QCM-D on mica for parallel QCM-D-AFM studies.

PubMed

Richter, Ralf P; Brisson, Alain

2004-05-25

Quartz crystal microbalance with dissipation monitoring (QCM-D) has developed into a recognized method to study adsorption processes in liquid, such as the formation of supported lipid bilayers and protein adsorption. However, the large intrinsic roughness of currently used gold-coated or silica-coated QCM-D sensors limits parallel structural characterization by atomic force microscopy (AFM). We present a method for coating QCM-D sensors with thin mica sheets operating in liquid with high stability and sensitivity. We define criteria to objectively assess the reliability of the QCM-D measurements and demonstrate that the mica-coated sensors can be used to follow the formation of supported lipid membranes and subsequent protein adsorption. This method allows combining QCM-D and AFM investigations on identical supports, providing detailed physicochemical and structural characterization of model membranes.

Orientation of ripples induced by ultrafast laser pulses on copper in different liquids

NASA Astrophysics Data System (ADS)

Maragkaki, Stella; Elkalash, Abdallah; Gurevich, Evgeny L.

2017-12-01

Formation of laser-induced periodic surface structures (LIPSS or ripples) was studied on a metallic surface of polished copper using irradiation with multiple femtosecond laser pulses in different environmental conditions (air, water, ethanol and methanol). Uniform LIPSS have been achieved by controlling the peak fluence and the overlapping rate. Ripples in both orientations, perpendicular and parallel to laser polarization, were observed in all liquids simultaneously. The orientation of these ripples in the center of the ablated line was changing with the incident light intensity. For low intensities the orientation of the ripples is perpendicular to the laser polarization, whereas for high intensities it turns parallel to it without considerable changes in the period. Multi-directional LIPSS formation was also observed for moderate peak fluence in liquid environments.

Method for selectively orienting induced fractures in subterranean earth formations

DOEpatents

Shuck, Lowell Z.

1977-02-01

The orientation of hydraulically-induced fractures in relatively deep subterranean earth formations is normally confined to vertical projections along a plane parallel to the maximum naturally occurring (tectonic) compressive stress field. It was found that this plane of maximum compressive stress may be negated and, in effect, re-oriented in a plane projecting generally orthogonal to the original tectonic stress plane by injecting liquid at a sufficiently high pressure into a wellbore fracture oriented in a plane parallel to the plane of tectonic stress for the purpose of stressing the surrounding earth formation in a plane generally orthogonal to the plane of tectonic stress. With the plane of maximum compressive stress re-oriented due to the presence of the induced compressive stress, liquid under pressure is injected into a second wellbore disposed within the zone influenced by the induced compressive stress but at a location in the earth formation laterally spaced from the fracture in the first wellbore for effecting a fracture in the second wellbore along a plane generally orthogonal to the fracture in the first wellbore.

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

DOE PAGES

Abraham, Mark James; Murtola, Teemu; Schulz, Roland; ...

2015-07-15

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. This work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. Finally, the latest best-in-class compressed trajectory storage format is supported.

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

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

Abraham, Mark James; Murtola, Teemu; Schulz, Roland

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. This work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. Finally, the latest best-in-class compressed trajectory storage format is supported.

How pattern is selected in drift wave turbulence: Role of parallel flow shear

NASA Astrophysics Data System (ADS)

Kosuga, Y.

2017-12-01

The role of parallel shear flow in the pattern selection problem in drift wave turbulence is discussed. Patterns of interest here are E × B convective cells, which include poloidally symmetric zonal flows and radially elongated streamers. The competition between zonal flow formation and streamer formation is analyzed in the context of modulational instability analysis, with the parallel flow shear as a parameter. For drift wave turbulence with k⊥ρs ≲ O (1 ) and without parallel flow coupling, zonal flows are preferred structures. While increasing the magnitude of parallel flow shear, streamer growth overcomes zonal flow growth. This is because the self-focusing effect of the modulational instability becomes more effective for streamers through density and parallel velocity modulation. As a consequence, the bursty release of free energy may result as the parallel flow shear increases.

Developing a Hadoop-based Middleware for Handling Multi-dimensional NetCDF

NASA Astrophysics Data System (ADS)

Li, Z.; Yang, C. P.; Schnase, J. L.; Duffy, D.; Lee, T. J.

2014-12-01

Climate observations and model simulations are collecting and generating vast amounts of climate data, and these data are ever-increasing and being accumulated in a rapid speed. Effectively managing and analyzing these data are essential for climate change studies. Hadoop, a distributed storage and processing framework for large data sets, has attracted increasing attentions in dealing with the Big Data challenge. The maturity of Infrastructure as a Service (IaaS) of cloud computing further accelerates the adoption of Hadoop in solving Big Data problems. However, Hadoop is designed to process unstructured data such as texts, documents and web pages, and cannot effectively handle the scientific data format such as array-based NetCDF files and other binary data format. In this paper, we propose to build a Hadoop-based middleware for transparently handling big NetCDF data by 1) designing a distributed climate data storage mechanism based on POSIX-enabled parallel file system to enable parallel big data processing with MapReduce, as well as support data access by other systems; 2) modifying the Hadoop framework to transparently processing NetCDF data in parallel without sequencing or converting the data into other file formats, or loading them to HDFS; and 3) seamlessly integrating Hadoop, cloud computing and climate data in a highly scalable and fault-tolerance framework.

Effect of angular momentum alignment and strong magnetic fields on the formation of protostellar discs

NASA Astrophysics Data System (ADS)

Gray, William J.; McKee, Christopher F.; Klein, Richard I.

2018-01-01

Star-forming molecular clouds are observed to be both highly magnetized and turbulent. Consequently, the formation of protostellar discs is largely dependent on the complex interaction between gravity, magnetic fields, and turbulence. Studies of non-turbulent protostellar disc formation with realistic magnetic fields have shown that these fields are efficient in removing angular momentum from the forming discs, preventing their formation. However, once turbulence is included, discs can form in even highly magnetized clouds, although the precise mechanism remains uncertain. Here, we present several high-resolution simulations of turbulent, realistically magnetized, high-mass molecular clouds with both aligned and random turbulence to study the role that turbulence, misalignment, and magnetic fields have on the formation of protostellar discs. We find that when the turbulence is artificially aligned so that the angular momentum is parallel to the initial uniform field, no rotationally supported discs are formed, regardless of the initial turbulent energy. We conclude that turbulence and the associated misalignment between the angular momentum and the magnetic field are crucial in the formation of protostellar discs in the presence of realistic magnetic fields.

Chocolate tablet aspects of cytherean Meshkenet Tessera

NASA Technical Reports Server (NTRS)

Raitala, J.

1993-01-01

Meshkenet Tessera structures were mapped from Magellan data and several resemblances to chocolate tablet boudinage were found. The complex fault sets display polyphase tectonic sequences of a few main deformation phases. Shear and tension have contributed to the areal deformation. Main faults cut the 1600-km long Meshkenet Tessera highland into bar-like blocks which have ridge and groove pattern oriented along or at high angles to the faults. The first approach to the surface block deformation is an assumption of initial parallel shear faulting followed by a chocolate tablet boudinage. Major faults which cut Meshkenet Tessera into rectangular blocks have been active repetitively while two progressive or superposed boudinage set formations have taken place at high angles during the relaxational or flattening type deformation of the area. Chocolate tablet boudinage is caused by a layer-parallel two-dimensional extension resulting in fracturing of the competent layer. Such structures, defined by two sets of boudin neck lines at right angles to each other, have been described by a number of authors. They develop in a flattening type of bulk deformation or during superposed deformation where the rock is elongated in two dimensions parallel to the surface. This is an attempt to describe and understand the formation and development of structures of Meshkenet Tessera which has complicated fault structures.

Towards a parallel collisionless shock in LAPD

NASA Astrophysics Data System (ADS)

Weidl, M. S.; Heuer, P.; Schaeffer, D.; Dorst, R.; Winske, D.; Constantin, C.; Niemann, C.

2017-09-01

Using a high-energy laser to produce a super-Alfvénic carbon-ion beam in a strongly magnetized helium plasma, we expect to be able to observe the formation of a collisionless parallel shock inside the Large Plasma Device. We compare early magnetic-field measurements of the resonant right-hand instability with analytical predictions and find excellent agreement. Hybrid simulations show that the carbon ions couple to the background plasma and compress it, although so far the background ions are mainly accelerated perpendicular to the mean-field direction.

Fiber optic cable-based high-resolution, long-distance VGA extenders

NASA Astrophysics Data System (ADS)

Rhee, Jin-Geun; Lee, Iksoo; Kim, Heejoon; Kim, Sungjoon; Koh, Yeon-Wan; Kim, Hoik; Lim, Jiseok; Kim, Chur; Kim, Jungwon

2013-02-01

Remote transfer of high-resolution video information finds more applications in detached display applications for large facilities such as theaters, sports complex, airports, and security facilities. Active optical cables (AOCs) provide a promising approach for enhancing both the transmittable resolution and distance that standard copper-based cables cannot reach. In addition to the standard digital formats such as HDMI, the high-resolution, long-distance transfer of VGA format signals is important for applications where high-resolution analog video ports should be also supported, such as military/defense applications and high-resolution video camera links. In this presentation we present the development of a compressionless, high-resolution (up to WUXGA, 1920x1200), long-distance (up to 2 km) VGA extenders based on serialized technique. We employed asynchronous serial transmission and clock regeneration techniques, which enables lower cost implementation of VGA extenders by removing the necessity for clock transmission and large memory at the receiver. Two 3.125-Gbps transceivers are used in parallel to meet the required maximum video data rate of 6.25 Gbps. As the data are transmitted asynchronously, 24-bit pixel clock time stamp is employed to regenerate video pixel clock accurately at the receiver side. In parallel to the video information, stereo audio and RS-232 control signals are transmitted as well.

SAPNEW: Parallel finite element code for thin shell structures on the Alliant FX-80

NASA Astrophysics Data System (ADS)

Kamat, Manohar P.; Watson, Brian C.

1992-11-01

The finite element method has proven to be an invaluable tool for analysis and design of complex, high performance systems, such as bladed-disk assemblies in aircraft turbofan engines. However, as the problem size increase, the computation time required by conventional computers can be prohibitively high. Parallel processing computers provide the means to overcome these computation time limits. This report summarizes the results of a research activity aimed at providing a finite element capability for analyzing turbomachinery bladed-disk assemblies in a vector/parallel processing environment. A special purpose code, named with the acronym SAPNEW, has been developed to perform static and eigen analysis of multi-degree-of-freedom blade models built-up from flat thin shell elements. SAPNEW provides a stand alone capability for static and eigen analysis on the Alliant FX/80, a parallel processing computer. A preprocessor, named with the acronym NTOS, has been developed to accept NASTRAN input decks and convert them to the SAPNEW format to make SAPNEW more readily used by researchers at NASA Lewis Research Center.

Parallel Microcracks-based Ultrasensitive and Highly Stretchable Strain Sensors.

PubMed

Amjadi, Morteza; Turan, Mehmet; Clementson, Cameron P; Sitti, Metin

2016-03-02

There is an increasing demand for flexible, skin-attachable, and wearable strain sensors due to their various potential applications. However, achieving strain sensors with both high sensitivity and high stretchability is still a grand challenge. Here, we propose highly sensitive and stretchable strain sensors based on the reversible microcrack formation in composite thin films. Controllable parallel microcracks are generated in graphite thin films coated on elastomer films. Sensors made of graphite thin films with short microcracks possess high gauge factors (maximum value of 522.6) and stretchability (ε ≥ 50%), whereas sensors with long microcracks show ultrahigh sensitivity (maximum value of 11,344) with limited stretchability (ε ≤ 50%). We demonstrate the high performance strain sensing of our sensors in both small and large strain sensing applications such as human physiological activity recognition, human body large motion capturing, vibration detection, pressure sensing, and soft robotics.

Dynamical Generation of Quasi-Stationary Alfvenic Double Layers and Charge Holes and Unified Theory of Quasi-Static and Alfvenic Auroral Arc Formation

NASA Astrophysics Data System (ADS)

Song, Y.; Lysak, R. L.

2015-12-01

Parallel E-fields play a crucial role for the acceleration of charged particles, creating discrete aurorae. However, once the parallel electric fields are produced, they will disappear right away, unless the electric fields can be continuously generated and sustained for a fairly long time. Thus, the crucial question in auroral physics is how to generate such a powerful and self-sustained parallel electric fields which can effectively accelerate charge particles to high energy during a fairly long time. We propose that nonlinear interaction of incident and reflected Alfven wave packets in inhomogeneous auroral acceleration region can produce quasi-stationary non-propagating electromagnetic plasma structures, such as Alfvenic double layers (DLs) and Charge Holes. Such Alfvenic quasi-static structures often constitute powerful high energy particle accelerators. The Alfvenic DL consists of localized self-sustained powerful electrostatic electric fields nested in a low density cavity and surrounded by enhanced magnetic and mechanical stresses. The enhanced magnetic and velocity fields carrying the free energy serve as a local dynamo, which continuously create the electrostatic parallel electric field for a fairly long time. The generated parallel electric fields will deepen the seed low density cavity, which then further quickly boosts the stronger parallel electric fields creating both Alfvenic and quasi-static discrete aurorae. The parallel electrostatic electric field can also cause ion outflow, perpendicular ion acceleration and heating, and may excite Auroral Kilometric Radiation.

High-performance parallel interface to synchronous optical network gateway

DOEpatents

St. John, Wallace B.; DuBois, David H.

1998-08-11

A digital system provides sending and receiving gateways for HIPPI interfaces. Electronic logic circuitry formats data signals and overhead signals in a data frame that is suitable for transmission over a connecting fiber optic link. Multiplexers route the data and overhead signals to a framer module. The framer module allocates the data and overhead signals to a plurality of 9-byte words that are arranged in a selected protocol. The formatted words are stored in a storage register for output through the gateway.

High-Speed Systolic Array Testbed.

DTIC Science & Technology

1987-10-01

applications since the concept was introduced by H.T. Kung In 1978. This highly parallel architecture of nearet neighbor data communciation and...must be addressed. For instance, should bit-serial or bit parallei computation be utilized. Does the dynamic range of the candidate applications or...numericai stability of the algorithms used require computations In fixed point and Integer format or the architecturally more complex and slower floating

Effects of imbalanced currents on large-format LiFePO4/graphite batteries systems connected in parallel

NASA Astrophysics Data System (ADS)

Shi, Wei; Hu, Xiaosong; Jin, Chao; Jiang, Jiuchun; Zhang, Yanru; Yip, Tony

2016-05-01

With the development and popularization of electric vehicles, it is urgent and necessary to develop effective management and diagnosis technology for battery systems. In this work, we design a parallel battery model, according to equivalent circuits of parallel voltage and branch current, to study effects of imbalanced currents on parallel large-format LiFePO4/graphite battery systems. Taking a 60 Ah LiFePO4/graphite battery system manufactured by ATL (Amperex Technology Limited, China) as an example, causes of imbalanced currents in the parallel connection are analyzed using our model, and the associated effect mechanisms on long-term stability of each single battery are examined. Theoretical and experimental results show that continuously increasing imbalanced currents during cycling are mainly responsible for the capacity fade of LiFePO4/graphite parallel batteries. It is thus a good way to avoid fast performance fade of parallel battery systems by suppressing variations of branch currents.

The formation of quasi-parallel shocks. [in space, solar and astrophysical plasmas

NASA Technical Reports Server (NTRS)

Cargill, Peter J.

1991-01-01

In a collisionless plasma, the coupling between a piston and the plasma must take place through either laminar or turbulent electromagnetic fields. Of the three types of coupling (laminar, Larmor and turbulent), shock formation in the parallel regime is dominated by the latter and in the quasi-parallel regime by a combination of all three, depending on the piston. In the quasi-perpendicular regime, there is usually a good separation between piston and shock. This is not true in the quasi-parallel and parallel regime. Hybrid numerical simulations for hot plasma pistons indicate that when the electrons are hot, a shock forms, but does not cleanly decouple from the piston. For hot ion pistons, no shock forms in the parallel limit: in the quasi-parallel case, a shock forms, but there is severe contamination from hot piston ions. These results suggest that the properties of solar and astrophysical shocks, such as particle acceleration, cannot be readily separated from their driving mechanism.

Parallel Grand Canonical Monte Carlo (ParaGrandMC) Simulation Code

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.

2016-01-01

This report provides an overview of the Parallel Grand Canonical Monte Carlo (ParaGrandMC) simulation code. This is a highly scalable parallel FORTRAN code for simulating the thermodynamic evolution of metal alloy systems at the atomic level, and predicting the thermodynamic state, phase diagram, chemical composition and mechanical properties. The code is designed to simulate multi-component alloy systems, predict solid-state phase transformations such as austenite-martensite transformations, precipitate formation, recrystallization, capillary effects at interfaces, surface absorption, etc., which can aid the design of novel metallic alloys. While the software is mainly tailored for modeling metal alloys, it can also be used for other types of solid-state systems, and to some degree for liquid or gaseous systems, including multiphase systems forming solid-liquid-gas interfaces.

Plasmonic Nanoholes in a Multi-Channel Microarray Format for Parallel Kinetic Assays and Differential Sensing

PubMed Central

Im, Hyungsoon; Lesuffleur, Antoine; Lindquist, Nathan C.; Oh, Sang-Hyun

2009-01-01

We present nanohole arrays in a gold film integrated with a 6-channel microfluidic chip for parallel measurements of molecular binding kinetics. Surface plasmon resonance effects in the nanohole arrays enable real-time label-free measurements of molecular binding events in each channel, while adjacent negative reference channels can record measurement artifacts such as bulk solution index changes, temperature variations, or changing light absorption in the liquid. Using this platform, streptavidin-biotin specific binding kinetics are measured at various concentrations with negative controls. A high-density microarray of 252 biosensing pixels is also demonstrated with a packing density of 106 sensing elements/cm2, which can potentially be coupled with a massively parallel array of microfluidic channels for protein microarray applications. PMID:19284776

DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0.

PubMed

Jiang, Xiaohui; Kumar, Kamal; Hu, Xin; Wallqvist, Anders; Reifman, Jaques

2008-09-08

Small-molecule docking is an important tool in studying receptor-ligand interactions and in identifying potential drug candidates. Previously, we developed a software tool (DOVIS) to perform large-scale virtual screening of small molecules in parallel on Linux clusters, using AutoDock 3.05 as the docking engine. DOVIS enables the seamless screening of millions of compounds on high-performance computing platforms. In this paper, we report significant advances in the software implementation of DOVIS 2.0, including enhanced screening capability, improved file system efficiency, and extended usability. To keep DOVIS up-to-date, we upgraded the software's docking engine to the more accurate AutoDock 4.0 code. We developed a new parallelization scheme to improve runtime efficiency and modified the AutoDock code to reduce excessive file operations during large-scale virtual screening jobs. We also implemented an algorithm to output docked ligands in an industry standard format, sd-file format, which can be easily interfaced with other modeling programs. Finally, we constructed a wrapper-script interface to enable automatic rescoring of docked ligands by arbitrarily selected third-party scoring programs. The significance of the new DOVIS 2.0 software compared with the previous version lies in its improved performance and usability. The new version makes the computation highly efficient by automating load balancing, significantly reducing excessive file operations by more than 95%, providing outputs that conform to industry standard sd-file format, and providing a general wrapper-script interface for rescoring of docked ligands. The new DOVIS 2.0 package is freely available to the public under the GNU General Public License.

Self-Assembled Structures of Benzoic Acid on Au(111) Surface

NASA Astrophysics Data System (ADS)

Vu, Thu-Hien; Wandlowski, Thomas

2017-06-01

Electrochemical scanning tunneling microscopy combined with cyclic voltammetry were employed to explore the self-assembly of benzoic acid (BA) on a Au(111) substrate surface in a 0.1-M HClO4 solution. At the negatively charged surface, BA molecules form two highly ordered physisorbed adlayers with their phenyl rings parallel to the substrate surface. High-resolution scanning tunneling microscopy images reveal the packing arrangement and internal molecular structures. The striped pattern and zigzag structure of the BA adlayers are composed of parallel rows of dimers, in which two BA molecules are bound through a pair of O-H···O hydrogen bonds. Increasing the electrode potential further to positive charge densities of Au(111) leads to the desorption of the physisorbed hydrogen-bonded networks and the formation of a chemisorbed adlayer. BA molecules change their orientation from planar to upright fashion, which is accompanied by the deprotonation of the carboxyl group. Furthermore, potential-induced formation and dissolution of BA adlayers were also investigated. Structural transitions between the various types of ordered adlayers occur according to a nucleation and growth mechanism.

Uniaxial cyclic strain enhances adipose-derived stem cell fusion with skeletal myocytes

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

Andersen, Jens Isak; Juhl, Morten; Nielsen, Thøger

2014-07-25

Highlights: • Uniaxial cyclic tensile strain (CTS) applied to ASCs alone or in coculture with myogenic precursors. • CTS promoted the formation of a highly ordered array of parallel ASCs. • Without biochemical supplements, CTS did not support advanced myogenic differentiation of ASCs. • Mechanical stimulation of cocultures boosted fusion of ASCs with skeletal myoblasts. - Abstract: Although adult muscle tissue possesses an exceptional capacity for regeneration, in the case of large defects, the restoration to original state is not possible. A well-known source for the de novo regeneration is the adipose-derived stem cells (ASCs), which can be readily isolatedmore » and have been shown to have a broad differentiation and regenerative potential. In this work, we employed uniaxial cyclic tensile strain (CTS), to mechanically stimulate human ASCs to participate in the formation skeletal myotubes in an in vitro model of myogenesis. The application of CTS for 48 h resulted in the formation of a highly ordered array of parallel ASCs, but failed to support skeletal muscle terminal differentiation. When the same stimulation paradigm was applied to cocultures with mouse skeletal muscle myoblasts, the percentage of ASCs contributing to the formation of myotubes significantly exceeded the levels reported in the literature hitherto. In perspective, the mechanical strain may be used to increase the efficiency of incorporation of ASCs in the skeletal muscles, which could be found useful in diverse traumatic or pathologic scenarios.« less

Parallel heater system for subsurface formations

DOEpatents

Harris, Christopher Kelvin [Houston, TX; Karanikas, John Michael [Houston, TX; Nguyen, Scott Vinh [Houston, TX

2011-10-25

A heating system for a subsurface formation is disclosed. The system includes a plurality of substantially horizontally oriented or inclined heater sections located in a hydrocarbon containing layer in the formation. At least a portion of two of the heater sections are substantially parallel to each other. The ends of at least two of the heater sections in the layer are electrically coupled to a substantially horizontal, or inclined, electrical conductor oriented substantially perpendicular to the ends of the at least two heater sections.

Parallel processing architecture for H.264 deblocking filter on multi-core platforms

NASA Astrophysics Data System (ADS)

Prasad, Durga P.; Sonachalam, Sekar; Kunchamwar, Mangesh K.; Gunupudi, Nageswara Rao

2012-03-01

Massively parallel computing (multi-core) chips offer outstanding new solutions that satisfy the increasing demand for high resolution and high quality video compression technologies such as H.264. Such solutions not only provide exceptional quality but also efficiency, low power, and low latency, previously unattainable in software based designs. While custom hardware and Application Specific Integrated Circuit (ASIC) technologies may achieve lowlatency, low power, and real-time performance in some consumer devices, many applications require a flexible and scalable software-defined solution. The deblocking filter in H.264 encoder/decoder poses difficult implementation challenges because of heavy data dependencies and the conditional nature of the computations. Deblocking filter implementations tend to be fixed and difficult to reconfigure for different needs. The ability to scale up for higher quality requirements such as 10-bit pixel depth or a 4:2:2 chroma format often reduces the throughput of a parallel architecture designed for lower feature set. A scalable architecture for deblocking filtering, created with a massively parallel processor based solution, means that the same encoder or decoder will be deployed in a variety of applications, at different video resolutions, for different power requirements, and at higher bit-depths and better color sub sampling patterns like YUV, 4:2:2, or 4:4:4 formats. Low power, software-defined encoders/decoders may be implemented using a massively parallel processor array, like that found in HyperX technology, with 100 or more cores and distributed memory. The large number of processor elements allows the silicon device to operate more efficiently than conventional DSP or CPU technology. This software programing model for massively parallel processors offers a flexible implementation and a power efficiency close to that of ASIC solutions. This work describes a scalable parallel architecture for an H.264 compliant deblocking filter for multi core platforms such as HyperX technology. Parallel techniques such as parallel processing of independent macroblocks, sub blocks, and pixel row level are examined in this work. The deblocking architecture consists of a basic cell called deblocking filter unit (DFU) and dependent data buffer manager (DFM). The DFU can be used in several instances, catering to different performance needs the DFM serves the data required for the different number of DFUs, and also manages all the neighboring data required for future data processing of DFUs. This approach achieves the scalability, flexibility, and performance excellence required in deblocking filters.

Parallel Force Assay for Protein-Protein Interactions

PubMed Central

Aschenbrenner, Daniela; Pippig, Diana A.; Klamecka, Kamila; Limmer, Katja; Leonhardt, Heinrich; Gaub, Hermann E.

2014-01-01

Quantitative proteome research is greatly promoted by high-resolution parallel format assays. A characterization of protein complexes based on binding forces offers an unparalleled dynamic range and allows for the effective discrimination of non-specific interactions. Here we present a DNA-based Molecular Force Assay to quantify protein-protein interactions, namely the bond between different variants of GFP and GFP-binding nanobodies. We present different strategies to adjust the maximum sensitivity window of the assay by influencing the binding strength of the DNA reference duplexes. The binding of the nanobody Enhancer to the different GFP constructs is compared at high sensitivity of the assay. Whereas the binding strength to wild type and enhanced GFP are equal within experimental error, stronger binding to superfolder GFP is observed. This difference in binding strength is attributed to alterations in the amino acids that form contacts according to the crystal structure of the initial wild type GFP-Enhancer complex. Moreover, we outline the potential for large-scale parallelization of the assay. PMID:25546146

Parallel force assay for protein-protein interactions.

PubMed

Aschenbrenner, Daniela; Pippig, Diana A; Klamecka, Kamila; Limmer, Katja; Leonhardt, Heinrich; Gaub, Hermann E

2014-01-01

Quantitative proteome research is greatly promoted by high-resolution parallel format assays. A characterization of protein complexes based on binding forces offers an unparalleled dynamic range and allows for the effective discrimination of non-specific interactions. Here we present a DNA-based Molecular Force Assay to quantify protein-protein interactions, namely the bond between different variants of GFP and GFP-binding nanobodies. We present different strategies to adjust the maximum sensitivity window of the assay by influencing the binding strength of the DNA reference duplexes. The binding of the nanobody Enhancer to the different GFP constructs is compared at high sensitivity of the assay. Whereas the binding strength to wild type and enhanced GFP are equal within experimental error, stronger binding to superfolder GFP is observed. This difference in binding strength is attributed to alterations in the amino acids that form contacts according to the crystal structure of the initial wild type GFP-Enhancer complex. Moreover, we outline the potential for large-scale parallelization of the assay.

Applications of Emerging Parallel Optical Link Technology to High Energy Physics Experiments

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

Chramowicz, J.; Kwan, S.; Prosser, A.

2011-09-01

Modern particle detectors depend upon optical fiber links to deliver event data to upstream trigger and data processing systems. Future detector systems can benefit from the development of dense arrangements of high speed optical links emerging from the telecommunications and storage area network market segments. These links support data transfers in each direction at rates up to 120 Gbps in packages that minimize or even eliminate edge connector requirements. Emerging products include a class of devices known as optical engines which permit assembly of the optical transceivers in close proximity to the electrical interfaces of ASICs and FPGAs which handlemore » the data in parallel electrical format. Such assemblies will reduce required printed circuit board area and minimize electromagnetic interference and susceptibility. We will present test results of some of these parallel components and report on the development of pluggable FPGA Mezzanine Cards equipped with optical engines to provide to collaborators on the Versatile Link Common Project for the HI-LHC at CERN.« less

Generation of Alfvenic Double Layers, Formation of Auroral Arcs, and Their Impact on Energy and Momentum Transfer in M-I Coupling System

NASA Astrophysics Data System (ADS)

Song, Y.; Lysak, R. L.

2017-12-01

Parallel electrostatic electric fields provide a powerful mechanism to accelerate auroral particles to high energy in the auroral acceleration region (AAR), creating both quasi-static and Alfvenic discrete aurorae. The total field-aligned current can be written as J||total=J||+J||D, where the displacement current is denoted as J||D=(1/4π)(∂E||/∂t), which describes the E||-generation (Song and Lysak, 2006). The generation of the total field-aligned current is related to spatial gradients of the parallel vorticity caused by the axial torque acting on field-aligned flux tubes in M-I coupling system. It should be noticed that parallel electric fields are not produced by the field-aligned current. In fact, the E||-generation is caused by Alfvenic interaction in the M-I coupling system, and is favored by a low plasma density and the enhanced localized azimuthal magnetic flux. We suggest that the nonlinear interaction of incident and reflected Alfven wave packets in the AAR can create reactive stress concentration, and therefore can generate the parallel electrostatic electric fields together with a seed low density cavity. The generated electric fields will quickly deepen the seed low density cavity, which can effectively create even stronger electrostatic electric fields. The electrostatic electric fields nested in a low density cavity and surrounded by enhanced azimuthal magnetic flux constitute Alfvenic electromagnetic plasma structures, such as Alfvenic Double Layers (DLs). The Poynting flux carried by Alfven waves can continuously supply energy from the generator region to the auroral acceleration region, supporting and sustaining Alfvenic DLs with long-lasting electrostatic electric fields which accelerate auroral particles to high energy. The generation of parallel electric fields and the formation of auroral arcs can redistribute perpendicular mechanical and magnetic stresses in auroral flux tubes, decoupling the magnetosphere from ionosphere drag locally. This may enhance the magnetotail earthward shear flows and rapidly buildup stronger parallel electric fields in the auroral acceleration region, leading to a sudden and violent tail energy release, if there is accumulated free magnetic energy in the tail.

Dust Dynamics in Protoplanetary Disks: Parallel Computing with PVM

NASA Astrophysics Data System (ADS)

de La Fuente Marcos, Carlos; Barge, Pierre; de La Fuente Marcos, Raúl

2002-03-01

We describe a parallel version of our high-order-accuracy particle-mesh code for the simulation of collisionless protoplanetary disks. We use this code to carry out a massively parallel, two-dimensional, time-dependent, numerical simulation, which includes dust particles, to study the potential role of large-scale, gaseous vortices in protoplanetary disks. This noncollisional problem is easy to parallelize on message-passing multicomputer architectures. We performed the simulations on a cache-coherent nonuniform memory access Origin 2000 machine, using both the parallel virtual machine (PVM) and message-passing interface (MPI) message-passing libraries. Our performance analysis suggests that, for our problem, PVM is about 25% faster than MPI. Using PVM and MPI made it possible to reduce CPU time and increase code performance. This allows for simulations with a large number of particles (N ~ 105-106) in reasonable CPU times. The performances of our implementation of the pa! rallel code on an Origin 2000 supercomputer are presented and discussed. They exhibit very good speedup behavior and low load unbalancing. Our results confirm that giant gaseous vortices can play a dominant role in giant planet formation.

Unique parallel radiations of high-mountainous species of the genus Sedum (Crassulaceae) on the continental island of Taiwan.

PubMed

Ito, Takuro; Yu, Chih-Chieh; Nakamura, Koh; Chung, Kuo-Fang; Yang, Qin-Er; Fu, Cheng-Xin; Qi, Zhe-Chen; Kokubugata, Goro

2017-08-01

We explored the temporal and spatial diversification of the plant genus Sedum L. (Crassulaceae) in Taiwan based on molecular analysis of nrITS and cpDNA sequences from East Asian Sedum members. Our phylogenetic and ancestral area reconstruction analysis showed that Taiwanese Sedum comprised two lineages that independently migrated from Japan and Eastern China. Furthermore, the genetic distances among species in these two clades were smaller than those of other East Asian Sedum clades, and the Taiwanese members of each clade occupy extremely varied habitats with similar niches in high-mountain regions. These data indicate that species diversification occurred in parallel in the two Taiwanese Sedum lineages, and that these parallel radiations could have occurred within the small continental island of Taiwan. Moreover, the estimated time of divergence for Taiwanese Sedum indicates that the two radiations might have been correlated to the formation of mountains in Taiwan during the early Pleistocene. We suggest that these parallel radiations may be attributable to the geographical dynamics of Taiwan and specific biological features of Sedum that allow them to adapt to new ecological niches. Copyright © 2017 Elsevier Inc. All rights reserved.

The microstructure and formation of duplex and black plessite in iron meteorites

NASA Technical Reports Server (NTRS)

Zhang, J.; Williams, D. B.; Goldstein, J. I.

1993-01-01

Two of the most common plessite structures, duplex and black plessite, in the taenite region of the Windmanstatten pattern of two iron meteorites (Grant and Carlton) are characterized using high-resolution electron microscopy and microanalysis techniques. Two types of gamma precipitates, found in the duplex plessite and black plessite regions, respectively, are identified, and their morphologies are described. The formation of the plessite structure is discussed using the information obtained in this study and results of a parallel investigation of decomposed martensitic Fe-Ni laboratory alloys.

Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein.

PubMed

Zou, Yu; Sun, Yunxiang; Zhu, Yuzhen; Ma, Buyong; Nussinov, Ruth; Zhang, Qingwen

2016-03-16

The aggregation of the copper-zinc superoxide dismutase (SOD1) protein is linked to familial amyotrophic lateral sclerosis, a progressive neurodegenerative disease. A recent experimental study has shown that the (147)GVIGIAQ(153) SOD1 C-terminal segment not only forms amyloid fibrils in isolation but also accelerates the aggregation of full-length SOD1, while substitution of isoleucine at site 149 by proline blocks its fibril formation. Amyloid formation is a nucleation-polymerization process. In this study, we investigated the oligomerization and the nucleus structure of this heptapeptide. By performing extensive replica-exchange molecular dynamics (REMD) simulations and conventional MD simulations, we found that the GVIGIAQ hexamers can adopt highly ordered bilayer β-sheets and β-barrels. In contrast, substitution of I149 by proline significantly reduces the β-sheet probability and results in the disappearance of bilayer β-sheet structures and the increase of disordered hexamers. We identified mixed parallel-antiparallel bilayer β-sheets in both REMD and conventional MD simulations and provided the conformational transition from the experimentally observed parallel bilayer sheets to the mixed parallel-antiparallel bilayer β-sheets. Our simulations suggest that the critical nucleus consists of six peptide chains and two additional peptide chains strongly stabilize this critical nucleus. The stabilized octamer is able to recruit additional random peptides into the β-sheet. Therefore, our simulations provide insights into the critical nucleus formation and the smallest stable nucleus of the (147)GVIGIAQ(153) peptide.

A global database with parallel measurements to study non-climatic changes

NASA Astrophysics Data System (ADS)

Venema, Victor; Auchmann, Renate; Aguilar, Enric

2015-04-01

n this work we introduce the rationale behind the ongoing compilation of a parallel measurements database, under the umbrella of the International Surface Temperatures Initiative (ISTI) and with the support of the World Meteorological Organization. We intend this database to become instrumental for a better understanding of inhomogeneities affecting the evaluation of long term changes in daily climate data. Long instrumental climate records are usually affected by non-climatic changes, due to, e.g., relocations and changes in instrumentation, instrument height or data collection and manipulation procedures. These so-called inhomogeneities distort the climate signal and can hamper the assessment of trends and variability. Thus to study climatic changes we need to accurately distinguish non-climatic and climatic signals. .The most direct way to study the influence of non-climatic changes on the distribution and to understand the reasons for these biases is the analysis of parallel measurements representing the old and new situation (in terms of e.g. instruments, location). According to the limited number of available studies and our understanding of the causes of inhomogeneity, we expect that they will have a strong impact on the tails of the distribution of temperatures and most likely of other climate elements. Our abilities to statistically homogenize daily data will be increased by systematically studying different causes of inhomogeneity replicated through parallel measurements. Current studies of non-climatic changes using parallel data are limited to local and regional case studies. However, the effect of specific transitions depends on the local climate and the most interesting climatic questions are about the systematic large-scale biases produced by transitions that occurred in many regions. Important potentially biasing transitions are the adoption of Stevenson screens, efforts to reduce undercatchment of precipitation or the move to automatic weather stations. Thus a large global parallel dataset is highly desirable as it allows for the study of systematic biases in the global record. In the ISTI Parallel Observations Science Team (POST), we will gather parallel data in their native format (to avoid undetectable conversion errors we will convert it to a standard format ourselves). We are interested in data from all climate variables at all time scales; from annual to sub-daily. High-resolution data is important for understanding the physical causes for the differences between the parallel measurements. For the same reason, we are also interested in other climate variables measured at the same station. For example, in case of parallel temperature measurements, the influencing factors are expected to be insolation, wind and clouds cover; in case of parallel precipitation measurements, wind and temperature are potentially important. Metadata that describe the parallel measurements is as important as the data itself and will be collected as well. For example, the types of the instruments, their siting, height, maintenance, etc. Because they are widely used to study moderate extremes, we will compute the indices of the Expert Team on Climate Change Detection and Indices (ETCCDI). In case the daily data cannot be shared, we would appreciate these indices from parallel measurements. For more information: http://tinyurl.com/ISTI-Parallel

Bandwidth scalable, coherent transmitter based on the parallel synthesis of multiple spectral slices using optical arbitrary waveform generation.

PubMed

Geisler, David J; Fontaine, Nicolas K; Scott, Ryan P; He, Tingting; Paraschis, Loukas; Gerstel, Ori; Heritage, Jonathan P; Yoo, S J B

2011-04-25

We demonstrate an optical transmitter based on dynamic optical arbitrary waveform generation (OAWG) which is capable of creating high-bandwidth (THz) data waveforms in any modulation format using the parallel synthesis of multiple coherent spectral slices. As an initial demonstration, the transmitter uses only 5.5 GHz of electrical bandwidth and two 10-GHz-wide spectral slices to create 100-ns duration, 20-GHz optical waveforms in various modulation formats including differential phase-shift keying (DPSK), quaternary phase-shift keying (QPSK), and eight phase-shift keying (8PSK) with only changes in software. The experimentally generated waveforms showed clear eye openings and separated constellation points when measured using a real-time digital coherent receiver. Bit-error-rate (BER) performance analysis resulted in a BER < 9.8 × 10(-6) for DPSK and QPSK waveforms. Additionally, we experimentally demonstrate three-slice, 4-ns long waveforms that highlight the bandwidth scalable nature of the optical transmitter. The various generated waveforms show that the key transmitter properties (i.e., packet length, modulation format, data rate, and modulation filter shape) are software definable, and that the optical transmitter is capable of acting as a flexible bandwidth transmitter.

Reconfigurable microfluidic hanging drop network for multi-tissue interaction and analysis.

PubMed

Frey, Olivier; Misun, Patrick M; Fluri, David A; Hengstler, Jan G; Hierlemann, Andreas

2014-06-30

Integration of multiple three-dimensional microtissues into microfluidic networks enables new insights in how different organs or tissues of an organism interact. Here, we present a platform that extends the hanging-drop technology, used for multi-cellular spheroid formation, to multifunctional complex microfluidic networks. Engineered as completely open, 'hanging' microfluidic system at the bottom of a substrate, the platform features high flexibility in microtissue arrangements and interconnections, while fabrication is simple and operation robust. Multiple spheroids of different cell types are formed in parallel on the same platform; the different tissues are then connected in physiological order for multi-tissue experiments through reconfiguration of the fluidic network. Liquid flow is precisely controlled through the hanging drops, which enable nutrient supply, substance dosage and inter-organ metabolic communication. The possibility to perform parallelized microtissue formation on the same chip that is subsequently used for complex multi-tissue experiments renders the developed platform a promising technology for 'body-on-a-chip'-related research.

High-performance parallel interface to synchronous optical network gateway

DOEpatents

St. John, Wallace B.; DuBois, David H.

1996-01-01

A system of sending and receiving gateways interconnects high speed data interfaces, e.g., HIPPI interfaces, through fiber optic links, e.g., a SONET network. An electronic stripe distributor distributes bytes of data from a first interface at the sending gateway onto parallel fiber optics of the fiber optic link to form transmitted data. An electronic stripe collector receives the transmitted data on the parallel fiber optics and reforms the data into a format effective for input to a second interface at the receiving gateway. Preferably, an error correcting syndrome is constructed at the sending gateway and sent with a data frame so that transmission errors can be detected and corrected in a real-time basis. Since the high speed data interface operates faster than any of the fiber optic links the transmission rate must be adapted to match the available number of fiber optic links so the sending and receiving gateways monitor the availability of fiber links and adjust the data throughput accordingly. In another aspect, the receiving gateway must have sufficient available buffer capacity to accept an incoming data frame. A credit-based flow control system provides for continuously updating the sending gateway on the available buffer capacity at the receiving gateway.

Novel high-fidelity realistic explosion damage simulation for urban environments

NASA Astrophysics Data System (ADS)

Liu, Xiaoqing; Yadegar, Jacob; Zhu, Youding; Raju, Chaitanya; Bhagavathula, Jaya

2010-04-01

Realistic building damage simulation has a significant impact in modern modeling and simulation systems especially in diverse panoply of military and civil applications where these simulation systems are widely used for personnel training, critical mission planning, disaster management, etc. Realistic building damage simulation should incorporate accurate physics-based explosion models, rubble generation, rubble flyout, and interactions between flying rubble and their surrounding entities. However, none of the existing building damage simulation systems sufficiently faithfully realize the criteria of realism required for effective military applications. In this paper, we present a novel physics-based high-fidelity and runtime efficient explosion simulation system to realistically simulate destruction to buildings. In the proposed system, a family of novel blast models is applied to accurately and realistically simulate explosions based on static and/or dynamic detonation conditions. The system also takes account of rubble pile formation and applies a generic and scalable multi-component based object representation to describe scene entities and highly scalable agent-subsumption architecture and scheduler to schedule clusters of sequential and parallel events. The proposed system utilizes a highly efficient and scalable tetrahedral decomposition approach to realistically simulate rubble formation. Experimental results demonstrate that the proposed system has the capability to realistically simulate rubble generation, rubble flyout and their primary and secondary impacts on surrounding objects including buildings, constructions, vehicles and pedestrians in clusters of sequential and parallel damage events.

The emergence of asymmetric normal fault systems under symmetric boundary conditions

NASA Astrophysics Data System (ADS)

Schöpfer, Martin P. J.; Childs, Conrad; Manzocchi, Tom; Walsh, John J.; Nicol, Andrew; Grasemann, Bernhard

2017-11-01

Many normal fault systems and, on a smaller scale, fracture boudinage often exhibit asymmetry with one fault dip direction dominating. It is a common belief that the formation of domino and shear band boudinage with a monoclinic symmetry requires a component of layer parallel shearing. Moreover, domains of parallel faults are frequently used to infer the presence of a décollement. Using Distinct Element Method (DEM) modelling we show, that asymmetric fault systems can emerge under symmetric boundary conditions. A statistical analysis of DEM models suggests that the fault dip directions and system polarities can be explained using a random process if the strength contrast between the brittle layer and the surrounding material is high. The models indicate that domino and shear band boudinage are unreliable shear-sense indicators. Moreover, the presence of a décollement should not be inferred on the basis of a domain of parallel faults alone.

Studying Electromagnetic Beam Instabilities in Laser Plasmas for Alfvénic Parallel Shock Formation

NASA Astrophysics Data System (ADS)

Dorst, R. S.; Heuer, P. V.; Weidl, M. S.; Schaeffer, D. B.; Constantin, C. G.; Vincena, S.; Tripathi, S.; Gekelman, W.; Winske, D.; Niemann, C.

2017-10-01

We present measurements of the collisionless interaction between an exploding laser-produced plasma (LPP) and a large, magnetized ambient plasma. The LPP is created by focusing a high energy laser on a target embedded in the ambient Large Plasma Device (LAPD) plasma at the University of California, Los Angeles. The resulting super-Alfvénic (MA = 5) ablated material moves parallel to the background magnetic field (300 G) through 12m (80 δ i) of the LAPD, interacting with the ambient Helium plasma (ni = 9 ×1012 cm-3) through electromagnetic beam instabilities. The debris is characterized by Langmuir probes and a time-resolved fluorescence monochromator. Waves in the magnetic field produced by the instabilities are diagnosed by an array of 3-axis `bdot' magnetic field probes. Measurements are compared to hybrid simulations of both the experiment and of parallel shocks.

Line-Focused Optical Excitation of Parallel Acoustic Focused Sample Streams for High Volumetric and Analytical Rate Flow Cytometry.

PubMed

Kalb, Daniel M; Fencl, Frank A; Woods, Travis A; Swanson, August; Maestas, Gian C; Juárez, Jaime J; Edwards, Bruce S; Shreve, Andrew P; Graves, Steven W

2017-09-19

Flow cytometry provides highly sensitive multiparameter analysis of cells and particles but has been largely limited to the use of a single focused sample stream. This limits the analytical rate to ∼50K particles/s and the volumetric rate to ∼250 μL/min. Despite the analytical prowess of flow cytometry, there are applications where these rates are insufficient, such as rare cell analysis in high cellular backgrounds (e.g., circulating tumor cells and fetal cells in maternal blood), detection of cells/particles in large dilute samples (e.g., water quality, urine analysis), or high-throughput screening applications. Here we report a highly parallel acoustic flow cytometer that uses an acoustic standing wave to focus particles into 16 parallel analysis points across a 2.3 mm wide optical flow cell. A line-focused laser and wide-field collection optics are used to excite and collect the fluorescence emission of these parallel streams onto a high-speed camera for analysis. With this instrument format and fluorescent microsphere standards, we obtain analysis rates of 100K/s and flow rates of 10 mL/min, while maintaining optical performance comparable to that of a commercial flow cytometer. The results with our initial prototype instrument demonstrate that the integration of key parallelizable components, including the line-focused laser, particle focusing using multinode acoustic standing waves, and a spatially arrayed detector, can increase analytical and volumetric throughputs by orders of magnitude in a compact, simple, and cost-effective platform. Such instruments will be of great value to applications in need of high-throughput yet sensitive flow cytometry analysis.

A direct-execution parallel architecture for the Advanced Continuous Simulation Language (ACSL)

NASA Technical Reports Server (NTRS)

Carroll, Chester C.; Owen, Jeffrey E.

1988-01-01

A direct-execution parallel architecture for the Advanced Continuous Simulation Language (ACSL) is presented which overcomes the traditional disadvantages of simulations executed on a digital computer. The incorporation of parallel processing allows the mapping of simulations into a digital computer to be done in the same inherently parallel manner as they are currently mapped onto an analog computer. The direct-execution format maximizes the efficiency of the executed code since the need for a high level language compiler is eliminated. Resolution is greatly increased over that which is available with an analog computer without the sacrifice in execution speed normally expected with digitial computer simulations. Although this report covers all aspects of the new architecture, key emphasis is placed on the processing element configuration and the microprogramming of the ACLS constructs. The execution times for all ACLS constructs are computed using a model of a processing element based on the AMD 29000 CPU and the AMD 29027 FPU. The increase in execution speed provided by parallel processing is exemplified by comparing the derived execution times of two ACSL programs with the execution times for the same programs executed on a similar sequential architecture.

Selective recognition of parallel and anti-parallel thrombin-binding aptamer G-quadruplexes by different fluorescent dyes

PubMed Central

Zhao, Dan; Dong, Xiongwei; Jiang, Nan; Zhang, Dan; Liu, Changlin

2014-01-01

G-quadruplexes (G4) have been found increasing potential in applications, such as molecular therapeutics, diagnostics and sensing. Both Thioflavin T (ThT) and N-Methyl mesoporphyrin IX (NMM) become fluorescent in the presence of most G4, but thrombin-binding aptamer (TBA) has been reported as the only exception of the known G4-forming oligonucleotides when ThT is used as a high-throughput assay to identify G4 formation. Here, we investigate the interactions between ThT/NMM and TBA through fluorescence spectroscopy, circular dichroism and molecular docking simulation experiments in the absence or presence of cations. The results display that a large ThT fluorescence enhancement can be observed only when ThT bind to the parallel TBA quadruplex, which is induced to form by ThT in the absence of cations. On the other hand, great promotion in NMM fluorescence can be obtained only in the presence of anti-parallel TBA quadruplex, which is induced to fold by K+ or thrombin. The highly selective recognition of TBA quadruplex with different topologies by the two probes may be useful to investigate the interactions between conformation-specific G4 and the associated proteins, and could also be applied in label-free fluorescent sensing of other biomolecules. PMID:25245945

Phototropic bending of non-elongating and radially growing woody stems results from asymmetrical xylem formation.

PubMed

Matsuzaki, Jun; Masumori, Masaya; Tange, Takeshi

2007-05-01

Active phototropic bending of non-elongating and radially growing portion of stems (woody stems) has not been previously documented, whereas negative gravitropic bending is well known. We found phototropic bending in woody stems and searched for the underlying mechanism. We inclined 1-year-old Quercus crispula Blume seedlings and unilaterally illuminated them from a horizontal direction perpendicular to ('normal' illumination) or parallel to ('parallel' illumination) the inclination azimuth. With normal illumination, active phototropic bending and xylem formation could be evaluated separately from the negative gravitropic response and vertical deflection resulting from the weight of the seedlings. One-year-old stems with normal illumination bent significantly, with asymmetrical xylem formation towards the illuminated upper surface and side of the stem, whereas those with parallel illumination showed non-significant lateral bending, with asymmetrical xylem formation only on the upper side. A mechanical model was built on the assumption that a bending moment resulted from the asymmetrical xylem formation during phototropic bending of the woody stems. The model fitted the relationship between the observed spatial distributions of the xylem and the observed lateral bending, and thus supported the hypothesis that phototropic bending of woody stems results from asymmetrical xylem formation, as such occurs during gravitropism.

Studies on the Simultaneous Formation of Aroma-Active and Toxicologically Relevant Vinyl Aromatics from Free Phenolic Acids during Wheat Beer Brewing.

PubMed

Langos, Daniel; Granvogl, Michael

2016-03-23

During the brewing process of wheat beer, the desired aroma-active vinyl aromatics 2-methoxy-4-vinylphenol and 4-vinylphenol as well as the undesired and toxicologically relevant styrene are formed from their respective precursors, free ferulic acid, p-coumaric acid, and cinnamic acid, deriving from the malts. Analysis of eight commercial wheat beers revealed high concentrations of 2-methoxy-4-vinylphenol and 4-vinylphenol always in parallel with high concentrations of styrene or low concentrations of the odorants in parallel with low styrene concentrations, suggesting a similar pathway. To better understand the formation of these vinyl aromatics, each process step of wheat beer brewing and the use of different strains of Saccharomyces cerevisiae were evaluated. During wort boiling, only a moderate decarboxylation of free phenolic acids and formation of desired and undesired vinyl aromatics were monitored due to the thermal treatment. In contrast, this reaction mainly occurred enzymatically catalyzed during fermentation with S. cerevisiae strain W68 with normal Pof(+) activity (phenolic off-flavor) resulting in a wheat beer eliciting the typical aroma requested by consumers due to high concentrations of 2-methoxy-4-vinylphenol (1790 μg/L) and 4-vinylphenol (937 μg/L). Unfortunately, also a high concentration of undesired styrene (28.3 μg/L) was observed. Using a special S. cerevisiae strain without Pof(+) activity resulted in a significant styrene reduction (

Gravitational Waves from Binary Mergers of Subsolar Mass Dark Black Holes

NASA Astrophysics Data System (ADS)

Shandera, Sarah; Jeong, Donghui; Gebhardt, Henry S. Grasshorn

2018-06-01

We explore the possible spectrum of binary mergers of subsolar mass black holes formed out of dark matter particles interacting via a dark electromagnetism. We estimate the properties of these dark black holes by assuming that their formation process is parallel to Population-III star formation, except that dark molecular cooling can yield a smaller opacity limit. We estimate the binary coalescence rates for the Advanced LIGO and Einstein telescope, and find that scenarios compatible with all current constraints could produce dark black holes at rates high enough for detection by Advanced LIGO.

Spontaneous formation of linearly arranged microcraters on sol-gel-derived silica-poly(vinylpyrrolidone) hybrid films induced by Bénard-Marangoni convection.

PubMed

Uchiyama, Hiroaki; Mantani, Yuto; Kozuka, Hiromitsu

2012-07-10

Complex, sophisticated surface patterns on micrometer and nanometer scales are obtained when solvent evaporates from solutions containing nonvolatile solutes dropped on a solid substrate. Such evaporation-driven pattern formation has been utilized as a fabrication process of highly ordered patterns in thin films. Here, we suggested the spontaneous pattern formation induced by Bénard-Marangoni convection triggered by solvent evaporation as a novel patterning process of sol-gel-derived organic-inorganic hybrid films. Microcraters of 1.0-1.5 μm in height and of 100-200 μm in width were spontaneously formed on the surface of silica-poly(vinylpyrrolidone) hybrid films prepared via temperature-controlled dip-coating process, where the surface patterns were linearly arranged parallel to the substrate withdrawal direction. Such highly ordered micropatterns were achieved by Bénard-Marangoni convection activated at high temperatures and the unidirectional flow of the coating solution on the substrate during dip-coating.

Transformation of shock-compressed graphite to hexagonal diamond in nanoseconds

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

Turneaure, Stefan J.; Sharma, Surinder M.; Volz, Travis J.

2017-10-01

The graphite-to-diamond transformation under shock compression has been of broad scientific interest since 1961. The formation of hexagonal diamond (HD) is of particular interest because it is expected to be harder than cubic diamond and due to its use in terrestrial sciences as a marker at meteorite impact sites. However, the formation of diamond having a fully hexagonal structure continues to be questioned and remains unresolved. Using real-time (nanosecond), in situ x-ray diffraction measurements, we show unequivocally that highly oriented pyrolytic graphite, shock-compressed along the c axis to 50 GPa, transforms to highly oriented elastically strained HD with the (100)HDmore » plane parallel to the graphite basal plane.« less

Development of a parallel FE simulator for modeling the whole trans-scale failure process of rock from meso- to engineering-scale

NASA Astrophysics Data System (ADS)

Li, Gen; Tang, Chun-An; Liang, Zheng-Zhao

2017-01-01

Multi-scale high-resolution modeling of rock failure process is a powerful means in modern rock mechanics studies to reveal the complex failure mechanism and to evaluate engineering risks. However, multi-scale continuous modeling of rock, from deformation, damage to failure, has raised high requirements on the design, implementation scheme and computation capacity of the numerical software system. This study is aimed at developing the parallel finite element procedure, a parallel rock failure process analysis (RFPA) simulator that is capable of modeling the whole trans-scale failure process of rock. Based on the statistical meso-damage mechanical method, the RFPA simulator is able to construct heterogeneous rock models with multiple mechanical properties, deal with and represent the trans-scale propagation of cracks, in which the stress and strain fields are solved for the damage evolution analysis of representative volume element by the parallel finite element method (FEM) solver. This paper describes the theoretical basis of the approach and provides the details of the parallel implementation on a Windows - Linux interactive platform. A numerical model is built to test the parallel performance of FEM solver. Numerical simulations are then carried out on a laboratory-scale uniaxial compression test, and field-scale net fracture spacing and engineering-scale rock slope examples, respectively. The simulation results indicate that relatively high speedup and computation efficiency can be achieved by the parallel FEM solver with a reasonable boot process. In laboratory-scale simulation, the well-known physical phenomena, such as the macroscopic fracture pattern and stress-strain responses, can be reproduced. In field-scale simulation, the formation process of net fracture spacing from initiation, propagation to saturation can be revealed completely. In engineering-scale simulation, the whole progressive failure process of the rock slope can be well modeled. It is shown that the parallel FE simulator developed in this study is an efficient tool for modeling the whole trans-scale failure process of rock from meso- to engineering-scale.

Anomalous resistivity due to low-frequency turbulence. [of collisionless plasma with limited acceleration of high velocity runaway electrons

NASA Technical Reports Server (NTRS)

Rowland, H. L.; Palmadesso, P. J.

1983-01-01

Large amplitude ion cyclotron waves have been observed on auroral field lines. In the presence of an electric field parallel to the ambient magnetic field these waves prevent the acceleration of the bulk of the plasma electrons leading to the formation of a runaway tail. It is shown that low-frequency turbulence can also limit the acceleration of high-velocity runaway electrons via pitch angle scattering at the anomalous Doppler resonance.

Ground testing of bioconvective variables such as morphological characterizations and mechanisms which regulate macroscopic patterns

NASA Technical Reports Server (NTRS)

Johnson, Adriel D.

1992-01-01

Conditions simulating low- and high-gravity, reveal changes in macroscopic pattern formation in selected microorganisms, but whether these structures are gravity dependent is not clear. Two theories have been identified in the fluid dynamics community which support macroscopic pattern formation. The first one is gravity dependent (fluid density models) where small concentrated regions of organisms sink unstably, and the second is gravity independent (wave reinforcement theory) where organisms align their movements in concert, such that either their swimming strokes beat in phase or their vortices entrain neighbors to follow parallel paths. Studies have shown that macroscopic pattern formation is consistent with the fluid density models for protozoa and algae and wave reinforcement hypothesis for caprine spermatozoa.

Exploiting Anti-T-shaped Graphene Architecture to Form Low Tortuosity, Sieve-like Interfaces for High-Performance Anodes for Li-Based Cells

PubMed Central

2017-01-01

Graphitic carbon anodes have long been used in Li ion batteries due to their combination of attractive properties, such as low cost, high gravimetric energy density, and good rate capability. However, one significant challenge is controlling, and optimizing, the nature and formation of the solid electrolyte interphase (SEI). Here it is demonstrated that carbon coating via chemical vapor deposition (CVD) facilitates high electrochemical performance of carbon anodes. We examine and characterize the substrate/vertical graphene interface (multilayer graphene nanowalls coated onto carbon paper via plasma enhanced CVD), revealing that these low-tortuosity and high-selection graphene nanowalls act as fast Li ion transport channels. Moreover, we determine that the hitherto neglected parallel layer acts as a protective surface at the interface, enhancing the anode performance. In summary, these findings not only clarify the synergistic role of the parallel functional interface when combined with vertical graphene nanowalls but also have facilitated the development of design principles for future high rate, high performance batteries. PMID:29392179

Product selectivity control induced by using liquid-liquid parallel laminar flow in a microreactor.

PubMed

Amemiya, Fumihiro; Matsumoto, Hideyuki; Fuse, Keishi; Kashiwagi, Tsuneo; Kuroda, Chiaki; Fuchigami, Toshio; Atobe, Mahito

2011-06-07

Product selectivity control based on a liquid-liquid parallel laminar flow has been successfully demonstrated by using a microreactor. Our electrochemical microreactor system enables regioselective cross-coupling reaction of aldehyde with allylic chloride via chemoselective cathodic reduction of substrate by the combined use of suitable flow mode and corresponding cathode material. The formation of liquid-liquid parallel laminar flow in the microreactor was supported by the estimation of benzaldehyde diffusion coefficient and computational fluid dynamics simulation. The diffusion coefficient for benzaldehyde in Bu(4)NClO(4)-HMPA medium was determined to be 1.32 × 10(-7) cm(2) s(-1) by electrochemical measurements, and the flow simulation using this value revealed the formation of clear concentration gradient of benzaldehyde in the microreactor channel over a specific channel length. In addition, the necessity of the liquid-liquid parallel laminar flow was confirmed by flow mode experiments.

Memory-based frame synchronizer. [for digital communication systems

NASA Technical Reports Server (NTRS)

Stattel, R. J.; Niswander, J. K. (Inventor)

1981-01-01

A frame synchronizer for use in digital communications systems wherein data formats can be easily and dynamically changed is described. The use of memory array elements provide increased flexibility in format selection and sync word selection in addition to real time reconfiguration ability. The frame synchronizer comprises a serial-to-parallel converter which converts a serial input data stream to a constantly changing parallel data output. This parallel data output is supplied to programmable sync word recognizers each consisting of a multiplexer and a random access memory (RAM). The multiplexer is connected to both the parallel data output and an address bus which may be connected to a microprocessor or computer for purposes of programming the sync word recognizer. The RAM is used as an associative memory or decorder and is programmed to identify a specific sync word. Additional programmable RAMs are used as counter decoders to define word bit length, frame word length, and paragraph frame length.

Shallow marine event sedimentation in a volcanic arc-related setting: The Ordovician Suri Formation, Famatina range, northwest Argentina

USGS Publications Warehouse

Mangano, M.G.; Buatois, L.A.

1996-01-01

The Loma del Kilome??tro Member of the Lower Ordovician Suri Formation records arc-related shelf sedimentation in the Famatina Basin of northwest Argentina. Nine facies, grouped into three facies assemblages, are recognized. Facies assemblage 1 [massive and parallel-laminated mudstones (facies A) locally punctuated by normally graded or parallel-laminated silty sandstones (facies B] records deposition from suspension fall-out and episodic storm-induced turbidity currents in an outer shelf setting. Facies assemblage 2 [massive and parallel-laminated mudstones (facies A) interbedded with rippled-top very fine-grained sandstones (facies D)] is interpreted as the product of background sedimentation alternating with distal storm events in a middle shelf environment. Facies assemblage 3 [normally graded coarse to fine-grained sandstones (facies C); parallel-laminated to low angle cross-stratified sandstones (facies E); hummocky cross-stratified sandstones and siltstones (facies F); interstratified fine-grained sandstones and mudstones (facies G); massive muddy siltstones and sandstones (facies H); tuffaceous sandstones (facies I); and interbedded thin units of massive and parallel-laminated mudstones (facies A)] is thought to represent volcaniclastic mass flow and storm deposition coupled with subordinated suspension fall-out in an inner-shelf to lower-shoreface setting. The Loma del Kilo??metro Member records regressive-transgressive sedimentation in a storm- and mass flow-dominated high-gradient shelf. Volcano-tectonic activity was the important control on shelf morphology, while relative sea-level change influenced sedimentation. The lower part of the succession is attributed to mud blanketing during high stand and volcanic quiescence. Progradation of the inner shelf to lower shoreface facies assemblage in the middle part represents an abrupt basinward shoreline migration. An erosive-based, non-volcaniclastic, turbidite unit at the base of this package suggests a sea level fall. Pyroclastic detritus, andesites, and a non-volcanic terrain were eroded and their detritus was transported basinward and redeposited by sediment gravity flows during the low stand. The local coexistence of juvenile pyroclastic detritus and fossils suggests reworking of rare ash-falls. The upper part of the Loma del Kilo??metre Member records a transgression with no evidence of contemporaneous volcanism. Biostratinomic, paleoecologic, and ichnologic analyses support this paleoenvironmental interpretations and provide independent evidence for the dominance of episodic sedimentation in an arc-related shallow marine setting. Fossil concentrations were mainly formed by event processes, such as storms and volcaniclastic mass flows. High depositional rates inhibited formation of sediment-starved biogenic concentrations. Collectively, trace fossils belong to the Cruziana ichnofacies. Low diversity, scarcity, and presence of relatively simple forms indicate benthic activity under stressful conditions, most probably linked to high sedimentation rates. Contrasting sedimentary dynamics between 'normal shelves' and their volcaniclastic counterparts produce distinct and particular signatures in the stratigraphic record. Arc-related shelves are typified by event deposition with significant participation of sediment gravity flows, relatively high sedimentation rates, textural and mineralogical immaturity of sediments, scarcity and low diversity of trace fossils, and dominance of transported and reworked faunal assemblages genetically related to episodic processes.

The Relation between Reconnected Flux, the Parallel Electric Field, and the Reconnection Rate in a Three-Dimensional Kinetic Simulation of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Wendel, D. E.; Olson, D. K.; Hesse, M.; Karimabadi, H.; Daughton, W. S.

2013-12-01

We investigate the distribution of parallel electric fields and their relationship to the location and rate of magnetic reconnection of a large particle-in-cell simulation of 3D turbulent magnetic reconnection with open boundary conditions. The simulation's guide field geometry inhibits the formation of topological features such as separators and null points. Therefore, we derive the location of potential changes in magnetic connectivity by finding the field lines that experience a large relative change between their endpoints, i.e., the quasi-separatrix layer. We find a correspondence between the locus of changes in magnetic connectivity, or the quasi-separatrix layer, and the map of large gradients in the integrated parallel electric field (or quasi-potential). Furthermore, we compare the distribution of parallel electric fields along field lines with the reconnection rate. We find the reconnection rate is controlled by only the low-amplitude, zeroth and first-order trends in the parallel electric field, while the contribution from high amplitude parallel fluctuations, such as electron holes, is negligible. The results impact the determination of reconnection sites within models of 3D turbulent reconnection as well as the inference of reconnection rates from in situ spacecraft measurements. It is difficult through direct observation to isolate the locus of the reconnection parallel electric field amidst the large amplitude fluctuations. However, we demonstrate that a positive slope of the partial sum of the parallel electric field along the field line as a function of field line length indicates where reconnection is occurring along the field line.

Parallel design patterns for a low-power, software-defined compressed video encoder

NASA Astrophysics Data System (ADS)

Bruns, Michael W.; Hunt, Martin A.; Prasad, Durga; Gunupudi, Nageswara R.; Sonachalam, Sekar

2011-06-01

Video compression algorithms such as H.264 offer much potential for parallel processing that is not always exploited by the technology of a particular implementation. Consumer mobile encoding devices often achieve real-time performance and low power consumption through parallel processing in Application Specific Integrated Circuit (ASIC) technology, but many other applications require a software-defined encoder. High quality compression features needed for some applications such as 10-bit sample depth or 4:2:2 chroma format often go beyond the capability of a typical consumer electronics device. An application may also need to efficiently combine compression with other functions such as noise reduction, image stabilization, real time clocks, GPS data, mission/ESD/user data or software-defined radio in a low power, field upgradable implementation. Low power, software-defined encoders may be implemented using a massively parallel memory-network processor array with 100 or more cores and distributed memory. The large number of processor elements allow the silicon device to operate more efficiently than conventional DSP or CPU technology. A dataflow programming methodology may be used to express all of the encoding processes including motion compensation, transform and quantization, and entropy coding. This is a declarative programming model in which the parallelism of the compression algorithm is expressed as a hierarchical graph of tasks with message communication. Data parallel and task parallel design patterns are supported without the need for explicit global synchronization control. An example is described of an H.264 encoder developed for a commercially available, massively parallel memorynetwork processor device.

Ultra-stretchable conductors based on buckled super-aligned carbon nanotube films.

PubMed

Yu, Yang; Luo, Shu; Sun, Li; Wu, Yang; Jiang, Kaili; Li, Qunqing; Wang, Jiaping; Fan, Shoushan

2015-06-14

Ultra-stretchable conductors are fabricated by coating super-aligned carbon nanotube (SACNT) films on pre-strained polydimethylsiloxane (PDMS) substrates and forming buckled SACNT structures on PDMS after release of the pre-strain. The parallel SACNT/PDMS conductors demonstrate excellent stability with normalized resistance changes of only 4.1% under an applied strain as high as 200%. The SACNT/PDMS conductors prepared with cross-stacked SACNT films show even lower resistance variation. The parallel SACNT/PDMS conductors exhibit high durability with a resistance increase of less than 5% after 10,000 cycles at 150% strain. In situ microscopic observations demonstrate that the buckled SACNT structures are straightened during the stretching process with reversible morphology evolution and thus the continuous SACNT conductive network can be protected from fracture. Due to the excellent electrical and mechanical properties of SACNT films and the formation of the buckled structure, SACNT/PDMS films exhibit high stretchability and durability, possessing great potential for use as ultra-stretchable conductors for wearable electronics, sensors, and energy storage devices.

High-performance parallel interface to synchronous optical network gateway

DOEpatents

St. John, W.B.; DuBois, D.H.

1996-12-03

Disclosed is a system of sending and receiving gateways interconnects high speed data interfaces, e.g., HIPPI interfaces, through fiber optic links, e.g., a SONET network. An electronic stripe distributor distributes bytes of data from a first interface at the sending gateway onto parallel fiber optics of the fiber optic link to form transmitted data. An electronic stripe collector receives the transmitted data on the parallel fiber optics and reforms the data into a format effective for input to a second interface at the receiving gateway. Preferably, an error correcting syndrome is constructed at the sending gateway and sent with a data frame so that transmission errors can be detected and corrected in a real-time basis. Since the high speed data interface operates faster than any of the fiber optic links the transmission rate must be adapted to match the available number of fiber optic links so the sending and receiving gateways monitor the availability of fiber links and adjust the data throughput accordingly. In another aspect, the receiving gateway must have sufficient available buffer capacity to accept an incoming data frame. A credit-based flow control system provides for continuously updating the sending gateway on the available buffer capacity at the receiving gateway. 7 figs.

An iterative method for systems of nonlinear hyperbolic equations

NASA Technical Reports Server (NTRS)

Scroggs, Jeffrey S.

1989-01-01

An iterative algorithm for the efficient solution of systems of nonlinear hyperbolic equations is presented. Parallelism is evident at several levels. In the formation of the iteration, the equations are decoupled, thereby providing large grain parallelism. Parallelism may also be exploited within the solves for each equation. Convergence of the interation is established via a bounding function argument. Experimental results in two-dimensions are presented.

Parallel collisionless shocks forming in simulations of the LAPD experiment

NASA Astrophysics Data System (ADS)

Weidl, Martin S.; Jenko, Frank; Niemann, Chris; Winske, Dan

2016-10-01

Research on parallel collisionless shocks, most prominently occurring in the Earth's bow shock region, has so far been limited to satellite measurements and simulations. However, the formation of collisionless shocks depends on a wide range of parameters and scales, which can be accessed more easily in a laboratory experiment. Using a kJ-class laser, an ongoing experimental campaign at the Large Plasma Device (LAPD) at UCLA is expected to produce the first laboratory measurements of the formation of a parallel collisionless shock. We present hybrid kinetic/MHD simulations that show how beam instabilities in the background plasma can be driven by ablating carbon ions from a target, causing non-linear density oscillations which develop into a propagating shock front. The free-streaming carbon ions can excite both the resonant right-hand instability and the non-resonant firehose mode. We analyze their respective roles and discuss optimizing their growth rates to speed up the process of shock formation.

Scalable Molecular Dynamics with NAMD

PubMed Central

Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus

2008-01-01

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654

Charge order-superfluidity transition in a two-dimensional system of hard-core bosons and emerging domain structures

NASA Astrophysics Data System (ADS)

Moskvin, A. S.; Panov, Yu. D.; Rybakov, F. N.; Borisov, A. B.

2017-11-01

We have used high-performance parallel computations by NVIDIA graphics cards applying the method of nonlinear conjugate gradients and Monte Carlo method to observe directly the developing ground state configuration of a two-dimensional hard-core boson system with decrease in temperature, and its evolution with deviation from a half-filling. This has allowed us to explore unconventional features of a charge order—superfluidity phase transition, specifically, formation of an irregular domain structure, emergence of a filamentary superfluid structure that condenses within of the charge-ordered phase domain antiphase boundaries, and formation and evolution of various topological structures.

Adding the 'heart' to hanging drop networks for microphysiological multi-tissue experiments.

PubMed

Rismani Yazdi, Saeed; Shadmani, Amir; Bürgel, Sebastian C; Misun, Patrick M; Hierlemann, Andreas; Frey, Olivier

2015-11-07

Microfluidic hanging-drop networks enable culturing and analysis of 3D microtissue spheroids derived from different cell types under controlled perfusion and investigating inter-tissue communication in multi-tissue formats. In this paper we introduce a compact on-chip pumping approach for flow control in hanging-drop networks. The pump includes one pneumatic chamber located directly above one of the hanging drops and uses the surface tension at the liquid-air-interface for flow actuation. Control of the pneumatic protocol provides a wide range of unidirectional pulsatile and continuous flow profiles. With the proposed concept several independent hanging-drop networks can be operated in parallel with only one single pneumatic actuation line at high fidelity. Closed-loop medium circulation between different organ models for multi-tissue formats and multiple simultaneous assays in parallel are possible. Finally, we implemented a real-time feedback control-loop of the pump actuation based on the beating of a human iPS-derived cardiac microtissue cultured in the same system. This configuration allows for simulating physiological effects on the heart and their impact on flow circulation between the organ models on chip.

Design and evaluation of an architecture for a digital signal processor for instrumentation applications

NASA Astrophysics Data System (ADS)

Fellman, Ronald D.; Kaneshiro, Ronald T.; Konstantinides, Konstantinos

1990-03-01

The authors present the design and evaluation of an architecture for a monolithic, programmable, floating-point digital signal processor (DSP) for instrumentation applications. An investigation of the most commonly used algorithms in instrumentation led to a design that satisfies the requirements for high computational and I/O (input/output) throughput. In the arithmetic unit, a 16- x 16-bit multiplier and a 32-bit accumulator provide the capability for single-cycle multiply/accumulate operations, and three format adjusters automatically adjust the data format for increased accuracy and dynamic range. An on-chip I/O unit is capable of handling data block transfers through a direct memory access port and real-time data streams through a pair of parallel I/O ports. I/O operations and program execution are performed in parallel. In addition, the processor includes two data memories with independent addressing units, a microsequencer with instruction RAM, and multiplexers for internal data redirection. The authors also present the structure and implementation of a design environment suitable for the algorithmic, behavioral, and timing simulation of a complete DSP system. Various benchmarking results are reported.

Anisotropic Formation of Quantum Turbulence Generated by a Vibrating Wire in Superfluid {}4{He}

NASA Astrophysics Data System (ADS)

Yano, H.; Ogawa, K.; Chiba, Y.; Obara, K.; Ishikawa, O.

2017-06-01

To investigate the formation of quantum turbulence in superfluid {}4{He}, we have studied the emission of vortex rings with a ring size of larger than 38 μm in diameter from turbulence generated by a vibrating wire. The emission rate of vortex rings from a turbulent region remains low until the beginning of high-rate emissions, suggesting that some of the vortex lines produced by the wire combine to form a vortex tangle, until an equilibrium is established between the rate of vortex line combination with the tangle and dissociation. The formation times of equilibrium turbulence are proportional to ɛ ^{-1.2} and ɛ ^{-0.6} in the directions perpendicular and parallel to the vibrating direction of the generator, respectively, indicating the anisotropic formation of turbulence. Here, ɛ is the generation power of the turbulence. This power dependence may be associated with the characteristics of quantum turbulence with a constant energy flux.

Hydrophilic strips for preventing air bubble formation in a microfluidic chamber.

PubMed

Choi, Munseok; Na, Yang; Kim, Sung-Jin

2015-12-01

In a microfluidic chamber, unwanted formation of air bubbles is a critical problem. Here, we present a hydrophilic strip array that prevents air bubble formation in a microfluidic chamber. The array is located on the top surface of the chamber, which has a large variation in width, and consists of a repeated arrangement of super- and moderately hydrophilic strips. This repeated arrangement allows a flat meniscus (i.e. liquid front) to form when various solutions consisting of a single stream or two parallel streams with different hydrophilicities move through the chamber. The flat meniscus produced by the array completely prevents the formation of bubbles. Without the array in the chamber, the meniscus shape is highly convex, and bubbles frequently form in the chamber. This hydrophilic strip array will facilitate the use of a microfluidic chamber with a large variation in width for various microfluidic applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Novel Way To Practice Slope.

ERIC Educational Resources Information Center

Kennedy, Jane B.

1997-01-01

Presents examples of using a tic-tac-toe format to practice finding the slope and identifying parallel and perpendicular lines from various equation formats. Reports the successful use of this format as a review in both precalculus and calculus classes before students work with applications of analytic geometry. (JRH)

Gate tunable parallel double quantum dots in InAs double-nanowire devices

NASA Astrophysics Data System (ADS)

Baba, S.; Matsuo, S.; Kamata, H.; Deacon, R. S.; Oiwa, A.; Li, K.; Jeppesen, S.; Samuelson, L.; Xu, H. Q.; Tarucha, S.

2017-12-01

We report fabrication and characterization of InAs nanowire devices with two closely placed parallel nanowires. The fabrication process we develop includes selective deposition of the nanowires with micron scale alignment onto predefined finger bottom gates using a polymer transfer technique. By tuning the double nanowire with the finger bottom gates, we observed the formation of parallel double quantum dots with one quantum dot in each nanowire bound by the normal metal contact edges. We report the gate tunability of the charge states in individual dots as well as the inter-dot electrostatic coupling. In addition, we fabricate a device with separate normal metal contacts and a common superconducting contact to the two parallel wires and confirm the dot formation in each wire from comparison of the transport properties and a superconducting proximity gap feature for the respective wires. With the fabrication techniques established in this study, devices can be realized for more advanced experiments on Cooper-pair splitting, generation of Parafermions, and so on.

Human telomere sequence DNA in water-free and high-viscosity solvents: G-quadruplex folding governed by Kramers rate theory.

PubMed

Lannan, Ford M; Mamajanov, Irena; Hud, Nicholas V

2012-09-19

Structures formed by human telomere sequence (HTS) DNA are of interest due to the implication of telomeres in the aging process and cancer. We present studies of HTS DNA folding in an anhydrous, high viscosity deep eutectic solvent (DES) comprised of choline choride and urea. In this solvent, the HTS DNA forms a G-quadruplex with the parallel-stranded ("propeller") fold, consistent with observations that reduced water activity favors the parallel fold, whereas alternative folds are favored at high water activity. Surprisingly, adoption of the parallel structure by HTS DNA in the DES, after thermal denaturation and quick cooling to room temperature, requires several months, as opposed to less than 2 min in an aqueous solution. This extended folding time in the DES is, in part, due to HTS DNA becoming kinetically trapped in a folded state that is apparently not accessed in lower viscosity solvents. A comparison of times required for the G-quadruplex to convert from its aqueous-preferred folded state to its parallel fold also reveals a dependence on solvent viscosity that is consistent with Kramers rate theory, which predicts that diffusion-controlled transitions will slow proportionally with solvent friction. These results provide an enhanced view of a G-quadruplex folding funnel and highlight the necessity to consider solvent viscosity in studies of G-quadruplex formation in vitro and in vivo. Additionally, the solvents and analyses presented here should prove valuable for understanding the folding of many other nucleic acids and potentially have applications in DNA-based nanotechnology where time-dependent structures are desired.

PFLOTRAN: Reactive Flow & Transport Code for Use on Laptops to Leadership-Class Supercomputers

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

Hammond, Glenn E.; Lichtner, Peter C.; Lu, Chuan

PFLOTRAN, a next-generation reactive flow and transport code for modeling subsurface processes, has been designed from the ground up to run efficiently on machines ranging from leadership-class supercomputers to laptops. Based on an object-oriented design, the code is easily extensible to incorporate additional processes. It can interface seamlessly with Fortran 9X, C and C++ codes. Domain decomposition parallelism is employed, with the PETSc parallel framework used to manage parallel solvers, data structures and communication. Features of the code include a modular input file, implementation of high-performance I/O using parallel HDF5, ability to perform multiple realization simulations with multiple processors permore » realization in a seamless manner, and multiple modes for multiphase flow and multicomponent geochemical transport. Chemical reactions currently implemented in the code include homogeneous aqueous complexing reactions and heterogeneous mineral precipitation/dissolution, ion exchange, surface complexation and a multirate kinetic sorption model. PFLOTRAN has demonstrated petascale performance using 2{sup 17} processor cores with over 2 billion degrees of freedom. Accomplishments achieved to date include applications to the Hanford 300 Area and modeling CO{sub 2} sequestration in deep geologic formations.« less

Synthesis and Characterization of High Molecular Weight Peptide Polymers and Copolymers Containing L-Dopa Residues

DTIC Science & Technology

1988-07-01

decapeptide (GLUE-12) with blocked lysines with DPPA for 24 hours. A parallel reaction was carried out to polymerize E- aminocaproic acid with DPPA for...shear adhesive strength tests. OPPA has also been used to prepare block copolymers between GLUE polypeptides and poly(e-amino caproic acid ). Concurrent...amino acid residues towards intramolecular or intermolecular bond formation. Polypeptides with repeating amino acid sequences have also been produced

Template-directed atomically precise self-organization of perfectly ordered parallel cerium silicide nanowire arrays on Si(110)-16 × 2 surfaces.

PubMed

Hong, Ie-Hong; Liao, Yung-Cheng; Tsai, Yung-Feng

2013-11-05

The perfectly ordered parallel arrays of periodic Ce silicide nanowires can self-organize with atomic precision on single-domain Si(110)-16 × 2 surfaces. The growth evolution of self-ordered parallel Ce silicide nanowire arrays is investigated over a broad range of Ce coverages on single-domain Si(110)-16 × 2 surfaces by scanning tunneling microscopy (STM). Three different types of well-ordered parallel arrays, consisting of uniformly spaced and atomically identical Ce silicide nanowires, are self-organized through the heteroepitaxial growth of Ce silicides on a long-range grating-like 16 × 2 reconstruction at the deposition of various Ce coverages. Each atomically precise Ce silicide nanowire consists of a bundle of chains and rows with different atomic structures. The atomic-resolution dual-polarity STM images reveal that the interchain coupling leads to the formation of the registry-aligned chain bundles within individual Ce silicide nanowire. The nanowire width and the interchain coupling can be adjusted systematically by varying the Ce coverage on a Si(110) surface. This natural template-directed self-organization of perfectly regular parallel nanowire arrays allows for the precise control of the feature size and positions within ±0.2 nm over a large area. Thus, it is a promising route to produce parallel nanowire arrays in a straightforward, low-cost, high-throughput process.

Template-directed atomically precise self-organization of perfectly ordered parallel cerium silicide nanowire arrays on Si(110)-16 × 2 surfaces

PubMed Central

2013-01-01

The perfectly ordered parallel arrays of periodic Ce silicide nanowires can self-organize with atomic precision on single-domain Si(110)-16 × 2 surfaces. The growth evolution of self-ordered parallel Ce silicide nanowire arrays is investigated over a broad range of Ce coverages on single-domain Si(110)-16 × 2 surfaces by scanning tunneling microscopy (STM). Three different types of well-ordered parallel arrays, consisting of uniformly spaced and atomically identical Ce silicide nanowires, are self-organized through the heteroepitaxial growth of Ce silicides on a long-range grating-like 16 × 2 reconstruction at the deposition of various Ce coverages. Each atomically precise Ce silicide nanowire consists of a bundle of chains and rows with different atomic structures. The atomic-resolution dual-polarity STM images reveal that the interchain coupling leads to the formation of the registry-aligned chain bundles within individual Ce silicide nanowire. The nanowire width and the interchain coupling can be adjusted systematically by varying the Ce coverage on a Si(110) surface. This natural template-directed self-organization of perfectly regular parallel nanowire arrays allows for the precise control of the feature size and positions within ±0.2 nm over a large area. Thus, it is a promising route to produce parallel nanowire arrays in a straightforward, low-cost, high-throughput process. PMID:24188092

Deep-sea tsunami deposits in the Miocene Nishizaki Formation of Boso Peninsula, Central Japan

NASA Astrophysics Data System (ADS)

Lee, I. T.; Ogawa, Y.

2003-12-01

Many sets of deep-sea deposits considered to be formed by return flow of tsunami were found from the middle Miocene Nishizaki Formation of Boso Peninsula, Central Japan, which is located near the convergent plate boundary at present as well as in the past, and has been frequently attacked by tsunami. The characteristics of the tsunami deposits in the Nishizaki Formation are as follows. Each set consists of 10-20 beds with parallel laminations formed under upper plane regime composed of alternated pumiceous beds in white and black colors. The white bed comprises coarse sands and pebbles with thickness of 5-10 cm. In contrast, the black bed is made of silts with thickness less than 1 cm. Among the 10-20 beds, the grain size is coarsest in the middle part of the set in general. The uppermost bed of each set shows cross-lamination formed by lower plane regime, gradually changing into finer graded bed on top. Sometimes, the lower part of the parallel laminated bed is associated with an underlying debrite or turbidite bed. Each set of these parallel-laminated beds is lenticular in shape thinning to the east in consistent with the generally eastward paleocurrent of the cross-lamination at the top. Such sedimentary characteristics are different from any event deposits reported in deep-sea but similar to the deep-sea K/T boundary deposits in the Caribbean region. Statistically, tsunami waves occur totally 12-13 times. Among them the height of 5-6th wave is known to be strongest. Interval time of each return flow is known to be 30-40 minutes, enough to settle the finer clastics at each bed top. The parallel-laminated parts have common dish structure and never trace fossils, indicating rather rapid deposition for the whole parts of the set. Consequently, the sedimentary characteristics shown from the parallel-laminated beds of the Nishizaki Formation are attributed to the return flow of tsunami to the deep-sea. We considered that such deep-sea parallel-laminated deposits of pumiceous clastics occur just after a large earthquake which forms the debrite or turbidite at the lowermost part.

Chenier plain genesis explained by feedbacks between waves, mud, and sand

NASA Astrophysics Data System (ADS)

Nardin, William; Fagherazzi, Sergio

2017-04-01

Cheniers are sandy ridges parallel to the coast established by high energy waves. Here we discuss ontogeny of chenier plains through dimensional analysis and numerical results from the morphodynamic model Delft3D-SWAN. Our results show that wave energy and inner-shelf slope play an important role in the formation of chenier plains. In our numerical experiments, waves affect chenier plain development in three ways: by winnowing coarse sediment from the mudflat, by eroding mud and accumulating sand over the beach during extreme wave events. We further show that different sediment characteristics and wave climates can lead to three alternative coastal landscapes: strand plains, mudflats, or the more complex chenier plains. Low inner-shelf slopes are the most favorable for strand plain and chenier plain formation, while high slopes decrease the likelihood of mudflat development and preservation.

Chenier plain development: feedbacks between waves, mud and sand

NASA Astrophysics Data System (ADS)

Nardin, W.; Fagherazzi, S.

2015-12-01

Cheniers are sandy ridges parallel to the coast established by high energy waves. Here we discuss Chenier plains ontogeny through dimensional analysis and numerical results from the morphodynamic model Delft3D-SWAN. Our results show that wave energy and shelf slope play an important role in the formation of Chenier plains. In our numerical experiments waves affect Chenier plain development in three ways: by winnowing sediment from the mudflat, by eroding mud and accumulating sand over the beach during extreme wave events. We further show that different sediment characteristics and wave climates can lead to three alternative coastal landscapes: strand plains, mudflats, or the more complex Chenier plains. Low inner-shelf slopes are the most favorable for strand plain and Chenier plain formation, while high slopes decrease the likelihood of mudflat development and preservation.

ExoCross: Spectra from molecular line lists

NASA Astrophysics Data System (ADS)

Yurchenko, Sergei N.; Al-Refaie, Ahmed; Tennyson, Jonathan

2018-03-01

ExoCross generates spectra and thermodynamic properties from molecular line lists in ExoMol, HITRAN, or several other formats. The code is parallelized and also shows a high degree of vectorization; it works with line profiles such as Doppler, Lorentzian and Voigt and supports several broadening schemes. ExoCross is also capable of working with the recently proposed method of super-lines. It supports calculations of lifetimes, cooling functions, specific heats and other properties. ExoCross converts between different formats, such as HITRAN, ExoMol and Phoenix, and simulates non-LTE spectra using a simple two-temperature approach. Different electronic, vibronic or vibrational bands can be simulated separately using an efficient filtering scheme based on the quantum numbers.

Crenulation cleavage development by partitioning of deformation into zones of progressive shearing (combined shearing, shortening and volume loss) and progressive shortening (no volume loss): quantification of solution shortening and intermicrolithon-movement

NASA Astrophysics Data System (ADS)

Stewart, L. K.

1997-11-01

An analytical method for determining amounts of cleavage-normal dissolution and cleavage-parallel shear movement that occurred between adjacent microlithons during crenulation cleavage seam formation within a deformed slate is developed for the progressive bulk inhomogeneous shortening (PBIS) mechanism of crenulation cleavage formation. The method utilises structural information obtained from samples where a diverging bed and vein are offset by a crenulation cleavage seam. Several samples analysed using this method produced ratios of relative, cleavage-parallel movement of microlithons to the material thickness removed by dissolution typically in the range of 1.1-3.4:1. The mean amount of solution shortening attributed to the formation of the cleavage seams examined is 24%. The results indicate that a relationship may exist between the width of microlithons and the amount of cleavage-parallel intermicrolithon-movement. The method presented here has the potential to help determine whether crenulation cleavage seams formed by the progressive bulk inhomogeneous shortening mechanism or by that involving cleavage-normal pressure solution alone.

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

Otto, C., Thomas, G.A.; Peticolas, W.L.; Rippe, K.

Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5{prime}-d-((A){sub 10}TAATTTTAAATATTT)-3{prime} (D1) and 5{prime}-d((T){sub 10}ATTAAAATTTATAAA)-3{prime} (D2) in H{sub 2}O and D{sub 2}O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5{prime}-d(AAATATTTAAAATTA-(T){sub 10})-3{prime} (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly(d(A)){center dot}poly(d(T)) and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due tomore » changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent with formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogeneous sequence and high A,T content are observed at 843 and 1,092 cm{sup {minus}1} in the spectra of the parallel-stranded duplex.« less

Magnetosheath Filamentary Structures Formed by Ion Acceleration at the Quasi-Parallel Bow Shock

NASA Technical Reports Server (NTRS)

Omidi, N.; Sibeck, D.; Gutynska, O.; Trattner, K. J.

2014-01-01

Results from 2.5-D electromagnetic hybrid simulations show the formation of field-aligned, filamentary plasma structures in the magnetosheath. They begin at the quasi-parallel bow shock and extend far into the magnetosheath. These structures exhibit anticorrelated, spatial oscillations in plasma density and ion temperature. Closer to the bow shock, magnetic field variations associated with density and temperature oscillations may also be present. Magnetosheath filamentary structures (MFS) form primarily in the quasi-parallel sheath; however, they may extend to the quasi-perpendicular magnetosheath. They occur over a wide range of solar wind Alfvénic Mach numbers and interplanetary magnetic field directions. At lower Mach numbers with lower levels of magnetosheath turbulence, MFS remain highly coherent over large distances. At higher Mach numbers, magnetosheath turbulence decreases the level of coherence. Magnetosheath filamentary structures result from localized ion acceleration at the quasi-parallel bow shock and the injection of energetic ions into the magnetosheath. The localized nature of ion acceleration is tied to the generation of fast magnetosonic waves at and upstream of the quasi-parallel shock. The increased pressure in flux tubes containing the shock accelerated ions results in the depletion of the thermal plasma in these flux tubes and the enhancement of density in flux tubes void of energetic ions. This results in the observed anticorrelation between ion temperature and plasma density.

Parallel production and verification of protein products using a novel high-throughput screening method.

PubMed

Tegel, Hanna; Yderland, Louise; Boström, Tove; Eriksson, Cecilia; Ukkonen, Kaisa; Vasala, Antti; Neubauer, Peter; Ottosson, Jenny; Hober, Sophia

2011-08-01

Protein production and analysis in a parallel fashion is today applied in laboratories worldwide and there is a great need to improve the techniques and systems used for this purpose. In order to save time and money, a fast and reliable screening method for analysis of protein production and also verification of the protein product is desired. Here, a micro-scale protocol for the parallel production and screening of 96 proteins in plate format is described. Protein capture was achieved using immobilized metal affinity chromatography and the product was verified using matrix-assisted laser desorption ionization time-of-flight MS. In order to obtain sufficiently high cell densities and product yield in the small-volume cultivations, the EnBase® cultivation technology was applied, which enables cultivation in as small volumes as 150 μL. Here, the efficiency of the method is demonstrated by producing 96 human, recombinant proteins, both in micro-scale and using a standard full-scale protocol and comparing the results in regard to both protein identity and sample purity. The results obtained are highly comparable to those acquired through employing standard full-scale purification protocols, thus validating this method as a successful initial screening step before protein production at a larger scale. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ultralow-Power Electronic Trapping of Nanoparticles with Sub-10 nm Gold Nanogap Electrodes.

PubMed

Barik, Avijit; Chen, Xiaoshu; Oh, Sang-Hyun

2016-10-12

We demonstrate nanogap electrodes for rapid, parallel, and ultralow-power trapping of nanoparticles. Our device pushes the limit of dielectrophoresis by shrinking the separation between gold electrodes to sub-10 nm, thereby creating strong trapping forces at biases as low as the 100 mV ranges. Using high-throughput atomic layer lithography, we manufacture sub-10 nm gaps between 0.8 mm long gold electrodes and pattern them into individually addressable parallel electronic traps. Unlike pointlike junctions made by electron-beam lithography or larger micron-gap electrodes that are used for conventional dielectrophoresis, our sub-10 nm gold nanogap electrodes provide strong trapping forces over a mm-scale trapping zone. Importantly, our technology solves the key challenges associated with traditional dielectrophoresis experiments, such as high voltages that cause heat generation, bubble formation, and unwanted electrochemical reactions. The strongly enhanced fields around the nanogap induce particle-transport speed exceeding 10 μm/s and enable the trapping of 30 nm polystyrene nanoparticles using an ultralow bias of 200 mV. We also demonstrate rapid electronic trapping of quantum dots and nanodiamond particles on arrays of parallel traps. Our sub-10 nm gold nanogap electrodes can be combined with plasmonic sensors or nanophotonic circuitry, and their low-power electronic operation can potentially enable high-density integration on a chip as well as portable biosensing.

Architecture studies and system demonstrations for optical parallel processor for AI and NI

NASA Astrophysics Data System (ADS)

Lee, Sing H.

1988-03-01

In solving deterministic AI problems the data search for matching the arguments of a PROLOG expression causes serious bottleneck when implemented sequentially by electronic systems. To overcome this bottleneck we have developed the concepts for an optical expert system based on matrix-algebraic formulation, which will be suitable for parallel optical implementation. The optical AI system based on matrix-algebraic formation will offer distinct advantages for parallel search, adult learning, etc.

Formation of Electrostatic Potential Drops in the Auroral Zone

NASA Technical Reports Server (NTRS)

Schriver, D.; Ashour-Abdalla, M.; Richard, R. L.

2001-01-01

In order to examine the self-consistent formation of large-scale quasi-static parallel electric fields in the auroral zone on a micro/meso scale, a particle in cell simulation has been developed. The code resolves electron Debye length scales so that electron micro-processes are included and a variable grid scheme is used such that the overall length scale of the simulation is of the order of an Earth radii along the magnetic field. The simulation is electrostatic and includes the magnetic mirror force, as well as two types of plasmas, a cold dense ionospheric plasma and a warm tenuous magnetospheric plasma. In order to study the formation of parallel electric fields in the auroral zone, different magnetospheric ion and electron inflow boundary conditions are used to drive the system. It has been found that for conditions in the primary (upward) current region an upward directed quasi-static electric field can form across the system due to magnetic mirroring of the magnetospheric ions and electrons at different altitudes. For conditions in the return (downward) current region it is shown that a quasi-static parallel electric field in the opposite sense of that in the primary current region is formed, i.e., the parallel electric field is directed earthward. The conditions for how these different electric fields can be formed are discussed using satellite observations and numerical simulations.

Microfluidic local perfusion chambers for the visualization and manipulation of synapses

PubMed Central

Taylor, Anne M.; Dieterich, Daniela C.; Ito, Hiroshi T.; Kim, Sally A.; Schuman, Erin M.

2010-01-01

Summary The polarized nature of neurons as well as the size and density of synapses complicates the manipulation and visualization of cell biological processes that control synaptic function. Here we developed a microfluidic local perfusion (μLP) chamber to access and manipulate synaptic regions and pre- and post-synaptic compartments in vitro. This chamber directs the formation of synapses in >100 parallel rows connecting separate neuron populations. A perfusion channel transects the parallel rows allowing access to synaptic regions with high spatial and temporal resolution. We used this chamber to investigate synapse-to-nucleus signaling. Using the calcium indicator dye, Fluo-4, we measured changes in calcium at dendrites and somata, following local perfusion of glutamate. Exploiting the high temporal resolution of the chamber, we exposed synapses to “spaced” or “massed” application of glutamate and then examined levels of pCREB in somata. Lastly, we applied the metabotropic receptor agonist, DHPG, to dendrites and observed increases in Arc transcription and Arc transcript localization. PMID:20399729

Comparison between Trichel pulse in negative corona and self-pulsing in other configurations

NASA Astrophysics Data System (ADS)

Xia, Qing; Zhang, Yu; He, Feng; Qin, Yu; Jiang, Zhaorui; Ouyang, Jiting

2018-02-01

We present here a comparison study on self-pulsing phenomena in negative corona, hollow cathode discharges (HCD) and parallel-plate discharge in air. The voltage-current (V-I) curve, the waveforms of self-pulsed currents, and the time-resolved images of the pulsed discharge are measured under various operating conditions. It is experimentally evidenced that the Trichel pulse in a negative corona and the self-pulsing in HCD and/or parallel-plate discharge have similar features as well as spatial-temporal developing process. It is suggested that they should have a similar mechanism that the pulsing reflects the mode transition of discharge between the low-current Townsend and the high-current normal glow. The pulse rising corresponds to the breakdown and formation of temporal glow discharge in a background of low-current Townsend discharge, while the decay edge relates to the transition back to Townsend discharge. The pulse interval is the re-building process of the space charge layer of high density to ensure the glow breakdown.

Solution- and solid-phase parallel synthesis of 4-alkoxy-substituted pyrimidines with high molecular diversity.

PubMed

Font, David; Heras, Montserrat; Villalgordo, José M

2003-01-01

A simple and straightforward methodology toward the synthesis of novel 2,6-disubstituted-4-alkoxypyrimidine derivatives of type 16 and 19 has been developed. This methodology, initially developed in solution, can be perfectly adapted to the solid support under analogous conditions, taking full advantage of automated parallel synthesis systems. This successful methodology benefits from the key role played by the thioether linkage placed at the 2-position in 3, 9, or 13 in a double manner: on one side, the steric effect exerted by the thioether linkage is likely to be responsible for the very high observed selectivity toward the formation of the O-alkylation products. On the other side, this sulfur linkage can serve not only as a robust point of attachment for the heterocycle, stable to a number of reaction conditions, but also as a means of introducing a new element of diversity through activation to the corresponding sulfone (safety-catch linker concept) and subsequent ipso-substitution reaction with a variety of different N-nucleophiles.

Observations of a field-aligned ion/ion-beam instability in a magnetized laboratory plasma

NASA Astrophysics Data System (ADS)

Heuer, P. V.; Weidl, M. S.; Dorst, R. S.; Schaeffer, D. B.; Bondarenko, A. S.; Tripathi, S. K. P.; Van Compernolle, B.; Vincena, S.; Constantin, C. G.; Niemann, C.; Winske, D.

2018-03-01

Collisionless coupling between super Alfvénic ions and an ambient plasma parallel to a background magnetic field is mediated by a set of electromagnetic ion/ion-beam instabilities including the resonant right hand instability (RHI). To study this coupling and its role in parallel shock formation, a new experimental configuration at the University of California, Los Angeles utilizes high-energy and high-repetition-rate lasers to create a super-Alfvénic field-aligned debris plasma within an ambient plasma in the Large Plasma Device. We used a time-resolved fluorescence monochromator and an array of Langmuir probes to characterize the laser plasma velocity distribution and density. The debris ions were observed to be sufficiently super-Alfvénic and dense to excite the RHI. Measurements with magnetic flux probes exhibited a right-hand circularly polarized frequency chirp consistent with the excitation of the RHI near the laser target. We compared measurements to 2D hybrid simulations of the experiment.

Observations of a field-aligned ion/ion-beam instability in a magnetized laboratory plasma

DOE PAGES

Heuer, P. V.; Weidl, M. S.; Dorst, R. S.; ...

2018-03-01

Collisionless coupling between super Alfvénic ions and an ambient plasma parallel to a background magnetic field is mediated by a set of electromagnetic ion/ion-beam instabilities including the resonant right hand instability (RHI). To study this coupling and its role in parallel shock formation, a new experimental configuration at the University of California, Los Angeles utilizes high-energy and high-repetition-rate lasers to create a super-Alfvénic field-aligned debris plasma within an ambient plasma in the Large Plasma Device. We used a time-resolved fluorescence monochromator and an array of Langmuir probes to characterize the laser plasma velocity distribution and density. The debris ions weremore » observed to be sufficiently super-Alfvénic and dense to excite the RHI. Measurements with magnetic flux probes exhibited a right-hand circularly polarized frequency chirp consistent with the excitation of the RHI near the laser target. To conclude, we compared measurements to 2D hybrid simulations of the experiment.« less

Anisotropy in Third-Order Nonlinear Optical Susceptibility of a Squarylium Dye in a Nematic Liquid Crystal

NASA Astrophysics Data System (ADS)

Jin, Zhao-Hui; Li, Zhong-Yu; Kasatani, Kazuo; Okamoto, Hiroaki

2006-03-01

A squarylium dye is dissolved in 4-cyano-4'-pentylbiphenyl (5CB) and oriented by sandwiching mixtures between two pieces of rubbed glass plates. The optical absorption spectra of the oriented squarylium dye-5CB layers exhibit high anisotropy. The third-order nonlinear optical responses and susceptibilities χ(3)e of squarylium dye in 5CB are measured with light polarizations parallel and perpendicular to the orientational direction by the resonant femtosecond degenerate four-wave mixing (DFWM) technique. Temporal profiles of the DFWM signal of the oriented squarylium dye-5CB layers with light polarizations parallel and perpendicular to the orientational direction are measured with a time resolution of 0.3 ps (FWHM), and are found to consist of two components, i.e., the coherent instantaneous nonlinear response and slow response due to the formation of excited molecules. A high anisotropic ratio of χ(3)e, 10.8±1.2, is observed for the oriented layers.

Observations of a field-aligned ion/ion-beam instability in a magnetized laboratory plasma

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

Heuer, P. V.; Weidl, M. S.; Dorst, R. S.

Collisionless coupling between super Alfvénic ions and an ambient plasma parallel to a background magnetic field is mediated by a set of electromagnetic ion/ion-beam instabilities including the resonant right hand instability (RHI). To study this coupling and its role in parallel shock formation, a new experimental configuration at the University of California, Los Angeles utilizes high-energy and high-repetition-rate lasers to create a super-Alfvénic field-aligned debris plasma within an ambient plasma in the Large Plasma Device. We used a time-resolved fluorescence monochromator and an array of Langmuir probes to characterize the laser plasma velocity distribution and density. The debris ions weremore » observed to be sufficiently super-Alfvénic and dense to excite the RHI. Measurements with magnetic flux probes exhibited a right-hand circularly polarized frequency chirp consistent with the excitation of the RHI near the laser target. To conclude, we compared measurements to 2D hybrid simulations of the experiment.« less

High-power, format-flexible, 885-nm vertical-cavity surface-emitting laser arrays

NASA Astrophysics Data System (ADS)

Wang, Chad; Talantov, Fedor; Garrett, Henry; Berdin, Glen; Cardellino, Terri; Millenheft, David; Geske, Jonathan

2013-03-01

High-power, format flexible, 885 nm vertical-cavity surface-emitting laser (VCSEL) arrays have been developed for solid-state pumping and illumination applications. In this approach, a common VCSEL size format was designed to enable tiling into flexible formats and operating configurations. The fabrication of a common chip size on ceramic submount enables low-cost volume manufacturing of high-power VCSEL arrays. This base VCSEL chip was designed to be 5x3.33 mm2, and produced up to 50 Watts of peak continuous wave (CW) power. To scale to higher powers, multiple chips can be tiled into a combination of series or parallel configurations tailored to the application driver conditions. In actively cooled CW operation, the VCSEL array chips were packaged onto a single water channel cooler, and we have demonstrated 0.5x1, 1x1, and 1x3 cm2 formats, producing 150, 250, and 500 Watts of peak power, respectively, in under 130 A operating current. In QCW operation, the 1x3 cm2 VCSEL module, which contains 18 VCSEL array chips packaged on a single water cooler, produced over 1.3 kW of peak power. In passively cooled packages, multiple chip configurations have been developed for illumination applications, producing over 300 Watts of peak power in QCW operating conditions. These VCSEL chips use a substrate-removed structure to allow for efficient thermal heatsinking to enable high-power operation. This scalable, format flexible VCSEL architecture can be applied to wavelengths ranging from 800 to 1100 nm, and can be used to tailor emission spectral widths and build high-power hyperspectral sources.

Interpretation of deep directional resistivity measurements acquired in high-angle and horizontal wells using 3-D inversion

NASA Astrophysics Data System (ADS)

Puzyrev, Vladimir; Torres-Verdín, Carlos; Calo, Victor

2018-05-01

The interpretation of resistivity measurements acquired in high-angle and horizontal wells is a critical technical problem in formation evaluation. We develop an efficient parallel 3-D inversion method to estimate the spatial distribution of electrical resistivity in the neighbourhood of a well from deep directional electromagnetic induction measurements. The methodology places no restriction on the spatial distribution of the electrical resistivity around arbitrary well trajectories. The fast forward modelling of triaxial induction measurements performed with multiple transmitter-receiver configurations employs a parallel direct solver. The inversion uses a pre-conditioned gradient-based method whose accuracy is improved using the Wolfe conditions to estimate optimal step lengths at each iteration. The large transmitter-receiver offsets, used in the latest generation of commercial directional resistivity tools, improve the depth of investigation to over 30 m from the wellbore. Several challenging synthetic examples confirm the feasibility of the full 3-D inversion-based interpretations for these distances, hence enabling the integration of resistivity measurements with seismic amplitude data to improve the forecast of the petrophysical and fluid properties. Employing parallel direct solvers for the triaxial induction problems allows for large reductions in computational effort, thereby opening the possibility to invert multiposition 3-D data in practical CPU times.

Construction Morphology and the Parallel Architecture of Grammar

ERIC Educational Resources Information Center

Booij, Geert; Audring, Jenny

2017-01-01

This article presents a systematic exposition of how the basic ideas of Construction Grammar (CxG) (Goldberg, 2006) and the Parallel Architecture (PA) of grammar (Jackendoff, 2002]) provide the framework for a proper account of morphological phenomena, in particular word formation. This framework is referred to as Construction Morphology (CxM). As…

Formation of quasiparallel Alfven solitons

NASA Technical Reports Server (NTRS)

Hamilton, R. L.; Kennel, C. F.; Mjolhus, E.

1992-01-01

The formation of quasi-parallel Alfven solitons is investigated through the inverse scattering transformation (IST) for the derivative nonlinear Schroedinger (DNLS) equation. The DNLS has a rich complement of soliton solutions consisting of a two-parameter soliton family and a one-parameter bright/dark soliton family. In this paper, the physical roles and origins of these soliton families are inferred through an analytic study of the scattering data generated by the IST for a set of initial profiles. The DNLS equation has as limiting forms the nonlinear Schroedinger (NLS), Korteweg-de-Vries (KdV) and modified Korteweg-de-Vries (MKdV) equations. Each of these limits is briefly reviewed in the physical context of quasi-parallel Alfven waves. The existence of these limiting forms serves as a natural framework for discussing the formation of Alfven solitons.

Convergent, Parallel and Correlated Evolution of Trophic Morphologies in the Subfamily Schizothoracinae from the Qinghai-Tibetan Plateau

PubMed Central

Qi, Delin; Chao, Yan; Guo, Songchang; Zhao, Lanying; Li, Taiping; Wei, Fulei; Zhao, Xinquan

2012-01-01

Schizothoracine fishes distributed in the water system of the Qinghai-Tibetan plateau (QTP) and adjacent areas are characterized by being highly adaptive to the cold and hypoxic environment of the plateau, as well as by a high degree of diversity in trophic morphology due to resource polymorphisms. Although convergent and parallel evolution are prevalent in the organisms of the QTP, it remains unknown whether similar evolutionary patterns have occurred in the schizothoracine fishes. Here, we constructed for the first time a tentative molecular phylogeny of the schizothoracine fishes based on the complete sequences of the cytochrome b gene. We employed this molecular phylogenetic framework to examine the evolution of trophic morphologies. We used Pagel's maximum likelihood method to estimate the evolutionary associations of trophic morphologies and food resource use. Our results showed that the molecular and published morphological phylogenies of Schizothoracinae are partially incongruent with respect to some intergeneric relationships. The phylogenetic results revealed that four character states of five trophic morphologies and of food resource use evolved at least twice during the diversification of the subfamily. State transitions are the result of evolutionary patterns including either convergence or parallelism or both. Furthermore, our analyses indicate that some characters of trophic morphologies in the Schizothoracinae have undergone correlated evolution, which are somewhat correlated with different food resource uses. Collectively, our results reveal new examples of convergent and parallel evolution in the organisms of the QTP. The adaptation to different trophic niches through the modification of trophic morphologies and feeding behaviour as found in the schizothoracine fishes may account for the formation and maintenance of the high degree of diversity and radiations in fish communities endemic to QTP. PMID:22470515

Adding the ‘heart’ to hanging drop networks for microphysiological multi-tissue experiments†

PubMed Central

Yazdi, Saeed Rismani; Shadmani, Amir; Bürgel, Sebastian C.; Misun, Patrick M.; Hierlemann, Andreas; Frey, Olivier

2017-01-01

Microfluidic hanging-drop networks enable culturing and analysis of 3D microtissue spheroids derived from different cell types under controlled perfusion and investigating inter-tissue communication in multi-tissue formats. In this paper we introduce a compact on-chip pumping approach for flow control in hanging-drop networks. The pump includes one pneumatic chamber located directly above one of the hanging drops and uses the surface tension at the liquid–air-interface for flow actuation. Control of the pneumatic protocol provides a wide range of unidirectional pulsatile and continuous flow profiles. With the proposed concept several independent hanging-drop networks can be operated in parallel with only one single pneumatic actuation line at high fidelity. Closed-loop medium circulation between different organ models for multi-tissue formats and multiple simultaneous assays in parallel are possible. Finally, we implemented a real-time feedback control-loop of the pump actuation based on the beating of a human iPS-derived cardiac microtissue cultured in the same system. This configuration allows for simulating physiological effects on the heart and their impact on flow circulation between the organ models on chip. PMID:26401602

One-dimension modeling on the parallel-plate ion extraction process based on a non-electron-equilibrium fluid model

NASA Astrophysics Data System (ADS)

Li, He-Ping; Chen, Jian; Guo, Heng; Jiang, Dong-Jun; Zhou, Ming-Sheng; Department of Engineering Physics Team

2017-10-01

Ion extraction from a plasma under an externally applied electric field involve multi-particle and multi-field interactions, and has wide applications in the fields of materials processing, etching, chemical analysis, etc. In order to develop the high-efficiency ion extraction methods, it is indispensable to establish a feasible model to understand the non-equilibrium transportation processes of the charged particles and the evolutions of the space charge sheath during the extraction process. Most of the previous studies on the ion extraction process are mainly based on the electron-equilibrium fluid model, which assumed that the electrons are in the thermodynamic equilibrium state. However, it may lead to some confusions with neglecting the electron movement during the sheath formation process. In this study, a non-electron-equilibrium model is established to describe the transportation of the charged particles in a parallel-plate ion extraction process. The numerical results show that the formation of the Child-Langmuir sheath is mainly caused by the charge separation. And thus, the sheath shielding effect will be significantly weakened if the charge separation is suppressed during the extraction process of the charged particles.

Genetic Dissection of Aversive Associative Olfactory Learning and Memory in Drosophila Larvae

PubMed Central

Widmann, Annekathrin; Artinger, Marc; Biesinger, Lukas; Boepple, Kathrin; Schlechter, Jana; Selcho, Mareike; Thum, Andreas S.

2016-01-01

Memory formation is a highly complex and dynamic process. It consists of different phases, which depend on various neuronal and molecular mechanisms. In adult Drosophila it was shown that memory formation after aversive Pavlovian conditioning includes—besides other forms—a labile short-term component that consolidates within hours to a longer-lasting memory. Accordingly, memory formation requires the timely controlled action of different neuronal circuits, neurotransmitters, neuromodulators and molecules that were initially identified by classical forward genetic approaches. Compared to adult Drosophila, memory formation was only sporadically analyzed at its larval stage. Here we deconstruct the larval mnemonic organization after aversive olfactory conditioning. We show that after odor-high salt conditioning larvae form two parallel memory phases; a short lasting component that depends on cyclic adenosine 3’5’-monophosphate (cAMP) signaling and synapsin gene function. In addition, we show for the first time for Drosophila larvae an anesthesia resistant component, which relies on radish and bruchpilot gene function, protein kinase C activity, requires presynaptic output of mushroom body Kenyon cells and dopamine function. Given the numerical simplicity of the larval nervous system this work offers a unique prospect for studying memory formation of defined specifications, at full-brain scope with single-cell, and single-synapse resolution. PMID:27768692

Genetic Dissection of Aversive Associative Olfactory Learning and Memory in Drosophila Larvae.

PubMed

Widmann, Annekathrin; Artinger, Marc; Biesinger, Lukas; Boepple, Kathrin; Peters, Christina; Schlechter, Jana; Selcho, Mareike; Thum, Andreas S

2016-10-01

Memory formation is a highly complex and dynamic process. It consists of different phases, which depend on various neuronal and molecular mechanisms. In adult Drosophila it was shown that memory formation after aversive Pavlovian conditioning includes-besides other forms-a labile short-term component that consolidates within hours to a longer-lasting memory. Accordingly, memory formation requires the timely controlled action of different neuronal circuits, neurotransmitters, neuromodulators and molecules that were initially identified by classical forward genetic approaches. Compared to adult Drosophila, memory formation was only sporadically analyzed at its larval stage. Here we deconstruct the larval mnemonic organization after aversive olfactory conditioning. We show that after odor-high salt conditioning larvae form two parallel memory phases; a short lasting component that depends on cyclic adenosine 3'5'-monophosphate (cAMP) signaling and synapsin gene function. In addition, we show for the first time for Drosophila larvae an anesthesia resistant component, which relies on radish and bruchpilot gene function, protein kinase C activity, requires presynaptic output of mushroom body Kenyon cells and dopamine function. Given the numerical simplicity of the larval nervous system this work offers a unique prospect for studying memory formation of defined specifications, at full-brain scope with single-cell, and single-synapse resolution.

Ongoing data reduction, theoretical studies and supporting research in magnetospheric physics

NASA Technical Reports Server (NTRS)

Scarf, F. L.; Greenstadt, E. W.

1984-01-01

Data from ISEE-3, Pioneer Venus Orbiter, and Voyager 1 and 2 were analyzed. The predictability of local shock macrostructure at ISEE-1, at the Earth's bow shock, from solar wind measurements made up-stream by ISEE-3, was conducted using computer graphic format. Morphology of quasi-parallel shock was reviewed. The review attempted to interrelate various measurements and computations involving the q-parallel structure and foreshock elements connected to it. A new classification for q-parallel morphology was suggested.

Vitamin D, Hypercalciuria and Kidney Stones

PubMed Central

Letavernier, Emmanuel; Daudon, Michel

2018-01-01

The estimated lifetime risk of nephrolithiasis is growing nowadays, and the formation of kidney stones is frequently promoted by hypercalciuria. Vitamin D, and especially its active metabolite calcitriol, increase digestive calcium absorption—as urinary calcium excretion is directly correlated with digestive calcium absorption, vitamin D metabolites could theoretically increase calciuria and promote urinary stone formation. Nevertheless, there was, until recently, low evidence that 25-hydroxyvitamin D serum levels would be correlated with kidney stone formation, even if high calcitriol concentrations are frequently observed in hypercalciuric stone formers. Low 25-hydroxyvitamin D serum levels have been associated with a broad spectrum of diseases, leading to a huge increase in vitamin D prescription in the general population. In parallel, an increased frequency of kidney stone episodes has been observed in prospective studies evaluating vitamin D alone or in association with calcium supplements, and epidemiological studies have identified an association between high 25-hydroxyvitamin D serum levels and kidney stone formation in some groups of patients. Moreover, urinary calcium excretion has been shown to increase in response to vitamin D supplements, at least in some groups of kidney stone formers. It seems likely that predisposed individuals may develop hypercalciuria and kidney stones in response to vitamin D supplements. PMID:29562593

Star Formation in M 33 (HerM33es)

NASA Astrophysics Data System (ADS)

Kramer, C.; Boquien, M.; Braine, J.; Buchbender, C.; Calzetti, D.; Gratier, P.; Mookerjea, B.; Relaño, M.; Verley, S.

2011-11-01

Within the key project "Herschel M 33 extended survey" (HerM33es), we are studying the physical and chemical processes driving star formation and galactic evolution in the nearby galaxy M 33, combining the study of local conditions affecting individual star formation with properties only becoming apparent on global scales. Here, we present recent results obtained by the HerM33es team. Combining Spitzer and Herschel data ranging from 3.6 μm to 500μm, along with H i, Hα, and GALEX UV data, we have studied the dust at high spatial resolutions of 150 pc, providing estimators of the total infrared (TIR) brightness and of the star formation rate. While the temperature of the warm dust at high brightness is driven by young massive stars, evolved stellar populations appear to drive the temperature of the cold dust. Plane-parallel models of photon dominated regions (PDRs) fail to reproduce fully the [C ii], [O i], and CO maps obtained in a first spectroscopic study of one 2' × 2' subregion of M 33, located on the inner, northern spiral arm and encompassing the H ii region BCLMP 302.

Origins of structure in globular proteins.

PubMed Central

Chan, H S; Dill, K A

1990-01-01

The principal forces of protein folding--hydrophobicity and conformational entropy--are nonspecific. A long-standing puzzle has, therefore, been: What forces drive the formation of the specific internal architectures in globular proteins? We find that any self-avoiding flexible polymer molecule will develop large amounts of secondary structure, helices and parallel and antiparallel sheets, as it is driven to increasing compactness by any force of attraction among the chain monomers. Thus structure formation arises from the severity of steric constraints in compact polymers. This steric principle of organization can account for why short helices are stable in globular proteins, why there are parallel and anti-parallel sheets in proteins, and why weakly unfolded proteins have some secondary structure. On this basis, it should be possible to construct copolymers, not necessarily using amino acids, that can collapse to maximum compactness in incompatible solvents and that should then have structural organization resembling that of proteins. Images PMID:2385597

The effect of asymmetrical electrode form after negative bias illuminated stress in amorphous IGZO thin film transistors

NASA Astrophysics Data System (ADS)

Su, Wan-Ching; Chang, Ting-Chang; Liao, Po-Yung; Chen, Yu-Jia; Chen, Bo-Wei; Hsieh, Tien-Yu; Yang, Chung-I.; Huang, Yen-Yu; Chang, Hsi-Ming; Chiang, Shin-Chuan; Chang, Kuan-Chang; Tsai, Tsung-Ming

2017-03-01

This paper investigates the degradation behavior of InGaZnO thin film transistors (TFTs) under negative bias illumination stress (NBIS). TFT devices with two different source and drain layouts were exanimated: one having a parallel format electrode and the other with UI format electrode. UI means that source/drain electrodes shapes is defined as a forked-shaped structure. The I-V curve of the parallel electrode exhibited a symmetric degradation under forward and reverse sweeping in the saturation region after 1000 s NBIS. In contrast, the I-V curve of the UI electrode structure under similar conditions was asymmetric. The UI electrode structure also shows a stretch-out phenomenon in its C-V measurement. Finally, this work utilizes the ISE-Technology Computer Aided Design (ISE-TCAD) system simulations, which simulate the electron field and IV curves, to analyze the mechanisms dominating the parallel and UI device degradation behaviors.

Evidence of a New Instability in Gyrokinetic Simulations of LAPD Plasmas

NASA Astrophysics Data System (ADS)

Terry, P. W.; Pueschel, M. J.; Rossi, G.; Jenko, F.; Told, D.; Carter, T. A.

2015-11-01

Recent experiments at the LArge Plasma Device (LAPD) have focused on structure formation driven by density and temperature gradients. A central difference relative to typical, tokamak-like plasmas stems from the linear geometry and absence of background magnetic shear. At sufficiently high β, strong excitation of parallel (compressional) magnetic fluctuations was observed. Here, linear and nonlinear simulations with the Gene code are used to demonstrate that these findings can be explained through the linear excitation of a Gradient-driven Drift Coupling mode (GDC). This recently-discovered instability, unlike other drift waves, relies on the grad-B drift due to parallel magnetic fluctuations in lieu of a parallel electron response, and can be driven by density or temperature gradients. The linear properties of the GDC for LAPD parameters are studied in detail, and the corresponding turbulence is investigated. It is found that, despite the very large collisionality in the experiment, many properties are recovered fairly well in the simulations. In addition to confirming the existence of the GDC, this opens up interesting questions regarding GDC activity in astrophysical and space plasmas. Supported by USDOE.

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

PubMed

Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

2014-06-14

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

Method for measuring pollutant formation

NASA Technical Reports Server (NTRS)

Stickler, David B. (Inventor); Annen, Kurt (Inventor)

2001-01-01

Diagnostic methods for determining an instantaneous rate of pollutant formation in a combustion system are based on measurement of chemiluminescence intensity generated simultaneously with the formation of the pollutant. The chemiluminescent signal is generated by an analog reaction which occurs in parallel with a key step in the formation of a specific pollutant of interest. The connection between the analog reaction and the pollution reaction is such that the chemiluminescent signal indicates the local, instantaneous formation rate of the pollutant of interest.

The Forest Method as a New Parallel Tree Method with the Sectional Voronoi Tessellation

NASA Astrophysics Data System (ADS)

Yahagi, Hideki; Mori, Masao; Yoshii, Yuzuru

1999-09-01

We have developed a new parallel tree method which will be called the forest method hereafter. This new method uses the sectional Voronoi tessellation (SVT) for the domain decomposition. The SVT decomposes a whole space into polyhedra and allows their flat borders to move by assigning different weights. The forest method determines these weights based on the load balancing among processors by means of the overload diffusion (OLD). Moreover, since all the borders are flat, before receiving the data from other processors, each processor can collect enough data to calculate the gravity force with precision. Both the SVT and the OLD are coded in a highly vectorizable manner to accommodate on vector parallel processors. The parallel code based on the forest method with the Message Passing Interface is run on various platforms so that a wide portability is guaranteed. Extensive calculations with 15 processors of Fujitsu VPP300/16R indicate that the code can calculate the gravity force exerted on 105 particles in each second for some ideal dark halo. This code is found to enable an N-body simulation with 107 or more particles for a wide dynamic range and is therefore a very powerful tool for the study of galaxy formation and large-scale structure in the universe.

Global Swath and Gridded Data Tiling

NASA Technical Reports Server (NTRS)

Thompson, Charles K.

2012-01-01

This software generates cylindrically projected tiles of swath-based or gridded satellite data for the purpose of dynamically generating high-resolution global images covering various time periods, scaling ranges, and colors called "tiles." It reconstructs a global image given a set of tiles covering a particular time range, scaling values, and a color table. The program is configurable in terms of tile size, spatial resolution, format of input data, location of input data (local or distributed), number of processes run in parallel, and data conditioning.

Biofilm formation and control in a simulated spacecraft water system - Two-year results

NASA Technical Reports Server (NTRS)

Schultz, John R.; Taylor, Robert D.; Flanagan, David T.; Carr, Sandra E.; Bruce, Rebekah J.; Svoboda, Judy V.; Huls, M. H.; Sauer, Richard L.; Pierson, Duane L.

1991-01-01

The ability of iodine to maintain microbial water quality in a simulated spacecraft water system is being studied. An iodine level of about 2.0 mg/L is maintained by passing ultrapure influent water through an iodinated ion exchange resin. Six liters are withdrawn daily and the chemical and microbial quality of the water is monitored regularly. Stainless steel coupons used to monitor biofilm formation are being analyzed by culture methods, epifluorescence microscopy, and scanning electron microscopy. Results from the first two years of operation show a single episode of high bacterial colony counts in the iodinated system. This growth was apparently controlled by replacing the iodinated ion exchange resin. Scanning electron microscopy indicates that the iodine has limited but not completely eliminated the formation of biofilm during the first two years of operation. Significant microbial contamination has been present continuously in a parallel noniodinated system since the third week of operation.

Growth of large aluminum nitride single crystals with thermal-gradient control

DOEpatents

Bondokov, Robert T; Rao, Shailaja P; Gibb, Shawn Robert; Schowalter, Leo J

2015-05-12

In various embodiments, non-zero thermal gradients are formed within a growth chamber both substantially parallel and substantially perpendicular to the growth direction during formation of semiconductor crystals, where the ratio of the two thermal gradients (parallel to perpendicular) is less than 10, by, e.g., arrangement of thermal shields outside of the growth chamber.

Growth of large aluminum nitride single crystals with thermal-gradient control

DOEpatents

Bondokov, Robert T.; Rao, Shailaja P.; Schowalter, Leo J.

2017-02-28

In various embodiments, non-zero thermal gradients are formed within a growth chamber both substantially parallel and substantially perpendicular to the growth direction during formation of semiconductor crystals, where the ratio of the two thermal gradients (parallel to perpendicular) is less than 10, by, e.g., arrangement of thermal shields outside of the growth chamber.

Staging memory for massively parallel processor

NASA Technical Reports Server (NTRS)

Batcher, Kenneth E. (Inventor)

1988-01-01

The invention herein relates to a computer organization capable of rapidly processing extremely large volumes of data. A staging memory is provided having a main stager portion consisting of a large number of memory banks which are accessed in parallel to receive, store, and transfer data words simultaneous with each other. Substager portions interconnect with the main stager portion to match input and output data formats with the data format of the main stager portion. An address generator is coded for accessing the data banks for receiving or transferring the appropriate words. Input and output permutation networks arrange the lineal order of data into and out of the memory banks.

Light-weight Parallel Python Tools for Earth System Modeling Workflows

NASA Astrophysics Data System (ADS)

Mickelson, S. A.; Paul, K.; Xu, H.; Dennis, J.; Brown, D. I.

2015-12-01

With the growth in computing power over the last 30 years, earth system modeling codes have become increasingly data-intensive. As an example, it is expected that the data required for the next Intergovernmental Panel on Climate Change (IPCC) Assessment Report (AR6) will increase by more than 10x to an expected 25PB per climate model. Faced with this daunting challenge, developers of the Community Earth System Model (CESM) have chosen to change the format of their data for long-term storage from time-slice to time-series, in order to reduce the required download bandwidth needed for later analysis and post-processing by climate scientists. Hence, efficient tools are required to (1) perform the transformation of the data from time-slice to time-series format and to (2) compute climatology statistics, needed for many diagnostic computations, on the resulting time-series data. To address the first of these two challenges, we have developed a parallel Python tool for converting time-slice model output to time-series format. To address the second of these challenges, we have developed a parallel Python tool to perform fast time-averaging of time-series data. These tools are designed to be light-weight, be easy to install, have very few dependencies, and can be easily inserted into the Earth system modeling workflow with negligible disruption. In this work, we present the motivation, approach, and testing results of these two light-weight parallel Python tools, as well as our plans for future research and development.

Probing amyloid fibril formation of the NFGAIL peptide by computer simulations

NASA Astrophysics Data System (ADS)

Melquiond, Adrien; Gelly, Jean-Christophe; Mousseau, Normand; Derreumaux, Philippe

2007-02-01

Amyloid fibril formation, as observed in Alzheimer's disease and type II diabetes, is currently described by a nucleation-condensation mechanism, but the details of the process preceding the formation of the nucleus are still lacking. In this study, using an activation-relaxation technique coupled to a generic energy model, we explore the aggregation pathways of 12 chains of the hexapeptide NFGAIL. The simulations show, starting from a preformed parallel dimer and ten disordered chains, that the peptides form essentially amorphous oligomers or more rarely ordered β-sheet structures where the peptides adopt a parallel orientation within the sheets. Comparison between the simulations indicates that a dimer is not a sufficient seed for avoiding amorphous aggregates and that there is a critical threshold in the number of connections between the chains above which exploration of amorphous aggregates is preferred.

The self in cyberspace. Identity formation in postmodern societies and Jung's Self as an objective psyche.

PubMed

Roesler, Christian

2008-06-01

Jung's concept of the Self is compared with current theories of identity formation in post-modern society concerning the question: is the self constituted through experience and cultural influences--as it is argued by current theories in the social sciences--or is it already preformed inside the person, as Jung argues? The impact of communication media on the formation of identity in today's societies is discussed with a focus on internet communication and virtual realities. The resulting types of identities are conceptualized as polycentric which has surprising parallels to Jung's idea of the Self. The epistemology of constructivism and parallels in Jung's thought are demonstrated. Jung's work in this respect often appears contradictory in itself but this can be dealt with by a postmodern approach which accepts a plurality of truths.

Seismic properties of lawsonite eclogites from the southern Motagua fault zone, Guatemala

NASA Astrophysics Data System (ADS)

Kim, Daeyeong; Wallis, Simon; Endo, Shunsuke; Ree, Jin-Han

2016-05-01

We present new data on the crystal preferred orientation (CPO) and seismic properties of omphacite and lawsonite in extremely fresh eclogite from the southern Motagua fault zone, Guatemala, to discuss the seismic anisotropy of subducting oceanic crust. The CPO of omphacite is characterized by (010)[001], and it shows P-wave seismic anisotropies (AVP) of 1.4%-3.2% and S-wave seismic anisotropies (AVS) of 1.4%-2.7%. Lawsonite exhibits (001) planes parallel to the foliation and [010] axes parallel to the lineation, and seismic anisotropies of 1.7%-6.6% AVP and 3.4%-14.7% AVS. The seismic anisotropy of a rock mass consisting solely of omphacite and lawsonite is 1.2%-4.1% AVP and 1.8%-6.8% AVS. For events that propagate more or less parallel to the maximum extension direction, X, the fast S-wave velocity (VS) polarization is parallel to the Z in the Y-Z section (rotated from the X-Z section), causing trench-normal seismic anisotropy for orthogonal subduction. Based on the high modal abundance and strong fabric of lawsonite, the AVS of eclogites is estimated as ~ 11.7% in the case that lawsonite makes up ~ 75% of the rock mass. On this basis, we suggest that lawsonite in both blueschist and eclogite may play important roles in the formation of complex pattern of seismic anisotropy observed in NE Japan: weak trench-parallel anisotropy in the forearc basin domains and trench-normal anisotropy in the backarc region.

On cooperative effects and aggregation of GNNQQNY and NNQQNY peptides

NASA Astrophysics Data System (ADS)

Nochebuena, Jorge; Ireta, Joel

2015-10-01

Some health disturbances like neurodegenerative diseases are associated to the presence of amyloids. GNNQQNY and NNQQNY peptides are considered as prototypical examples for studying the formation of amyloids. These exhibit quite different aggregation behaviors despite they solely differ in size by one residue. To get insight into the reasons for such difference, we have examined association energies of aggregates (parallel β-sheets, fibril-spines, and crystal structures) from GNNQQNY and NNQQY using density functional theory. As we found that GNNQQNY tends to form a zwitterion in the crystal structure, we have investigated the energetics of parallel β-sheets and fibril-spines in the canonical and zwitterionic states. We found that the formation of GNNQQNY aggregates is energetically more favored than the formation of the NNQQNY ones. We show that the latter is connected to the network of hydrogen bonds formed by each aggregate. Moreover, we found that the formation of some NNQQNY aggregates is anticooperative, whereas cooperative with GNNQQNY. These results have interesting implications for deciphering the factors determining peptide aggregation propensities.

Biomechanics of far cortical locking.

PubMed

Bottlang, Michael; Feist, Florian

2011-02-01

The development of far cortical locking (FCL) was motivated by a conundrum: locked plating constructs provide inherently rigid stabilization, yet they should facilitate biologic fixation and secondary bone healing that relies on flexible fixation to stimulate callus formation. Recent studies have confirmed that the high stiffness of standard locked plating constructs can suppress interfragmentary motion to a level that is insufficient to reliably promote secondary fracture healing by callus formation. Furthermore, rigid locking screws cause an uneven stress distribution that may lead to stress fracture at the end screw and stress shielding under the plate. This review summarizes four key features of FCL constructs that have been shown to enhance fixation and healing of fractures: flexible fixation, load distribution, progressive stiffening, and parallel interfragmentary motion. Specifically, flexible fixation provided by FCL reduces the stiffness of a locked plating construct by 80% to 88% to actively promote callus proliferation similar to an external fixator. Load is evenly distributed between FCL screws to mitigate stress risers at the end screw. Progressive stiffening occurs by near cortex support of FCL screws and provides additional support under elevated loading. Finally, parallel interfragmentary motion by the S-shaped flexion of FCL screws promotes symmetric callus formation. In combination, these features of FCL constructs have been shown to induce more callus and to yield significantly stronger and more consistent healing compared with standard locked plating constructs. As such, FCL constructs function as true internal fixators by replicating the biomechanical behavior and biologic healing response of external fixators.

Biomechanics of Far Cortical Locking

PubMed Central

Bottlang, Michael; Feist, Florian

2011-01-01

The development of FCL was motivated by a conundrum: locked plating constructs provide inherently rigid stabilization, yet they should facilitate biological fixation and secondary bone healing that relies on flexible fixation to stimulate callus formation. Recent studies have confirmed that the high stiffness of standard locked plating constructs can suppress interfragmentary motion to a level that is insufficient to reliably promote secondary fracture healing by callus formation. Furthermore, rigid locking screws cause an uneven stress distribution that may lead to stress fracture at the end screw and stress shielding under the plate. This review summarizes four key features of FCL constructs that have shown to enhance fixation and fracture healing: Flexible fixation, load distribution, progressive stiffening, and parallel interfragmentary motion. Specifically, flexible fixation provided by FCL reduces the stiffness of a locked plating construct by 80–88% to actively promote callus proliferation similar to an external fixator. Load distribution is evenly shared between FCL screws to mitigate stress risers at the end screw. Progressive stiffening occurs by near cortex support of FCL screws and provides additional support under elevated loading. Finally, parallel interfragmentary motion by s-shaped flexion of FCL screws has shown to induce symmetric callus formation. In combination, these features of FCL constructs have shown to induce more callus and to yield significantly stronger and more consistent healing compared to standard locked plating constructs. As such, FCL constructs function as true internal fixators by replicating the biomechanical behavior and biological healing response of external fixators. PMID:21248556

JSD: Parallel Job Accounting on the IBM SP2

NASA Technical Reports Server (NTRS)

Saphir, William; Jones, James Patton; Walter, Howard (Technical Monitor)

1995-01-01

The IBM SP2 is one of the most promising parallel computers for scientific supercomputing - it is fast and usually reliable. One of its biggest problems is a lack of robust and comprehensive system software. Among other things, this software allows a collection of Unix processes to be treated as a single parallel application. It does not, however, provide accounting for parallel jobs other than what is provided by AIX for the individual process components. Without parallel job accounting, it is not possible to monitor system use, measure the effectiveness of system administration strategies, or identify system bottlenecks. To address this problem, we have written jsd, a daemon that collects accounting data for parallel jobs. jsd records information in a format that is easily machine- and human-readable, allowing us to extract the most important accounting information with very little effort. jsd also notifies system administrators in certain cases of system failure.

X-Raying the Star Formation History of the Universe.

PubMed

Cavaliere; Giacconi; Menci

2000-01-10

The current models of early star and galaxy formation are based upon the hierarchical growth of dark matter halos, within which the baryons condense into stars after cooling down from a hot diffuse phase. The latter is replenished by infall of outer gas into the halo potential wells; this includes a fraction previously expelled and preheated because of momentum and energy fed back by the supernovae which follow the star formation. We identify such an implied hot phase with the medium known to radiate powerful X-rays in clusters and in groups of galaxies. We show that the amount of the hot component required by the current star formation models is enough to be observable out to redshifts z approximately 1.5 in forthcoming deep surveys from Chandra and X-Ray Multimirror Mission, especially in case the star formation rate is high at such and earlier redshifts. These X-ray emissions constitute a necessary counterpart and will provide a much-wanted probe of the star formation process itself (in particular, of the supernova feedback) to parallel and complement the currently debated data from optical and IR observations of the young stars.

The influence of stimulus format on drawing—a functional imaging study of decision making in portrait drawing

PubMed Central

Miall, R.C.; Nam, Se-Ho; Tchalenko, J.

2014-01-01

To copy a natural visual image as a line drawing, visual identification and extraction of features in the image must be guided by top-down decisions, and is usually influenced by prior knowledge. In parallel with other behavioral studies testing the relationship between eye and hand movements when drawing, we report here a functional brain imaging study in which we compared drawing of faces and abstract objects: the former can be strongly guided by prior knowledge, the latter less so. To manipulate the difficulty in extracting features to be drawn, each original image was presented in four formats including high contrast line drawings and silhouettes, and as high and low contrast photographic images. We confirmed the detailed eye–hand interaction measures reported in our other behavioral studies by using in-scanner eye-tracking and recording of pen movements with a touch screen. We also show that the brain activation pattern reflects the changes in presentation formats. In particular, by identifying the ventral and lateral occipital areas that were more highly activated during drawing of faces than abstract objects, we found a systematic increase in differential activation for the face-drawing condition, as the presentation format made the decisions more challenging. This study therefore supports theoretical models of how prior knowledge may influence perception in untrained participants, and lead to experience-driven perceptual modulation by trained artists. PMID:25128710

High-throughput measurements of biochemical responses using the plate::vision multimode 96 minilens array reader.

PubMed

Huang, Kuo-Sen; Mark, David; Gandenberger, Frank Ulrich

2006-01-01

The plate::vision is a high-throughput multimode reader capable of reading absorbance, fluorescence, fluorescence polarization, time-resolved fluorescence, and luminescence. Its performance has been shown to be quite comparable with other readers. When the reader is integrated into the plate::explorer, an ultrahigh-throughput screening system with event-driven software and parallel plate-handling devices, it becomes possible to run complicated assays with kinetic readouts in high-density microtiter plate formats for high-throughput screening. For the past 5 years, we have used the plate::vision and the plate::explorer to run screens and have generated more than 30 million data points. Their throughput, performance, and robustness have speeded up our drug discovery process greatly.

Evaluating Statistical Targets for Assembling Parallel Mixed-Format Test Forms

ERIC Educational Resources Information Center

Debeer, Dries; Ali, Usama S.; van Rijn, Peter W.

2017-01-01

Test assembly is the process of selecting items from an item pool to form one or more new test forms. Often new test forms are constructed to be parallel with an existing (or an ideal) test. Within the context of item response theory, the test information function (TIF) or the test characteristic curve (TCC) are commonly used as statistical…

Liquid-Nitrogen Test for Blocked Tubes

NASA Technical Reports Server (NTRS)

Wagner, W. R.

1984-01-01

Nondestructive test identifies obstructed tube in array of parallel tubes. Trickle of liquid nitrogen allowed to flow through tube array until array accumulates substantial formation of frost from moisture in air. Flow stopped and warm air introduced into inlet manifold to heat tubes in array. Tubes still frosted after others defrosted identified as obstructed tubes. Applications include inspection of flow systems having parallel legs.

Outrunning damage: Electrons vs X-rays-timescales and mechanisms.

PubMed

Spence, John C H

2017-07-01

Toward the end of his career, Zewail developed strong interest in fast electron spectroscopy and imaging, a field to which he made important contributions toward his aim of making molecular movies free of radiation damage. We therefore compare here the atomistic mechanisms leading to destruction of protein samples in diffract-and-destroy experiments for the cases of high-energy electron beam irradiation and X-ray laser pulses. The damage processes and their time-scales are compared and relevant elastic, inelastic, and photoelectron cross sections are given. Inelastic mean-free paths for ejected electrons at very low energies in insulators are compared with the bioparticle size. The dose rate and structural damage rate for electrons are found to be much lower, allowing longer pulses, reduced beam current, and Coulomb interactions for the formation of smaller probes. High-angle electron scattering from the nucleus, which has no parallel in the X-ray case, tracks the slowly moving nuclei during the explosion, just as the gain of the XFEL (X-ray free-electron laser) has no parallel in the electron case. Despite reduced damage and much larger elastic scattering cross sections in the electron case, leading to not dissimilar elastic scattering rates (when account is taken of the greatly increased incident XFEL fluence), progress for single-particle electron diffraction is seen to depend on the effort to reduce emittance growth due to Coulomb interactions, and so allow formation of intense sub-micron beams no larger than a virus.

Outrunning damage: Electrons vs X-rays—timescales and mechanisms

PubMed Central

Spence, John C. H.

2017-01-01

Toward the end of his career, Zewail developed strong interest in fast electron spectroscopy and imaging, a field to which he made important contributions toward his aim of making molecular movies free of radiation damage. We therefore compare here the atomistic mechanisms leading to destruction of protein samples in diffract-and-destroy experiments for the cases of high-energy electron beam irradiation and X-ray laser pulses. The damage processes and their time-scales are compared and relevant elastic, inelastic, and photoelectron cross sections are given. Inelastic mean-free paths for ejected electrons at very low energies in insulators are compared with the bioparticle size. The dose rate and structural damage rate for electrons are found to be much lower, allowing longer pulses, reduced beam current, and Coulomb interactions for the formation of smaller probes. High-angle electron scattering from the nucleus, which has no parallel in the X-ray case, tracks the slowly moving nuclei during the explosion, just as the gain of the XFEL (X-ray free-electron laser) has no parallel in the electron case. Despite reduced damage and much larger elastic scattering cross sections in the electron case, leading to not dissimilar elastic scattering rates (when account is taken of the greatly increased incident XFEL fluence), progress for single-particle electron diffraction is seen to depend on the effort to reduce emittance growth due to Coulomb interactions, and so allow formation of intense sub-micron beams no larger than a virus. PMID:28653018

Hubble's View of Little Blue Dots

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2018-02-01

The recent discovery of a new type of tiny, star-forming galaxy is the latest in a zoo of detections shedding light on our early universe. What can we learn from the unique little blue dots found in archival Hubble data?Peas, Berries, and DotsGreen pea galaxies identified by citizen scientists with Galaxy Zoo. [Richard Nowell Carolin Cardamone]As telescope capabilities improve and we develop increasingly deeper large-scale surveys of our universe, we continue to learn more about small, faraway galaxies. In recent years, increasing sensitivity first enabled the detection of green peas luminous, compact, low-mass (10 billion solar masses; compare this to the Milky Ways 1 trillion solar masses!) galaxies with high rates of star formation.Not long thereafter, we discovered galaxies that form stars similarly rapidly, but are even smaller only 330 million solar masses, spanning less than 3,000 light-years in size. These tiny powerhouses were termed blueberries for their distinctive color.Now, scientists Debra and Bruce Elmegreen (of Vassar College and IBM Research Division, respectively) report the discovery of galaxies that have even higher star formation rates and even lower masses: little blue dots.Exploring Tiny Star FactoriesThe Elmegreens discovered these unique galaxies by exploring archival Hubble data. The Hubble Frontier Fields data consist of deep images of six distant galaxy clusters and the parallel fields next to them. It was in the archival data for two Frontier Field Parallels, those for clusters Abell 2744 and MAS J0416.1-2403, that the authors noticed several galaxies that stand out as tiny, bright, blue objects that are nearly point sources.Top: a few examples of the little blue dots recently identified in two Hubble Frontier Field Parallels. Bottom: stacked images for three different groups of little blue dots. [Elmegreen Elmegreen 2017]The authors performed a search through the two Frontier Field Parallels, discovering a total of 55 little blue dots with masses spanning 105.8107.4solar masses, specific star formation rates of 10-7.4, and redshifts of 0.5 z 5.4.Exploring these little blue dots, the Elmegreens find that the galaxies sizes tend to be just a few hundred light-years across. They are gas-dominated; gas currently outweighs stars in these galaxies by perhaps a factor of five. Impressively, based on the incredibly high specific star formation rates observed in these little blue dots, they appear to have formed all of their stars in the last 1% of the age of the universe for them.An Origin for Globulars?Log-log plot of star formation rate vs. mass for the three main groups of little blue dots (red, green, and blue markers), a fourth group of candidates with different properties (brown markers), and previously discovered local blueberry galaxies. The three main groups of little blue dots appear to be low-mass analogs of blueberries. [Elmegreen Elmegreen 2017]Intriguingly, this rapid star formation might be the key to answering a long-standing question: where do globular clusters come from? The Elmegreens propose that little blue dots might actually be an explanation for the origin of these orbiting, spherical, low-metallicity clusters of stars.The authors demonstrate that, if the current star formation rates observed in little blue dots were to persist for another 50 Myr before feedback or gas exhaustion halted star production, the little blue dots could form enough stars to create clusters of roughly a million solar masses which is large enough to explain the globular clusters we observe today.If little blue dots indeed rapidly produced such star clusters in the past, the clusters could later be absorbed into the halos of todays spiral and elliptical galaxies, appearing to us as the low-metallicity globular clusters that orbit large galaxies today.CitationDebra Meloy Elmegreen and Bruce G. Elmegreen 2017 ApJL 851 L44. doi:10.3847/2041-8213/aaa0ce

Colloid-based multiplexed method for screening plant biomass-degrading glycoside hydrolase activities in microbial communities

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

Reindl, W.; Deng, K.; Gladden, J.M.

2011-05-01

The enzymatic hydrolysis of long-chain polysaccharides is a crucial step in the conversion of biomass to lignocellulosic biofuels. The identification and characterization of optimal glycoside hydrolases is dependent on enzyme activity assays, however existing methods are limited in terms of compatibility with a broad range of reaction conditions, sample complexity, and especially multiplexity. The method we present is a multiplexed approach based on Nanostructure-Initiator Mass Spectrometry (NIMS) that allowed studying several glycolytic activities in parallel under diverse assay conditions. Although the substrate analogs carried a highly hydrophobic perfluorinated tag, assays could be performed in aqueous solutions due colloid formation ofmore » the substrate molecules. We first validated our method by analyzing known {beta}-glucosidase and {beta}-xylosidase activities in single and parallel assay setups, followed by the identification and characterization of yet unknown glycoside hydrolase activities in microbial communities.« less

Dielectric monitoring of carbon nanotube network formation in curing thermosetting nanocomposites

NASA Astrophysics Data System (ADS)

Battisti, A.; Skordos, A. A.; Partridge, I. K.

2009-08-01

This paper focuses on monitoring of carbon nanotube (CNT) network development during the cure of unsaturated polyester nanocomposites by means of electrical impedance spectroscopy. A phenomenological model of the dielectric response is developed using equivalent circuit analysis. The model comprises two parallel RC elements connected in series, each of them giving rise to a semicircular arc in impedance complex plane plots. An established inverse modelling methodology is utilized for the estimation of the parameters of the corresponding equivalent circuit. This allows a quantification of the evolution of two separate processes corresponding to the two parallel RC elements. The high frequency process, which is attributed to CNT aggregates, shows a monotonic decrease in characteristic time during the cure. In contrast, the low frequency process, which corresponds to inter-aggregate phenomena, shows a more complex behaviour explained by the interplay between conductive network development and the cross-linking of the polymer.

Orogenic structural inheritance and rifted passive margin formation

NASA Astrophysics Data System (ADS)

Salazar Mora, Claudio A.; Huismans, Ritske S.

2016-04-01

Structural inheritance is related to mechanical weaknesses in the lithosphere due to previous tectonic events, e.g. rifting, subduction and collision. The North and South Atlantic rifted passive margins that formed during the breakup of Western Gondwana, are parallel to the older Caledonide and the Brasiliano-Pan-African orogenic belts. In the South Atlantic, 'old' mantle lithospheric fabric resulting from crystallographic preferred orientation of olivine is suggested to play a role during rifted margin formation (Tommasi and Vauchez, 2001). Magnetometric and gravimetric mapping of onshore structures in the Camamu and Almada basins suggest that extensional faults are controlled by two different directions of inherited older Brasiliano structures in the upper lithosphere (Ferreira et al., 2009). In the South Atlantic Campos Basin, 3D seismic data indicate that inherited basement structures provide a first order control on basin structure (Fetter, 2009). Here we investigate the role of structural inheritance on the formation of rifted passive margins with high-resolution 2D thermo-mechanical numerical experiments. The numerical domain is 1200 km long and 600 km deep and represents the lithosphere and the sublithospheric mantle. Model experiments were carried out by creating self-consistent orogenic inheritance where a first phase of orogen formation is followed by extension. We focus in particular on the role of varying amount of orogenic shortening, crustal rheology, contrasting styles of orogen formation on rifted margin style, and the time delay between orogeny and subsequent rifted passive formation. Model results are compared to contrasting structural styles of rifted passive margin formation as observed in the South Atlantic. Ferreira, T.S., Caixeta, J.M., Lima, F.D., 2009. Basement control in Camamu and Almada rift basins. Boletim de Geociências da Petrobrás 17, 69-88. Fetter, M., 2009. The role of basement tectonic reactivation on the structural evolution of Campos Basin, offshore Brazil: Evidence from 3D seismic analysis and section restoration. Marine and Petroleum Geology 26, 873-886. Tommasi, A., Vauchez, A., 2001. Continental rifting parallel to ancient collisional belts: An effect of the mechanical anisotropy of the lithospheric mantle. Earth and Planetary Science Letters 185, 199-210.

Parallel Tracks as Quasi-steady States for the Magnetic Boundary Layers in Neutron-star Low-mass X-Ray Binaries

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

Erkut, M. Hakan; Çatmabacak, Onur, E-mail: mherkut@gmail.com

The neutron stars in low-mass X-ray binaries (LMXBs) are usually thought to be weakly magnetized objects accreting matter from their low-mass companions in the form of a disk. Albeit weak compared to those in young neutron-star systems, the neutron-star magnetospheres in LMXBs can play an important role in determining the correlations between spectral and temporal properties. Parallel tracks appearing in the kilohertz (kHz) quasi-periodic oscillation (QPO) frequency versus X-ray flux plane can be used as a tool to study the magnetosphere–disk interaction in neutron-star LMXBs. For dynamically important weak fields, the formation of a non-Keplerian magnetic boundary layer at themore » innermost disk truncated near the surface of the neutron star is highly likely. Such a boundary region may harbor oscillatory modes of frequencies in the kHz range. We generate parallel tracks using the boundary region model of kHz QPOs. We also present the direct application of our model to the reproduction of the observed parallel tracks of individual sources such as 4U 1608–52, 4U 1636–53, and Aql X-1. We reveal how the radial width of the boundary layer must vary in the long-term flux evolution of each source to regenerate the parallel tracks. The run of the radial width looks similar for different sources and can be fitted by a generic model function describing the average steady behavior of the boundary region over the long term. The parallel tracks then correspond to the possible quasi-steady states the source can occupy around the average trend.« less

Parallel Tracks as Quasi-steady States for the Magnetic Boundary Layers in Neutron-star Low-mass X-Ray Binaries

NASA Astrophysics Data System (ADS)

Erkut, M. Hakan; Çatmabacak, Onur

2017-11-01

The neutron stars in low-mass X-ray binaries (LMXBs) are usually thought to be weakly magnetized objects accreting matter from their low-mass companions in the form of a disk. Albeit weak compared to those in young neutron-star systems, the neutron-star magnetospheres in LMXBs can play an important role in determining the correlations between spectral and temporal properties. Parallel tracks appearing in the kilohertz (kHz) quasi-periodic oscillation (QPO) frequency versus X-ray flux plane can be used as a tool to study the magnetosphere-disk interaction in neutron-star LMXBs. For dynamically important weak fields, the formation of a non-Keplerian magnetic boundary layer at the innermost disk truncated near the surface of the neutron star is highly likely. Such a boundary region may harbor oscillatory modes of frequencies in the kHz range. We generate parallel tracks using the boundary region model of kHz QPOs. We also present the direct application of our model to the reproduction of the observed parallel tracks of individual sources such as 4U 1608-52, 4U 1636-53, and Aql X-1. We reveal how the radial width of the boundary layer must vary in the long-term flux evolution of each source to regenerate the parallel tracks. The run of the radial width looks similar for different sources and can be fitted by a generic model function describing the average steady behavior of the boundary region over the long term. The parallel tracks then correspond to the possible quasi-steady states the source can occupy around the average trend.

A highly parallel multigrid-like method for the solution of the Euler equations

NASA Technical Reports Server (NTRS)

Tuminaro, Ray S.

1989-01-01

We consider a highly parallel multigrid-like method for the solution of the two dimensional steady Euler equations. The new method, introduced as filtering multigrid, is similar to a standard multigrid scheme in that convergence on the finest grid is accelerated by iterations on coarser grids. In the filtering method, however, additional fine grid subproblems are processed concurrently with coarse grid computations to further accelerate convergence. These additional problems are obtained by splitting the residual into a smooth and an oscillatory component. The smooth component is then used to form a coarse grid problem (similar to standard multigrid) while the oscillatory component is used for a fine grid subproblem. The primary advantage in the filtering approach is that fewer iterations are required and that most of the additional work per iteration can be performed in parallel with the standard coarse grid computations. We generalize the filtering algorithm to a version suitable for nonlinear problems. We emphasize that this generalization is conceptually straight-forward and relatively easy to implement. In particular, no explicit linearization (e.g., formation of Jacobians) needs to be performed (similar to the FAS multigrid approach). We illustrate the nonlinear version by applying it to the Euler equations, and presenting numerical results. Finally, a performance evaluation is made based on execution time models and convergence information obtained from numerical experiments.

High performance cellular level agent-based simulation with FLAME for the GPU.

PubMed

Richmond, Paul; Walker, Dawn; Coakley, Simon; Romano, Daniela

2010-05-01

Driven by the availability of experimental data and ability to simulate a biological scale which is of immediate interest, the cellular scale is fast emerging as an ideal candidate for middle-out modelling. As with 'bottom-up' simulation approaches, cellular level simulations demand a high degree of computational power, which in large-scale simulations can only be achieved through parallel computing. The flexible large-scale agent modelling environment (FLAME) is a template driven framework for agent-based modelling (ABM) on parallel architectures ideally suited to the simulation of cellular systems. It is available for both high performance computing clusters (www.flame.ac.uk) and GPU hardware (www.flamegpu.com) and uses a formal specification technique that acts as a universal modelling format. This not only creates an abstraction from the underlying hardware architectures, but avoids the steep learning curve associated with programming them. In benchmarking tests and simulations of advanced cellular systems, FLAME GPU has reported massive improvement in performance over more traditional ABM frameworks. This allows the time spent in the development and testing stages of modelling to be drastically reduced and creates the possibility of real-time visualisation for simple visual face-validation.

Terrain types and local-scale stratigraphy of grooved terrain on ganymede

NASA Technical Reports Server (NTRS)

Murchie, Scott L.; Head, James W.; Helfenstein, Paul; Plescia, Jeffrey B.

1986-01-01

Grooved terrain is subdivided on the basis of pervasive morphology into: (1) groove lanes - elongate parallel groove bands, (2) grooved polygons - polygonal domains of parallel grooves, (3) reticulate terrain - polygonal domains of orthogonal grooves, and (4) complex grooved terrain - polygons with several complexly cross-cutting groove sets. Detailed geologic mapping of select areas, employing previously established conventions for determining relative age relations, reveals a general three-stage sequence of grooved terrain emplacement: first, dissection of the lithosphere by throughgoing grooves, and pervasive deformation of intervening blocks; second, extensive flooding and continued deformation of the intervening blocks; third, repeated superposition of groove lanes concentrated at sites of initial throughgoing grooves. This sequence is corroborated by crater-density measurements. Dominant orientations of groove sets are parallel to relict zones of weakness that probably were reactivated during grooved terrain formation. Groove lane morphology and development consistent with that predicted for passive rifts suggests a major role of global expansion in grooved terrain formation.

Automated Performance Prediction of Message-Passing Parallel Programs

NASA Technical Reports Server (NTRS)

Block, Robert J.; Sarukkai, Sekhar; Mehra, Pankaj; Woodrow, Thomas S. (Technical Monitor)

1995-01-01

The increasing use of massively parallel supercomputers to solve large-scale scientific problems has generated a need for tools that can predict scalability trends of applications written for these machines. Much work has been done to create simple models that represent important characteristics of parallel programs, such as latency, network contention, and communication volume. But many of these methods still require substantial manual effort to represent an application in the model's format. The NIK toolkit described in this paper is the result of an on-going effort to automate the formation of analytic expressions of program execution time, with a minimum of programmer assistance. In this paper we demonstrate the feasibility of our approach, by extending previous work to detect and model communication patterns automatically, with and without overlapped computations. The predictions derived from these models agree, within reasonable limits, with execution times of programs measured on the Intel iPSC/860 and Paragon. Further, we demonstrate the use of MK in selecting optimal computational grain size and studying various scalability metrics.

Architectural element analysis within the Kayenta Formation (Lower Jurassic) using ground-probing radar and sedimentological profiling, southwestern Colorado

NASA Astrophysics Data System (ADS)

Stephens, Mark

1994-05-01

A well exposed outcrop in the Kayenta Formation (Lower Jurassic) in southwestern Colorado was examined in order to delineate the stratigraphy in the subsurface and test the usefulness of ground-probing radar (GPR) in three-dimensional architectural studies. Two fluvial styles are present within the Kayenta Formation. Sandbodies within the lower third of the outcrop are characterized by parallel laminations that can be followed in the cliff-face for well over 300 m. These sandbodies are sheet-like in appearance, and represent high-energy flood deposits that most likely resulted from episodic floods. The remainder of the outcrop is characterized by concave-up channel deposits with bank-attached and mid-channel macroforms. Their presence suggests a multiple channel river system. The GPR data collected on the cliff-top, together with sedimentological data, provided a partial three-dimensional picture of the paleo-river system within the Kayenta Formation. The 3-D picture consists of stacked channel-bar lenses approximately 50 m in diameter. The GPR technique offers a very effective means of delineating the subsurface stratigraphy. Its high resolution capabilities, easy mobility, and rapid rate of data collection make it a useful tool. Its shallow penetration depth and limitation to low-conductivity environments are its only drawbacks.

Formation of laser-induced periodic surface structures on niobium by femtosecond laser irradiation

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

Pan, A.; Dias, A.; Gomez-Aranzadi, M.

2014-05-07

The surface morphology of a Niobium sample, irradiated in air by a femtosecond laser with a wavelength of 800 nm and pulse duration of 100 fs, was examined. The period of the micro/nanostructures, parallel and perpendicularly oriented to the linearly polarized fs-laser beam, was studied by means of 2D Fast Fourier Transform analysis. The observed Laser-Induced Periodic Surface Structures (LIPSS) were classified as Low Spatial Frequency LIPSS (periods about 600 nm) and High Spatial Frequency LIPSS, showing a periodicity around 300 nm, both of them perpendicularly oriented to the polarization of the incident laser wave. Moreover, parallel high spatial frequency LIPSS were observedmore » with periods around 100 nm located at the peripheral areas of the laser fingerprint and overwritten on the perpendicular periodic gratings. The results indicate that this method of micro/nanostructuring allows controlling the Niobium grating period by the number of pulses applied, so the scan speed and not the fluence is the key parameter of control. A discussion on the mechanism of the surface topology evolution was also introduced.« less

Unidirectional spin density wave state in metallic (Sr 1-xLax) 2IrO 4

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

Chen, Xiang; Schmehr, Julian L.; Islam, Zahirul

Materials that exhibit both strong spin–orbit coupling and electron correlation effects are predicted to host numerous new electronic states. One prominent example is the J eff = 1/2 Mott state in Sr 2IrO 4, where introducing carriers is predicted to manifest high temperature superconductivity analogous to the S=1/2 Mott state of La 2CuO 4. While bulk super- conductivity currently remains elusive, anomalous quasiparticle behaviors paralleling those in the cuprates such as pseudogap formation and the formation of a d-wave gap are observed upon electron-doping Sr 2IrO 4. Here we establish a magnetic parallel between electron-doped Sr 2IrO 4 and hole-dopedmore » La 2CuO 4 by unveiling a spin density wave state in electron-doped Sr 2IrO 4. Our magnetic resonant X-ray scattering data reveal the presence of an incom- mensurate magnetic state reminiscent of the diagonal spin density wave state observed in the monolayer cuprate (La 1-xSr x) 2CuO 4. This link supports the conjecture that the quenched Mott phases in electron-doped Sr 2IrO 4 and hole-doped La 2CuO 4 support common competing electronic phases.« less

Robotic platform for parallelized cultivation and monitoring of microbial growth parameters in microwell plates.

PubMed

Knepper, Andreas; Heiser, Michael; Glauche, Florian; Neubauer, Peter

2014-12-01

The enormous variation possibilities of bioprocesses challenge process development to fix a commercial process with respect to costs and time. Although some cultivation systems and some devices for unit operations combine the latest technology on miniaturization, parallelization, and sensing, the degree of automation in upstream and downstream bioprocess development is still limited to single steps. We aim to face this challenge by an interdisciplinary approach to significantly shorten development times and costs. As a first step, we scaled down analytical assays to the microliter scale and created automated procedures for starting the cultivation and monitoring the optical density (OD), pH, concentrations of glucose and acetate in the culture medium, and product formation in fed-batch cultures in the 96-well format. Then, the separate measurements of pH, OD, and concentrations of acetate and glucose were combined to one method. This method enables automated process monitoring at dedicated intervals (e.g., also during the night). By this approach, we managed to increase the information content of cultivations in 96-microwell plates, thus turning them into a suitable tool for high-throughput bioprocess development. Here, we present the flowcharts as well as cultivation data of our automation approach. © 2014 Society for Laboratory Automation and Screening.

Utilizing borehole electrical images to interpret lithofacies of fan-delta: A case study of Lower Triassic Baikouquan Formation in Mahu Depression, Junggar Basin, China

NASA Astrophysics Data System (ADS)

Yuan, Rui; Zhang, Changmin; Tang, Yong; Qu, Jianhua; Guo, Xudong; Sun, Yuqiu; Zhu, Rui; Zhou, Yuanquan (Nancy)

2017-11-01

Large-scale conglomerate fan-delta aprons were typical deposits on the slope of Mahu Depression during the Early Triassic. Without outcrops, it is difficult to study the lithofacies only by examining the limited cores from the main oil-bearing interval of the Baikouquan Formation. Borehole electrical imaging log provides abundant high-resolution geologic information that is obtainable only from real rocks previously. Referring to the lithology and sedimentary structure of cores, a case study of fan-deltas in the Lower Triassic Baikouquan Formation of the Mahu Depression presents a methodology for interpreting the complicated lithofacies utilizing borehole electrical images. Eleven types of lithologies and five types of sedimentary structures are summarized in borehole electrical images. The sediments are fining upward from gravel to silt and clay in the Baikouquan Formation. Fine-pebbles and granules are the main deposits in T1b1 and T1b2, but sandstones, siltstones and mudstones are more developed in T1b3. The main sedimentary textures are massive beddings, cross beddings and scour-and-fill structures. Parallel and horizontal beddings are more developed in T1b3 relatively. On integrated analysis of the lithology and sedimentary structure, eight lithofacies from electrical images, referred to as image lithofacies, is established for the fan-deltas. Granules to coarse-pebbles within massive beddings, granules to coarse-pebbles within cross and parallel beddings, siltstones within horizontal and massive beddings are the most developed lithofacies respectively in T1b1, T1b2 and T1b3. It indicates a gradual rise of the lake level of Mahu depression during the Early Triassic, with the fan-delta aprons retrograding towards to the margin of the basin. Therefore, the borehole electrical imaging log compensate for the limitation of cores of the Baikouquan Formation, providing an effective new approach to interpret the lithofacies of fan-delta.

The formation of magnetic silicide Fe3Si clusters during ion implantation

NASA Astrophysics Data System (ADS)

Balakirev, N.; Zhikharev, V.; Gumarov, G.

2014-05-01

A simple two-dimensional model of the formation of magnetic silicide Fe3Si clusters during high-dose Fe ion implantation into silicon has been proposed and the cluster growth process has been computer simulated. The model takes into account the interaction between the cluster magnetization and magnetic moments of Fe atoms random walking in the implanted layer. If the clusters are formed in the presence of the external magnetic field parallel to the implanted layer, the model predicts the elongation of the growing cluster in the field direction. It has been proposed that the cluster elongation results in the uniaxial magnetic anisotropy in the plane of the implanted layer, which is observed in iron silicide films ion-beam synthesized in the external magnetic field.

IPython: components for interactive and parallel computing across disciplines. (Invited)

NASA Astrophysics Data System (ADS)

Perez, F.; Bussonnier, M.; Frederic, J. D.; Froehle, B. M.; Granger, B. E.; Ivanov, P.; Kluyver, T.; Patterson, E.; Ragan-Kelley, B.; Sailer, Z.

2013-12-01

Scientific computing is an inherently exploratory activity that requires constantly cycling between code, data and results, each time adjusting the computations as new insights and questions arise. To support such a workflow, good interactive environments are critical. The IPython project (http://ipython.org) provides a rich architecture for interactive computing with: 1. Terminal-based and graphical interactive consoles. 2. A web-based Notebook system with support for code, text, mathematical expressions, inline plots and other rich media. 3. Easy to use, high performance tools for parallel computing. Despite its roots in Python, the IPython architecture is designed in a language-agnostic way to facilitate interactive computing in any language. This allows users to mix Python with Julia, R, Octave, Ruby, Perl, Bash and more, as well as to develop native clients in other languages that reuse the IPython clients. In this talk, I will show how IPython supports all stages in the lifecycle of a scientific idea: 1. Individual exploration. 2. Collaborative development. 3. Production runs with parallel resources. 4. Publication. 5. Education. In particular, the IPython Notebook provides an environment for "literate computing" with a tight integration of narrative and computation (including parallel computing). These Notebooks are stored in a JSON-based document format that provides an "executable paper": notebooks can be version controlled, exported to HTML or PDF for publication, and used for teaching.

Formative Research regarding Kidney Disease Health Information in a Latino American Sample: Associations among Message Frame, Threat, Efficacy, Message Effectiveness, and Behavioral Intention

ERIC Educational Resources Information Center

Maguire, Katheryn C.; Gardner, Jay; Sopory, Pradeep; Jian, Guowei; Roach, Marcia; Amschlinger, Joe; Moreno, Marcia; Pettey, Gary; Piccone, Gianfranco

2010-01-01

Using prospect theory and the extended parallel process model, this study examined the effect of gain/loss message framing on perceptions of severity, susceptibility, response efficacy, and self efficacy (derived from the extended parallel process model), as well as perception of message effectiveness and behavioral intention in a community based…

Dimer formation of perylene: An ultracold spectroscopic and computational study

NASA Astrophysics Data System (ADS)

Birer, Ö.; Yurtsever, E.

2015-10-01

The electronic spectra of perylene inside helium nanodroplets recorded by the depletion method are presented. The results show two broad peaks in addition to sharp monomer vibronic transitions due to dimer formation. In order to understand the details of the spectra, first the dimer formation is studied by DFT and SCS-MP2 calculations and then the electronic spectra are calculated at the minima of the potential energy surface (PES). Theoretical calculations show that there are two low-lying energetically degenerate dimer structures; namely a parallel displaced one and a rotated stacked one. PES around these minima is very flat with a number of local minima at higher energies which at the experimental temperatures cannot be populated. Even though thermodynamically these two structures are equally populated, dynamical considerations point out that in helium droplet the parallel displaced geometry is encouraged by the natural alignment of the molecules due to the acquired angular momentum following the pick-up process. The calculated spectrum of the parallel displaced geometry predicts the positions of the dimer transitions within 30 nm of the experimental spectrum. Furthermore, the difference between the two dimer transitions is accurately predicted to be about 25 nm while the experimental difference was about 20 nm. Such a small difference could only be detected due to the ultracold conditions helium nanodroplets provided.

Parallel hyperbolic PDE simulation on clusters: Cell versus GPU

NASA Astrophysics Data System (ADS)

Rostrup, Scott; De Sterck, Hans

2010-12-01

Increasingly, high-performance computing is looking towards data-parallel computational devices to enhance computational performance. Two technologies that have received significant attention are IBM's Cell Processor and NVIDIA's CUDA programming model for graphics processing unit (GPU) computing. In this paper we investigate the acceleration of parallel hyperbolic partial differential equation simulation on structured grids with explicit time integration on clusters with Cell and GPU backends. The message passing interface (MPI) is used for communication between nodes at the coarsest level of parallelism. Optimizations of the simulation code at the several finer levels of parallelism that the data-parallel devices provide are described in terms of data layout, data flow and data-parallel instructions. Optimized Cell and GPU performance are compared with reference code performance on a single x86 central processing unit (CPU) core in single and double precision. We further compare the CPU, Cell and GPU platforms on a chip-to-chip basis, and compare performance on single cluster nodes with two CPUs, two Cell processors or two GPUs in a shared memory configuration (without MPI). We finally compare performance on clusters with 32 CPUs, 32 Cell processors, and 32 GPUs using MPI. Our GPU cluster results use NVIDIA Tesla GPUs with GT200 architecture, but some preliminary results on recently introduced NVIDIA GPUs with the next-generation Fermi architecture are also included. This paper provides computational scientists and engineers who are considering porting their codes to accelerator environments with insight into how structured grid based explicit algorithms can be optimized for clusters with Cell and GPU accelerators. It also provides insight into the speed-up that may be gained on current and future accelerator architectures for this class of applications. Program summaryProgram title: SWsolver Catalogue identifier: AEGY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v3 No. of lines in distributed program, including test data, etc.: 59 168 No. of bytes in distributed program, including test data, etc.: 453 409 Distribution format: tar.gz Programming language: C, CUDA Computer: Parallel Computing Clusters. Individual compute nodes may consist of x86 CPU, Cell processor, or x86 CPU with attached NVIDIA GPU accelerator. Operating system: Linux Has the code been vectorised or parallelized?: Yes. Tested on 1-128 x86 CPU cores, 1-32 Cell Processors, and 1-32 NVIDIA GPUs. RAM: Tested on Problems requiring up to 4 GB per compute node. Classification: 12 External routines: MPI, CUDA, IBM Cell SDK Nature of problem: MPI-parallel simulation of Shallow Water equations using high-resolution 2D hyperbolic equation solver on regular Cartesian grids for x86 CPU, Cell Processor, and NVIDIA GPU using CUDA. Solution method: SWsolver provides 3 implementations of a high-resolution 2D Shallow Water equation solver on regular Cartesian grids, for CPU, Cell Processor, and NVIDIA GPU. Each implementation uses MPI to divide work across a parallel computing cluster. Additional comments: Sub-program numdiff is used for the test run.

Light fluorous-tagged traceless one-pot synthesis of benzimidazoles facilitated by microwave irradiation.

PubMed

Tseng, Chih-Chung; Tasi, Cheng-Hsun; Sun, Chung-Ming

2012-06-01

A novel protocol for rapid assemble of benzimidazole framework has been demonstrated. This method incorporated with light fluorous-tag provides a convenient method for diversification of benzimidazoles and for easy purification via fluorous solid-phase extraction (F-SPE) in a parallel manner. The key transformation of this study involves in situ reduction of aromatic nitro compound, amide formation, cyclization and aromatization promoted by microwave irradiation in a one-pot fashion. The strategy is envisaged to be applied for the establishment of drug-like small molecule libraries for high throughput screening.

In situ patterned micro 3D liver constructs for parallel toxicology testing in a fluidic device

PubMed Central

Skardal, Aleksander; Devarasetty, Mahesh; Soker, Shay; Hall, Adam R

2017-01-01

3D tissue models are increasingly being implemented for drug and toxicology testing. However, the creation of tissue-engineered constructs for this purpose often relies on complex biofabrication techniques that are time consuming, expensive, and difficult to scale up. Here, we describe a strategy for realizing multiple tissue constructs in a parallel microfluidic platform using an approach that is simple and can be easily scaled for high-throughput formats. Liver cells mixed with a UV-crosslinkable hydrogel solution are introduced into parallel channels of a sealed microfluidic device and photopatterned to produce stable tissue constructs in situ. The remaining uncrosslinked material is washed away, leaving the structures in place. By using a hydrogel that specifically mimics the properties of the natural extracellular matrix, we closely emulate native tissue, resulting in constructs that remain stable and functional in the device during a 7-day culture time course under recirculating media flow. As proof of principle for toxicology analysis, we expose the constructs to ethyl alcohol (0–500 mM) and show that the cell viability and the secretion of urea and albumin decrease with increasing alcohol exposure, while markers for cell damage increase. PMID:26355538

In situ patterned micro 3D liver constructs for parallel toxicology testing in a fluidic device.

PubMed

Skardal, Aleksander; Devarasetty, Mahesh; Soker, Shay; Hall, Adam R

2015-09-10

3D tissue models are increasingly being implemented for drug and toxicology testing. However, the creation of tissue-engineered constructs for this purpose often relies on complex biofabrication techniques that are time consuming, expensive, and difficult to scale up. Here, we describe a strategy for realizing multiple tissue constructs in a parallel microfluidic platform using an approach that is simple and can be easily scaled for high-throughput formats. Liver cells mixed with a UV-crosslinkable hydrogel solution are introduced into parallel channels of a sealed microfluidic device and photopatterned to produce stable tissue constructs in situ. The remaining uncrosslinked material is washed away, leaving the structures in place. By using a hydrogel that specifically mimics the properties of the natural extracellular matrix, we closely emulate native tissue, resulting in constructs that remain stable and functional in the device during a 7-day culture time course under recirculating media flow. As proof of principle for toxicology analysis, we expose the constructs to ethyl alcohol (0-500 mM) and show that the cell viability and the secretion of urea and albumin decrease with increasing alcohol exposure, while markers for cell damage increase.

Formation of organic layer on femtosecond laser-induced periodic surface structures

NASA Astrophysics Data System (ADS)

Yasumaru, Naoki; Sentoku, Eisuke; Kiuchi, Junsuke

2017-05-01

Two types of laser-induced periodic surface structures (LIPSS) formed on titanium by femtosecond (fs) laser pulses (λ = 800 nm, τ = 180 fs, ν = 1 kHz) in air were investigated experimentally. At a laser fluence F above the ablation threshold, LIPSS with a minimum mean spacing of D < λ⁄2 were observed perpendicular to the laser polarization direction. In contrast, for F slightly below than the ablation threshold, ultrafine LIPSS with a minimum value of D < λ/10 were formed parallel to the polarization direction. The surface roughness of the parallel-oriented LIPSS was almost the same as that of the non-irradiated surface, unlike the high roughness of the perpendicular-oriented LIPSS. In addition, although the surface state of the parallel-oriented LIPSS was the same as that of the non-irradiated surface, the perpendicular-oriented LIPSS were covered with an organic thin film similar to a cellulose derivative that cannot be easily formed by conventional chemical synthesis. The results of these surface analyses indicate that these two types of LIPSS are formed through different mechanisms. This fs-laser processing technique may become a new technology for the artificial synthesis of cellulose derivatives.

Changes in collagen fibril network organization and proteoglycan distribution in equine articular cartilage during maturation and growth

PubMed Central

Hyttinen, Mika M; Holopainen, Jaakko; René van Weeren, P; Firth, Elwyn C; Helminen, Heikki J; Brama, Pieter A J

2009-01-01

The aim of this study was to record growth-related changes in collagen network organization and proteoglycan distribution in intermittently peak-loaded and continuously lower-level-loaded articular cartilage. Cartilage from the proximal phalangeal bone of the equine metacarpophalangeal joint at birth, at 5, 11 and 18 months, and at 6–10 years of age was collected from two sites. Site 1, at the joint margin, is unloaded at slow gaits but is subjected to high-intensity loading during athletic activity; site 2 is a continuously but less intensively loaded site in the centre of the joint. The degree of collagen parallelism was determined with quantitative polarized light microscopy and the parallelism index for collagen fibrils was computed from the cartilage surface to the osteochondral junction. Concurrent changes in the proteoglycan distribution were quantified with digital densitometry. We found that the parallelism index increased significantly with age (up to 90%). At birth, site 2 exhibited a more organized collagen network than site 1. In adult horses this situation was reversed. The superficial and intermediate zones exhibited the greatest reorganization of collagen. Site 1 had a higher proteoglycan content than site 2 at birth but here too the situation was reversed in adult horses. We conclude that large changes in joint loading during growth and maturation in the period from birth to adulthood profoundly affect the architecture of the collagen network in equine cartilage. In addition, the distribution and content of proteoglycans are modified significantly by altered joint use. Intermittent peak-loading with shear seems to induce higher collagen parallelism and a lower proteoglycan content in cartilage than more constant weight-bearing. Therefore, we hypothesize that the formation of mature articular cartilage with a highly parallel collagen network and relatively low proteoglycan content in the peak-loaded area of a joint is needed to withstand intermittent stress and shear, whereas a constantly weight-bearing joint area benefits from lower collagen parallelism and a higher proteoglycan content. PMID:19732210

Conformation and structural changes of diblock copolymers with octopus-like micelle formation in the presence of external stimuli

NASA Astrophysics Data System (ADS)

Dammertz, K.; Saier, A. M.; Marti, O.; Amirkhani, M.

2014-04-01

External stimuli such as vapours and electric fields can be used to manipulate the formation of AB-diblock copolymers on surfaces. We study the conformational variation of PS-b-PMMA (polystyrene-block-poly(methyl methacrylate)), PS and PMMA adsorbed on mica and their response to saturated water or chloroform atmospheres. Using specimens with only partial polymer coverage, new unanticipated effects were observed. Water vapour, a non-solvent for all three polymers, was found to cause high surface mobility. In contrast, chloroform vapour (a solvent for all three polymers) proved to be less efficient. Furthermore, the influence of an additional applied electric field was investigated. A dc field oriented parallel to the sample surface induces the formation of polymer islands which assemble into wormlike chains. Moreover, PS-b-PMMA forms octopus-like micelles (OLMs) on mica. Under the external stimuli mentioned above, the wormlike formations of OLMs are able to align in the direction of the external electric field. In the absence of an electric field, the OLMs disaggregate and exhibit phase separated structures under chloroform vapour.

Photonic crystal biosensor microplates with integrated fluid networks for high throughput applications in drug discovery

NASA Astrophysics Data System (ADS)

Choi, Charles J.; Chan, Leo L.; Pineda, Maria F.; Cunningham, Brian T.

2007-09-01

Assays used in pharmaceutical research require a system that can not only detect biochemical interactions with high sensitivity, but that can also perform many measurements in parallel while consuming low volumes of reagents. While nearly all label-free biosensor transducers to date have been interfaced with a flow channel, the liquid handling system is typically aligned and bonded to the transducer for supplying analytes to only a few sensors in parallel. In this presentation, we describe a fabrication approach for photonic crystal biosensors that utilizes nanoreplica molding to produce a network of sensors that are automatically self-aligned with a microfluidic network in a single process step. The sensor/fluid network is inexpensively produced on large surface areas upon flexible plastic substrates, allowing the device to be incorporated into standard format 96-well microplates. A simple flow scheme using hydrostatic pressure applied through a single control point enables immobilization of capture ligands upon a large number of sensors with 220 nL of reagent, and subsequent exposure of the sensors to test samples. A high resolution imaging detection instrument is capable of monitoring the binding within parallel channels at rates compatible with determining kinetic binding constants between the immobilized ligands and the analytes. The first implementation of this system is capable of monitoring the kinetic interactions of 11 flow channels at once, and a total of 88 channels within an integrated biosensor microplate in rapid succession. The system was initially tested to characterize the interaction between sets of proteins with known binding behavior.

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

Kahlenberg, Volker; Konzett, Juergen; Kaindl, Reinhard

High-pressure synthesis experiments in the system Na{sub 2}O-Y{sub 2}O{sub 3}-SiO{sub 2} revealed the existence of a previously unknown polymorph of NaYSi{sub 2}O{sub 6} or Na{sub 3}Y{sub 3}[Si{sub 3}O{sub 9}]{sub 2} which was quenched from 3.0 GPa and 1000 deg. C. Structural investigations on this modification have been performed using single-crystal X-ray diffraction data collected at ambient conditions. Furthermore, unpolarized micro-Raman spectra have been obtained from single-crystal material. The high-P modification of NaYSi{sub 2}O{sub 6} crystallizes in the centrosymmetric space group C2/c with 12 formula units per cell (a=8.2131(9) A, b=10.3983(14) A, c=17.6542(21) A, {beta}=100.804(9){sup o}, V=1481.0(3) A{sup 3}, R(|F|)=0.033 formore » 1142 independent observed reflections) and belongs to the group of cyclo-silicates. Basic building units are isolated three-membered [Si{sub 3}O{sub 9}] rings located in layers parallel to (010). Within a single layer the rings are concentrated in strings parallel to [100]. The sequence of directedness of up (U) or down (D) pointing tetrahedra of a single ring is UUU or DDD, respectively. Stacking of the layers parallel to b results in the formation of a three-dimensional structure in which yttrium and sodium cations are incorporated for charge compensation. In more detail, four non-tetrahedral cation positions can be differentiated which are coordinated by 6 and 8 oxygen ligands. Refinements of the site occupancies did not reveal any indication for mixed Na-Y populations on these positions. Finally, several geometrical parameters of rings occurring in cyclo-trisilicate structures have been compiled and are discussed. - Graphical abstract: Projection of the whole structure of high-P NaYSi{sub 2}O{sub 6} parallel to [100].« less

Archimedes' principle for characterisation of recombinant whole cell biocatalysts.

PubMed

Schmitt, Steven; Walser, Marcel; Rehmann, Michael; Oesterle, Sabine; Panke, Sven; Held, Martin

2018-02-14

The ability of whole cells to catalyse multistep reactions, often yielding synthetically demanding compounds later used by industrial biotech or pharma, makes them an indispensable tool of synthetic chemistry. The complex reaction network employed by cellular catalysts and the still only moderate predictive power of modelling approaches leaves this tool challenging to engineer. Frequently, large libraries of semi-rationally generated variants are sampled in high-throughput mode in order to then identify improved catalysts. We present a method for space- and time-efficient processing of very large libraries (10 7 ) of recombinant cellular catalysts, in which the phenotypic characterisation and the isolation of positive variants for the entire library is done within one minute in a single, highly parallelized operation. Specifically, product formation in nanolitre-sized cultivation vessels is sensed and translated into the formation of catalase as a reporter protein. Exposure to hydrogen peroxide leads to oxygen gas formation and thus to a density shift of the cultivation vessel. Exploiting Archimedes' principle, this density shift and the resulting upward buoyancy force can be used for batch-wise library sampling. We demonstrate the potential of the method for both, screening and selection protocols, and envision a wide applicability of the system for biosensor-based assays.

Parallel Processing at the High School Level.

ERIC Educational Resources Information Center

Sheary, Kathryn Anne

This study investigated the ability of high school students to cognitively understand and implement parallel processing. Data indicates that most parallel processing is being taught at the university level. Instructional modules on C, Linux, and the parallel processing language, P4, were designed to show that high school students are highly…

A high-performance spatial database based approach for pathology imaging algorithm evaluation

PubMed Central

Wang, Fusheng; Kong, Jun; Gao, Jingjing; Cooper, Lee A.D.; Kurc, Tahsin; Zhou, Zhengwen; Adler, David; Vergara-Niedermayr, Cristobal; Katigbak, Bryan; Brat, Daniel J.; Saltz, Joel H.

2013-01-01

Background: Algorithm evaluation provides a means to characterize variability across image analysis algorithms, validate algorithms by comparison with human annotations, combine results from multiple algorithms for performance improvement, and facilitate algorithm sensitivity studies. The sizes of images and image analysis results in pathology image analysis pose significant challenges in algorithm evaluation. We present an efficient parallel spatial database approach to model, normalize, manage, and query large volumes of analytical image result data. This provides an efficient platform for algorithm evaluation. Our experiments with a set of brain tumor images demonstrate the application, scalability, and effectiveness of the platform. Context: The paper describes an approach and platform for evaluation of pathology image analysis algorithms. The platform facilitates algorithm evaluation through a high-performance database built on the Pathology Analytic Imaging Standards (PAIS) data model. Aims: (1) Develop a framework to support algorithm evaluation by modeling and managing analytical results and human annotations from pathology images; (2) Create a robust data normalization tool for converting, validating, and fixing spatial data from algorithm or human annotations; (3) Develop a set of queries to support data sampling and result comparisons; (4) Achieve high performance computation capacity via a parallel data management infrastructure, parallel data loading and spatial indexing optimizations in this infrastructure. Materials and Methods: We have considered two scenarios for algorithm evaluation: (1) algorithm comparison where multiple result sets from different methods are compared and consolidated; and (2) algorithm validation where algorithm results are compared with human annotations. We have developed a spatial normalization toolkit to validate and normalize spatial boundaries produced by image analysis algorithms or human annotations. The validated data were formatted based on the PAIS data model and loaded into a spatial database. To support efficient data loading, we have implemented a parallel data loading tool that takes advantage of multi-core CPUs to accelerate data injection. The spatial database manages both geometric shapes and image features or classifications, and enables spatial sampling, result comparison, and result aggregation through expressive structured query language (SQL) queries with spatial extensions. To provide scalable and efficient query support, we have employed a shared nothing parallel database architecture, which distributes data homogenously across multiple database partitions to take advantage of parallel computation power and implements spatial indexing to achieve high I/O throughput. Results: Our work proposes a high performance, parallel spatial database platform for algorithm validation and comparison. This platform was evaluated by storing, managing, and comparing analysis results from a set of brain tumor whole slide images. The tools we develop are open source and available to download. Conclusions: Pathology image algorithm validation and comparison are essential to iterative algorithm development and refinement. One critical component is the support for queries involving spatial predicates and comparisons. In our work, we develop an efficient data model and parallel database approach to model, normalize, manage and query large volumes of analytical image result data. Our experiments demonstrate that the data partitioning strategy and the grid-based indexing result in good data distribution across database nodes and reduce I/O overhead in spatial join queries through parallel retrieval of relevant data and quick subsetting of datasets. The set of tools in the framework provide a full pipeline to normalize, load, manage and query analytical results for algorithm evaluation. PMID:23599905

Formation and evolution of bubbly screens in confined oscillating bubbly liquids.

PubMed

Shklyaev, Sergey; Straube, Arthur V

2010-01-01

We consider the dynamics of dilute monodisperse bubbly liquid confined by two plane solid walls and subject to small-amplitude high-frequency oscillations normal to the walls. The initial state corresponds to the uniform distribution of bubbles and motionless liquid. The period of external driving is assumed much smaller than typical relaxation times for a single bubble but larger than the period of volume eigenoscillations. The time-averaged description accounting for the two-way coupling between the liquid and the bubbles is applied. We show that the model predicts accumulation of bubbles in thin sheets parallel to the walls. These singular structures, which are formally characterized by infinitely thin width and infinitely high concentration, are referred to as bubbly screens. The formation of a bubbly screen is described analytically in terms of a self-similar solution, which is in agreement with numerical simulations. We study the evolution of bubbly screens and detect a one-dimensional stationary state, which is shown to be unconditionally unstable.

Pattern formation and filamentation in low temperature, magnetized plasmas - a numerical approach

NASA Astrophysics Data System (ADS)

Menati, Mohamad; Konopka, Uwe; Thomas, Edward

2017-10-01

In low-temperature discharges under the influence of high magnetic field, pattern and filament formation in the plasma has been reported by different groups. The phenomena present themselves as bright plasma columns (filaments) oriented parallel to the magnetic field lines at high magnetic field regime. The plasma structure can filament into different shapes from single columns to spiral and bright rings when viewed from the top. In spite of the extensive experimental observations, the observed effects lack a detailed theoretical and numerical description. In an attempt to numerically explain the plasma filamentation, we present a simplified model for the plasma discharge and power deposition into the plasma. Based on the model, 2-D and 3-D codes are being developed that solve Poisson's equation along with the fluid equations to obtain a self-consistent description of the plasma. The model and preliminary results applied to the specific plasma conditions will be presented. This work was supported by the US Dept. of Energy and NSF, DE-SC0016330, PHY-1613087.

Formation and evolution of bubbly screens in confined oscillating bubbly liquids

NASA Astrophysics Data System (ADS)

Shklyaev, Sergey; Straube, Arthur V.

2010-01-01

We consider the dynamics of dilute monodisperse bubbly liquid confined by two plane solid walls and subject to small-amplitude high-frequency oscillations normal to the walls. The initial state corresponds to the uniform distribution of bubbles and motionless liquid. The period of external driving is assumed much smaller than typical relaxation times for a single bubble but larger than the period of volume eigenoscillations. The time-averaged description accounting for the two-way coupling between the liquid and the bubbles is applied. We show that the model predicts accumulation of bubbles in thin sheets parallel to the walls. These singular structures, which are formally characterized by infinitely thin width and infinitely high concentration, are referred to as bubbly screens. The formation of a bubbly screen is described analytically in terms of a self-similar solution, which is in agreement with numerical simulations. We study the evolution of bubbly screens and detect a one-dimensional stationary state, which is shown to be unconditionally unstable.

Lipid tubules Formed by Flow-Controlled Hydration

NASA Astrophysics Data System (ADS)

Yuan, Jing; Hirst, Linda S.

2007-03-01

Self-assembled cylindrical tubules from lipid molecules have attracted considerable attention because of their interesting supramolecular structures and technological applications. Schnur et al. [1] reported the formation of tubular microstructures from a series of diacetylenic phospholipids after liposomes were cooled through their chain melting transition. After that, several methods have been developed to fabricate such unique microstructures mainly by means of deforming preformed Giant unilamellar vesicles. Here we present a simple strategy to construct lipid microtubules through a flow-controlled lipid hydration. Fluorescent microscopy and Confocal Laser Microscopy were used to visualize the formation and the structure of the lipid tubules. Tubules were found to develop following the direction of the dynamic flow with highly parallel alignment. At high flow speeds, partial cross-linking of the lipid tubules was observed. To demonstrate the generality of this method, different types of phospholipids, such as Phosphatidic Acid (PA), Phosphatidylserine (PS), Phosphatidylethanolamine (PE), and Phosphatidylglycerol (PG) were investigated. [1] J.M. Schnur et al, Science, 264, 945 (1994).

An Educational Intervention to Train Community Pharmacists in Providing Specialized Asthma Care

PubMed Central

Smith, Lorraine; Armour, Carol; Krass, Ines

2006-01-01

Objectives The development, implementation, and evaluation of an educational intervention to facilitate specialized asthma care provision by community pharmacists. Design Formative evaluation and a parallel group repeated measures design were used to test the effect of an educational intervention on pharmacist satisfaction and practice behavior as well as patient outcomes. The educational intervention was based on practitioner needs and principles of adult learning using flexible delivery formats. Assessment In the intervention area, 15 pharmacists were trained with the educational intervention, and they provided specialized asthma care to 52 patients over 6 months, while in the control area, 12 pharmacists provided “usual care” to 50 patients. The intervention pharmacists were highly satisfied with the education received and rated most aspects highly. Improvements in patient clinical, humanistic, and economic outcomes in the intervention area were obtained. Conclusion The positive results of the educational intervention demonstrate the effectiveness of an educational approach grounded in the theory that inducing behavioral changes in pharmacy practitioners results in improved patient outcomes. PMID:17149447

Transformation of shock-compressed graphite to hexagonal diamond in nanoseconds

PubMed Central

Turneaure, Stefan J.; Sharma, Surinder M.; Volz, Travis J.; Winey, J. M.; Gupta, Yogendra M.

2017-01-01

The graphite-to-diamond transformation under shock compression has been of broad scientific interest since 1961. The formation of hexagonal diamond (HD) is of particular interest because it is expected to be harder than cubic diamond and due to its use in terrestrial sciences as a marker at meteorite impact sites. However, the formation of diamond having a fully hexagonal structure continues to be questioned and remains unresolved. Using real-time (nanosecond), in situ x-ray diffraction measurements, we show unequivocally that highly oriented pyrolytic graphite, shock-compressed along the c axis to 50 GPa, transforms to highly oriented elastically strained HD with the (100)HD plane parallel to the graphite basal plane. These findings contradict recent molecular dynamics simulation results for the shock-induced graphite-to-diamond transformation and provide a benchmark for future theoretical simulations. Additionally, our results show that an earlier report of HD forming only above 170 GPa for shocked pyrolytic graphite may lead to incorrect interpretations of meteorite impact events. PMID:29098183

Transformation of shock-compressed graphite to hexagonal diamond in nanoseconds

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

Turneaure, Stefan J.; Sharma, Surinder M.; Volz, Travis J.

The graphite-to-diamond transformation under shock compression has been of broad scientific interest since 1961. The formation of hexagonal diamond (HD) is of particular interest because it is expected to be harder than cubic diamond and due to its use in terrestrial sciences as a marker at meteorite impact sites. However, the formation of diamond having a fully hexagonal structure continues to be questioned and remains unresolved. Using real-time (nanosecond), in situ x-ray diffraction measurements, we show unequivocally that highly oriented pyrolytic graphite, shock-compressed along the c axis to 50 GPa, transforms to highly oriented elastically strained HD with the (100)HDmore » plane parallel to the graphite basal plane. These findings contradict recent molecular dynamics simulation results for the shock-induced graphite-to-diamond transformation and provide a benchmark for future theoretical simulations. Additionally, our results show that an earlier report of HD forming only above 170 GPa for shocked pyrolytic graphite may lead to incorrect interpretations of meteorite impact events.« less

Transformation of shock-compressed graphite to hexagonal diamond in nanoseconds

DOE PAGES

Turneaure, Stefan J.; Sharma, Surinder M.; Volz, Travis J.; ...

2017-10-27

The graphite-to-diamond transformation under shock compression has been of broad scientific interest since 1961. The formation of hexagonal diamond (HD) is of particular interest because it is expected to be harder than cubic diamond and due to its use in terrestrial sciences as a marker at meteorite impact sites. However, the formation of diamond having a fully hexagonal structure continues to be questioned and remains unresolved. Using real-time (nanosecond), in situ x-ray diffraction measurements, we show unequivocally that highly oriented pyrolytic graphite, shock-compressed along the c axis to 50 GPa, transforms to highly oriented elastically strained HD with the (100)HDmore » plane parallel to the graphite basal plane. These findings contradict recent molecular dynamics simulation results for the shock-induced graphite-to-diamond transformation and provide a benchmark for future theoretical simulations. Additionally, our results show that an earlier report of HD forming only above 170 GPa for shocked pyrolytic graphite may lead to incorrect interpretations of meteorite impact events.« less

Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations

NASA Technical Reports Server (NTRS)

Norman, Michael L.

1997-01-01

Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.

Application of Coaxial Ion Gun for Film Generation and Ion Implantation

NASA Astrophysics Data System (ADS)

Takatsu, Mikio; Asai, Tomohiko; Kurumi, Satoshi; Suzuki, Kaoru; Hirose, Hideharu; Masutani, Shigeyuki

A magnetized coaxial plasma gun (MCPG) is here utilized for deposition on high-melting-point metals. MCPGs have hitherto been studied mostly in the context of nuclear fusion research, for particle and magnetic helicity injection and spheromak formation. During spheromak formation, the electrode materials are ionized and mixed into the plasmoid. In this study, this ablation process by gun-current sputtering is enhanced for metallic thin-film generation. In the proposed system geometry, only ionized materials are electromagnetically accelerated by the self-Lorentz force, with ionized operating gas as a magnetized thermal plasmoid, contributing to the thin-film deposition. This reduces the impurity and non-uniformity of the deposited thin-film. Furthermore, as the ions are accelerated in a parallel direction to the injection axis, vertical implantation of the ions into the substrate surface is achieved. To test a potential application of the developed system, experiments were conducted involving the formation of a buffer layer on hard ceramics, for use in dental materials.

Clustering on Magnesium Surfaces - Formation and Diffusion Energies.

PubMed

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and [Formula: see text]. In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a [Formula: see text], clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface [Formula: see text] is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich-Schwoebel barriers converge as the step height is three atomic layers or thicker. Adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.

Microplate-based filter paper assay to measure total cellulase activity.

PubMed

Xiao, Zhizhuang; Storms, Reginald; Tsang, Adrian

2004-12-30

The standard filter paper assay (FPA) published by the International Union of Pure and Applied Chemistry (IUPAC) is widely used to determine total cellulase activity. However, the IUPAC method is not suitable for the parallel analyses of large sample numbers. We describe here a microplate-based method for assaying large sample numbers. To achieve this, we reduced the enzymatic reaction volume to 60 microl from the 1.5 ml used in the IUPAC method. The modified 60-microl format FPA can be carried out in 96-well assay plates. Statistical analyses showed that the cellulase activities of commercial cellulases from Trichoderma reesei and Aspergillus species determined with our 60-microl format FPA were not significantly different from the activities measured with the standard FPA. Our results also indicate that the 60-microl format FPA is quantitative and highly reproducible. Moreover, the addition of excess beta-glucosidase increased the sensitivity of the assay by up to 60%. 2004 Wiley Periodicals, Inc.

High-performance computing — an overview

NASA Astrophysics Data System (ADS)

Marksteiner, Peter

1996-08-01

An overview of high-performance computing (HPC) is given. Different types of computer architectures used in HPC are discussed: vector supercomputers, high-performance RISC processors, various parallel computers like symmetric multiprocessors, workstation clusters, massively parallel processors. Software tools and programming techniques used in HPC are reviewed: vectorizing compilers, optimization and vector tuning, optimization for RISC processors; parallel programming techniques like shared-memory parallelism, message passing and data parallelism; and numerical libraries.

Critical Role of Nitric Oxide-cGMP Cascade in the Formation of cAMP-Dependent Long-Term Memory

ERIC Educational Resources Information Center

Aonuma, Hitoshi; Mizunami, Makoto; Matsumoto, Yukihisa; Unoki, Sae

2006-01-01

Cyclic AMP pathway plays an essential role in formation of long-term memory (LTM). In some species, the nitric oxide (NO)-cyclic GMP pathway has been found to act in parallel and complementary to the cAMP pathway for LTM formation. Here we describe a new role of the NO-cGMP pathway, namely, stimulation of the cAMP pathway to induce LTM. We have…

Cytological, molecular mechanisms and temperature stress regulating production of diploid male gametes in Dianthus caryophyllus L.

PubMed

Zhou, Xuhong; Mo, Xijun; Gui, Min; Wu, Xuewei; Jiang, Yalian; Ma, Lulin; Shi, Ziming; Luo, Ying; Tang, Wenru

2015-12-01

In plant evolution, because of its key role in sexual polyploidization or whole genome duplication events, diploid gamete formation is considered as an important component in diversification and speciation. Environmental stress often triggers unreduced gamete production. However, the molecular, cellular mechanisms and adverse temperature regulating diplogamete production in carnation remain poorly understood. Here, we investigate the cytological basis for 2n male gamete formation and describe the isolation and characterization of the first gene, DcPS1 (Dianthus Caryophyllus Parallel Spindle 1). In addition, we analyze influence of temperature stress on diploid gamete formation and transcript levels of DcPS1. Cytological evidence indicated that 2n male gamete formation is attributable to abnormal spindle orientation at male meiosis II. DcPS1 protein is conserved throughout the plant kingdom and carries domains suggestive of a regulatory function. DcPS1 expression analysis show DcPS1 gene probably have a role in 2n pollen formation. Unreduced pollen formation in various cultivation was sensitive to high or low temperature which was probably regulated by the level of DcPS1 transcripts. In a broader perspective, these findings can have potential applications in fundamental polyploidization research and plant breeding programs. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

The influence of stimulus format on drawing--a functional imaging study of decision making in portrait drawing.

PubMed

Miall, R C; Nam, Se-Ho; Tchalenko, J

2014-11-15

To copy a natural visual image as a line drawing, visual identification and extraction of features in the image must be guided by top-down decisions, and is usually influenced by prior knowledge. In parallel with other behavioral studies testing the relationship between eye and hand movements when drawing, we report here a functional brain imaging study in which we compared drawing of faces and abstract objects: the former can be strongly guided by prior knowledge, the latter less so. To manipulate the difficulty in extracting features to be drawn, each original image was presented in four formats including high contrast line drawings and silhouettes, and as high and low contrast photographic images. We confirmed the detailed eye-hand interaction measures reported in our other behavioral studies by using in-scanner eye-tracking and recording of pen movements with a touch screen. We also show that the brain activation pattern reflects the changes in presentation formats. In particular, by identifying the ventral and lateral occipital areas that were more highly activated during drawing of faces than abstract objects, we found a systematic increase in differential activation for the face-drawing condition, as the presentation format made the decisions more challenging. This study therefore supports theoretical models of how prior knowledge may influence perception in untrained participants, and lead to experience-driven perceptual modulation by trained artists. Copyright © 2014. Published by Elsevier Inc.

High-spatial-frequency periodic surface structures on steel substrate induced by subnanosecond laser pulses

NASA Astrophysics Data System (ADS)

Hikage, Haruki; Nosaka, Nami; Matsuo, Shigeki

2017-11-01

By irradiation with 0.5 ns laser pulses at a wavelength λ = 1.064 µm, laser-induced periodic surface structures (LIPSS) were fabricated on a steel substrate. In addition to low-spatial-frequency LIPSS (LSFL), a high-spatial-frequency LIPSS (HSFL) of period Λ ∼ 0.4λ with two-dimensional expansion was formed, although it is generally recognized that HSFL are formed only by ultrafast laser pulses. The wavevector of the observed HSFL was perpendicular to the electric field of the irradiated laser pulse (each ridge/groove of the HSFL was parallel to the electric field). We discuss the relationship between the formation of HSFL and the pulse duration.

Structural Insights into the Quadruplex-Duplex 3' Interface Formed from a Telomeric Repeat: A Potential Molecular Target.

PubMed

Russo Krauss, Irene; Ramaswamy, Sneha; Neidle, Stephen; Haider, Shozeb; Parkinson, Gary N

2016-02-03

We report here on an X-ray crystallographic and molecular modeling investigation into the complex 3' interface formed between putative parallel stranded G-quadruplexes and a duplex DNA sequence constructed from the human telomeric repeat sequence TTAGGG. Our crystallographic approach provides a detailed snapshot of a telomeric 3' quadruplex-duplex junction: a junction that appears to have the potential to form a unique molecular target for small molecule binding and interference with telomere-related functions. This unique target is particularly relevant as current high-affinity compounds that bind putative G-quadruplex forming sequences only rarely have a high degree of selectivity for a particular quadruplex. Here DNA junctions were assembled using different putative quadruplex-forming scaffolds linked at the 3' end to a telomeric duplex sequence and annealed to a complementary strand. We successfully generated a series of G-quadruplex-duplex containing crystals, both alone and in the presence of ligands. The structures demonstrate the formation of a parallel folded G-quadruplex and a B-form duplex DNA stacked coaxially. Most strikingly, structural data reveals the consistent formation of a TAT triad platform between the two motifs. This triad allows for a continuous stack of bases to link the quadruplex motif with the duplex region. For these crystal structures formed in the absence of ligands, the TAT triad interface occludes ligand binding at the 3' quadruplex-duplex interface, in agreement with in silico docking predictions. However, with the rearrangement of a single nucleotide, a stable pocket can be produced, thus providing an opportunity for the binding of selective molecules at the interface.

Model of formation of Ishtar Terra, Venus

NASA Astrophysics Data System (ADS)

Ansan, V.; Vergely, P.; Masson, Ph.

1996-08-01

For more than a decade, the radar mapping of Venus' surface has revealed that it results from a complex volcanic and tectonic history, especially in the northern latitudes. Ishtar Terra (0°E-62°E) consists of a high plateau, Lakshmi Planum, surrounded by highlands, Freyja Montes to the north and Maxwell Montes to the east. The latter is the highest relief of Venus, standing more than 10 km in elevation. The high resolution of Magellan radar images (120-300 m) allows us to interpret them in terms of tectonics and propose a model of formation for the central part of Ishtar Terra. The detailed tectonic interpretations are based on detailed structural and geologic cartography. The geologic history of Ishtar Terra resulted from two distinct, opposite tectonic stages with an important, transitional volcanic activity. First, Lakshmi Planum, the oldest part of Ishtar Terra is an extensive and complexly fractured plateau that can be compared to a terrestrial craton. Then the plateau is partially covered by fluid lava flows that may be similar to Deccan traps, in India. Second, after the extensional deformation of Lakshmi Planum and its volcanic activity, Freyja and Maxwell Montes formed by WSW-ENE horizontal crustal shortening. The latter produced a series of NNW-SSE parallel, sinuous, folds and imbricated structures that overlapped Lakshmi Planum westward. So these mountain belts have the same structural characteristics as terrestrial fold-and-thrust belts. These mountain belts also display evidence of a late volcanic stage and a subsequent period of relaxation that created grabens parallel to the highland trend, especially in Maxwell Montes.

Collagen production of osteoblasts revealed by ultra-high voltage electron microscopy.

PubMed

Hosaki-Takamiya, Rumiko; Hashimoto, Mana; Imai, Yuichi; Nishida, Tomoki; Yamada, Naoko; Mori, Hirotaro; Tanaka, Tomoyo; Kawanabe, Noriaki; Yamashiro, Takashi; Kamioka, Hiroshi

2016-09-01

In the bone, collagen fibrils form a lamellar structure called the "twisted plywood-like model." Because of this unique structure, bone can withstand various mechanical stresses. However, the formation of this structure has not been elucidated because of the difficulty of observing the collagen fibril production of the osteoblasts via currently available methods. This is because the formation occurs in the very limited space between the osteoblast layer and bone matrix. In this study, we used ultra-high-voltage electron microscopy (UHVEM) to observe collagen fibril production three-dimensionally. UHVEM has 3-MV acceleration voltage and enables us to use thicker sections. We observed collagen fibrils that were beneath the cell membrane of osteoblasts elongated to the outside of the cell. We also observed that osteoblasts produced collagen fibrils with polarity. By using AVIZO software, we observed collagen fibrils produced by osteoblasts along the contour of the osteoblasts toward the bone matrix area. Immediately after being released from the cell, the fibrils run randomly and sparsely. But as they recede from the osteoblast, the fibrils began to run parallel to the definite direction and became thick, and we observed a periodical stripe at that area. Furthermore, we also observed membrane structures wrapped around filamentous structures inside the osteoblasts. The filamentous structures had densities similar to the collagen fibrils and a columnar form and diameter. Our results suggested that collagen fibrils run parallel and thickly, which may be related to the lateral movement of the osteoblasts. UHVEM is a powerful tool for observing collagen fibril production.

Friction and Environmental Sensitivity of Molybdenum Disulfide: Effects of Microstructure

NASA Astrophysics Data System (ADS)

Curry, John F.

For nearly a century, molybdenum disulfide has been employed as a solid lubricant to reduce the friction and wear between surfaces. MoS2 is in a class of unique materials, transition metal dichalcogens (TMDC), that have a single crystal structure forming lamellae that interact via weak van der Waals forces. This dissertation focuses on the link between the microstructure of MoS2 and the energetics of running film formation to reduce friction, and effects of environmental sensitivities on performance. Nitrogen impinged MoS2 films are utilized as a comparator to amorphous PVD deposited MoS2 in many of the studies due to the highly ordered surface parallel basal texture of sprayed films. Comparisons showed that films with a highly ordered structure can reduce high friction behavior during run-in. It is thought that shear induced reorientation of amorphous films contributes to typically high initial friction during run-in. In addition to a reduction in initial friction, highly ordered MoS2 films are shown to be more resistant to penetration from oxidative aging processes. High sensitivity, low-energy ion scattering (HS-LEIS) enabled depth profiles that showed oxidation limited to the first monolayer for ordered films and throughout the depth (4-5 nm) for amorphous films. X-ray photoelectron spectroscopy supported these findings, showing far more oxidation in amorphous films than ordered films. Many of these results show the benefits of a well run-in coating, yet transient increases in initial friction can still be noticed after only 5 - 10 minutes. It was found that the transient return to high initial friction after dwell times past 5 - 10 minutes was not due to adsorbed species such as water, but possibly an effect of basal plane relaxation to a commensurate state. Additional techniques and methods were developed to study the effect of adsorbed water and load on running film formation via spiral orbit XRD studies. Spiral orbit experiments enabled large enough worn areas for study in the XRD. Diffraction patterns for sputtered coatings at high loads (1N) showed more intense signals for surface parallel basal plane representation than lower loads (100mN). Tests run in dry and humid nitrogen (20% RH), however, showed no differences in reorientation of basal planes. Microstructure was found to be an important factor in determining the tribological performance of MoS2 films in a variety of testing conditions and environments. These findings will be useful in developing a mechanistic framework that better understands the energetics of running film formation and how different environments play a role.

Parallel processing data network of master and slave transputers controlled by a serial control network

DOEpatents

Crosetto, D.B.

1996-12-31

The present device provides for a dynamically configurable communication network having a multi-processor parallel processing system having a serial communication network and a high speed parallel communication network. The serial communication network is used to disseminate commands from a master processor to a plurality of slave processors to effect communication protocol, to control transmission of high density data among nodes and to monitor each slave processor`s status. The high speed parallel processing network is used to effect the transmission of high density data among nodes in the parallel processing system. Each node comprises a transputer, a digital signal processor, a parallel transfer controller, and two three-port memory devices. A communication switch within each node connects it to a fast parallel hardware channel through which all high density data arrives or leaves the node. 6 figs.

Parallel processing data network of master and slave transputers controlled by a serial control network

DOEpatents

Crosetto, Dario B.

1996-01-01

The present device provides for a dynamically configurable communication network having a multi-processor parallel processing system having a serial communication network and a high speed parallel communication network. The serial communication network is used to disseminate commands from a master processor (100) to a plurality of slave processors (200) to effect communication protocol, to control transmission of high density data among nodes and to monitor each slave processor's status. The high speed parallel processing network is used to effect the transmission of high density data among nodes in the parallel processing system. Each node comprises a transputer (104), a digital signal processor (114), a parallel transfer controller (106), and two three-port memory devices. A communication switch (108) within each node (100) connects it to a fast parallel hardware channel (70) through which all high density data arrives or leaves the node.

Why Video Games Can Be a Good Fit for Formative Assessment

ERIC Educational Resources Information Center

Bauer, Malcolm; Wylie, Caroline; Jackson, Tanner; Mislevy, Bob; Hoffman-John, Erin; John, Michael; Corrigan, Seth

2017-01-01

This paper explores the relation between formative assessment principles and their analogues in video games that game designers have been developing over the past 35 years. We identify important parallels between the two that should enable effective and efficient use of well-designed video games in the classroom as part of an overall learning…

The Effects of Blogging on Reading Engagement in the Upper Elementary Grades

ERIC Educational Resources Information Center

Ray, Holly Wilson

2013-01-01

With children growing up as digital natives, they have become accustomed to a fast paced, multitasking environment. In this digital landscape, children's brains learn in a parallel format, with instant information, as opposed to the traditional linear format with one skill being introduced at a time. Today's education methods used to…

Novel microfluidic system for online monitoring of biofilm dynamics by electrical impedance spectroscopy and amperometry

NASA Astrophysics Data System (ADS)

Bruchmann, Julia; Sachsenheimer, Kai; Schwartz, Thomas; Rapp, Bastian E.

2016-03-01

Biofilm formation is ubiquitous in nature where microorganisms attach to surfaces and form highly adapted and protected communities. In technical and industrial systems like drinking water supply, food production or shipping industry biofilms are a major cause of product contamination, biofouling, and biocorrosion. Therefore, understanding of biofilm formation and means of preventing biofilm formation is important to develop novel biofilm treatment strategies. A system allowing directly online detection and monitoring biofilm formation is necessary. However, until today, there are little to none technical systems featuring a non-destructive real-time characterization of biofilm formation in a highthroughput manner. This paper presents such a microfluidic system based on electrical impedance spectroscopy (EIS) and amperomertic current measurement. The sensor consists of four modules, each housing 24 independent electrodes within 12 microfluidic channels. Attached biomass on the electrodes is monitored as increased inhibition in charge transfer by EIS and a change in metabolic activity is measured as change in produced electric current by amperometry. This modular sensor system is highly adaptable and suitable for a broad range of microbiological applications. Among others, biofilm formation processes can be characterized online, biofilm manipulation like inactivation or destabilization can be monitored in real-time and gene expression can be analyzed in parallel. The use of different electrode designs allows effective biofilm studies during all biofilm phases. The whole system was recently extended by an integrated pneumatic microfluidic pump which enables easy handling procedures. Further developments of this pumping module will allow a fully- automated computer-controlled valving and pumping.

Sweet-sensitive protein from bovine taste buds: isolation and assay.

PubMed

Dastoli, F R; Price, S

1966-11-18

Using refractometry and ultraviolet-difference spectroscopy to indicate interaction between proteins and coinpounds of low molecular weight, we found a protein fraction in bovine tongue extracts that coinplexes sugars and saccharin. The strengths of the coinzplexes parallel the degrees of sweetness of the compounds, and the effects of pH upon formation of complexes parallel the effects of pH upon sensitivity of taste buds to sweet compounds in vivo.

Dopaminergic neurons write and update memories with cell-type-specific rules

PubMed Central

Aso, Yoshinori; Rubin, Gerald M

2016-01-01

Associative learning is thought to involve parallel and distributed mechanisms of memory formation and storage. In Drosophila, the mushroom body (MB) is the major site of associative odor memory formation. Previously we described the anatomy of the adult MB and defined 20 types of dopaminergic neurons (DANs) that each innervate distinct MB compartments (Aso et al., 2014a, 2014b). Here we compare the properties of memories formed by optogenetic activation of individual DAN cell types. We found extensive differences in training requirements for memory formation, decay dynamics, storage capacity and flexibility to learn new associations. Even a single DAN cell type can either write or reduce an aversive memory, or write an appetitive memory, depending on when it is activated relative to odor delivery. Our results show that different learning rules are executed in seemingly parallel memory systems, providing multiple distinct circuit-based strategies to predict future events from past experiences. DOI: http://dx.doi.org/10.7554/eLife.16135.001 PMID:27441388

Characterizing chlorine oxidation of dissolved organic matter and disinfection by-product formation with fluorescence spectroscopy and parallel factor analysis

NASA Astrophysics Data System (ADS)

Beggs, Katherine M. H.; Summers, R. Scott; McKnight, Diane M.

2009-12-01

Relationships between chlorine demand and disinfection by-product (DBP) formation during chlorination and fluorescence of dissolved organic matter (DOM) were developed. Fluorescence excitation and emission (EEM) spectroscopy was employed, and parameters including fluorescence index, redox index, and overall fluorescence intensity (OFI) were correlated to chlorine demand and DBP formation. The EEMs were also analyzed using a well established global parallel factor analysis (PARAFAC) model which resolves the fluorescence signal into 13 components, including quinone-like and protein-like components. Over an 8-day chlorination period the OFI and sum of the 13 PARAFAC loadings decreased by more than 70%. The remaining identified quinone-like compounds within the DOM were shifted to a more oxidized state. Quinone fluorescence was strongly correlated to both reduced fluorescence intensity and to chlorine demand which indicates that fluorescence may be used to track the chlorine oxidation of DOM. Quinone fluorescence was also correlated strongly with both classes of regulated DBPs: total trihalomethanes and haloacetic acids. Quinone-like components were found to be strongly correlated to overall, short-term, and long-term specific DBP formation. The results of this study show that fluorescence is a useful tool in tracking both DOM oxidation and DBP formation during chlorination.

Jet formation and equatorial superrotation in Jupiter's atmosphere: Numerical modelling using a new efficient parallel code

NASA Astrophysics Data System (ADS)

Rivier, Leonard Gilles

Using an efficient parallel code solving the primitive equations of atmospheric dynamics, the jet structure of a Jupiter like atmosphere is modeled. In the first part of this thesis, a parallel spectral code solving both the shallow water equations and the multi-level primitive equations of atmospheric dynamics is built. The implementation of this code called BOB is done so that it runs effectively on an inexpensive cluster of workstations. A one dimensional decomposition and transposition method insuring load balancing among processes is used. The Legendre transform is cache-blocked. A "compute on the fly" of the Legendre polynomials used in the spectral method produces a lower memory footprint and enables high resolution runs on relatively small memory machines. Performance studies are done using a cluster of workstations located at the National Center for Atmospheric Research (NCAR). BOB performances are compared to the parallel benchmark code PSTSWM and the dynamical core of NCAR's CCM3.6.6. In both cases, the comparison favors BOB. In the second part of this thesis, the primitive equation version of the code described in part I is used to study the formation of organized zonal jets and equatorial superrotation in a planetary atmosphere where the parameters are chosen to best model the upper atmosphere of Jupiter. Two levels are used in the vertical and only large scale forcing is present. The model is forced towards a baroclinically unstable flow, so that eddies are generated by baroclinic instability. We consider several types of forcing, acting on either the temperature or the momentum field. We show that only under very specific parametric conditions, zonally elongated structures form and persist resembling the jet structure observed near the cloud level top (1 bar) on Jupiter. We also study the effect of an equatorial heat source, meant to be a crude representation of the effect of the deep convective planetary interior onto the outer atmospheric layer. We show that such heat forcing is able to produce strong equatorial superrotating winds, one of the most striking feature of the Jovian circulation.

TORUS: Radiation transport and hydrodynamics code

NASA Astrophysics Data System (ADS)

Harries, Tim

2014-04-01

TORUS is a flexible radiation transfer and radiation-hydrodynamics code. The code has a basic infrastructure that includes the AMR mesh scheme that is used by several physics modules including atomic line transfer in a moving medium, molecular line transfer, photoionization, radiation hydrodynamics and radiative equilibrium. TORUS is useful for a variety of problems, including magnetospheric accretion onto T Tauri stars, spiral nebulae around Wolf-Rayet stars, discs around Herbig AeBe stars, structured winds of O supergiants and Raman-scattered line formation in symbiotic binaries, and dust emission and molecular line formation in star forming clusters. The code is written in Fortran 2003 and is compiled using a standard Gnu makefile. The code is parallelized using both MPI and OMP, and can use these parallel sections either separately or in a hybrid mode.

Connectionism, parallel constraint satisfaction processes, and gestalt principles: (re) introducing cognitive dynamics to social psychology.

PubMed

Read, S J; Vanman, E J; Miller, L C

1997-01-01

We argue that recent work in connectionist modeling, in particular the parallel constraint satisfaction processes that are central to many of these models, has great importance for understanding issues of both historical and current concern for social psychologists. We first provide a brief description of connectionist modeling, with particular emphasis on parallel constraint satisfaction processes. Second, we examine the tremendous similarities between parallel constraint satisfaction processes and the Gestalt principles that were the foundation for much of modem social psychology. We propose that parallel constraint satisfaction processes provide a computational implementation of the principles of Gestalt psychology that were central to the work of such seminal social psychologists as Asch, Festinger, Heider, and Lewin. Third, we then describe how parallel constraint satisfaction processes have been applied to three areas that were key to the beginnings of modern social psychology and remain central today: impression formation and causal reasoning, cognitive consistency (balance and cognitive dissonance), and goal-directed behavior. We conclude by discussing implications of parallel constraint satisfaction principles for a number of broader issues in social psychology, such as the dynamics of social thought and the integration of social information within the narrow time frame of social interaction.

Laser Ray Tracing in a Parallel Arbitrary Lagrangian-Eulerian Adaptive Mesh Refinement Hydrocode

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

Masters, N D; Kaiser, T B; Anderson, R W

2009-09-28

ALE-AMR is a new hydrocode that we are developing as a predictive modeling tool for debris and shrapnel formation in high-energy laser experiments. In this paper we present our approach to implementing laser ray-tracing in ALE-AMR. We present the equations of laser ray tracing, our approach to efficient traversal of the adaptive mesh hierarchy in which we propagate computational rays through a virtual composite mesh consisting of the finest resolution representation of the modeled space, and anticipate simulations that will be compared to experiments for code validation.

Derivatives of Δ 2-pyrazoline-products of 1,5-diaminotetrazole interaction with chalcone: Molecular structure and spectral properties

NASA Astrophysics Data System (ADS)

Kolos, N. N.; Paponov, B. V.; Orlov, V. D.; Lvovskaya, M. I.; Doroshenko, A. O.; Shishkin, O. V.

2006-03-01

1,5-diaminotetrazole at conditions of its interaction with chalcones (1,3-diphenylpropenones) in hot DMF undergoes Dimroth rearrangement to 5-tetrazolylhydrazine, which results in formation of 1-(5-tetrazolyl)-3,5-diaryl-Δ 2-pyrazolines ( I). Structure of the obtained products was confirmed by their parallel synthesis and X-ray structural analysis. Unusual fluorescence behavior of the tetrazolopyrazolynes in polar solvents was attributed to the dissociation of their highly acidic tetrazole N-H group. The last hypothesis was confirmed at the investigation of the protolytic interactions of I with tertiary amine.

AEgIS at ELENA: outlook for physics with a pulsed cold antihydrogen beam

NASA Astrophysics Data System (ADS)

Doser, M.; Aghion, S.; Amsler, C.; Bonomi, G.; Brusa, R. S.; Caccia, M.; Caravita, R.; Castelli, F.; Cerchiari, G.; Comparat, D.; Consolati, G.; Demetrio, A.; Di Noto, L.; Evans, C.; Fanì, M.; Ferragut, R.; Fesel, J.; Fontana, A.; Gerber, S.; Giammarchi, M.; Gligorova, A.; Guatieri, F.; Haider, S.; Hinterberger, A.; Holmestad, H.; Kellerbauer, A.; Khalidova, O.; Krasnický, D.; Lagomarsino, V.; Lansonneur, P.; Lebrun, P.; Malbrunot, C.; Mariazzi, S.; Marton, J.; Matveev, V.; Mazzotta, Z.; Müller, S. R.; Nebbia, G.; Nedelec, P.; Oberthaler, M.; Pacifico, N.; Pagano, D.; Penasa, L.; Petracek, V.; Prelz, F.; Prevedelli, M.; Rienaecker, B.; Robert, J.; Røhne, O. M.; Rotondi, A.; Sandaker, H.; Santoro, R.; Smestad, L.; Sorrentino, F.; Testera, G.; Tietje, I. C.; Widmann, E.; Yzombard, P.; Zimmer, C.; Zmeskal, J.; Zurlo, N.

2018-03-01

The efficient production of cold antihydrogen atoms in particle traps at CERN's Antiproton Decelerator has opened up the possibility of performing direct measurements of the Earth's gravitational acceleration on purely antimatter bodies. The goal of the AEgIS collaboration is to measure the value of g for antimatter using a pulsed source of cold antihydrogen and a Moiré deflectometer/Talbot-Lau interferometer. The same antihydrogen beam is also very well suited to measuring precisely the ground-state hyperfine splitting of the anti-atom. The antihydrogen formation mechanism chosen by AEgIS is resonant charge exchange between cold antiprotons and Rydberg positronium. A series of technical developments regarding positrons and positronium (Ps formation in a dedicated room-temperature target, spectroscopy of the n=1-3 and n=3-15 transitions in Ps, Ps formation in a target at 10 K inside the 1 T magnetic field of the experiment) as well as antiprotons (high-efficiency trapping of ?, radial compression to sub-millimetre radii of mixed ? plasmas in 1 T field, high-efficiency transfer of ? to the antihydrogen production trap using an in-flight launch and recapture procedure) were successfully implemented. Two further critical steps that are germane mainly to charge exchange formation of antihydrogen-cooling of antiprotons and formation of a beam of antihydrogen-are being addressed in parallel. The coming of ELENA will allow, in the very near future, the number of trappable antiprotons to be increased by more than a factor of 50. For the antihydrogen production scheme chosen by AEgIS, this will be reflected in a corresponding increase of produced antihydrogen atoms, leading to a significant reduction of measurement times and providing a path towards high-precision measurements. This article is part of the Theo Murphy meeting issue `Antiproton physics in the ELENA era'.

Control mechanism of double-rotator-structure ternary optical computer

NASA Astrophysics Data System (ADS)

Kai, SONG; Liping, YAN

2017-03-01

Double-rotator-structure ternary optical processor (DRSTOP) has two characteristics, namely, giant data-bits parallel computing and reconfigurable processor, which can handle thousands of data bits in parallel, and can run much faster than computers and other optical computer systems so far. In order to put DRSTOP into practical application, this paper established a series of methods, namely, task classification method, data-bits allocation method, control information generation method, control information formatting and sending method, and decoded results obtaining method and so on. These methods form the control mechanism of DRSTOP. This control mechanism makes DRSTOP become an automated computing platform. Compared with the traditional calculation tools, DRSTOP computing platform can ease the contradiction between high energy consumption and big data computing due to greatly reducing the cost of communications and I/O. Finally, the paper designed a set of experiments for DRSTOP control mechanism to verify its feasibility and correctness. Experimental results showed that the control mechanism is correct, feasible and efficient.

Understanding the crack formation of graphite particles in cycled commercial lithium-ion batteries by focused ion beam - scanning electron microscopy

NASA Astrophysics Data System (ADS)

Lin, Na; Jia, Zhe; Wang, Zhihui; Zhao, Hui; Ai, Guo; Song, Xiangyun; Bai, Ying; Battaglia, Vincent; Sun, Chengdong; Qiao, Juan; Wu, Kai; Liu, Gao

2017-10-01

The structure degradation of commercial Lithium-ion battery (LIB) graphite anodes with different cycling numbers and charge rates was investigated by focused ion beam (FIB) and scanning electron microscopy (SEM). The cross-section image of graphite anode by FIB milling shows that cracks, resulted in the volume expansion of graphite electrode during long-term cycling, were formed in parallel with the current collector. The crack occurs in the bulk of graphite particles near the lithium insertion surface, which might derive from the stress induced during lithiation and de-lithiation cycles. Subsequently, crack takes place along grain boundaries of the polycrystalline graphite, but only in the direction parallel with the current collector. Furthermore, fast charge graphite electrodes are more prone to form cracks since the tensile strength of graphite is more likely to be surpassed at higher charge rates. Therefore, for LIBs long-term or high charge rate applications, the tensile strength of graphite anode should be taken into account.

78 FR 59859 - Defense Federal Acquisition Regulation Supplement: Allowability of Legal Costs for Whistleblower...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-30

... considered in the formation of a final rule. ADDRESSES: Submit comments identified by DFARS Case 2013-D022... (for DoD only) and two FAR cases (for title 41 agencies), which are independent, but parallel... response to this interim rule in the formation of the final rule. List of Subjects in 48 CFR Parts 216 and...

A Quick and Parallel Analytical Method Based on Quantum Dots Labeling for ToRCH-Related Antibodies

NASA Astrophysics Data System (ADS)

Yang, Hao; Guo, Qing; He, Rong; Li, Ding; Zhang, Xueqing; Bao, Chenchen; Hu, Hengyao; Cui, Daxiang

2009-12-01

Quantum dot is a special kind of nanomaterial composed of periodic groups of II-VI, III-V or IV-VI materials. Their high quantum yield, broad absorption with narrow photoluminescence spectra and high resistance to photobleaching, make them become a promising labeling substance in biological analysis. Here, we report a quick and parallel analytical method based on quantum dots for ToRCH-related antibodies including Toxoplasma gondii, Rubella virus, Cytomegalovirus and Herpes simplex virus type 1 (HSV1) and 2 (HSV2). Firstly, we fabricated the microarrays with the five kinds of ToRCH-related antigens and used CdTe quantum dots to label secondary antibody and then analyzed 100 specimens of randomly selected clinical sera from obstetric outpatients. The currently prevalent enzyme-linked immunosorbent assay (ELISA) kits were considered as “golden standard” for comparison. The results show that the quantum dots labeling-based ToRCH microarrays have comparable sensitivity and specificity with ELISA. Besides, the microarrays hold distinct advantages over ELISA test format in detection time, cost, operation and signal stability. Validated by the clinical assay, our quantum dots-based ToRCH microarrays have great potential in the detection of ToRCH-related pathogens.

Striped Data Server for Scalable Parallel Data Analysis

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

Chang, Jin; Gutsche, Oliver; Mandrichenko, Igor

A columnar data representation is known to be an efficient way for data storage, specifically in cases when the analysis is often done based only on a small fragment of the available data structures. A data representation like Apache Parquet is a step forward from a columnar representation, which splits data horizontally to allow for easy parallelization of data analysis. Based on the general idea of columnar data storage, working on the [LDRD Project], we have developed a striped data representation, which, we believe, is better suited to the needs of High Energy Physics data analysis. A traditional columnar approachmore » allows for efficient data analysis of complex structures. While keeping all the benefits of columnar data representations, the striped mechanism goes further by enabling easy parallelization of computations without requiring special hardware. We will present an implementation and some performance characteristics of such a data representation mechanism using a distributed no-SQL database or a local file system, unified under the same API and data representation model. The representation is efficient and at the same time simple so that it allows for a common data model and APIs for wide range of underlying storage mechanisms such as distributed no-SQL databases and local file systems. Striped storage adopts Numpy arrays as its basic data representation format, which makes it easy and efficient to use in Python applications. The Striped Data Server is a web service, which allows to hide the server implementation details from the end user, easily exposes data to WAN users, and allows to utilize well known and developed data caching solutions to further increase data access efficiency. We are considering the Striped Data Server as the core of an enterprise scale data analysis platform for High Energy Physics and similar areas of data processing. We have been testing this architecture with a 2TB dataset from a CMS dark matter search and plan to expand it to multiple 100 TB or even PB scale. We will present the striped format, Striped Data Server architecture and performance test results.« less

Multiprocessor graphics computation and display using transputers

NASA Technical Reports Server (NTRS)

Ellis, Graham K.

1988-01-01

A package of two-dimensional graphics routines was developed to run on a transputer-based parallel processing system. These routines were designed to enable applications programmers to easily generate and display results from the transputer network in a graphic format. The graphics procedures were designed for the lowest possible network communication overhead for increased performance. The routines were designed for ease of use and to present an intuitive approach to generating graphics on the transputer parallel processing system.

A novel G-quadruplex motif in the Human MET promoter region.

PubMed

Yan, Jing; Zhao, Deming; Dong, Liping; Pan, Shuang; Hao, Fengjin; Guan, Yifu

2017-12-22

It is known that the guanine-rich strands in proto-oncogene promoters can fold into G-quadruplex structures to regulate gene expression. An intramolecular parallel G-quadruplex has been identified in MET promoter. It acts as a repressor in regulating MET expression. However, the full guanine-rich region in MET promoter forms a hybrid parallel/antiparallel G-quadruplex structure under physiological conditions, which means there are some antiparallel and hybrid parallel/antiparallel G-quadruplex structures in this region. In the present study, our data indicate that g3-5 truncation adopts an intramolecular hybrid parallel/antiparallel G-quadruplex under physiological conditions in vitro The g3-5 G-quadruplex structure significantly stops polymerization by Klenow fragment in K + buffer. Furthermore, the results of circular dichroism (CD) spectra and polymerase stop assay directly demonstrate that the G-quadruplex structure in g3-5 fragment can be stabilized by the G-quadruplex ligand TMPyP4 (5,10,15,20-tetra-(N-methyl-4-pyridyl) porphine). But the dual luciferase assay indicates TMPyP4 has no effect on the formation of g3-5 G-quadruplex in HepG2 cells. The findings in the present study will enrich our understanding of the G-quadruplex formation in proto-oncogene promoters and the mechanisms of gene expression regulation. © 2017 The Author(s).

Application of Formation MicroScanner Log in Structural Analysis of an Ultra-slow Spreading Environment, ODP Hole 1105A

NASA Astrophysics Data System (ADS)

Zarian, P.; Casey, J. F.; Miller, J.

2002-12-01

One of the unconventional research efforts that have been directed to reveal the structure of the lower oceanic crust is the application of Formation MicroScanner log in an ultra-slow spreading environment. Hole 1105A was cored during ODP Leg 179 to a depth of 158m on the Atlantis Platform in the Southwest Indian Ridge with a relative high recovery of 82.8% of gabbroic rocks. Open-hole logs, including FMS borehole images were acquired after the coring operation. Detailed modal, grain size and microstructural analyses of 147 thin sections reveal the relationships between deformation intensity, modal composition and rheology. The microstructural analyses showed that the majority of the oxide-rich gabbros exhibit high deformation intensity textures, which are present only in a few of the oxide-free gabbros. The oxide-rich gabbros represent ductile deformation zones and control the location of major deformation zones within these rocks. Oxide-rich layers can be clearly identified on electrical images and enabled the identification of different deformation features.The calibration of borehole images with core data provides us with more detailed information about the geometry of these oxide-rich layers within the magma chamber such as the dip and true pseudo-stratigraphic thickness of these layers. Also within the intervals of no core recovery, electrical images provide valuable information of the borehole wall. Brittle deformation features such as natural mineralized fractures can be documented throughout the borehole. Statistical results show that oxide-rich layers are relatively steep with an average dip of about 50 degrees and have a dominant E-W strike which is parallel to the ridge. These layers may represent the insitu crystallization of cummulate layers on a magma chamber wall elongated parallel to the ridge, or they may represent shear zones associated with near surface high angle normal faults that cut the main low angle detachment surface which caused the unroofing of the lower oceanic crust at the inner corner of the Ridge-Transform Intersection. These ductile shear zones appear to strike in a ridge parallel orientation, may have acted as syntectonic permeable pathways for fractionated melts infiltrated during the unroofing. Core-log integration also demonstrates the capabilities of electrical borehole images for structural analyses within a hard rock environment.

PWHATSHAP: efficient haplotyping for future generation sequencing.

PubMed

Bracciali, Andrea; Aldinucci, Marco; Patterson, Murray; Marschall, Tobias; Pisanti, Nadia; Merelli, Ivan; Torquati, Massimo

2016-09-22

Haplotype phasing is an important problem in the analysis of genomics information. Given a set of DNA fragments of an individual, it consists of determining which one of the possible alleles (alternative forms of a gene) each fragment comes from. Haplotype information is relevant to gene regulation, epigenetics, genome-wide association studies, evolutionary and population studies, and the study of mutations. Haplotyping is currently addressed as an optimisation problem aiming at solutions that minimise, for instance, error correction costs, where costs are a measure of the confidence in the accuracy of the information acquired from DNA sequencing. Solutions have typically an exponential computational complexity. WHATSHAP is a recent optimal approach which moves computational complexity from DNA fragment length to fragment overlap, i.e., coverage, and is hence of particular interest when considering sequencing technology's current trends that are producing longer fragments. Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engineered PWHATSHAP, a parallel, high-performance version of WHATSHAP. PWHATSHAP is embedded in a toolkit developed in Python and supports genomics datasets in standard file formats. Building on WHATSHAP, PWHATSHAP exhibits the same complexity exploring a number of possible solutions which is exponential in the coverage of the dataset. The parallel implementation on multi-core architectures allows for a relevant reduction of the execution time for haplotyping, while the provided results enjoy the same high accuracy as that provided by WHATSHAP, which increases with coverage. Due to its structure and management of the large datasets, the parallelisation of WHATSHAP posed demanding technical challenges, which have been addressed exploiting a high-level parallel programming framework. The result, PWHATSHAP, is a freely available toolkit that improves the efficiency of the analysis of genomics information.

Structural studies on a high-pressure polymorph of NaYSi 2O 6

NASA Astrophysics Data System (ADS)

Kahlenberg, Volker; Konzett, Jürgen; Kaindl, Reinhard

2007-06-01

High-pressure synthesis experiments in the system Na 2O-Y 2O 3-SiO 2 revealed the existence of a previously unknown polymorph of NaYSi 2O 6 or Na 3Y 3[Si 3O 9] 2 which was quenched from 3.0 GPa and 1000 °C. Structural investigations on this modification have been performed using single-crystal X-ray diffraction data collected at ambient conditions. Furthermore, unpolarized micro-Raman spectra have been obtained from single-crystal material. The high-P modification of NaYSi 2O 6 crystallizes in the centrosymmetric space group C2/ c with 12 formula units per cell ( a=8.2131(9) Å, b=10.3983(14) Å, c=17.6542(21) Å, β=100.804(9)°, V=1481.0(3) Å 3, R(| F|)=0.033 for 1142 independent observed reflections) and belongs to the group of cyclo-silicates. Basic building units are isolated three-membered [Si 3O 9] rings located in layers parallel to (010). Within a single layer the rings are concentrated in strings parallel to [100]. The sequence of directedness of up ( U) or down ( D) pointing tetrahedra of a single ring is UUU or DDD, respectively. Stacking of the layers parallel to b results in the formation of a three-dimensional structure in which yttrium and sodium cations are incorporated for charge compensation. In more detail, four non-tetrahedral cation positions can be differentiated which are coordinated by 6 and 8 oxygen ligands. Refinements of the site occupancies did not reveal any indication for mixed Na-Y populations on these positions. Finally, several geometrical parameters of rings occurring in cyclo-trisilicate structures have been compiled and are discussed.

Human Gingival Fibroblasts Display a Non-Fibrotic Phenotype Distinct from Skin Fibroblasts in Three-Dimensional Cultures

PubMed Central

Mah, Wesley; Jiang, Guoqiao; Olver, Dylan; Cheung, Godwin; Kim, Ben; Larjava, Hannu; Häkkinen, Lari

2014-01-01

Scar formation following skin injury can be a major psychosocial and physiological problem. However, the mechanisms of scar formation are still not completely understood. Previous studies have shown that wound healing in oral mucosa is faster, associates with a reduced inflammatory response and results to significantly reduced scar formation compared with skin wounds. In the present study, we hypothesized that oral mucosal fibroblasts from human gingiva are inherently distinct from fibroblasts from breast and abdominal skin, two areas prone to excessive scar formation, which may contribute to the preferential wound healing outcome in gingiva. To this end, we compared the phenotype of human gingival and skin fibroblasts cultured in in vivo-like three-dimensional (3D) cultures that mimic the cells' natural extracellular matrix (ECM) niche. To establish 3D cultures, five parallel fibroblast lines from human gingiva (GFBLs) and breast skin (SFBLs) were seeded in high density, and cultured for up to 21 days in serum and ascorbic acid containing medium to induce expression of wound-healing transcriptome and ECM deposition. Cell proliferation, morphology, phenotype and expression of wound healing and scar related genes were analyzed by real-time RT-PCR, Western blotting and immunocytochemical methods. The expression of a set of genes was also studied in three parallel lines of human abdominal SFBLs. Findings showed that GFBLs displayed morphologically distinct organization of the 3D cultures and proliferated faster than SFBLs. GFBLs expressed elevated levels of molecules involved in regulation of inflammation and ECM remodeling (MMPs) while SFBLs showed significantly higher expression of TGF-β signaling, ECM and myofibroblast and cell contractility-related genes. Thus, GFBLs display an inherent phenotype conducive for fast resolution of inflammation and ECM remodeling, characteristic for scar-free wound healing, while SFBLs have a profibrotic, scar-prone phenotype. PMID:24608113

Trihalomethane and nonpurgeable total organic-halide formation potentials of the Mississippi river

USGS Publications Warehouse

Rathbun, R.E.

1996-01-01

Trihalomethane and nonpurgeable total organic-hallide formation potentials were determined for water samples from 12 sites along the Mississippi River from Minneapolis, MN, to New Orleans, LA, for the summer and fall of 1991 and the spring of 1992. The formation potentials increased with distance upstream, approximately paralleling the increase of the dissolved organic- carbon concentration. The pH and the dissolved organic-carbon and free- chlorine concentrations were significant variables in the prediction of the formation potentials. The trihalomethane formation potential increased as the pH increased, whereas the nonpurgeable total organic-halide formation potential decreased. All formation potentials increased as the dissolved organic-carbon and free-chlorine concentrations increased, with the dissolved organic-carbon concentration having a much greater effect.

Pit-chain in Noctis Labyrinthus

NASA Image and Video Library

2002-12-20

These pit-chain features in this NASA Mars Odyssey image of south Noctis Labryinthus are oriented parallel to grabens in the area, suggesting that tensional stresses may have been responsible for their formation.

Investigation on the photoreactions of nitrate and nitrite ions with selected azaarenes in water

PubMed

Beitz; Bechmann; Mitzner

1999-01-01

The photoreactions of selected azaarenes with nitrate and nitrite ions were investigated under irradiation at lambda = 313 nm. The excitation of both anions leads to several photochemical reactions forming mainly hydroxyl radicals and nitrogen oxides. The purification capability of natural waters i.e. the oxidation of inorganic and organic substances results from the formation of hydroxyl radicals. Nitrated isomers of azaarenes were found among the main products of the investigated photoreactions. The nitrogen oxides were responsible for the production of nitrated derivatives which possess a high toxic potential. Their formation was explained by the parallel occurance of two mechanism, a molecular and a radical one. The molecular mechanism became more important with increasing ionisation potentials of the azaarenes. The spectrum of oxidized products corresponded to the one got in the photoreactions of azaarenes with hydrogen peroxide. The formation of several oxidation and nitration products of the pyridine ring with its low electron density was explained by the reaction of excited states of azaarenes. The photoreactions with nitrite ions only led to the formation of oxidized and nitrated products. Nitroso products were not formed. The reactivity of nitrogen monoxide is too low for its reaction with the azaarenes.

LPS-induced NF-{kappa}B expression in THP-1Blue cells correlates with neopterin production and activity of indoleamine 2,3-dioxygenase

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

Schroecksnadel, Sebastian; Jenny, Marcel; Division of Medical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck

2010-09-03

Research highlights: {yields} LPS induces NF-{kappa}B, neopterin formation and tryptophan degradation in THP-1 cells. {yields} Close dose- and time-dependent correlations exist between these biochemical events. {yields} Data provides some evidence for a parallel induction of them upon TLR stimulation. {yields} Results can be of considerable relevance also in vivo. -- Abstract: Neopterin production is induced in human monocyte-derived macrophages and dendritic cells upon stimulation with Th1-type cytokine interferon-{gamma} (IFN-{gamma}). In parallel, IFN-{gamma} induces the tryptophan-(trp)-degrading enzyme indoleamine 2,3-dioxygenase (IDO) and triggers the formation of reactive oxygen species (ROS). Translocation of the signal transduction element nuclear factor-{kappa}B (NF-{kappa}B) is induced bymore » ROS and accelerates the pro-inflammatory response by activation of other pro-inflammatory pathways. Therefore, a close relationship between NF-{kappa}B expression, the production of neopterin and the degradation of trp can be assumed, although this has not been demonstrated so far. In the present in vitro study we compared the influence of lipopolysaccharide (LPS) on NF-{kappa}B activation, neopterin formation and the degradation of trp in THP-1Blue cells, which represent the human myelomonocytic cell line THP-1 stably transfected with an NF-{kappa}B inducible reporter system. In cells stimulated with LPS, a significant induction of NF-{kappa}B was observed, and this was paralleled by an increase of kynureunine (kyn) and neopterin concentrations and a decline of trp. The increase of the kyn to trp quotient indicates accelerated IDO activity. Higher LPS concentrations and longer incubation of cells were associated with higher activities of all three biochemical pathways and significant correlations existed between NF-{kappa}B activation, neopterin release and trp degradation (all p < 0.001). We conclude that there is a parallel induction of NF-{kappa}B, neopterin formation and trp degradation in monocytic THP-1 cells, which is elicited by pro-inflammatory triggers like LPS during innate immune responses.« less

Investigation into the formation of the scrape-off layer density shoulder in JET ITER-like wall L-mode and H-mode plasmas

NASA Astrophysics Data System (ADS)

Wynn, A.; Lipschultz, B.; Cziegler, I.; Harrison, J.; Jaervinen, A.; Matthews, G. F.; Schmitz, J.; Tal, B.; Brix, M.; Guillemaut, C.; Frigione, D.; Huber, A.; Joffrin, E.; Kruzei, U.; Militello, F.; Nielsen, A.; Walkden, N. R.; Wiesen, S.; Contributors, JET

2018-05-01

The low temperature boundary layer plasma (scrape-off layer or SOL) between the hot core and the surrounding vessel determines the level of power loading, erosion and implantation of material surfaces, and thus the viability of tokamak-based fusion as an energy source. This study explores mechanisms affecting the formation of flattened density profiles, so-called ‘density shoulders’, in the low-field side (LFS) SOL, which modify ion and neutral fluxes to surfaces—and subsequent erosion. We find that increases in SOL parallel resistivity, Λdiv (=[L || ν eiΩi]/c sΩe), postulated to lead to shoulder growth through changes in SOL turbulence characteristics, correlates with increases in SOL shoulder amplitude, A s, only under a subset of conditions (D2-fuelled L-mode density scans with outer strike point on the horizontal target). Λdiv fails to correlate with A s for cases of N2 seeding or during sweeping of the strike point across the horizontal target. The limited correlation of Λdiv and A s is also found for H-mode discharges. Thus, while it may be necessary for Λdiv to be above a threshold of ~1 for shoulder formation and/or growth, another mechanism is required. More significantly, we find that in contrast to parallel resistivity, outer divertor recycling, as quantified by the total outer divertor Balmer D α emission, I-D α , does scale with A s where Λdiv does and even where Λdiv does not. Divertor recycling could lead to SOL density shoulder formation through: (a) reducing the parallel to the field flow (loss) of ions out of the SOL to the divertor; and (b) changes in radial electric fields which lead to E  ×  B poloidal flows as well as potentially affecting SOL turbulence birth characteristics. Thus, changes in divertor recycling may be the sole process involved in bringing about SOL density shoulders or it may be that it acts in tandem with parallel resistivity.

Mountains on Io: High-resolution Galileo observations, initial interpretations, and formation models

USGS Publications Warehouse

Turtle, E.P.; Jaeger, W.L.; Keszthelyi, L.P.; McEwen, A.S.; Milazzo, M.; Moore, J.; Phillips, C.B.; Radebaugh, J.; Simonelli, D.; Chuang, F.; Schuster, P.; Alexander, D.D.A.; Capraro, K.; Chang, S.-H.; Chen, A.C.; Clark, J.; Conner, D.L.; Culver, A.; Handley, T.H.; Jensen, D.N.; Knight, D.D.; LaVoie, S.K.; McAuley, M.; Mego, V.; Montoya, O.; Mortensen, H.B.; Noland, S.J.; Patel, R.R.; Pauro, T.M.; Stanley, C.L.; Steinwand, D.J.; Thaller, T.F.; Woncik, P.J.; Yagi, G.M.; Yoshimizu, J.R.; Alvarez Del Castillo, E.M.; Beyer, R.; Branston, D.; Fishburn, M.B.; Muller, Birgit; Ragan, R.; Samarasinha, N.; Anger, C.D.; Cunningham, C.; Little, B.; Arriola, S.; Carr, M.H.; Asphaug, E.; Morrison, D.; Rages, K.; Banfield, D.; Bell, M.; Burns, J.A.; Carcich, B.; Clark, B.; Currier, N.; Dauber, I.; Gierasch, P.J.; Helfenstein, P.; Mann, M.; Othman, O.; Rossier, L.; Solomon, N.; Sullivan, R.; Thomas, P.C.; Veverka, J.; Becker, T.; Edwards, K.; Gaddis, L.; Kirk, R.; Lee, E.; Rosanova, T.; Sucharski, R.M.; Beebe, R.F.; Simon, A.; Belton, M.J.S.; Bender, K.; Fagents, S.; Figueredo, P.; Greeley, R.; Homan, K.; Kadel, S.; Kerr, J.; Klemaszewski, J.; Lo, E.; Schwarz, W.; Williams, D.; Williams, K.; Bierhaus, B.; Brooks, S.; Chapman, C.R.; Merline, B.; Keller, J.; Tamblyn, P.; Bouchez, A.; Dyundian, U.; Ingersoll, A.P.; Showman, A.; Spitale, J.; Stewart, S.; Vasavada, A.; Breneman, H.H.; Cunningham, W.F.; Johnson, T.V.; Jones, T.J.; Kaufman, J.M.; Klaasen, K.P.; Levanas, G.; Magee, K.P.; Meredith, M.K.; Orton, G.S.; Senske, D.A.; West, A.; Winther, D.; Collins, G.; Fripp, W.J.; Head, J. W.; Pappalardo, R.; Pratt, S.; Prockter, L.; Spaun, N.; Colvin, T.; Davies, M.; DeJong, E.M.; Hall, J.; Suzuki, S.; Gorjian, Z.; Denk, T.; Giese, B.; Koehler, U.; Neukum, G.; Oberst, J.; Roatsch, T.; Tost, W.; Wagner, R.; Dieter, N.; Durda, D.; Geissler, P.; Greenberg, R.J.; Hoppa, G.; Plassman, J.; Tufts, R.; Fanale, F.P.; Granahan, J.C.

2001-01-01

During three close flybys in late 1999 and early 2000 the Galileo spacecraft ac-quired new observations of the mountains that tower above Io's surface. These images have revealed surprising variety in the mountains' morphologies. They range from jagged peaks several kilometers high to lower, rounded structures. Some are very smooth, others are covered by numerous parallel ridges. Many mountains have margins that are collapsing outward in large landslides or series of slump blocks, but a few have steep, scalloped scarps. From these observations we can gain insight into the structure and material properties of Io's crust as well as into the erosional processes acting on Io. We have also investigated formation mechanisms proposed for these structures using finite-element analysis. Mountain formation might be initiated by global compression due to the high rate of global subsidence associated with Io's high resurfacing rate; however, our models demonstrate that this hypothesis lacks a mechanism for isolating the mountains. The large fraction (???40%) of mountains that are associated with paterae suggests that in some cases these features are tectonically related. Therefore we have also simulated the stresses induced in Io's crust by a combination of a thermal upwelling in the mantle with global lithospheric compression and have shown that this can focus compressional stresses. If this mechanism is responsible for some of Io's mountains, it could also explain the common association of mountains with paterae. Copyright 2001 by the American Geophysical Union.

An investigation of the effect of instruction in physics on the formation of mental models for problem-solving in the context of simple electric circuits

NASA Astrophysics Data System (ADS)

Beh, Kian Lim

2000-10-01

This study was designed to explore the effect of a typical traditional method of instruction in physics on the formation of useful mental models among college students for problem-solving using simple electric circuits as a context. The study was also aimed at providing a comprehensive description of the understanding regarding electric circuits among novices and experts. In order to achieve these objectives, the following two research approaches were employed: (1) A students survey to collect data from 268 physics students; and (2) An interview protocol to collect data from 23 physics students and 24 experts (including 10 electrical engineering graduates, 4 practicing electrical engineers, 2 secondary school physics teachers, 8 physics lecturers, and 4 electrical engineers). Among the major findings are: (1) Most students do not possess accurate models of simple electric circuits as presented implicitly in physics textbooks; (2) Most students display good procedural understanding for solving simple problems concerning electric circuits but have no in-depth conceptual understanding in terms of practical knowledge of current, voltage, resistance, and circuit connections; (3) Most students encounter difficulty in discerning parallel connections that are drawn in a non-conventional format; (4) After a year of college physics, students show significant improvement in areas, including practical knowledge of current and voltage, ability to compute effective resistance and capacitance, ability to identify circuit connections, and ability to solve problems; however, no significance was found in practical knowledge of resistance and ability to connect circuits; and (5) The differences and similarities between the physics students and the experts include: (a) Novices perceive parallel circuits more in terms of 'branch', 'current', and 'resistors with the same resistance' while experts perceive parallel circuits more in terms of 'node', 'voltage', and 'less resistance'; and (b) Both novices and experts use phrases such as 'side-by side' and 'one on top of the other' in describing parallel circuits which emphasize the geometry of the standard circuit drawing when describing parallel resistors.

Parallel simulations of Grover's algorithm for closest match search in neutron monitor data

NASA Astrophysics Data System (ADS)

Kussainov, Arman; White, Yelena

We are studying the parallel implementations of Grover's closest match search algorithm for neutron monitor data analysis. This includes data formatting, and matching quantum parameters to a conventional structure of a chosen programming language and selected experimental data type. We have employed several workload distribution models based on acquired data and search parameters. As a result of these simulations, we have an understanding of potential problems that may arise during configuration of real quantum computational devices and the way they could run tasks in parallel. The work was supported by the Science Committee of the Ministry of Science and Education of the Republic of Kazakhstan Grant #2532/GF3.

H2 formation on interstellar dust grains: The viewpoints of theory, experiments, models and observations

NASA Astrophysics Data System (ADS)

Wakelam, Valentine; Bron, Emeric; Cazaux, Stephanie; Dulieu, Francois; Gry, Cécile; Guillard, Pierre; Habart, Emilie; Hornekær, Liv; Morisset, Sabine; Nyman, Gunnar; Pirronello, Valerio; Price, Stephen D.; Valdivia, Valeska; Vidali, Gianfranco; Watanabe, Naoki

2017-12-01

Molecular hydrogen is the most abundant molecule in the universe. It is the first one to form and survive photo-dissociation in tenuous environments. Its formation involves catalytic reactions on the surface of interstellar grains. The micro-physics of the formation process has been investigated intensively in the last 20 years, in parallel of new astrophysical observational and modeling progresses. In the perspectives of the probable revolution brought by the future satellite JWST, this article has been written to present what we think we know about the H2 formation in a variety of interstellar environments.

gadfly: A pandas-based Framework for Analyzing GADGET Simulation Data

NASA Astrophysics Data System (ADS)

Hummel, Jacob A.

2016-11-01

We present the first public release (v0.1) of the open-source gadget Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing simulation data from the astrophysical simulation codes gadget and gizmo using pandas, a thoroughly documented, open-source library providing high-performance, easy-to-use data structures that is quickly becoming the standard for data analysis in python. Gadfly is a framework for analyzing particle-based simulation data stored in the HDF5 format using pandas DataFrames. The package enables efficient memory management, includes utilities for unit handling, coordinate transformations, and parallel batch processing, and provides highly optimized routines for visualizing smoothed-particle hydrodynamics data sets.

Atmospheric tomography using a fringe pattern in the sodium layer.

PubMed

Baharav, Y; Ribak, E N; Shamir, J

1994-02-15

We wish to measure and separate the contribution of atmospheric turbulent layers for multiconjugate adaptive optics. To this end, we propose to create a periodic fringe pattern in the sodium layer and image it with a modified Hartmann sensor. Overlapping sections of the fringes are imaged by a lenslet array onto contiguous areas in a large-format camera. Low-layer turbulence causes an overall shift of the fringe pattern in each lenslet, and high-attitude turbulence results in internal deformations in the pattern. Parallel Fourier analysis permits separation of the atmospheric layers. Two mirrors, one conjugate to a ground layer and the other conjugate to a single high-altitude layer, are shown to widen the field of view significantly compared with existing methods.

Endoscopic evaluation of food bolus formation and its relationship with the number of chewing cycles.

PubMed

Fukatsu, H; Nohara, K; Kotani, Y; Tanaka, N; Matsuno, K; Sakai, T

2015-08-01

It is known that solid food is transported to the pharynx actively in parallel to it being crushed by chewing and mixed with saliva in the oral cavity. Therefore, food bolus formation should be considered to take place from the oral cavity to the pharynx. In previous studies, the chewed food was evaluated after the food had been removed from the oral cavity. However, it has been pointed out that spitting food out of the oral cavity interferes with natural food bolus formation. Therefore, we observed food boluses immediately before swallowing using an endoscope to establish a method to evaluate the food bolus-forming function, and simultaneously performed endoscopic evaluation of food bolus formation and its relationship with the number of chewing cycles. The subject was inserted the endoscope nasally and instructed to eat two coloured samples of boiled rice simultaneously in two ingestion conditions ('as usual' and 'chewing well'). The condition of the food bolus was graded into three categories for each item of grinding, mixing and aggregation and scored 2, 1 and 0. The score of aggregation was high under both ingestion conditions. The scores of grinding and mixing tended to be higher in subjects with a high number of chewing cycles, and the score of aggregation was high regardless of the number of chewing cycles. It was suggested that food has to be aggregated, even though the number of chewing cycles is low and the food is not ground or mixed for a food bolus to reach the swallowing threshold. © 2015 John Wiley & Sons Ltd.

Parallelizing serial code for a distributed processing environment with an application to high frequency electromagnetic scattering

NASA Astrophysics Data System (ADS)

Work, Paul R.

1991-12-01

This thesis investigates the parallelization of existing serial programs in computational electromagnetics for use in a parallel environment. Existing algorithms for calculating the radar cross section of an object are covered, and a ray-tracing code is chosen for implementation on a parallel machine. Current parallel architectures are introduced and a suitable parallel machine is selected for the implementation of the chosen ray-tracing algorithm. The standard techniques for the parallelization of serial codes are discussed, including load balancing and decomposition considerations, and appropriate methods for the parallelization effort are selected. A load balancing algorithm is modified to increase the efficiency of the application, and a high level design of the structure of the serial program is presented. A detailed design of the modifications for the parallel implementation is also included, with both the high level and the detailed design specified in a high level design language called UNITY. The correctness of the design is proven using UNITY and standard logic operations. The theoretical and empirical results show that it is possible to achieve an efficient parallel application for a serial computational electromagnetic program where the characteristics of the algorithm and the target architecture critically influence the development of such an implementation.

Proteomic analysis of fibroblastema formation in regenerating hind limbs of Xenopus laevis froglets and comparison to axolotl

PubMed Central

2014-01-01

Background To gain insight into what differences might restrict the capacity for limb regeneration in Xenopus froglets, we used High Performance Liquid Chromatography (HPLC)/double mass spectrometry to characterize protein expression during fibroblastema formation in the amputated froglet hindlimb, and compared the results to those obtained previously for blastema formation in the axolotl limb. Results Comparison of the Xenopus fibroblastema and axolotl blastema revealed several similarities and significant differences in proteomic profiles. The most significant similarity was the strong parallel down regulation of muscle proteins and enzymes involved in carbohydrate metabolism. Regenerating Xenopus limbs differed significantly from axolotl regenerating limbs in several ways: deficiency in the inositol phosphate/diacylglycerol signaling pathway, down regulation of Wnt signaling, up regulation of extracellular matrix (ECM) proteins and proteins involved in chondrocyte differentiation, lack of expression of a key cell cycle protein, ecotropic viral integration site 5 (EVI5), that blocks mitosis in the axolotl, and the expression of several patterning proteins not seen in the axolotl that may dorsalize the fibroblastema. Conclusions We have characterized global protein expression during fibroblastema formation after amputation of the Xenopus froglet hindlimb and identified several differences that lead to signaling deficiency, failure to retard mitosis, premature chondrocyte differentiation, and failure of dorsoventral axial asymmetry. These differences point to possible interventions to improve blastema formation and pattern formation in the froglet limb. PMID:25063185

Legacy Extragalactic UV Survey (LEGUS) With the Hubble Space Telescope. I. Survey Description

NASA Astrophysics Data System (ADS)

Calzetti, D.; Lee, J. C.; Sabbi, E.; Adamo, A.; Smith, L. J.; Andrews, J. E.; Ubeda, L.; Bright, S. N.; Thilker, D.; Aloisi, A.; Brown, T. M.; Chandar, R.; Christian, C.; Cignoni, M.; Clayton, G. C.; da Silva, R.; de Mink, S. E.; Dobbs, C.; Elmegreen, B. G.; Elmegreen, D. M.; Evans, A. S.; Fumagalli, M.; Gallagher, J. S., III; Gouliermis, D. A.; Grebel, E. K.; Herrero, A.; Hunter, D. A.; Johnson, K. E.; Kennicutt, R. C.; Kim, H.; Krumholz, M. R.; Lennon, D.; Levay, K.; Martin, C.; Nair, P.; Nota, A.; Östlin, G.; Pellerin, A.; Prieto, J.; Regan, M. W.; Ryon, J. E.; Schaerer, D.; Schiminovich, D.; Tosi, M.; Van Dyk, S. D.; Walterbos, R.; Whitmore, B. C.; Wofford, A.

2015-02-01

The Legacy ExtraGalactic UV Survey (LEGUS) is a Cycle 21 Treasury program on the Hubble Space Telescope aimed at the investigation of star formation and its relation with galactic environment in nearby galaxies, from the scales of individual stars to those of ˜kiloparsec-size clustered structures. Five-band imaging from the near-ultraviolet to the I band with the Wide-Field Camera 3 (WFC3), plus parallel optical imaging with the Advanced Camera for Surveys (ACS), is being collected for selected pointings of 50 galaxies within the local 12 Mpc. The filters used for the observations with the WFC3 are F275W(λ2704 Å), F336W(λ3355 Å), F438W(λ4325 Å), F555W(λ5308 Å), and F814W(λ8024 Å) the parallel observations with the ACS use the filters F435W(λ4328 Å), F606W(λ5921 Å), and F814W(λ8057 Å). The multiband images are yielding accurate recent (≲50 Myr) star formation histories from resolved massive stars and the extinction-corrected ages and masses of star clusters and associations. The extensive inventories of massive stars and clustered systems will be used to investigate the spatial and temporal evolution of star formation within galaxies. This will, in turn, inform theories of galaxy evolution and improve the understanding of the physical underpinning of the gas-star formation relation and the nature of star formation at high redshift. This paper describes the survey, its goals and observational strategy, and the initial scientific results. Because LEGUS will provide a reference survey and a foundation for future observations with the James Webb Space Telescope and with ALMA, a large number of data products are planned for delivery to the community. Based on observations obtained with the NASA/ESA Hubble Space Telescope at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy under NASA Contract NAS 5-26555.

Pyronin Y (basic xanthene dye)-bentonite composite: A spectroscopic study

NASA Astrophysics Data System (ADS)

Tabak, A.; Kaya, M.; Yilmaz, N.; Meral, K.; Onganer, Y.; Caglar, B.; Sungur, O.

2014-02-01

The expansion by 1.43 Angstrom of basal spacing and the shift to higher frequencies of in-plane ring vibrations of the Pyronin Y molecule at 1603 and 1527 cm-1 on the formation of Pyronin Y-bentonite composite exhibited that the dye cations might be oriented as a monolayer form in the interlamellar spacing with aromatic rings parallel to clay layers. Thermal analysis results of this composite compared to those of raw bentonite signified the different outer sphere water entities associated with the replacement of inorganic cations with organic dye cations and the gradual decomposition of the organic molecule in the interlamellar spacing. Thermo-Infrared spectra of Pyronin Y-bentonite sample up to high temperatures showed the thermal stability of the dye-clay composite as a result of the presence of π interactions. The pore structure characteristics of Pyronin Y-bentonite composite exhibited the increase in the number of mesopores during formation of the composite.

Design of a novel bioreactor and application in vascular tissue engineering

NASA Astrophysics Data System (ADS)

Zhang, Zhi-Xiong; Xi, Ting-Fei; Wang, Ying-Jun; Chen, Xiao-Song; Zhang, Jian; Wang, Chun-Ren; Gu, Yong-Quan; Chen, Liang; Li, Jian-Xin; Chen, Bing

2008-11-01

Endothelial cells (ECs) detachment under high shear stress at the early period of transplantation resulted in thrombosis and occlusion. To solve this problem, we developed a novel bioreactor. The bioreactor mimicked the formation of pulsatile flow in physiological conditions. Human umbilical vein ECs were seeded onto the lumen of living tissue conduits grown within dog peritoneal cavity. The shear stress generated by the bioreactor was increased step by step from 1.5 ± 0.8 dyn/cm 2 to 5.3 ± 2.4 dyn/cm 2, and was applied to ECs after static culture for 2 days. The results showed that completely confluent monolayer ECs were elongated, and were oriented parallel to the flow direction. The bioreactor could provide good environment for formation of endothelium. Stepwise increase shear stress could strengthen cell-cell and cell-extracellular matrix. The flow conditions of the bioreactor play a key role to determine the quality of the ECs lining.

Packet telemetry and packet telecommand - The new generation of spacecraft data handling techniques

NASA Technical Reports Server (NTRS)

Hooke, A. J.

1983-01-01

Because of rising costs and reduced reliability of spacecraft and ground network hardware and software customization, standardization Packet Telemetry and Packet Telecommand concepts are emerging as viable alternatives. Autonomous packets of data, within each concept, which are created within ground and space application processes through the use of formatting techniques, are switched end-to-end through the space data network to their destination application processes through the use of standard transfer protocols. This process may result in facilitating a high degree of automation and interoperability because of completely mission-independent-designed intermediate data networks. The adoption of an international guideline for future space telemetry formatting of the Packet Telemetry concept, and the advancement of the NASA-ESA Working Group's Packet Telecommand concept to a level of maturity parallel to the of Packet Telemetry are the goals of the Consultative Committee for Space Data Systems. Both the Packet Telemetry and Packet Telecommand concepts are reviewed.

Exploration of ground instability factor causing slumping and related dewatering in high methane-flux and gentle continental slope off Shimokita Peninsula, NE Japan

NASA Astrophysics Data System (ADS)

Morita, S.; Nakajima, T.; Goto, S.; Yamada, Y.; Kawamura, K.

2012-12-01

A great number of slump (submarine landslide) units have been identified by reflection seismic surveys performed off Shimokita Peninsula, NE Japan (Morita, et al., 2011). A 3-D seismic data revealed typical deformations caused by slumping and related dewatering in the Pliocene and upper formations. The slumping was generated primarily by layer-parallel slip in a very gentle (<1 degree) and flat continental slope. The size of slump units extends over 30 km in both width and slip direction in maximum. The slump units often exhibit an imbrication structure formed by repeated thrusting in the bottom layers, being mostly composed of the thrust blocks and little matrix. The dewatering structure is observed as widespread parallel dikes of which distribution is strongly dependent on the imbrication of the slump units. Slip planes of the slumps are traceable in seismic data because of the layer-parallel slip. The layers which correspond to the slip planes proved to be generally characterized as low-amplitude layers having some thickness, and some of the slip planes exhibit flattened features under the slump units of the imbrication structure accompanied by parallel dikes. This implies that excess fluid in the slip plane caused the lubrication to enhance the slumping and was drained through the parallel dikes during slumping. Some typical structures related to natural gas, e.g. enhanced reflection, gas chimney, have been identified in the seismic data. The shakedown cruise of D/V Chikyu in 2006 reported a recovery of gas hydrate in nearby area (Higuchi et al., 2009). A shallow sulfate-methane interface (SMI) of 3.5-12 mbsf has been reported in the survey area (Kotani et al., 2007). These features indicate that a high methane flux in the area is likely an important ground instability factor to cause the slumping and the dewatering phenomena. We recognize that the set of the slump units in the survey area is one of the most suitable targets to approach mechanism of submarine landslides so that we started exploring the feasibility of a scientific drilling in this survey area.

The language parallel Pascal and other aspects of the massively parallel processor

NASA Technical Reports Server (NTRS)

Reeves, A. P.; Bruner, J. D.

1982-01-01

A high level language for the Massively Parallel Processor (MPP) was designed. This language, called Parallel Pascal, is described in detail. A description of the language design, a description of the intermediate language, Parallel P-Code, and details for the MPP implementation are included. Formal descriptions of Parallel Pascal and Parallel P-Code are given. A compiler was developed which converts programs in Parallel Pascal into the intermediate Parallel P-Code language. The code generator to complete the compiler for the MPP is being developed independently. A Parallel Pascal to Pascal translator was also developed. The architecture design for a VLSI version of the MPP was completed with a description of fault tolerant interconnection networks. The memory arrangement aspects of the MPP are discussed and a survey of other high level languages is given.

Physical and chemical controls on ore shoots - insights from 3D modeling of an orogenic gold deposit

NASA Astrophysics Data System (ADS)

Vollgger, S. A.; Tomkins, A. G.; Micklethwaite, S.; Cruden, A. R.; Wilson, C. J. L.

2016-12-01

Many ore deposits have irregular grade distributions with localized elongate and well-mineralized rock volumes commonly referred to as ore shoots. The chemical and physical processes that control ore shoot formation are rarely understood, although transient episodes of elevated permeability are thought to be important within the brittle and brittle-ductile crust, due to faulting and fracturing associated with earthquake-aftershock sequences or earthquake swarms. We present data from an orogenic gold deposit in Australia where the bulk of the gold is contained in abundant fine arsenopyrite crystals associated with a fault-vein network within tight upright folds. The deposit-scale fault network is connected to a deeper network of thrust faults (tens of kilometers long). Using 3D implicit modeling of geochemical data, based on radial basis functions, gold grades and gold-arsenic element ratios were interpolated and related to major faults, vein networks and late intrusions. Additionally, downhole bedding measurements were used to model first order (mine-scale) fold structures. The results show that ore shoot plunges are not parallel with mine-scale or regional fold plunges, and that bedding parallel faults related to flexural slip folding play a pivotal role on ore shoot attitudes. 3D fault slip and dilation tendency analysis indicate that fault reactivation and formation of linking faults are associated with large volumes of high-grade ore. We suggest slip events on the large-scale thrust network allowed mineralizing fluids to rapidly migrate over large distances and become supersaturated in elements such as gold, promoting widespread precipitation and high nucleation densities of arsenopyrite upon fluid-rock interaction at trap sites within the deposit.

Large-scale parallel lattice Boltzmann-cellular automaton model of two-dimensional dendritic growth

NASA Astrophysics Data System (ADS)

Jelinek, Bohumir; Eshraghi, Mohsen; Felicelli, Sergio; Peters, John F.

2014-03-01

An extremely scalable lattice Boltzmann (LB)-cellular automaton (CA) model for simulations of two-dimensional (2D) dendritic solidification under forced convection is presented. The model incorporates effects of phase change, solute diffusion, melt convection, and heat transport. The LB model represents the diffusion, convection, and heat transfer phenomena. The dendrite growth is driven by a difference between actual and equilibrium liquid composition at the solid-liquid interface. The CA technique is deployed to track the new interface cells. The computer program was parallelized using the Message Passing Interface (MPI) technique. Parallel scaling of the algorithm was studied and major scalability bottlenecks were identified. Efficiency loss attributable to the high memory bandwidth requirement of the algorithm was observed when using multiple cores per processor. Parallel writing of the output variables of interest was implemented in the binary Hierarchical Data Format 5 (HDF5) to improve the output performance, and to simplify visualization. Calculations were carried out in single precision arithmetic without significant loss in accuracy, resulting in 50% reduction of memory and computational time requirements. The presented solidification model shows a very good scalability up to centimeter size domains, including more than ten million of dendrites. Catalogue identifier: AEQZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, UK Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 29,767 No. of bytes in distributed program, including test data, etc.: 3131,367 Distribution format: tar.gz Programming language: Fortran 90. Computer: Linux PC and clusters. Operating system: Linux. Has the code been vectorized or parallelized?: Yes. Program is parallelized using MPI. Number of processors used: 1-50,000 RAM: Memory requirements depend on the grid size Classification: 6.5, 7.7. External routines: MPI (http://www.mcs.anl.gov/research/projects/mpi/), HDF5 (http://www.hdfgroup.org/HDF5/) Nature of problem: Dendritic growth in undercooled Al-3 wt% Cu alloy melt under forced convection. Solution method: The lattice Boltzmann model solves the diffusion, convection, and heat transfer phenomena. The cellular automaton technique is deployed to track the solid/liquid interface. Restrictions: Heat transfer is calculated uncoupled from the fluid flow. Thermal diffusivity is constant. Unusual features: Novel technique, utilizing periodic duplication of a pre-grown “incubation” domain, is applied for the scaleup test. Running time: Running time varies from minutes to days depending on the domain size and number of computational cores.

Xyce Parallel Electronic Simulator : users' guide, version 2.0.

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

Hoekstra, Robert John; Waters, Lon J.; Rankin, Eric Lamont

2004-06-01

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator capable of simulating electrical circuits at a variety of abstraction levels. Primarily, Xyce has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability the current state-of-the-art in the following areas: {sm_bullet} Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. {sm_bullet} Improved performance for allmore » numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. {sm_bullet} Device models which are specifically tailored to meet Sandia's needs, including many radiation-aware devices. {sm_bullet} A client-server or multi-tiered operating model wherein the numerical kernel can operate independently of the graphical user interface (GUI). {sm_bullet} Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing of computing platforms. These include serial, shared-memory and distributed-memory parallel implementation - which allows it to run efficiently on the widest possible number parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. One feature required by designers is the ability to add device models, many specific to the needs of Sandia, to the code. To this end, the device package in the Xyce These input formats include standard analytical models, behavioral models look-up Parallel Electronic Simulator is designed to support a variety of device model inputs. tables, and mesh-level PDE device models. Combined with this flexible interface is an architectural design that greatly simplifies the addition of circuit models. One of the most important feature of Xyce is in providing a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia now has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods) research and development can be performed. Ultimately, these capabilities are migrated to end users.« less

3-D Hybrid Kinetic Modeling of the Interaction Between the Solar Wind and Lunar-like Exospheric Pickup Ions in Case of Oblique/ Quasi-Parallel/Parallel Upstream Magnetic Field

NASA Technical Reports Server (NTRS)

Lipatov, A. S.; Farrell, W. M.; Cooper, J. F.; Sittler, E. C., Jr.; Hartle, R. E.

2015-01-01

The interactions between the solar wind and Moon-sized objects are determined by a set of the solar wind parameters and plasma environment of the space objects. The orientation of upstream magnetic field is one of the key factors which determines the formation and structure of bow shock wave/Mach cone or Alfven wing near the obstacle. The study of effects of the direction of the upstream magnetic field on lunar-like plasma environment is the main subject of our investigation in this paper. Photoionization, electron-impact ionization and charge exchange are included in our hybrid model. The computational model includes the self-consistent dynamics of the light (hydrogen (+), helium (+)) and heavy (sodium (+)) pickup ions. The lunar interior is considered as a weakly conducting body. Our previous 2013 lunar work, as reported in this journal, found formation of a triple structure of the Mach cone near the Moon in the case of perpendicular upstream magnetic field. Further advances in modeling now reveal the presence of strong wave activity in the upstream solar wind and plasma wake in the cases of quasiparallel and parallel upstream magnetic fields. However, little wave activity is found for the opposite case with a perpendicular upstream magnetic field. The modeling does not show a formation of the Mach cone in the case of theta(Sub B,U) approximately equal to 0 degrees.

Development of the Large-Scale Statistical Analysis System of Satellites Observations Data with Grid Datafarm Architecture

NASA Astrophysics Data System (ADS)

Yamamoto, K.; Murata, K.; Kimura, E.; Honda, R.

2006-12-01

In the Solar-Terrestrial Physics (STP) field, the amount of satellite observation data has been increasing every year. It is necessary to solve the following three problems to achieve large-scale statistical analyses of plenty of data. (i) More CPU power and larger memory and disk size are required. However, total powers of personal computers are not enough to analyze such amount of data. Super-computers provide a high performance CPU and rich memory area, but they are usually separated from the Internet or connected only for the purpose of programming or data file transfer. (ii) Most of the observation data files are managed at distributed data sites over the Internet. Users have to know where the data files are located. (iii) Since no common data format in the STP field is available now, users have to prepare reading program for each data by themselves. To overcome the problems (i) and (ii), we constructed a parallel and distributed data analysis environment based on the Gfarm reference implementation of the Grid Datafarm architecture. The Gfarm shares both computational resources and perform parallel distributed processings. In addition, the Gfarm provides the Gfarm filesystem which can be as virtual directory tree among nodes. The Gfarm environment is composed of three parts; a metadata server to manage distributed files information, filesystem nodes to provide computational resources and a client to throw a job into metadata server and manages data processing schedulings. In the present study, both data files and data processes are parallelized on the Gfarm with 6 file system nodes: CPU clock frequency of each node is Pentium V 1GHz, 256MB memory and40GB disk. To evaluate performances of the present Gfarm system, we scanned plenty of data files, the size of which is about 300MB for each, in three processing methods: sequential processing in one node, sequential processing by each node and parallel processing by each node. As a result, in comparison between the number of files and the elapsed time, parallel and distributed processing shorten the elapsed time to 1/5 than sequential processing. On the other hand, sequential processing times were shortened in another experiment, whose file size is smaller than 100KB. In this case, the elapsed time to scan one file is within one second. It implies that disk swap took place in case of parallel processing by each node. We note that the operation became unstable when the number of the files exceeded 1000. To overcome the problem (iii), we developed an original data class. This class supports our reading of data files with various data formats since it converts them into an original data format since it defines schemata for every type of data and encapsulates the structure of data files. In addition, since this class provides a function of time re-sampling, users can easily convert multiple data (array) with different time resolution into the same time resolution array. Finally, using the Gfarm, we achieved a high performance environment for large-scale statistical data analyses. It should be noted that the present method is effective only when one data file size is large enough. At present, we are restructuring the new Gfarm environment with 8 nodes: CPU is Athlon 64 x2 Dual Core 2GHz, 2GB memory and 1.2TB disk (using RAID0) for each node. Our original class is to be implemented on the new Gfarm environment. In the present talk, we show the latest results with applying the present system for data analyses with huge number of satellite observation data files.

Extending Automatic Parallelization to Optimize High-Level Abstractions for Multicore

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

Liao, C; Quinlan, D J; Willcock, J J

2008-12-12

Automatic introduction of OpenMP for sequential applications has attracted significant attention recently because of the proliferation of multicore processors and the simplicity of using OpenMP to express parallelism for shared-memory systems. However, most previous research has only focused on C and Fortran applications operating on primitive data types. C++ applications using high-level abstractions, such as STL containers and complex user-defined types, are largely ignored due to the lack of research compilers that are readily able to recognize high-level object-oriented abstractions and leverage their associated semantics. In this paper, we automatically parallelize C++ applications using ROSE, a multiple-language source-to-source compiler infrastructuremore » which preserves the high-level abstractions and gives us access to their semantics. Several representative parallelization candidate kernels are used to explore semantic-aware parallelization strategies for high-level abstractions, combined with extended compiler analyses. Those kernels include an array-base computation loop, a loop with task-level parallelism, and a domain-specific tree traversal. Our work extends the applicability of automatic parallelization to modern applications using high-level abstractions and exposes more opportunities to take advantage of multicore processors.« less

Methods and apparatus for capture and storage of semantic information with sub-files in a parallel computing system

DOEpatents

Faibish, Sorin; Bent, John M; Tzelnic, Percy; Grider, Gary; Torres, Aaron

2015-02-03

Techniques are provided for storing files in a parallel computing system using sub-files with semantically meaningful boundaries. A method is provided for storing at least one file generated by a distributed application in a parallel computing system. The file comprises one or more of a complete file and a plurality of sub-files. The method comprises the steps of obtaining a user specification of semantic information related to the file; providing the semantic information as a data structure description to a data formatting library write function; and storing the semantic information related to the file with one or more of the sub-files in one or more storage nodes of the parallel computing system. The semantic information provides a description of data in the file. The sub-files can be replicated based on semantically meaningful boundaries.

A Structure-Toxicity Study of Aß42 Reveals a New Anti-Parallel Aggregation Pathway

PubMed Central

Vignaud, Hélène; Bobo, Claude; Lascu, Ioan; Sörgjerd, Karin Margareta; Zako, Tamotsu; Maeda, Mizuo; Salin, Benedicte; Lecomte, Sophie; Cullin, Christophe

2013-01-01

Amyloid beta (Aβ) peptides produced by APP cleavage are central to the pathology of Alzheimer’s disease. Despite widespread interest in this issue, the relationship between the auto-assembly and toxicity of these peptides remains controversial. One intriguing feature stems from their capacity to form anti-parallel ß-sheet oligomeric intermediates that can be converted into a parallel topology to allow the formation of protofibrillar and fibrillar Aβ. Here, we present a novel approach to determining the molecular aspects of Aß assembly that is responsible for its in vivo toxicity. We selected Aß mutants with varying intracellular toxicities. In vitro, only toxic Aß (including wild-type Aß42) formed urea-resistant oligomers. These oligomers were able to assemble into fibrils that are rich in anti-parallel ß-sheet structures. Our results support the existence of a new pathway that depends on the folding capacity of Aß . PMID:24244667

Formation of a parallel-stranded DNA homoduplex by d(GGA) repeat oligonucleotides.

PubMed Central

Suda, T; Mishima, Y; Asakura, H; Kominami, R

1995-01-01

The GGA9-H molecules consisting of a double helical stretch followed by a single-stranded 3'-terminal overhang of nine GGA sequence repeats exhibited a gel mobility-shifted band in a concentration-dependent manner, suggestive of the intermolecular complex formation. The position of the shifted band in a gel was almost identical to that of the Y-shaped dimer marker of the same molecular weight that had the two double-helices at one side. This suggests that GGA9-H dimerizes in a parallel orientation without the formation of four-stranded hairpin structure. Since the GGA9-H homoduplex was stably formed at pH 4, 7 and 9, the formation does not require protonation or deprotonation of the N1 position of adenines. Neither does it require the N7 group of guanines responsible for Hoogsteen base pairing from the methylation interference and modification studies. Modification of the N7 group of guanines with dimethyl sulfate (DMS) did not inhibit the association and also the N7 group in the homoduplex was not protected from DMS. On the other hand, the GAA9-H having the G to A base substitution did not show such an association with either GGA9-H or GAA9-H. These results suggest that the homoduplex formation may be due to G.G base pairing through non-Hoogsteen hydrogen bonds. Images PMID:7479009

Clog Retard of a Vortex Throttle Joule-Thomson Cryocooler: Further Experimental Verification

NASA Astrophysics Data System (ADS)

Maytal, B.-Z.

2010-04-01

The demand of high purity gas supply for Joule-Thomson cryocoolers and liquefiers is crucial in order to avoid plug formation at the delicate throttling device. A throttle which would tolerate higher level of contamination is greatly desirable for more reliable operation. The vortex throttle has such a potential. A series of vortex throttles were applied to a miniature Joule-Thomson cryocooler and tested with precisely contaminated coolant. The instantaneous flow rate and the mode of its decay indicate the rate and nature of plug formation. Each experiment was a simultaneous run of two cryocoolers in parallel at similar conditions: one with a traditional throttle of short hole, and the other one with the vortex throttle. The clog retard behavior of the vortex throttle was verified. It runs about 2.5 times longer than the traditional one, while being fed by water vapor contaminated nitrogen at the levels of 5 and 17 PPM. The contamination level by carbon dioxide was 80 PPM and exhibited a different behavior of clog formation. Its effect on the cryocooler temperature stability with the vortex throttle was quite minor.

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

DOE PAGES

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

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

Chu, Haijian; Huang, Hanchen; Wang, Jian

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

Experimental investigation of homogeneous charge compression ignition combustion of biodiesel fuel with external mixture formation in a CI engine.

PubMed

Ganesh, D; Nagarajan, G; Ganesan, S

2014-01-01

In parallel to the interest in renewable fuels, there has also been increased interest in homogeneous charge compression ignition (HCCI) combustion. HCCI engines are being actively developed because they have the potential to be highly efficient and to produce low emissions. Even though HCCI has been researched extensively, few challenges still exist. These include controlling the combustion at higher loads and the formation of a homogeneous mixture. To obtain better homogeneity, in the present investigation external mixture formation method was adopted, in which the fuel vaporiser was used to achieve excellent HCCI combustion in a single cylinder air-cooled direct injection diesel engine. In continuation of our previous works, in the current study a vaporised jatropha methyl ester (JME) was mixed with air to form a homogeneous mixture and inducted into the cylinder during the intake stroke to analyze the combustion, emission and performance characteristics. To control the early ignition of JME vapor-air mixture, cooled (30 °C) Exhaust gas recirculation (EGR) technique was adopted. The experimental result shows 81% reduction in NOx and 72% reduction in smoke emission.

A study on the probability of twin plane formation during the nucleation of AgBr and AgCl crystals in the aqueous gelatin solution

NASA Astrophysics Data System (ADS)

Ohzeki, Katsuhisa; Hosoya, Yoichi

2007-07-01

A study was made on the probability of twin plane formation during the nucleation of AgBr and AgCl crystals. The growth condition was controlled to keep the number of the nuclei, neither decreasing owing to their dissolution, nor increasing owing to the formation of a new nucleus during the growth process. Under the condition, the nuclei were grown to have {1 1 1} faces on their surfaces by controlling pAg in a reaction solution and by use of growth modifier in case of AgCl crystal formation. The number of twin planes in each crystal was judged according to a conventional way on the basis of its morphology. The dependence of the number of twin planes per crystal on the probability of twin plain formation was in accordance with Poisson distribution, indicating the random formation of a twin plane on the {1 1 1} faces of a nucleus. The result that the ratio of number of AgCl crystals with parallel twin planes to all the multiply twinned crystals was about 10% supports the random formation of a twin plane and suggests that the twin plane formation took place on {1 1 1} surfaces at the possible eight corner of a nucleus. On the other hand, the ratio of the number of AgBr crystals with parallel twin planes to all the multiply twinned crystals was more than 50%. The result was explained by the anisotropic growth of a singly twinned nucleus according to the higher growth rate of {1 0 0} surfaces than that of {1 1 1} surfaces.

Arc/Forearc Lengthening at Plate Triple Junctions and the Formation of Ophiolitic Soles

NASA Astrophysics Data System (ADS)

Casey, John; Dewey, John

2013-04-01

The principal enigma of large obducted ophiolite slabs is that they clearly must have been generated by some form of organized sea-floor spreading/plate-accretion, such as may be envisioned for the oceanic ridges, yet the volcanics commonly have arc affinity (Miyashiro) with boninites (high-temperature/low-pressure, high Mg and Si andesites), which are suggestive of a forearc origin. PT conditions under which boninites and metamorphic soles form and observations of modern forearc systems lead us to the conclusion that ophiolite formation is associated with overidding plate spreading centers that intersect the trench to form ridge-trench-trench of ridge-trench-tranform triple junctions. The spreading centers extend and lengthen the forearc parallel to the trench and by definition are in supra-subduction zone (SSZ) settings. Many ophiolites likewise have complexly-deformed associated mafic-ultramafic assemblages that suggest fracture zone/transform t along their frontal edges, which in turn has led to models involving the nucleation of subduction zones on fracture zones or transpressional transforms. Hitherto, arc-related sea-floor-spreading has been considered to be either pre-arc (fore-arc boninites) or post-arc (classic Karig-style back arc basins that trench-parallell split arcs). Syn-arc boninites and forearc oceanic spreading centers that involve a stable ridge/trench/trench triple or a ridge-trench-transform triple junction, the ridge being between the two upper plates, are consistent with large slab ophiolite formation in a readied obduction settting. The direction of subduction must be oblique with a different sense in the two subduction zones and the oblique subduction cannot be partitioned into trench orthogonal and parallel strike-slip components. As the ridge spreads, new oceanic lithosphere is created within the forearc, the arc and fore-arc lengthen significantly, and a syn-arc ophiolite forearc complex is generated by this mechanism. The ophiolite ages along arc-strike; a distinctive diachronous MORB-like to boninitic to arc volcanic stratigraphy develops vertically in the forearc and eruption centers progressively migrate from the forearc back to the main arc massif with time. Dikes in the ophiolite are highly oblique to the trench (as are back-arc magnetic anomalies. Boninites and high-mg andesites are generated in the fore-arc under the aqueous, low pressure/high temperature, regime at the ridge above the instantaneously developed subducting and dehydrating slab. Subducted slab refrigeration of the hanging wall ensues and accretion of MORB metabasites to the hanging wall of the subduction channel initiates. Mafic protolith garnet/two pyroxene granulites to greenschists accrete and form the inverted P and T metamorphic sole prior to obduction. Sole accretion of lithosphere begins at about 1000°C and the full retrogressive sole may be fully formed within ten to fifteen million years of accretion, at which time low grade subduction melanges accrete. Obduction of the SSZ forearc ophiolite with its subjacent metamorphic sole occurs whenever the oceanic arc attempts subduction of a stable buoyant continental or back arc margin.

Paleocene Pacific Plate reorganization mirrored in formation of the Suvarov Trough, Manihiki Plateau

NASA Astrophysics Data System (ADS)

Pietsch, Ricarda; Uenzelmann-Neben, Gabriele

2016-10-01

The Suvarov Trough is a graben structure that deviates from the Danger Islands Troughs within the Manihiki Plateau, a Large Igneous Province (LIP) located in the Central Pacific. New high-resolution seismic reflection data provide evidence that the graben formed in two phases during the Paleocene (65-45 Ma). In a first phase extension occurred in southwestward direction, pulling apart the northern part of the Suvarov Trough and a parallel trending unnamed trough. In a second phase a change of extensional force direction occurred from southwest to west-northwest, forming the southern part of the Suvarov Trough that extends onto the High Plateau. The formation of the Suvarov Trough is accompanied by a series of normal fault systems that apparently formed simultaneously. Comparing the seismic results to existing Pacific paleo strain reconstructions, the timing of increased strain and local deformation direction fits well to our findings. We thus suggest that the multiple strike directions of the Suvarov Trough represent an extensional structure that was caused by the major, stepwise Pacific Plate reorganization during the Paleocene.

ABM Drag_Pass Report Generator

NASA Technical Reports Server (NTRS)

Fisher, Forest; Gladden, Roy; Khanampornpan, Teerapat

2008-01-01

dragREPORT software was developed in parallel with abmREPORT, which is described in the preceding article. Both programs were built on the capabilities created during that process. This tool generates a drag_pass report that summarizes vital information from the MRO aerobreaking drag_pass build process to facilitate both sequence reviews and provide a high-level summarization of the sequence for mission management. The script extracts information from the ENV, SSF, FRF, SCMFmax, and OPTG files, presenting them in a single, easy-to-check report providing the majority of parameters needed for cross check and verification as part of the sequence review process. Prior to dragReport, all the needed information was spread across a number of different files, each in a different format. This software is a Perl script that extracts vital summarization information and build-process details from a number of source files into a single, concise report format used to aid the MPST sequence review process and to provide a high-level summarization of the sequence for mission management reference. This software could be adapted for future aerobraking missions to provide similar reports, review and summarization information.

Magnetized Collisionless Shock Studies Using High Velocity Plasmoids

NASA Astrophysics Data System (ADS)

Weber, Thomas; Intrator, T.

2013-04-01

Magnetized collisionless shocks are ubiquitous throughout the cosmos and are observed to accelerate particles to relativistic velocities, amplify magnetic fields, transport energy, and create non-thermal distributions. They exhibit transitional scale lengths much shorter than the collisional mean free path and are mediated by collective interactions rather than Coulomb collisions. The Magnetized Shock Experiment (MSX) leverages advances in Field Reversed Configuration (FRC) plasmoid formation and acceleration to produce highly supersonic and super-Alfvénic supercritical shocks with pre-existing magnetic field at perpendicular, parallel or oblique angles to the direction of propagation. Adjustable shock speed, density, and magnetic field provide unique access to a range of parameter space relevant to a variety of naturally occurring shocks. This effort examines experimentally, analytically, and numerically the physics of collisionless shock formation, structure, and kinetic effects in a laboratory setting and draw comparisons between experimental data and astronomical observations. Supported by DOE Office of Fusion Energy Sciences and National Nuclear Security Administration under LANS contract DE-AC52-06NA25369 Approved for Public Release: LA-UR-12-22886

GRAVIDY, a GPU modular, parallel direct-summation N-body integrator: dynamics with softening

NASA Astrophysics Data System (ADS)

Maureira-Fredes, Cristián; Amaro-Seoane, Pau

2018-01-01

A wide variety of outstanding problems in astrophysics involve the motion of a large number of particles under the force of gravity. These include the global evolution of globular clusters, tidal disruptions of stars by a massive black hole, the formation of protoplanets and sources of gravitational radiation. The direct-summation of N gravitational forces is a complex problem with no analytical solution and can only be tackled with approximations and numerical methods. To this end, the Hermite scheme is a widely used integration method. With different numerical techniques and special-purpose hardware, it can be used to speed up the calculations. But these methods tend to be computationally slow and cumbersome to work with. We present a new graphics processing unit (GPU), direct-summation N-body integrator written from scratch and based on this scheme, which includes relativistic corrections for sources of gravitational radiation. GRAVIDY has high modularity, allowing users to readily introduce new physics, it exploits available computational resources and will be maintained by regular updates. GRAVIDY can be used in parallel on multiple CPUs and GPUs, with a considerable speed-up benefit. The single-GPU version is between one and two orders of magnitude faster than the single-CPU version. A test run using four GPUs in parallel shows a speed-up factor of about 3 as compared to the single-GPU version. The conception and design of this first release is aimed at users with access to traditional parallel CPU clusters or computational nodes with one or a few GPU cards.

Airfoil-based electromagnetic energy harvester containing parallel array motion between moving coil and multi-pole magnets towards enhanced power density.

PubMed

Leung, Chung Ming; Wang, Ya; Chen, Wusi

2016-11-01

In this letter, the airfoil-based electromagnetic energy harvester containing parallel array motion between moving coil and trajectory matching multi-pole magnets was investigated. The magnets were aligned in an alternatively magnetized formation of 6 magnets to explore enhanced power density. In particular, the magnet array was positioned in parallel to the trajectory of the tip coil within its tip deflection span. The finite element simulations of the magnetic flux density and induced voltages at an open circuit condition were studied to find the maximum number of alternatively magnetized magnets that was required for the proposed energy harvester. Experimental results showed that the energy harvester with a pair of 6 alternatively magnetized linear magnet arrays was able to generate an induced voltage (V o ) of 20 V, with an open circuit condition, and 475 mW, under a 30 Ω optimal resistance load operating with the wind speed (U) at 7 m/s and a natural bending frequency of 3.54 Hz. Compared to the traditional electromagnetic energy harvester with a single magnet moving through a coil, the proposed energy harvester, containing multi-pole magnets and parallel array motion, enables the moving coil to accumulate a stronger magnetic flux in each period of the swinging motion. In addition to the comparison made with the airfoil-based piezoelectric energy harvester of the same size, our proposed electromagnetic energy harvester generates 11 times more power output, which is more suitable for high-power-density energy harvesting applications at regions with low environmental frequency.

Two-dimensional parallel array technology as a new approach to automated combinatorial solid-phase organic synthesis

PubMed

Brennan; Biddison; Frauendorf; Schwarcz; Keen; Ecker; Davis; Tinder; Swayze

1998-01-01

An automated, 96-well parallel array synthesizer for solid-phase organic synthesis has been designed and constructed. The instrument employs a unique reagent array delivery format, in which each reagent utilized has a dedicated plumbing system. An inert atmosphere is maintained during all phases of a synthesis, and temperature can be controlled via a thermal transfer plate which holds the injection molded reaction block. The reaction plate assembly slides in the X-axis direction, while eight nozzle blocks holding the reagent lines slide in the Y-axis direction, allowing for the extremely rapid delivery of any of 64 reagents to 96 wells. In addition, there are six banks of fixed nozzle blocks, which deliver the same reagent or solvent to eight wells at once, for a total of 72 possible reagents. The instrument is controlled by software which allows the straightforward programming of the synthesis of a larger number of compounds. This is accomplished by supplying a general synthetic procedure in the form of a command file, which calls upon certain reagents to be added to specific wells via lookup in a sequence file. The bottle position, flow rate, and concentration of each reagent is stored in a separate reagent table file. To demonstrate the utility of the parallel array synthesizer, a small combinatorial library of hydroxamic acids was prepared in high throughput mode for biological screening. Approximately 1300 compounds were prepared on a 10 μmole scale (3-5 mg) in a few weeks. The resulting crude compounds were generally >80% pure, and were utilized directly for high throughput screening in antibacterial assays. Several active wells were found, and the activity was verified by solution-phase synthesis of analytically pure material, indicating that the system described herein is an efficient means for the parallel synthesis of compounds for lead discovery. Copyright 1998 John Wiley & Sons, Inc.

High-Performance Psychometrics: The Parallel-E Parallel-M Algorithm for Generalized Latent Variable Models. Research Report. ETS RR-16-34

ERIC Educational Resources Information Center

von Davier, Matthias

2016-01-01

This report presents results on a parallel implementation of the expectation-maximization (EM) algorithm for multidimensional latent variable models. The developments presented here are based on code that parallelizes both the E step and the M step of the parallel-E parallel-M algorithm. Examples presented in this report include item response…

Bilingual parallel programming

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

Foster, I.; Overbeek, R.

1990-01-01

Numerous experiments have demonstrated that computationally intensive algorithms support adequate parallelism to exploit the potential of large parallel machines. Yet successful parallel implementations of serious applications are rare. The limiting factor is clearly programming technology. None of the approaches to parallel programming that have been proposed to date -- whether parallelizing compilers, language extensions, or new concurrent languages -- seem to adequately address the central problems of portability, expressiveness, efficiency, and compatibility with existing software. In this paper, we advocate an alternative approach to parallel programming based on what we call bilingual programming. We present evidence that this approach providesmore » and effective solution to parallel programming problems. The key idea in bilingual programming is to construct the upper levels of applications in a high-level language while coding selected low-level components in low-level languages. This approach permits the advantages of a high-level notation (expressiveness, elegance, conciseness) to be obtained without the cost in performance normally associated with high-level approaches. In addition, it provides a natural framework for reusing existing code.« less

Cloud parallel processing of tandem mass spectrometry based proteomics data.

PubMed

Mohammed, Yassene; Mostovenko, Ekaterina; Henneman, Alex A; Marissen, Rob J; Deelder, André M; Palmblad, Magnus

2012-10-05

Data analysis in mass spectrometry based proteomics struggles to keep pace with the advances in instrumentation and the increasing rate of data acquisition. Analyzing this data involves multiple steps requiring diverse software, using different algorithms and data formats. Speed and performance of the mass spectral search engines are continuously improving, although not necessarily as needed to face the challenges of acquired big data. Improving and parallelizing the search algorithms is one possibility; data decomposition presents another, simpler strategy for introducing parallelism. We describe a general method for parallelizing identification of tandem mass spectra using data decomposition that keeps the search engine intact and wraps the parallelization around it. We introduce two algorithms for decomposing mzXML files and recomposing resulting pepXML files. This makes the approach applicable to different search engines, including those relying on sequence databases and those searching spectral libraries. We use cloud computing to deliver the computational power and scientific workflow engines to interface and automate the different processing steps. We show how to leverage these technologies to achieve faster data analysis in proteomics and present three scientific workflows for parallel database as well as spectral library search using our data decomposition programs, X!Tandem and SpectraST.

Field characterization of elastic properties across a fault zone reactivated by fluid injection

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

Jeanne, Pierre; Guglielmi, Yves; Rutqvist, Jonny

In this paper, we studied the elastic properties of a fault zone intersecting the Opalinus Clay formation at 300 m depth in the Mont Terri Underground Research Laboratory (Switzerland). Four controlled water injection experiments were performed in borehole straddle intervals set at successive locations across the fault zone. A three-component displacement sensor, which allowed capturing the borehole wall movements during injection, was used to estimate the elastic properties of representative locations across the fault zone, from the host rock to the damage zone to the fault core. Young's moduli were estimated by both an analytical approach and numerical finite differencemore » modeling. Results show a decrease in Young's modulus from the host rock to the damage zone by a factor of 5 and from the damage zone to the fault core by a factor of 2. In the host rock, our results are in reasonable agreement with laboratory data showing a strong elastic anisotropy characterized by the direction of the plane of isotropy parallel to the laminar structure of the shale formation. In the fault zone, strong rotations of the direction of anisotropy can be observed. Finally, the plane of isotropy can be oriented either parallel to bedding (when few discontinuities are present), parallel to the direction of the main fracture family intersecting the zone, and possibly oriented parallel or perpendicular to the fractures critically oriented for shear reactivation (when repeated past rupture along this plane has created a zone).« less

Field characterization of elastic properties across a fault zone reactivated by fluid injection

DOE PAGES

Jeanne, Pierre; Guglielmi, Yves; Rutqvist, Jonny; ...

2017-08-12

In this paper, we studied the elastic properties of a fault zone intersecting the Opalinus Clay formation at 300 m depth in the Mont Terri Underground Research Laboratory (Switzerland). Four controlled water injection experiments were performed in borehole straddle intervals set at successive locations across the fault zone. A three-component displacement sensor, which allowed capturing the borehole wall movements during injection, was used to estimate the elastic properties of representative locations across the fault zone, from the host rock to the damage zone to the fault core. Young's moduli were estimated by both an analytical approach and numerical finite differencemore » modeling. Results show a decrease in Young's modulus from the host rock to the damage zone by a factor of 5 and from the damage zone to the fault core by a factor of 2. In the host rock, our results are in reasonable agreement with laboratory data showing a strong elastic anisotropy characterized by the direction of the plane of isotropy parallel to the laminar structure of the shale formation. In the fault zone, strong rotations of the direction of anisotropy can be observed. Finally, the plane of isotropy can be oriented either parallel to bedding (when few discontinuities are present), parallel to the direction of the main fracture family intersecting the zone, and possibly oriented parallel or perpendicular to the fractures critically oriented for shear reactivation (when repeated past rupture along this plane has created a zone).« less

Parallel 3D Finite Element Numerical Modelling of DC Electron Guns

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

Prudencio, E.; Candel, A.; Ge, L.

2008-02-04

In this paper we present Gun3P, a parallel 3D finite element application that the Advanced Computations Department at the Stanford Linear Accelerator Center is developing for the analysis of beam formation in DC guns and beam transport in klystrons. Gun3P is targeted specially to complex geometries that cannot be described by 2D models and cannot be easily handled by finite difference discretizations. Its parallel capability allows simulations with more accuracy and less processing time than packages currently available. We present simulation results for the L-band Sheet Beam Klystron DC gun, in which case Gun3P is able to reduce simulation timemore » from days to some hours.« less

Tension is required for fibripositor formation.

PubMed

Kapacee, Zoher; Richardson, Susan H; Lu, Yinhui; Starborg, Tobias; Holmes, David F; Baar, Keith; Kadler, Karl E

2008-05-01

Embryonic tendon cells (ETCs) have actin-rich fibripositors that accompany parallel bundles of collagen fibrils in the extracellular matrix. To study fibripositor function, we have developed a three-dimensional cell culture system that promotes and maintains fibripositors. We show that ETCs cultured in fixed-length fibrin gels replace the fibrin during ~6 days in culture with parallel bundles of narrow-diameter collagen fibrils that are uniaxially aligned with fibripositors, thereby generating a tendon-like construct. Fibripositors occurred simultaneously with onset of parallel collagen fibrils. Interestingly, the constructs have a tendon-like crimp. In initial experiments to study the effects of tension, we showed that cutting the constructs resulted in loss of tension, loss of fibripositors and the appearance of immature fibrils with no preferred orientation.

Petascale computation of multi-physics seismic simulations

NASA Astrophysics Data System (ADS)

Gabriel, Alice-Agnes; Madden, Elizabeth H.; Ulrich, Thomas; Wollherr, Stephanie; Duru, Kenneth C.

2017-04-01

Capturing the observed complexity of earthquake sources in concurrence with seismic wave propagation simulations is an inherently multi-scale, multi-physics problem. In this presentation, we present simulations of earthquake scenarios resolving high-detail dynamic rupture evolution and high frequency ground motion. The simulations combine a multitude of representations of model complexity; such as non-linear fault friction, thermal and fluid effects, heterogeneous fault stress and fault strength initial conditions, fault curvature and roughness, on- and off-fault non-elastic failure to capture dynamic rupture behavior at the source; and seismic wave attenuation, 3D subsurface structure and bathymetry impacting seismic wave propagation. Performing such scenarios at the necessary spatio-temporal resolution requires highly optimized and massively parallel simulation tools which can efficiently exploit HPC facilities. Our up to multi-PetaFLOP simulations are performed with SeisSol (www.seissol.org), an open-source software package based on an ADER-Discontinuous Galerkin (DG) scheme solving the seismic wave equations in velocity-stress formulation in elastic, viscoelastic, and viscoplastic media with high-order accuracy in time and space. Our flux-based implementation of frictional failure remains free of spurious oscillations. Tetrahedral unstructured meshes allow for complicated model geometry. SeisSol has been optimized on all software levels, including: assembler-level DG kernels which obtain 50% peak performance on some of the largest supercomputers worldwide; an overlapping MPI-OpenMP parallelization shadowing the multiphysics computations; usage of local time stepping; parallel input and output schemes and direct interfaces to community standard data formats. All these factors enable aim to minimise the time-to-solution. The results presented highlight the fact that modern numerical methods and hardware-aware optimization for modern supercomputers are essential to further our understanding of earthquake source physics and complement both physic-based ground motion research and empirical approaches in seismic hazard analysis. Lastly, we will conclude with an outlook on future exascale ADER-DG solvers for seismological applications.

Fast I/O for Massively Parallel Applications

NASA Technical Reports Server (NTRS)

OKeefe, Matthew T.

1996-01-01

The two primary goals for this report were the design, contruction and modeling of parallel disk arrays for scientific visualization and animation, and a study of the IO requirements of highly parallel applications. In addition, further work in parallel display systems required to project and animate the very high-resolution frames resulting from our supercomputing simulations in ocean circulation and compressible gas dynamics.

Modeling Nanocomposites for Molecular Dynamics (MD) Simulations

DTIC Science & Technology

2015-01-01

Parallel Simulator ( LAMMPS ) is used as the MD simulator [9], the coordinates must be formatted for use in LAMMPSs. VMD has a set of tools (TopoTools...that can be used to generate a LAMMPS -readable format [6]. 3 Figure 4. Ethylene Monomer Produced From Coordinates in PDB and Rendered Using...where, i and j are the atom subscripts. Simulations are performed using LAMMPS simulation software. Periodic boundary conditions are

Comparison of three-dimensional fluorescence analysis methods for predicting formation of trihalomethanes and haloacetic acids.

PubMed

Peleato, Nicolás M; Andrews, Robert C

2015-01-01

This work investigated the application of several fluorescence excitation-emission matrix analysis methods as natural organic matter (NOM) indicators for use in predicting the formation of trihalomethanes (THMs) and haloacetic acids (HAAs). Waters from four different sources (two rivers and two lakes) were subjected to jar testing followed by 24hr disinfection by-product formation tests using chlorine. NOM was quantified using three common measures: dissolved organic carbon, ultraviolet absorbance at 254 nm, and specific ultraviolet absorbance as well as by principal component analysis, peak picking, and parallel factor analysis of fluorescence spectra. Based on multi-linear modeling of THMs and HAAs, principle component (PC) scores resulted in the lowest mean squared prediction error of cross-folded test sets (THMs: 43.7 (μg/L)(2), HAAs: 233.3 (μg/L)(2)). Inclusion of principle components representative of protein-like material significantly decreased prediction error for both THMs and HAAs. Parallel factor analysis did not identify a protein-like component and resulted in prediction errors similar to traditional NOM surrogates as well as fluorescence peak picking. These results support the value of fluorescence excitation-emission matrix-principal component analysis as a suitable NOM indicator in predicting the formation of THMs and HAAs for the water sources studied. Copyright © 2014. Published by Elsevier B.V.

New type of kinematic indicator in bed-parallel veins, Late Jurassic-Early Cretaceous Vaca Muerta Formation, Argentina: E-W shortening during Late Cretaceous vein opening

NASA Astrophysics Data System (ADS)

Ukar, Estibalitz; Lopez, Ramiro G.; Gale, Julia F. W.; Laubach, Stephen E.; Manceda, Rene

2017-11-01

In the Late Jurassic-Early Cretaceous Vaca Muerta Formation, previously unrecognized yet abundant structures constituting a new category of kinematic indicator occur within bed-parallel fibrous calcite veins (BPVs) in shale. Domal shapes result from localized shortening and thickening of BPVs and the intercalation of centimeter-thick, host-rock shale inclusions within fibrous calcite beef, forming thrust fault-bounded pop-up structures. Ellipsoidal and rounded structures show consistent orientations, lineaments of interlayered shale and fibrous calcite, and local centimeter-scale offset thrust faults that at least in some cases cut across the median line of the BPV and indicate E-W shortening. Continuity of crystal fibers shows the domal structures are contemporaneous with BPV formation and help establish timing of fibrous vein growth in the Late Cretaceous, when shortening directions were oriented E-W. Differences in the number of opening stages and the deformational style of the different BPVs indicate they may have opened at different times. The new domal kinematic indicators described in this study are small enough to be captured in core. When present in the subsurface, domal structures can be used to either infer paleostress orientation during the formation of BPVs or to orient core in cases where the paleostress is independently known.

Neotectonic Activity from Karewa Sediments, Kashmir Himalaya, India

NASA Astrophysics Data System (ADS)

Agarwal, K. K.; Shah, R. A.; Achyuthan, H.; Singh, D. S.; Srivastava, S.; Khan, I.

2018-01-01

Intermontane basin sedimentation occurred during Pliocene-Pleistocene in the Karewa Basin which formed after the continent-continent collision resulting in the formation of Himalayan orogenic belt around Eocene. These are elongated, narrow, thrust bounded basins which have formed during the late stages of orogeny. Situated at a height of 1700-1800 m above sea level, the Karewa basin received sediments because of ponding of a pre-existing river system and the tectonic movements along the Great Himalayan Ranges in the north and the Pir-Panjal ranges in the south along active faults. About 1300 m thick sediments of largely fluvio-lacustrine, glacio-fluvio-lacustrine and eolian origin are exposed having evidences of neotectonically formed structural features such as folds and faults. Folds are more prominent in the Lower Karewa formation (Hirpur Formation) while faults (mostly normal faults) are abundant in the Upper Karewas (Nagum Formation). Drainage in the area varies from dendritic to anastomosing to parallel. Anastomosing drainage suggests sudden decrease in gradient while presence of linear features such as faults and ridges is evident by parallel drainage. Study of morphometric parameters such as stream length (Lsm) and stream length ratios (RL), bifurcation ratio (Rb), drainage density (D), form factor (Rf), circularity ratio (Rc), and elongation ratio (Re) also indicate intense tectonic activity in the recent past.

Parallel Architectures and Parallel Algorithms for Integrated Vision Systems. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Choudhary, Alok Nidhi

1989-01-01

Computer vision is regarded as one of the most complex and computationally intensive problems. An integrated vision system (IVS) is a system that uses vision algorithms from all levels of processing to perform for a high level application (e.g., object recognition). An IVS normally involves algorithms from low level, intermediate level, and high level vision. Designing parallel architectures for vision systems is of tremendous interest to researchers. Several issues are addressed in parallel architectures and parallel algorithms for integrated vision systems.

Parallel Implementation of a High Order Implicit Collocation Method for the Heat Equation

NASA Technical Reports Server (NTRS)

Kouatchou, Jules; Halem, Milton (Technical Monitor)

2000-01-01

We combine a high order compact finite difference approximation and collocation techniques to numerically solve the two dimensional heat equation. The resulting method is implicit arid can be parallelized with a strategy that allows parallelization across both time and space. We compare the parallel implementation of the new method with a classical implicit method, namely the Crank-Nicolson method, where the parallelization is done across space only. Numerical experiments are carried out on the SGI Origin 2000.

Adapting high-level language programs for parallel processing using data flow

NASA Technical Reports Server (NTRS)

Standley, Hilda M.

1988-01-01

EASY-FLOW, a very high-level data flow language, is introduced for the purpose of adapting programs written in a conventional high-level language to a parallel environment. The level of parallelism provided is of the large-grained variety in which parallel activities take place between subprograms or processes. A program written in EASY-FLOW is a set of subprogram calls as units, structured by iteration, branching, and distribution constructs. A data flow graph may be deduced from an EASY-FLOW program.

Morphology, structure, and magnetism of FeCo thin films electrodeposited on hydrogen-terminated Si(111) surfaces.

PubMed

Zarpellon, J; Jurca, H F; Mattoso, N; Klein, J J; Schreiner, W H; Ardisson, J D; Macedo, W A A; Mosca, D H

2007-12-15

In this work we describe the fabrication of FeCo alloy (less than 10 at% Co) thin films from aqueous ammonium sulfate solutions onto n-type Si(111) substrates using potentiostatic electrodeposition at room temperature. The incorporation of Co into the deposits tends to inhibit Fe silicide formation and to protect deposits against oxidation under air exposure. As the incorporation of Co was progressively increased, the sizes of nuclei consisting of FeCo alloy increased, leading to films with a highly oriented body-centered cubic structure with crystalline texture, where (110) planes remain preferentially oriented parallel to the film surface.

Efficient Parallel Kernel Solvers for Computational Fluid Dynamics Applications

NASA Technical Reports Server (NTRS)

Sun, Xian-He

1997-01-01

Distributed-memory parallel computers dominate today's parallel computing arena. These machines, such as Intel Paragon, IBM SP2, and Cray Origin2OO, have successfully delivered high performance computing power for solving some of the so-called "grand-challenge" problems. Despite initial success, parallel machines have not been widely accepted in production engineering environments due to the complexity of parallel programming. On a parallel computing system, a task has to be partitioned and distributed appropriately among processors to reduce communication cost and to attain load balance. More importantly, even with careful partitioning and mapping, the performance of an algorithm may still be unsatisfactory, since conventional sequential algorithms may be serial in nature and may not be implemented efficiently on parallel machines. In many cases, new algorithms have to be introduced to increase parallel performance. In order to achieve optimal performance, in addition to partitioning and mapping, a careful performance study should be conducted for a given application to find a good algorithm-machine combination. This process, however, is usually painful and elusive. The goal of this project is to design and develop efficient parallel algorithms for highly accurate Computational Fluid Dynamics (CFD) simulations and other engineering applications. The work plan is 1) developing highly accurate parallel numerical algorithms, 2) conduct preliminary testing to verify the effectiveness and potential of these algorithms, 3) incorporate newly developed algorithms into actual simulation packages. The work plan has well achieved. Two highly accurate, efficient Poisson solvers have been developed and tested based on two different approaches: (1) Adopting a mathematical geometry which has a better capacity to describe the fluid, (2) Using compact scheme to gain high order accuracy in numerical discretization. The previously developed Parallel Diagonal Dominant (PDD) algorithm and Reduced Parallel Diagonal Dominant (RPDD) algorithm have been carefully studied on different parallel platforms for different applications, and a NASA simulation code developed by Man M. Rai and his colleagues has been parallelized and implemented based on data dependency analysis. These achievements are addressed in detail in the paper.

Design and Performance of a 1 ms High-Speed Vision Chip with 3D-Stacked 140 GOPS Column-Parallel PEs †.

PubMed

Nose, Atsushi; Yamazaki, Tomohiro; Katayama, Hironobu; Uehara, Shuji; Kobayashi, Masatsugu; Shida, Sayaka; Odahara, Masaki; Takamiya, Kenichi; Matsumoto, Shizunori; Miyashita, Leo; Watanabe, Yoshihiro; Izawa, Takashi; Muramatsu, Yoshinori; Nitta, Yoshikazu; Ishikawa, Masatoshi

2018-04-24

We have developed a high-speed vision chip using 3D stacking technology to address the increasing demand for high-speed vision chips in diverse applications. The chip comprises a 1/3.2-inch, 1.27 Mpixel, 500 fps (0.31 Mpixel, 1000 fps, 2 × 2 binning) vision chip with 3D-stacked column-parallel Analog-to-Digital Converters (ADCs) and 140 Giga Operation per Second (GOPS) programmable Single Instruction Multiple Data (SIMD) column-parallel PEs for new sensing applications. The 3D-stacked structure and column parallel processing architecture achieve high sensitivity, high resolution, and high-accuracy object positioning.

Glycoprotein biosynthesis in animal cells grown in suspension culture. Assembly of lipid-linked saccharides and formation of protein-bound 'high-mannose' oligosaccharides.

PubMed Central

Bailey, D S; Burke, J; Sinclair, R; Mukherjee, B B

1981-01-01

Glycoprotein biosynthesis was studied with mouse L-cells grown in suspension culture. Glucose-deprived cells incorporated [3H]mannose into 'high-mannose' protein-bound oligosaccharides and a few relatively high-molecular-weight lipid-linked oligosaccharides. The latter were retained by DEAE-cellulose and turned over quite slowly during pulse--chase experiments. Increased heterogeneity in size of lipid-linked oligosaccharides developed during prolonged glucose deprivation. Sequential elongation of lipid-linked oligosaccharides was also observed, and conditions that prevented the assembly of the higher lipid-linked oligosaccharides also prevented the formation of the larger protein-bound 'high-mannose' oligosaccharides. In parallel experiments, [3H]mannose was incorporated into a total polyribosome fraction, suggesting that mannose residues were transferred co-translationally to nascent protein. Membrane preparations from these cells catalysed the assembly from UDP-N-acetyl-D-[6-3H]glucosamine and GDP-D-[U-14C]mannose of polyisoprenyl diphosphate derivatives whose oligosaccharide moieties were heterogeneous in size. Elongation of the N-acetyl-D-[6-3H]glucosamine-initiated glycolipids with mannose residues produced several higher lipid-linked oligosaccharides similar to those seen during glucose deprivation in vivo. Glucosylation of these mannose-containing oligosaccharides from UDP-D-[6-3H]glucose was restricted to those of a relatively high molecular weight. Protein-bound saccharides formed in vitro were mainly smaller in size than those assembled on the lipid acceptors. These results support the involvement of lipid-linked saccharides in the synthesis of asparagine-linked glycoproteins, but show both in vivo and in vitro that protein-bound 'high-mannose' oligosaccharide formation can occur independently of higher lipid-linked oligosaccharide synthesis. PMID:7306042

Effects of Propylene Carbonate Content in CsPF 6 -Containing Electrolytes on the Enhanced Performances of Graphite Electrode for Lithium-Ion Batteries

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

Zheng, Jianming; Yan, Pengfei; Cao, Ruiguo

2016-02-15

The effects Of propylene carbonate (PC) content in CsPF6-containing electrolytes on the performances of graphite electrode in lithium half cells and in graphite parallel to LiNi0.80Co0.15Al0.05O2 (NCA) full cells are investigated. It is found that the performance of graphite electrode is significantly-affected by PC content in the CsPF6-containing electrolytes. An optimal PC content of 20% by weight in the solvent mixtures is identified. The enhanced electrochemical performance of graphite electrode can be attributed to the synergistic effects of the PC solvent and the Cs+ additive. The synergistic effects of Cs+ additive and appropriate amount of PC enable the formation ofmore » a robust, ultrathin, and compact solid electrolyte interphase (SEI) layer on the surface of graphite electrode, which is only permeable for desolvated Li+ ions and allows fast Li+ ion transport through it. Therefore, this SEI layer effectively suppresses the PC cointercalation and largely alleviates the Li dendrite formation on graphite electrode during lithiation even at relatively high current densities. The presence of low-melting-point PC solvent improves the sustainable operation of graphite parallel to NCA full cells under a wide temperature range. The fundamental findings also shed light On the importance of manipulating/maintaining the electrode/electrolyte interphasial stability in various energy-storage devices.« less

X-ray computed tomography comparison of individual and parallel assembled commercial lithium iron phosphate batteries at end of life after high rate cycling

NASA Astrophysics Data System (ADS)

Carter, Rachel; Huhman, Brett; Love, Corey T.; Zenyuk, Iryna V.

2018-03-01

X-ray computed tomography (X-ray CT) across multiple length scales is utilized for the first time to investigate the physical abuse of high C-rate pulsed discharge on cells wired individually and in parallel.. Manufactured lithium iron phosphate cells boasting high rate capability were pulse power tested in both wiring conditions with high discharge currents of 10C for a high number of cycles (up to 1200) until end of life (<80% of initial discharge capacity retained). The parallel assembly reached end of life more rapidly for reasons unknown prior to CT investigations. The investigation revealed evidence of overdischarge in the most degraded cell from the parallel assembly, compared to more traditional failure in the individual cell. The parallel-wired cell exhibited dissolution of copper from the anode current collector and subsequent deposition throughout the separator near the cathode of the cell. This overdischarge-induced copper deposition, notably impossible to confirm with other state of health (SOH) monitoring methods, is diagnosed using CT by rendering the interior current collector without harm or alteration to the active materials. Correlation of CT observations to the electrochemical pulse data from the parallel-wired cells reveals the risk of parallel wiring during high C-rate pulse discharge.

Enhancing GIS Capabilities for High Resolution Earth Science Grids

NASA Astrophysics Data System (ADS)

Koziol, B. W.; Oehmke, R.; Li, P.; O'Kuinghttons, R.; Theurich, G.; DeLuca, C.

2017-12-01

Applications for high performance GIS will continue to increase as Earth system models pursue more realistic representations of Earth system processes. Finer spatial resolution model input and output, unstructured or irregular modeling grids, data assimilation, and regional coordinate systems present novel challenges for GIS frameworks operating in the Earth system modeling domain. This presentation provides an overview of two GIS-driven applications that combine high performance software with big geospatial datasets to produce value-added tools for the modeling and geoscientific community. First, a large-scale interpolation experiment using National Hydrography Dataset (NHD) catchments, a high resolution rectilinear CONUS grid, and the Earth System Modeling Framework's (ESMF) conservative interpolation capability will be described. ESMF is a parallel, high-performance software toolkit that provides capabilities (e.g. interpolation) for building and coupling Earth science applications. ESMF is developed primarily by the NOAA Environmental Software Infrastructure and Interoperability (NESII) group. The purpose of this experiment was to test and demonstrate the utility of high performance scientific software in traditional GIS domains. Special attention will be paid to the nuanced requirements for dealing with high resolution, unstructured grids in scientific data formats. Second, a chunked interpolation application using ESMF and OpenClimateGIS (OCGIS) will demonstrate how spatial subsetting can virtually remove computing resource ceilings for very high spatial resolution interpolation operations. OCGIS is a NESII-developed Python software package designed for the geospatial manipulation of high-dimensional scientific datasets. An overview of the data processing workflow, why a chunked approach is required, and how the application could be adapted to meet operational requirements will be discussed here. In addition, we'll provide a general overview of OCGIS's parallel subsetting capabilities including challenges in the design and implementation of a scientific data subsetter.

Physics Structure Analysis of Parallel Waves Concept of Physics Teacher Candidate

NASA Astrophysics Data System (ADS)

Sarwi, S.; Supardi, K. I.; Linuwih, S.

2017-04-01

The aim of this research was to find a parallel structure concept of wave physics and the factors that influence on the formation of parallel conceptions of physics teacher candidates. The method used qualitative research which types of cross-sectional design. These subjects were five of the third semester of basic physics and six of the fifth semester of wave course students. Data collection techniques used think aloud and written tests. Quantitative data were analysed with descriptive technique-percentage. The data analysis technique for belief and be aware of answers uses an explanatory analysis. Results of the research include: 1) the structure of the concept can be displayed through the illustration of a map containing the theoretical core, supplements the theory and phenomena that occur daily; 2) the trend of parallel conception of wave physics have been identified on the stationary waves, resonance of the sound and the propagation of transverse electromagnetic waves; 3) the influence on the parallel conception that reading textbooks less comprehensive and knowledge is partial understanding as forming the structure of the theory.

Optimal parallel solution of sparse triangular systems

NASA Technical Reports Server (NTRS)

Alvarado, Fernando L.; Schreiber, Robert

1990-01-01

A method for the parallel solution of triangular sets of equations is described that is appropriate when there are many right-handed sides. By preprocessing, the method can reduce the number of parallel steps required to solve Lx = b compared to parallel forward or backsolve. Applications are to iterative solvers with triangular preconditioners, to structural analysis, or to power systems applications, where there may be many right-handed sides (not all available a priori). The inverse of L is represented as a product of sparse triangular factors. The problem is to find a factored representation of this inverse of L with the smallest number of factors (or partitions), subject to the requirement that no new nonzero elements be created in the formation of these inverse factors. A method from an earlier reference is shown to solve this problem. This method is improved upon by constructing a permutation of the rows and columns of L that preserves triangularity and allow for the best possible such partition. A number of practical examples and algorithmic details are presented. The parallelism attainable is illustrated by means of elimination trees and clique trees.

The CAnadian NIRISS Unbiased Cluster Survey (CANUCS)

NASA Astrophysics Data System (ADS)

Ravindranath, Swara; NIRISS GTO Team

2017-06-01

CANUCS GTO program is a JWST spectroscopy and imaging survey of five massive galaxy clusters and ten parallel fields using the NIRISS low-resolution grisms, NIRCam imaging and NIRSpec multi-object spectroscopy. The primary goal is to understand the evolution of low mass galaxies across cosmic time. The resolved emission line maps and line ratios for many galaxies, with some at resolution of 100pc via the magnification by gravitational lensing will enable determining the spatial distribution of star formation, dust and metals. Other science goals include the detection and characterization of galaxies within the reionization epoch, using multiply-imaged lensed galaxies to constrain cluster mass distributions and dark matter substructure, and understanding star-formation suppression in the most massive galaxy clusters. In this talk I will describe the science goals of the CANUCS program. The proposed prime and parallel observations will be presented with details of the implementation of the observation strategy using JWST proposal planning tools.

GANDALF - Graphical Astrophysics code for N-body Dynamics And Lagrangian Fluids

NASA Astrophysics Data System (ADS)

Hubber, D. A.; Rosotti, G. P.; Booth, R. A.

2018-01-01

GANDALF is a new hydrodynamics and N-body dynamics code designed for investigating planet formation, star formation and star cluster problems. GANDALF is written in C++, parallelized with both OPENMP and MPI and contains a PYTHON library for analysis and visualization. The code has been written with a fully object-oriented approach to easily allow user-defined implementations of physics modules or other algorithms. The code currently contains implementations of smoothed particle hydrodynamics, meshless finite-volume and collisional N-body schemes, but can easily be adapted to include additional particle schemes. We present in this paper the details of its implementation, results from the test suite, serial and parallel performance results and discuss the planned future development. The code is freely available as an open source project on the code-hosting website github at https://github.com/gandalfcode/gandalf and is available under the GPLv2 license.

Emerging Adults’ Lived Experience of Formative Family Stress: The Family’s Lasting Influence

PubMed Central

Valdez, Carmen R.; Chavez, Tom; Woulfe, Julie

2014-01-01

In this article, we use a phenomenology framework to explore emerging adults’ formative experiences of family stress. Fourteen college students participated in a qualitative interview about their experience of family stress. We analyzed the interviews using the empirical phenomenological psychology method. Participants described a variety of family stressors, including parental conflict and divorce, physical or mental illness, and emotional or sexual abuse by a family member. Two general types of parallel processes were essential to the experience of family stress for participants. First, the family stressor was experienced in shifts and progressions reflecting the young person’s attempts to manage the stressor, and second, these shifts and progressions were interdependent with deeply personal psychological meanings of self, sociality, physical and emotional expression, agency, place, space, project, and discourse. We describe each one of these parallel processes, and their subprocesses, and conclude with implications for mental health practice and research. PMID:23771635

Emerging adults' lived experience of formative family stress: the family's lasting influence.

PubMed

Valdez, Carmen R; Chavez, Tom; Woulfe, Julie

2013-08-01

In this article, we use a phenomenology framework to explore emerging adults' formative experiences of family stress. Fourteen college students participated in a qualitative interview about their experience of family stress. We analyzed the interviews using the empirical phenomenological psychology method. Participants described a variety of family stressors, including parental conflict and divorce, physical or mental illness, and emotional or sexual abuse by a family member. Two general types of parallel processes were essential to the experience of family stress for participants. First, the family stressor was experienced in shifts and progressions reflecting the young person's attempts to manage the stressor, and second, these shifts and progressions were interdependent with deeply personal psychological meanings of self, sociality, physical and emotional expression, agency, place, space, project, and discourse. We describe each of these parallel processes and their subprocesses, and conclude with implications for mental health practice and research.

Bis(1,3-dimethyl-1H-imidazolium) hexa-fluoro-silicate: the second monoclinic polymorph.

PubMed

Tian, Chong; Nie, Wanli; Borzov, Maxim V

2013-01-01

The title compound, 2C5H9N2 (+)·SiF6 (2-), (I), crystallized as a new polymorph, different from the previously reported one (Ia) [Light et al. (2007 ▶) private communication (refcode: NIQFAV). CCDC, Cambridge, England]. The symmetry [space groups P21/n for (I) and C2/c for(Ia)] and crystal packing patterns are markedly different for this pair of polymorphs. In (I), all imidazolium cations in the lattice are nearly parallel to each other, whereas a herringbone arrangement can be found in (Ia). In (I), each SiF6 (2-) dianion forms four short C-H⋯F contacts with adjacent C5H9N2 (+) cations, resulting in the formation of layers parallel to the ac plane. In (Ia), the C-H⋯F contacts are generally longer and result in the formation of layers along the bc plane.

Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel β-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.

PubMed

Yazawa, Koji; Suzuki, Furitsu; Nishiyama, Yusuke; Ohata, Takuya; Aoki, Akihiro; Nishimura, Katsuyuki; Kaji, Hironori; Shimizu, Tadashi; Asakura, Tetsuo

2012-11-25

The accurate (1)H positions of alanine tripeptide, A(3), with anti-parallel and parallel β-sheet structures could be determined by highly resolved (1)H DQMAS solid-state NMR spectra and (1)H chemical shift calculation with gauge-including projector augmented wave calculations.

The Relationships of Upper Plate Ridge-Trench-Trench and Ridge-Trench-Transform Triple Junction Evolution to Arc Lengthening, Subduction Zone initiation and Ophiolitic Forearc Obduction

NASA Astrophysics Data System (ADS)

Casey, J.; Dewey, J. F.

2013-12-01

The principal enigma of large obducted ophiolite slabs is that they clearly must have been generated by some form of organized sea-floor spreading/plate-accretion, such as may be envisioned for the oceanic ridges, yet the volcanics commonly have arc affinity (Miyashiro) with boninites (high-temperature/low-pressure, high Mg and Si andesites), which are suggestive of a forearc origin. PT conditions under which boninites and metamorphic soles form and observations of modern forearc systems lead us to the conclusion that ophiolite formation is associated with overriding plate spreading centers that intersect the trench to form ridge-trench-trench of ridge-trench-tranform triple junctions. The spreading centers extend and lengthen the forearc parallel to the trench and by definition are in supra-subduction zone (SSZ) settings. Many ophiolites likewise have complexly-deformed associated mafic-ultramafic assemblages that suggest fracture zone/transform along their frontal edges, which in turn has led to models involving the nucleation of subduction zones on fracture zones or transpressional transforms. Hitherto, arc-related sea-floor-spreading has been considered to be either pre-arc (fore-arc boninites) or post-arc (classic Karig-style back arc basins that trench-parallel split arcs). Syn-arc boninites and forearc oceanic spreading centers that involve a stable ridge/trench/trench triple or a ridge-trench-transform triple junction, the ridge being between the two upper plates, are consistent with large slab ophiolite formation in an obduction-ready settting. The direction of subduction must be oblique with a different sense in the two subduction zones and the oblique subduction cannot be partitioned into trench orthogonal and parallel strike-slip components. As the ridge spreads, new oceanic lithosphere is created within the forearc, the arc and fore-arc lengthen significantly, and a syn-arc ophiolite forearc complex is generated by this mechanism. The ophiolite ages along arc-strike; a distinctive diachronous MORB-like to boninitic to arc volcanic stratigraphy develops vertically in the forearc and eruption centers progressively migrate from the forearc back to the main arc massif with time. Dikes in the ophiolite are commonly highly oblique to the trench (as are back-arc magnetic anomalies in modern environments). Boninites and high-mg andesites are generated in the fore-arc under the aqueous, low pressure/high temperature, regime at the ridge above the instantaneously developed subducting and dehydrating slab. We review both modern subduction environments and ancient obducted ophiolite analogues that illustrate this tectonic model for subduction initiation and the creation and rapid divergent-convergent plate tectonic transitions to ophiolitic forearcs.

Time and space resolved spectroscopic investigation during anode plume formation in a high-current vacuum arc

NASA Astrophysics Data System (ADS)

Khakpour, A.; Methling, R.; Uhrlandt, D.; Franke, St.; Gortschakow, S.; Popov, S.; Batrakov, A.; Weltmann, K. D.

2017-05-01

This paper presents time and space resolved results of spectroscopic measurements during the formation of an anode plume in the late current pulse phase of a high-current vacuum arc. The formation of the anode plume is investigated systematically based on the occurrence of high-current anode spots, depending on gap distance and current for AC 100 Hz and CuCr7525 butt contacts with a diameter of 10 mm. The anode plume is observed after the extinction of anode spot type 2 in which both the anode and cathode are active. It is concluded from the spatial profiles of the atomic and ionic radiation, parallel and perpendicular to anode surface, that the inner part of the plume is dominated by Cu I radiation, whereas a halo of light emitted by Cu II covers the plume. The radiation intensity of Cu III lines is quite low across the whole anode plume. Upper level excited state densities corresponding to Cu I lines at 510.55, 515.32, 521.82, 578.21 nm are determined. The temporal evolution of the resulting excitation temperature in the centre of the plume varies from 8500 K to 6000 K at 500 µs to 100 µs before current zero, respectively. The density calculated for Cu I at position in the plume is in the range of 1-5  ×  1019 m-3.

Generation and evolution of anisotropic turbulence and related energy transfer in a multi-species solar wind

NASA Astrophysics Data System (ADS)

Maneva, Yana; Poedts, Stefaan

2017-04-01

The electromagnetic fluctuations in the solar wind represent a zoo of plasma waves with different properties, whose wavelengths range from largest fluid scales to the smallest dissipation scales. By nature the power spectrum of the magnetic fluctuations is anisotropic with different spectral slopes in parallel and perpendicular directions with respect to the background magnetic field. Furthermore, the magnetic field power spectra steepen as one moves from the inertial to the dissipation range and we observe multiple spectral breaks with different slopes in parallel and perpendicular direction at the ion scales and beyond. The turbulent dissipation of magnetic field fluctuations at the sub-ion scales is believed to go into local ion heating and acceleration, so that the spectral breaks are typically associated with particle energization. The gained energy can be in the form of anisotropic heating, formation of non-thermal features in the particle velocity distributions functions, and redistribution of the differential acceleration between the different ion populations. To study the relation between the evolution of the anisotropic turbulent spectra and the particle heating at the ion and sub-ion scales we perform a series of 2.5D hybrid simulations in a collisionless drifting proton-alpha plasma. We neglect the fast electron dynamics and treat the electrons as an isothermal fluid electrons, whereas the protons and a minor population of alpha particles are evolved in a fully kinetic manner. We start with a given wave spectrum and study the evolution of the magnetic field spectral slopes as a function of the parallel and perpendicular wave¬numbers. Simultaneously, we track the particle response and the energy exchange between the parallel and perpendicular scales. We observe anisotropic behavior of the turbulent power spectra with steeper slopes along the dominant energy-containing direction. This means that for parallel and quasi-parallel waves we have steeper spectral slope in parallel direction, whereas for highly oblique waves the dissipation occurs predominantly in perpendicular direction and the spectral slopes are steeper across the background magnetic field. The value of the spectral slopes depends on the angle of propagation, the spectral range, as well as the plasma properties. In general the dissipation is stronger at small scales and the corresponding spectral slopes there are steeper. For parallel and quasi-parallel propagation the prevailing energy cascade remains along the magnetic field, whereas for initially isotropic oblique turbulence the cascade develops mainly in perpendicular direction.

High-pressure, high-temperature synthesis of superhard boron suboxide

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

Hubert, H.; Garvie, L.A.J.; Leinenweber, K.

A multianvil device was used to investigate the formation of B{sub x}O phases produced in the 2 to 10 GPa pressure range with temperatures between 1,000 and 1,800 C. Amorphous and crystalline B and BP were oxidized using B{sub 2}O{sub 3} and CrO{sub 3}. Using powder X-ray diffraction and parallel electron energy-loss spectroscopy (PEELS), the authors were unable to detect graphitic or diamond-structured B{sub 2}O, reported in previous studies. The refractory boride B{sub 6}O, which has the {alpha}-rhombohedral boron structure, is the dominant suboxide in the P and T range of the investigation. PEELS with a transmission electron microscope wasmore » used to characterize the boron oxides.« less

Parallel tempering simulation of the three-dimensional Edwards-Anderson model with compact asynchronous multispin coding on GPU

NASA Astrophysics Data System (ADS)

Fang, Ye; Feng, Sheng; Tam, Ka-Ming; Yun, Zhifeng; Moreno, Juana; Ramanujam, J.; Jarrell, Mark

2014-10-01

Monte Carlo simulations of the Ising model play an important role in the field of computational statistical physics, and they have revealed many properties of the model over the past few decades. However, the effect of frustration due to random disorder, in particular the possible spin glass phase, remains a crucial but poorly understood problem. One of the obstacles in the Monte Carlo simulation of random frustrated systems is their long relaxation time making an efficient parallel implementation on state-of-the-art computation platforms highly desirable. The Graphics Processing Unit (GPU) is such a platform that provides an opportunity to significantly enhance the computational performance and thus gain new insight into this problem. In this paper, we present optimization and tuning approaches for the CUDA implementation of the spin glass simulation on GPUs. We discuss the integration of various design alternatives, such as GPU kernel construction with minimal communication, memory tiling, and look-up tables. We present a binary data format, Compact Asynchronous Multispin Coding (CAMSC), which provides an additional 28.4% speedup compared with the traditionally used Asynchronous Multispin Coding (AMSC). Our overall design sustains a performance of 33.5 ps per spin flip attempt for simulating the three-dimensional Edwards-Anderson model with parallel tempering, which significantly improves the performance over existing GPU implementations.

Preliminary Diffusive Clearance of Silicon Nanopore Membranes in a Parallel Plate Configuration for Renal Replacement Therapy

PubMed Central

Kim, Steven; Heller, James; Iqbal, Zohora; Kant, Rishi; Kim, Eun Jung; Durack, Jeremy; Saeed, Maythem; Do, Loi; Hetts, Steven; Wilson, Mark; Brakeman, Paul; Fissell, William H.; Roy, Shuvo

2015-01-01

Silicon nanopore membranes (SNM) with compact geometry and uniform pore size distribution have demonstrated a remarkable capacity for hemofiltration. These advantages could potentially be used for hemodialysis. Here we present an initial evaluation of the SNM’s mechanical robustness, diffusive clearance, and hemocompatibility in a parallel plate configuration. Mechanical robustness of the SNM was demonstrated by exposing membranes to high flows (200ml/min) and pressures (1,448mmHg). Diffusive clearance was performed in an albumin solution and whole blood with blood and dialysate flow rates of 25ml/min. Hemocompatibility was evaluated using scanning electron microscopy and immunohistochemistry after 4-hours in an extra-corporeal porcine model. The pressure drop across the flow cell was 4.6mmHg at 200ml/min. Mechanical testing showed that SNM could withstand up to 775.7mmHg without fracture. Urea clearance did not show an appreciable decline in blood versus albumin solution. Extra-corporeal studies showed blood was successfully driven via the arterial-venous pressure differential without thrombus formation. Bare silicon showed increased cell adhesion with a 4.1 fold increase and 1.8 fold increase over polyethylene-glycol (PEG)-coated surfaces for tissue plasminogen factor (t-PA) and platelet adhesion (CD-41), respectively. These initial results warrant further design and development of a fully scaled SNM-based parallel plate dialyzer for renal replacement therapy. PMID:26692401

HeinzelCluster: accelerated reconstruction for FORE and OSEM3D.

PubMed

Vollmar, S; Michel, C; Treffert, J T; Newport, D F; Casey, M; Knöss, C; Wienhard, K; Liu, X; Defrise, M; Heiss, W D

2002-08-07

Using iterative three-dimensional (3D) reconstruction techniques for reconstruction of positron emission tomography (PET) is not feasible on most single-processor machines due to the excessive computing time needed, especially so for the large sinogram sizes of our high-resolution research tomograph (HRRT). In our first approach to speed up reconstruction time we transform the 3D scan into the format of a two-dimensional (2D) scan with sinograms that can be reconstructed independently using Fourier rebinning (FORE) and a fast 2D reconstruction method. On our dedicated reconstruction cluster (seven four-processor systems, Intel PIII@700 MHz, switched fast ethernet and Myrinet, Windows NT Server), we process these 2D sinograms in parallel. We have achieved a speedup > 23 using 26 processors and also compared results for different communication methods (RPC, Syngo, Myrinet GM). The other approach is to parallelize OSEM3D (implementation of C Michel), which has produced the best results for HRRT data so far and is more suitable for an adequate treatment of the sinogram gaps that result from the detector geometry of the HRRT. We have implemented two levels of parallelization for four dedicated cluster (a shared memory fine-grain level on each node utilizing all four processors and a coarse-grain level allowing for 15 nodes) reducing the time for one core iteration from over 7 h to about 35 min.

P-body components, Dhh1 and Pat1, are involved in tRNA nuclear-cytoplasmic dynamics

PubMed Central

Hurto, Rebecca L.; Hopper, Anita K.

2011-01-01

The nuclear-cytoplasmic distribution of tRNA depends on the balance between tRNA nuclear export/re-export and retrograde tRNA nuclear import in Saccharomyces cerevisiae. The distribution of tRNA is sensitive to nutrient availability as cells deprived of various nutrients exhibit tRNA nuclear accumulation. Starvation induces numerous events that result in translational repression and P-body formation. This study investigated the possible coordination of these responses with tRNA nuclear-cytoplasmic distribution. Dhh1 and Pat1 function in parallel to promote translation repression and P-body formation in response to starvation. Loss of both, Dhh1 and Pat1, results in a failure to repress translation and to induce P-body formation in response to glucose starvation. This study reports that nutrient deprived dhh1 pat1 cells also fail to accumulate tRNA within nuclei. Conversely, inhibition of translation initiation and induction of P-body formation by overproduction of Dhh1 or Pat1 cause tRNA nuclear accumulation in nutrient-replete conditions. Also, loss of the mRNA decapping activator, Lsm1, causes tRNA nuclear accumulation. However, the coordination between P-body formation, translation repression, and tRNA distribution is limited to the early part of the P-body formation/translation repression pathway as loss of mRNA decapping or 5′ to 3′ degradation does not influence tRNA nuclear-cytoplasmic dynamics. The data provide the first link between P-body formation/translation initiation and tRNA nuclear-cytoplasmic dynamics. The current model is that Dhh1 and Pat1 function in parallel to promote starvation-induced tRNA nuclear accumulation. PMID:21398402

Development of HgCdTe large format MBE arrays and noise-free high speed MOVPE EAPD arrays for ground based NIR astronomy

NASA Astrophysics Data System (ADS)

Finger, G.; Baker, I.; Downing, M.; Alvarez, D.; Ives, D.; Mehrgan, L.; Meyer, M.; Stegmeier, J.; Weller, H. J.

2017-11-01

Large format near infrared HgCdTe 2Kx2K and 4Kx4K MBE arrays have reached a level of maturity which meets most of the specifications required for near infrared (NIR) astronomy. The only remaining problem is the persistence effect which is device specific and not yet fully under control. For ground based multi-object spectroscopy on 40 meter class telescopes larger pixels would be advantageous. For high speed near infrared fringe tracking and wavefront sensing the only way to overcome the CMOS noise barrier is the amplification of the photoelectron signal inside the infrared pixel by means of the avalanche gain. A readout chip for a 320x256 pixel HgCdTe eAPD array will be presented which has 32 parallel video outputs being arranged in such a way that the full multiplex advantage is also available for small sub-windows. In combination with the high APD gain this allows reducing the readout noise to the subelectron level by applying nondestructive readout schemes with subpixel sampling. Arrays grown by MOVPE achieve subelectron readout noise and operate with superb cosmetic quality at high APD gain. Efforts are made to reduce the dark current of those arrays to make this technology also available for large format focal planes of NIR instruments offering noise free detectors for deep exposures. The dark current of the latest MOVPE eAPD arrays is already at a level adequate for noiseless broad and narrow band imaging in scientific instruments.

How to avoid glucose degradation products in peritoneal dialysis fluids.

PubMed

Erixon, Martin; Wieslander, Anders; Lindén, Torbjörn; Carlsson, Ola; Forsbäck, Gunita; Svensson, Eva; Jönsson, Jan Ake; Kjellstrand, Per

2006-01-01

The formation of glucose degradation products (GDPs) during sterilization of peritoneal dialysis fluids (PDFs) is one of the most important aspects of biocompatibility of glucose-containing PDFs. Producers of PDFs are thus trying to minimize the level of GDPs in their products. 3,4-Dideoxyglucosone-3-ene (3,4-DGE) has been identified as the most bioreactive GDP in PDFs. It exists in a temperature-dependent equilibrium with a pool of 3-deoxyglucosone (3-DG) and is a precursor in the irreversible formation of 5-hydroxymethyl furaldehyde (5-HMF). The aim of the present study was to investigate how to minimize GDPs in PDFs and how different manufacturers have succeeded in doing so. Glucose solutions at different pHs and concentrations were heat sterilized and 3-DG, 3,4-DGE, 5-HMF, formaldehyde, and acetaldehyde were analyzed. Conventional as well as biocompatible fluids from different manufacturers were analyzed in parallel for GDP concentrations. The concentrations of 3-DG and 3,4-DGE produced during heat sterilization decreased when pH was reduced to about 2. Concentration of 5-HMF decreased when pH was reduced to 2.6. After further decrease to a pH of 2.0, concentration of 5-HMF increased slightly, and below a pH of 2.0 it increased considerably, together with formaldehyde; 3-DG continued to drop and 3,4-DGE remained constant. Inhibition of cell growth was paralleled by 3,4-DGE concentration at pH 2.0 - 6.0. A high glucose concentration lowered concentrations of 3,4-DGE and 3-DG at pH 5.5 and of 5-HMF at pH 1. At pH 2.2 and 3.2, glucose concentration had a minor effect on the formation of GDPs. All conventional PDFs contained high levels of 3,4-DGE and 3-DG. Concentrations were considerably lower in the biocompatible fluids. However, the concentration of 5-H M F was slightly higher in all the biocompatible fluids. The best way to avoid reactive GDPs is to have a pH between 2.0 and 2.6 during sterilization. If pHs outside this range are used, it becomes more important to have high glucose concentration during the sterilization process. There are large variations in GDPs, both within and between biocompatible and conventionally manufactured PDFs.

Combinatorial development of antibacterial Zr-Cu-Al-Ag thin film metallic glasses.

PubMed

Liu, Yanhui; Padmanabhan, Jagannath; Cheung, Bettina; Liu, Jingbei; Chen, Zheng; Scanley, B Ellen; Wesolowski, Donna; Pressley, Mariyah; Broadbridge, Christine C; Altman, Sidney; Schwarz, Udo D; Kyriakides, Themis R; Schroers, Jan

2016-05-27

Metallic alloys are normally composed of multiple constituent elements in order to achieve integration of a plurality of properties required in technological applications. However, conventional alloy development paradigm, by sequential trial-and-error approach, requires completely unrelated strategies to optimize compositions out of a vast phase space, making alloy development time consuming and labor intensive. Here, we challenge the conventional paradigm by proposing a combinatorial strategy that enables parallel screening of a multitude of alloys. Utilizing a typical metallic glass forming alloy system Zr-Cu-Al-Ag as an example, we demonstrate how glass formation and antibacterial activity, two unrelated properties, can be simultaneously characterized and the optimal composition can be efficiently identified. We found that in the Zr-Cu-Al-Ag alloy system fully glassy phase can be obtained in a wide compositional range by co-sputtering, and antibacterial activity is strongly dependent on alloy compositions. Our results indicate that antibacterial activity is sensitive to Cu and Ag while essentially remains unchanged within a wide range of Zr and Al. The proposed strategy not only facilitates development of high-performing alloys, but also provides a tool to unveil the composition dependence of properties in a highly parallel fashion, which helps the development of new materials by design.

Combinatorial development of antibacterial Zr-Cu-Al-Ag thin film metallic glasses

NASA Astrophysics Data System (ADS)

Liu, Yanhui; Padmanabhan, Jagannath; Cheung, Bettina; Liu, Jingbei; Chen, Zheng; Scanley, B. Ellen; Wesolowski, Donna; Pressley, Mariyah; Broadbridge, Christine C.; Altman, Sidney; Schwarz, Udo D.; Kyriakides, Themis R.; Schroers, Jan

2016-05-01

Metallic alloys are normally composed of multiple constituent elements in order to achieve integration of a plurality of properties required in technological applications. However, conventional alloy development paradigm, by sequential trial-and-error approach, requires completely unrelated strategies to optimize compositions out of a vast phase space, making alloy development time consuming and labor intensive. Here, we challenge the conventional paradigm by proposing a combinatorial strategy that enables parallel screening of a multitude of alloys. Utilizing a typical metallic glass forming alloy system Zr-Cu-Al-Ag as an example, we demonstrate how glass formation and antibacterial activity, two unrelated properties, can be simultaneously characterized and the optimal composition can be efficiently identified. We found that in the Zr-Cu-Al-Ag alloy system fully glassy phase can be obtained in a wide compositional range by co-sputtering, and antibacterial activity is strongly dependent on alloy compositions. Our results indicate that antibacterial activity is sensitive to Cu and Ag while essentially remains unchanged within a wide range of Zr and Al. The proposed strategy not only facilitates development of high-performing alloys, but also provides a tool to unveil the composition dependence of properties in a highly parallel fashion, which helps the development of new materials by design.

Combinatorial development of antibacterial Zr-Cu-Al-Ag thin film metallic glasses

PubMed Central

Liu, Yanhui; Padmanabhan, Jagannath; Cheung, Bettina; Liu, Jingbei; Chen, Zheng; Scanley, B. Ellen; Wesolowski, Donna; Pressley, Mariyah; Broadbridge, Christine C.; Altman, Sidney; Schwarz, Udo D.; Kyriakides, Themis R.; Schroers, Jan

2016-01-01

Metallic alloys are normally composed of multiple constituent elements in order to achieve integration of a plurality of properties required in technological applications. However, conventional alloy development paradigm, by sequential trial-and-error approach, requires completely unrelated strategies to optimize compositions out of a vast phase space, making alloy development time consuming and labor intensive. Here, we challenge the conventional paradigm by proposing a combinatorial strategy that enables parallel screening of a multitude of alloys. Utilizing a typical metallic glass forming alloy system Zr-Cu-Al-Ag as an example, we demonstrate how glass formation and antibacterial activity, two unrelated properties, can be simultaneously characterized and the optimal composition can be efficiently identified. We found that in the Zr-Cu-Al-Ag alloy system fully glassy phase can be obtained in a wide compositional range by co-sputtering, and antibacterial activity is strongly dependent on alloy compositions. Our results indicate that antibacterial activity is sensitive to Cu and Ag while essentially remains unchanged within a wide range of Zr and Al. The proposed strategy not only facilitates development of high-performing alloys, but also provides a tool to unveil the composition dependence of properties in a highly parallel fashion, which helps the development of new materials by design. PMID:27230692

Effect of Gold on the Microstructural Evolution and Integrity of a Sintered Silver Joint

NASA Astrophysics Data System (ADS)

Muralidharan, Govindarajan; Leonard, Donovan N.; Meyer, Harry M.

2017-07-01

There is a need for next-generation, high-performance power electronic packages and systems employing wide-bandgap devices to operate at high temperatures in automotive and electric grid applications. Sintered silver joints are currently being evaluated as an alternative to Pb-free solder joints. Of particular interest is the development of joints based on silver paste consisting of nano- or micron-scale particles that can be processed without application of external pressure. The microstructural evolution at the interface of a pressureless-sintered silver joint formed between a SiC die with Ti/Ni/Au metallization and an active metal brazed (AMB) substrate with Ag metallization at 250°C has been evaluated using scanning electron microscopy (SEM), x-ray microanalysis, and x-ray photoelectron spectroscopy (XPS). Results from focused ion beam (FIB) cross-sections show that, during sintering, pores in the sintered region near to the Au layer tend to be narrow and elongated with long axis oriented parallel to the interface. Further densification results in formation of many small, relatively equiaxed pores aligned parallel to the interface, creating a path for easy crack propagation. X-ray microanalysis results confirm interdiffusion between Au and Ag and that a region with poor mechanical strength is formed at the edge of this region of interdiffusion.

Massively parallel haplotyping on microscopic beads for the high-throughput phase analysis of single molecules.

PubMed

Boulanger, Jérôme; Muresan, Leila; Tiemann-Boege, Irene

2012-01-01

In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method capable of analyzing in parallel hundreds of thousands single molecules in one experiment. In this method, multiple PCR reactions amplify different polymorphic regions of a single DNA molecule on a magnetic bead compartmentalized in an emulsion drop. The allelic states of the amplified polymorphisms are identified with fluorescently labeled probes that are then decoded from images taken of the arrayed beads by a microscope. This method can evaluate the phase of up to 3 polymorphisms separated by up to 5 kilobases in hundreds of thousands single molecules. We tested the sensitivity of the method by measuring the number of mutant haplotypes synthesized by four different commercially available enzymes: Phusion, Platinum Taq, Titanium Taq, and Phire. The digital nature of the method makes it highly sensitive to detecting haplotype ratios of less than 1:10,000. We also accurately quantified chimera formation during the exponential phase of PCR by different DNA polymerases.

A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Cα–H hydrogen bonds

PubMed Central

Mueller, Benjamin K.; Subramaniam, Sabareesh; Senes, Alessandro

2014-01-01

Carbon hydrogen bonds between Cα–H donors and carbonyl acceptors are frequently observed between transmembrane helices (Cα–H···O=C). Networks of these interactions occur often at helix−helix interfaces mediated by GxxxG and similar patterns. Cα–H hydrogen bonds have been hypothesized to be important in membrane protein folding and association, but evidence that they are major determinants of helix association is still lacking. Here we present a comprehensive geometric analysis of homodimeric helices that demonstrates the existence of a single region in conformational space with high propensity for Cα–H···O=C hydrogen bond formation. This region corresponds to the most frequent motif for parallel dimers, GASright, whose best-known example is glycophorin A. The finding suggests a causal link between the high frequency of occurrence of GASright and its propensity for carbon hydrogen bond formation. Investigation of the sequence dependency of the motif determined that Gly residues are required at specific positions where only Gly can act as a donor with its “side chain” Hα. Gly also reduces the steric barrier for non-Gly amino acids at other positions to act as Cα donors, promoting the formation of cooperative hydrogen bonding networks. These findings offer a structural rationale for the occurrence of GxxxG patterns at the GASright interface. The analysis identified the conformational space and the sequence requirement of Cα–H···O=C mediated motifs; we took advantage of these results to develop a structural prediction method. The resulting program, CATM, predicts ab initio the known high-resolution structures of homodimeric GASright motifs at near-atomic level. PMID:24569864

Characterizing a gravitational lens in the molecular Einstein ring SMG 18423+5938

NASA Astrophysics Data System (ADS)

Carilli, Chris

2011-10-01

We propose a single orbit exposure of the strongly lensed submm galaxy {SMG}, MM18423+5938, using WFC3 110W. MM1842 is the brightest SMG with a published spectroscopic redshift {z = 3.9296}, and has an apparent star formation rate of order 1e4 Mo/yr. Recent EVLA observations reveal a complete Einstein ring for the CO emission, confirming the strong lensing hypothesis for MM1842. Using the CFHT, we have identified the lensing galaxy at the center of the CO ring, with z_phot 1.0. MM1842 is the archetype, and best studied, of the new population of strongly lensed SMGs that have recently been identified in shallow, wide field submm surveys. These systems represent the formation of massive galaxies at high redshift in luminous starburst events. MM1842 presents a unique opportunity to study the physical processes involved in early galaxy formation at unprecedented physical resolution. The goal of this modest HST request is to obtain detailed information on the stellar distribution in the lensing galaxy. Such information is fundamental to accurate lens modeling of the system, as has been clearly demonstrated with the CASTLES HST survey. In parallel, we are performing high resolution imaging {0.1"} of the very luminous CO, atomic fine structure line, and dust continuum emission from MM1842 with the EVLA and IRAM PdBI. Using the lens model, we can then trace back the gas distribution and dynamics in the source-plane at an effective physical resolution approaching 100pc. The proposed HST observations are crucial to constrain the lens model, and thereby enable a truly breath-taking, high physical resolution study of massive galaxy formation in the early Universe.

Transparent Glass Ceramics Doped by Chromium(III) and Chromium(III) and Neodymium(III) as New Materials for Lasers and Luminescent Solar Concentrators.

DTIC Science & Technology

1987-04-30

1.5 ZrO2 * 0.3 As203, 0.024 Cr203, melted under various conditions. Parallel measurements of X-ray diffraction, optical and EPR spectra reveal the...optical and EPR spectra reveal the different formation of gahnite from precursor glass or petalite-like phase. Introduction In a number of recent...conditions on optical and EPR spectra of Cr(III). Further on the parallel changes of spectra and x-ray diffraction patterns are indica- ted. The gahnite

Parallel File System I/O Performance Testing On LANL Clusters

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

Wiens, Isaac Christian; Green, Jennifer Kathleen

2016-08-18

These are slides from a presentation on parallel file system I/O performance testing on LANL clusters. I/O is a known bottleneck for HPC applications. Performance optimization of I/O is often required. This summer project entailed integrating IOR under Pavilion and automating the results analysis. The slides cover the following topics: scope of the work, tools utilized, IOR-Pavilion test workflow, build script, IOR parameters, how parameters are passed to IOR, *run_ior: functionality, Python IOR-Output Parser, Splunk data format, Splunk dashboard and features, and future work.

High-throughput sample adaptive offset hardware architecture for high-efficiency video coding

NASA Astrophysics Data System (ADS)

Zhou, Wei; Yan, Chang; Zhang, Jingzhi; Zhou, Xin

2018-03-01

A high-throughput hardware architecture for a sample adaptive offset (SAO) filter in the high-efficiency video coding video coding standard is presented. First, an implementation-friendly and simplified bitrate estimation method of rate-distortion cost calculation is proposed to reduce the computational complexity in the mode decision of SAO. Then, a high-throughput VLSI architecture for SAO is presented based on the proposed bitrate estimation method. Furthermore, multiparallel VLSI architecture for in-loop filters, which integrates both deblocking filter and SAO filter, is proposed. Six parallel strategies are applied in the proposed in-loop filters architecture to improve the system throughput and filtering speed. Experimental results show that the proposed in-loop filters architecture can achieve up to 48% higher throughput in comparison with prior work. The proposed architecture can reach a high-operating clock frequency of 297 MHz with TSMC 65-nm library and meet the real-time requirement of the in-loop filters for 8 K × 4 K video format at 132 fps.

A parallel solver for huge dense linear systems

NASA Astrophysics Data System (ADS)

Badia, J. M.; Movilla, J. L.; Climente, J. I.; Castillo, M.; Marqués, M.; Mayo, R.; Quintana-Ortí, E. S.; Planelles, J.

2011-11-01

HDSS (Huge Dense Linear System Solver) is a Fortran Application Programming Interface (API) to facilitate the parallel solution of very large dense systems to scientists and engineers. The API makes use of parallelism to yield an efficient solution of the systems on a wide range of parallel platforms, from clusters of processors to massively parallel multiprocessors. It exploits out-of-core strategies to leverage the secondary memory in order to solve huge linear systems O(100.000). The API is based on the parallel linear algebra library PLAPACK, and on its Out-Of-Core (OOC) extension POOCLAPACK. Both PLAPACK and POOCLAPACK use the Message Passing Interface (MPI) as the communication layer and BLAS to perform the local matrix operations. The API provides a friendly interface to the users, hiding almost all the technical aspects related to the parallel execution of the code and the use of the secondary memory to solve the systems. In particular, the API can automatically select the best way to store and solve the systems, depending of the dimension of the system, the number of processes and the main memory of the platform. Experimental results on several parallel platforms report high performance, reaching more than 1 TFLOP with 64 cores to solve a system with more than 200 000 equations and more than 10 000 right-hand side vectors. New version program summaryProgram title: Huge Dense System Solver (HDSS) Catalogue identifier: AEHU_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHU_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 87 062 No. of bytes in distributed program, including test data, etc.: 1 069 110 Distribution format: tar.gz Programming language: Fortran90, C Computer: Parallel architectures: multiprocessors, computer clusters Operating system: Linux/Unix Has the code been vectorized or parallelized?: Yes, includes MPI primitives. RAM: Tested for up to 190 GB Classification: 6.5 External routines: MPI ( http://www.mpi-forum.org/), BLAS ( http://www.netlib.org/blas/), PLAPACK ( http://www.cs.utexas.edu/~plapack/), POOCLAPACK ( ftp://ftp.cs.utexas.edu/pub/rvdg/PLAPACK/pooclapack.ps) (code for PLAPACK and POOCLAPACK is included in the distribution). Catalogue identifier of previous version: AEHU_v1_0 Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 533 Does the new version supersede the previous version?: Yes Nature of problem: Huge scale dense systems of linear equations, Ax=B, beyond standard LAPACK capabilities. Solution method: The linear systems are solved by means of parallelized routines based on the LU factorization, using efficient secondary storage algorithms when the available main memory is insufficient. Reasons for new version: In many applications we need to guarantee a high accuracy in the solution of very large linear systems and we can do it by using double-precision arithmetic. Summary of revisions: Version 1.1 Can be used to solve linear systems using double-precision arithmetic. New version of the initialization routine. The user can choose the kind of arithmetic and the values of several parameters of the environment. Running time: About 5 hours to solve a system with more than 200 000 equations and more than 10 000 right-hand side vectors using double-precision arithmetic on an eight-node commodity cluster with a total of 64 Intel cores.

Parallel artificial liquid membrane extraction as an efficient tool for removal of phospholipids from human plasma.

PubMed

Ask, Kristine Skoglund; Bardakci, Turgay; Parmer, Marthe Petrine; Halvorsen, Trine Grønhaug; Øiestad, Elisabeth Leere; Pedersen-Bjergaard, Stig; Gjelstad, Astrid

2016-09-10

Generic Parallel Artificial Liquid Membrane Extraction (PALME) methods for non-polar basic and non-polar acidic drugs from human plasma were investigated with respect to phospholipid removal. In both cases, extractions in 96-well format were performed from plasma (125μL), through 4μL organic solvent used as supported liquid membranes (SLMs), and into 50μL aqueous acceptor solutions. The acceptor solutions were subsequently analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) using in-source fragmentation and monitoring the m/z 184→184 transition for investigation of phosphatidylcholines (PC), sphingomyelins (SM), and lysophosphatidylcholines (Lyso-PC). In both generic methods, no phospholipids were detected in the acceptor solutions. Thus, PALME appeared to be highly efficient for phospholipid removal. To further support this, qualitative (post-column infusion) and quantitative matrix effects were investigated with fluoxetine, fluvoxamine, and quetiapine as model analytes. No signs of matrix effects were observed. Finally, PALME was evaluated for the aforementioned drug substances, and data were in accordance with European Medicines Agency (EMA) guidelines. Copyright © 2016 Elsevier B.V. All rights reserved.

Progress on H5Part: A Portable High Performance Parallel DataInterface for Electromagnetics Simulations

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

Adelmann, Andreas; Gsell, Achim; Oswald, Benedikt

Significant problems facing all experimental andcomputationalsciences arise from growing data size and complexity. Commonto allthese problems is the need to perform efficient data I/O ondiversecomputer architectures. In our scientific application, thelargestparallel particle simulations generate vast quantitiesofsix-dimensional data. Such a simulation run produces data foranaggregate data size up to several TB per run. Motived by the needtoaddress data I/O and access challenges, we have implemented H5Part,anopen source data I/O API that simplifies the use of the HierarchicalDataFormat v5 library (HDF5). HDF5 is an industry standard forhighperformance, cross-platform data storage and retrieval that runsonall contemporary architectures from large parallel supercomputerstolaptops. H5Part, whichmore » is oriented to the needs of the particlephysicsand cosmology communities, provides support for parallelstorage andretrieval of particles, structured and in the future unstructuredmeshes.In this paper, we describe recent work focusing on I/O supportforparticles and structured meshes and provide data showing performance onmodernsupercomputer architectures like the IBM POWER 5.« less

Parallel nano-assembling of a multifunctional GO/HapNP coating on ultrahigh-purity magnesium for biodegradable implants

NASA Astrophysics Data System (ADS)

Santos, C.; Piedade, C.; Uggowitzer, P. J.; Montemor, M. F.; Carmezim, M. J.

2015-08-01

This work reports the one-step fabrication of a novel coating on ultra high purity magnesium using a parallel nano assembling process. The multifunctional biodegradable surface was obtained by adding hydroxyapatite nanoparticles (HapNP) plus graphene oxide (GO). The coating was characterized by scanning electron microscope (SEM), transmission electron microscope (TEM), X-ray diffractometer (XRD), micro-Raman spectroscopy. The thin phosphate coating (thickness of 1 μm) reveals a uniform coverage with cypress like structures. The incorporation of HapNP and GO promotes the hydrophilic behavior of the coating surface. The results revealed that the proposed coating can be used to tailor the surface properties such as wettability by adjusting the contents of HapNP and GO. The in vitro degradation rate of the coated magnesium suggests that the presence of HapNP and GO/HapNP in the phosphate coating decreased the current density compared to the single phosphate coating and uncoated magnesium. This study also reveals the HapNP/GO/phosphate coating induces apatite formation, showing suitable degradability that makes it a promising coating candidate for enhanced bone regeneration.

Sharp organic interface of molecular C60 chains and a pentacene derivative SAM on Au(788): A combined STM & DFT study

NASA Astrophysics Data System (ADS)

Wang, Jun; Tang, Jian-Ming; Larson, Amanda M.; Miller, Glen P.; Pohl, Karsten

2013-12-01

Controlling the molecular structure of the donor-acceptor interface is essential to overcoming the efficiency bottleneck in organic photovoltaics. We present a study of self-assembled fullerene (C60) molecular chains on perfectly ordered 6,13-dichloropentacene (DCP) monolayers forming on a vicinal Au(788) surface using scanning tunneling microscopy in conjunction with density functional theory calculations. DCP is a novel pentacene derivative optimized for photovoltaic applications. The molecules form a brick-wall patterned centered rectangular lattice with the long axis parallel to the monatomic steps that separate the 3.9 nm wide Au(111) terraces. The strong interaction between the C60 molecules and the gold substrate is well screened by the DCP monolayer. At submonolayer C60 coverage, the fullerene molecules form long parallel chains, 1.1 nm apart, with a rectangular arrangement instead of the expected close-packed configuration along the upper step edges. The perfectly ordered DCP structure is unaffected by the C60 chain formation. The controlled sharp highly-ordered organic interface has the potential to improve the conversion efficiency in organic photovoltaics.

Understanding the crack formation of graphite particles in cycled commercial lithium-ion batteries by focused ion beam - scanning electron microscopy

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

Lin, Na; Jia, Zhe; Wang, Zhihui

Here in this paper, the structure degradation of commercial Lithium-ion battery (LIB) graphite anodes with different cycling numbers and charge rates was investigated by focused ion beam (FIB) and scanning electron microscopy (SEM). The cross-section image of graphite anode by FIB milling shows that cracks, resulted in the volume expansion of graphite electrode during long-term cycling, were formed in parallel with the current collector. The crack occurs in the bulk of graphite particles near the lithium insertion surface, which might derive from the stress induced during lithiation and de-lithiation cycles. Subsequently, crack takes place along grain boundaries of the polycrystallinemore » graphite, but only in the direction parallel with the current collector. Furthermore, fast charge graphite electrodes are more prone to form cracks since the tensile strength of graphite is more likely to be surpassed at higher charge rates. Therefore, for LIBs long-term or high charge rate applications, the tensile strength of graphite anode should be taken into account.« less

Understanding the crack formation of graphite particles in cycled commercial lithium-ion batteries by focused ion beam - scanning electron microscopy

DOE PAGES

Lin, Na; Jia, Zhe; Wang, Zhihui; ...

2017-10-01

Here in this paper, the structure degradation of commercial Lithium-ion battery (LIB) graphite anodes with different cycling numbers and charge rates was investigated by focused ion beam (FIB) and scanning electron microscopy (SEM). The cross-section image of graphite anode by FIB milling shows that cracks, resulted in the volume expansion of graphite electrode during long-term cycling, were formed in parallel with the current collector. The crack occurs in the bulk of graphite particles near the lithium insertion surface, which might derive from the stress induced during lithiation and de-lithiation cycles. Subsequently, crack takes place along grain boundaries of the polycrystallinemore » graphite, but only in the direction parallel with the current collector. Furthermore, fast charge graphite electrodes are more prone to form cracks since the tensile strength of graphite is more likely to be surpassed at higher charge rates. Therefore, for LIBs long-term or high charge rate applications, the tensile strength of graphite anode should be taken into account.« less

Nonlinear Electron Acoustic Waves in the Inner Magnetosphere

NASA Astrophysics Data System (ADS)

Dillard, C. S.; Vasko, I.; Mozer, F.; Agapitov, O. V.

2017-12-01

The Van Allen Probes observe intense broad-band electrostatic wave activity in the inner magnetosphere. The high-resolution electric field measurements show that these broad-band wave activity is made of large-amplitude electrostatic solitary waves propagating generally along the background magnetic field with velocities of a few thousands km/s. There are generally two types of the observed solitary waves. The solitary waves with the bipolar parallel electric field are interpreted as electron phase space holes, while the nature of solitary waves with asymmetric parallel electric field has remained puzzling. In the present work we show that asymmetric solitary waves propagate with velocities (1000-5000 km/s) and have spatial scales (100 m-1 km) similar to those for electron-acoustic waves existing due to two temperature electron population. Through the numerical fluid simulation we show that the spikes are produced from the initially harmonic electron-acoustic perturbation due to the nonlinear steepening. Through the analysis of the modified KdV equation we show that the steepening is arrested at some moment by the collisionless Landau dissipation and results in formation of the observed asymmetric spikes (shocklets).

Impacts of Spontaneous Hot Flow Anomalies on the Magnetosheath and Magnetopause

NASA Technical Reports Server (NTRS)

Omidi, N.; Berchem, J.; Sibeck, D.; Zhang, H.

2016-01-01

Spacecraft observations and global hybrid (kinetic ions and fluid electrons) simulations have demonstrated that ion dissipation processes at the quasi-parallel bow shock are associated with the formation of structures called spontaneous hot flow anomalies (SHFAs). Previous simulations and recent spacecraft observations have also established that SHFAs result in the formation of magnetosheath filamentary structures(MFS). In this paper we demonstrate that in addition to MFS, SHFAs also result in the formation of magnetos heath cavities that are associated with decreases in density, velocity, and magnetic field and enhancements in temperature. We use the results of a global MHD run to determine the change in the magnetosheath properties associated with cavities due to ion kinetic effects. The results also show the formation of regions of high flow speed called magnetosheath jets whose properties as a function of solar wind Mach number are described in this study. Comparing the properties of the simulated magnetosheath cavities and jets to past spacecraft observations provides good agreement in both cases. We also demonstrate that pressure variations associated with cavities and SHFAs in the sheath result in a continuous sunward and anti sunward magnetopause motion. This result is consistent with previous suggestions that SHFAs may be responsible for the generation of ion cyclotron waves and precipitation of ring current protons in the outer magnetosphere.

Impacts of spontaneous hot flow anomalies on the magnetosheath and magnetopause

NASA Astrophysics Data System (ADS)

Omidi, N.; Berchem, J.; Sibeck, D.; Zhang, H.

2016-04-01

Spacecraft observations and global hybrid (kinetic ions and fluid electrons) simulations have demonstrated that ion dissipation processes at the quasi-parallel bow shock are associated with the formation of structures called spontaneous hot flow anomalies (SHFAs). Previous simulations and recent spacecraft observations have also established that SHFAs result in the formation of magnetosheath filamentary structures (MFS). In this paper we demonstrate that in addition to MFS, SHFAs also result in the formation of magnetosheath cavities that are associated with decreases in density, velocity, and magnetic field and enhancements in temperature. We use the results of a global MHD run to determine the change in the magnetosheath properties associated with cavities due to ion kinetic effects. The results also show the formation of regions of high flow speed called magnetosheath jets whose properties as a function of solar wind Mach number are described in this study. Comparing the properties of the simulated magnetosheath cavities and jets to past spacecraft observations provides good agreement in both cases. We also demonstrate that pressure variations associated with cavities and SHFAs in the sheath result in a continuous sunward and antisunward magnetopause motion. This result is consistent with previous suggestions that SHFAs may be responsible for the generation of ion cyclotron waves and precipitation of ring current protons in the outer magnetosphere.

Penn State University ground software support for X-ray missions.

NASA Astrophysics Data System (ADS)

Townsley, L. K.; Nousek, J. A.; Corbet, R. H. D.

1995-03-01

The X-ray group at Penn State is charged with two software development efforts in support of X-ray satellite missions. As part of the ACIS instrument team for AXAF, the authors are developing part of the ground software to support the instrument's calibration. They are also designing a translation program for Ginga data, to change it from the non-standard FRF format, which closely parallels the original telemetry format, to FITS.

Modeling of Composite Scenes Using Wires, Plates and Dielectric Parallelized (WIPL-DP)

DTIC Science & Technology

2006-06-01

formation and solves the data communications problem. The ability to perform subsurface imaging to depths of 200’ have already been demonstrated by...perform subsurface imaging to depths of 200’ have already been demonstrated by Brown in [3] and presented in Figure 3 above. Furthermore, reference [3...transmitter platform for use in image formation and solves the data communications problem. The ability to perform subsurface imaging to depths of 200

Integration experiences and performance studies of A COTS parallel archive systems

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

Chen, Hsing-bung; Scott, Cody; Grider, Bary

2010-01-01

Current and future Archive Storage Systems have been asked to (a) scale to very high bandwidths, (b) scale in metadata performance, (c) support policy-based hierarchical storage management capability, (d) scale in supporting changing needs of very large data sets, (e) support standard interface, and (f) utilize commercial-off-the-shelf(COTS) hardware. Parallel file systems have been asked to do the same thing but at one or more orders of magnitude faster in performance. Archive systems continue to move closer to file systems in their design due to the need for speed and bandwidth, especially metadata searching speeds such as more caching and lessmore » robust semantics. Currently the number of extreme highly scalable parallel archive solutions is very small especially those that will move a single large striped parallel disk file onto many tapes in parallel. We believe that a hybrid storage approach of using COTS components and innovative software technology can bring new capabilities into a production environment for the HPC community much faster than the approach of creating and maintaining a complete end-to-end unique parallel archive software solution. In this paper, we relay our experience of integrating a global parallel file system and a standard backup/archive product with a very small amount of additional code to provide a scalable, parallel archive. Our solution has a high degree of overlap with current parallel archive products including (a) doing parallel movement to/from tape for a single large parallel file, (b) hierarchical storage management, (c) ILM features, (d) high volume (non-single parallel file) archives for backup/archive/content management, and (e) leveraging all free file movement tools in Linux such as copy, move, ls, tar, etc. We have successfully applied our working COTS Parallel Archive System to the current world's first petaflop/s computing system, LANL's Roadrunner, and demonstrated its capability to address requirements of future archival storage systems.« less

Integration experiments and performance studies of a COTS parallel archive system

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

Chen, Hsing-bung; Scott, Cody; Grider, Gary

2010-06-16

Current and future Archive Storage Systems have been asked to (a) scale to very high bandwidths, (b) scale in metadata performance, (c) support policy-based hierarchical storage management capability, (d) scale in supporting changing needs of very large data sets, (e) support standard interface, and (f) utilize commercial-off-the-shelf (COTS) hardware. Parallel file systems have been asked to do the same thing but at one or more orders of magnitude faster in performance. Archive systems continue to move closer to file systems in their design due to the need for speed and bandwidth, especially metadata searching speeds such as more caching andmore » less robust semantics. Currently the number of extreme highly scalable parallel archive solutions is very small especially those that will move a single large striped parallel disk file onto many tapes in parallel. We believe that a hybrid storage approach of using COTS components and innovative software technology can bring new capabilities into a production environment for the HPC community much faster than the approach of creating and maintaining a complete end-to-end unique parallel archive software solution. In this paper, we relay our experience of integrating a global parallel file system and a standard backup/archive product with a very small amount of additional code to provide a scalable, parallel archive. Our solution has a high degree of overlap with current parallel archive products including (a) doing parallel movement to/from tape for a single large parallel file, (b) hierarchical storage management, (c) ILM features, (d) high volume (non-single parallel file) archives for backup/archive/content management, and (e) leveraging all free file movement tools in Linux such as copy, move, Is, tar, etc. We have successfully applied our working COTS Parallel Archive System to the current world's first petafiop/s computing system, LANL's Roadrunner machine, and demonstrated its capability to address requirements of future archival storage systems.« less

MPI, HPF or OpenMP: A Study with the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Hribar, Michelle; Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1999-01-01

Porting applications to new high performance parallel and distributed platforms is a challenging task. Writing parallel code by hand is time consuming and costly, but the task can be simplified by high level languages and would even better be automated by parallelizing tools and compilers. The definition of HPF (High Performance Fortran, based on data parallel model) and OpenMP (based on shared memory parallel model) standards has offered great opportunity in this respect. Both provide simple and clear interfaces to language like FORTRAN and simplify many tedious tasks encountered in writing message passing programs. In our study we implemented the parallel versions of the NAS Benchmarks with HPF and OpenMP directives. Comparison of their performance with the MPI implementation and pros and cons of different approaches will be discussed along with experience of using computer-aided tools to help parallelize these benchmarks. Based on the study,potentials of applying some of the techniques to realistic aerospace applications will be presented

MPI, HPF or OpenMP: A Study with the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Jin, H.; Frumkin, M.; Hribar, M.; Waheed, A.; Yan, J.; Saini, Subhash (Technical Monitor)

1999-01-01

Porting applications to new high performance parallel and distributed platforms is a challenging task. Writing parallel code by hand is time consuming and costly, but this task can be simplified by high level languages and would even better be automated by parallelizing tools and compilers. The definition of HPF (High Performance Fortran, based on data parallel model) and OpenMP (based on shared memory parallel model) standards has offered great opportunity in this respect. Both provide simple and clear interfaces to language like FORTRAN and simplify many tedious tasks encountered in writing message passing programs. In our study, we implemented the parallel versions of the NAS Benchmarks with HPF and OpenMP directives. Comparison of their performance with the MPI implementation and pros and cons of different approaches will be discussed along with experience of using computer-aided tools to help parallelize these benchmarks. Based on the study, potentials of applying some of the techniques to realistic aerospace applications will be presented.

Consumption of a diet low in advanced glycation end products for 4 weeks improves insulin sensitivity in overweight women.

PubMed

Mark, Alicja Budek; Poulsen, Malene Wibe; Andersen, Stine; Andersen, Jeanette Marker; Bak, Monika Judyta; Ritz, Christian; Holst, Jens Juul; Nielsen, John; de Courten, Barbora; Dragsted, Lars Ove; Bügel, Susanne Gjedsted

2014-01-01

OBJECTIVE High-heat cooking of food induces the formation of advanced glycation end products (AGEs), which are thought to impair glucose metabolism in type 2 diabetic patients. High intake of fructose might additionally affect endogenous formation of AGEs. This parallel intervention study investigated whether the addition of fructose or cooking methods influencing the AGE content of food affect insulin sensitivity in overweight individuals. RESEARCH DESIGN AND METHODS Seventy-four overweight women were randomized to follow either a high- or low-AGE diet for 4 weeks, together with consumption of either fructose or glucose drinks. Glucose and insulin concentrations-after fasting and 2 h after an oral glucose tolerance test-were measured before and after the intervention. Homeostasis model assessment of insulin resistance (HOMA-IR) and insulin sensitivity index were calculated. Dietary and urinary AGE concentrations were measured (liquid chromatography tandem mass spectrometry) to estimate AGE intake and excretion. RESULTS When adjusted for changes in anthropometric measures during the intervention, the low-AGE diet decreased urinary AGEs, fasting insulin concentrations, and HOMA-IR, compared with the high-AGE diet. Addition of fructose did not affect any outcomes. CONCLUSIONS Diets with high AGE content may increase the development of insulin resistance. AGEs can be reduced by modulation of cooking methods but is unaffected by moderate fructose intake.

The Russell gold deposit, Carolina Slate Belt, North Carolina

USGS Publications Warehouse

Klein, T.L.; Cunningham, C.G.; Logan, M.A.V.; Seal, R.R.

2007-01-01

Gold deposits have been mined in the Carolina slate belt from the early 1800s to recent times, with most of the production from large mines in South Carolina. The Russell mine, one of the larger producers in North Carolina, is located in the central Uwharrie Mountains, and produced over 470 kg of gold. Ore grades averaged about 3.4 grams per tonne (g/ t), with higher-grade zones reported. The Russell deposit is interpreted to be a sediment-hosted, gold-rich, base-metal poor, volcanogenic massive sulfide deposit in which gold was remobilized, in part, during Ordovician metamorphism. The ore was deposited syngenetically with laminated siltstones of the late Proterozoic Tillery Formation that have been metamorphosed to a lower greenschist facies. The Tillery Formation regionally overlies subaerial to shallow marine rhyolitic volcanic and volcaniclastic rocks of the Uwharrie Formation and underlies the marine volcanic and sedimentary rocks of the Cid Formation. Recent mapping has shown that a rhyolitic dome near the Russell mine was extruded during the deposition of the lower part of the Tillery Formation, at about the same time as ore deposition. Relict mafic, rock fragments present in the ore zones suggest contemporaneous bimodal (rhyolite-basalt) volcanism. The maximum formation age of the Russell deposit is younger than 558 Ma, which is similar to that of the larger, well known Brewer, Haile, and Ridgeway deposits of South Carolina. Gold was mined from at least six zones that are parallel to the regional metamorphic foliation. These strongly deformed zones consist of northeast-trending folds, high-angle reverse faults, and asymmetric doubly plunging folds overturned to the southeast. The dominant structure at the mine is an asymmetric doubly plunging anticline with the axis trending N 45?? E, probably related to late Ordovician (456 ?? 2 Ma) regional metamorphism and deformation. Two stages of pyrite growth are recognized. Stage 1, primary, spongy pyrite, is present in thin massive sulfide layers parallel to bedding and intergrown with pyrrhotite, chalcopyrite, sphalerite, and sparse arsenopyrite. Stage 2, secondary pyrite, is present as euhedral, idiomorphic rims on spongy pyrite and as veinlets that parallel the regional foliation. Stage 1 pyrite was deposited syngenetically or diagenetically during or soon after sedimentation. Stage 2 pyrite overgrowths and veins resulted from recrystallization or remobilization of stage 1 pyrite, probably during deformation related to Ordovician regional metamorphism. It is proposed that the spongy texture of the stage 1 pyrite represents nucleation and growth of pyrite on organic matter, possibly of bacterial origin. Other textures, such as geometric voids in spongy pyrite, As-rich zones surrounding central voids, 60-??m ring structures composed of spongy pyrite, and layers of spongy pyrite interlayered with bedding laminations, also appear to indicate replacement of organic matter by pyrite. Stage 1 pyrite contains up to 0.06 wt percent gold. The ??34S values of pyrite in and near pyritic ore (3.5-4.5???), in the rhyolite dome (5.1-5.4???) and in the Tillery Formation (5.9-6.2???) are interpreted to reflect mixing of sulfur derived from igneous and seawater sources. Whole-rock ??18O values of nearby unaltered mudstone are about 11 per mil whereas those from altered mudstone at the deposit are 7.4 to 10.6 per mil. The lower ?? 18O values are interpreted to indicate possible high-temperature exchange between relatively low ??18O hydrothermal fluids and the wall rocks. Gold, As, K, and Mo are enriched relative to the regional background in both the ore zones and in pyrite veins and disseminations in the nearby rhyolite dome, suggesting a possible genetic link between the rhyolitic volcanism and the gold mineralization. ?? 2007 Society of Economic Geologists, Inc.

Research in parallel computing

NASA Technical Reports Server (NTRS)

Ortega, James M.; Henderson, Charles

1994-01-01

This report summarizes work on parallel computations for NASA Grant NAG-1-1529 for the period 1 Jan. - 30 June 1994. Short summaries on highly parallel preconditioners, target-specific parallel reductions, and simulation of delta-cache protocols are provided.

The effect of anisotropic heat transport on magnetic islands in 3-D configurations

NASA Astrophysics Data System (ADS)

Schlutt, M. G.; Hegna, C. C.

2012-08-01

An analytic theory of nonlinear pressure-induced magnetic island formation using a boundary layer analysis is presented. This theory extends previous work by including the effects of finite parallel heat transport and is applicable to general three dimensional magnetic configurations. In this work, particular attention is paid to the role of finite parallel heat conduction in the context of pressure-induced island physics. It is found that localized currents that require self-consistent deformation of the pressure profile, such as resistive interchange and bootstrap currents, are attenuated by finite parallel heat conduction when the magnetic islands are sufficiently small. However, these anisotropic effects do not change saturated island widths caused by Pfirsch-Schlüter current effects. Implications for finite pressure-induced island healing are discussed.

Re-forming supercritical quasi-parallel shocks. II - Mechanism for wave generation and front re-formation

NASA Technical Reports Server (NTRS)

Winske, D.; Thomas, V. A.; Omidi, N.; Quest, K. B.

1990-01-01

This paper continues the study of Thomas et al. (1990) in which hybrid simulations of quasi-parallel shocks were performed in one and two spatial dimensions. To identify the wave generation processes, the electromagnetic structure of the shock is examined by performing a number of one-dimensional hybrid simulations of quasi-parallel shocks for various upstream conditions. In addition, numerical experiments were carried out in which the backstreaming ions were removed from calculations to show their fundamental importance in reformation process. The calculations show that the waves are excited before ions can propagate far enough upstream to generate resonant modes. At some later times, the waves are regenerated at the leading edge of the interface, with properties like those of their initial interactions.

Multi-threaded parallel simulation of non-local non-linear problems in ultrashort laser pulse propagation in the presence of plasma

NASA Astrophysics Data System (ADS)

Baregheh, Mandana; Mezentsev, Vladimir; Schmitz, Holger

2011-06-01

We describe a parallel multi-threaded approach for high performance modelling of wide class of phenomena in ultrafast nonlinear optics. Specific implementation has been performed using the highly parallel capabilities of a programmable graphics processor.

The stress shadow effect: a mechanical analysis of the evenly-spaced parallel strike-slip faults in the San Andreas fault system

NASA Astrophysics Data System (ADS)

Zuza, A. V.; Yin, A.; Lin, J. C.

2015-12-01

Parallel evenly-spaced strike-slip faults are prominent in the southern San Andreas fault system, as well as other settings along plate boundaries (e.g., the Alpine fault) and within continental interiors (e.g., the North Anatolian, central Asian, and northern Tibetan faults). In southern California, the parallel San Jacinto, Elsinore, Rose Canyon, and San Clemente faults to the west of the San Andreas are regularly spaced at ~40 km. In the Eastern California Shear Zone, east of the San Andreas, faults are spaced at ~15 km. These characteristic spacings provide unique mechanical constraints on how the faults interact. Despite the common occurrence of parallel strike-slip faults, the fundamental questions of how and why these fault systems form remain unanswered. We address this issue by using the stress shadow concept of Lachenbruch (1961)—developed to explain extensional joints by using the stress-free condition on the crack surface—to present a mechanical analysis of the formation of parallel strike-slip faults that relates fault spacing and brittle-crust thickness to fault strength, crustal strength, and the crustal stress state. We discuss three independent models: (1) a fracture mechanics model, (2) an empirical stress-rise function model embedded in a plastic medium, and (3) an elastic-plate model. The assumptions and predictions of these models are quantitatively tested using scaled analogue sandbox experiments that show that strike-slip fault spacing is linearly related to the brittle-crust thickness. We derive constraints on the mechanical properties of the southern San Andreas strike-slip faults and fault-bounded crust (e.g., local fault strength and crustal/regional stress) given the observed fault spacing and brittle-crust thickness, which is obtained by defining the base of the seismogenic zone with high-resolution earthquake data. Our models allow direct comparison of the parallel faults in the southern San Andreas system with other similar strike-slip fault systems, both on Earth and throughout the solar system (e.g., the Tiger Stripe Fractures on Enceladus).

Parallel community climate model: Description and user`s guide

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

Drake, J.B.; Flanery, R.E.; Semeraro, B.D.

This report gives an overview of a parallel version of the NCAR Community Climate Model, CCM2, implemented for MIMD massively parallel computers using a message-passing programming paradigm. The parallel implementation was developed on an Intel iPSC/860 with 128 processors and on the Intel Delta with 512 processors, and the initial target platform for the production version of the code is the Intel Paragon with 2048 processors. Because the implementation uses a standard, portable message-passing libraries, the code has been easily ported to other multiprocessors supporting a message-passing programming paradigm. The parallelization strategy used is to decompose the problem domain intomore » geographical patches and assign each processor the computation associated with a distinct subset of the patches. With this decomposition, the physics calculations involve only grid points and data local to a processor and are performed in parallel. Using parallel algorithms developed for the semi-Lagrangian transport, the fast Fourier transform and the Legendre transform, both physics and dynamics are computed in parallel with minimal data movement and modest change to the original CCM2 source code. Sequential or parallel history tapes are written and input files (in history tape format) are read sequentially by the parallel code to promote compatibility with production use of the model on other computer systems. A validation exercise has been performed with the parallel code and is detailed along with some performance numbers on the Intel Paragon and the IBM SP2. A discussion of reproducibility of results is included. A user`s guide for the PCCM2 version 2.1 on the various parallel machines completes the report. Procedures for compilation, setup and execution are given. A discussion of code internals is included for those who may wish to modify and use the program in their own research.« less

Apparatus for suppressing formation of vortices in the coolant fluid of a nuclear reactor and associated method

DOEpatents

Ekeroth, D.E.; Garner, D.C.; Hopkins, R.J.; Land, J.T.

1993-11-30

An apparatus and method are provided for suppressing the formation of vortices in circulating coolant fluid of a nuclear reactor. A vortex-suppressing plate having a plurality of openings therein is suspended within the lower plenum of a reactor vessel below and generally parallel to the main core support of the reactor. The plate is positioned so as to intersect vortices which may form in the circulating reactor coolant fluid. The intersection of the plate with such vortices disrupts the rotational flow pattern of the vortices, thereby disrupting the formation thereof. 3 figures.

Apparatus for suppressing formation of vortices in the coolant fluid of a nuclear reactor and associated method

DOEpatents

Ekeroth, Douglas E.; Garner, Daniel C.; Hopkins, Ronald J.; Land, John T.

1993-01-01

An apparatus and method are provided for suppressing the formation of vortices in circulating coolant fluid of a nuclear reactor. A vortex-suppressing plate having a plurality of openings therein is suspended within the lower plenum of a reactor vessel below and generally parallel to the main core support of the reactor. The plate is positioned so as to intersect vortices which may form in the circulating reactor coolant fluid. The intersection of the plate with such vortices disrupts the rotational flow pattern of the vortices, thereby disrupting the formation thereof.

Shallow lacustrine system of the Permian Pedra de Fogo Formation, Western Gondwana, Parnaíba Basin, Brazil

NASA Astrophysics Data System (ADS)

Araújo, Raphael Neto; Nogueira, Afonso César Rodrigues; Bandeira, José; Angélica, Rômulo Simões

2016-04-01

The Permian Period of the Parnaíba Basin, northern Brazil, represented here by deposits from the Pedra de Fogo Formation, records important events that occurred in Western Gondwana near its boundary with the Mesozoic Era. The analysis of outcrop based facies from the Permian Pedra de Fogo Formation, which is 100 m thick, carried out along the eastern and western borders of the Parnaiba Basin, allowed the identification of eleven sedimentary facies, which were grouped into three distinct facies associations (FA), representative of a shallow lacustrine system associated with mudflats and ephemeral rivers. Bioturbation, desiccation cracks, silcretes and various siliceous concretions characterize the Pedra de Fogo deposits. The FA1 mudflat deposits occur predominantly at the base of the Pedra de Fogo Formation and consist of laminated claystone/mudstone, mudcrack-bearing sandstones/mudstones and sandstones exhibiting cross-lamination, massive and megaripple bedding. Popcorn-like silicified nodules and casts indicate evaporite deposits. Other common features are silica concretions, silicified tepees and silcretes. FA2 represents nearshore deposits and consists of fine-grained sandstones with evenly parallel lamination, climbing ripple cross-lamination, massive and megaripple bedding and mudstone/siltstone showing evenly parallel lamination. FA3 refers to wadi/inundite deposits, generally organized as fining-upward cycles of metric size, composed of conglomerates and medium-grained pebbly sandstones showing massive bedding and cross-stratification, as well as claystone/siltstone showing evenly parallel to undulate lamination. Scour-and-fill features are isolated in predominantly tabular deposits composed of mudstones interbedded with fine to medium-grained sandstones showing planar to slightly undulate lamination. Silicified plant remains previously classified as belonging to the Psaronius genus found in the uppermost levels of the Pedra de Fogo Formation, near the contact with the Motuca Formation, are considered here as excellent biostratigraphic markers. Fish remains, ostracods, bryozoans and scolecodonts represent other fossils that are present in the succession. Mudflat deposits developed in an arid and hot climate probably in the Early Permian. Semi-arid conditions prevailed in the Middle Permian allowing the proliferation of fauna and flora in adjacent humid regions and onto the lake margin. The climate variation was responsible for the contraction and expansion phases of the lake, fed by sporadic sheet floods carrying plant remains. The reestablishment of the arid climate, at the end of Permian, marks the final sedimentation of the Pedra de Fogo Formation, linked to the consolidation of the Pangaea Supercontinent. This last event was concomitant with the deposition of the Motuca Formation red beds and the development of extensive ergs related to the Triassic Sambaíba Formation in Western Gondwana.

PEM-PCA: a parallel expectation-maximization PCA face recognition architecture.

PubMed

Rujirakul, Kanokmon; So-In, Chakchai; Arnonkijpanich, Banchar

2014-01-01

Principal component analysis or PCA has been traditionally used as one of the feature extraction techniques in face recognition systems yielding high accuracy when requiring a small number of features. However, the covariance matrix and eigenvalue decomposition stages cause high computational complexity, especially for a large database. Thus, this research presents an alternative approach utilizing an Expectation-Maximization algorithm to reduce the determinant matrix manipulation resulting in the reduction of the stages' complexity. To improve the computational time, a novel parallel architecture was employed to utilize the benefits of parallelization of matrix computation during feature extraction and classification stages including parallel preprocessing, and their combinations, so-called a Parallel Expectation-Maximization PCA architecture. Comparing to a traditional PCA and its derivatives, the results indicate lower complexity with an insignificant difference in recognition precision leading to high speed face recognition systems, that is, the speed-up over nine and three times over PCA and Parallel PCA.

Parallel multiscale simulations of a brain aneurysm

PubMed Central

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

2012-01-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work. PMID:23734066

Parallel multiscale simulations of a brain aneurysm.

PubMed

Grinberg, Leopold; Fedosov, Dmitry A; Karniadakis, George Em

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr . The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

Parallel multiscale simulations of a brain aneurysm

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

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em, E-mail: george_karniadakis@brown.edu

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm.more » The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.« less

The Parallel System for Integrating Impact Models and Sectors (pSIMS)

NASA Technical Reports Server (NTRS)

Elliott, Joshua; Kelly, David; Chryssanthacopoulos, James; Glotter, Michael; Jhunjhnuwala, Kanika; Best, Neil; Wilde, Michael; Foster, Ian

2014-01-01

We present a framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. We present the pSIMS design and use example assessments to demonstrate its multi-model, multi-scale, and multi-sector versatility.

Statistical Analysis of NAS Parallel Benchmarks and LINPACK Results

NASA Technical Reports Server (NTRS)

Meuer, Hans-Werner; Simon, Horst D.; Strohmeier, Erich; Lasinski, T. A. (Technical Monitor)

1994-01-01

In the last three years extensive performance data have been reported for parallel machines both based on the NAS Parallel Benchmarks, and on LINPACK. In this study we have used the reported benchmark results and performed a number of statistical experiments using factor, cluster, and regression analyses. In addition to the performance results of LINPACK and the eight NAS parallel benchmarks, we have also included peak performance of the machine, and the LINPACK n and n(sub 1/2) values. Some of the results and observations can be summarized as follows: 1) All benchmarks are strongly correlated with peak performance. 2) LINPACK and EP have each a unique signature. 3) The remaining NPB can grouped into three groups as follows: (CG and IS), (LU and SP), and (MG, FT, and BT). Hence three (or four with EP) benchmarks are sufficient to characterize the overall NPB performance. Our poster presentation will follow a standard poster format, and will present the data of our statistical analysis in detail.

On-line electrochemistry-bioaffinity screening with parallel HR-LC-MS for the generation and characterization of modified p38α kinase inhibitors.

PubMed

Falck, David; de Vlieger, Jon S B; Giera, Martin; Honing, Maarten; Irth, Hubertus; Niessen, Wilfried M A; Kool, Jeroen

2012-04-01

In this study, an integrated approach is developed for the formation, identification and biological characterization of electrochemical conversion products of p38α mitogen-activated protein kinase inhibitors. This work demonstrates the hyphenation of an electrochemical reaction cell with a continuous-flow bioaffinity assay and parallel LC-HR-MS. Competition of the formed products with a tracer (SKF-86002) that shows fluorescence enhancement in the orthosteric binding site of the p38α kinase is the readout for bioaffinity. Parallel HR-MS(n) experiments provided information on the identity of binders and non-binders. Finally, the data produced with this on-line system were compared to electrochemical conversion products generated off-line. The electrochemical conversion of 1-{6-chloro-5-[(2R,5S)-4-(4-fluorobenzyl)-2,5-dimethylpiperazine-1-carbonyl]-3aH-indol-3-yl}-2-morpholinoethane-1,2-dione resulted in eight products, three of which showed bioaffinity in the continuous-flow p38α bioaffinity assay used. Electrochemical conversion of BIRB796 resulted, amongst others, in the formation of the reactive quinoneimine structure and its corresponding hydroquinone. Both products were detected in the p38α bioaffinity assay, which indicates binding to the p38α kinase.

Parallelization of NAS Benchmarks for Shared Memory Multiprocessors

NASA Technical Reports Server (NTRS)

Waheed, Abdul; Yan, Jerry C.; Saini, Subhash (Technical Monitor)

1998-01-01

This paper presents our experiences of parallelizing the sequential implementation of NAS benchmarks using compiler directives on SGI Origin2000 distributed shared memory (DSM) system. Porting existing applications to new high performance parallel and distributed computing platforms is a challenging task. Ideally, a user develops a sequential version of the application, leaving the task of porting to new generations of high performance computing systems to parallelization tools and compilers. Due to the simplicity of programming shared-memory multiprocessors, compiler developers have provided various facilities to allow the users to exploit parallelism. Native compilers on SGI Origin2000 support multiprocessing directives to allow users to exploit loop-level parallelism in their programs. Additionally, supporting tools can accomplish this process automatically and present the results of parallelization to the users. We experimented with these compiler directives and supporting tools by parallelizing sequential implementation of NAS benchmarks. Results reported in this paper indicate that with minimal effort, the performance gain is comparable with the hand-parallelized, carefully optimized, message-passing implementations of the same benchmarks.

AEgIS at ELENA: outlook for physics with a pulsed cold antihydrogen beam.

PubMed

Doser, M; Aghion, S; Amsler, C; Bonomi, G; Brusa, R S; Caccia, M; Caravita, R; Castelli, F; Cerchiari, G; Comparat, D; Consolati, G; Demetrio, A; Di Noto, L; Evans, C; Fanì, M; Ferragut, R; Fesel, J; Fontana, A; Gerber, S; Giammarchi, M; Gligorova, A; Guatieri, F; Haider, S; Hinterberger, A; Holmestad, H; Kellerbauer, A; Khalidova, O; Krasnický, D; Lagomarsino, V; Lansonneur, P; Lebrun, P; Malbrunot, C; Mariazzi, S; Marton, J; Matveev, V; Mazzotta, Z; Müller, S R; Nebbia, G; Nedelec, P; Oberthaler, M; Pacifico, N; Pagano, D; Penasa, L; Petracek, V; Prelz, F; Prevedelli, M; Rienaecker, B; Robert, J; Røhne, O M; Rotondi, A; Sandaker, H; Santoro, R; Smestad, L; Sorrentino, F; Testera, G; Tietje, I C; Widmann, E; Yzombard, P; Zimmer, C; Zmeskal, J; Zurlo, N

2018-03-28

The efficient production of cold antihydrogen atoms in particle traps at CERN's Antiproton Decelerator has opened up the possibility of performing direct measurements of the Earth's gravitational acceleration on purely antimatter bodies. The goal of the AEgIS collaboration is to measure the value of g for antimatter using a pulsed source of cold antihydrogen and a Moiré deflectometer/Talbot-Lau interferometer. The same antihydrogen beam is also very well suited to measuring precisely the ground-state hyperfine splitting of the anti-atom. The antihydrogen formation mechanism chosen by AEgIS is resonant charge exchange between cold antiprotons and Rydberg positronium. A series of technical developments regarding positrons and positronium (Ps formation in a dedicated room-temperature target, spectroscopy of the n =1-3 and n =3-15 transitions in Ps, Ps formation in a target at 10 K inside the 1 T magnetic field of the experiment) as well as antiprotons (high-efficiency trapping of [Formula: see text], radial compression to sub-millimetre radii of mixed [Formula: see text] plasmas in 1 T field, high-efficiency transfer of [Formula: see text] to the antihydrogen production trap using an in-flight launch and recapture procedure) were successfully implemented. Two further critical steps that are germane mainly to charge exchange formation of antihydrogen-cooling of antiprotons and formation of a beam of antihydrogen-are being addressed in parallel. The coming of ELENA will allow, in the very near future, the number of trappable antiprotons to be increased by more than a factor of 50. For the antihydrogen production scheme chosen by AEgIS, this will be reflected in a corresponding increase of produced antihydrogen atoms, leading to a significant reduction of measurement times and providing a path towards high-precision measurements.This article is part of the Theo Murphy meeting issue 'Antiproton physics in the ELENA era'. © 2018 The Author(s).

An Ornithopod-Dominated Tracksite from the Lower Cretaceous Jiaguan Formation (Barremian–Albian) of Qijiang, South-Central China: New Discoveries, Ichnotaxonomy, Preservation and Palaeoecology

PubMed Central

Xing, Lida; Lockley, Martin G.; Marty, Daniel; Zhang, Jianping; Wang, Yan; Klein, Hendrik; McCrea, Richard T.; Buckley, Lisa G.; Belvedere, Matteo; Mateus, Octávio; Gierliński, Gerard D.; Piñuela, Laura; Persons, W. Scott; Wang, Fengping; Ran, Hao; Dai, Hui; Xie, Xianming

2015-01-01

The historically-famous Lotus Fortress site, a deep 1.5–3.0-meter-high, 200-meter-long horizonal notch high up in near-vertical sandstone cliffs comprising the Cretaceous Jiaguan Formation, has been known since the 13th Century as an impregnable defensive position. The site is also extraordinary for having multiple tetrapod track-bearing levels, of which the lower two form the floor of part of the notch, and yield very well preserved asseamblages of ornithopod, bird (avian theropod) and pterosaur tracks. Trackway counts indicate that ornithopods dominate (69%) accounting for at least 165 trackmakers, followed by bird (18%), sauropod (10%), and pterosaur (3%). Previous studies designated Lotus Fortress as the type locality of Caririchnium lotus and Wupus agilis both of which are recognized here as valid ichnotaxa. On the basis of multiple parallel trackways both are interpreted as representing the trackways of gregarious species. C. lotus is redescribed here in detail and interpreted to indicate two age cohorts representing subadults that were sometimes bipedal and larger quadrupedal adults. Two other previously described dinosaurian ichnospecies, are here reinterpreted as underprints and considered nomina dubia. Like a growing number of significant tetrapod tracksites in China the Lotus Fortress site reveals new information about the composition of tetrapod faunas from formations in which the skeletal record is sparse. In particular, the site shows the relatively high abundance of Caririchium in a region where saurischian ichnofaunas are often dominant. It is also the only site known to have yielded Wupus agilis. In combination with information from other tracksites from the Jiaguan formation and other Cretaceous formations in the region, the track record is proving increasingly impotant as a major source of information on the vertebrate faunas of the region. The Lotus Fortress site has been developed as a spectacular, geologically-, paleontologically- and a culturally-significant destination within Qijiang National Geological Park. PMID:26492525

An Ornithopod-Dominated Tracksite from the Lower Cretaceous Jiaguan Formation (Barremian-Albian) of Qijiang, South-Central China: New Discoveries, Ichnotaxonomy, Preservation and Palaeoecology.

PubMed

Xing, Lida; Lockley, Martin G; Marty, Daniel; Zhang, Jianping; Wang, Yan; Klein, Hendrik; McCrea, Richard T; Buckley, Lisa G; Belvedere, Matteo; Mateus, Octávio; Gierliński, Gerard D; Piñuela, Laura; Persons, W Scott; Wang, Fengping; Ran, Hao; Dai, Hui; Xie, Xianming

2015-01-01

The historically-famous Lotus Fortress site, a deep 1.5-3.0-meter-high, 200-meter-long horizonal notch high up in near-vertical sandstone cliffs comprising the Cretaceous Jiaguan Formation, has been known since the 13th Century as an impregnable defensive position. The site is also extraordinary for having multiple tetrapod track-bearing levels, of which the lower two form the floor of part of the notch, and yield very well preserved asseamblages of ornithopod, bird (avian theropod) and pterosaur tracks. Trackway counts indicate that ornithopods dominate (69%) accounting for at least 165 trackmakers, followed by bird (18%), sauropod (10%), and pterosaur (3%). Previous studies designated Lotus Fortress as the type locality of Caririchnium lotus and Wupus agilis both of which are recognized here as valid ichnotaxa. On the basis of multiple parallel trackways both are interpreted as representing the trackways of gregarious species. C. lotus is redescribed here in detail and interpreted to indicate two age cohorts representing subadults that were sometimes bipedal and larger quadrupedal adults. Two other previously described dinosaurian ichnospecies, are here reinterpreted as underprints and considered nomina dubia. Like a growing number of significant tetrapod tracksites in China the Lotus Fortress site reveals new information about the composition of tetrapod faunas from formations in which the skeletal record is sparse. In particular, the site shows the relatively high abundance of Caririchium in a region where saurischian ichnofaunas are often dominant. It is also the only site known to have yielded Wupus agilis. In combination with information from other tracksites from the Jiaguan formation and other Cretaceous formations in the region, the track record is proving increasingly impotant as a major source of information on the vertebrate faunas of the region. The Lotus Fortress site has been developed as a spectacular, geologically-, paleontologically- and a culturally-significant destination within Qijiang National Geological Park.

Waterfalls drive parallel evolution in a freshwater goby

PubMed Central

Kano, Yuichi; Nishida, Shin; Nakajima, Jun

2012-01-01

Waterfalls may affect fish distribution and genetic structure within drainage networks even to the extent of leading evolutionary events. Here, parallel evolution was studied by focusing on waterfall and the landlocked freshwater goby Rhinogobius sp. YB (YB), which evolved from amphidromous R. brunneus (BR). The fish fauna was surveyed at 30 sites in 11 rivers on Iriomote Island, Japan, the geography of which was characterized by terraces/tablelands with many waterfalls. We found that all YB individuals were distributed only above waterfalls (height 6.8–58.7 m), whereas BR, and other fishes, were mostly distributed below waterfalls. Mitochondrial DNA analysis showed that every YB local population above the waterfall was independently evolved from BR. In contrast, cluster analysis of nine morphological characters, such as fin color and body pattern, showed that the morphology of YB individuals held a similarity beyond the genetic divergence, suggesting parallel evolution has occurred relating to their morphology. Genetic distance between each YB local population and BR was significantly correlated with waterfall height (r2 = 0.94), suggesting that the waterfalls have been heightened due to the constant geological erosion and that their height represents the isolation period of YB local populations from BR (ca. 11,000–88,000 years). Each local population of BR was once landlocked in upstream by waterfall formation, consequently evolving to YB in each site. Although the morphology of YB had a high degree of similarity among local populations, finer scale analysis showed that the morphology of YB was significantly correlated with the genetic distance from BR. Consequently, there could be simultaneous multiple phases of allopatric/parallel evolution of the goby due to variations in waterfall height on this small island. PMID:22957183

Correlation of generation interval and scale of large-scale submarine landslides using 3D seismic data off Shimokita Peninsula, Northeast Japan

NASA Astrophysics Data System (ADS)

Nakamura, Yuki; Ashi, Juichiro; Morita, Sumito

2016-04-01

To clarify timing and scale of past submarine landslides is important to understand formation processes of the landslides. The study area is in a part of continental slope of the Japan Trench, where a number of large-scale submarine landslide (slump) deposits have been identified in Pliocene and Quaternary formations by analysing METI's 3D seismic data "Sanrikuoki 3D" off Shimokita Peninsula (Morita et al., 2011). As structural features, swarm of parallel dikes which are likely dewatering paths formed accompanying the slumping deformation, and slip directions are basically perpendicular to the parallel dikes. Therefore, parallel dikes are good indicator for estimation of slip directions. Slip direction of each slide was determined one kilometre grid in the survey area of 40 km x 20 km. The remarkable slip direction varies from Pliocene to Quaternary in the survey area. Parallel dike structure is also available for the distinguishment of the slump deposit and normal deposit on time slice images. By tracing outline of slump deposits at each depth, we identified general morphology of the overall slump deposits, and calculated the volume of the extracted slump deposits so as to estimate the scale of each event. We investigated temporal and spatial variation of depositional pattern of the slump deposits. Calculating the generation interval of the slumps, some periodicity is likely recognized, especially large slump do not occur in succession. Additionally, examining the relationship of the cumulative volume and the generation interval, certain correlation is observed in Pliocene and Quaternary. Key words: submarine landslides, 3D seismic data, Shimokita Peninsula

Investigating the Formation and Sub-Structure of Unmagnetized Collisionless Shocks

NASA Astrophysics Data System (ADS)

Endrizzi, Douglass; Egedal, J.; Forest, C.; Greess, S.; Millet-Ayala, A.; Olson, J.; Ready, A.; Waleffe, R.; Gota, H.

2017-10-01

Collisionless shocks, where the shock thickness is much smaller than the collisional mean free path, are ubiquitous astrophysical phenomena. In all shocks, the Rankine-Hugoniot jump conditions are satisfied through entropy generation at the interface; the shock propagation angle with respect to the magnetic field affects the mechanism by which this entropy is generated. Two experiments on the Big Red Ball (BRB) at UW-Madison explored the formation mechanisms of parallel and perpendicular, unmagnetized and magnetized collisionless shocks with large (1 - 3 m) system sizes. In the first experiment, a 1 m diameter theta-pinch drove a supersonic (3 < M < 4) compressive flow perpendicular to the background magnetic field. In the second, a compact toroid ([cite TriAlpha]) was fired supersonically (4 < M < 5) parallel to the background magnetic field. Triple, Langmuir, emissive, and magnetic probes were used to measure electron density, temperature, plasma potential, and fluctuations in magnetic fields. Results showing the transition from above to below MA = 1 , measurements of electron precursors, exploration of subshock structure, evidence of instabilities in the shock formation process, and future work will be presented. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE 1256259.

Tuning the mesomorphic properties of phenoxy-terminated smectic liquid crystals: the effect of fluoro substitution.

PubMed

Thompson, Matthew; Carkner, Carolyn; Mosey, Nicholas J; Kapernaum, Nadia; Lemieux, Robert P

2015-05-21

The mesomorphic properties of phenoxy-terminated 5-alkoxy-2-(4-alkoxyphenyl)pyrimidine liquid crystals can be tuned in a predictable fashion with fluoro substituents on the phenoxy end-group. We show that an ortho-fluoro substituent promotes the formation of a tilted smectic C (SmC) phase whereas a para-fluoro substituent promotes the formation of an orthogonal smectic A (SmA) phase. The balance between SmA and SmC phases may be understood in terms of the energetic preference of the phenoxy end-groups to self-assemble via arene-arene interactions in a parallel or antiparallel geometry, and how these non-covalent interactions may cause either a suppression or enhancement of out-of-layer fluctuations at the interface of smectic layers. Calculations of changes in the potential energy of association ΔE for non-covalent dimers of fluoro-substituted n-butyloxybenzene molecules in parallel and antiparallel geometries support this hypothesis. We also show how mesomorphic properties can be further tuned by difluoro and perfluoro substitution, including difluoro substitution at the ortho positions, which uniquely promotes the formation of a SmC-nematic phase sequence.

A comparison of the primal and semi-dual variational formats of gradient-extended crystal inelasticity

NASA Astrophysics Data System (ADS)

Carlsson, Kristoffer; Runesson, Kenneth; Larsson, Fredrik; Ekh, Magnus

2017-10-01

In this paper we discuss issues related to the theoretical as well as the computational format of gradient-extended crystal viscoplasticity. The so-called primal format uses the displacements, the slip of each slip system and the dissipative stresses as the primary unknown fields. An alternative format is coined the semi-dual format, which in addition includes energetic microstresses among the primary unknown fields. We compare the primal and semi-dual variational formats in terms of advantages and disadvantages from modeling as well as numerical viewpoints. Finally, we perform a series of representative numerical tests to investigate the rate of convergence with finite element mesh refinement. In particular, it is shown that the commonly adopted microhard boundary condition poses a challenge in the special case that the slip direction is parallel to a grain boundary.

High-Throughput Effect-Directed Analysis Using Downscaled in Vitro Reporter Gene Assays To Identify Endocrine Disruptors in Surface Water

PubMed Central

2018-01-01

Effect-directed analysis (EDA) is a commonly used approach for effect-based identification of endocrine disruptive chemicals in complex (environmental) mixtures. However, for routine toxicity assessment of, for example, water samples, current EDA approaches are considered time-consuming and laborious. We achieved faster EDA and identification by downscaling of sensitive cell-based hormone reporter gene assays and increasing fractionation resolution to allow testing of smaller fractions with reduced complexity. The high-resolution EDA approach is demonstrated by analysis of four environmental passive sampler extracts. Downscaling of the assays to a 384-well format allowed analysis of 64 fractions in triplicate (or 192 fractions without technical replicates) without affecting sensitivity compared to the standard 96-well format. Through a parallel exposure method, agonistic and antagonistic androgen and estrogen receptor activity could be measured in a single experiment following a single fractionation. From 16 selected candidate compounds, identified through nontargeted analysis, 13 could be confirmed chemically and 10 were found to be biologically active, of which the most potent nonsteroidal estrogens were identified as oxybenzone and piperine. The increased fractionation resolution and the higher throughput that downscaling provides allow for future application in routine high-resolution screening of large numbers of samples in order to accelerate identification of (emerging) endocrine disruptors. PMID:29547277

Sedimentary facies and gas accumulation model of Lower Shihezi Formation in Shenguhao area, northern Ordos basin, China

NASA Astrophysics Data System (ADS)

Lin, Weibing; Chen, Lin; Lu, Yongchao; Zhao, Shuai

2017-04-01

The Lower Shihezi formation of lower Permian series in Shenguhao develops the highest gas abundance of upper Paleozoic in China, which has already commercially produced on a large scale. The structural location of Shenguhao belongs to the transition zone of Yimeng uplift and Yishan slope of northern Ordos basin, China. Based on the data of core, well logging and seismic, the sedimentary facies and gas accumulation model have been studied in this paper. Sedimentary facies analysis shows that the braided delta is the major facies type developed in this area during the period of Lower Shihezi formation. The braided delta can be further divided into two microfacies, distributary channel and flood plain. The distributary channel sandbody develops the characteristics of scour surface, trough cross beddings and normal grading sequences. Its seismic reflection structure is with the shape of flat top and concave bottom. Its gamma-ray logging curve is mainly in a box or bell shape. The flood plain is mainly composed of thick mudstones. Its seismic reflection structure is with the shape of parallel or sub-parallel sheet. Its gamma-ray logging curve is mainly in a linear tooth shape. On the whole, the distribution of sandbody is characterized by large thickness, wide area and good continuity. Based on the analysis of the sea level change and the restoration of the ancient landform in the period of Lower Shihezi formation, the sea level relative change and morphology of ancient landform have been considered as the main controlling factors for the development and distribution of sedimentary facies. The topography was with big topographic relief, and the sea level was relatively low in the early stage of Low Shihezi formation. The sandbody distributed chiefly along the landform depressions. The sandbody mainly developed in the pattern of multiple vertical superpositions with thick layer. In the later stage, landform gradually converted to be flat, and strata tended to be gentle. With the sea level gradually increasing, the lateral continuity of sandbody gradually became worse and gradually transformed into the pattern of single and isolated. The analysis of the typical gas accumulation profile of the Lower Shihezi Formation in the study area reveals that the formation of gas pools is mainly controlled by the distribution of sedimentary facies, faults and high point of structures. Generally, the types of gas pool developed in the study area can be divided into up dip pinch out gas pool, fault block gas pool and microstructure gas pool. The coal bearing strata of the underlying Taiyuan Formation and Shanxi Formation are the main hydrocarbon source rocks of the Lower Shihezi Formation. The gas transporting channel and lateral sealing composed by fault and sandbody constitute the key to form an effective gas pool, which usually made up of good lateral sealing, great thickness and good connectivity.

Solution-processed parallel tandem polymer solar cells using silver nanowires as intermediate electrode.

PubMed

Guo, Fei; Kubis, Peter; Li, Ning; Przybilla, Thomas; Matt, Gebhard; Stubhan, Tobias; Ameri, Tayebeh; Butz, Benjamin; Spiecker, Erdmann; Forberich, Karen; Brabec, Christoph J

2014-12-23

Tandem architecture is the most relevant concept to overcome the efficiency limit of single-junction photovoltaic solar cells. Series-connected tandem polymer solar cells (PSCs) have advanced rapidly during the past decade. In contrast, the development of parallel-connected tandem cells is lagging far behind due to the big challenge in establishing an efficient interlayer with high transparency and high in-plane conductivity. Here, we report all-solution fabrication of parallel tandem PSCs using silver nanowires as intermediate charge collecting electrode. Through a rational interface design, a robust interlayer is established, enabling the efficient extraction and transport of electrons from subcells. The resulting parallel tandem cells exhibit high fill factors of ∼60% and enhanced current densities which are identical to the sum of the current densities of the subcells. These results suggest that solution-processed parallel tandem configuration provides an alternative avenue toward high performance photovoltaic devices.

New approach to the boundary-parallel plastic / viscous diapiric flow patterns in the curvilinear boundary zones: an implication for structural geology studies

NASA Astrophysics Data System (ADS)

Sarkarinejad, Khalil

2010-05-01

New approach to the boundary-parallel plastic / viscous diapiric flow patterns in the curvilinear boundary zones: an implication for structural geology studies Khalil Sarkarinejad and Abdolreza Partabian Department of Earth Sciences, College of Sciences, Shiraz University, Shiraz, Iran (Sarkarinejad@geology.susc.ac.ir). In the oceanic diverging away plates, the asthenospheric flow at solidus high-temperature conditions typically produces mineral foliations and lineations in peridotites. Foliation and lineation of mantle are defined by preferred flattening and alignment of olivine, pyroxene and spinel. In the areas with steep foliations trajectories which are associated with the steeply plunging stretching lineation trajectories, reflecting localized vertical flow and has been related to mantle diapir. The mantle flow patterns are well documented through detail structural mapping of the Neyriz ophiolite along the Zagros inclined dextral transpression and Oman ophiolite. Such models of the diverging asthenaspheric mantle flow and formation of mantle diapir are rarely discussed and paid any attention in the mathematical models of transpressional deformation in converging continental crusts. Systematic measurements of the mineral preferred orientations and construction of the foliation and lineation trajectories of the Zagros high-strain zone reveal two diapers with the shape of the inclined NW-SE boundary-parallel semi-ellipses shape and one rotated asymmetric diapir. These diapers made of quartzo-feldspathic gneiss and garnet amphibolite core with phyllite, phyllonite, muscovite schist and deformed conglomerate as a cover sequences. These boundary-parallel and rotated diapirs are formed by the interaction of Afro-Arabian lower to middle continental detachment and hot subdacting Tethyan oceanic crust, due to increasing effective pressure and temperature. The plastic/viscous gneissic diapers were squeezed between in Zagros transpression curvilinear boundary zones in an angle alpha=25°. Constructed finite strain ellipsoid based on the X-axes of the elliptical shaped deformed markers of the diapir cover sequences show trend X-axis of the strain ellipsoid making an angle phai=2° with the boundary zones. The steep plunging stretching lineation primarily controlled by the plastic/viscous flow. This also show that during inclined upwelling boundary-parallel diapers, X-, Y-axes of the strain ellipsoid rotated clockwise and Z-axis experienced counter clockwise rotation with triclinic symmetries relative to the Zagros curvilinear transpression boundary zones with an orientation of N42°plus/minus 24°W.

Pore Fluid Extraction by Reactive Solitary Waves in 3-D

NASA Astrophysics Data System (ADS)

Omlin, Samuel; Malvoisin, Benjamin; Podladchikov, Yury Y.

2017-09-01

In the lower crust, viscous compaction is known to produce solitary porosity and fluid pressure waves. Metamorphic (de)volatilization reactions can also induce porosity changes in response to the propagating fluid pressure anomalies. Here we present results from high-resolution simulations using Graphic Processing Unit parallel processing with a model that includes both viscous (de)compaction and reaction-induced porosity changes. Reactive porosity waves propagate in a manner similar to viscous porosity waves, but through a different mechanism involving fluid release and trap in the solid by reaction. These waves self-generate from red noise or an ellipsoidal porosity anomaly with the same characteristic size and abandon their source region to propagate at constant velocity. Two waves traveling at different velocities pass through each other in a soliton-like fashion. Reactive porosity waves thus provide an additional mechanism for fluid extraction at shallow depths with implications for ore formation, diagenesis, metamorphic veins formation, and fluid extraction from subduction zones.

Aluminum integral foams with tailored density profile by adapted blowing agents

NASA Astrophysics Data System (ADS)

Hartmann, Johannes; Fiegl, Tobias; Körner, Carolin

2014-05-01

The goal of the present work is the variation of the structure of aluminum integral foams regarding the thickness of the integral solid skin as well as the density profile. A modified die casting process, namely integral foam molding, is used in which an aluminum melt and blowing agent particles (magnesium hydride MgH2) are injected in a permanent steel mold. The high solidification rates at the cooled walls of the mold lead to the formation of a solid skin. In the inner region, hydrogen is released by thermal decomposition of MgH2 particles. Thus, the pore formation takes place parallel to the continuing solidification of the melt. The thickness of the solid skin and the density profile of the core strongly depend on the interplay between solidification velocity and kinetics of hydrogen release. By varying the melt and blowing agent properties, the structure of integral foams can be systematically changed to meet the requirements of the desired field of application of the produced component.

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

DOE PAGES

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-10-25

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

Quasi-discrete particle motion in an externally imposed, ordered structure in a dusty plasma at high magnetic field

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

Thomas, Edward, E-mail: etjr@auburn.edu; Konopka, Uwe; Lynch, Brian

Dusty plasmas have been studied in argon, radio frequency (rf) glow discharge plasmas at magnetic fields up to 2.5 T where the electrons and ions are strongly magnetized. Plasmas are generated between two parallel plate electrodes where the lower, powered electrode is solid and the upper electrode supports a dual mesh consisting of #24 brass and #30 aluminum wire cloth. In this experiment, we study the formation of imposed ordered structures and particle dynamics as a function of magnetic field. Through observations of trapped particles and the quasi-discrete (i.e., “hopping”) motion of particles between the trapping locations, it is possible tomore » make a preliminary estimate of the potential structure that confines the particles to a grid structure in the plasma. This information is used to gain insight into the formation of the imposed grid pattern of the dust particles in the plasma.« less

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy.

PubMed

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-01-01

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic , using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic .

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

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

Pryor, Alan; Ophus, Colin; Miao, Jianwei

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

Chronic administration of sulbutiamine improves long term memory formation in mice: possible cholinergic mediation.

PubMed

Micheau, J; Durkin, T P; Destrade, C; Rolland, Y; Jaffard, R

1985-08-01

Thiamine deficiency in both man and animals is known to produce memory dysfunction and cognitive disorders which have been related to an impairment of cholinergic activity. The present experiment was aimed at testing whether, inversely, chronic administration of large doses of sulbutiamine would have a facilitative effect on memory and would induce changes in central cholinergic activity. Accordingly mice received 300 mg/kg of sulbutiamine daily for 10 days. They were then submitted to an appetitive operant level press conditioning test. When compared to control subjects, sulbutiamine treated mice learned the task at the same rate in a single session but showed greatly improved performance when tested 24 hr after partial acquisition of the same task. Parallel neurochemical investigations showed that the treatment induced a slight (+ 10%) but significant increase in hippocampal sodium-dependent high affinity choline uptake. The present findings and previous results suggest that sulbutiamine improves memory formation and that this behavioral effect could be mediated by an increase in hippocampal cholinergic activity.

Deficiency of cyclin-dependent kinase inhibitors p21{sup Cip1} and p27{sup Kip1} accelerates atherogenesis in apolipoprotein E-deficient mice

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

Akyuerek, Levent M.; Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Goeteborg, SE-405 30; Boehm, Manfred

2010-05-28

Cyclin-dependent kinase inhibitors, p21{sup Cip1} and p27{sup Kip1}, are upregulated during vascular cell proliferation and negatively regulate growth of vascular cells. We hypothesized that absence of either p21{sup Cip1} or p27{sup Kip1} in apolipoprotein E (apoE)-deficiency may increase atherosclerotic plaque formation. Compared to apoE{sup -/-} aortae, both apoE{sup -/-}/p21{sup -/-} and apoE{sup -/-}/p27{sup -/-} aortae exhibited significantly more atherosclerotic plaque following a high-cholesterol regimen. This increase was particularly observed in the abdominal aortic regions. Deficiency of p27{sup Kip1} accelerated plaque formation significantly more than p21{sup -/-} in apoE{sup -/-} mice. This increased plaque formation was in parallel with increased intima/mediamore » area ratios. Deficiency of p21{sup Cip1} and p27{sup Kip1} accelerates atherogenesis in apoE{sup -/-} mice. These findings have significant implications for our understanding of the molecular basis of atherosclerosis associated with excessive proliferation of vascular cells.« less

Xenia: A Probe of Cosmic Chemical Evolution

NASA Technical Reports Server (NTRS)

Kouveliotou, Chryssa; Piro, L.

2008-01-01

Xenia is a concept study for a medium-size astrophysical cosmology mission addressing the Cosmic Origins key objective of NASA's Science Plan. The fundamental goal of this objective is to understand the formation and evolution of structures on various scales from the early Universe to the present time (stars, galaxies and the cosmic web). Xenia will use X-and y-ray monitoring and wide field X-ray imaging and high-resolution spectroscopy to collect essential information from three major tracers of these cosmic structures: the Warm Hot Intergalactic Medium (WHIM), Galaxy Clusters and Gamma Ray Bursts (GRBs). Our goal is to trace the chemo-dynamical history of the ubiquitous warm hot diffuse baryon component in the Universe residing in cosmic filaments and clusters of galaxies up to its formation epoch (at z =0-2) and to map star formation and galaxy metal enrichment into the re-ionization era beyond z 6. The concept of Xenia (Greek for "hospitality") evolved in parallel with the Explorer of Diffuse Emission and GRB Explosions (EDGE), a mission proposed by a multinational collaboration to the ESA Cosmic Vision 2015. Xenia incorporates the European and Japanese collaborators into a U.S. led mission that builds on the scientific objectives and technological readiness of EDGE.

Galaxy Interactions, Tidal Debris, and the Origin of Intracluster Light in the Coma Cluster

NASA Astrophysics Data System (ADS)

Gregg, Michael

1999-07-01

We propose to obtain deep WFPC2 and parallel STIS images of low surface brightness tidal debris that we have recently discovered in the Coma cluster; the material is being stripped from its parent galaxy and added to the general cluster background. These images will enable direct study of the brightest blue and red supergiants, globular clusters, and star forming regions which may be present, or will place strong limits on the numbers of such objects and any recent star formation. We also propose similar observations of the parent spiral, NGC4911, in the core of Coma; it is losing its ISM to the hot cluster gas and as well as the low surface brightness tidal debris. By imaging this galaxy, we will get a high resolution look at the interaction between the galaxy and interstellar medium, as well as any ram-pressure induced star formation. The tidal features in Coma appear to be adding material to the background light and cD galaxy envelopes at a significant rate; determining the nature of the added stellar population and the interactions which produce it are critical to understanding the formation and evolution of cD galaxies and clusters.

Xenia: A Probe of Cosmic Chemical Evolution

NASA Astrophysics Data System (ADS)

Kouveliotou, Chryssa; Piro, L.; Xenia Collaboration

2008-03-01

Xenia is a concept study for a medium-size astrophysical cosmology mission addressing the Cosmic Origins key objective of NASA's Science Plan. The fundamental goal of this objective is to understand the formation and evolution of structures on various scales from the early Universe to the present time (stars, galaxies and the cosmic web). Xenia will use X-and γ-ray monitoring and wide field X-ray imaging and high-resolution spectroscopy to collect essential information from three major tracers of these cosmic structures: the Warm Hot Intergalactic Medium (WHIM), Galaxy Clusters and Gamma Ray Bursts (GRBs). Our goal is to trace the chemo-dynamical history of the ubiquitous warm hot diffuse baryon component in the Universe residing in cosmic filaments and clusters of galaxies up to its formation epoch (at z =0-2) and to map star formation and galaxy metal enrichment into the re-ionization era beyond z 6. The concept of Xenia (Greek for "hospitality") evolved in parallel with the Explorer of Diffuse Emission and GRB Explosions (EDGE), a mission proposed by a multinational collaboration to the ESA Cosmic Vision 2015. Xenia incorporates the European and Japanese collaborators into a U.S. led mission that builds on the scientific objectives and technological readiness of EDGE.

First results from the HST Grism Lens-Amplified Survey from Space (GLASS)

NASA Astrophysics Data System (ADS)

WANG, XIN; Schmidt, K. B.; Treu, T.; GLASS Team

2014-01-01

GLASS is a cycle-21 large program with the Hubble Space Telescope, targeting 10 massive clusters, including the 6 Frontier Fields, using the WFC3 and ACS grisms. The program consists of 140 primary orbits and 140 parallel orbits. Using the clusters as cosmic telescopes, GLASS is taking spectra of faint background galaxies with unprecedented sensitivity and angular resolution. GLASS has 3 primary science drivers, although a variety of other science investigations are possible in combination with existing and planned imaging campaigns. The first key science goal is to shed light upon the role of galaxies in reionizing the universe, the topology of high redshift intergalactic/interstellar medium and Lyman alpha escape fraction. The second key science goal is to study gas accretion, star formation and outflows by mapping spatially resolved star formation and metallicity gradients in galaxies at z=1.3-2.3. The third key science goal is to study the environmental dependence of galaxy evolution, by mapping spatially resolved star formation in galaxies in the cluster cores and infalling regions. We present the details of the program and results from the first cluster observed by GLASS MACS0717.5+3745.

Extracellular matrix dynamics during vertebrate axis formation.

PubMed

Czirók, András; Rongish, Brenda J; Little, Charles D

2004-04-01

The first evidence for the dynamics of in vivo extracellular matrix (ECM) pattern formation during embryogenesis is presented below. Fibrillin 2 filaments were tracked for 12 h throughout the avian intraembryonic mesoderm using automated light microscopy and algorithms of our design. The data show that these ECM filaments have a reproducible morphogenic destiny that is characterized by directed transport. Fibrillin 2 particles initially deposited in the segmental plate mesoderm are translocated along an unexpected trajectory where they eventually polymerize into an intricate scaffold of cables parallel to the anterior-posterior axis. The cables coalesce near the midline before the appearance of the next-formed somite. Moreover, the ECM filaments define global tissue movements with high precision because the filaments act as passive motion tracers. Quantification of individual and collective filament "behaviors" establish fate maps, trajectories, and velocities. These data reveal a caudally propagating traveling wave pattern in the morphogenetic movements of early axis formation. We conjecture that within vertebrate embryos, long-range mechanical tension fields are coupled to both large-scale patterning and local organization of the ECM. Thus, physical forces or stress fields are essential requirements for executing an emergent developmental pattern-in this case, paraxial fibrillin cable assembly.

Impact of structural and autocyclic basin-floor topography on the depositional evolution of the deep-water Valparaiso forearc basin, central Chile

USGS Publications Warehouse

Laursen, J.; Normark, W.R.

2003-01-01

The Valparaiso Basin constitutes a unique and prominent deep-water forearc basin underlying a 40-km by 60-km mid-slope terrace at 2.5-km water depth on the central Chile margin. Seismic-reflection data, collected as part of the CONDOR investigation, image a 3-3.5-km thick sediment succession that fills a smoothly sagged, margin-parallel, elongated trough at the base of the upper slope. In response to underthrusting of the Juan Ferna??ndez Ridge on the Nazca plate, the basin fill is increasingly deformed in the seaward direction above seaward-vergent outer forearc compressional highs. Syn-depositional growth of a large, margin-parallel monoclinal high in conjunction with sagging of the inner trough of the basin created stratal geometries similar to those observed in forearc basins bordered by large accretionary prisms. Margin-parallel compressional ridges diverted turbidity currents along the basin axis and exerted a direct control on sediment depositional processes. As structural depressions became buried, transverse input from point sources on the adjacent upper slope formed complex fan systems with sediment waves characterising the overbank environment, common on many Pleistocene turbidite systems. Mass failure as a result of local topographic inversion formed a prominent mass-flow deposit, and ultimately resulted in canyon formation and hence a new focused point source feeding the basin. The Valparaiso Basin is presently filled to the spill point of the outer forearc highs, causing headward erosion of incipient canyons into the basin fill and allowing bypass of sediment to the Chile Trench. Age estimates that are constrained by subduction-related syn-depositional deformation of the upper 700-800m of the basin fill suggest that glacio-eustatic sea-level lowstands, in conjunction with accelerated denudation rates, within the past 350 ka may have contributed to the increase in simultaneously active point sources along the upper slope as well as an increased complexity of proximal depositional facies.

Teaching RLC Parallel Circuits in High-School Physics Class

ERIC Educational Resources Information Center

Simon, Alpár

2015-01-01

This paper will try to give an alternative treatment of the subject "parallel RLC circuits" and "resonance in parallel RLC circuits" from the Physics curricula for the XIth grade from Romanian high-schools, with an emphasis on practical type circuits and their possible applications, and intends to be an aid for both Physics…

Biomimetic engineering of a generic cell-on-membrane architecture by microfluidic engraving for on-chip bioassays.

PubMed

Lee, Sang-Wook; Noh, Ji-Yoon; Park, Seung Chul; Chung, Jin-Ho; Lee, Byoungho; Lee, Sin-Doo

2012-05-22

We develop a biomimetic cell-on-membrane architecture in close-volume format which allows the interfacial biocompatibility and the reagent delivery capability for on-chip bioassays. The key concept lies in the microfluidic engraving of lipid membranes together with biological cells on a supported substrate with topographic patterns. The simultaneous engraving process of a different class of fluids is promoted by the front propagation of an air-water interface inside a flow-cell. This highly parallel, microfluidic cell-on-membrane approach opens a door to the natural biocompatibility in mimicking cellular stimuli-response behavior essential for diverse on-chip bioassays that can be precisely controlled in the spatial and temporal manner.

Supercomputer simulations of structure formation in the Universe

NASA Astrophysics Data System (ADS)

Ishiyama, Tomoaki

2017-06-01

We describe the implementation and performance results of our massively parallel MPI†/OpenMP‡ hybrid TreePM code for large-scale cosmological N-body simulations. For domain decomposition, a recursive multi-section algorithm is used and the size of domains are automatically set so that the total calculation time is the same for all processes. We developed a highly-tuned gravity kernel for short-range forces, and a novel communication algorithm for long-range forces. For two trillion particles benchmark simulation, the average performance on the fullsystem of K computer (82,944 nodes, the total number of core is 663,552) is 5.8 Pflops, which corresponds to 55% of the peak speed.

Characterization and mechanism of He plasma pretreatment of nanoscale polymer masks for improved pattern transfer fidelity

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

Weilnboeck, F.; Metzler, D.; Kumar, N.

2011-12-26

Roughening of nanoscale polymer masks during plasma etching (PE) limits feature critical dimensions in current and future lithographic technologies. Roughness formation of 193 nm photoresist (PR) is mechanistically explained by plasma-induced changes in mechanical properties introduced at the PR surface ({approx}2 nm) by ions and in parallel in the material bulk ({approx}200 nm) by ultraviolet (UV) plasma radiation. Synergistic roughening of polymer masks can be prevented by pretreating PR patterns with a high dose of He plasma UV exposure to saturate bulk material modifications. During subsequent PE, PR patterns are stabilized and exhibit improved etch resistance and reduced surface/line-edge roughness.

HeNCE: A Heterogeneous Network Computing Environment

DOE PAGES

Beguelin, Adam; Dongarra, Jack J.; Geist, George Al; ...

1994-01-01

Network computing seeks to utilize the aggregate resources of many networked computers to solve a single problem. In so doing it is often possible to obtain supercomputer performance from an inexpensive local area network. The drawback is that network computing is complicated and error prone when done by hand, especially if the computers have different operating systems and data formats and are thus heterogeneous. The heterogeneous network computing environment (HeNCE) is an integrated graphical environment for creating and running parallel programs over a heterogeneous collection of computers. It is built on a lower level package called parallel virtual machine (PVM).more » The HeNCE philosophy of parallel programming is to have the programmer graphically specify the parallelism of a computation and to automate, as much as possible, the tasks of writing, compiling, executing, debugging, and tracing the network computation. Key to HeNCE is a graphical language based on directed graphs that describe the parallelism and data dependencies of an application. Nodes in the graphs represent conventional Fortran or C subroutines and the arcs represent data and control flow. This article describes the present state of HeNCE, its capabilities, limitations, and areas of future research.« less

An intercalation-locked parallel-stranded DNA tetraplex

DOE PAGES

Tripathi, S.; Zhang, D.; Paukstelis, P. J.

2015-01-27

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

Using fluorescence-parallel factor analysis for assessing disinfection by-product formation and natural organic matter removal efficiency in secondary treated synthetic drinking waters.

PubMed

Watson, Kalinda; Farré, Maria José; Leusch, Frederic D L; Knight, Nicole

2018-05-28

Parallel factor (PARAFAC) analysis of fluorescence excitation-emission matrices (EEMs) was used to investigate the organic matter and DBP formation characteristics of untreated, primary treated (enhanced coagulation; EC) and secondary treated synthetic waters prepared using a Suwannee River natural organic matter (SR-NOM) isolate. The organic matter was characterised by four different fluorescence components; two humic acid-like (C1 and C2) and two protein-like (C3 and C4). Secondary treatment methods tested, following EC treatment, were; powdered activated carbon (PAC), granular activated carbon (GAC), 0.1% silver-impregnated activated carbon (SIAC), and MIEX® resin. Secondary treatments were more effective at removing natural organic matter (NOM) and fluorescent DBP-precursor components than EC alone. The formation of a suite of 17 DBPs including chlorinated, brominated and iodinated trihalomethanes (THMs), dihaloacetonitriles (DHANs), chloropropanones (CPs), chloral hydrate (CH) and trichloronitromethane (TCNM) was determined after chlorinating water sampled before and after each treatment step. Regression analysis was used to investigate the relationship between peak component fluorescence intensity (F MAX ), DBP concentration and speciation, and more commonly used aggregate parameters such as DOC, UV 254 and SUVA 254 . PARAFAC component 1 (C1) was in general a better predictor of DBP formation than other aggregate parameters, and was well correlated (R ≥ 0.80) with all detected DBPs except dibromochloromethane (DBCM) and dibromoacetonitrile (DBAN). These results indicate that the fluorescence-PARAFAC approach could provide a robust analytical tool for predicting DBP formation, and for evaluating the removal of NOM fractions relevant to DBP formation during water treatment. Copyright © 2018. Published by Elsevier B.V.

Flow Field and Nutrient Dynamics Control Over Formation of Parallel Vegetation Patterns in the Florida Everglades

NASA Astrophysics Data System (ADS)

Engel, V.; Cheng, Y.; Stieglitz, M.

2009-12-01

Pattern formation in vegetated communities reflects the underlying mechanisms governing resource utilization and distribution across the landscape. An example of a patterned ecosystem is the Florida Everglades, which is characterized by parallel and slightly elevated peat "ridges" separated by deeper water "slough" communities (R&S). Ridges are dominated by sawgrass (Cladium jamaiscence). These patterns are thought to be aligned with and develop in response to the historic surface water flow direction, though the precise mechanisms which lead to their formation are poorly understood. Over the years this R&S habitat has degraded in areas where the natural flow regime, hydroperiod, and water depths have been impacted by human development. Managing and restoring this habitat has been an objective of the U.S. Federal and Florida State governments since the Comprehensive Everglades Restoration Plan (CERP) was authorized in 2000. It is imperative, however, to develop a mechanistic understanding of ridge-slough formation before the potential benefits of hydrologic forecasts associated with CERP can be evaluated. Recently, Cheng et al (see Cheng et al, session NG14) employed a simple 2D advection-diffusion model developed by Rietkerk et al (2004) to describe for the first time, the formation of parallel stripes from hydrologic interactions. To simulate parallel stripes, Cheng et al retained the basic equations of the Rietkerk model but allowed for constant advection of water and nutrient in one direction to simulate slope conditions, with evapotranspiration driven advection of water and nutrient perpendicular to the downhill flow direction. We employ this modeling framework and parameterize the model with Everglades field data to simulate ridge-slough formation. In this model, the relatively higher rates of evapotranspiration on the ridges compared to the sloughs create hydraulic gradients which carry dissolved nutrients from the sloughs to the faster growing ridges. With time, the patches aggregate and spread laterally in the direction of the downhill flow. The characteristic wavelengths and spatial patterning of the ridge-slough habitat found in the historic Everglades is reproduced by the model. Nutrient distributions across the landscape and across the ridge-slough interfaces also match observations. Perturbations to the system are modeled in the form of altered hydraulic gradients and nutrient input functions, similar to actual stressors on the system. Under the altered conditions, a loss of patterning in the habitat is observed, in some cases leading to ridge expansion into the sloughs, and in others leading to a complete loss of vegetation pattern. Simulations indicate that the hydrologic changes required to regenerate coherence in the ridge slough patterns in degraded areas are different from those in which the system originally formed. Plant-nutrient interactions and the overall nutrient status are shown to be a major determinant in how the system will respond to hydrologic changes associated with CERP.

Assembly of Layered Monetite-Chitosan Nanocomposite and Its Transition to Organized Hydroxyapatite.

PubMed

Ruan, Qichao; Liberman, David; Zhang, Yuzheng; Ren, Dongni; Zhang, Yunpeng; Nutt, Steven; Moradian-Oldak, Janet

2016-06-13

Bioinspired synthesis of hierarchically structured calcium phosphate (CaP) material is a highly promising strategy for developing improved bone substitute materials. However, synthesis of CaP materials with outstanding mechanical properties still remains an ongoing challenge. Inspired by the formation of lamellar structure in nacre, we designed an organic matrix composed of chitosan and cis-butenediolic acid (maleic acid, MAc) that could assemble into a layered complex and further guide the mineralization of monetite crystals, resulting in the formation of organized and parallel arrays of monetite platelets with a brick-and-mortar structure. Using the layered monetite-chitosan composite as a precursor, we were able to synthesize hydroxyapatite (HAp) with multiscale hierarchically ordered structure via a topotactic phase transformation process. On the nanoscale, needlelike HAp crystallites assembled into organized bundles that aligned to form highly oriented plates on the microscale. On the large-scale level, these plates with different crystal orientations were stacked together to form a layered structure. The organized structures and composite feature yielded CaP materials with improved mechanical properties close to those of bone. Our study introduces a biomimetic approach that may be practical for the design of advanced, mechanically robust materials for biomedical applications.

Dyke-sill relationships in Karoo dolerites as indicators of propagation and emplacement processes of mafic magmas in the shallow crust

NASA Astrophysics Data System (ADS)

Coetzee, A.; Kisters, A. F. M.

2017-04-01

This paper describes the spatial and temporal relationships between Karoo-age (ca. 180 Ma) dolerite dykes and a regional-scale saucer-sill complex from the Secunda (coal mine) Complex in the northeastern parts of the Karoo Basin of South Africa. Unlike parallel dyke swarms of regional extensional settings, mafic dykes commonly show curved geometries and highly variable orientations, short strike extents and complex cross-cutting and intersecting relationships. Importantly, the dyke networks originate from the upper contacts of the first-order dolerite sill-saucer structure and are not the feeders of the saucer complex. Cross-cutting relationships indicate the largely contemporaneous formation of dykes and the inner sill and inclined sheets of the underlying saucer. Systematic dykes form a distinct boxwork-type pattern of two high-angle, interconnected dyke sets. The formation and orientation of this dyke set is interpreted to be related to the stretching of roof strata above elongated magma lobes that facilitated the propagation of the inner sill, similar to the "cracked lid" model described for large saucer complexes in Antarctica. Dyke patterns generally reflect the saucer emplacement process and the associated deformation of wall rocks rather than far-field regional stresses.

Supramolecular organization and chiral resolution of p-terphenyl-m-dicarbonitrile on the Ag(111) surface.

PubMed

Marschall, Matthias; Reichert, Joachim; Seufert, Knud; Auwärter, Willi; Klappenberger, Florian; Weber-Bargioni, Alexander; Klyatskaya, Svetlana; Zoppellaro, Giorgio; Nefedov, Alexei; Strunskus, Thomas; Wöll, Christof; Ruben, Mario; Barth, Johannes V

2010-05-17

The supramolecular organization and layer formation of the non-linear, prochiral molecule [1, 1';4',1'']-terphenyl-3,3"-dicarbonitrile adsorbed on the Ag(111) surface is investigated by scanning tunneling microscopy (STM) and near-edge X-ray absorption fine-structure spectroscopy (NEXAFS). Upon two-dimensional confinement the molecules are deconvoluted in three stereoisomers, that is, two mirror-symmetric trans- and one cis-species. STM measurements reveal large and regular islands following room temperature deposition, whereby NEXAFS confirms a flat adsorption geometry with the electronic pi-system parallel to the surface plane. The ordering within the expressed supramolecular arrays reflects a substrate templating effect, steric constraints and the operation of weak lateral interactions mainly originating from the carbonitrile endgroups. High-resolution data at room temperature reveal enantiormorphic characteristics of the molecular packing schemes in different domains of the arrays, indicative of chiral resolution during the 2D molecular self-assembly process. At submonolayer coverage supramolecular islands coexist with a disordered fluid phase of highly mobile molecules. Following thermal quenching (down to 6 K) we find extended supramolecular ribbons stabilised again by attractive and directional noncovalent interactions, the formation of which reflects a chiral resolution of trans-species.

The Role of Grain Orientation and Grain Boundary Characteristics in the Mechanical Twinning Formation in a High Manganese Twinning-Induced Plasticity Steel

NASA Astrophysics Data System (ADS)

Shterner, Vadim; Timokhina, Ilana B.; Rollett, Anthony D.; Beladi, Hossein

2018-04-01

In the current study, the dependence of mechanical twinning on grain orientation and grain boundary characteristics was investigated using quasi in-situ tensile testing. The grains of three main orientations (i.e., <111>, <110>, and <100> parallel to the tensile axis (TA)) and certain characteristics of grain boundaries (i.e., the misorientation angle and the inclination angle between the grain boundary plane normal and the TA) were examined. Among the different orientations, <111> and <100> were the most and the least favored orientations for the formation of mechanical twins, respectively. The <110> orientation was intermediate for twinning. The annealing twin boundaries appeared to be the most favorable grain boundaries for the nucleation of mechanical twinning. No dependence was found for the inclination angle of annealing twin boundaries, but the orientation of grains on either side of the annealing twin boundary exhibited a pronounced effect on the propensity for mechanical twinning. Annealing twin boundaries adjacent to high Taylor factor grains exhibited a pronounced tendency for twinning regardless of their inclination angle. In general, grain orientation has a significant influence on twinning on a specific grain boundary.

Abandoned rail corridors in Texas : a policy and infrastructure evaluation.

DOT National Transportation Integrated Search

2011-03-01

The use of existing and abandoned railroad rights-of-way has been a proven method of acquiring linear : corridors for the construction of roadways since the formation of the Texas Highway Department. Either : paralleling existing rail lines or re-usi...

Imaging Cold Gas to 1 kpc scales in high-redshift galaxies with the ngVLA

NASA Astrophysics Data System (ADS)

Casey, Caitlin; Narayanan, Desika; Dave, Romeel; Hung, Chao-Ling; Champagne, Jaclyn; Carilli, Chris Luke; Decarli, Roberto; Murphy, Eric J.; Popping, Gergo; Riechers, Dominik; Somerville, Rachel S.; Walter, Fabian

2017-01-01

The next generation Very Large Array (ngVLA) will revolutionize our understanding of the distant Universe via the detection of cold molecular gas in the first galaxies. Its impact on studies of galaxy characterization via detailed gas dynamics will provide crucial insight on dominant physical drivers for star-formation in high redshift galaxies, including the exchange of gas from scales of the circumgalactic medium down to resolved clouds on mass scales of ~10^5 M_sun. In this study, we employ a series of high-resolution, cosmological, hydrodynamic zoom simulations from the MUFASA simulation suite and a CASA simulator to generate mock ngVLA observations. Based on a direct comparison between the inferred results from our mock observations and the cosmological simulations, we investigate the capabilities of ngVLA to constrain the mode of star formation, dynamical mass, and molecular gas kinematics in individual high-redshift galaxies using cold gas tracers like CO(1-0) and CO(2-1). Using the Despotic radiative transfer code that encompasses simultaneous thermal and statistical equilibrium in calculating the molecular and atomic level populations, we generate parallel mock observations of high-J transitions of CO and C+ from ALMA for comparison. The factor of 100 times improvement in mapping speed for the ngVLA beyond the Jansky VLA and the proposed ALMA Band 1 will make these detailed, high-resolution imaging and kinematic studies routine at z=2 and beyond.

The Effect of High N-DOPED Anatase TiO2 on the Band Gap Narrowing and Redshift by First-Principles

NASA Astrophysics Data System (ADS)

Hou, Qingyu; Jin, Yongjun; Ying, Chun; Zhao, Erjun; Zhang, Yue; Dong, Hongying

2012-10-01

Anatase TiO2 supercells were studied by first-principles, in which one was undoped and another three were high N-doping. Partial densities of states, band structure, population and absorption spectrum were calculated. The calculated results indicated that in the condition of TiO2-xNx (x = 0.0625, 0.125, 0.25), the higher the doping concentration is, the shorter will be the lattice parameters parallel to the direction of c-axis. The strength of covalent bond significantly varied. The formation energy increases at first, and then decreases. The doping models become less stable as N-doping concentration increases. Meanwhile, the narrower the band gap is, the more significant will be the redshift, which is in agreement with the experimental results.

Disruption of Chemoreceptor Signaling Arrays by High Levels of CheW, the Receptor-Kinase Coupling Protein

PubMed Central

Cardozo, Marcos J.; Massazza, Diego A.; Parkinson, John S.; Studdert, Claudia A.

2017-01-01

Summary During chemotactic signaling by Escherichia coli, the small cytoplasmic CheW protein couples the histidine kinase CheA to chemoreceptor control. Although essential for assembly and operation of receptor signaling complexes, CheW in stoichiometric excess disrupts chemotactic behavior. To explore the mechanism of the CheW excess effect, we measured the physiological consequences of high cellular levels of wild-type CheW and of several CheW variants with reduced or enhanced binding affinities for receptor molecules. We found that high levels of CheW interfered with trimer assembly, prevented CheA activation, blocked cluster formation, disrupted chemotactic ability, and elevated receptor methylation levels. The severity of these effects paralleled the receptor binding affinities of the CheW variants. Because trimer formation may be an obligate step in the assembly of ternary signaling complexes and higher-order receptor arrays, we suggest that all CheW excess effects stem from disruption of trimer assembly. We propose that the CheW-binding sites in receptor dimers overlap their trimer contact sites and that high levels of CheW saturate the receptor binding sites, preventing trimer assembly. The CheW-trapped receptor dimers seem to be improved substrates for methyltransferase reactions, but cannot activate CheA or assemble into clusters, processes that are essential for chemotactic signaling. PMID:20487303

The NAS parallel benchmarks

NASA Technical Reports Server (NTRS)

Bailey, David (Editor); Barton, John (Editor); Lasinski, Thomas (Editor); Simon, Horst (Editor)

1993-01-01

A new set of benchmarks was developed for the performance evaluation of highly parallel supercomputers. These benchmarks consist of a set of kernels, the 'Parallel Kernels,' and a simulated application benchmark. Together they mimic the computation and data movement characteristics of large scale computational fluid dynamics (CFD) applications. The principal distinguishing feature of these benchmarks is their 'pencil and paper' specification - all details of these benchmarks are specified only algorithmically. In this way many of the difficulties associated with conventional benchmarking approaches on highly parallel systems are avoided.

On magnetohydrodynamic thermal instabilities in magnetic flux tubes. [in plane parallel stellar atmosphere in LTE and hydrostatic equilibrium

NASA Technical Reports Server (NTRS)

Massaglia, S.; Ferrari, A.; Bodo, G.; Kalkofen, W.; Rosner, R.

1985-01-01

The stability of current-driven filamentary modes in magnetic flux tubes embedded in a plane-parallel atmosphere in LTE and in hydrostatic equilibrium is discussed. Within the tube, energy transport by radiation only is considered. The dominant contribution to the opacity is due to H- ions and H atoms (in the Paschen continuum). A region in the parameter space of the equilibrium configuration in which the instability is effective is delimited, and the relevance of this process for the formation of structured coronae in late-type stars and accretion disks is discussed.

Subglacial Depositional Processes in the Port Askaig Formation (Neoproterozoic) of Ireland

NASA Astrophysics Data System (ADS)

Knight, J.

2004-12-01

The Port Askaig Formation was deposited during the Vendian glaciation (c. 650 Ma) and is a range of tillites that outcrop discontinuously from Banffshire (Scotland) to Connemara (Ireland). Sedimentary structures commonly observed include dropstones and sediment drapes, interpreted as deposition from a floating glacial ice shelf in a shallow marginal sea. Other structures, such as intersecting clastic dikes, have been interpreted as evidence for subaerial exposure of the tillite surface. Exposures of the Port Askaig Formation were examined at its Irish type area at Kiltyfanned Lough, County Donegal. Here, homogeneous sandy beds with internal planar bedding structures are separated by laminated fine sand beds which have erosional upper surfaces. The laminated beds are clast-free and individual laminae are laterally continuous and undisturbed. Larger clasts lie bed-parallel and are draped by overlying beds. Occasionally drapes are asymmetric with a thickened sediment prow, suggestive of flow direction. The clastic dikes are polygonal in plan view, may be isolated or interconnected, and are often arranged in parallel sheets which pinch out laterally. Internally, the clastic dikes are infilled with coarse sand to gravel. Infills are often aligned parallel to dike margins. The presence of draped and deformed sediments suggest a subglacial environment with free water availability. The flat-lying morphology of clasts also favours a subglacial rather than a full marine environment. The morphology and disposition of clastic dikes is interpreted as due to subglacial hydrofracturing of a till sheet and upward passage of sediment-charged water through the fracture zone, which is known from late Pleistocene and Precambrian tillites elsewhere. Variations in water availability can be reconciled by a sub-ice shelf depositional model with spatial and temporal changes in tidally-induced ice-bed coupling.

Trend Switching Processes in Financial Markets

NASA Astrophysics Data System (ADS)

Preis, Tobias; Stanley, H. Eugene

For an intriguing variety of switching processes in nature, the underlying complex system abruptly changes at a specific point from one state to another in a highly discontinuous fashion. Financial market fluctuations are characterized by many abrupt switchings creating increasing trends ("bubble formation") and decreasing trends ("bubble collapse"), on time scales ranging from macroscopic bubbles persisting for hundreds of days to microscopic bubbles persisting only for very short time scales. Our analysis is based on a German DAX Future data base containing 13,991,275 transactions recorded with a time resolution of 10- 2 s. For a parallel analysis, we use a data base of all S&P500 stocks providing 2,592,531 daily closing prices. We ask whether these ubiquitous switching processes have quantifiable features independent of the time horizon studied. We find striking scale-free behavior of the volatility after each switching occurs. We interpret our findings as being consistent with time-dependent collective behavior of financial market participants. We test the possible universality of our result by performing a parallel analysis of fluctuations in transaction volume and time intervals between trades. We show that these financial market switching processes have features similar to those present in phase transitions. We find that the well-known catastrophic bubbles that occur on large time scales - such as the most recent financial crisis - are no outliers but in fact single dramatic representatives caused by the formation of upward and downward trends on time scales varying over nine orders of magnitude from the very large down to the very small.

Efficient diagonalization of the sparse matrices produced within the framework of the UK R-matrix molecular codes

NASA Astrophysics Data System (ADS)

Galiatsatos, P. G.; Tennyson, J.

2012-11-01

The most time consuming step within the framework of the UK R-matrix molecular codes is that of the diagonalization of the inner region Hamiltonian matrix (IRHM). Here we present the method that we follow to speed up this step. We use shared memory machines (SMM), distributed memory machines (DMM), the OpenMP directive based parallel language, the MPI function based parallel language, the sparse matrix diagonalizers ARPACK and PARPACK, a variation for real symmetric matrices of the official coordinate sparse matrix format and finally a parallel sparse matrix-vector product (PSMV). The efficient application of the previous techniques rely on two important facts: the sparsity of the matrix is large enough (more than 98%) and in order to get back converged results we need a small only part of the matrix spectrum.

SequenceL: Automated Parallel Algorithms Derived from CSP-NT Computational Laws

NASA Technical Reports Server (NTRS)

Cooke, Daniel; Rushton, Nelson

2013-01-01

With the introduction of new parallel architectures like the cell and multicore chips from IBM, Intel, AMD, and ARM, as well as the petascale processing available for highend computing, a larger number of programmers will need to write parallel codes. Adding the parallel control structure to the sequence, selection, and iterative control constructs increases the complexity of code development, which often results in increased development costs and decreased reliability. SequenceL is a high-level programming language that is, a programming language that is closer to a human s way of thinking than to a machine s. Historically, high-level languages have resulted in decreased development costs and increased reliability, at the expense of performance. In recent applications at JSC and in industry, SequenceL has demonstrated the usual advantages of high-level programming in terms of low cost and high reliability. SequenceL programs, however, have run at speeds typically comparable with, and in many cases faster than, their counterparts written in C and C++ when run on single-core processors. Moreover, SequenceL is able to generate parallel executables automatically for multicore hardware, gaining parallel speedups without any extra effort from the programmer beyond what is required to write the sequen tial/singlecore code. A SequenceL-to-C++ translator has been developed that automatically renders readable multithreaded C++ from a combination of a SequenceL program and sample data input. The SequenceL language is based on two fundamental computational laws, Consume-Simplify- Produce (CSP) and Normalize-Trans - pose (NT), which enable it to automate the creation of parallel algorithms from high-level code that has no annotations of parallelism whatsoever. In our anecdotal experience, SequenceL development has been in every case less costly than development of the same algorithm in sequential (that is, single-core, single process) C or C++, and an order of magnitude less costly than development of comparable parallel code. Moreover, SequenceL not only automatically parallelizes the code, but since it is based on CSP-NT, it is provably race free, thus eliminating the largest quality challenge the parallelized software developer faces.

A high-speed linear algebra library with automatic parallelism

NASA Technical Reports Server (NTRS)

Boucher, Michael L.

1994-01-01

Parallel or distributed processing is key to getting highest performance workstations. However, designing and implementing efficient parallel algorithms is difficult and error-prone. It is even more difficult to write code that is both portable to and efficient on many different computers. Finally, it is harder still to satisfy the above requirements and include the reliability and ease of use required of commercial software intended for use in a production environment. As a result, the application of parallel processing technology to commercial software has been extremely small even though there are numerous computationally demanding programs that would significantly benefit from application of parallel processing. This paper describes DSSLIB, which is a library of subroutines that perform many of the time-consuming computations in engineering and scientific software. DSSLIB combines the high efficiency and speed of parallel computation with a serial programming model that eliminates many undesirable side-effects of typical parallel code. The result is a simple way to incorporate the power of parallel processing into commercial software without compromising maintainability, reliability, or ease of use. This gives significant advantages over less powerful non-parallel entries in the market.

Three-dimensional assembly of tissue-engineered cartilage constructs results in cartilaginous tissue formation without retainment of zonal characteristics.

PubMed

Schuurman, W; Harimulyo, E B; Gawlitta, D; Woodfield, T B F; Dhert, W J A; van Weeren, P R; Malda, J

2016-04-01

Articular cartilage has limited regenerative capabilities. Chondrocytes from different layers of cartilage have specific properties, and regenerative approaches using zonal chondrocytes may yield better replication of the architecture of native cartilage than when using a single cell population. To obtain high seeding efficiency while still mimicking zonal architecture, cell pellets of expanded deep zone and superficial zone equine chondrocytes were seeded and cultured in two layers on poly(ethylene glycol)-terephthalate-poly(butylene terephthalate) (PEGT-PBT) scaffolds. Scaffolds seeded with cell pellets consisting of a 1:1 mixture of both cell sources served as controls. Parallel to this, pellets of superficial or deep zone chondrocytes, and combinations of the two cell populations, were cultured without the scaffold. Pellet cultures of zonal chondrocytes in scaffolds resulted in a high seeding efficiency and abundant cartilaginous tissue formation, containing collagen type II and glycosaminoglycans (GAGs) in all groups, irrespective of the donor (n = 3), zonal population or stratified scaffold-seeding approach used. However, whereas total GAG production was similar, the constructs retained significantly more GAG compared to pellet cultures, in which a high percentage of the produced GAGs were secreted into the culture medium. Immunohistochemistry for zonal markers did not show any differences between the conditions. We conclude that spatially defined pellet culture in 3D scaffolds is associated with high seeding efficiency and supports cartilaginous tissue formation, but did not result in the maintenance or restoration of the original zonal phenotype. The use of pellet-assembled constructs leads to a better retainment of newly produced GAGs than the use of pellet cultures alone. Copyright © 2013 John Wiley & Sons, Ltd.

Global Magnetohydrodynamic Simulation Using High Performance FORTRAN on Parallel Computers

NASA Astrophysics Data System (ADS)

Ogino, T.

High Performance Fortran (HPF) is one of modern and common techniques to achieve high performance parallel computation. We have translated a 3-dimensional magnetohydrodynamic (MHD) simulation code of the Earth's magnetosphere from VPP Fortran to HPF/JA on the Fujitsu VPP5000/56 vector-parallel supercomputer and the MHD code was fully vectorized and fully parallelized in VPP Fortran. The entire performance and capability of the HPF MHD code could be shown to be almost comparable to that of VPP Fortran. A 3-dimensional global MHD simulation of the earth's magnetosphere was performed at a speed of over 400 Gflops with an efficiency of 76.5 VPP5000/56 in vector and parallel computation that permitted comparison with catalog values. We have concluded that fluid and MHD codes that are fully vectorized and fully parallelized in VPP Fortran can be translated with relative ease to HPF/JA, and a code in HPF/JA may be expected to perform comparably to the same code written in VPP Fortran.

A review of the theory, methods and recent applications of high-throughput single-cell droplet microfluidics

NASA Astrophysics Data System (ADS)

Lagus, Todd P.; Edd, Jon F.

2013-03-01

Most cell biology experiments are performed in bulk cell suspensions where cell secretions become diluted and mixed in a contiguous sample. Confinement of single cells to small, picoliter-sized droplets within a continuous phase of oil provides chemical isolation of each cell, creating individual microreactors where rare cell qualities are highlighted and otherwise undetectable signals can be concentrated to measurable levels. Recent work in microfluidics has yielded methods for the encapsulation of cells in aqueous droplets and hydrogels at kilohertz rates, creating the potential for millions of parallel single-cell experiments. However, commercial applications of high-throughput microdroplet generation and downstream sensing and actuation methods are still emerging for cells. Using fluorescence-activated cell sorting (FACS) as a benchmark for commercially available high-throughput screening, this focused review discusses the fluid physics of droplet formation, methods for cell encapsulation in liquids and hydrogels, sensors and actuators and notable biological applications of high-throughput single-cell droplet microfluidics.

A Low-Power High-Speed Smart Sensor Design for Space Exploration Missions

NASA Technical Reports Server (NTRS)

Fang, Wai-Chi

1997-01-01

A low-power high-speed smart sensor system based on a large format active pixel sensor (APS) integrated with a programmable neural processor for space exploration missions is presented. The concept of building an advanced smart sensing system is demonstrated by a system-level microchip design that is composed with an APS sensor, a programmable neural processor, and an embedded microprocessor in a SOI CMOS technology. This ultra-fast smart sensor system-on-a-chip design mimics what is inherent in biological vision systems. Moreover, it is programmable and capable of performing ultra-fast machine vision processing in all levels such as image acquisition, image fusion, image analysis, scene interpretation, and control functions. The system provides about one tera-operation-per-second computing power which is a two order-of-magnitude increase over that of state-of-the-art microcomputers. Its high performance is due to massively parallel computing structures, high data throughput rates, fast learning capabilities, and advanced VLSI system-on-a-chip implementation.

Structure of junctions of multiwalled carbon nanotubes with tetragonal cross section and flattened nanotubes revealed by electron-beam tomography

NASA Astrophysics Data System (ADS)

Nagano, Yuta; Kohno, Hideo

2017-11-01

Multiwalled carbon nanotubes with tetragonal cross section frequently form junctions with flattened multi-walled carbon nanotubes, a kind of carbon nanoribbon. The three-dimensional structure of the junctions is revealed by transmission-electron-microscopy-based tomography. Two types of junction, parallel and diagonal, are found. The formation mechanism of these two types of junction is discussed in terms of the origami mechanism that was previously proposed to explain the formation of carbon nanoribbons and nanotetrahedra.

Characterizing parallel file-access patterns on a large-scale multiprocessor

NASA Technical Reports Server (NTRS)

Purakayastha, A.; Ellis, Carla; Kotz, David; Nieuwejaar, Nils; Best, Michael L.

1995-01-01

High-performance parallel file systems are needed to satisfy tremendous I/O requirements of parallel scientific applications. The design of such high-performance parallel file systems depends on a comprehensive understanding of the expected workload, but so far there have been very few usage studies of multiprocessor file systems. This paper is part of the CHARISMA project, which intends to fill this void by measuring real file-system workloads on various production parallel machines. In particular, we present results from the CM-5 at the National Center for Supercomputing Applications. Our results are unique because we collect information about nearly every individual I/O request from the mix of jobs running on the machine. Analysis of the traces leads to various recommendations for parallel file-system design.

Complexes of horseradish peroxidase with formate, acetate, and carbon monoxide.

PubMed

Carlsson, Gunilla H; Nicholls, Peter; Svistunenko, Dimitri; Berglund, Gunnar I; Hajdu, Janos

2005-01-18

Carbon monoxide, formate, and acetate interact with horseradish peroxidase (HRP) by binding to subsites within the active site. These ligands also bind to catalases, but their interactions are different in the two types of enzymes. Formate (notionally the "hydrated" form of carbon monoxide) is oxidized to carbon dioxide by compound I in catalase, while no such reaction is reported to occur in HRP, and the CO complex of ferrocatalase can only be obtained indirectly. Here we describe high-resolution crystal structures for HRP in its complexes with carbon monoxide and with formate, and compare these with the previously determined HRP-acetate structure [Berglund, G. I., et al. (2002) Nature 417, 463-468]. A multicrystal X-ray data collection strategy preserved the correct oxidation state of the iron during the experiments. Absorption spectra of the crystals and electron paramagnetic resonance data for the acetate and formate complexes in solution correlate electronic states with the structural results. Formate in ferric HRP and CO in ferrous HRP bind directly to the heme iron with iron-ligand distances of 2.3 and 1.8 A, respectively. CO does not bind to the ferric iron in the crystal. Acetate bound to ferric HRP stacks parallel with the heme plane with its carboxylate group 3.6 A from the heme iron, and without an intervening solvent molecule between the iron and acetate. The positions of the oxygen atoms in the bound ligands outline a potential access route for hydrogen peroxide to the iron. We propose that interactions in this channel ensure deprotonation of the proximal oxygen before binding to the heme iron.

Embryonic vasculogenesis and hematopoietic specification

USDA-ARS?s Scientific Manuscript database

Vasculogenesis is the process by which blood vessels are formed de novo. In mammals, vasculogenesis occurs in parallel with hematopoiesis, the formation of blood cells. Thus, it is debated whether vascular endothelial cells and blood cells are derived from a common progenitor. Whether or not this is...

Broadband hybrid electromagnetic and piezoelectric energy harvesting from ambient vibrations and pneumatic vortices induced by running subway trains.

DOT National Transportation Integrated Search

2017-05-01

The airfoil-based electromagnetic energy harvester containing parallel array motion between moving coil and : trajectory matching multi-pole magnets was investigated. The magnets were aligned in an alternatively : magnetized formation of 6 magnets to...

Formation of Crenulated Clinoforms on Continental Shelves

DTIC Science & Technology

2004-09-30

SE, parallel to the bathymetric contours and to the direction of the Western Adriatic Coastal Current ( WACC ), but close to the clinoform roll-over...storms, due to enhanced wave shear stresses causing sediment resuspension and to the strengthening of the WACC . This process contributes to the

A Lightweight Remote Parallel Visualization Platform for Interactive Massive Time-varying Climate Data Analysis

NASA Astrophysics Data System (ADS)

Li, J.; Zhang, T.; Huang, Q.; Liu, Q.

2014-12-01

Today's climate datasets are featured with large volume, high degree of spatiotemporal complexity and evolving fast overtime. As visualizing large volume distributed climate datasets is computationally intensive, traditional desktop based visualization applications fail to handle the computational intensity. Recently, scientists have developed remote visualization techniques to address the computational issue. Remote visualization techniques usually leverage server-side parallel computing capabilities to perform visualization tasks and deliver visualization results to clients through network. In this research, we aim to build a remote parallel visualization platform for visualizing and analyzing massive climate data. Our visualization platform was built based on Paraview, which is one of the most popular open source remote visualization and analysis applications. To further enhance the scalability and stability of the platform, we have employed cloud computing techniques to support the deployment of the platform. In this platform, all climate datasets are regular grid data which are stored in NetCDF format. Three types of data access methods are supported in the platform: accessing remote datasets provided by OpenDAP servers, accessing datasets hosted on the web visualization server and accessing local datasets. Despite different data access methods, all visualization tasks are completed at the server side to reduce the workload of clients. As a proof of concept, we have implemented a set of scientific visualization methods to show the feasibility of the platform. Preliminary results indicate that the framework can address the computation limitation of desktop based visualization applications.

X-Ray and TeV Gamma-Ray Emission from Parallel Electron-Positron or Electron-Proton Beams in BL Lacertae Objects

NASA Astrophysics Data System (ADS)

Krawczynski, H.

2007-04-01

In this paper we discuss models of the X-ray and TeV γ-ray emission from BL Lac objects based on parallel electron-positron or electron-proton beams that form close to the central black hole, due to the strong electric fields generated by the accretion disk and possibly also by the black hole itself. Fitting the energy spectrum of the BL Lac object Mrk 501, we obtain tight constraints on the beam properties. Launching a sufficiently energetic beam requires rather strong magnetic fields close to the black hole (~100-1000 G). However, the model fits imply that the magnetic field in the emission region is only ~0.02 G. Thus, the particles are accelerated close to the black hole and propagate a considerable distance before instabilities trigger the dissipation of energy through synchrotron and self-Compton emission. We discuss various approaches to generate enough power to drive the jet and, at the same time, to accelerate particles to ~20 TeV energies. Although the parallel beam model has its own problems, it explains some of the long-standing problems that plague models based on Fermi-type particle acceleration, such as the presence of a very high minimum Lorentz factor of accelerated particles. We conclude with a brief discussion of the implications of the model for the difference between the processes of jet formation in BL Lac-type objects and those in quasars.

X-ray and TeV Gamma-Ray Emission from Parallel Electron-Positron or Electron-Proton Beams in BL Lac Objects

NASA Astrophysics Data System (ADS)

Krawczynski, Henric

2007-04-01

In this contribution we discuss models of the X-rays and TeV gamma-ray emission from BL Lac objects based on parallel electron-positron or electron-proton beams that form close to the central black hole owing to the strong electric fields generated by the accretion disk and possibly also by the black hole itself. Fitting the energy spectrum of the BL Lac object Mrk 501, we obtain tight constrains on the beam properties. Launching a sufficiently energetic beam requires rather strong magnetic fields close to the black hole 100-1000 G. However, the model fits imply that the magnetic field in the emission region is only 0.02 G. Thus, the particles are accelerated close to the black hole and propagate a considerable distance before instabilities trigger the dissipation of energy through synchrotron and self-Compton emission. We discuss various approaches to generate enough power to drive the jet and, at the same time, to accelerate particles to 20 TeV energies. Although the parallel beam model has its own problems, it explains some of the long-standing problems that plague models based on Fermi type particle acceleration, like the presence of a very high minimum Lorentz factor of accelerated particles. We conclude with a brief discussion of the implications of the model for the difference between the processes of jet formation in BL Lac type objects and in quasars.

A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library.

PubMed

Waugh, Caryll; Cromer, Deborah; Grimm, Andrew; Chopra, Abha; Mallal, Simon; Davenport, Miles; Mak, Johnson

2015-04-09

Massive, parallel sequencing is a potent tool for dissecting the regulation of biological processes by revealing the dynamics of the cellular RNA profile under different conditions. Similarly, massive, parallel sequencing can be used to reveal the complexity of viral quasispecies that are often found in the RNA virus infected host. However, the production of cDNA libraries for next-generation sequencing (NGS) necessitates the reverse transcription of RNA into cDNA and the amplification of the cDNA template using PCR, which may introduce artefact in the form of phantom nucleic acids species that can bias the composition and interpretation of original RNA profiles. Using HIV as a model we have characterised the major sources of error during the conversion of viral RNA to cDNA, namely excess RNA template and the RNaseH activity of the polymerase enzyme, reverse transcriptase. In addition we have analysed the effect of PCR cycle on detection of recombinants and assessed the contribution of transfection of highly similar plasmid DNA to the formation of recombinant species during the production of our control viruses. We have identified RNA template concentrations, RNaseH activity of reverse transcriptase, and PCR conditions as key parameters that must be carefully optimised to minimise chimeric artefacts. Using our optimised RT-PCR conditions, in combination with our modified PCR amplification procedure, we have developed a reliable technique for accurate determination of RNA species using NGS technology.

Sensitive and label-free detection of miRNA-145 by triplex formation.

PubMed

Aviñó, Anna; Huertas, César S; Lechuga, Laura M; Eritja, Ramon

2016-01-01

The development of new strategies for detecting microRNAs (miRNAs) has become a crucial step in the diagnostic field. miRNA profiles depend greatly on the sample and the analytical platform employed, leading sometimes to contradictory results. In this work, we study the use of modified parallel tail-clamps to detect a miRNA sequence involved in tumor suppression by triplex formation. Thermal denaturing curves and circular dichroism (CD) measurements have been performed to confirm that parallel clamps carrying 8-aminoguanine form the most stable triplex structures with their target miRNA. The modified tail-clamps have been tested as bioreceptors in a surface plasmon resonance (SPR) biosensor for the detection of miRNA-145. The detection limit was improved 2.4 times demonstrating that a stable triplex structure is formed between target miRNA and 8-aminoguanine tail-clamp bioreceptor. This new approach is an essential step toward the label-free and reliable detection of miRNA signatures for diagnostic purposes.

High Performance Computing at NASA

NASA Technical Reports Server (NTRS)

Bailey, David H.; Cooper, D. M. (Technical Monitor)

1994-01-01

The speaker will give an overview of high performance computing in the U.S. in general and within NASA in particular, including a description of the recently signed NASA-IBM cooperative agreement. The latest performance figures of various parallel systems on the NAS Parallel Benchmarks will be presented. The speaker was one of the authors of the NAS (National Aerospace Standards) Parallel Benchmarks, which are now widely cited in the industry as a measure of sustained performance on realistic high-end scientific applications. It will be shown that significant progress has been made by the highly parallel supercomputer industry during the past year or so, with several new systems, based on high-performance RISC processors, that now deliver superior performance per dollar compared to conventional supercomputers. Various pitfalls in reporting performance will be discussed. The speaker will then conclude by assessing the general state of the high performance computing field.

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

Aceves, Salvador M.; Ledesma-Orozco, Elias Rigoberto; Espinosa-Loza, Francisco

A pressure vessel apparatus for cryogenic capable storage of hydrogen or other cryogenic gases at high pressure includes an insert with a parallel inlet duct, a perpendicular inlet duct connected to the parallel inlet. The perpendicular inlet duct and the parallel inlet duct connect the interior cavity with the external components. The insert also includes a parallel outlet duct and a perpendicular outlet duct connected to the parallel outlet duct. The perpendicular outlet duct and the parallel outlet duct connect the interior cavity with the external components.

Parallel fabrication of macroporous scaffolds.

PubMed

Dobos, Andrew; Grandhi, Taraka Sai Pavan; Godeshala, Sudhakar; Meldrum, Deirdre R; Rege, Kaushal

2018-07-01

Scaffolds generated from naturally occurring and synthetic polymers have been investigated in several applications because of their biocompatibility and tunable chemo-mechanical properties. Existing methods for generation of 3D polymeric scaffolds typically cannot be parallelized, suffer from low throughputs, and do not allow for quick and easy removal of the fragile structures that are formed. Current molds used in hydrogel and scaffold fabrication using solvent casting and porogen leaching are often single-use and do not facilitate 3D scaffold formation in parallel. Here, we describe a simple device and related approaches for the parallel fabrication of macroporous scaffolds. This approach was employed for the generation of macroporous and non-macroporous materials in parallel, in higher throughput and allowed for easy retrieval of these 3D scaffolds once formed. In addition, macroporous scaffolds with interconnected as well as non-interconnected pores were generated, and the versatility of this approach was employed for the generation of 3D scaffolds from diverse materials including an aminoglycoside-derived cationic hydrogel ("Amikagel"), poly(lactic-co-glycolic acid) or PLGA, and collagen. Macroporous scaffolds generated using the device were investigated for plasmid DNA binding and cell loading, indicating the use of this approach for developing materials for different applications in biotechnology. Our results demonstrate that the device-based approach is a simple technology for generating scaffolds in parallel, which can enhance the toolbox of current fabrication techniques. © 2018 Wiley Periodicals, Inc.

Parallel Spectral Acquisition with an Ion Cyclotron Resonance Cell Array.

PubMed

Park, Sung-Gun; Anderson, Gordon A; Navare, Arti T; Bruce, James E

2016-01-19

Mass measurement accuracy is a critical analytical figure-of-merit in most areas of mass spectrometry application. However, the time required for acquisition of high-resolution, high mass accuracy data limits many applications and is an aspect under continual pressure for development. Current efforts target implementation of higher electrostatic and magnetic fields because ion oscillatory frequencies increase linearly with field strength. As such, the time required for spectral acquisition of a given resolving power and mass accuracy decreases linearly with increasing fields. Mass spectrometer developments to include multiple high-resolution detectors that can be operated in parallel could further decrease the acquisition time by a factor of n, the number of detectors. Efforts described here resulted in development of an instrument with a set of Fourier transform ion cyclotron resonance (ICR) cells as detectors that constitute the first MS array capable of parallel high-resolution spectral acquisition. ICR cell array systems consisting of three or five cells were constructed with printed circuit boards and installed within a single superconducting magnet and vacuum system. Independent ion populations were injected and trapped within each cell in the array. Upon filling the array, all ions in all cells were simultaneously excited and ICR signals from each cell were independently amplified and recorded in parallel. Presented here are the initial results of successful parallel spectral acquisition, parallel mass spectrometry (MS) and MS/MS measurements, and parallel high-resolution acquisition with the MS array system.

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.

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

PubMed

Samadian, Soroush; Bruce, Jeff P; Pugh, Trevor J

2018-03-01

Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

Insights into the Hendra virus NTAIL-XD complex: Evidence for a parallel organization of the helical MoRE at the XD surface stabilized by a combination of hydrophobic and polar interactions.

PubMed

Erales, Jenny; Beltrandi, Matilde; Roche, Jennifer; Maté, Maria; Longhi, Sonia

2015-08-01

The Hendra virus is a member of the Henipavirus genus within the Paramyxoviridae family. The nucleoprotein, which consists of a structured core and of a C-terminal intrinsically disordered domain (N(TAIL)), encapsidates the viral genome within a helical nucleocapsid. N(TAIL) partly protrudes from the surface of the nucleocapsid being thus capable of interacting with the C-terminal X domain (XD) of the viral phosphoprotein. Interaction with XD implies a molecular recognition element (MoRE) that is located within N(TAIL) residues 470-490, and that undergoes α-helical folding. The MoRE has been proposed to be embedded in the hydrophobic groove delimited by helices α2 and α3 of XD, although experimental data could not discriminate between a parallel and an antiparallel orientation of the MoRE. Previous studies also showed that if the binding interface is enriched in hydrophobic residues, charged residues located close to the interface might play a role in complex formation. Here, we targeted for site directed mutagenesis two acidic and two basic residues within XD and N(TAIL). ITC studies showed that electrostatics plays a crucial role in complex formation and pointed a parallel orientation of the MoRE as more likely. Further support for a parallel orientation was afforded by SAXS studies that made use of two chimeric constructs in which XD and the MoRE were covalently linked to each other. Altogether, these studies unveiled the multiparametric nature of the interactions established within this complex and contribute to shed light onto the molecular features of protein interfaces involving intrinsically disordered regions. Copyright © 2015 Elsevier B.V. All rights reserved.

The paradigm compiler: Mapping a functional language for the connection machine

NASA Technical Reports Server (NTRS)

Dennis, Jack B.

1989-01-01

The Paradigm Compiler implements a new approach to compiling programs written in high level languages for execution on highly parallel computers. The general approach is to identify the principal data structures constructed by the program and to map these structures onto the processing elements of the target machine. The mapping is chosen to maximize performance as determined through compile time global analysis of the source program. The source language is Sisal, a functional language designed for scientific computations, and the target language is Paris, the published low level interface to the Connection Machine. The data structures considered are multidimensional arrays whose dimensions are known at compile time. Computations that build such arrays usually offer opportunities for highly parallel execution; they are data parallel. The Connection Machine is an attractive target for these computations, and the parallel for construct of the Sisal language is a convenient high level notation for data parallel algorithms. The principles and organization of the Paradigm Compiler are discussed.

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.

Corridor One:An Integrated Distance Visualization Enuronments for SSI+ASCI Applications

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

Christopher R. Johnson, Charles D. Hansen

2001-10-29

The goal of Corridor One: An Integrated Distance Visualization Environment for ASCI and SSI Application was to combine the forces of six leading edge laboratories working in the areas of visualization and distributed computing and high performance networking (Argonne National Laboratory, Lawrence Berkeley National Laboratory, Los Alamos National Laboratory, University of Illinois, University of Utah and Princeton University) to develop and deploy the most advanced integrated distance visualization environment for large-scale scientific visualization and demonstrate it on applications relevant to the DOE SSI and ASCI programs. The Corridor One team brought world class expertise in parallel rendering, deep image basedmore » rendering, immersive environment technology, large-format multi-projector wall based displays, volume and surface visualization algorithms, collaboration tools and streaming media technology, network protocols for image transmission, high-performance networking, quality of service technology and distributed computing middleware. Our strategy was to build on the very successful teams that produced the I-WAY, ''Computational Grids'' and CAVE technology and to add these to the teams that have developed the fastest parallel visualizations systems and the most widely used networking infrastructure for multicast and distributed media. Unfortunately, just as we were getting going on the Corridor One project, DOE cut the program after the first year. As such, our final report consists of our progress during year one of the grant.« less

A parallel architecture of interpolated timing recovery for high- speed data transfer rate and wide capture-range

NASA Astrophysics Data System (ADS)

Higashino, Satoru; Kobayashi, Shoei; Yamagami, Tamotsu

2007-06-01

High data transfer rate has been demanded for data storage devices along increasing the storage capacity. In order to increase the transfer rate, high-speed data processing techniques in read-channel devices are required. Generally, parallel architecture is utilized for the high-speed digital processing. We have developed a new architecture of Interpolated Timing Recovery (ITR) to achieve high-speed data transfer rate and wide capture-range in read-channel devices for the information storage channels. It facilitates the parallel implementation on large-scale-integration (LSI) devices.

DVS-SOFTWARE: An Effective Tool for Applying Highly Parallelized Hardware To Computational Geophysics

NASA Astrophysics Data System (ADS)

Herrera, I.; Herrera, G. S.

2015-12-01

Most geophysical systems are macroscopic physical systems. The behavior prediction of such systems is carried out by means of computational models whose basic models are partial differential equations (PDEs) [1]. Due to the enormous size of the discretized version of such PDEs it is necessary to apply highly parallelized super-computers. For them, at present, the most efficient software is based on non-overlapping domain decomposition methods (DDM). However, a limiting feature of the present state-of-the-art techniques is due to the kind of discretizations used in them. Recently, I. Herrera and co-workers using 'non-overlapping discretizations' have produced the DVS-Software which overcomes this limitation [2]. The DVS-software can be applied to a great variety of geophysical problems and achieves very high parallel efficiencies (90%, or so [3]). It is therefore very suitable for effectively applying the most advanced parallel supercomputers available at present. In a parallel talk, in this AGU Fall Meeting, Graciela Herrera Z. will present how this software is being applied to advance MOD-FLOW. Key Words: Parallel Software for Geophysics, High Performance Computing, HPC, Parallel Computing, Domain Decomposition Methods (DDM)REFERENCES [1]. Herrera Ismael and George F. Pinder, Mathematical Modelling in Science and Engineering: An axiomatic approach", John Wiley, 243p., 2012. [2]. Herrera, I., de la Cruz L.M. and Rosas-Medina A. "Non Overlapping Discretization Methods for Partial, Differential Equations". NUMER METH PART D E, 30: 1427-1454, 2014, DOI 10.1002/num 21852. (Open source) [3]. Herrera, I., & Contreras Iván "An Innovative Tool for Effectively Applying Highly Parallelized Software To Problems of Elasticity". Geofísica Internacional, 2015 (In press)

Method and apparatus for fabrication of high gradient insulators with parallel surface conductors spaced less than one millimeter apart

DOEpatents

Sanders, David M.; Decker, Derek E.

1999-01-01

Optical patterns and lithographic techniques are used as part of a process to embed parallel and evenly spaced conductors in the non-planar surfaces of an insulator to produce high gradient insulators. The approach extends the size that high gradient insulating structures can be fabricated as well as improves the performance of those insulators by reducing the scale of the alternating parallel lines of insulator and conductor along the surface. This fabrication approach also substantially decreases the cost required to produce high gradient insulators.

In situ conversion process systems utilizing wellbores in at least two regions of a formation

DOEpatents

Vinegar, Harold J [Bellaire, TX; Hsu, Chia-Fu [Granada Hills, CA

2011-09-27

A system for heating a subsurface formation is described. The system includes a plurality of elongated heaters located in a plurality of openings in the formation. At least two of the heaters are substantially parallel to each other for at least a portion of the lengths of the heaters. At least two of the heaters have first end portions in a first region of the formation and second end portions in a second region of the formation. A source of time-varying current is configured to apply time-varying current to at least two of the heaters. The first end portions of at least two heaters are configured to have substantially the same voltage applied to them. The second portions of at least two heaters are configured to have substantially the same voltage applied to them.

Ripple formation on Si surfaces during plasma etching in Cl2

NASA Astrophysics Data System (ADS)

Nakazaki, Nobuya; Matsumoto, Haruka; Sonobe, Soma; Hatsuse, Takumi; Tsuda, Hirotaka; Takao, Yoshinori; Eriguchi, Koji; Ono, Kouichi

2018-05-01

Nanoscale surface roughening and ripple formation in response to ion incidence angle has been investigated during inductively coupled plasma etching of Si in Cl2, using sheath control plates to achieve the off-normal ion incidence on blank substrate surfaces. The sheath control plate consisted of an array of inclined trenches, being set into place on the rf-biased electrode, where their widths and depths were chosen in such a way that the sheath edge was pushed out of the trenches. The distortion of potential distributions and the consequent deflection of ion trajectories above and in the trenches were then analyzed based on electrostatic particle-in-cell simulations of the plasma sheath, to evaluate the angular distributions of ion fluxes incident on substrates pasted on sidewalls and/or at the bottom of the trenches. Experiments showed well-defined periodic sawtooth-like ripples with their wave vector oriented parallel to the direction of ion incidence at intermediate off-normal angles, while relatively weak corrugations or ripplelike structures with the wave vector perpendicular to it at high off-normal angles. Possible mechanisms for the formation of surface ripples during plasma etching are discussed with the help of Monte Carlo simulations of plasma-surface interactions and feature profile evolution. The results indicate the possibility of providing an alternative to ion beam sputtering for self-organized formation of ordered surface nanostructures.

Development of gallium arsenide high-speed, low-power serial parallel interface modules: Executive summary

NASA Technical Reports Server (NTRS)

1988-01-01

Final report to NASA LeRC on the development of gallium arsenide (GaAS) high-speed, low power serial/parallel interface modules. The report discusses the development and test of a family of 16, 32 and 64 bit parallel to serial and serial to parallel integrated circuits using a self aligned gate MESFET technology developed at the Honeywell Sensors and Signal Processing Laboratory. Lab testing demonstrated 1.3 GHz clock rates at a power of 300 mW. This work was accomplished under contract number NAS3-24676.

The NAS parallel benchmarks

NASA Technical Reports Server (NTRS)

Bailey, D. H.; Barszcz, E.; Barton, J. T.; Carter, R. L.; Lasinski, T. A.; Browning, D. S.; Dagum, L.; Fatoohi, R. A.; Frederickson, P. O.; Schreiber, R. S.

1991-01-01

A new set of benchmarks has been developed for the performance evaluation of highly parallel supercomputers in the framework of the NASA Ames Numerical Aerodynamic Simulation (NAS) Program. These consist of five 'parallel kernel' benchmarks and three 'simulated application' benchmarks. Together they mimic the computation and data movement characteristics of large-scale computational fluid dynamics applications. The principal distinguishing feature of these benchmarks is their 'pencil and paper' specification-all details of these benchmarks are specified only algorithmically. In this way many of the difficulties associated with conventional benchmarking approaches on highly parallel systems are avoided.

High-energy physics software parallelization using database techniques

NASA Astrophysics Data System (ADS)

Argante, E.; van der Stok, P. D. V.; Willers, I.

1997-02-01

A programming model for software parallelization, called CoCa, is introduced that copes with problems caused by typical features of high-energy physics software. By basing CoCa on the database transaction paradimg, the complexity induced by the parallelization is for a large part transparent to the programmer, resulting in a higher level of abstraction than the native message passing software. CoCa is implemented on a Meiko CS-2 and on a SUN SPARCcenter 2000 parallel computer. On the CS-2, the performance is comparable with the performance of native PVM and MPI.

Fast polyenergetic forward projection for image formation using OpenCL on a heterogeneous parallel computing platform.

PubMed

Zhou, Lili; Clifford Chao, K S; Chang, Jenghwa

2012-11-01

Simulated projection images of digital phantoms constructed from CT scans have been widely used for clinical and research applications but their quality and computation speed are not optimal for real-time comparison with the radiography acquired with an x-ray source of different energies. In this paper, the authors performed polyenergetic forward projections using open computing language (OpenCL) in a parallel computing ecosystem consisting of CPU and general purpose graphics processing unit (GPGPU) for fast and realistic image formation. The proposed polyenergetic forward projection uses a lookup table containing the NIST published mass attenuation coefficients (μ∕ρ) for different tissue types and photon energies ranging from 1 keV to 20 MeV. The CT images of interested sites are first segmented into different tissue types based on the CT numbers and converted to a three-dimensional attenuation phantom by linking each voxel to the corresponding tissue type in the lookup table. The x-ray source can be a radioisotope or an x-ray generator with a known spectrum described as weight w(n) for energy bin E(n). The Siddon method is used to compute the x-ray transmission line integral for E(n) and the x-ray fluence is the weighted sum of the exponential of line integral for all energy bins with added Poisson noise. To validate this method, a digital head and neck phantom constructed from the CT scan of a Rando head phantom was segmented into three (air, gray∕white matter, and bone) regions for calculating the polyenergetic projection images for the Mohan 4 MV energy spectrum. To accelerate the calculation, the authors partitioned the workloads using the task parallelism and data parallelism and scheduled them in a parallel computing ecosystem consisting of CPU and GPGPU (NVIDIA Tesla C2050) using OpenCL only. The authors explored the task overlapping strategy and the sequential method for generating the first and subsequent DRRs. A dispatcher was designed to drive the high-degree parallelism of the task overlapping strategy. Numerical experiments were conducted to compare the performance of the OpenCL∕GPGPU-based implementation with the CPU-based implementation. The projection images were similar to typical portal images obtained with a 4 or 6 MV x-ray source. For a phantom size of 512 × 512 × 223, the time for calculating the line integrals for a 512 × 512 image panel was 16.2 ms on GPGPU for one energy bin in comparison to 8.83 s on CPU. The total computation time for generating one polyenergetic projection image of 512 × 512 was 0.3 s (141 s for CPU). The relative difference between the projection images obtained with the CPU-based and OpenCL∕GPGPU-based implementations was on the order of 10(-6) and was virtually indistinguishable. The task overlapping strategy was 5.84 and 1.16 times faster than the sequential method for the first and the subsequent digitally reconstruction radiographies, respectively. The authors have successfully built digital phantoms using anatomic CT images and NIST μ∕ρ tables for simulating realistic polyenergetic projection images and optimized the processing speed with parallel computing using GPGPU∕OpenCL-based implementation. The computation time was fast (0.3 s per projection image) enough for real-time IGRT (image-guided radiotherapy) applications.

An Overview of High-performance Parallel Big Data transfers over multiple network channels with Transport Layer Security (TLS) and TLS plus Perfect Forward Secrecy (PFS)

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

Fang, Chin; Corttrell, R. A.

This Technical Note provides an overview of high-performance parallel Big Data transfers with and without encryption for data in-transit over multiple network channels. It shows that with the parallel approach, it is feasible to carry out high-performance parallel "encrypted" Big Data transfers without serious impact to throughput. But other impacts, e.g. the energy-consumption part should be investigated. It also explains our rationales of using a statistics-based approach for gaining understanding from test results and for improving the system. The presentation is of high-level nature. Nevertheless, at the end we will pose some questions and identify potentially fruitful directions for futuremore » work.« less

Should essays and other "open-ended"-type questions retain a place in written summative assessment in clinical medicine?

PubMed

Hift, Richard J

2014-11-28

Written assessments fall into two classes: constructed-response or open-ended questions, such as the essay and a number of variants of the short-answer question, and selected-response or closed-ended questions; typically in the form of multiple-choice. It is widely believed that constructed response written questions test higher order cognitive processes in a manner that multiple-choice questions cannot, and consequently have higher validity. An extensive review of the literature suggests that in summative assessment neither premise is evidence-based. Well-structured open-ended and multiple-choice questions appear equivalent in their ability to assess higher cognitive functions, and performance in multiple-choice assessments may correlate more highly than the open-ended format with competence demonstrated in clinical practice following graduation. Studies of construct validity suggest that both formats measure essentially the same dimension, at least in mathematics, the physical sciences, biology and medicine. The persistence of the open-ended format in summative assessment may be due to the intuitive appeal of the belief that synthesising an answer to an open-ended question must be both more cognitively taxing and similar to actual experience than is selecting a correct response. I suggest that cognitive-constructivist learning theory would predict that a well-constructed context-rich multiple-choice item represents a complex problem-solving exercise which activates a sequence of cognitive processes which closely parallel those required in clinical practice, hence explaining the high validity of the multiple-choice format. The evidence does not support the proposition that the open-ended assessment format is superior to the multiple-choice format, at least in exit-level summative assessment, in terms of either its ability to test higher-order cognitive functioning or its validity. This is explicable using a theory of mental models, which might predict that the multiple-choice format will have higher validity, a statement for which some empiric support exists. Given the superior reliability and cost-effectiveness of the multiple-choice format consideration should be given to phasing out open-ended format questions in summative assessment. Whether the same applies to non-exit-level assessment and formative assessment is a question which remains to be answered; particularly in terms of the educational effect of testing, an area which deserves intensive study.

Crackling sound generation during the formation of liquid bridges: A lattice gas model

NASA Astrophysics Data System (ADS)

Almeida, Alexandre B.; Buldyrev, Sergey V.; Alencar, Adriano M.

2013-08-01

Due to abnormal mechanical instabilities, liquid bridges may form in the small airways blocking airflow. Liquid bridge ruptures during inhalation are the major cause of the crackling adventitious lung sound, which can be heard using a simple stethoscope. Recently, Vyshedskiy and colleagues (2009) [1] described and characterized a crackle sound originated during expiration. However, the mechanism and origin of the expiratory crackle are still controversial. Thus, in this paper, we propose a mechanism for expiratory crackles. We hypothesize that the expiratory crackle sound is a result of the energy released in the form of acoustic waves during the formation of the liquid bridge. The magnitude of the energy released is proportional to the difference in free energy prior and after the bridge formation. We use a lattice gas model to describe the liquid bridge formation between two parallel planes. Specifically, we determine the surface free energy and the conditions of the liquid bridge formation between two parallel planes separated by a distance 2h by a liquid droplet of volume Ω and contact angle Θ, using both Monte Carlo simulation of a lattice gas model and variational calculus based on minimization of the surface area with the volume and the contact angle constrained. We numerically and analytically determine the phase diagram of the system as a function of the dimensionless parameter hΩ and Θ. We can distinguish two different phases: one droplet and one liquid bridge. We observe a hysteresis curve for the energy changes between these two states, and a finite size effect in the bridge formation. We compute the release of free energy during the formation of the liquid bridge and discuss the results in terms of system size. We also calculate the force exerted from liquid bridge on the planes by studying the dependence of the free energy on the separation between the planes 2h. The simulation results are in agreement with the analytical solution.

Internationalization of MBA Programs in Asia-Pacific: Looking beyond Business Study Missions.

ERIC Educational Resources Information Center

Teck-Meng, Tan; And Others

1997-01-01

Internationalization of the curriculum in the Nanyang University (Singapore) master's program in business administration (MBA) is described, highlighting its parallels with formation of government policy initiatives that encourage regional expansion of Singapore businesses. Lessons learned from the internationalization experiences of MBA programs…

Parallel-In-Time For Moving Meshes

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

Falgout, R. D.; Manteuffel, T. A.; Southworth, B.

2016-02-04

With steadily growing computational resources available, scientists must develop e ective ways to utilize the increased resources. High performance, highly parallel software has be- come a standard. However until recent years parallelism has focused primarily on the spatial domain. When solving a space-time partial di erential equation (PDE), this leads to a sequential bottleneck in the temporal dimension, particularly when taking a large number of time steps. The XBraid parallel-in-time library was developed as a practical way to add temporal parallelism to existing se- quential codes with only minor modi cations. In this work, a rezoning-type moving mesh is appliedmore » to a di usion problem and formulated in a parallel-in-time framework. Tests and scaling studies are run using XBraid and demonstrate excellent results for the simple model problem considered herein.« less

Design of a dataway processor for a parallel image signal processing system

NASA Astrophysics Data System (ADS)

Nomura, Mitsuru; Fujii, Tetsuro; Ono, Sadayasu

1995-04-01

Recently, demands for high-speed signal processing have been increasing especially in the field of image data compression, computer graphics, and medical imaging. To achieve sufficient power for real-time image processing, we have been developing parallel signal-processing systems. This paper describes a communication processor called 'dataway processor' designed for a new scalable parallel signal-processing system. The processor has six high-speed communication links (Dataways), a data-packet routing controller, a RISC CORE, and a DMA controller. Each communication link operates at 8-bit parallel in a full duplex mode at 50 MHz. Moreover, data routing, DMA, and CORE operations are processed in parallel. Therefore, sufficient throughput is available for high-speed digital video signals. The processor is designed in a top- down fashion using a CAD system called 'PARTHENON.' The hardware is fabricated using 0.5-micrometers CMOS technology, and its hardware is about 200 K gates.

Geologic mapping of Northern Atla Regio on Venus: Preliminary data

NASA Technical Reports Server (NTRS)

Nikishin, A. M.; Burba, G. A.

1993-01-01

The Northern part of Atla Regio within the frame of C1-formate Magellan photo map 15N197 was mapped geologically at scale 1:8,000,000. This is a part of Russia's contribution into C1 geologic mapping efforts. The map is reproduced here being reduced about twice. The map shows that the Northern Atla area is predominantly a volcanic plain with numerous volcanic features: shield volcanoes, domes and hills with various morphology, corona-like constructions, radar bright and dark spots often with flow-like outlines. Relatively small areas of tessera occurred in the area are mainly semi-flooded with the plain material. Tesserae are considered to be the oldest terrains within the map sheet. There are many lineated terrains in the region. They are interpreted as the old, almost-buried tesserae (those with crossed lineaments) or partly buried ridge belts (those with parallel lineaments). These lineated terrains have an intermediate age between the young volcanic plains and the old tessera areas. Two prominent high volcanic shields are located within the region - Ozza Mons and Sapas Mona. The most prominent structure in Northern Atla is Ganis Chasma rift. The rift cuts volcanic plain and is considered to be under formation during approximately the same time with Ozza Mons shield. Ganis Chasma rift valley is highly fractured and bounded with fault scarps. Rift shoulder uplifts are typical for Ganis Chasma. There are few relatively young volcanic features inside the rift valley. The analysis of fracturing and rift valley geometry shows the rift originated due to 5-10 percent crustal extention followed by the crustal subsidence. The age sequence summary for the main terrain types in the region is (from older to younger ones): tesserae; lineated terrains with crossed lineaments; lineated terrains with parallel lineaments; volcanic plains; and prominent volcanic shields and Ganis Chasma rift valley. The geologic structure of Atla Regio as it appeared now with the Magellan high resolution images is very close to that of Beta Regio. Such conclusion coincide with the earlier ones based on the coarser data.

Plains tectonism on Venus: The deformation belts of Lavinia Planitia

NASA Technical Reports Server (NTRS)

Squyres, Steven W.; Jankowski, David G.; Simons, Mark; Solomon, Sean C.; Hager, Bradford H.; Mcgill, George E.

1993-01-01

High-resolution radar images from the Magellan spacecraft have revealed the first details of the morphology of the Lavinia Planitia region of Venus. A number of geologic units can be distinguished, including volcanic plains units with a range of ages. Transecting these plains over much of the Lavinia region are two types of generally orthogonal features that we interpret to be compressional wrinkle ridges and extensional grooves. The dominant tectonic features of Lavinia are broad elevated belts of intense deformation that transect the plains with complex geometry. They are many tens to a few hundred kilometers wide, as much as 1000 km long, and elevated hundreds of meters above the surrounding plains. Two classes of deformation belts are seen in the Lavinia region. 'Ridge belts' are composed of parallel ridges, each a few hundred meters in elevation, that we interpret to be folds. Typical fold spacings are 5-10 km. 'Fracture belts' are dominated instead by intense faulting, with faults in some instances paired to form narrow grabens. There is also some evidence for modest amounts of horizontal shear distributed across both ridge and fracture belts. Crosscutting relationships among the belts show there to be a range in belt ages. In western Lavinia, in particular, many ridge and fracture belts appear to bear a relationship to the much smaller wrinkle ridges and grooves on the surrounding plains: ridge morphology tends to dominate belts that lie more nearly parallel to local plains wrinkle ridges, and fracture morphology tends to dominate belts that lie more nearly parallel to local plains grooves. We use simple models to explore the formation of ridge and fracture belts. We show that convective motions in the mantle can couple to the crust to cause horizontal stresses of a magnitude sufficient to induce the formation of deformation belts like those observed in Lavinia. We also use the small-scale wavelengths of deformation observed within individual ridge belts to place an approximate lower limit on the venusian thermal gradient in the Lavinia region at the time of deformation.

Tectonic control of complex slope failures in the Ameka River Valley (Lower Gibe Area, central Ethiopia): Implications for landslide formation

NASA Astrophysics Data System (ADS)

Kycl, Petr; Rapprich, Vladislav; Verner, Kryštof; Novotný, Jan; Hroch, Tomáš; Mišurec, Jan; Eshetu, Habtamu; Tadesse Haile, Ezra; Alemayehu, Leta; Goslar, Tomasz

2017-07-01

Even though major faults represent important landslide controlling factors, the role the tectonic setting in actively spreading rifts plays in the development of large complex landslides is seldom discussed. The Ameka complex landslide area is located on the eastern scarp of the Gibe Gorge, approximately 45 km to the west of the Main Ethiopian Rift and 175 km to the southwest of Addis Ababa. Investigation of the complex landslide failures required a combination of satellite and airborne data-based geomorphology, geological field survey complemented with structural analysis, radiocarbon geochronology and vertical electric sounding. The obtained observations confirmed the multiphase evolution of the landslide area. We have documented that, apart from climatic and lithological conditions, the main triggering factor of the Ameka complex landslide is the tectonic development of this area. The E-W extension along the NNE-SSW trending Main Ethiopian Rift is associated with the formation of numerous parallel normal faults, such as the Gibe Gorge fault and the almost perpendicular scissor faults. The geometry of the slid blocks of coherent lithology have inherited the original tectonic framework, which suggests the crucial role tectonics play in the fragmentation of the compact rock-masses, and the origin and development of the Ameka complex landslide area. Similarly, the main scarps were also parallel to the principal tectonic features. The local tectonic framework is dominated by faults of the same orientation as the regional structures of the Main Ethiopian Rift. Such parallel tectonic frameworks display clear links between the extension of the Main Ethiopian Rift and the tectonic development of the landslide area. The Ameka complex landslide developed in several episodes over thousands of years. According to the radiocarbon data, the last of the larger displaced blocks (representing only 2% of the total area) most likely slid down in the seventh century AD. The main scarps, namely the high scarps in the western part, are unstable over the long term and toppling and falling-type slope movements can be expected here in the future.

Initiation of and distributed deformation at and around stylolite interfaces: Insights from detailed microstructural analysis

NASA Astrophysics Data System (ADS)

Ebner, M.; Piazolo, S.; Koehn, D.

2009-04-01

In the present contribution we investigate the microstructure of bedding parallel and bedding normal stylolites in carbonate rocks. We focused our study on micro-stylolites which represent an initial stage of this localised pressure solution process as stylolite roughness amplitude is a function of strain. We use electron backscatter diffraction analysis (EBSD) and orientation contrast imaging to address the following issues: (i) What causes the initiation of stylolite interfaces at a submicroscopic scale, (ii) is there distributed deformation around the stylolite interface and (iii) what is the role of the interface (residuum)? Our findings demonstrate that the characteristic stylolite teeth are initiated at a pre-existing heterogeneity in the host-rock. This quenched noise in carbonate rocks is typically composed of clay particles in the submicron scale. In addition, qtz-grains are present along especially pronounced stylolite peaks. The stylolite interface evolves with increasing strain from individual clay particles separated by grain-grain contacts of calcite along the interface to a continuous layer of clay and oxides. Thickness variation of the residuum along the interface is inferred to be strongly influenced by the pre-existing distribution of pinning particles that are more resistant to dissolution. Another important observation is that a shaped preferred orientation (SPO) exists in a halo around the stylolite. This SPO increases with proximity to the stylolite interface. Within this halo, crystal plastic deformation is expressed by subgrain formation with subgrain boundaries usually aligned parallel to shortening direction. Bedding normal (tectonic) stylolites which overprint already compacted beds i.e. with a pre-existing sedimentary SPO parallel to the bedding plane exhibit a SPO at a high angle to the sedimentary SPO. We conclude that stylolite roughness is primarily caused by pre-existing heterogeneities in the host-rock which are more resistant to dissolution e.g. clay particles and/or qtz grains. Secondly, we demonstrate that stylolite formation is not a process that is restricted to the stylolite interface itself but a process that is active in a broader zone around the actual interface.

Parallel Computing:. Some Activities in High Energy Physics

NASA Astrophysics Data System (ADS)

Willers, Ian

This paper examines some activities in High Energy Physics that utilise parallel computing. The topic includes all computing from the proposed SIMD front end detectors, the farming applications, high-powered RISC processors and the large machines in the computer centers. We start by looking at the motivation behind using parallelism for general purpose computing. The developments around farming are then described from its simplest form to the more complex system in Fermilab. Finally, there is a list of some developments that are happening close to the experiments.

A scalable neuroinformatics data flow for electrophysiological signals using MapReduce.

PubMed

Jayapandian, Catherine; Wei, Annan; Ramesh, Priya; Zonjy, Bilal; Lhatoo, Samden D; Loparo, Kenneth; Zhang, Guo-Qiang; Sahoo, Satya S

2015-01-01

Data-driven neuroscience research is providing new insights in progression of neurological disorders and supporting the development of improved treatment approaches. However, the volume, velocity, and variety of neuroscience data generated from sophisticated recording instruments and acquisition methods have exacerbated the limited scalability of existing neuroinformatics tools. This makes it difficult for neuroscience researchers to effectively leverage the growing multi-modal neuroscience data to advance research in serious neurological disorders, such as epilepsy. We describe the development of the Cloudwave data flow that uses new data partitioning techniques to store and analyze electrophysiological signal in distributed computing infrastructure. The Cloudwave data flow uses MapReduce parallel programming algorithm to implement an integrated signal data processing pipeline that scales with large volume of data generated at high velocity. Using an epilepsy domain ontology together with an epilepsy focused extensible data representation format called Cloudwave Signal Format (CSF), the data flow addresses the challenge of data heterogeneity and is interoperable with existing neuroinformatics data representation formats, such as HDF5. The scalability of the Cloudwave data flow is evaluated using a 30-node cluster installed with the open source Hadoop software stack. The results demonstrate that the Cloudwave data flow can process increasing volume of signal data by leveraging Hadoop Data Nodes to reduce the total data processing time. The Cloudwave data flow is a template for developing highly scalable neuroscience data processing pipelines using MapReduce algorithms to support a variety of user applications.

A scalable neuroinformatics data flow for electrophysiological signals using MapReduce

PubMed Central

Jayapandian, Catherine; Wei, Annan; Ramesh, Priya; Zonjy, Bilal; Lhatoo, Samden D.; Loparo, Kenneth; Zhang, Guo-Qiang; Sahoo, Satya S.

2015-01-01

Data-driven neuroscience research is providing new insights in progression of neurological disorders and supporting the development of improved treatment approaches. However, the volume, velocity, and variety of neuroscience data generated from sophisticated recording instruments and acquisition methods have exacerbated the limited scalability of existing neuroinformatics tools. This makes it difficult for neuroscience researchers to effectively leverage the growing multi-modal neuroscience data to advance research in serious neurological disorders, such as epilepsy. We describe the development of the Cloudwave data flow that uses new data partitioning techniques to store and analyze electrophysiological signal in distributed computing infrastructure. The Cloudwave data flow uses MapReduce parallel programming algorithm to implement an integrated signal data processing pipeline that scales with large volume of data generated at high velocity. Using an epilepsy domain ontology together with an epilepsy focused extensible data representation format called Cloudwave Signal Format (CSF), the data flow addresses the challenge of data heterogeneity and is interoperable with existing neuroinformatics data representation formats, such as HDF5. The scalability of the Cloudwave data flow is evaluated using a 30-node cluster installed with the open source Hadoop software stack. The results demonstrate that the Cloudwave data flow can process increasing volume of signal data by leveraging Hadoop Data Nodes to reduce the total data processing time. The Cloudwave data flow is a template for developing highly scalable neuroscience data processing pipelines using MapReduce algorithms to support a variety of user applications. PMID:25852536

A transient analysis of frost formation on a parallel plate evaporator

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

Martinez-Frias, J.; Aceves, S.M.; Hernandez-Guerrero, A.

1996-12-31

This paper presents the development of a transient model for evaluating frost formation on a parallel plate evaporator for heat pump applications. The model treats the frost layer as a porous substance, and applies the equations of conservation of mass, momentum and energy to calculate the growth and densification of the frost layer. Empirical correlations for thermal conductivity and tortuosity as a function of density are incorporated from previous studies. Frost growth is calculated as a function of time, Reynolds number, longitudinal location, plate temperature, and ambient air temperature and humidity. The main assumptions are: ideal gas behavior for airmore » and water vapor, uniform frost density and thermal conductivity across the thickness of the frost layer; and quasi-steady conditions during the whole process. The mathematical model is validated by comparing the predicted values of frost thickness and frost density with results obtained in recent experimental studies. A good agreement was obtained in the comparison. The frost formation model calculates pressure drop and heat transfer resistance that result from the existence of the frost layer, and it can therefore be incorporated into a heat pump model to evaluate performance losses due to frosting as a function of weather conditions and time of operation since the last evaporator defrost.« less

Assessing trihalomethanes (THMs) and N-nitrosodimethylamine (NDMA) formation potentials in drinking water treatment plants using fluorescence spectroscopy and parallel factor analysis.

PubMed

Yang, Liyang; Kim, Daekyun; Uzun, Habibullah; Karanfil, Tanju; Hur, Jin

2015-02-01

The formation of disinfection byproducts (DBPs) is a major challenge in drinking water treatments. This study explored the applicability of fluorescence excitation-emission matrices and parallel factor analysis (EEM-PARAFAC) for assessing the formation potentials (FPs) of trihalomethanes (THMs) and N-nitrosodimethylamine (NDMA), and the treatability of THM and NDMA precursors in nine drinking water treatment plants. Two humic-like and one tryptophan-like components were identified for the samples using PARAFAC. The total THM FP (TTHM FP) correlated strongly with humic-like component C2 (r=0.874), while NDMA FP showed a moderate and significant correlation with the tryptophan-like component C3 (r=0.628). The reduction by conventional treatment was more effective for C2 than C3, and for TTHM FP than NDMA FP. The treatability of DOM and TTHM FP correlated negatively with the absorption spectral slope (S275-295) and biological index (BIX) of the raw water, but it correlated positively with humification index (HIX). Our results demonstrated that PARAFAC components were valuable for assessing DBPs FP in drinking water treatments, and also that the raw water quality could affect the treatment efficiency. Copyright © 2014 Elsevier Ltd. All rights reserved.

3D Resistive MHD Simulations of Formation, Compression, and Acceleration of Compact Tori

NASA Astrophysics Data System (ADS)

Woodruff, Simon; Meyer, Thomas; Stuber, James; Romero-Talamas, Carlos; Brown, Michael; Kaur, Manjit; Schaffner, David

2017-10-01

We present results from extended resistive 3D MHD simulations (NIMROD) pertaining to a new formation method for toroidal plasmas using a reconnection region that forms in a radial implosion, and results from the acceleration of CTs along a drift tube that are accelerated by a coil and are allowed to go tilt unstable and form a helical minimum energy state. The new formation method results from a reconnection region that is generated between two magnetic compression coils that are ramped to 320kV in 2 μs. When the compressing field is aligned anti-parallel to a pre-existing CT, a current sheet and reconnection region forms that accelerates plasma radially inwards up to 500km/s which stagnates and directed energy converts to thermal, raising temperatures to 500eV. When field is aligned parallel to the pre-existing CT, the configuration can be accelerated along a drift tube. For certain ratios of magnetic field to density, the CT goes tilt-unstable forming a twisted flux rope, which can also be accelerated and stagnated on an end wall, where temperature and field increases as the plasma compresses. We compare simulation results with adiabatic scaling relations. Work supported by ARPA-E ALPHA program and DARPA.

Characterization of the seismically imaged Tuscarora fold system and implications for layer parallel shortening in the Pennsylvania salient

NASA Astrophysics Data System (ADS)

Mount, Van S.; Wilkins, Scott; Comiskey, Cody S.

2017-12-01

The Tuscarora fold system (TFS) is located in the Pennsylvania salient in the foreland of the Valley and Ridge province. The TFS is imaged in high quality 3D seismic data and comprises a system of small-scale folds within relatively flat-lying Lower Silurian Tuscarora Formation strata. We characterize the TFS structures and infer layer parallel shortening (LPS) directions and magnitudes associated with deformation during the Alleghany Orogeny. Previously reported LPS data in our study area are from shallow Devonian and Carboniferous strata (based on outcrop and core analyses) above the shallowest of three major detachments recognized in the region. Seismic data allows us to characterize LPS at depth in strata beneath the shallow detachment. Our LPS data (orientations and inferred magnitudes) are consistent with the shallow data leading us to surmise that LPS during Alleghanian deformation fanned around the salient and was distributed throughout the stratigraphic section - and not isolated to strata above the shallow detachment. We propose that a NW-SE oriented Alleghanian maximum principal stress was perturbed by deep structure associated with the non-linear margin of Laurentia resulting in fanning of shortening directions within the salient.

Propagation of acoustic shock waves between parallel rigid boundaries and into shadow zones

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

Desjouy, C., E-mail: cyril.desjouy@gmail.com; Ollivier, S.; Dragna, D.

2015-10-28

The study of acoustic shock propagation in complex environments is of great interest for urban acoustics, but also for source localization, an underlying problematic in military applications. To give a better understanding of the phenomenon taking place during the propagation of acoustic shocks, laboratory-scale experiments and numerical simulations were performed to study the propagation of weak shock waves between parallel rigid boundaries, and into shadow zones created by corners. In particular, this work focuses on the study of the local interactions taking place between incident, reflected, and diffracted waves according to the geometry in both regular or irregular – alsomore » called Von Neumann – regimes of reflection. In this latter case, an irregular reflection can lead to the formation of a Mach stem that can modify the spatial distribution of the acoustic pressure. Short duration acoustic shock waves were produced by a 20 kilovolts electric spark source and a schlieren optical method was used to visualize the incident shockfront and the reflection/diffraction patterns. Experimental results are compared to numerical simulations based on the high-order finite difference solution of the two dimensional Navier-Stokes equations.« less

T-cell libraries allow simple parallel generation of multiple peptide-specific human T-cell clones.

PubMed

Theaker, Sarah M; Rius, Cristina; Greenshields-Watson, Alexander; Lloyd, Angharad; Trimby, Andrew; Fuller, Anna; Miles, John J; Cole, David K; Peakman, Mark; Sewell, Andrew K; Dolton, Garry

2016-03-01

Isolation of peptide-specific T-cell clones is highly desirable for determining the role of T-cells in human disease, as well as for the development of therapies and diagnostics. However, generation of monoclonal T-cells with the required specificity is challenging and time-consuming. Here we describe a library-based strategy for the simple parallel detection and isolation of multiple peptide-specific human T-cell clones from CD8(+) or CD4(+) polyclonal T-cell populations. T-cells were first amplified by CD3/CD28 microbeads in a 96U-well library format, prior to screening for desired peptide recognition. T-cells from peptide-reactive wells were then subjected to cytokine-mediated enrichment followed by single-cell cloning, with the entire process from sample to validated clone taking as little as 6 weeks. Overall, T-cell libraries represent an efficient and relatively rapid tool for the generation of peptide-specific T-cell clones, with applications shown here in infectious disease (Epstein-Barr virus, influenza A, and Ebola virus), autoimmunity (type 1 diabetes) and cancer. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Passing in Command Line Arguments and Parallel Cluster/Multicore Batching in R with batch.

PubMed

Hoffmann, Thomas J

2011-03-01

It is often useful to rerun a command line R script with some slight change in the parameters used to run it - a new set of parameters for a simulation, a different dataset to process, etc. The R package batch provides a means to pass in multiple command line options, including vectors of values in the usual R format, easily into R. The same script can be setup to run things in parallel via different command line arguments. The R package batch also provides a means to simplify this parallel batching by allowing one to use R and an R-like syntax for arguments to spread a script across a cluster or local multicore/multiprocessor computer, with automated syntax for several popular cluster types. Finally it provides a means to aggregate the results together of multiple processes run on a cluster.

Introduction to a system for implementing neural net connections on SIMD architectures

NASA Technical Reports Server (NTRS)

Tomboulian, Sherryl

1988-01-01

Neural networks have attracted much interest recently, and using parallel architectures to simulate neural networks is a natural and necessary application. The SIMD model of parallel computation is chosen, because systems of this type can be built with large numbers of processing elements. However, such systems are not naturally suited to generalized communication. A method is proposed that allows an implementation of neural network connections on massively parallel SIMD architectures. The key to this system is an algorithm permitting the formation of arbitrary connections between the neurons. A feature is the ability to add new connections quickly. It also has error recovery ability and is robust over a variety of network topologies. Simulations of the general connection system, and its implementation on the Connection Machine, indicate that the time and space requirements are proportional to the product of the average number of connections per neuron and the diameter of the interconnection network.

Introduction to a system for implementing neural net connections on SIMD architectures

NASA Technical Reports Server (NTRS)

Tomboulian, Sherryl

1988-01-01

Neural networks have attracted much interest recently, and using parallel architectures to simulate neural networks is a natural and necessary application. The SIMD model of parallel computation is chosen, because systems of this type can be built with large numbers of processing elements. However, such systems are not naturally suited to generalized elements. A method is proposed that allows an implementation of neural network connections on massively parallel SIMD architectures. The key to this system is an algorithm permitting the formation of arbitrary connections between the neurons. A feature is the ability to add new connections quickly. It also has error recovery ability and is robust over a variety of network topologies. Simulations of the general connection system, and its implementation on the Connection Machine, indicate that the time and space requirements are proportional to the product of the average number of connections per neuron and the diameter of the interconnection network.

Mother Centriole Distal Appendages Mediate Centrosome Docking at the Immunological Synapse and Reveal Mechanistic Parallels with Ciliogenesis.

PubMed

Stinchcombe, Jane C; Randzavola, Lyra O; Angus, Karen L; Mantell, Judith M; Verkade, Paul; Griffiths, Gillian M

2015-12-21

Cytotoxic T lymphocytes (CTLs) are highly effective serial killers capable of destroying virally infected and cancerous targets by polarized release from secretory lysosomes. Upon target contact, the CTL centrosome rapidly moves to the immunological synapse, focusing microtubule-directed release at this point [1-3]. Striking similarities have been noted between centrosome polarization at the synapse and basal body docking during ciliogenesis [1, 4-8], suggesting that CTL centrosomes might dock with the plasma membrane during killing, in a manner analogous to primary cilia formation [1, 4]. However, questions remain regarding the extent and function of centrosome polarization at the synapse, and recent reports have challenged its role [9, 10]. Here, we use high-resolution transmission electron microscopy (TEM) tomography analysis to show that, as in ciliogenesis, the distal appendages of the CTL mother centriole contact the plasma membrane directly during synapse formation. This is functionally important as small interfering RNA (siRNA) targeting of the distal appendage protein, Cep83, required for membrane contact during ciliogenesis [11], impairs CTL secretion. Furthermore, the regulatory proteins CP110 and Cep97, which must dissociate from the mother centriole to allow cilia formation [12], remain associated with the mother centriole in CTLs, and neither axoneme nor transition zone ciliary structures form. Moreover, complete centrosome docking can occur in proliferating CTLs with multiple centriole pairs. Thus, in CTLs, centrosomes dock transiently with the membrane, within the cell cycle and without progression into ciliogenesis. We propose that this transient centrosome docking without cilia formation is important for CTLs to deliver rapid, repeated polarized secretion directed by the centrosome. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Direct participation of DNA in the formation of singlet oxygen and base damage under UVA irradiation.

PubMed

Yagura, Teiti; Schuch, André Passaglia; Garcia, Camila Carrião Machado; Rocha, Clarissa Ribeiro Reily; Moreno, Natália Cestari; Angeli, José Pedro Friedmann; Mendes, Davi; Severino, Divinomar; Bianchini Sanchez, Angelica; Di Mascio, Paolo; de Medeiros, Marisa Helena Gennari; Menck, Carlos Frederico Martins

2017-07-01

UVA light is hardly absorbed by the DNA molecule, but recent works point to a direct mechanism of DNA lesion by these wavelengths. UVA light also excite endogenous chromophores, which causes DNA damage through ROS. In this study, DNA samples were irradiated with UVA light in different conditions to investigate possible mechanisms involved in the induction of DNA damage. The different types of DNA lesions formed after irradiation were determined through the use of endonucleases, which recognize and cleave sites containing oxidized bases and cyclobutane pyrimidine dimers (CPDs), as well as through antibody recognition. The formation of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxodG) was also studied in more detail using electrochemical detection. The results show that high NaCl concentration and concentrated DNA are capable of reducing the induction of CPDs. Moreover, concerning damage caused by oxidative stress, the presence of sodium azide and metal chelators reduce their induction, while deuterated water increases the amounts of oxidized bases, confirming the involvement of singlet oxygen in the generation of these lesions. Curiously, however, high concentrations of DNA also enhanced the formation of oxidized bases, in a reaction that paralleled the increase in the formation of singlet oxygen in the solution. This was interpreted as being due to an intrinsic photosensitization mechanism, depending directly on the DNA molecule to absorb UVA and generate singlet oxygen. Therefore, the DNA molecule itself may act as a chromophore for UVA light, locally producing a damaging agent, which may lead to even greater concerns about the deleterious impact of sunlight. Copyright © 2017 Elsevier Inc. All rights reserved.

Little Blue Dots in the Hubble Space Telescope Frontier Fields: Precursors to Globular Clusters?

NASA Astrophysics Data System (ADS)

Elmegreen, Debra Meloy; Elmegreen, Bruce G.

2017-12-01

Galaxies with stellar masses < {10}7.4 {M}ȯ and specific star formation rates {sSFR}> {10}-7.4 yr‑1 were examined on images of the Hubble Space Telescope Frontier Field Parallels for Abell 2744 and MACS J0416.1-02403. They appear as unresolved “Little Blue Dots” (LBDs). They are less massive and have higher specific star formation rates (sSFRs) than “blueberries” studied by Yang et al. and higher sSFRs than “Blue Nuggets” studied by Tacchella et al. We divided the LBDs into three redshift bins and, for each, stacked the B435, V606, and I814 images convolved to the same stellar point-spread function (PSF). Their radii were determined from PSF deconvolution to be ∼80 to ∼180 pc. The high sSFRs suggest that their entire stellar mass has formed in only 1% of the local age of the universe. The sSFRs at similar epochs in local dwarf galaxies are lower by a factor of ∼100. Assuming that the star formation rate is {ε }{ff}{M}{gas}/{t}{ff} for efficiency {ε }{ff}, gas mass M gas, and free-fall time, t ff, the gas mass and gas-to-star mass ratio are determined. This ratio exceeds 1 for reasonable efficiencies, and is likely to be ∼5 even with a high {ε }{ff} of 0.1. We consider whether these regions are forming today’s globular clusters. With their observed stellar masses, the maximum likely cluster mass is ∼ {10}5 {M}ȯ , but if star formation continues at the current rate for ∼ 10{t}{ff}∼ 50 {Myr} before feedback and gas exhaustion stop it, then the maximum cluster mass could become ∼ {10}6 {M}ȯ .

Cooling beyond the boundary value in supercritical fluids under vibration

NASA Astrophysics Data System (ADS)

Sharma, D.; Erriguible, A.; Amiroudine, S.

2017-12-01

Supercritical fluids when subjected to simultaneous quench and vibration have been known to cause various intriguing flow phenomena and instabilities depending on the relative direction of temperature gradient and vibration. Here we describe a surprising and interesting phenomenon wherein temperature in the fluid falls below the imposed boundary value when the walls are quenched and the direction of vibration is normal to the temperature gradient. We define these regions in the fluid as sink zones, because they act like sink for heat within the fluid domain. The formation of these zones is first explained using a one-dimensional (1D) analysis with acceleration in constant direction. Subsequently, the effect of various boundary conditions and the relative direction of the temperature gradient to acceleration are analyzed, highlighting the necessary conditions for the formation of sink zones. It is found that the effect of high compressibility and the action of self-weight (due to high acceleration) causes the temperature to change in the bulk besides the usual action of piston effect. This subsequently affects the overall temperature profile thereby leading to the formation of sink zones. Though the examined 1D cases differ from the current two-dimensional (2D) cases, owing to the direction of acceleration being normal as compared to parallel in case of former, the explanations pertaining to 1D cases are judiciously utilized to elucidate the formation of sink zones in 2D supercritical fluids subjected to thermal quench and vibrational acceleration. The appearance of sink zones is found to be dependent on several factors such as proximity to the critical point and acceleration. A surface three-dimensional plot illustrating the effect of these parameters on onset time of sink zones is presented to further substantiate these arguments.

Parallel Fixed Point Implementation of a Radial Basis Function Network in an FPGA

PubMed Central

de Souza, Alisson C. D.; Fernandes, Marcelo A. C.

2014-01-01

This paper proposes a parallel fixed point radial basis function (RBF) artificial neural network (ANN), implemented in a field programmable gate array (FPGA) trained online with a least mean square (LMS) algorithm. The processing time and occupied area were analyzed for various fixed point formats. The problems of precision of the ANN response for nonlinear classification using the XOR gate and interpolation using the sine function were also analyzed in a hardware implementation. The entire project was developed using the System Generator platform (Xilinx), with a Virtex-6 xc6vcx240t-1ff1156 as the target FPGA. PMID:25268918

Toroidal equilibrium states with reversed magnetic shear and parallel flow in connection with the formation of Internal Transport Barriers

NASA Astrophysics Data System (ADS)

Kuiroukidis, Ap.; Throumoulopoulos, G. N.

2015-08-01

We construct nonlinear toroidal equilibria of fixed diverted boundary shaping with reversed magnetic shear and flows parallel to the magnetic field. The equilibria have hole-like current density and the reversed magnetic shear increases as the equilibrium nonlinearity becomes stronger. Also, application of a sufficient condition for linear stability implies that the stability is improved as the equilibrium nonlinearity correlated to the reversed magnetic shear gets stronger with a weaker stabilizing contribution from the flow. These results indicate synergetic stabilizing effects of reversed magnetic shear, equilibrium nonlinearity and flow in the establishment of Internal Transport Barriers (ITBs).

Morphology, directed self-assembly and pattern transfer from a high molecular weight polystyrene-block-poly(dimethylsiloxane) block copolymer film

NASA Astrophysics Data System (ADS)

Cheng, Li-Chen; Bai, Wubin; Fernandez Martin, Eduardo; Tu, Kun-Hua; Ntetsikas, Konstantinos; Liontos, George; Avgeropoulos, Apostolos; Ross, C. A.

2017-04-01

The self-assembly of block copolymers with large feature sizes is inherently challenging as the large kinetic barrier arising from chain entanglement of high molecular weight (MW) polymers limits the extent over which long-range ordered microdomains can be achieved. Here, we illustrate the evolution of thin film morphology from a diblock copolymer of polystyrene-block-poly(dimethylsiloxane) exhibiting total number average MW of 123 kg mol-1, and demonstrate the formation of layers of well-ordered cylindrical microdomains under appropriate conditions of binary solvent mix ratio, commensurate film thickness, and solvent vapor annealing time. Directed self-assembly of the block copolymer within lithographically patterned trenches occurs with alignment of cylinders parallel to the sidewalls. Fabrication of ordered cobalt nanowire arrays by pattern transfer was also implemented, and their magnetic properties and domain wall behavior were characterized.

Nanophotonics for Lab-on-Chip Applications

NASA Astrophysics Data System (ADS)

Seitz, Peter

Optical methods are the preferred measurement techniques for biosensors and lab-on-chip applications. Their key properties are sensitivity, selectivity and robustness. To simplify the systems and their operation, it is desirable to employ label-free optical methods, requiring the functionalization of interfaces. Evanescent electromagnetic waves are probing the optical proper ties near the interfaces, a few 100 nm deep into the sample fluid. The sensitivity of these measurements can be improved with optical micro-resonators, in particular whispering gallery mode devices. Q factors as high as 2x108 have been achieved in practice. The resulting narrow-linewidth resonances and an unexpected thermo-optic effect make it possible to detect single biomolecules using a label-free biosensor principle. Future generations of biosensors and labs-on-chip for point-of-care and high-troughput screening applications will require large numbers of parallel measurement channels, necessitating optical micro-resonators in array format produced very cost-effectively.

Unstart coupling mechanism analysis of multiple-modules hypersonic inlet.

PubMed

Hu, Jichao; Chang, Juntao; Wang, Lei; Cao, Shibin; Bao, Wen

2013-01-01

The combination of multiplemodules in parallel manner is an important way to achieve the much higher thrust of scramjet engine. For the multiple-modules scramjet engine, when inlet unstarted oscillatory flow appears in a single-module engine due to high backpressure, how to interact with each module by massflow spillage, and whether inlet unstart occurs in other modules are important issues. The unstarted flowfield and coupling characteristic for a three-module hypersonic inlet caused by center module II and side module III were, conducted respectively. The results indicate that the other two hypersonic inlets are forced into unstarted flow when unstarted phenomenon appears on a single-module hypersonic inlet due to high backpressure, and the reversed flow in the isolator dominates the formation, expansion, shrinkage, and disappearance of the vortexes, and thus, it is the major factor of unstart coupling of multiple-modules hypersonic inlet. The coupling effect among multiple modules makes hypersonic inlet be more likely unstarted.

Mineralization of collagen may occur on fibril surfaces: evidence from conventional and high-voltage electron microscopy and three-dimensional imaging

NASA Technical Reports Server (NTRS)

Landis, W. J.; Hodgens, K. J.; Song, M. J.; Arena, J.; Kiyonaga, S.; Marko, M.; Owen, C.; McEwen, B. F.

1996-01-01

The interaction between collagen and mineral crystals in the normally calcifying leg tendons from the domestic turkey, Meleagris gallopavo, has been investigated at an ultrastructural level with conventional and high-voltage electron microscopy, computed tomography, and three-dimensional image reconstruction methods. Specimens treated by either aqueous or anhydrous techniques and resin-embedded were appropriately sectioned and regions of early tendon mineralization were photographed. On the basis of individual photomicrographs, stereoscopic pairs of images, and tomographic three-dimensional image reconstructions, platelet-shaped crystals may be demonstrated for the first time in association with the surface of collagen fibrils. Mineral is also observed in closely parallel arrays within collagen hole and overlap zones. The mineral deposition at these spatially distinct locations in the tendon provides insight into possible means by which calcification is mediated by collagen as a fundamental event in skeletal and dental formation among vertebrates.

Kinesiology Workbook and Laboratory Manual.

ERIC Educational Resources Information Center

Harris, Ruth W.

This manual is written for students in anatomy, kinesiology, or introductory biomechanics courses. The book is divided into two sections, a kinesiology workbook and a laboratory manual. The two sections parallel each other in content and format. Each is divided into three corresponding sections: (1) Anatomical bases for movement description; (2)…

[Series: Medical Applications of the PHITS Code (2): Acceleration by Parallel Computing].

PubMed

Furuta, Takuya; Sato, Tatsuhiko

2015-01-01

Time-consuming Monte Carlo dose calculation becomes feasible owing to the development of computer technology. However, the recent development is due to emergence of the multi-core high performance computers. Therefore, parallel computing becomes a key to achieve good performance of software programs. A Monte Carlo simulation code PHITS contains two parallel computing functions, the distributed-memory parallelization using protocols of message passing interface (MPI) and the shared-memory parallelization using open multi-processing (OpenMP) directives. Users can choose the two functions according to their needs. This paper gives the explanation of the two functions with their advantages and disadvantages. Some test applications are also provided to show their performance using a typical multi-core high performance workstation.

Resolutions of the Coulomb operator: VIII. Parallel implementation using the modern programming language X10.

PubMed

Limpanuparb, Taweetham; Milthorpe, Josh; Rendell, Alistair P

2014-10-30

Use of the modern parallel programming language X10 for computing long-range Coulomb and exchange interactions is presented. By using X10, a partitioned global address space language with support for task parallelism and the explicit representation of data locality, the resolution of the Ewald operator can be parallelized in a straightforward manner including use of both intranode and internode parallelism. We evaluate four different schemes for dynamic load balancing of integral calculation using X10's work stealing runtime, and report performance results for long-range HF energy calculation of large molecule/high quality basis running on up to 1024 cores of a high performance cluster machine. Copyright © 2014 Wiley Periodicals, Inc.

New NAS Parallel Benchmarks Results

NASA Technical Reports Server (NTRS)

Yarrow, Maurice; Saphir, William; VanderWijngaart, Rob; Woo, Alex; Kutler, Paul (Technical Monitor)

1997-01-01

NPB2 (NAS (NASA Advanced Supercomputing) Parallel Benchmarks 2) is an implementation, based on Fortran and the MPI (message passing interface) message passing standard, of the original NAS Parallel Benchmark specifications. NPB2 programs are run with little or no tuning, in contrast to NPB vendor implementations, which are highly optimized for specific architectures. NPB2 results complement, rather than replace, NPB results. Because they have not been optimized by vendors, NPB2 implementations approximate the performance a typical user can expect for a portable parallel program on distributed memory parallel computers. Together these results provide an insightful comparison of the real-world performance of high-performance computers. New NPB2 features: New implementation (CG), new workstation class problem sizes, new serial sample versions, more performance statistics.

The behaviour of water and sodium chloride solution confined into asbestos nanotube

NASA Astrophysics Data System (ADS)

Fomin, Yu. D.; Ryzhov, V. N.; Tsiok, E. N.

2016-08-01

We present the molecular simulation study of the behaviour of water and sodium chloride solution confined in lizardite asbestos nanotube which is a typical example of hydrophilic confinement. The local structure and orientational and dynamic properties are studied. It is shown that at low enough temperatures there is a well-defined orientational ordering of the water molecules. At high local densities corresponding to the maxima of the density distribution function, the water molecules are oriented parallel to the axis of the tube. It is also shown that the diffusion coefficient drops about two orders of magnitude comparing to the bulk case. The behaviour of sodium chloride solutions is also considered and the formation of double layer is observed.

Friction and wear of single-crystal manganese-zinc ferrite

NASA Technical Reports Server (NTRS)

Miyoshi, K.; Buckley, D. H.

1979-01-01

Sliding friction experiments were conducted with single crystal manganese-zinc ferrite in contact with itself and with transition metals. Results indicate mating highest atomic density directions (110) on matched crystallographic planes exhibit the lowest coefficient of friction, indicating that direction is important in the friction behavior of ferrite. Matched parallel high atomic density planes and crystallographic directions at the interface exhibit low coefficients of friction. The coefficients of friction for ferrite in contact with various metals are related to the relative chemical activity of these metals. The more active the metal, the higher the coefficient of friction. Cracking and the formation of hexagon- and rectangular-shaped platelet wear debris due to cleavages of (110) planes are observed on the ferrite surfaces as a result of sliding.

The Snow Data System at NASA JPL

NASA Astrophysics Data System (ADS)

Horn, J.; Painter, T. H.; Bormann, K. J.; Rittger, K.; Brodzik, M. J.; Skiles, M.; Burgess, A. B.; Mattmann, C. A.; Ramirez, P.; Joyce, M.; Goodale, C. E.; McGibbney, L. J.; Zimdars, P.; Yaghoobi, R.

2017-12-01

The Snow Data System at NASA JPL includes data processing pipelines built with open source software, Apache 'Object Oriented Data Technology' (OODT). Processing is carried out in parallel across a high-powered computing cluster. The pipelines use input data from satellites such as MODIS, VIIRS and Landsat. They apply algorithms to the input data to produce a variety of outputs in GeoTIFF format. These outputs include daily data for SCAG (Snow Cover And Grain size) and DRFS (Dust Radiative Forcing in Snow), along with 8-day composites and MODICE annual minimum snow and ice calculations. This poster will describe the Snow Data System, its outputs and their uses and applications. It will also highlight recent advancements to the system and plans for the future.

The Snow Data System at NASA JPL

NASA Astrophysics Data System (ADS)

Joyce, M.; Laidlaw, R.; Painter, T. H.; Bormann, K. J.; Rittger, K.; Brodzik, M. J.; Skiles, M.; Burgess, A. B.; Mattmann, C. A.; Ramirez, P.; Goodale, C. E.; McGibbney, L. J.; Zimdars, P.; Yaghoobi, R.

2016-12-01

The Snow Data System at NASA JPL includes data processing pipelines built with open source software, Apache 'Object Oriented Data Technology' (OODT). Processing is carried out in parallel across a high-powered computing cluster. The pipelines use input data from satellites such as MODIS, VIIRS and Landsat. They apply algorithms to the input data to produce a variety of outputs in GeoTIFF format. These outputs include daily data for SCAG (Snow Cover And Grain size) and DRFS (Dust Radiative Forcing in Snow), along with 8-day composites and MODICE annual minimum snow and ice calculations. This poster will describe the Snow Data System, its outputs and their uses and applications. It will also highlight recent advancements to the system and plans for the future.

Transformations of C2-C4 alcohols on the surface of a copper catalyst

NASA Astrophysics Data System (ADS)

Magaeva, A. A.; Lyamina, G. V.; Sudakova, N. N.; Shilyaeva, L. P.; Vodyankina, O. V.

2007-10-01

The interaction of monoatomic alcohols C2-C4 with the surface of a copper catalyst preliminarily oxidized under various conditions was studied by the temperature-programmed reaction method to determine the detailed mechanism of partial oxidation. The conditions of oxygen preadsorption on the surface of copper for the preparation of the desired products were determined. The selective formation of carbonyl compounds was shown to occur at the boundary between reduced and oxidized copper surface regions. The role played by Cu2O was the deep oxidation of alcohols to CO2. Alcohols with branched hydrocarbon structures experienced parallel partial oxidation and dehydrogenation, which was related to the high stability of intermediate keto-type compounds.

Innovative design of composite structures: Further studies in the use of a curvilinear fiber format to improve structural efficiency

NASA Technical Reports Server (NTRS)

Hyer, Michael W.; Charette, Robert F.

1988-01-01

Further studies to determine the potential for using a curvilinear fiber format in the design of composite laminates are reported. The curvilinear format is in contrast to the current practice of having the fibers aligned parallel to each other and in a straight line. The problem of a plate with a central circular hole is used as a candidate problem for this study. The study concludes that for inplane tensile loading the curvilinear format is superior. The limited results to date on compression buckling loads indicate that the curvilinear designs are poorer in resistant buckling. However, for the curvilinear design of interest, the reduction in buckling load is minimal and so overall there is a gain in considering the curvilinear design.

Formation of Gas-Phase Formate in Thermal Reactions of Carbon Dioxide with Diatomic Iron Hydride Anions.

PubMed

Jiang, Li-Xue; Zhao, Chongyang; Li, Xiao-Na; Chen, Hui; He, Sheng-Gui

2017-04-03

The hydrogenation of carbon dioxide involves the activation of the thermodynamically very stable molecule CO 2 and formation of a C-H bond. Herein, we report that HCO 2 - and CO can be formed in the thermal reaction of CO 2 with a diatomic metal hydride species, FeH - . The FeH - anions were produced by laser ablation, and the reaction with CO 2 was analyzed by mass spectrometry and quantum-chemical calculations. Gas-phase HCO 2 - was observed directly as a product, and its formation was predicted to proceed by facile hydride transfer. The mechanism of CO 2 hydrogenation in this gas-phase study parallels similar behavior of a condensed-phase iron catalyst. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Scalable Unix commands for parallel processors : a high-performance implementation.

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

Ong, E.; Lusk, E.; Gropp, W.

2001-06-22

We describe a family of MPI applications we call the Parallel Unix Commands. These commands are natural parallel versions of common Unix user commands such as ls, ps, and find, together with a few similar commands particular to the parallel environment. We describe the design and implementation of these programs and present some performance results on a 256-node Linux cluster. The Parallel Unix Commands are open source and freely available.

High order parallel numerical schemes for solving incompressible flows

NASA Technical Reports Server (NTRS)

Lin, Avi; Milner, Edward J.; Liou, May-Fun; Belch, Richard A.

1992-01-01

The use of parallel computers for numerically solving flow fields has gained much importance in recent years. This paper introduces a new high order numerical scheme for computational fluid dynamics (CFD) specifically designed for parallel computational environments. A distributed MIMD system gives the flexibility of treating different elements of the governing equations with totally different numerical schemes in different regions of the flow field. The parallel decomposition of the governing operator to be solved is the primary parallel split. The primary parallel split was studied using a hypercube like architecture having clusters of shared memory processors at each node. The approach is demonstrated using examples of simple steady state incompressible flows. Future studies should investigate the secondary split because, depending on the numerical scheme that each of the processors applies and the nature of the flow in the specific subdomain, it may be possible for a processor to seek better, or higher order, schemes for its particular subcase.

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics.

PubMed

Kelly, Benjamin J; Fitch, James R; Hu, Yangqiu; Corsmeier, Donald J; Zhong, Huachun; Wetzel, Amy N; Nordquist, Russell D; Newsom, David L; White, Peter

2015-01-20

While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.

Parallel computing in experimental mechanics and optical measurement: A review (II)

NASA Astrophysics Data System (ADS)

Wang, Tianyi; Kemao, Qian

2018-05-01

With advantages such as non-destructiveness, high sensitivity and high accuracy, optical techniques have successfully integrated into various important physical quantities in experimental mechanics (EM) and optical measurement (OM). However, in pursuit of higher image resolutions for higher accuracy, the computation burden of optical techniques has become much heavier. Therefore, in recent years, heterogeneous platforms composing of hardware such as CPUs and GPUs, have been widely employed to accelerate these techniques due to their cost-effectiveness, short development cycle, easy portability, and high scalability. In this paper, we analyze various works by first illustrating their different architectures, followed by introducing their various parallel patterns for high speed computation. Next, we review the effects of CPU and GPU parallel computing specifically in EM & OM applications in a broad scope, which include digital image/volume correlation, fringe pattern analysis, tomography, hyperspectral imaging, computer-generated holograms, and integral imaging. In our survey, we have found that high parallelism can always be exploited in such applications for the development of high-performance systems.

ParCAT: A Parallel Climate Analysis Toolkit

NASA Astrophysics Data System (ADS)

Haugen, B.; Smith, B.; Steed, C.; Ricciuto, D. M.; Thornton, P. E.; Shipman, G.

2012-12-01

Climate science has employed increasingly complex models and simulations to analyze the past and predict the future of our climate. The size and dimensionality of climate simulation data has been growing with the complexity of the models. This growth in data is creating a widening gap between the data being produced and the tools necessary to analyze large, high dimensional data sets. With single run data sets increasing into 10's, 100's and even 1000's of gigabytes, parallel computing tools are becoming a necessity in order to analyze and compare climate simulation data. The Parallel Climate Analysis Toolkit (ParCAT) provides basic tools that efficiently use parallel computing techniques to narrow the gap between data set size and analysis tools. ParCAT was created as a collaborative effort between climate scientists and computer scientists in order to provide efficient parallel implementations of the computing tools that are of use to climate scientists. Some of the basic functionalities included in the toolkit are the ability to compute spatio-temporal means and variances, differences between two runs and histograms of the values in a data set. ParCAT is designed to facilitate the "heavy lifting" that is required for large, multidimensional data sets. The toolkit does not focus on performing the final visualizations and presentation of results but rather, reducing large data sets to smaller, more manageable summaries. The output from ParCAT is provided in commonly used file formats (NetCDF, CSV, ASCII) to allow for simple integration with other tools. The toolkit is currently implemented as a command line utility, but will likely also provide a C library for developers interested in tighter software integration. Elements of the toolkit are already being incorporated into projects such as UV-CDAT and CMDX. There is also an effort underway to implement portions of the CCSM Land Model Diagnostics package using ParCAT in conjunction with Python and gnuplot. ParCAT is implemented in C to provide efficient file IO. The file IO operations in the toolkit use the parallel-netcdf library; this enables the code to use the parallel IO capabilities of modern HPC systems. Analysis that currently requires an estimated 12+ hours with the traditional CCSM Land Model Diagnostics Package can now be performed in as little as 30 minutes on a single desktop workstation and a few minutes for relatively small jobs completed on modern HPC systems such as ORNL's Jaguar.

Clues to the formation of Enceladus' south-polar terrain from simulations of funiscular plains formation

NASA Astrophysics Data System (ADS)

Bland, M. T.; McKinnon, W. B.

2013-12-01

Cassini imaging and thermal data have demonstrated that Enceladus' four south-polar linear-fractures are the source of both Enceladus' cryovolcanic plume and its extreme thermal emission. These long (130 km), parallel 'tiger stripes' are located within a young, quasi-circular, south-polar depression characterized by extensive tectonic deformation that includes sets of both small-scale fractures (possibly relic tiger stripes) [Patthoff and Kattenhorn 2011], and large-amplitude circumferential ridges. Between the tiger stripes themselves are broad regions of periodic, low amplitude (50-100 m), short-wavelength (1 km) ridges (dubbed 'funiscular' terrain) that generally run parallel to the larger tiger stripe fractures but occasionally intersect them at small angles [Spencer et al. 2009]. The formation of the south polar terrain (SPT) may be related to localized melting of Enceladus' ice layer [e.g., Collins and Goodman, 2007] but the detailed formation kinematics of the SPT and its specific tectonic structures is far from certain. Here we constrain the formation of the SPT by simulating the development of funiscular terrain specifically. This terrain dominates the central portion of the SPT, including regions immediately adjacent to the tiger stripes. The stripes are, in effect, large-scale fractures imbedded within the funiscular terrain; thus, any kinematic or dynamic prescription for SPT formation must account for funiscular morphology. The simplest formation mechanism consistent with the funiscular ridges is that of low-amplitude, short-wavelength folding of a thin surface layer. Barr and Pruess [2010] demonstrated the plausibility of this mechanism using an analytical model developed for folds forming on lava flow tops. We extend their analysis using finite element modeling of the contraction of a thin, brittle lithosphere overlying ductile ice. We find fold morphologies consistent with the funiscular terrain (50-100 m amplitude, 1.5 km wavelengths) for lithospheric thicknesses of 250-500 m assuming weak (~100 kPa) near surface ice and 10% shortening. Creation of short wavelengths and tight fold hinges requires kinematic fold growth that shortens the fold wavelength subsequent to establishment of a longer, initial dominant wavelength. Thicker lithospheres (1 km) also reproduce the deformation if strains exceed 10%, though fold amplitudes are lower and wavelengths longer in this case. The thin lithosphere required to produce funiscular morphologies require exceedingly high heat flow if intact (low porosity) ice is assumed (≥1 W m-2). Significant lithospheric porosity that depresses the ice thermal conductivity (e.g., by a factor of ~3 for 30% porosity [Shoshany et al. 2002]) is likely required, and could decrease the necessary heat flux to ~300 mW m-2. The thin lithosphere necessary for its formation might account for the funiscular terrain's limited spatial extent adjacent to the tiger stripes, the locus of SPT thermal activity. A compressive stress regime between the tensile tiger stripes suggests local accommodation of strain in a dominantly extensional setting that is likely modulated by tidally-induced shear.

Parallelized multi–graphics processing unit framework for high-speed Gabor-domain optical coherence microscopy

PubMed Central

Tankam, Patrice; Santhanam, Anand P.; Lee, Kye-Sung; Won, Jungeun; Canavesi, Cristina; Rolland, Jannick P.

2014-01-01

Abstract. Gabor-domain optical coherence microscopy (GD-OCM) is a volumetric high-resolution technique capable of acquiring three-dimensional (3-D) skin images with histological resolution. Real-time image processing is needed to enable GD-OCM imaging in a clinical setting. We present a parallelized and scalable multi-graphics processing unit (GPU) computing framework for real-time GD-OCM image processing. A parallelized control mechanism was developed to individually assign computation tasks to each of the GPUs. For each GPU, the optimal number of amplitude-scans (A-scans) to be processed in parallel was selected to maximize GPU memory usage and core throughput. We investigated five computing architectures for computational speed-up in processing 1000×1000 A-scans. The proposed parallelized multi-GPU computing framework enables processing at a computational speed faster than the GD-OCM image acquisition, thereby facilitating high-speed GD-OCM imaging in a clinical setting. Using two parallelized GPUs, the image processing of a 1×1×0.6  mm3 skin sample was performed in about 13 s, and the performance was benchmarked at 6.5 s with four GPUs. This work thus demonstrates that 3-D GD-OCM data may be displayed in real-time to the examiner using parallelized GPU processing. PMID:24695868

Parallelized multi-graphics processing unit framework for high-speed Gabor-domain optical coherence microscopy.

PubMed

Tankam, Patrice; Santhanam, Anand P; Lee, Kye-Sung; Won, Jungeun; Canavesi, Cristina; Rolland, Jannick P

2014-07-01

Gabor-domain optical coherence microscopy (GD-OCM) is a volumetric high-resolution technique capable of acquiring three-dimensional (3-D) skin images with histological resolution. Real-time image processing is needed to enable GD-OCM imaging in a clinical setting. We present a parallelized and scalable multi-graphics processing unit (GPU) computing framework for real-time GD-OCM image processing. A parallelized control mechanism was developed to individually assign computation tasks to each of the GPUs. For each GPU, the optimal number of amplitude-scans (A-scans) to be processed in parallel was selected to maximize GPU memory usage and core throughput. We investigated five computing architectures for computational speed-up in processing 1000×1000 A-scans. The proposed parallelized multi-GPU computing framework enables processing at a computational speed faster than the GD-OCM image acquisition, thereby facilitating high-speed GD-OCM imaging in a clinical setting. Using two parallelized GPUs, the image processing of a 1×1×0.6  mm3 skin sample was performed in about 13 s, and the performance was benchmarked at 6.5 s with four GPUs. This work thus demonstrates that 3-D GD-OCM data may be displayed in real-time to the examiner using parallelized GPU processing.

Optoelectronic associative recall using motionless-head parallel readout optical disk

NASA Astrophysics Data System (ADS)

Marchand, P. J.; Krishnamoorthy, A. V.; Ambs, P.; Esener, S. C.

1990-12-01

High data rates, low retrieval times, and simple implementation are presently shown to be obtainable by means of a motionless-head 2D parallel-readout system for optical disks. Since the optical disk obviates mechanical head motions for access, focusing, and tracking, addressing is performed exclusively through the disk's rotation. Attention is given to a high-performance associative memory system configuration which employs a parallel readout disk.

Finger-like pattern formation in dilute surfactant pentaethylene glycol monododecyl ether solutions.

PubMed

Kubo, Yoshihide; Yokoyama, Yasuhiro; Tanaka, Shinpei

2013-04-07

We report here peculiar finger-like patterns observed during the phase separation process of dilute micellar pentaethylene glycol monododecyl ether solutions. The patterns were composed of parallel and periodic threads of micelle-rich domains. Prior to this pattern formation, the phase separation always started with the appearance of water-rich domains rimmed by the micelle-rich domains. It was found that these rims played a significant role in the pattern formation. We explain this pattern formation using a simple simulation model with disconnectable springs. The simulation results suggested that the spatially inhomogeneous elasticity or connectivity of a transient gel of worm-like micelles was responsible for the rim formation. The rims thus formed lead rim-induced nucleation, growth, and elongation of the domains owing to their small mobility and the elastic frustration around them. These rim-induced processes eventually produce the observed finger-like patterns.

Performance Refactoring of Instrumentation, Measurement, and Analysis Technologies for Petascale Computing. The PRIMA Project

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

Malony, Allen D.; Wolf, Felix G.

2014-01-31

The growing number of cores provided by today’s high-­end computing systems present substantial challenges to application developers in their pursuit of parallel efficiency. To find the most effective optimization strategy, application developers need insight into the runtime behavior of their code. The University of Oregon (UO) and the Juelich Supercomputing Centre of Forschungszentrum Juelich (FZJ) develop the performance analysis tools TAU and Scalasca, respectively, which allow high-­performance computing (HPC) users to collect and analyze relevant performance data – even at very large scales. TAU and Scalasca are considered among the most advanced parallel performance systems available, and are used extensivelymore » across HPC centers in the U.S., Germany, and around the world. The TAU and Scalasca groups share a heritage of parallel performance tool research and partnership throughout the past fifteen years. Indeed, the close interactions of the two groups resulted in a cross-­fertilization of tool ideas and technologies that pushed TAU and Scalasca to what they are today. It also produced two performance systems with an increasing degree of functional overlap. While each tool has its specific analysis focus, the tools were implementing measurement infrastructures that were substantially similar. Because each tool provides complementary performance analysis, sharing of measurement results is valuable to provide the user with more facets to understand performance behavior. However, each measurement system was producing performance data in different formats, requiring data interoperability tools to be created. A common measurement and instrumentation system was needed to more closely integrate TAU and Scalasca and to avoid the duplication of development and maintenance effort. The PRIMA (Performance Refactoring of Instrumentation, Measurement, and Analysis) project was proposed over three years ago as a joint international effort between UO and FZJ to accomplish these objectives: (1) refactor TAU and Scalasca performance system components for core code sharing and (2) integrate TAU and Scalasca functionality through data interfaces, formats, and utilities. As presented in this report, the project has completed these goals. In addition to shared technical advances, the groups have worked to engage with users through application performance engineering and tools training. In this regard, the project benefits from the close interactions the teams have with national laboratories in the United States and Germany. We have also sought to enhance our interactions through joint tutorials and outreach. UO has become a member of the Virtual Institute of High-­Productivity Supercomputing (VI-­HPS) established by the Helmholtz Association of German Research Centres as a center of excellence, focusing on HPC tools for diagnosing programming errors and optimizing performance. UO and FZJ have conducted several VI-­HPS training activities together within the past three years.« less

Performance Refactoring of Instrumentation, Measurement, and Analysis Technologies for Petascale Computing: the PRIMA Project

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

Malony, Allen D.; Wolf, Felix G.

2014-01-31

The growing number of cores provided by today’s high-end computing systems present substantial challenges to application developers in their pursuit of parallel efficiency. To find the most effective optimization strategy, application developers need insight into the runtime behavior of their code. The University of Oregon (UO) and the Juelich Supercomputing Centre of Forschungszentrum Juelich (FZJ) develop the performance analysis tools TAU and Scalasca, respectively, which allow high-performance computing (HPC) users to collect and analyze relevant performance data – even at very large scales. TAU and Scalasca are considered among the most advanced parallel performance systems available, and are used extensivelymore » across HPC centers in the U.S., Germany, and around the world. The TAU and Scalasca groups share a heritage of parallel performance tool research and partnership throughout the past fifteen years. Indeed, the close interactions of the two groups resulted in a cross-fertilization of tool ideas and technologies that pushed TAU and Scalasca to what they are today. It also produced two performance systems with an increasing degree of functional overlap. While each tool has its specific analysis focus, the tools were implementing measurement infrastructures that were substantially similar. Because each tool provides complementary performance analysis, sharing of measurement results is valuable to provide the user with more facets to understand performance behavior. However, each measurement system was producing performance data in different formats, requiring data interoperability tools to be created. A common measurement and instrumentation system was needed to more closely integrate TAU and Scalasca and to avoid the duplication of development and maintenance effort. The PRIMA (Performance Refactoring of Instrumentation, Measurement, and Analysis) project was proposed over three years ago as a joint international effort between UO and FZJ to accomplish these objectives: (1) refactor TAU and Scalasca performance system components for core code sharing and (2) integrate TAU and Scalasca functionality through data interfaces, formats, and utilities. As presented in this report, the project has completed these goals. In addition to shared technical advances, the groups have worked to engage with users through application performance engineering and tools training. In this regard, the project benefits from the close interactions the teams have with national laboratories in the United States and Germany. We have also sought to enhance our interactions through joint tutorials and outreach. UO has become a member of the Virtual Institute of High-Productivity Supercomputing (VI-HPS) established by the Helmholtz Association of German Research Centres as a center of excellence, focusing on HPC tools for diagnosing programming errors and optimizing performance. UO and FZJ have conducted several VI-HPS training activities together within the past three years.« less

Topology of polymer chains under nanoscale confinement.

PubMed

Satarifard, Vahid; Heidari, Maziar; Mashaghi, Samaneh; Tans, Sander J; Ejtehadi, Mohammad Reza; Mashaghi, Alireza

2017-08-24

Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of l p under a spherical confinement of radius R c . At low values of l p /R c , the entropy of the linear chain leads to the formation of independent contacts along the chain and accordingly, increases the fraction of series topology with respect to other topologies. However, at high l p /R c , the fraction of cross and parallel topologies are enhanced in the chain topological circuits with cross becoming predominant. At an intermediate confining regime, we identify a critical value of l p /R c , at which all topological states have equal probability. Confinement thus equalizes the probability of more complex cross and parallel topologies to the level of the more simple, non-cooperative series topology. Moreover, our topology analysis reveals distinct behaviours for ring- and linear polymers under weak confinement; however, we find no difference between ring- and linear polymers under strong confinement. Under weak confinement, ring polymers adopt parallel and series topologies with equal likelihood, while linear polymers show a higher tendency for series arrangement. The radial distribution analysis of the topology reveals a non-uniform effect of confinement on the topology of polymer chains, thereby imposing more pronounced effects on the core region than on the confinement surface. Additionally, our results reveal that over a wide range of confining radii, loops arranged in parallel and cross topologies have nearly the same contact orders. Such degeneracy implies that the kinetics and transition rates between the topological states cannot be solely explained by contact order. We expect these findings to be of general importance in understanding chaperone assisted protein folding, chromosome architecture, and the evolution of molecular folds.

High Order Semi-Lagrangian Advection Scheme

NASA Astrophysics Data System (ADS)

Malaga, Carlos; Mandujano, Francisco; Becerra, Julian

2014-11-01

In most fluid phenomena, advection plays an important roll. A numerical scheme capable of making quantitative predictions and simulations must compute correctly the advection terms appearing in the equations governing fluid flow. Here we present a high order forward semi-Lagrangian numerical scheme specifically tailored to compute material derivatives. The scheme relies on the geometrical interpretation of material derivatives to compute the time evolution of fields on grids that deform with the material fluid domain, an interpolating procedure of arbitrary order that preserves the moments of the interpolated distributions, and a nonlinear mapping strategy to perform interpolations between undeformed and deformed grids. Additionally, a discontinuity criterion was implemented to deal with discontinuous fields and shocks. Tests of pure advection, shock formation and nonlinear phenomena are presented to show performance and convergence of the scheme. The high computational cost is considerably reduced when implemented on massively parallel architectures found in graphic cards. The authors acknowledge funding from Fondo Sectorial CONACYT-SENER Grant Number 42536 (DGAJ-SPI-34-170412-217).

Mechanism of inverted-chirp infrasonic radiation from sprites

NASA Astrophysics Data System (ADS)

de Larquier, Sebastien; Pasko, Victor P.

2010-12-01

Farges and Blanc (2010) reported inverted-chirp infrasonic signals with high frequencies arriving before low frequencies, possibly emitted by sprite discharges and observed on the ground at close range (<100 km) from the source. In the present work a parallel version of a 2-D FDTD model of infrasound propagation in a realistic atmosphere is applied to demonstrate that the observed morphology of infrasound signals is consistent with general scaling of diameters of sprite streamers inversely proportionally to the air density. The smaller structures at lower altitudes radiate higher infrasonic frequencies that arrive first at the observational point on the ground, while the low frequency components are delayed because they originate at lower air densities at higher altitudes. The results demonstrate that strong absorption of high frequency infrasonic components at high altitudes (i.e., ˜0.2 dB/km for 8 Hz at 70 km) may also contribute to formation of inverted-chirp signals observed on the ground at close range.

The anomalously high melting temperature of bilayer ice.

PubMed

Kastelowitz, Noah; Johnston, Jessica C; Molinero, Valeria

2010-03-28

Confinement of water usually depresses its melting temperature. Here we use molecular dynamics simulations to determine the liquid-crystal equilibrium temperature for water confined between parallel hydrophobic or mildly hydrophilic plates as a function of the distance between the surfaces. We find that bilayer ice, an ice polymorph in which the local environment of each water molecule strongly departs from the most stable tetrahedral structure, has the highest melting temperature (T(m)) of the series of l-layer ices. The melting temperature of bilayer ice is not only unusually high compared to the other confined ices, but also above the melting point of bulk hexagonal ice. Recent force microscopy experiments of water confined between graphite and a tungsten tip reveal the formation of ice at room temperature [K. B. Jinesh and J. W. M. Frenken, Phys. Rev. Lett. 101, 036101 (2008)]. Our results suggest that bilayer ice, for which we compute a T(m) as high as 310 K in hydrophobic confinement, is the crystal formed in those experiments.

Closed timelike curves produced by pairs of moving cosmic strings - Exact solutions

NASA Technical Reports Server (NTRS)

Gott, J. Richard, III

1991-01-01

Exact solutions of Einstein's field equations are presented for the general case of two moving straight cosmic strings that do not intersect. The solutions for parallel cosmic strings moving in opposite directions show closed timelike curves (CTCs) that circle the two strings as they pass, allowing observers to visit their own past. Similar results occur for nonparallel strings, and for masses in (2+1)-dimensional spacetime. For finite string loops the possibility that black-hole formation may prevent the formation of CTCs is discussed.

Brainhack: a collaborative workshop for the open neuroscience community.

PubMed

Cameron Craddock, R; S Margulies, Daniel; Bellec, Pierre; Nolan Nichols, B; Alcauter, Sarael; A Barrios, Fernando; Burnod, Yves; J Cannistraci, Christopher; Cohen-Adad, Julien; De Leener, Benjamin; Dery, Sebastien; Downar, Jonathan; Dunlop, Katharine; R Franco, Alexandre; Seligman Froehlich, Caroline; J Gerber, Andrew; S Ghosh, Satrajit; J Grabowski, Thomas; Hill, Sean; Sólon Heinsfeld, Anibal; Matthew Hutchison, R; Kundu, Prantik; R Laird, Angela; Liew, Sook-Lei; J Lurie, Daniel; G McLaren, Donald; Meneguzzi, Felipe; Mennes, Maarten; Mesmoudi, Salma; O'Connor, David; H Pasaye, Erick; Peltier, Scott; Poline, Jean-Baptiste; Prasad, Gautam; Fraga Pereira, Ramon; Quirion, Pierre-Olivier; Rokem, Ariel; S Saad, Ziad; Shi, Yonggang; C Strother, Stephen; Toro, Roberto; Q Uddin, Lucina; D Van Horn, John; W Van Meter, John; C Welsh, Robert; Xu, Ting

2016-01-01

Brainhack events offer a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well as parallel educational sessions, Brainhack fosters novel collaborations around the interests of its attendees. Here we provide an overview of its structure, past events, and example projects. Additionally, we outline current innovations such as regional events and post-conference publications. Through introducing Brainhack to the wider neuroscience community, we hope to provide a unique conference format that promotes the features of collaborative, open science.

Formation Flying With Decentralized Control in Libration Point Orbits

NASA Technical Reports Server (NTRS)

Folta, David; Carpenter, J. Russell; Wagner, Christoph

2000-01-01

A decentralized control framework is investigated for applicability of formation flying control in libration orbits. The decentralized approach, being non-hierarchical, processes only direct measurement data, in parallel with the other spacecraft. Control is accomplished via linearization about a reference libration orbit with standard control using a Linear Quadratic Regulator (LQR) or the GSFC control algorithm. Both are linearized about the current state estimate as with the extended Kalman filter. Based on this preliminary work, the decentralized approach appears to be feasible for upcoming libration missions using distributed spacecraft.

Broad source fringe formation with a Fresnel biprism and a Mach-Zehnder interferometer.

PubMed

Leon, S C

1987-12-15

A biprism is used to combine identical spatially incoherent wavefronts that have been split by an amplitude splitting interferometer such as the Mach-Zehnder. The performance of this composite interferometer is evaluated by tracing the chief ray through parallel optical systems using Snell's law and trigonometry. Fringes formed in spatially incoherent light with this optical system are compared with those formed using the Mach-Zehnder and grating interferometers. It is shown that the combination can exhibit extended source fringe formation capability greatly exceeding that of the Mach-Zehnder interferometer.