatomical models produced by three-dimensional printing appeal to both educators and researchers who can utilize the technology to improve visualization proficiency. (3, 4) The real benefits of this method result from the tangible experience a researcher can have with data that cannot be adequately conveyed through a computer screen. The translation of pre-clinical 3D data to a physical object that is an exact copy of the test subject is a powerful tool for visualization and communication, especially for relating imaging research to students, or those in other fields. Here, we provide a detailed method for printing plastic models of bone and organ structures derived from X-ray CT scans utilizing an Albira X-ray CT system in conjunction with PMOD, ImageJ, Meshlab, Netfabb, and ReplicatorG software packages.

Zernike phase contrast cryo-electron tomography of whole bacterial cells

PubMed Central

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. PMID:24075950

Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site

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

Akparov, V. Kh., E-mail: valery@akparov.ru; Timofeev, V. I., E-mail: tostars@mail.ru; Maghsoudi, N. N., E-mail: maghsudi@yahoo.com

2017-03-15

Crystals of porcine pancreatic carboxypeptidase B (CPB) were grown by the capillary counter-diffusion method in the presence of polyethylene glycol and zinc acetate. The three-dimensional structure of CPB was determined at 1.40 Å resolution using the X-ray diffraction data set collected from the crystals of the enzyme at the SPring 8 synchrotron facility and was refined to R{sub fact} = 17.19%, R{sub free} = 19.78%. The structure contains five zinc atoms, two of which are present in the active site of the enzyme, and an acetate ion. The arrangement of an additional zinc atom in the active site and themore » acetate ion is different from that reported by Yoshimoto et al.« less

Three-dimensional structure of photosystem II from Thermosynechococcus elongates in complex with terbutryn

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

Gabdulkhakov, A. G., E-mail: azat@vega.protes.ru; Dontsova, M. V.; Saenger, W.

Photosystem II is a key component of the photosynthetic pathway producing oxygen at the thylakoid membrane of cyanobacteria, green algae, and plants. The three-dimensional structure of photosystem II from the cyanobacterium Thermosynechococcus elongates in a complex with herbicide terbutryn (a photosynthesis inhibitor) was determined for the first time by X-ray diffraction and refined at 3.2 Angstrom-Sign resolution (R{sub factor} = 26.9%, R{sub free} = 29.9%, rmsd for bond lengths is 0.013 Angstrom-Sign , and rmsd for bond angles is 2.2 Degree-Sign ). The terbutryn molecule was located in the binding pocket of the mobile plastoquinone. The atomic coordinates of themore » refined structure of photosystem II in a complex with terbutryn were deposited in the Protein Data Bank.« less

Super-resolution three-dimensional fluorescence and optical diffraction tomography of live cells using structured illumination generated by a digital micromirror device.

PubMed

Shin, Seungwoo; Kim, Doyeon; Kim, Kyoohyun; Park, YongKeun

2018-06-15

We present a multimodal approach for measuring the three-dimensional (3D) refractive index (RI) and fluorescence distributions of live cells by combining optical diffraction tomography (ODT) and 3D structured illumination microscopy (SIM). A digital micromirror device is utilized to generate structured illumination patterns for both ODT and SIM, which enables fast and stable measurements. To verify its feasibility and applicability, the proposed method is used to measure the 3D RI distribution and 3D fluorescence image of various samples, including a cluster of fluorescent beads, and the time-lapse 3D RI dynamics of fluorescent beads inside a HeLa cell, from which the trajectory of the beads in the HeLa cell is analyzed using spatiotemporal correlations.

High resolution magnetic resonance imaging of the calcaneus: age-related changes in trabecular structure and comparison with dual X-ray absorptiometry measurements

NASA Technical Reports Server (NTRS)

Ouyang, X.; Selby, K.; Lang, P.; Engelke, K.; Klifa, C.; Fan, B.; Zucconi, F.; Hottya, G.; Chen, M.; Majumdar, S.;

Painting Supramolecular Polymers in Organic Solvents by Super-resolution Microscopy

PubMed Central

2018-01-01

Despite the rapid development of complex functional supramolecular systems, visualization of these architectures under native conditions at high resolution has remained a challenging endeavor. Super-resolution microscopy was recently proposed as an effective tool to unveil one-dimensional nanoscale structures in aqueous media upon chemical functionalization with suitable fluorescent probes. Building upon our previous work, which enabled photoactivation localization microscopy in organic solvents, herein, we present the imaging of one-dimensional supramolecular polymers in their native environment by interface point accumulation for imaging in nanoscale topography (iPAINT). The noncovalent staining, typical of iPAINT, allows the investigation of supramolecular polymers’ structure in situ without any chemical modification. The quasi-permanent adsorption of the dye to the polymer is exploited to identify block-like arrangements within supramolecular fibers, which were obtained upon mixing homopolymers that were prestained with different colors. The staining of the blocks, maintained by the lack of exchange of the dyes, permits the imaging of complex structures for multiple days. This study showcases the potential of PAINT-like strategies such as iPAINT to visualize multicomponent dynamic systems in their native environment with an easy, synthesis-free approach and high spatial resolution. PMID:29697958

Temperature and velocity structure functions in the upper troposhere and lower stratosphere from aircraft measurements (Invited)

NASA Astrophysics Data System (ADS)

Wroblewski, D. E.; Werne, J.; Cote, O.; Hacker, J.; Dobosy, R.

2010-12-01

High-resolution turbulence measurements of temperature and three components of velocity were acquired from the GROB 520T EGRETT high altitude research aircraft equipped with three NOAA/FRD built BAT probes. The research campaign spanned eight years with the goal of characterizing clear air turbulence (CAT) and optical turbulence (OpT) in the upper troposphere and lower stratosphere (UTLS), focusing on scales from 1 meter to 1 km, a range that encompasses three-dimensional phenomena critical to CAT and OpT, but for which a dearth of experimental data exists. This talk will cover structure function analysis from 129 separate level flight segments representing 41 hours of flight time and 12,600 km of flight distance. The scaling behavior for sub 100- meter scales will be discussed, with an emphasis on Kelvin-Helmholtz (KH) shear layer development as a phenomenological model for this scale range. Comparisons with micro-scale, direct numerical simulations of KH billows will be presented.

MicroCT angiography detects vascular formation and regression in skin wound healing.

PubMed

Urao, Norifumi; Okonkwo, Uzoagu A; Fang, Milie M; Zhuang, Zhen W; Koh, Timothy J; DiPietro, Luisa A

2016-07-01

Properly regulated angiogenesis and arteriogenesis are essential for effective wound healing. Tissue injury induces robust new vessel formation and subsequent vessel maturation, which involves vessel regression and remodeling. Although formation of functional vasculature is essential for healing, alterations in vascular structure over the time course of skin wound healing are not well understood. Here, using high-resolution ex vivo X-ray micro-computed tomography (microCT), we describe the vascular network during healing of skin excisional wounds with highly detailed three-dimensional (3D) reconstructed images and associated quantitative analysis. We found that relative vessel volume, surface area and branching number are significantly decreased in wounds from day 7 to days 14 and 21. Segmentation and skeletonization analysis of selected branches from high-resolution images as small as 2.5μm voxel size show that branching orders are decreased in the wound vessels during healing. In histological analysis, we found that the contrast agent fills mainly arterioles, but not small capillaries nor large veins. In summary, high-resolution microCT revealed dynamic alterations of vessel structures during wound healing. This technique may be useful as a key tool in the study of the formation and regression of wound vessels. Copyright © 2016 Elsevier Inc. All rights reserved.

Morphological control of three-dimensional carbon nanotube anode for high-capacity lithium-ion battery

NASA Astrophysics Data System (ADS)

Kang, Chiwon; Lee, Hoo-Jeong

2018-05-01

In this paper, we report the results of modulating the processing conditions (mainly, temperature) of a two-step method consisting of sputtering deposition of a Ni catalytic layer and chemical vapor deposition (CVD) of carbon nanotubes (CNTs) on a three-dimensional (3D)-structured Cu mesh to control the morphology of CNTs for advanced Li-ion battery (LIB) applications. We disclosed that CNT growth at a low temperature (700 °C) produced small-diameter CNTs (CNT_S) with an average diameter of ∼20 nm, while that at a high temperature (750 °C) produced large-diameter CNTs (CNT_L) with an average diameter of 200–300 nm. The high-resolution transmission electron microscopy (HR-TEM) and Raman analyses manifested poorly crystalline CNTs for both samples. CNTS showed a specific capacity of 476 mAh g‑1, which is ∼176% superior to that of CNTL (271 mAh g‑1) and ∼128% higher than the theoretical capacity of the state-of-the-art graphites and recently reported nanostructured carbon-based anode materials.

Charge density wave order in 1D mirror twin boundaries of single-layer MoSe 2

DOE PAGES

Barja, Sara; Wickenburg, Sebastian; Liu, Zhen-Fei; ...

2016-04-18

Here, We provide direct evidence for the existence of isolated, one-dimensional charge density waves at mirror twin boundaries (MTBs) of single-layer semiconducting MoSe 2. Such MTBs have been previously observed by transmission electron microscopy and have been predicted to be metallic in MoSe 2 and MoS 2. Our low-temperature scanning tunnelling microscopy/spectroscopy measurements revealed a substantial bandgap of 100 meV opening at the Fermi energy in the otherwise metallic one-dimensional structures. We found a periodic modulation in the density of states along the MTB, with a wavelength of approximately three lattice constants. In addition to mapping the energy-dependent densitymore » of states, we determined the atomic structure and bonding of the MTB through simultaneous high-resolution non-contact atomic force microscopy. Density functional theory calculations based on the observed structure reproduced both the gap opening and the spatially resolved density of states.« less

BIM-Sim: Interactive Simulation of Broadband Imaging Using Mie Theory

NASA Astrophysics Data System (ADS)

Berisha, Sebastian; van Dijk, Thomas; Bhargava, Rohit; Carney, P. Scott; Mayerich, David

2017-02-01

Understanding the structure of a scattered electromagnetic (EM) field is critical to improving the imaging process. Mechanisms such as diffraction, scattering, and interference affect an image, limiting the resolution and potentially introducing artifacts. Simulation and visualization of scattered fields thus plays an important role in imaging science. However, the calculation of scattered fields is extremely time-consuming on desktop systems and computationally challenging on task-parallel systems such as supercomputers and cluster systems. In addition, EM fields are high-dimensional, making them difficult to visualize. In this paper, we present a framework for interactively computing and visualizing EM fields scattered by micro and nano-particles. Our software uses graphics hardware for evaluating the field both inside and outside of these particles. We then use Monte-Carlo sampling to reconstruct and visualize the three-dimensional structure of the field, spectral profiles at individual points, the structure of the field at the surface of the particle, and the resulting image produced by an optical system.

Three-dimensional optoacoustic mesoscopy of the tumor heterogeneity in vivo using high depth-to-resolution multispectral optoacoustic tomography

NASA Astrophysics Data System (ADS)

Li, Jiao; Zhang, Songhe; Chekkoury, Andrei; Glasl, Sarah; Vetschera, Paul; Koberstein-Schwarz, Benno; Omar, Murad; Ntziachristos, Vasilis

2017-03-01

Multispectral optoacoustic mesoscopy (MSOM) has been recently introduced for cancer imaging, it has the potential for high resolution imaging of cancer development in vivo, at depths beyond the diffusion limit. Based on spectral features, optoacoustic imaging is capable of visualizing angiogenesis and imaging cancer heterogeneity of malignant tumors through endogenous hemoglobin. However, high-resolution structural and functional imaging of whole tumor mass is limited by modest penetration and image quality, due to the insufficient capability of ultrasound detectors and the twodimensional scan geometry. In this study, we introduce a novel multi-spectral optoacoustic mesoscopy (MSOM) for imaging subcutaneous or orthotopic tumors implanted in lab mice, with the high-frequency ultrasound linear array and a conical scanning geometry. Detailed volumetric images of vasculature and oxygen saturation of tissue in the entire tumors are obtained in vivo, at depths up to 10 mm with the desirable spatial resolutions approaching 70μm. This unprecedented performance enables the visualization of vasculature morphology and hypoxia conditions has been verified with ex vivo studies. These findings demonstrate the potential of MSOM for preclinical oncological studies in deep solid tumors to facilitate the characterization of tumor's angiogenesis and the evaluation of treatment strategies.

An efficient photogrammetric stereo matching method for high-resolution images

NASA Astrophysics Data System (ADS)

Li, Yingsong; Zheng, Shunyi; Wang, Xiaonan; Ma, Hao

2016-12-01

Stereo matching of high-resolution images is a great challenge in photogrammetry. The main difficulty is the enormous processing workload that involves substantial computing time and memory consumption. In recent years, the semi-global matching (SGM) method has been a promising approach for solving stereo problems in different data sets. However, the time complexity and memory demand of SGM are proportional to the scale of the images involved, which leads to very high consumption when dealing with large images. To solve it, this paper presents an efficient hierarchical matching strategy based on the SGM algorithm using single instruction multiple data instructions and structured parallelism in the central processing unit. The proposed method can significantly reduce the computational time and memory required for large scale stereo matching. The three-dimensional (3D) surface is reconstructed by triangulating and fusing redundant reconstruction information from multi-view matching results. Finally, three high-resolution aerial date sets are used to evaluate our improvement. Furthermore, precise airborne laser scanner data of one data set is used to measure the accuracy of our reconstruction. Experimental results demonstrate that our method remarkably outperforms in terms of time and memory savings while maintaining the density and precision of the 3D cloud points derived.

Three-dimensional Hessian matrix-based quantitative vascular imaging of rat iris with optical-resolution photoacoustic microscopy in vivo

NASA Astrophysics Data System (ADS)

Zhao, Huangxuan; Wang, Guangsong; Lin, Riqiang; Gong, Xiaojing; Song, Liang; Li, Tan; Wang, Wenjia; Zhang, Kunya; Qian, Xiuqing; Zhang, Haixia; Li, Lin; Liu, Zhicheng; Liu, Chengbo

2018-04-01

For the diagnosis and evaluation of ophthalmic diseases, imaging and quantitative characterization of vasculature in the iris are very important. The recently developed photoacoustic imaging, which is ultrasensitive in imaging endogenous hemoglobin molecules, provides a highly efficient label-free method for imaging blood vasculature in the iris. However, the development of advanced vascular quantification algorithms is still needed to enable accurate characterization of the underlying vasculature. We have developed a vascular information quantification algorithm by adopting a three-dimensional (3-D) Hessian matrix and applied for processing iris vasculature images obtained with a custom-built optical-resolution photoacoustic imaging system (OR-PAM). For the first time, we demonstrate in vivo 3-D vascular structures of a rat iris with a the label-free imaging method and also accurately extract quantitative vascular information, such as vessel diameter, vascular density, and vascular tortuosity. Our results indicate that the developed algorithm is capable of quantifying the vasculature in the 3-D photoacoustic images of the iris in-vivo, thus enhancing the diagnostic capability of the OR-PAM system for vascular-related ophthalmic diseases in vivo.

High-resolution three-dimensional partially coherent diffraction imaging.

PubMed

Clark, J N; Huang, X; Harder, R; Robinson, I K

2012-01-01

The wave properties of light, particularly its coherence, are responsible for interference effects, which can be exploited in powerful imaging applications. Coherent diffractive imaging relies heavily on coherence and has recently experienced rapid growth. Coherent diffractive imaging recovers an object from its diffraction pattern by computational phasing with the potential of wavelength-limited resolution. Diminished coherence results in reconstructions that suffer from artefacts or fail completely. Here we demonstrate ab initio phasing of partially coherent diffraction patterns in three dimensions, while simultaneously determining the coherence properties of the illuminating wavefield. Both the dramatic improvements in image interpretability and the three-dimensional evaluation of the coherence will have broad implications for quantitative imaging of nanostructures and wavefield characterization with X-rays and electrons.

Classification of trabeculae into three-dimensional rodlike and platelike structures via local inertial anisotropy.

PubMed

Vasilić, Branimir; Rajapakse, Chamith S; Wehrli, Felix W

2009-07-01

Trabecular bone microarchitecture is a significant determinant of the bone's mechanical properties and is thus of major clinical relevance in predicting fracture risk. The three-dimensional nature of trabecular bone is characterized by parameters describing scale, topology, and orientation of structural elements. However, none of the current methods calculates all three types of parameters simultaneously and in three dimensions. Here the authors present a method that produces a continuous classification of voxels as belonging to platelike or rodlike structures that determines their orientation and estimates their thickness. The method, dubbed local inertial anisotropy (LIA), treats the image as a distribution of mass density and the orientation of trabeculae is determined from a locally calculated tensor of inertia at each voxel. The orientation entropies of rods and plates are introduced, which can provide new information about microarchitecture not captured by existing parameters. The robustness of the method to noise corruption, resolution reduction, and image rotation is demonstrated. Further, the method is compared with established three-dimensional parameters including the structure-model index and topological surface-to-curve ratio. Finally, the method is applied to data acquired in a previous translational pilot study showing that the trabecular bone of untreated hypogonadal men is less platelike than that of their eugonadal peers.

SOMAR-LES: A framework for multi-scale modeling of turbulent stratified oceanic flows

NASA Astrophysics Data System (ADS)

Chalamalla, Vamsi K.; Santilli, Edward; Scotti, Alberto; Jalali, Masoud; Sarkar, Sutanu

2017-12-01

A new multi-scale modeling technique, SOMAR-LES, is presented in this paper. Localized grid refinement gives SOMAR (the Stratified Ocean Model with Adaptive Resolution) access to small scales of the flow which are normally inaccessible to general circulation models (GCMs). SOMAR-LES drives a LES (Large Eddy Simulation) on SOMAR's finest grids, forced with large scale forcing from the coarser grids. Three-dimensional simulations of internal tide generation, propagation and scattering are performed to demonstrate this multi-scale modeling technique. In the case of internal tide generation at a two-dimensional bathymetry, SOMAR-LES is able to balance the baroclinic energy budget and accurately model turbulence losses at only 10% of the computational cost required by a non-adaptive solver running at SOMAR-LES's fine grid resolution. This relative cost is significantly reduced in situations with intermittent turbulence or where the location of the turbulence is not known a priori because SOMAR-LES does not require persistent, global, high resolution. To illustrate this point, we consider a three-dimensional bathymetry with grids adaptively refined along the tidally generated internal waves to capture remote mixing in regions of wave focusing. The computational cost in this case is found to be nearly 25 times smaller than that of a non-adaptive solver at comparable resolution. In the final test case, we consider the scattering of a mode-1 internal wave at an isolated two-dimensional and three-dimensional topography, and we compare the results with Legg (2014) numerical experiments. We find good agreement with theoretical estimates. SOMAR-LES is less dissipative than the closure scheme employed by Legg (2014) near the bathymetry. Depending on the flow configuration and resolution employed, a reduction of more than an order of magnitude in computational costs is expected, relative to traditional existing solvers.

AFM Structural Characterization of Drinking Water Biofilm ...

EPA Pesticide Factsheets

Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodology will allow future in situ investigations to temporally monitor mixed culture drinking water biofilm structural changes during disinfection treatments. Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodo

Three-dimensional surface reconstruction for industrial computed tomography

NASA Technical Reports Server (NTRS)

Vannier, M. W.; Knapp, R. H.; Gayou, D. E.; Sammon, N. P.; Butterfield, R. L.; Larson, J. W.

1985-01-01

Modern high resolution medical computed tomography (CT) scanners can produce geometrically accurate sectional images of many types of industrial objects. Computer software has been developed to convert serial CT scans into a three-dimensional surface form, suitable for display on the scanner itself. This software, originally developed for imaging the skull, has been adapted for application to industrial CT scanning, where serial CT scans thrrough an object of interest may be reconstructed to demonstrate spatial relationships in three dimensions that cannot be easily understood using the original slices. The methods of three-dimensional reconstruction and solid modeling are reviewed, and reconstruction in three dimensions from CT scans through familiar objects is demonstrated.

THE THREE DIMENSIONAL STRUCTURE OF ASPERGILLUS NIGER PECTIN LYASE AT 1.7-A RESOLUTION. (U915444)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

DRAGON Grid: A Three-Dimensional Hybrid Grid Generation Code Developed

NASA Technical Reports Server (NTRS)

Liou, Meng-Sing

2000-01-01

Because grid generation can consume 70 percent of the total analysis time for a typical three-dimensional viscous flow simulation for a practical engineering device, payoffs from research and development could reduce costs and increase throughputs considerably. In this study, researchers at the NASA Glenn Research Center at Lewis Field developed a new hybrid grid approach with the advantages of flexibility, high-quality grids suitable for an accurate resolution of viscous regions, and a low memory requirement. These advantages will, in turn, reduce analysis time and increase accuracy. They result from an innovative combination of structured and unstructured grids to represent the geometry and the computation domain. The present approach makes use of the respective strengths of both the structured and unstructured grid methods, while minimizing their weaknesses. First, the Chimera grid generates high-quality, mostly orthogonal meshes around individual components. This process is flexible and can be done easily. Normally, these individual grids are required overlap each other so that the solution on one grid can communicate with another. However, when this communication is carried out via a nonconservative interpolation procedure, a spurious solution can result. Current research is aimed at entirely eliminating this undesired interpolation by directly replacing arbitrary grid overlapping with a nonstructured grid called a DRAGON grid, which uses the same set of conservation laws over the entire region, thus ensuring conservation everywhere. The DRAGON grid is shown for a typical film-cooled turbine vane with 33 holes and 3 plenum compartments. There are structured grids around each geometrical entity and unstructured grids connecting them. In fiscal year 1999, Glenn researchers developed and tested the three-dimensional DRAGON grid-generation tools. A flow solver suitable for the DRAGON grid has been developed, and a series of validation tests are underway.

Three-Dimensional Super-Resolution: Theory, Modeling, and Field Tests Results

NASA Technical Reports Server (NTRS)

Bulyshev, Alexander; Amzajerdian, Farzin; Roback, Vincent E.; Hines, Glenn; Pierrottet, Diego; Reisse, Robert

2014-01-01

Many flash lidar applications continue to demand higher three-dimensional image resolution beyond the current state-of-the-art technology of the detector arrays and their associated readout circuits. Even with the available number of focal plane pixels, the required number of photons for illuminating all the pixels may impose impractical requirements on the laser pulse energy or the receiver aperture size. Therefore, image resolution enhancement by means of a super-resolution algorithm in near real time presents a very attractive solution for a wide range of flash lidar applications. This paper describes a superresolution technique and illustrates its performance and merits for generating three-dimensional image frames at a video rate.

Single-particle cryo-electron microscopy of Rift Valley fever virus

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

Sherman, Michael B.; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555; Freiberg, Alexander N.

2009-04-25

Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human and veterinary pathogen causing acute hepatitis in ruminants and has the potential to cause hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T = 12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure providesmore » a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit vaccines.« less

Integrated Aeromechanics with Three-Dimensional Solid-Multibody Structures

NASA Technical Reports Server (NTRS)

Datta, Anubhav; Johnson, Wayne

2014-01-01

A full three-dimensional finite element-multibody structural dynamic solver is coupled to a three-dimensional Reynolds-averaged Navier-Stokes solver for the prediction of integrated aeromechanical stresses and strains on a rotor blade in forward flight. The objective is to lay the foundations of all major pieces of an integrated three-dimensional rotor dynamic analysis - from model construction to aeromechanical solution to stress/strain calculation. The primary focus is on the aeromechanical solution. Two types of three-dimensional CFD/CSD interfaces are constructed for this purpose with an emphasis on resolving errors from geometry mis-match so that initial-stage approximate structural geometries can also be effectively analyzed. A three-dimensional structural model is constructed as an approximation to a UH-60A-like fully articulated rotor. The aerodynamic model is identical to the UH-60A rotor. For preliminary validation measurements from a UH-60A high speed flight is used where CFD coupling is essential to capture the advancing side tip transonic effects. The key conclusion is that an integrated aeromechanical analysis is indeed possible with three-dimensional structural dynamics but requires a careful description of its geometry and discretization of its parts.

Nonhydrostatic simulation of hyperpycnal river plumes on sloping continental shelves: Flow structures and nonhydrostatic effect

NASA Astrophysics Data System (ADS)

Tseng, Chien-Yung; Chou, Yi-Ju

2018-04-01

A three-dimensional nonhydrostatic coastal model SUNTANS is used to study hyperpycnal plumes on sloping continental shelves with idealized domain setup. The study aims to examine the nonhydrostatic effect of the plunging hyperpycnal plume and the associated flow structures on different shelf slopes. The unstructured triangular grid in SUNTANS allows for local refinement of the grid size for regions in which the flow varies abruptly, while retaining low-cost computation using the coarse grid resolution for regions in which the flow is more uniform. These nonhydrostatic simulations reveal detailed three-dimensional flow structures in both transient and steady states. Via comparison with the hydrostatic simulation, we show that the nonhydrostatic effect is particularly important before plunging, when the plume is subject to significant changes in both the along-shore and vertical directions. After plunging, where the plume becomes an undercurrent that is more spatially uniform, little difference is found between the hydrostatic and nonhydrostatic simulations in the present gentle- and mild-slope cases. A grid-dependence study shows that the nonhydrostatic effect can be seen only when the grid resolution is sufficiently fine that the calculation is not overly diffusive. A depth-integrated momentum budget analysis is then conducted to show that the flow convergence due to plunging is an important factor in the three-dimensional flow structures. Moreover, it shows that the nonhydrostatic effect becomes more important as the slope increases, and in the steep-slope case, neglect of transport of the vertical momentum during plunging in the hydrostatic case further leads to an erroneous prediction for the undercurrent.

Visualizing the root-PDL-bone interface using high-resolution microtomography

NASA Astrophysics Data System (ADS)

Dalstra, Michel; Cattaneo, Paolo M.; Herzen, Julia; Beckmann, Felix

2008-08-01

The root/periodontal ligament/bone (RPB) interface is important for a correct understanding of the load transfer mechanism of masticatory forces and orthodontic loads. It is the aim of this study to assess the three-dimensional structure of the RPB interface using high-resolution microtomography. A human posterior jaw segment, obtained at autopsy from a 22-year old male donor was first scanned using a tomograph at the HASYLAB/DESY synchrotron facility (Hamburg, Germany) at 31μm resolution. Afterwards the first molar and its surrounding bone were removed with a 10mm hollow core drill. From this cylindrical sample smaller samples were drilled out in the buccolingual direction with a 1.5mm hollow core drill. These samples were scanned at 4μm resolution. The scans of the entire segment showed alveolar bone with a thin lamina dura, supported by an intricate trabecular network. Although featuring numerous openings between the PDL and the bone marrow on the other side to allow blood vessels to transverse, the lamina dura seems smooth at this resolution. First at high resolution, however, it becomes evident that it is irregular with bony spiculae and pitted surfaces. Therefore the stresses in the bone during physiological or orthodontic loading are much higher than expected from a smooth continuous alveolus.

Dental magnetic resonance imaging: making the invisible visible.

PubMed

Idiyatullin, Djaudat; Corum, Curt; Moeller, Steen; Prasad, Hari S; Garwood, Michael; Nixdorf, Donald R

2011-06-01

Clinical dentistry is in need of noninvasive and accurate diagnostic methods to better evaluate dental pathosis. The purpose of this work was to assess the feasibility of a recently developed magnetic resonance imaging (MRI) technique, called SWeep Imaging with Fourier Transform (SWIFT), to visualize dental tissues. Three in vitro teeth, representing a limited range of clinical conditions of interest, imaged using a 9.4T system with scanning times ranging from 100 seconds to 25 minutes. In vivo imaging of a subject was performed using a 4T system with a 10-minute scanning time. SWIFT images were compared with traditional two-dimensional radiographs, three-dimensional cone-beam computed tomography (CBCT) scanning, gradient-echo MRI technique, and histological sections. A resolution of 100 μm was obtained from in vitro teeth. SWIFT also identified the presence and extent of dental caries and fine structures of the teeth, including cracks and accessory canals, which are not visible with existing clinical radiography techniques. Intraoral positioning of the radiofrequency coil produced initial images of multiple adjacent teeth at a resolution of 400 μm. SWIFT MRI offers simultaneous three-dimensional hard- and soft-tissue imaging of teeth without the use of ionizing radiation. Furthermore, it has the potential to image minute dental structures within clinically relevant scanning times. This technology has implications for endodontists because it offers a potential method to longitudinally evaluate teeth where pulp and root structures have been regenerated. Copyright © 2011 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Numerical solution to the glancing sidewall oblique shock wave/turbulent boundary layer interaction in three dimension

NASA Technical Reports Server (NTRS)

Anderson, B. H.; Benson, T. J.

1983-01-01

A supersonic three-dimensional viscous forward-marching computer design code called PEPSIS is used to obtain a numerical solution of the three-dimensional problem of the interaction of a glancing sidewall oblique shock wave and a turbulent boundary layer. Very good results are obtained for a test case that was run to investigate the use of the wall-function boundary-condition approximation for a highly complex three-dimensional shock-boundary layer interaction. Two additional test cases (coarse mesh and medium mesh) are run to examine the question of near-wall resolution when no-slip boundary conditions are applied. A comparison with experimental data shows that the PEPSIS code gives excellent results in general and is practical for three-dimensional supersonic inlet calculations.

Numerical solution to the glancing sidewall oblique shock wave/turbulent boundary layer interaction in three-dimension

NASA Technical Reports Server (NTRS)

Anderson, B. H.; Benson, T. J.

1983-01-01

A supersonic three-dimensional viscous forward-marching computer design code called PEPSIS is used to obtain a numerical solution of the three-dimensional problem of the interaction of a glancing sidewall oblique shock wave and a turbulent boundary layer. Very good results are obtained for a test case that was run to investigate the use of the wall-function boundary-condition approximation for a highly complex three-dimensional shock-boundary layer interaction. Two additional test cases (coarse mesh and medium mesh) are run to examine the question of near-wall resolution when no-slip boundary conditions are applied. A comparison with experimental data shows that the PEPSIS code gives excellent results in general and is practical for three-dimensional supersonic inlet calculations.

X-ray phase contrast tomography from whole organ down to single cells

NASA Astrophysics Data System (ADS)

Krenkel, Martin; Töpperwien, Mareike; Bartels, Matthias; Lingor, Paul; Schild, Detlev; Salditt, Tim

2014-09-01

We use propagation based hard x-ray phase contrast tomography to explore the three dimensional structure of neuronal tissues from the organ down to sub-cellular level, based on combinations of synchrotron radiation and laboratory sources. To this end a laboratory based microfocus tomography setup has been built in which the geometry was optimized for phase contrast imaging and tomography. By utilizing phase retrieval algorithms, quantitative reconstructions can be obtained that enable automatic renderings without edge artifacts. A high brightness liquid metal microfocus x-ray source in combination with a high resolution detector yielding a resolution down to 1.5 μm. To extend the method to nanoscale resolution we use a divergent x-ray waveguide beam geometry at the synchrotron. Thus, the magnification can be easily tuned by placing the sample at different defocus distances. Due to the small Fresnel numbers in this geometry the measured images are of holographic nature which poses a challenge in phase retrieval.

Vertical velocity structure and geometry of clear air convective elements

NASA Technical Reports Server (NTRS)

Rowland, J. R.; Arnold, A.

1975-01-01

The paper discusses observations of individual convective elements with a high-power narrow-beam scanning radar, an FM-CW radar, and an acoustic sounder, including the determination of the vertical air velocity patterns of convective structures with the FM-CW radar and acoustic sounder. Data are presented which link the observed velocity structure and geometrical patterns to previously proposed models of boundary layer convection. It is shown that the high-power radar provides a clear three-dimensional picture of convective cells and fields over a large area with a resolution of 150 m, where the convective cells are roughly spherical. Analysis of time-height records of the FM-CW radar and acoustic sounder confirms the downdraft-entrainment mechanism of the convective cell. The Doppler return of the acoustic sounder and the insect-trail slopes on FM-CW radar records are independent but redundant methods for obtaining the vertical velocity patterns of convective structures.

Three-dimensional large-eddy simulations of the early phase of contrail-to-cirrus transition: effects of atmospheric turbulence and radiative transfer

DOE PAGES

Paoli, Roberto; Thouron, Odile; Cariolle, Daniel; ...

2017-12-08

Here, this article presents the results from numerical experiments of the early phase of contrail-cirrus formation using a limited set of fully three-dimensional, high-resolution large-eddy-simulations. The focus is laid on the interplay between atmospheric turbulence and the radiative transfer (and to a limited extent the ambient ice relative humidity), and how this interaction affects the contrail evolution and the characteristics of the resulting contrail-cirrus one hour after emission. Turbulence is sustained via a large-scale stochastic forcing that creates a non-uniform shear in addition to pure turbulent fluctuations. This effect manifests in the formation of vertically sheared structures of ice crystals.more » When radiative transfer is activated, ice tends to redistribute more uniformly along the vertical direction forming spotty vertical structures. For the conditions analyzed in this study, atmospheric turbulence, inclusive of non-uniform turbulent shear and turbulent fluctuations, affects primarily the contrail width whereas the microphysical properties such ice water path and ice mass are controlled by radiative transfer and relative humidity.« less

Three-dimensional large-eddy simulations of the early phase of contrail-to-cirrus transition: effects of atmospheric turbulence and radiative transfer

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

Paoli, Roberto; Thouron, Odile; Cariolle, Daniel

Here, this article presents the results from numerical experiments of the early phase of contrail-cirrus formation using a limited set of fully three-dimensional, high-resolution large-eddy-simulations. The focus is laid on the interplay between atmospheric turbulence and the radiative transfer (and to a limited extent the ambient ice relative humidity), and how this interaction affects the contrail evolution and the characteristics of the resulting contrail-cirrus one hour after emission. Turbulence is sustained via a large-scale stochastic forcing that creates a non-uniform shear in addition to pure turbulent fluctuations. This effect manifests in the formation of vertically sheared structures of ice crystals.more » When radiative transfer is activated, ice tends to redistribute more uniformly along the vertical direction forming spotty vertical structures. For the conditions analyzed in this study, atmospheric turbulence, inclusive of non-uniform turbulent shear and turbulent fluctuations, affects primarily the contrail width whereas the microphysical properties such ice water path and ice mass are controlled by radiative transfer and relative humidity.« less

Serial sectioning for examination of photoreceptor cell architecture by focused ion beam technology

PubMed Central

Mustafi, Debarshi; Avishai, Amir; Avishai, Nanthawan; Engel, Andreas; Heuer, Arthur; Palczewski, Krzysztof

2011-01-01

Structurally deciphering complex neural networks requires technology with sufficient resolution to allow visualization of single cells and their intimate surrounding connections. Scanning electron microscopy (SEM), coupled with serial ion ablation (SIA) technology, presents a new avenue to study these networks. SIA allows ion ablation to remove nanometer sections of tissue for SEM imaging, resulting in serial section data collection for three-dimensional reconstruction. Here we highlight a method for preparing retinal tissues for imaging of photoreceptors by SIA-SEM technology. We show that this technique can be used to visualize whole rod photoreceptors and the internal disc elements from wild-type (wt) mice. The distance parameters of the discs and photoreceptors are in good agreement with previous work with other methods. Moreover, we show that large planes of retinal tissue can be imaged at high resolution to display the packing of normal rods. Finally, SIA-SEM imaging of retinal tissue from a mouse model (Nrl−/−) with phenotypic changes akin to the human disease enhanced S-cone syndrome (ESCS) revealed a structural profile of overall photoreceptor ultrastructure and internal elements that accompany this disease. Overall, this work presents a new method to study photoreceptor cells at high structural resolution that has a broad applicability to the visual neuroscience field. PMID:21439323

Diffusion-prepared stimulated-echo turbo spin echo (DPsti-TSE): An eddy current-insensitive sequence for three-dimensional high-resolution and undistorted diffusion-weighted imaging.

PubMed

Zhang, Qinwei; Coolen, Bram F; Versluis, Maarten J; Strijkers, Gustav J; Nederveen, Aart J

2017-07-01

In this study, we present a new three-dimensional (3D), diffusion-prepared turbo spin echo sequence based on a stimulated-echo read-out (DPsti-TSE) enabling high-resolution and undistorted diffusion-weighted imaging (DWI). A dephasing gradient in the diffusion preparation module and rephasing gradients in the turbo spin echo module create stimulated echoes, which prevent signal loss caused by eddy currents. Near to perfect agreement of apparent diffusion coefficient (ADC) values between DPsti-TSE and diffusion-weighted echo planar imaging (DW-EPI) was demonstrated in both phantom transient signal experiments and phantom imaging experiments. High-resolution and undistorted DPsti-TSE was demonstrated in vivo in prostate and carotid vessel wall. 3D whole-prostate DWI was achieved with four b values in only 6 min. Undistorted ADC maps of the prostate peripheral zone were obtained at low and high imaging resolutions with no change in mean ADC values [(1.60 ± 0.10) × 10 -3 versus (1.60 ± 0.02) × 10 -3  mm 2 /s]. High-resolution 3D DWI of the carotid vessel wall was achieved in 12 min, with consistent ADC values [(1.40 ± 0.23) × 10 -3  mm 2 /s] across different subjects, as well as slice locations through the imaging volume. This study shows that DPsti-TSE can serve as a robust 3D diffusion-weighted sequence and is an attractive alternative to the traditional two-dimensional DW-EPI approaches. Copyright © 2017 John Wiley & Sons, Ltd.

Resolution enhancement using simultaneous couple illumination

NASA Astrophysics Data System (ADS)

Hussain, Anwar; Martínez Fuentes, José Luis

2016-10-01

A super-resolution technique based on structured illumination created by a liquid crystal on silicon spatial light modulator (LCOS-SLM) is presented. Single and simultaneous pairs of tilted beams are generated to illuminate a target object. Resolution enhancement of an optical 4f system is demonstrated by using numerical simulations. The resulting intensity images are recorded at a charged couple device (CCD) and stored in the computer memory for further processing. One dimension enhancement can be performed with only 15 images. Two dimensional complete improvement requires 153 different images. The resolution of the optical system is extended three times compared to the band limited system.

Resolution analysis of finite fault source inversion using one- and three-dimensional Green's functions 1. Strong motions

USGS Publications Warehouse

Graves, R.W.; Wald, D.J.

2001-01-01

We develop a methodology to perform finite fault source inversions from strong motion data using Green's functions (GFs) calculated for a three-dimensional (3-D) velocity structure. The 3-D GFs are calculated numerically by inserting body forces at each of the strong motion sites and then recording the resulting strains along the target fault surface. Using reciprocity, these GFs can be recombined to represent the ground motion at each site for any (heterogeneous) slip distribution on the fault. The reciprocal formulation significantly reduces the required number of 3-D finite difference computations to at most 3NS, where NS is the number of strong motion sites used in the inversion. Using controlled numerical resolution tests, we have examined the relative importance of accurate GFs for finite fault source inversions which rely on near-source ground motions. These experiments use both 1-D and 3-D GFs in inversions for hypothetical rupture models in order (1) to analyze the ability of the 3-D methodology to resolve trade-offs between complex source phenomena and 3-D path effects, (2) to address the sensitivity of the inversion results to uncertainties in the 3-D velocity structure, and (3) to test the adequacy of the 1-D GF method when propagation effects are known to be three-dimensional. We find that given "data" from a prescribed 3-D Earth structure, the use of well-calibrated 3-D GFs in the inversion provides very good resolution of the assumed slip distribution, thus adequately separating source and 3-D propagation effects. In contrast, using a set of inexact 3-D GFs or a set of hybrid 1-D GFs allows only partial recovery of the slip distribution. These findings suggest that in regions of complex geology the use of well-calibrated 3-D GFs has the potential for increased resolution of the rupture process relative to 1-D GFs. However, realizing this full potential requires that the 3-D velocity model and associated GFs should be carefully validated against the true 3-D Earth structure before performing the inverse problem with actual data. Copyright 2001 by the American Geophysical Union.

Three-dimensional-printed gas dynamic virtual nozzles for x-ray laser sample delivery

PubMed Central

Nelson, Garrett; Kirian, Richard A.; Weierstall, Uwe; Zatsepin, Nadia A.; Faragó, Tomáš; Baumbach, Tilo; Wilde, Fabian; Niesler, Fabian B. P.; Zimmer, Benjamin; Ishigami, Izumi; Hikita, Masahide; Bajt, Saša; Yeh, Syun-Ru; Rousseau, Denis L.; Chapman, Henry N.; Spence, John C. H.; Heymann, Michael

2016-01-01

Reliable sample delivery is essential to biological imaging using X-ray Free Electron Lasers (XFELs). Continuous injection using the Gas Dynamic Virtual Nozzle (GDVN) has proven valuable, particularly for time-resolved studies. However, many important aspects of GDVN functionality have yet to be thoroughly understood and/or refined due to fabrication limitations. We report the application of 2-photon polymerization as a form of high-resolution 3D printing to fabricate high-fidelity GDVNs with submicron resolution. This technique allows rapid prototyping of a wide range of different types of nozzles from standard CAD drawings and optimization of crucial dimensions for optimal performance. Three nozzles were tested with pure water to determine general nozzle performance and reproducibility, with nearly reproducible off-axis jetting being the result. X-ray tomography and index matching were successfully used to evaluate the interior nozzle structures and identify the cause of off-axis jetting. Subsequent refinements to fabrication resulted in straight jetting. A performance test of printed nozzles at an XFEL provided high quality femtosecond diffraction patterns. PMID:27410079

Observing the overall rocking motion of a protein in a crystal

NASA Astrophysics Data System (ADS)

Ma, Peixiang; Xue, Yi; Coquelle, Nicolas; Haller, Jens D.; Yuwen, Tairan; Ayala, Isabel; Mikhailovskii, Oleg; Willbold, Dieter; Colletier, Jacques-Philippe; Skrynnikov, Nikolai R.; Schanda, Paul

2015-10-01

The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall `rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1-100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.

Three-dimensional microscopy of the Rad51 recombination protein during meiotic prophase.

PubMed Central

Franklin, A E; McElver, J; Sunjevaric, I; Rothstein, R; Bowen, B; Cande, W Z

1999-01-01

An open question in meiosis is whether the Rad51 recombination protein functions solely in meiotic recombination or whether it is also involved in the chromosome homology search. To address this question, we have performed three-dimensional high-resolution immunofluorescence microscopy to visualize native Rad51 structures in maize male meiocytes. Maize has two closely related RAD51 genes that are expressed at low levels in differentiated tissues and at higher levels in mitotic and meiotic tissues. Cells and nuclei were specially fixed and embedded in polyacrylamide to maintain both native chromosome structure and the three dimensionality of the specimens. Analysis of Rad51 in maize meiocytes revealed that when chromosomes condense during leptotene, Rad51 is diffuse within the nucleus. Rad51 foci form on the chromosomes at the beginning of zygotene and rise to approximately 500 per nucleus by mid-zygotene when chromosomes are pairing and synapsing. During chromosome pairing, we consistently found two contiguous Rad51 foci on paired chromosomes. These paired foci may identify the sites where DNA sequence homology is being compared. During pachytene, the number of Rad51 foci drops to seven to 22 per nucleus. This higher number corresponds approximately to the number of chiasmata in maize meiosis. These observations are consistent with a role for Rad51 in the homology search phase of chromosome pairing in addition to its known role in meiotic recombination. PMID:10330467

Does Explosive Nuclear Burning Occur in Tidal Disruption Events of White Dwarfs by Intermediate-mass Black Holes?

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

Tanikawa, Ataru; Sato, Yushi; Hachisu, Izumi

We investigate nucleosynthesis in tidal disruption events (TDEs) of white dwarfs (WDs) by intermediate-mass black holes. We consider various types of WDs with different masses and compositions by means of three-dimensional (3D) smoothed particle hydrodynamics (SPH) simulations. We model these WDs with different numbers of SPH particles, N , from a few 10{sup 4} to a few 10{sup 7} in order to check mass resolution convergence, where SPH simulations with N > 10{sup 7} (or a space resolution of several 10{sup 6} cm) have unprecedentedly high resolution in this kind of simulation. We find that nuclear reactions become less activemore » with increasing N and that these nuclear reactions are excited by spurious heating due to low resolution. Moreover, we find no shock wave generation. In order to investigate the reason for the absence of a shock wave, we additionally perform one-dimensional (1D) SPH and mesh-based simulations with a space resolution ranging from 10{sup 4} to 10{sup 7} cm, using a characteristic flow structure extracted from the 3D SPH simulations. We find shock waves in these 1D high-resolution simulations, one of which triggers a detonation wave. However, we must be careful of the fact that, if the shock wave emerged in an outer region, it could not trigger the detonation wave due to low density. Note that the 1D initial conditions lack accuracy to precisely determine where a shock wave emerges. We need to perform 3D simulations with ≲10{sup 6} cm space resolution in order to conclude that WD TDEs become optical transients powered by radioactive nuclei.« less

New optical tomographic & topographic techniques for biomedical applications

NASA Astrophysics Data System (ADS)

Buytaert, Jan

The mammalian middle ear contains the eardrum and the three auditory ossicles, and forms an impedance match between sound in air and pressure waves in the fluid of the inner ear. Without this intermediate system, with its unsurpassed efficiency and dynamic range, we would be practically deaf. Physics-based modeling of this extremely complex mechanical system is necessary to help our basic understanding of the functioning of hearing. Highly realistic models will make it possible to predict the outcome of surgical interventions and to optimize design of ossicle prostheses and active middle ear implants. To obtain such models and with realistic output, basic input data is still missing. In this dissertation I developed and used two new optical techniques to obtain two essential sets of data: accurate three-dimensional morphology of the middle ear structures, and elasticity parameters of the eardrum. The first technique is a new method for optical tomography of macroscopic biomedical objects, which makes it possible to measure the three-dimensional geometry of the middle ear ossicles and soft tissues which are connecting and suspending them. I made a new and high-resolution version of this orthogonal-plane fluorescence optical sectioning method, to obtain micrometer resolution in macroscopic specimens. The result is thus a complete 3-D model of the middle (and inner) ear of gerbil in unprecedented quality. On top of high-resolution morphological models of the middle ear structures, I applied the technique in other fields of research as well. The second device works according to a new optical profilometry technique which allows to measure shape and deformations of the eardrum and other membranes or objects. The approach is called projection moire profilometry, and creates moire interference fringes which contain the height information. I developed a setup which uses liquid crystal panels for grid projection and optical demodulation. Hence no moving parts are present and the setup is entirely digitally controlled. This measurement method is developed to determine the elasticity parameters of the eardrum in-situ. Other surface shapes however can also be measured.

The Three-Dimensional Point Spread Function of Aberration-Corrected Scanning Transmission Electron Microscopy

PubMed Central

Lupini, A.R.; de Jonge, N.

2012-01-01

Aberration-correction reduces the depth of field in scanning transmission electron microscopy (STEM) and thus allows three-dimensional imaging by depth-sectioning. This imaging mode offers the potential for sub-Ångstrom lateral resolution and nanometer-scale depth sensitivity. For biological samples, which may be many microns across and where high lateral resolution may not always be needed, optimizing the depth resolution even at the expense of lateral resolution may be desired, aiming to image through thick specimens. Although there has been extensive work examining and optimizing the probe formation in two-dimensions, there is less known about the probe shape along the optical axis. Here the probe shape is examined in three-dimensions in an attempt to better understand the depth-resolution in this mode. Examples are presented of how aberrations change the probe shape in three-dimensions, and it is found that off-axial aberrations may need to be considered for focal series of large areas. It is shown that oversized or annular apertures theoretically improve the vertical resolution for 3D imaging of nanoparticles. When imaging nanoparticles of several nanometer size, regular STEM can thereby be optimized such that the vertical full width at half maximum approaches that of the aberration corrected STEM with a standard aperture. PMID:21878149

Three-dimensional gas exchange pathways in pome fruit characterized by synchrotron x-ray computed tomography.

PubMed

Verboven, Pieter; Kerckhofs, Greet; Mebatsion, Hibru Kelemu; Ho, Quang Tri; Temst, Kristiaan; Wevers, Martine; Cloetens, Peter; Nicolaï, Bart M

2008-06-01

Our understanding of the gas exchange mechanisms in plant organs critically depends on insights in the three-dimensional (3-D) structural arrangement of cells and voids. Using synchrotron radiation x-ray tomography, we obtained for the first time high-contrast 3-D absorption images of in vivo fruit tissues of high moisture content at 1.4-microm resolution and 3-D phase contrast images of cell assemblies at a resolution as low as 0.7 microm, enabling visualization of individual cell morphology, cell walls, and entire void networks that were previously unknown. Intercellular spaces were always clear of water. The apple (Malus domestica) cortex contains considerably larger parenchyma cells and voids than pear (Pyrus communis) parenchyma. Voids in apple often are larger than the surrounding cells and some cells are not connected to void spaces. The main voids in apple stretch hundreds of micrometers but are disconnected. Voids in pear cortex tissue are always smaller than parenchyma cells, but each cell is surrounded by a tight and continuous network of voids, except near brachyssclereid groups. Vascular and dermal tissues were also measured. The visualized network architecture was consistent over different picking dates and shelf life. The differences in void fraction (5.1% for pear cortex and 23.0% for apple cortex) and in gas network architecture helps explain the ability of tissues to facilitate or impede gas exchange. Structural changes and anisotropy of tissues may eventually lead to physiological disorders. A combined tomography and internal gas analysis during growth are needed to make progress on the understanding of void formation in fruit.

Ultrasonic three-dimensional on-chip cell culture for dynamic studies of tumor immune surveillance by natural killer cells.

PubMed

Christakou, Athanasia E; Ohlin, Mathias; Önfelt, Björn; Wiklund, Martin

2015-08-07

We demonstrate a simple method for three-dimensional (3D) cell culture controlled by ultrasonic standing waves in a multi-well microplate. The method gently arranges cells in a suspension into a single aggregate in each well of the microplate and, by this, nucleates 3D tissue-like cell growth for culture times between two and seven days. The microplate device is compatible with both high-resolution optical microscopy and maintenance in a standard cell incubator. The result is a scaffold- and coating-free method for 3D cell culture that can be used for controlling the cellular architecture, as well as the cellular and molecular composition of the microenvironment in and around the formed cell structures. We demonstrate the parallel production of one hundred synthetic 3D solid tumors comprising up to thousands of human hepatocellular carcinoma (HCC) HepG2 cells, we characterize the tumor structure by high-resolution optical microscopy, and we monitor the functional behavior of natural killer (NK) cells migrating, docking and interacting with the tumor model during culture. Our results show that the method can be used for determining the collective ability of a given number of NK cells to defeat a solid tumor having a certain size, shape and composition. The ultrasound-based method itself is generic and can meet any demand from applications where it is advantageous to monitor cell culture from production to analysis of 3D tissue or tumor models using microscopy in one single microplate device.

A high-resolution 3D ultrasonic system for rapid evaluation of the anterior and posterior segment.

PubMed

Peyman, Gholam A; Ingram, Charles P; Montilla, Leonardo G; Witte, Russell S

2012-01-01

Traditional ultrasound imaging systems for ophthalmology employ slow, mechanical scanning of a single-element ultrasound transducer. The goal was to demonstrate rapid examination of the anterior and posterior segment with a three-dimensional (3D) commercial ultrasound system incorporating high-resolution linear probe arrays. The 3D images of the porcine eye were generated in approximately 10 seconds by scanning one of two commercial linear arrays (25- and 50-MHz). Healthy enucleated pig eyes were compared with those with induced injury or placement of a foreign material (eg, metal). Rapid, volumetric imaging was also demonstrated in one human eye in vivo. The 50-MHz probe provided exquisite volumetric images of the anterior segment at a depth up to 15 mm and axial resolution of 30 μm. The 25-MHz probe provided a larger field of view (lateral X depth: 20 × 30 mm), sufficient for capturing the entire anterior and posterior segments of the pig eye, at a resolution of 60 μm. A 50-MHz scan through the human eyelid illustrated detailed structures of the Meibomian glands, cilia, cornea, and anterior segment back to the posterior capsule. The 3D system with its high-frequency ultrasound arrays, fast data acquisition, and volume rendering capability shows promise for investigating anterior and posterior structures of the eye. Copyright 2012, SLACK Incorporated.

Small-angle x-ray scattering study of polymer structure: Carbosilane dendrimers in hexane solution

NASA Astrophysics Data System (ADS)

Shtykova, E. V.; Feigin, L. A.; Volkov, V. V.; Malakhova, Yu. N.; Streltsov, D. R.; Buzin, A. I.; Chvalun, S. N.; Katarzhanova, E. Yu.; Ignatieva, G. M.; Muzafarov, A. M.

2016-09-01

The three-dimensional organization of monodisperse hyper-branched macromolecules of regular structure—carbosilane dendrimers of zero, third, and sixth generations—has been studied by small-angle X-ray scattering (SAXS) in solution. The use of modern methods of SAXS data interpretation, including ab initio modeling, has made it possible to determine the internal architecture of the dendrimers in dependence of the generation number and the number of cyclosiloxane end groups (forming the shell of dendritic macromolecules) and show dendrimers to be spherical. The structural results give grounds to consider carbosilane dendrimers promising objects for forming crystals with subsequent structural analysis and determining their structure with high resolution, as well as for designing new materials to be used in various dendrimer-based technological applications.

Equally sloped X-ray microtomography of living insects with low radiation dose and improved resolution capability

NASA Astrophysics Data System (ADS)

Yao, Shengkun; Fan, Jiadong; Zong, Yunbing; He, You; Zhou, Guangzhao; Sun, Zhibin; Zhang, Jianhua; Huang, Qingjie; Xiao, Tiqiao; Jiang, Huaidong

2016-03-01

Three-dimensional X-ray imaging of living specimens is challenging due to the limited resolution of conventional absorption contrast X-ray imaging and potential irradiation damage of biological specimens. In this letter, we present microtomography of a living specimen combining phase-contrast imaging and a Fourier-based iterative algorithm termed equally sloped tomography. Non-destructive 3D imaging of an anesthetized living yellow mealworm Tenebrio molitor was demonstrated with a relatively low dose using synchrotron generated X-rays. Based on the high-quality 3D images, branching tracheoles and different tissues of the insect in a natural state were identified and analyzed, demonstrating a significant advantage of the technique over conventional X-ray radiography or histotomy. Additionally, the insect survived without problem after a 1.92-s X-ray exposure and subsequent absorbed radiation dose of ˜1.2 Gy. No notable physiological effects were observed after reviving the insect from anesthesia. The improved static tomographic method demonstrated in this letter shows advantage in the non-destructive structural investigation of living insects in three dimensions due to the low radiation dose and high resolution capability, and offers many potential applications in biological science.

Equally sloped X-ray microtomography of living insects with low radiation dose and improved resolution capability

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

Yao, Shengkun; Fan, Jiadong; Zong, Yunbing

Three-dimensional X-ray imaging of living specimens is challenging due to the limited resolution of conventional absorption contrast X-ray imaging and potential irradiation damage of biological specimens. In this letter, we present microtomography of a living specimen combining phase-contrast imaging and a Fourier-based iterative algorithm termed equally sloped tomography. Non-destructive 3D imaging of an anesthetized living yellow mealworm Tenebrio molitor was demonstrated with a relatively low dose using synchrotron generated X-rays. Based on the high-quality 3D images, branching tracheoles and different tissues of the insect in a natural state were identified and analyzed, demonstrating a significant advantage of the technique overmore » conventional X-ray radiography or histotomy. Additionally, the insect survived without problem after a 1.92-s X-ray exposure and subsequent absorbed radiation dose of ∼1.2 Gy. No notable physiological effects were observed after reviving the insect from anesthesia. The improved static tomographic method demonstrated in this letter shows advantage in the non-destructive structural investigation of living insects in three dimensions due to the low radiation dose and high resolution capability, and offers many potential applications in biological science.« less

Comparative analysis of three-dimensional structures of homodimers of uridine phosphorylase from Salmonella typhimurium in the unligated state and in a complex with potassium ion

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

Lashkov, A. A.; Zhukhlistova, N. E.; Gabdulkhakov, A. G.

2009-03-15

The spatial organization of the homodimer of unligated uridine phosphorylase from Salmonella typhimurium (St UPh) was determined with high accuracy. The structure was refined at 1.80 A resolution to R{sub work} = 16.1% and R{sub free} = 20.0%. The rms deviations for the bond lengths, bond angles, and chiral angles are 0.006 A, 1.042{sup o}, and 0.071{sup o}, respectively. The coordinate error estimated by the Luzzati plot is 0.166 A. The coordinate error based on the maximum likelihood is 0.199 A. A comparative analysis of the spatial organization of the homodimer in two independently refined structures and the structure ofmore » the homodimer St UPh in the complex with a K{sup +} ion was performed. The substrate-binding sites in the homodimers StUPhs in the unligated state were found to act asynchronously. In the presence of a potassium ion, the three-dimensional structures of the subunits in the homodimer are virtually identical, which is apparently of importance for the synchronous action of both substrate-binding sites. The atomic coordinates of the refined structure of the homodimer and structure factors have been deposited in the Protein Data Bank (PDB ID code 3DPS).« less

Analysis of human plasma lipids by using comprehensive two-dimensional gas chromatography with dual detection and with the support of high-resolution time-of-flight mass spectrometry for structural elucidation.

PubMed

Salivo, Simona; Beccaria, Marco; Sullini, Giuseppe; Tranchida, Peter Q; Dugo, Paola; Mondello, Luigi

2015-01-01

The main focus of the present research is the analysis of the unsaponifiable lipid fraction of human plasma by using data derived from comprehensive two-dimensional gas chromatography with dual quadrupole mass spectrometry and flame ionization detection. This approach enabled us to attain both mass spectral information and analyte percentage data. Furthermore, gas chromatography coupled with high-resolution time-of-flight mass spectrometry was used to increase the reliability of identification of several unsaponifiable lipid constituents. The synergism between both the high-resolution gas chromatography and mass spectrometry processes enabled us to attain a more in-depth knowledge of the unsaponifiable fraction of human plasma. Additionally, information was attained on the fatty acid and triacylglycerol composition of the plasma samples, subjected to investigation by using comprehensive two-dimensional gas chromatography with dual quadrupole mass spectrometry and flame ionization detection and high-performance liquid chromatography with atmospheric pressure chemical ionization quadrupole mass spectrometry, respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High resolution three-dimensional robotic synthetic tracked aperture ultrasound imaging: feasibility study

NASA Astrophysics Data System (ADS)

Zhang, Haichong K.; Fang, Ting Yun; Finocchi, Rodolfo; Boctor, Emad M.

2017-03-01

Three dimensional (3D) ultrasound imaging is becoming a standard mode for medical ultrasound diagnoses. Conventional 3D ultrasound imaging is mostly scanned either by using a two dimensional matrix array or by motorizing a one dimensional array in the elevation direction. However, the former system is not widely assessable due to its cost, and the latter one has limited resolution and field-of-view in the elevation axis. Here, we propose a 3D ultrasound imaging system based on the synthetic tracked aperture approach, in which a robotic arm is used to provide accurate tracking and motion. While the ultrasound probe is moved by a robotic arm, each probe position is tracked and can be used to reconstruct a wider field-of-view as there are no physical barriers that restrict the elevational scanning. At the same time, synthetic aperture beamforming provides a better resolution in the elevation axis. To synthesize the elevational information, the single focal point is regarded as the virtual element, and forward and backward delay-andsum are applied to the radio-frequency (RF) data collected through the volume. The concept is experimentally validated using a general ultrasound phantom, and the elevational resolution improvement of 2.54 and 2.13 times was measured at the target depths of 20 mm and 110 mm, respectively.

Serial block face scanning electron microscopy--the future of cell ultrastructure imaging.

PubMed

Hughes, Louise; Hawes, Chris; Monteith, Sandy; Vaughan, Sue

2014-03-01

One of the major drawbacks in transmission electron microscopy has been the production of three-dimensional views of cells and tissues. Currently, there is no one suitable 3D microscopy technique that answers all questions and serial block face scanning electron microscopy (SEM) fills the gap between 3D imaging using high-end fluorescence microscopy and the high resolution offered by electron tomography. In this review, we discuss the potential of the serial block face SEM technique for studying the three-dimensional organisation of animal, plant and microbial cells.

Six dimensional X-ray Tensor Tomography with a compact laboratory setup

NASA Astrophysics Data System (ADS)

Sharma, Y.; Wieczorek, M.; Schaff, F.; Seyyedi, S.; Prade, F.; Pfeiffer, F.; Lasser, T.

2016-09-01

Attenuation based X-ray micro computed tomography (XCT) provides three-dimensional images with micrometer resolution. However, there is a trade-off between the smallest size of the structures that can be resolved and the measurable sample size. In this letter, we present an imaging method using a compact laboratory setup that reveals information about micrometer-sized structures within samples that are several orders of magnitudes larger. We combine the anisotropic dark-field signal obtained in a grating interferometer and advanced tomographic reconstruction methods to reconstruct a six dimensional scattering tensor at every spatial location in three dimensions. The scattering tensor, thus obtained, encodes information about the orientation of micron-sized structures such as fibres in composite materials or dentinal tubules in human teeth. The sparse acquisition schemes presented in this letter enable the measurement of the full scattering tensor at every spatial location and can be easily incorporated in a practical, commercially feasible laboratory setup using conventional X-ray tubes, thus allowing for widespread industrial applications.

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

PubMed

Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun

2018-06-01

The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods. Copyright © 2018 Elsevier Inc. All rights reserved.

Enabling high-precision nonlinear three-dimensional photoprocessing of premeditated designs on a conventional multiphoton imaging system

NASA Astrophysics Data System (ADS)

Garsha, Karl E.

2004-06-01

There is an increasing amount of interest in functionalized microstructural, microphotonic and microelectromechanical systems (MEMS) for use in biological applications. By scanning a tightly focused ultra-short pulsed laser beam inside a wide variety of commercially available polymer systems, the flexibility of the multiphoton microscope can be extended to include routine manufacturing of micro-devices with feature sizes well below the diffraction limit. Compared with lithography, two-photon polymerization has the unique ability to additively realize designs with high resolution in three dimensions; this permits the construction of cross-linked components and structures with hollow cavities. In light of the increasing availability of multiphoton imaging systems at research facilities, femtosecond laser manufacturing becomes particularly attractive in that the modality provides a readily accessible, rapid and high-accuracy 3-D processing capability to biological investigators interested in culture scaffolds and biomimetic tissue engineering, bio-MEMS, biomicrophotonics and microfluidics applications. This manuscript overviews recent efforts towards to enabling user accessible 3-D micro-manufacturing capabilities on a conventional proprietary-based imaging system. Software which permits the off-line design of microstructures and leverages the extensibility of proprietary LCSM image acquisition software to realize designs is introduced. The requirements for multiphoton photo-disruption (ablation) are in some ways analogous to those for multiphoton polymerization. Hence, "beam-steering" also facilitates precision photo-disruption of biological tissues with 3-D resolution, and applications involving tissue microdissection and intracellular microsurgery or three-dimensionally resolved fluorescence recovery after photobleaching (FRAP) studies can benefit from this work as well.

Numerical design of advanced multi-element airfoils

NASA Technical Reports Server (NTRS)

Mathias, Donovan L.; Cummings, Russell M.

1994-01-01

The current study extends the application of computational fluid dynamics to three-dimensional high-lift systems. Structured, overset grids are used in conjunction with an incompressible Navier-Stokes flow solver to investigate flow over a two-element high-lift configuration. The computations were run in a fully turbulent mode using the one-equation Baldwin-Barth turbulence model. The geometry consisted of an unswept wing which spanned a wind tunnel test section. Flows over full and half-span Fowler flap configurations were computed. Grid resolution issues were investigated in two dimensional studies of the flapped airfoil. Results of the full-span flap wing agreed well with experimental data and verified the method. Flow over the wing with the half-span was computed to investigate the details of the flow at the free edge of the flap. The results illustrated changes in flow streamlines, separation locations, and surface pressures due to the vortex shed from the flap edge.

A metallo-DNA nanowire with uninterrupted one-dimensional silver array

NASA Astrophysics Data System (ADS)

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Hattori, Yoshikazu; Saneyoshi, Hisao; Ono, Akira; Tanaka, Yoshiyuki

2017-10-01

The double-helix structure of DNA, in which complementary strands reversibly hybridize to each other, not only explains how genetic information is stored and replicated, but also has proved very attractive for the development of nanomaterials. The discovery of metal-mediated base pairs has prompted the generation of short metal-DNA hybrid duplexes by a bottom-up approach. Here we describe a metallo-DNA nanowire—whose structure was solved by high-resolution X-ray crystallography—that consists of dodecamer duplexes held together by four different metal-mediated base pairs (the previously observed C-Ag-C, as well as G-Ag-G, G-Ag-C and T-Ag-T) and linked to each other through G overhangs involved in interduplex G-Ag-G. The resulting hybrid nanowires are 2 nm wide with a length of the order of micrometres to millimetres, and hold the silver ions in uninterrupted one-dimensional arrays along the DNA helical axis. The hybrid nanowires are further assembled into three-dimensional lattices by interactions between adenine residues, fully bulged out of the double helix.

Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs

PubMed Central

Baker, T. S.; Olson, N. H.; Fuller, S. D.

1999-01-01

Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-Å) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical. PMID:10585969

Multispectral high-resolution hologram generation using orthographic projection images

NASA Astrophysics Data System (ADS)

Muniraj, I.; Guo, C.; Sheridan, J. T.

2016-08-01

We present a new method of synthesizing a digital hologram of three-dimensional (3D) real-world objects from multiple orthographic projection images (OPI). A high-resolution multiple perspectives of 3D objects (i.e., two dimensional elemental image array) are captured under incoherent white light using synthetic aperture integral imaging (SAII) technique and their OPIs are obtained respectively. The reference beam is then multiplied with the corresponding OPI and integrated to form a Fourier hologram. Eventually, a modified phase retrieval algorithm (GS/HIO) is applied to reconstruct the hologram. The principle is validated experimentally and the results support the feasibility of the proposed method.

Transport of phase space densities through tetrahedral meshes using discrete flow mapping

NASA Astrophysics Data System (ADS)

Bajars, Janis; Chappell, David J.; Søndergaard, Niels; Tanner, Gregor

2017-01-01

Discrete flow mapping was recently introduced as an efficient ray based method determining wave energy distributions in complex built up structures. Wave energy densities are transported along ray trajectories through polygonal mesh elements using a finite dimensional approximation of a ray transfer operator. In this way the method can be viewed as a smoothed ray tracing method defined over meshed surfaces. Many applications require the resolution of wave energy distributions in three-dimensional domains, such as in room acoustics, underwater acoustics and for electromagnetic cavity problems. In this work we extend discrete flow mapping to three-dimensional domains by propagating wave energy densities through tetrahedral meshes. The geometric simplicity of the tetrahedral mesh elements is utilised to efficiently compute the ray transfer operator using a mixture of analytic and spectrally accurate numerical integration. The important issue of how to choose a suitable basis approximation in phase space whilst maintaining a reasonable computational cost is addressed via low order local approximations on tetrahedral faces in the position coordinate and high order orthogonal polynomial expansions in momentum space.

A three-dimensional metal grid mesh as a practical alternative to ITO

NASA Astrophysics Data System (ADS)

Jang, Sungwoo; Jung, Woo-Bin; Kim, Choelgyu; Won, Phillip; Lee, Sang-Gil; Cho, Kyeong Min; Jin, Ming Liang; An, Cheng Jin; Jeon, Hwan-Jin; Ko, Seung Hwan; Kim, Taek-Soo; Jung, Hee-Tae

2016-07-01

The development of a practical alternative to indium tin oxide (ITO) is one of the most important issues in flexible optoelectronics. In spite of recent progress in this field, existing approaches to prepare transparent electrodes do not satisfy all of their essential requirements. Here, we present a new substrate-embedded tall (~350 nm) and thin (~30 nm) three-dimensional (3D) metal grid mesh structure with a large area, which is prepared via secondary sputtering. This structure satisfies most of the essential requirements of transparent electrodes for practical applications in future opto-electronics: excellent optoelectronic performance (a sheet resistance of 9.8 Ω □-1 with a transmittance of 85.2%), high stretchability (no significant change in resistance for applied strains <15%), a sub-micrometer mesh period, a flat surface (a root mean square roughness of approximately 5 nm), no haze (approximately 0.5%), and strong adhesion to polymer substrates (it survives attempted detachment with 3M Scotch tape). Such outstanding properties are attributed to the unique substrate-embedded 3D structure of the electrode, which can be obtained with a high aspect ratio and in high resolution over large areas with a simple process. As a demonstration of its suitability for practical applications, our transparent electrode was successfully tested in a flexible touch screen panel. We believe that our approach opens up new practical applications in wearable electronics.The development of a practical alternative to indium tin oxide (ITO) is one of the most important issues in flexible optoelectronics. In spite of recent progress in this field, existing approaches to prepare transparent electrodes do not satisfy all of their essential requirements. Here, we present a new substrate-embedded tall (~350 nm) and thin (~30 nm) three-dimensional (3D) metal grid mesh structure with a large area, which is prepared via secondary sputtering. This structure satisfies most of the essential requirements of transparent electrodes for practical applications in future opto-electronics: excellent optoelectronic performance (a sheet resistance of 9.8 Ω □-1 with a transmittance of 85.2%), high stretchability (no significant change in resistance for applied strains <15%), a sub-micrometer mesh period, a flat surface (a root mean square roughness of approximately 5 nm), no haze (approximately 0.5%), and strong adhesion to polymer substrates (it survives attempted detachment with 3M Scotch tape). Such outstanding properties are attributed to the unique substrate-embedded 3D structure of the electrode, which can be obtained with a high aspect ratio and in high resolution over large areas with a simple process. As a demonstration of its suitability for practical applications, our transparent electrode was successfully tested in a flexible touch screen panel. We believe that our approach opens up new practical applications in wearable electronics. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr03060b

Three-dimensional printing of complex biological structures by freeform reversible embedding of suspended hydrogels

PubMed Central

Hinton, Thomas J.; Jallerat, Quentin; Palchesko, Rachelle N.; Park, Joon Hyung; Grodzicki, Martin S.; Shue, Hao-Jan; Ramadan, Mohamed H.; Hudson, Andrew R.; Feinberg, Adam W.

2015-01-01

We demonstrate the additive manufacturing of complex three-dimensional (3D) biological structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels, enables 3D printing of hydrated materials with an elastic modulus <500 kPa including alginate, collagen, and fibrin. Computer-aided design models of 3D optical, computed tomography, and magnetic resonance imaging data were 3D printed at a resolution of ~200 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains were mechanically robust and recreated complex 3D internal and external anatomical architectures. PMID:26601312

Comparison of three-dimensional visualization techniques for depicting the scala vestibuli and scala tympani of the cochlea by using high-resolution MR imaging.

PubMed

Hans, P; Grant, A J; Laitt, R D; Ramsden, R T; Kassner, A; Jackson, A

1999-08-01

Cochlear implantation requires introduction of a stimulating electrode array into the scala vestibuli or scala tympani. Although these structures can be separately identified on many high-resolution scans, it is often difficult to ascertain whether these channels are patent throughout their length. The aim of this study was to determine whether an optimized combination of an imaging protocol and a visualization technique allows routine 3D rendering of the scala vestibuli and scala tympani. A submillimeter T2 fast spin-echo imaging sequence was designed to optimize the performance of 3D visualization methods. The spatial resolution was determined experimentally using primary images and 3D surface and volume renderings from eight healthy subjects. These data were used to develop the imaging sequence and to compare the quality and signal-to-noise dependency of four data visualization algorithms: maximum intensity projection, ray casting with transparent voxels, ray casting with opaque voxels, and isosurface rendering. The ability of these methods to produce 3D renderings of the scala tympani and scala vestibuli was also examined. The imaging technique was used in five patients with sensorineural deafness. Visualization techniques produced optimal results in combination with an isotropic volume imaging sequence. Clinicians preferred the isosurface-rendered images to other 3D visualizations. Both isosurface and ray casting displayed the scala vestibuli and scala tympani throughout their length. Abnormalities were shown in three patients, and in one of these, a focal occlusion of the scala tympani was confirmed at surgery. Three-dimensional images of the scala vestibuli and scala tympani can be routinely produced. The combination of an MR sequence optimized for use with isosurface rendering or ray-casting algorithms can produce 3D images with greater spatial resolution and anatomic detail than has been possible previously.

A new general circulation model of Jupiter's atmosphere based on the UKMO Unified Model: Three-dimensional evolution of isolated vortices and zonal jets in mid-latitudes

NASA Astrophysics Data System (ADS)

Yamazaki, Y. H.; Skeet, D. R.; Read, P. L.

2004-04-01

We have been developing a new three-dimensional general circulation model for the stratosphere and troposphere of Jupiter based on the dynamical core of a portable version of the Unified Model of the UK Meteorological Office. Being one of the leading terrestrial GCMs, employed for operational weather forecasting and climate research, the Unified Model has been thoroughly tested and performance tuned for both vector and parallel computers. It is formulated as a generalized form of the standard primitive equations to handle a thick atmosphere, using a scaled pressure as the vertical coordinate. It is able to accurately simulate the dynamics of a three-dimensional fully compressible atmosphere on the whole or a part of a spherical shell at high spatial resolution in all three directions. Using the current version of the GCM, we examine the characteristics of the Jovian winds in idealized configurations based on the observed vertical structure of temperature. Our initial focus is on the evolution of isolated eddies in the mid-latitudes. Following a brief theoretical investigation of the vertical structure of the atmosphere, limited-area cyclic channel domains are used to numerically investigate the nonlinear evolution of the mid-latitude winds. First, the evolution of deep and shallow cyclones and anticyclones are tested in the atmosphere at rest to identify a preferred horizontal and vertical structure of the vortices. Then, the dependency of the migration characteristics of the vortices are investigated against modelling parameters to find that it is most sensitive to the horizontal diffusion. We also examine the hydrodynamical stability of observed subtropical jets in both northern and southern hemispheres in the three-dimensional nonlinear model as initial value problems. In both cases, it was found that the prominent jets are unstable at various scales and that vorteces of various sizes are generated including those comparable to the White Ovals and the Great Red Spot.

Intracranial arterial wall imaging using three-dimensional high isotropic resolution black blood MRI at 3.0 Tesla.

PubMed

Qiao, Ye; Steinman, David A; Qin, Qin; Etesami, Maryam; Schär, Michael; Astor, Brad C; Wasserman, Bruce A

2011-07-01

To develop a high isotropic-resolution sequence to evaluate intracranial vessels at 3.0 Tesla (T). Thirteen healthy volunteers and 4 patients with intracranial stenosis were imaged at 3.0T using 0.5-mm isotropic-resolution three-dimensional (3D) Volumetric ISotropic TSE Acquisition (VISTA; TSE, turbo spin echo), with conventional 2D-TSE for comparison. VISTA was repeated for 6 volunteers and 4 patients at 0.4-mm isotropic-resolution to explore the trade-off between SNR and voxel volume. Wall signal-to-noise-ratio (SNR(wall) ), wall-lumen contrast-to-noise-ratio (CNR(wall-lumen) ), lumen area (LA), wall area (WA), mean wall thickness (MWT), and maximum wall thickness (maxWT) were compared between 3D-VISTA and 2D-TSE sequences, as well as 3D images acquired at both resolutions. Reliability was assessed by intraclass correlations (ICC). Compared with 2D-TSE measurements, 3D-VISTA provided 58% and 74% improvement in SNR(wall) and CNR(wall-lumen) , respectively. LA, WA, MWT and maxWT from 3D and 2D techniques highly correlated (ICCs of 0.96, 0.95, 0.96, and 0.91, respectively). CNR(wall-lumen) using 0.4-mm resolution VISTA decreased by 27%, compared with 0.5-mm VISTA but with reduced partial-volume-based overestimation of wall thickness. Reliability for 3D measurements was good to excellent. The 3D-VISTA provides SNR-efficient, highly reliable measurements of intracranial vessels at high isotropic-resolution, enabling broad coverage in a clinically acceptable time. Copyright © 2011 Wiley-Liss, Inc.

Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes▿

PubMed Central

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

2011-01-01

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur. PMID:21965559

Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

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

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott

2012-02-13

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF)more » CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.« less

3-D characterization of weathered building limestones by high resolution synchrotron X-ray microtomography.

PubMed

Rozenbaum, O

2011-04-15

Understanding the weathering processes of building stones and more generally of their transfer properties requires detailed knowledge of the porosity characteristics. This study aims at analyzing three-dimensional images obtained by X-ray microtomography of building stones. In order to validate these new results a weathered limestone previously characterised (Rozenbaum et al., 2007) by two-dimensional image analysis was selected. The 3-D images were analysed by a set of mathematical tools that enable the description of the pore and solid phase distribution. Results show that 3-D image analysis is a powerful technique to characterise the morphological, structural and topological differences due to weathering. The paper also discusses criteria for mathematically determining whether a stone is weathered or not. Copyright © 2011 Elsevier B.V. All rights reserved.

Compton imaging tomography for nondestructive evaluation of spacecraft thermal protection systems

NASA Astrophysics Data System (ADS)

Romanov, Volodymyr; Burke, Eric; Grubsky, Victor

2017-02-01

Here we present new results of in situ nondestructive evaluation (NDE) of spacecraft thermal protection system materials obtained with POC-developed NDE tool based on a novel Compton Imaging Tomography (CIT) technique recently pioneered and patented by Physical Optics Corporation (POC). In general, CIT provides high-resolution three-dimensional Compton scattered X-ray imaging of the internal structure of evaluated objects, using a set of acquired two-dimensional Compton scattered X-ray images of consecutive cross sections of these objects. Unlike conventional computed tomography, CIT requires only one-sided access to objects, has no limitation on the dimensions and geometry of the objects, and can be applied to large multilayer non-uniform objects with complicated geometries. Also, CIT does not require any contact with the objects being imaged during its application.

Laser-etch patterning of metal oxide coated carbon nanotube 3D architectures.

PubMed

Aksu, Cemile; Ingram, Wade; Bradford, Philip D; Jur, Jesse S

2018-08-17

This paper describes a way to fabricate novel hybrid low density nanostructures containing both carbon nanotubes (CNTs) and ceramic nanotubes. Using atomic layer deposition, a thin film of aluminum oxide was conformally deposited on aligned multiwall CNT foams in which the CNTs make porous, three-dimensional interconnected networks. A CO 2 laser was used to etch pure alumina nanotube structures by burning out the underlying CNT substrate in discrete locations via the printed laser pattern. Structural and morphological transitions during the calcination process of aluminum oxide coated CNTs were investigated through in situ transmission electron microscopy and high-resolution scanning electron microscopy. Laser parameters were optimized to etch the CNT away (i.e. etching speed, power and focal length) while minimizing damage to the alumina nanotubes due to overheating. This study opens a new route for fabricating very low density three dimensionally patterned materials with areas of dissimilar materials and properties. To demonstrate the attributes of these structures, the etched areas were used toward anisotropic microfluidic liquid flow. The demonstration used the full thickness of the material to make complex pathways for the liquid flow in the structure. Through tuning of processing conditions, the alumina nanotube (etched) regions became hydrophilic while the bulk material remained hydrophobic and electrically conductive.

A novel left heart simulator for the multi-modality characterization of native mitral valve geometry and fluid mechanics.

PubMed

Rabbah, Jean-Pierre; Saikrishnan, Neelakantan; Yoganathan, Ajit P

2013-02-01

Numerical models of the mitral valve have been used to elucidate mitral valve function and mechanics. These models have evolved from simple two-dimensional approximations to complex three-dimensional fully coupled fluid structure interaction models. However, to date these models lack direct one-to-one experimental validation. As computational solvers vary considerably, experimental benchmark data are critically important to ensure model accuracy. In this study, a novel left heart simulator was designed specifically for the validation of numerical mitral valve models. Several distinct experimental techniques were collectively performed to resolve mitral valve geometry and hemodynamics. In particular, micro-computed tomography was used to obtain accurate and high-resolution (39 μm voxel) native valvular anatomy, which included the mitral leaflets, chordae tendinae, and papillary muscles. Three-dimensional echocardiography was used to obtain systolic leaflet geometry. Stereoscopic digital particle image velocimetry provided all three components of fluid velocity through the mitral valve, resolved every 25 ms in the cardiac cycle. A strong central filling jet (V ~ 0.6 m/s) was observed during peak systole with minimal out-of-plane velocities. In addition, physiologic hemodynamic boundary conditions were defined and all data were synchronously acquired through a central trigger. Finally, the simulator is a precisely controlled environment, in which flow conditions and geometry can be systematically prescribed and resultant valvular function and hemodynamics assessed. Thus, this work represents the first comprehensive database of high fidelity experimental data, critical for extensive validation of mitral valve fluid structure interaction simulations.

Development of fine-resolution analyses and expanded large-scale forcing properties. Part I: Methodology and evaluation

DOE PAGES

Li, Zhijin; Vogelmann, Andrew M.; Feng, Sha; ...

2015-01-20

We produce fine-resolution, three-dimensional fields of meteorological and other variables for the U.S. Department of Energy’s Atmospheric Radiation Measurement (ARM) Southern Great Plains site. The Community Gridpoint Statistical Interpolation system is implemented in a multiscale data assimilation (MS-DA) framework that is used within the Weather Research and Forecasting model at a cloud-resolving resolution of 2 km. The MS-DA algorithm uses existing reanalysis products and constrains fine-scale atmospheric properties by assimilating high-resolution observations. A set of experiments show that the data assimilation analysis realistically reproduces the intensity, structure, and time evolution of clouds and precipitation associated with a mesoscale convective system.more » Evaluations also show that the large-scale forcing derived from the fine-resolution analysis has an overall accuracy comparable to the existing ARM operational product. For enhanced applications, the fine-resolution fields are used to characterize the contribution of subgrid variability to the large-scale forcing and to derive hydrometeor forcing, which are presented in companion papers.« less

Three-dimensional optical coherence tomography of the embryonic murine cardiovascular system

NASA Astrophysics Data System (ADS)

Luo, Wei; Marks, Daniel L.; Ralston, Tyler S.; Boppart, Stephen A.

2006-03-01

Optical coherence tomography (OCT) is an emerging high-resolution real-time biomedical imaging technology that has potential as a novel investigational tool in developmental biology and functional genomics. In this study, murine embryos and embryonic hearts are visualized with an OCT system capable of 2-µm axial and 15-µm lateral resolution and with real-time acquisition rates. We present, to our knowledge, the first sets of high-resolution 2- and 3-D OCT images that reveal the internal structures of the mammalian (murine) embryo (E10.5) and embryonic (E14.5 and E17.5) cardiovascular system. Strong correlations are observed between OCT images and corresponding hematoxylin- and eosin-stained histological sections. Real-time in vivo embryonic (E10.5) heart activity is captured by spectral-domain optical coherence tomography, processed, and displayed at a continuous rate of five frames per second. With the ability to obtain not only high-resolution anatomical data but also functional information during cardiovascular development, the OCT technology has the potential to visualize and quantify changes in murine development and in congenital and induced heart disease, as well as enable a wide range of basic in vitro and in vivo research studies in functional genomics.

Three-dimensional Optical Coherence Tomography for Optical Biopsy of Lymph Nodes and Assessment of Metastatic Disease

PubMed Central

John, Renu; Adie, Steven G.; Chaney, Eric J.; Marjanovic, Marina; Tangella, Krishnarao V.; Boppart, Stephen A.

2013-01-01

Background Numerous techniques have been developed for localizing lymph nodes before surgical resection and for their histological assessment. Nondestructive high-resolution transcapsule optical imaging of lymph nodes offers the potential for in situ assessment of metastatic involvement, potentially during surgical procedures. Methods Three-dimensional optical coherence tomography (3-D OCT) was used for imaging and assessing resected popliteal lymph nodes from a preclinical rat metastatic tumor model over a 9-day time-course study after tumor induction. The spectral-domain OCT system utilized a center wavelength of 800 nm, provided axial and transverse resolutions of 3 and 12 µm, respectively, and performed imaging at 10,000 axial scans per second. Results OCT is capable of providing high-resolution labelfree images of intact lymph node microstructure based on intrinsic optical scattering properties with penetration depths of ~1–2 mm. The results demonstrate that OCT is capable of differentiating normal, reactive, and metastatic lymph nodes based on microstructural changes. The optical scattering and structural changes revealed by OCT from day 3 to day 9 after the injection of tumor cells into the lymphatic system correlate with inflammatory and immunological changes observed in the capsule, precortical regions, follicles, and germination centers found during histopathology. Conclusions We report for the first time a longitudinal study of 3-D transcapsule OCT imaging of intact lymph nodes demonstrating microstructural changes during metastatic infiltration. These results demonstrate the potential of OCT as a technique for intraoperative, real-time in situ 3-D optical biopsy of lymph nodes for the intraoperative staging of cancer. PMID:22688663

Nano-Optics for Chemical and Materials Characterization

NASA Astrophysics Data System (ADS)

Beversluis, Michael; Stranick, Stephan

2007-03-01

Light microscopy can provide non-destructive, real-time, three-dimensional imaging with chemically-specific contrast, but diffraction frequently limits the resolution to roughly 200 nm. Recently, structured illumination techniques have allowed fluorescence imaging to reach 50 nm resolution [1]. Since these fluorescence techniques were developed for use in microbiology, a key challenge is to take the resolution-enhancing features and apply them to contrast mechanisms like vibrational spectroscopy (e.g., Raman and CARS microscopy) that provide morphological and chemically specific imaging.. We are developing a new hybrid technique that combines the resolution enhancement of structured illumination microscopy with scanning techniques that can record hyperspectral images with 100 nm spatial resolution. We will show such superresolving images of semiconductor nanostructures and discuss the advantages and requirements for this technique. Referenence: 1. M. G. L. Gustafsson, P. Natl. Acad. Sci. USA 102, 13081-13086 (2005).

Three-dimensionality of the bulk electronic structure in WTe 2

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

Wu, Yun; Jo, Na Hyun; Mou, Daixiang

Inmore » this paper, we use temperature- and field-dependent resistivity measurements (Shubnikov–de Haas quantum oscillations) and ultrahigh-resolution, tunable, vacuum ultraviolet laser-based angle-resolved photoemission spectroscopy (ARPES) to study the three-dimensionality (3D) of the bulk electronic structure in WTe 2 , a type II Weyl semimetal. The bulk Fermi surface (FS) consists of two pairs of electron pockets and two pairs of hole pockets along the Χ–Γ–Χ direction as detected by using an incident photon energy of 6.7 eV, which is consistent with the previously reported data. However, if using an incident photon energy of 6.36 eV, another pair of tiny electron pockets is detected on both sides of the Γ point, which is in agreement with the small quantum oscillation frequency peak observed in the magnetoresistance. Therefore, the bulk, 3D FS consists of three pairs of electron pockets and two pairs of hole pockets in total. With the ability of fine tuning the incident photon energy, we demonstrate the strong three-dimensionality of the bulk electronic structure in WTe 2 . Finally, the combination of resistivity and ARPES measurements reveals the complete, and consistent, picture of the bulk electronic structure of this material.« less

Three-dimensionality of the bulk electronic structure in WTe 2

DOE PAGES

Wu, Yun; Jo, Na Hyun; Mou, Daixiang; ...

2017-05-18

Inmore » this paper, we use temperature- and field-dependent resistivity measurements (Shubnikov–de Haas quantum oscillations) and ultrahigh-resolution, tunable, vacuum ultraviolet laser-based angle-resolved photoemission spectroscopy (ARPES) to study the three-dimensionality (3D) of the bulk electronic structure in WTe 2 , a type II Weyl semimetal. The bulk Fermi surface (FS) consists of two pairs of electron pockets and two pairs of hole pockets along the Χ–Γ–Χ direction as detected by using an incident photon energy of 6.7 eV, which is consistent with the previously reported data. However, if using an incident photon energy of 6.36 eV, another pair of tiny electron pockets is detected on both sides of the Γ point, which is in agreement with the small quantum oscillation frequency peak observed in the magnetoresistance. Therefore, the bulk, 3D FS consists of three pairs of electron pockets and two pairs of hole pockets in total. With the ability of fine tuning the incident photon energy, we demonstrate the strong three-dimensionality of the bulk electronic structure in WTe 2 . Finally, the combination of resistivity and ARPES measurements reveals the complete, and consistent, picture of the bulk electronic structure of this material.« less

Crystal structure of the HA3 subcomponent of Clostridium botulinum type C progenitor toxin.

PubMed

Nakamura, Toshio; Kotani, Mao; Tonozuka, Takashi; Ide, Azusa; Oguma, Keiji; Nishikawa, Atsushi

2009-01-30

The Clostridium botulinum type C 16S progenitor toxin contains a neurotoxin and several nontoxic components, designated nontoxic nonhemagglutinin (HA), HA1 (HA-33), HA2 (HA-17), HA3a (HA-22-23), and HA3b (HA-53). The HA3b subcomponent seems to play an important role cooperatively with HA1 in the internalization of the toxin by gastrointestinal epithelial cells via binding of these subcomponents to specific oligosaccharides. In this study, we investigated the sugar-binding specificity of the HA3b subcomponent using recombinant protein fused to glutathione S-transferase and determined the three-dimensional structure of the HA3a-HA3b complex based on X-ray crystallography. The crystal structure was determined at a resolution of 2.6 A. HA3b contains three domains, domains I to III, and the structure of domain I resembles HA3a. In crystal packing, three HA3a-HA3b molecules are assembled to form a three-leaved propeller-like structure. The three HA3b domain I and three HA3a alternate, forming a trimer of dimers. In a database search, no proteins with high structural homology to any of the domains (Z score >10) were found. Especially, HA3a and HA3b domain I, mainly composed of beta-sheets, reveal a unique fold. In binding assays, HA3b bound sialic acid with high affinity, but did not bind galactose, N-acetylgalactosamine, or N-acetylglucosamine. The electron density of liganded N-acetylneuraminic acid was determined by crystal soaking. In the sugar-complex structure, the N-acetylneuraminic acid-binding site was located in the cleft formed between domains II and III of HA3b. This report provides the first determination of the three-dimensional structure of the HA3a-HA3b complex and its sialic acid binding site. Our results will provide useful information for elucidating the mechanism of assembly of the C16S toxin and for understanding the interactions with oligosaccharides on epithelial cells and internalization of the botulinum toxin complex.

Fine Metal Mask 3-Dimensional Measurement by using Scanning Digital Holographic Microscope

NASA Astrophysics Data System (ADS)

Shin, Sanghoon; Yu, Younghun

2018-04-01

For three-dimensional microscopy, fast and high axial resolution are very important. Extending the depth of field for digital holographic is necessary for three-dimensional measurements of thick samples. We propose an optical sectioning method for optical scanning digital holography that is performed in the frequency domain by spatial filtering of a reconstructed amplitude image. We established a scanning dual-wavelength off-axis digital holographic microscope to measure samples that exhibit a large amount of coherent noise and a thickness larger than the depth of focus of the objective lens. As a demonstration, we performed a three-dimensional measurement of a fine metal mask with a reconstructed sectional phase image and filtering with a reconstructed amplitude image.

Comparison of radiograph-based texture analysis and bone mineral density with three-dimensional microarchitecture of trabecular bone.

PubMed

Ranjanomennahary, P; Ghalila, S Sevestre; Malouche, D; Marchadier, A; Rachidi, M; Benhamou, Cl; Chappard, C

2011-01-01

Hip fracture is a serious health problem and textural methods are being developed to assess bone quality. The authors aimed to perform textural analysis at femur on high-resolution digital radiographs compared to three-dimensional (3D) microarchitecture comparatively to bone mineral density. Sixteen cadaveric femurs were imaged with an x-ray device using a C-MOS sensor. One 17 mm square region of interest (ROI) was selected in the femoral head (FH) and one in the great trochanter (GT). Two-dimensional (2D) textural features from the co-occurrence matrices were extracted. Site-matched measurements of bone mineral density were performed. Inside each ROI, a 16 mm diameter core was extracted. Apparent density (Dapp) and bone volume proportion (BV/TV(Arch)) were measured from a defatted bone core using Archimedes' principle. Microcomputed tomography images of the entire length of the core were obtained (Skyscan 1072) at 19.8 microm of resolution and usual 3D morphometric parameters were computed on the binary volume after calibration from BV/TV(Arch). Then, bone surface/bone volume, trabecular thickness, trabecular separation, and trabecular number were obtained by direct methods without model assumption and the structure model index was calculated. In univariate analysis, the correlation coefficients between 2D textural features and 3D morphological parameters reached 0.83 at the FH and 0.79 at the GT. In multivariate canonical correlation analysis, coefficients of the first component reached 0.95 at the FH and 0.88 at the GT. Digital radiographs, widely available and economically viable, are an alternative method for evaluating bone microarchitectural structure.

Impacts of SST Patterns on Rapid Intensification of Typhoon Megi (2010)

NASA Astrophysics Data System (ADS)

Kanada, Sachie; Tsujino, Satoki; Aiki, Hidenori; Yoshioka, Mayumi K.; Miyazawa, Yasumasa; Tsuboki, Kazuhisa; Takayabu, Izuru

2017-12-01

Typhoon Megi (2010), a very intense tropical cyclone with a minimum central pressure of 885 hPa, was characterized by especially rapid intensification. We investigated this intensification process by a simulation experiment using a high-resolution (0.02° × 0.02°) three-dimensional atmosphere-ocean coupled regional model. We also performed a sensitivity experiment with a time-fixed sea surface temperature (SST). The coupled model successfully simulated the minimum central pressure of Typhoon Megi, whereas the fixed SST experiment simulated an excessively low minimum central pressure of 839 hPa. The simulation results also showed a close relationship between the radial SST profiles and the rapid intensification process. Because the warm sea increased near-surface water vapor and hence the convective available potential energy, the high SST in the eye region facilitated tall and intense updrafts inside the radius of maximum wind speed and led to the start of rapid intensification. In contrast, high SST outside this radius induced local secondary updrafts that inhibited rapid intensification even if the mean SST in the core region exceeded 29.0°C. These secondary updrafts moved inward and eventually merged with the primary eyewall updrafts. Then the storm intensified rapidly when the high SST appeared in the eye region. Thus, the changes in the local SST pattern around the storm center strongly affected the rapid intensification process by modulating the radial structure of core convection. Our results also show that the use of a high-resolution three-dimensional atmosphere-ocean coupled model offers promise for improving intensity forecasts of tropical cyclones.

Fabrication of three-dimensional collagen scaffold using an inverse mould-leaching process.

PubMed

Ahn, SeungHyun; Lee, SuYeon; Cho, Youngseok; Chun, Wook; Kim, GeunHyung

2011-09-01

Natural biopolymers, such as collagen or chitosan, are considered ideal for biomedical scaffolds. However, low processability of the materials has hindered the fabrication of designed pore structures controlled by various solid freeform-fabrication methods. A new technique to fabricate a biomedical three-dimensional collagen scaffold, supplemented with a sacrificial poly(ethylene oxide) mould is proposed. The fabricated collagen scaffold shows a highly porous surface and a three-dimensional structure with high porosity as well as mechanically stable structure. To show its feasibility for biomedical applications, fibroblasts/keratinocytes were co-cultured on the scaffold, and the cell proliferation and cell migration of the scaffold was more favorable than that obtained with a spongy-type collagen scaffold.

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

PubMed

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.

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

PubMed Central

Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S.; Carazo, Jose Maria

2016-01-01

Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application—3DIANA—specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es. PMID:26772592

High-resolution neutron diffraction study of CuNCN: New evidence of structure anomalies at low temperature

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

Jacobs, Philipp; Houben, Andreas; Dronskowski, Richard, E-mail: drons@HAL9000.ac.rwth-aachen.de

Copper carbodiimide (CuNCN) is the nitrogen-containing analogue of cupric oxide. Based on high-resolution neutron-diffraction data, CuNCN's lattice parameters are derived as a function of the temperature. In accordance with a recent synchrotron study, a clear trend in the cell parameter a is observed accompanying the changing magnetic behavior. With decreasing temperature, a slowly decreases to a minimum at ∼100 K after which it rises again. The same trend—albeit more pronounced—is observed for the c lattice parameter at ∼35 K. The herein presented neutron powder-diffraction data also support the conjectured sequence of transitions from the high-temperature one-dimensional resonating valence-bond (RVB) statemore » to a transient two-dimensional RVB state and eventually, at lowest temperatures, into another two-dimensional RVB state, presumably the ground state.« less

Three-dimensional hard and soft tissue imaging of the human cochlea by scanning laser optical tomography (SLOT)

PubMed Central

Mohebbi, Saleh; Andrade, José; Nolte, Lena; Meyer, Heiko; Heisterkamp, Alexander; Majdani, Omid

2017-01-01

The present study focuses on the application of scanning laser optical tomography (SLOT) for visualization of anatomical structures inside the human cochlea ex vivo. SLOT is a laser-based highly efficient microscopy technique which allows for tomographic imaging of the internal structure of transparent specimens. Thus, in the field of otology this technique is best convenient for an ex vivo study of the inner ear anatomy. For this purpose, the preparation before imaging comprises decalcification, dehydration as well as optical clearing of the cochlea samples in toto. Here, we demonstrate results of SLOT imaging visualizing hard and soft tissue structures with an optical resolution of down to 15 μm using extinction and autofluorescence as contrast mechanisms. Furthermore, the internal structure can be analyzed nondestructively and quantitatively in detail by sectioning of the three-dimensional datasets. The method of X-ray Micro Computed Tomography (μCT) has been previously applied to explanted cochlea and is solely based on absorption contrast. An advantage of SLOT is that it uses visible light for image formation and thus provides a variety of contrast mechanisms known from other light microscopy techniques, such as fluorescence or scattering. We show that SLOT data is consistent with μCT anatomical data and provides additional information by using fluorescence. We demonstrate that SLOT is applicable for cochlea with metallic cochlear implants (CI) that would lead to significant artifacts in μCT imaging. In conclusion, the present study demonstrates the capability of SLOT for resolution visualization of cleared human cochleae ex vivo using multiple contrast mechanisms and lays the foundation for a broad variety of additional studies. PMID:28873437

Three-dimensional Model of Human Platelet Integrin αIIbβ3 in Solution Obtained by Small Angle Neutron Scattering*

PubMed Central

Nogales, Aurora; García, Carolina; Pérez, Javier; Callow, Phil; Ezquerra, Tiberio A.; González-Rodríguez, José

2010-01-01

Integrin αIIbβ3 is the major membrane protein and adhesion receptor at the surface of blood platelets, which after activation plays a key role in platelet plug formation in hemostasis and thrombosis. Small angle neutron scattering (SANS) and shape reconstruction algorithms allowed formation of a low resolution three-dimensional model of whole αIIbβ3 in Ca2+/detergent solutions. Model projections after 90° rotation along its long axis show an elongated and “arched” form (135°) not observed before and a “handgun” form. This 20-nm-long structure is well defined, despite αIIbβ3 multidomain nature and expected segmental flexibility, with the largest region at the top, followed by two narrower and smaller regions at the bottom. Docking of this SANS envelope into the high resolution structure of αIIbβ3, reconstructed from crystallographic and NMR data, shows that the solution structure is less constrained, allows tentative assignment of the disposition of the αIIb and β3 subunits and their domains within the model, and points out the structural analogies and differences of the SANS model with the crystallographic models of the recombinant ectodomains of αIIbβ3 and αVβ3 and with the cryo-electron microscopy model of whole αIIbβ3. The ectodomain is in the bent configuration at the top of the model, where αIIb and β3 occupy the concave and convex sides, respectively, at the arched projection, with their bent knees at its apex. It follows the narrower transmembrane region and the cytoplasmic domains at the bottom end. αIIbβ3 aggregated in Mn2+/detergent solutions, which impeded to get its SANS model. PMID:19897481

All sky imaging Fabry-Perot spectrometer for optical investigation of the upper atmosphere

NASA Astrophysics Data System (ADS)

Sekar, R.; Gurubaran, S.; Sridharan, R.

1993-06-01

A simple optical design, keeping in view of the available components, has been worked out to develop the 'all sky imaging Fabry-Perot spectrometer' to study the spatial structures in thermospheric winds and temperature. This system comprises three subsystems, namely, (1) field widening front-end optics, (2) high resolution Fabry-Perot spectrometer and (3) a two-dimensional detector. The design details of the above imaging spectrometer that has been commissioned for routine observations from Mt. Abu along with the first results on OI 6300 A airglow emission are presented and discussed.

Development, implementation and evaluation of satellite-aided agricultural monitoring systems

NASA Technical Reports Server (NTRS)

Cicone, R. (Principal Investigator); Crist, E.; Metzler, M.; Parris, T.

1982-01-01

Research supporting the use of remote sensing for inventory and assessment of agricultural commodities is summarized. Three task areas are described: (1) corn and soybean crop spectral/temporal signature characterization; (2) efficient area estimation technology development; and (3) advanced satellite and sensor system definition. Studies include an assessment of alternative green measures from MSS variables; the evaluation of alternative methods for identifying, labeling or classification targets in an automobile procedural context; a comparison of MSS, the advanced very high resolution radiometer and the coastal zone color scanner, as well as a critical assessment of thematic mapper dimensionally and spectral structure.

Three-dimensional structures of unligated uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 Å resolution and its complex with an antibacterial drug

NASA Astrophysics Data System (ADS)

Balaev, V. V.; Lashkov, A. A.; Gabdulkhakov, A. G.; Dontsova, M. V.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

2015-07-01

Uridine phosphorylases play an essential role in the cellular metabolism of some antibacterial agents. Acute infectious diseases (bubonic plague, yersiniosis, pseudotuberculosis, etc., caused by bacteria of the genus Yersinia) are treated using both sulfanilamide medicines and antibiotics, including trimethoprim. The action of an antibiotic on a bacterial cell is determined primarily by the character of its interactions with cellular components, including those which are not targets (for example, with pyrimidine phosphorylases). This type of interaction should be taken into account in designing drugs. The three-dimensional structure of uridine phosphorylase from the bacterium Yersinia pseudotuberculosis ( YptUPh) with the free active site was determined for the first time by X-ray crystallography and refined at 1.40 Å resolution (DPI = 0.062 Å; ID PDB: 4OF4). The structure of the complex of YptUPh with the bacteriostatic drug trimethoprim was studied by molecular docking and molecular dynamics methods. The trimethoprim molecule was shown to be buffered by the enzyme YptUPh, resulting in a decrease in the efficiency of the treatment of infectious diseases caused by bacteria of the genus Yersinia with trimethoprim.

Structure formation in organic thin films observed in real time by energy dispersive near-edge x-ray absorption fine-structure spectroscopy

NASA Astrophysics Data System (ADS)

Scholz, M.; Sauer, C.; Wiessner, M.; Nguyen, N.; Schöll, A.; Reinert, F.

2013-08-01

We study the structure formation of 1,4,5,8-naphthalene-tetracarboxylicacid-dianhydride (NTCDA) multilayer films on Ag(111) surfaces by energy dispersive near-edge x-ray absorption fine-structure spectroscopy (NEXAFS) and photoelectron spectroscopy. The time resolution of seconds of the method allows us to identify several sub-processes, which occur during the post-growth three-dimensional structural ordering, as well as their characteristic time scales. After deposition at low temperature the NTCDA molecules are preferentially flat lying and the films exhibit no long-range order. Upon annealing the molecules flip into an upright orientation followed by an aggregation in a transient phase which exists for several minutes. Finally, three-dimensional islands are established with bulk-crystalline structure involving substantial mass transport on the surface and morphological roughening. By applying the Kolmogorov-Johnson-Mehl-Avrami model the activation energies of the temperature-driven sub-processes can be derived from the time evolution of the NEXAFS signal.

Advanced morphological and biochemical magnetic resonance imaging of cartilage repair procedures in the knee joint at 3 Tesla.

PubMed

Welsch, Goetz H; Mamisch, Tallal C; Hughes, Timothy; Domayer, Stephan; Marlovits, Stefan; Trattnig, Siegfried

2008-09-01

Morphological and biochemical magnetic resonance imaging (MRI) is due to high field MR systems, advanced coil technology, and sophisticated sequence protocols capable of visualizing articular cartilage in vivo with high resolution in clinical applicable scan time. Several conventional two-dimensional (2D) and three-dimensional (3D) approaches show changes in cartilage structure. Furthermore newer isotropic 3D sequences show great promise in improving cartilage imaging and additionally in diagnosing surrounding pathologies within the knee joint. Functional MR approaches are additionally able to provide a specific measure of the composition of cartilage. Cartilage physiology and ultra-structure can be determined, changes in cartilage macromolecules can be detected, and cartilage repair tissue can thus be assessed and potentially differentiated. In cartilage defects and following nonsurgical and surgical cartilage repair, morphological MRI provides the basis for diagnosis and follow-up evaluation, whereas biochemical MRI provides a deeper insight into the composition of cartilage and cartilage repair tissue. A combination of both, together with clinical evaluation, may represent a desirable multimodal approach in the future, also available in routine clinical use.

Analysis of high-rise constructions with the using of three-dimensional models of rods in the finite element program PRINS

NASA Astrophysics Data System (ADS)

Agapov, Vladimir

2018-03-01

The necessity of new approaches to the modeling of rods in the analysis of high-rise constructions is justified. The possibility of the application of the three-dimensional superelements of rods with rectangular cross section for the static and dynamic calculation of the bar and combined structures is considered. The results of the eighteen-story spatial frame free vibrations analysis using both one-dimensional and three-dimensional models of rods are presented. A comparative analysis of the obtained results is carried out and the conclusions on the possibility of three-dimensional superelements application in static and dynamic analysis of high-rise constructions are given on its basis.

Ground Penetrating Radar Imaging of Ancient Clastic Deposits: A Tool for Three-Dimensional Outcrop Studies

NASA Astrophysics Data System (ADS)

Akinpelu, Oluwatosin Caleb

The growing need for better definition of flow units and depositional heterogeneities in petroleum reservoirs and aquifers has stimulated a renewed interest in outcrop studies as reservoir analogues in the last two decades. Despite this surge in interest, outcrop studies remain largely two-dimensional; a major limitation to direct application of outcrop knowledge to the three dimensional heterogeneous world of subsurface reservoirs. Behind-outcrop Ground Penetrating Radar (GPR) imaging provides high-resolution geophysical data, which when combined with two dimensional architectural outcrop observation, becomes a powerful interpretation tool. Due to the high resolution, non-destructive and non-invasive nature of the GPR signal, as well as its reflection-amplitude sensitivity to shaly lithologies, three-dimensional outcrop studies combining two dimensional architectural element data and behind-outcrop GPR imaging hold significant promise with the potential to revolutionize outcrop studies the way seismic imaging changed basin analysis. Earlier attempts at GPR imaging on ancient clastic deposits were fraught with difficulties resulting from inappropriate field techniques and subsequent poorly-informed data processing steps. This project documents advances in GPR field methodology, recommends appropriate data collection and processing procedures and validates the value of integrating outcrop-based architectural-element mapping with GPR imaging to obtain three dimensional architectural data from outcrops. Case studies from a variety of clastic deposits: Whirlpool Formation (Niagara Escarpment), Navajo Sandstone (Moab, Utah), Dunvegan Formation (Pink Mountain, British Columbia), Chinle Formation (Southern Utah) and St. Mary River Formation (Alberta) demonstrate the usefulness of this approach for better interpretation of outcrop scale ancient depositional processes and ultimately as a tool for refining existing facies models, as well as a predictive tool for subsurface reservoir modelling. While this approach is quite promising for detailed three-dimensional outcrop studies, it is not an all-purpose panacea; thick overburden, poor antenna-ground coupling in rough terrains typical of outcrops, low penetration and rapid signal attenuation in mudstone and diagenetic clay- rich deposits often limit the prospects of this novel technique.

Four-dimensional MRI of renal function in the developing mouse.

PubMed

Xie, Luke; Subashi, Ergys; Qi, Yi; Knepper, Mark A; Johnson, G Allan

2014-09-01

The major roles of filtration, metabolism and high blood flow make the kidney highly vulnerable to drug-induced toxicity and other renal injuries. A method to follow kidney function is essential for the early screening of toxicity and malformations. In this study, we acquired high spatiotemporal resolution (four dimensional) datasets of normal mice to follow changes in kidney structure and function during development. The data were acquired with dynamic contrast-enhanced MRI (via keyhole imaging) and a cryogenic surface coil, allowing us to obtain a full three-dimensional image (isotropic resolution, 125 microns) every 7.7 s over a 50-min scan. This time course permitted the demonstration of both contrast enhancement and clearance. Functional changes were measured over a 17-week course (at 3, 5, 7, 9, 13 and 17 weeks). The time dimension of the MRI dataset was processed to produce unique image contrasts to segment the four regions of the kidney: cortex (CO), outer stripe (OS) of the outer medulla (OM), inner stripe (IS) of the OM and inner medulla (IM). Local volumes, time-to-peak (TTP) values and decay constants (DC) were measured in each renal region. These metrics increased significantly with age, with the exception of DC values in the IS and OS. These data will serve as a foundation for studies of normal renal physiology and future studies of renal diseases that require early detection and intervention. Copyright © 2014 John Wiley & Sons, Ltd.

Bacterial Transcription as a Target for Antibacterial Drug Development

PubMed Central

Ma, Cong; Yang, Xiao

2016-01-01

SUMMARY Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design. PMID:26764017

Single-particle cryo-electron microscopy of Rift Valley fever virus

PubMed Central

Sherman, Michael B.; Freiberg, Alexander N.; Holbrook, Michael R.; Watowich, Stanley J.

2009-01-01

Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human veterinary pathogen causing acute hepatitis in ruminants and has the potential to Single-particle cryo-EM reconstruction of RVFV MP-12 hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T=12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure provides a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit-vaccines. PMID:19304307

Adaptive optics improves multiphoton super-resolution imaging

NASA Astrophysics Data System (ADS)

Zheng, Wei; Wu, Yicong; Winter, Peter; Shroff, Hari

2018-02-01

Three dimensional (3D) fluorescence microscopy has been essential for biological studies. It allows interrogation of structure and function at spatial scales spanning the macromolecular, cellular, and tissue levels. Critical factors to consider in 3D microscopy include spatial resolution, signal-to-noise (SNR), signal-to-background (SBR), and temporal resolution. Maintaining high quality imaging becomes progressively more difficult at increasing depth (where optical aberrations, induced by inhomogeneities of refractive index in the sample, degrade resolution and SNR), and in thick or densely labeled samples (where out-of-focus background can swamp the valuable, in-focus-signal from each plane). In this report, we introduce our new instrumentation to address these problems. A multiphoton structured illumination microscope was simply modified to integrate an adpative optics system for optical aberrations correction. Firstly, the optical aberrations are determined using direct wavefront sensing with a nonlinear guide star and subsequently corrected using a deformable mirror, restoring super-resolution information. We demonstrate the flexibility of our adaptive optics approach on a variety of semi-transparent samples, including bead phantoms, cultured cells in collagen gels and biological tissues. The performance of our super-resolution microscope is improved in all of these samples, as peak intensity is increased (up to 40-fold) and resolution recovered (up to 176+/-10 nm laterally and 729+/-39 nm axially) at depths up to 250 μm from the coverslip surface.

Low-cost three-dimensional millimeter-wave holographic imaging system based on a frequency-scanning antenna.

PubMed

Amin Nili, Vahid; Mansouri, Ehsan; Kavehvash, Zahra; Fakharzadeh, Mohammad; Shabany, Mahdi; Khavasi, Amin

2018-01-01

In this paper, a closed-form two-dimensional reconstruction technique for hybrid frequency and mechanical scanning millimeter-wave (MMW) imaging systems is proposed. Although being commercially implemented in many imaging systems as a low-cost real-time solution, the results of frequency scanning systems have been reconstructed numerically or have been reported as the captured raw data with no clear details. Furthermore, this paper proposes a new framework to utilize the captured data of different frequencies for three-dimensional (3D) reconstruction based on novel proposed closed-form relations. The hybrid frequency and mechanical scanning structure, together with the proposed reconstruction method, yields a low-cost MMW imaging system with a satisfying performance. The extracted reconstruction formulations are validated through numerical simulations, which show comparable image quality with conventional MMW imaging systems, i.e., switched-array (SA) and phased-array (PA) structures. Extensive simulations are also performed in the presence of additive noise, demonstrating the acceptable robustness of the system against system noise compared to SA and comparable performance with PA. Finally, 3D reconstruction of the simulated data shows a depth resolution of better than 10 cm with minimum degradation of lateral resolution in the 10 GHz frequency bandwidth.

Evolution of a double-front Rayleigh-Taylor system using a graphics-processing-unit-based high-resolution thermal lattice-Boltzmann model.

PubMed

Ripesi, P; Biferale, L; Schifano, S F; Tripiccione, R

2014-04-01

We study the turbulent evolution originated from a system subjected to a Rayleigh-Taylor instability with a double density at high resolution in a two-dimensional geometry using a highly optimized thermal lattice-Boltzmann code for GPUs. Our investigation's initial condition, given by the superposition of three layers with three different densities, leads to the development of two Rayleigh-Taylor fronts that expand upward and downward and collide in the middle of the cell. By using high-resolution numerical data we highlight the effects induced by the collision of the two turbulent fronts in the long-time asymptotic regime. We also provide details on the optimized lattice-Boltzmann code that we have run on a cluster of GPUs.

Microfabrication technology by femtosecond laser direct scanning using two-photon photo-polymerization

NASA Astrophysics Data System (ADS)

Zhou, Ming; Liu, Li-Peng; Dai, Qi-Xun; Pan, Chuan-Peng

2005-01-01

Two-photon absorption (TPA) is confined at the focus under tight-focusing conditions, which provides a novel concept for micro-fabrication using two-photon photo-polymerization in resin. The development of three-dimensional micro-fabrication by femtosecond laser was introduced at first, then the merits of femtosecond two-photon photo-polymerization was expatiated. Femtosecond laser direct scanning three-dimensional (3D) micro-fabrication system was set up and corresponding controlling software was developed. We demonstrated a fabrication of three-dimensional microstructures using photo-polymerization of resin by two-photon absorption. The precision of micro-machining and the spatial resolution reached 1um because of TPA. The dependence of fabricated line width to the micro-fabrication speed was investigated. Benzene ring, CHINA and layer-by-layer of log structures were fabricated in this 3D- micro-fabrication system as examples.

Two-dimensional transport in structured optical force landscapes

NASA Astrophysics Data System (ADS)

Xiao, Ke

The overdamped transport of a Brownian particle in a structured force landscape has been studied extensively for a century. Even such well-studied examples as Brownian transport in a one-dimensional tilted washboard potential continue to yield surprising results, with recent discoveries including the giant enhancement of diffusion at the depinning transition, and the so-called "thermal ratchet effect". The transport phenomena in higher-dimensional systems should be substantially richer, but remain largely unexplored. In this Thesis we study the biased diffusion of colloidal spheres through two-dimensional force landscapes created with holographic optical tweezers (HOT). These studies take advantage of holographic video microscopy (HVM), which enables us to follow spheres' three-dimensional motions with nanometer resolution while simultaneously measuring their radii and refractive indexes with part-per-thousand resolution. Using these techniques we investigated the kinetically and statistically locked-in transport of colloidal spheres through arrays of optical traps, and confirmed previously untested predictions for kinetically locked-in transport that can be used for sorting applications with previously unheard finesse. Extending this result to highly structured two-dimensional landscapes, we developed prismatic optical fractionation, in which objects with different physical properties are deflected into different directions, a phenomenon analogous to a prism dispersing different wavelengths of light into different directions. Our simulational and experimental studies revealed the important role that thermal fluctuations play in establishing the hierarchy of kinetically locked-in states. We also investigated Brownian motion in a two-dimensional optical force landscape that varies in time. The traps for these studies were arranged in particular pattern called a "Fibonacci spiral" that is both the densest arrangement of circular objects with a circular domain and also particularly endowed with useful and interesting symmetries. Periodically rotating this pattern gives rise to transport in the both radial and azimuthal dimensions, whose direction depends on the angle and speed of rotation as well as the inter-trap separation. This deceptively simple system displays an extremely rich pattern of flux reversals in both dimensions and creates new avenues for studying the departure from equilibrium in noise-driven machines.

Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography.

PubMed

Yu, Young-Sang; Farmand, Maryam; Kim, Chunjoong; Liu, Yijin; Grey, Clare P; Strobridge, Fiona C; Tyliszczak, Tolek; Celestre, Rich; Denes, Peter; Joseph, John; Krishnan, Harinarayan; Maia, Filipe R N C; Kilcoyne, A L David; Marchesini, Stefano; Leite, Talita Perciano Costa; Warwick, Tony; Padmore, Howard; Cabana, Jordi; Shapiro, David A

2018-03-02

Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a set of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices.

Angular reconstitution-based 3D reconstructions of nanomolecular structures from superresolution light-microscopy images

PubMed Central

Salas, Desirée; Le Gall, Antoine; Fiche, Jean-Bernard; Valeri, Alessandro; Ke, Yonggang; Bron, Patrick; Bellot, Gaetan

2017-01-01

Superresolution light microscopy allows the imaging of labeled supramolecular assemblies at a resolution surpassing the classical diffraction limit. A serious limitation of the superresolution approach is sample heterogeneity and the stochastic character of the labeling procedure. To increase the reproducibility and the resolution of the superresolution results, we apply multivariate statistical analysis methods and 3D reconstruction approaches originally developed for cryogenic electron microscopy of single particles. These methods allow for the reference-free 3D reconstruction of nanomolecular structures from two-dimensional superresolution projection images. Since these 2D projection images all show the structure in high-resolution directions of the optical microscope, the resulting 3D reconstructions have the best possible isotropic resolution in all directions. PMID:28811371

Synchrotron radiation microbeam X-ray diffraction for nondestructive assessments of local structural properties of faceted InGaN/GaN quantum wells

NASA Astrophysics Data System (ADS)

Sakaki, Atsushi; Funato, Mitsuru; Kawamura, Tomoaki; Araki, Jun; Kawakami, Yoichi

2018-03-01

Synchrotron radiation (SR) X-ray diffraction with a sub-µm spatial resolution is used to nondestructively evaluate the local thickness and alloy composition of three-dimensionally faceted InGaN/GaN quantum wells (QWs). The (0001) facet QW on a trapezoidal structure composed of (0001), \\{ 11\\bar{2}2\\} , and \\{ 11\\bar{2}0\\} facets is nonuniform, most likely owing to the migration of adatoms between facets. The thickness and composition markedly vary within a short distance for the \\{ 11\\bar{2}2\\} facet QW of another pyramidal structure. The QW parameters acquired by SR microbeam X-ray diffraction reproduce the local emission property assessed by cathodoluminescence, thereby indicating the high reliability of this method.

Structure of the Si(111)-(5×2)-Au Surface

NASA Astrophysics Data System (ADS)

Abukawa, Tadashi; Nishigaya, Yoshiki

2013-01-01

The structure of the Si(111)-(5×2)-Au surface, one of the long-standing problems in surface science, has been solved by means of Weissenberg reflection high-energy electron diffraction. The arrangement of the Au atoms and their positions with respect to the substrate were determined from a three-dimensional Patterson function with a lateral resolution of 0.3 Å based on a large amount of diffraction data. The new structural model consists of six Au atoms in a 5×2 unit, which agrees with the recently confirmed Au coverage of 0.6 ML [I. Barke , Phys. Rev. B 79, 155301 (2009).PRBMDO1098-0121]. The model has a distinct ×2 periodicity, and includes a Au dimer. The model is also compatible with previously obtained STM images.

Characterization of alterations in diabetic myocardial tissue using high resolution MRI.

PubMed

Loganathan, Rajaprasad; Bilgen, Mehmet; Al-Hafez, Baraa; Smirnova, Irina V

2006-02-01

Cardiovascular complications, including diabetic cardiomyopathy, are the major cause of fatalities in diabetes. Diabetic cardiomyopathy is expressed in part through fibrosis and left ventricular hypertrophy, increasing myocardial stiffness leading to heart failure. In order to search for curative interventions, precise evaluation of the diabetic heart pathology is extremely important. Magnetic resonance imaging (MRI) is ideally suited for the assessment of heart disorders due to its high resolution, three-dimensional properties and dimensional accuracy. In this study streptozotocin injected Sprague-Dawley rats were used as a model of type 1 diabetes to characterize abnormalities in the diabetic left ventricle (LV). High resolution MRI using a 9.4 T horizontal bore scanner was performed on control and 7 weeks diabetic rats. In the diabetic rats as compared to controls, we found increased LV wall volume to body weight ratio, suggestive of LV hypertrophy; increased LV wall mean pixel intensity, and decreased T2 relaxation time, both suggestive of changes in the diabetic tissue properties, perhaps due to presence of fibrosis which was detected through increase in the collagen fractional area. In addition, changes in the LV cavity area were observed and quantified in post-mortem diabetic hearts indicative of stiffer and less resilient LV myocardial tissue with diabetes. Together the data suggest that LV hypertrophy and fibrosis may be a major factor underlying structural and functional abnormalities in the diabetic heart, and MRI is a valuable tool to non-invasively monitor the pathological changes in diabetic cardiomyopathy.

Rapid, semi-automatic fracture and contact mapping for point clouds, images and geophysical data

NASA Astrophysics Data System (ADS)

Thiele, Samuel T.; Grose, Lachlan; Samsu, Anindita; Micklethwaite, Steven; Vollgger, Stefan A.; Cruden, Alexander R.

2017-12-01

The advent of large digital datasets from unmanned aerial vehicle (UAV) and satellite platforms now challenges our ability to extract information across multiple scales in a timely manner, often meaning that the full value of the data is not realised. Here we adapt a least-cost-path solver and specially tailored cost functions to rapidly interpolate structural features between manually defined control points in point cloud and raster datasets. We implement the method in the geographic information system QGIS and the point cloud and mesh processing software CloudCompare. Using these implementations, the method can be applied to a variety of three-dimensional (3-D) and two-dimensional (2-D) datasets, including high-resolution aerial imagery, digital outcrop models, digital elevation models (DEMs) and geophysical grids. We demonstrate the algorithm with four diverse applications in which we extract (1) joint and contact patterns in high-resolution orthophotographs, (2) fracture patterns in a dense 3-D point cloud, (3) earthquake surface ruptures of the Greendale Fault associated with the Mw7.1 Darfield earthquake (New Zealand) from high-resolution light detection and ranging (lidar) data, and (4) oceanic fracture zones from bathymetric data of the North Atlantic. The approach improves the consistency of the interpretation process while retaining expert guidance and achieves significant improvements (35-65 %) in digitisation time compared to traditional methods. Furthermore, it opens up new possibilities for data synthesis and can quantify the agreement between datasets and an interpretation.

Utilizing High-Performance Computing to Investigate Parameter Sensitivity of an Inversion Model for Vadose Zone Flow and Transport

NASA Astrophysics Data System (ADS)

Fang, Z.; Ward, A. L.; Fang, Y.; Yabusaki, S.

2011-12-01

High-resolution geologic models have proven effective in improving the accuracy of subsurface flow and transport predictions. However, many of the parameters in subsurface flow and transport models cannot be determined directly at the scale of interest and must be estimated through inverse modeling. A major challenge, particularly in vadose zone flow and transport, is the inversion of the highly-nonlinear, high-dimensional problem as current methods are not readily scalable for large-scale, multi-process models. In this paper we describe the implementation of a fully automated approach for addressing complex parameter optimization and sensitivity issues on massively parallel multi- and many-core systems. The approach is based on the integration of PNNL's extreme scale Subsurface Transport Over Multiple Phases (eSTOMP) simulator, which uses the Global Array toolkit, with the Beowulf-Cluster inspired parallel nonlinear parameter estimation software, BeoPEST in the MPI mode. In the eSTOMP/BeoPEST implementation, a pre-processor generates all of the PEST input files based on the eSTOMP input file. Simulation results for comparison with observations are extracted automatically at each time step eliminating the need for post-process data extractions. The inversion framework was tested with three different experimental data sets: one-dimensional water flow at Hanford Grass Site; irrigation and infiltration experiment at the Andelfingen Site; and a three-dimensional injection experiment at Hanford's Sisson and Lu Site. Good agreements are achieved in all three applications between observations and simulations in both parameter estimates and water dynamics reproduction. Results show that eSTOMP/BeoPEST approach is highly scalable and can be run efficiently with hundreds or thousands of processors. BeoPEST is fault tolerant and new nodes can be dynamically added and removed. A major advantage of this approach is the ability to use high-resolution geologic models to preserve the spatial structure in the inverse model, which leads to better parameter estimates and improved predictions when using the inverse-conditioned realizations of parameter fields.

Selective separation of fluorinated compounds from complex organic mixtures by pyrolysis-comprehensive two-dimensional gas chromatography coupled to high-resolution time-of-flight mass spectrometry.

PubMed

Nakajima, Yoji; Arinami, Yuko; Yamamoto, Kiyoshi

2014-12-29

The usefulness of comprehensive two-dimensional gas chromatography (GC×GC) was demonstrated for the selective separation of fluorinated compounds from organic mixtures, such as kerosene/perfluorokerosene mixtures, pyrolysis products derived from polyethylene/ethylene-tetrafluoroethylene alternating copolymer mixture and poly[2-(perfluorohexyl)ethyl acrylate]. Perfluorocarbons were completely separated from hydrocarbons in the two-dimensional chromatogram. Fluorohydrocarbons in the pyrolysis products of polyethylene/ethylene-tetrafluoroethylene alternating copolymer mixture were selectively isolated from their hydrocarbon counterparts and regularly arranged according to their chain length and fluorine content in the two-dimensional chromatogram. A reliable structural analysis of the fluorohydrocarbons was achieved by combining effective GC×GC positional information with accurate mass spectral data obtained by high-resolution time-of-flight mass spectrometry (HRTOF-MS). 2-(Perfluorohexyl)ethyl acrylate monomer, dimer, and trimer as well as 2-(perfluorohexyl)ethyl alcohol in poly[2-(perfluorohexyl)ethyl acrylate] pyrolysis products were detected in the bottommost part of the two-dimensional chromatogram with separation from hydrocarbons possessing terminal structure information about the polymer, such as α-methylstyrene. Pyrolysis-GC×GC/HRTOF-MS appeared particularly suitable for the characterization of fluorinated polymer microstructures, such as monomer sequences and terminal groups. Copyright © 2014 Elsevier B.V. All rights reserved.

Three-Dimensional Printing of Complex Structures by Freeform Reversible Embedding of Suspended Hydrogels (FRESH)

NASA Astrophysics Data System (ADS)

Feinberg, Adam

We demonstrate the additive manufacturing of complex three-dimensional (3D) structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels (FRESH), enables 3D printing of hydrated materials with an elastic modulus less than 500 kPa including alginate, collagen, hyaluronic acid and fibrin. A range of crosslinking mechanisms can be used depending on the polymer being printed, including ionic, enzymatic, pH, thermal and light based approaches. CAD models of 3D optical, computed tomography, and magnetic resonance imaging data can be 3D printed at a resolution of 100 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains are mechanically robust and recreate complex 3D internal and external anatomical architectures. Recent advances have improved the resolution and broadened the range of materials that can be FRESH 3D printed. This work was supported in part by the NIH Director's New Innovator Award (DP2HL117750) and the NSF CAREER Award (1454248).

Super-resolution photoacoustic microscopy using a localized near-field of a plasmonic nanoaperture: a three-dimensional simulation study

NASA Astrophysics Data System (ADS)

Park, Byullee; Lee, Hongki; Upputuri, Paul Kumar; Pramanik, Manojit; Kim, Donghyun; Kim, Chulhong

2018-02-01

Super-resolution microscopy has been increasingly important to delineate nanoscale biological structures or nanoparticles. With these increasing demands, several imaging modalities, including super-resolution fluorescence microscope (SRFM) and electron microscope (EM), have been developed and commercialized. These modalities achieve nanoscale resolution, however, SRFM cannot image without fluorescence, and sample preparation of EM is not suitable for biological specimens. To overcome those disadvantages, we have numerically studied the possibility of superresolution photoacoustic microscopy (SR-PAM) based on near-field localization of light. Photoacoustic (PA) signal is generally acquired based on optical absorption contrast; thus it requires no agents or pre-processing for the samples. The lateral resolution of the conventional photoacoustic microscopy is limited to 200 nm by diffraction limit, therefore reducing the lateral resolution is a major research impetus. Our approach to breaking resolution limit is to use laser pulses of extremely small spot size as a light source. In this research, we simulated the PA signal by constructing the three dimensional SR-PAM system environment using the k-Wave toolbox. As the light source, we simulated ultrashort light pulses using geometrical nanoaperture with near-field localization of surface plasmons. Through the PA simulation, we have successfully distinguish cuboids spaced 3 nm apart. In the near future, we will develop the SR-PAM and it will contribute to biomedical and material sciences.

Two-dimensional mesh embedding for Galerkin B-spline methods

NASA Technical Reports Server (NTRS)

Shariff, Karim; Moser, Robert D.

1995-01-01

A number of advantages result from using B-splines as basis functions in a Galerkin method for solving partial differential equations. Among them are arbitrary order of accuracy and high resolution similar to that of compact schemes but without the aliasing error. This work develops another property, namely, the ability to treat semi-structured embedded or zonal meshes for two-dimensional geometries. This can drastically reduce the number of grid points in many applications. Both integer and non-integer refinement ratios are allowed. The report begins by developing an algorithm for choosing basis functions that yield the desired mesh resolution. These functions are suitable products of one-dimensional B-splines. Finally, test cases for linear scalar equations such as the Poisson and advection equation are presented. The scheme is conservative and has uniformly high order of accuracy throughout the domain.